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Agentic and Language Techniques Research 2

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Absence of effect of prenatal ethanol on adult emotionality and ethanol consumption in rats. Lower peak blood ethanol concentrations after 1 and 2 g of ethanol per kg were found in pregnant rats than in virgin females. No significant differences in adult "emotionality" or ethanol consumption were found in rats exposed to prenatal alcohol and in pair-fed and untreated controls.

[blood <Organism_substance>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Sox9 neural crest determinant gene controls patterning and closure of the posterior frontal cranial suture. Cranial suture development involves a complex interaction of genes and tissues derived from neural crest cells (NCC) and paraxial mesoderm. In mice, the posterior frontal (PF) suture closes during the first month of life while other sutures remain patent throughout the life of the animal. Given the unique NCC origin of PF suture complex (analogous to metopic suture in humans), we performed quantitative real-time PCR and immunohistochemistry to study the expression pattern of the NCC determinant gene Sox9 and select markers of extracellular matrix. Our results indicated a unique up-regulated expression of Sox9, a regulator of chondrogenesis, during initiation of PF suture closure, along with the expression of specific cartilage markers (Type II Collagen and Type X Collagen), as well as cartilage tissue formation in the PF suture. This process was followed by expression of bone markers (Type I Collagen and Osteocalcin), suggesting endochondral ossification. Moreover, we studied the effect of haploinsufficiency of the NCC determinant gene Sox9 in the NCC derived PF suture complex. A decrease in dosage of Sox9 by haploinsufficiency in NCC-derived tissues resulted in delayed PF suture closure. These results demonstrate a unique development of the PF suture complex and the role of Sox9 as an important contributor to timely and proper closure of the PF suture through endochondral ossification.

[neural crest <Tissue>] [posterior frontal cranial suture <Multi-tissue_structure>] [Cranial suture <Multi-tissue_structure>] [tissues <Tissue>] [neural crest cells <Cell>] [NCC <Cell>] [paraxial mesoderm <Multi-tissue_structure>] [posterior frontal (PF) suture <Multi-tissue_structure>] [sutures <Multi-tissue_structure>] [NCC <Cell>] [PF suture <Multi-tissue_structure>] [metopic suture <Multi-tissue_structure>] [NCC <Cell>] [extracellular matrix <Cellular_component>] [PF suture <Multi-tissue_structure>] [cartilage <Tissue>] [cartilage tissue <Tissue>] [PF suture <Multi-tissue_structure>] [bone <Tissue>] [NCC <Cell>] [NCC <Cell>] [PF suture <Multi-tissue_structure>] [NCC-derived tissues <Tissue>] [PF suture <Multi-tissue_structure>] [PF suture <Multi-tissue_structure>] [PF suture <Multi-tissue_structure>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Definition of pathogens It remains difficult to determine whether the organisms detected by the DNA Detection Kit are true pathogens. This also applies, although to a much lesser degree, to conventional blood culture analysis. However, detected organisms were considered to be pathogens if the results of culture tests from samples of the suspected infectious sites coincided with the results of DNA Detection Kit or blood culture analysis. The culture data of sputum, urine, pus and drainage fluid were used to define the pathogens. A decision as to whether an identified organism was a pathogen was taken based on the decision tree shown in Figure 1. Thus, when the same organism was detected by both DNA Detection Kit and blood culture analysis, the detected organism was considered an infectious pathogen. If there was a discrepancy between the organism that was detected by SeptiFast analysis and that detected by blood culture analysis, or if an organism was only detected in one of these tests, then other samples taken from the infection site were analyzed. If this second culture test of the suspected infectious site revealed the presence of the same organism, this organism was considered to be a pathogen. If the microbial strain was only detected once for a sample, we then checked the second culture results in the suspected infectious sites. If this result identified the same strain as that identified by SeptiFast analysis then it was decided that this strain was a pathogen. However, if the strain was still only detected in some of the assays, we next determined if the patient involved suffered from sepsis. Sepsis is defined as SIRS caused by infection. The definition of sepsis that we used was based on the International Sepsis Forum Definition of Infection at the ICU Consensus Conference [7]. However, if the underlying disease is acute lymphoma leukemia (ALL), malignant lymphoma (ML), or acute myelogenous leukemia (AML), the definition of infection is defined as the ability to detect infectious organisms by blood culture analysis. If the patient was not defined as having sepsis when whole blood was administered to the patient, we decided that the strain detected by subsequent DNA Detection Kit or blood culture analysis was not a pathogen. Figure 1 Flowchart for pathogen decision. Samples were defined as negative for pathogens if a pathogen could not be detected by any method of analysis within seven days, and if another type of culture test did not detect this pathogen but could detect other organisms. CoNS bacteria, which are represented by the Staphylococcus epidermidis (S. epidermidis) and Streptococcus spp. are indigenous bacteria and often cause contamination in assays of pathogens. Therefore, when CoNS or Streptococcus spp. were detected by blood culture and SeptiFast analysis, the following criteria were applied to define whether these strains represented a pathogenic infection: (1) Tests were performed at least twice within 48 hours before and after CoNS were detected by blood culture or SeptiFast analysis; (2) CoNS or Streptococcus spp. were detected in two different blood culture tests that were separately performed twice within 48 hours; and, (3) CoNS or Streptococcus spp. were detected twice or more in tests that were performed three times [11-15]. If a sample's results met any of these three criteria, then the sample was evaluated as a pathogen. The distinction between pathogen and contamination was also determined for CoNS or Streptococcus spp. from the crossing point (Cp) obtained using the LightCycler analysis software v4.05. The Cp represents the point in the amplification cycle where the amplification curve crosses the detection threshold. When CoNS or Streptococcus spp. were detected using the LightCycler analysis software v4.05, a Cp of less than 20 was defined as indicating a pathogen and a Cp of over 20 was defined as contamination by checking the amplification curve.

[blood <Organism_substance>] [blood <Organism_substance>] [sputum <Organism_substance>] [urine <Organism_substance>] [pus <Organism_substance>] [fluid <Organism_substance>] [blood <Organism_substance>] [blood <Organism_substance>] [malignant lymphoma <Pathological_formation>] [ML <Pathological_formation>] [blood <Organism_substance>] [whole blood <Organism_substance>] [blood <Organism_substance>] [blood <Organism_substance>] [blood <Organism_substance>] [blood <Organism_substance>] [sample <Organism_substance>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Determination of eprosartan in human plasma and urine by LC/MS/MS. A protein precipitation, liquid chromatography/tandem mass spectrometry (LC/MS/MS) method has been developed and validated for the determination of eprosartan in human plasma and urine. The solvent system also served as a protein precipitation reagent. The chromatographic separation was achieved on a CAPCELL PAK C18 column (50 mmx2.0 mm, 5 microm, Shiseido). A mobile phase was consisted of 0.5% formic acid in water and 0.5% formic acid in acetonitrile (72:28). Detection was by positive ion electrospray tandem mass spectrometry on a Sciex API3000. The standard curves, which ranged from 5 to 2000 ng/mL in human plasma and from 0.25 to 50 microg/mL in urine, were fitted to a 1/x weighted quadratic regression model. The method proved to be accurate, specific and sensitive enough to be successfully applied to a pharmacokinetic study.

[plasma <Organism_substance>] [urine <Organism_substance>] [plasma <Organism_substance>] [urine <Organism_substance>] [plasma <Organism_substance>] [urine <Organism_substance>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Discussion Among adolescent boys in Chapaevsk, Russia, higher serum levels of sum of dioxin-like compounds and sum of dioxin TEQs were positively associated with increased age, consumption of fish, local meats other than chicken, and inversely with weeks of gestation. The age association was found despite a narrow age range of slightly over two years in our study. Although not statistically significant, the distance the boy lived from the Khimprom factory at the time of blood draw was inversely associated with serum levels of sum of dioxin-like compounds and sum of dioxin TEQs. As expected, serum PCBs, specifically PCB 118, were strongly associated with both sum of dioxin-like compounds and sum of dioxin TEQs. There was no association between the distance of the residence from the Khimprom plant during the pregnancy and subsequent serum dioxin levels. One potential explanation for the lack of association may include misclassification of distance since the mother was asked to recall a time period more than 14 years prior to the study. However, we would expect that the mother would be able to recall residential history at the time of the birth of their son. Mother's self-reported estimates of current residential distance from Khimprom was generally accurate; twenty-one of twenty-nine mothers correctly categorized their current residential distance from the Khimprom plants based on cross-referencing using GIS mapping. Other explanations include that prenatal exposure 14 or more years prior to the current serum sample is not as strong a predictor as are exposures resulting from present residential location. Although there was no association of case status (cryptorchidism or hypospadias) with dioxin levels, we did not have sufficient power to definitively assess this relationship. Perinatal history (e.g. weeks of breastfeeding) was generally not associated with exposure measures in this population; this may be a function of older age of the children. However, there are limited data on the relationship of perinatal factors with organochlorine exposures in this age group so a null finding is of interest given reports that differences in organochlorine levels among breastfed and non-breastfed are generally no longer discernable by early school age [24,25] and, furthermore, that dietary intake after this age contributes significantly to total dioxin intake [26]. In prior studies, substantial emphasis has been placed on pre- and early postnatal (via breastfeeding) exposures because of particular vulnerability during fetal and early infant development. The exposure risk factors during peri-adolescence, another period of potential developmental vulnerability, has not been studied in-detail, therefore, the identification of exposure risk factors specific to this period will enhance our understanding of this critical period. Although data on levels of PCDD/PCDFs in children is limited, our results suggest that the mean total TEQs among Chapaevsk adolescents were higher than most values previously reported in non-occupationally exposed populations of comparable or even older ages. Figure 2 shows a comparison of the mean PCDD/PCDFs TEQ levels in Chapaevsk boys with other populations (TEQ from dioxin-like PCBs was not included, since some of these studies did not report them). The mean TEQs of pooled blood samples from 10 year-old German boys in rural and urban settings was 8.2 pg TEQ/g lipid for an urban industrial area, 9.0 pg TEQ/g lipid for an industrial area within a rural setting, and 10.1 pg TEQ/g lipid for a rural area [27]. In comparison, the mean TEQ in the Chapevsk boys was 19.3 pg TEQ/g lipid. With the exception of children described by Wuthe et al. [27], subjects in the other studies in Figure 2 were significantly older than the Chapaevsk boys. Despite age differences, the mean TEQ in Chapaevsk boys was comparable to or even higher than the mean TEQ in older populations from other countries. For example, they were higher than mean TEQs of 18.4 pg TEQ/g lipid in adults (40.6 years old average) from South Germany [27] or 16.4 pg TEQ/g lipid from 20 year old Japanese women [28] or pooled samples from randomly selected males and females 18-69 years of age from the Spanish city of Mataro [29], which were 12.5 and 14.7 pg TEQ/g lipid respectively. The mean levels in adult female (mean age 41 years) non-factory workers in the Russian city of Shelekhovo were also lower at 14.5 pg TEQ/g lipid [30]. Mean TEQs for the general population (mean age 44.2 years) in Germany, collected in 1997-98 [31], and median TEQs for long-term workers of pulp and paper mill and non-workers in the U.S. in 1996 [32] were similar to levels found in the Chapaevsk boys. The mean levels in the study in Germany were 20.71 pg TEQ/g lipid and in the U.S. the median levels were 19.1 pg TEQ/g lipid for community residents and 21.2 pg TEQ/g lipid for low exposure workers. Figure 2 Mean PCDD/PCDFs TEQ levels in Chapaevsk boys in comparison with other populations. Although TCDD was largely below the detection limits in this small pilot sample, the two boys with detectable values had high TCDD levels (17.9 and 21.7 pg/g lipid), suggesting that exposure for at least some portion of this population is substantially higher than typical of this age group. In comparison, in a cohort of adult (mean age of 58 years) fishermen from a polluted region of Finland, the mean TCDD concentration was 19 pg/g lipid [33]. In adult (mean age of 53 years) residents from Calcasieu Parish, Louisiana, which is near a chemical industrial complex, the mean TCDD level was 7.6 pg/g lipid [34]. Not only were the dioxin levels in these two children higher than those found in these studies, but the adults in the previous studies were several decades older and therefore would be expected to have higher dioxin body burdens than younger children [35]. Potential explanations for the large number of non-detectable samples for TCDD include the small sample volume and young age of the subjects. In our future studies in this population, we will collect larger volumes of serum for dioxin analysis. In one of the few studies on dioxin-like compounds in which children were included, Eskenazi and coworkers [36] evaluated the relationship between serum TCDD concentrations and age at exposure of female residents of Seveso, Italy. Residents near the ICMESA chemical plant in Seveso were exposed to some of the highest known residential levels of 2,3,7,8-TCDD as a result of an explosion at the plant. Archived serum collected near the time of the accident was used to measure exposures. Residents closest to the plant had a median 2,3,7,8-TCDD level of 272 ppt (IQR 92 - 883 ppt). Residential proximity to the plant and younger age (up to 13 years old) were the strongest predictors of an individual's serum 2,3,7,8-TCDD level. Other predictors included being outdoors at the time of explosion and consumption of homegrown food. The higher levels found in children were most likely a result of increased exposure as a result of activity patterns and a greater proportionate consumption of food, water and air than adults [37]. Although the exposure scenario (an acute high exposure event) is different than the chronic low/moderate exposure occurring in Chapaevsk, the results from Seveso suggest that children may be at increased risk for high dioxin exposure from environmental contamination. In our study, although distance from the Khimprom plants was a weak predictor of serum dioxin-like compounds, consumption of local foods (specifically meat and fish), as in the Seveso study, was a strong predictor of sum of dioxin-like compounds and dioxin TEQs. This finding is notable given concerns regarding environmental dioxin contamination in the community and suggests that food may be one of the more, if not most, important routes of environmental contaminant exposure for residents in this setting. In other settings, contaminated food generally contributes much more substantially to human organochlorine burden than air or soil (which may be related to residential proximity to pollutant sources) [6]. We will investigate this issue in more detail in our ongoing study.

[serum <Organism_substance>] [meats <Organism_subdivision>] [blood <Organism_substance>] [serum <Organism_substance>] [serum <Organism_substance>] [serum <Organism_substance>] [serum sample <Organism_substance>] [fetal <Developing_anatomical_structure>] [blood samples <Organism_substance>] [samples <Organism_substance>] [sample <Organism_substance>] [body <Organism_subdivision>] [samples <Organism_substance>] [sample <Organism_substance>] [serum <Organism_substance>] [serum <Organism_substance>] [serum <Organism_substance>] [serum <Organism_substance>] [serum <Organism_substance>] [meat <Organism_subdivision>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Induction of apoptosis in skeletal tissues: phosphate-mediated chick chondrocyte apoptosis is calcium dependent. In an earlier study, we have shown that Pi induced apoptosis of terminally differentiated hypertrophic chondrocytes. To ascertain whether Ca2+ modulates Pi-induced cell death, we asked the following two questions: First, can we prevent Pi-induced apoptosis by removing Ca2+ from the culture medium; alternatively, can we potentiate cell death by increasing the Ca2+ concentration? Second, can we inhibit chondrocyte apoptosis by blocking Pi transport? We also explored the mechanism of apoptosis by evaluating mitochondrial activity and reactive oxygen species (ROS) generation in cells treated with the ion pair. We noted that EDTA and EGTA blocked Pi-induced apoptosis in a dose-dependent manner. While high levels of Ca2+ alone had little effect on chondrocyte viability, the cation enhanced Pi-dependent cell death and greatly increased Pi uptake. When Pi transport was blocked, there was complete inhibition of cell killing. The process of cell death was characterized by mitochondrial hyperpolarization; two hours following apoptogen treatment, there was a significant decrease in the mitochondrial membrane potential. Coincident with the changes in mitochondrial function, there was an increase in intracellular Ca2+ that was maintained throughout the experimental period. A raised Ca2+ signal was observed in blebs at the cell membrane. Finally, we noted that, 75 minutes after treatment with the ion pair, there was a six-fold elevation in ROS levels. This increase declined to baseline values after three hours. Based on these observations, we suggest that, at the cartilage mineralization front, an elevation in local environmental Ca2+ and Pi concentrations modulates oxidative metabolism, and triggers apoptosis of terminally differentiated chondrocytes.

[skeletal tissues <Tissue>] [chondrocyte <Cell>] [chondrocytes <Cell>] [cell <Cell>] [cell <Cell>] [chondrocyte <Cell>] [mitochondrial <Cellular_component>] [cells <Cell>] [chondrocyte <Cell>] [cell <Cell>] [cell <Cell>] [cell <Cell>] [mitochondrial <Cellular_component>] [mitochondrial membrane <Cellular_component>] [mitochondrial <Cellular_component>] [intracellular <Immaterial_anatomical_entity>] [cell membrane <Cellular_component>] [cartilage <Tissue>] [chondrocytes <Cell>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Confocal and scanning microscopic images of mammoth's and human hair. Taphonomic changes, indicated by arrow-heads and straight white arrow in the confocal image. Bacterial-fungal colonies are shown by broken arrows. Red arrow indicates space between cuticle and hair shaft due to shrinkage. Extensive taphonomic changes in YUK are evident. Note the preservation of the cuticle in the human hair in contrast to the craters in the cuticles of the mammoth's hair. Bacterial biofilms are a feature of human hair; mammoth's hair was protected from bacterial invasion in permafrost.

[hair <Multi-tissue_structure>] [hair shaft <Multi-tissue_structure>] [hair <Multi-tissue_structure>] [hair <Multi-tissue_structure>] [hair <Multi-tissue_structure>] [hair <Multi-tissue_structure>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

[Biotechnological and biomedical aspects of production and study of metal cation-phospholipid complexes]. Problems relating to the technology of a phospholipid preparation from natural materials, liposome production, and studies into the mechanisms of interaction between metal (trace elements) cations and model bilayer lipid membranes are discussed. The proposed technology of extraction allows for preparation of phospholipids utilizable for liposome formation. The cation specificity of lipid bilayers is found to be determined by the presence of anionic phosphate adsorption sites on their surface.

[bilayer lipid membranes <Cellular_component>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

[Treatment of squamous intraepithelial lesion of type CIN2 et CIN3 with laser CO2 vaporization: retrospective study of 52 cases]. OBJECTIVES: This study was carried out over an 8-year period in order to evaluate the long-term effectiveness of laser CO2 vaporization in the treatment of squamous intraepithelial lesion of type CIN2 and CIN3. MATERIALS AND METHODS: A retrospective study of 52 cases of cervical lesions of type CIN2 and CIN3 treated in first intention by laser CO2 vaporization was carried out at the hospital Jeanne-de-Flandre in CHRU of Lille from 1996 to 2003. This treatment was performed on only high-grade exo-cervical lesions, of small size (<2cm2), after a complete colposcopic examination. RESULTS: Fifty-two patients were treated by first-intention laser vaporization only. Mean age was 29.4 years and 51.9% were nulliparous. At the first cyto-colposcopic control, there were 17 persistent lesions (32.7%). Among the 35 patients without persistent lesion, 29 achieved cure (absence of recurrence), 4 presented a recurrence and 2 were lost to follow-up. CONCLUSION: The current data of the literature concerning the treatment by laser CO2 vaporization authorize application of this method for certain high-grade exocervical lesions after a complete colposcopic examination. This type of treatment remains less aggressive than a surgical treatment. The high rate of residual lesions in particular in the event of CIN3 can be due to an incomplete destruction of the lesion. Patients should thus be advised that monitoring is an integral part of the treatment. Laser vaporization could be limited to CIN1 and CIN2 lesions.

