bluuebunny/crossref_metadata_2025_split huggingface dataset:
Filling annotation gaps in yeast genomes using genome-wide contact maps
Authors: Marie-Nelly Hervé , Marbouty Martial , Cournac Axel , Liti Gianni , Fischer Gilles , Zimmer Christophe , Koszul Romain 
Published: April 2014

Abstract
Motivations: De novo sequencing of genomes is followed by annotation analyses aiming at identifying functional genomic features such as genes, non-coding RNAs or regulatory sequences, taking advantage of diverse datasets. These steps sometimes fail at detecting non-coding functional sequences: for example, origins of replication, centromeres and rDNA positions have proven difficult to annotate with high confidence. Here, we demonstrate an unconventional application of Chromosome Conformation Capture (3C) technique, which typically aims at deciphering the average 3D organization of genomes, by showing how functional information about the sequence can be extracted solely from the chromosome contact map.
Results: Specifically, we describe a combined experimental and bioinformatic procedure that determines the genomic positions of centromeres and ribosomal DNA clusters in yeasts, including species where classical computational approaches fail. For instance, we determined the centromere positions in Naumovozyma castellii , where these coordinates could not be obtained previously. Although computed centromere positions were characterized by conserved synteny with neighboring species, no consensus sequences could be found, suggesting that centromeric binding proteins or mechanisms have significantly diverged. We also used our approach to refine centromere positions in Kuraishia capsulata and to identify rDNA positions in Debaryomyces hansenii . Our study demonstrates how 3C data can be used to complete the functional annotation of eukaryotic genomes.
Availability and implementation: The source code is provided in the Supplementary Material. This includes a zipped file with the Python code and a contact matrix of Saccharomyces cerevisiae .
Contact: romain.koszul@pasteur.fr
Supplementary information: Supplementary data are available at Bioinformatics online
Polymorphism in the ADRB2 Gene Explains a Small Portion of Intersubject Variability in Pain Relative to Cervical Dilation in the First Stage of Labor
Authors: Terkawi Abdullah S. , Jackson William M. , Hansoti Shehnaz , Tabassum Rabeena , Flood Pamela 
Published: April 2014

Abstract

Background:
Variability in labor pain has been associated with demographic, clinical, and psychological factors. Polymorphisms of the β2-adrenergic receptor gene (ADRB2) influence sensitivity to experimental pain in humans and are a risk factor for chronic pain. The authors hypothesized that polymorphisms in ADRB2 may influence labor pain.

Methods:
After Institutional Review Board approval and written informed consent, the authors prospectively obtained hourly pain reports from 233 nulliparous parturients during the first stage of labor, of which 199 were included in the current analysis. DNA from blood samples was genotyped at polymorphisms in the genes for the β2-adrenergic receptor, the μ opioid receptor subtype 1, catechol-O-methyltransferase, fatty acid amide hydrolase, and the oxytocin receptor. Labor pain as a function of cervical dilation was modeled with previously described methods. Patient covariates, ADRB2 genotype, and obstetrical and anesthesia treatment were evaluated as covariates in the model.

Results:
Labor pain more rapidly became severe in parturients heterozygous or homozygous for the G allele at rs1042714 in the ADRB2 gene. Labor pain increased more rapidly after artificial rupture of membranes, augmentation with oxytocin, and in younger women. Inclusion of covariates explained approximately 10% of the variability between subjects. ADRB2 genotype explained less than 1% of the intersubject variability.

Conclusion:

ADRB2 genotype correlates with labor pain but explained less than 1% of the intersubject variance in the model.
Evolutionary multiplayer games
Authors: Gokhale Chaitanya S. , Traulsen Arne 
Published: April 2014

