bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of sex and early maternal abuse on adrenocorticotropin hormone and cortisol responses to the corticotropin-releasing hormone challenge during the first 3 years of life in group-living rhesus monkeys
Authors: Sanchez Mar M. , Mccormack Kai , Grand Alison P. , Fulks Richelle , Graff Anne , Maestripieri Dario 
Published: January 2010

AbstractIn this study we investigated the development of the hypothalamic–pituitary–adrenal (HPA) axis in 21 group-living rhesus monkeys infants that were physically abused by their mothers in the first few months of life and in 21 nonabused controls. Cortisol and adrenocorticotropin hormone (ACTH) responses to a corticotropin-releasing hormone (CRH) challenge were assessed at 6-month intervals during the subjects' first 3 years of life. Abused infants exhibited greater cortisol responses to CRH than controls across the 3 years. Abused infants also exhibited blunted ACTH secretion in response to CRH, especially at 6 months of age. Although there were no significant sex differences in abuse experienced early in life, females showed a greater cortisol response to CRH than males at all ages. There were no significant sex differences in the ACTH response to CRH, or significant interactions between sex and abuse in the ACTH or cortisol response. Our findings suggest that early parental maltreatment results in greater adrenocortical, and possibly also pituitary, responsiveness to challenges later in life. These long-term alterations in neuroendocrine function may be one the mechanisms through which infant abuse results in later psychopathologies. Our study also suggests that there are developmental sex differences in adrenal function that occur irrespective of early stressful experience. The results of this study can enhance our understanding of the long-term effects of child maltreatment as well as our knowledge of the development of the HPA axis in human and nonhuman primates.
The relation of weight change to depressive symptoms in adolescence
Authors: Felton Julia , Cole David A. , Tilghman-Osborne Carlos , Maxwell Melissa A. 
Published: January 2010

AbstractTheDiagnostic and Statistical Manual of Mental Disorderslists weight gain or weight loss as a symptom of depression at all ages, but no study of adolescent depression has examined its relation to actual (not just self-reported) weight change. In the current longitudinal study, 215 adolescents provided physical and self-report measures of change in weight, body mass, and body fat over a 4-month time interval. They also completed psychological measures of body dissatisfaction, problematic eating attitudes, and depressive symptoms. The relation between physical measures of weight change and depressive symptoms varied with age. These relations were explained by individual differences in body dissatisfaction, eating attitudes, and behaviors, leading to questions about weight change as a symptom of depression in adolescence.
Nitric oxide synthase isoforms and the effect of their inhibition on meiotic maturation of porcine oocytes
Authors: Chmelíková Eva , Ješeta Michal , Sedmíková Markéta , Petr Jaroslav , Tůmová Lenka , Kott Tomáš , Lipovová Petra , Jílek František 
Published: January 2010

SummaryIn this paper we assessed: (i) the change in nitric oxide synthase (NOS) isoforms' expression and intracellular localization and in NOS mRNA in porcine oocytes during meiotic maturation; (ii) the effect of NOS inhibition byNω-nitro-l-arginine methyl ester (l-NAME) and aminoguanidine (AG) on meiotic maturation of cumulus–oocyte complexes (COC) as well as denuded oocytes (DO); and (iii) nitric oxide (NO) formation in COC. All three NOS isoforms (eNOS, iNOS and nNOS) and NOS mRNA (eNOS mRNA, iNOS mRNA and nNOS mRNA) were found in both porcine oocytes and their cumulus cells except for nNOS mRNA, which was not detected in the cumulus cells. NOS isoforms differed in their intracellular localization in the oocyte: while iNOS protein was dispersed in the oocyte cytoplasm, nNOS was localized in the oocyte cytoplasm and in germinal vesicles (GV) and eNOS was present in dots in the cytoplasm, GV and was associated with meiotic spindles.l-NAME inhibitor significantly suppressed metaphase (M)I to MII transition (5.0 mM experimental group: 34.9% MI, control group: 9.5% MI) and at the highest concentration (10.0 mM) also affected GV breakdown (GVBD); in contrast also AG inhibited primarily GVBD. The majority of the oocytes (10.0 mM experimental group: 60.8%, control group: 1.2%) was not able to resume meiosis. AG significantly inhibited GVBD in DO, butl-NAME had no significant effect on the GVBD of these cells. During meiotic maturation, NO is formed in COC and the NO formed by cumulus cells is necessary for the process of GVBD.
Expression of melatonin (MT1, MT2) and melatonin-related receptors in the adult rat testes and during development
Authors: Izzo Gaia , Francesco Aniello , Ferrara Diana , Campitiello Maria Rosaria , Serino Ismene , Minucci Sergio , d'Istria Michela 
Published: January 2010

