bluuebunny/crossref_metadata_2025_split huggingface dataset:
EPIP: MHC-I epitope prediction integrating mass spectrometry derived motifs and tissue-specific expression profiles
Authors: Hu Weipeng , Qiu Si , Li Youping , Lin Xinxin , Zhang Le , Xiang Haitao , Han Xing , Zhu Sitao , Chen Lei , Li Sha , Li Wenhui , Ren Zhe , Hou GuiXue , Lin Zhilong , Lu Jianliang , Liu Geng , Li Bo , Lee Leo J 
Published: March 2019

AbstractBackgroundAccurate prediction of epitopes presented by human leukocyte antigen (HLA) is crucial for personalized cancer immunotherapies targeting T cell epitopes. Mass spectrometry (MS) profiling of eluted HLA ligands, which provides high-throughput measurements of HLA associated peptides in vivo, can be used to faithfully model the presentation of epitopes on the cell surface. In addition, gene expression profiles measured by RNA-seq data in a specific cell/tissue type can significantly improve the performance of epitope presentation prediction. However, although large amount of high-quality MS data of HLA-bound peptides is being generated in recent years, few provide matching RNA-seq data, which makes incorporating gene expression into epitope prediction difficult.MethodsWe collected publicly available HLA peptidome and matching RNA-seq data of 34 cell lines derived from various sources. We built position score specific matrixes (PSSMs) for 21 HLA-I alleles based on these MS data, then used logistic regression (LR) to model the relationship among PSSM score, gene expression and peptide length to predict whether a peptide could be presented in each of the cell line. We further built a universal LR model, termed Epitope Presentation Integrated Prediction (EPIP), based on more than 180,000 unique HLA ligands collected from public sources and ~3,000 HLA ligands generated by ourselves, to predict epitope presentation for 66 common HLA-I alleles.ResultsWhen evaluating EPIP on large, independent HLA eluted ligand datasets, it performed substantially better than other popular methods, including MixMHCpred (v2.0), NetMHCpan (v4.0), and MHCflurry (v1.2.2), with an average 0.1% positive predictive value (PPV) of 52.01%, compared to 37.24%, 36.96%, 24.90% and 23.76% achieved by MixMHCpred, NetMHCpan-4.0 (EL), NetMHCpan-4.0 (BA) and MHCflurry, respectively. It is also comparable to EDGE, a recent deep learning-based model that is not publicly available, on predicting epitope presentation and selecting immunogenic cancer neoantigens. However, the simplicity and flexibility of EPIP makes it easier to be applied in diverse situations, and we demonstrated this by generating MS data for the HCC4006 cell line and adding the support of HLA-A*33:03 to EPIP. EPIP is publicly available as a web tool < http://epip.genomics.cn/>.Conclusionswe have developed an easy to use, publicly available epitope prediction tool, EPIP, that incorporates information from both MS and RNA-seq data, and demonstrated its superior performance over existing public methods.
GPseudoClust: deconvolution of shared pseudo-profiles at single-cell resolution
Authors: Strauss Magdalena E , Kirk Paul DW , Reid John E , Wernisch Lorenz 
Published: March 2019

AbstractMotivationMany methods have been developed to cluster genes on the basis of their changes in mRNA expression over time, using bulk RNA-seq or microarray data. However, single-cell data may present a particular challenge for these algorithms, since the temporal ordering of cells is not directly observed. One way to address this is to first use pseudotime methods to order the cells, and then apply clustering techniques for time course data. However, pseudotime estimates are subject to high levels of uncertainty, and failing to account for this uncertainty is liable to lead to erroneous and/or over-confident gene clusters.ResultsThe proposed method, GPseudoClust, is a novel approach that jointly infers pseudotem-poral ordering and gene clusters, and quantifies the uncertainty in both. GPseudoClust combines a recent method for pseudotime inference with nonparametric Bayesian clustering methods, efficient MCMC sampling, and novel subsampling strategies which aid computation. We consider a broad array of simulated and experimental datasets to demonstrate the effectiveness of GPseudoClust in a range of settings.AvailabilityAn implementation is available on GitHub: https://github.com/magStra/nonparametricSummaryPSM and https://github.com/magStra/GPseudoClust.Contactms58@sanger.ac.ukSupplementary informationSupplementary materials are available.
Shared resources between visual attention and visual working memory are allocated through rhythmic sampling
Authors: Balestrieri Elio , Ronconi Luca , Melcher David 
Published: March 2019

