bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spontaneous fungal peritonitis: a rare but severe complication of liver cirrhosis
Authors: Gravito-Soares Marta , Gravito-Soares Elisa , Lopes Sandra , Ribeiro Graça , Figueiredo Pedro 
Published: June 2017

Introduction and aim
Spontaneous bacterial peritonitis is the most common infectious complication in cirrhosis. Spontaneous fungal peritonitis is rare and remains unknown. In this work, spontaneous fungal peritonitis as well as risk factors and prognosis are characterized.

Patients and methods
A retrospective case–control study of 253 consecutive admissions by peritonitis in cirrhotic patients was carried out between 2006 and 2015. Comparison of patients with spontaneous fungal peritonitis (cases) and spontaneous bacterial peritonitis with positive microbiologic ascitic fluid culture (controls) was performed. Variables such as sociodemographic and clinical features, cirrhosis etiology, liver dysfunction scores, ascitic and laboratory parameters, invasive procedures, and prognosis were evaluated.

Results
Of the 231 patients, eight (3.5%) developed spontaneous fungal peritonitis, 62.5% of cases being coinfected with bacteria. Candida spp. was isolated in 87.5% of cases, mainly Candida albicans (37.5%) and C. krusei (25.0%). Patients with spontaneous fungal peritonitis had higher ascitic fluid lactate dehydrogenase (288.4±266.6 vs. 161.0±179.5; P=0.011), blood leukocyte count (15187.5±5432.3 vs. 10969.8±6949.5; P=0.028), blood urea nitrogen (69.8±3.1 vs. 36.3±25.5; P=0.001), higher number of invasive procedures (colonoscopy: 25.0 vs. 0.8%, P=0.001; urinary catheterization: 87.5 vs. 49.6%, P=0.038; nasogastric intubation: 87.5 vs. 26.9%, P=0.001), and longer duration of hospital stay (30.0±32.9 vs. 18.9±17.0 days; P=0.031). No statistical difference was found between the two groups for Model for End-Stage Liver Disease, Model for End-Stage Liver Disease–sodium, and Child–Pugh scores. Spontaneous fungal peritonitis was associated with a worse prognosis, particularly severe sepsis/septic shock (87.5 vs. 42.8%, P=0.023), admission in the gastroenterology intensive care unit (87.5 vs. 24.4%; P=0.001), and overall (62.5 vs. 31.9%; P=0.039) or 30-day mortality (50.0 vs. 24.4%; P=0.034), with a mean diagnosis-death time of 17.6±11.5 days.

Conclusion
Despite being a rare condition, spontaneous fungal peritonitis was associated with worse prognosis and higher mortality than SBP. The ascitic fluid lactate dehydrogenase, blood leukocyte count and urea nitrogen, invasive procedures, and longer admission time were independent risk factors for spontaneous fungal peritonitis.
Survey Instruments to Assess Patient Experiences With Access and Coordination Across Health Care Settings
Authors: Quinn Martha , Robinson Claire , Forman Jane , Krein Sarah L. , Rosland Ann-Marie 
Published: June 2017

Background:
Improving access can increase the providers a patient sees, and cause coordination challenges. For initiatives that increase care across health care settings, measuring patient experiences with access and care coordination will be crucial.

Objectives:
Map existing survey measures of patient experiences with access and care coordination expected to be relevant to patients accessing care across settings. Preliminarily examine whether aspects of access and care coordination important to patients are represented by existing measures.

Research Design:
Structured literature review of domains and existing survey measures related to access and care coordination across settings. Survey measures, and preliminary themes from semistructured interviews of 10 patients offered VA-purchased Community Care, were mapped to identified domains.

Results:
We identified 31 existing survey instruments with 279 items representing 6 access and 5 care coordination domains relevant to cross-system care. Domains frequently assessed by existing measures included follow-up coordination, primary care access, cross-setting coordination, and continuity. Preliminary issues identified in interviews, but not commonly assessed by existing measures included: (1) acceptability of distance to care site given patient’s clinical situation; (2) burden on patients to access and coordinate care and billing; (3) provider familiarity with Veteran culture and VA processes.

