bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interpretable detection of novel human viruses from genome sequencing data
Authors: Bartoszewicz Jakub M. , Seidel Anja , Renard Bernhard Y. 
Published: January 2020

ABSTRACTViruses evolve extremely quickly, so reliable methods for viral host prediction are necessary to safeguard biosecurity and biosafety alike. Novel human-infecting viruses are difficult to detect with standard bioinformatics workflows. Here, we predict whether a virus can infect humans directly from next-generation sequencing reads. We show that deep neural architectures significantly outperform both shallow machine learning and standard, homology-based algorithms, cutting the error rates in half and generalizing to taxonomic units distant from those presented during training. Further, we develop a suite of interpretability tools and show that it can be applied also to other models beyond the host prediction task. We propose a new approach for convolutional filter visualization to disentangle the information content of each nucleotide from its contribution to the final classification decision. Nucleotide-resolution maps of the learned associations between pathogen genomes and the infectious phenotype can be used to detect regions of interest in novel agents, for example the SARS-CoV-2 coronavirus, unknown before it caused a COVID-19 pandemic in 2020. All methods presented here are implemented as easy-to-install packages enabling analysis of NGS datasets without requiring any deep learning skills, but also allowing advanced users to easily train and explain new models for genomics.
dnmt1function is required to maintain retinal stem cells within the ciliary marginal zone of the zebrafish eye
Authors: Angileri Krista M. , Gross Jeffrey M. 
Published: January 2020

AbstractThe ciliary marginal zone (CMZ) of the zebrafish retina contains a population of actively proliferating resident stem cells, which generate retinal neurons throughout life. The maintenance methyltransferase,dnmt1, is expressed within the CMZ. Loss of dnmt1 function results in gene misregulation and cell death in a variety of developmental contexts, however, its role in retinal stem cell (RSC) maintenance is currently unknown. Here, we demonstrate that zebrafishdnmt1s872mutants possess severe defects in RSC maintenance within the CMZ. Using a combination of immunohistochemistry,in situhybridization, and a transgenic reporter assay, our results demonstrate a requirement for dnmt1 activity in the regulation of RSC proliferation, gene expression and in the repression of endogenous retroelements (REs). Ultimately, cell death is elevated in thednmt1-/-CMZ, but in ap53-independent manner. Using a transgenic reporter for RE transposition activity, we demonstrate increased transposition in thednmt1-/-CMZ. Taken together our data identify a critical role for dnmt1 function in RSC maintenance in the vertebrate eye.
Insights into Cross-species Evolution of Novel Human Coronavirus SARS-CoV-2 and Defining Immune Determinants for Vaccine Development
Authors: Ramaiah Arunachalam , Arumugaswami Vaithilingaraja 
Published: January 2020

ABSTRACTNovel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak in the city of Wuhan, China during December 2019, has now spread to various countries across the globe triggering a heightened containment effort. This human pathogen is a member of betacoronavirus genus carrying 30 kilobase of single positive-sense RNA genome. Understanding the evolution, zoonotic transmission, and source of this novel virus would help accelerating containment and prevention efforts. The present study reported detailed analysis of SARS-CoV-2 genome evolution and potential candidate peptides for vaccine development. This new coronavirus genotype might have been evolved from a bat-coronavirus by accumulating non-synonymous mutations, indels, and recombination events. Structural proteins Spike (S), and Membrane (M) had extensive mutational changes, whereas Envelope (E) and Nucleocapsid (N) proteins were very conserved suggesting differential selection pressures exerted on SARS-CoV-2 during evolution. Interestingly, SARS-CoV-2 Spike protein contains a 39 nucleotide sequence insertion relative to SARS-like bat-SL-CoVZC45/2017. Furthermore, we identified eight high binding affinity (HBA) CD4 T-cell epitopes in the S, E, M and N proteins, which can be commonly recognized by HLA-DR alleles of Asia and Asia-Pacific Region population. These immunodominant epitopes can be incorporated in universal subunit SARS-CoV-2 vaccine. Diverse HLA types and variations in the epitope binding affinity may contribute to the wide range of immunopathological outcomes of circulating virus in humans. Our findings emphasize the requirement for continuous surveillance of SARS-CoV-2 strains in live animal markets to better understand the viral adaptation to human host and to develop practical solutions to prevent the emergence of novel pathogenic SARS-CoV-2 strains.
The crystal structure of the TonB-dependent transporter YncD reveals a positively charged substrate binding site
Authors: Grinter Rhys , Lithgow Trevor 
Published: January 2020

