bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of a new Infectious Pancreatic Necrosis Virus (IPNV) isolate in Atlantic salmon (Salmo salar L.) that causes mortality in resistant fish
Authors: Hillestad Borghild , Johannessen Stein , Melingen Geir Olav , Moghadam Hooman K. 
Published: May 2021

AbstractInfectious pancreatic necrosis (IPN) is an important viral disease of salmonids that can affect fish during various life cycles. In Atlantic salmon, selecting for genetically resistant animals against IPN has been one of the most highly praised success stories in the history of fish breeding. The findings that resistance against this disease has a significant genetic component, which is mainly controlled by variations in a single gene, has helped to reduce the IPN outbreaks over the past decade to a great extent. In this paper, we present the identification of a new isolate of the IPN virus, from a field outbreak, that had caused mortality, even in the genetically resistant animals. We recovered and assembled the full-length genome of this virus, following deep-sequencing of an infected tissue. The comparative sequence analysis revealed that for the critical amino acid motifs, previously found to be associated with the degree of virulence, the newly identified isolate is similar to the virus’s avirulent form. However, we detected a set of deduced amino acid residues, particularly in the hypervariable region of the polyprotein, that collectively are unique to this strain compared to all other reference sequences assessed in this study. We suggest that these mutations have likely equipped the virus with the capacity to escape the host defence mechanism more efficiently, even in the genetically deemed IPN resistant animals.
Cryo-ET reveals two major tubulin-based cytoskeleton structures inToxoplasma gondii
Authors: Sun Stella Y. , Segev-Zarko Li-av , Chen Muyuan , Pintilie Grigore D. , Schmid Michael F. , Ludtke Steven J. , Boothroyd John C. , Chiu Wah 
Published: May 2021

SUMMARYIn the obligate intracellular parasite,Toxoplasma gondii, the subpellicular microtubules (SPMTs) help maintain shape, while the apical conoid (also tubulin-based) is implicated in invasion. Here, we use cryo-electron tomography to determine the molecular structures of the SPMTs and the conoid-fibrils (CFs) in vitrified and detergent-lysed parasites. Subvolume densities from detergent-extracted parasites yielded averaged density maps at subnanometer resolutions, and these were related back to their architecturein situ. An intraluminal spiral (IS) lines the interior of the 13-protofilament SPMTs, revealing a preferred orientation of these microtubules relative to the parasite’s long axis. Each CF is composed of 9 tubulin protofilaments, that produce a comma-shaped cross-section, plus additional associated components. Conoid protrusion, a crucial step in invasion, is associated with an altered pitch of each CF. The use of basic building blocks of protofilaments and different accessory proteins in one organism, illustrates the versatility of these critical structures.
Automatic instance segmentation of mitochondria in electron microscopy data
Authors: Nightingale Luke , de Folter Joost , Spiers Helen , Strange Amy , Collinson Lucy M , Jones Martin L 
Published: May 2021

ABSTRACTWe present a new method for rapid, automated, large-scale 3D mitochondria instance segmentation, developed in response to the ISBI 2021 MitoEM Challenge. In brief, we trained separate machine learning algorithms to predict (1) mitochondria areas and (2) mitochondria boundaries in image volumes acquired from both rat and human cortex with multi-beam scanning electron microscopy. The predictions from these algorithms were combined in a multi-step post-processing procedure, that resulted in high semantic and instance segmentation performance. All code is provided via a public repository.
The gut bacterial natural product colibactin triggers induction of latent viruses in diverse bacteria
Authors: Silpe Justin E. , Wong Joel W. H. , Owen Siân V. , Baym Michael , Balskus Emily P. 
Published: May 2021

AbstractColibactin is a chemically unstable small molecule genotoxin produced by multiple different bacteria, including members of the human gut microbiome.1,2 While the biological activity of colibactin has been extensively investigated in mammalian systems,3 little is known about its effects on other microorganisms. Here, we discover that colibactin targets bacteria carrying prophages, inducing lytic development via the bacterial SOS response. DNA, added exogenously, protects bacteria from colibactin, as does expressing a colibactin resistance protein (ClbS) in non-colibactin-producing cells. The prophage-inducing effects we observe apply broadly across taxonomically diverse phage-bacteria systems. Finally, we identify bacteria that possess colibactin resistance genes but lack colibactin biosynthetic genes. Many of these bacteria are infected with predicted prophages, and we show that the expression of their ClbS homologs provides immunity from colibactin-triggered induction. Our study reveals a mechanism by which colibactin production could impact microbiomes and highlights an underappreciated role for microbial natural products in influencing population-level events such as phage outbreaks.
Generative neural networks separate common and specific transcriptional responses
Authors: Lee Alexandra J. , Mould Dallas L. , Crawford Jake , Hu Dongbo , Powers Rani K. , Doing Georgia , Costello James C. , Hogan Deborah A. , Greene Casey S. 
Published: May 2021

