bluuebunny/crossref_metadata_2025_split huggingface dataset:
The study of rotavirus phylogenetic diversity, re-assortment and interspecies transmission and associated virome in Northern Irish livestock and wildlife
Authors: Tregaskis Paula Lagan , Mooney Mark , Lemon Ken 
Published: April 2019

Background
Rotavirus (RV) is a highly infectious pathogen of livestock causing diarrhoea and dehydration, and substantial economic loss. RV is an RNA virus with a segmented genome that has evolved significantly creating diverse strains. RV is believed to be endemic within livestock and the genotyping of positive isolates will allow the diversity of the rotavirus to be phylogenetically mapped for evidence of re-assortment and interspecies transmission. Rotavirus positive samples and rotavirus negative samples were examined using a metagenomics approach through next generation sequencing (NGS) to study the virome of symptomatic animals.

Methods
RV in symptomatic livestock, and a small subset of wildlife and exotic animal faeces samples (n=326), originating from Northern Ireland, were screened by RT PCR for the RV VP6 gene. NGS libraries using a de novo metagenomics approach were run on the MiSeq reagent V3 600 cycle as pairend reads. Data was quality checked by Fast QC, assembled in SPAdes, processed through NCBI blast (n) and then MEGAN to display the taxonomical content.

Results
The prevalence of RV VP6 gene was n=108 (33 %). Initial Sanger sequencing results showed porcine G3, G4 and G5 and bovine P7 and P13 strains. Preliminary metagenomic results indicates re-assortment and interspecies transmission with a positive bovine sample showing RV acquired re-assortment from human and equine RV strains. Analysis shows there is a large viral community present in both RV positive and RV negative animals. The metagenomic profiling through NGS data set will give a better understanding of the symptomatic virome in livestock.
A SLIC answer to a continuing problem
Authors: Hammond Robert 
Published: April 2019

Background
The burden of Anti-Microbial Resistance (AMR) is a growing problem globally. Here we present a device that determines susceptibility rapidly from primary human or animal samples and could turn the tide of AMR. SLIC (Scattered Light Integrating Collector) is a sensitive device for the detection of microbes based on the scattering of laser light.

Methods
Proof of concept studies were carried out initially to establish the lower limit of detection. This was found to be 10–50 c.f.u. ml−1. This exquisite sensitivity allowed us to commence work establishing rapid MICs. Starting with an inoculum of 105/ml bacteria and using a relevant range of antibiotic concentrations the MIC can be established in less than one microbial doubling period.

Results
The rapid and sensitive detection SLIC affords allows for fast growing organisms such as E. coli and S. aureus to have their MICs established in less than 10 min, for any antibiotic. For slow growing organisms such as M. bovis we are able to establish an MIC in H. influenzae and Mycoplasma spp.

Conclusion
As bacterial quantification is continuously monitored we are able to see the action of antibiotics in real time. Using this facility, we can readily distinguish between lytic antibiotics and bactericidal but non-lytic antibiotics. This provides the opportunity to gain new insights into the mechanisms of action and the effect antibiotics have on microbes in a new way in a novel Point-of-Care device.
Applying Next Generation Sequencing Technology to Hepatitis C genotyping in a routine diagnostic laboratory
Authors: May Sophie 
Published: April 2019

Background
To meet the target of Hepatitis C elimination in the UK, a rapid and high throughput method of genotyping is desirable. Current methods target the NS5B region with a nested PCR followed by Sanger sequencing. Drawbacks include insufficient information to guide second line treatment in the event of failure and poor sensitivity compared to assays targeting the 5’UTR.

Method
Previously tested HCV positive patient samples were selected and RNA extracted using an ultra-centrifugation manual extraction method. A two-step reverse transcription long range PCR generated amplicons which were quantified using the Qubit fluorometer and libraries prepared using the Nextera XT library preparation kit. Sequencing was performed using an Illumina Miseq and genomes were assembled using a Linex-based bioinformatics pipeline.

