bluuebunny/crossref_metadata_2025_split huggingface dataset:
Two-dimensional characterization of ELM precursors in NSTX
Authors: Sechrest Y. , Munsat T. , Battaglia D.J. , Zweben S.J. 
Published: November 2012

Abstract
Gas puff imaging has been used to capture the two-dimensional evolution of edge-localized mode (ELM) precursors. Precursor events were observed preceding ELMs and ELM-induced H–L back-transitions in radio-frequency heated H-mode plasmas, and the growth of the precursor mode through the ELM filamentation was imaged in the plane perpendicular to the local B-field. Strong edge intensity modulations appeared to propagate in the electron diamagnetic direction while steadily drifting radially outwards. Intensity fluctuations were observed at frequencies around 20 kHz and wavenumbers of 0.05–0.2 cm−1. Upon growing to a trigger point, precursor fluctuations were seen to form filamentary structures and move into the scrape-off layer (SOL) explosively with radial velocities peaking at 8 km s−1. Once in the SOL, filaments reverse their propagation direction and travel in the ion diamagnetic direction. Edge intensity fluctuations are strongly correlated with magnetic signals from Mirnov coils, and toroidally distributed coils estimated toroidal mode numbers of n = 5–10. Quantitatively similar precursors have been observed in ohmic H-mode plasmas as well, though significantly fewer events are seen in the ohmic cases and none were observed in the near-threshold NBI H-modes studied.
MetaGeneTack: ab initio detection of frameshifts in metagenomic sequences
Authors: Tang Shiyuyun , Antonov Ivan , Borodovsky Mark 
Published: November 2012

Abstract
Summary: Frameshift (FS) prediction is important for analysis and biological interpretation of metagenomic sequences. Since a genomic context of a short metagenomic sequence is rarely known, there is not enough data available to estimate parameters of species-specific statistical models of protein-coding and non-coding regions. The challenge of ab initio FS detection is, therefore, two fold: (i) to find a way to infer necessary model parameters and (ii) to identify positions of frameshifts (if any). Here we describe a new tool, MetaGeneTack, which uses a heuristic method to estimate parameters of sequence models used in the FS detection algorithm. It is shown on multiple test sets that the MetaGeneTack FS detection performance is comparable or better than the one of earlier developed program FragGeneScan.
Availability and implementation: MetaGeneTack is available as a web server at http://exon.gatech.edu/GeneTack/cgi/metagenetack.cgi. Academic users can download a standalone version of the program from http://exon.gatech.edu/license_download.cgi.
Contact: borodovsky@gatech.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Pathway hunting by random survival forests
Authors: Chen Xi , Ishwaran Hemant 
Published: November 2012

AbstractMotivation: Pathway or gene set analysis has been widely applied to genomic data. Many current pathway testing methods use univariate test statistics calculated from individual genomic markers, which ignores the correlations and interactions between candidate markers. Random forests-based pathway analysis is a promising approach for incorporating complex correlation and interaction patterns, but one limitation of previous approaches is that pathways have been considered separately, thus pathway cross-talk information was not considered.Results: In this article, we develop a new pathway hunting algorithm for survival outcomes using random survival forests, which prioritize important pathways by accounting for gene correlation and genomic interactions. We show that the proposed method performs favourably compared with five popular pathway testing methods using both synthetic and real data. We find that the proposed methodology provides an efficient and powerful pathway modelling framework for high-dimensional genomic data.Availability: The R code for the analysis used in this article is available upon request.Contact: xi.steven.chen@gmail.comSupplementary information: Supplementary data are available at Bioinformatics online.
PBSIM: PacBio reads simulator—toward accurate genome assembly
Authors: Ono Yukiteru , Asai Kiyoshi , Hamada Michiaki 
Published: November 2012