AbstractEvolutionary game theory has become one of the most diverse and far reaching theories in biology. Applications of this theory range from cell dynamics to social evolution. However, many applications make it clear that inherent non-linearities of natural systems need to be taken into account. One way of introducing such non-linearities into evolutionary games is by the inclusion of multiple players. An example is of social dilemmas, where group benefits could e.g. increase less than linear with the number of cooperators. Such multiplayer games can be introduced in all the fields where evolutionary game theory is already well established. However, the inclusion of non-linearities can help to advance the analysis of systems which are known to be complex, e.g. in the case of non-Mendelian inheritance. We review the diachronic theory and applications of multiplayer evolutionary games and present the current state of the field. Our aim is a summary of the theoretical results from well-mixed populations in infinite as well as finite populations. We also discuss examples from three fields where the theory has been successfully applied, ecology, social sciences and population genetics. In closing, we probe certain future directions which can be explored using the complexity of multiplayer games while preserving the promise of simplicity of evolutionary games.
KmerStream: Streaming algorithms for k-mer abundance estimation
Authors: Melsted Páll , Halldórsson Bjarni V. 
Published: April 2014

AbstractMotivation: Several applications in bioinformatics, such as genome assemblers and error corrections methods, rely on counting and keeping track of k-mers (substrings of length k). Histograms of k-mer frequencies can give valuable insight into the underlying distribution and indicate the error rate and genome size sampled in the sequencing experiment.Results: We present KmerStream, a streaming algorithm for computing statistics for high throughput sequencing data based on the frequency of k-mers. The algorithm runs in time linear in the size of the input and the space requirement are logarithmic in the size of the input. This very low space requirement allows us to deal with much larger datasets than previously presented algorithms. We derive a simple model that allows us to estimate the error rate of the sequencing experiment, as well as the genome size, using only the aggregate statistics reported by KmerStream and validate the accuracy on sequences from a PhiX control.As an application we show how KmerStream can be used to compute the error rate of a DNA sequencing experiment. We run KmerStream on a set of 2656 whole genome sequenced individuals and compare the error rate to quality values reported by the sequencing equipment. We discover that while the quality values alone are largely reliable as a predictor of error rate, there is considerable variability in the error rates between sequencing runs, even when accounting for reported quality values.Availability: The tool KmerStream is written in C++ and is released under a GPL license. It is freely available at https://github.com/pmelsted/KmerStreamContact:pmelsted@hi.is
Phenotypic and Transcriptional Analysis of Divergently Selected Maize Populations Reveals the Role of Developmental Timing in Seed Size Determination
Authors: Sekhon Rajandeep S. , Hirsch Candice N. , Childs Kevin L. , Breitzman Matthew W. , Kell Paul , Duvick Susan , Spalding Edgar P. , Buell C. Robin , de Leon Natalia , Kaeppler Shawn M. 
Published: April 2014

AbstractSeed size is a component of grain yield and an important trait in crop domestication. To understand the mechanisms governing seed size in maize (Zea mays), we examined transcriptional and developmental changes during seed development in populations divergently selected for large and small seed size from Krug, a yellow dent maize cultivar. After 30 cycles of selection, seeds of the large seed population (KLS30) have a 4.7-fold greater weight and a 2.6-fold larger size compared with the small seed population (KSS30). Patterns of seed weight accumulation from the time of pollination through 30 d of grain filling showed an earlier onset, slower rate, and earlier termination of grain filling in KSS30 relative to KLS30. This was further supported by transcriptome patterns in seeds from the populations and derived inbreds. Although the onset of key genes was earlier in small seeds, similar maximum transcription levels were observed in large seeds at later stages, suggesting that functionally weaker alleles, rather than transcript abundance, may be the basis of the slow rate of seed filling in KSS30. Gene coexpression networks identified several known genes controlling cellularization and proliferation as well as novel genes that will be useful candidates for biotechnological approaches aimed at altering seed size in maize and other cereals.
Influence of land use and climate on recent forest expansion: a case study in the Eurosiberian–Mediterranean limit of north‐west Spain
Authors: Álvarez‐Martínez Jose Manuel , Suárez‐Seoane Susana , Stoorvogel Jetse J. , de Luis Calabuig Estanislao 
Published: April 2014

Summary

In Mediterranean mountainous areas, forests have expanded in recent decades because traditional management practices have been abandoned or reduced. However, understanding the ecological mechanisms behind landscape change is a complex undertaking because the influence of land use may be reinforced or constrained by abiotic factors such as climate. In this work, we evaluated their combined effects on recent forest expansion across climatic, topographic and management gradients.