AbstractThe outer membrane of Gram-negative bacteria is highly impermeable to hydrophilic molecules larger than 600 Da, protecting these bacteria from toxins present in the environment. In order to transport nutrients across this impermeable membrane, Gram-negative bacteria utilise a diverse family of outer-membrane proteins called TonB-dependent transporters. The majority of this family transport iron-containing substrates. However, it is becoming increasingly clear that TonB-dependent transporters target chemically diverse substrates. In this work, we investigate the structure and phylogenetic distribution of the TonB-dependent transporter YncD. We show that while YncD is present in some enteropathogens includingE. coliandSalmonellaspp., it is also widespread in Gamma and Betaproteobacteria of environmental origin. We determine the structure of YncD, showing that despite a distant evolutionary relationship, it shares structural features with the ferriccitrate transporter FecA, including a compact positively-charged substrate-binding site. Despite these shared features, we show that YncD does not contribute to the growth ofE. coliin pure culture under-iron limiting conditions or with ferric-citrate as an iron source. Previous studies on transcriptional regulation inE. colishow that YncD is not induced under iron-limiting conditions and is unresponsive to the Ferric uptake regulator (Fur). These observations combined with the data we present, suggest that YncD is not responsible for the transport of an iron-containing substrate.
The genetic structure and adaptation of Andean highlanders and Amazonian dwellers is influenced by the interplay between geography and culture
Authors: Borda Victor , Alvim Isabela , Aquino Marla M , Silva Carolina , Soares-Souza Giordano B , Leal Thiago P , Scliar Marilia O , Zamudio Roxana , Zolini Camila , Padilla Carlos , Cáceres Omar , Levano Kelly , Sanchez Cesar , Trujillo Omar , Flores-Villanueva Pedro O. , Dean Michael , Fuselli Silvia , Machado Moara , Romero Pedro E. , Tassi Francesca , Yeager Meredith , O’Connor Timothy D. , Gilman Robert H , Tarazona-Santos Eduardo , Guio Heinner 
Published: January 2020

AbstractWestern South America was one of the worldwide cradles of civilization. The well known Inca Empire was thetip of the icebergof a cultural and biological evolutionary process that started 14-11 thousand years ago. Genetic data from 18 Peruvian populations reveal that: (1) The between-population homogenization of the central-southern Andes and its differentiation with respect to Amazonian populations of similar latitudes do not extend northward. Instead, longitudinal gene flow between the northern coast of Peru, Andes and Amazonia accompanied cultural and socioeconomic interactions revealed by archeological studies. This pattern recapitulates the environmental and cultural differentiation between the fertile north, where altitudes are lower; and the arid south, where the Andes are higher, acting as a genetic barrier between the sharply different environments of the Andes and Amazonia (2). The genetic homogenization between the populations of the arid Andes is not only due to migration during the Inca Empire or the subsequent colonial period. It started at least during the earlier expansion of the pre-Inca Wari Empire (600-1000 YBP) (3) This demographic history allowed for cases of positive natural selection in the high and arid Andes vs. the low Amazon tropical forest: in the Andes,HAND2-AS1(heart and neural crest derivatives expressed 2 antisense RNA1, related with cardiovascular function) andDUOX2(dual oxidase 2, related to thyroid function and innate immunity) genes; in the Amazon, the gene encoding for the CD45 protein, essential for antigen recognition by T/B lymphocytes in viral-host interaction, consistent with thehost-virus arms racehypothesis.
Identification of Relevant Genetic Alterations in Cancer using Topological Data Analysis
Authors: Rabadán Raúl , Mohamedi Yamina , Rubin Udi , Chu Tim , Elliott Oliver , Arnés Luis , Cal Santiago , Obaya Álvaro J. , Levine Arnold J. , Cámara Pablo G. 
Published: January 2020

