bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association between aerobic fitness in late pregnancy and duration of labor in nulliparous women
Authors: KARDEL KRISTIN R. , JOHANSEN BJØRN , VOLDNER NANNA , IVERSEN PER OLE , HENRIKSEN TORE 
Published: June 2009

AbstractIt is established that the level of physical activity in the population generally is too low, and data indicate that pregnant women are no exception. Studies of the effects of aerobic fitness on delivery outcomes are limited. In this observational study, we investigated the effect of aerobic fitness on duration of labor in nulliparous women who started labor spontaneously. Maximal oxygen uptake was measured in 40 nulliparous women at 35–37 weeks of gestation. Duration of labor was defined as the time between 3 cm cervical dilation with regular uterine contractions and delivery. The mean (SD) maximal oxygen uptake was 2.1 (0.3) L/min and duration of labor 583 (317) minutes. Duration of labor was inversely associated with maximal oxygen uptake after adjusting for birthweight (p = 0.034). We conclude that measurement of maximal oxygen uptake is safe in pregnancy at 35–37 weeks and that increased aerobic fitness was associated with shorter labor in nulliparous women who started labor spontaneously.
Is there any relation between development of persistent non‐reassuring fetal heart rate pattern and acutely increased uterine artery vascular flow resistance during dinoprostone use in prolonged pregnancies?
Authors: KARCAALTINCABA DENIZ , AKDAG DERYA , KANDEMIR OMER , YALVAC SERDAR , GUVEN EMINE SEDA GUVENDAG , HABERAL ALI 
Published: June 2009

AbstractObjective. To investigate the relation between changes in Doppler parameters of fetal and uterine arteries and development of persistent non‐reassuring fetal heart rate (FHR) pattern during induction of labor with dinoprostone (Propess®) in pregnancies at ≥41 weeks gestation. Design. Prospective cohort study. Setting. Etlik Zubeyde Hanim Women's Hospital, Turkey. Sample. One hundred forty‐one prolonged pregnancies. Methods. Doppler parameters of umbilical, middle cerebral, and uterine arteries were measured before and 4–6 hours after dinoprostone application between uterine contractions. Non‐reassuring FHR pattern and persistent non‐reassuring FHR pattern criteria were defined based on NICE 2007 guidelines. Women with successful spontaneous vaginal delivery were recruited as a control group (n = 108), while women who underwent cesarean delivery due to persistent non‐reassuring FHR pattern were recruited as a study group (n = 15). Main outcome measures. Prediction of non‐reassuring FHR pattern with Doppler analysis of uterine and fetal arteries. Results. After dinoprostone application there was significant enhancement in uterine artery resistance index (RI) in the study group compared to the control group (p = 0.002). Receiver operating characteristics curve analysis identified a uterine artery RI increase value of 0.11 as the optimal threshold for prediction of persistent non‐reassuring FHR pattern with 73.3% sensitivity and 69.4% specificity. Logistic regression analysis demonstrated that an increase in the uterine artery RI was predictive for persistent non‐reassuring FHR pattern (odds ratio (OR) 4.97; 95% CI 1.5–16.8). Conclusion. Acute increase in uterine artery RI due to dinoprostone use may end with persistent non‐reassuring FHR pattern in prolonged pregnancies. This may allow earlier prediction of persistent non‐reassuring FHR pattern development and risk assessment.
Short and long‐term effects of antenatal corticosteroids assessed in a cohort of 7,827 children born preterm
Authors: ERIKSSON LENA , HAGLUND BENGT , EWALD UWE , ODLIND VIVECA , KIELER HELLE 
Published: July 2009

