bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proximity-dependent proteomics of theChlamydia trachomatisinclusion membrane reveals functional interactions with endoplasmic reticulum exit sites
Authors: Dickinson Mary S. , Anderson Lindsey N. , Webb-Robertson Bobbie-Jo M. , Hansen Joshua R. , Smith Richard D. , Wright Aaron T. , Hybiske Kevin 
Published: March 2018

AbstractChlamydia trachomatisis the most common bacterial sexually transmitted infection, responsible for millions of infections each year. Despite this high prevalence, the elucidation of the molecular mechanisms ofChlamydiapathogenesis has been difficult due to limitations in genetic tools and its intracellular developmental cycle. Within a host epithelial cell, chlamydiae replicate within a vacuole called the inclusion. ManyChlamydia–host interactions are thought to be mediated by the Inc family of type III secreted proteins that are anchored in the inclusion membrane, but their array of host targets are largely unknown. To investigate how the inclusion membrane proteome changes over the course of an infected cell, we have adapted the APEX system of proximity-dependent biotinylation. APEX is capable of specifically labeling proteins within a 20 nm radius in living cells. We transformedC. trachomatisto express the enzyme APEX fused to known inclusion membrane proteins, allowing biotinylation and pull-down of inclusion-associated proteins. Using quantitative mass spectrometry against APEX labeled samples, we identified over 400 proteins associated with the inclusion membrane at early, middle, and late stages of epithelial cell infection. This system was sensitive enough to detect inclusion interacting proteins early in the developmental cycle, at 8 hours post infection, a previously intractable time point. Mass spectrometry analysis revealed a novel, early association betweenC. trachomatisinclusions and endoplasmic reticulum exit sites (ERES), functional regions of the ER where COPII-coated vesicles originate. Pharmacological and genetic disruption of ERES function severely restricted early chlamydial growth and the development of infectious progeny. APEX is therefore a powerful in situ approach for identifying critical protein interactions on the membranes of pathogen-containing vacuoles. Furthermore, the data derived from proteomic mapping ofChlamydiainclusions has illuminated an important functional role for ERES in promoting chlamydial developmental growth.
Structural transition and antibody binding of Ebola GP and Zika E proteins from pre-fusion to fusion-initiation states
Authors: Lappala-Vernon A , Nishima W , Miner J C , Fenimore P W , Fischer W , Hraber P T , Zhang M , McMahon B H , Tung C-S 
Published: March 2018

AbstractMembrane fusion proteins are responsible for viral entry into host cells– a crucial first step in viral infection. These proteins undergo large conformational changes from pre-fusion to fusion initiation structures, and, despite differences in viral genomes and disease etiology, many fusion proteins are arranged as trimers. Structural information for both pre-fusion and fusion initiation states is critical for understanding virus neutralization by the host immune system. In the case of Ebola glycoprotein (GP) and Zika envelope protein (Zika E), pre-fusion state structures have been identified experimentally, but only partial structures of fusion initiation states have been described. While the fusion initiation structure is in an energetically unfavorable state that is difficult to solve experimentally, the existing structural information combined with computational approaches enabled the modeling of fusion initiation state structures of both proteins. These structural models provide an improved understanding of four different neutralizing antibodies in the prevention of viral host entry.
Eco-evolutionary community turnover following environmental change
Authors: Lasky Jesse R. 
Published: March 2018