Conclusions:
Existing survey instruments assess many aspects of patient experiences with access and care coordination in cross-system care. Systems assessing cross-system care should consider whether patient surveys accurately reflect the level of patients’ concerns with burden to access and coordinate care, and adequately reflect the impact of clinical severity and cultural familiarity on patient preferences.
Nonhuman Primate (Rhesus Macaque) Models of Severe Pressure-Targeted Hemorrhagic and Polytraumatic Hemorrhagic Shock
Authors: Sheppard Forest R. , Macko Antoni R. , Glaser Jacob J. , Vernon Philip J. , Burdette Alexander J. , Paredes Ruth Madelaine , Koeller Craig A. , Pusateri Anthony E. , Tadaki Douglas K. , Cardin Sylvain 
Published: June 2017

ABSTRACT

Background:
We endeavored to develop clinically translatable nonhuman primate (NHP) models of severe polytraumatic hemorrhagic shock.

Methods:
NHPs were randomized into five severe pressure-targeted hemorrhagic shock (PTHS) ± additional injuries scenarios: 30-min PTHS (PTHS-30), 60-min PTHS (PTHS-60), PTHS-60 + soft tissue injury (PTHS-60+ST), PTHS-60+ST + femur fracture (PTHS-60+ST+FF), and decompensated PTHS+ST+FF (PTHS-D). Physiologic parameters were recorded and blood samples collected at five time points with animal observation through T = 24 h. Results presented as mean ± SEM; statistics: log transformation followed by two-way ANOVA with Bonferroni multiple comparisons, Wilcoxon nonparametric test for comparisons, and the Friedmans’ one-way ANOVA; significance: P < 0.05.

Results:
Percent blood loss was 40% ± 2, 59% ± 3, 52% ± 3, 49% ± 2, and 54% ± 2 for PTHS-30, PTHS-60, PTHS-60+ST, PTHS-60+ST+FF, and PTHS-D, respectively. All animals survived to T = 24 h except one in each of the PTHS-60 and PTHS-60+ST+FF groups and seven in the PTHS-D group. Physiologic, coagulation, and inflammatory parameters demonstrated increasing derangements with increasing model severity.

Conclusion:
NHPs exhibit a high degree of resilience to hemorrhagic shock and polytrauma as evidenced by moderate perturbations in metabolic, coagulation, and immunologic outcomes with up to 60 min of profound hypotension regardless of injury pattern. Extending the duration of PTHS to the point of decompensation in combination with polytraumatic injury, evoked derangements consistent with those observed in severely injured trauma patients which would require ICU care. Thus, we have successfully established a clinically translatable NHP trauma model for use in testing therapeutic interventions to trauma.
Guillain–Barré syndrome and Zika virus outbreaks
Authors: Nascimento Osvaldo J.M. , da Silva Ivan R.F. 
Published: June 2017

Purpose of review
Arboviruses have been associated with central and peripheral nervous system injuries, in special the flaviviruses. Guillain–Barré syndrome (GBS), transverse myelitis, meningoencephalitis, ophthalmological manifestations, and other neurological complications have been recently associated to Zika virus (ZIKV) infection. In this review, we aim to analyze the epidemiological aspects, possible pathophysiology, and what we have learned about the clinical and laboratory findings, as well as treatment of patients with ZIKV-associated neurological complications.

Recent findings
In the last decades, case series have suggested a possible link between flaviviruses and development of GBS. Recently, large outbreaks of ZIKV infection in Asia and the Americas have led to an increased incidence of GBS in these territories. Rapidly, several case reports and case series have reported an increase of all clinical forms and electrophysiological patterns of GBS, also including cases with associated central nervous system involvement. Finally, cases suggestive of acute transient polyneuritis, as well as acute and progressive postinfectious neuropathies associated to ZIKV infection have been reported, questioning the usually implicated mechanisms of neuronal injury.

Summary
The recent ZIKV outbreaks have triggered the occurrence of a myriad of neurological manifestations likely associated to this arbovirosis, in special GBS and its variants.
The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions
Authors: Bolouri Hamid , Farrar Jason E. , Triche Timothy , Ries Rhonda E. , Lim Emilia L. , Alonzo Todd A. , Ma Yussanne , Moore Richard , Mungall Andrew J. , Marra Marco A. , Zhang Jinghui , Ma Xiaotu , Liu Yu , Liu Yanling , Guidry Auvil Jaime M. , Davidsen Tanja M. , Gesuwan Patee , Hermida Leandro C. , Salhia Bodour , Capone Stephen , Ramsingh Giridharan , Zwaan Christian Michel , Noort Sanne , Piccolo Stephen R. , Kolb E. Anders , Gamis Alan S. , Smith Malcolm A. , Gerhard Daniela S. , Meshinchi Soheil 
Published: June 2017

