bluuebunny/crossref_metadata_2025_split huggingface dataset:
A parental transcriptional response to microsporidia infection induces inherited immunity in offspring
Authors: Willis Alexandra R. , Zhao Winnie , Sukhdeo Ronesh , Wadi Lina , El Jarkass Hala Tamim , Claycomb Julie M. , Reinke Aaron W. 
Published: October 2020

AbstractInherited immunity is an emerging field and describes how the transfer of immunity from parents to offspring can promote progeny survival in the face of infection. The mechanisms of how inherited immunity is induced are mostly unknown. The intracellular parasiteNematocida parisiiis a natural microsporidian pathogen ofCaenorhabditis elegans. Here, we show thatN. parisii-infected worms produce primed offspring that are resistant to microsporidia infection. We find that immunity is induced in a dose dependent manner and lasts for a single generation. Intergenerational immunity prevents host cell invasion byN. parisiiand also enhances survival to the bacterial pathogenPseudomonas aeruginosa. Further, we show that inherited immunity is triggered by the host transcriptional response to infection, which can also be induced through maternal somatic depletion of negative regulators PALS-22 and the retinoblastoma protein ortholog LIN-35. We show that other biotic and abiotic stresses, such as viral infection and cadmium exposure, that induce a similar transcriptional response to microsporidia can also induce immunity in progeny. Our results demonstrate that distinct stimuli can induce inherited immunity to provide resistance against multiple classes of pathogens. These results show that activation of an innate immune response can provide protection against pathogens not only within a generation, but also in the next generation.
HiC-DC+: systematic 3D interaction calls and differential analysis for Hi-C and HiChIP
Authors: Sahin Merve , Wong Wilfred , Zhan Yingqian , Van Deynze Kinsey , Koche Richard , Leslie Christina S. 
Published: October 2020

AbstractWe present HiC-DC+, a software tool for Hi-C/Hi-ChIP interaction calling and differential analysis using an efficient implementation of the HiC-DC statistical framework. HiC-DC+ integrates with popular preprocessing and visualization tools, includes TAD and A/B compartment callers, and outperformed existing tools in H3K27ac HiChIP benchmarking as validated by CRISPRi-FlowFISH. Differential HiC-DC+ analysis recovered global principles of 3D organization during cohesin perturbation and differentiation, including TAD aggregation, enhancer hubs, and promoter-enhancer loop dynamics.
Expansion of gamma-butyrolactone signaling molecule biosynthesis to phosphotriester natural products
Authors: Kudo Yuta , Awakawa Takayoshi , Du Yi-Ling , Jordan Peter A. , Creamer Kaitlin E. , Jensen Paul R. , Linington Roger G. , Ryan Katherine S. , Moore Bradley S. 
Published: October 2020

AbstractBacterial hormones, such as the iconic gamma-butyrolactone A-factor, are essential signaling molecules that regulate diverse physiological processes, including specialized metabolism. These low molecular weight compounds are common inStreptomycesspecies and display species-specific structural differences. Recently, unusual gamma-butyrolactone natural products called salinipostins were isolated from the marine actinomycete genusSalinisporabased on their anti-malarial properties. As the salinipostins possess a rare phosphotriester motif of unknown biosynthetic origin, we set out to explore its construction by the widely conserved 9-genesptoperon inSalinisporaspecies. We show through a series of in vivo and in vitro studies that thesptgene cluster dually encodes the saliniphostins and newly identified A-factor-like gamma-butyrolactones (Sal-GBLs). Remarkably, homologous biosynthetic gene clusters are widely distributed amongst many actinomycete genera, includingStreptomyces,suggesting the significance of this operon in bacteria.
Aberrant Epithelial Differentiation Contributes to Pathogenesis in a Murine Model of Congenital Tufting Enteropathy
Authors: Das Barun , Okamoto Kevin , Rabalais John , Young Jocelyn , Barrett Kim E. , Sivagnanam Mamata 
Published: October 2020