AbstractAttention and Visual Working Memory (VWM) are among the most theoretically detailed and empirically tested constructs in human cognition. Nevertheless, the nature of the interrelation between selective attention and VWM still presents a fundamental controversy: do they rely on the same cognitive resources or not? The present study aims at disentangling this issue by capitalizing on recent evidence showing that attention is a rhythmic phenomenon, oscillating over short time windows. Using a dual-task approach, we combined a classic VWM task with a detection task in which we densely sampled detection performance during the time between the memory and the test array. Our results show that an increment in VWM load was related to a worse detection of near threshold visual stimuli and, importantly, to the presence of an oscillatory pattern in detection performance at ∼5 Hz. Furthermore, our findings suggest that the frequency of this sampling rhythm changes according to the strategic allocation of attentional resources to either the VWM or the detection task. This pattern of results is consistent with a central sampling attentional rhythm which allocates shared attentional resources both to the flow of external visual stimulation and also to the internal maintenance of visual information.
A Role for Gαz in regulating seizure susceptibility
Authors: Hultman Rainbo , Boms Okechi , Mague Stephen , Hughes Dalton , Nadler Victor , Dzirasa Kafui , Casey Patrick J. 
Published: March 2019

AbstractMuch about the molecular mechanisms underlying seizure susceptibility remains unknown. A number of studies have indicated that the neurotrophic factor BDNF plays an important role in mediating seizure susceptibility. Recently, we found that the heterotrimeric G – protein, Gz, which is known to endogenously couple to monoaminergic receptors, such as serotonin, norepinephrine and dopamine receptors, regulates BDNF-induced signaling and development in cortical neurons. Interestingly, several of the receptors that Gz endogenously couples to have also been shown to be associated with seizure phenotypes (5HT1A-serotonin and D2 dopamine). Here we characterized seizure susceptibility in Gz-null mice, behaviorally and electrographically, finding that Gz-null mice have increased seizure susceptibility using a modified version of the pilocarpine model of status epilepticus. Local field potential (LFP) data recorded from six brain regions-amygdala, dorsal hippocampus, ventral hippocampus, motor cortex, somatosensory cortex, and thalamus-showed robust electrographic seizure activity for Gz-null mice compared with low or no seizure activity in wild-type controls.
Risk of differential cancer types over age in families with Li-Fraumeni syndrome: a validation study using multi-center cohorts
Authors: Shin Seung Jun , Dodd Elissa , Peng Gang , Bojadzieva Jasmina , Chen Jingxiao , Amos Chris , Mai Phuong L. , Savage Sharon A. , Ballinger Mandy L. , Thomas David M. , Yuan Ying , Strong Louise C. , Wang Wenyi 
Published: March 2019

ABSTRACTLi-Fraumeni syndrome (LFS) is a rare hereditary cancer syndrome associated with an autosomal dominant mutation inheritance in the TP53 tumor suppressor gene and a wide spectrum of cancer diagnoses. An accurate estimation of the penetrance of different cancer types in LFS is crucial to improve the clinical characterization and management of high-risk individuals of LFS. Our competing risk-based statistical model incorporates the pedigree structure efficiently into the penetrance estimation and corrects for the ascertainment bias. A set of TP53 penetrance for three cancer types (breast, BR/sarcoma, SA/others, OT) involved in LFS is then estimated from 186 pediatric-sarcoma families collected at MD Anderson Cancer Center. The penetrance was then validated on a mixed cohort of clinically ascertained families with cancer (total number of families=668). The age-dependent onset probability distributions of specific cancer types are different. For breast cancer, the TP53 penetrance goes up at an earlier age than the reported BRCA1/2 penetrance. We validated the prediction performance of the penetrance estimates via two independent cohorts combined (BR=85, SA=540, OT=158). We obtained areas under the ROC curves (AUCs) of 0.92 (BR), 0.75 (SA), and 0.81 (OT). Our R package, LFSPRO, provides risk estimates for the diagnosis of breast cancer, sarcoma, other cancers or death before cancer diagnosis in future.SignificanceCancer-specific penetrance can facilitate clinical characterization of LFS and will contribute to the management of families at high risk of LFS.
Chromosome-wide co-fluctuation of stochastic gene expression in mammalian cells
Authors: Sun Mengyi , Zhang Jianzhi 
Published: March 2019

