bluuebunny/crossref_metadata_2025_split huggingface dataset:
Polymorphism ofMC4RAsp298Asn site and its relationship with backfat thickness in commercial pigs
Authors: Xiao-Hui Yang , Yuan Liu , Hui Tang , Ning-Bo Zhang , Ying Wu , Shu-Dong Wei , Yun-Liang Jiang 
Published: March 2009

AbstractMelanocortin-4 receptor (MC4R) is a member of the superfamily of G-protein-coupled receptors (GPCRs), which affects body weight, energy homeostasis and food intake in humans and mice. In this study, the Asp298Asn polymorphism of theMC4Rgene was investigated in Laiwu, Yorkshire×Laiwu and commercial cross-bred pig populations using polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP), and the relationship of this mutation with backfat thickness was analysed. The results indicated that only genotype 11 exists in 33 individuals of Laiwu pigs, and three genotypes (11, 12 and 22) were detected in Yorkshire×Laiwu and commercial cross-bred populations. The distributions of allele and genotype frequencies in Yorkshire×Laiwu and commercial cross-bred populations were similar, with the frequency of allele 1 being higher than that of allele 2. In commercial cross-bred pigs, the mean backfat thickness of individuals with genotype 22 was significantly higher than that of individuals with genotypes 12 (P<0.01) and 11 (P<0.05). This study provides evidence that the Asp298Asn polymorphism of theMC4Rgene is associated with backfat thickness in commercial cross-bred pigs with Western pigs as parental lines and, therefore, can be used as a DNA marker for breeding in such populations of pigs.
Isolation and culture of bone marrow mesenchymal stem cells from human fetus and their biological properties
Authors: Yi-Hua Zhang , Zhong-Ying Dou , Wen-Zheng Shen , Chun-Rong Yang , Zhi-Min Gao 
Published: March 2009

AbstractThe population doubling number (70–80 times) of human fetal bone marrow mesenchymal stem cells (BMMSCs) is about two times higher than that (30–40 times) of adult BMMSCs, and their differentiation capacity is superior to that of their adult counterparts. In this study, BMMSCs were isolated from long bones of 2- to 3-month-old human abortuses by rinsing and selectively culturing whole marrow cells. Basic medium and serum concentration were optimized and growth curves plotted, both by MTT [3-(4,5-dimethylthiazol-2-yl)-2,5-di-phenyltetrazolium bromide] reduction assay. Isolated cells were identified by flow cytometry and immunocytochemistry for their antigen markers. The biosafety of isolated cells was evaluated by karyotype analysis and a tumour-forming experiment. The results indicated that lengthwise scissoring of fetal long bones and rinsing of their marrow cells was practical and useful for recovery of BMMSCs from the investigated human abortuses. In this experiment, α-MEM (minimum essential medium, alpha medium)+20% FCS (fetal calf serum) was the best for in vitro culture of BMMSCs. The third-passage BMMSCs expressed Oct4, SSEA3 and SSEA4 besides the surface markers of their adult counterparts. The population doubling time of the BMMSCs of passage 6, 12 and 24 were 34, 36 and 40 h, respectively. Cells in all passages showed a diploid karyotype and formed no tumours in nude mice. The BMMSCs used in this study proved to be biologically safe and ideal seed cells for research on human tissue engineering and regeneration medicine.
In vitro differentiation of chicken spermatogonial stem cells into adipocytes
Authors: Fei Yu , Jian-Hui Ge , Li-Gang Ni , Xian-Hong He , Qi Xu , Bi-Chun Li 
Published: March 2009

AbstractSpermatogonial stem cells (SSCs), which were isolated from chicken (Gallus gallus) embryo testes 16 days after laying, were cultured, subcultured, and induced into adipocytes in vitro. The differentiated cells were identified by oil red-O staining. Dexamethasone, insulin and 3-isobutyl-1-methylxanthine (IBMX) were tested for their induction potential. About 7–21 days after induction, SSCs differentiated into adipocytes, and the resulting adipocytes strongly expressed peroxisome proliferation activation receptor-γ (PPAR-γ). The assay outcome showed that an optimal treatment consisted of dexamethasone, insulin and IBMX application for 3 days and insulin for 1 day (3 cycles), then insulin for 21 days. The differentiation ratio was 85%, better than the combined use of dexamethasone, insulin and IBMX (P<0.01). However, the combination of the three derivatives triggered a stronger induction than any of them used alone (P<0.01). This study has demonstrated the potential of chicken embryonic SSCs to differentiate in vitro into adipocytes.
Income and the use of health care: an empirical study of Egypt and Lebanon
Authors: ELGAZZAR HEBA 
Published: March 2009

