bluuebunny/crossref_metadata_2025_split huggingface dataset:
BALSA: Integrated secondary analysis for whole-genome and whole-exome sequencing, accelerated by GPU
Authors: Luo Ruibang , Wong Yiu-Lun , Law Wai-Chun , Lee Lap-Kei , Liu Chi-Man , Cheung Jeanno , Lam Tak-Wah 
Published: January 2018

This paper reports an integrated solution, called BALSA, for the secondary analysis of next generation sequencing data; it exploits the computational power of GPU and an intricate memory management to give a fast and accurate analysis. From raw reads to variants (including SNPs and Indels), BALSA, using just a single computing node with a commodity GPU board, takes 5.5 hours to process 50-fold whole genome sequencing (~750 million 100bp paired-end reads), or just 25 minutes for 210-fold whole exome sequencing. BALSA’s speed is rooted at its parallel algorithms to effectively exploit a GPU to speed up processes like alignment, realignment and statistical testing. BALSA incorporates a 16-genotype model to support the calling of SNPs and Indels and achieves competitive variant calling accuracy and sensitivity when compared to the ensemble of six popular variant callers. BALSA also supports efficient identification of somatic SNVs and CNVs; experiments showed that BALSA recovers all the previously validated somatic SNVs and CNVs, and it is more sensitive for somatic Indel detection. BALSA outputs variants in VCF format. A pileup-like SNAPSHOT format, while maintaining the same fidelity as BAM in variant calling, enables efficient storage and indexing, and facilitates the App development of downstream analyses.
BALSA is available at: http://sourceforge.net/p/balsa
Shotgun proteomics reveals physiological response to ocean acidification in Crassostrea gigas
Authors: Timmins-Schiffman Emma , Coffey William D , Hua Wilber , Nunn Brook L , Dickinson Gary H , Roberts Steven B 
Published: January 2018

Background. Ocean acidification as a result of increased anthropogenic CO2 emissions is occurring in marine and estuarine environments worldwide. The coastal ocean experiences additional daily and seasonal fluctuations in pH that can be lower than projected end of century open ocean pH reductions. Projected and current ocean acidification have wide-ranging effects on many aquatic organisms, however the exact mechanisms of the impacts of ocean acidification on many of these animals remains to be characterized.
Methods. In order to assess the impact of ocean acidification on marine invertebrates, Pacific oysters (Crassostrea gigas) were exposed to one of four different pCO2 levels for four weeks: 400 µatm (pH 8.0), 800 µatm (pH 7.7), 1000 µatm (pH 7.6), or 2800 µatm (pH 7.3). At the end of 4 weeks a variety of physiological parameters were measured to assess the impacts of ocean acidification: tissue glycogen content and fatty acid profile, shell micromechanical properties, and response to acute heat shock. To determine the effects of ocean acidification on the underlying molecular physiology of oysters and their stress response, some of the oysters from 400 µatm and 2800 µatm were exposed to an additional mechanical stress and shotgun proteomics were done on oysters from high and low pCO2 and from with and without mechanical stress.
Results. At the end of the four week exposure period, oysters in all four pCO2 environments deposited new shell, but growth rate was not different among the treatments. However, micromechanical properties of the new shell were compromised by elevated pCO2. Elevated pCO2 affected neither whole body fatty acid composition, nor glycogen content, nor mortality rate associated with acute heat shock. Shotgun proteomics revealed that several physiological pathways were significantly affected by ocean acidification, including antioxidant response, carbohydrate metabolism, and transcription and translation. Additionally, the proteomic response to a second stress differed with pCO2, with numerous processes significantly affected by mechanical stimulation at high versus low pCO2 (all proteomics data are available in the ProteomeXchange under the identifier PXD000835).
Discussion. Oyster physiology is significantly altered by exposure to elevated pCO2, indicating changes in energy resource use. This is especially apparent in the assessment of the effects of pCO2 on the proteomic response to a second stress. The altered stress response illustrates that ocean acidification may impact how oysters respond to other changes in their environment. These data contribute to an integrative view of the effects of ocean acidification on oysters as well as physiological trade-offs during environmental stress.
Approaches to describing inter-rater reliability of the overall clinical appearance of febrile infants and toddlers in the Emergency Department.
Authors: Walsh Paul , Thornton Justin M. , Walker Nicholas , McCoy John Gary , Baal Joe , Baal Jed , Mendoza Nanse , Banimahd MD Faried , Asato Julie 
Published: January 2018

