bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tests of species‐specific models reveal the importance of drought in postglacial range shifts of a Mediterranean‐climate tree: insights from integrative distributional, demographic and coalescent modelling andABCmodel selection
Authors: Bemmels Jordan B. , Title Pascal O. , Ortego Joaquín , Knowles L. Lacey 
Published: August 2016

AbstractPast climate change has caused shifts in species distributions and undoubtedly impacted patterns of genetic variation, but the biological processes mediating responses to climate change, and their genetic signatures, are often poorly understood. We test six species‐specific biologically informed hypotheses about such processes in canyon live oak (Quercus chrysolepis) from the California Floristic Province. These hypotheses encompass the potential roles of climatic niche, niche multidimensionality, physiological trade‐offs in functional traits, and local‐scale factors (microsites and local adaptation within ecoregions) in structuring genetic variation. Specifically, we use ecological niche models (ENMs) to construct temporally dynamic landscapes where the processes invoked by each hypothesis are reflected by differences in local habitat suitabilities. These landscapes are used to simulate expected patterns of genetic variation under each model and evaluate the fit of empirical data from 13 microsatellite loci genotyped in 226 individuals from across the species range. Using approximate Bayesian computation (ABC), we obtain very strong support for two statistically indistinguishable models: a trade‐off model in which growth rate and drought tolerance drive habitat suitability and genetic structure, and a model based on the climatic niche estimated from a genericENM, in which the variables found to make the most important contribution to theENMhave strong conceptual links to drought stress. The two most probable models for explaining the patterns of genetic variation thus share a common component, highlighting the potential importance of seasonal drought in driving historical range shifts in a temperate tree from a Mediterranean climate where summer drought is common.
Evaluation of a novel lentiviral vaccine expressing KMP11‐HASPB fusion protein against Leishmania infantum in BALB/c mice
Authors: Mortazavidehkordi N. , Farjadfar A. , Khanahmad H. , Ghayour Najafabadi Z. , Hashemi N. , Fallah A. , Najafi A. , Kia V. , Hejazi S. H. 
Published: August 2016

SummaryHydrophilic acylated surface protein B (HASPB) is an immunogenic Leishmania protein against which antibodies are produced in the sera of cutaneous and visceral Leishmaniasis (VL) patients. Kinetoplastid membrane protein 11 (KMP11) is another protein antigen of Leishmania which is reported as a promising candidate for vaccination of VL. It is a highly conserved surface protein present in all members of kinetoplastid family and is expressed in both promastigotes and amastigotes. In this study, the coding sequence of KMP11 and HASPB was cloned into a pCDH‐cGFP lentiviral vector as a fusion protein. The gene expression was confirmed using RT‐PCR and Western blot methods. After injection of the recombinant KMP11‐HASPB‐expressing lentiviruses to BALB/c mice, using ELISA technique, a significant increase in IFN‐γ and IL‐4 as well as IgG1 and IgG2a was observed compared to the control group. Furthermore, the number of parasites in the liver and spleen of vaccinated mice decreased significantly compared with the control group.
Subglacial emplacement of tills and meltwater deposits at the base of overdeepened bedrock troughs
Authors: Buechi Marius W. , Frank Stephan M. , Graf Hans Rudolf , Menzies John , Anselmetti Flavio S. 
Published: August 2016

AbstractThe sedimentary infills of subglacially eroded bedrock troughs in the Alps are underexplored archives for the timing, extent and character of Pleistocene glaciations but may contain excellent records of the Quaternary landscape evolution over several glacial–interglacial cycles. The onset of sedimentation in these bedrock troughs is often reflected by diamicts and gravels directly overlying bedrock in the deepest basin segments. Subglacial or proglacial depositional environments have been proposed for these coarse‐grained basal units but their characteristics and origin remain controversial. This article presents results from drill cores that recovered a coarse‐grained basal unit in a major buried bedrock‐trough system in the Lower Glatt Valley, northern Switzerland. The excellent core recovery allowed a detailed study combining macroscopic, microscopic and geochemical methods and gives unprecedented insights into the transition from erosion to deposition in overdeepened bedrock troughs. These results show that the basal infill comprises diamicts, interpreted as subglacial tills, separated by thin sorted interbeds, originating from subglacial cavity deposition. The stacking of these units is interpreted to represent repeated switching between a coupled and decoupled ice–bed‐interface indicating an ever‐transforming mosaic of subglacial bed conditions. Decoupling in response to high basal water pressures is probably promoted by the confined subglacial hydraulic conditions resulting from the bedrock acting as aquitards, the narrow reverse sloping outlet and a large catchment area. While stratigraphic and lithological evidence suggests that erosion and the onset of basal sedimentation occurred during the same glaciation, different scenarios for the relative timing of infilling in relation to formation and glaciation of the bedrock trough are discussed. Overlying deltaic and glaciolacustrine sediments suggest deposition during subsequent deglaciation of the bedrock trough. The basal sediment characteristics are in agreement with previous reports in hydrogeological and seismic exploration and suggest the occurrence of similar basal successions in other subglacially overdeepened basins in the Alps and elsewhere.
Effect of resistance training on phase angle in older women: A randomized controlled trial
Authors: Souza M. F. , Tomeleri C. M. , Ribeiro A. S. , Schoenfeld B. J. , Silva A. M. , Sardinha L. B. , Cyrino E. S. 
Published: August 2016