AbstractIn middle-income Arab countries such as Egypt and Lebanon, income-associated equity in health care remains an elusive policy objective in part due to a relatively high reliance on out-of-pocket payments in financing care. This article examines the effect of income on the use of outpatient and inpatient health care services in Egypt and Lebanon using econometric analysis of cross-sectional data from the World Health Organization. In light of noticeable differences in income and public financing arrangements, these two countries serve as interesting case studies. Multivariate regression results suggest that Egyptian respondents were more likely to use health services than their Lebanese counterparts, holding all else constant, and that this effect was particularly evident for outpatient care. A higher income and insurance increased the likelihood of outpatient use more so than inpatient use, with these effects more pronounced in Lebanon. Overall, lower-income groups tended to report having worse health levels and paying more out-of-pocket on health care as a share of income than did higher-income groups. At the same time, these socioeconomic disparities in health appeared to be greater in Lebanon than in Egypt. Economic barriers to the use of health services are discussed within the context of health financing policy reforms aimed at improving equity in access to care in countries such as Egypt and Lebanon.
Proteolytic activation of human pancreatitis-associated protein is required for peptidoglycan binding and bacterial aggregation
Authors: Medveczky Péter , Szmola Richárd , Sahin-Tóth Miklós 
Published: March 2009

PAP (pancreatitis-associated protein) is a 16 kDa lectin-like protein, which becomes robustly up-regulated in the pancreatic juice during acute pancreatitis. Trypsin cleaves the N-terminus of PAP, which in turn forms insoluble fibrils. PAP and its paralogue, the pancreatic stone protein, induce bacterial aggregation and, more recently, PAP was shown to bind to the peptidoglycan of Gram-positive bacteria and exert a direct bactericidal effect. However, the role of N-terminal processing in the antibacterial function of PAP has remained unclear. In the present study, we demonstrate that N-terminal cleavage of PAP by trypsin at the Arg37–Ile38 peptide bond or by elastase at the Ser35–Ala36 peptide bond is a prerequisite for binding to the peptidoglycan of the Gram-positive bacterium Bacillus subtilis. The tryptic site in PAP was also efficiently cleaved by nprE (extracellular neutral metalloprotease) secreted from B. subtilis. Trypsin-mediated processing of PAP resulted in the formation of the characteristic insoluble PAP species, whereas elastase-processed PAP remained soluble. N-terminally processed PAP induced rapid aggregation of B. subtilis without significant bacterial killing. The bacteria-aggregating activities of trypsin-processed and elastase-processed PAP were comparable. In contrast with previous reports, the Gram-negative Escherichia coli bacterium was not aggregated. We conclude that N-terminal processing is necessary for the peptidoglycan binding and bacteria-aggregating activity of PAP and that trypsin-processed and elastase-processed forms are functionally equivalent. The observations also extend the complement of proteases capable of PAP processing, which now includes trypsins, pancreatic elastases and bacterial zinc metalloproteases of the thermolysin type.
Characterization of Citrus sinensis type 1 mitochondrial alternative oxidase and expression analysis in biotic stress
Authors: Daurelio Lucas Damián , Checa Susana Karina , Barrio Jorgelina Morán , Ottado Jorgelina , Orellano Elena Graciela 
Published: March 2009

The higher plant mitochondrial electron transport chain contains an alternative pathway that ends with the AOX (alternative oxidase). The AOX proteins are encoded by a small gene family composed of two discrete gene subfamilies. Aox1 is present in both monocot and eudicot plants, whereas Aox2 is only present in eudicot plants. We isolated a genomic clone from Citrus sinensis containing the Aox1a gene. The orange Aox1a consists of four exons interrupted by three introns and its promoter harbours diverse putative stress-specific regulatory motifs including pathogen response elements. The role of the Aox1a gene was evaluated during the compatible interaction between C. sinensis and Xanthomonas axonopodis pv. citri and no induction of the Aox1a at the transcriptional level was observed. On the other hand, Aox1a was studied in orange plants during non-host interactions with Pseudomonas syringae pv. tomato and Xanthomonas campestris pv. vesicatoria, which result in hypersensitive response. Both phytopathogens produced a strong induction of Aox1a, reaching a maximum at 8 h post-infiltration. Exogenous application of salicylic acid produced a slight increase in the steady-state level of Aox1a, whereas the application of fungi elicitors showed the highest induction. These results suggest that AOX1a plays a role during biotic stress in non-host plant pathogen interaction.
The Development of Swallowing Respiratory Coordination
Authors: Huckabee Maggie-Lee 
Published: March 2009

