bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differences in the transcriptome signatures of two genetically related Entamoeba histolytica cell lines derived from the same isolate with different pathogenic properties
Authors: Biller Laura , Davis Paul H , Tillack Manuela , Matthiesen Jenny , Lotter Hannelore , Stanley Samuel L , Tannich Egbert , Bruchhaus Iris 
Published: January 2010

Abstract

Background
The availability of two genetically very similar cell lines (A and B) derived from the laboratory isolate Entamoeba histolytica HM-1:IMSS, which differ in their virulence properties, provides a powerful tool for identifying pathogenicity factors of the causative agent of human amoebiasis. Cell line A is incapable inducing liver abscesses in gerbils, whereas interaction with cell line B leads to considerable abscess formation. Phenotypic characterization of both cell lines revealed that trophozoites from the pathogenic cell line B have a larger cell size, an increased growth rate in vitro, an increased cysteine peptidase activity and higher resistance to nitric oxide stress. To find proteins that may serve as virulence factors, the proteomes of both cell lines were previously studied, resulting in the identification of a limited number of differentially synthesized proteins. This study aims to identify additional genes, serving as virulence factors, or virulence markers.

Results
To obtain a comprehensive picture of the differences between the cell lines, we compared their transcriptomes using an oligonucleotide-based microarray and confirmed findings with quantitative real-time PCR. Out of 6242 genes represented on the array, 87 are differentially transcribed (≥two-fold) in the two cell lines. Approximately 50% code for hypothetical proteins. Interestingly, only 19 genes show a five-fold or higher differential expression. These include three rab7 GTPases, which were found with a higher abundance in the non-pathogenic cell line A. The aig1-like GTPases are of special interest because the majority of them show higher levels of transcription in the pathogenic cell line B. Only two molecules were found to be differentially expressed between the two cell lines in both this study and our previous proteomic approach.

Conclusions
In this study we have identified a defined set of genes that are differentially transcribed between the non-pathogenic cell line A and the pathogenic cell line B of E. histolytica. The identification of transcription profiles unique for amoebic cell lines with pathogenic phenotypes may help to elucidate the transcriptional framework of E. histolytica pathogenicity and serve as a basis for identifying transcriptional markers and virulence factors.
Divergent adaptive and innate immunological responses are observed in humans following blunt trauma
Authors: Kasten Kevin R , Goetzman Holly S , Reid Maria R , Rasper Alison M , Adediran Samuel G , Robinson Chad T , Cave Cindy M , Solomkin Joseph S , Lentsch Alex B , Johannigman Jay A , Caldwell Charles C 
Published: January 2010

AbstractBackgroundThe immune response to trauma has traditionally been modeled to consist of the systemic inflammatory response syndrome (SIRS) followed by the compensatory anti-inflammatory response syndrome (CARS). We investigated these responses in a homogenous cohort of male, severe blunt trauma patients admitted to a University Hospital surgical intensive care unit (SICU). After obtaining consent, peripheral blood was drawn up to 96 hours following injury. The enumeration and functionality of both myeloid and lymphocyte cell populations were determined.ResultsNeutrophil numbers were observed to be elevated in trauma patients as compared to healthy controls. Further, neutrophils isolated from trauma patients had increased raft formation and phospho-Akt. Consistent with this, the neutrophils had increased oxidative burst compared to healthy controls. In direct contrast, blood from trauma patients contained decreased naïve T cell numbers. Upon activation with a T cell specific mitogen, trauma patient T cells produced less IFN-gamma as compared to those from healthy controls. Consistent with these results, upon activation, trauma patient T cells were observed to have decreased T cell receptor mediated signaling.ConclusionsThese results suggest that following trauma, there are concurrent and divergent immunological responses. These consist of a hyper-inflammatory response by the innate arm of the immune system concurrent with a hypo-inflammatory response by the adaptive arm.
Microbiological quality of drinking water from dispensers in Italy
Authors: Liguori Giorgio , Cavallotti Ivan , Arnese Antonio , Amiranda Ciro , Anastasi Daniela , Angelillo Italo F 
Published: January 2010

Abstract

Background
Water coolers are popular in office buildings and commercial stores and the quality of this source of drinking water has the potential to cause waterborne outbreaks, especially in sensitive and immunocompromised subjects. The aim of this study was to determine the quality of water plumbed in coolers from commercial stores in comparison with tap water in Italy.