Abstract
Motivation: PacBio sequencers produce two types of characteristic reads (continuous long reads: long and high error rate and circular consensus sequencing: short and low error rate), both of which could be useful for de novo assembly of genomes. Currently, there is no available simulator that targets the specific generation of PacBio libraries.
Results: Our analysis of 13 PacBio datasets showed characteristic features of PacBio reads (e.g. the read length of PacBio reads follows a log-normal distribution). We have developed a read simulator, PBSIM, that captures these features using either a model-based or sampling-based method. Using PBSIM, we conducted several hybrid error correction and assembly tests for PacBio reads, suggesting that a continuous long reads coverage depth of at least 15 in combination with a circular consensus sequencing coverage depth of at least 30 achieved extensive assembly results.
Availability: PBSIM is freely available from the web under the GNU GPL v2 license (http://code.google.com/p/pbsim/).
Contact: mhamada@k.u-tokyo.ac.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
HD-CNV: hotspot detector for copy number variants
Authors: Butler Jenna L. , Osborne Locke Marjorie Elizabeth , Hill Kathleen A. , Daley Mark 
Published: November 2012

Abstract
Summary: Copy number variants (CNVs) are a major source of genetic variation. Comparing CNVs between samples is important in elucidating their potential effects in a wide variety of biological contexts. HD-CNV (hotspot detector for copy number variants) is a tool for downstream analysis of previously identified CNV regions from multiple samples, and it detects recurrent regions by finding cliques in an interval graph generated from the input. It creates a unique graphical representation of the data, as well as summary spreadsheets and UCSC (University of California, Santa Cruz) Genome Browser track files. The interval graph, when viewed with other software or by automated graph analysis, is useful in identifying genomic regions of interest for further study.
Availability and implementation: HD-CNV is an open source Java code and is freely available, with tutorials and sample data from http://daleylab.org.
Contact: jcamer7@uwo.ca
Binary Interval Search: a scalable algorithm for counting interval intersections
Authors: Layer Ryan M. , Skadron Kevin , Robins Gabriel , Hall Ira M. , Quinlan Aaron R. 
Published: November 2012

Abstract
Motivation: The comparison of diverse genomic datasets is fundamental to understand genome biology. Researchers must explore many large datasets of genome intervals (e.g. genes, sequence alignments) to place their experimental results in a broader context and to make new discoveries. Relationships between genomic datasets are typically measured by identifying intervals that intersect, that is, they overlap and thus share a common genome interval. Given the continued advances in DNA sequencing technologies, efficient methods for measuring statistically significant relationships between many sets of genomic features are crucial for future discovery.
Results: We introduce the Binary Interval Search (BITS) algorithm, a novel and scalable approach to interval set intersection. We demonstrate that BITS outperforms existing methods at counting interval intersections. Moreover, we show that BITS is intrinsically suited to parallel computing architectures, such as graphics processing units by illustrating its utility for efficient Monte Carlo simulations measuring the significance of relationships between sets of genomic intervals.
Availability: https://github.com/arq5x/bits.
Contact: arq5x@virginia.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Demethylesterification of Cell Wall Pectins in Arabidopsis Plays a Role in Seed Germination
Authors: Müller Kerstin , Levesque-Tremblay Gabriel , Bartels Sebastian , Weitbrecht Karin , Wormit Alexandra , Usadel Bjoern , Haughn George , Kermode Allison R. 
Published: November 2012

Abstract
The methylesterification status of cell wall homogalacturonans, mediated through the action of pectin methylesterases (PMEs), influences the biophysical properties of plant cell walls such as elasticity and porosity, important parameters for cell elongation and water uptake. The completion of seed germination requires cell wall extensibility changes in both the radicle itself and in the micropylar tissues surrounding the radicle. In wild-type seeds of Arabidopsis (Arabidopsis thaliana), PME activities peaked around the time of testa rupture but declined just before the completion of germination (endosperm weakening and rupture). We overexpressed an Arabidopsis PME inhibitor to investigate PME involvement in seed germination. Seeds of the resultant lines showed a denser methylesterification status of their cell wall homogalacturonans, but there were no changes in the neutral sugar and uronic acid composition of the cell walls. As compared with wild-type seeds, the PME activities of the overexpressing lines were greatly reduced throughout germination, and the low steady-state levels neither increased nor decreased. The most striking phenotype was a significantly faster rate of germination, which was not connected to altered testa rupture morphology but to alterations of the micropylar endosperm cells, evident by environmental scanning electron microscopy. The transgenic seeds also exhibited an apparent reduced sensitivity to abscisic acid with respect to its inhibitory effects on germination. We speculate that PME activity contributes to the temporal regulation of radicle emergence in endospermic seeds by altering the mechanical properties of the cell walls and thereby the balance between the two opposing forces of radicle elongation and mechanical resistance of the endosperm.
iRootHair: A Comprehensive Root Hair Genomics Database
Authors: Kwasniewski Miroslaw , Nowakowska Urszula , Szumera Jakub , Chwialkowska Karolina , Szarejko Iwona 
Published: November 2012