Phase angle (PhA) is an angular‐derived bioelectrical impedance parameter based on resistance and reactance that has been widely used in different populations as an objective indicator of cellular health. The purpose of this study was to analyze the effect of resistance training (RT) on PhA in older women. Forty‐one older women (67.2 ± 4.5 years, 64.0 ± 12.3 kg, 154.7 ± 5.2 cm, and 26.6 ± 4.8 kg/m2) were randomly assigned to one of two groups: a training group (TG, n = 19) that underwent progressive RT for 12 weeks (eight exercises, three sets of 10–15 repetitions maximum, three times per week) or a control group (CG, n = 22) that did not perform any type of exercise during the intervention period. Resistance, reactance, PhA, total body water (TBW), intracellular (ICW) and extracellular (ECW) water were assessed by spectral bioelectrical impedance. There was a significant group by time interaction (P < 0.05) for PhA, TBW, and ICW in which only the TG increased their scores after the intervention period (PhA = +6.5%, TBW = +2.8%, and ICW = +5.1%). The results suggest that progressive RT promotes an increase in PhA in older women. Therefore, the PhA seems to be a good parameter to assess changes in cellular health during RT intervention.
Full-Genome Sequence Analysis of a Reassortant Strain of
Bluetongue virus
Serotype 16 from Southern India
Authors: Kumar Lalit , Batra Kanisht , Chaudhary Deepika , Gupta Akhil Kumar , Dalal Anita , Kalyanaraman Brindha , Irulappan Ganesan P. , Kumar Vinay , Maan Sushila 
Published: August 2016

ABSTRACT

The complete genome sequence of a reassortant field strain (IND2014/01) of
Bluetongue virus
(BTV) serotype 16, isolated from sheep from southern India in 2014, was sequenced. The total genome size was 19,186 bp. Sequence comparisons of all genome segments, except segment 5 (Seg-5), showed that IND2014/01 belonged to the major eastern topotype of BTV.
Complete Genome Sequences of Three Historically Important, Spatiotemporally Distinct, and Genetically Divergent Strains of Zika Virus: MR-766, P6-740, and PRVABC-59
Authors: Yun Sang-Im , Song Byung-Hak , Frank Jordan C. , Julander Justin G. , Polejaeva Irina A. , Davies Christopher J. , White Kenneth L. , Lee Young-Min 
Published: August 2016

ABSTRACT
Here, we report the 10,807-nucleotide-long consensus RNA genome sequences of three spatiotemporally distinct and genetically divergent Zika virus strains, with the functionality of their genomic sequences substantiated by reverse genetics: MR-766 (African lineage, Uganda, 1947), P6-740 (Asian lineage, Malaysia, 1966), and PRVABC-59 (Asian lineage-derived American strain, Puerto Rico, 2015).
Genome Sequence of a Multidrug-Resistant Strain of
Bacillus pumilus
, CB01, Isolated from the Feces of an American Crow,
Corvus brachyrhynchos
Authors: Nelson R. Lee , Castro Michael A. , Katti Madhusudan , Eisen Jonathan A. , Van Laar Tricia A. 
Published: August 2016

ABSTRACT

Avian species have the potential to serve as important reservoirs for the spread of pathogenic microorganisms. Here, we report the genome sequence of a drug-resistant strain of
Bacillus pumilus
, CB01, isolated from the feces of an American crow,
Corvus brachyrhynchos
.
Genome Sequence and Annotation of
Colletotrichum higginsianum
, a Causal Agent of Crucifer Anthracnose Disease
Authors: Zampounis Antonios , Pigné Sandrine , Dallery Jean-Félix , Wittenberg Alexander H. J. , Zhou Shiguo , Schwartz David C. , Thon Michael R. , O'Connell Richard J. 
Published: August 2016

