bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiple types of genomic variation contribute to adaptive traits in the mustelid subfamily Guloninae
Authors: Derežanin Lorena , Blažytė Asta , Dobrynin Pavel , Duchêne David A. , Horacio Grau José , Jeon Sungwon , Kliver Sergei , Koepfli Klaus-Peter , Meneghini Dorina , Preick Michaela , Tomarovsky Andrey , Totikov Azamat , Fickel Jörns , Förster Daniel W. 
Published: September 2021

AbstractSpecies of the mustelid subfamily Guloninae inhabit diverse habitats on multiple continents, and occupy a variety of ecological niches. They differ in feeding ecologies, reproductive strategies and morphological adaptations. To identify candidate loci associated with adaptations to their respective environments, we generated a de novo assembly of the tayra (Eira barbara), the earliest diverging species in the subfamily, and compared this with the genomes available for the wolverine (Gulo gulo) and the sable (Martes zibellina). Our comparative genomic analyses included searching for signs of positive selection, examining changes in gene family sizes, as well as searching for species-specific structural variants (SVs). Among candidate loci associated with phenotypic traits, we observed many related to diet, body condition and reproduction. For example, for the tayra, which has an atypical gulonine reproductive strategy of aseasonal breeding, we observe species-specific changes in many pregnancy-related genes. For the wolverine, a circumpolar hypercarnivore that must cope with seasonal food scarcity, we observed many changes in genes associated with diet and body condition. All types of genomic variation examined contributed substantially to the identification of candidate loci. This strongly argues for consideration of variation other than single nucleotide polymorphisms in comparative genomics studies aiming to identify loci of adaptive significance.
csdR, an R package for differential co-expression analysis
Authors: Pettersen Jakob P. , Almaas Eivind 
Published: September 2021

AbstractBackgroundDifferential co-expression network analysis has become an important tool to gain understanding of biological phenotypes and diseases. The CSD algorithm is a method to generate differential co-expression networks by comparing gene co-expressions from two different conditions. Each of the gene pairs is assigned conserved (C), specific (S) and differentiated (D) scores based on the co-expression of the gene pair between the two conditions. The result of the procedure is a network where the nodes are genes and the links are the gene pairs with the highest C-, S-, and D-scores. However, the existing CSD-implementations suffer from poor computational performance, difficult user procedures and lack of documentation.ResultsWe created the R-package csdR aimed at reaching good performance together with ease of use, sufficient documentation, and with the ability to play well with other tools for data analysis. csdR was benchmarked on a realistic dataset with 20, 645 genes. After verifying that the chosen number of iterations gave sufficient robustness, we tested the performance against the two existing CSD implementations. csdR was superior in performance to one of the implementations, whereas the other did not run. Our implementation can utilize multiple processing cores. However, we were unable to achieve more than ∼ 2.7 parallel speedup with saturation reached at about 10 cores.ConclusionsThe results suggest that csdR is a useful tool for differential co-expression analysis and is able to generate robust results within a workday on datasets of realistic sizes when run on a workstation or compute server.
Engaging the ‘A’ Class Antibody: Variable-Heavy (VH) region influencing IgA1&2 engagement of FcαRI and superantigen proteins G, A, and L
Authors: Ling Wei-Li , Su Chinh Tran-To , Lua Wai-Heng , Yeo Joshua Yi , Poh Jun-Jie , Ng Yuen-Ling , Wipat Anil , Gan Samuel Ken-En 
Published: September 2021