AbstractLarge-scale cancer genomic studies enable the systematic identification of mutations that lead to the genesis and progression of tumors, uncovering the underlying molecular mechanisms and potential therapies. While some such mutations are recurrently found in many tumors, many others exist solely within a few samples, precluding detection by conventional recurrence-based statistical approaches. Integrated analysis of somatic mutations and RNA expression data across 12 tumor types reveals that mutations of cancer genes are usually accompanied by substantial changes in expression. We use topological data analysis to leverage this observation and uncover 38 elusive candidate cancer-associated genes, including inactivating mutations of the metalloproteinase ADAMTS12 in lung adenocarcinoma. We show thatADAMTS12−/−mice have a five-fold increase in the susceptibility to develop lung tumors, confirming the role ofADAMTS12as a tumor suppressor gene. Our results demonstrate that data integration through topological techniques can increase our ability to identify previously unreported cancer-related alterations.
MAGGIE: leveraging genetic variation to identify DNA sequence motifs mediating transcription factor binding and function
Authors: Shen Zeyang , Hoeksema Marten A , Ouyang Zhengyu , Benner Christopher , Glass Christopher K 
Published: January 2020

AbstractGenetic variation in regulatory elements can alter transcription factor (TF) binding by mutating a TF binding motif, which in turn may affect the activity of the regulatory elements. However, it is unclear which TFs are prone to be affected by a given variant. Current motif analysis tools either prioritize TFs based on motif enrichment without linking to a function or are limited in their applications due to the assumption of linearity between motifs and their functional effects. Here, we present MAGGIE, a novel method for identifying motifs mediating TF binding and function. By leveraging measurements from diverse genotypes, MAGGIE uses a statistical approach to link mutation of a motif to changes of an epigenomic feature without assuming a linear relationship. We benchmark MAGGIE across various applications using both simulated and biological datasets and demonstrate its improvement in sensitivity and specificity compared to the state-of-the-art motif analysis approaches. We use MAGGIE to reveal insights into the divergent functions of distinct NF-κB factors in the pro-inflammatory macrophages, showing its promise in discovering novel functions of TFs. The Python package for MAGGIE is freely available athttps://github.com/zeyang-shen/maggie.
Combined impact of pesticides and other environmental stressors on taxonomic richness of freshwater animals in irrigation ponds
Authors: Ito Hiroshi C. , Shiraishi Hiroaki , Nakagawa Megumi , Takamura Noriko 
Published: January 2020

AbstractRice paddy irrigation ponds can sustain surprisingly high taxonomic richness and make significant contributions to regional biodiversity. We evaluated the impacts of pesticides and other environmental stressors on the taxonomic richness of freshwater animals in 21 irrigation ponds in Japan. We sampled a wide range of freshwater animals (reptiles, amphibians, fishes, mollusks, crustaceans, insects, annelids, bryozoans, and sponges) and surveyed environmental variables related to pesticide contamination, eutrophication, decreased macrophyte coverage, physical habitat destruction, and invasive alien species. Statistical analyses comprised contraction of highly correlated environmental variables, best-subset model selection, stepwise model selection, and permutation tests. Results showed that: (i) probenazole (fungicide) was the unique significant stressor on fish (i.e., contamination with this compound had a significantly negative correlation with fish taxonomic richness), (ii) the interaction of BPMC (insecticide; also known as fenobucarb) and bluegill (invasive alien fish) was a significant stressor on a “large insect” category (Coleoptera, Ephemeroptera, Hemiptera, Lepidoptera, Odonata, and Trichoptera), (iii) the interaction of BPMC and concrete bank was a significant stressor on an “invertebrate” category, (iv) the combined impacts of BPMC and the other stressors on the invertebrate and large insect categories resulted in an estimated mean loss of taxonomic richness by 15% and 77%, respectively, in comparison with a hypothetical pond with preferable conditions.
Modelling the combined effects of hydrogen traps and surface films on hydrogen permeation in ferritic steels
Authors: Zhi Huihui , Yu Haiyang , Gao Lei , Zhang Zhiliang , Su Yanjing 
Published: January 2020