ABSTRACTGene expression is subject to stochastic noise, but to what extent and by which means such stochastic variations are coordinated among different genes are unclear. We hypothesize that neighboring genes on the same chromosome co-fluctuate in expression because of their common chromatin dynamics, and verify it at the genomic scale using allele-specific single-cell RNA-sequencing data of mouse cells. Unexpectedly, the co-fluctuation extends to genes that are over 60 million bases apart. We provide evidence that this long-range effect arises in part from chromatin co-accessibilities of linked loci attributable to three-dimensional proximity, which is much closer intra-chromosomally than inter-chromosomally. We further show that genes encoding components of the same protein complex tend to be chromosomally linked, likely resulting from natural selection for intracellular among-component dosage balance. These findings have implications for both the evolution of genome organization and optimal design of synthetic genomes in the face of gene expression noise.
Genetic Polymorphisms and Molecular Mechanisms Mediating Oncolytic Potency of Reovirus Strains
Authors: Mohamed Adil , Clements Derek R. , Konda Prathyusha , Gujar Shashi A. , Lee Patrick W. , Smiley James R. , Shmulevitz Maya 
Published: March 2019

ABSTRACTThe Dearing strain of Mammalian orthoreovirus (T3D) is undergoing clinical trials as an oncolytic virotherapeutic agent. In this study, a comprehensive phenotypic and genetic comparison of T3D virus stocks from various laboratories and commercial sources revealed that T3D laboratory strains differ substantially in their oncolytic activitiesin vitroandin vivo. Superior replication of the most-oncolytic T3D lab strain was attributed to several mechanistic advantages: virus-cell binding, viral RNA transcriptase activity, viral inclusion morphology, and differential activation of RIG-I versus NFκB-dependent signalling pathways. Viral S4, M1 and L3 gene segments were each independently associated with a distinct mechanistic advantage. Furthermore, the specific missense polymorphisms that governed replication potency were identified, and utilized to generate a hybrid of T3D laboratory strains with further-augmented replication in tumor cells. Together, the results depict an elaborate balance between reovirus replication and host-cell signaling to achieve optimal oncolytic reovirus efficacy.
Analysing drivers and outcomes of job and professional satisfaction at health centres in Portugal
Authors: Santana Silvina , Loureiro Sandra Maria Correia 
Published: March 2019

PurposeThe purpose of this paper is to analyse antecedents, associations and outcomes of job and professional satisfaction of doctors and nurses in Portuguese health centres.Design/methodology/approachThe authors have used structural equation modelling to examine the causal relationships between multiple variables placed in a path model reflecting the theoretical foundation.FindingsThe percentage of those satisfied or very satisfied with their jobs was just above 50 per cent. Doctors’ satisfaction stems from personal achievement and the formal component of work environment, leading them to strongly recommend their work in the health centre to dear ones but not to put aside other job options. Nurses’ level of job satisfaction seems to be affected by co-workers and interpersonal relationships beside personal achievement and has more strong and multifaceted impact on their feelings and behaviour that goes from recommending their job position to considering to quit job and even regretting the option made in terms of career.Originality/valueThis study represents the first attempt to conceptualise and test a simultaneous model comprising antecedents and outcomes of both job satisfaction and professional satisfaction in primary care, investigating also differences between genders and professions. Results shed light on determinants of satisfaction among specialised staff in Portuguese primary care and how they affect commitment to the organisation and the way career choice is regarded.
Examining cannabis protective behavioral strategy use using multiple methods
Authors: Prince Mark A. , Jenzer Tiffany , Brown Whitney , Hetelekides Eleftherios M. , Mumm Rachel A. , Collins R. Lorraine 
Published: March 2019

