bluuebunny/crossref_metadata_2025_split huggingface dataset:
REHE: Fast Variance Components Estimation for Linear Mixed Models
Authors: Yue Kun , Ma Jing , Thornton Timothy , Shojaie Ali 
Published: February 2021

AbstractLinear mixed models are widely used in ecological and biological applications, especially in genetic studies. Reliable estimation of variance components is crucial for using linear mixed models. However, standard methods, such as the restricted maximum likelihood (REML), are computationally inefficient and may be unstable with small samples. Other commonly used methods, such as the Haseman-Elston (HE) regression, may yield negative estimates of variances. Utilizing regularized estimation strategies, we propose the restricted Haseman-Elston (REHE) regression and REHE with resampling (reREHE) estimators, along with an inference framework for REHE, as fast and robust alternatives that provide non-negative estimates with comparable accuracy to REML. The merits of REHE are illustrated using real data and benchmark simulation studies.
Microbial populations are shaped by dispersal and recombination in a low biomass subseafloor habitat
Authors: Anderson Rika E. , Graham Elaina D. , Huber Julie A. , Tully Benjamin J. 
Published: February 2021

The subseafloor is a vast habitat that supports microorganisms that have a global scale impact on geochemical cycles. Many of the endemic microbial communities inhabiting the subseafloor consist of small populations under growth-limited conditions. For small populations, stochastic evolutionary events can have large impacts on intraspecific population dynamics and allele frequencies. These conditions are fundamentally different from those experienced by most microorganisms in surface environments, and it is unknown how small population sizes and growth-limiting conditions influence evolution and population structure in the subsurface. Using a two-year, high-resolution environmental time-series, we examine the dynamics of microbial populations from cold, oxic crustal fluids collected from the subseafloor site North Pond, located near the mid-Atlantic ridge. Our results reveal rapid shifts in overall abundance, allele frequency, and strain abundance across the time points observed, with evidence for homologous recombination between coexisting lineages. We show that the subseafloor aquifer is a dynamic habitat that hosts microbial metapopulations that disperse frequently through the crustal fluids, enabling gene flow and recombination between microbial populations. The dynamism and stochasticity of microbial population dynamics in North Pond suggests that these forces are important drivers in the evolution of microbial populations in the vast subseafloor habitat.Significance StatementThe cold, oxic subseafloor is an understudied habitat that is difficult to access, yet important to global biogeochemical cycles and starkly different compared to microbial habitats on the surface of the Earth. Our understanding of microbial evolution and population dynamics is largely molded by studies of microbes living in surface habitats that can host 10-1,000 times more microbial biomass than is frequently observed in the subsurface. This study provides an opportunity to observe population dynamics within a low biomass, growth-limited environment and reveals that microbial populations in the subseafloor are influenced by changes in selection pressure and gene sweeps. In addition, recombination between strains that have dispersed from elsewhere within the aquifer has an important impact on the evolution of microbial populations. Much of the microbial life on the planet exists under growth-limited conditions and the subseafloor provides a natural laboratory to explore how life evolves in such environments.
Mutation of lipoprotein processing pathway genelspAor inhibition of LspA activity by globomycin increases MRSA resistance to β-lactam antibiotics
Authors: Fingleton Claire , Zeden Merve S. , Bueno Emilio , Cava Felipe , O’Gara James P. 
Published: February 2021

AbstractTheStaphylococcus aureuscell envelope comprises numerous components, including peptidoglycan (PG), wall teichoic acids (WTA), lipoteichoic acids (LTA), targeted by antimicrobial drugs. MRSA resistance to methicillin is mediated by themecA-encoded β-lactam-resistant transpeptidase, penicillin binding protein 2a (PBP2a). However, PBP2a-dependent β-lactam resistance is also modulated by the activity of pathways involved in the regulation or biosynthesis of PG, WTA or LTA. Here, we report that mutation of the lipoprotein signal peptidase II gene,lspA, from the lipoprotein processing pathway, significantly increased β-lactam resistance in MRSA. Mutation oflgt, which encodes diacylglycerol transferase (Lgt) responsible for synthesis of the LspA substrate did not impact β-lactam susceptibility. Consistent with previous reports,lgtandlspAmutations impaired growth in chemically defined media, but not in complex broth. MRSA exposure to the LspA inhibitor globomycin also increased β-lactam resistance. Mutation oflgtin anlspAbackground restored β-lactam resistance to wild type. ThelspAmutation had no effect on PBP2a expression, PG composition or autolytic activity indicating a potential role for WTA or LTA. ThelspAandlgtmutants exhibited marginally increased resistance to the D-alanine pathway inhibitor D-cycloserine. In addition, mutation oflgtand multicopylspAexpression, but not mutation oflspA, significantly increased susceptibility to the lipoteichoic acid synthase inhibitor Congo red revealing complex interplay between lipoprotein processing mutations and the expression/stability of cell surface glycopolymers. These findings indicate that accumulation of the LspA substrate, diacylglyceryl lipoprotein, increases MRSA resistance to β-lactam antibiotics through impacts on cell envelope components other than PG.
Nonsense-mediated decay is highly stable across individuals and tissues
Authors: Teran Nicole A. , Nachun Daniel , Eulalio Tiffany , Ferraro Nicole M. , Smail Craig , Rivas Manuel A. , Montgomery Stephen B. 
Published: February 2021