AbstractObjective. To study the benefits of antenatal corticosteroids (ACS) in clinical settings and to evaluate the occurrence of long‐term neuro‐sensory effects such as epilepsy and cerebral palsy (CP). Design. Observational population‐based study including all births between gestational weeks 24 and 34 during 1976–1997 in Sweden. Exposure to ACS was evaluated at hospital level. Children were followed up to their ninth birthday. Sample and methods. Seven thousand eight hundred twenty‐seven infants of which 5,632 were exposed to ACS. Data on hospital ACS routines was based on questionnaires and interviews with physicians and pharmacy sales. Outcomes were obtained from the national health registers and assessed according to gender of the child. Logistic regression was used to assess associations. Main outcome measures. Neonatal death, low Apgar score, respiratory distress syndrome (RDS), bronchopulmonary dysplasia (BPD), intraventricular hemorrhage (IVH), retinopathy of prematurity (ROP), CP, and epilepsy. Results. After adjustment, exposed infants had reduced risks of RDS (OR 0.80, 95% CI 0.70–0.92), late neonatal death (OR 0.86, 95% CI 0.57–1.29), BPD (OR 0.87, 95% CI 0.62–1.22), ROP (OR 0.80, 95% CI 0.48–1.32), IVH (OR 0.93, 95% CI 0.67–1.3), and CP (OR 0.82, 95% CI 0.58–1.15). Males had a higher risk of epilepsy (OR 1.74, 95% CI 0.85–3.55) than females (OR 0.50, 95% CI 0.25–1.03). Conclusion. The results confirm the beneficial effect of ACS regarding RDS in clinical settings. Except for a tendency to increased risk of epilepsy among male infants there were no increased risks of neuro‐sensory outcomes.
A pipeline for the quantitative analysis of CG dinucleotide methylation using mass spectrometry
Authors: Thompson Reid F. , Suzuki Masako , Lau Kevin W. , Greally John M. 
Published: June 2009

Abstract
Motivation: DNA cytosine methylation is an important epigenetic regulator, critical for mammalian development and the control of gene expression. Numerous techniques using either restriction enzyme or affinity-based approaches have been developed to interrogate cytosine methylation status genome-wide, however these assays must be validated by a more quantitative approach, such as MALDI-TOF mass spectrometry of bisulphite-converted DNA (commercialized as Sequenom's EpiTYPER assay using the MassArray system). Here, we present an R package (‘MassArray’) that assists in assay design and uses the standard Sequenom output file as the input to a pipeline of analyses not available as part of the commercial software. The tools in this package include bisulphite conversion efficiency calculation, sequence polymorphism flagging and visualization tools that combine multiple experimental replicates and create tracks for genome browser viewing.
Contact: jgreally@aecom.yu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Comparative study on ChIP-seq data: normalization and binding pattern characterization
Authors: Taslim Cenny , Wu Jiejun , Yan Pearlly , Singer Greg , Parvin Jeffrey , Huang Tim , Lin Shili , Huang Kun 
Published: June 2009

Abstract
Motivation: Antibody-based Chromatin Immunoprecipitation assay followed by high-throughput sequencing technology (ChIP-seq) is a relatively new method to study the binding patterns of specific protein molecules over the entire genome. ChIP-seq technology allows scientist to get more comprehensive results in shorter time. Here, we present a non-linear normalization algorithm and a mixture modeling method for comparing ChIP-seq data from multiple samples and characterizing genes based on their RNA polymerase II (Pol II) binding patterns.
Results: We apply a two-step non-linear normalization method based on locally weighted regression (LOESS) approach to compare ChIP-seq data across multiple samples and model the difference using an Exponential-NormalK mixture model. Fitted model is used to identify genes associated with differential binding sites based on local false discovery rate (fdr). These genes are then standardized and hierarchically clustered to characterize their Pol II binding patterns. As a case study, we apply the analysis procedure comparing normal breast cancer (MCF7) to tamoxifen-resistant (OHT) cell line. We find enriched regions that are associated with cancer (P &lt; 0.0001). Our findings also imply that there may be a dysregulation of cell cycle and gene expression control pathways in the tamoxifen-resistant cells. These results show that the non-linear normalization method can be used to analyze ChIP-seq data across multiple samples.
Availability: Data are available at http://www.bmi.osu.edu/~khuang/Data/ChIP/RNAPII/
Contact: taslim.2@osu.edu; khuang@bmi.osu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Error control variability in pathway-based microarray analysis
Authors: Gold David L. , Miecznikowski Jeffrey C. , Liu Song 
Published: June 2009