SummaryIt is well known that melatonin provokes reproductive alterations in response to changes in hours of daylight in seasonally breeding mammals, exerting a regulatory role at different levels of the hypothalamic–pituitary–gonadal axis. Although it has also been demonstrated that melatonin may affect testicular activity in vertebrates, until now, very few data support the hypothesis of a local action of melatonin in the male gonads. The aim of this study was to investigate whether MT1, MT2 melatonin receptors and the H9 melatonin-related receptor, are expressed in the adult rat testes and during development. A semi-quantitative RT-PCR method was used to analyse the expression of MT1, MT2 and H9 receptors mRNAs in several rat tissues, mainly focusing on testes during development and adult life. Our results provide molecular evidences of the presence of both MT1 and, for the first time, MT2 melatonin receptors as well as of the H9 melatonin-related receptor in the examined tissues, including adult testes. During development MT1 and MT2 transcripts are expressed at lower levels in testes of rats from 1 day to 1 week of age, lightly increased at 2 weeks of age and remained permanently expressed throughout development until 6 months. These data strongly support the hypothesis that melatonin acts directly in male vertebrate gonads suggesting that rat testes may be a suitable model to verify the role of indolamine in vertebrate testicular activity.
Effect of retinoid X receptor α (RXRα) on apoptosis in primary cultured porcine pre-adipocytes
Authors: Ya-Qiu Lin , He-Lin Zhuang , Gong-She Yang 
Published: January 2010

AbstractUsing semi-quantitative reverse transcriptase polymerase chain reaction (semi-qRT-PCR), cell transfection, Hoechst 33342, acridine orange (AO) and flow cytometry methods, apoptotic changes in porcine pre-adipocytes treated with 9-cis retinoic acid (9-cisRA)–retinoid X receptor α (RXRα) ligand, transfected with pEnhanced green fluorescent proteins C2–RXRα (pEGFPC2–RXRα) or RXRα–small interfering RNA (RXRα–siRNA), respectively, were investigated. Observations of morphologic changes showed changes in cell structure, cellular shrinkage and condensation of chromatin, pyknosis of the nucleus into a compact body, complete fragmentation within the nuclear membrane, continuous budding and shedding, and, finally conversion of the cell into several apoptotic bodies wrapped in membranes of different sizes. Compared with the control group, the apoptotic rate was significantly lowered in the 10 nmol/l 9-cisRA-treated group, and significantly higher in the 10 μmol/l 9-cisRA-treated group (both P<0.05). Gene expression of RXRα was significantly up-regulated and down-regulated when cultured pre-adipocytes were transfected with pEGFPC2–RXRα or RXRα–siRNA (P<0.05), respectively; the apoptotic rate decreased in the pEGFPC2–RXRα group and significantly increased in the RXRα–siRNA group when compared with a control group (P<0.05). This implies that RXRα inhibits the apoptosis of porcine pre-adipocytes.
Attributable Costs of Surgical Site Infection and Endometritis after Low Transverse Cesarean Delivery
Authors: Olsen Margaret A. , Butler Anne M. , Willers Denise M. , Gross Gilad A. , Hamilton Barton H. , Fraser Victoria J. 
Published: January 2010

