bluuebunny/crossref_metadata_2025_split huggingface dataset:
Correlation in Domain Fluctuations Navigates Target Search of a Viral Peptide along RNA
Authors: Prusty Sangram , Sarkar Raju , Roy Susmita 
Published: June 2021

ABSTRACTBiological macromolecules often exhibit correlation in fluctuations involving distinct domains. This study decodes their functional implications in RNA-protein recognition and target-specific binding. The target search of a peptide along RNA in viral TAR-Tat complex is closely monitored using atomistic simulations, steered molecular dynamics simulations, free energy calculations, and a machine-learning-based clustering technique. An anti-correlated domain fluctuation is identified between the tetraloop and the bulge region in the apo form of TAR RNA that sets a hierarchy in the domain-specific fluctuations at each binding event and that directs succeeding binding footsteps. Thus, at each binding footstep, the dynamic partner selects an RNA location for binding where it senses higher fluctuation, which is conventionally reduced upon binding. This event stimulates an alternate domain-fluctuation which then dictates sequential binding footstep/s and thus, the search progresses. Our cross-correlation maps show that the fluctuations relay from one domain to another specific domain till the anti-correlation between that inter-domain fluctuations sustains. Artificial attenuation of that hierarchical domain fluctuation inhibits specific RNA binding. The binding is completed with the arrival of a few long-lived water molecules that mediate slightly distant RNA-protein sites and finally stabilizes the overall complex. The study underscores the functional importance of naturally designed fluctuating RNA motifs (bulge, tetraloop) and their interplay in dictating the directionality of the search in a highly dynamic environment.
Interrogation of the Dynamic Properties of Higher-Order Heterochromatin Using CRISPR/dCas9
Authors: Gao Yuchen , Han Mengting , Shang Stephen , Wang Haifeng , Qi Lei S. 
Published: June 2021

ABSTRACTEukaryotic chromosomes feature large regions of compact, repressed heterochromatin hallmarked by Heterochromatin Protein 1 (HP1). HP1 proteins play multi-faceted roles in shaping heterochromatin, and in cells, HP1 tethering to individual gene promoters leads to epigenetic modifications and silencing. However, emergent properties of HP1 at supranucleosomal scales remain difficult to study in cells due to lack of appropriate tools. Here, we develop CRISPR-Engineered Chromatin Organization (EChO), combining live cell CRISPR imaging with inducible large-scale recruitment of chromatin proteins to native genomic targets. We demonstrate that human HP1α tiling across kilobase-scale genomic DNA forms novel contacts with natural heterochromatin, integrates two distantly targeted regions, and reversibly changes chromatin from a diffuse to compact state. The compact state exhibits delayed disassembly kinetics and represses transcription across over 600 kilobases. These findings support a polymer model of HP1α-mediated chromatin regulation and highlight the utility of CRISPR-EChO in studying supranucleosomal chromatin organization in living cells.
Implicating Gene and Cell Networks Responsible for Differential COVID-19 Host Responses via an Interactive Single Cell Web Portal
Authors: Jin Kang , Bardes Eric E. , Mitelpunkt Alexis , Wang Jake Y. , Bhatnagar Surbhi , Sengupta Soma , Krummel Daniel Pomeranz , Rothenberg Marc E. , Aronow Bruce J. 
Published: June 2021

SummaryNumerous studies have provided single-cell transcriptome profiles of host responses to SARS-CoV-2 infection. Critically lacking however is a datamine that allows users to compare and explore cell profiles to gain insights and develop new hypotheses. To accomplish this, we harmonized datasets from COVID-19 and other control condition blood, bronchoalveolar lavage, and tissue samples, and derived a compendium of gene signature modules per cell type, subtype, clinical condition, and compartment. We demonstrate approaches to probe these via a new interactive web portal (http://toppcell.cchmc.org/COVID-19). As examples, we develop three hypotheses: (1) a multicellular signaling cascade among alternatively differentiated monocyte-derived macrophages whose tasks include T cell recruitment and activation; (2) novel platelet subtypes with drastically modulated expression of genes responsible for adhesion, coagulation and thrombosis; and (3) a multilineage cell activator network able to drive extrafollicular B maturation via an ensemble of genes strongly associated with risk for developing post-viral autoimmunity.
Logical and experimental modeling of cytokine and eicosanoid signaling in psoriatic keratinocytes
Authors: Tsirvouli Eirini , Ashcroft Felicity , Johansen Berit , Kuiper Martin 
Published: June 2021