[squamous intraepithelial lesion <Pathological_formation>] [squamous intraepithelial lesion <Pathological_formation>] [cervical lesions <Pathological_formation>] [exo-cervical lesions <Pathological_formation>] [lesions <Pathological_formation>] [lesion <Pathological_formation>] [exocervical lesions <Pathological_formation>] [lesions <Pathological_formation>] [lesion <Pathological_formation>] [lesions <Pathological_formation>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Abbreviations Ac-DEVD-AMC = N-acetyl-Asp-Glu-Val-Asp-7-amino-4-methylcoumarin; Ac-DEVD-CHO = N-acetyl-Asp-Glu-Val-Asp-aldehyde; COX = cyclooxygenase; Deltapsim = mitochondrial membrane potential; DAPI = 4',6-diamidino-2-phenylindole; DMEM = Dulbecco's modified Eagle's medium; ELISA = enzyme-linked immunosorbent assay; FCS = fetal calf serum; FLS = fibroblast-like synoviocytes; IL = interleukin; JC-1 = 5,5',6,6'-tetrachloro-1,1',3,3'-tetraethylbenzimidazole carbocyanide iodide; MTT = 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide; PBS = phosphate-buffered saline; PGE2 = prostaglandin E2; RA = rheumatoid arthritis.

[mitochondrial membrane <Cellular_component>] [fetal <Developing_anatomical_structure>] [serum <Organism_substance>] [FLS <Cell>] [fibroblast-like synoviocytes <Cell>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

MoClo cloning protocol Restriction-ligations were set up by pipetting in one tube approximately 40 fmol (~100 ng of DNA for a 4 kb plasmid) of each DNA component (PCR product or plasmid), 10 U of the required restriction enzyme (BsaI or BpiI) and 10 U T4 DNA ligase (using high concentration ligase, 20 U/microl) in Promega ligation buffer in a final reaction volume of 20 microl. The reaction was incubated in a thermocycler for 5 hours at 37degreesC, 5 min at 50degreesC and 10 min at 80degreesC. The reaction mix was then added to 100 microl chemically competent DH10b cells, incubated for 15-30 min on ice and transformed by heat shock. 800 microl of liquid LB was then added to the transformation, and the cells were let to recover 45 min at 37degreesC. Different aliquots of the transformation were plated on LB plates containing the appropriate antibiotic. The number of colonies was counted for one or two selected plates (containing countable number of colonies), or from a section of the plates when very high number of colonies were obtained even for the lowest volume plated. The number of colonies was then extrapolated for the entire transformation. For level 2-2 cloning, two type IIS enzymes were required, BpiI and BsaI. The same protocol was used as described above except that 10 U and 2.5 U were used for the enzymes BpiI and BsaI, respectively. To optimize efficiency of the restriction-ligation for the final construct containing 11 transcription units (cL2-13*), a variation of this protocol was used as follows. The reaction mix was set up containing 20 U ligase, 5 U BpiI and 5 U BsaI, in a total reaction volume of 20 microl. The mix was incubated in a thermocycler with the following parameters: incubation for 2 minutes at 37degreesC, 5 minutes at 16degreesC, both steps repeated 45 times, followed by incubation for 5 minutes at 50degreesC and 10 minutes at 80degreesC. The reaction mix was transformed in E. coli chemically competent cells as described above.

[DH10b cells <Cell>] [cells <Cell>] [competent cells <Cell>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

(a) Schematic drawing of the magnetic tweezers. A DNA molecule is attached at one end to the bottom of the flow cell and at the other end to a magnetic bead. This molecule can be pulled and twisted using small magnets placed above the flow cell. The position of the magnetic bead is measured using an inverted microscope placed beneath the flow cell. The bead position and thus the end-to-end distance of the DNA molecule is determined using video microscopy and image analysis. (b) Extension of a DNA molecule versus the number of turns applied by the magnets for various stretching forces. At low force, contraction of the molecule is symmetrical under positive and negative applied turns. At higher force, the molecule's extension initially remains constant for positive applied turns. The induced torque increases linearly with the number of applied turns, as depicted in the top graph until a buckling transition allows the system to saturate its torsional constraint through the formation of plectonemes.

[cell <Cell>] [cell <Cell>] [cell <Cell>] [plectonemes <Cellular_component>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Epstein-Barr virus-associated nonsmall cell lung carcinoma: undifferentiated "lymphoepithelioma-like" carcinoma as a distinct entity with better prognosis. BACKGROUND: Epstein-Barr virus (EBV) infection in nonsmall cell lung carcinoma (NSCLC) has been demonstrated in some ethnic groups. The pathobiology and the role of EBV and oncoprotein expression in these tumors have not been studied extensively. In this study, the authors investigated EBV-encoded RNA-1 (EBER1) transcripts by in situ hybridization and the expression of latent membrane protein-1 (LMP-1) and bcl-2 protein by immunohistochemistry in NSCLC patients from Taiwan, where nasopharyngeal carcinoma is endemic. METHODS: A total of 127 cases of NSCLC (43 cases of squamous cell carcinoma [SCC], 67 cases of adenocarcinoma [AD], 12 cases of large cell carcinoma [LCC], and 5 cases of lymphoepithelioma-like carcinoma [LE]) were included. A sensitive polymerase chain reaction-derived, digoxigenin-labeled DNA probe for in situ detection of EBER1 transcripts was performed for the detection of EBV. Immunohistochemistry using the avidin-biotin-immunoperoxidase method was also performed to evaluate the expression of bcl-2 and LMP-1. RESULTS: EBER1 was detected in 11 of the 127 NSCLC cases (8.7%; 6 SCC cases and 5 LE cases). All 5 LE cases were EBV-positive, whereas only 6 of the 43 SCC cases (14%), 0 of 67 AD cases, and 12 LCC cases were EBV-positive (P < 0.05). All five LE cases showed diffuse, strong, positive staining of tumor cells; five of the six SCC cases showed diffuse but weak staining. Among the nontumor epithelial cells, there was no EBER1 staining of any of the 11 EBER1-positive cases. The mean age of the LE patients was 10 years younger than that of the patients with other histological types. All 5 LE patients were nonsmokers, whereas 3 of the 6 patients with EBER1-positive SCC (50%) were smokers. EBER1 expression did not correlate with the 2-year survival rate of overall cases, but all 5 LE patients were alive without clinical evidence of disease at last follow-up. Gender, lymph node or distant metastasis, and clinical stage were not found to have any correlation with EBER1 expression (P > 0.05). All LE cases had bcl-2 oncoprotein expression (100%). This frequency was significantly different from other histologic types (P < 0.05). The LMP-1 detection rate was low and demonstrated no correlation with bcl-2 expression. CONCLUSIONS: In this study, the authors found that the primary LE of the lung is associated with young age, a history of not smoking, high bcl-2 immunoreactivity, and better survival rate. These characteristics demonstrate that EBV-associated LE of the lung is a unique entity. The findings of the current study suggest that EBV infection may play a different role in the tumorigenesis of primary LE of the lung than it does in other EBER1-positive NSCLCs.

[nonsmall cell lung carcinoma <Pathological_formation>] ["lymphoepithelioma-like" carcinoma <Pathological_formation>] [nonsmall cell lung carcinoma <Pathological_formation>] [NSCLC <Pathological_formation>] [tumors <Pathological_formation>] [NSCLC <Pathological_formation>] [nasopharyngeal carcinoma <Pathological_formation>] [NSCLC <Pathological_formation>] [squamous cell carcinoma <Pathological_formation>] [SCC <Pathological_formation>] [adenocarcinoma <Pathological_formation>] [AD <Pathological_formation>] [large cell carcinoma <Pathological_formation>] [LCC <Pathological_formation>] [lymphoepithelioma-like carcinoma <Pathological_formation>] [LE <Pathological_formation>] [NSCLC <Pathological_formation>] [SCC <Pathological_formation>] [LE <Pathological_formation>] [LE <Pathological_formation>] [SCC <Pathological_formation>] [AD <Pathological_formation>] [LCC <Pathological_formation>] [LE <Pathological_formation>] [tumor cells <Cell>] [SCC <Pathological_formation>] [nontumor epithelial cells <Cell>] [LE <Pathological_formation>] [LE <Pathological_formation>] [SCC <Pathological_formation>] [LE <Pathological_formation>] [lymph node <Multi-tissue_structure>] [LE <Pathological_formation>] [LE <Pathological_formation>] [lung <Organ>] [LE <Pathological_formation>] [lung <Organ>] [LE <Pathological_formation>] [lung <Organ>] [EBER1-positive NSCLCs <Pathological_formation>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

An unusual case of benign mucous membrane pemphigoid. This case of benign mucous membrane pemphigoid (BMMP) is unusual in that blistering, scarring lesions were confined to the skin for 15 years before mucous membranes were involved. The onset of this disorder at the age of 38 is also unusual. Detailed immunological investigation was performed on this patient but the results in no way clarify the present confusion regarding the immunopathological processes in BMMP related to those operative in bullous pemphigoid.

[mucous membrane <Multi-tissue_structure>] [mucous membrane <Multi-tissue_structure>] [lesions <Pathological_formation>] [skin <Organ>] [mucous membranes <Multi-tissue_structure>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Heart sound and electrocardiogram recording devices for telemedicine environments. There is currently a worldwide trend to bring healthcare services as close as possible to the patient, either through home healthcare systems, or telemedicine. There is thus a general need for equipment that can capture patient data electronically for automated review or analysis by a medical practitioner. This paper presents prototype systems that were developed with the ultimate aim for use in telemedicine settings in rural Africa. These devices can be used to electronically capture data on patients from several sensors in a quick an easy manner. In our presented cases we focus on cardiovascular information. One of the main advantages of the proposed systems is that the data are captured simultaneously from multiple sensors. The data can be stored and sent electronically for review and analysis, and knowledge-based systems or neural network type models can be used in the future for semi-autonomous screening of the recordings, before a patient is referred to a specialist.

[Heart <Organ>] [cardiovascular <Anatomical_system>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Introduction Hip fractures in the aged constitute a major health problem with substantial morbidity [1], mortality [2, 3], and, as the ageing population increases, an increasing burden on the health care system [4]. Fracture risk varies markedly between countries [5]. In a study by Kanis et al. [6], comparing 10-year probability of hip fracture, all countries except Norway had lower risk than Sweden. Other countries categorized at very high risk (>75% of the risk of Sweden) were Iceland, Denmark and the US. At the age of 80, the estimated probability of sustaining a hip fracture the next 10 years is 8.6% and 17.7% in Norwegian men and women, respectively [7], and a report from the Norwegian capital Oslo calculated an overall annual fracture rate of 118.0 in women and 44.0 in men per 10,000 [8]. Several recent studies are reporting declining fracture incidence [9-14]. Although the Norwegian hip fracture rates remain the highest reported in the world, data from Oslo in 1996-1997 indicated no increasing incidence rates compared to the 1988-1989 [8].Within Norway, considerable geographic differences have been reported, with substantially lower rates in smaller cities and rural areas compared to Oslo [7, 15]. However, these are reports based on sporadic studies in few regions and in limited time periods [16, 17]. From 1985 to 2003, the Norwegian Institute of Public Health commissioned four Norwegian hospitals, representing 10% of the population, to run a national injury registry [18]. The registry collected a variety of data connected to the actual injury itself and the event leading to the injury. In the city of Harstad in Northern Norway, the registration continued and has been running for more than 23 years. Throughout the years of the National Injury Registry, the injury rates in Harstad closely resembled the rates of the national registry [18]. With reference to the recent reports suggesting stabilizing hip fracture incidence internationally as well as nationally, and regional differences within Norway, we have used the hip fracture data in the Harstad Injury Registry to: Describe age- and sex-specific incidence of hip fractures in Harstad, Northern Norway and make comparison with rates from the Norwegian capital Oslo Describe time trends in hip fracture incidence in Harstad from 1994 to 2008 Describe place of injury and seasonal variations in hip fracture incidence in Harstad Compare 3-month, 6-month, and 1-year mortality after hip fracture between women and men in Harstad

[Hip <Organism_subdivision>] [hip <Organism_subdivision>] [hip <Organism_subdivision>] [hip <Organism_subdivision>] [hip <Organism_subdivision>] [hip <Organism_subdivision>] [hip <Organism_subdivision>] [hip <Organism_subdivision>] [hip <Organism_subdivision>] [hip <Organism_subdivision>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Hypocholesterolaemic and antioxidant effects of Glycyrrhiza glabra (Linn) in rats. The hypocholesterolaemic and antioxidant effects of Glycyrrhiza glabra (GG) root powder were examined in hypercholesterolaemic male albino rats. A 4-week administration of GG root powder (5 and 10 gm% in diet) to hypercholesterolaemic rats resulted in significant reduction in plasma, hepatic total lipids, cholesterol, triglycerides and plasma low-density lipoprotein and VLDL-cholesterol accompanied by significant increases in HDL-cholesterol levels. Furthermore, significant increases in fecal cholesterol, neutral sterols and bile acid excretion along with an increase in hepatic HMG-CoA reductase activity and bile acid production were observed in these animals. The root powder administration to hypercholesterolaemic rats also decreased hepatic lipid peroxidation with a concomitant increase in superoxide dismutase (SOD) and catalase activities and total ascorbic acid content. Thus, the hypocholesterolaemic and antioxidant effects of GG root appeared to be mediated via (i) accelerated cholesterol, neutral sterol and bile acid elimination through fecal matter with an increased hepatic bile acid production and (ii) improving the activities of hepatic SOD, catalase and increasing the ascorbic acid content. The normo-cholesterolaemic animals when fed with GG root powder at 10 gm% level, registered a significant decline in plasma lipid profiles and an increase in HDL-cholesterol content. The antioxidant status of these animals also was improved upon treatment.

[root <Organ>] [root <Organ>] [plasma <Organism_substance>] [hepatic <Organ>] [plasma <Organism_substance>] [fecal <Organism_substance>] [hepatic <Organ>] [root <Organ>] [hepatic <Organ>] [root <Organ>] [fecal matter <Organism_substance>] [hepatic <Organ>] [hepatic <Organ>] [root <Organ>] [plasma <Organism_substance>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Pharmacokinetic-pharmacodynamic analysis. The mean (90% CI) slope estimate from the linezolid concentration-R-R interval analysis was -0.0017 (-0.0022 to -0.0011) ms/ng/ml. This translates to mean (90% CI) predicted decreases in heart rate of approximately 1.5 (1.0 to 2.0) and 3.0 (2.1 to 4.1) beats/min at the mean Cmax following the administration of 600- and 1,200-mg linezolid doses, respectively. The study-specific mean correction factor estimated from baseline data was 0.278, which is slightly less than Fridericia's correction (0.333). Evaluation of the various correction factors showed that QTcF most appropriately resolves the relationship between the QT interval and the heart rate in the baseline data from the present study. This is evident upon inspection of Fig. 4, since the slope between the QTcF interval and the R-R interval is closest to zero when this correction is applied. Fig. 4. Evaluation of various heart rate correction factors for the QT interval versus the R-R interval. The predicted line in each figure represents the fit from a linear mixed-effect model with R-R interval as a fixed effect and subject-specific random effects for intercept and slope. The results from the concentration-QTcF analysis are graphically depicted in Fig. 5. The mean (90% CI) slope estimate from the linezolid concentration-QTcF analysis was -0.0145 (-0.0768 to 0.0477) ms/mug/ml. At the geometric mean Cmax following the infusion of linezolid at 600 mg (14.9 mug/ml) and 1,200 mg (30.5 mug/ml), the mean (90% CI) predicted placebo-adjusted changes from the baseline QTcF were -0.217 (-1.14 to 0.710) and -0.444 (-2.34 to 1.45) ms, respectively, thus confirming a lack of a relationship between linezolid concentrations and QTc interval. Fig. 5. QTcF interval versus plasma linezolid concentrations.

[heart <Organ>] [heart <Organ>] [heart <Organ>] [plasma <Organism_substance>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Sickle cell disease: continuous arterial spin-labeling perfusion MR imaging in children. Cerebral blood flow (CBF) was measured with continuous arterial spin-labeling perfusion magnetic resonance (MR) imaging in 14 children with sickle cell disease and seven control subjects. Mean CBF values were higher in patients (P <.005) than in control subjects in all cerebral artery territories. Three patients had decreased CBF in right anterior and middle cerebral artery territories compared with CBF on the left, and one patient had a profound decrease in CBF in all three territories in the right hemisphere. Baseline CBF was significantly decreased in territories seen as unaffected on conventional MR images and MR angiograms in four children with sickle cell disease.

[Sickle cell <Cell>] [arterial <Multi-tissue_structure>] [Cerebral <Organ>] [blood <Organism_substance>] [arterial <Multi-tissue_structure>] [sickle cell <Cell>] [cerebral artery <Multi-tissue_structure>] [right anterior <Multi-tissue_structure>] [cerebral artery <Multi-tissue_structure>] [right hemisphere <Organism_subdivision>] [sickle cell <Cell>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

A generative model for image segmentation based on label fusion. We propose a nonparametric, probabilistic model for the automatic segmentation of medical images, given a training set of images and corresponding label maps. The resulting inference algorithms rely on pairwise registrations between the test image and individual training images. The training labels are then transferred to the test image and fused to compute the final segmentation of the test subject. Such label fusion methods have been shown to yield accurate segmentation, since the use of multiple registrations captures greater inter-subject anatomical variability and improves robustness against occasional registration failures. To the best of our knowledge, this manuscript presents the first comprehensive probabilistic framework that rigorously motivates label fusion as a segmentation approach. The proposed framework allows us to compare different label fusion algorithms theoretically and practically. In particular, recent label fusion or multiatlas segmentation algorithms are interpreted as special cases of our framework. We conduct two sets of experiments to validate the proposed methods. In the first set of experiments, we use 39 brain MRI scans-with manually segmented white matter, cerebral cortex, ventricles and subcortical structures-to compare different label fusion algorithms and the widely-used FreeSurfer whole-brain segmentation tool. Our results indicate that the proposed framework yields more accurate segmentation than FreeSurfer and previous label fusion algorithms. In a second experiment, we use brain MRI scans of 282 subjects to demonstrate that the proposed segmentation tool is sufficiently sensitive to robustly detect hippocampal volume changes in a study of aging and Alzheimer's Disease.

[brain <Organ>] [white matter <Multi-tissue_structure>] [cerebral cortex <Multi-tissue_structure>] [ventricles <Multi-tissue_structure>] [subcortical structures <Multi-tissue_structure>] [brain <Organ>] [brain <Organ>] [hippocampal <Multi-tissue_structure>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Acute ablation of Langerhans cells enhances skin immune responses. Understanding the function of Langerhans cells (LCs) in vivo has been complicated by conflicting results from LC-deficient mice. Human Langerin-DTA mice constitutively lack LCs and develop exaggerated contact hypersensitivity (CHS) responses. Murine Langerin-diphtheria toxin receptor (DTR) mice allow for the inducible elimination of LCs and Langerin(+) dermal dendritic cells (dDCs) after administration of diphtheria toxin, which results in reduced CHS. When Langerin(+) dDCs have partially repopulated the skin but LCs are still absent, CHS returns to normal. Thus, LCs appear to be suppressive in human Langerin-DTA mice and redundant in murine Langerin-DTR mice. To determine whether inducible versus constitutive LC ablation explains these results, we engineered human Langerin-DTR mice in which diphtheria toxin ablates LCs without affecting Langerin(+) dDCs. The inducible ablation of LCs in human Langerin-DTR mice resulted in increased CHS. Thus, LC-mediated suppression does not require their absence during ontogeny or during the steady-state and is consistent with a model in which LCs actively suppress Ag-specific CHS responses.

