bluuebunny/crossref_metadata_2025_split huggingface dataset:
OASIS evaluation of the French surveillance network for antimicrobial resistance in diseased animals (RESAPATH): success factors at the basis of a well-performing volunteer system
Authors: Mader R. , Jarrige N. , Haenni M. , Bourély C. , Madec J.-Y. , Amat J.-P. 
Published: April 2021

SummaryAntimicrobial resistance is a One Health issue requiring the development of surveillance systems in the human, environmental and animal sectors. In Europe, the surveillance of antimicrobial resistance on zoonotic pathogens and indicator bacteria in healthy food-producing animals has been implemented on a legal basis, while countries are also expected to extend their surveillance to diseased animals in the frame of national action plans. In this context, evaluating existing antimicrobial resistance surveillance systems in veterinary medicine is important to improve systems in place, but also to help other countries learn from these experiences, understand success factors and anticipate challenges. With this aim, the French surveillance network for antimicrobial resistance in bacteria from diseased animals (RESAPATH) was evaluated using the OASIS assessment tool. Key performance factors included (i) a strong and inclusive central institutional organization defining clear and well-accepted surveillance objectives, scope and procedures, (ii) strong skills in epidemiology and microbiology and (iii) a win-win approach enabling the volunteer participation of 71 field laboratories and where a free annual proficiency testing plays a pivotal role. The main area of improvement of RESAPATH was its time-consuming data management system.
Portrait of a genus: the genetic diversity ofZea
Authors: Chen Lu , Luo Jingyun , Jin Minliang , Yang Ning , Liu Xiangguo , Peng Yong , Li Wenqiang , Qing Liu , Yin Yuejia , Ye Xinnan , Yan Jiali , Zhang Qinghua , Zhang Xiaoting , Gui Songtao , Wu Shenshen , Wang Yuebin , Luo Yun , Jiang Chengling , Deng Min , Jin Min , Jian Liumei , Yu Yanhui , Zhang Maolin , Yang Xiaohong , Hufford Matthew B. , Fernie Alisdair R. , Warburton Marilyn L. , Ross-Ibarra Jeffrey , Yan Jianbing 
Published: April 2021

AbstractMaize is a globally valuable commodity and one of the most extensively studied genetic model organisms. However, we know surprisingly little about the extent and potential utility of the genetic variation found in the wild relatives of maize. Here, we characterize a high-density genomic variation map from ~700 genomes encompassing maize and all wild taxa of the genusZea, identifying over 65 million single nucleotide polymorphisms (SNPs), 8 million Insertion/Deletion (InDel) polymorphisms, and over one thousand novel inversions. The variation map reveals evidence of selection within taxa displaying novel adaptations such as perenniality and regrowth. We focus in detail on evidence of convergent adaptation in highland teosinte and temperate maize. This study not only indicates the key role of hormone related pathways in highland adaptation and flowering time related pathways in high latitude adaptation, but also identifies significant overlap in the genes underlying adaptations to both environments. To show how this data can identify useful genetic variants, we generated and characterized novel mutant alleles for two flowering time candidate genes. This work provides the most extensive sampling to date of the genetic diversity inherent in the genusZea, resolving questions on evolution and identifying adaptive variants for direct use in modern breeding.
Automatic structural analysis of bioinspired percolating network materials using graph theory
Authors: Vecchio Drew , Mahler Samuel , Hammig Mark D. , Kotov Nicholas A. 
Published: April 2021