Abstract
Research exists that evaluates the mechanics of swallowing respiratory coordination in healthy children and adults as well and individuals with swallowing impairment. The research program summarized in this article represents a systematic examination of swallowing respiratory coordination across the lifespan as a means of behaviorally investigating mechanisms of cortical modulation. Using time-locked recordings of submental surface electromyography, nasal airflow, and thyroid acoustics, three conditions of swallowing were evaluated in 20 adults in a single session and 10 infants in 10 sessions across the first year of life. The three swallowing conditions were selected to represent a continuum of volitional through nonvolitional swallowing control on the basis of a decreasing level of cortical activation. Our primary finding is that, across the lifespan, brainstem control strongly dictates the duration of swallowing apnea and is heavily involved in organizing the integration of swallowing and respiration, even in very early infancy. However, there is evidence that cortical modulation increases across the first 12 months of life to approximate more adult-like patterns of behavior. This modulation influences primarily conditions of volitional swallowing; sleep and naïve swallows appear to not be easily adapted by cortical regulation. Thus, it is attention, not arousal that engages cortical mechanisms.
The Interaction of Pulmonary Physiology and Swallowing: A Juggling Act for the Physician and Speech-Language Pathologist
Authors: Dikeman Karen J. , Kazandjian Marta S. , Tun Elbert , Niyazova Panina , Tsai Tien-Tsai , Russo Daniel J. 
Published: March 2009

Abstract
Patients who are dependent upon tracheostomy and/or ventilator use present a particular challenge to health-care providers. The interaction of pulmonary physiology and deglutition is complex, as illustrated in the course of patients who are in the weaning process. Speech language pathologists (SLPs) should work closely with their physician colleagues to understand the influence of multiple medical co-morbidities on intervention. In traditional medicine, the clinician's objective is to connect a patient's many symptoms and complaints to a single disease entity. However, in caring for the ventilator dependent geriatric population, a symptom such as dysphagia typically results from the interplay of various, multi-organ symptoms, and conditions. This article strives to demonstrate the “juggling act” that the physician and SLP must balance between the patient's current medical condition, pulmonary dysfunction, and disordered swallowing. Clinical case studies illustrate the benefit of swallowing intervention on quality of life. While the care of patients with tracheostomy and ventilator dependence requires a team approach, with respiratory therapy and nursing vital members, this article emphasizes the roles of the SLP and physician.
DIYA: a bacterial annotation pipeline for any genomics lab
Authors: Stewart Andrew C. , Osborne Brian , Read Timothy D. 
Published: March 2009

Abstract
Summary:DIYA (Do-It-Yourself Annotator) is a modular and configurable open source pipeline software, written in Perl, used for the rapid annotation of bacterial genome sequences. The software is currently used to take DNA contigs as input, either in the form of complete genomes or the result of shotgun sequencing, and produce an annotated sequence in Genbank file format as output.
Availability: Distribution and source code are available at (https://sourceforge.net/projects/diyg/).
Contact: tread@emory.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
The use of gene ontology evidence codes in preventing classifier assessment bias
Authors: Rogers Mark F. , Ben-Hur Asa 
Published: March 2009