AbstractMotivation: The decision to commit some or many false positives in practice rests with the investigator. Unfortunately, not all error control procedures perform the same. Our problem is to choose an error control procedure to determine a P-value threshold for identifying differentially expressed pathways in high-throughput gene expression studies. Pathway analysis involves fewer tests than differential gene expression analysis, on the order of a few hundred. We discuss and compare methods for error control for pathway analysis with gene expression data.Results: In consideration of the variability in test results, we find that the widely used Benjamini and Hochberg's (BH) false discovery rate (FDR) analysis is less robust than alternative procedures. BH's error control requires a large number of hypothesis tests, a reasonable assumption for differential gene expression analysis, though not the case with pathway-based analysis. Therefore, we advocate through a series of simulations and applications to real gene expression data that researchers control the number of false positives rather than the FDR.Availability: Our R package, EPath.omg is available at http://sphhp.buffalo.edu/biostat/research/software.Contact: dlgold@buffalo.eduSupplementary information: Supplementary data are available at Bioinformatics online.
A genetic programming approach for Burkholderia Pseudomallei diagnostic pattern discovery
Authors: Yang Zheng Rong , Lertmemongkolchai Ganjana , Tan Gladys , Felgner Philip L. , Titball Richard 
Published: June 2009

Abstract
Motivation: Finding diagnostic patterns for fighting diseases like Burkholderia pseudomallei using biomarkers involves two key issues. First, exhausting all subsets of testable biomarkers (antigens in this context) to find a best one is computationally infeasible. Therefore, a proper optimization approach like evolutionary computation should be investigated. Second, a properly selected function of the antigens as the diagnostic pattern which is commonly unknown is a key to the diagnostic accuracy and the diagnostic effectiveness in clinical use.
Results: A conversion function is proposed to convert serum tests of antigens on patients to binary values based on which Boolean functions as the diagnostic patterns are developed. A genetic programming approach is designed for optimizing the diagnostic patterns in terms of their accuracy and effectiveness. During optimization, it is aimed to maximize the coverage (the rate of positive response to antigens) in the infected patients and minimize the coverage in the non-infected patients while maintaining the fewest number of testable antigens used in the Boolean functions as possible. The final coverage in the infected patients is 96.55% using 17 of 215 (7.4%) antigens with zero coverage in the non-infected patients. Among these 17 antigens, BPSL2697 is the most frequently selected one for the diagnosis of Burkholderia Pseudomallei. The approach has been evaluated using both the cross-validation and the Jack–knife simulation methods with the prediction accuracy as 93% and 92%, respectively. A novel approach is also proposed in this study to evaluate a model with binary data using ROC analysis.
Contact: z.r.yang@ex.ac.uk
libAnnotationSBML: a library for exploiting SBML annotations
Authors: Swainston Neil , Mendes Pedro 
Published: June 2009

Abstract
Summary: The Systems Biology Markup Language (SBML) is an established community XML format for the markup of biochemical models. With the introduction of SBML level 2 version 3, specific model entities, such as species or reactions, can now be annotated using ontological terms. These annotations, which are encoded using the resource description framework (RDF), provide the facility to specify definite terms to individual components, allowing software to unambiguously identify such components and thus link the models to existing data resources.
libSBML is an application programming interface library for the manipulation of SBML files. While libSBML provides the facilities for reading and writing such annotations from and to models, it is beyond the scope of libSBML to provide interpretation of these terms. The libAnnotationSBML library introduced here acts as a layer on top of libSBML linking SBML annotations to the web services that describe these ontological terms. Two applications that use this library are described: SbmlSynonymExtractor finds name synonyms of SBML model entities and SbmlReactionBalancer checks SBML files to determine whether specifed reactions are elementally balanced.
Availability: http://mcisb.sourceforge.net/
Contact: neil.swainston@manchester.ac.uk
Transcriptional landscape estimation from tiling array data using a model of signal shift and drift
Authors: Nicolas Pierre , Leduc Aurélie , Robin Stéphane , Rasmussen Simon , Jarmer Hanne , Bessières Philippe 
Published: June 2009