[Langerhans cells <Cell>] [skin <Organ>] [Langerhans cells <Cell>] [LCs <Cell>] [LC <Cell>] [LCs <Cell>] [LCs <Cell>] [Langerin(+) dermal dendritic cells <Cell>] [dDCs <Cell>] [Langerin(+) dDCs <Cell>] [skin <Organ>] [LCs <Cell>] [LCs <Cell>] [LC <Cell>] [LCs <Cell>] [Langerin(+) dDCs <Cell>] [LCs <Cell>] [LC <Cell>] [LCs <Cell>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Basilar papilla The basilar papilla is found in a recess that opens into the saccular space at one end, and is limited by a thin contact membrane at the other. The contact membrane separates the endolymphatic fluid in the papillar recess from the perilymphatic fluid at the round window (Lewis and Narins 1999; Wever 1985). The recess perimeter is roughly oval in shape; in the bullfrog, Rana catesbeiana, its major axis is approximately 200 mum long, while the minor axis measures approximately 150 mum (Van Bergeijk 1957). In the leopard frog, Rana pipiens pipiens, it is of similar size (personal observation, RLMS & JMS). The oval perimeter of the lumen is formed from limbic tissue; a substance unique to the inner ear, and similar to cartilage (Wever 1985). The sensory epithelium is approximately 100 mum long. It occupies a curved area that is symmetrical in the major axis of the elliptical lumen. It contains approximately 60 hair cells (measured in Rana catesbeiana), from which the stereovilli protrude into the lumen and connect to the tectorial membrane (Frishkopf and Flock 1974). Typically the orientation of the hair cells, as defined by the direction to which the v-shape of the stereovilli bundle points (Lewis et al. 1985), is away from the sacculus in Ranidae. The tectorial membrane spans the lumen of the papillar recess. It occludes about half the lumen, and consequently takes an approximately semi-circular shape when viewed from the saccular side (Frishkopf and Flock 1974; Wever 1985). The membrane has pores at the surface closest to the epithelium, into which the tips of the hair bundles project (Lewis and Narins 1999).4

[Basilar papilla <Multi-tissue_structure>] [basilar papilla <Multi-tissue_structure>] [saccular space <Immaterial_anatomical_entity>] [contact membrane <Multi-tissue_structure>] [contact membrane <Multi-tissue_structure>] [endolymphatic fluid <Organism_substance>] [papillar <Multi-tissue_structure>] [perilymphatic fluid <Organism_substance>] [lumen <Immaterial_anatomical_entity>] [limbic tissue <Tissue>] [inner ear <Multi-tissue_structure>] [cartilage <Tissue>] [sensory epithelium <Tissue>] [elliptical lumen <Immaterial_anatomical_entity>] [hair cells <Cell>] [stereovilli <Cellular_component>] [lumen <Immaterial_anatomical_entity>] [tectorial membrane <Multi-tissue_structure>] [hair cells <Cell>] [stereovilli <Cellular_component>] [sacculus <Multi-tissue_structure>] [tectorial membrane <Multi-tissue_structure>] [lumen <Immaterial_anatomical_entity>] [papillar <Multi-tissue_structure>] [lumen <Immaterial_anatomical_entity>] [saccular <Multi-tissue_structure>] [membrane <Multi-tissue_structure>] [epithelium <Tissue>] [hair <Multi-tissue_structure>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Oesophageal candidiasis and croup in a child with defective neutrophil motility. Severe oesophageal candidiasis and croup due to involvement of the larynx developed insidiously in a girl aged 20 months. There had been delayed separation of the umbilical cord and repeated infections associated with a defect of neutrophil motility. The significance of the early clinical features was not fully appreciated and the diagnosis considered only when stricture of the oesophagus became evident. She was treated with oral ketoconazole 100 mg daily. After one month's treatment there was striking radiological improvement apart from the persistence of the oesophageal stricture. The croup resolved completely but there was only partial relief of dysphagia because of the residual stricture. We would emphasis that candidiasis should be anticipated and treated vigorously in children with such a defect of neutrophil motility.

[Oesophageal <Organ>] [neutrophil <Cell>] [oesophageal <Organ>] [larynx <Multi-tissue_structure>] [neutrophil <Cell>] [oesophagus <Organ>] [oesophageal <Organ>] [neutrophil <Cell>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Immunoglobulins associated with elevated riboflavin binding by plasma from cancer patients. Plasma from 182 patients with different malignant diseases was tested for riboflavin binding by immunoglobulins, which have been recently identified as major carriers of this micronutrient. A wide range of binding (5.9 to 130 pmole/ml plasma) was observed, and significant elevations were found for patients having breast cancer (21.2 +/- 1.9, P less than 0.05) and melanoma (25.7 +/- 1.9, P less than 0.001) compared to controls (15.5 +/- 1.9). The proteins responsible for a majority of the higher binding were identified as immunoglobulins, based on their elution from gel filtration columns and the removal of 57-88% of the non-albumin binding by treating of plasma with Protein A-agarose. The binding was only weakly related to the total concentration of immunoglobulins (r = 0.11 by linear regression analysis), however, and is apparently due to a subclass that is elevated in some types of cancer. Elevated levels of these immunoglobulins may contribute to the lower urinary levels and clearance of riboflavin in cancer.

[plasma <Organism_substance>] [cancer <Pathological_formation>] [Plasma <Organism_substance>] [breast cancer <Pathological_formation>] [melanoma <Pathological_formation>] [plasma <Organism_substance>] [urinary <Organism_substance>] [cancer <Pathological_formation>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Neural network analysis of spectroscopic data of lycopene and beta-carotene content in food samples compared to HPLC-UV-vis. In this study a neural network (NN) model was designed to predict lycopene and beta-carotene concentrations in food samples, combined with a simple and fast technique, such as UV-vis spectroscopy. The measurement of the absorbance at 446 and 502 nm of different beta-carotene and lycopene standard mixtures was used to optimize a neural network based on a multilayer perceptron (MLP) (learning and verification process). Then, for validation purposes, the optimized NN has been applied to determine the concentration of both compounds in food samples (fresh tomato, tomato concentrate, tomato sauce, ketchup, tomato juice, watermelon, medlar, green pepper, and carrots), comparing the NN results with the known values of these compounds obtained by analytical techniques (UV-vis and HPLC). It was concluded that when the MLP-NN is used within the range studied, the optimized NN is able to estimate the beta-carotene and lycopene concentrations in food samples with an adequate accuracy, solving the UV-vis interference of beta-carotene and lycopene.

[concentrate <Organism_substance>] [juice <Organism_substance>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Inhibition of calmodulin-dependent myosin light-chain kinase by growth-hormone-releasing factor and vasoactive intestinal peptide. In view of the ability of calmodulin to bind vasoactive intestinal peptide (VIP) and growth-hormone-releasing factor (GRF) with high affinity [Stallwood, Brugger, Baggenstoss, Stemmer, Shiraga, Landers and Paul (1992) J. Biol. Chem. 267, 19617-19621], the effects of these neuropeptides on a model calmodulin-dependent enzyme, myosin light-chain kinase (MLCK), were studied. Both peptides were potent inhibitors of MLCK activity. The inhibition of enzyme activity by VIP and GRF was progressively overcome with increasing calmodulin concentrations, with no inhibition observed at a saturating calmodulin concentration. Nanomolar concentrations of MLCK blocked the formation of calmodulin-[125I-Tyr10]VIP complexes. These data provide support for a functional role of VIP and GRF binding by calmodulin.

[intestinal <Multi-tissue_structure>] [intestinal <Multi-tissue_structure>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Oscillatory alpha-band mechanisms and the deployment of spatial attention to anticipated auditory and visual target locations: supramodal or sensory-specific control mechanisms? Oscillatory alpha-band activity (8-15 Hz) over parieto-occipital cortex in humans plays an important role in suppression of processing for inputs at to-be-ignored regions of space, with increased alpha-band power observed over cortex contralateral to locations expected to contain distractors. It is unclear whether similar processes operate during deployment of spatial attention in other sensory modalities. Evidence from lesion patients suggests that parietal regions house supramodal representations of space. The parietal lobes are prominent generators of alpha oscillations, raising the possibility that alpha is a neural signature of supramodal spatial attention. Furthermore, when spatial attention is deployed within vision, processing of task-irrelevant auditory inputs at attended locations is also enhanced, pointing to automatic links between spatial deployments across senses. Here, we asked whether lateralized alpha-band activity is also evident in a purely auditory spatial-cueing task and whether it had the same underlying generator configuration as in a purely visuospatial task. If common to both sensory systems, this would provide strong support for "supramodal" attention theory. Alternately, alpha-band differences between auditory and visual tasks would support a sensory-specific account. Lateralized shifts in alpha-band activity were indeed observed during a purely auditory spatial task. Crucially, there were clear differences in scalp topographies of this alpha activity depending on the sensory system within which spatial attention was deployed. Findings suggest that parietally generated alpha-band mechanisms are central to attentional deployments across modalities but that they are invoked in a sensory-specific manner. The data support an "interactivity account," whereby a supramodal system interacts with sensory-specific control systems during deployment of spatial attention.

[parieto-occipital cortex <Multi-tissue_structure>] [cortex <Multi-tissue_structure>] [lesion <Pathological_formation>] [parietal regions <Organism_subdivision>] [parietal lobes <Multi-tissue_structure>] [neural <Multi-tissue_structure>] [scalp <Multi-tissue_structure>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Abdominal approach for the ligation of bleeding oesophageal varices. The conventional surgical treatment of bleeding oesophageal varices in the emergency situation is based upon the Boerema-Crile operation of transthoracic oesophagotomy and ligation of the varices. This and the other methods of treatment of this condition in current practice are discussed. Two cases are reported in which a transabdominal oesophagogastrotomy was used to approach the site of bleeding. This operation is described and the theoretical and practical advantages it appears to offer over the standard approach are considered.

[Abdominal <Organism_subdivision>] [oesophageal varices <Multi-tissue_structure>] [oesophageal varices <Multi-tissue_structure>] [transthoracic <Organism_subdivision>] [varices <Multi-tissue_structure>] [transabdominal <Organism_subdivision>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

The LHRH pulse generator: a mediobasal hypothalamic location. The location and mechanism of LHRH pulse generator are discussed based on our series of experiments. Suckling stimulus is a novel stimulus that inhibits LH pulses without any cooperation from ovarian steroids, unlike other stimuli such as stress, photoperiod etc. It is directly involved in suppressing the activity of the LHRH pulse generator. The information from teats suckled by pups or babies is conveyed dorsally to the mediobasal hypothalamus (MBH), where the LHRH pulse generator may be located. Experiments using various types of deafferentation and fetal brain tissue transplantation confirmed that the LHRH pulse generator is located in the MBH and suggested that LHRH pulse generator consists of nonLHRH neurons. Endogenous excitatory amino acid is one of the possible neurotransmitters that regulate LHRH release at the nerve terminal in ME.

[mediobasal hypothalamic <Multi-tissue_structure>] [ovarian <Organ>] [mediobasal hypothalamus <Multi-tissue_structure>] [fetal brain tissue <Tissue>] [nerve terminal <Multi-tissue_structure>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Neurologic diagnosis and treatment in patients with computed tomography and nasal endoscopy negative facial pain. OBJECTIVE: To determine the helpfulness of specialist neurology referral for patients with facial pain, a normal sinus computed tomography (CT) scan, and normal nasal endoscopy findings. STUDY DESIGN: Prospective identification of patients and analysis of data approved by the Institutional Review Board. METHODS: The data of 104 consecutive patients presenting with facial pain, a normal sinus CT scan, and normal nasal endoscopy findings were reviewed. The patients presented to a single rhinologist in a tertiary care institution. All patients were referred for specialist neurologic evaluation and potential treatment. Further information was obtained from a patient survey. RESULTS: Of the 104 patients, 81 were women and 23 were men. The average age was 46 years (range, 22-85). Fifty-six had clear CT scans, 48 had minimal change, and all had negative endoscopies. Twenty-nine had previous unsuccessful sinus surgery. The average follow-up period was 10.5 months. Forty of 75 patients seeing a neurologist were seen on multiple occasions. Four percent of patients seen by a neurologist had an unsuspected serious intracranial diagnosis. The most common diagnoses were migraine (37%), rebound headache (17%), chronic daily headache (17%), and obstructive sleep apnea (16%). Overall, 58% improved on medical therapy; 60% of those with a clear CT scan improved, and 53% of those with minimal change on CT scan improved (P = .749). CONCLUSIONS: Facial pain remains a difficult symptom to diagnose and treat in rhinologic practice. Patients often undergo surgery without help. Most patients with facial pain, a normal sinus CT scan, and normal endoscopy findings benefit from neurologic consultation. Serious intracranial pathologic conditions can be excluded and diagnosis-specific pharmacogenetic therapy instituted with improvement in more than 50%.

[nasal <Organism_subdivision>] [facial <Organism_subdivision>] [facial <Organism_subdivision>] [sinus <Immaterial_anatomical_entity>] [nasal <Organism_subdivision>] [facial <Organism_subdivision>] [sinus <Immaterial_anatomical_entity>] [nasal <Organism_subdivision>] [sinus <Immaterial_anatomical_entity>] [intracranial <Immaterial_anatomical_entity>] [Facial <Organism_subdivision>] [facial <Organism_subdivision>] [sinus <Immaterial_anatomical_entity>] [intracranial <Immaterial_anatomical_entity>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Neutrophil function in chronic neutrophilic leukemia: defective respiratory burst in response to phorbol esters. Functional analyses were performed on neutrophils isolated from 6 patients from two institutions who displayed features of chronic neutrophilic leukemia (CNL). These neutrophils demonstrated a consistent deficiency (44 +/- 8% of control values) in superoxide anion (O2-) production in response to the phorbol ester, phorbol myristate acetate (PMA). O2- production in response to chemotactic peptides was near normal (82.3 +/- 10.7% of control values). Bacterial killing was normal in the two patients studied, and chemotaxis was diminished in response to zymosan-activated plasma and to high concentrations of chemotactic peptides in the patients studied. Cytosolic C kinase activity was decreased in one of the two patients studied. These results suggest that a deficient O2- release in response to PMA is a hallmark of neutrophils in CNL and may provide a diagnostic indicator of this condition.

[Neutrophil <Cell>] [neutrophilic <Cell>] [respiratory <Anatomical_system>] [neutrophils <Cell>] [neutrophilic <Cell>] [neutrophils <Cell>] [plasma <Organism_substance>] [neutrophils <Cell>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Conclusions Myocardial ischaemia during DCMR is independently predictive of cardiac events among patients with previous myocardial revascularisation.

[Myocardial <Multi-tissue_structure>] [cardiac <Organ>] [myocardial <Multi-tissue_structure>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Endoscopic injection therapy for acute upper GI bleeding. In summary, we have found this technique to be useful in patients in whom coagulation therapy is not possible or effective. It must still be considered a technique which is undergoing evaluation. Prospective randomized trials comparing this therapy with other currently available therapies such a electrocoagulation, laser and conservative management must be completed to firmly define its place in treatment strategy for acute upper GI bleeding.

[upper GI <Organism_subdivision>] [upper GI <Organism_subdivision>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

3.2. Molecular Mechanisms Mediating the Perinatal Beta-Cell Adaptive Response to Early-Life Stressors Molecular mechanisms responsible for impaired beta-cell mass formation after IUCR or IUPR have come under investigation. First, it has been proposed that IUCR can result in a reduction of the embryonic beta-cell progenitor pool leading to inappropriate postnatal beta-cell formation. Stanger et al. [108] demonstrated that selective genetic reduction in the size of PDX-1+ pancreatic progenitors during the fetal period results in impaired beta-cell formation during the postnatal period with consequent development of glucose intolerance during adulthood. Consistent with this, maternal food restriction leads to significant reduction in PDX-1+ and neurogenin-3+ pancreatic precursors during embryonic development in rats, diminished postnatal beta-cell formation, and inability to expand beta-cell mass in response to pregnancy [47, 94]. The UPI model is also characterized by a permanent decrease in islet PDX-1 mRNA expression. This decrease has recently been shown to be due to progressive epigenetic silencing of the Pdx1 gene locus secondary to proximal promoter methylation [69, 109], and it may be responsible for the decreased rate of beta-cell replication and inappropriate postnatal beta-cell mass development [69, 110]. In the same way of thinking, studies have demonstrated that the maintenance of methylated histone H3 Lys4 by Set7/9, a member of the SET methyltransferase family, is crucial to Pdx1 activity in beta-cell lines [111-113]. This led to the hypothesis that Set7/9 may represent a novel chromatin-modifying protein that functions in part through its recruitment to target genes by cell-specific transcription factors such as Pdx1. Since then, a role of histone methyl transferases, particularly set7, has also been demonstrated in the sustained deleterious effects of chronic hyperglycemia on human microvascular endothelial cells [114]. Such an epigenetic change could potentially be involved in the deleterious effect of high glucose upon the fetal pancreas in the IUED models. Another mechanism proposed to explain reduced beta-cell formation after IUCR is related to prenatal glucocorticoid exposure. Administration of either dexamethasone or carbenoxolone (to inhibit 11 beta-hydroxysteroid dehydrogenase type 2) to normal pregnant rats also causes fetal growth retardation and the adult offspring are hypertensive and hyperglycemic, with hyperactive hypothalamic-pituitary-adrenal axis [115]. Maternal undernutrition significantly increased both fetal and maternal corticosterone concentrations in rats [116]. Subsequently, maternal and/or fetal overexposure to glucocorticoids (via administration of dexamethasone) impairs both fetal and postnatal beta-cell formation in rodents and nonhuman primates [94, 117-119]. Seckl et al. [115] have shown that fetal corticosterone concentrations are inversely correlated with fetal insulin content and postnatal beta-cell formation in rats. Evidence suggests that glucocorticoids can exert a direct effect on the developing fetal pancreas via transcriptional modulation of transcription factors involved in beta-cell formation and differentiation [117]. Glucocorticoid receptors are present in the pancreas during embryonic development of rodents and humans [117], and glucocorticoids can bind to the Pdx1 promoter and thus suppress fetal endocrine cell differentiation [117]. Glucocorticoid treatment has been shown to significantly reduce fetal expression of key endocrine transcription factors such as Pdx1 and Pax6 but simultaneously increase expression of transcription factors that regulate development of the exocrine pancreas [119]. It has also been demonstrated that the UPI or the low-protein IUPR offspring experience increased oxidative stress and impaired mitochondrial function [96, 120]. The mitochondrial dysfunction was not limited to just the beta cell, as mitochondria from both the liver and skeletal muscle exhibit decreased oxidation of pyruvate, subsequently leading to the development of features commonly found in T2D [100, 121]. Also exposure to a Western-style diet before and during pregnancy (an IUEO model) alters the redox state as early as preimplantation development, leading to mild oxidative stress associated with inflammation. The finding that administration of antioxidants to the dam reverses oxidative stress and completely prevents the development of glucose intolerance and increased adiposity in the adult offspring suggests that oxidative stress plays an important role in the development of adiposity in this case [122]. Some studies in the low-protein IUPR model have demonstrated that oxidative stress is not limited to just mitochondrial DNA damage, but also to genomic DNA, impacting cell-cycle regulation and gene expression [123]. While DNA is being targeted throughout by ROS, there are particular regions that are known to be more sensitive to ROS-mediated damage, for example, telomeres. Telomeres comprise GC-rich repeats and are found at the ends of each chromosome. They are known to shorten with each cellular division and, hence, can act as a mitotic clock, registering the number of replicative divisions to have taken place within the cell. Investigations using an IUPR model have indeed reported a decrease in longevity in the offspring [123, 124] accompanied by reduction in mitochondrial antioxidant defences [96, 125] and telomere length in islets [125]. Pancreatic islet development has been shown to be influenced by a number of growth factors including the insulin-like growth factors, IGF-I and IGF-II whose expression in utero is regulated by nutrient and hormone concentrations. IUPR modifies expression of both IGF genes in a variety of fetal tissues. In an IUPR rat model with a decreased beta-cell mass and beta-cell replication and an increased rate of beta-cell apoptosis, gene expression for IGF-II but not IGF-I was found reduced in the fetal pancreas [126]. In a different IUPR model with more severe global food restriction which induced hyperinsulinemia and an increase in beta-cell mass in their fetuses [90], the fetal phenotype was unexpectedly associated with an increase in pancreatic IGF-I expression, islet IGF-1R [91], and IRS-2 [92]. In the fetal GK/Par rat exposed to mild hyperglycemia during gestation (a model of IUED), data from our group suggest that the beta-cell deficit (reduced by more than 50%) starts as early as fetal age E16 and reflects decreased beta-cell proliferation, a limitation of beta-cell neogenesis from precursors, and increased apoptosis of both beta cells and their precursors [86]. Notably, Pdx1 and Neurogenin3 expression were decreased on E18 but normally expressed on E13 [86]. Defective signalling through the Igf2/Igf1-R pathway may represent the primary instrumental anomaly since Igf2 and Igf1-R protein expressions are already decreased within the GK/Par pancreatic rudiment at E13, at a time when beta-cell mass (first wave of beta-cell expansion) is in fact normal [31]. Low levels of pancreatic Igf2 associated with beta-cell mass deficiency are maintained thereafter within the fetal pancreas [87]. Crossbreeding protocols between nondiabetic W and diabetic GK rats showed that, in late gestation (E18), pancreatic Igf2 protein expression was as low in GKmother/GKfather and Wmother/GKfather crosses as in GKmother/GKfather crosses [87]. These findings rather support the hypothesis that the pancreatic Igf2 anomaly in the GK diabetic model is linked to a genetic determinism. This view is also consistent with the results of genetic analyses that linked a locus containing the gene encoding Igf2 to diabetes in the GK rat [127]. The Igf2 gene is subjected to paternal genomic imprinting. However, because the Igf2 expression is similarly affected in fetuses, regardless of whether the father is W or GK [87], we cannot conclude with a simple change of Igf2 gene imprinting in the GK rat. Finally, our understanding of the underlying mechanisms for reduced BCM in response to inappropriate perinatal nutrition is growing rapidly. However, the relative contribution of the many intrinsic and extrinsic factors which contribute to the adaptive response of the developing endocrine pancreas is still to be established.