Objectives To measure inter-rater agreement of overall clinical appearance of febrile children aged less than 24 months and to compare methods for doing so.
Study Design and setting We performed an observational study of inter-rater reliability of the assessment of febrile children in a county hospital emergency department serving a mixed urban and rural population. Two emergency medicine healthcare providers independently evaluated the overall clinical appearance of children less than 24 months of age who had presented for fever. They recorded the initial ‘gestalt’ assessment of whether or not the child was ill appearing or if they were unsure. They then repeated this assessment after examining the child. Each rater was blinded to the other’s assessment. Our primary analysis was graphical. We also calculated Cohen’s κ, Gwet’s agreement coefficient and other measures of agreement and weighted variants of these. We examined the effect of time between exams and patient and provider characteristics on inter-rater agreement.
Results We analyzed 159 of the 173 patients enrolled. Median age was 9.5 months (lower and upper quartiles 4.9-14.6), 99/159 (62%) were boys and 22/159 (14%) were admitted. Overall 118/159 (74%) and 119/159 (75%) were classified as well appearing on initial ‘gestalt’ impression by both examiners. Summary statistics varied from 0.223 for weighted κ to 0.635 for Gwet’s AC2. Inter rater agreement was affected by the time interval between the evaluations and the age of the child but not by the experience levels of the rater pairs. Classifications of ‘not ill appearing’ were more reliable than others.
Conclusion The inter-rater reliability of emergency providers' assessment of overall clinical appearance was adequate when described graphically and by Gwet’s AC. Different summary statistics yield different results for the same dataset.
Tracheostomy in children with congenital heart disease: a national analysis of the Kids' Inpatient Database.
Authors: Maxwell Bryan G , Nelson McMillan Kristen 
Published: January 2018

Background: While single-institution studies reported the indications and outcomes of tracheostomy in children with congenital heart disease (CHD), no national analyses have been performed. We sought to examine the indications, performance, outcomes, and resource utilization of tracheostomy in children with CHD using a nationally representative database.
Methods: We identified all children undergoing tracheostomy in the Kids’ Inpatient Database 1997 through 2009, and we compared children with CHD to children without CHD. Within the CHD group, we compared children whose tracheostomy occurred in the same hospital admissions as a cardiac operation to those whose tracheostomy occurred without a cardiac operation in the same admission.
Results: Tracheostomy was performed in n=2,495 children with CHD, which represents 9.6% of all tracheostomies performed in children (n=25,928), and 3.5% of all admissions for children with CHD (n=355,460). Over the study period, there was an increasing trend in the proportion of all tracheostomies that were done in children with CHD (p<0.0001) and an increasing trend in the proportion of admissions for children with CHD that involved a tracheostomy (p<0.0001). The population of children with CHD undergoing tracheostomy differed markedly in baseline characteristics, outcomes, and resource utilization. Similarly, the subgroup of children whose tracheostomy was performed in the same admission as a cardiac operation differed significantly from those whose tracheostomy was not.
Conclusions: Tracheostomy is an increasingly common procedure in children with CHD despite being associated with significantly greater resource utilization and in-hospital mortality. The population of children with CHD who undergo tracheostomy differs markedly from that of children without CHD who undergo tracheostomy, and important differences are observed between children who undergo tracheostomy in the same admission as a cardiac surgical procedure and those who undergo tracheostomy in a nonsurgical admission, as well as between children with single-ventricle physiology and children with two-ventricle physiology.
Translation, adaptation, validation and performance of the American Weight Efficacy Lifestyle Questionnaire Short Form (WEL-SF) to a Norwegian version: A cross-sectional study
Authors: Flølo Tone Nygaard , Andersen John Roger , Nielsen Hans Jørgen , Nativig Gerd Karin 
Published: January 2018

