bluuebunny/crossref_metadata_2025 huggingface dataset:
Pidgins and Creoles
Authors: Baptista Marlyse
Published: February 2017

This chapter offers an overview of the controversies surrounding the study of creole syntax while evaluating representative studies. This overview includes proposals that cast creoles as a “type” of languages, proposals that view creoles as interlanguages and resulting from second language acquisition, and proposals that consider them as hybrid grammars yielding innovative feature recombinations due to language contact. It also discusses the benefits of the Atlas of Pidgin and Creole Structures, as it lays out a promising new direction in the investigation of pidgins and creoles by offering systematic comparisons of a large sample of creoles and their source languages. This collaborative Atlas provides broad empirical coverage, testing the hypotheses reflected by the various positions and schools of thought discussed in this chapter while unveiling the rich diversity of creole syntactic features.
Intergroup Contact and the Struggle for Social Justice
Authors: Durrheim Kevin , Dixon John
Published: February 2017

Early research on intergroup contact in social psychology had a clear social change agenda. Authors like Clark and Allport directly addressed themes of power and inequality as they studied the effects of contact to support desegregation activism in the United States. During the subsequent decades the focus on inequality, power, and social change was replaced with the quest for a generalized theory of prejudice reduction. This chapter shows how this change in focus took place; it considers the ways in which some contact research continues to ignore social justice concerns today; and it reflects on the effects of this focus. Finally, the chapter sketches—in broad outline—a model of the way intergroup contact functions to reproduce social situations and the experiences of people who participate in these situations.
The Ethics of War
Authors: Frowe Helen , Lazar Seth
Published: February 2017

War is not the only or even the major cause of human suffering. But it is the cause for which we are most often most directly responsible. Our voluntary choices result in huge increases in mortality, massive refugee crises, and the dislocation of whole generations. So while there are other equally pressing problems facing humanity, none of them raises as pointed moral questions as those to do with whether and when we may take our polities to war and how we must fight if we do so. This Handbook offers a guide to thinking through the morality of war, from the perspective of contemporary analytical just war theory. This introduction explains the methodological and substantive choices made in designing the volume, then summarizes the key insights of the chapters to follow.
Is Pelvic-Floor Muscle Training a Physical Therapy or a Behavioral Therapy? A Call to Name and Report the Physical, Cognitive, and Behavioral Elements
Authors: Frawley Helena C. , Dean Sarah G. , Slade Susan C. , Hay-Smith E. Jean C.
Published: February 2017

This perspective article explores whether pelvic-floor muscle training (PFMT) for the management of female urinary incontinence and prolapse is a physical therapy or a behavioral therapy. The primary aim is to demonstrate that it is both. A secondary aim is to show that the plethora of terms used for PFMT is potentially confusing and that current terminology inadequately represents the full intent, content, and delivery of this complex intervention. While physical therapists may be familiar with exercise terms, the details are often incompletely reported; furthermore, physical therapists are less familiar with the terminology used in accurately representing cognitive and behavioral therapy interventions, which results in these elements being even less well reported. Thus, an additional aim is to provide greater clarity in the terminology used in the reporting of PFMT interventions, specifically, descriptions of the exercise and behavioral elements. First, PFMT is described as a physical therapy and as an exercise therapy informed predominantly by the discipline of physical therapy. However, effective implementation requires use of the cognitive and behavioral perspectives of the discipline of psychology. Second, the theoretical underpinning of the psychology-informed elements of PFMT is summarized. Third, to address some identified limitations and confusion in current terminology and reporting, recommendations for ways in which physical therapists can incorporate the psychology-informed elements of PFMT alongside the more familiar exercise therapy–informed elements are made. Fourth, an example of how both elements can be described and reported in a PFMT intervention is provided. In summary, this perspective explores the underlying concepts of PFMT to demonstrate that it is both a physical intervention and a behavioral intervention and that it can and should be described as such, and an example of the integration of these elements into clinical practice is provided.
Gross Motor Trajectories During the First Year of Life for Preterm Infants With Very Low Birth Weight
Authors: Su Yu-Han , Jeng Suh-Fang , Hsieh Wu-Shiun , Tu Yu-Kang , Wu Yen-Tzu , Chen Li-Chiou
Published: February 2017

Background

Early identification of motor dysfunction in preterm infants with very low birth weight (VLBW) is important in order to provide early intervention.

Objective

This study was to examine the motor trajectories of preterm infants with VLBW during their first year of life and to investigate the predictive ability and influencing factors of the trajectories.

Design and Methods

A total of 342 preterm infants with VLBW were prospectively assessed for motor development by the Alberta Infant Motor Scales at 4, 6, 9, and 12 months and for developmental outcomes using the Bayley Scales of Infant and Toddler Development, second edition, at 24 months. Perinatal and socio-environmental factors were collected at baseline. Growth mixture modeling was used to explore the patterns of infants’ motor trajectories during their first year of life. Logistic regression analyses were applied to examine the influencing factors associated with motor trajectories and their predictability of 24-month developmental outcomes.