AbstractCo-occurring species often differ in intraspecific genetic diversity, which in turn can affect adaptation in response to environmental change. Specifically, the simultaneous evolutionary responses of co-occurring species to temporal environmental change may influence community dynamics. Local adaptation along environmental gradients combined with gene flow can promote genetic diversity of traits under selection within populations. Here I build off existing quantitative genetic theory to study community dynamics of locally adapted species in response to temporal environmental change. I show that species with greater gene flow have lower equilibrium population size due to maladaptive immigrant genotypes (migration load). However, following abrupt environmental change that leaves all species initially maladapted, high gene flow species adapt faster due to greater standing genetic diversity. As a result, communities may undergo a transient reversal in relative abundance, sometimes only after substantial lag periods. If constant temporal environmental change is applied, the community exhibits a shift toward stable dominance by species with intermediate gene flow. High gene flow species can sometimes increase abundance under environmental change if environmental change supresses superior competitor but lower gene flow species. The community dynamics observed here parallel the purely ecological successional dynamics following disturbances and are analogous to the transient benefit of hypermutator alleles under changing environments. My results demonstrate how interspecific variation in life history can have far-reaching impacts on eco-evolutionary community response to environmental change.
Social intelligence model with multiple internal models
Authors: Isomura Takuya , Parr Thomas , Friston Karl 
Published: March 2018

AbstractTo exhibit social intelligence, animals have to recognize who they are communicating with. One way to make this inference is to select among multiple internal generative models of each conspecific. This induces an interesting problem: when receiving sensory input generated by a particular conspecific, how does an animal know which internal model to update? We consider a theoretical and neurobiologically plausible solution that enables inference and learning under multiple generative models by integrating active inference and (online) Bayesian model selection. This scheme fits sensory inputs under each generative model. Model parameters are then updated in proportion to the probability it could have generated the current input (i.e., model evidence). We show that a synthetic bird who employs the proposed scheme successfully learns and distinguishes (real zebra finch) birdsongs generated by several different birds. These results highlight the utility of having multiple internal models to make inferences in complicated social environments.
Lipid perturbation-activated IRE-1 modulates autophagy and lipolysis during endoplasmic reticulum stress
Authors: Koh Jhee Hong , Wang Lei , Beaudoin-Chabot Caroline , Thibault Guillaume 
Published: March 2018

ABSTRACTMetabolic disorders such as obesity and nonalcoholic fatty liver disease (NAFLD) are emerging diseases that affect the global population. One facet of these disorders is attributed to the disturbance of membrane lipid composition. Perturbation of endoplasmic reticulum (ER) homeostasis through changes in membrane phospholipid composition results in activation of the unfolded protein response (UPR) and causes dramatic translational and transcriptional changes in the cell. To restore cellular homeostasis, the three highly conserved UPR transducers ATF6, IRE1, and PERK mediate cellular processes upon ER stress. The role of the UPR in proteotoxic stress caused by the accumulation of misfolded proteins is well understood but much less so under lipid perturbation-induced UPR (UPRLP). We found that genetically disrupted phosphatidylcholine synthesis inC. eleganscauses, lipid perturbation, lipid droplet accumulation, and induced ER stress, all hallmarks of NAFLD. Transcriptional profiling of UPRLPanimals shows a unique subset of genes modulated in an UPR-dependent manner that is unaffected by proteotoxic stress (UPRPT). Among these, we identified autophagy genesbec-1andlgg-1and the lipid droplet-associated lipaseatgl-1to be modulated by IRE-1. Considering the important role of lipid homeostasis and how its impairment contributes to the pathology of metabolic diseases, our data uncovers the indispensable role of a fully functional UPR program in regulating lipid homeostasis in the face of chronic ER stress and lipotoxicity.
Open-pFind enables precise, comprehensive and rapid peptide identification in shotgun proteomics
Authors: Chi Hao , Liu Chao , Yang Hao , Zeng Wen-Feng , Wu Long , Zhou Wen-Jing , Niu Xiu-Nan , Ding Yue-He , Zhang Yao , Wang Rui-Min , Wang Zhao-Wei , Chen Zhen-Lin , Sun Rui-Xiang , Liu Tao , Tan Guang-Ming , Dong Meng-Qiu , Xu Ping , Zhang Pei-Heng , He Si-Min 
Published: March 2018