We used orthorectified aerial photographs from the second half of the twentieth century (1956, 1974, 1983, 1990 and 2004) to monitor changes in forest distribution in a set of 20 head‐water basins in the Cantabrian Mountains of north‐west Spain, at the Eurosiberian–Mediterranean limit. In particular, we evaluated the role of land‐use history (comparing natural vs. anthropic basins) and microclimate (comparing shaded vs. sunny aspects) of forest gain/loss rates and spatial distribution shifts. Finally, we applied Species Distribution Modelling techniques (MaxEnt and BIOMOD) in the stated scenarios of land‐use history and microclimate, to assess habitat suitability for forest expansion on the basis of topography, soil properties and mesoclimatic variables.

Forest cover increased from 10.72% in 1956 to 27.67% in 2004 in the area. The rate of expansion was significantly higher in natural basins and, particularly, on shaded slopes. In all cases, the mean elevation of new forest patches increased during the study period, which was particularly evident on natural sunny slopes. The performance of the models and the magnitude of the effects varied across land‐use histories and microclimatic conditions. Soil properties and temperature and precipitation in late spring and early summer were the main drivers of forest expansion in modelling exercises, although expansion rates and upward altitudinal shifts were primarily controlled by land‐use history and the biogeographic origin of the forests.

Synthesis. The combination of monitoring and modelling techniques used in this work contributed to the understanding of forest expansion in cultural systems, indicating that ecological succession is not a homogeneous process, but varies spatially due to human and abiotic constraints since historical times.
Rhizobial galactoglucan determines the predatory pattern of Myxococcus xanthus and protects Sinorhizobium meliloti from predation
Authors: Pérez Juana , Jiménez‐Zurdo José I. , Martínez‐Abarca Francisco , Millán Vicenta , Shimkets Lawrence J. , Muñoz‐Dorado José 
Published: April 2014

SummaryMyxococcus xanthus is a social bacterium that preys on prokaryotic and eukaryotic microorganisms. Co‐culture of M. xanthus with reference laboratory strains and field isolates of the legume symbiont Sinorhizobium meliloti revealed two different predatory patterns that resemble frontal and wolf‐pack attacks. Use of mutants impaired in the two types of M. xanthus surface motility (A or adventurous and S or social motility) and a csgA mutant, which is unable to form macroscopic travelling waves known as ripples, has demonstrated that both motility systems but not rippling are required for efficient predation. To avoid frontal attack and reduce killing rates, rhizobial cells require a functional expR gene. ExpR regulates expression of genes involved in a variety of functions. The use of S. meliloti mutants impaired in several of these functions revealed that the exopolysaccharide galactoglucan (EPS II) is the major determinant of the M. xanthus predatory pattern. The data also suggest that this biopolymer confers an ecological advantage to rhizobial survival in soil, which may have broad environmental implications.
Cyclic Pentanone Peroxide: Sensitiveness and Suitability as a Model for Triacetone Triperoxide
Authors: Bali Mark S. , Armitt David , Wallace Lynne , Day Anthony I. 
Published: April 2014

AbstractResearch to counter the threat of organic peroxides such as triacetone triperoxide (TATP) is at times hampered by their inherent extreme sensitiveness and volatility. This work describes an approach to lowering some risks associated with the handling of TATP in the laboratory through the use of an analog species, tripentanone triperoxide (TPTP). Sensitiveness has been tested via standard methods. GCMS analysis has shown that TPTP degrades via similar mechanisms to TATP under a range of conditions. Slight differences in product composition were traced to side reactions which may also affect impurities present in homemade TATP synthesis. A pilot field trial was conducted to evaluate TPTP as a substitute for TATP in explosive detection dog (EDD) scent training. The degradation studies have yielded insights into the complexities of the acidic degradation of cyclic peroxides with potential forensic application, and TPTP's inadequacy as a TATP pseudoscent is a valuable example of the limitations of such training aids.
A Comparison of Hypothermic Deaths in South Australia and Sweden
Authors: Bright Fiona M. , Winskog Calle , Walker Melissa , Byard Roger W. 
Published: April 2014