Results
A total of 150 samples were tested, with full HCV genomes obtained for genotypes 1–6 and the sensitivity of the assay corresponded to around 1000 IU  ml−1. Where previous sequence data for resistance associated variants (RAVs) was available, mutations were consistent. Furthermore, the assay identified a 2 k/1b recombinant and allowed the typing of previously unassigned genotypes, demonstrating its utility in the diverse local population.

Conclusion
This study displayed the utility of a whole genome sequencing approach to HCV. A major benefit of whole genome analysis was the inclusion of regions targeted by antiviral therapy such as NS5A and NS3. This allowed the identification of RAVs in patients experiencing treatment failure. Its application to dried blood spots is currently being investigated as part of a wider screening programme.
Cerebellar Modulation of Mesolimbic Dopamine Transmission is Functionally Asymmetrical
Authors: Holloway Zade R. , Paige Nick B. , Comstock Josiah F. , Nolen Hunter G. , Sable Helen J. , Lester Deranda B. 
Published: April 2019

AbstractCerebral and cerebellar hemispheres are known to be asymmetrical in structure and function, and previous literature supports that asymmetry extends to the neural dopamine systems. Using in vivo fixed-potential amperometry with carbon-fiber microelectrodes in anesthetized mice, the current study assessed hemispheric lateralization of stimulation-evoked dopamine in the nucleus accumbens (NAc) and the influence of the cerebellum in regulating this reward-associated pathway. Our results suggest that cerebellar output can modulate mesolimbic dopamine transmission, and this modulation contributes to asymmetrically lateralized dopamine release. Dopamine release did not differ between hemispheres when evoked by medial forebrain bundle (MFB) stimulation; however, dopamine release was significantly greater in the right NAc relative to the left when evoked by electrical stimulation of the cerebellar dentate nucleus (DN). Furthermore, cross-hemispheric talk between the left and right cerebellar DN does not seem to influence mesolimbic release given that lidocaine infused into the DN opposite to the stimulated DN did not alter release. These studies may provide a neurochemical mechanism for studies identifying the cerebellum as a relevant node for reward, motivational behavior, saliency, and inhibitory control. An increased understanding of the lateralization of dopaminergic systems may reveal novel targets for pharmacological interventions in neuropathology of the cerebellum and extending projections.
Graph-Based Method for Anomaly Detection in Functional Brain Network using Variational Autoencoder
Authors: Mirakhorli Jalal , Mirakhorli Mojgan 
Published: April 2019

AbstractFunctional neuroimaging techniques using resting-state functional MRI (rs-fMRI) have accelerated progress in brain disorders and dysfunction studies. Since, there are the slight differences between healthy and disorder brains, investigation in the complex topology of human brain functional networks is difficult and complicated task with the growth of evaluation criteria. Recently, graph theory and deep learning applications have spread widely to understanding human cognitive functions that are linked to gene expression and related distributed spatial patterns. Irregular graph analysis has been widely applied in many brain recognition domains, these applications might involve both node-centric and graph-centric tasks. In this paper, we discuss about individual Variational Autoencoder and Graph Convolutional Network (GCN) for the region of interest identification areas of brain which do not have normal connection when apply certain tasks. Here, we identified a framework of Graph Auto-Encoder (GAE) with hyper sphere distributer for functional data analysis in brain imaging studies that is underlying non-Euclidean structure, in learning of strong rigid graphs among large scale data. In addition, we distinguish the possible mode correlations in abnormal brain connections.
Carryover effects of temperature and pCO2across multiple Olympia oyster populations
Authors: Spencer Laura H , Venkataraman Yaamini R , Crim Ryan , Ryan Stuart , Horwith Micah J , Roberts Steven B 
Published: April 2019