[Beta-Cell <Cell>] [beta-cell <Cell>] [embryonic beta-cell <Cell>] [beta-cell <Cell>] [pancreatic <Organ>] [fetal <Developing_anatomical_structure>] [beta-cell <Cell>] [pancreatic <Organ>] [embryonic <Developing_anatomical_structure>] [beta-cell <Cell>] [beta-cell <Cell>] [islet <Multi-tissue_structure>] [beta-cell <Cell>] [beta-cell <Cell>] [beta-cell lines <Cell>] [cell <Cell>] [microvascular endothelial cells <Cell>] [fetal pancreas <Organ>] [beta-cell <Cell>] [fetal <Developing_anatomical_structure>] [hypothalamic <Organ>] [pituitary <Organ>] [adrenal <Organ>] [fetal <Developing_anatomical_structure>] [fetal <Developing_anatomical_structure>] [fetal <Developing_anatomical_structure>] [beta-cell <Cell>] [fetal <Developing_anatomical_structure>] [fetal <Developing_anatomical_structure>] [beta-cell <Cell>] [fetal pancreas <Organ>] [beta-cell <Cell>] [pancreas <Organ>] [embryonic <Developing_anatomical_structure>] [fetal endocrine cell <Cell>] [fetal <Developing_anatomical_structure>] [exocrine pancreas <Organ>] [mitochondrial <Cellular_component>] [mitochondrial <Cellular_component>] [beta cell <Cell>] [mitochondria <Cellular_component>] [liver <Organ>] [skeletal muscle <Organ>] [mitochondrial <Cellular_component>] [cell <Cell>] [cellular <Cell>] [cell <Cell>] [mitochondrial <Cellular_component>] [islets <Multi-tissue_structure>] [Pancreatic islet <Multi-tissue_structure>] [fetal tissues <Tissue>] [beta-cell <Cell>] [beta-cell <Cell>] [beta-cell <Cell>] [fetal pancreas <Organ>] [beta-cell <Cell>] [fetuses <Developing_anatomical_structure>] [fetal <Developing_anatomical_structure>] [pancreatic <Organ>] [islet <Multi-tissue_structure>] [fetal <Developing_anatomical_structure>] [beta-cell <Cell>] [fetal <Developing_anatomical_structure>] [beta-cell <Cell>] [beta-cell <Cell>] [beta cells <Cell>] [pancreatic rudiment <Organ>] [beta-cell <Cell>] [beta-cell <Cell>] [pancreatic <Organ>] [beta-cell <Cell>] [fetal pancreas <Organ>] [pancreatic <Organ>] [pancreatic <Organ>] [fetuses <Developing_anatomical_structure>] [endocrine pancreas <Organ>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Percutaneous coronary intervention for the very late stent thrombosis in right coronary artery. A: a balloon angioplasty was performed to treat total occlusion of the stented right coronary artery. B: final coronary angiogram showed good distal flow without residual stenosis.

[coronary <Multi-tissue_structure>] [right coronary artery <Multi-tissue_structure>] [right coronary artery <Multi-tissue_structure>] [coronary <Multi-tissue_structure>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Sensitivity analysis of the influence of source-term and environmental parameters on the radiological risk of coal-fired plants. A sensitivity analysis was undertaken to determine the influence of different source-term and environmental parameters on the radiological risks from a coal-fired plant (CFP). It was found that the release rate of radionuclides and the effective release height most significantly influence radiological risk. Site characteristics, such as rain scavenging coefficients and food acquirement habits, have a lesser influence, and some parameters, such as time delay before ingestion of contaminated food, have practically no influence on the radiological impact of a CFP. The contribution to radiation risks of different exposure modes (i.e. inhalation, ingestion and contact with ground surface) were also analyzed, as well as of specific radionuclides and human body organs. Results of the sensitivity analysis were interpreted in terms of the characteristics of the fuel, facilities and site of a CFP. It is concluded that by proper choice of coal, furnace, ash filtration and stack height, as well as by proper siting, the radiological impact of a CFP can be drastically reduced.

[body organs <Organ>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Involvement of de novo ceramide synthesis in radiocontrast-induced renal tubular cell injury. We reported previously that various radiocontrast media cause apoptosis in porcine proximal tubular (LLC-PK(1)) cells, in which reduction in B-cell lymphoma (Bcl)-2 expression and caspase-3 activation are implicated. In the present study, we investigated a role for ceramide in radiocontrast media-induced apoptosis in renal tubular cells. LLC-PK(1) cells were exposed to radiocontrast media for 30 min, followed by incubation for 24 h in normal medium. Cell viability was assessed by 2-(2-methoxy-4-nitrophenyl)-3-(4-nitrophenyl)-5-(2,4-disulfophenyl)-2H-tetrazolium monosodium salt assay, while apoptosis was determined by terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling stain. Immunofluorescent stains were performed using antibodies against phosphorylated Akt (pAkt) and cAMP response element binding protein (CREB) (pCREB), and ceramide. The mRNA expression and protein content of Bcl-2 were determined by reverse transcriptase-polymerase chain reaction and enzyme immunoassay, respectively. In vivo model of contrast-induced renal injury was induced in mice with unilateral renal occlusion. The cell injury induced by the nonionic radiocontrast medium ioversol was reversed by inhibiting de novo ceramide synthesis with fumonisin B(1) (FB(1)) and L-cycloserine, but not by suppressing sphingomyelin breakdown with D609. FB(1) reversed ioversol-induced decrease in the immunoreactivities of pAkt and pCREB, reduction in Bcl-2 expression and caspase-3 activation. Like ioversol, C2 ceramide and the Akt inhibitor Src homology-6 induced apoptosis by reducing pAkt and pCREB-like immunoreactivities, lowering Bcl-2 expression and enhancing caspase-3 activity. Indeed, various radiocontrast media, excluding iodixanol which showed the least nephrotoxicity, enhanced ceramide-like immunoreactivity. The role for de novo ceramide synthesis was also shown in the in vivo model of radiocontrast nephropathy. We demonstrated here for the first time that the enhancement of de novo ceramide synthesis contributes to radiocontrast nephropathy.

[renal tubular cell <Cell>] [proximal tubular (LLC-PK(1)) cells <Cell>] [renal tubular cells <Cell>] [LLC-PK(1) cells <Cell>] [Cell <Cell>] [renal <Organ>] [renal <Organ>] [cell <Cell>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Results primary pancreatic sarcomas are extremely rare. Pancreatic sarcomas are more aggressive than other pancreatic neoplasms.

[pancreatic sarcomas <Pathological_formation>] [Pancreatic sarcomas <Pathological_formation>] [pancreatic neoplasms <Pathological_formation>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

The Acute Dialysis Quality Initiative--part IV: membranes for CRRT. The extracorporeal membrane used in a continuous renal replacement therapy (CRRT) for the treatment of a critically ill patient with acute renal failure (ARF) is vitally important for several reasons, including its influence on biocompatibility and filter performance. The clinical relevance of membrane-related biocompatibility markers traditionally used in chronic hemodialysis remains unclear in CRRT. Numerous approaches may be used to assess membrane and filter performance in CRRT, but no specific methodology is accepted widely at present. Although a potential benefit of certain membranes used for CRRT is adsorptive removal of inflammatory mediators, this issue has not been assessed carefully in well-designed clinical trials. These and other issues should be the subject of future clinical research efforts.

[membranes <Multi-tissue_structure>] [extracorporeal membrane <Multi-tissue_structure>] [renal <Organ>] [renal <Organ>] [membrane <Multi-tissue_structure>] [membrane <Multi-tissue_structure>] [membranes <Multi-tissue_structure>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

[Anomalous origin of the right coronary artery from the left sinus of Valsalva: case report and literature review]. We describe the case of a patient in whom evaluation of effort angina revealed a tight stenosis of a right coronary artery anomalously arising from the left sinus of Valsalva, which was successfully treated by stent implantation. The abnormal origin of the right coronary artery from the left aortic sinus coursing between the aorta and the pulmonary trunk is a rare congenital anomaly. It may remain asymptomatic, but can also cause major cardiac events, even in the absence of coronary atherosclerosis. We discuss the clinical importance of this anomaly and review the literature concerning current views and therapy.

[right coronary artery <Multi-tissue_structure>] [sinus <Immaterial_anatomical_entity>] [right coronary artery <Multi-tissue_structure>] [sinus <Immaterial_anatomical_entity>] [right coronary artery <Multi-tissue_structure>] [aortic sinus <Immaterial_anatomical_entity>] [aorta <Multi-tissue_structure>] [pulmonary trunk <Multi-tissue_structure>] [cardiac <Organ>] [coronary <Multi-tissue_structure>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Management of extremity trauma and related infections occurring in the aquatic environment. Wounds sustained in oceans, lakes, and streams are exposed to a milieu of bacteria rarely encountered in typical land-based injuries. These include Vibrio species, Aeromonas hydrophila, Pseudomonas and Plesiomonas species, Erysipelothrix rhusiopathiae, Mycobacterium marinum, and other microbes. Failure to recognize and treat these less common pathogens in a timely manner may result in significant morbidity or death. Initial antibiotic therapy should address common gram-positive and gram-negative aquatic bacteria, depending on the environment. Trauma occurring in brackish or salt water should be treated with doxycycline and ceftazidime, or a fluoroquinolone (eg, ciprofloxacin or levofloxacin). Freshwater wounds should be managed with ciprofloxacin, levofloxacin, or a third- or fourth-generation cephalosporin (eg, ceftazidime). Injuries sustained in a marine or freshwater environment may result from bites or venomous stings of aquatic organisms as well as from accidental trauma. Musculoskeletal trauma caused by venomous underwater species (eg, stingrays, stinging fish, sea urchins, and coral) requires immediate neutralization of the heat-labile toxin with immersion in nonscalding water for 30 to 90 minutes. Appropriate management of aquatic wounds requires recognition of the mechanism of injury, neutralization of venom, antibiotic administration, radiographic assessment, surgical debridement with irrigation, wound cultures, and structural repair or amputation as indicated by the severity of the injury.

[Wounds <Pathological_formation>] [wounds <Pathological_formation>] [Musculoskeletal trauma <Pathological_formation>] [wounds <Pathological_formation>] [wound <Pathological_formation>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Effect of Trail on the expression of endogenous M2. (A) Effect of Trail on the level of endogenous M2 protein. The expression level of endogenous M2 protein in HeLa cells was determined using western blot 4 h following Trail (250 mug/ml) treatment. (B) Effect of Trail on the endogenous M2 mRNA. The expression level of endogenous M2 mRNA in HeLa cells was detected using RNase protection assay 4 h following Trail (250 mug/ml) treatment. (C) Effect of Trail on the synthesis of endogenous M2 protein. HeLa cells were first treated with 250 mug/ml Trail followed by pulse labeling of newly synthesized proteins with [35S]methionine. M2 protein was then immunoprecipitated and separated by SDS-PAGE for autoradiography as described in Materials and Methods.

[HeLa cells <Cell>] [HeLa cells <Cell>] [HeLa cells <Cell>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

[The assessment of flow velocity in carotid and intracranial arteries in three different age groups]. In this report we assess the systolic maximal flow velocity in carotid and intracranial arteries in 191 subjects with no history of cerebral vascular disease in 3 age groups: 20-40 years (1 group), 41-60 years (2 group), and above 60 years (3 group). The subjects were assessed using Sonomed Transcranial Doppler Spectrograph according to generally accepted principles. The purpose of the study was to establish the mean value of maximal flow velocity in each particular artery in three age groups, and to observe the changes in this parameter with age. The results were analyzed using statistical methods and a significant decrease in blood flow, Vmax, was found in all investigated arteries. A mean decrease of 8.02% in flow velocity Vmax was found, when comparing groups 2 and 1, and difference 15.99% comparing 3 and 1.

[carotid <Multi-tissue_structure>] [intracranial arteries <Multi-tissue_structure>] [carotid <Multi-tissue_structure>] [intracranial arteries <Multi-tissue_structure>] [cerebral vascular <Multi-tissue_structure>] [artery <Multi-tissue_structure>] [blood <Organism_substance>] [arteries <Multi-tissue_structure>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Antishock trousers: a collective review. Antishock trousers have become an integral part of emergency medical care for many traumatic and life-threatening emergencies. This article represents a summary of the current state of knowledge concerning the use of this device. A brief history of the development of antishock garments is discussed. This is followed by a discussion of human clinical studies and results of clinical research on hemodynamics, respiration, use in head injury, and effects on vascular hemostasis. Indications, contraindications, complications, and recommended procedure for use are discussed. Based on randomized prospective studies, antishock garments have not, as yet, been shown to improve patient morbidity or mortality. Proper use of antishock garments requires an understanding of both their function and their limitations.

[head <Organism_subdivision>] [vascular <Multi-tissue_structure>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

2.2. Iris and Ciliary Body Serotonin is present in mammalian iris-ciliary body complex (ICB) at higher concentration that in non-mammalian species [5, 45, 73, 129, 137]. Moreover, the presence of serotonergic nerves has been demonstrated in studies conducted on the ICB of various species [102, 137, 138]. Experimental evidence and radioligand analyses have defined the presence at this level of three different types of serotonin receptors [10, 28, 85, 136, 137], i.e. 5-HT1A, 5-HT2A/2C and 5-HT7 [98], one linked to a stimulation of inositol phosphates (5-HT2 subtype), while the others two are linked to cAMP activity. The plausibility of the existence of more than one 5-HT receptor type in the ciliary body is confirmed by intraocular pressure (IOP) experiments. Topical application of serotonin has been reported to both elevate [84] and lower [88] IOP in rabbit. A large number of reports have shown that serotonin agonists and antagonists can produce increases and decreases in IOP when given orally, topically to the eye or when they are directly injected in the anterior chamber [10, 26, 34, 35, 64, 75, 84, 87, 88, 112, 113, 126, 136, 137]. A rationale for such apparently contradictory results may be due to the different sites of action, i.e. which class of serotonin receptor is activated. In fact, in rabbit the administration of 5-methyl-urapidil (a combined 5-HT1A agonist/alpha1 adrenoreceptor antagonist) and 8-OH-DPAT (8-hydroxydypropylaminotetralin, a 5HT1A agonist) reduces IOP, while the administration of 5-CT (5-carboxamidotryptamine, a 5-HT1A and 5-HT7 agonist) increases IOP [36, 84, 99]. Chidlow, Le Corre and Osborne [28] have recently demonstrated that, in section taken through the whole eye and ciliary body, prominent 5-HT1A and 5-HT7 receptor messenger ribonucleic acid signals were obtained. These signals were evident in both the pigmented and non-pigmented epithelial cell layers of the pars plicata region of the ciliary processes, but not in the pars plana or in the ciliary musculature. 5-HT1A and 5-HT7 signals were apparent in the posterior processes but not in the iris processes. The presence of both receptors in the ciliary body would certainly provide an explanation for the shallow displacement curves observed in [3H]5-HT binding studies with the tissue [110], since this ligand can be used to label both receptors. Because the ciliary epithelium of the pars plicata is responsible for the secretion of aqueous humor, an obvious function for these two receptors would be an involvement in the control of aqueous production and, consequently, of the IOP level. Further, the almost identical distribution of the 5-HT1A and 5-HT7 messengers ribonucleic acid indicate that the receptors may be co-localized in epithelial cells. The presence of two serotonin receptors with opposing effects on cAMP in the same cell layer prompts the suggestion that they could act antagonistically. The agonism of 5-HT1A receptors, negatively coupled to cAMP, reduces IOP by decreasing the production of aqueous humor, like beta-receptor antagonists which, diminishing the content of cAMP at the postjunctional site, lowers the aqueous humor secretion with a consequent decrease in IOP [98]. On the contrary, the administration of 5-CT induces a rise in IOP, which is partly or entirely caused by an increase in aqueous humor secretion mediated by 5-HT7 receptors [84]. The other type of serotonin receptor present in the ICB is a 5-HT2 type. Serotonin stimulates the accumulation of inositol phosphates in the ICB and this effect is partially counteracted by the 5-HT2 antagonists ketanserin, methysergide and mianserin [98]. Studies with ketanserin have demonstrated that, when orally or topically applied, it lowers IOP in animals, healthy volunteers and in glaucomatous patients [26, 34, 37, 64, 75, 88, 113, 126]. It has been emphasized that ketanserin also possesses an affinity for alpha1-adrenoreceptors [27, 36, 139], and for this reason the effects of ketanserin on IOP may not be entirely caused by its action on 5-HT2 receptors. However, data from human studies conducted after oral or topical administration of ketanserin, in which were determined the variations of IOP, total outflow facility and pupil diameter, demonstrated that the alpha1-adrenoreceptor blocking effect exerted by ketanserin should represent a further aspect of its mechanism of action, probably due to a functional sharing of these receptors [64, 87]. Lastly, already in 1992 Martin and co-workers showed the occurrence of a significant correlation between the content of serotonin in the aqueous humor and IOP in the human eye [85]. In 1981, Moro and his collaborators found that intravitreal injection of 5, 6-dihydroxytryptamine, a serotonergic neurotoxin, causes miosis [91]. The identification of 5-HT7, but not of 5-HT1 receptors in the rabbit iris, suggests that this population of serotonergic receptors is involved in the relaxation of the sphincter of the pupil. In fact, one of the function correlate to 5-HT7 receptor activation includes smooth muscle relaxation observed in a variety of isolated tissue preparations, in which elevation of cAMP concentration was also detected [3, 44]. Further evidence for the mediation of the relaxant response via the 5-HT7 receptor is provided by the localization of messenger ribonucleic acid transcripts encoding the 5-HT7 receptor in many blood vessels [67]. This hypothesized mechanism of action is also supported by the fact that various other receptor types, also positively coupled to cAMP, in the iris cause relaxation of the sphincter muscle [1, 28].

