bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effect of post‐cesarean rectal misoprostol on intestinal motility
Authors: Adanikin Abiodun I. , Orji Ernest O. , Fasubaa Olusola B. , Onwudiegwu Uche , Ijarotimi Omotade A. , Olaniyan Oluwaseyi 
Published: August 2012

AbstractObjectiveTo determine whether rectally administered misoprostol can induce intestinal motility compared with oxytocin infusion when used to prevent primary postpartum hemorrhage after cesarean delivery.MethodsIn a prospective randomized double‐blind study in Nigeria, 218 parturients undergoing cesarean delivery who had risk factors for primary postpartum hemorrhage were enrolled between July 1, 2010, and March 31, 2011. Participants received 600 μg of rectal misoprostol or 20 intravenous units of oxytocin for 4 hours after surgery. The primary outcome was time until passage of flatus. Adverse effects, need for additional analgesic, and length of hospital stay were also assessed.ResultsThe misoprostol group had a significantly shorter mean postoperative interval to passage of flatus (20.27 ± 7.77 hours versus 38.34 ± 10.98 hours; P < 0.001) and commencement of regular diet (21.08 ± 7.69 hours versus 39.13 ± 10.94 hours; P < 0.001). Gastrointestinal adverse effects were more frequent, albeit not significantly, in the misoprostol group: nausea, 6.4% versus 1.8%; vomiting, 7.3% versus 2.8%; and abdominal distension, 3.7% versus 2.8%. The need for additional analgesic was the same in the 2 groups.ConclusionAfter cesarean delivery, rectal misoprostol had the added benefit of inducing intestinal motility. Misoprostol might be considered in a clinical setting where postoperative ileus is anticipated.
Use of early transverse annular compression sutures for complete placenta previa during cesarean delivery
Authors: Huang Yi‐Ying , Zhuang Jing‐Yi , Bao Yi‐Rong , Ying Hao , Wang De‐Fen 
Published: August 2012

AbstractObjectiveTo compare the difference in maternal outcomes between early and late use of transverse annular compression sutures (TACS) during cesarean delivery among women with complete placenta previa (CPP).MethodsA retrospective study of 36 women with CPP was conducted. Percentiles of blood loss before TACS were calculated. The transfusion rate, sensitivity, specificity, Youden index, positive predictive value, and negative predictive value were also estimated. Patients were assigned to either the early TACS group or the late TACS group based on the highest Youden index. Maternal outcomes of the 2 groups were compared.ResultsThe Youden index for transfusion rate was highest when blood loss before TACS reached 500 mL. Blood loss before intervention in the late TACS group was significantly higher than in the early TACS group (735.0 ± 123.7 mL versus 396.9 ± 76.3 mL; P < 0.001). More women in the late TACS group than in the early TACS group required blood transfusion (60.0% versus 12.5%; P = 0.004) and the volume of blood transfused was significantly lower in the early TACS group than in the late TACS group (137.5 ± 377.5 mL versus 806.7 ± 619.3 mL; P = 0.001).ConclusionEarly implementation of TACS could lead to improved maternal outcomes.
Provenance and climate change inferred from Sr–Nd–Pb isotopes of late Quaternary sediments in the Huanghe (Yellow River) Delta, China
Authors: Hu Bangqi , Li Guogang , Li Jun , Bi Jianqiang , Zhao Jingtao , Bu Ruyuan 
Published: August 2012

AbstractWe present a provenance study of core ZK2 from the Huanghe (Yellow River) Delta in order to assess the impacts of climate change on the sediment supplies during the last glacial–interglacial cycle. Facies analysis and sequence stratigraphy methods are used to construct the age model. Sr isotopic compositions of ZK2 range from 0.716389 to 0.723884, with 87Sr/86Sr increased with decreasing grain size. Nd and Pb isotopic compositions display two large major excursions during Marine Oxygen Isotope stages (MIS) 2 and 4, with less radiogenic εNd and lower 208Pb/204Pb, 207Pb/204Pb, and 206Pb/204Pb values during these periods. These excursions have been explained in terms of changes in the mixing proportion of sediments from the Loess Plateau and Ordos Plateau, resulting from East Asian monsoon intensity variations. The weak summer monsoon precipitation resulted in decreased erosion of Loess Plateau during MIS 2, 4 and the middle of MIS 3. Meanwhile, both the intensified East Asian winter monsoon and the southward expansions of Mu Us desert significantly enhanced the eolian sand entering the Huanghe. Therefore, our results highlight the impact of monsoon variability on erosion patterns in the Huanghe basin.
Evaluating Pulmonary Vein Isolation
Authors: Shah Dipen 
Published: August 2012