AbstractPrecise interpretation of the effects of protein-truncating variants (PTVs) is important for accurate determination of variant impact. Current methods for assessing the ability of PTVs to induce nonsense-mediated decay (NMD) focus primarily on the position of the variant in the transcript. We used RNA-sequencing of the Genotype Tissue Expression v8 cohort to compute the efficiency of NMD using allelic imbalance for 2,320 rare (genome aggregation database minor allele frequency <=1%) PTVs across 809 individuals in 49 tissues. We created an interpretable predictive model using penalized logistic regression in order to evaluate the comprehensive influence of variant annotation, tissue, and inter-individual variation on NMD. We found that variant position, allele frequency, including ultra-rare and singleton variants, and conservation were predictive of allelic imbalance. Furthermore, we found that NMD effects were highly concordant across tissues and individuals. Due to this high consistency, we demonstratein silicothat utilizing peripheral tissues or cell lines provides accurate prediction of NMD for PTVs.
Horizontal transfer of microbial toxin genes to gall midge genomes
Authors: Verster Kirsten I. , Tarnopol Rebecca L. , Akalu Saron M. , Whiteman Noah K. 
Published: February 2021

AbstractA growing body of evidence points to a role for horizontal gene transfer (HGT) in the evolution of animal novelties. Previously, we discovered the horizontal transfer of the gene encoding the eukaryotic genotoxin cytolethal distending toxin B (CdtB) from theAcyrthosiphon pisumSecondary Endosymbiont (APSE) bacteriophage to drosophilid and aphid genomes. Here, we report thatcdtBis also found in the nuclear genome of the gall-forming ‘swede midge’Contarinia nasturtii(Diptera: Cecidomyiidae). We subsequently searched genome sequences of all available cecidomyiid species for evidence of microbe-to-insect HGT events. We found evidence of pervasive transfer of APSE-like toxin genes to cecidomyiid nuclear genomes. Many of the toxins encoded by these horizontally transferred genes target eukaryotic cells, rather than prokaryotes. In insects, catalytic residues important for toxin function are conserved. Phylogenetic analyses of HGT candidates indicated APSE phages were often not the ancestral donor of the toxin gene to cecidomyiid genomes, suggesting a broader pool of microbial donor lineages. We used a phylogenetic signal statistic to test a transfer-by-proximity hypothesis for HGT, which showed, that prokaryotic-to-insect HGT was more likely to occur between taxa in common environments. Our study highlights the horizontal transfer of genes encoding a new functional class of proteins in insects, toxins that target eukaryotic cells, which is potentially important in mediating interactions with eukaryotic pathogens and parasites.Significance StatementThe diversity of genes encoded by phages infecting bacterial symbionts of eukaryotes represents an enormous, relatively unexplored pool of new eukaryotic genes through horizontal gene transfer (HGT). In this study, we discovered pervasive HGT of toxin genes encoded byAcyrthosiphon pisumsecondary endosymbiont (APSE) bacteriophages and other microbes to the nuclear genomes of gall midges (Diptera: Cecidomyiidae). We found five toxin genes were transferred horizontally from phage, bacteria, or fungi into genomes of several cecidomyiid species. These genes wereaip56, cdtB, lysozyme, rhs, andsltxB. Most of the toxins encoded by these genes antagonize eukaryotic cells, and we posit that they may play a protective role in the insect immune system.
Thermal flexibility is a repeatable mechanism to cope with environmental stressors in a passerine bird
Authors: Robertson Joshua K. , Mastromonaco Gabriela F. , Burness Gary 
Published: February 2021