Abstract
The specialized root epidermis cells of higher plants produce long, tubular outgrowths called root hairs. Root hairs play an important role in nutrient and water uptake, and they serve as a valuable model in studies of plant cell morphogenesis. More than 1,300 articles that describe the biological processes of these unique cells have been published to date. As new fields of root hair research are emerging, the number of new papers published each year and the volumes of new relevant data are continuously increasing. Therefore, there is a general need to facilitate studies on root hair biology by collecting, presenting, and sharing the available information in a systematic, curated manner. Consequently, in this paper, we present a comprehensive database of root hair genomics, iRootHair, which is accessible as a Web-based service. The current version of the database includes information about 153 root hair-related genes that have been identified to date in dicots and monocots along with their putative orthologs in higher plants with sequenced genomes. In order to facilitate the use of the iRootHair database, it is subdivided into interrelated, searchable sections that describe genes, processes of root hair formation, root hair mutants, and available references. The database integrates bioinformatics tools with a focus on sequence identification and annotation. iRootHair is a unique resource for root hair research that integrates the large volume of data related to root hair genomics in a single, curated, and expandable database that is freely available at www.iroothair.org.
Rapid Reversion from Monomer to Dimer Regenerates the Ultraviolet-B Photoreceptor UV RESISTANCE LOCUS8 in Intact Arabidopsis Plants
Authors: Heilmann Monika , Jenkins Gareth I. 
Published: November 2012

Abstract
Arabidopsis (Arabidopsis thaliana) UV RESISTANCE LOCUS8 (UVR8) is a photoreceptor that specifically mediates photomorphogenic responses to ultraviolet (UV)-B in plants. UV-B photoreception induces the conversion of the UVR8 dimer into a monomer that interacts with the CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1) protein to regulate gene expression. However, it is not known how the dimeric photoreceptor is regenerated in plants. Here, we show, by using inhibitors of protein synthesis and degradation via the proteasome, that the UVR8 dimer is not regenerated by rapid de novo synthesis following destruction of the monomer. Rather, regeneration occurs by reversion from the monomer to the dimer. However, regeneration of dimeric UVR8 in darkness following UV-B exposure occurs much more rapidly in vivo than in vitro with illuminated plant extracts or purified UVR8, indicating that rapid regeneration requires intact cells. Rapid dimer regeneration in vivo requires protein synthesis, the presence of a carboxyl-terminal 27-amino acid region of UVR8, and the presence of COP1, which is known to interact with the carboxyl-terminal region. However, none of these factors can account fully for the difference in regeneration kinetics in vivo and in vitro, indicating that additional proteins or processes are involved in UVR8 dimer regeneration in vivo.
Sick leave during pregnancy: a longitudinal study of rates and risk factors in a Norwegian population
Authors: Dørheim SK , Bjorvatn B , Eberhard‐Gran M 
Published: November 2012