AbstractPulmonary vein isolation is the electrophysiological endpoint of complete conduction block at the level of the veno‐atrial junction and must be explicitly distinguished from encircling PV ablation which frequently does not result in isolation.The prerequisites for successful PV isolation include a knowledge of the individual anatomy of the PVs and the left atrium, appropriate positioning of circular mapping catheters, and a knowledge of the electrophysiology of PV activation, in addition to effective ablation tools. Excessive ablation, and possibly complications, can be avoided by the recognition of non‐PV myocardial contributions to electrograms recorded from within the PVs. The posterior wall of the left atrial appendage contributes far‐field electrograms to recordings from all or nearly all left superior PVs, the low anterior left atrium to 80% of left inferior PV recordings and the superior vena cava to 23% of right superior PV recordings. Recognition of these far‐field components is feasible and accurate in sinus rhythm as well as during ongoing atrial fibrillation. Finally, the creation of temporally stable PV isolation remains a currently unsolved problem although prolonged post isolation surveillance, may be helpful.
Genetic Background of Arrhythmogenic Right Ventricular Dysplasia/Cardiomyopathy: Time to Start Asian Registry!
Authors: Horie Minoru , Ishida Katsuya , Nishio Yukiko , Nagaoka Iori , Matsui Keiji 
Published: August 2012

AbstractArrhythmogenic right venticular dysplasia/cardiomyopathy (ARVD/C) is an inherited cardiomyopathy with a very low penetrance affecting the right ventricle (RV) and presenting palpitation and syncope due to ventricular tachycardia (VT) originating from RV. The VT can degenerate into ventricular fibrillation and sudden cardiac death. The genetic background of ARVD/C has recently been found to be heterogeneous, mainly resulting from cell adhesion abnormalities due to mutations in five different genes encoding members of the desmosome complex. In Asian countries, however, the genetic aspect of the disease has not been fully studied, although the clinical features of Asian ARVD/C patients are different from those in Western countries in the penetrance of phenotypes, relation to Brugada syndrome and link to RV outflow tract ventricular tachycardia. It is of urgent need to have a registry of Asian ARVD/C patients and to conduct a more detailed genetic survey on the candidate genes, including desomosomal ones.
Identification and Radiofrequency Catheter Ablation of a Nonsustained Atrial Tachycardia at the Septal Mitral Annulus with the Use of a Noncontact Mapping System: A Case Report
Authors: Narita Sumito , Tsuchiya Takeshi , Ushinohama Hiroya , Ando Shin‐ichi 
Published: August 2012

AbstractHere we report a case of a 16‐year old female with symptomatic nonsustained atrial tachycardia (NSAT) originating from the septal mitral annulus. NSAT was induced by atrial burst pacing after an intravenous isoproterenol (ISP) injection. The array mode of the noncontact mapping system (NCM) allowed us to quickly identify the tachycardia focus at the septal mitral annulus, where the contact bipolar voltage map revealed no low voltage area (<0.5 mV). The NSAT was eliminated by a radiofrequency energy application to the identified tachycardia focus during sinus rhythm, and the patient has been free from any symptoms during 10 months of follow‐up.
ST‐T Abnormalities on ECG in Relation to Cardiovascular Risk Factors
Authors: Chinushi Yuko , Watanabe Hiroshi , Chinushi Masaomi , Aizawa Yoshifusa 
Published: August 2012

Background: Significance of an ST‐T abnormality in subjects with no apparent heart diseases is to be determined.Subjects and methods: The study involved 44,990 adults (16,368 males and 28,622 females) aged 40‐85 years who under went an annual health examination. Cardiovascular risks (CVRs) were considered positive if 1) body mass index was ≥ 25Kg/m2, 2) systolic blood pressure (BP) ≥ 130 mmHg and/or diastolic BP ≥ 85mmHg, 3) triglyceride ≥ 150 mg/ dl, 4) HDL‐C level ≤ 40mg/dl for men and ≤ 50mg/dl for women, or 5) fasting blood glucose ≤ 110 mg/dl. The relation between CVRs and ST‐T abnormalities were evaluated.Results: ST‐T abnormalities were found in 6.49% in males, and more frequently in females: 8.45%. Each CVR and the number of combined CVRs were risk factors for ST‐T abnormalities on ECG (P < 0.0001 for a trend). On the other hand, ECG‐based LVH was found in 5.7% but showed no relation with CVRs or their com binations. ST‐T abnormalities may represent preclinical cardiac involvement of CVRs more sensitively than LVH on ECG and ECG findings may be used in mass examinations.Conclusions: ST‐T abnormalities without apparent heart diseas may be considered to be nonspecific but this cross‐sectional study showed that they are related to CVRs and may be used as an early marker of preclinical cardiac damage by CVRs.
The Relationship between Optimization for Cardiac Resynchronization Therapy by Measurement of dp/dt and the Middle‐to‐long‐term Prognosis of Heart Failure Patients
Authors: Kabutoya Tomoyuki , Mitsuhashi Takeshi , Watanabe Tomonori , Nakagami Rieko , Hata Yoshihito , Shimada Kazuyuki , Kario Kazuomi 
Published: August 2012