ABSTRACT

Colletotrichum higginsianum
is an ascomycete fungus causing anthracnose disease on numerous cultivated plants in the family
Brassicaceae
, as well as the model plant
Arabidopsis thaliana
. We report an assembly of the nuclear genome and gene annotation of this pathogen, which was obtained using a combination of PacBio long-read sequencing and optical mapping.
Draft Genome Sequence of Phosphate-Solubilizing Bacterium
Paraburkholderia tropica
Strain P-31 Isolated from Pomegranate (
Punica granatum
) Rhizosphere
Authors: Kaur Chandandeep , Selvakumar Govindan , Ganeshamurthy Arakalgud Nanjundiah 
Published: August 2016

ABSTRACT

We report the 8.9 Mb draft genome sequence of phosphate-solubilizing bacterium
Paraburkholderia tropica
strain P-31, isolated from pomegranate (
Punica granatum
) rhizosphere. The draft genome sequence of
Paraburkholderia tropica
strain P-31 consists of 8,881,246 bp with a G+C content of 64.7%, 8,039 protein-coding genes, and 49 RNAs.
Genome Sequences of
Ralstonia insidiosa
Type Strain ATCC 49129 and Strain FC1138, a Strong Biofilm Producer Isolated from a Fresh-Cut Produce-Processing Plant
Authors: Xu Yunfeng , Nagy Attila , Yan Xianghe , Haley Bradd J. , Kim Seon Woo , Liu Nancy T. , Nou Xiangwu 
Published: August 2016

ABSTRACT

Ralstonia insidiosa
is an opportunistic pathogen and a strong biofilm producer. Here, we present the complete genome sequences of
R. insidiosa
FC1138 and ATCC 49129. Both strains have two circular chromosomes of approximately 3.9 and 1.9 Mb and a 50-kb plasmid. ATCC 49129 also possesses a megaplasmid of approximately 318 kb.
Draft Genome Sequence of Endophytic Bacterium
Enterobacter asburiae
PDA134, Isolated from Date Palm (
Phoenix dactylifera
L.) Roots
Authors: Yaish Mahmoud W. 
Published: August 2016

ABSTRACT

In this report, a draft of the
Enterobacter asburiae
strain PDA134 genome was sequenced. This bacterial strain was isolated from the root tissue of a date palm, where it has the ability to produce 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase and indole-3-acetic acid (IAA) under salinity stress.
Draft Genome Sequence of an Industrially Important
Bacillus
sp. from Mandarmani Coastal Waters in Midnapur District, West Bengal, India
Authors: Ray Chaudhuri Shaon 
Published: August 2016

ABSTRACT

Reported here is the draft genome sequence of an amylase-, protease-, DNase-, oxidase-, gelatinase-, and catalase-producing, Gram-positive diplobacillus (
Bacillus
sp. SM1 strain MCC2138), which was isolated from marine coastal waters and has the ability to degum raw silk fabric as well as Ramie fiber. The genome comprises 1.76 Mb with a GC content of 34.5%.
Vitamin D deficiency in Malaysian adolescents aged 13 years: findings from the Malaysian Health and Adolescents Longitudinal Research Team study (MyHeARTs)
Authors: Al-Sadat Nabilla , Majid Hazreen Abdul , Sim Pei Ying , Su Tin Tin , Dahlui Maznah , Abu Bakar Mohd Fadzrel , Dzaki Najat , Norbaya Saidatul , Murray Liam , Cantwell Marie M , Jalaludin Muhammad Yazid ,   MyHeART study group
Published: August 2016