ObjectiveTo describe the prevalence of, reasons given for, and factors associated with sick leave during pregnancy.DesignLongitudinal, population‐based descriptive study.SettingAkershus University Hospital, Norway.PopulationAll women scheduled to give birth at the hospital (November 2008 to April 2010).MethodsConsenting women were handed a questionnaire at the routine ultrasound check at 17 weeks of gestation. Women returning this questionnaire received a second questionnaire at 32 weeks of gestation. Multiple logistic regression analyses were performed to examine associations with somatic, psychiatric and social factors.Main outcome measuresRates and duration of sick leave.ResultsBy 32 weeks of gestation, 63.2% of the 2918 women included were on sick leave, and 75.3% had been on sick leave at some point during their pregnancy. Pelvic girdle pain and fatigue/sleep problems were the main reasons given for sick leave. Being on sick leave in all trimesters was strongly associated with hyperemesis, exercising less than weekly, chronic pain before or during pregnancy, infertility treatment (all P < 0.001); younger maternal age, conflicts in the workplace (both P < 0.01); multiparity, previous depression, insomnia and lower education (all P < 0.05). Sick leave was associated with elective caesarean section and higher infant birthweight (P < 0.01). Adjustment of the work situation was associated with 1 week shorter duration of sick leave.ConclusionsMost women receive sick leave during pregnancy, but sick leave might not be caused by pregnancy alone. Previous medical and psychiatric history, work conditions and socio‐economic factors need to be addressed to understand sick leave during pregnancy.
Timing of administration of prophylactic antibiotics for caesarean section: a systematic review and meta‐analysis
Authors: Baaqeel H , Baaqeel R 
Published: November 2012

BackgroundProphylactic antibiotics reduce infectious morbidity from caesarean section. The timing of their administration, however, is a matter of controversy.ObjectivesTo examine maternal and neonatal infectious morbidity in women receiving preoperative prophylaxis compared with those receiving intraoperative administration.Search strategyMedline, Embase, Current Controlled Trials and Cochrane Central were searched from their inception dates to December 2011.Selection criteriaRandomised controlled trials of a single dose of any antibiotic comparing preoperative with intraoperative administration were selected.Data collection and analysisTrial characteristics, outcomes and quality measures, based on the Cochrane tool for risk of bias, were independently extracted. The random effect model of DerSimonian and Laird to estimate relative risks (RRs) for maternal and neonatal outcomes was used.Main resultsSix trials met the inclusion criteria, reporting on 2313 women and 2345 newborns. Preoperative administration was associated with a significant 41% reduction in the rate of endometritis compared with intraoperative administration (RR 0.59; 95% confidence interval [95% CI] 0.37–0.94; I2 0%). In the preoperative group, there were nonsignificant reductions in the rates of wound infection (RR 0.71; 95% CI 0.44–1.14; I2 0%), maternal febrile morbidity (RR 0.94; 95% CI 0.46–1.95; I2 0%), neonatal sepsis (RR 0.81; 95% CI 0.47–1.41; I2 0%), neonatal septic work‐up (RR 0.93; 95% CI 0.71–1.21; I2 0%) and neonatal intensive‐care unit admission (RR 0.92; 95% CI 0.65–1.28; I2 0%). There were nonsignificant increases in the rates of maternal pyelonephritis (RR 1.09; 95% CI 0.49–2.43; I2 0%) and neonatal pneumonia (RR 3.36; 95% CI 0.55–20.47; I2 0%).ConclusionsCompared with intraoperative administration, preoperative antibiotics significantly reduce the rate of endometritis. The lack of neonatal adverse effects should be cautiously interpreted given the limited power of the trials to detect such effects.
Enhanced AMPA receptor activity increases operant alcohol self‐administration and cue‐induced reinstatement
Authors: Cannady Reginald , Fisher Kristen R. , Durant Brandon , Besheer Joyce , Hodge Clyde W. 
Published: November 2012