Background: The relationship between optimization according to left ventricular (LV) dp/dt, changes in LV performance, and prognosis of heart failure patients who undergo cardiac resynchronization therapy (CRT) remains unclear.Methods: We studied 27 consecutive patients who underwent CRT implantation (18 males, 9 females; age, 67.3 ± 8.3 years). We measured LV dp/dt to determine the timing of LV‐right ventricular (RV) sequential pacing. Echocardiographic examination was performed before and after the CRT procedure to assess LV ejection fraction (LVEF) and LV end‐diastolic diameter (LVEDD). Primary endpoints were all‐cause death and cardiac hospitalization.Results: An increase in LV dp/dt during CRT was significantly associated with an increase in LVEF (r = 0.47, p = 0.018), but was not associated with a decrease in LVEDD. The mean follow‐up period was 14 ± 13 months, and six endpoints were observed. In the control group, no subjects encountered any of the endpoints, and they had higher LVEDD reductions (5.7 ± 8.4 vs. ± 2.5 ± 4.6 mm; p = 0.034) than those in the event group. Cox regression analysis revealed that a reduction in LVEDD was a significant predictor of event‐free survival.Conclusions: The measurement of LV dp/dt might be useful for the optimization of CRT. Reductions in LVEDD are necessary to achieve improvements in the long‐term prognosis of CRT patients.
TRFolder-W: a web server for telomerase RNA structure prediction in yeast genomes
Authors: Zhang Dong , Xue Xingran , Malmberg Russell L. , Cai Liming 
Published: August 2012

Abstract
Summary: TRFolder-W is a web server capable of predicting core structures of telomerase RNA (TR) in yeast genomes. TRFolder is a command-line Python toolkit for TR-specific structure prediction. We developed a web-version built on the django web framework, leveraging the work done previously, to include enhancements to increase flexibility of usage. To date, there are five core sub-structures commonly found in TR of fungal species, which are the template region, downstream pseudoknot, boundary element, core-closing stem and triple helix. The aim of TRFolder-W is to use the five core structures as fundamental units to predict potential TR genes for yeast, and to provide a user-friendly interface. Moreover, the application of TRFolder-W can be extended to predict the characteristic structure on species other than fungal species.
Availability: The web server TRFolder-W is available at http://rna-informatics.uga.edu/?f=software&p=TRFolder-w.
Contact: cai@cs.uga.edu
Supplementary information: http://rna-informatics.uga.edu/?f=software&p=TRFolder-w-supplement.
Qualitative translation of relations from BioPAX to SBML qual
Authors: Büchel Finja , Wrzodek Clemens , Mittag Florian , Dräger Andreas , Eichner Johannes , Rodriguez Nicolas , Le Novère Nicolas , Zell Andreas 
Published: August 2012

Abstract
Motivation: The biological pathway exchange language (BioPAX) and the systems biology markup language (SBML) belong to the most popular modeling and data exchange languages in systems biology. The focus of SBML is quantitative modeling and dynamic simulation of models, whereas the BioPAX specification concentrates mainly on visualization and qualitative analysis of pathway maps. BioPAX describes reactions and relations. In contrast, SBML core exclusively describes quantitative processes such as reactions. With the SBML qualitative models extension (qual), it has recently also become possible to describe relations in SBML. Before the development of SBML qual, relations could not be properly translated into SBML. Until now, there exists no BioPAX to SBML converter that is fully capable of translating both reactions and relations.
Results: The entire nature pathway interaction database has been converted from BioPAX (Level 2 and Level 3) into SBML (Level 3 Version 1) including both reactions and relations by using the new qual extension package. Additionally, we present the new webtool BioPAX2SBML for further BioPAX to SBML conversions. Compared with previous conversion tools, BioPAX2SBML is more comprehensive, more robust and more exact.
Availability: BioPAX2SBML is freely available at http://webservices.cs.uni-tuebingen.de/ and the complete collection of the PID models is available at http://www.cogsys.cs.uni-tuebingen.de/downloads/Qualitative-Models/.
Contact: finja.buechel@uni-tuebingen.de
Supplementary Information: Supplementary data are available at Bioinformatics online.
Information-theoretic analysis and prediction of protein atomic burials: on the search for an informational intermediate between sequence and structure
Authors: Rocha Juliana R. , van der Linden Marx G. , Ferreira Diogo C. , Azevêdo Paulo H. , Pereira de Araújo Antônio F. 
Published: August 2012

