bluuebunny/crossref_metadata_2025_split huggingface dataset:
Binding From both sides: TolR and full-length OmpA bind and maintain the local structure of the E. coli cell wall
Authors: Boags Alister T. , Samsudin Firdaus , Khalid Syma 
Published: September 2018

SUMMARYWe present a molecular modeling and simulation study of the of the E. coli cell envelope, with a particular focus on the role of TolR, a native protein of the E. coli inner membrane in interactions with the cell wall. TolR has been proposed to bind to peptidoglycan, but the only structure of this protein thus far is in a conformation in which the putative peptidoglycan binding domain is not accessible. We show that a model of the extended conformation of the protein in which this domain is exposed, binds peptidoglycan largely through electrostatic interactions. We show that non-covalent interactions of TolR and OmpA with the cell wall, from the inner membrane and outer membrane sides respectively, maintain the position of the cell wall even in the absence of Braun’s lipoprotein. When OmpA is truncated to remove the peptidoglycan binding domain, TolR is able to pull the cell wall down towards the inner membrane. The charged residues that mediate the cell-wall interactions of TolR in our simulations, are conserved across a number of species of Gram-negative bacteria.
Inferring high-dimensional pathways of trait acquisition in evolution and disease
Authors: Greenbury Sam F. , Barahona Mauricio , Johnston Iain G. 
Published: September 2018

AbstractThe explosion of data throughout the sciences provides unprecedented opportunities to learn about the dynamics of evolution and disease progression. Here, we describe a highly generalisable statistical platform to infer the dynamic pathways by which many, potentially interacting, discrete traits are acquired or lost over time in biological processes. The platform uses HyperTraPS (hypercubic transition path sampling) to learn progression pathways from cross-sectional, longitudinal, or phylogenetically-linked data with unprecedented efficiency, readily distinguishing multiple competing pathways, and identifying the most parsimonious mechanisms underlying given observations. Its Bayesian structure quantifies uncertainty in pathway structure and allows interpretable predictions of behaviours, such as which symptom a patient will acquire next. We exploit the model’s topology to provide visualisation tools for intuitive assessment of multiple, variable pathways. We apply the method to ovarian cancer progression and the evolution of multidrug resistance in tuberculosis, demonstrating its power to reveal previously undetected dynamic pathways.
MoMo: Discovery of statistically significant post-translational modification motifs
Authors: Cheng Alice , Grant Charles E. , Noble William S. , Bailey Timothy L. 
Published: September 2018

AbstractMotivationPost-translational modifications (PTMs) of proteins are associated with many significant biological functions and can be identified in high throughput using tandem mass spectrometry. Many PTMs are associated with short sequence patterns called “motifs” that help localize the modifying enzyme. Accordingly, many algorithms have been designed to identify these motifs from mass spectrometry data. Accurate statistical confidence estimates for discovered motifs are critically important for proper interpretation and in the design of downstream experimental validation.ResultsWe describe a method for assigning statistical confidence estimates to PTM motifs, and we demonstrate that this method provides accurate p-values on both simulated and real data. Our methods are implemented in MoMo, a software tool for discovering motifs among sets of PTMs that we make available as a web server and as downloadable source code. MoMo reimplements the two most widely used PTM motif discovery algorithms—motif-x and MoDL—while offering many enhancements. Relative to motif-x, MoMo offers improved statistical confidence estimates and more accurate calculation of motif scores. The MoMo web server offers more proteome databases, more input formats, larger inputs and longer running times than the motif-x web server. Finally, our study demonstrates that the confidence estimates produced by motif-x are inaccurate. This inaccuracy stems in part from the common practice of drawing “background” peptides from an unshuffled proteome database. Our results thus suggest that many of the hundreds of papers that use motif-x to find motifs may be reporting results that lack statistical support.Availabilityhttp://meme-suite.orgContacttimothybailey@unr.edu
Generality and opponency of rostromedial tegmental (RMTg) roles in valence processing
Authors: Li Hao , Pullmann Dominika , Cho Jennifer Y. , Eid Maya , Jhou Thomas C. 
Published: September 2018

SummaryThe rostromedial tegmental nucleus (RMTg), a GABAergic afferent to midbrain dopamine (DA) neurons, has been hypothesized to encode aversive stimuli. However, this encoding pattern has only been demonstrated for a limited number of stimuli, and its influence on the ventral tegmental (VTA) responses to aversive stimuli is untested. Here, we found that RMTg neurons show average inhibitions to rewarding stimuli and excitations to aversive stimuli of greatly varying sensory modalities and timescales. Notably, negative valence-encoding neurons are particularly enriched in subpopulations projecting to the VTA versus other targets. Additionally, RMTg neurons also dynamically encode “opponent” changes in motivational states induced by removal of sustained stimuli. Finally, excitotoxic RMTg lesions impair conditioned place aversion to multiple aversive stimuli, and greatly reduce aversive stimulus-induced inhibitions in VTA neurons, particularly in putative DA-like neurons. Together, our findings indicate a broad RMTg role in encoding aversion and potentially driving DA responses and behavior.
Evolutionary branching of host resistance induced by density-dependent mortality
Authors: Zu Jian , Fu Shuting , Li Miaolei , Gu Yuexi 
Published: September 2018