AbstractInterest in IgA as an alternative therapeutic and diagnostic antibody has increased over the years, yet much remains to be investigated especially given their importance in activating immune cells in blood and in mucosal immunity. Recent whole antibody-based investigations have shown significant distal effects between the variable (V) and constant (C)-regions that can be mitigated by the different hinge regions of the human IgA subtypes A1 and A2. Diving deeper into the mechanisms underlying this, systematic VH manipulations retaining the CDRs were performed on a panel of 28 IgA1s and A2s across the Trastuzumab and Pertuzumab models, revealed distal effects on FcαRI binding. Further insights from structural modelling showed these effects to also be mitigated by the differing glycosylation patterns in IgA1 and 2 to explain reversal of trends of IgA1s and 2s effected by slight changes in the CDRs. IgAs bound at the Fc showed similar trends but magnitudes better binding to Her2 with that bound by ppL, showing that ppL can sterically hinder Her2 antigen binding. Contrary to canonical knowledge, we found strong evidence of IgAs binding SpG that was narrowed to be at the CH2-3 region, and that the likely binding with SpA was beyond VH3 FWR and most likely at the CH1. VH1 was found to be the most suitable framework (FWRs) for CDR-grafting for both IgA1 and 2. With relevance to interactions with the microbiome at mucosal surfaces, mechanistic insight of how these IgAs can interact bacterial superantigens proteins G, A, and L are also discovered for potential future interventions.One Sentence SummaryAn insight into the mechanism of distal V-region effects on FCAR and superantigens proteins G, A, and L by both IgA1 and A2.
Fitness landscape analysis of a tRNA gene reveals that the wild type allele is sub-optimal, yet mutationally robust
Authors: Gabzi Tzahi , Pilpel Yitzhak , Friedlander Tamar 
Published: September 2021

AbstractFitness landscape mapping and the prediction of evolutionary trajectories on these landscapes are major tasks in evolutionary biology research. Evolutionary dynamics is tightly linked to the landscape topography, but this relation is not straightforward. Here, we analyze a fitness landscape of a yeast tRNA gene, previously measured under four different conditions. We find that the wild type allele is sub-optimal, and 8%-10% of its variants are fitter. We rule out the possibilities that the wild type is fittest on average on multiple conditions or located on a local fitness maximum. Instead, we find that the wild type is mutationally robust (‘flat’), while more fit variants are typically mutationally fragile. Similar observations of mutational robustness or flatness have been so far made in very few cases, predominantly in viral genomes.
scoMorphoFISH: A Deep-Learning enabled toolbox for single-cell single-mRNA quantification and correlative (ultra-)morphometry
Authors: Siegerist Florian , Hay Eleonora , Dikou Juan Saydou , Büscher Anja , Oh Jun , Ribback Silvia , Zimmermann Uwe , Bräsen Jan Hinrich , Lenoir Olivia , Endlich Karlhans , Tharaux Pierre-Louis , Endlich Nicole 
Published: September 2021

AbstractIncreasing the information depth of single kidney biopsies can improve diagnostic precision, personalized medicine and accelerate basic kidney research. Until now, information on mRNA abundance and morphologic analysis has been obtained from different samples, missing out on the spatial context and single-cell correlation of findings. Herein, we present scoMorphoFISH, a modular toolbox to get spatial single-cell single-mRNA expression data optimized for routinely generated kidney biopsies. Deep-Learning was used to virtually dissect tissue sections in tissue compartments and cell types to which single-cell expression data was assigned. Furthermore, we show correlative and spatial single-cell expression quantification with super-resolved podocyte foot process morphometry on the same histological section. In contrast to bulk analysis methods, this approach will help to identify local transcription changes even in less frequent kidney cell types on a spatial single-cell level with single-mRNA resolution. As this method performs well with standard formalin-fixed paraffin-embedded samples and we provide pretrained DL-networks embedded in a comprehensive image analysis workflow, this method can be applied immediately in a variety of settings.
Revealing Free Energy Landscape from MD Data via Conditional Angle Partition Tree
Authors: Jiang Hangjin , Li Han , Wong Wing Hung , Fan Xiaodan 
Published: September 2021