Results

Preterm infants with VLBW showed 3 distinct motor trajectories: stably normal (55%), deteriorating (32%), and persistently delayed (13%). Furthermore, the motor trajectories were predictive of 24-month cognitive and motor outcomes. Perinatal factors including lower birth weight, male gender, moderate to severe bronchopulmonary dysplasia, stage III to IV retinopathy of prematurity, and major brain damage were associated with a risk of deteriorating and persistently delayed trajectories (all P < .05). Socio-environmental factors had no association with motor trajectories.

Limitations

The small sample size of the infants with a persistently delayed trajectory may have limited the assessment of some influencing factors.

Conclusion

The identified early motor trajectories, predictive values, and influencing factors provide insightful implications for early detection and prevention of motor -disorders in preterm infants with VLBW.
Genotypic Diversity of Phytophthora cinnamomi and P. plurivora in Maryland’s Nurseries and Mid-Atlantic Forests
Authors: Beaulieu Justine , Ford Blaine , Balci Yilmaz
Published: February 2017

Genetic diversity of two Phytophthora spp.—P. cinnamomi (102 isolates), commonly encountered in Maryland nurseries and forests in the Mid-Atlantic United States, and P. plurivora (186 isolates), a species common in nurseries—was characterized using amplified fragment length polymorphism. Expected heterozygosity and other indices suggested a lower level of diversity among P. cinnamomi than P. plurivora isolates. Hierarchical clustering showed P. cinnamomi isolates separated into four clusters, and two of the largest clusters were closely related, containing 80% of the isolates. In contrast, P. plurivora isolates separated into six clusters, one of which included approximately 40% of the isolates. P. plurivora isolates recovered from the environment (e.g., soil and water) were genotypically more diverse than those found causing lesions. For both species, isolate origin (forest versus nursery or among nurseries) was a significant factor of heterozygosity. Clonal groups existed within P. cinnamomi and P. plurivora and included isolates from both forest and nurseries, suggesting that a pathway from nurseries to forests or vice versa exists.
Predicting susceptibility to tuberculosis based on gene expression profiling in dendritic cells
Authors: Blischak John D. , Tailleux Ludovic , Myrthil Marsha , Charlois Cécile , Bergot Emmanuel , Dinh Aurélien , Morizot Gloria , Chény Olivia , Von Platen Cassandre , Herrmann Jean-Louis , Brosch Roland , Barreiro Luis B. , Gilad Yoav
Published: February 2017

Tuberculosis (TB) is a deadly infectious disease, which kills millions of people every year. The causative pathogen,Mycobac-terium tuberculosis(MTB), is estimated to have infected up to a third of the world’s population; however, only approximately 10% of infected healthy individuals progress to active TB. Despite evidence for heritability, it is not currently possible to predict who may develop TB. To explore approaches to classify susceptibility to TB, we infected with MTB dendritic cells (DCs) from putatively resistant individuals diagnosed with latent TB, and from susceptible individuals that had recovered from active TB. We measured gene expression levels in infected and non-infected cells and found hundreds of differentially expressed genes between susceptible and resistant individuals in the non-infected cells. We further found that genetic polymorphisms nearby the differentially expressed genes between susceptible and resistant individuals are more likely to be associated with TB susceptibility in published GWAS data. Lastly, we trained a classifier based on the gene expression levels in the non-infected cells, and demonstrated decent performance on our data and an independent data set. Overall, our promising results from this small study suggest that training a classifier on a larger cohort may enable us to accurately predict TB susceptibility.
Interactions between genetic variation and cellular environment in skeletal muscle gene expression
Authors: Taylor D. Leland , Knowles David A. , Scott Laura J. , Ramirez Andrea H. , Paolo Casale Franceso , Wolford Brooke N. , Guan Li , Varshney Arushi , Oliveira Albanus Ricardo , Parker Stephen C.J. , Narisu Narisu , Chines Peter S. , Erdos Michael R. , Welch Ryan P. , Kinnunen Leena , Saramies Jouko , Sundvall Jouko , Lakka Timo A. , Laakso Markku , Tuomilehto Jaakko , Koistinen Heikki A. , Stegle Oliver , Boehnke Michael , Birney Ewan , Collins Francis S.
Published: February 2017

From whole organisms to individual cells, responses to environmental conditions are influenced by genetic makeup, where the effect of genetic variation on a trait depends on the environmental context. RNA-sequencing quantifies gene expression as a molecular trait, and is capable of capturing both genetic and environmental effects. In this study, we explore opportunities of using allele-specific expression (ASE) to discovercisacting genotype-environment interactions (GxE) - genetic effects on gene expression that depend on an environmental condition. Treating 17 common, clinical traits as approximations of the cellular environment of 267 skeletal muscle biopsies, we identify 10 candidate interaction quantitative trait loci (iQTLs) across 6 traits (12 unique gene-environment trait pairs; 10% FDR per trait) including sex, systolic blood pressure, and low-density lipoprotein cholesterol. Although using ASE is in principle a promising approach to detect GxE effects, replication of such signals can be challenging as validation requires harmonization of environmental traits across cohorts and a sufficient sampling of heterozygotes for a transcribed SNP. Comprehensive discovery and replication will require large human transcriptome datasets, or the integration of multiple transcribed SNPs, coupled with standardized clinical phenotyping.
CAFE MOCHA:An Integrated Platform for Discovering Clinically Relevant Molecular Changes in Cancer; an Example of Distant Metastasis and Recurrence-linked Classifiers in Head and Neck Squamous Cell Carcinoma
Authors: Krishnan Neeraja M , Mohanraj I , Hariharan Janani , Panda Binay
Published: February 2017

Background

CAFE MOCHA(Clinical Association of Functionally Established MOlecular CHAnges) is an integrated GUI-driven computational and statistical framework to discover molecular signatures linked to a specific clinical attribute in a cancer type. We testedCAFE MOCHAin head and neck squamous cell carcinoma (HNSCC) for discovering a signature linked to distant metastasis and recurrence (MR) in 517 tumors from TCGA and validated the signature in 18 tumors from an independent cohort.