PurposeCannabis use among young adults is increasing, despite being associated with several negative consequences. Protective behavioral strategies (PBSs) are a potential mechanism of behavior change for reducing substance use, yet PBS use for cannabis is not well understood. The purpose of this paper is to further define and measure the PBS construct for cannabis.Design/methodology/approachA community sample of cannabis users (n=54) participated in eight focus groups discussing the use of PBSs. Participants completed surveys regarding demographics, cannabis use habits and cannabis problems. The authors also administered an existing measure of cannabis PBS and asked them to generate new or unique protective strategies that they had used or had heard of others using.FindingsThematic analysis of qualitative focus group data provided information about cannabis users’ reasons for regulating cannabis use (e.g. health or legal problems, interpersonal) as well as strategies to moderate cannabis use or attenuate their risk for experiencing adverse consequences (e.g. distraction, existential/spiritual strategies). Analyses of quantitative survey data revealed that use of PBSs was negatively correlated with cannabis outcomes. Perceived helpfulness of strategies was an important predictor of decreased cannabis use and adverse consequences.Research limitations/implicationsFindings expand the understanding of the definition and measurement of strategies for regulating cannabis use and reducing related risk of experiencing adverse consequences.Originality/valueThis is the first study to examine cannabis-related PBS using both qualitative and quantitative methods, which provide insights into the definition of PBS and for future refinements of PBS measurement.
Barriers and enablers to women in fire and emergency leadership roles
Authors: Parkinson Debra , Duncan Alyssa , Archer Frank 
Published: March 2019

Purpose
The purpose of this paper is to understand what (if any) actual and perceived barriers exist for women to take on fire and emergency management leadership roles within the Department of Environment, Land, Water and Planning, Victoria, Australia.

Design/methodology/approach
An anonymous quantitative online survey was used to collect data about opinions and thoughts of staff. This informed the qualitative component of the research – in-depth, semi-structured interviews and a focus group. The combination of these techniques provides deeper insight into the nature of the barriers for women.

Findings
Respondents identified real barriers for women accessing leadership roles in fire and emergency. Reflecting the wider literature on barriers to women in executive roles, those identified related to sexism, career penalties not faced by men for family responsibilities, and assumptions of women helping other women’s careers. There were more men in senior roles, leaving senior women isolated and often overlooked. Women had fewer role models and sponsors than men and less developed networks, finding it harder to access training and deployments. The context was described by most as “a boys’ club”, where men were seen to dominate meetings and stereotype the abilities of women.

Originality/value
This paper analyses the barriers to women in fire and emergency leadership roles within a masculine workplace and is rare in including a qualitative aspect to the issue in the Australian context.
Investigating the transformative impact of bank transparency on consumers’ financial well-being
Authors: Losada-Otálora Mauricio , Alkire (née Nasr) Linda 
Published: March 2019