AbstractThis study explores the evolutionary dynamics of host resistance in a susceptible-infected model with density-dependent mortality. We assume that the resistant ability of susceptible host will adaptively evolve, a different type of host differs in its susceptibility to infection, but the resistance to a pathogen involves a cost such that a less susceptible host results in a lower birth rate. By using the methods of adaptive dynamics and critical function analysis, we find that the evolutionary outcome relies mainly on the trade-off relationship between host resistance and its fertility. Firstly, we show that if the trade-off curve is globally con-cave, then a continuously stable strategy is predicted. In contrast, if the trade-off curve is weakly convex in the vicinity of singular strategy, then the evolutionary branching of host resistance is possible. Moreover, the bifurcation analysis shows that independent of the trade-off curve, the values of continuously stable strategy and evolutionary branching point will always increase as the demographic parameters increase. Secondly, after evolutionary branching in the host resistance has occurred, we examine the coevolutionary dynamics of the dimorphic host population and find that for a type of concave-convex-concave trade-off curve, the final evolutionary outcome may contain a relatively higher susceptible host and a relatively higher resistant host, which can continuously stably coexist on a long-term evo-lutionary timescale. Numerical simulation further shows that eventually the equilibrium population densities of the dimorphic susceptible host might be very close to each other. Finally, we find that for a type of sigmoidal trade-off curve, due to the high cost in terms of the birth rate, always the branch with higher resistance will go extinct, the eventual evolutionary outcome includes a monomorphic host with relatively lower resistance. Particularly, in this case we find that the evolution of costly host resistance may reduce the equilibrium population density of susceptible host, instead it may increase the equilibrium population density of infected host.
Efficient curation of genebanks using next generation sequencing reveals substantial duplication of germplasm accessions
Authors: Singh Narinder , Wu Shuangye , Raupp W. John , Sehgal Sunish , Arora Sanu , Tiwari Vijay , Vikram Prashant , Singh Sukhwinder , Chhuneja Parveen , Gill Bikram S. , Poland Jesse 
Published: September 2018

ABSTRACTGenebanks are valuable resources for crop improvement through the acquisition, ex-situ conservation and sharing of unique germplasm among plant breeders and geneticists. With over seven million existing accessions and increasing storage demands and costs, genebanks need efficient characterization and curation to make them more accessible and usable and to reduce operating costs, so that the crop improvement community can most effectively leverage this vast resource of untapped novel genetic diversity. However, the sharing and inconsistent documentation of germplasm often results in unintentionally duplicated collections with poor characterization and many identical accessions that can be hard or impossible to identify without passport information and unmatched accession identifiers. Here we demonstrate the use of genotypic information from these accessions using a cost-effective next generation sequencing platform to find and remove duplications. We identify and characterize over 50% duplicated accessions both within and across genebank collections of Aegilops tauschii, an important wild relative of wheat and source of genetic diversity for wheat improvement. We present a pipeline to identify and remove identical accessions within and among genebanks and curate globally unique accessions. We also show how this approach can also be applied to future collection efforts to avoid the accumulation of identical material. When coordinated across global genebanks, this approach will ultimately allow for cost effective and efficient management of germplasm and better stewarding of these valuable resources.
Dystroglycan is a scaffold for extracellular axon guidance decisions
Authors: Lindenmaier L. Bailey , Parmentier Nicolas , Guo Caying , Tissir Fadel , Wright Kevin M 
Published: September 2018

SummaryAxon guidance requires interactions between extracellular signaling molecules and transmembrane receptors, but how appropriate context-dependent decisions are coordinated outside the cell remains unclear. Here we show that the transmembrane glycoprotein Dystroglycan interacts with a changing set of environmental cues that regulate the trajectories of extending axons throughout the brain and spinal cord. Dystroglycan operates primarily as an extracellular scaffold during axon guidance, as it functions non-cell autonomously and does not require signaling through its intracellular domain. We identify the transmembrane receptor Celsr3/Adgrc3 as a binding partner for Dystroglycan, and show that this interaction is critical for specific axon guidance events in vivo. These findings establish Dystroglycan as a multifunctional scaffold that coordinates extracellular matrix proteins, secreted cues, and transmembrane receptors to regulate axon guidance.
Critical success factors in the management of ideas as an essential component of innovation and business excellence
Authors: Santos Gilberto , Afonseca José , Lopes Nuno , Félix Maria João , Murmura Federica 
Published: September 2018

Purpose
This research aims to focus on the idea management system (IMS) with the main purpose of identifying and describing the factors that promote success in managing ideas, grounded on the analysis of case studies.