ABSTRACTMimicking numerous biological membranes and nanofiber-based tissues, there are multiple materials that are structured as percolating nanoscale networks (PPNs). They reveal unique combination of properties and the family of PNN-based composites and nanoporous materials is rapidly expanding. Their technological significance and the necessity of their structural design require a unifying approach for their structural description. However, their complex aperiodic architectures are difficult to describe using traditional methods that are tailored for crystals. A related problem is the lack of computational tools that enable one to capture and enumerate the patterns of stochastically branching fibrils that are typical for these composites. Here, we describe a conceptual methodology and a computational package,StructuralGT,to automatically produce a graph theoretical (GT) description of PNNs from various micrographs. Using nanoscale networks formed by aramid nanofibers (ANFs) as examples, we demonstrate structural analysis of PNNs with 13 GT parameters. Unlike qualitative assessments of physical features employed previously,StructuralGTallows quantitative description of the complex structural attributes of PNNs enumerating the network’s morphology, connectivity, and transfer patterns. Accurate conversion and analysis of micrographs is possible for various levels of noise, contrast, focus, and magnification while a dedicated graphical user interface provides accessibility and clarity. The GT parameters are expected to be correlated to material properties of PNNs (e.g. ion transport, conductivity, stiffness) and utilized by machine learning tools for effectual materials design.Table of Content
Chemotherapy induces a YAP1-dependent fetal conversion to human Colorectal Cancer cells that is predictive of poor patient outcome
Authors: Solé Laura , Lobo-Jarne Teresa , Villanueva Alberto , Vert Anna , Guillén Yolanda , Sangrador Irene , Barbachano Antonio , Lop Joan , Guix Marta , Salido Marta , Bellosillo Beatriz , García-Romero Raquel , Garrido Marta , González Jessica , Martínez-Iniesta María , Lopez-Arribillaga Erika , Salazar Ramón , Montagut Clara , Torres Ferrán , Iglesias Mar , Celià-Terrassa Toni , Muñoz Alberto , Bigas Anna , Espinosa Lluís 
Published: April 2021

AbstractCurrent therapy against colorectal cancer is based on DNA-damaging agents that eradicate highly proliferative malignant cells. Whether sublethal chemotherapy affects tumor cell behavior and impacts on patient outcome is primarily unstudied. We now show that sublethal chemotherapy imposes a quiescent-like state to p53 wildtype human colorectal cancer (CRC) cells that is linked to the acquisition of a fetal phenotype downstream of YAP1, similar to that observed after intestinal damage. CRC cells displaying this fetal phenotype exhibit tumor- initiating activity comparable to untreated cells but superior metastatic capacity. Notably, nuclear YAP1 accumulation, or detection of the fetal signature in tumors predict poor prognosis in CRC patients carrying p53 wildtype tumors. Collectively, our results uncover a potential adverse response of tumor cells to suboptimal chemotherapy, and identify nuclear YAP1 and fetal conversion of colorectal tumors as biomarkers for prognosis and therapy prescription.Statement of significanceChemotherapy induces a quiescent-like phenotype to colorectal cancer cells that is linked to the acquisition of a YAP1-dependent fetal signature. Notably, this signature is predictive of patient outcome in different cohorts of human colorectal cancer.
Sequence specificity in DNA binding is determined by association rather than dissociation
Authors: Marklund Emil , Mao Guanzhong , Deindl Sebastian , Elf Johan 
Published: April 2021

AbstractSequence-specific binding of proteins to DNA is essential for accessing genetic information. Here, we derive a simple equation for target-site recognition, which uncovers a previously unrecognized coupling between the macroscopic association and dissociation rates of the searching protein. Importantly, this relationship makes it possible to recover the relevant microscopic rates from experimentally determined macroscopic ones. We directly test the equation by observing the binding and unbinding of individuallacrepressor (LacI) molecules during target search. We find that LacI dissociates from different target sequences with essentially identical microscopic dissociation rates. Instead, sequence specificity is determined by the efficiency with which the protein recognizes different targets, effectively reducing its risk of being retained on a non-target sequence. Our theoretical framework also accounts for the coupling between off-target binding and unbinding of the catalytically inactive Cas9 (dCas9), showing that the binding pathway can be obtained from macroscopic data.One Sentence SummaryAssociation and dissociation rates are anti-correlated for reactions that include a nonspecific probing step.
SMaSH:A scalable, general marker gene identification framework for single-cell RNA sequencing and Spatial Transcriptomics
Authors: Nelson M. E. , Riva S. G. , Cvejic A. 
Published: April 2021