[Iris <Multi-tissue_structure>] [Ciliary Body <Multi-tissue_structure>] [iris-ciliary body complex <Multi-tissue_structure>] [ICB <Multi-tissue_structure>] [nerves <Multi-tissue_structure>] [ICB <Multi-tissue_structure>] [ciliary body <Multi-tissue_structure>] [intraocular <Immaterial_anatomical_entity>] [eye <Organ>] [anterior chamber <Multi-tissue_structure>] [eye <Organ>] [ciliary body <Multi-tissue_structure>] [epithelial cell <Cell>] [pars plicata <Multi-tissue_structure>] [ciliary <Multi-tissue_structure>] [pars plana <Multi-tissue_structure>] [ciliary musculature <Multi-tissue_structure>] [iris <Multi-tissue_structure>] [ciliary body <Multi-tissue_structure>] [tissue <Tissue>] [ciliary epithelium <Tissue>] [pars plicata <Multi-tissue_structure>] [epithelial cells <Cell>] [cell <Cell>] [humor <Organism_substance>] [humor <Organism_substance>] [ICB <Multi-tissue_structure>] [ICB <Multi-tissue_structure>] [pupil <Multi-tissue_structure>] [humor <Organism_substance>] [eye <Organ>] [iris <Multi-tissue_structure>] [sphincter <Tissue>] [pupil <Multi-tissue_structure>] [smooth muscle <Tissue>] [tissue <Tissue>] [blood vessels <Multi-tissue_structure>] [iris <Multi-tissue_structure>] [sphincter muscle <Tissue>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Primary hyperparathyroidism and the heart: cardiac abnormalities correlated to clinical and biochemical data. Comparing patients with primary hyperparathyroidism (PHP) to a normocalcemic control population, those with PHP have a higher incidence of cardiovascular disease and cardiac abnormalities. This study aimed at correlating cardiac findings (valvular and myocardial calcification, myocardial hypertrophy) with clinical data (age, sex, clinical manifestation, nephrolithiasis, nephrocalcinosis, hypertension, skeletal abnormalities, hypercalcemic syndrome) and biochemical data (serum calcium, serum phosphate, serum iPTH level, serum creatinine). A group of 132 consecutive patients with surgically verified PHP (94 women, 38 men; ages 15-86, mean age 57 +/- 16 years) were included in this study. Blood chemistry, clinical presentation, radiography, and echocardiography were carried out in all patients for univariate and multivariate analyses of all parameters. There was no statistical correlation between clinical symptoms, biochemical data, and cardiac calcific alterations. Typical skeletal manifestations (osteolysis/subperiostal resorption) and valvular calcifications were significantly correlated to left ventricular hypertrophy (p = 0.005). Cardiac abnormalities such as calcific myocardial deposits or mitral and aortic valvular calcifications do not correlate with laboratory findings and clinical presentation at the time of diagnosis. There was no biochemical or clinical variable that could predict the frequency or severity of valvular sclerosis or calcific deposits in the myocardium. However, PHP-related skeletal abnormalities and valvular calcification were predicting factors for left ventricular hypertrophy, a reversible cardiac manifestation of PHP. Myocardial hypertrophy is more often found with classic symptomatic PHP with osseous abnormalities.

[heart <Organ>] [cardiac <Organ>] [cardiovascular <Multi-tissue_structure>] [cardiac <Organ>] [cardiac <Organ>] [valvular <Multi-tissue_structure>] [myocardial <Multi-tissue_structure>] [myocardial <Multi-tissue_structure>] [skeletal <Anatomical_system>] [serum <Organism_substance>] [serum <Organism_substance>] [serum <Organism_substance>] [serum <Organism_substance>] [Blood <Organism_substance>] [cardiac <Organ>] [skeletal <Anatomical_system>] [valvular <Multi-tissue_structure>] [left ventricular <Multi-tissue_structure>] [Cardiac <Organ>] [myocardial <Multi-tissue_structure>] [mitral <Multi-tissue_structure>] [aortic valvular <Multi-tissue_structure>] [valvular <Multi-tissue_structure>] [myocardium <Multi-tissue_structure>] [skeletal <Anatomical_system>] [valvular <Multi-tissue_structure>] [left ventricular <Multi-tissue_structure>] [cardiac <Organ>] [Myocardial <Multi-tissue_structure>] [osseous <Organ>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Background Previous publications indicate that acupuncture is efficient for the treatment of pelvic girdle pain, PGP, in pregnant women. However, the use of acupuncture for PGP is rare due to insufficient documentation of adverse effects of this treatment in this specific condition. The aim of the present work was to assess adverse effects of acupuncture on the pregnancy, mother, delivery and the fetus/neonate in comparison with women that received stabilising exercises as adjunct to standard treatment or standard treatment alone.

[pelvic girdle <Multi-tissue_structure>] [fetus <Developing_anatomical_structure>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Abbreviations ARDS: acute respiratory distress syndrome; CMV: conventional mechanical ventilation; HFOV: high-frequency oscillation ventilation; LPS: lipopolysaccharide; PEEP: positive end-expiratory pressure; VILI: ventilator-induced lung injury.

[respiratory <Anatomical_system>] [lung <Organ>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Multicentre study on peri- and postoperative central venous oxygen saturation in high-risk surgical patients. INTRODUCTION: Low central venous oxygen saturation (ScvO2) has been associated with increased risk of postoperative complications in high-risk surgery. Whether this association is centre-specific or more generalisable is not known. The aim of this study was to assess the association between peri- and postoperative ScvO2 and outcome in high-risk surgical patients in a multicentre setting. METHODS: Three large European university hospitals (two in Finland, one in Switzerland) participated. In 60 patients with intra-abdominal surgery lasting more than 90 minutes, the presence of at least two of Shoemaker's criteria, and ASA (American Society of Anesthesiologists) class greater than 2, ScvO2 was determined preoperatively and at two hour intervals during the operation until 12 hours postoperatively. Hospital length of stay (LOS) mortality, and predefined postoperative complications were recorded. RESULTS: The age of the patients was 72 +/- 10 years (mean +/- standard deviation), and simplified acute physiology score (SAPS II) was 32 +/- 12. Hospital LOS was 10.5 (8 to 14) days, and 28-day hospital mortality was 10.0%. Preoperative ScvO2 decreased from 77% +/- 10% to 70% +/- 11% (p < 0.001) immediately after surgery and remained unchanged 12 hours later. A total of 67 postoperative complications were recorded in 32 patients. After multivariate analysis, mean ScvO2 value (odds ratio [OR] 1.23 [95% confidence interval (CI) 1.01 to 1.50], p = 0.037), hospital LOS (OR 0.75 [95% CI 0.59 to 0.94], p = 0.012), and SAPS II (OR 0.90 [95% CI 0.82 to 0.99], p = 0.029) were independently associated with postoperative complications. The optimal value of mean ScvO2 to discriminate between patients who did or did not develop complications was 73% (sensitivity 72%, specificity 61%). CONCLUSION: Low ScvO2 perioperatively is related to increased risk of postoperative complications in high-risk surgery. This warrants trials with goal-directed therapy using ScvO2 as a target in high-risk surgery patients.

[central venous <Multi-tissue_structure>] [central venous <Multi-tissue_structure>] [abdominal <Organism_subdivision>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Melanoma/skin cancer screening clinics: experiences in The Netherlands. In 1989 and 1990 we conducted two free melanoma/skin screening clinics in Oss and Arnhem in the Netherlands. The study was carried out along the lines of the recent campaigns supported by the American Academy of Dermatology. Of 2564 persons screened, 53 had melanoma or nonmelanoma skin cancer (2.1%). Compliance with follow-up for persons with suspected melanoma/skin cancer was adequate (93 of 103; 90.3%).

[Melanoma <Pathological_formation>] [skin cancer <Pathological_formation>] [melanoma <Pathological_formation>] [skin <Organ>] [melanoma <Pathological_formation>] [nonmelanoma skin cancer <Pathological_formation>] [melanoma <Pathological_formation>] [skin cancer <Pathological_formation>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

2.1. Biological samples Placental tissues from the first trimester legally induced abortions (8-12 weeks of gestation) were obtained from the Department of Obstetrics and Gynecology at the Broussais, Saint Vincent de Paul and Cochin Hospitals. Second trimester placental tissues were collected at the time of termination of pregnancy at 15 and 25 weeks of gestation (in weeks of amenorrhea) in trisomy 21-affected pregnancies. Fetal Down syndrome was diagnosed by karyotyping of amniotic fluid cells. The indication of amniocentesis was the maternal age. Term placentas were obtained after elective cesarean section from healthy mothers near term with uncomplicated pregnancies. With written informed consent of the pregnant woman, the following samples were collected at term: a fragment of the placenta, umbilical cord fetal blood and maternal blood. The placenta biopsy sample was collected at a depth of 1 cm and at a distance of 8 cm from the edge of the placenta, with the maternal side facing upward. The use of these biological samples was approved by local ethical committee. Villous cytotrophoblastic cells were isolated by sequential enzymatic digestion of chorionic villi from the first trimester, second trimester and term placenta and purified on a discontinuous percoll gradient, as described previously.47-49 These cells were positively stained for cytokeratin 7 at 95%, indicating the cytotrophoblastic origin of the cells. Placental fibroblasts were isolated by prolonged enzymatic digestion from first trimester chorionic villi as in Malassine et al.50 Fibroblastic cells (1.25 x 105 cells/mL) were plated on 35-mm plastic dishes (TPP, Switzerland) and cultured for 48 h, and the culture medium was changed daily. These cultured fibroblasts were characterized using immunocytochemistry. It was found that 98% of the cells were vimentin positive and also positive for a monoclonal antibody against specific fibroblast antigen (clone ASO2, Dianova, Hamburg, Germany). Owing to the limited amount of cells, only DNA was extracted.

[Placental tissues <Tissue>] [placental tissues <Tissue>] [Fetal <Developing_anatomical_structure>] [amniotic fluid cells <Cell>] [placentas <Organ>] [fragment <Organ>] [placenta <Organ>] [umbilical cord fetal blood <Organism_substance>] [blood <Organism_substance>] [placenta biopsy sample <Organ>] [placenta <Organ>] [Villous cytotrophoblastic cells <Cell>] [chorionic villi <Multi-tissue_structure>] [placenta <Organ>] [cells <Cell>] [cells <Cell>] [Placental fibroblasts <Cell>] [chorionic villi <Multi-tissue_structure>] [Fibroblastic cells <Cell>] [fibroblasts <Cell>] [cells <Cell>] [fibroblast <Cell>] [cells <Cell>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Summary Kindt et al.1 published a report entitled "Intestinal immune activation in presumed post-infectious functional syspepsia" in the August issue of Neurogastroenterology and Motility in 2009. By comparing the signs of inflammation and the degree of hyperplasia of the enterochromaffin cells (EC) in duodenal biopsies obtained from patients with presumed post-infectious functional dyspepsia (PI-FD) and unspecified-onset functional dyspepsia (U-FD), they showed that PI-FD is associated with persistence of focal T-cell aggregates, decrease in CD4+ cells and increased macrophage counts surrounding the crypts, without any significant differences in the numbers of EC or chromogranin A (CA)-positive cells (mast cells). This finding may indicate impaired ability of the immune system in these cases to terminate the inflammatory response after an acute insult.

[Intestinal <Multi-tissue_structure>] [enterochromaffin cells <Cell>] [EC <Cell>] [T-cell <Cell>] [CD4+ cells <Cell>] [macrophage <Cell>] [crypts <Multi-tissue_structure>] [EC <Cell>] [chromogranin A (CA)-positive cells <Cell>] [mast cells <Cell>] [immune system <Anatomical_system>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Breast cancer The incidence of breast cancer is no higher than in the rest of the population. Tamoxifen should not be used as it may worsen symptoms [43]. Women need also specific management for treatment of HAE. Short term prophylaxis: three options are available: attenuated androgens, tranexamic acid or C1Inh concentrate. There is no specific problem for the use of theses drugs for short course in female patients. In case of short term prophylaxis with attenuated androgens, no virilisation has been observed [44,45]. Acute attack treatment: there is no specific problem for the use of C1inh concentrate, tranexamic acid, icatibant; or ecallantide in female patients.

[Breast cancer <Pathological_formation>] [breast cancer <Pathological_formation>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Methods Therefore, we developed a reciprocal system of a full-length HIV packaging cell line and a shortened HI-viral shuttle vector. The Tat-deficient packaging construct is stably integrated in a VSVG-pseudotyped cell line and transactivated by the shuttle vector by expression of TATGFP from a heterologous promoter which also indicates positive cells. Expression of the HI-viral structure proteins is driven by a natural 5' LTR promoter and a 3' polyadenylation signal, whereas the envelope expression out of the shuttle vector is achieved by an IRES. This system of two vectors is tightly controllable and bypasses the problem of limited packaging capacity into HIV-1 virions.

[full-length HIV packaging cell line <Cell>] [VSVG-pseudotyped cell line <Cell>] [cells <Cell>] [envelope <Cellular_component>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Ca++ distribution after Na+ pump inhibition in cultured neonatal rat myocardial cells. The influence of inhibition of the Na+ pump, with secondary stimulation of Na+-Ca++ exchange, on cellular Ca++ distribution is examined using the on-line scintillation disk technique and cultured neonatal rat myocardial cells. Under control conditions, La+++ displaced 78.1 +/- 1.13% (SEM) of the total cell associated 45Ca. Application of 1 mm ouabain or reduction of [K+]o to 0.5 mM resulted in a net increase of 10.6 +/- 1.3% and 13.8 +/- 2%, respectively, in total cell-associated Ca++. Of this added 45Ca, 75.9 +/- 2.7% and 78.4 +/- 2.1%, respectively remained La+++-displaceable. The 45Ca-binding characteristics of isolated sarcolemma, prepared from the cultured neonatal rat myocardial cells using the gas dissection technique, were examined. When treated with either ouabain or low [K+]o solutions, sarcolemmal 45Ca binding did not change. This result indicates that functional, intact tissue is necessary to observe the Ca++ increase. Treatment of the cells with verapamil before and during ouabain exposure failed to inhibit the ouabain-induced increase in cell-associated 45Ca. The evidence indicates that inhibition of the Na+-pump, and secondary stimulation of Na+-Ca++ exchange, result in a net increase of 11-15% in cell-associated Ca++, 78% of which remains La+++-displaceable and is, therefore, localized to the sarcolemma-glycocalyx complex.

[myocardial cells <Cell>] [cellular <Cell>] [myocardial cells <Cell>] [cell <Cell>] [cell <Cell>] [sarcolemma <Cellular_component>] [myocardial cells <Cell>] [sarcolemmal <Cellular_component>] [tissue <Tissue>] [cells <Cell>] [cell <Cell>] [sarcolemma <Cellular_component>] [glycocalyx <Cellular_component>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Segmental atrial contraction in patients restored to sinus rhythm after cardioversion for chronic atrial fibrillation: a colour Doppler tissue imaging study. AIMS: There is little known about segmental atrial function in patients with atrial arrhythmias. We evaluated segmental atrial contractility using colour Doppler tissue imaging (CDTI) in patients with chronic atrial fibrillation (CAF) who were successfully restored and maintained in sinus rhythm (SR). METHODS AND RESULTS: We compared the segmental atrial contractility in 39 CAF patients who were successfully cardioverted and maintained in SR for 6 months. Follow up echocardiograms were performed at baseline, 1 week, 1 month and 6 months and compared to a normal age matched cohort (n = 34). Using CDTI, mean peak velocities of atrial contraction were measured from annular, mid and superior segments of lateral and septal walls of the left atrium and right atrium in the apical four-chamber view. Segmental velocities from the posterior and anterior walls of the left atrium were measured from the apical two-chamber view. Segmental left atrial velocities improved over time in the CAF group, with the majority of the recovery occurring in the first month, but failed to normalise even at 6 months. In comparison, the right atrial velocities in the AF group had normalised at 1 month. CONCLUSION: Patients with CAF have persistent segmental left atrial dysfunction even 6 months after restoration and maintenance of SR, though right atrial velocities appear to normalise. This differential recovery indicates that left atrial function remains subnormal in patients with CAF despite maintenance of SR, suggesting underlying atrial myopathy or fibrosis as a consequence of CAF.

[atrial <Multi-tissue_structure>] [sinus <Immaterial_anatomical_entity>] [atrial <Multi-tissue_structure>] [tissue <Tissue>] [atrial <Multi-tissue_structure>] [atrial <Multi-tissue_structure>] [atrial <Multi-tissue_structure>] [tissue <Tissue>] [atrial <Multi-tissue_structure>] [sinus <Immaterial_anatomical_entity>] [atrial <Multi-tissue_structure>] [atrial <Multi-tissue_structure>] [lateral <Multi-tissue_structure>] [septal walls <Multi-tissue_structure>] [left atrium <Multi-tissue_structure>] [right atrium <Multi-tissue_structure>] [left atrium <Multi-tissue_structure>] [left atrial <Multi-tissue_structure>] [right atrial <Multi-tissue_structure>] [left atrial <Multi-tissue_structure>] [right atrial <Multi-tissue_structure>] [left atrial <Multi-tissue_structure>] [atrial <Multi-tissue_structure>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

SUMMARY Both the innate and adaptive immune subsystems are necessary to provide an effective immune response whether to an actual pathogenic agent or to an immunization. Further, effective immunizations must induce long-term stimulation of both the humoral and cell-mediated arms of the adaptive system by the production of effector cells for the current infection and memory cells for future infections with the pathogenic agent. At least seven different types of vaccines are currently in use or in development that produce this effective immunity and have contributed greatly to the prevention of infectious disease around the world.

[immune subsystems <Anatomical_system>] [cell <Cell>] [effector cells <Cell>] [memory cells <Cell>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Listerine: past, present and future--a test of thyme. Listerine, a mouthrinse composed of a mixture of essential oils, was created in 1879 and was originally formulated as a surgical antiseptic. In spite of its known antimicrobial properties it was thought of as a product in search of a use and promoted as a deterrent for halitosis and as a floor cleaner. In the last several years Listerine has emerged as a bona fide therapeutic agent for reduction of plaque induced oral diseases. In contrast to the inconsistent history of Listerine, systemic antibiotics discovered in the 1940's were heralded as miracle drugs. However, the value of prophylactic usage of antibiotics has come under scrutiny as a result of increasing resistance and adverse reactions. Moreover, reports by both American and British professional societies have led to a re-evaluation of the relative risks associated with plaque induced bacteremia when twice-yearly visits to dental professionals are compared to daily activities. These new recommendations and revelations open the door for local antimicrobial approaches to reduce the challenge of plaque-induced bacteremias. These issues will be discussed in the context of Listerine, its intricate and complicated past, and its connection to current uses in oral health and beyond.