Abstract
Motivation: It has been recently suggested that atomic burials, as expressed by molecular central distances, contain sufficient information to determine the tertiary structure of small globular proteins. A possible approach to structural determination from sequence could therefore involve a sequence-to-burial intermediate prediction step whose accuracy, however, is theoretically limited by the mutual information between these two variables. We use a non-redundant set of globular protein structures to estimate the mutual information between local amino acid sequence and atomic burials. Discretizing central distances of or atoms in equiprobable burial levels, we estimate relevant mutual information measures that are compared with actual predictions obtained from a Naive Bayesian Classifier (NBC) and a Hidden Markov Model (HMM).
Results: Mutual information density for 20 amino acids and two or three burial levels were estimated to be roughly 15% of the unconditional burial entropy density. Lower estimates for the mutual information between local amino acid sequence and burial of a single residue indicated an increase in mutual information with the number of burial levels up to at least five or six levels. Prediction schemes were found to efficiently extract the available burial information from local sequence. Lower estimates for the mutual information involving single burials are consistently approached by predictions from the NBC and actually surpassed by predictions from the HMM. Near-optimal prediction for the HMM is indicated by the agreement between its density of prediction information and the corresponding density of mutual information between input and output representations.
Availability: The dataset of protein structures and the prediction implementations are available at http://www.btc.unb.br/ (in ‘Software’).
Contact: aaraujo@unb.br
Supplementary information: Supplementary data are available at Bioinformatics online.
Static network structure can be used to model the phenotypic effects of perturbations in regulatory networks
Authors: Feiglin Ariel , Hacohen Adar , Sarusi Avital , Fisher Jasmin , Unger Ron , Ofran Yanay 
Published: August 2012

Abstract
Motivation: Biological processes are dynamic, whereas the networks that depict them are typically static. Quantitative modeling using differential equations or logic-based functions can offer quantitative predictions of the behavior of biological systems, but they require detailed experimental characterization of interaction kinetics, which is typically unavailable. To determine to what extent complex biological processes can be modeled and analyzed using only the static structure of the network (i.e. the direction and sign of the edges), we attempt to predict the phenotypic effect of perturbations in biological networks from the static network structure.
Results: We analyzed three networks from different sources: The EGFR/MAPK and PI3K/AKT network from a detailed experimental study, the TNF regulatory network from the STRING database and a large network of all NCI-curated pathways from the Protein Interaction Database. Altogether, we predicted the effect of 39 perturbations (e.g. by one or two drugs) on 433 target proteins/genes. In up to 82% of the cases, an algorithm that used only the static structure of the network correctly predicted whether any given protein/gene is upregulated or downregulated as a result of perturbations of other proteins/genes.
Conclusion: While quantitative modeling requires detailed experimental data and heavy computations, which limit its scalability for large networks, a wiring-based approach can use available data from pathway and interaction databases and may be scalable. These results lay the foundations for a large-scale approach of predicting phenotypes based on the schematic structure of networks.
Contact: yanay@ofranlab.org
Supplementary information: Supplementary data are available at Bioinformatics online.
RIsearch: fast RNA–RNA interaction search using a simplified nearest-neighbor energy model
Authors: Wenzel Anne , Akbaşli Erdinç , Gorodkin Jan 
Published: August 2012