AbstractBackground & AimsCongenital Tufting Enteropathy (CTE) is an intractable diarrheal disease of infancy caused by mutation of Epithelial Cell Adhesion Molecule (EpCAM). The cellular and molecular basis of CTE pathology has been elusive. We hypothesized that the loss of EpCAM in CTE results in altered lineage differentiation and defects in absorptive enterocytes thereby contributing to CTE pathogenesis.MethodsIntestine from CTE mice was evaluated for specific markers by RT-qPCR, western blotting and immunostaining. Body weight, blood glucose and intestinal enzyme activity were also investigated. A CTE enteroid model was used to assess whether the decreased census of secretory cells could be rescued.ResultsCTE mice exhibited alterations in brush-border function, disaccharidase activity and glucose absorption, potentially contributing to nutrient malabsorption and impaired weight gain. Altered cell differentiation in CTE mice led to decreased secretory cells and increased numbers of absorptive cells, though the absorptive enterocytes lacked key features, causing brush border malfunction. Further, treatment with Notch signaling inhibitor, DAPT, increased the numbers of major secretory cell types in CTE enteroids (Graphical abstract 1).ConclusionsAlterations in intestinal epithelial cell differentiation in CTE mice favor an increase in absorptive cells at the expense of secretory cells. Although the proportion of absorptive enterocytes is increased, they lack key functional properties. We conclude that these effects underlie pathogenic features of CTE such as malabsorption and diarrhea, and ultimately the failure to thrive seen in patients. The ability of DAPT to reverse aberrant differentiation suggests a possible therapeutic strategy.SynopsisA murine model of Congenital Tufting Enteropathy exhibits altered intestinal cell differentiation, leading to increased absorptive and decreased secretory cells, which can be reversed with DAPT. Absorptive enterocytes in these mice are also dysfunctional, contributing to disease pathogenesis.Graphical Abstract
Compact and evenly distributedk-mer binning for genomic sequences
Authors: Nyström-Persson Johan , Keeble-Gagnère Gabriel , Zawad Niamat 
Published: October 2020

AbstractThe processing ofk-mers (subsequences of lengthk) is at the foundation of many sequence processing algorithms in bioinformatics, includingk-mer counting for genome size estimation, genome assembly, and taxonomic classification for metagenomics. Minimizers - orderedm-mers wherem < k- are often used to groupk-mers into bins as a first step in such processing. However, minimizers are known to generate bins of very different sizes, which can pose challenges for distributed and parallel processing, as well as generally increase memory requirements. Furthermore, although various minimizer orderings have been proposed, their practical value for improving tool efficiency has not yet been fully explored. Here we present Discount, a distributedk-mer counting tool based on Apache Spark, which we use to investigate the behaviour of various minimizer orderings in practice when applied to metagenomics data. Using this tool, we then introduce the universal frequency ordering, a new combination of frequency counted minimizers and universalk-mer hitting sets, which yields both evenly distributed binning and small bin sizes. We show that this ordering allows Discount to perform distributedk-mer counting on a large dataset in as little as 1/8 of the memory of comparable approaches, making it the most efficient out-of-core distributedk-mer counting method available.
Direct measurements of mRNA translation kinetics in living cells
Authors: Metelev Mikhail , Volkov Ivan L. , Lundin Erik , Gynnå Arvid H. , Elf Johan , Johansson Magnus 
Published: October 2020

ABSTRACTRibosome mediated mRNA translation is central to life as we know it. The cycle of translation has, however, not been characterized in a living cell. Here we have developed a live-cell ribosome-labeling method, which allows us to characterize the whole processes of finding an mRNA and translating it, using single-molecule tracking techniques. We find that more than 90% of both bacterial ribosomal subunits are engaged in elongation at any particular time, and that neither of the subunits, in general, continues translation from one open reading frame to the next on a poly-cistronic mRNA. Furthermore, we find that a variety of previously published orthogonal ribosomes, with altered anti-Shine-Dalgarno sequences, show significant binding to endogenous mRNAs, with the rate of translation initiation only modestly affected. Hence, our results suggest that other mRNA elements than the SD sequence play major roles in directing the ribosome to the correct translation start sites.
BMP signalling facilitates transit amplification in the developing chick and human cerebellum
Authors: Rook V , Haldipur P , Millen K , Butts T , Wingate RJ 
Published: October 2020