AbstractGenome-wide transcriptome profiling identifies genes that are prone to differential expression across contexts (“common DEGs”), as well as genes with changes specific to the experimental manipulation. Distinguishing common DEGs from those that are specifically changed in a context of interest allows more efficient prediction of which genes are specific to a given biological process under scrutiny. Currently, commonly differentially expressed genes or pathways can only be identified through the laborious manual curation of highly controlled experiments, an inordinately time-consuming and impractical endeavor. Here we pioneer an approach for identifying common patterns using generative neural networks. This approach produces a background set of transcriptomic experiments from which a null distribution of gene and pathway changes can be generated. By comparing the set of differentially expressed genes found in a target experiment against the generated background set, common results can be easily separated from specific ones. This “Specific cOntext Pattern Highlighting In Expression data” (SOPHIE) approach is broadly applicable to new platforms or any species with a large collection of gene expression data. We apply SOPHIE to diverse datasets including those from human, human cancer, and the bacterial pathogen Pseudomonas aeruginosa. SOPHIE identifies common DEGs in concordance with previously described, manually and systematically determined common DEGs. Further, molecular validation indicates that SOPHIE detects highly specific, but low magnitude, biologically relevant, transcriptional changes. SOPHIE’s measure of specificity can complement log fold change values generated from traditional differential expression analyses. For example, by filtering the set of differentially expressed genes, one can identify those genes that are specifically relevant to the experimental condition of interest. Consequently, these results can inform future research directions.
Preservation of HIV-1 Gag helical bundle symmetry by bevirimat is central to maturation inhibition
Authors: Pak Alexander J. , Purdy Michael D. , Yeager Mark , Voth Gregory A. 
Published: May 2021

AbstractThe assembly and maturation of human immunodeficiency virus type-1 (HIV-1) requires proteolytic cleavage of the Gag polyprotein. The rate-limiting step resides at the junction between the capsid protein CA and spacer peptide 1, which assembles as a six-helix bundle (6HB). bevirimat (BVM), the first-in-class maturation inhibitor drug, targets the 6HB and impedes proteolytic cleavage, yet the molecular mechanisms of its activity, and relatedly, the escape mechanisms of mutant viruses, remain unclear. Here, we employed extensive molecular dynamics (MD) simulations and free energy calculations to quantitatively investigate molecular structure-activity relationships, comparing wild-type and mutant viruses in the presence and absence of BVM and inositol hexakisphosphate (IP6), an assembly cofactor. Our analysis shows that the efficacy of BVM is directly correlated with preservation of six-fold symmetry in the 6HB, which exists as an ensemble of structural states. We identified two primary escape mechanisms, and both lead to loss of symmetry, thereby facilitating helix uncoiling to aid access of protease. Our findings also highlight specific interactions that can be targeted for improved inhibitor activity and support the use of MD simulations for future inhibitor design.
The view from the front line: shifting beneficiary accountability and interrelatedness in the time of a global pandemic
Authors: Yates David , Difrancesco Rita Maria 
Published: May 2021

PurposeWe discuss the beneficiary accountability implications that arose due to the COVID-19 pandemic (and resultant social distancing restrictions) for a branch of a religious non-governmental organisation (NGO) based in mainland Spain, whose main beneficiaries are homeless individuals.Design/methodology/approachWe utilise a singular case method to observe accountability implications in the case organisation. We also utilise two sources of primary data: eight semi-structured interviews with volunteers of the NGO branch, supported by auto-ethnographic data recorded in forty-six diary entries throughout the period of research.FindingsAs the main mechanism for the discharge of beneficiary accountability for the case organisation is through action, this was affected greatly by the COVID-19 pandemic and social distancing measures. Beneficiary accountability (discharged through action) changed rapidly, resulting in neglect of previous beneficiaries, carrying profound implications for charitable actors, beneficiaries and the organisation.Research limitations/implicationsOur case focuses on that of a small organisation, and therefore the generalisability of findings will be somewhat limited and context specific. The number of interviews (eight) is also relatively small.Practical implicationsInsights can be drawn for the management of volunteers, alignment of personally held accountabilities of internal actors with those of organisations and emotional aspects of accountability for NGO managers and organisers.Originality/valueNGO accountability theorisation is enhanced via the use of Levinas' Judaic writings concerning the importance of the ritual practice of ethics for the individual involved in charitable action. The intertwined nature of personal accountability of volunteers and beneficiary accountability for the organisation is emphasised.
Learning accounting through visual representations
Authors: Sithole Seedwell , Datt Ragini , de Lange Paul , Tharapos Meredith 
Published: May 2021

Purpose
The purpose of this study is to investigate the effectiveness of diagrammatic visualisation techniques versus sentential learning contexts in an accounting subject using the theoretical lens of cognitive load theory (CLT).