Abstract
Motivation: Regulatory, non-coding RNAs often function by forming a duplex with other RNAs. It is therefore of interest to predict putative RNA–RNA duplexes in silico on a genome-wide scale. Current computational methods for predicting these interactions range from fast complementary-based searches to those that take intramolecular binding into account. Together these methods constitute a trade-off between speed and accuracy, while leaving room for improvement within the context of genome-wide screens. A fast pre-filtering of putative duplexes would therefore be desirable.
Results: We present RIsearch, an implementation of a simplified Turner energy model for fast computation of hybridization, which significantly reduces runtime while maintaining accuracy. Its time complexity for sequences of lengths m and n is with a much smaller pre-factor than other tools. We show that this energy model is an accurate approximation of the full energy model for near-complementary RNA–RNA duplexes. RIsearch uses a Smith–Waterman-like algorithm using a dinucleotide scoring matrix which approximates the Turner nearest-neighbor energies. We show in benchmarks that we achieve a speed improvement of at least 2.4× compared with RNAplex, the currently fastest method for searching near-complementary regions. RIsearch shows a prediction accuracy similar to RNAplex on two datasets of known bacterial short RNA (sRNA)–messenger RNA (mRNA) and eukaryotic microRNA (miRNA)–mRNA interactions. Using RIsearch as a pre-filter in genome-wide screens reduces the number of binding site candidates reported by miRNA target prediction programs, such as TargetScanS and miRanda, by up to 70%. Likewise, substantial filtering was performed on bacterial RNA–RNA interaction data.
Availability: The source code for RIsearch is available at: http://rth.dk/resources/risearch.
Contact: gorodkin@rth.dk
Supplementary information: Supplementary data are available at Bioinformatics online.
HSPIR: a manually annotated heat shock protein information resource
Authors: R. Ratheesh Kumar , N. S. Nagarajan , S. P. Arunraj , Sinha Devanjan , Veedin Rajan Vinoth Babu , Esthaki Vinoth Kumar , D’Silva Patrick 
Published: August 2012

AbstractSummary: Heat shock protein information resource (HSPIR) is a concerted database of six major heat shock proteins (HSPs), namely, Hsp70, Hsp40, Hsp60, Hsp90, Hsp100 and small HSP. The HSPs are essential for the survival of all living organisms, as they protect the conformations of proteins on exposure to various stress conditions. They are a highly conserved group of proteins involved in diverse physiological functions, including de novo folding, disaggregation and protein trafficking. Moreover, their critical role in the control of disease progression made them a prime target of research. Presently, limited information is available on HSPs in reference to their identification and structural classification across genera. To that extent, HSPIR provides manually curated information on sequence, structure, classification, ontology, domain organization, localization and possible biological functions extracted from UniProt, GenBank, Protein Data Bank and the literature. The database offers interactive search with incorporated tools, which enhances the analysis. HSPIR is a reliable resource for researchers exploring structure, function and evolution of HSPs.Availability: http://pdslab.biochem.iisc.ernet.in/hspir/Contact: patrick@biochem.iisc.ernet.inSupplementary information: Supplementary data are available at Bioinformatics online.
Quality of life monitoring in ambulatory heart failure patients: temporal changes and prognostic value
Authors: Lupón Josep , Gastelurrutia Paloma , de Antonio Marta , González Beatriz , Cano Lucía , Cabanes Roser , Urrutia Agustín , Díez Crisanto , Coll Ramón , Altimir Salvador , Bayes‐Genis Antoni 
Published: August 2012

AimsHeart failure (HF) is a chronic condition that typically affects a patient's quality of life (QoL). Little is known about long‐term QoL monitoring in HF. This study aimed to evaluate the temporal changes and prognostic value of QoL assessment in a real‐life cohort of HF patients.Methods and resultsThe Minnesota Living with Heart Failure Questionnaire was used to monitor QoL at baseline and at 1, 3, and 5 years for 1151 consecutive patients {71.7% men, median age 69 years [25th–75th percentiles (P25–P75) 59–76]} in an HF unit. Follow‐up for prognosis assessment was extended to 6 years. The number of answered questionnaires was 1151 at baseline, 746 at 1 year, 268 at 3 years, and 240 at 5 years. QoL scores showed a steep decrease (indicating QoL improvement) during the first year [29 (P25–P75 16–43) at baseline vs. 15 (P25–P75 8–27) at 1 year, P < 0.001], which was tempered, yet significant up to 5 years [12 (P25–P75 7–23) at 3 years vs. 10 (P25–P75 5–21) at 5 years, P = 0.012]. We recorded 457 deaths during follow‐up. In a comprehensive multivariable Cox regression analysis, baseline QoL remained a significant prognosticator during follow‐up [hazard ratio (HR)Cox for death 1.012, 95% confidence interval 1.006–1.018, P < 0.001]. QoL monitoring showed that a score increase ≥10% between consecutive assessments stratified high‐risk patients within the next 12 months (P = 0.008).ConclusionBoth baseline and follow‐up QoL monitoring were useful for patient risk stratification in a real‐life HF cohort. Worse QoL may warn of a worse prognosis. Widespread QoL monitoring in routine clinical practice is recommended.