Purpose
The purpose of this study is to develop a model extending Oriani’s formula by introducing a normalised concentration to simulate hydrogen diffusion in a multi-material system such as coated steels, under the presence of traps.

Design/methodology/approach
Implemented through the finite element method based on the analogy between mass diffusion and heat transfer, the governing equation was applied to investigate the combined effects of hydrogen traps and surface oxide films on hydrogen permeation in ferritic steels.

Findings
This study shows that the effective diffusivity varies over several orders of magnitude depending on the traps and films. This explains the divergence of measured hydrogen diffusivities in steels. It is revealed that hydrogen permeation in steels with Pd or Ni film is a trapping-dominant transport process, while hydrogen permeation in steel with oxide film is a process controlled by both trapping effect and retarding effect of oxide film. The oxide film enhances total hydrogen concentration within the steel substrate and is therefore detrimental. The Pd or Ni film has a little influence on total hydrogen concentration distribution depending on trapping energy.

Originality/value
Hydrogen flux curves and transient hydrogen concentration distributions can be directly obtained through the developed model. The proposed approach can also be extended to investigate other interstitial (i.e. carbon, oxygen and nitrogen) diffusion with traps revisited in complex systems.
Multidisciplinary design optimization using knowledge management applied to an electronic throttle
Authors: Mcharek Mehdi , Azib Toufik , Hammadi Moncef , Larouci Cherif , Choley Jean-Yves 
Published: January 2020

Purpose
Within the current industrial context, companies aim to decrease the design process time and cost. The multidisciplinary design optimization (MDO) appears as a solution to accelerate the process and support designers in different stages of the design cycle. However, this relatively new concept needs to be integrated efficiently in the industrial environment and issues related to collaboration, data management, traceability and reuse need to be overcome.

Design/methodology/approach
The aim of this work is to efficiently integrate the MDO in the industrial design cycle by means of knowledge management (KM) techniques. To take into account the industrial environment, the methodology was applied in a collaborative software.

Findings
An example of collaborative design and optimization of an electronic throttle body (ETB) controller is presented with industrial requirements. The design problem was solved successfully and demonstrates the efficiency of the methodology in collaborative environments.

Originality/value
The contributions of this work lie in the structuration of the knowledge to support MDO and the definition of a general way to connect the existent MDO tools to the knowledge base. This methodology will enable to freely link different steps of the design process and reduce considerably the setting time of MDO in industries.
Stochastic investigation of graphene structures with efficient polynomial models
Authors: Zygiridis Theodoros , Amanatiadis Stamatis A. , Karamanos Theodosios , Kantartzis Nikolaos V. 
Published: January 2020

Purpose
The extraordinary properties of graphene render it ideal for diverse contemporary and future applications. Aiming at the investigation of certain aspects commonly overlooked in pertinent works, the authors study wave-propagation phenomena supported by graphene layers within a stochastic framework, i.e. when uncertainty in various factors affects the graphene’s surface conductivity. Given that the consideration of an increasing number of graphene sheets may increase the stochastic dimensionality of the corresponding problem, efficient surrogates with reasonable computational cost need to be developed.

Design/methodology/approach
The authors exploit the potential of generalized Polynomial Chaos (PC) expansions and develop low-cost surrogates that enable the efficient extraction of the necessary statistical properties displayed by stochastic graphene-related quantities of interest (QoI). A key step is the incorporation of an initial variance estimation, which unveils the significance of each input parameter and facilitates the selection of the most appropriate basis functions, by favoring anisotropic formulae. In addition, the impact of controlling the allowable input interactions in the expansion terms is investigated, aiming at further PC-basis elimination.

