bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying Reproducible Transcription Regulator Coexpression Patterns with Single Cell Transcriptomics
Authors: Morin Alexander , Chu C. Pan , Pavlidis Paul 
Published: February 2024

AbstractThe proliferation of single cell transcriptomics has potentiated our ability to unveil patterns that reflect dynamic cellular processes such as the regulation of gene transcription. In this study, we leverage a broad collection of single cell RNA-seq data to identify the gene partners whose expression is most coordinated with each human and mouse transcription regulator (TR). We assembled 120 human and 103 mouse scRNA-seq datasets from the literature (>28 million cells), constructing a single cell coexpression network for each. We aimed to understand the consistency of TR coexpression profiles across a broad sampling of biological contexts, rather than examine the preservation of context-specific signals. Our workflow therefore explicitly prioritizes the patterns that are most reproducible across cell types. Towards this goal, we characterize the similarity of each TR’s coexpression within and across species. We create single cell coexpression rankings for each TR, demonstrating that this aggregated information recovers literature curated targets on par with ChIP-seq data. We then combine the coexpression and ChIP-seq information to identify candidate regulatory interactions supported across methods and species. Finally, we highlight interactions for the important neural TR ASCL1 to demonstrate how our compiled information can be adopted for community use.Author SummaryA common way to analyze gene expression (transcriptomics) data is to correlate gene transcript levels across samples for every pair of genes (coexpression). Coordinated expression between genes may imply a shared biological function, though this warrants cautious interpretation given assumptions about cellular processes inferred from RNA abundances alone. Still, coexpression inference is often used to nominate genes whose expression may be controlled by transcription regulators (TRs). The rapid generation of diverse single cell transcriptomics data has unlocked our ability to discover coexpression patterns across individual cells — though these signals are often noisy. Reproducible patterns across studies can help distinguish meaningful biological relationships from spurious correlations. We used this study to analyze a broad collection of single cell data spanning numerous tissues in human and mouse to infer global TR coexpression patterns. We aimed to learn which interactions were generally observable, to better potentiate future examinations of reproducible coexpression in specific contexts. We evaluate the predictive performance of these global single cell coexpression rankings using independent gene regulation evidence, and highlight TR-gene pairs that are supported across data modalities as well as species. By disseminating these rankings, we hope that other researchers can extract insight for their own TRs of interest.
Dynamic modulation of social gaze by sex and familiarity in marmoset dyads
Authors: Xing Feng , Sheffield Alec G. , Jadi Monika P. , Chang Steve W. C. , Nandy Anirvan S. 
Published: February 2024

SummarySocial communication relies on the ability to perceive and interpret the direction of others’ attention, and is commonly conveyed through head orientation and gaze direction in humans and nonhuman primates. However, traditional social gaze experiments in nonhuman primates require restraining head movements, significantly limiting their natural behavioral repertoire. Here, we developed a novel framework for accurately tracking facial features and three-dimensional head gaze orientations of multiple freely moving common marmosets (Callithrix jacchus). By combining deep learning-based computer vision tools with triangulation algorithms, we were able to track the facial features of marmoset dyads within an arena. This method effectively generates dynamic 3D geometrical facial frames while overcoming common challenges like occlusion. To detect the head gaze direction, we constructed a virtual cone, oriented perpendicular to the facial frame. Using this pipeline, we quantified different types of interactive social gaze events, including partner-directed gaze and joint gaze to a shared spatial location. We observed clear effects of sex and familiarity on both interpersonal distance and gaze dynamics in marmoset dyads. Unfamiliar pairs exhibited more stereotyped patterns of arena occupancy, more sustained levels of social gaze across social distance, and increased social gaze monitoring. On the other hand, familiar pairs exhibited higher levels of joint gazes. Moreover, males displayed significantly elevated levels of gazes toward females’ faces and the surrounding regions, irrespective of familiarity. Our study reveals the importance of two key social factors in driving the gaze behaviors of a prosocial primate species and lays the groundwork for a rigorous quantification of primate behaviors in naturalistic settings.
WITHDRAWN: Gammaherpesvirus infection alters transfer RNA splicing and triggers tRNA cleavage
Authors: Manning Aidan C. , Bashir Mahmoud M. , Jimenez Ariana R. , Upton Heather E. , Collins Kathleen , Lowe Todd M. , Tucker Jessica M. 
Published: February 2024