Abstract
Motivation: The biological community's reliance on computational annotations of protein function makes correct assessment of function prediction methods an issue of great importance. The fact that a large fraction of the annotations in current biological databases are based on computational methods can lead to bias in estimating the accuracy of function prediction methods. This can happen since predicting an annotation that was derived computationally in the first place is likely easier than predicting annotations that were derived experimentally, leading to over-optimistic classifier performance estimates.
Results: We illustrate this phenomenon in a set of controlled experiments using a nearest neighbor classifier that uses PSI-BLAST similarity scores. Our results demonstrate that the source of Gene Ontology (GO) annotations used to assess a protein function predictor can have a highly significant influence on classifier accuracy: the average accuracy over four species and over GO terms in the biological process namespace increased from 0.72 to 0.87 when the classifier was given access to annotations that are assigned evidence codes that indicate a possible computational source, instead of experimentally determined annotations. Slightly smaller increases were observed in the other namespaces. In these comparisons the total number of annotations and their distribution across GO terms were kept the same.
Conclusion: In conclusion, taking into account GO evidence codes is required for reporting accuracy statistics that do not overestimate a model's performance, and is of particular importance for a fair comparison of classifiers that rely on different information sources.
Contact: rogersma@cs.colostate.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Performance of Residents and Anesthesiologists in a Simulation-based Skill Assessment
Authors: Murray David J. , Boulet John R. , Avidan Michael , Kras Joseph F. , Henrichs Bernadette , Woodhouse Julie , Evers Alex S. 
Published: March 2009

Background
Anesthesiologists and anesthesia residents are expected to acquire and maintain skills to manage a wide range of acute intraoperative anesthetic events. The purpose of this study was to determine whether an inventory of simulated intraoperative scenarios provided a reliable and valid measure of anesthesia residents' and anesthesiologists' skill.

Methods
Twelve simulated acute intraoperative scenarios were designed to assess the performance of 64 residents and 35 anesthesiologists. The participants were divided into four groups based on their training and experience. There were 31 new CA-1, 12 advanced CA-1, and 22 CA-2/CA-3 residents as well as a group of 35 experienced anesthesiologists who participated in the assessment. Each participant managed a set of simulated events. The advanced CA-1 residents, CA-2/CA-3 residents, and 35 anesthesiologists managed 8 of 12 intraoperative simulation exercises. The 31 CA-1 residents each managed 3 intraoperative scenarios.

Results
The new CA-1 residents received lower scores on the simulated intraoperative events than the other groups of participants. The advanced CA-1 residents, CA-2/CA-3 residents, and anesthesiologists performed similarly on the overall assessment. There was a wide range of scores obtained by individuals in each group. A number of the exercises were difficult for the majority of participants to recognize and treat, but most events effectively discriminated among participants who achieved higher and lower overall scores.

Conclusion
This simulation-based assessment provided a valid method to distinguish the skills of more experienced anesthesia residents and anesthesiologists from residents in early training. The overall score provided a reliable measure of a participant's ability to recognize and manage simulated acute intraoperative events. Additional studies are needed to determine whether these simulation-based assessments are valid measures of clinical performance.
Persistent Low-frequency Spontaneous Discharge in A-fiber and C-fiber Primary Afferent Neurons during an Inflammatory Pain Condition
Authors: Xiao Wen-Hua , Bennett Gary J. 
Published: March 2009

Background
Primary afferent nociceptor sensitization and its accompanying spontaneous discharge are believed to be the proximate cause of the spontaneous pain and hypersensitivity that follow an acute tissue injury. Evidence for this comes almost entirely from studies limited to the first few minutes to an hour or two after injury, when the inflammatory reaction to injury has just begun. However, there is evidence that inflammatory pain mechanisms differ from acute pain mechanisms and that the mechanisms that drive and modulate inflammatory pain may evolve over time.

Methods
The authors surveyed spontaneous afferent discharge in rats with hind paw inflammation evoked by complete Freund adjuvant over the entire 14 days of the inflammatory pain condition, as determined in parallel experiments assessing allodynia and hyperalgesia.

Results
Inflammation-evoked heat hyperalgesia, mechanoallodynia, and mechanohyperalgesia began within hours, persisted until at least day 7, and resolved by day 14. A large percentage (23%) of A fibers had spontaneous discharge 2 days after inflammation, but the incidence was much reduced (to 7-9%) by 7 and 14 days. At all times, the A-fiber discharge frequency was low (<3.0 Hz) or very low (<0.3 Hz). A large percentage (24%) of C fibers had spontaneous discharge 2 and 7 days after inflammation, but this also declined to near control levels by day 14; C-fiber discharge frequency was also always low (most at 0.3-1.0 Hz).