ABSTRACTShotgun proteomics has grown rapidly in recent decades, but a large fraction of tandem mass spectrometry (MS/MS) data in shotgun proteomics are not successfully identified. We have developed a novel database search algorithm, Open-pFind, to efficiently identify peptides even in an ultra-large search space which takes into account unexpected modifications, amino acid mutations, semi- or non-specific digestion and co-eluting peptides. Tested on two metabolically labeled MS/MS datasets, Open-pFind reported 50.5‒117.0% more peptide-spectrum matches (PSMs) than the seven other advanced algorithms. More importantly, the Open-pFind results were more credible judged by the verification experiments using stable isotopic labeling. Tested on four additional large-scale datasets, 70‒85% of the spectra were confidently identified, and high-quality spectra were nearly completely interpreted by Open-pFind. Further, Open-pFind was over 40 times faster than the other three open search algorithms and 2‒3 times faster than three restricted search algorithms. Re-analysis of an entire human proteome dataset consisting of ∼25 million spectra using Open-pFind identified a total of 14,064 proteins encoded by 12,723 genes by requiring at least two uniquely identified peptides. In this search results, Open-pFind also excelled in an independent test for false positives based on the presence or absence of olfactory receptors. Thus, a practical use of the open search strategy has been realized by Open-pFind for the truly global-scale proteomics experiments of today and in the future.
Prestimulus neural alpha power predicts confidence in discriminating identical tones
Authors: Wöstmann Malte , Waschke Leonhard , Obleser Jonas 
Published: March 2018

AbstractThere is growing evidence that the power of prestimulus neural alpha oscillations (∼10 Hz) holds information on a perceiver’s bias or confidence in an ensuing perceptual decision, rather than perceptual sensitivity per se. Obviously, however, confidence also depends on the physical evidence available in the stimulus as well as on task performance. If prestimulus alpha power has a direct impact on decision confidence, this link should hold independent of variations in stimulus evidence and performance. We tested this assertion in a paradigm where human listeners (n = 17) rated their confidence in the discrimination of the pitch of two identical tones. Lower prestimulus alpha power in the electroencephalogram (EEG) was predictive of higher confidence ratings, but not of the decision outcome (i.e., judging the first or the second tone as being higher in pitch). Importantly, the link between prestimulus alpha power and decision confidence was not mediated by auditory evoked activity. Our findings demonstrate that the link between prestimulus alpha power and decision confidence does not hinge on physical evidence in the stimulus or task performance. Instead, these results speak to a model wherein low prestimulus alpha power increases neural baseline excitability, which is reflected in enhanced stimulus-evoked neural responses and higher confidence.Significance statementIn order to understand the mechanistic relevance of neural oscillations for perception, we here relate these directly to changes in human auditory decision confidence. Human subjects rated their confidence in the discrimination of the pitch of two tones, which were, unbeknownst to the listener, physically identical. In the absence of changing evidence in the physical stimulus or changes in task performance, we demonstrate that prestimulus alpha power negatively relates to decision confidence. Our results support a model of cortical alpha oscillations as a proxy for neural baseline excitability in which lower prestimulus alpha power does not lead to more precise but rather to overall amplified neural representations.
Identifying the genetic basis of variation in cell behaviour in human iPS cell lines from healthy donors
Authors: Vigilante Alessandra , Laddach Anna , Moens Nathalie , Meleckyte Ruta , Leha Andreas , Ghahramani Arsham , Culley Oliver J. , Kathuria Annie , Hurling Chloe , Vickers Alice , Tewary Mukul , Zandstra Peter ,   HipSci Consortium, Durbin Richard , Fraternali Franca , Stegle Oliver , Birney Ewan , Luscombe Nicholas M. , Danovi Davide , Watt Fiona M. 
Published: March 2018

AbstractLarge cohorts of human iPSCs from healthy donors are potentially a powerful tool for investigating the relationship between genetic variants and cellular phenotypes. Here we integrate high content imaging, gene expression and DNA sequence datasets for over 100 human iPSC lines to identify the genetic basis of inter-individual variability in cell behaviour. By applying a dimensionality reduction approach, Probabilistic Estimation of Expression Residuals (PEER), we identified genes that correlated in expression with intrinsic (genetic) and extrinsic (ECM) factors. However, variation in mRNA levels could not account for outlier cell behaviour. Instead, we identified rare, deleterious SNVs in the coding sequence of genes involved in ECM adhesion that occurred in cell lines that were outliers for one or more phenotypes such as cell spreading. These also correlated with altered germ layer differentiation on micropatterned surfaces. Our study thus establishes a strategy for integrating genetic and cell biological measurements for high-throughput analysis.
Hierarchy, Morphology, and Adaptive Radiation: a Test of Osborn’s Law in the Carnivora
Authors: Slater Graham J. , Friscia Anthony R. 
Published: March 2018