AbstractPsoriasis is characterized by chronic inflammation, perpetuated by a Th17-dependent signaling loop between the immune system and keratinocytes that could involve phospholipase A2(PLA2)-dependent eicosanoid release. A prior knowledge network supported by experimental observations was used to encode the regulatory network of psoriatic keratinocytes in a computational model for studying the mode of action of a cytosolic (c) PLA2α inhibitor. A combination of evidence derived from the computational model and experimental data suggests that Th17 cytokines stimulate pro-inflammatory cytokine expression in psoriatic keratinocytes via activation of cPLA2α-PGE2-EP4 signaling, which could be suppressed using the anti-psoriatic calcipotriol. cPLA2α inhibition and calcipotriol showed overlapping and distinct modes of action. Model analyses revealed the immunomodulatory role of Th1 cytokines, the modulation of the physiological states of keratinocytes by Th17 cytokines, and how Th1 and Th17 cells together promote the development of psoriasis. Model simulations additionally suggest novel drug targets, including EP4 and PRKACA, for treatment that may restore a normal phenotype. Our work illustrates how the study of complex diseases can benefit from an integrated systems approach.
TSEBRA: Transcript Selector for BRAKER
Authors: Gabriel Lars , Hoff Katharina J. , Brůna Tomáš , Borodovsky Mark , Stanke Mario 
Published: June 2021

AbstractBackgroundBRAKER is a suite of automatic pipelines, BRAKER1 and BRAKER2, for the accurate annotation of protein-coding genes in eukaryotic genomes. Each pipeline trains statistical models of protein-coding genes based on provided evidence and, then predicts protein-coding genes in genomic sequences using both the extrinsic evidence and statistical models. For training and prediction, BRAKER1 and BRAKER2 incorporate complementary extrinsic evidence: BRAKER1 uses only RNA-seq data while BRAKER2 uses only a database of cross-species proteins. The BRAKER suite has so far not been able to reliably exceed the accuracy of BRAKER1 and BRAKER2 when incorporating both types of evidence simultaneously. Currently, for a novel genome project where both RNA-seq and protein data are available, the best option is to run both pipelines independently, and to pick one, likely better output. Therefore, one or another type of the extrinsic evidence would remain unexploited.ResultsWe present TSEBRA, a software that selects gene predictions (transcripts) from the sets generated by BRAKER1 and BRAKER2. TSEBRA uses a set of rules to compare scores of overlapping transcripts based on their support by RNA-seq and homologous protein evidence. We show in computational experiments on genomes of 11 species that TSEBRA achieves higher accuracy than either BRAKER1 or BRAKER2 running alone and that TSEBRA compares favorably with the combiner tool EVidenceModeler.ConclusionTSEBRA is an easy-to-use and fast software tool. It can be used in concert with the BRAKER pipeline to generate a gene prediction set supported by both RNA-seq and homologous protein evidence.
Evidence for a vocal signature in the rat and its reinforcing effects
Authors: Vielle Cassandre , Montanari Christian , Pelloux Yann , Baunez Christelle 
Published: June 2021