Abstract
Motivation: High-density oligonucleotide tiling array technology holds the promise of a better description of the complexity and the dynamics of transcriptional landscapes. In organisms such as bacteria and yeasts, transcription can be measured on a genome-wide scale with a resolution &gt;25 bp. The statistical models currently used to handle these data remain however very simple, the most popular being the piecewise constant Gaussian model with a fixed number of breakpoints.
Results: This article describes a new methodology based on a hidden Markov model that embeds the segmentation of a continuous-valued signal in a probabilistic setting. For a computationally affordable cost, this framework (i) alleviates the difficulty of choosing a fixed number of breakpoints, and (ii) permits retrieving more information than a unique segmentation by giving access to the whole probability distribution of the transcription profile. Importantly, the model is also enriched and accounts for subtle effects such as signal ‘drift’ and covariates. Relevance of this framework is demonstrated on a Bacillus subtilis dataset.
Availability: A software is distributed under the GPL.
Contact: pierre.nicolas@jouy.inra.fr
Supplementary information: Supplementary data is available at Bioinformatics online.
The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction
Authors: Huttenhower Curtis , Hibbs Matthew A. , Myers Chad L. , Caudy Amy A. , Hess David C. , Troyanskaya Olga G. 
Published: June 2009

Abstract
Motivation: Rapidly expanding repositories of highly informative genomic data have generated increasing interest in methods for protein function prediction and inference of biological networks. The successful application of supervised machine learning to these tasks requires a gold standard for protein function: a trusted set of correct examples, which can be used to assess performance through cross-validation or other statistical approaches. Since gene annotation is incomplete for even the best studied model organisms, the biological reliability of such evaluations may be called into question.
Results: We address this concern by constructing and analyzing an experimentally based gold standard through comprehensive validation of protein function predictions for mitochondrion biogenesis in Saccharomyces cerevisiae. Specifically, we determine that (i) current machine learning approaches are able to generalize and predict novel biology from an incomplete gold standard and (ii) incomplete functional annotations adversely affect the evaluation of machine learning performance. While computational approaches performed better than predicted in the face of incomplete data, relative comparison of competing approaches—even those employing the same training data—is problematic with a sparse gold standard. Incomplete knowledge causes individual methods' performances to be differentially underestimated, resulting in misleading performance evaluations. We provide a benchmark gold standard for yeast mitochondria to complement current databases and an analysis of our experimental results in the hopes of mitigating these effects in future comparative evaluations.
Availability: The mitochondrial benchmark gold standard, as well as experimental results and additional data, is available at http://function.princeton.edu/mitochondria
Contact: ogt@cs.princeton.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Effect of piboserod, a 5‐HT4serotonin receptor antagonist, on left ventricular function in patients with symptomatic heart failure
Authors: Kjekshus John K. , Torp‐Pedersen Christian , Gullestad Lars , Køber Lars , Edvardsen Thor , Olsen Inge C. , Sjaastad Ivar , Qvigstad Eirik , Skomedal Tor , Osnes Jan‐Bjørn , Levy Finn Olav 
Published: July 2009

AimsMyocardial 5‐HT4serotonin (5‐HT) receptors are increased and activated in heart failure (HF). Blockade of 5‐HT4receptors reduced left ventricular (LV) remodelling in HF rats. We evaluated the effect of piboserod, a potent, selective, 5‐HT4serotonin receptor antagonist, on LV function in patients with HF.Methods and resultsThis was a prospective, double‐blind, parallel group trial in patients with NYHA class II–IV HF and LV ejection fraction (EF) ≤0.35. Patients receiving standard HF treatment were randomized to placebo (n= 70) or piboserod 80 mg (n= 67) for 24 weeks including 4 weeks up titration. The primary endpoint was LVEF measured by cardiac magnetic resonance imaging (MRI). Secondary endpoints were LV volumes, N‐terminal pro‐brain natriuretic peptide, norepinephrine, quality of life, and 6 min walk test. Piboserod significantly increased LVEF by 1.7% vs. placebo (CI 0.3, 3.2,P= 0.020), primarily through reduced end‐systolic volume from 165 to 158 mL (P= 0.060). There was a trend for greater increase in LVEF (2.7%, CI −1.1, 6.6,P= 0.15) in a small subset of patients not on chronic β‐blocker therapy. There was no significant effect on neurohormones, quality of life, or exercise tolerance. Patients on piboserod reported more adverse events, but numbers were too small to identify specific safety issues.ConclusionAlthough patients with chronic HF had a small but significant improvement in LVEF when treated with piboserod for 24 weeks, the result was not reflected in significant changes in other efficacy parameters, and its clinical relevance remains uncertain.Clinicaltrials.gov, NCT 00421746
Nested Patch PCR for Highly Multiplexed Amplification of Genomic Loci
Authors: Varley Katherine E. , Mitra Robi D. 
Published: July 2009