AbstractDeciphering the free energy landscape of biomolecular structure space is crucial for understanding many complex molecular processes, such as protein-protein interaction, RNA folding, and protein folding. A major source of current dynamic structure data is Molecular Dynamics (MD) simulations. Several methods have been proposed to investigate the free energy landscape from MD data, but all of them rely on the assumption that kinetic similarity is associated with global geometric similarity, which may lead to unsatisfactory results. In this paper, we proposed a new method called Conditional Angle Partition Tree to reveal the hierarchical free energy landscape by correlating local geometric similarity with kinetic similarity. Its application on the benchmark alanine dipeptide MD data showed a much better performance than existing methods in exploring and understanding the free energy landscape. We also applied it to the MD data of Villin HP35. Our results are more reasonable on various aspects than those from other methods and very informative on the hierarchical structure of its energy landscape.
Validity and sensitivity of an inertial measurement unit-driven biomechanical model of motor variability for gait
Authors: Bailey Christopher A. , Uchida Thomas K. , Nantel Julie , Graham Ryan B. 
Published: September 2021

AbstractMotor variability in gait is frequently linked to fall risk, yet field-based biomechanical joint evaluations are scarce. We evaluated the validity and sensitivity of an inertial measurement unit (IMU)-driven biomechanical model of joint angle variability for gait. Fourteen healthy young adults completed seven-minute trials of treadmill gait at several speeds and arm swing amplitudes. Joint kinematics were estimated by IMU- and optoelectronic-based models using OpenSim. We calculated range of motion (ROM), magnitude of variability (meanSD), local dynamic stability (λmax), persistence of ROM fluctuations (DFAα), and regularity (SaEn) of each angle over 200 continuous strides, and evaluated model accuracy (e.g., RMSD: root mean square difference), consistency (ICC2,1: intraclass correlation), biases, limits of agreement, and sensitivity to within-participant gait responses (effects of Speed and Swing). RMSDs of joint angles were 1.7–7.5° (pooled mean of 4.8°), excluding ankle inversion. ICCs were mostly good– excellent in the primary plane of motion for ROM and in all planes for meanSD and λmax, but were poor–moderate for DFAα and SaEn. Modeled Speed and Swing responses for ROM, meanSD, and λmax were similar. Results suggest that the IMU-driven model is valid and sensitive for field-based assessments of joint angles and several motor variability features.
Open social innovation for surplus food recovery and aid during COVID-19 crisis: the case of Fondazione Banco Alimentare Onlus
Authors: Penco Lara , Ciacci Andrea , Benevolo Clara , Torre Teresina 
Published: September 2021

PurposeThe study analyses the role that open social innovation (OSI) perspective played for Fondazione Banco Alimentare Onlus (FBAO), a food bank in Italy, in responding to the COVID-19 crisis. It answers the following research question: how does a crisis, such as the COVID-19 pandemic, stimulate the adoption of OSI practices to revamp the activities of FBAO and facilitate appropriate solutions to carry out its social mission?Design/methodology/approachThis study employs a qualitative approach. It is based on a single case study.FindingsThe study shows how COVID-19 has stimulated the adoption of OSI practices to continue to meet the social mission, creating innovative projects or finding new ways to do the same things.Research limitations/implicationsThe study is based on a single case study.Practical implicationsThe paper contributes insights into the literature on OSI, examining how inbound and outbound OSI mechanisms can modify business models and increase the adaptation capacity of food banks and their effectiveness. In addition, it provides a rich context in which the social value drivers provided by OSI are studied.Originality/valueThis paper applies the OSI to a food bank to evaluate what this action mode produces for the food bank during a health crisis. Specifically, this is the first paper that studies the COVID-19 crisis response of a food bank from the OSI perspective, focusing on the inbound and outbound OSI processes that characterized the entire network of relationships.
An optimized double-integral-sliding-mode-controller for a PV microgrid
Authors: Pradhan Swati Sucharita , Pradhan Raseswari , Subudhi Bidyadhar 
Published: September 2021

Purpose
The dynamics of the PV microgrid (PVMG) system are highly nonlinear and uncertain in nature. It is encountered with parametric uncertainties and disturbances. This system cannot be controlled properly by conventional linear controllers. H− controller and sliding mode controller (SMC) may capable of controlling it with ease. Due to its inherent dynamics, SMC introduces unwanted chattering into the system output waveforms. This paper aims to propose a controller to reduce this chattering.