Background: Researchers have emphasized a need to identify predictors that can explain the variability in weight management after bariatric surgery. Eating self-efficacy has demonstrated predictive impact on patients’ adherence to recommended eating habits following multidisciplinary treatment programs, but has to a limited extent been subject for research after bariatric surgery. Recently an American short form version (WEL-SF) of the commonly used Weight Efficacy Lifestyle Questionnaire (WEL) was available for research and clinical purposes.
Objectives: We intended to translate and culturally adapt the WEL-SF to Norwegian conditions, and to evaluate the new versions’ psychometrical properties in a Norwegian population of morbidly obese patients eligible for bariatric surgery.
Design: Cross-sectional
Methods: A total of 225 outpatients selected for Laparoscopic sleeve gastrectomy (LSG) were recruited; 114 non-operated and 111 operated patients, respectively. The questionnaire was translated through forward and backward procedures. Structural properties were assessed performing principal component analysis (PCA), correlation and regression analysis were conducted to evaluate convergent validity and sensitivity, respectively. Data was assessed by mean, median, item response, missing values, floor- and ceiling effect, Cronbach`s alpha and alpha if item deleted.
Results: The PCA resulted in one factor with eigenvalue>1, explaining 63.0% of the variability. The WEL-SF sum scores were positively correlated with the Self-efficacy and quality of life instruments (p<0.001). The WEL-SF was associated with body mass index (BMI) (p<0.001) and changes in BMI (p=0.026). A very high item response was obtained with only one missing value (0.4%). The ceiling effect was in average 0.9 and 17.1% in the non-operated and operated sample, respectively. Strong internal consistency (r =0.92) was obtained, and Cronbach’s alpha remained high (0.86-0.92) if single items were deleted.
Conclusion: The Norwegian version of WEL-SF appears to be a valid questionnaire on eating self-efficacy, with acceptable psychometrical properties in a population of morbidly obese patients
A global phylogenetic analysis in order to determine the host species and geography dependent features present in the evolution of avian H9N2 Influenza Hemagglutinin
Authors: Dalby Andrew R , Iqbal Munir 
Published: January 2018

A complete phylogenetic analysis of all of the H9N2 hemagglutinin sequences that were collected between 1966 and 2012 was carried out in order to build a picture of the geographical and host specific evolution of the hemagglutinin protein. To improve the quality and applicability of the output data the sequences were divided into subsets based upon location and host species.
The phylogenetic analysis of hemagglutinin reveals that the protein has distinct lineages between China and the Middle East, and that wild birds in both regions retain a distinct form of the H9 molecule, from the same lineage as the ancestral hemagglutinin. The results add further evidence to the hypothesis that the current predominant H9N2 hemagglutinin lineage might have originated in Southern China. The study also shows that there are sampling problems that affect the reliability of this and any similar analysis. This raises questions about the surveillance of H9N2 and the need for wider sampling of the virus in the environment.
The results of this analysis are also consistent with a model where hemagglutinin has predominantly evolved by neutral drift punctuated by occasional selection events. These selective events have produced the current pattern of distinct lineages in the Middle East, Korea and China. This interpretation is in agreement with existing studies that have shown that there is widespread intra-country sequence evolution.
Structure determination of Murine Norovirus NS6 proteases with C-terminal extensions designed to probe protease-substrate interactions
Authors: Fernandes Humberto , Leen Eoin N , Cromwell Jnr Hamlet , Pfeil Marc-Philipp , Curry Stephen 
Published: January 2018