INTRODUCTIONNested Patch polymerase chain reaction (PCR) amplifies a large number (greater than 90) of targeted loci from genomic DNA simultaneously in the same reaction. These amplified loci can then be sequenced on a second-generation sequencing machine to detect single nucleotide polymorphisms (SNPs) and mutations. The reaction is highly specific: 90% of sequencing reads match targeted loci. Nested Patch PCR can be performed on many samples in parallel, and by using sample-specific DNA barcodes, these can be pooled and sequenced in a single reaction. Thus, the Nested Patch PCR protocol that is described here provides an easy workflow to identify SNPs and mutations across many targeted loci for many samples in parallel.
Use of Fluorescence In Situ Hybridization and the daime Image Analysis Program for the Cultivation-Independent Quantification of Microorganisms in Environmental and Medical Samples
Authors: Daims Holger 
Published: July 2009

INTRODUCTIONConventional cultivation-based methods to measure microbial abundance are unsuitable for quantifying uncultured microorganisms that constitute the majority of microbial life in most environmental or medical samples. This problem is solved by the quantification approach described here, which combines fluorescence in situ hybridization (FISH) with rRNA-targeted probes and digital image analysis. By measuring the areas of probe-labeled biomass in randomly recorded image pairs, an unbiased estimate of the relative biovolume of the population of interest can be obtained. This approach expresses abundance as “biovolume fraction” (relative to the total biovolume of the whole microbial community). This value equals the share of biochemical reaction space occupied by the quantified population and thus can be more relevant ecologically than absolute cell numbers (e.g., a few large cells can contain the same biovolume as many small cells). Another advantage lies in the complete independence of this method from the morphology of the quantified organisms. Regardless of whether the target microbes occur as single cells in plankton samples, as filaments, or as dense aggregates in biofilms, this cultivation-independent method allows the composition of complex microbial communities to be determined.
Adhesive Micropatterns for Cells: A Microcontact Printing Protocol
Authors: Théry Manuel , Piel Matthieu 
Published: July 2009

INTRODUCTIONThis protocol describes a simple, fast, and efficient method for making adhesive micropatterns that can be used to control individual cell shape and adhesion patterns. It is based on the use of an elastomeric stamp containing microfeatures to print proteins on the substrate of choice. The process can be subdivided into three parts. First, a silicon master is fabricated, which contains the microfeatures of interest. Once fabricated, the master can be used multiple times to make stamps. Masters with customized patterns can also be purchased commercially. Second, a polydimethylsiloxane (PDMS) stamp is fabricated. Unlike fabrication of the master, this step can be performed without specialized equipment. The PDMS stamp is inked with extracellular matrix proteins. Proteins are printed on a substrate (e.g., a tissue culture polystyrene dish or a glass coverslip covered with a thin layer of polystyrene). The nonprinted areas are back-filled with poly-L-lysine-polyethylene glycol, which renders them resistant to cell adhesion. The production of these micropatterned substrates can be completed in <2 h. The third and final portion of the protocol describes the deposition of cells onto the micropatterned substrate.
Using Progressive Methods for Global Multiple Sequence Alignment
Authors: Mount David W. 
Published: July 2009

INTRODUCTIONFinding a global optimal alignment of more than two sequences that includes matches, mismatches, and gaps and that takes into account the degree of variation in all of the sequences at the same time is especially difficult. The dynamic programming algorithm used for optimal alignment of pairs of sequences can be extended to global alignment of three sequences, but for more than three sequences, only a small number of relatively short sequences may be analyzed. Thus, approximate methods are used for global sequence alignment. One class of these methods is progressive global alignment, which starts with an alignment of the most alike sequences and then builds an alignment by adding more sequences. This article introduces three programs that use progressive alignment methodology.