Design/methodology/approach
This paper presents redesign of the SMC by modifying its sliding surface and tuning its parameters by employing water-evaporation-optimization (WEO) based metaheuristic algorithm.

Findings
By using this proposed water-evaporation-optimization algorithm-double integral sliding mode controller (WEOA-DISMC), the chattering magnitude is diminished greatly. Further, to examine which controller between H8 controller and proposed WEOA-DISMC performs better in both normal and uncertain situations, a comparative analysis has been made in this paper. The considered comparison parameters are reference tracking, disturbance rejection and robust stability.

Originality/value
WEO tuned DISMC for PVMG system is the contribution.
The impact of corporate social responsibility (CSR) priming on consumers’ consumption and lifestyle choices with intertemporal tradeoffs
Authors: Fatemi Hajar , Dube Laurette 
Published: September 2021

PurposeThis paper aims to study the unexplored possibility that priming firms’ corporate social responsibility (CSR) activity in consumers’ minds may impact consumers’ preference for non-firm related consumption and lifestyle choice options with intertemporal trade-offs.Design/methodology/approachAcross four experimental studies, the authors looked at the impact of CSR priming on the preference of participants for later larger versus sooner smaller money (Study 1), saving versus spending (Study 2) and healthy versus unhealthy food choices (Studies 3 and 4). These choice options were not related to the focal firm that practiced CSR. The authors measured the changes in participants’ consideration of future consequences (CFC) as a potential mediator for the results.FindingsThe participants in the CSR condition showed a higher CFC and a higher preference for the options with long-term benefits and immediate costs over the ones with long-term costs and immediate benefits, i.e. later larger over sooner smaller money, saving over spending and healthy over unhealthy food. The authors documented a mediation role for CFC.Research limitations/implicationsAll the participants in the studies were from the USA. Looking at the cultural differences can enrich the understanding of the impact of CSR on preference for the options with intertemporal trade-offs. Furthermore, this paper builds its theoretical justification based on the assumption of individuals’ acceptance of CSR activities. Nevertheless, consumers may have skepticism about these activities. Future studies may investigate the effect of CSR skepticism of individuals on the proposed effects. Additionally, investigating the moderating roles of individuals’ characteristics like their prosocial concern or their knowledge about choice options might be an avenue for future research.Practical implicationsThe findings highlight the benefits of CSR priming on consumers’ welfare and normative behavior. Firms may use the findings to understand and manage the impact of other firms’ CSR communications on the evaluation of their own products.Originality/valueThis research is the first to highlight the impact of CSR priming on consumers’ non-firm-related consumption and lifestyle choices with intertemporal trade-offs. The results showed the positive effect of priming firms’ CSR activities on consumers’ CFC and the mediating role of CFC.
Towards competence-oriented higher education: a systematic literature review of the different perspectives on successful exit profiles
Authors: Brauer Sanna 
Published: September 2021

PurposeThe twenty-first century education system seeks to meet the societal demands of economic effectiveness and the unique professional development needs of individuals. This paper aims to discuss the qualities of competence-oriented educational processes and the recent movement towards competence-based curricula in higher education.Design/methodology/approachThis study follows a systematic literature review (SLR) methodology to explore the concept of competence within the context of educational science. The subsequent thematic synthesis analyses the findings of reviewed publications regarding graduate attributes in competence-oriented higher education and their perspectives and working-life expectations on exit profiles.FindingsInterest in competence-oriented education, training and learning has grown in recent years, resulting in numerous theoretical and technical pedagogical applications in higher education. Nonetheless, ambiguous terminology presents a significant challenge, which is demonstrated by the inconsistent language of the study's results. Moreover, there is an obvious need for teachers' in-service training. The qualitative synthesis of this article will be useful for both educational and working life sectors to inform and promote different perspectives on competence-oriented educational processes. A clear articulation of competences is crucial for reforming higher education to meet students' interests and recognise their work-life needs.Originality/valueThe concept of competence has been under-investigated in higher education research and practices. This study offers novel insights and practical implications for competence-oriented learning concerning the paradigmatic change across higher education.
Business adversity during the COVID-19 crisis and beyond: the way forward for small and medium enterprises in India
Authors: Nair Saji Thazhungal Govindan 
Published: September 2021