ObjectiveTo determine the prevalence of vitamin D deficiency (<37.5 nmol/L) among young adolescents in Malaysia and its association with demographic characteristics, anthropometric measures and physical activity.DesignThis is a cross-sectional study among Form 1 (year 7) students from 15 schools selected using a stratified random sampling design. Information regarding sociodemographic characteristics, clinical data and environmental factors was collected and blood samples were taken for total vitamin D. Descriptive and multivariable logistic regression was performed on the data.SettingNational secondary schools in Peninsular Malaysia.Participants1361 students (mean age 12.9±0.3 years) (61.4% girls) completed the consent forms and participated in this study. Students with a chronic health condition and/or who could not understand the questionnaires due to lack of literacy were excluded.Main outcome measuresVitamin D status was determined through measurement of sera 25-hydroxyvitamin D (25(OH)D). Body mass index (BMI) was classified according to International Obesity Task Force (IOTF) criteria. Self-reported physical activity levels were assessed using the validated Malay version of the Physical Activity Questionnaire for Older Children (PAQ-C).ResultsDeficiency in vitamin D was seen in 78.9% of the participants. The deficiency was significantly higher in girls (92.6%, p<0.001), Indian adolescents (88.6%, p<0.001) and urban-living adolescents (88.8%, p<0.001). Females (OR=8.98; 95% CI 6.48 to 12.45), adolescents with wider waist circumference (OR=2.64; 95% CI 1.65 to 4.25) and in urban areas had higher risks (OR=3.57; 95% CI 2.54 to 5.02) of being vitamin D deficient.ConclusionsThe study shows a high prevalence of vitamin D deficiency among young adolescents. Main risk factors are gender, ethnicity, place of residence and obesity.
Risk Factors and Cognitive Relevance of Cortical Cerebral Microinfarcts in Patients With Ischemic Stroke or Transient Ischemic Attack
Authors: Wang Zhaolu , van Veluw Susanne J. , Wong Adrian , Liu Wenyan , Shi Lin , Yang Jie , Xiong Yunyun , Lau Alexander , Biessels Geert Jan , Mok Vincent C.T. 
Published: August 2016

Background and Purpose—
It was recently demonstrated that cerebral microinfarcts (CMIs) can be detected in vivo using 3.0 tesla (T) magnetic resonance imaging. We investigated the prevalence, risk factors, and the longitudinal cognitive consequence of cortical CMIs on 3.0T magnetic resonance imaging, in patients with ischemic stroke or transient ischemic attack.

Methods—
A total of 231 patients undergoing 3.0T magnetic resonance imaging were included. Montreal Cognitive Assessment was used to evaluate global cognitive functions and cognitive domains (memory, language, and attention visuospatial and executive functions). Cognitive changes were represented by the difference in Montreal Cognitive Assessment score between baseline and 28-month after stroke/transient ischemic attack. The cross-sectional and longitudinal associations between cortical CMIs and cognitive functions were explored using ANCOVA and regression models.

Results—

Cortical CMIs were observed in 34 patients (14.7%), including 13 patients with acute (hyperintense on diffusion-weighted imaging) and 21 with chronic CMIs (isointense on diffusion-weighted imaging). Atrial fibrillation was a risk factor for all cortical CMIs (odds ratio, 4.8; 95% confidence interval, 1.5–14.9;
P
=0.007). Confluent white matter hyperintensities was associated with chronic CMIs (odds ratio, 2.8; 95% confidence interval, 1.0–7.8;
P
=0.047). The presence of cortical CMIs at baseline was associated with worse visuospatial functions at baseline and decline over 28-month follow-up (β=0.5; 95% confidence interval, 0.1–1.0;
P
=0.008, adjusting for brain atrophy, white matter hyperintensities, lacunes, and microbleeds).

Conclusions—
Cortical CMIs are a common finding in patients with stroke/transient ischemic attack. Associations between CMI with atrial fibrillation and white matter hyperintensities suggest that these lesions have a heterogeneous cause, involving microembolism and cerebral small vessel disease. CMI seemed to preferentially impact visuospatial functions as assessed by a cognitive screening test.
Two new species of Helicascus (Morosphaeriaceae) from submerged wood in northern Thailand
Authors: LUO ZONG-LONG , YANG JING , LIU JIAN-KUI , SU HONG-YAN , BAHKALI ALI H. , HYDE KEVIN D. 
Published: August 2016

Helicascus species from submerged wood in aquatic habitats in northern Thailand were studied based on morphology and analysis of DNA sequence data. Descriptions and illustrations of H. elaterascus and a new species H. chiangraiensis are provided. H. chiangraiensis is characterized by unilocular ascostromata, fissitunicate asci with a long, narrow and coiled endoascus, ascospores with 2–4 large refractive guttules. The phylogenetic analysis based on combined ITS, LSU and SSU sequence data placed the species in Morosphaeriaceae (Pleosporales).
Two new Chrysosporium (Onygenaceae, Onygenales) from China
Authors: ZHANG YAN-WEI , CHEN WANHAO , ZENG GUIPING , ZOU XIAO , WEN TINGCHI , HAN YANFENG , QIU SHU-YI , LIANG ZONG-QI 
Published: August 2016