Methods
For each sample, microbial parameters and chemical indicators of contamination were evaluated and information about the date of installation, time since last ordinary and extraordinary maintenance of water coolers was collected.

Results
In all samples the chemical parameters (nitrite, ammonium, free active chlorine residual) did not exceed the reference values of the drinking water regulation; the pH value in 86.8% samples of the carbonated waters was lower than the reference limit. The microbiological results indicated that the bacteria count at 22°C and 37°C was higher than the required values in 71% and 81% for the non-carbonated water and in 86% and 88% for the carbonated one, respectively. Enterococcus spp. and Escherichia coli were not detected in any of the water samples. Pseudomonas aeruginosa was found in only one sample of the tap water and in 28.9% and 23.7% of the non-carbonated and carbonated water samples, respectively. No statistically significant differences in bacterial counts at 22°C and 37°C have been found between the non-carbonated and carbonated water from the sampled coolers in relation with the time since the last filter was substituted. The bacteriological quality of tap water was superior to that of non-carbonated and carbonated water from coolers.

Conclusion
The results emphasize the importance of adopting appropriate routinely monitoring system in order to prevent or to diminish the chances of contamination of this water source.
Transcriptional regulatory network triggered by oxidative signals configures the early response mechanisms of japonica rice to chilling stress
Authors: Yun Kil-Young , Park Myoung Ryoul , Mohanty Bijayalaxmi , Herath Venura , Xu Fuyu , Mauleon Ramil , Wijaya Edward , Bajic Vladimir B , Bruskiewich Richard , de los Reyes Benildo G 
Published: January 2010

AbstractBackgroundThe transcriptional regulatory network involved in low temperature response leading to acclimation has been established inArabidopsis. In japonica rice, which can only withstand transient exposure to milder cold stress (10°C), an oxidative-mediated network has been proposed to play a key role in configuring early responses and short-term defenses. The components, hierarchical organization and physiological consequences of this network were further dissected by a systems-level approach.ResultsRegulatory clusters responding directly to oxidative signals were prominent during the initial 6 to 12 hours at 10°C. Early events mirrored a typical oxidative response based on striking similarities of the transcriptome to disease, elicitor and wounding induced processes. Targets of oxidative-mediated mechanisms are likely regulated by several classes of bZIP factors acting on as1/ocs/TGA-like element enriched clusters, ERF factors acting on GCC-box/JAre-like element enriched clusters and R2R3-MYB factors acting on MYB2-like element enriched clusters.Temporal induction of several H2O2-induced bZIP, ERF and MYB genes coincided with the transient H2O2spikes within the initial 6 to 12 hours. Oxidative-independent responses involveDREB/CBF,RAP2andRAV1factors acting on DRE/CRT/rav1-like enriched clusters and bZIP factors acting on ABRE-like enriched clusters. Oxidative-mediated clusters were activated earlier than ABA-mediated clusters.ConclusionGenome-wide, physiological and whole-plant level analyses established a holistic view of chilling stress response mechanism of japonica rice. Early response regulatory network triggered by oxidative signals is critical for prolonged survival under sub-optimal temperature. Integration of stress and developmental responses leads to modulated growth and vigor maintenance contributing to a delay of plastic injuries.
Prostaglandin E2-induced colonic secretion in patients with and without colorectal neoplasia
Authors: Kaltoft Nicolai , Tilotta Maria C , Witte Anne-Barbara , Osbak Philip S , Poulsen Steen S , Bindslev Niels , Hansen Mark B 
Published: January 2010

Abstract

Background
The pathogenesis for colorectal cancer remains unresolved. A growing body of evidence suggests a direct correlation between cyclooxygenase enzyme expression, prostaglandin E2 metabolism and neoplastic development. Thus further understanding of the regulation of epithelial functions by prostaglandin E2 is needed. We hypothesized that patients with colonic neoplasia have altered colonic epithelial ion transport and express functionally different prostanoid receptor levels in this respect.

