bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative genomics and transcriptomic response to root exudates of six rice root-associatedBurkholderia sensu latospecies
Authors: Wallner Adrian , Klonowska Agnieszka , Guigard Ludivine , King Eoghan , Rimbault Isabelle , Ngonkeu Eddy , Nguyen Phuong , Béna Gilles , Moulin Lionel 
Published: October 2022

AbstractBeyond being a reliable nutrient provider, some bacteria will perceive the plant as a potential host and undertake root colonization leading to mutualistic or parasitic interactions. Bacteria of theBurkholderiaandParaburkholderiagenera are frequently found in the rhizosphere of rice. While the latter are often described as plant growth promoting species,Burkholderiaare often studied for their human opportunistic traits. Here, we used root exudate stimulation on threeBurkholderiaand threeParaburkholderiastrains isolated from rice roots to characterize their preliminary adaptation to the rice host at the transcriptomic level. Instead of the awaited genus-dependent adaptation, we observed a strongly species-specific response for all tested strains. While all bacteria originate from the rice environment, there are great disparities in their levels of adaptation following the sensing of root exudates. We further report the shared major functions that were differentially regulated in this early step of bacterial adaptation to plant colonization, including amino acids and putrescine metabolism, the Entner-Doudoroff (ED) pathway as well as cyclic diguanylate monophosphate (c-di-GMP) cycling.
Modeling Single-Cell Dynamics Using Unbalanced Parameterized Monge Maps
Authors: Eyring Luca Vincent , Klein Dominik , Palla Giovanni , Becker Soeren , Weiler Philipp , Kilbertus Niki , Theis Fabian J. 
Published: October 2022

AbstractOptimal Transport (OT) has proven useful to infer single-cell trajectories of developing biological systems by aligning distributions across time points. Recently, Parameterized Monge Maps (PMM) were introduced to learn the optimal map between two distributions. Here, we apply PMM to model single-cell dynamics and show that PMM fails to account for asymmetric shifts in cell state distributions. To alleviate this limitation, we propose Unbalanced Parameterised Monge Maps (UPMM). We first describe the novel formulation and show on synthetic data how our method extends discrete unbalanced OT to the continuous domain. Then, we demonstrate that UPMM outperforms well-established trajectory inference methods on real-world developmental single-cell data.
Structure of human phagocyte NADPH oxidase in the resting state
Authors: Liu Rui , Song Kangcheng , Wu Jing-Xiang , Geng Xiao-Peng , Zheng Liming , Gao Xiaoyin , Peng Hailin , Chen Lei 
Published: October 2022

AbstractPhagocyte oxidase plays an essential role in the first line of host defense against pathogens. It oxidizes intracellular NADPH to reduce extracellular oxygen to produce superoxide anions for pathogen killing. The resting phagocyte oxidase is a heterodimeric complex formed by two transmembrane proteins NOX2 and p22. Despite the functional importance of this complex, its structure remains elusive. Here we reported the cryo-EM structure of the human NOX2-p22 complex in nanodisc in the resting state. The structure shows that p22 is formed by four transmembrane helices and interacts with NOX2 through its M1 and M4 helices. Hydrophobic residues on M3, M4, and M5 of NOX2 contribute to the complex formation. Structural analysis suggests that the cytosolic factors activate the NOX2-p22 complex by stabilizing the dehydrogenase domain (DH) in a productive docked conformation which is efficient for electron transfer between DH and the transmembrane domain.
Pervasive mRNA uridylation in fission yeast catalysed by both Cid1 and Cid16 terminal uridyltransferases
Authors: Lipińska-Zubrycka L , Grochowski M , Bähler J , Małecki M 
Published: October 2022

AbstractMessenger RNA uridylation is pervasive and conserved among eukaryotes, but the consequences of this modification for mRNA fate are still under debate. Utilising a simple model organism to study uridylation may facilitate efforts to understand the cellular function of this process. Here we demonstrate that uridylation can be detected using simple bioinformatics approach. We utilise it to unravel widespread transcript uridylation in fission yeast and demonstrate the contribution of both Cid1 and Cid16, the only two annotated terminal uridyltransferases (TUT-ases) in this yeast.To detect uridylation in transcriptome data, we used a RNA-sequencing (RNA-seq) library preparation protocol involving initial linker ligation to fragmented RNA. We next explored the data to detect uridylation marks. Our analysis shows that uridylation in yeast is pervasive, similarly to the ones in multicellular organisms. Importantly, our results confirm the role of the cytoplasmic uridyltransferase Cid1 as the primary uridylation catalyst. However, we also observed an auxiliary role of the second uridyltransferase, Cid16. Thus both fission yeast uridyltransferases are involved in mRNA uridylation. Intriguingly, we found no physiological phenotype of the single and double deletion mutants of cid1 and cid16 and only limited impact of uridylation on steady-state mRNA levels.Our work establishes fission yeast as a potent model to study uridylation in a simple eukaryote, and we demonstrate that it is possible to detect uridylation marks in RNA-seq data without the need for specific methodologies.
MTCH2 cooperates with MFN2 and lysophosphatidic acid synthesis to sustain mitochondrial fusion
Authors: Goldman Andres , Mullokandov Michael , Zaltsman Yehudit , Regev Limor , Zaidman Smadar , Gross Atan 
Published: October 2022