Methods

The platform integrates mutations and indels, gene expression, DNA methylation and copy number variations to discover a classifier first, predict an incoming tumour for the same by pulling defined class variables into a single framework that incorporates a coordinate geometry-based algorithm, called Complete Specificity Margin Based Clustering (CSMBC) with 100% specificity.CAFE MOCHAclassifies an incoming tumour sample using either a matched normal or a built-in database of normal tissues. The application is packed and deployed using theinstall4jmulti-platform installer.

Results

We testedCAFE MOCHAto discover a signature for distant metastasis and recurrence in HNSCC. The signature MR44 in HNSCC yielded 80% sensitivity and 100% specificity in the discovery stage and 100% sensitivity and 100% specificity in the validation stage.

Conclusions

CAFE MOCHAis a cancer type- and clinical attribute-agnostic computational and statistical framework to discover integrated molecular signature for a specific clinical attribute.

CAFE MOCHAis available in GitHub (https://github.com/binaypanda/CAFEMOCHA).
Microvessel Chaste: An Open Library for Spatial Modelling of Vascularized Tissues
Authors: Grogan J.A. , Connor A.J. , Markelc B. , Muschel R.J. , Maini P.K. , Byrne H.M. , Pitt-Francis J.M.
Published: February 2017

Spatial models of vascularized tissues are widely used in computational physiology, to study for example, tumour growth, angiogenesis, osteogenesis, coronary perfusion and oxygen delivery. Composition of such models is time-consuming, with many researchers writing custom software for this purpose. Recent advances in imaging have produced detailed three-dimensional (3D) datasets of vascularized tissues at the scale of individual cells. To fully exploit such data there is an increasing need for software that allows user-friendly composition of efficient, 3D models of vascularized tissue growth, and comparison of predictions with in vivo or in vitro experiments and other models. Microvessel Chaste is a new open-source library for building spatial models of vascularized tissue growth. It can be used to simulate vessel growth and adaptation in response to mechanical and chemical stimuli, intra- and extra-vascular transport of nutrient, growth factor and drugs, and cell proliferation in complex 3D geometries. The library provides a comprehensive Python interface to solvers implemented in C++, allowing user-friendly model composition, and integration with experimental data. Such integration is facilitated by interoperability with a growing collection of scientific Python software for image processing, statistical analysis, model annotation and visualization. The library is available under an open-source Berkeley Software Distribution (BSD) licence at https://jmsgrogan.github.io/MicrovesselChaste. This article links to two reproducible example problems, showing how the library can be used to model tumour growth and angiogenesis with realistic vessel networks.
Normalization of Mass Spectrometry Data (NOMAD)
Authors: Murie Carl , Sandri Brian , Griffin Timothy J. , Wendt Christine , Larsson Ola
Published: February 2017

Motivation

iTRAQ reagent-based mass spectrometry (MS) is a commonly used technology for identification and quantification of proteins in biological samples. Such studies are often performed over multiple MS runs, potentially resulting in introduction of MS run bias that could affect downstream analysis. iTRAQ MS data have therefore commonly been normalized using a reference sample which is included in each MS run. We show, however, that such normalization does not efficiently remove systematic MS run bias. A linear model approach was previously proposed to improve on the reference normalization approach but does not computationally scale to larger data. Here we describe the NOMAD (normalization of mass spectrometry data) R package which implements a computationally efficient ANOVA normalization approach with protein assembly functionality.

Results

NOMAD provides the same advantages as the linear regression solution but is more computationally efficient which allows superior scaling to larger sample sizes. Moreover, NOMAD efficiently removes bias which allows for valid across MS run comparisons.

Availability

The NOMAD Bioconductor package:www.bioconductor.org

Contact

ola.larsson@ki.se;carl.murie@ki.se
VREX: An Open-Source Toolbox for Creating 3D Virtual Reality Experiments
Authors: Vasser Madis , Kängsepp Markus , Magomedkerimov Murad , Kilvits Kälver , Stafinjak Vladislav , Kivisik Taavi , Vicente Raul , Aru Jaan
Published: February 2017

Background

We present VREX, a free open-source Unity toolbox for virtual reality research in the fields of experimental psychology and neuroscience.

Results

Different study protocols about perception, attention, cognition and memory can be constructed using the toolbox. VREX provides a procedural generation of (interconnected) rooms that can be automatically furnished with a click of a button. VREX includes a menu system for creating and storing experiments with different stages. Researchers can combine different rooms and environments to perform end-to-end experiments including different testing situations and data collection. For fine-tuned control VREX also comes with an editor where all the objects in the virtual room can be manually placed and adjusted in the 3D world.