AbstractSpatial transcriptomics is revolutionising the study of single-cell RNA and tissue-wide cell heterogeneity, but few robust methods connecting spatially resolved cells to so-called marker genes from single-cell RNA sequencing, which generate significant insight gleaned from spatial methods, exist. Here we presentSMaSH, a general computational framework for extracting key marker genes from single-cell RNA sequencing data for spatial transcriptomics approaches.SMaSHextracts robust and biologically well-motivated marker genes, which characterise the given data-set better than existing and limited computational approaches for global marker gene calculation.
SorCS2 deletion leads to altered neuronal lysosome activity
Authors: Almeida Sérgio , Miranda André M. , Tóth Andrea E. , Nielsen Morten S. , Oliveira Tiago Gil 
Published: April 2021

AbstractVps10p domain receptors are important for regulating intracellular protein sorting within the central nervous system and as such constitute risk factors for different brain pathologies. Here, we show that removal of SorCS2 leads to altered lysosomal activity in mouse primary neurons. SorCS2-/-neurons show elevated lysosomal markers such as LAMP1 and acidic hydrolases including cathepsin B and D. Despite increased levels, SorCS2-/-neurons fail to degrade cathepsin specific substrates in a live context. SorCS2-deficient mice present an increase in lysolipids, which may contribute to membrane permeabilization and increased susceptibility to lysosomal stress. Our findings highlight SorCS2 as an important factor for a balanced neuronal lysosome milieu.
Performance Determinants of Unsupervised Clustering Methods for Microbiome Data
Authors: Shi Yushu , Zhang Liangliang , Peterson Christine , Do Kim-Anh , Jenq Robert 
Published: April 2021

ABSTRACTBackgroundIn microbiome data analysis, unsupervised clustering is often used to identify naturally occurring clusters, which can then be assessed for associations with characteristics of interest. In this work, we systematically compared beta diversity and clustering methods commonly used in microbiome analyses. We applied these to four published datasets where highly distinct microbiome profiles could be seen between sample groups.ResultsAlthough no single method outperformed the others consistently, we did identify key scenarios where certain methods can underperform. Specifically, the Bray Curtis metric resulted in poor clustering in a dataset where high-abundance OTUs were relatively rare. In contrast, the unweighted UniFrac metric clustered poorly when used on a dataset with a high prevalence of low-abundance OTUs. To test our proposition, we systematically modified properties of the poorly performing datasets and found that this approach resulted in improved Bray Curtis and unweighted UniFrac performance. Based on these observations, we rationally combined the Bray Curtis metric and the unweighted UniFrac metrics and found that this new beta diversity metric showed high performance across all datasets. We also evaluated our findings by examining a clinical dataset where clusters are less separated.ConclusionsOur systematic evaluation of clustering performance in these five datasets demonstrates that there is no existing clustering method that universally performs best across all datasets. We propose a combined metric of Bray Curtis and unweighted UniFrac that capitalizes on the complementary strengths of the two metrics.
Structure and Stability of the designer protein WRAP-T and its permutants
Authors: Mylemans Bram , Lee Xiao Yin , Laier Ina , Helsen Christine , Voet Arnout R.D. 
Published: April 2021

Abstractβ-Propeller proteins are common natural disc-like pseudo-symmetric proteins that contain multiple repeats (‘blades’) each consisting of a 4-stranded anti-parallelβ-sheet. So far, 4- to 12-bladedβ-propellers have been discovered in nature showing large functional and sequential variation. Using computational design approaches, we created perfectly symmetricβ-propellers out of natural pseudo-symmetric templates. These proteins are useful tools to study protein evolution of this very diverse fold. While the 7-bladed architecture is the most common, no symmetric 7-bladed monomer has been created and characterized so far. Here we describe such a engineered protein, based on a highly symmetric natural template, and test the effects of circular permutation on its stability. Geometrical analysis of this protein and other artificial symmetrical proteins reveals no systematic constraint that could be used to help in engineering of this fold, and suggests sequence constraints unique to eachβ-propeller sub-family.
The diffusion of accounting reform in Sri Lanka: an analysis of two layers of diffusion among three levels of government
Authors: Dissanayake Thusitha , Dellaportas Steven , Yapa Prem W.S. 
Published: April 2021