Noroviruses are positive-sense single-stranded RNA viruses. They encode an NS6 protease that cleaves a viral polyprotein at specific sites to produce mature viral proteins. In an earlier study we obtained crystals of murine norovirus (MNV) NS6 protease in which crystal contacts were mediated by specific insertion of the C-terminus of one protein (which contains residues P5-P1 of the NS6-7 cleavage junction) into the peptide binding site of an adjacent molecule, forming an adventitious protease-product complex. We sought to reproduce this crystal form to investigate protease-substrate complexes by extending the C-terminus of NS6 construct to include residues on the C-terminal (P´) side of the cleavage junction. We report the crystallization and crystal structure determination of inactive mutants of murine norovirus NS6 protease with C-terminal extensions of one, two and four residues from the N-terminus of the adjacent NS7 protein (NS6 1´, NS6 2´, NS6 4´). We also determined the structure of a chimeric extended NS6 protease in which the P4 P4′ sequence of the NS6-7 cleavage site was replaced with the corresponding sequence from the NS2-3 cleavage junction (NS6 4´ 2|3).
The constructs NS6 1′ and NS6 2′ yielded crystals that diffracted anisotropically. We found that, although the uncorrected data could be phased by molecular replacement, refinement of the structures stalled unless the data were ellipsoidally truncated and corrected with anisotropic B-factors. These corrections significantly improved phasing by molecular replacement and subsequent refinement.
The refined structures of all four extended NS6 proteases are very similar in structure to the mature MNV NS6 — and in one case reveal additional details of a surface loop. Although the packing arrangement observed showed some similarities to those observed in the adventitious protease-product crystals reported previously, in no case were specific protease-substrate interactions observed.
Effects of anesthetics pentobarbital sodium and chloral hydrate on urine proteome
Authors: Zhao Mindi , Gao Youhe 
Published: January 2018

Background. Urine can be a better source than blood for biomarker discovery since it accumulates many changes. The urine proteome is susceptible to many factors including anesthesia. Pentobarbital sodium and chloral hydrate are commonly used anesthetics in animal experiments.
Methods. This study demonstrated effects of these two anesthetics on the rat urine proteome using liquid chromatography–tandem mass spectrometry (LC-MS/MS).
Results. With anesthesia, the urinary protein-to-creatinine ratio of all rats increased two fold. The relative abundance of 22 and 23 urinary proteins were changed with pentobarbital sodium or chloral hydrate anesthesia, respectively, as determined by label-free quantification. Among these changed proteins, fifteen had been considered as candidate biomarkers such as uromodulin, sixteen had been considered stable in healthy human urine, which are more likely to be considered as potential biomarkers when changed, such as transferrin.
Discussion. The pattern of changed urinary proteins provides clues to the discovery of urinary proteins regulatory mechanisms. When determining candidate biomarker, anesthetic-related effects can be excluded in future biomarker discovery studies. Since anesthetics take effects via nervous system, this study is the first to provide clues that protein handling function of kidney may possibly be regulated by nervous system.
The “Rosetta Stone” for deciphering the anatomy of the stem turtle Condorchelys antiqua (Early-Middle Jurassic; Chubut, Argentina)
Authors: Sterli Juliana , de la Fuente Marcelo , Rougier Guillermo 
Published: January 2018

Background. Condorchelys antiqua is a stem turtle previously described from the Queso Rallado Locality, Cañadón Asfalto Formation (Early-Middle Jurassic), Chubut, Argentina. In 2014 a skull (MPEF-PV 10900) and an articulated shell with associated postcranial remains (MPEF-PV 10884) of C. antiqua were discovered in the mentioned locality.
Methods. The new specimens have been prepared by L. Reiner (technician at the Museo Egidio Feruglio) and then studied using the regular paleontological methodology (e.g., direct observations and under the microscope, photography, and drawings). The new data provided by these two specimens, plus some other isolated remains that were re-prepared, allowed us to score a 25% more of the characters of C. antiqua in the most complete up to date matrix for Mesozoic turtles. The matrix was build in Mesquite and analyzed under maximum parsimony in TNT. We performed two rounds of Tree Bisection Reconnection and calculated a strict consensus. Branch supports were provided using bootstrap, jackknife, and Bremer support.
Results. We regard the specimen MPEF-PV 10900 as represented by the basicranium and some previously unknown skull bones like the maxilla, frontal, parietal, and postorbital. This specimen also shows that there were no teeth in the pterygoid of C. antiqua. On the other hand, specimen MPEF-PV 10884 is an almost complete carapace and plastron with 4 thoracic vertebrae and ribs, scapular and pelvic girdles, humerus, left radius, femur, tibia, fibula, 2 metatarsal/carpals, 2 phalanges, 1 ungual phalanx and 1 chevron bone. The preliminary cladistic analysis resulted in 750 most parsimonious trees of 893 steps. The result of the analysis corroborates the position of C. antiqua as a stem turtle more derived than the Triassic and Australochelys africanus. Condorchelys antiqua is recovered in a polytomy together with other early-middle Jurassic turtles (e.g., Kayentachelys aprix and Indochelys spatulata) and the clade formed by the remaining turtles.
Discussion. Although many new characters have been scored for C. antiqua in the phylogenetic analysis, this new information did not resolved the phylogenetic position for this taxon. We consider that more information about I. spatulata and K. aprix could help to better understand the relationships among these basal taxa. On the other hand, these new specimens of C. antiqua bring valuable information to decipher the anatomy of the poorly known non-shell postcranial elements of these Early to Middle Jurassic stem turtles. In light of the recently suggested aquatic preferences of C. antiqua, the next step on this research would be to explore other adaptations to the aquatic environment using postcranial elements, particularly the limb bones.
Sex differences in beliefs and attitudes towards mental illness: An examination of mental health literacy in a community sample
Authors: Gibbons Ray J , Thorsteinsson Einar B , Loi Natasha M 
Published: January 2018