AbstractCase files from Forensic Science South Australia and the Swedish National Forensic Database were reviewed over a 6‐year period from 2006 to 2011 for cases where hypothermia either caused, or significantly contributed to, death. Data were analyzed for age, sex, time of year/season, place of discovery, circumstances of death, and underlying medical conditions. Despite the considerable demographic, geographic, and climatological differences, hypothermic deaths occurred at very similar rates in South Australia (3.9/100,000) and Sweden (3.3/100,000). Deaths from hypothermia in South Australia occurred predominantly indoors at home addresses, involving elderly females with multiple underlying illnesses and limited outside contacts. In contrast, Swedish hypothermic deaths generally occurred outdoors and involved middle‐aged elderly males. These data show that hypothermia may be a risk in warmer climates particularly for elderly, socially isolated individuals.
Application of Volume‐of‐Fluid Method to Analyze the Viscosity Effect on the Spine Formation of Bloodstains
Authors: Park Chan‐Seong , Ihm Chun‐Hwa , Cho Nam‐Soo , Chung Nak‐Eun 
Published: April 2014

AbstractIn bloodstain pattern analysis, the blood droplet volume and surface impact velocity play an important role, and many related experimental studies have been carried out. If an appropriate computational fluid dynamics (CFD) model that could solve bloodstain patterns, especially spine formation bloodstain patterns, can be obtained, the blood droplet volume and impact speeds at various crime scenes can be predicted more accurately. For this purpose, Flow‐3D software using the volume‐of‐fluid method was applied to analyze the behavior of human blood droplets during an impact event, especially focusing on the viscous effect on splashing, which forms the spine which can be used to predict the impact velocity. To obtain a non‐Newtonian viscosity model of blood for a computational fluid dynamic analysis, the venous blood samples of 163 people were tested using a hemorheology instrument. Among the venous blood samples of 163 people, 37 samples for which all blood test results were in a normal range were selected for the non‐Newtonian viscosity modeling. From the CFD analysis, it could be concluded that a non‐Newtonian viscosity model is more appropriate than a constant viscosity model for predicting splashing that forms the spine. The gradient of the non‐Newtonian model at a high shear rate has more of an effect on spine formation than that at a low shear rate. The lowest viscosity with a high velocity at the outer front of the radiating flow plays an important role in forming the splashing pattern.
Sharp Force Injury Fatalities: A Retrospective Study (1982–2012) in Brescia (Italy)
Authors: Vassalini Marzia , Verzeletti Andrea , De Ferrari Francesco 
Published: April 2014

AbstractA retrospective study was carried out on postmortem examination data of 131 sharp force‐related casualties recorded by the Brescia Institute of Forensic Medicine between 1982 and 2012. The objective was to identify relevant parameters that may be used to distinguish the manner of deaths between homicide, suicide, and accident. The following variables were considered: manner of death; demographic data; scene; type of sharp object; location and numbers of wounds; the presence of hesitation marks/defense wounds; toxicological findings; psychiatric history. There were 92 homicides, 28 suicides, and 11 accidents. Most victims were male, with an average age of 43. Injuries in isolation were present in 9.8% of homicides, in 35.7% of suicides, and in 54.5% of accidents. Most injuries involved the left anterior chest in homicides and the forearms in suicides. This study underlines the importance of a meticulous postmortem examination of injuries on the body and their relationship with other results from the death scene investigation.
Acute coronary syndrome diagnosis at hospital discharge: How often do we get it right in the emergency department?
Authors: Handrinos Alex , Braitberg George , Mosley Ian Trevor 
Published: April 2014