PurposeThe purpose of this study is to evaluate the implementation of accrual accounting among two layers of government in Sri Lanka. This study examines the process of diffusion and application among and between provincial governments and local governments to assess the barriers and enablers on the implementation of accrual accounting.Design/methodology/approachThe study relies on data collected through interviews with 30 accounting and finance personnel from all levels of government active in the diffusion process. Interviews were conducted to gather and assess their insights and perceptions on the diffusion of accrual accounting. The data are examined initially using Rogers (1995) “diffusion of innovation” theory to explain the factors influencing the diffusion and adoption of accrual accounting at two levels of government but the analysed primarily by comparing the perspectives of respondents between the different layers of government.FindingsThe findings show that the adoption of accrual accounting was more effective among local governments compared with provincial governments. The lack of effective communication and engagement from the leaders of the innovation failed to persuade provincial government adopters of the true value of the accounting reform. This is contrasted with local governments who openly adopted accrual accounting but not in response to pressure from provincial government, who have oversight responsibility for local governments, but in response to funding protocols initiated by the central government to account for grant funding.Research limitations/implicationsThe findings of the study should be interpreted with caution as the data are obtained from the narrow cohort of accounting and finance professionals and may not reflect the views or experience of all stakeholders involved in the diffusion of accrual accounting.Originality/valueThe paper contributes to the diffusion of accounting innovation literature by examining the role of key players in different layers of government, particularly visible among provincial governments where the lack of engagement delayed its commitment to the implementation of accrual accounting.
An empirical study of commerce students (undergraduate and postgraduate) for insurance industry in India
Authors: Gupta Ruchi 
Published: April 2021

Purpose
The purpose of this study is to find out the awareness, attitude and career preference of commerce students (undergraduate (UG) and post-graduate (PG)) for the insurance industry in India.

Design/methodology/approach
The data were collected from 800 commerce students (400 male students and 400 female students) through a structured questionnaire. The questionnaire had 18 items related to awareness, attitude and career preference for insurance. The reliability of the tool was assessed by Cronbach’s alpha. To establish the relationship between variables, cross-tabulation techniques that involved Chi-square tests were used. The conclusion was drawn based on probability values (p-value) taking the critical as 0.05 (Bivariate). The data was analyzed using SPSS.

Findings
The results revealed that commerce students-UG and PG were aware of the basics of insurance, irrespective of their gender and family income. The students have a positive attitude toward insurance, but lack awareness regarding career options in the insurance industry.

Research limitations/implications
This study included only UG and PG commerce students of Allahabad University and its constituent colleges, hence its findings cannot be generalized for the entire country.

Practical implications
This study can be beneficial to insurance companies in framing their policies as India has a huge young population. There is a need to make the students in higher education aware of the benefits of insurance to cover any unforeseen economic loss and also to make them aware of the career options in the insurance industry.

Originality/value
The present study bridges the gap between existing studies regarding awareness, attitude and career preference of students with gender and family income. To date, no study has been done to find the awareness and attitude of students toward the insurance industry, neither in terms of their becoming prospective customers nor in terms of career preference.
Disruption of qualifications in manufacturing: challenges and prospects
Authors: Tūtlys Vidmantas , Spöttl Georg 
Published: April 2021

Purpose
This paper aims to disclose the implications of the 4th Industrial Revolution for vocational and professional qualifications and their systems. It also seeks to enhance more active discussion of experts and researchers about the change of vocational and professional qualifications created by the advent of the 4th Industrial Revolution.