[plaque <Organism_substance>] [oral <Organism_subdivision>] [plaque <Organism_substance>] [plaque <Organism_substance>] [oral <Organism_subdivision>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Is there an upper limit of intracranial pressure in patients with severe head injury if cerebral perfusion pressure is maintained? Authors of recent studies have championed the importance of maintaining cerebral perfusion pressure (CPP) to prevent secondary brain injury following traumatic head injury. Data from these studies have provided little information regarding outcome following severe head injury in patients with an intracranial pressure (ICP) greater than 40 mm Hg, however, in July 1997 the authors instituted a protocol for the management of severe head injury in patients with a Glasgow Coma Scale score lower than 9. The protocol was focused on resuscitation from acidosis, maintenance of a CPP greater than 60 mm Hg through whatever means necessary as well as elevation of the head of the bed, mannitol infusion, and ventriculostomy with cerebrospinal fluid drainage for control of ICP. Since the institution of this protocol, nine patients had a sustained ICP greater than 40 mm Hg for 2 or more hours, and five of these had an ICP greater than 75 mm Hg on insertion of the ICP monitor and later experienced herniation and expired within 24 hours. Because of the severe nature of the injuries demonstrated on computerized tomography scans and their physical examinations, these patients were not aggressively treated under this protocol. The authors vigorously attempted to maintain a CPP greater than 60 mm Hg with intensive fluid resuscitation and the administration of pressor agents in the four remaining patients who had developed an ICP higher than 40 mm Hg after placement of the ICP monitor. Two patients had an episodic ICP greater than 40 mm Hg for more than 36 hours, the third patient had an episodic ICP greater than of 50 mm Hg for more than 36 hours, and the fourth patient had an episodic ICP greater than 50 mm Hg for more than 48 hours. On discharge, all four patients were able to perform normal activities of daily living with minimal assistance and experience ongoing improvement. Data from this preliminary study indicate that intense, aggressive management of CPP can lead to good neurological outcomes despite extremely high ICP. Aggressive CPP therapy should be performed and maintained even though apparently lethal ICP levels may be present. Further study is needed to support these encouraging results.

[intracranial <Immaterial_anatomical_entity>] [head <Organism_subdivision>] [cerebral <Organ>] [cerebral <Organ>] [brain <Organ>] [head <Organism_subdivision>] [head <Organism_subdivision>] [intracranial <Immaterial_anatomical_entity>] [head <Organism_subdivision>] [cerebrospinal fluid <Organism_substance>] [fluid <Organism_substance>] [neurological <Anatomical_system>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Figures and Tables Figure 1 Allergen and particle dose-response experiments in BALB/cA and NIH mice Levels of serum OVA-specific IgE (A, D), IgG1 (B, E) and IgG2a (C, F) on day 26 after injection into one hind footpad of 100 (open columns), 50 (gray) or 10 (black) mug OVA combined with 100, 40, 10 or 0 mug PSP, or buffer (HBSS (hatched)), in BALB/cA (A, B, C) and NIH (D, E, F) mice. On day 21 the mice were boostered with the same OVA dose in the footpad. The PSP-control ("PSP ctr") group was given 100 mug PSP on day 0, followed by HBSS injection on day 21 (diamonds). Values (arbitrary units, AU) for individual mice (circles) and median values (columns) for groups of eight mice are shown. Dotted lines indicate the lower or higher detection limits for the ELISA assays. Note different scales for the two strains of mice. Figure 2 The adjuvant effect of PSP on OVA-specific IgE and IgG2a responses in different strains of mice Levels of serum OVA-specific IgE (A) and IgG2a (B) on day 26 after injection into one hind footpad of HBSS (open columns), 10 mug OVA (gray), 40 mug PSP (hatched) or 10 mug OVA + 40 mug PSP (black) in different mouse strains. On day 21 all mice were boostered with 10 mug OVA in the footpad. Vertical straight lines indicate separate experiments. Values (arbitrary units, AU) for individual mice (circles) and median values (columns) for groups of mice are shown. Dotted lines indicate the lower detection limits for the ELISA assays. Brackets indicate statistically significant differences between groups (p < 0.05). All experiments were performed twice with similar results, with eight mice per group. Figure 3 The primary cellular response in the draining lymph node The primary cellular response in the draining PLN was determined five days after a single injection of HBSS (open columns), 10 mug OVA (gray), 40 mug PSP (hatched) or 10 mug OVA + 40 mug PSP (black) into both hind footpads of BALB/cA, NIH and C3H/HeN mice. The total lymph node cell numbers (A) and IL-4 (B), IFN-gamma (C) and IL-10 (D) secreted from the PLN cells after ex vivo stimulation with Con A were determined. Values for individual samples (circles) and group median values (columns) are shown. Dotted lines indicate the lower detection limits for the cytokine ELISA assays, and brackets indicate statistically significant differences between groups (p < 0.05).

[serum <Organism_substance>] [hind footpad <Organism_subdivision>] [footpad <Organism_subdivision>] [serum <Organism_substance>] [hind footpad <Organism_subdivision>] [footpad <Organism_subdivision>] [cellular <Cell>] [lymph node <Multi-tissue_structure>] [cellular <Cell>] [PLN <Multi-tissue_structure>] [lymph node cell <Cell>] [PLN cells <Cell>] [samples <Cell>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

SUMMARY This is a prospective study carried out to determine the outcome of patients who refuse cystectomy after receiving neoadjuvant chemotherapy for muscle-invasive bladder cancer. Sixty-three patients were evaluated between 1995 and 2001 who declined to undergo a planned cystectomy because they achieved a complete clinical response to neoadjuvant cisplatin-based chemotherapy. Herr assessed patient, tumor and treatment features for a median follow- up of 86 months, all patients being followed-up for more than 5 years. Forty patients (64%) survived, with 54% of them having an intact functioning bladder. The number and size of invasive tumors were strongly associated with the overall survival. The most significant treatment variable predicting better survival was complete resection of the invasive tumor on restaging transurethral resection (TUR) before starting chemotherapy. Of 23 patients (36%) who subsequently died of disease, 19 (30%) relapsed with invasive cancer in the bladder. Over 90% of the surviving patients had solitary, small and low-stage invasive tumors completely resected and 83% survived without relapses in the bladder.[1]

[muscle-invasive bladder cancer <Pathological_formation>] [tumor <Pathological_formation>] [bladder <Organ>] [tumors <Pathological_formation>] [tumor <Pathological_formation>] [cancer <Pathological_formation>] [bladder <Organ>] [tumors <Pathological_formation>] [bladder <Organ>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Brainstem auditory-evoked potential evaluation in children with meningitis. Brainstem auditory-evoked potential (BAEP) was performed on 101 children with meningitis to assess the incidence of hearing impairment. Fifty-two (51.5%) children had bacterial meningitis, six (5.9%) had viral meningitis, and 43 (42.6%) had aseptic meningitis. Fifty-one (50.5%) patients were assessed before discharge and 50 (49.5%) 9 days to 17 months later (mean = 4 months). BAEP impairment was found in 28 (27.7%) of 101 patients; 24 had sensorineural and four had conductive type of hearing loss, and 17 (60.7%) had unilateral and 11 (39.3%) had bilateral impairment. Hearing threshold was elevated in 22 (21.8%) patients, and the other six had increased latency and interpeak latencies with normal threshold. Frequency of BAEP impairment or hearing loss associated with bacterial meningitis was 34.6% and 30.8%, respectively; frequency associated with aseptic meningitis was 20.9% and 13.9%, respectively. One child with viral meningitis (coxsackie virus) had mild BAEP impairment. Most of the BAEP impairment in the bacterial meningitis group was associated with H. influenzae. Prospective BAEP study was performed in 20 patients randomly at 0.3 to 18 months to assess hearing status after antibiotic treatment, 10 with normal and 10 with abnormal BAEP. All the initially normal BAEP patients remained normal. Of the 10 patients with abnormal BAEP results initially, four returned to normal, two improved, three remained unchanged, and one deteriorated. The incidence of hearing loss after bacterial and aseptic meningitis is high. BAEP is useful to screen for possible hearing loss in children with meningitis, and follow-up BAEP is necessary for those patients with initially abnormal BAEP.

[Brainstem <Multi-tissue_structure>] [Brainstem <Multi-tissue_structure>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Mapping of the L-methylmalonyl-CoA mutase gene to mouse chromosome 17. In humans, methylmalonyl acidemia is caused by a deficiency of L-methylmalonyl-CoA mutase (MUT) controlled by a gene that has been mapped to chromosome 6. The mouse homolog of this gene has now been mapped to mouse chromosome 17. Recombinant inbred and congenic strains place the mouse Mut locus 1.06 cM distal to H-2, between Pgk-2 and Ce-2. The relative order of syntenic probes flanking H-2 on mouse chromosome 17 and HLA on human chromosome 6 is shown to be different.

[chromosome 17 <Cellular_component>] [chromosome 6 <Cellular_component>] [chromosome 17 <Cellular_component>] [chromosome 17 <Cellular_component>] [chromosome 6 <Cellular_component>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

TBX21: a functional variant predicts improvement in asthma with the use of inhaled corticosteroids. TBX21 encodes for the transcription factor T-bet (T-box expressed in T cells), which influences naive T lymphocyte development and has been implicated in asthma pathogenesis. Specifically, the T-bet knockout mouse spontaneously develops airway hyperresponsiveness and other changes consistent with asthma. Because airway responsiveness is moderated by the use of inhaled corticosteroids in asthma, it is conceivable that genetic variation in TBX21 may alter asthma phenotypes in a treatment-specific fashion. Here we demonstrate that the nonsynonymous variation in TBX21 coding for replacement of histidine 33 with glutamine is associated with significant improvement in the PC(20) (a measure of airway responsiveness) of asthmatic children in a large clinical trial spanning 4 years. We note that this increase occurs only in the children randomized to inhaled corticosteroids and that it dramatically enhances the overall improvement in PC(20) associated with inhaled corticosteroid usage. The average PC(20) at trial end for subjects on inhaled corticosteroids possessing a variant allele was in the normal range for nonasthmatics. In cellular models, we show that the TBX21 variant increases T helper 1 and decreases T helper 2 cytokine expression comparably with wild type. TBX21 may thus be an important determinant pharmacogenetic response to the therapy of asthma with inhaled corticosteroids.

[T cells <Cell>] [T lymphocyte <Cell>] [airway <Multi-tissue_structure>] [airway <Multi-tissue_structure>] [airway <Multi-tissue_structure>] [T helper 1 <Cell>] [T helper 2 <Cell>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Outcomes of cefazolin versus ceftriaxone therapy in treating lower respiratory tract infections in adults. OBJECTIVE: To determine whether choice of a first- versus third-generation cephalosporin as initial therapy for lower respiratory tract infections in hospitalized adults affects the course and duration of care, both of which may influence antimicrobial treatment cost. DESIGN: Retrospective analysis of discharge abstracts and hospital pharmacy records. SETTING: Forty-eight US acute-care hospitals. PATIENTS: One thousand ninety-two hospitalized adults (aged > 17 y) with principal diagnoses of lower respiratory tract infections (DRGs 79-80, 89-90). INTERVENTIONS: Cefazolin or ceftriaxone, given as sole antimicrobial therapy for at least one day. MAIN OUTCOME MEASURES: (1) The number of patients who received another parenteral antibiotic anytime prior to hospital discharge; (2) the number of days during which patients received any parenteral antibiotic while in the hospital; and (3) the number of days patients remained hospitalized following the start of antibiotic therapy. RESULTS: Patients treated with cefazolin (n = 763) were more likely to receive another parenteral antibiotic while in the hospital (30.3 vs. 20.7 percent; p < 0.001) and received more total days of therapy (7.2 vs. 6.7 d; p < 0.05) than those treated with ceftriaxone (n = 329). Although the time to hospital discharge did not differ in the full sample (9.2 d for both groups), it was greater among those receiving cefazolin (8.6 vs. 8.0 d; p < 0.05) when patients with lengths of stay exceeding 24 days were excluded from both groups. CONCLUSIONS: In addition to acquisition cost, differences in course and duration of care should be considered when determining the most cost-effective choice for antimicrobial therapy.

[lower respiratory tract <Multi-tissue_structure>] [lower respiratory tract <Multi-tissue_structure>] [lower respiratory tract <Multi-tissue_structure>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

MOR1K expression and binding pattern. (A) The schematic diagram illustrates the exonic composition and relative positions of PCR primers designed to amplify the major MOR1 isoform and the newly identified alternative MOR1K isoform. The relative positions of translation initiation start and stop codons are designated by ATG and TGA, respectively. The predicted protein structure of MOR1 and MOR1K isoforms is schematically presented. Translation of the MOR1K variant results in a 6TM receptor, truncated at the N-terminus. (B) Real-time PCR was performed on total RNA samples from the human brain regions known to express MOR1. Primers specific for exons 1 and 2 were used to measure MOR1 and primers specific for exons 13 and exon 2 were used to measure MOR1K[32]. GAP3DH was used as a control for cDNA loading and PCR efficiency. (C) Confocal images of C-terminally MYC-tagged MOR1 or FLAG-tagged MOR1K overexpressed in HEK293 cells and stained with either Anti-MYC-Tag Antibody (Alexa Fluor 647 Conjugate) or Anti-DYKDDDDK Tag Antibody (Alexa Fluor 555 conjugate). Cells transfected with MOR1 showed membrane expression of receptor, while cell transfected with MOR1K express receptor only intracellular. (D) Confocal images of C-terminally FLAG-tagged MOR1K overexpressed in Be2C cells and stained with either Anti-FLAG M2 Antibody Alexa Fluor Conjugate or fluorescent-labeled naloxone (FNAL). Cells transfected with MOR1K showed intracellular retention of FNAL that co-localized with antibody-labeled receptor. (E) The binding of naloxone to MOR1K was assessed using flow cytometry to measure FNAL retention. Be2C cells transfected with either MOR1 or MOR1K isoforms showed increased retention of FNAL at concentrations of 0.1 and 1 muM. FNAL retention was abolished in the presence of 10 muM unlabelled naloxone (Nal). In panel E, data are presented as mean + SEM. *P < 0.05 different from controls).

[brain <Organ>] [HEK293 cells <Cell>] [Cells <Cell>] [membrane <Cellular_component>] [cell <Cell>] [intracellular <Immaterial_anatomical_entity>] [Be2C cells <Cell>] [Cells <Cell>] [intracellular <Immaterial_anatomical_entity>] [Be2C cells <Cell>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Focal congenital alveolar proteinosis associated with abnormal surfactant protein B messenger RNA. Two siblings presented with typical clinical features of congenital pulmonary alveolar proteinosis (PAP). Necropsy of one sibling revealed scattered foci of the diagnostic histologic changes in the lung tissue. In contrast to infantile and adult PAP, focal distribution is uncommon in congenital PAP. Defective expression of the granulocyte-macrophage colony-stimulating factor receptor was ruled out. The surfactant protein B (SP-B) content in the lung tissue of the autopsied patient was low, and a deletion in the SP-B messenger RNA was detected. We speculate that the PAP in our patients was related to the reduced quantity and/or to the altered quality of SP-B.

[alveolar <Multi-tissue_structure>] [pulmonary alveolar <Multi-tissue_structure>] [foci <Pathological_formation>] [lung tissue <Tissue>] [focal <Pathological_formation>] [lung tissue <Tissue>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Printing solution Several transfection reagents were tested (data not shown), and we found that the X-tremeGENE siRNA transfection reagent (Roche) gave good transfection efficiencies both for plasmids and siRNAs, and chose to use this reagent for all transfected cell microarray experiments in the present study. For printing the arrays, one major challenge is to find a good balance between high transfection efficiency and spatially confined spots to avoid cross-contamination between the spots. In order to optimize the reverse transfection protocol for HEK 293ind-ICER IIgamma cells (see below) and X-tremeGENE transfection reagent, we investigated the effect of varying the concentrations of gelatine and sucrose in the printing solution. These reagents have been reported to influence both the transfection efficiency and spot integrity (6,27). Sucrose was observed to be specifically beneficial for obtaining high transfection efficiency when storing the arrays for several weeks before use (data not shown). Figure 1A and B show representative images of the observed effects of varying the concentrations of gelatine and sucrose. We observed that the transfection efficiency increased with increasing gelatine concentration (tested in the range 0.01-0.40%). However, an increased disturbance of the spatial definition of the spots was observed with increasing concentrations of gelatine or sucrose (tested in the range 0-100 mM). A combined effect of the concentrations of gelatine and sucrose was also observed, as low concentrations of gelatine allowed us to use higher concentrations of sucrose than with higher concentrations of gelatine before cells spread outside the spots. Based on several optimizing experiments, we found that 3 microl X-tremeGENE solution per microgram nucleic acid, 25 mM sucrose and 0.1% gelatine in the final printing solution reproducibly gave spatial restricted transfection with high transfection efficiency printing the arrays with both a pipette tip and a hand-held arrayer (see below). Figure 1. Effects of sucrose and gelatine concentrations on spot integrity and transfection efficiency. (A) Array printed with pDsRed (50 ng/microl) in a printing solution with different gelatine and sucrose concentrations. Scanning image of the whole array and magnifications of specific spots. (B) Array printed with pEGFP (50 ng/microl) in a printing solution with 25 mM sucrose and four different concentrations of gelatine. Top: Box plot of the fluorescence intensities in each spot (n = 32-34). Bottom: Scanning image showing squares of seven times five spots for the four gelatine concentrations. From left to right: 0.01, 0.05, 0.1 and 0.2% gelatine. The DNA-lipid-gelatine-sucrose solutions were printed manually with a 10 microl pipette tip (A) or by MicroCasterTM manual arrayer system (B). In a 1.5 ml microcentrifuge tube, plasmid (1 microg/microl) and siRNA were mixed with growth medium without fetal calf serum (FCS), 0.5 microl 1.5 M sucrose and 3 microl X-tremeGENE per microgram nucleic acid to a final volume of 22.5 microl. After 15-20 min of incubation, 7.5 microl 0.4% gelatine (Type B, G9391, Sigma) was added to give 30 microl printing solution. The gelatine solution was prepared as described by Ziauddin and Sabatini (1). To achieve sufficient level of expression from the transfected plasmids, 25-50 ng/microl pEGFP-N1 or pDsRed-express-N1 and 50-75 ng/microl of CRE or NFkappaB reporter plasmids was used. For siRNA studies, 2-30 ng/microl siRNA in the final printing solution was used.

[plasmids <Cellular_component>] [cell <Cell>] [HEK 293ind-ICER IIgamma cells <Cell>] [cells <Cell>] [fetal <Developing_anatomical_structure>] [serum <Organism_substance>] [plasmids <Cellular_component>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Tarsoconjunctival flap after division

[Tarsoconjunctival flap <Multi-tissue_structure>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Additional File 1 Appendix 1. Indications for liver function tests with no obvious liver disease, and consequent investigations

[liver <Organ>] [liver <Organ>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

The proenkephalin-A-derivative Met-enkephalin-Arg-Gly-Leu is not present in the feline species. No opioid octapeptide Met-enkephalin-Arg-Gly-Leu was detected either in the brain or in the adrenal gland of the cat using a specific radioimmunoassay. Whereas it was possible to determine the Met-enkephalin and Leu-enkephalin contents. The Met-enkephalin versus Leu-enkephalin concentration ratio was around five in each area of the brain assayed. The presence of authentic Met-enkephalin and Leu-enkephalin was confirmed by high performance liquid chromatography analysis. All in all, these data seem to indicate that the cat proenkephalin is partly different from that previously analysed in mammalian species including humans, rats and cows.