AbstractPredicting how populations will respond to ocean change across generations is critical to effective conservation of marine species. One emerging factor is the influence of parental exposures on offspring phenotype, known as intergenerational carryover effects. Parental exposure may deliver beneficial or detrimental characteristics to offspring that can influence larval recruitment patterns, thus shaping how populations and community structure respond to ocean change. Impacts of adult exposure to elevated winter temperature and pCO2on reproduction and offspring viability were examined in the Olympia oyster (Ostrea lurida) using three populations of adult, hatchery-rearedO. lurida,plus an additional cohort spawned from one of the populations. Oysters were sequentially exposed to elevated temperature (+4°C, at 10°C), followed by elevated pCO2(+2204 µatm, at 3045 µatm) during winter months. Male gametes were more developed after elevated temperature exposure and less developed after high pCO2exposure, but there was no impact on female gametes or sex ratios. Oysters previously exposed to elevated winter temperature released larvae earlier, regardless of pCO2exposure. Those exposed to elevated winter temperature as a sole treatment released more larvae on a daily basis, but when also exposed to high pCO2there was no effect. These combined results indicate that elevated winter temperature acceleratesO. luridaspermatogenesis, resulting in earlier larval release and increased production, with elevated pCO2exposure negating effects of elevated temperature. Altered recruitment patterns may therefore follow warmer winters due to precocious spawning, but these effects may be masked by coincidental high pCO2. Offspring were reared in common conditions for one year, then deployed for three months in four estuarine bays with distinct environmental conditions. Offspring of parents exposed to elevated pCO2had higher survival rates in two of the four bays. This carryover effect demonstrates that parental conditions can have substantial ecologically relevant impacts that should be considered when predicting impacts of environmental change. Furthermore, Olympia oysters may be more resilient in certain environments when progenitors are pre-conditioned in stressful conditions. Combined with other recent studies, our work suggests that the Olympia may be more equipped than other oysters for the challenge of a changing ocean.
The splicing factor hnRNP M is a critical regulator of innate immune gene expression in macrophages
Authors: West K.O. , Scott H.M. , Torres-Odio S. , West A.P. , Patrick K.L. , Watson R.O. 
Published: April 2019

ABSTRACTWhile transcriptional control mechanisms of innate immune gene expression are well characterized, almost nothing is known about how pre-mRNA splicing decisions influence, or are influenced by, macrophage activation. Here, we demonstrate that the splicing factor hnRNP M is a critical repressor of innate immune gene expression and that its function is regulated by pathogen sensing cascades. Loss of hnRNP M leads to hyperinduction of a unique regulon of inflammatory and antimicrobial genes, including IL6, Mx1, and Gbp5, following a variety of innate immune stimuli. While mutating specific serines on hnRNP M had little effect on its ability to control pre-mRNA splicing or transcript levels of “housekeeping” genes in resting macrophages, it greatly impacted the protein’s ability to dampen induction of specific innate immune transcripts following activation of pathogen sensing cascades. These data reveal a previously unappreciated role for pattern recognition receptor signaling in controlling splicing factor phosphorylation and establish pre-mRNA splicing as a critical regulatory node in defining innate immune outcomes.
Separation and detection of minimal length isomeric glycopeptide neoantigen epitopes centering GSTA region of MUC1 by LC-MS
Authors: Zhou Dapeng , Xiao Kaijie , Tian Zhixin 
Published: April 2019

AbstractMUC1 ranks No.2 on the list of targets for cancer immunotherapy. We previously reported monoclonal antibodies binding to glycopeptide neoantigen epitopes centering GSTA sequence of the highly glycosylated tandem repeat region of MUC1. Epitopes centering GSTA sequence are also predicted by NetMHC programs to bind to MHC molecules, although empirical data are lacking. Detecting isomeric MUC1 glycopeptide epitopes by mass spectrometry (MS) remains a technical challenge since antigenic epitopes are often shorter than 10 amino acids. MUC1 digests by Arg-C-specific endopeptidase clostripain could generate heterogenous icosapeptides, but isomeric 20-residue glycopetides could not be separated by liquid chromatography. In this study, we used pronase fromStreptomyces griseus, which has no amino acid sequence preference for enzymatic cleavage sites, to digest a pair of synthetic glycopeptide isomers RPAPGST(Tn)APPAHG and RPAPGS(Tn)TAPPAHG, and analyzed the digests by LC-MS using electron transfer dissociation (ETD) and higher-energy collisional dissociation (HCD) methods. The results showed that glycopeptide isomers containing 8 to 11 amino acids could be efficiently generated by pronase digestion. Such glycopeptide isomers of minimal epitope lengths were clearly distinguished by characteristic MS/MS ion patterns and elution profiles of liquid chromatography. A glycopeptide library was generated which may serve as standards for measuring neoantigen epitopes centering GSTA sequence.
Tacit knowledge as a multilayer phenomenon: the “onion” model
Authors: Asher Dan , Popper Micha 
Published: April 2019