AbstractWhile the term “language” is used for human and non-human primates, “vocal communication” is rather used for rodents or other species. The main difference is that there is, to date, no evidence for a vocal signature in the well-known 50- and 22-kHz ultrasonic vocalizations (USV) emitted by rats. Here, we show that rats can recognize the identity of the USV emitter since they self-administer preferentially playback of 50-kHz USV emitted by a stranger rat over those emitted by their cage-mate. In a second experiment, we show that the familiarity with the USV emitter also modulate the effect of USV playback during cocaine self-administration, since only stranger, but not familiar, 50-kHz USV decrease drug intake. Finally, to study the neurobiological substrate of those processes, we have tested the effects of the subthalamic nucleus (STN) lesion on these various conditions. STN-lesioned rats did not lever press much for any USV playback, whatever their emotional valence, nor did they seem able to differentiate familiar from stranger peer. Advocating for the existence of a vocal signature in rats, these results highlight the importance of ultrasonic communication in socio-affective influence of behavior, such as the influence of proximal social factors on drug consumption and confirm the role of the subthalamic nucleus on this influence.
Single-molecule imaging reveals the coupling of translation and mRNA decay
Authors: Dave Pratik , Griesbach Esther , Roth Gregory , Mateju Daniel , Chao Jeffrey A. 
Published: June 2021

SUMMARYThe relationship between mRNA translation and decay is incompletely understood, with conflicting reports suggesting that translation can either promote decay or stabilize mRNAs. The effect of translation on mRNA decay has mainly been studied using ensemble measurements and global inhibitors of transcription and translation, which can mask the underlying mechanisms. We developed a single-molecule imaging approach to control the translation of a specific transcript that enabled simultaneous measurement of translation and mRNA decay. Our results demonstrate that mRNAs undergoing translation are degraded faster than non-translating ones, although with slower kinetics than translation-coupled degradation of transcripts targeted by NMD. Furthermore, our results indicate that miRNAs mediate efficient degradation of both translating and non-translating target mRNAs. Single-molecule measurements of translation and decay reveal a predominant role of mRNA decay in miRNA-mediated regulation. Simultaneous visualization of translation and decay on single mRNAs provides a framework to study how these processes are interconnected in cells.
Operationalising ethnicity in accountability: insights from an ethnic group within the Salvation Army
Authors: Joannides De Lautour Vassili , Hoque Zahirul , Wickramasinghe Danture 
Published: June 2021

PurposeThis paper explores how ethnicity is implicated in an etic–emic understanding through day-to-day practices and how such practices meet external accountability demands. Addressing the broader question of how ethnicity presents in an accounting situation, it examines the mundane level responses to those accountability demands manifesting an operationalisation of the ethnicity of the people who make those responses.Design/methodology/approachThe study followed ethnomethodology principles whereby one of the researchers acted both as an active member and as a researcher within a Salvation Army congregation in Manchester (UK), while the others acted as post-fieldwork reflectors.FindingsThe conceivers and guardians of an accountability system relating to the Zimbabwean-Mancunian Salvationist congregation see account giving practices as they appear (etic), not as they are thought and interiorised (emic). An etic–emic misunderstanding on both sides occurs in the situation of a practice variation in a formal accountability system. This is due to the collision of one ethnic group's emics with the emics of conceivers. Such day-to-day practices are thus shaped by ethnic orientations of the participants who operationalise the meeting of accountability demands. Hence, while ethnicity is operationalised in emic terms, accounting is seen as an etic construct. Possible variations between etic requirements and emic practices can realise this operationalisation.Research limitations/implicationsThe authors’ findings were based on one ethnic group's emic construction of accountability. Further research may extend this to multi-ethnic settings with multiple etic/emic combinations.Originality/valueThis study contributed to the debate on both epistemological and methodological issues in accountability. As it is ill-defined or neglected in the literature, the authors offer a working conceptualisation of ethnicity – an operating cultural unit being implicated in both accounting and accountability.
Passenger aircraft emissions analysis at Ordu-Giresun International Airport, Turkey in 2017
Authors: Orhan Ilkay 
Published: June 2021

Purpose
The purpose of this study is to present the pollutant gas produced by hydrocarbons (HC), carbon monoxide (CO) and nitrogen oxides (NOx) and the quantity of fuel burned from commercial aircraft at Ordu-Giresun International Airport, Turkey during the landing and take-off (LTO) cycles in 2017.

Design/methodology/approach
The flight data recorded by the General Directorate of State Airports Authority and the aircraft engine emission data from International Civil Aviation Organization (ICAO) Engine Exhaust Emission Databank were used for calculation. The aircraft and engine types used by the airlines for flight at Ordu-Giresun International Airport were determined. To evaluate the effect of taxi time on emission amounts, analysis and evaluations were made by taking different taxi times into consideration.