Methods
Patients referred for colonoscopy were included and grouped into patients with and without colorectal neoplasia. Patients without endoscopic findings of neoplasia served as controls. Biopsy specimens were obtained from normally appearing mucosa in the sigmoid part of colon. Biopsies were mounted in miniaturized modified Ussing air-suction chambers. Indomethacin (10 μM), various stimulators and inhibitors of prostanoid receptors and ion transport were subsequently added to the chamber solutions. Electrogenic ion transport parameters (short circuit current and slope conductance) were recorded. Tissue pathology and tissue damage before and after experiments was assessed by histology.

Results
Baseline short circuit current and slope conductance did not differ between the two groups. Patients with neoplasia were significantly more sensitive to indomethacin with a decrease in short circuit current of 15.1 ± 2.6 μA·cm-2 compared to controls, who showed a decrease of 10.5 ± 2.1 μA·cm-2 (p = 0.027). Stimulation or inhibition with theophylline, ouabain, bumetanide, forskolin or the EP receptor agonists prostaglandin E2, butaprost, sulprostone and prostaglandin E1 (OH) did not differ significantly between the two groups. Histology was with normal findings in both groups.

Conclusions
Epithelial electrogenic transport is more sensitive to indomethacin in normal colonic mucosa from patients with previous or present colorectal neoplasia compared to colonic mucosa from control patients. Stimulated epithelial electrogenic transport through individual prostanoid subtype receptors EP1, EP2, EP3, and EP4 is not significantly different between neoplasia diseased patients and controls. This indicates that increased indomethacin-sensitive mechanisms in colonic mucosa from neoplasia diseased patients are not related to differences in functional expression of EP receptor subtypes.
Diagnoses and visit length in complementary and mainstream medicine
Authors: Heiligers Phil JM , de Groot Judith , Koster Dick , van Dulmen Sandra 
Published: January 2010

Abstract

Background
The demand for complementary medicine (CM) is growing worldwide and so is the supply. So far, there is not much insight in the activities in Dutch CM practices nor in how these activities differ from mainstream general practice. Comparisons on diagnoses and visit length can offer an impression of how Dutch CM practices operate.

Methods
Three groups of regularly trained physicians specialized in CM participated in this study: 16 homeopathic physicians, 13 physician acupuncturists and 11 naturopathy physicians. Every CM physician was asked to include a maximum of 75 new patients within a period of six months. For each patient an inclusion registration form had to be completed and the activities during a maximum of five repeat visits were subsequently registered. Registrations included patient characteristics, diagnoses and visit length. These data could be compared with similar data from general practitioners (GPs) participating in the second Dutch national study in general practice (DNSGP-2). Differences between CM practices and between CM and mainstream GP data were tested using multilevel regression analysis.

Results
The CM physicians registered activities in a total of 5919 visits in 1839 patients. In all types of CM practices general problems (as coded in the ICPC) were diagnosed more often than in mainstream general practice, especially fatigue, allergic reactions and infections. Psychological problems and problems with the nervous system were also diagnosed more frequently. In addition, each type of CM physician encountered specific health problems: in acupuncture problems with the musculoskeletal system prevailed, in homeopathy skin problems and in naturopathy gastrointestinal problems. Comparisons in visit length revealed that CM physicians spent at least twice as much time with patients compared to mainstream GPs.

Conclusions
CM physicians differed from mainstream GPs in diagnoses, partly related to general and partly to specific diagnoses. Between CM practices differences were found on specific domains of complaints. Visit length was much longer in CM practices compared to mainstream GP visits, and such ample time may be one of the attractive features of CM for patients.
Developing counseling skills through pre-recorded videos and role play: a pre- and post-intervention study in a Pakistani medical school
Authors: Ahsen Noor F , Batul Syeda A , Ahmed Ahsen N , Imam Sardar Z , Iqbal Humaira , Shamshair Khayyam , Ali Hammad 
Published: January 2010

Abstract

Background
Interactive methods like role play, recorded video scenarios and objective structured clinical exam (OSCE) are being regularly used to teach and assess communication skills of medical students in the western world. In developing countries however, they are still in the preliminary phases of execution in most institutes. Our study was conducted in a naïve under resourced setup to assess the impact of such teaching methodologies on the counseling skills of medical students.