AbstractHenry Fairfield Osborn’s law of adaptive radiation was intended to explain the early proliferation of morphological and functional variation in diversifying clades. Yet, despite much theoretical development and empirical testing, questions remain regarding the taxonomic levels at which adaptive radiation occurs, the traits involved, and its frequency across the tree of life. Here, we evaluate support for this “early burst” model of adaptive radiation in 14 ecomorphological traits plus body mass for the extant mammalian order Carnivora. Strong support for an early burst adaptive radiation is recovered for molar grinding area, a key proxy for diet. However, we find no evidence for early burst–like dynamics in body mass or multivariate trait data, suggesting a decoupling of evolutionary modes among traits driven by dietary specialization. Furthermore, the signal of an early burst is only recovered for Carnivora, and not in family–level clades. The lack of support for the early burst model of morphological adaptive radiation in previous phylogenetic studies may be a consequence of focusing on the wrong traits at the wrong taxonomic levels. Osborn’s law predicted that adaptive radiation should be hierarchically structured, and the search for its signature and understanding of its prevalence will require a renewed focus on functional traits and their evolution over higher-level clades.
Motivation trajectory of attending performing arts: the role of knowledge
Authors: Obaidalahe Zakia , Steils Nadia 
Published: March 2018

PurposeThis study concerns the attendance motivations for cultural services based on the audience’s level of knowledge. The purpose of this paper is to define the role played by general knowledge (e.g. cultural education) and specific knowledge (e.g. communication around a cultural product) in the attendance motivation trajectory of a cultural service.Design/methodology/approachThe study uses in-depth interviews with 20 visitors to two public theatres, one in Belgium and one in France.FindingsThe results identify a tripartite motivation in the decision to attend a performance, corresponding to four visitor segments defined according to their level of general and specific knowledge.Originality/valueThe recommendations arising from the study are that potential audience members be targeted according to their particular profile and that their cultural tastes be developed by raising their level of general knowledge, an element that goes beyond the suggested motivation trajectory.
Measuring compression caused by garments
Authors: Ellis Brett , Kirkpatrick Erin , Kothari Phan Sonal , Imler Stacy , Beckham Haskell 
Published: March 2018

PurposeStretch fabrics are employed to create compression in garments for medical, sports, and fitness applications. Although potential correlations between wearing compression garments and physiological or performance metrics have been studied, such correlations require knowledge of the actual compression caused by garments. The purpose of this paper is to demonstrate, compare, and contrast different methods for measuring compression delivered by an exemplar compression garment.Design/methodology/approachThe exemplar compression garment is a plain jersey knit maternity band. The compression delivered by this garment was determined via three different methods – Tekscan pressure mapping system, Hohenstein Measurement System (HOSY), and a fabric-based analytical model employing uniaxial fabric tensile data.FindingsHOSY and the fabric-based model, assuming a circular cross section for the garment, provided comparable results for compression versus garment height. However, these methods did not capture the varying compression delivered at different transverse locations when the subject was noncircular in cross section. Assuming an elliptical cross section, the fabric-based model predicted results that were comparable to those measured by the Tekscan system: for example, compressions were approximately 130-160 percent greater at the hip, and approximately 60-100 percent lower at the posterior, than HOSY revealed. Further, the Tekscan system allows the effect of movement on compression to be captured.Originality/valueThis paper compares and contrasts three compression measurement methods and demonstrates the importance of angular position and height dependencies. Further, the fabric-based model is presented as a tool to assist design of compression garments.
Assessing primary care data quality
Authors: Lim Yvonne Mei Fong , Yusof Maryati , Sivasampu Sheamini 
Published: March 2018

Purpose
The purpose of this paper is to assess National Medical Care Survey data quality.