Withdrawal statementThe authors have withdrawn this manuscript due to a duplicate posting of manuscript number BIORXIV/2024/592122. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author. The correct preprint can be found at doi:https://doi.org/10.1101/2024.05.01.592122.
Transmission-blocking activity of artesunate, chloroquine and methylene blue onPlasmodium vivaxgametocytes
Authors: Chaumeau Victor , Wasisakun Praphan , Watson James A. , Oo Thidar , Aryalamloed Sarang , Sue Mu Phang , Htoo Gay Nay , Tha Naw Moo , Archusuksan Laypaw , Sawasdichai Sunisa , Gornsawun Gornpan , Mehra Somya , White Nicholas J. , Nosten François H. 
Published: February 2024

ABSTRACTPlasmodium vivaxis now the main cause of malaria outside Africa. The gametocytocidal effects of antimalarial drugs are important to reduce malaria transmissibility, particularly in low transmission settings, but they are not well characterized forP. vivax. The transmission-blocking effects of chloroquine, artesunate and methylene blue onP. vivaxgametocytes were assessed. Blood specimens were collected from patients presenting with vivax malaria, incubated with or without the tested drugs, and then fed to mosquitos from a laboratory-adapted colony ofAnopheles dirus(a major malaria vector in Southeast Asia). The effects on oocyst and sporozoite development were analyzed under a multi-level Bayesian model accounting for assay variability and the heterogeneity of mosquitoPlasmodium-infection. Artesunate and methylene blue, but not chloroquine, exhibited potent transmission-blocking effects. Gametocyte exposures to artesunate and methylene blue reduced the mean oocyst count 469 fold (95%CI: 345 to 650) and 1438 fold (95%CI: 970 to 2064) respectively. The corresponding estimates for the sporozoite stage were a 148 fold reduction (95%CI: 61 to 470) and a 536 fold reduction (95%CI: 246 to 1311) in the mean count, respectively. In contrast, high chloroquine exposures reduced the mean oocyst count by only 1.40 fold (95%CI: 1.20 to 1.64) and the mean sporozoite count 1.34 fold (95%CI: 1.12 to 1.66). This suggests that patients with vivax malaria often remain infectious to anopheline mosquitos after treatment with chloroquine. Immediate initiation of primaquine radical cure or use of artemisinin combination therapies would reduce the transmissibility ofP. vivaxinfections.
“Fruit basket upset”: spatially explicit crop mixture responses to climatic and economic pressures
Authors: Robertson Richard , Petsakos Athanasios , Song Chun , Cenacchi Nicola , Gotor Elisabetta 
Published: February 2024

PurposeThe choice of crops to produce at a location depends to a large degree on the climate. As the climate changes and food demand evolves, farmers may need to produce a different mix of crops. This study assesses how much cropland may be subject to such upheavals at the global scale, and then focuses on China as a case study to examine how spatial heterogeneity informs different contexts for adaptation within a country.Design/methodology/approachA global agricultural economic model is linked to a cropland allocation algorithm to generate maps of cropland distribution under historical and future conditions. The mix of crops at each location is examined to determine whether it is likely to experience a major shift.FindingsTwo-thirds of rainfed cropland and half of irrigated cropland are likely to experience substantial upheaval of some kind.Originality/valueThis analysis helps establish a global context for the local changes that producers might face under future climate and socioeconomic changes. The scale of the challenge means that the agricultural sector needs to prepare for these widespread and diverse upheavals.
Mediated crises and strategic crisis communication of third sector organizations: a content analysis of crisis reporting in six countries
Authors: Schwarz Andreas , Diers-Lawson Audra 
Published: February 2024

PurposeThis study aims to contribute to strategic crisis communication research by exploring international media representations of third sector crises and crisis response; expanding the range of crisis types beyond transgressions; and developing a framework that integrates framing and crisis communication theory.Design/methodology/approachQuantitative content analysis was applied to identify patterns in crisis reporting of 18 news media outlets in Canada, Germany, India, Switzerland, UK and US. Using an inductive framing approach, crisis coverage of nonprofit organizations (NPOs) and intergovernmental organizations (IGOs) between 2015 and 2018 was analyzed across a wide range of crises, including but not limited to prominent cases such as Oxfam, Kids Company, or the Islamic Research Foundation.FindingsThe news media in six countries report more internal crises in the third sector than external crises. The most frequent crisis types were fraud and corruption, sexual violence/personal exploitation and attacks on organizations. Exploratory factor analysis revealed three components of crisis response strategies quoted in the media, conditional rebuild, defensive and justified denial strategies. Causal attributions and conditional rebuild strategies significantly influenced media evaluations of organizational crisis response. Three frames of third sector crises were detected; the critique, the damage and the victim frame. These frames emphasize different crisis types, causes, crisis response strategies and evaluations of crisis response.Originality/valueThe study reveals the particularities of crises and crisis communication in the third sector and identifies factors that influence mediated portrayals of crises and crisis response strategies of nonprofit organizations (NPOs) from an international comparative perspective. The findings have relevant implications for crisis communication theory and practice.
Nested insider-partial mediator: South Korea’s mediation in the US–DPRK crisis in 2017–2018
Authors: Schiff Amira 
Published: February 2024