AbstractThe external granule layer (EGL) is a transient proliferative layer that gives rise to cerebellar granule cell neurons. Extensive EGL proliferation characterises the foliated structure of amniote cerebella, but the factors that regulate EGL formation, amplification within it, and differentiation from it, are incompletely understood. Here, we characterise bone morphogenic protein (BMP) signalling during cerebellar development in chick and human and show that while in chick BMP signalling correlates with external granule layer formation, in humans BMP signalling is maintained throughout the external granule layer after the onset of foliation. We also show via Immunohistochemical labelling of phosphorylated Smad1/5/9 the comparative spatiotemporal activity of BMP signalling in chick and human. Usingin-ovoelectroporation in chick, we demonstrate that BMP signalling is necessary for subpial migration of granule cell precursors and hence the formation of the external granule layer (EGL) prior to transit amplification. However, altering BMP signalling does not block the formation of mature granule neurons but significantly disrupts that pattern of morphological transitions that accompany transit amplification. Our results elucidate two key, temporally distinct roles for BMP signallingin vivoin organising first the assembly of the EGL from the rhombic lip and subsequently the tempo of granule neuron production within the EGL.Significance statementImproper development of cerebellar granule neurons can manifest in a plethora of neurodevelopmental disorders, including but not limited to medulloblastoma and autism. Many studies have sought to understand the role of developmental signalling pathways in granule cell neurogenesis, using genetic manipulation in transgenic mice. To complement these insights, we have used comparative assessment of BMP signalling during development in chick and human embryos andin vivomanipulation of the chick to understand and segregate the spatiotemporal roles of BMP signalling, yielding important insights on evolution and in consideration of future therapeutic avenues that target BMP signalling.
The Evolution of Immune Sensitivity under Immunopathological and Autoimmune Costs
Authors: Aldakak Lafi , Rühli Frank , Galipaud Matthias , Bender Nicole 
Published: October 2020

AbstractHosts with high immune sensitivity benefit from rapid recovery but suffer multiple costs thereof. We distinguish between immunopathological costs due to collateral damage and autoimmune costs due to false positives against self. Selection on sensitivity follows different trajectories depending on the cost nature and the overlap degree between host- and parasitic molecular signatures. Increased parasite virulence selects for higher immune sensitivity under immunopathological costs but low sensitivity when the costs are autoimmune, contradicting previous theoretical results. Longer lifespan of the host selects for low sensitivity under immunopathology to avoid accumulated tissue damage. Under autoimmune costs, hosts with a shorter lifespan cannot afford to shorten it further due to autoimmunity and evolve lower immune sensitivity. Longer lifespan selects for high or low sensitivity depending on the presence of immune memory. These results extend our understanding of selection on immune sensitivity and help explain phenomena like the cytokine shock and chronic infections.
Measuring pro-poor growth: a comparative study and a fuzzy logic-based method
Authors: Kacem Rami Haj , Kacem Saoussen Bel Hadj 
Published: October 2020