Purpose
This paper aims to clarify the term “tacit knowledge” and suggests the “onion model” as a way to explore conceptually linked layers of tacit knowledge. The model allows the application of different methodologies to elicit tacit knowledge in each layer, the ability to infer tacit knowledge in other layers from tacit knowledge gained in another layer and the exploration of the dynamics of tacit knowledge among the various layers presented in the model. Conceptual and practical advantages compared to prior works on tacit knowledge are discussed.

Design/methodology/approach
The main theoretical and methodological dilemmas discussed in the literature regarding tacit knowledge are reviewed. The “onion model” presented in this paper suggests an approach and methodologies that address the issues raised in the literature. The different layers of the model are demonstrated by prior research studies.

Findings
The “onion model” discussed in this study points to various layers of tacit knowledge and the links among them, allowing a research-based approach, as well as various practices.

Research limitations/implications
This paper discusses different layers of tacit knowledge relying on previous works that have dealt with these layers independently. The model as a whole and the dynamics among the layers are yet to be empirically investigated.

Practical implications
The “onion model” provides a conceptual framework that can be used for research and diagnosis aimed at exploring tacit knowledge that can serve individual and organizational development.

Originality/value
The approach discussed in this paper addresses some major problems discussed in the literature on tacit knowledge.
Investigating the role of UTAUT and e-service quality in internet banking adoption setting
Authors: Rahi Samar , Abd.Ghani Mazuri 
Published: April 2019

PurposeTechnology adoption is a great challenge in the banking sector of Pakistan. A recent report issued by state bank of Pakistan revealed that there is a squeak growth, only 3 percent, in internet banking adoption. In order to effectively delve into the issue of internet banking adoption, the purpose of this paper is to use unified theory of acceptance and use of technology factors, namely performance expectancy and effort expectancy and e-service quality (E-SQ), as theoretical lens for this study.Design/methodology/approachThe research model was empirically tested using 398 valid responses from customers of commercial banks in Pakistan. The theoretical model was tested using structural equation modeling.FindingsFindings indicate that performance expectancy, effort expectancy, website design, customer service, assurance and reliability have direct influence on user intention to adopt internet banking. Results revealed that approximately 79 percent of variance in user intention to adopt internet banking was explained by predictors. In addition, the mediating role of performance expectancy and effort expectancy among website design, customer service and user intention was also confirmed.Practical implicationsFor researchers, this study provides a base of integrated technology model and it suggests using this model in other online domains such as mobile payment and online web-shopping for further refinement. For policymakers, understanding the key constructs is important to design, refine and implement new internet banking website that, in turn, will boost internet banking adoption trend among users of commercial banks.Originality/valueThis paper makes a unique contribution toward information system and services marketing literature. The study schematized that website design, customer service, assurance and reliability are the key dimensions of E-SQ and significantly influence the user intention to adopt internet banking.
Genome‐wide association study identified genes in the response to Salmonella pullorum infection in chickens
Authors: Xiao L. , He C. , Luo L. , Yang K. , Yang L. , Xu K. , Zheng Y. , Gu C. , Huang Q. , Meng H. 
Published: April 2019