Findings
As a result of the emission analysis, the amount of fuel consumed by the aircraft were calculated as 6,551.52 t/y, and the emission amounts for CO, HC and NOx were estimated as 66.81, 4.20 and 79.97 t/y, respectively.

Practical implications
This study is aimed to reveal the effect and contribution of taxi time on the emitted emission at the airport during the LTO phase of the aircraft.

Originality/value
This study helps aviation authorities explain the importance of developing procedures that ensure the delivery of aircraft to flights in minimum time by raising awareness of the impact of taxi time on emitted emissions, and contributes to the determination of an aircraft emission inventory at Ordu-Giresun International Airport.
China’s arable land wasting problem
Authors: Chen Wensheng 
Published: June 2021

PurposeChina's population–land contradiction is a crucial issue, and by deeply analyzing causes of wasting arable land, this article recommends some policies to avoid waste.Design/methodology/approachBased on the current high-, middle- and low-class differentiation in the agricultural products' consumption structure against urban residents' rapid income growth, this article proposes that agricultural products with distinctive regional characteristics should be developed according to regional natural agricultural resources and market demand, so as to ensure that China's scarce arable land can be used effectively.FindingsChoices in regional agricultural production relate to operational farmers' enthusiasm for profitability and production, residential farmers' ability to ensure their own food security, agriculture's sustainable development and arable land resources' optimal allocation. Therefore, the varietal structure of agricultural products and regional production layout should be compatibly decided according to consumer demand and resource endowment.Originality/valueDuring the process of industrialization and urbanization, wasting of arable land has become a social development problem. On the basis of agriculture's regional resource endowment, this article reconstructs the functional positioning of various Chinese agricultural regions and solves the difficult problem of consumption structure transformation and homogeneous competition through the geographical division of labor, thereby optimizing allocation of arable land resources.
Corporate governance and COVID-19: a literature review
Authors: Koutoupis Andreas , Kyriakogkonas Panagiotis , Pazarskis Michail , Davidopoulos Leonidas 
Published: June 2021

Purpose
The purpose of this study is to review the literature on corporate governance (CG); environmental, social and governance (ESG) issues and corporate social responsibility (CSR) during the Coronavirus disease 2019 (COVID-19) pandemic and addresses three research questions: What are the characteristics of the literature on CG and COVID-19? What are the themes in CG in the COVID-19 era? and What are key areas of future research on CG and COVID-19?

Design/methodology/approach
The authors attempted a systematic literature review of 62 studies published in 2020. The authors used four criteria to identify characteristics of the literature on CG and COVID-19 and three criteria to identify key themes in the literature addressing CG and the pandemic. The authors analyzed answers to the above research questions and proposals from studies reviewed to guide future research.

Findings
CG in the context of COVID-19 has been studied mostly in developed countries and within a theoretical framework. As accounting data are insufficient, more research is required in all countries (developed, emerging and other). Further, there are no conclusive results regarding the relevance of ESG and CSR to financial performance. Future research should use additional methodologies and data sources to fully explain the impact of COVID-19 on CG.

Practical implications
Practitioners and policymakers could benefit from the study, as the authors present key challenges to CG for the present and the future.

Originality/value
This study is the first to provide a systematic literature review on CG during the COVID-19 pandemic and presents current trends, challenges and avenues for future research.
Analysis and visualization of COVID-19 discourse on Twitter using data science: a case study of the USA, the UK and India
Authors: Ilyas Haider , Anwar Ahmed , Yaqub Ussama , Alzamil Zamil , Appelbaum Deniz 
Published: June 2021

Purpose
This paper aims to understand, examine and interpret the main concerns and emotions of the people regarding COVID-19 pandemic in the UK, the USA and India using Data Science measures.

Design/methodology/approach
This study implements unsupervised and supervised machine learning methods, i.e. topic modeling and sentiment analysis on Twitter data for extracting the topics of discussion and calculating public sentiment.