[brain <Organ>] [adrenal gland <Organ>] [brain <Organ>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

The septic abscess wall: a cytokine-generating organ associated with portal venous cytokinemia, hepatic outflow fibrosis, sinusoidal congestion, inflammatory cell sequestration, hepatocellular lipid deposition, and focal cell death. An acute septic inflammatory response with access to the portal circulation was created in a rat model using an intra-abdominal abscess composed of a sterile agar pellet, or one contaminated with 102 Escherichia coli (E. coli) and 109 Bacteriodes fragilis (B. fragilis). After 3 days postimplantation, a well-formed intra-abdominal abscess occurred whose wall showed IL-6 DNA by PCR and IL-6 mRNA by in situ hybridization. Portal venous blood draining into the liver from the intra-abdominal abscess had increased levels of TNF-alpha, IL-1beta, and IL-6 in both sterile and septic groups compared with a control normal animal group. Increased levels of these cytokines were also found in suprahepatic inferior vena caval blood, but were correlated with the higher portal vein levels, suggesting a gradient from abscess wall to portal vein into the systemic circulation via the liver. Liver histology demonstrated sinusoidal congestion centering on the central vein, growing worse with progression from normal in control, to sterile, to septic. Similarly, the degree of intrahepatic myeloperoxidase-positive inflammatory cell infiltration and hepatocellular lipid deposition and apoptosis also increased from control, to sterile, to septic. Gene expression by in situ hybridization demonstrated a significant increase in IL-6 and fibrinogen mRNAs in cells surrounding the central vein in sterile and septic animals, being greatest in animals with sepsis, associated with an increased deposition of collagen in the central vein area, most prominent in the septic liver. The pericentral vein cells with IL-6 and fibrinogen mRNA increases paralleled the increases in cells containing IL-6 and fibrinogen mRNAs in the abscess walls of sterile and septic animals, respectively. The data suggest that an intra-abdominal abscess, especially when contaminated with gram-negative bacteria, induces mRNA-generated cytokine responses in the abscess wall that are related to increased portal venous levels of the inflammatory cytokines TNF-alpha, IL-1beta, and IL-6 perfusing the liver. These, in turn, induce localized production of IL-6 and fibrinogen mRNAs in cells at the central vein area with resultant outflow fibrosis and increased inflammatory cell sequestration within the liver lobular sinuses. This is associated with a generalized inflammatory response and intrahepatic portal sinusoid congestion. There is also increased hepatocellular lipid deposition and apoptosis. Thus, the cytokine production of the abscess wall itself appears to be a major mediator of the septic hepatic response.

[septic abscess wall <Multi-tissue_structure>] [organ <Organ>] [portal venous <Multi-tissue_structure>] [hepatic <Organ>] [sinusoidal <Tissue>] [inflammatory cell <Cell>] [hepatocellular <Cell>] [cell <Cell>] [abdominal abscess <Pathological_formation>] [abdominal abscess <Pathological_formation>] [wall <Tissue>] [Portal venous blood <Organism_substance>] [liver <Organ>] [abdominal abscess <Pathological_formation>] [suprahepatic inferior vena caval blood <Organism_substance>] [portal vein <Multi-tissue_structure>] [abscess wall <Multi-tissue_structure>] [portal vein <Multi-tissue_structure>] [liver <Organ>] [Liver <Organ>] [sinusoidal <Tissue>] [central vein <Multi-tissue_structure>] [inflammatory cell <Cell>] [hepatocellular <Cell>] [cells <Cell>] [central vein <Multi-tissue_structure>] [central vein <Multi-tissue_structure>] [septic liver <Organ>] [pericentral vein cells <Cell>] [cells <Cell>] [abscess walls <Multi-tissue_structure>] [abdominal abscess <Pathological_formation>] [abscess wall <Multi-tissue_structure>] [portal venous <Multi-tissue_structure>] [liver <Organ>] [cells <Cell>] [central vein <Multi-tissue_structure>] [inflammatory cell <Cell>] [liver lobular sinuses <Multi-tissue_structure>] [hepatocellular <Cell>] [abscess wall <Multi-tissue_structure>] [septic hepatic <Organ>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Impact of dexamethasone-induced immunosuppression on the duration and level of shedding of Escherichia coli O157:H7 in calves. The goal of this study was to determine whether immunosuppression plays a role in the level and duration of fecal shedding of Escherichia coli O157. Immunosuppression was induced in calves by administering dexamethasone. Six 1-week-old Holstein bull calves were injected intramuscularly with dexamethasone and orally inoculated with 10(9) CFU of a mixture of three nalidixic-acid resistant strains of E. coli O157:H7. Five 1-week-old Holstein bull calves that were given the same oral inoculation of E. coli O157:H7, but not the dexamethasone injections, served as controls. All calves were examined daily and fecal samples were collected three times a week for detection and enumeration of the nalidixic-acid resistant E. coli O157. Four weeks after the last calf stopped shedding, all calves were necropsied and samples from the gastrointestinal tract were taken for the detection of the nalidixic-acid resistant E. coli O157. Dexamethasone-injected calves shed at higher levels (P = 0.04) on days 4 and 7 postinoculation, but not thereafter. None of the samples collected at necropsy were positive for E. coli O157. Data from this study suggest that there may be a time-dependent relationship between dexamethasone immunosuppression and the fecal concentration of E. coli O157 but that transient immunosuppression does not appear to prolong shedding of E. coli O157.

[fecal <Organism_substance>] [intramuscularly <Tissue>] [fecal <Organism_substance>] [gastrointestinal tract <Organism_subdivision>] [fecal <Organism_substance>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Background HIV-1 infectivity depends on free cholesterol incorporated into the viral envelope. Here, we analyze HIV infectivity in the presence of drugs that stimulate cholesterol efflux.

[envelope <Cellular_component>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

(a) Sequence alignment of PY-NLSs. The homologous regions of C-NLS of the EWS protein, NLS of Sam68 and FUS/TLS protein and M9 NLS of hnRNP A1 and hnRNP M, classified as PY-NLS are in yellow boxes. Phosphorylated Y656 of the EWS protein and Y440 of Sam68 are indicated (in red). Positions of identical residues in SAM68 and EWS C-NLS are indicated in bold and residues with identical charges are underlined. Known positions of the FUS/TLS mutations in ALS are in bold. (b) Subcellular localization of YFP, the C-terminally tagged EWS-YFP, EWS(Y656A)-YFP, EWS(Y656F)-YFP, and EWS(Y656D)-YFP (in green). Nuclei are shown by DAPI staining (in blue). Bars, 15 mum.

[Subcellular <Cellular_component>] [Nuclei <Cellular_component>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Antisense technologies have a future fighting neurodegenerative diseases. Our growing understanding of the role that unfavorable patterns of gene expression play in the etiology of neurodegenerative disease emphasizes the need for strategies to selectively block the biosynthesis of harmful proteins in the brain. Antisense technologies are ideally suited to this purpose. Tailor-designed to target specific RNA, antisense oligonucleotides and ribozymes offer tools to suppress the production of proteins mediating neurodegeneration. Although technical limitations must still be overcome, the antisense approach represents a novel and exciting strategy for intervention in diseases of the central nervous system.

[brain <Organ>] [central nervous system <Anatomical_system>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Tail flick test CSLE did not show any difference compared with control, at all the tested doses [Figure 4]. Morphine showed a significant increase of latency time at 45, 60 and 75 min. Figure 4 Effect of CSLE (100, 200 and 500 mg/kg) and morphine on the latency response of mice in the tail flick test. Values are presented as the mean +/- SEM (n = 5) *P < 0.05, significant increase from control

[tail <Organism_subdivision>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

The origin of yolk-DNA in Xenopus laevis. Xenopus laevis serum and plasma was found to contain an average of 25 microgram DNA/ml. Isolated X. laevis oocytes incubated in medium containing 25 microgram DNA/ml labeled with either 125I, 32P or 14C and from three different sources (bovine, E. coli and X. laevis), incorporated the label at an average rate of 0.11 ng.mm-2.hr-1. Sucrose gradient fractionation of oocytes revealed that 40-75% of the acid-precipitable label incorporated was associated with the yolk platelets. Additional incubations of oocytes in unlabeled medium demonstrated that the DNA incorporated into the yolk platelets was undergoing turnover; only 20% of the yolk-associated DNA was still present after a one-week incubation. Our data suggest that yolk-DNA arises by the adventitious uptake of DNA present in the maternal serum by vitellogenic oocytes.

[yolk <Developing_anatomical_structure>] [serum <Organism_substance>] [plasma <Organism_substance>] [oocytes <Cell>] [oocytes <Cell>] [yolk platelets <Cell>] [oocytes <Cell>] [yolk platelets <Cell>] [yolk <Developing_anatomical_structure>] [yolk <Developing_anatomical_structure>] [serum <Organism_substance>] [oocytes <Cell>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Analysis of processivity of mungbean dideoxynucleotide-sensitive DNA polymerase and detection of the activity and expression of the enzyme in the meristematic and meiotic tissues and following DNA damaging agent. Analysis of the processivity of mungbean ddNTP-sensitive DNA polymerase showed the incorporation of approximately 35-40 nucleotides per binding event in the replication assays involving M13 ss DNA template with 5'-labeled 17-mer primer. Optimal processivity was obtained with 100-150 mM KCl and 6-8 mM Mg2+ at pH 7.5. The enzyme showed preference for Mg2+ over Mn2+ as the metal activator for processivity. 2', 3' dideoxythymidine 5' triphosphate (ddTTP) and rat DNA pol beta antibody strongly influenced distributive synthesis. Considerable enhancement in processivity was noticed at 1mM ATP and 2-4 mM spermidine while higher concentrations of spermidine caused distributive synthesis. The enzyme was found to be active in both meristematic and meiotic tissues and distinctly induced by EMS treatment. DNA-binding assays revealed distinct binding ability of the enzyme to template/primer and damaged DNA substrate. Together these observations illustrate the probable involvement of the enzyme in replication and repair machinery in higher plants.

[meristematic <Tissue>] [meiotic tissues <Tissue>] [meristematic <Tissue>] [meiotic tissues <Tissue>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

An introduction to evidence-based practice for hand surgeons and therapists. Evidence-based practice is a methodical approach to clinical practice where experience, best research evidence, and patient goals and values are integrated to make optimal decisions when making a diagnosis, selecting a diagnostic test, picking an intervention or determining prognosis. There are five steps in this process. Hand surgeons and therapists can use the evidence-based process to attain optimal management of individual patients, manage their overall practice, guide the ongoing professional development, and deal with funding and policy makers.

[hand <Organism_subdivision>] [Hand <Organism_subdivision>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Long-term immunosuppression in burned patients assessed by in vitro neutrophil oxidative burst (Phagoburst). OBJECTIVE: To assess the duration and magnitude of immunosuppression induced by burns as measured by the neutrophil oxidative burst in vitro. DESIGN: Prospective exploratory cohort study. SETTING: Tertiary referral unit, University Hospital, Linkoping, Sweden (National Burn Unit). PATIENTS AND HEALTHY VOLUNTEERS (CONTROLS): Twenty-eight subjects consecutively admitted to the Burn Unit. The mean total burn surface area (TBSA%) was 36 (range 13-87) and mean age 44 years (range 14-89). Patients' data were collected prospectively in the burn unit, which also included sequential organ failure assessment (SOFA) score. INTERVENTIONS: None. MEASUREMENTS AND RESULTS: To assess the changes in the oxidative capacity of neutrophils after the burn, blood samples for the Phagoburst analysis were taken on admission and at least once every second week for the duration of stay in hospital and thereafter monthly up to 12 months after the burn. Neutrophils were stimulated in vitro by Escherichia coli, phorbol 12-phorbol myristate 13-acetate (PMA), and peptide N-formyl-Met-Leu-Phe (fMLP). Oxidative burst was measured by flow cytometry. Oxidative capacity of the neutrophils decreased similarly for all three stimulants: there was a pathological decrease shortly after admission, with the lowest value occurring between days 7 and 10, followed by a gradual recovery during the ensuing months. Full recovery (to the values of the controls) was seen first 3.5 months after the burn. Using multiple regression, we found that only age and time since the burn significantly (p<0.05) affected the oxidative burst. White cell count (WCC) and C-reactive protein (CRP) values returned to reference ranges long before the oxidative burst. CONCLUSIONS: This study provides evidence that immunosuppression in those injured by burns, as assessed by the in vitro oxidative burst of neutrophils, remains long after the event of the burn (up to 3.5 months after burn). Absence of correlations to TBSA%, FTB%, blood transfusion, opiates provided, and multiple organ failure score and laboratory infection variables together with the finding that decreased oxidative burst was uniform after the injury, suggesting that this immunosuppression is primarily due to the general metabolic response rather than recurring infections.

[neutrophil <Cell>] [neutrophil <Cell>] [organ <Organ>] [neutrophils <Cell>] [blood samples <Organism_substance>] [Neutrophils <Cell>] [neutrophils <Cell>] [White cell <Cell>] [neutrophils <Cell>] [blood <Organism_substance>] [organ <Organ>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Subject disposition. Data from 110 enrolled subjects were eligible for analysis. The demographics of the study subjects, by site, are recorded in Table 1. The population studied was predominantly not HIV infected (92%), and by the study entry criteria, their probability of infection was considered to be low. The risk categories assigned at the time of study entry were combined into groups for analysis, based on the predisposition for PCP. The analysis groups were as follows: (i) HIV/AIDS, (ii) lung transplant (one subject with a dual organ transplant [lung/kidney] was included in this category), (iii) all other organ transplants and allogeneic hematopoietic stem cell transplants (HSCT), (iv) leukemia, other hematological disorders, and autologous HSCT, (v) other solid tumors, and (vi) other nonmalignant conditions. Table 1. Subject enrollment, disposition, and demographics by sitea Characteristic Valueb Site 1 Site 2 Site 3 Site 4 Enrollment Unique subjects 18 29 22 62 Subjects entering into primary analysisc 18 22 22 48 Subjects with repeat visits 0 0 0 16 No. of samples assayed 18 22 22 70 Gender Male 7 10 13 29 Female 11 12 9 19 Race Caucasian 12 4 0 48 Black 6 13 0 0 Other (nonwhite) 0 5 0 0 No data 0 0 22 0 Mean (range) age (yr) 57 (26-78) 54 (21-75) 52 (26-74) 56 (23-73) Pretest probability of PCP Moderate 0 3 4 0 Low 18 19 18 48 Sample type BAL 18 20 20 43 Sputum 0 1 1 0 Other LRT 0 1 1 5 At-risk group HIV/AIDS 0 3 6 0 Lung transplant 8 0 1 31 Other transplants 1 7 3 0 Leukemia 1 1 7 0 Other solid tumors 2 1 1 7 Other nonmalignant conditions 6 10 4 10 a The testing and enrollment sites for the study were Duke University School of Medicine, Durham, NC; Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY; Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland; and Medizinische Universitat and Landeskrankenhaus Natters, Innsbruck, Austria. b Except where otherwise indicated, values are numbers of patients. c Subjects were excluded from analysis if they withdrew consent or if there was inadequate sample left for PCR testing.

[lung <Organ>] [organ <Organ>] [lung <Organ>] [kidney <Organ>] [organ <Organ>] [allogeneic hematopoietic stem cell <Cell>] [solid tumors <Pathological_formation>] [Sputum <Organism_substance>] [Lung <Organ>] [solid tumors <Pathological_formation>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Multiple phosphotyrosine phosphatase mRNAs are expressed in the human lung fibroblast cell line WI-38. Protein tyrosine phosphatases are important components of signal transduction pathways. The authors have used reverse transcription/polymerase chain reactions to accomplish a comprehensive examination of the RNA expression for 58 distinct mammalian protein tyrosine and dual specificity phosphatase (PTPase) and PTPase-like genes in the normal human diploid fibroblast cell line WI-38. Thirty-seven of these PTPase genes express easily measurable RNA, and four simultaneously express the RNA for two or more isoforms. Messages for an additional eight PTPase genes are detectable at low levels. Only 14 known PTPase genes do not express measurable RNA under our conditions. For purposes of comparison, the authors also assessed the PTPases expressed in the WI-38 cell line using highly degenerate primers to conserved motifs found in the classical tyrosine-specific PTPases. Only eight of the 22 classic tyrosine-specific PTPases detected using the specific primers were detected using these degenerate primers. Our panel of specific PTPase primers should be very useful for semiquantitatively assessing the repertoire of PTPases expressed by cells.

[lung fibroblast cell line WI-38 <Cell>] [diploid fibroblast cell line WI-38 <Cell>] [WI-38 cell line <Cell>] [cells <Cell>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Magnetic resonance imaging of axial plan with intravenous contrast gadolinium-BOPTA demonstrating a mass adherent to the right ventricular wall.

[intravenous <Multi-tissue_structure>] [ventricular wall <Multi-tissue_structure>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Conclusion: This study demonstrates that surgery plus chemotherapy and radiation therapy is helpful for treating patients with pelvic Ewing's sarcoma, particularly in achieving local control.

[pelvic Ewing's sarcoma <Pathological_formation>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Prolonged control of patterned biofilm formation by bio-inert surface chemistry. A bio-inert surface chemistry was developed that can confine biofilm formation in designed patterns for at least 26 days.

[biofilm <Cell>] [biofilm <Cell>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

[Histopathologic examination of rectal carcinoma]. In patients with rectal carcinoma, the histopathological evaluation of the surgical specimen provides pivotal prognostic and therapeutic information. Important parameters are tumor site, depth of invasion, histological type and grade, pattern of invasion (diffusely infiltrating versus expanding margin), degree of peritumoral lymphocytic infiltration, and tumor involvement of surgical margins and lymph nodes. Evaluation of the circumferential (deep, lateral) margin is of utmost importance. It should be labeled with ink in the gross specimen and should be examined histologically using several tissue blocks. The number of lymph node metastases and the total number of lymph nodes examined should be reported. A histological evaluation of the distal mesorectum in its entirety is recommended to detect discontinuous distal mesorectal tumor spread. The histopathological findings should be summarized using the TNM-classification.

[rectal carcinoma <Pathological_formation>] [rectal carcinoma <Pathological_formation>] [surgical specimen <Pathological_formation>] [tumor <Pathological_formation>] [peritumoral lymphocytic <Cell>] [tumor <Pathological_formation>] [surgical margins <Tissue>] [lymph nodes <Multi-tissue_structure>] [circumferential (deep, lateral) margin <Tissue>] [specimen <Pathological_formation>] [tissue <Tissue>] [lymph node metastases <Pathological_formation>] [lymph nodes <Multi-tissue_structure>] [distal mesorectum <Multi-tissue_structure>] [distal mesorectal tumor <Pathological_formation>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Costs of hip fracture. Rehabilitation of 180 patients in primary health care. Costs related to functional status were calculated for 180 consecutive hip fracture patients (mean age 78 years) who were admitted from their own home and rehabilitated in primary health care. Within 4 months after the fracture, 75 percent of the patients had been discharged to their own home, 9 percent were dead, and the short-term medical treatment costs per patient were SEK 43,000, whereas the total costs including communal help and costs for living accommodations after discharge were twice as high. The total costs per patient for long-term medical treatment (from 4 months up to 3 years after fracture) were 7 percent of the short-term medical treatment costs. Patients with a cervical fracture discharged to their own home and with good functional status consumed only one fifth of the resources that patients with a trochanteric fracture discharged to institutional care and who had reduced functional status consumed. A substantial part of the costs can be saved by improved organization of rehabilitation after discharge from the hospital. A further cost reduction would require a combination of technologic, social, and organizational changes aimed at early discharge and continued follow-up in primary health care.