AbstractFor many vertebrates, urban environments are characterised by frequent environmental stressors. Coping with such stressors can demand that urban individuals activate energetically costly physiological pathways (e.g. the fight-or-flight response) more regularly than rural-living conspecifics. However, urban environments also commonly demand appreciable expenditure toward thermoregulation, owing to their often extreme climatic variations. To date, whether and how vertebrates can balance expenditure toward both the physiological stress response and thermoregulation, and thus persist in an urbanising world, remains an unanswered and urgent question among ecologists.In some species, changes in body surface temperature (Ts) and peripheral heat loss (qTot) that accompany the stress response are thought to balance energetic expenditure toward thermoregulation and responding to a stressor. Thus, augmentation of stressinduced thermal responses may be a mechanism by which urban individuals cope with simultaneously high thermoregulatory and stress-physiological demands.We tested whether stress-induced changes in Tsand qTot: (1) differed between urban- and rural-origin individuals, (2) reduce thermoregulatory demands in urban individuals relative to rural conspecifics, and (3) meet an essential first criterion for evolutionary responses to selection (variability among, and consistency within, individuals).Using the black-capped chickadee (Poecile atricapillus; n = 19), we show that neither rapid nor chronic changes in Tsand qTotfollowing exposure to randomised stressors differed between urban- and rural-origin individuals (nurban= 9; nrural= 10). Nevertheless, we do find that stress-induced changes in Tsand qTotare highly repeatable across chronic time periods (RTs= 0.61; RqTot= 0.67) and display signatures of stabilising or directional selection (i.e. reduced variability and increase repeatability relative to controls).Our findings suggest that, although urban individuals appear no more able to balance expenditure toward thermoregulation and the stress response than rural conspecifics, the capacity to do so may be subject to selection in some species. To our knowledge this is also the first study to report repeatability of any theorised stress-induced trade-off.
Unfazed: parent-of-origin detection for large and smallde novovariants
Authors: Belyeu Jonathan R. , Sasani Thomas A. , Pedersen Brent S. , Quinlan Aaron R. 
Published: February 2021

AbstractSummaryUnfazedis a command-line tool to determine the parental gamete of origin forde novomutations from paired-end Illumina DNA sequencing reads.Unfazeduses variant information for a sequenced trio to identify the parental gamete of origin by linking phase-informative inherited variants tode novomutations using read-based phasing. It achieves a high success rate by chaining reads into haplotype groups, thus increasing the search space for informative sites. Unfazed provides a simple command-line interface and scales well to large inputs, determining parent-of-origin for nearly 30,000de novovariants in under 60 hours.AvailabilityUnfazed is available athttps://github.com/ibelyeu/unfazed.
TheC. elegansDAF-19M module: a shift from general ciliogenesis to ciliary and behavioral specialization
Authors: Ahn Soungyub , Yang Heeseung , Son Sangwon , Park Dongjun , Yim Hyunsoo , Swoboda Peter , Lee Junho 
Published: February 2021

AbstractIn animals, cilia are important for the interaction with environments and the proper function of tissues and organs. Understanding the distinctive identities of each type of ciliated cell is essential for therapeutic solutions for ciliopathies, complex disorders with impairments of various organs caused by defective cilia development and function. Here, we report a regulatory module consisting of a cascade of transcription factors and their target genes that confer the cell type-specific ciliary identities on the IL2 ciliated neurons inC. elegans. We found that DAF-19M, isoform of the soleC. elegansRFX transcription factor DAF-19, through X-box promoter motif variants, heads a regulatory module in IL2 neurons, comprising the core target genesklp-6(kinesin),osm-9(TRP channel), andcwp-4(novel); under the overall control of terminal selector proteins UNC-86 and CFI-1. Considering the conservation of this DAF-19M module in IL2 neurons for nictation, a dauer larva-specific behavior, and in male-specific neurons for mating behavior, we propose the existence of an evolutionarily adaptable, hard-wired genetic module for distinct behaviors that share the feature “recognizing the environment.”
Integrated DC-AC and AC-DC converter using H-converter for wide range voltage applications
Authors: R. Saravanan , S. Vijayshankar , Sathyaseelan Sathyaseelan , K. Suresh 
Published: February 2021

Purpose
This paper aims to propose Hidden Converter (H-Converter) combined with dual port 3Ø inverter for energy storage application to produce wide range of voltage. Some of the application required wide range of voltages, but problem from E-chopper is either boost or buck mode of operations, both modes are not possible. To overcome this drawback, H-Converter is combined with dual port 3Ø inverter controlled by carrier-based pulse width modulation (CB-PWM) technique is added with zero sequence injection.

Design/methodology/approach
Hidden converter is a bidirectional DC-DC chopper used to convert fixed DC to variable DC and vice versa in both buck and boost modes of operations. Dual port inverter is combined with hidden DC-DC converter can produce wide range of voltages.

Findings
The bidirectional DC-AC converter requires less power for processing and consumes less power losses by using modest carrier built- pulse width modulation scheme through proposed zero structure addition.