Purpose
The purpose of this paper is to advance our understanding of international crisis mediation by introducing and examining the nested insider-partial mediator (NIPM) concept, a nuanced perspective on IPM behavior. This study challenges the traditional view of effective mediators as external, unbiased entities by delving into the behavior and contribution of mediators who are deeply embedded in the conflict environment, such as South Korea’s unique position in navigating the US–DPRK crisis in 2017–2018. By analyzing South Korea’s dual role as mediator and negotiator and its employment of both nondirective and directive mediation strategies, the paper demonstrates the potential effectiveness of NIPMs in managing complex biases and contributing to de-escalation in intense crisis scenarios.

Design/methodology/approach
This paper uses a focused single-case study approach to analyze South Korea’s role as an NIPM. Using a process-tracing methodology, it examines how contextual factors such as relationships, interests and inherent biases influenced South Korea’s mediation strategies in this complex geopolitical scenario. Empirical evidence was retrieved from public sources, including official statements and press interviews, providing an empirical foundation for understanding NIPM behavior. This approach facilitates a detailed study of South Korea’s unique mediation role within the intricate dynamics of the Korean Peninsula conflict.

Findings
The study’s findings illustrate the pivotal role NIPMs can play in complex international conflicts, underlining the significant potential of NIPMs in crisis prevention. The findings highlight South Korea’s adept navigation through intricate geopolitical dynamics, leveraging its unique insider position and established relationships with both the USA and North Korea. This behavior was instrumental in mitigating a potentially explosive situation, steering the crisis toward negotiation and de-escalation. The research underscores the effectiveness of the NIPM framework in understanding the nuanced behavior of mediators who are deeply integrated into multi-level conflicts, influenced by their connections, interests and inherent biases.

Originality/value
This research not only broadens the theoretical framework of insider-partial mediation by introducing the concept of NIPM, but also has practical implications for policymakers and practitioners in leveraging regional mediation strategies for international crisis mitigation. The study underscores the importance of mediators’ deep-rooted connections, biases and vested interests in influencing their mediation tactics, thus offering a comprehensive understanding of the multifaceted nature of international mediation in complex geopolitical conflicts.
Shared professional logics amongst managers and bureaucrats in Brazilian social security: a street-level mixed-methods study
Authors: de Andrade Luiz Henrique Alonso , Pekkola Elias 
Published: February 2024

PurposeThis research addresses the professional logics of street-level managers (SLMs) and bureaucrats (SLBs) working in the Brazilian National Social Security Agency (INSS) through their perceptions of distributive justice and discretion. Since SLMs have the authority to influence SLBs' actions, we investigate whether these two groups hold similar viewpoints.Design/methodology/approachWe integrate the administrative data and survey responses (n = 678) with earlier thematic content analysis (n = 350) in three stages: mean-testing, regression analyses and complementary qualitative analysis, integrated through a mixed-methods matrix.FindingsWhilst no significant differences emerge in distributive justice ideas between groups, SLMs demand wider benefit-granting discretion, praising professionalism whilst adopting managerial posture and jargon.Research limitations/implicationsThe study adds to the theoretical discussions concerning SLM’s influence on SLB’s decision-making, suggesting that other factors outweigh it. The finding concerning the managers’ demand for wider discretion asks for further in-depth approaches.Practical implicationsFindings supply valuable insights for policymakers and managers steering administrative reforms, by questioning whether some roles SLMs play are limited to symbolic levels. Further, SLBs’ heterogenous formations might be more relevant to policy divergence than managerial influence and perhaps an underutilised source of innovation.Originality/valueBy approaching street-level management professional logics within a Global South welfare state through a mixed-methods approach, this study offers a holistic understanding of complex dynamics, providing novel insights for public sector management.
Gender diversity and corporate financial distress in the Pakistan stock market: the interacting effect of family-controlled companies
Authors: Muien Hafiz Muhammad , Nordin Sabariah , Badru Bazeet Olayemi 
Published: February 2024