[hip <Organism_subdivision>] [hip <Organism_subdivision>] [cervical <Organism_subdivision>] [trochanteric <Multi-tissue_structure>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Results and Discussion Figure 4 shows the frequency response of the device before and after plating cells. In the frequency range measured (4-600 Hz), only two clear peaks can be seen in the bare device. After cells had adhered to the surface, there is a shift in both the resonant frequency and the height of these peaks. Table 1 shows the results for this trial and a second trial where the experiment was repeated to confirm the initial results. At a plating density of 1300 cells/mm2, there were approximately 140 cells on the portion of the cantilever free to vibrate (dimensions shown in Figure 1). Table 1 Cantilever response data from two trials Experiment #1 Experiment #2 Freq. 1 (kHz) Amp. 1 (deg) Freq. 2 (kHz) Amp. 2 (deg) Freq. 1 (kHz) Amp. 1 (deg) Freq. 2 (kHz) Amp. 2 (deg) Initial 313.0 .086 375.5 .055 313.9 .091 376.5 .071 With cells 307.5 .031 371.0 .018 308 .052 370.5 .043 Change 5.5 .055 4.5 .037 5.9 .039 6.0 .028 Figure 4 Phase angle vs. frequency. (left) Phase angle of impedance with linear regression line. (right) To provide an easier comparison, phase angles have been levelled with respect to the linear regression line that passes through each set of data. The addition of cells causes the peaks to shift to lower frequencies and decrease in amplitude. The two peaks shown were the only detectable resonances despite the relatively wide frequency range measured. The electrical detection of resonances is critically compromised by the strong damping imposed by the cell media, making these measurements more challenging than those carried out in air or in a vacuum where resonance peaks show much larger amplitude [18]. In the desired in vivo application for this work, as a sensor for stent healing, it can be expected that in the course of normal healing the stent will be fully populated with a significantly thicker layer of endothelial cells. In the case of restenosis, this lining would be even thicker. This may hamper any movement of the cantilever and cause the peaks to eventually become undetectable. Frequent measurements of the resonant frequencies will differentiate this end state with the possibility of device failure. The noninvasive nature of these measurements that can be transmitted wirelessly to an external device make this an attractive and low risk option for monitoring healing.

[cells <Cell>] [cells <Cell>] [cells <Cell>] [cells <Cell>] [cells <Cell>] [cells <Cell>] [cell <Cell>] [endothelial cells <Cell>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Miscellaneous Proteins Apart from the above-described proteins, several other molecules are also associated with the pathological lesions of AD, and some of these can be regarded as amateur chaperones. Acute phase proteins, such as alpha1-antichymotrypsin (ACT), alpha2-macroglobulin (alpha2M), and SAP, are all associated with Abeta deposition [129-132]. ACT is a serine protease inhibitor of the serpin family, and in AD, ACT levels are upregulated, and binding of ACT with Abeta induces Abeta fibrillogenesis [133-135]. Furthermore, when ACT is overexpressed in transgenic mice, an increased plaque load in the brains of these mice and impaired spatial learning is observed [134, 135]. alpha2M also binds Abeta, although in contrast to ACT, this binding prevents Abeta fibril formation and fibril-associated neurotoxicity [136, 137]. alpha2M promotes the protease-mediated degradation of alpha2M/Abeta complexes and contributes to clearance of Abeta from the brain (discussed in paragraph 4) [138, 139]. The glycoprotein SAP belongs to the pentraxin family and is a common component of all known types of amyloid fibrils. SAP is upregulated in AD and protects amyloid fibrils from proteolysis in vitro [140, 141]. SAP not only colocalizes with SPs and interacts with aggregated Abeta; SAP oligomers also bind and activate C1 [142]. Both C1 and SAP may bind to fibrillar Abeta deposits in vivo and induce microglial activation, as cultured human microglial cells show an increase in cytokine production after co-stimulation of Abeta with C1q and SAP [104]. These observations further strengthen the above-noted suggestion that not only Abeta, but also several Abeta-binding proteins, are capable of activating the complement system, and thus, contribute to neuroinflammation in AD. In addition, both alpha2M and ACT, in contrast to SAP, can be regarded as amateur chaperones, as they regulate conformational changes of Abeta. Tissue-type plasminogen activator (tPA) regulates activation of plasminogen into plasmin and is expressed in various regions of the brain especially in the hippocampus [143]. Several reports suggested an important role for tPA in AD, as the tPA system is involved in Abeta turnover [144, 145]. Fibrillar forms of Abeta stimulate tPA activity in vitro, whereas in AD patients, a reduction of tPA activity is observed in the affected areas [144, 146]. Although tPA has no effect on conformational changes of Abeta, it might play a role in the clearance of Abeta from the brain (paragraph 4]. The actin-regulatory protein gelsolin is found both intracellularly and in plasma [147, 148]. Plasma gelsolin can be considered an amateur chaperone, as it binds Abeta and not only inhibits its Abeta fibrillization but is also capable of degrading preformed Abeta fibrils [149, 150]. Furthermore, gelsolin inhibits Abeta-mediated neurotoxicity [151]. One of the major gangliosides in the brain is GM1. Soluble Abeta binds GM1 and the formed complexes accelerate Abeta fibrillogenesis by acting as a seed for Abeta [152]. In the presence of GM1, Abeta is more neurotoxic than Abeta alone, and cholesterol-rich membranes demonstrate accelerated Abeta binding due to the formation of GM1 clusters [153, 154]. As GM1 is a major component of lipid rafts and recent studies suggest that Abeta accumulation in these lipid rafts is an early event in AD development, GM1 might play an important role in the early steps in AD pathogenesis [155, 156]. In summary, several proteins are associated with Abeta aggregates in the AD brain and contribute to the aggregation of Abeta and should, therefore, be considered as amateur chaperones. In addition, they might play a role in triggering inflammation.

[pathological lesions <Pathological_formation>] [plaque <Cell>] [brains <Organ>] [fibril <Pathological_formation>] [brain <Organ>] [amyloid fibrils <Pathological_formation>] [amyloid fibrils <Pathological_formation>] [fibrillar <Pathological_formation>] [microglial <Cell>] [microglial cells <Cell>] [brain <Organ>] [hippocampus <Multi-tissue_structure>] [Fibrillar <Pathological_formation>] [brain <Organ>] [cellularly <Cell>] [plasma <Organism_substance>] [Plasma <Organism_substance>] [fibrils <Pathological_formation>] [brain <Organ>] [membranes <Cellular_component>] [lipid rafts <Organism_substance>] [lipid rafts <Organism_substance>] [AD brain <Organ>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Image-directed and color Doppler studies of gallbladder tumors. Thirteen cases of primary adenocarcinoma of the gallbladder (GB), 1 of malignant fibrous histocytoma, 3 of metastatic adenocarcinoma, 5 of adenoma, 5 of polypus, 2 of xanthogranuloma, 6 of chronic cholecystitis, 4 of acute cholecystitis, and 8 of subacute cholecystitis were studied by image-directed and color Doppler ultrasonography (CDUS). All of the 14 cases of primary GB cancer (10 masses, 4 thickening wall) were found to have a high velocity arterial blood flow signal in the wall of the GB. In contrast, the 3 cases of metastatic cancer of the GB had no blood flow signal in the wall of the GB. For the 30 cases of benign lesions of the GB, only in 12 cases was a low velocity blood flow signal found. Nine of 10 cases of primary GB malignancy were found to have high velocity arterial blood flow signals in the tumor masses. No blood flow signal was observed in the masses of 13 cases (3 of metastatic adenocarcinoma, 5 of adenoma, 5 of polypus). An abnormal high velocity arterial blood flow signal observed within masses in the GB or in the GB wall is a significant feature of primary GB cancer and thus helps to differentiate primary GB cancer from metastatic and benign lesions of the GB.

[gallbladder tumors <Pathological_formation>] [adenocarcinoma <Pathological_formation>] [gallbladder <Organ>] [GB <Organ>] [malignant fibrous histocytoma <Pathological_formation>] [metastatic adenocarcinoma <Pathological_formation>] [adenoma <Pathological_formation>] [polypus <Pathological_formation>] [xanthogranuloma <Pathological_formation>] [GB cancer <Pathological_formation>] [wall <Multi-tissue_structure>] [arterial blood <Organism_substance>] [wall <Multi-tissue_structure>] [GB <Organ>] [metastatic cancer <Pathological_formation>] [GB <Organ>] [blood <Organism_substance>] [wall <Multi-tissue_structure>] [GB <Organ>] [benign lesions <Pathological_formation>] [GB <Organ>] [blood <Organism_substance>] [GB malignancy <Pathological_formation>] [arterial blood <Organism_substance>] [tumor <Pathological_formation>] [blood <Organism_substance>] [metastatic adenocarcinoma <Pathological_formation>] [adenoma <Pathological_formation>] [polypus <Pathological_formation>] [arterial blood <Organism_substance>] [GB <Organ>] [GB wall <Multi-tissue_structure>] [GB cancer <Pathological_formation>] [GB cancer <Pathological_formation>] [metastatic <Pathological_formation>] [benign lesions <Pathological_formation>] [GB <Organ>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

2.1. Genome sequencing, assembly and validation DNA shotgun libraries with average insert sizes of 1.6 and 6.5 kb were constructed in pUC118 (TaKaRa), whereas a fosmid library with average insert size of 37 kb was constructed in pCC1FOS (EPICENTRE) as described previously.18,19 A total of 50 400 clones (34 560, 10 752 and 5088 clones from libraries with 1.6, 6.5 and 37 kb inserts, respectively) were subjected to sequencing from both ends of the inserts on either ABI 3730xl DNA Analyzer (Applied Biosystems) or Base Station DNA Fragment Analyzer BST-0100 (MJ Research, Inc.). Sequence reads were trimmed at a threshold quality value of 20 by Phred and assembled by Phrap and CONSED assembly tools.20,21 For alignment and validation of contigs, Optical Mapping (OpGen) was used. Gaps between contigs were closed by sequencing PCR products, which bridge two neighboring contigs. Finally, each base of K. setae NBRC 14216T genome was ensured to be sequenced from multiple clones and from both directions with Phrap quality score >=70 or from one direction with Phrap quality score >=40. Chromosomal terminus was determined after attaching adenine and thymine homopolymers to the naked 3' ends of the chromosome as described previously.5

[chromosome <Cellular_component>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

CONCLUSION Intra-operative monitoring of partial pressure of tissue oxygen (PtiO2 ) is a very sensitive method of detecting the decrease of oxygen for cell utilization, due to decreased blood flow, during temporary clipping and after definitive clipping, in middle cerebral artery incidental unruptured aneurysm surgery. "Basal values", obtained without the influence of subarachnoid blood, were lower than expected in "uninjured" brain, and this fact, although unexplained, should be kept in mind in future investigation in this field. Although values that could be predictive of brain ischemia could not be established, an incomplete recovery or continuous decrease in PtiO2 values after definitive clipping should be considered an indicator of high risk for the development of post-operative brain infarction, and, therefore, an indication for verification of the position of the clip.

[tissue <Tissue>] [cell <Cell>] [blood <Organism_substance>] [cerebral artery <Multi-tissue_structure>] [aneurysm <Pathological_formation>] [subarachnoid blood <Organism_substance>] [brain <Organ>] [brain <Organ>] [brain <Organ>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

a, b Radiographs of the left elbow and forearm 5 months after the surgery

[elbow <Organism_subdivision>] [forearm <Organism_subdivision>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

COMMENTS Recurrent anterior vaginal wall prolapse can develop in more than 20% of patients undergoing traditional anterior colporrhaphy. In light of this high recurrence rate many surgeons have been incorporating synthetic or allograft mesh to augment the repair. In this study there are some shortcomings, including retrospective design, short follow-up for a study spanning almost six years and a lack of validated questionnaires. Authors report a negative experience with porcine dermis, both in terms of success and extrusion rate. However, others have reported better outcome[1] which may be due to different follow-up times and outcome measures. Apart from this, biological grafts are also associated with allergic reactions and disease transmission. There is paucity of data regarding prospective randomized trials on the use of these biomaterials prior to their widespread human need which might help in reducing such type of experiences. Unless such data are available surgeons should give serious thought prior to embarking on the use of such biological materials.[2]

[anterior vaginal wall <Multi-tissue_structure>] [dermis <Multi-tissue_structure>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

RNA extraction and reverse transcription Total RNA were extracted from cells using either Trizol reagent (Invitrogen) or RNeasy kit (Qiagen) and treated with DNaseI reagent (Macherey-Nagel) for 30 min at room temperature. Reverse transcriptions were performed using 1microg total RNA and the High capacity cDNA reverse transcription kit with RNase Inhibitor (Applied Biosystems).

[cells <Cell>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Methodologies for measuring carcinogen adducts in humans. In summary, although some of the more optimistic aspirations for human biomonitoring studies envisaged a decade ago have not been realized thus far, some considerable advances have been made. The examples cited above indicate that the feasibility of biomonitoring has been clearly established. In addition, they demonstrate the need for preliminary biomarker testing and validation through transitional studies prior to their field application. In the next decade of research into carcinogen adducts in humans, continued improvements in the reproducibility and specificity of assays for DNA adducts will be needed. Perhaps the increasing use of hybrid methodologies to concentrate adducts followed by specific chemical analyses will allow such adducts to be monitored more precisely. Of course, further basic research into the mechanisms of carcinogenesis will allow the measurement of specific novel markers which are more closely tied to the disease endpoint than adducts. The development of new assays for determining metabolic phenotypes and genotypes relevant to carcinogenesis should improve our estimates of susceptibility (46-48). Such new approaches along with the sustained improvement of current assays will allow molecular approaches to continue to enrich cancer epidemiology in the future.

[cancer <Pathological_formation>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Regulation of glucosyl- and fructosyltransferase synthesis by continuous cultures of Streptococcus mutans. Streptococcus mutans strains Ingbritt, and its derivative B7 which had been passaged through monkeys, have been used to investigate how the synthesis of extracellular glucosyl- and fructosyltransferases is regulated. The most active enzyme from carbon-limited continuous cultures was a fructosyltransferase; enzymes catalysing the formation of water-insoluble glucans from sucrose were relatively inactive. Dextransucrase (EC 2.4.1.5), which catalyses soluble glucan synthesis, was most active in the supernatant fluid from cultures grown with excess glucose, fructose or sucrose, but full activity was detected only when the enzyme was incubated with both sucrose and dextran. Little dextransucrase activity was detected in carbon-limited cultures. It is concluded that glucosyl- and fructosyltransferases are constitutive enzymes in that they are synthesized at similar rates during growth with an excess of the substrate or of the products of the reactions which they catalyse. Although the Ingbritt strain was originally isolated from a carious lesion, it is now a poor source of glucosyltransferase activity. Glucosyltransferases were extremely active in cultures of a recent clinical isolate, strain 3209, and were apparently induced during growth with excess glucose.

[extracellular <Immaterial_anatomical_entity>] [carious lesion <Pathological_formation>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Tonometry in normal and scarred corneas, and in postkeratoplasty eyes: a comparative study of the Goldmann, the ProTon and the Schiotz tonometers. PURPOSE: Clinical comparison of intraocular pressure (IOP) measured with the Goldmann applanation tonometer (GAT), the ProTon tonometer (PT), and the Schiotz tonometer (ST), in normal eyes, eyes with scarred corneas and postkeratoplasty eyes. MATERIAL AND METHODS: The IOP readings with GAT, PT, and ST were compared in 125 eyes with normal corneas (Group A), 17 eyes with scarred corneas (Group B), and in 21 postkeratoplasty eyes (Group C). The data were statistically analysed at 95% confidence interval; linear regression analysis and paired t-test were done. RESULTS: The mean differences and their standard deviation [SD] between GAT and PT readings, and GAT and ST readings respectively were: [1] in Group A: -0.23 [SD 2.75] mmHg and +0.24 [SD 3.18] mmHg respectively; [2] in Group B: -1.8 [SD 12.67] mmHg and -4.5 [SD 9.95 mmHg; and [3] in Group C: +0.24 [SD 8.72] mmHg and -0.12 [SD 8.7] mmHg. They were not statistically significant. In Group A the 95% confidence interval between GAT and PT readings was -5.27 mmHg to 5.73 mmHg, and between GAT and ST readings, -6.12 mmHg to 6.59 mmHg. Ninety six [77%] eyes with the PT and 84 [69%] eyes with ST measurements were within 3 mmHg of GAT pressure. The correlation coefficients [r] for PT and ST were 0.93 [P = 0.0000] and 0.88 [P = 0.0000] respectively. In Group B 95% confidence interval between GAT and PT readings was -27.17 mmHg to 23.51 mmHg, and between GAT and ST measurement, -24.37 mmHg to 15.44 mmHg. The correlation coefficients [r] for the PT and ST were 0.112 [P = 0.660] and 0.630 [P = 0.006] respectively. In group C, the 95% confidence interval between GAT and PT measurements was -17.20 mmHg to 17.67 mmHg, and between GAT and ST measurements, -17.51 mmHg to 17.27 mmHg. The correlation coefficients [r] for the PT and the ST were 0.780 [P = 0.0000] and 0.740 [P = 0.0001] respectively. CONCLUSIONS: In clinical practice PT appears to have a higher level of accuracy than ST in normal corneas. In scarred corneas and post-penetrating keratoplasty eyes, because of high SD for mean differences and wide confidence interval of 95%, both PT and ST are inaccurate in measuring IOP as compared to GAT in such eyes.

[corneas <Multi-tissue_structure>] [eyes <Organ>] [intraocular <Immaterial_anatomical_entity>] [eyes <Organ>] [eyes <Organ>] [corneas <Multi-tissue_structure>] [eyes <Organ>] [eyes <Organ>] [corneas <Multi-tissue_structure>] [eyes <Organ>] [corneas <Multi-tissue_structure>] [eyes <Organ>] [eyes <Organ>] [eyes <Organ>] [corneas <Multi-tissue_structure>] [corneas <Multi-tissue_structure>] [eyes <Organ>] [eyes <Organ>]

You are provided with a text. Your objective is to identify, extract and classify all anatomical entities mentioned in the text, maintaining the order in which they appear. Types are [Pathological_formation, Organ, Tissue, Multi-tissue_structure, Developing_anatomical_structure, Cell, Anatomical_system, Organism_subdivision, Organism_substance, Cellular_component, Immaterial_anatomical_entity]. The entities should be presented in the following format: [entity <type>].

Study of freeze-thaw effects and CSF pH on tissue RNA integrity We have long suspected, on the basis of our tissue banking experience, that most of the molecular degradation that occurs in banked tissue is due to repeated freeze-thaw cycles, which occur due to improper handling during dissection for tissue retrieval or due to freezer malfunctions. Our freezers are currently protected by temperature-sensitive alarms that automatically telephone maintenance and tissue banking personnel when the temperature reaches a certain level. More protection is preferable, with CO2 tanks for backup cooling the optimum (but expensive) approach. We plan to systematically investigate the effects of thawing and refreezing on RNA integrity, by deliberately thawing and freezing small samples of brain tissue over varying time intervals and temperatures.

[tissue <Tissue>] [tissue <Tissue>] [tissue <Tissue>] [tissue <Tissue>] [tissue <Tissue>] [samples <Tissue>] [brain tissue <Tissue>]