Background.Accurate data on costs attributable to hospital-acquired infections are needed to determine their economic impact and the cost-benefit of potential preventive strategies.Objective.To determine the attributable costs of surgical site infection (SSI) and endometritis (EMM) after cesarean section by means of 2 different methods.Design.Retrospective cohort.Setting.Barnes-Jewish Hospital, a 1,250-bed academic tertiary care hospital.Patients.There were 1,605 women who underwent low transverse cesarean section from July 1999 through June 2001.Methods.Attributable costs of SSI and EMM were determined by generalized least squares (GLS) and propensity score matched-pairs by means of administrative claims data to define underlying comorbidities and procedures. For the matched-pairs analyses, uninfected control patients were matched to patients with SSI or with EMM on the basis of their propensity to develop infection, and the median difference in costs was calculated.Results.The attributable total hospital cost of SSI calculated by GLS was $3,529 and by propensity score matched-pairs was $2,852. The attributable total hospital cost of EMM calculated by GLS was $3,956 and by propensity score matched-pairs was $3,842. The majority of excess costs were associated with room and board and pharmacy costs.Conclusions.The costs of SSI and EMM were lower than SSI costs reported after more extensive operations. The attributable costs of EMM calculated by the 2 methods were very similar, whereas the costs of SSI calculated by propensity score matched-pairs were lower than the costs calculated by GLS. The difference in costs determined by the 2 methods needs to be considered by investigators who are performing cost analyses of hospital-acquired infections.
WellReader: a MATLAB program for the analysis of fluorescence and luminescence reporter gene data
Authors: Boyer Frédéric , Besson Bruno , Baptist Guillaume , Izard Jérôme , Pinel Corinne , Ropers Delphine , Geiselmann Johannes , de Jong Hidde 
Published: January 2010

Abstract
Motivation: Fluorescent and luminescent reporter gene systems in combination with automated microplate readers allow real-time monitoring of gene expression on the population level at high precision and sampling density. This generates large amounts of data for the analysis of which computer tools are missing to date.
Results: We have developed WellReader, a MATLAB program for the analysis of fluorescent and luminescent reporter gene data. WellReader allows the user to load the output files of microplate readers, remove outliers, correct for background effects and smooth and fit the data. Moreover, it computes biologically relevant quantities from the measured signals, notably promoter activities and protein concentrations, and compares the resulting expression profiles of different genes under different conditions.
Availability: WellReader is available under a LGPL licence at http://prabi1.inrialpes.fr/trac/wellreader.
Contact: hidde.de-jong@inria.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
Computational quantification of metabolic fluxes from a single isotope snapshot: application to an animal biopsy
Authors: Binsl Thomas W. , Alders David J.C. , Heringa Jaap , Groeneveld A.B. Johan , van Beek Johannes H.G.M. 
Published: January 2010

Abstract
Motivation: Quantitative determination of metabolic fluxes in single tissue biopsies is difficult. We report a novel analysis approach and software package for in vivo flux quantification using stable isotope labeling.
Results: We developed a protocol based on brief, timed infusion of 13C isotope-enriched substrates for the tricarboxylic acid (TCA) cycle followed by quick freezing of tissue biopsies. NMR measurements of tissue extracts were used for flux estimation based on a computational model of carbon transitions between TCA cycle metabolites and related amino acids. To this end, we developed a computational framework in which metabolic systems can be flexibly assembled, simulated and analyzed. Flux parameters were quantified from NMR multiplets by a partial grid search followed by repeated Nelder–Mead optimizations implemented on a computer grid. We implemented a model of the TCA cycle and showed by extensive simulations that the timed infusion protocol reliably quantitates multiple fluxes. Experimental validation of the method was done in vivo on hearts of anesthetized pigs under two different conditions: basal state (n = 7) and cardiac stress caused by infusion of dobutamine (n = 7). About nine tissue samples (40–200 mg dry-weight) were taken per heart. TCA cycle flux was 6.11 ± 0.28 (SEM) μmol/min · gdw at baseline versus 9.29 ± 1.03 μmol/min · gdw for dobutamine stress. Oxygen consumption calculated from the TCA cycle flux and from ‘gold standard’ blood gas-based measurements were close, correlating with r=0.88 (P &lt; 10−4). Spatial heterogeneity in metabolic fluxes is detectable amongst the small samples. We propose that our novel isotope snapshot methodology is suitable for flux measurements in biopsies in vivo.
Availability: Non-profit organizations will, upon request, be granted a non-exclusive license to use the software for internal research and teaching purposes at no charge. A web interface for using the software on our computer grid is available under http://www.ibi.vu.nl/programs/
Contact: hans.van.beek@falw.vu.nl
Supplementary information: Supplementary data are available at Bioinformatics online.
Exploring classification strategies with the CoEPrA 2006 contest
Authors: Demir-Kavuk Ozgur , Riedesel Henning , Knapp Ernst-Walter 
Published: January 2010