PurposeThis paper has two purposes. The first is to provide a critical evaluation of current methods of measuring monetary versus non-monetary pro-poor growth. The second is to propose an alternative method based on the fuzzy logic aggregation approach, which allows including both monetary and non-monetary indicators simultaneously for measuring the “global pro-poor growth”.Design/methodology/approachThe methodology that we propose is based on the fuzzy logic approach to aggregate both monetary and non-monetary indicators simultaneously and thus to calculate the “Global Welfare Index”. This index will be considered as the main global wellbeing indicator based on which a “Global Growth Incidence Curve” is constructed to analyze the pro-poor growth. 10; Also, an application of the main previous procedures for measuring monetary vs non-monetary pro-poor growth is presented to compare their results and to discuss their advantages and limitations.FindingsEmpirical validation using Tunisian data reveals that on one hand, results of the pro-poor growth analysis are very sensitive to the used measurement method and may lead to different conclusions. On the other hand, our alternative procedure may provide a more appropriate analysis of pro-poor growth given that it takes into consideration the multidimensional aspect of poverty while remaining faithful to the fundamental principle of pro-poor growth measurement.Originality/valueThe proposed method for constructing the “Global Growth Incidence Curve” is original given that it presents a new procedure to take into account both monetary and non-monetary indicators simultaneously, which allows having a more global view of the phenomenon. Also, the comparative study of the different proposed methods in the literature of measuring pro-poor growth is useful to identify their limitations and advantages.
The importance of trust for electronic commerce satisfaction: an entrepreneurial perspective
Authors: Shirazi Farid , Adam Nawal Abdalla , Shanmugam Mohana , Schultz Carsten D. 
Published: October 2020

PurposeSocial commerce has seen a prosperous growth following the rise of social media, in particular, social networking sites have established novel ways to communicate and transact between firms and people. The rise of new technologies has also directed to changes in how entrepreneurs convey their business. Despite intensive social commerce research, the challenges of social commerce for entrepreneurs have attracted less attention and especially neglected the role of trust and satisfaction in electronic commerce.Design/methodology/approachThis research use a survey to collect data. The authors use structural equation modeling-partial least square (SEM-PLS) to analysis the data. This quantitative research provides new insights in the food industry.FindingsThis research thus provides insights into social commerce by analyzing the role of trust in the relationship between customers' social media activities and customers' satisfaction. The present study finds a mediating effect of trust in developing satisfaction. Social media activities facilitate a positive level of trust that in turn creates a satisfying environment for customers in social commerce. The research provides theoretical and practical implications at the end of the study.Originality/valueThe findings provide good knowledge for the food industry to stay connected with customers and develop their satisfaction.
The impact of political connection and risk committee on corporate financial performance: evidence from financial firms in Malaysia
Authors: Aldhamari Redhwan , Mohamad Nor Mohamad Naimi , Boudiab Mourad , Mas'ud Abdulsalam 
Published: October 2020

Purpose
This study aims to examine the association between the effectiveness of risk committee (RC) and firms’ performance in Malaysian context. It also explores whether political connection has an impact on the relationship.

Design/methodology/approach
This study, using a principle components analysis, derives a factor score for RC attributes to proxy the effectiveness of RC. It also uses both accounting and market performance to measure the company performance.

Findings
Using a sample of financial firms from 2004 to 2018, this study finds that both accounting and market performance are higher for firms with an effective RC. It also finds that the effectiveness of RC in monitoring and management of risks is more pronounced for politically connected firms (PCFs). In further tests, the paper finds that RC attributes (i.e. RC independence, qualification and gender) are positively and significantly associated with accounting performance, while those of RC existence and overlap are positively and significantly related to market performance. The study also finds that RC size (RC diligence) has a positive (negative) impact on financial firms accounting and market performance. The further analysis also shows that PCFs with a separate as well as larger RCs experience both higher accounting and market performance. This study’s results are robust for concerns of endogeneity.

Practical implications
The findings of this study resolve the ongoing debates surrounding political connection by suggesting financial firms not to have politically connected board members as doing so may deteriorate their performance. This study’s results are also useful for investors, regulators and policymakers.

Originality/value
To the best of the authors’ knowledge, this study, for the first time, introduces on the interaction term between the effectiveness of RCs and political connection to empirically explore how an effective RC may reduce the potential risk of political ties. As such, this study adds to the literature and sheds light on an aspect of risk (i.e. risk stems from establishing close link with the government) that is growing in importance.
Exploring critical influencing factors for the site selection failure of waste-to-energy projects in China caused by the “not in my back yard” effect
Authors: Cong Xuhui , Wang Liang , Ma Li , Skibnewski M. 
Published: October 2020