AbstractLong‐term alcohol exposure produces neuroadaptations that contribute to the progression of alcohol abuse disorders. Chronic alcohol consumption results in strengthened excitatory neurotransmission and increased α‐amino‐3‐hydroxyl‐5‐methyl‐4‐isoxazole‐propionate receptors (AMPA) receptor signaling in animal models. However, the mechanistic role of enhanced AMPA receptor activity in alcohol‐reinforcement and alcohol‐seeking behavior remains unclear. This study examined the role of enhanced AMPA receptor function using the selective positive allosteric modulator, aniracetam, in modulating operant alcohol self‐administration and cue‐induced reinstatement. Male alcohol‐preferring (P‐) rats, trained to self‐administer alcohol (15%, v/v) versus water were pre‐treated with aniracetam to assess effects on maintenance of alcohol self‐administration. To determine reinforcer specificity, P‐rats were trained to self‐administer sucrose (0.8%, w/v) versus water, and effects of aniracetam were tested. The role of aniracetam in modulating relapse of alcohol‐seeking was assessed using a response contingent cue‐induced reinstatement procedure in P‐rats trained to self‐administer 15% alcohol. Aniracetam pre‐treatment significantly increased alcohol‐reinforced responses relative to vehicle treatment. This increase was not attributed to aniracetam‐induced hyperactivity as aniracetam pre‐treatment did not alter locomotor activity. AMPA receptor involvement was confirmed because 6,7‐dinitroquinoxaline‐2,3‐dione (AMPA receptor antagonist) blocked the aniracetam‐induced increase in alcohol self‐administration. Aniracetam did not alter sucrose‐reinforced responses in sucrose‐trained P‐rats, suggesting that enhanced AMPA receptor activity is selective in modulating the reinforcing function of alcohol. Finally, aniracetam pre‐treatment potentiated cue‐induced reinstatement of alcohol‐seeking behavior versus vehicle‐treated P‐rats. These data suggest that enhanced glutamate activity at AMPA receptors may be key in facilitating alcohol consumption and seeking behavior, which could ultimately contribute to the development of alcohol abuse disorders.
Renal pericytes: regulators of medullary blood flow
Authors: Kennedy‐Lydon T. M. , Crawford C. , Wildman S. S. P. , Peppiatt‐Wildman C. M. 
Published: November 2012

AbstractRegulation of medullary blood flow (MBF) is essential in maintaining normal kidney function. Blood flow to the medulla is supplied by the descending vasa recta (DVR), which arise from the efferent arterioles of juxtamedullary glomeruli. DVR are composed of a continuous endothelium, intercalated with smooth muscle‐like cells called pericytes. Pericytes have been shown to alter the diameter of isolated and in situ DVR in response to vasoactive stimuli that are transmitted via a network of autocrine and paracrine signalling pathways. Vasoactive stimuli can be released by neighbouring tubular epithelial, endothelial, red blood cells and neuronal cells in response to changes in NaCl transport and oxygen tension. The experimentally described sensitivity of pericytes to these stimuli strongly suggests their leading role in the phenomenon of MBF autoregulation. Because the debate on autoregulation of MBF fervently continues, we discuss the evidence favouring a physiological role for pericytes in the regulation of MBF and describe their potential role in tubulo‐vascular cross‐talk in this region of the kidney. Our review also considers current methods used to explore pericyte activity and function in the renal medulla.
Recent advances in laparoscopic surgery
Authors: Lee Wei‐Jei , Chan Chien‐Pin , Wang Bing‐Yen 
Published: November 2012

AbstractLaparoscopic surgery has been widely adopted and new technical innovation, procedures and evidence based knowledge are persistently emerging. This review documents recent major advancements in laparoscopic surgery. A PubMed search was made in order to identify recent advances in this field. We reviewed the recent data on randomized trials in this field as well as papers of systematic review. Laparoscopic cholecystectomy is the most frequently performed procedure, followed by laparoscopic bariatric surgery. Although bile duct injuries are relatively uncommon (0.15%–0.6%), intraoperative cholangiography still plays a role in reducing the cost of litigation. Laparoscopic bariatric surgery is the most commonly performed laparoscopic gastrointestinal surgery in the USA, and laparoscopic Nissen fundoplication is the treatment of choice for intractable gastroesophageal reflux disease. Recent randomized trials have demonstrated that laparoscopic gastric and colorectal cancer resection are safe and oncologically correct procedures. Laparoscopic surgery has also been widely developed in hepatic, pancreatic, gynecological and urological surgery. Recently, SILS and robotic surgery have penetrated all specialties of abdominal surgery. However, evidence‐based medicine has failed to show major advantages in SILS, and the disadvantage of robotic surgery is the high costs related to purchase and maintenance of technology. Laparoscopic surgery has become well developed in recent decades and is the choice of treatment in abdominal surgery. Recently developed SILS techniques and robotic surgery are promising but their benefits remain to be determined.