Abstract
Motivation: In silico methods to classify compounds as potential drugs that bind to a specific target become increasingly important for drug design. To build classification devices training sets of drugs with known activities are needed. For many such classification problems, not only qualitative but also quantitative information of a specific property (e.g. binding affinity) is available. The latter can be used to build a regression scheme to predict this property for new compounds. Predicting a compound property explicitly is generally more difficult than classifying that the property lies below or above a given threshold value. Hence, an indirect classification that is based on regression may lead to poorer results than a direct classification scheme. In fact, initially researchers are only interested to classify compounds as potential drugs. The activities of these compounds are subsequently measured in wet lab.
Results: We propose a novel approach that uses available quantitative information directly for classification rather than first using a regression scheme. It uses a new type of loss function called weighted biased regression. Application of this method to four widely studied datasets of the CoEPrA contest (Comparative Evaluation of Prediction Algorithms, http://coepra.org) shows that it can outperform simple classification methods that do not make use of this additional quantitative information.
Availability: A stand alone application is available at the webpage http://agknapp.chemie.fu-berlin.de/agknapp/index.php?menu=software&page=PeptideClassifier that can be used to build a model for a peptide training set to be submitted.
Contact: odemir@chemie.fu-berlin.de
Supplementary Information: Supplementary data are available at Bioinformatics online.
Correcting population stratification in genetic association studies using a phylogenetic approach
Authors: Li Mingyao , Reilly Muredach P. , Rader Daniel J. , Wang Li-San 
Published: January 2010

Abstract
Motivation: The rapid development of genotyping technology and extensive cataloguing of single nucleotide polymorphisms (SNPs) across the human genome have made genetic association studies the mainstream for gene mapping of complex human diseases. For many diseases, the most practical approach is the population-based design with unrelated individuals. Although having the advantages of easier sample collection and greater power than family-based designs, unrecognized population stratification in the study samples can lead to both false-positive and false-negative findings and might obscure the true association signals if not appropriately corrected.
Methods: We report PHYLOSTRAT, a new method that corrects for population stratification by combining phylogeny constructed from SNP genotypes and principal coordinates from multi-dimensional scaling (MDS) analysis. This hybrid approach efficiently captures both discrete and admixed population structures.
Results: By extensive simulations, the analysis of a synthetic genome-wide association dataset created using data from the Human Genome Diversity Project, and the analysis of a lactase-height dataset, we show that our method can correct for population stratification more efficiently than several existing population stratification correction methods, including EIGENSTRAT, a hybrid approach based on MDS and clustering, and STRATSCORE , in terms of requiring fewer random SNPs for inference of population structure. By combining the flexibility and hierarchical nature of phylogenetic trees with the advantage of representing admixture using MDS, our hybrid approach can capture the complex population structures in human populations effectively.
Software Availability: Codes can be downloaded from http://people.pcbi.upenn.edu/∼lswang/phylostrat/
Contact: mingyao@upenn.edu; iswang@upenn.edu.
Supplementary information: Supplementary data are available at Bioinformatics online.
A hidden Ising model for ChIP-chip data analysis
Authors: Mo Qianxing , Liang Faming 
Published: January 2010

Abstract
Motivation: Chromatin immunoprecipitation (ChIP) coupled with tiling microarray (chip) experiments have been used in a wide range of biological studies such as identification of transcription factor binding sites and investigation of DNA methylation and histone modification. Hidden Markov models are widely used to model the spatial dependency of ChIP-chip data. However, parameter estimation for these models is typically either heuristic or suboptimal, leading to inconsistencies in their applications. To overcome this limitation and to develop an efficient software, we propose a hidden ferromagnetic Ising model for ChIP-chip data analysis.
Results: We have developed a simple, but powerful Bayesian hierarchical model for ChIP-chip data via a hidden Ising model. Metropolis within Gibbs sampling algorithm is used to simulate from the posterior distribution of the model parameters. The proposed model naturally incorporates the spatial dependency of the data, and can be used to analyze data with various genomic resolutions and sample sizes. We illustrate the method using three publicly available datasets and various simulated datasets, and compare it with three closely related methods, namely TileMap HMM, tileHMM and BAC. We find that our method performs as well as TileMap HMM and BAC for the high-resolution data from Affymetrix platform, but significantly outperforms the other three methods for the low-resolution data from Agilent platform. Compared with the BAC method which also involves MCMC simulations, our method is computationally much more efficient.
Availability: A software called iChip is freely available at http://www.bioconductor.org/.
Contact: moq@mskcc.org
Prevalence and pharmacological treatment of left‐ventricular dysfunction in patients undergoing vascular surgery
Authors: Flu Willem‐Jan , van Kuijk Jan‐Peter , Galal Wael , Kuiper Ruud , van de Ven Louis L. , Verhagen Hence J.M. , Bax Jeroen J. , Poldermans Don 
Published: January 2010