Conclusions

VREX simplifies the generation and setup of complicated VR scenes and experiments for researchers. VREX can be downloaded and easily installed fromvrex.mozello.com
Structure of a AAA+ unfoldase in the process of unfolding substrate
Authors: Ripstein Zev. A , Huang Rui , Augustyniak Rafal , Kay Lewis E. , Rubinstein John L.
Published: February 2017

AAA+ unfoldases are thought to unfold substrate through the central pore of their hexameric structures, but how this process occurs is not known. VAT, theThermoplasma acidophilumhomologue of eukaryotic CDC48/p97, works in conjunction with the proteasome to degrade misfolded or damaged proteins. We show that in the presence of ATP, VAT with its regulatory N-terminal domains removed unfolds other VAT complexes as substrate. We captured images of this transient process by electron cryomicroscopy (cryo-EM) to reveal the structure of the substrate-bound intermediate. Substrate binding breaks the six-fold symmetry of the complex, allowing five of the six VAT subunits to constrict into a tight helix that grips an ~80 Å stretch of unfolded protein. The structure suggests a processive hand-over-hand unfolding mechanism, where each VAT subunit releases the substrate in turn before re-engaging further along the target protein, thereby unfolding it.
North Andean origin and diversification of the largest ithomiine butterfly genus
Authors: De-Silva Donna Lisa , Mota Luísa L. , Chazot Nicolas , Mallarino Ricardo , Silva-Brandão Karina L. , Gómez Piñerez Luz Miryam , Freitas André V.L. , Lamas Gerardo , Joron Mathieu , Mallet James , Giraldo Carlos E. , Uribe Sandra , Särkinen Tiina , Knapp Sandra , Jiggins Chris D. , Willmott Keith R. , Elias Marianne
Published: February 2017

The Neotropics harbour the most diverse flora and fauna on Earth. The Andes are a major centre of diversification and source of diversity for adjacent areas in plants and vertebrates, but studies on insects remain scarce, even though they constitute the largest fraction of terrestrial biodiversity. Here, we combine molecular and morphological characters to generate a dated phylogeny of the butterfly genusPteronymia(Nymphalidae: Danainae), which we use to infer spatial, elevational and temporal diversification patterns. We first propose six taxonomic changes that raise the generic species total to 53, makingPteronymiathe most diverse genus of the tribe Ithomiini. Our biogeographic reconstruction shows thatPteronymiaoriginated in the Northern Andes, where it diversified extensively. Some lineages colonized lowlands and adjacent montane areas, but diversification here remained scarce. The recent colonization of lowland areas was reflected by an increase in the rate of evolution of species elevational ranges towards present. By contrast, speciation rate decelerated with time, with no extinction. The geological history of the Andes and adjacent regions have likely contributed toPteronymiadiversification by providing compartmentalized habitats and an array of biotic and abiotic conditions, and by limiting dispersal between some areas while promoting interchange across others.
The mammalian kinetochore independently regulates its passive and active force-generating interfaces with microtubules
Authors: Long Alexandra F. , Udy Dylan B. , Dumont Sophie
Published: February 2017

The kinetochore links chromosomes to dynamic spindle microtubules and drives both chromosome congression and segregation. To do so, the kinetochore must hold on to depolymerizing and polymerizing microtubules. At metaphase, one sister kinetochore couples to depolymerizing microtubules, pulling its sister along polymerizing microtubules [1,2]. Distinct kinetochore-microtubule interfaces mediate these behaviors: active interfaces transduce microtubule depolymerization into mechanical work, and passive interfaces generate friction as the kinetochore slides along microtubules [3,4]. We do not know the physical and molecular nature [5–7] of these interfaces, or how they are regulated to support diverse mitotic functions in mammalian cells. To address this question, we focus on the mechanical role of the essential load-bearing protein Hec1 [8–11]. Hec1’s affinity for microtubules is regulated by Aurora B phosphorylation on its N-terminal tail [12–15], but its role at the passive and active interfaces remains unclear. Here, we use laser ablation to trigger cellular pulling on mutant kinetochores and decouple sistersin vivo, and thereby separately probe Hec1’s role as it moves on polymerizing versus depolymerizing microtubules. We show that Hec1 phosphorylation tunes passive friction along polymerizing microtubules, modulating both the magnitude and timescale of responses to force. In contrast, we find that Hec1 phosphorylation does not affect the kinetochore’s ability to grip depolymerizing microtubules, or switch to this active force-generating state. Together, the data suggest that different kinetochore interfaces engage with growing and shrinking microtubules, and that passive friction can be regulated without disrupting active force generation. Through this mechanism, the kinetochore can modulate its grip on microtubules as its functional needs change during mitosis, and yet retain its ability to couple to microtubules powering chromosome movement.
Prediction of Molecular Mechanisms of Breast Cancer Metastasis
Authors: Siwo Geoffrey H. , Stolovitzky Gustavo A. , Assefa Solomon
Published: February 2017