Methods
Fifty four 4th year MBBS students were identified to be evaluated for communication skills by trained facilitators in a pre-intervention OSCE. The same group of students was given a demonstration of ideal skill level by means of videos and role playing sessions in addition to real life interaction with patients during hospital and community rotations. A post-intervention evaluation was carried out six months later through OSCE and direct observation through structured checklist (DOS) in hospital and community settings. The combined and individual performance levels of these students were analyzed.

Results
There was a statistically significant difference in the communication skills of students when assessed in the post-intervention OSCE (p = 0.000). Individual post-intervention percentages of study participants displayed improvement as well (n = 45, p = 0.02). No difference was observed between the scores of male and female students when assessed for two specific competencies of antenatal care and breast feeding counseling (p = 0.11). The mean DOS (%) score of 12 randomly selected students was much lower as compared to the post-intervention (%) score but the difference between them was statistically non significant, a result that may have been affected by the small sample size as well as other factors that may come into play in real clinical settings and were not explored in this study (59.41 ± 7.8 against 82.43 ± 22.08, p = 0.88).

Conclusions
Videos and role play in combination with community and clinical exposure are effective modes of teaching counseling skills to medical students. They can be successfully utilized even in a limited resource setup, as demonstrated by our trial.
Malaria incidence and prevalence on Pemba Island before the onset of the successful control intervention on the Zanzibar Archipelago
Authors: Jaenisch Thomas , Sullivan David J , Dutta Arup , Deb Saikat , Ramsan Mahdi , Othman Mashavu K , Gaczkowski Roger , Tielsch James , Sazawal Sunil 
Published: January 2010

Abstract

Background
Malaria incidence has been reported to decrease substantially in parts of sub-Saharan Africa, including the Zanzibar Archipelago in East Africa. A cohort study with an intensive follow-up on Pemba Island just before the onset of the highly successful malaria control intervention was conducted. The reported estimates of parasite prevalence and incidence can serve as a robust baseline to evaluate the effect size of the successful interventions and the potential contribution of quality controls and other factors associated with research studies in the decreased estimate of transmission.

Methods
In a rural clinic, two successive cohorts of 537 children total aged 2-23 months were followed for six months each with an intensive visitation schedule of bi-weekly follow-up. Robust estimates of incidence and prevalence according to four different malaria definitions were obtained.

Results
Malaria incidence and prevalence placed Pemba Island in a hyperendemic rather than holoendemic setting for the years 2003-2005. Overall parasite prevalence was estimated to be 39% - with monthly estimates varying between 30% and 50%. Incidence of malaria varied between 2.3 and 3.8 malaria episodes per year based on a diagnosis of fever and various microscopy-based parasite thresholds and between 4.8 and 5.7 based on a diagnosis of fever and 100 parasites/microliter analogous to detection by rapid diagnostic tests. Both parasite densities and malaria incidence increased with age and rainy season. Malaria incidence also varied substantially between the individual villages within the study area.

Conclusions
Pemba Island was previously considered holo-endemic for Malaria. The data suggest that the transmission situation on Pemba Island was significantly lower in 2003-2005 suggesting a hyper-endemic or meso-endemic transmission environment. The figures were obtained just before the onset of the highly successful malaria control intervention by impregnated bed nets and IRS on the Zanzibar Archipelago and provide robust estimates of the malaria transmission situation prior to the control programme. Together with other published data, the results suggest that malaria transmission had started to decrease before the onset of the control programme. The local heterogeneity in malaria incidence highlights the importance of a micro-epidemiological approach in the context of malaria control and elimination.
Constitutively overexpressed 21 kDa protein in Hodgkin lymphoma and aggressive non-Hodgkin lymphomas identified as cytochrome B5b (CYB5B)
Authors: Murphy Derek , Parker Jeremy , Zhou Minglong , Fadlelmola Faisal M , Steidl Christian , Karsan Aly , Gascoyne Randy D , Chen Hong , Banerjee Diponkar 
Published: January 2010