Design/methodology/approach
Research is based on the case studies of the design and development of vocational and professional qualifications focused on the skills requirements of the 4th Industrial Revolution. There are analyzed and compared two cases of the international (EU) projects aiming to design and implement new qualifications in the metalworking industry and the case of introduction of additional qualifications in Germany. The main research methods include content analysis of the qualifications descriptors and vocational education and training (VET) curricula, a meta-analysis of the research on the implications of Industry 4.0 for VET.

Findings
The choices of the structure and contents of qualifications and VET curricula in the context of the 4th Industrial Revolution are defined by the specific state of technologies and work organizations in the enterprises, limitations of VET providers, individual skills needs of learners, national and sectoral policies in the field of qualifications and curricula. It requires compromises between the concept of solid qualifications based on the holistic orientation to work processes and the trends toward flexible curriculum; between the design of new qualifications and adjustment of the existing ones, as well as between the individualistic and collective approaches to qualifications.

Research limitations/implications
The research is focused on the development of qualifications in the manufacturing sector (metalworking and engineering industry). The paper contributes to the theoretical discussions and research of qualifications, competence, VET and human resource development by suggesting a theoretical framework for the analysis of the development of qualifications in the context of the 4th Industrial Revolution, as well as by stressing the importance of holistic view to this development which should comprise both policies and practices of the design of qualifications, curriculum design, education and training and assessment of learning outcomes.

Originality/value
The paper provides insight into the implications of the 4th Industrial Revolution to the key processes of the national systems of qualifications by referring to the cases of current efforts to adjust qualifications in the metalworking sector and engineering industry. It also suggests possible scenarios for the future development of vocational and professional qualifications in the context of the 4th Industrial Revolution.
Comparison between maintenance policies based on q-Weibull and Weibull models
Authors: Assis Edilson M. , Figueirôa Filho Celso Luiz Santiago , Lima Gabriel Costa , Salles Gisele Maria de Oliveira , Pinto Ailton 
Published: April 2021

PurposeThe purpose of this article is to compare maintenance policies based on Weibull and q-Weibull models.Design/methodology/approachThis paper uses analytical developments, several figures and tables for graphical and numerical comparison. Previously published hydropower equipment data are used as examples.FindingsModels for optimal maintenance interval determination based on q-Weibull distribution were defined. Closed-form expressions were found, and this allows the application of the method with small computational effort.Practical implicationsThe use of the q-Weibull model to guide the definition of maintenance strategy allows decision-making to be more consistent with sample data. The flexibility of the q-Weibull model is able to produce failure rate modeling with five different formats: decreasing, constant, increasing, unimodal and U-shaped. In this way, the maintenance strategies resulting from this model should be more assertive.Originality/valueExpressions for determining the optimal interval of preventive maintenance were deduced from q-Weibull distribution. Expected costs per maintenance cycle of Brazilian hydropower equipment were calculated with q-Weibull and Weibull distributions. These results were compared in terms of absolute values and trends. Although a large number of works on corrective and preventive maintenance have been proposed, no applications of the q-Weibull distribution were found in literature.
Empathy impairs virtue: the influence of empathy and vulnerability on charitable giving
Authors: Wei Chuang , Yu Zhaoji , Li Yongli 
Published: April 2021

PurposeOnline charitable giving is prevalent, and how to attract individuals' attention to donate is essential for charities. Little is known about the interaction effect of empathy (donor) and vulnerability (receiver) on donate intention. To bridge this gap, this study aims to investigate whether the influence of empathy on charitable giving would be moderated by receivers' vulnerability, and if yes, what is the mechanism.Design/methodology/approachFive experiments were conducted in the context of charitable giving with 1,303 participants to test our hypotheses.FindingsWhen empathetic individuals confronted high vulnerable receivers, they were less likely to donate; otherwise, they were more likely to donate when they confronted low vulnerable receivers, and this interaction effect was mediated by concern about self.Originality/valueThe present research identifies a novel moderator of the effect of empathy on charitable giving and elucidates the underlying mechanism of concern about self. Based on these findings, the authors provide actionable implications for charities by demonstrating the interaction effect of empathy and vulnerability on donate intention.