PurposeAs the benefit of gender diversity continues to receive significant attention, a holistic investigation of its effect on corporate financial distress (CFD) is lacking. Therefore, this study examines the effects of board gender diversity, measured in different forms, such as the presence and proportion of female directors, family-affiliated female directors and the chief executive officer (CEO) gender, on CFD in Pakistan. The study also investigates the interacting effects of family-controlled (20 and 50% family-owned) companies on the association between board gender diversity and CFD.Design/methodology/approachThe study applied the pooled cross-sectional logistic regression model to examine the effect of board gender diversity (presence and proportion of female directors, family-affiliated female directors and CEO gender) on CFD through a sample of 285 non-financial companies in Pakistan over the period of 2006–2017.FindingsThe results reveal that gender diversity on boards is significantly and negatively associated with CFD in Pakistan. In addition, when family ownership is 50% or more, the interacting effect of family control is found to be significant, while gender effects remain negative. The results suggest that female directors contribute to the long-term viability of companies, especially family-owned companies. Female directors are also found to be more prevalent in family-owned companies compared to their non-family counterparts.Research limitations/implicationsThe findings imply that female directors may efficiently manage and control all functions necessary to guarantee the company's long-term prosperity. Similarly, gender effects can outweigh the detrimental impact of family control when female directors are in reasonable numbers and of high quality in the boardroom.Practical implicationsThe practical relevance of the findings is that female directors play a significant role on the corporate board. Thus, it is a wakeup call for Pakistani companies to recognize the critical role and uniqueness of women on the corporate ladder. Family companies can also galvanize on the uniqueness of women to improve their governance structure.Originality/valueThis study adds to the literature on the benefits of gender diversity in family and non-family-owned companies. Specifically, this study applied multiple measures of gender diversity and family control in a single study. In addition, the study was conducted in a country that is ranked as the second worst country in the Global Gender Gap Index 2022, implying that investigating this type of research would go a long way towards changing the minds of corporate executives and regulators about the critical role that women can play in the economy.
Earnings predictability or truthfulness? Which one investors care more about
Authors: Fan Shihui , Zhou Yan 
Published: February 2024

Purpose
This study aims to investigate the impact of earnings predictability and truthfulness on nonprofessional investors’ investment willingness.

Design/methodology/approach
Earnings predictability is captured by quarterly earnings autocorrelation, and earnings truthfulness is indicated by real earnings management (REM). The average of investment attractiveness and willingness measures investment willingness. The authors use experiments to isolate the impact of quarterly earnings autocorrelation and REM on investors’ investment behaviors.

Findings
From the 2 × 2 design, the authors observe that investors weight more on earnings predictability than earnings truthfulness.

Research limitations/implications
The generalization of the findings may be constrained for the following reasons. First, the authors use only one proxy, REM, to measure earnings truthfulness. In addition, the authors provide the participants, Amazon Mechanical Turk, with earnings predictability. Results may no longer hold if each participant has different understanding and analysis of earnings predictability.

Practical implications
In periods of unprecedented and severe financial uncertainty (i.e. the COVID-19 pandemic), investors rely more on earnings predictability than on earnings truthfulness. The study assists managers to strategically emphasize the predictability of earnings to attract investors, especially when firms face financial challenges or uncertainty.

Social implications
This study contributes to understanding investor behavior and the critical role of earnings predictability and truthfulness in shaping investment decisions.

Originality/value
This paper contributes to the literature of earnings properties in financial reporting, particularly by shedding light on the nuanced interplay between earnings predictability and earnings truthfulness. The research also demonstrates that elevated earnings autocorrelation indirectly stimulates investment willingness by enhancing the investors’ perception of earnings persistence of targeted firms.
Does supply chain analytics adoption impacts sustainable performance? A consideration of technophobia as an influencing factor
Authors: Lyu Xianwei , Dastane Omkar , He Xiaoguang 
Published: February 2024

Purpose
Food SMEs is the backbone of local and world economy. Even while food SMEs are aware of the potential advantages of implementing supply chain analytics (SCA), only a small number of companies use data-based decision-making. This is because of technophobia. In light of this, the purpose of this study is to investigate the factors that have an impact on SCA adoption which in turn influence the sustainable performance of firms.

Design/methodology/approach
The data were collected from 221 managers working in food-related SMEs in China by using a questionnaire-based survey. The framework of this study was validated using a rigorous statistical procedure using the technique, namely, partial least squares structural equation modelling.

Findings
The findings of this study suggest that all modified UTAUT components (i.e. performance expectancy, effort expectancy, social influence, facilitating conditions and technophobia) significantly influence SCA adoption. Moreover, the existing study highlights and confirms the significance of adopting SCA to improve sustainable performance.

Originality/value
This research is novel, as it extends and investigates the theoretical framework based on UTAUT theory in SCA context and its impact on sustainable organizational performance. In addition, the factor of technophobia is tested in SCA context. This study has several contributory managerial implications for food SMEs.