Design/methodology/approach
The present study used four groups of students; two groups completed a task using diagrammatic visualisation learning materials, with one of the groups undertaking their leaning activities collaboratively and another on an individual basis, whereas two comparison groups were given a sentential learning context without diagrams, with one group undertaking their leaning activities collaboratively and the other individually. In addition to performance grades, cognitive load self-report scores were also elicited from participants.

Findings
The findings of this study indicate support for diagrammatic visualisation techniques for students working collaboratively. Compared with sentential learners, the authors find significantly improved test performance for students who work collaboratively in a diagrammatic visualisation environment. Students in the visualisation environments obtained higher grades than those in the sentential group. In terms of mental effort, students in the visualisation conditions reported the lowest cognitive load.

Practical implications
The authors conclude that diagrammatic visualisation learning techniques enhance student performance outcomes, particularly for those who work collaboratively. CLT assists in the understanding of the mental processes involved in learning. Instructional designers need to consider CLT when developing diagrammatic visualisation material to enable students to obtain the best possible learning outcomes.

Originality/value
This study addresses a gap in the literature by examining the use of diagrammatic visualisation materials as an alternative to text when learning accounting. The study explores the effect of visualisation material on students’ cognitive load by analysing their mental effort. The study contributes useful findings on visualisation as a conduit to enhancing the understanding of accounting using CLT principles.
New results for the realization of interfered direct-form digital filters with single two's complement nonlinearity
Authors: Kumar Mani Kant , Jha Nishant 
Published: May 2021

PurposeThis paper deals with the problem of input/output-to-state stability (IOSS) of direct-form digital filters, which simultaneously contain external disturbances and two's complement nonlinearity. The nonlinearity under consideration is confined to the sector [–1, 1], which contains saturation, zeroing, two's complement and triangular.Design/methodology/approachThe proposed condition is based on IOSS approach, which is capable of providing a framework for checking and analysing the stability of nonlinear system based on input as well as output information.FindingsA linear matrix inequality (LMI)-based new sufficient criterion for the IOSS of the suggested system is obtained. The obtained criterion is capable of detecting the output-to-state stability (OSS) and asymptotic stability of direct-form digital filters with zero external disturbances. In addition, state-norm estimator for the filter under consideration is constructed by adopting an exponential-decay IOSS criterion. Several examples are provided to illustrate the usefulness of the proposed criteria.Originality/valueThe result of the paper is introduced for the first time, and it is suitable for stability analysis of interfered direct-form digital filter with two's complement overflow using IOSS approach.
Formation and management of public debt sustainability on the example of the Republic of Kazakhstan and the Russian Federation
Authors: Mukhtarkhan Asset 
Published: May 2021

Purpose
The purpose of this paper is to study debt sustainability of countries with a resource-based economy on the example of the Republic of Kazakhstan and the Russian Federation.

Design/methodology/approach
Macroeconomic indicators and data on external and internal public debt of the Republic of Kazakhstan and the Russian Federation for the period from 2007 to 2019 were analyzed using quantitative, qualitative, comparative, descriptive and graphical methods. Based on the collected data, the indicators were calculated, analyzed and compared, taking into account the threshold values, using The Debt Sustainability Framework for Low-Income Countries of the International Monetary Fund and the World Bank.

Findings
The results of the study showed that the indicators of the public debt of both the Republic of Kazakhstan and the Russian Federation, during the period covered by the study, were in the zone of reduced risk and were stable. In addition, the study revealed a slight shift in the structure of the public debt of the Republic of Kazakhstan toward a decrease in the share of domestic borrowing (from 67% to 55%), whereas in the structure of the Russian public debt, the share of domestic borrowing increased significantly (from 52% to 74%).

Originality/value
The results of this study can be applied by scientists to analyze the sustainability of public debt in various countries and regions, as well as by officials to determine the fiscal and budgetary policies of the Republic of Kazakhstan and the Russian Federation, as well as other states.
Prioritizing Green HRM practices from policymaker’s perspective
Authors: Mehrajunnisa Mehrajunnisa , Jabeen Fauzia , Faisal Mohd Nishat , Mehmood Khalid 
Published: May 2021

Purpose
This study aims to identify and prioritize Green human resource management (GHRM) practices from the policymaker’s perspective in the United Arab Emirates (UAE)-based manufacturing and service sectors to facilitate sustainable environmental performance.

Design/methodology/approach
Drawing upon the ability–motivation–opportunity (AMO) and corporate environmentalism theory, this study uses the analytic hierarchy process (AHP), a multi-criteria decision-making model, to rank the most influential enablers of GHRM practices. Data were collected from 24 C-suite executives of UAE-based manufacturing and service units.