Findings
Governments and policymakers remained the focus of public discussion on Twitter during the first three months of the pandemic. Overall, public sentiment toward the pandemic remained neutral except for the USA.

Originality/value
This paper proposes a Data Science-based approach to better understand the public topics of concern during the COVID-19 pandemic.
The family CEO’s effect on succession planning: founder status, difficulties with letting go and gender differences
Authors: Umans Ine , Lybaert Nadine , Steijvers Tensie , Voordeckers Wim 
Published: June 2021

PurposeThe purpose of this paper is to investigate several antecedents of succession planning in family firms: founder status, the family chief executive officer (CEO)’s inability to let go and the family CEO’s gender.Design/methodology/approachThis study conducts moderated mediation analysis on a sample of 259 family firms.FindingsThe results show that family firms led by founders show lower succession planning levels than family firms led by descendant family CEOs. This effect is mediated by the family CEO’s inability to let go. Furthermore, the influence of the emotion of being unable to let go on succession planning is dependent on the family CEO’s gender. This influence is smaller when the family CEO is female than when the family CEO is male.Originality/valueThe study introduces the family CEO’s inability to let go as a mediator in the founder-succession planning relationship. The results add empirical evidence to the debate about gender influences in family firms. By showing that emotions have a different outcome concerning succession planning depending on the family CEO’s gender, this study enriches gender research. The study also contributes to the family business field by introducing relational theory as a valuable theoretical framework to include gender in succession research.
Gender stereotyping and self-stereotyping among Danish managers
Authors: Smith Nina , Eriksson Tor , Smith Valdemar 
Published: June 2021

PurposeThe purpose of this paper is to describe how gender stereotypes and self-stereotypes of Danish managers vary among managers at different job levels, from lower level managers to CEO level, in a large survey of Danish private-sector managers.Design/methodology/approachThis study is explorative. Measures of stereotypes and self-stereotypes are constructed and analyzed with regressions models that control for a large number of individual and firm characteristics.FindingsThe results document significant gender differences in stereotyping among managers. Male managers have significantly more masculine stereotypes of successful leaders, and they rate themselves higher on masculine traits than female managers. For CEOs, the picture is different. Stereotypes do not differ by gender and female CEOs have more pronounced masculine stereotypes than female managers at lower levels. Female managers at the age of 50 are the least gender stereotyping managers. Younger female managers have significantly more masculine stereotypes about the role as a successful leader.Research limitations/implicationsThis study is based on cross-sectional data and does not claim to uncover causal relationships.Practical implicationsThe results suggest that gender stereotypes and self-stereotypes among Danish private-sector managers are not going to change quickly indicating that new government policies with more focus on gender equalization and affirmative actions are called for.Originality/valueMost earlier studies of stereotypes concerning female managers are based on studies of samples drawn from the general population or consisting of students. This study makes use of a large sample of managerial employees from all levels of the corporate hierarchy in different types of firms.
Review of research for two decades for women leadership in higher education around the world and in Vietnam: a comparative analysis
Authors: Maheshwari Greeni , Nayak Rajkishore , Ngyyen Tu 
Published: June 2021

Purpose
The purpose of this paper is to find the studies conducted on women leadership in higher education (WLHE) in the past 20 years to understand as to how the trend has changed over the past two decades around the world and particularly in Vietnam for women leaders in higher education institutions.

Design/methodology/approach
This paper used a systematic review of 93 articles published in the past 20 years in WLHE. The articles were classified based on the country of research and the research methods used.

Findings
The study concluded that most of the research in WLHE had been done in the USA and Canada, with a dearth of literature on WLHE in Asia, and only six studies so far have been done in Vietnam, with only two studies being done before 2017. Vietnam is gaining importance in research in WLHE may be because of the increased female labour participation rate and growth in the gross domestic product.

Practical implications
This study provided some recommendations at the societal, institutional and individual levels, which can help in women empowerment and help women take up the leadership roles.

Originality/value
Although a variety of reviews have been conducted focusing on different areas in higher education, there is a small number of literature review studies in the field of women leaders in higher education, especially in Vietnam and Asia. Hence, the current study will add this missing part to the growing body of literature in WLHE.