Design/methodology/approach
Data completeness and representativeness were computed for all observations while other data quality measures were assessed using a 10 per cent sample from the National Medical Care Survey database; i.e., 12,569 primary care records from 189 public and private practices were included in the analysis.

Findings
Data field completion ranged from 69 to 100 per cent. Error rates for data transfer from paper to web-based application varied between 0.5 and 6.1 per cent. Error rates arising from diagnosis and clinical process coding were higher than medication coding. Data fields that involved free text entry were more prone to errors than those involving selection from menus. The authors found that completeness, accuracy, coding reliability and representativeness were generally good, while data timeliness needs to be improved.

Research limitations/implications
Only data entered into a web-based application were examined. Data omissions and errors in the original questionnaires were not covered.

Practical implications
Results from this study provided informative and practicable approaches to improve primary health care data completeness and accuracy especially in developing nations where resources are limited.

Originality/value
Primary care data quality studies in developing nations are limited. Understanding errors and missing data enables researchers and health service administrators to prevent quality-related problems in primary care data.
The different impact of personal social capital and intra-organizational SC
Authors: Ben-Hador Batia , Eckhaus Eyal 
Published: March 2018

PurposeThis study relates to two levels of organization social capital (SC): personal SC and intra-organizational SC. Personal SC is the utility derived from the person’s relationship, and his positioning in networks, inside and out of the organization. Intra-organizational SC is the benefit derived from interactions within, and between groups in the organization, and is based on trust, reciprocity, common goals, sharing information and knowledge. The purpose of this paper is to examine the difference between the SC levels by their connections to employee energy and success, before and after crisis.Design/methodology/approachIn order to test the hypotheses, the authors used the Enron e-mails corpus, the texts were analyzed using SQL.FindingsThe findings suggest that the impact of personal SC and intra-organizational SC, on employee energy and success is different. Personal SC was found to have a higher impact on those two variables, than intra-organizational SC. After crisis, this gap became larger.Originality/valueThe importance of the findings is in the distinction between the SC levels, and their different impact on the employees. However, the situation of Enron employees at that time implies that the more important level of SC is the intra-organizational SC.
Whither competition in Malaysia’s banking industry ex post a restructuring
Authors: Chung Tinfah , Mohd Ariff 
Published: March 2018

Purpose
The purpose of this paper is to report how banking competition has fared ex post a major consolidation exercise completed during 2002-2004, which led to a complete restructuring of the sector in Malaysia. Nothing is known about the competitiveness of banking system ex post a major consolidation of banks in any country including Malaysia, a middle-income economy.

Design/methodology/approach
The authors apply two models, the Panzar and Rosse (1997) and the Lerner index (1934). The two competitiveness measures are quite refined, well received by researchers, but has yet been applied to measure banking sector competitiveness of a middle-income country to characterize post-merger behavior using post-global-crisis data set. The data were complemented by documentary analysis, including brand documents, descriptions of internal processes and copies of employee magazine articles.

Findings
The results indicate that, after 11 years of consolidation, the banking sector is not operating under perfect or monopolistic competition. Malaysia’s banking industry continues to benefit the charter holders at increasingly lower level because a cartel-like environment still provides trade-off of competition costs before 2002/2004 with the costs from a cartel-like industry structures now. There is only a weak evidence that, in recent years, the banking sector is moving toward more competition.

Research limitations/implications
The chosen area of research is to test the response of the banking sector ex post consolidation after a crisis. It enables researcher to compare results with those of other countries and may not be generalizable.

Practical implications
The findings reported in this study using corroborating measures for the first time, appear to suggest increasing concentration from consolidation may lead to the undesirable cartel-like industry structure where the exercise of market power in the name of stability may not be welfare promoting.

Originality/value
This paper fulfills an identified need to study how the banking sector has performed ex post consolidation after a crisis.