Findings
The proposed stochastic methodology is assessed via comparisons with reference Monte-Carlo results, and the developed reduced basis models are shown to be sufficiently reliable, being at the same time computationally cheaper than standard PC expansions. In this context, different graphene configurations with varying numbers of random inputs are modeled, and interesting conclusions are drawn regarding their stochastic responses.

Originality/value
The statistical properties of surface-plasmon polaritons and other QoIs are predicted reliably in diverse graphene configurations, when the surface conductivity displays non-trivial uncertainty levels. The suggested PC methodology features simple implementation and low complexity, yet its performance is not compromised, compared to other standard approaches, and it is shown to be capable of delivering valid results.
Critical success factors of the continued usage of digital library successful implementation in military-context
Authors: Abdul Rahman Abdul Rahim , Mohezar Suhana , Habidin Nurul Fadly , Mohd Fuzi Nursyazwani 
Published: January 2020

Purpose
This paper aims to identify the critical success factors of the continued usage of digital library (DL) successful implementation from the perspective of users with organisation support factors as key antecedents.

Design/methodology/approach
Based on the extensive literature review, this study has constructed a conceptual framework based on organisational support perspectives and updated Delone and McLean’s information system success model. A pilot study was carried out on a sample of 105 respondents from military-context. A survey instrument including 22 measurement items was designed to identify the level of DL information system (IS) successful implementation practices in military context. Descriptive statistical analysis and reliability analysis were used to analyse the data with SPSS software.

Findings
The findings indicate that training and education, DL environment and communication support, continuation of usage intention, net benefits and user satisfaction are the critical success factors that play key role in ensuring the continued usage DL successful implementation in military context. The military-context DL needs to obtain critical success factors of DL practices implementation to sustain its continued usage, particularly for the active users of its members.

Research limitations/implications
This study only considered the military personnel who have visited the five main military libraries. For practical implications, the development of instruments in this study may be valuable tools to evaluate DL in other DL settings in Malaysian context other than academic settings.

Originality/value
This study makes a new contribution to DL IS successful implementation practices in military context. This study also provides important information for decision-makers involved in DL IS successful implementation practices and provides useful reference for future researchers in this research area.
Mixed methods research in tourism and hospitality journals
Authors: Truong Dao , Xiaoming Liu Rose , Yu Jing (Jasper) 
Published: January 2020

Purpose
This paper aims to examine mixed methods research (MMR) that appeared in eight tourism and hospitality journals (“Annals of Tourism Research”, “Tourism Management”, “Journal of Travel Research”, “Journal of Sustainable Tourism”, “International Journal of Contemporary Hospitality Management”, “International Journal of Hospitality Management”, “Journal of Hospitality Marketing and Management” and “Journal of Hospitality and Tourism Research”) from 1998 to 2019.

Design/methodology/approach
This review paper was a mixed methods design and was conducted in three phases. In the first phase, a content analysis was performed to determine if each article could be classified as non-empirical, qualitative, quantitative or mixed methods. In the second phase, descriptive statistics was used to present the number and characteristics of MMR articles. In the third phase, the contributions of MMR to addressing particular issues in tourism and hospitality studies were investigated.

Findings
This study identified 753 mixed methods articles, wherein 482 articles (64%) were published in the chosen tourism publication outlets and 271 (36%) in the chosen hospitality publication outlets. MMR studies having a dominant focus on specific methods (459 articles; 61%) outnumbered those having an equal focus on the qualitative and quantitative parts (294 articles; 39%). In case one method was dominant, this was typically the quantitative. Sequential data collection was prevalent in most of the cases (94.2%). The contributions of MMR to addressing generic and specific research problems were also analyzed.

Originality/value
This is the first comparison of MMR in major tourism and hospitality journals.