Purpose
The novel coronavirus (COVID-19) leaves Indian business teetering on the edge of survival. This paper aims to set out to assess the impact of the pandemic shocks on the small and medium business segments in India. The research also explores the strategies that potentially take the segments back to recovery and growth.

Design/methodology/approach
The findings draw on the perspectives of academic and business people, and the authors use linear and nonlinear regression modelling under three recovery scenarios to support our arguments.

Findings
Evidence suggests that the shocks to business are manifold and the severity of most of the issues will aggravate as the recovery prolongs.

Practical implications
The paper explains the rationale of realistic strategies and compares its effects across potent recoveries. The findings are useful for both academics and business and relates to the strategic decisions that would be taken by small and medium enterprises to expedite recovery from the crisis.

Originality/value
The research is unique in surveying the academics and entrepreneurs about the impact of COVID-19 on Indian business.
Mutual fund manager turnover: an empirical investigation of performance
Authors: Ghalke Avinash , Kulkarni Shripad 
Published: September 2021

PurposeWhen a fund manager leaves, the investment strategy of the fund changes or remains the same. The departing fund manager's resignation is either forced or voluntary. The study investigates the relationship between the portfolio manager's transition and the fund's investment strategy and how the change affects the mutual fund returns in the subsequent period.Design/methodology/approachThe authors examine 148 fund manager changes in India between April 2005–March 2018 using three performance measures: abnormal return (fund return minus benchmark return), Jensen's alpha and Carhart four-factor alpha. The analysis includes an event study methodology, followed by a two-step Fama–MacBeth regression approach.FindingsContrary to the previous studies conducted in the developed markets, the authors find that fund performance improves irrespective of whether the fund manager change is forced or voluntary. The outperformance after the fund manager's exit is significant for funds belonging to the larger fund families.Originality/valueIn the context of investment management, the authors provide a conceptual framework to understand the effect of fund manager exit on mutual fund performance. The authors substantiate their arguments with empirical evidence. To the best of the authors' understanding, this is the first research to examine the effect of changing mutual fund managers in an emerging market setting.
FDI inflow, ICT and economic performance of India: an empirical investigation
Authors: Nayak Suryakanta , Sahoo Dukhabandhu 
Published: September 2021

PurposeThe aim of this study is to examine the impact of foreign direct investment (FDI) inflow and information and communication technology (ICT) on the economic performance of India by analysing annual data from 1991 to 2019.Design/methodology/approachThis study has used data collected from secondary sources. The variables considered for the analysis are based on the review of theoretical and empirical literature. Moreover, apart from the quantitative variables, two qualitative variables have also been considered through the use of dummy variables. The Cobb–Douglas, Transcendental logarithmic and Simultaneous equations models have been used for the study.FindingsThe result reveals that the partial elasticities of the per-capita gross domestic product (PCGDP) of India with respect to FDI, mobile density (MD) and internet density (ID) are 0.074, 0.024 and 0.036, respectively. The positive and significant coefficient of the interaction among FDI, MD and ID in the estimation of the transcendental logarithmic function indicates the importance of ICT infrastructure in extracting the best out of FDI (the coefficient is 0.011 for the model without any control variables and it is 0.005 with control variables).Originality/valueThe findings of this study are more reliable as the latest available data have been analysed through the appropriate econometric models. This study will be useful for the policymakers in the formulation of policies with regard to foreign capital and digitalisation.