Design/methodology/approach
The method used consists of a case study and semi-structured interviews with those directly responsible for the management of ideas from four companies, which are presented in this paper.

Findings
The main findings, critical for the success of an IMS, are as follow: the involvement of top management, evidence of results, establishment of goals and objectives, dissemination of good results, willingness to share and develop ideas, complete transparency in the management of ideas, maintenance of dynamic and proactive attitudes and mainly recognition. All have been described.

Research limitations/implications
This work presents a preliminary framework for further research toward the study of CSFs inherent to IMSs that is still bound by the limited number of case studies presented. Further research should be undertaken to broaden and consolidate the presented CFSs and their pertinence.

Originality/value
This study, although limited to four case studies, presents conclusive results that support managers of suggestion systems/IMSs in improving or deploying such systems. The main factors were identified and described. They can contribute to the effectiveness of employee suggestion system. It can be reasoned from this investigation that the contributions from employees toward the success of a company leads to excellence in business.
The right to be included
Authors: Dali Keren 
Published: September 2018

PurposeIn the spirit of the growing Time is Up movement in North America, this paper aims to focus on the human dimension of academic learning environments and delves into the reasons for the continuous oppression, discrimination and bullying (ODB) of faculty members with disabilities in academia, showing the particularly detrimental effect of ODB in the small professionally oriented field of information science.Design/methodology/approachThe conceptualizing of continuous ODB of people with disabilities in academia is done by carefully scrutinizing the state of affairs; presenting a nuanced survey of utilized terminology; providing a new and inclusive definition of everyday oppression; introducing a new model of an oppressive workplace environment experienced by people with disabilities; showing the centrality of information behaviours and phenomena in ODB; highlighting the high relevance of this discussion to learning science; and outlining potential detrimental effects of ODB on the psychological climate in and the process of professional higher education.FindingsThe model of an oppressive workplace environment experienced by people with disabilities is presented.Originality/valueUnlike previous models of ODB at the workplace, the current model puts information phenomena as decisive factors in continuous ODB against people with disabilities; particular attention is paid to information avoidance behaviours; distorted or delayed information messages transmitted by managers to employees; gossip as an informal information-based tactic of ODB; the insufficient protection of privacy and confidentiality of information about disabilities and personal health; and vague information messages that diminish the usefulness of university policies on disabilities.
Finding eWOM customers from customer reviews
Authors: Zhao Pengfei , Wu Ji , Hua Zhongsheng , Fang Shijian 
Published: September 2018

PurposeThe purpose of this paper is to identify electronic word-of-mouth (eWOM) customers from customer reviews. Thus, firms can precisely leverage eWOM customers to increase their product sales.Design/methodology/approachThis research proposed a framework to analyze the content of consumer-generated product reviews. Specific algorithms were used to identify potential eWOM reviewers, and then an evaluation method was used to validate the relationship between product sales and the eWOM reviewers identified by the authors’ proposed method.FindingsThe results corroborate that online product reviews that are made by the eWOM customers identified by the authors’ proposed method are more related to product sales than customer reviews that are made by non-eWOM customers and that the predictive power of the reviews generated by eWOM customers are significantly higher than the reviews generated by non-eWOM customers.Research limitations/implicationsThe proposed method is useful in the data set, which is based on one type of products. However, for other products, the validity must be tested. Previous eWOM customers may have no significant influence on product sales in the future. Therefore, the proposed method should be tested in the new market environment.Practical implicationsBy combining the method with the previous customer segmentation method, a new framework of customer segmentation is proposed to help firms understand customers’ value specifically.Originality/valueThis study is the first to identify eWOM customers from online reviews and to evaluate the relationship between reviewers and product sales.
Procurement risk management under uncertainty: a review
Authors: Hong Zhen , Lee C.K.M. , Zhang Linda 
Published: September 2018