Objectives: The current study investigated mental health literacy in an Australian sample to examine the influence sex has in the identification of and attitudes towards various aspects of mental illness.
Method: An online questionnaire was completed by 373 participants (267 female, M = 34.87). Participants were randomly assigned a vignette depicting an individual exhibiting the symptoms of one of three types of mental illness and asked to answer questions relating to aspects of mental health literacy.
Results: Males exhibited poorer mental health literacy skills compared to females. Males were less likely to correctly identify the type of mental illness, more likely to rate symptoms as less serious and to perceive the individual as having greater personal control over such symptoms.
Conclusion: Generally, the sample was relatively proficient at correctly identifying mental illness but overall males displayed poorer mental health literacy skills than females.
Crustacean amphipods from marsh ponds: a nutritious feed resource with potential for application in Integrated Multi-Trophic Aquaculture
Authors: Jiménez-Prada Pablo , Hachero-Cruzado Ismael , Giráldez Inmaculada , Fernández-Diaz Catalina , Vilas César , Cañavate José Pedro , Guerra-García José Manuel 
Published: January 2018

Coastal protection, nutrient cycling, erosion control, water purification, and carbon sequestration are ecosystem services provided by salt marshes. Additionally, salt ponds offer coastal breeding and a nursery habitat for fishes and they provide abundant invertebrates, such as amphipods, which are potentially useful as a resource in aquaculture. Fishmeal and fish oil are necessary food resources to support aquaculture of carnivorous species due to their omega-3 long-chain polyunsaturated fatty acids (n-3 LC-PUFA). Currently, aquaculture depends on limited fisheries and feed with elevated n-3 LC-PUFA levels, but the development of more sustainable food sources is necessary. Amphipods appear to be a potential high quality alternative feed resource for aquaculture. Hence, a nutritional study was carried out for several main amphipod species—Microdeutopus gryllotalpa,Monocorophium acherusicum,Gammarus insensibilis,Melita palmataandCymadusa filosa—in terrestrial ponds in the South of Spain. These species showed high protein content (up to 40%), high n-3 PUFA and phospholipid levels, and high levels of phophatidylcholine (PC), phosphatidylethanolamine (PE) and triacylglycerols (TAG), the latter being significantly high forM. acherusicum.M. gryllotalpaandM. acherusicumshowed the highest proportion of lipids (19.15% and 18.35%, respectively). Isoleucine, glycine and alanine were the dominant amino acids in all species. In addition, amphipods collected from ponds showed low levels of heavy metals. Furthermore, the biochemical profiles of the five species of amphipods have been compared with other studied alternative prey. Therefore, pond amphipods are good candidates to be used as feed, and are proposed as a new sustainable economic resource to be used in aquaculture.G. insensibilismay be the best for intensive culture as an alternative feed resource because it shows: (1) adequate n-3 PUFA and PL composition; (2) high levels of glycine, alanine, tyrosine, isoleucine and lysine; (3) high natural densities; (4) large body size (≥1 cm), and (5) high concentration of calcium. Moreover, a combined culture of amphipods and fishes in these marsh ponds seems a promising and environmentally sustainable way to develop Integrate Multi-Trophic Aquaculture (IMTA) in these ecosystems.