Fungal isolates GZUIFR-EM14.2002 and GZUIFR-EM66601 were respectively isolated from Chinese soil samples under the snake skin in Guizhou Province and from the soil samples under the feathers in Hubei Province, China. Morphological and molecular evidence support both isolates as new species of Chrysosporium. Phylogenetic analysis based on ITS-5.8S rDNA sequences grouped GZUIFR-EM14.2002 together with C. lucknowense and C. mephiticum. GZUIFR-EM14.2002, which could be distinguished from the latter two species by the presence of abundant intercalary conidia, was named C. guizhouense sp. nov. In the phylogenetic tree, GZUIFR-EM66601 was most closely related to C. submersum and C. siglerae, GZUIFR-EM66601 differed from the other two species in having small obovate to ellipsoidal conidia and no intercalary conidia; this strain was designated as C. hubeiense sp. nov. Holotypes and their isolates had been deposited in GZAC, Guiyang, Guizhou Province, China.
CloneCNA: detecting subclonal somatic copy number alterations in heterogeneous tumor samples from whole-exome sequencing data
Authors: Yu Zhenhua , Li Ao , Wang Minghui 
Published: August 2016

AbstractBackgroundCopy number alteration is a main genetic structural variation that plays an important role in tumor initialization and progression. Accurate detection of copy number alterations is necessary for discovering cancer-causing genes. Whole-exome sequencing has become a widely used technology in the last decade for detecting various types of genomic aberrations in cancer genomes. However, there are several major issues encountered in these detection problems, including normal cell contamination, tumor aneuploidy, and intra-tumor heterogeneity. Especially, deciphering the intra-tumor heterogeneity is imperative for identifying clonal and subclonal copy number alterations.ResultsWe introduce CloneCNA, a novel bioinformatics tool for efficiently addressing these issues and automatically detecting clonal and subclonal somatic copy number alterations from heterogeneous tumor samples. CloneCNA fully explores the log ratio of read counts between paired tumor-normal samples and tumor B allele frequency of germline heterozygous SNP positions, further employs efficient statistical models to quantitatively represent copy number status of tumor sample containing multiple clones. We examine CloneCNA on simulated heterogeneous and real tumor samples, and the results demonstrate that CloneCNA has higher power to detect copy number alterations than existing methods.ConclusionsCloneCNA, a novel algorithm is developed to efficiently and accurately identify somatic copy number alterations from heterogeneous tumor samples. We demonstrate the statistical framework of CloneCNA represents a remarkable advance for tumor whole-exome sequencing data. We expect that CloneCNA will promote cancer-focused studies for investigating the role of clonal evolution and elucidating critical events benefiting tumor tumourigenesis and progression.
A scalable assembly-free variable selection algorithm for biomarker discovery from metagenomes
Authors: Gkanogiannis Anestis , Gazut Stéphane , Salanoubat Marcel , Kanj Sawsan , Brüls Thomas 
Published: August 2016

Abstract
Background
Metagenomics holds great promises for deepening our knowledge of key bacterial driven processes, but metagenome assembly remains problematic, typically resulting in representation biases and discarding significant amounts of non-redundant sequence information. In order to alleviate constraints assembly can impose on downstream analyses, and/or to increase the fraction of raw reads assembled via targeted assemblies relying on pre-assembly binning steps, we developed a set of binning modules and evaluated their combination in a new “assembly-free” binning protocol.

Results
We describe a scalable multi-tiered binning algorithm that combines frequency and compositional features to cluster unassembled reads, and demonstrate i) significant runtime performance gains of the developed modules against state of the art software, obtained through parallelization and the efficient use of large lock-free concurrent hash maps, ii) its relevance for clustering unassembled reads from high complexity (e.g., harboring 700 distinct genomes) samples, iii) its relevance to experimental setups involving multiple samples, through a use case consisting in the “de novo” identification of sequences from a target genome (e.g., a pathogenic strain) segregating at low levels in a cohort of 50 complex microbiomes (harboring 100 distinct genomes each), in the background of closely related strains and the absence of reference genomes, iv) its ability to correctly identify clusters of sequences from the E. coli O104:H4 genome as the most strongly correlated to the infection status in 53 microbiomes sampled from the 2011 STEC outbreak in Germany, and to accurately cluster contigs of this pathogenic strain from a cross-assembly of these 53 microbiomes.

Conclusions
We present a set of sequence clustering (“binning”) modules and their application to biomarker (e.g., genomes of pathogenic organisms) discovery from large synthetic and real metagenomics datasets. Initially designed for the “assembly-free” analysis of individual metagenomic samples, we demonstrate their extension to setups involving multiple samples via the usage of the “alignment-free” d2S statistic to relate clusters across samples, and illustrate how the clustering modules can otherwise be leveraged for de novo “pre-assembly” tasks by segregating sequences into biologically meaningful partitions.