AbstractObjectiveAcute coronary syndrome (ACS) encompasses unstable angina (UA), non‐ST elevation myocardial infarction (NSTEMI) and ST segment myocardial infarction (STEMI). In 2007–2008 in Australia, there were 95 000 hospitalisations for ACS. There is limited data about the level of agreement between the ED and hospital discharge diagnosis. The objective of the present study is to describe the proportion of ED patients with a concordant ACS hospital discharge diagnosis and determine factors associated with this.MethodsThe present study was a retrospective case series of consecutive presentations of patients with ACS to the EDs of Southern Health, Victoria, Australia, during a 6 month period between August 2011 and January 2012.ResultsOne thousand and twenty‐eight patients diagnosed with ACS in the ED were identified. Hospital discharge diagnosis was recorded for 704 cases. The mean age was 63 years (SD 14.5) and 69% were male. One hundred and nineteen patients (16.9%) were diagnosed with a STEMI, 322 (45.7%) with a NSTEMI and 263 (37.4%) with UA. There were 68.3% who had a concordant discharge diagnosis of ACS. An ED diagnosis of STEMI (87.4), English as the primary language (OR 1.81 [1.13–2.89]) and chest pain as the presenting complaint (OR 2.70 [1.72–4.23]) were associated with a concordant diagnosis of ACS.ConclusionAlmost one‐third of patients who are admitted to the hospital with ACS have a different hospital discharge diagnosis. English as a primary language and presenting with chest pain are associated with a more concordant diagnosis. More research needs to be performed to better understand these findings.
Occupational fall injuries presenting to the emergency department
Authors: Son Hyung Min , Kim Sun Hyu , Shin Sang Do , Ryoo Hyun Wook , Ryu Hyun Ho , Lee Ji Ho 
Published: April 2014

AbstractObjectivesThis study was performed to evaluate occupational and fall injuries presenting to the ED, the risk factors associated with falls among all occupational injuries, and factors affecting prognosis.MethodsData from ED‐based Occupational Injury Surveillance System were analysed to investigate the occupational injuries. The 2147 occupational injury subjects were divided into two groups: fall (n = 213, 9.9%) and non‐fall (n = 1934, 90.1%). Data including baseline and clinical characteristics were compared between the groups.ResultsThe mean age was older in the fall group (46 vs 42 years old). The rate of construction site‐related injury was 32% in the fall group and only 8% in the non‐fall group. Injury occurrence during regular working hours (09.00 hours to 18.00 hours) was 70% in the fall group and 57% in the non‐fall group. Injury severity using the Excess Mortality Ratio‐adjusted Injury Severity Score (EMR‐ISS) was more severe in the fall group than in the non‐fall group, and days away from work were longer in the fall group than the non‐fall group. Older age, compared with an age <29 years old and presence in a construction area during regular working hours were factors associated with fall injuries. Factors affecting prolonged absence for work were older age, higher EMR‐ISS, fall injury and poor workplace environmental conditions.ConclusionRisk factors associated with fall‐related occupational injuries include older age and being at a construction area during regular working hours. Falls among occupational injuries are more severe than other injuries and result in longer work loss.
Review article: Ventricular assist devices in the emergency department
Authors: Partyka Christopher , Taylor Ben 
Published: April 2014

AbstractVentricular assist devices (VADs) have become an indispensable tool in the management of end‐stage cardiac failure, both as a means of bridging to cardiac transplantation and as destination therapy for long‐term quality of life improvement. Although the technology continues to advance and these devices continue to be refined, they are still associated with significant complications. This article reviews the basics of VAD function and physiology, as well as the myriad to complications that follow their implantation. This review aims to provide a systematic approach to the troubleshooting, diagnosis and management of both VAD‐associated complications and the resuscitation of the decompensated VAD patient presenting to the ED.
Review article: Elevated troponin: Diagnostic gold or fool's gold?
Authors: Rahman Atifur , Broadley Simon A 
Published: April 2014

AbstractTroponin is a highly sensitive biomarker of myocardial injury and has been used extensively in everyday clinical practice in the community as well as in hospitals for the diagnosis of acute myocardial infarction (AMI) and for risk stratification of patients with acute coronary symptoms. Dynamic elevations in biomarkers (troponin) are considered fundamental to the diagnosis of AMI. Unfortunately, many clinical conditions can cause troponin elevation in the absence of myocardial ischaemia, and elevated levels sometimes pose a diagnostic dilemma. In some cases, inappropriate diagnosis of ‘AMI’ based primarily on a raised troponin can have a deleterious impact on an individual, including on driving, insurance and other medicolegal matters. An incorrect diagnosis of myocardial infarction can also lead to the oversight of serious life‐threatening alternative causes of troponin elevation (e.g. pulmonary embolism). This article discusses the role of troponin in our everyday clinical practice in the ED.