Metastasis -the spread of cancer to other parts of the body- causes 90% of cancer deaths, underlies major health complications in cancer patients and renders most cancers incurable. Unfortunately, the molecular mechanisms underlying the process are poorly understood and therapeutics to block it remain elusive. Here, we present a computational technique for scanning genome-scale regulatory networks for potential genes associated with metastasis. First, we demonstrate that in the breast cancer cell line MCF7, the commonly dysregulated cancer biomarkers TP53, ERBB2, ESR1 and PGR are closely connected to known metastasis genes with a significant proportion being 2nddegree neighbors of a given biomarker. Next, we identify genes whose 2nddegree neighbors are connected in a similar manner to these biomarkers. Consequently, these are referred to as metastasis associated genes or MAGs. We identify 190 genes that are TP53-MAGs, 22 ERBB2-MAGs, 240 ESR1-MAGs and 84 PGR-MAGs (FDR adjustedP<0.001). Analysis of the MAGs reveals statistically significant enrichment with biological functions previously associated with metastasis including the extracellular matrix (ECM) receptor interaction, focal adhesion, cytokine-cytokine receptor interaction and chemokine signaling. The biological significance of MAGs is further supported by their enrichment with experimentally validated binding sites for transcription factors that regulate metastasis, for example BACH1- a master regulator of breast cancer metastasis to bone. The predicted MAGs are also clinically relevant as therapeutic targets for metastasis blocking agents. Specifically, genes that are perturbed by drugs and miRNAs that influence metastasis are enriched with MAGs. Furthermore, some MAGs are associated with patient survival and provide insights into the proclivity for breast cancer subtypes to preferentially spread to specific organs. The results of this study imply that aberrations in primary tumors may constrict metastasis trajectories. This could enable the prediction of organ specific metastases based on aberrations in the primary tumor and lay a foundation for future studies on individualized or personalized models of metastasis. The approach is potentially scalable across other cancers and has clinical implications.
Holotomography: refractive index as an intrinsic imaging contrast for 3-D label-free live cell imaging
Authors: Kim Doyeon , Lee SangYun , Lee Moosung , Oh JunTaek , Yang Su-A , Park YongKeun
Published: February 2017

Live cell imaging provides essential information in the investigation of cell biology and related pathophysiology. Refractive index (RI) can serve as intrinsic optical imaging contrast for 3-D label-free and quantitative live cell imaging, and provide invaluable information to understand various dynamics of cells and tissues for the study of numerous fields. Recently significant advances have been made in imaging methods and analysis approaches utilizing RI, which are now being transferred to biological and medical research fields, providing novel approaches to investigate the pathophysiology of cells. To provide insight how RI can be used as an imaging contrast for imaging of biological specimens, here we provide the basic principle of RI-based imaging techniques and summarize recent progress on applications, ranging from microbiology, hematology, infectious diseases, hematology, and histopathology.
Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromosome conformation capture data
Authors: Jiao Wen-Biao , Accinelli Gonzalo Garcia , Hartwig Benjamin , Kiefer Christiane , Baker David , Severing Edouard , Willing Eva-Maria , Piednoel Mathieu , Woetzel Stefan , Madrid-Herrero Eva , Huettel Bruno , Hümann Ulrike , Reinhard Richard , Koch Marcus A. , Swan Daniel , Clavijo Bernardo , Coupland George , Schneeberger Korbinian
Published: February 2017

Long-read sequencing can overcome the weaknesses of short reads in the assembly of eukaryotic genomes; however, at present additional scaffolding is needed to achieve chromosome-level assemblies. We generated Pacific Biosciences (PacBio) long-read data of the genomes of three relatives of the model plant Arabidopsis thaliana and assembled all three genomes into only a few hundred contigs. To improve the contiguities of these assemblies, we generated BioNano Genomics optical mapping and Dovetail Genomics chromosome conformation capture data for genome scaffolding. Despite their technical differences, optical mapping and chromosome conformation capture performed similarly and doubled N50 values. After improving both integration methods, assembly contiguity reached chromosome-arm-levels. We rigorously assessed the quality of contigs and scaffolds using Illumina mate-pair libraries and genetic map information. This showed that PacBio assemblies have high sequence accuracy but can contain several misassemblies, which join unlinked regions of the genome. Most, but not all, of these misjoints were removed during the integration of the optical mapping and chromosome conformation capture data. Even though none of the centromeres were fully assembled, the scaffolds revealed large parts of some centromeric regions, even including some of the heterochromatic regions, which are not present in gold standard reference sequences.
Microbial strain-level population structure and genetic diversity from metagenomes
Authors: Truong Duy Tin , Tett Adrian , Pasolli Edoardo , Huttenhower Curtis , Segata Nicola
Published: February 2017