PurposeThe purpose of this paper is twofold, first providing researchers with an overview about the uncertainties occurred in procurement including applicable approaches for analyzing different uncertain scenarios, and second proposing directions to inspire future research by identifying research gaps.Design/methodology/approachPapers related to supply chain risk management and procurement risk management (PRM) from 1995–2017 in several major databases are extracted by keywords and then further filtered based on the relevance to the topic, number of citations and publication year. A total of over 156 papers are selected. Definitions and current approaches related to procurement risks management are reviewed.FindingsFive main risks in procurement process are identified. Apart from summarizing current strategies, suggestions are provided to facilitate strategy selection to handle procurement risks. Seven major future challenges and implications related PRM and different uncertainties are also indicated in this paper.Research limitations/implicationsProcurement decisions making under uncertainty has attracted considerable attention from researchers and practitioners. Despite the increasing awareness for risk management for supply chain, no detail and holistic review paper studied on procurement uncertainty. Managing procurement risk not only need to mitigate the risk of price and lead time, but also need to have sophisticated analysis techniques in supply and demand uncertainty.Originality/valueThe contribution of this review paper is to discuss the implications of the research findings and provides insight about future research. A novel research framework is introduced as reference guide for researchers to apply innovative approach of operations research to resolve the procurements uncertainty problems.
A TISM modeling of critical success factors of blockchain based cloud services
Authors: Prasad Sanjay , Shankar Ravi , Gupta Rachita , Roy Sreejit 
Published: September 2018

Purpose
Over last few years, a major innovation known as blockchain technology has emerged as potentially one of the most disruptive technology of recent times. The purpose of this paper is to identify and analyze various critical success factors (CSFs) that can facilitate success of blockchain-based cloud services. Further, this paper aims to analyze and understand mutual interactions among these CSFs.

Design/methodology/approach
In this paper, 19 CSFs have been identified through literature review and expert opinions. The hierarchical framework developed using total interpretive structural modeling has revealed the inter-dependencies among these CSFs. The methodology employed in this study provides a mechanism to conduct an exploratory study by identifying the factors and analyzing their interactions through the development of a hierarchical framework. This research further categorizes CSFs into multiple clusters based on their driving power and dependence power.

Findings
This paper has identified 19 CSFs, namely, user engagement, industry collaboration, rich ecosystem, blockchain technology standardization, regulatory clarity, cost efficiency, energy efficiency (wasted resources), handling blockchain bloat, miner incentives, business case alignment to blockchain capability, sidechains development, blockchain talent pool availability, leadership readiness for a decentralized consensus based technology, technology investment and maturity, trust on blockchain networks, integration with other cloud services, robust and mature smart contracts platform, blockchain security and user control on data (privacy). Further, driver and dependent variables have been identified.

Research limitations/implications
Future research can discover and detail the sub-factors behind the 19 CSFs identified in this paper. Additionally, more work can be done to extend the current structural model for blockchain-based services to a more functional form.

Practical implications
It provides a comprehensive list of CSFs that are relevant for development of blockchain-based cloud services. This will help industry leaders to strategically focus on the main drivers that will ensure that businesses get maximum benefit of this disruptive technology.

Originality/value
This study makes a significant contribution in the literature of blockchain-based cloud services, which captures the perspective of different stakeholders. This study is one of the first (if not the first) systematic research on adoption of blockchain-based services. It creates the foundation to carry out further research in this area.
Impact of service quality on satisfaction and loyalty at manufacturer-distributor dyad
Authors: Gandhi Surjit Kumar , Sachdeva Anish , Gupta Ajay 
Published: September 2018

PurposeThe purpose of this paper is to investigate the role played by service quality (SQ) in manufacturer–distributor working partnerships in the context of Indian small and medium enterprises (SMEs), and present two models which propose and validate that contributions toward SQ, made by both the manufacturing unit and distribution firm lead to satisfaction which consequently results in business-to-business (B2B) loyalty.Design/methodology/approachThe research design for this study includes a combination of literature review, exploratory interviews with a focus group and a questionnaire survey conducted through interview schedule from 101 information rich and willing respondents working in SMEs of northern India.FindingsThe paper brings out scales foe measuring organizational (internal) and distributor (external) SQ. Further, two models using structural equation modeling are developed. Model-I examines the effect of organizational SQ on distributor SQ. Model-II examines the impact of distributor SQ on satisfaction and loyalty and also tests a set of four propositions related to their working relationship. The models are empirically tested and are found to be fit.Research limitations/implicationsFuture researchers may validate these scales, and empirically test the proposed models in alternate settings. Insights derived from this study may be transferred to other partnerships, which may exist in a manufacturing supply chain including suppliers, employees, retailers and end consumers.Practical implicationsThis study would be of interest to SME practitioners interested in improving SQ with their distributors. The study also finds support for strengthening collaborative relationships with B2B partners to achieve a win-win situation.Originality/valueThere are very few empirical studies that measure SQ w.r.t. distribution function in SMEs and the concept is in nascent stage, especially in Indian setting.