Conclusions
The pain, allodynia, and hyperalgesia associated with an established inflammatory condition are associated with a persistent low-frequency spontaneous discharge in both A-fiber and C-fiber sensory afferents.
Hydrocortisone Preserves the Vascular Barrier by Protecting the Endothelial Glycocalyx
Authors: Chappell Daniel , Jacob Matthias , Hofmann-Kiefer Klaus , Bruegger Dirk , Rehm Markus , Conzen Peter , Welsch Ulrich , Becker Bernhard F. 
Published: March 2009

Background
Hydrocortisone protects against ischemia-reperfusion injury, reduces paracellular permeability for macromolecules, and is routinely applied in the prevention of interstitial edema. Healthy vascular endothelium is coated by the endothelial glycocalyx, diminution of which increases capillary permeability, suggesting that the glycocalyx is a target for hydrocortisone action.

Methods
Isolated guinea pig hearts were perfused with Krebs-Henseleit buffer. Hydrocortisone was applied in a stress dose (10 microg/ml) before inducing 20 min of ischemia (37 degrees C). Hearts were reperfused for 20 min at constant flow (baseline perfusion pressure, 70 cm H2O) with Krebs-Henseleit buffer or Krebs-Henseleit buffer plus 2 g% hydroxyethyl starch (130 kd). Coronary net fluid filtration was assessed directly by measuring transudate formation on the epicardial surface. Hearts were perfusion fixed to visualize the glycocalyx.

Results
Ischemia-induced degradation of the glycocalyx enhanced coronary perfusion pressure (118.8 +/- 17.3 cm H2O) and increased vascular permeability (8 +/- 0.2 microl x min(-1) x cm H2O(-1) at baseline vs. 34 +/- 3.3 microl x min(-1) x cm H2O(-1) after reperfusion). Enzymatic digestion of the glycocalyx (heparinase) elicited similar effects. Hydrocortisone reduced postischemic oxidative stress, perfusion pressure (86.3 +/- 6.4 cm H2O), and transudate formation (11 +/- 0.6 microl x min(-1) x cm H2O(-1)). Applying colloid augmented this (70.6 +/- 5.6 cm H2O and 9 +/- 0.5 microl x min(-1) x cm H2O(-1)). Postischemic shedding of syndecan-1, heparan sulfate, and hyaluronan was inhibited by hydrocortisone, as was release of histamine from resident mast cells. Electron microscopy revealed a mostly intact glycocalyx after hydrocortisone treatment, but not after heparinase treatment.

Conclusions
Hydrocortisone preserves the endothelial glycocalyx, sustaining the vascular barrier and reducing interstitial edema. The effect of colloids suggests that prevention of postischemic rise in coronary resistance by hydrocortisone could also be based on alleviation of endothelial swelling. Stabilization of myocardial mast cells by hydrocortisone may account for the mitigated inflammatory affect of ischemia-reperfusion.
Differential Presynaptic Effects of Opioid Agonists on Aδ- and C-afferent Glutamatergic Transmission to the Spinal Dorsal Horn
Authors: Ikoma Miho , Kohno Tatsuro , Baba Hiroshi 
Published: March 2009

Background
Although intrathecal administration of opioids produces antinociceptive effects in the spinal cord, it has not been established whether intrathecal opioid application more effectively terminates C fiber-mediated pain than A fiber-mediated pain. Here, the authors focus on the differences in opioid actions on Adelta- and C-afferent responses.

Methods
Using the whole cell patch clamp technique, the authors investigated the presynaptic inhibitory actions of micro-, delta-, and kappa-opioid receptor agonists on primary afferent-evoked excitatory postsynaptic currents (EPSCs) in substantia gelatinosa neurons of adult rat spinal cord slices.

Results
The micro agonist DAMGO (0.1, 1 microM) reduced the amplitude of glutamatergic monosynaptic Adelta- or C fiber-evoked EPSCs. C fiber-evoked EPSCs were inhibited to a greater extent than Adelta fiber-evoked EPSCs. The delta agonist DPDPE (1, 10 microM) produced modest inhibition of Adelta- or C fiber-evoked EPSCs. In contrast, the kappa agonist U69593 (1 microM) did not affect the amplitude of either Adelta or C fiber-evoked EPSCs.

Conclusions
These results indicate that opioids suppress excitatory synaptic transmission mainly through activation of micro receptors on primary afferent C fibers. Given that the substantia gelatinosa is the main termination of Adelta and C fibers transmitting nociceptive information, the current findings may partially explain the different potency of opioid agonists.