Among the human health conditions linked to microbial communities, phenotypes are often associated with only a subset of strains within causal microbial groups. Although it has been critical for decades in microbial physiology to characterize individual strains, this has been challenging when using culture-independent high-throughput metagenomics. We introduce StrainPhlAn, a novel metagenomic strain identification approach, and apply it to characterize the genetic structure of thousands of strains from more than 125 species in more than 1500 gut metagenomes drawn from populations spanning North and South American, European, Asian, and African countries. The method relies on per-sample dominant sequence variant reconstruction within species-specific marker genes. It identified primarily subject-specific strain variants (<5% inter-subject strain sharing), and we determined that a single strain typically dominated each species and was retained over time (for >70% of species). Microbial population structure was correlated in several distinct ways with the geographic structure of the host population. In some cases, discrete subspecies (e.g., for Eubacterium rectale and Prevotella copri) or continuous microbial genetic variations (e.g., for Faecalibacterium prausnitzii) were associated with geographically distinct human populations, whereas few strains occurred in multiple unrelated cohorts. We further estimated the genetic variability of gut microbes, with Bacteroides species appearing remarkably consistent (0.45% median number of nucleotide variants between strains), whereas P. copri was among the most plastic gut colonizers. We thus characterize here the population genetics of previously inaccessible intestinal microbes, providing a comprehensive strain-level genetic overview of the gut microbial diversity.
Detached eddy simulations for high speed axial flow fuel pumps with swept and straight blade impellers
Authors: Tao Ran , Xiao Ruofu , Wang Fujun
Published: February 2017

Purpose

High speed axial flow pumps are widely used in aircraft fuel systems. Conventional axial flow pumps often generate radial secondary flows at partial-load conditions which influence the flow structure and form a “saddle-shaped” region in the Q-H curve that can destabilize the operation. Thus, the “saddle-shaped” Q-H region must be eliminated. The paper aims to discuss these issues.

Design/methodology/approach

The swept stacking method is often used for radial flow control in turbo-machinery impeller blade design. Hence, this study uses the swept stacking method to design a high speed axial flow pump. The detached eddy simulation method and experiments are used to compare the performance of a swept blade impeller in a high speed axial fuel pump with the original straight blade impeller. Both the pump performance and internal flow characteristics are studied.

Findings

The results show separation vortices in the impeller with the straight blade design at partial-load conditions that are driven by the rotating centrifugal force to gather near the shroud. The swept geometry provides an extra force which is opposite to the rotating centrifugal force that creates a new radial equilibrium which turns the flow back towards the middle of the blade which eliminates the vortices and the “saddle-shaped” Q-H region. The swept blade impeller also improves the critical cavitation performance. Analysis of the pressure pulsations shows that the swept blade design does not affect the stability.

Originality/value

This study is the initial application of swept blades for axial flow liquid pumps. The results show how the swept stacking changes the radial equilibrium of the high density, high viscosity flow and the effects on the mass transfer and pressure pulsations. The swept blade effectively improves the operating stability of high speed fuel pumps.
Do non-staggered board elections matter to earnings quality and the value relevance of earnings and book value?
Authors: Chiang Shuling , Kleinman Gary , Lee Picheng
Published: February 2017

Purpose

The purpose of this paper is to examine the impact of non-staggered voting for members of the board of directors on earnings quality and the value relevance of earnings and book value.

Design/methodology/approach

The authors used a sample of Taiwanese firms whose board was elected as a whole every three years from 2003 to 2013. The authors used multiple regression analysis to test whether board of directors elections and corporate governance affected earnings quality and the value relevance of earnings and book value.

Findings

The authors found that elections led to lower earnings quality, but better corporate governance led to greater earnings quality. In the presence of board elections, earnings have reduced value relevance but book value had increased value relevance. Finally, given board elections, the relative value relevance of earnings and book value on stock price was not fully moderated by strong corporate governance.

Research limitations/implications

The results presented here indicate the importance of better corporate governance in diffusing suspicions of management occasioned by the use of discretionary accruals in years in which board elections take place. Better corporate governance regimes led to a more positive relationship of discretionary accruals to earnings persistence, even in the presence of directorial elections. Similarly, better corporate governance regimes led to a more positive relationship between earnings per share and stock prices. Limitations include the restriction of the testing locale to Taiwan. That said, many companies around the globe use non-staggered board elections. Accordingly, these results suggest issues of importance to corporate governance advocates beyond Taiwan as well.

Originality/value

This study deepens the field’s understanding of the impact of corporate governance arrangements and schedules for electing board of directors’ members on issues of interest to stockholders.
The Optimization of Electrophoresis on a Glass Microfluidic Chip and its Application in Forensic Science
Authors: Han Jun P. , Sun Jing , Wang Le , Liu Peng , Zhuang Bin , Zhao Lei , Liu Yao , Li Cai X.
Published: February 2017

Microfluidic chips offer significant speed, cost, and sensitivity advantages, but numerous parameters must be optimized to provide microchip electrophoresis detection. Experiments were conducted to study the factors, including sieving matrices (the concentration and type), surface modification, analysis temperature, and electric field strengths, which all impact the effectiveness of microchip electrophoresis detection of DNA samples. Our results showed that the best resolution for ssDNA was observed using 4.5% w/v (7 M urea) lab‐fabricated LPA gel, dynamic wall coating of the microchannel, electrophoresis temperatures between 55 and 60°C, and electrical fields between 350 and 450 V/cm on the microchip‐based capillary electrophoresis (μCE) system. One base‐pair resolution could be achieved in the 19‐cm‐length microchannel. Furthermore, both 9947A standard genomic DNA and DNA extracted from blood spots were demonstrated to be successfully separated with well‐resolved DNA peaks in 8 min. Therefore, the microchip electrophoresis system demonstrated good potential for rapid forensic DNA analysis.
A rapid method for selecting suitable animal species for studying pathogen interactions with plasma protein ligands in vivo
Authors: Naudin Clément , Schumski Ariane , Salo‐Ahen Outi M. H. , Herwald Heiko , Smeds Emanuel
Published: February 2017