AbstractWe present the molecular landscape of pediatric acute myeloid leukemia (AML), characterizing nearly 1,000 participants in Children’s Oncology Group (COG) AML trials. The COG/NCI TARGET AML initiative assessed cases by whole-genome, targeted DNA, mRNA, miRNA sequencing and CpG methylation profiling. Validated DNA variants revealed diverse, infrequent mutations with fewer than 40 genes mutated in >2% of cases. In contrast, somatic structural variants, including novel gene fusions and focalMBNL1,ZEB2, andELF1deletions, were disproportionately prevalent in young as compared to adult patients. Conversely,DNMT3AandTP53mutations, common in adults, are conspicuously absent from virtually all pediatric cases. NovelGATA2,FLT3, andCBLmutations, recurrentMYC-ITD, NRAS, KRAS, andWT1mutations are frequent in pediatric AML. Deletions, mutations, and promoter DNA hypermethylation convergently impact Wnt signaling, Polycomb repression, innate immune cell interactions, and a cluster of zinc finger genes associated withKMT2Arearrangements. These results highlight the need for, and facilitate the development of age-tailored targeted therapies for the treatment of pediatric AML.
Non-latching positive feedback enables robust bimodality by de-coupling expression noise from the mean
Authors: Razooky Brandon S. , Cao Youfang , Perelson Alan S. , Simpson Michael L. , Weinberger Leor S. 
Published: June 2017

ABSTRACTFundamental to biological decision-making is the ability to generate bimodal expression patterns where two alternate expression states simultaneously exist. Here, we use a combination of single-cell analysis and mathematical modeling to examine the sources of bimodality in the transcriptional program controlling HIV’s fate decision between active replication and viral latency. We find that the HIV Tat protein manipulates the intrinsic toggling of HIV’s promoter, the LTR, to generate bimodal ON-OFF expression, and that transcriptional positive feedback from Tat shifts and expands the regime of LTR bimodality. This result holds for both minimal synthetic viral circuits and full-length virus. Strikingly, computational analysis indicates that the Tat circuit’s non-cooperative ‘non-latching’ feedback architecture is optimized to slow the promoter’s toggling and generate bimodality by stochastic extinction of Tat. In contrast to the standard Poisson model, theory and experiment show that non-latching positive feedback substantially dampens the inverse noise-mean relationship to maintain stochastic bimodality despite increasing mean-expression levels. Given the rapid evolution of HIV, the presence of a circuit optimized to robustly generate bimodal expression appears consistent with the hypothesis that HIV’s decision between active replication and latency provides a viral fitness advantage. More broadly, the results suggest that positive-feedback circuits may have evolved not only for signal amplification but also for robustly generating bimodality by decoupling expression fluctuations (noise) from mean expression levels.
Brain-state invariant thalamo-cortical coordination revealed by non-linear encoders
Authors: Viejo Guillaume , Cortier Thomas , Peyrache Adrien 
Published: June 2017

AbstractUnderstanding how neurons cooperate to integrate sensory inputs and guide behavior is a fundamental problem in neuroscience. A large body of methods have been developed to study neuronal firing at the single cell and population levels, generally seeking interpretability as well as predictivity. However, these methods are usually confronted with the lack of ground-truth necessary to validate the approach. Here, using neuronal data from the head-direction (HD) system, we present evidence demonstrating how gradient boosted trees, a non-linear and supervised Machine Learning tool, can learn the relationship between behavioral parameters and neuronal responses with high accuracy by optimizing the information rate. Interestingly, and unlike other classes of Machine Learning methods, the intrinsic structure of the trees can be interpreted in relation to behavior (e.g. to recover the tuning curves) or to study how neurons cooperate with their peers in the network. We show how the method, unlike linear analysis, reveals that the coordination in thalamo-cortical circuits is qualitatively the same during wakefulness and sleep, indicating a brain-state independent feed-forward circuit. Machine Learning tools thus open new avenues for benchmarking model-based characterization of spike trains.Author summaryThe thalamus is a brain structure that relays sensory information to the cortex and mediates cortico-cortical interaction. Unraveling the dialogue between the thalamus and the cortex is thus a central question in neuroscience, with direct implications on our understanding of how the brain operates at the macro scale and of the neuronal basis of brain disorders that possibly result from impaired thalamo-cortical networks, such as absent epilepsy and schizophrenia. Methods that are classically used to study the coordination between neuronal populations are usually sensitive to the ongoing global dynamics of the networks, in particular desynchronized (wakefulness and REM sleep) and synchronized (non-REM sleep) states. They thus fail to capture the underlying temporal coordination. By analyzing recordings of thalamic and cortical neuronal populations of the HD system in freely moving mice during exploration and sleep, we show how a general non-linear encoder captures a brain-state independent temporal coordination where the thalamic neurons leading their cortical targets by 20-50ms in all brain states. This study thus demonstrates how methods that do not assume any models of neuronal activity may be used to reveal important aspects of neuronal dynamics and coordination between brain regions.
vqtl: AnRpackage for Mean-Variance QTL Mapping
Authors: Corty Robert W. , Valdar William 
Published: June 2017