AimsThis study evaluated the prevalence of left‐ventricular (LV) dysfunction in vascular surgery patients and pharmacological treatment, according ESC guidelines.Methods and resultsEchocardiography was performed pre‐operatively in 1005 consecutive patients. Left ventricular ejection fraction (LVEF) ≤50% defined systolic LV dysfunction. Diastolic LV dysfunction was diagnosed based on E/A‐ratio, pulmonary vein flow, and deceleration time. Optimal pharmacological treatment to improve LV function was considered as: (i) angiotensin‐blocking agent (ACE‐I/ARB) in patients with LVEF ≤40%; (ii) ACE‐I/ARB and β‐blocker in patients with LVEF ≤40% + heart failure symptoms or previous myocardial infarction; and (iii) a diuretic in patients with symptomatic heart failure, regardless of LVEF. Left‐ventricular dysfunction was present in 506 patients (50%), of whom 209 (41%) had asymptomatic diastolic LV dysfunction, 194 (39%) had asymptomatic systolic LV dysfunction, and 103 (20%) had symptomatic heart failure. Treatment with ACE‐I/ARB and/or β‐blocker could be initiated/improved in 67 (34%) of the 199 patients with (a)symptomatic LVEF ≤40%. A diuretic could be initiated in 32 patients (31%) with symptomatic heart failure (regardless of LVEF).ConclusionsThis study demonstrates a high prevalence of LV dysfunction in vascular surgery patients and under‐utilization of ESC recommended pharmacological treatment. Standard pre‐operative evaluation of LV function could be argued based on our results to reduce this observed care gap.
Long‐term association between self‐reported signs and symptoms and heart failure hospitalizations: the Atherosclerosis Risk In Communities (ARIC) Study
Authors: Avery Christy L. , Mills Katherine T. , Chambless Lloyd E. , Chang Patricia P. , Folsom Aaron R. , Mosley Thomas H. , Ni Hanyu , Rosamond Wayne D. , Wagenknecht Lynne , Wood Joy , Heiss Gerardo 
Published: January 2010

AimsAlthough studies of the accuracy of heart failure (HF) classification scoring systems are available, few have examined their performance when restricted to self‐reported items.Methods and resultsWe evaluated the association between a simplified version of the Gothenburg score, a validated HF score comprised of cardiac and pulmonary signs and symptoms and medication use, and incident HF hospitalizations in 15 430 Atherosclerosis Risk in Communities (ARIC) Study participants. Gothenburg scores (range: 0–3) were constructed using self‐reported items obtained at study baseline (1987–89). Incident HF hospitalization over 14.7 years of follow‐up was defined as the first identified hospitalization with an ICD‐9 discharge code of 428 (n = 1668). Self‐reported Gothenburg scores demonstrated very high agreement with the original metric comprised of self‐reported and clinical measures and were directly associated with incident HF hospitalizations: [score = 1: hazard rate ratio (HRR) = 1.23 (1.07–1.42); score = 2: HRR = 2.17 (1.92–2.43); score = 3: HRR = 3.98 (3.37–4.70)].ConclusionIn a population‐based cohort, self‐reported Gothenburg criteria items were associated with hospitalized HF over a prolonged follow‐up time. The association was also consistent across groups defined by sex and race, suggesting that this simple score deserves further study as a screening tool for the identification of individuals at high risk of HF in resource‐limited settings.