PurposeThis study aims to explore the critical influencing factors that lead to the site selection failure of waste-to-energy (WtE) projects in China under the influence of the “Not In My Back Yard” (NIMBY) effect, which can provide references to improve the decision-making process of similar projects in the future.Design/methodology/approachThe fuzzy decision-making trial and evaluation laboratory (DEMATEL) method was used to propose an analytical framework for exploring the critical influencing factors affecting the site selection failure of WtE projects. The causal relationship between different influencing factors is finally determined on the basis of the opinions of 12 experts from universities, government departments, consulting units, planning and design units, construction units and WtE enterprises.FindingsResults showed that six crucial factors resulted in the site selection failure of WtE projects from the NIMBY effect perspective: “Insufficient public participation,” “Near the place of residence,” “Nonstandard government decision-making processes,” “Low information disclosure,” “Destroys the surrounding environment,” and “Imperfect compensation scheme.”Originality/valueResults can determine the priorities and causal relationships among the various influencing factors. The decision-making optimization suggestions can provide reference for decision- makers, thereby possibly promoting the scientific and standardization of site selection decision process.
Modelling performance measurement barriers of humanitarian supply chain
Authors: Patil Anchal , Shardeo Vipulesh , Madaan Jitender 
Published: October 2020

PurposeHumanitarian supply chain (HSC) has been constantly challenged with multiple issues due to the complex dynamics of the disaster. These issues are inevitable and interrelated. The issues produce undesirable cascading effects that make performance measurement complicated. This paper aims to identify and model the critical barriers in the HSC.Design/methodology/approachThe study identifies 17 barriers through the relevant literature and interviews with the stakeholders related to humanitarian organization (HO) in the developing economy. The barriers have been identified from strategic, technological, organizational, economic and operational point of view. Further, the barriers were ranked based on the degree of influence using the grey analytic network process (ANP) approach. The interrelationship among the influential barriers is established through modified total interpretive structural modelling (mTISM). To analyse and demonstrate the iterative consensus among the stakeholders, kappa statistics was adopted.FindingsThe barriers have been ranked to determine their extent of influence and modelled to reveal the interrelationship among them. The issues concerned with skills of personnel are the most influential barrier. Other three critical barriers identified are: chaotic operative environment, conflicting objectives of HO and lack of funding for information technology (IT) infrastructure. Appropriate funds need to be allocated towards IT infrastructure and personnel training.Originality/valueBoth quantitative and qualitative performance measurement frameworks had been proposed earlier for HSC. However, limited literature addresses the implementation issues with the available frameworks. This study advances the knowledge on performance measurement barriers of HSC and develops a functional description to identify the critical role of performance measurement in HOs. The study proposes a new version of the interpretive structure modelling, using mTISM technique, to determine the contextual interactions between various HSC performance measurement barriers.
Numerical approach to interpret the attributes of porous journal bearings using couple-stress fluid
Authors: Patil Shalini M. , Vinay C.V. , P.A. Dinesh 
Published: October 2020

Purpose
The purpose of this paper is to study the amalgamated consequences of nonNewtonian fluid and permeability for nonporous journal spinning with constant tangential velocity inside a rough porous bearing.

Design/methodology/approach
The flow is assumed to have developed under low Reynolds number, and the flow is governed by reduced Navier–Stokes equations. Based on Stokes theory for couple-stress fluid, a closed form of nonNewtonian Reynolds equation is obtained. Finite difference based multigrid method is adopted to study the various parameters of journal bearings.

Findings
It is found that bearing attributes such as pressure distribution and weight carrying capacity are commanding for nonNewtonian couple-stress fluid compared to the classical Newtonian case.

Originality/value
The multigrid method for the Reynolds equation is used, which accelerates the convergence rate of the solution and is independent of the grid size. The effects of couple-stress fluid promote the enhanced pressure distribution in the fluid. Both increased weight bearing capacity and delayed squeezing time reduce the skin-friction and hence take longer time to come in contact with each other.

Peer review
The peer review history for this article is available at: https://publons.com/publon/10.1108/ILT-02-2020-0051/