ABSTRACTWe presentvqtl, anRpackage for mean-variance QTL mapping. This QTL mapping approach tests for genetic loci that influence the mean of the phenotype, termed mean QTL, the variance of the phenotype, termed variance QTL, or some combination of the two, termed mean-variance QTL. It is unique in its ability to correct for variance heterogeneity arising not only from the QTL itself but also from nuisance factors, such as sex, batch, or housing. This package provides functions to conduct genome scans, run permutations to assess the statistical significance, and make informative plots to communicate results. Because it is inter-operable with the popularqtlpackage and uses many of the same data structures and input patterns, it will be straightforward for geneticists to analyze future experiments withvqtlas well as re-analyze past experiments, possibly discovering new QTL.
Faster carbon accumulation in global forest soils
Authors: Zhang Weixin , Chen Yuanqi , Shi Leilei , Wang Xiaoli , Liu Yongwen , Rao Xingquan , Lin Yongbiao , Shao Yuanhu , Li Xiaobo , Liu Shengjie , Piao Shilong , Zhu Weixing , Zou Xiaoming , Fu Shenglei 
Published: June 2017

AbstractComparing soil organic carbon (SOC) stocks across space and time is a fundamental issue in global ecology. However, the conventional approach fails to determine SOC stock in an equivalent volume of mineral-soil, and therefore, SOC stock changes can be under- or overestimates if soils swell or shrink during forest development or degradation. Here, we propose to estimate SOC stock as the product of mineral-soil mass in an equivalent mineral-soil volume and SOC concentration expressed as g C Kg-1mineral-soil. This method enables researchers to compare SOC stocks across space and time. Our results show an unaccounted SOC accumulation of 2.4 - 10.1 g C m-2year-1in the 1m surface mineral-soils in global forests. This unaccounted SOC amounts to an additional C sink of 0.12 – 0.25 Pg C year-1, which equals 30 – 62% of the previously estimated annual SOC accumulation in global forests. This finding suggests that forest soils are stronger C sinks than previously recognized.
Compositional Mediation Analysis for Microbiome Studies
Authors: Sohn Michael B. , Li Hongzhe 
Published: June 2017

AbstractMotivated by recent advances in causal mediation analysis and problems in the analysis of microbiome data, we consider the setting where the effect of a treatment on an outcome is transmitted through perturbing the microbial communities or compositional mediators. Compositional and high-dimensional nature of such mediators makes the standard mediation analysis not directly applicable to our setting. We propose a sparse compositional mediation model that can be used to estimate the causal direct and indirect (or mediation) effects utilizing the algebra for compositional data in the simplex space. We also propose tests of total and component-wise mediation effects using bootstrap. We conduct extensive simulation studies to assess the performance of the proposed method and apply the method to a real metagenomic dataset to investigate the effect of fat intake on body mass index mediated through the gut microbiome composition.
Phylogeographic separation and formation of sexually discrete lineages in a global population ofYersinia pseudotuberculosis
Authors: Seecharran Tristan , Kalin-Mänttäri Laura , Koskela Katja A. , Nikkari Simo , Dickins Benjamin , Corander Jukka , Skurnik Mikael , McNally Alan 
Published: June 2017