Originality/value
By using this proposed strategy H-Converter can produce wide range of voltage in both the sides and mostly power is processed in the 3Ø inverter with a one stage conversion with less power loss. As a result, with one stage power conversion has more efficiency because of less power loss. This proposed converter has designed by analysis, and the real time result is tested in an experiment.
Stakeholder interaction for sustainability in seaports. Analysing the implementation and its linkages to overarching interaction efforts
Authors: Fobbe Lea , Hilletofth Per 
Published: February 2021

PurposeThis study aims to analyse how and to what extent stakeholder interaction for sustainability is implemented in organisations and the linkages to the overarching interaction efforts.Design/methodology/approachThis study was conducted in the context of seaports. To examine interaction activities with stakeholders for sustainability and how they are implemented, the study uses content analysis of sustainability reports.FindingsThe results show that the majority of ports recognise the importance of stakeholder interaction to create value and guide organisational sustainability; however, it is implemented to varying levels and degrees, which affects the form and extent of the overarching interaction efforts. The paper proposes four categories of implementing stakeholder interaction, showing the linkages to the number of stakeholder groups involved, sustainability dimensions covered and interaction approaches used.Originality/valueThis paper contributes to sustainability, stakeholder and management literature by highlighting different levels of implementation of stakeholder interaction for sustainability and its linkages to overarching efforts that may affect the sustainable development of an organisation. The results of this study provide a better understanding of stakeholder interaction within organisational sustainability approaches and implementation in sustainability-oriented business models. As organisations seek to increase their sustainability performance, these insights may be useful for both academia and practice.
Entropy generation analysis of electrical magnetohydrodynamic flow of TiO2-Cu/H2O hybrid nanofluid with partial slip
Authors: M. Venkata Subba Rao , Gireesha B.J. , Gangadhar Kotha , P. Manasa Seshakumari , Sindhu S. 
Published: February 2021

Purpose
This paper aims to address the magnetohydrodynamic boundary layer flow of hybrid mixture across a stretching surface under the influence of electric field.

Design/methodology/approach
The local similarity transformations are implemented to reformulate the governing partial differential equations into coupled non-linear ordinary differential equations of higher order. The numerical solutions are obtained for the simplified governing equations with the aid of finite difference technique.

Findings
The velocity, temperature and entropy generation are examined thoroughly for the effects of different budding parameters related to present analysis by means of graphs. It is obtained that owing to the effect of magnetic field along with slip factor, the fluid motion slowdown. However, the flow velocity enhances for the rising estimations of an electric field which tends to resolve sticky effects.

Originality/value
The three-dimensional plots are drawn to understand the nature of physical quantities. To ensure the precision, the obtained solutions are compared with the existing one for certain specific conditions. A good concurrence is observed between the proposed results and previously recorded outcomes.
A three-dimensional shoulder protector based on ergonomics for workers
Authors: Eom Ran-i , Lee Yejin 
Published: February 2021

PurposeThe use of shoulder protectors is strongly recommended when carrying objects on the shoulder to ensure the health and safety of workers. Thus, this study aimed to develop and verify an ergonomic shoulder protector that considers human body shape and carrying posture from an ergonomic perspective. Ultimately, this study will present a shoulder protector with enhanced fit and safety for carrying workers at construction sites.Design/methodology/approachThe shoulder protector was designed and printed using three-dimensional printing technology with variable side neck points and shoulder point heights to reflect the human body's shoulder line shape and to position the carried object stably on the shoulder. The developed shoulder protectors were evaluated in terms of their fit according to the work posture of the carrier, adherence upon motion and durability through structural analysis.FindingsThe design of the shoulder protector for carrying workers followed the shoulder line. It is best placed above the side neck point by 1.0 cm and above the shoulder point by 2.0 cm. Its length is slightly shorter than the human shoulder for superior fit and safety.Originality/valueThe final shoulder protector (FSP) for carrying workers reflects the body curvature while enhancing fit and safety by considering activity and protective factors. As functional studies and evaluations on the need for protectors are scarce, this study provides fundamental data in the evaluation of protective gears.
The pattern design of fabrics produced by three-channel rotor-spun colorful melange yarn
Authors: Pan Bo , Yang Xiao Yi , Yang Rui Hua 
Published: February 2021

PurposeThe purpose of this article is to design and make fabrics with colorful melange yarns spun by a three-channel rotor spinning machine.Design/methodology/approachThe three-channel digital rotor-spun machine controls the blending proportion by adjusting the feeding of three-primary color fiber slivers online, so that a piece of colorful yarn presents a variety of colors along the longitudinal direction where constant yarn linear density can be produced flexibly. Various fabric patterns can be produced by three-channel rotor-spun colorful melange yarn with different periods of color.FindingsThe fabric, made by the rotor-spun colorful melange yarn, is rich in color, clear in layers, soft in the hand and has a hazy three-dimensional effect. The product is environmentally friendly and saves energy.Originality/valueAn innovative idea to develop various colorful fabrics is proposed by combining their pattern with colorful melange yarn produced by a three-channel rotor spinning machine.