Species tropism constitutes a serious problem for developing relevant animal models of infection. Human pathogens can express virulence factors that show specific selectivity to human proteins, while their affinity for orthologs from other species can vary significantly. Suitable animal species must be used to analyse whether virulence factors are potential targets for drug development. We developed an assay that rapidly predicts applicable animal species for studying virulence factors binding plasma proteins. We used two well‐characterized Staphylococcus aureus proteins, SSL7 and Efb, to develop an ELISA‐based inhibition assay using plasma from different animal species. The interaction between SSL7 and human C5 and the binding of Efb to human fibrinogen and human C3 was studied. Affinity experiments and Western blot analyses were used to validate the assay. Human, monkey and cat plasma interfered with binding of SSL7 to human C5. Binding of Efb to human fibrinogen was blocked in human, monkey, gerbil and pig plasma, while human, monkey, gerbil, rabbit, cat and guinea pig plasma inhibited the binding of Efb to human C3. These results emphasize the importance of choosing correct animal models, and thus, our approach is a rapid and cost‐effective method that can be used to prevent unnecessary animal experiments.
Revealing the Diversity of Natural Hydrologic Regimes in California with Relevance for Environmental Flows Applications
Authors: Lane Belize A. , Dahlke Helen E. , Pasternack Gregory B. , Sandoval‐Solis Samuel
Published: February 2017

Alterations to flow regimes for water management objectives have degraded river ecosystems worldwide. These alterations are particularly profound in Mediterranean climate regions such as California with strong climatic variability and riverine species highly adapted to the resulting flooding and drought disturbances. However, defining environmental flow targets for Mediterranean rivers is complicated by extreme hydrologic variability and often intensive water management legacies. Improved understanding of the diversity of natural streamflow patterns and their spatial arrangement across Mediterranean regions is needed to support the future development of effective flow targets at appropriate scales for management applications with minimal resource and data requirements. Our study addresses this need through the development of a spatially explicit reach‐scale hydrologic classification for California. Dominant hydrologic regimes and their physio‐climatic controls are revealed, using available unimpaired and naturalized streamflow time‐series and generally publicly available geospatial datasets. This methodology identifies eight natural flow classes representing distinct flow sources, hydrologic characteristics, and catchment controls over rainfall‐runoff response. The study provides a broad‐scale hydrologic framework upon which flow‐ecology relationships could subsequently be established towards reach‐scale environmental flows applications in a complex, highly altered Mediterranean region.
Prices and heterogeneous search costs
Authors: Moraga‐González José Luis , Sándor Zsolt , Wildenbeest Matthijs R.
Published: February 2017

We study price formation in a model of consumer search for differentiated products in which consumers have heterogeneous search costs. We provide conditions under which a pure‐strategy symmetric Nash equilibrium exists and is unique. Search costs affect two margins—the intensive search margin (or search intensity) and the extensive search margin (or the decision to search rather than to not search at all). These two margins affect the elasticity of demand in opposite directions and whether lower search costs result in higher or lower prices depends on the properties of the search cost density.
Cannabis use and symptom severity in individuals at ultra high risk for psychosis: a meta‐analysis
Authors: Carney R. , Cotter J. , Firth J. , Bradshaw T. , Yung A. R.
Published: February 2017

Objective

We aimed to assess whether individuals at ultra high risk (UHR) for psychosis have higher rates of cannabis use and cannabis use disorders (CUDs) than non‐UHR individuals and determine whether UHR cannabis users have more severe psychotic experiences than non‐users.

Method

We conducted a meta‐analysis of studies reporting cannabis use in the UHR group and/or positive or negative symptoms among UHR cannabis users and non‐users. Logit event rates were calculated for cannabis use, in addition to odds ratios to assess the difference between UHR and controls. Severity of clinical symptoms in UHR cannabis users and non‐users was compared using Hedges’ g.

Results

Thirty unique studies were included (UHR n = 4205, controls n = 667) containing data from cross‐sectional and longitudinal studies, and randomised control trials. UHR individuals have high rates of current (26.7%) and lifetime (52.8%) cannabis use, and CUDs (12.8%). Lifetime use and CUDs were significantly higher than controls (lifetime OR: 2.09; CUD OR: 5.49). UHR cannabis users had higher rates of unusual thought content and suspiciousness than non‐users.