PurposeGrounded in Transformative Service Research, the purpose of this paper is to explore the mechanisms by which bank information transparency influences consumer’s financial well-being (FWB). The authors propose that customer attitudes toward the brand and the subjectively perceived ability of individuals to deal with the financial challenges explain the enhancement of FWB driven by bank information transparency.Design/methodology/approachA survey was conducted to test the proposed hypotheses. In total, 400 bank customers of five commercial banks in Colombia were approached and asked to fill out a pen and paper questionnaire. Serial mediation analysis was applied to test the hypotheses.FindingsThis research shows that bank information transparency can uplift the FWB of customers. Furthermore, the positive effect of bank information transparency on the FWB occurs because the shared information improves the positive attitudes toward banks and the perceived financial self-efficacy of customers.Research limitations/implicationsThis paper heeds the call of current literature for improved explanations of the relationship between attempts to inform consumers about financial services and their FWB.Practical implicationsThis research shows that managers who embrace the challenging task of improving the FWB of their customers should design strategies for more transparent information sharing with their customers. However, these strategies should be designed not only to deliver information to customers but also to increase the perceived disclosure, accuracy and clarity of shared information.Originality/valueThis pioneering study aims to explain the effects of bank information transparency on the FWB of consumers by drawing on interdisciplinary literature. This research is important as many banks aim to increase their information transparency without a clear understanding of the effects of these actions on consumers and therefore in many instances their efforts fail. A key contribution of this study is identifying concrete mechanisms (i.e. brand attitudes and self-efficacy) that help managers to improve customers’ FWB via information transparency. Accordingly, the authors offer suggestions for better information transparency strategy implementation.
Income security, social comparisons and materialism
Authors: Chatterjee Devlina , Kumar Mahendra , Dayma Kapil K. 
Published: March 2019

Purpose
The purpose of this paper is to understand the effect of perceived income security (IS), materialistic values and socially driven aspirations on the financial well-being (FWB) of young Indian adults.

Design/methodology/approach
A questionnaire was designed using available scales for FWB and materialism. Questions were incorporated to measure social comparison and IS. A structural equation approach using data from 327 respondents was used to test a hypothesized model of FWB.

Findings
The IS has the largest positive effect, while unemployment has the largest negative effect on FWB. Overt materialism (OM) negatively affects FWB. Socially motivated aspirations have an indirect negative effect mediated by OM. Among demographic variables, income, education and stable employment increase FWB. Males have lower levels of FWB.

Research limitations/implications
The data includes 327 respondents that were polled using convenience sampling. The results may not be generalizable to India at large.

Social implications
A common consideration when choosing a job is the salary. However, we find that IS affects subsequent FWB to a much greater extent than income level and materialistic aspirations.

Originality/value
This is the first study to look at the relative importance of materialistic aspirations vs IS in determining FWB. The results will help policy makers in devising policies and financial service providers in designing products and services that will increase the FWB of Indians.
Consumer’s initial trust formation in IOB’s acceptance
Authors: Kaabachi Souheila , Ben Mrad Selima , O’Leary Bay 
Published: March 2019

Purpose
The purpose of this paper is to explore how variables like propensity to trust, website usability, social influence, customer awareness about internet-only banks (IOBs) and perceived compatibility influence customers’ initial trust formation toward IOBs’ acceptance. The model is based on the technology acceptance model, diffusion of innovation theory and theory of reasoned action.

Design/methodology/approach
A non-probability convenience sample of 239 IOBs’ potential adopters from France was used to test the structural equation model between initial trust antecedents and IOB’s usage intention.

Findings
Findings confirm the important role of trust in initiating customers’ relationship with IOBs and show that social influence, compatibility and website usability contribute the most to IOB’s initial trust formation. Indeed, it has been found that the level of consumer information about IOBs and propensity to trust have a moderate impact on consumer’s initial trust. Results revealed that there is a general lack of consumer’s awareness about IOB’s services features.

Practical implications
To promote the trustworthiness of their sites and services to potential consumers, IOBs should enhance WOM by using social network applications. IOBs need to develop marketing communication campaigns in which they can educate potential customers about IOB’s features. In addition, IOBs should demonstrate to their customers that IOBs’ banking system is consistent with their current lifestyle. IOBs are encouraged to develop a favorable impression by investing heavily on their website usability and information design.

Originality/value
This study contributes significantly to the marketing research literature related to consumer trust and electronic banking literature. Indeed, only a few marketing studies have been conducted about IOBs. The results show the role played by initial trust formation in the case of IOBs. In addition, it points out the importance of five trust cues: individual cues, knowledge cues, institutional cues, cognitive cues and social cues (social influence).