SummaryPullorum is a bacterial disease that threatens the modern poultry industry. Over the years, research on this topic has focused mainly on its epidemiology, whereas the hosts’ genetic basis of infection is still vague. In order to identify chickens’ genes associated with pullorum, we sequenced 300 New Pudong chicken by double digest genotyping‐by‐sequencing. We obtained 1 527 953 SNPs for a genome‐wide association analysis, which identified 43 genome‐wide significant markers. Most of the significant SNPs were in the interval of 57.7–59.0 Mb on chromosome 5. The gene set enrichment analysis suggests a potential manner for bacterial infection and remaining inside the host. This work provides basic data for the purification, prevention and treatment of pullorum disease.
CRA Reputation and Bond Yield: Evidence from the Chinese Bond Market
Authors: Hu Xiaolu , Huang Haozhi , Shi Jing , Wang Hua 
Published: April 2019

AbstractThe paper examines the reputation effect of credit rating agencies (CRAs) in China. We find a negative association between CRAs’ reputation and public bonds’ offering yield spreads after controlling for endogeneity. Analyses of the correlation between CRA reputation and bond return volatility in the aftermarket and cross‐sectional variations of reputation effects alongside a host of information environment proxies for issuers, we identify the information channel through which CRA reputation plays its role. This is further supported when we utilize an exogenous event, the introduction of an independent CRA (the China Bond Rating Co. Ltd), to explore the potential changes of the reputation effect.
Treatment and outcome of Unicentric Castleman Disease: a retrospective analysis of 71 cases
Authors: Boutboul David , Fadlallah Jehane , Chawki Sylvain , Fieschi Claire , Malphettes Marion , Dossier Antoine , Gérard Laurence , Mordant Pierre , Meignin Véronique , Oksenhendler Eric , Galicier Lionel 
Published: April 2019

SummaryWe retrospectively analysed 71 cases of Unicentric Castleman disease, a rare, usually asymptomatic, benign lymphoproliferative disorder presenting as a unique nodal mass. Although surgery is considered as the gold standard therapy, only 38 patients (54%) underwent initial surgical resection and 95% were cured. An additional 9 patients had surgery after an attempt at medical reduction. Reduction therapy was used in 21 patients with a 55% response rate, but without evidence for an optimal regimen. Radiotherapy was limited to 8 patients because of associated toxicity. Watch and wait was considered in 13 asymptomatic patients and 11 of these remained stable for up to 17 years.
Cultures of conflict: Protests, violent repression, and community values
Authors: Akkuş Birol , Postmes Tom , Stroebe Katherine , Baray Gamze 
Published: April 2019

What are the cultural origins of societal conflicts that revolve around democratization, women's rights, and modern libertarian values? We propose that deep‐seated differences in community‐based collective values (at the micro‐level) may be related to why people support anti‐government protestandwhy they support repression of such protests (at the macro‐level). The hypothesis was examined among residents of Turkey (N = 500). Cultural values, measured at the individual level and community level with the community collectivism scale, correlated with political orientation and emotions, as well as with subsequent support for anti‐governmental protest or its repression. The main conclusions are that both support for protest and support for repression are related to the cultural values people hold and their subsequent political orientations and emotions. Micro‐level cultural values in local communities may thus play a role in explaining macro‐level socio‐political divides.
PERIODIC, COMPLETE‐PARTICIPATION TRADE IN THE LAGOS‐ROCHETEAU MODEL
Authors: Liao Mouhua 
Published: April 2019

ABSTRACTThis paper contributes to a recent policy discussion regarding the costs and benefits of setting up a centralized electronic trading platform to replace over‐the‐counter (OTC) markets. We modify the Lagos and Rocheteau (2009, henceforth LR) asset trading model by replacing their investor‐dealer random matching and bilateral trade with a centralized competitive market that opens periodically. This arrangement preserves the main tension and trade‐off in LR. We then analyse and quantify when to introduce a centralized market and how frequently it should open in order to make it as efficiently as the decentralized OTC market in LR.