Conclusion

Ultra high risk individuals have high rates of cannabis use and CUDs, and cannabis users had more severe positive symptoms. Targeting substance use during the UHR phase may have significant benefits to an individual's long‐term outcome.
Regulatory T cells and type 2 innate lymphoid cell‐dependent asthma
Authors: Aron J. L. , Akbari O.
Published: February 2017

Group 2 innate lymphoid cells (ILC2s) are a recently identified group of cells with the potent capability to produce Th2‐type cytokines such as interleukin (IL)‐5 and IL‐13. Several studies suggest that ILC2s play an important role in the development of allergic diseases and asthma. Activation of pulmonary ILC2s in murine models lacking T and B cells induces eosinophilia and airway hyper‐reactivity (AHR), which are cardinal features of asthma. More importantly, numerous recent studies have highlighted the role of ILC2s in asthma persistence and exacerbation among human subjects, and thus, regulation of pulmonary ILC2s is a major area of investigation aimed at curbing allergic lung inflammation and exacerbation. Emerging evidence reveals that a group of regulatory T cells, induced Tregs (iTregs), effectively suppress the production of ILC2‐driven, pro‐inflammatory cytokines IL‐5 and IL‐13. The inhibitory effects of iTregs are blocked by preventing direct cellular contact or by inhibiting the ICOS‐ICOS‐ligand (ICOSL) pathway, suggesting that both direct contact and ICOS‐ICOSL interaction are important in the regulation of ILC2 function. Also, cytokines such as IL‐10 and TGF‐β1 significantly reduce cytokine secretion by ILC2s. Altogether, these new findings uncover iTregs as potent regulators of ILC2 activation and implicate their utility as a therapeutic approach for the treatment of ILC2‐mediated allergic asthma and respiratory disease.
Physical activity outside of organised sports is associated with functional performance
Authors: Tocci Noah , Howell David R. , Sugimoto Dai , Stracciolini Andrea , Morse Jen , Meehan William P.
Published: February 2017

Aim

The purpose of this study was to determine whether high levels of strenuous physical activity outside of organised sports are associated with better functional test performance.

Methods

Youth athletes (n = 445, mean = 14.2 ± 2.5 years) reported their frequency of strenuous physical activity outside of organised sports. The functional performance tests: vertical jump height, pro agility test time, estimated maximal oxygen uptake (VO2 max), front plank time and postural stability were measured and compared between groups.

Results

Athletes in the five or more times a week group demonstrated faster pro agility times (5.37 ± 0.43 seconds) than the never group (5.59 ± 0.56 seconds; p = 0.002) and the 1–4 times a week group (5.52 ± 0.47 seconds; p = 0.005). The five or more times a week group demonstrated higher mean vertical jump height (42.9 ± 13.3 vs. 40.3 ± 10.8 cm; p = 0.009) and higher estimated VO2 max (48.1 vs. 45.6 mL/kg/minute; p = 0.001) than the 1–4 times a week group.

Conclusion

Youth athletes who engaged in strenuous physical activity outside of organised sports five or more times a week performed best on functional performance tests.
Cerebral amyloidoma is characterized by B‐cell clonality and a stable clinical course
Authors: Heß Katharina , Purrucker Jan , Hegenbart Ute , Brokinkel Benjamin , Berndt Rouven , Keyvani Kathy , Monoranu Camelia M. , Löhr Mario , Reifenberger Guido , Munoz‐Bendix Christopher , Kalla Jörg , Groß Justus , Schick Uta , Kollmer Jennifer , Klapper Wolfram , Röcken Christoph , Hasselblatt Martin , Paulus Werner
Published: February 2017

Amyloidomas are rare amyloid‐containing lesions, which may also occur in the central nervous system. Etiology, pathogenesis and clinical course are poorly understood. To gain more insight into the biology of cerebral amyloidoma, they aimed to characterize its histopathological, molecular and clinical features in a retrospective series of seven patients. FFPE tissue specimens were examined using immunohistochemistry, chromogenic in situ hybridization (CISH) for light chains kappa and lambda as well as an IgH gene clonality analysis. Follow‐up information was gathered by reviewing patient records and imaging results. Median age of the three males and four females was 50 years (range: 35–53 years). All cerebral amyloidomas were located supratentorially and were classified as lambda light chain amyloidosis (AL‐λ; n = 6) and kappa light chain amyloidosis (AL‐κ; n = 1) on immunohistochemistry and CISH. B‐cell clonality was confirmed by IgH gene clonality assay in all cases examined. After a median follow‐up of 21 months, all patients were alive and showed stable disease. No progression to systemic disease was observed. In conclusion, their data suggest that cerebral amyloidoma is a local disease characterized by B‐cell clonality and associated with a stable clinical course.
Age of Bilingual Exposure Is Related to the Contribution of Phonological and Semantic Knowledge to Successful Reading Development
Authors: Jasińska Kaja K. , Petitto Laura‐Ann
Published: February 2017

Bilingual children's reading as a function of age of first bilingual language exposure (AoE) was examined. Bilingual (varied AoE) and monolingual children (N = 421) were compared in their English language and reading abilities (6–10 years) using phonological awareness, semantic knowledge, and reading tasks. Structural equation modeling was applied to determine how bilingual AoE predicts reading outcomes. Early exposed bilinguals outperformed monolinguals on phonological awareness and word reading. Phonology and semantic (vocabulary) knowledge differentially predicted reading depending on the bilingual experience and AoE. Understanding how bilingual experiences impact phonological awareness and semantic knowledge, and in turn, impact reading outcomes is relevant for our understanding of what language and reading skills are best to focus on, and when, to promote optimal reading success.