AbstractBackgroundWe have previously reported a novel constitutively overexpressed 21 kDa protein in Hodgkin Lymphoma (HL) and aggressive Non-Hodgkin Lymphomas (NHL). The objective of the current study was to 1) identify this protein using two independent methods, 2) study the expression of the protein and its encoding mRNA in reactive lymph nodes, normal lymphocytes and CD34+ bone marrow precursor cells, 3) analyse patterns of expression of the protein in tissue microarrays assembled from a large number of diagnostic clinical biopsies from patients with HL, and 4) determine the copy number variation and mutation status of the encoding gene in HL cell lines.ResultsPeptide sequencing by LC-MS/MS and protein identification by protein array screening identified a single protein, CYB5B. No mutations were detected in theCYB5Bgene in HL cell lines. Quantitative PCR showedCYB5Bgene expression was increased in HL and NHL cell lines. Array CGH using a submegabase resolution tiling array revealed gains in theCYB5Blocus in HL cell lines KMH2 and L428. Membrane expression was seen in Reed-Sternberg cells in clinical biopsies from patients with HL but not in reactive lymph nodes. Bone marrow CD34+ precursor cells were CYB5B negative on the cell surface. RT-PCR assays of RNA extracted from T and B cell enriched fractions obtained from normal peripheral blood mononuclear cells, reactive lymph nodes, tonsils and normal bone marrow samples showed no evidence of increased mRNA levels ofCYB5Bin comparison to housekeeping geneGAPDH.ConclusionsThe 21 kDa protein overexpressed in HL and aggressive NHL is identical to CYB5B.CYB5Bgene expression is increased in a subset of HL and NHL cell lines tested. This is associated withCYB5Bgene amplification in HL cell lines KMH2 and L428. CYB5B may be a potential target for antibody-based therapy of HL and aggressive NHL as although cytoplasmic expression is present in reactive lymphocytes, it is not expressed on the cell surface of non-neoplastic lymphocytes or bone marrow precursor cells.
Cell-specific targeting of lentiviral vectors mediated by fusion proteins derived from Sindbis virus, vesicular stomatitis virus, or avian sarcoma/leukosis virus
Authors: Zhang Xian-Yang , Kutner Robert H , Bialkowska Agnieszka , Marino Michael P , Klimstra William B , Reiser Jakob 
Published: January 2010

Abstract

Background
The ability to efficiently and selectively target gene delivery vectors to specific cell types in vitro and in vivo remains one of the formidable challenges in gene therapy. We pursued two different strategies to target lentiviral vector delivery to specific cell types. In one of the strategies, vector particles bearing a membrane-bound stem cell factor sequence plus a separate fusion protein based either on Sindbis virus strain TR339 glycoproteins or the vesicular stomatitis virus G glycoprotein were used to selectively transduce cells expressing the corresponding stem cell factor receptor (c-kit). An alternative approach involved soluble avian sarcoma/leukosis virus receptors fused to cell-specific ligands including stem cell factor and erythropoietin for targeting lentiviral vectors pseudotyped with avian sarcoma/leukosis virus envelope proteins to cells that express the corresponding receptors.

Results
The titers of unconcentrated vector particles bearing Sindbis virus strain TR339 or vesicular stomatitis virus G fusion proteins plus stem cell factor in the context of c-kit expressing cells were up to 3.2 × 105 transducing units per ml while vector particles lacking the stem cell factor ligand displayed titers that were approximately 80 fold lower. On cells that lacked the c-kit receptor, the titers of stem cell factor-containing vectors were approximately 40 times lower compared to c-kit-expressing cells.
Lentiviral vectors pseudotyped with avian sarcoma/leukosis virus subgroup A or B envelope proteins and bearing bi-functional bridge proteins encoding erythropoietin or stem cell factor fused to the soluble extracellular domains of the avian sarcoma/leukosis virus subgroup A or B receptors resulted in efficient transduction of erythropoietin receptor or c-kit-expressing cells. Transduction of erythropoietin receptor-expressing cells mediated by bi-functional bridge proteins was found to be dependent on the dose, the correct subgroup-specific virus receptor and the correct envelope protein. Furthermore, transduction was completely abolished in the presence of anti-erythropoietin antibody.

Conclusions
Our results indicate that the avian sarcoma/leukosis virus bridge strategy provides a reliable approach for cell-specific lentiviral vector targeting. The background levels were lower compared to alternative strategies involving Sindbis virus strain TR339 or vesicular stomatitis virus fusion proteins.