AbstractYersinia pseudotuberculosisis a Gram negative intestinal pathogen of humans and has been responsible for several nation-wide gastro-intestinal outbreaks. Large-scale population genomic studies have been performed on the other human pathogenicYersinia, Y. pestisandY. enterocoliticaallowing a high-resolution understanding of the ecology, evolution and dissemination of these pathogens. However, to date no large-scale global population genomic analysis ofY. pseudotuberculosishas been performed. Here we present analyses of the genomes of 134 strains ofY. pseudotuberculosisisolated from around the world, from multiple ecosystems since 1960’s. Our data display a phylogeographic split within the population, with an Asian ancestry and subsequent dispersal of successful clonal lineages into Europe and the rest of the world. These lineages can be differentiated by CRISPR cluster arrays, and we show that the lineages are limited with respect to inter-lineage genetic exchange. This restriction of genetic exchange maintains the discrete lineage structure in the population despite co-existence of lineages for thousands of years in multiple countries. Our data highlights how CRISPR can be informative of the evolutionary trajectory of bacterial lineages, and merits further study across bacteria.
A multi-parent advanced generation inter-cross population for genetic analysis of multiple traits in cowpea (Vigna unguiculataL. Walp.)
Authors: Huynh Bao-Lam , Ehlers Jeffrey D. , Munoz-Amatriain Maria , Lonardi Stefano , Santos Jansen R. P. , Ndeve Arsenio , Batieno Benoit J. , Boukar Ousmane , Cisse Ndiaga , Drabo Issa , Fatokun Christian , Kusi Francis , Agyare Richard Y. , Guo Yi-Ning , Herniter Ira , Lo Sassoum , Wanamaker Steve I. , Close Timothy J. , Roberts Philip A. 
Published: June 2017

AbstractDevelopment and analysis of Multiparent Advanced Generation Inter-Cross (MAGIC) populations have been conducted with several crop plants to harness the potential for dissecting the genetic structure of traits and improving breeding populations. We developed a first MAGIC population for cowpea (Vigna unguiculataL. Walp.) from eight founder parents which are genetically diverse and carry many abiotic and biotic stress resistance, seed quality and agronomic traits relevant to cowpea improvement in sub-Saharan Africa (SSA) where cowpea is vitally important in the human diet and in local economies. The eight parents were inter-crossed using structured matings to ensure the population would have balanced representation from each of the founder parents, followed by single-seed descent, resulting in 365 F8 recombinant inbred lines (RILs) each carrying a mosaic of genome blocks contributed from all founders. This was confirmed by SNP genotyping with the cowpea Illumina 60K iSelect BeadArray. Following filtering to eliminate duplicates, sister lines and accidental selfing events, a core set of 305 F8 RILs was chosen as the primary population. The F8 lines were on average 99.74% homozygous while also diverse in agronomic traits including flowering time, growth habit, maturity, yield potential and seed characteristics across environments. Trait-associated SNPs were identified for most of the parental traits. Loci with major effects on photoperiod sensitivity and seed size were also verified by genetic mapping in biparental RIL populations. The distribution of recombination frequency varied considerably between chromosomes, with recombination hotspots distributed mostly in the telomeric regions. Due to its broad genetic base, this cowpea MAGIC population promises breakthroughs in genetic gain and high-resolution genetic mapping for gene discovery, enhancement of breeding populations and, for some lines, direct releases as new varieties.
A systematic survey of centrality measures for protein-protein interaction networks
Authors: Ashtiani Minoo , Salehzadeh-Yazdi Ali , Razaghi-Moghadam Zahra , Hennig Holger , Wolkenhauer Olaf , Mirzaie Mehdi , Jafari Mohieddin 
Published: June 2017

AbstractBackgroundNumerous centrality measures have been introduced to identify “central” nodes in large networks. The availability of a wide range of measures for ranking influential nodes leaves the user to decide which measure may best suit the analysis of a given network. The choice of a suitable measure is furthermore complicated by the impact of the network topology on ranking influential nodes by centrality measures. To approach this problem systematically, we examined the centrality profile of nodes of yeast protein-protein interaction networks (PPINs) in order to detect which centrality measure is succeeding in predicting influential proteins. We studied how different topological network features are reflected in a large set of commonly used centrality measures.ResultsWe used yeast PPINs to compare 27 common of centrality measures. The measures characterize and assort influential nodes of the networks. We applied principal component analysis (PCA) and hierarchical clustering and found that the most informative measures depend on the network’s topology. Interestingly, some measures had a high level of contribution in comparison to others in all PPINs, namely Latora closeness, Decay, Lin, Freeman closeness, Diffusion, Residual closeness and Average distance centralities.ConclusionsThe choice of a suitable set of centrality measures is crucial for inferring important functional properties of a network. We concluded that undertaking data reduction using unsupervised machine learning methods helps to choose appropriate variables (centrality measures). Hence, we proposed identifying the contribution proportions of the centrality measures with PCA as a prerequisite step of network analysis before inferring functional consequences, e.g., essentiality of a node.