Findings
Top management orientation for Green, Green organizational culture and Green corporate strategic planning were the most critical enablers that promote GHRM practices in the UAE’s manufacturing and service firms. Past research has mostly overlooked the strategic variables and focused only on organizational level antecedents based on HR bundles of practices.

Research limitations/implications
Data were collected only from UAE firms, hence limiting its generalizability. The study shall help organizations operating in emerging countries adopt the best GHRM practices toward Green goal agendas.

Originality/value
This research provides an AHP framework that can be used to conceptualize and prioritize GHRM practices, which aids in a firm’s Green decision-making and transition toward sustainable Green growth. This study furthers understanding of GHRM practices play out at the various levels-of-analysis within organizations to present a comprehensive paucity of integrative and multi-level studies over recent years. The study may be relevant for other organizations in other national contexts with similar governance homogeneity.
A novel series-parallel hybrid robot for climbing transmission tower
Authors: Yao Yanzhang , Wang Wei , Qiao Yue , He Zhihang , Liu Fusheng , Li Xuelong , Liu Xinxin , Zou Dehua , Zhang Tong 
Published: May 2021

Purpose
The purpose of this paper is to describe the design and development of a novel series-parallel robot, which aims to climb on the transmission tower.

Design methodology approach
This study introduces a hybrid robot, which consists of adsorption and two 3-degree of freedom (DOF) translation parallel legs connected by a body linkage. The DOF of the legs ensures that the robot can move on the climbing plane, also contribute to a compact design of the robot. An electromagnet is used to adsorb onto the transmission tower, simplifying the overall structure. Based on the robot design, this paper further defines its climbing gait and adopt the 6th B-spline curves for climbing trajectory planning under different working environments.

Findings
The developed prototype that implements the design of the robot, which was used in simulation and experiments, showing that the robot is capable of climbing in the test environments with the planned climbing gait.

Originality value
The hybrid robot is able to climb under varying degrees of inclinations and cross the obstacles, and the magnetic attraction can ensure stable climbing.
Corporate cash holdings and firm life cycle: evidence from China
Authors: Rehman Ajid Ur , Ahmad Tanveer , Hussain Shahzad , Hassan Shoaib 
Published: May 2021

Purpose
The purpose of this paper is to investigate how corporate cash holdings changes across firm life cycle and how firms undergo heterogeneous dynamic cash adjustment as they advance from one stage to the next stage.

Design/methodology/approach
This study uses an extensive data set of 2,994 Chinese A-listed firms. The authors use generalized method of moments (GMM) and Fisher Panel unit root testing to investigate the targeting behavior of Chinese firms.

Findings
The uni-variate investigation reveals that firms in the growth stage exhibits the highest cash levels and firms in the decline stage report the lowest cash levels. As growth firms have high investment needs, they may require raising external capital to meet investment needs. To avoid the costly external financing, firms in growth stage tend to hold more cash. The GMM estimation reveals that along all the phases of firm life cycle there are evidences of trade-off behavior of corporate cash holdings. The authors report that adjustment rate increases as firms enters into the growth stage.

Practical implications
The findings provide both theoretical and practical insight to align cash policies with the available strategic choices along firm life cycle in an emerging market characterized by market imperfections.

Originality/value
The study is unique from the context that it is applying robust methodology to one of rarely investigated area in corporate cash policy. The peculiar Chinese study setting characterized by higher information asymmetry, high cost of external financing and heterogeneous access to financing sources provide theoretical and empirical underpinnings to investigate and gain insight about how corporate cash policy can be aligned with strategic choices available across different stages of life cycle.
Unmasking conflict in vertical coopetition
Authors: Rajala Anni , Tidström Annika 
Published: May 2021

Purpose
The purpose of this study is to increase understanding about vertical coopetition from the perspective of interrelated conflict episodes on multiple levels.

Design/methodology/approach
The empirical part is based on a qualitative single case study of a coopetitive buyer-supplier relationship in the manufacturing sector.

Findings
Conflicts in vertical coopetition evolve from being merely functional and task-related to becoming dysfunctional and relationship-related, as the level of competition increases. The nature of conflict episodes influences the development of vertical coopetition, and therefore, the interrelatedness of conflict episodes is important to acknowledge.

Practical implications
Although a conflict is considered functional within a company, it may still be dysfunctional as far as the coopetitive relationship with the buyer or seller is concerned. Competition may trigger conflicts related to protecting own technology and knowledge, which may lead to termination of the cooperation, therefore coopetition should be managed in a way that balance sharing and protecting important knowledge to get advantages of coopetition.

Originality/value
The findings enhance prior research on vertical coopetition by offering new perspectives on causes of conflicts, their management, outcomes and types. The value of taking a multilevel approach lies in the ability to show how conflicts occur and influence other conflicts through the interrelatedness of conflict elements on different levels.