AbstractMitochondrial dynamics is critical to sustain normal mitochondrial function and is linked to the response of cells to stressful conditions. Fusion of the outer mitochondrial membrane (OMM) is regulated by mitofusin 1 (MFN1) and 2 (MFN2), yet the differential contribution of each of these proteins to this process is less understood. Mitochondrial carrier homolog 2 (MTCH2) was shown to compensate for MFN2’s loss, however its exact function in mitochondrial fusion remains poorly understood. Here we determined the mitochondrial fusion-interplay between MFN1, MFN2 and MTCH2 and demonstrate that MFN2 and MTCH2 play separate, but redundant, roles required for mitochondrial fusion. Loss of either MFN2 or MTCH2 elicits mitochondrial fragmentation that retains mitochondrial plasticity, while loss of both proteins completely impairs mitochondrial fusion. We also show that expression of an MFN2 mutant targeted to the endoplasmic reticulum (ER) is sufficient to restore mitochondrial elongation in MTCH2 KO cells and that this restoration depends on the synthesis of the pro-mitochondrial fusion lipid lysophosphatidic acid (LPA). Moreover, silencing of MFN2 or inhibition of de novo LPA synthesis, revealed the requirement of MTCH2 to sustain mitochondrial plasticity in response to stress. Thus, we unmask two cooperative mechanisms that sustain mitochondrial fusion: one in the OMM, dependent on MTCH2 and MFN1, and independent of MFN2; and a second mechanism in the ER that relies on MFN2 and LPA synthesis.
A corset of adhesions during development establishes individual neural stem cell niches and controls adult behaviour
Authors: Banach-Latapy Agata , Rincheval Vincent , Briand David , Guénal Isabelle , Spéder Pauline 
Published: October 2022

ABSTRACTNeural stem cells (NSCs) reside in a defined cellular microenvironment, the niche, which supports the generation and integration of neuronal lineages. The mechanisms building a sophisticated niche structure around NSCs, and their functional relevance for neurogenesis are yet to be understood. In the Drosophila larval brain, the cortex glia (CG) encase individual NSC lineages, organizing the stem cell population and newborn neurons into a stereotypic structure. We first found that lineage information is dominant over stem cell fate. We then discovered that, in addition to timing, the balance between multiple adhesion complexes supports the individual encasing of NSC lineages. An intra-lineage adhesion through homophilic Neuroglian interactions provides strong binding between cells of a same lineage, while a weaker interaction through Neurexin-IV exists between CG to NSC lineages. Their loss leads to random, aberrant grouping of several NSC lineages together, and to altered axonal projection of newborn neurons. Further, we link the loss of these two adhesion complexes during development to locomotor hyperactivity in the resulting adults. Altogether, our findings identify a corset of adhesions building a neurogenic niche at the scale of individual stem cell and provide the proof-of-principle that mechanisms supporting niche formation during development define adult behaviour.
Geometric constraints on human brain function
Authors: Pang James C. , Aquino Kevin M. , Oldehinkel Marianne , Robinson Peter A. , Fulcher Ben D. , Breakspear Michael , Fornito Alex 
Published: October 2022

ABSTRACTThe brain’s anatomy constrains its function, but precisely how remains unclear. Here, we show that human cortical and subcortical activity, measured with magnetic resonance imaging under spontaneous and diverse task-evoked conditions, can be parsimoniously understood as resulting from excitations of fundamental, resonant modes of the brain’s geometry (i.e., its shape) rather than modes from complex inter-regional connectivity, as classically assumed. We then use these modes to show that task-evoked activations across >10,000 brain maps are not confined to focal areas, as widely believed, but instead excite brain-wide modes with wavelengths spanning >60 mm. Finally, we confirm theoretical predictions that the close link between geometry and function is explained by a dominant role for wave-like dynamics, showing that such dynamics can reproduce numerous canonical spatiotemporal properties of spontaneous and evoked recordings. Our findings challenge prevailing views of brain function and identify a previously under-appreciated role of brain geometry that is predicted by a unifying and physically principled approach.
Analysis of the structure and time-series evolution of knowledge label network from a complex perspective
Authors: Wang Xu , Feng Xin , Guo Yuan 
Published: October 2022

PurposeThe research on social media-based academic communication has made great progress with the development of the mobile Internet era, and while a large number of research results have emerged, clarifying the topology of the knowledge label network (KLN) in this field and showing the development of its knowledge labels and related concepts is one of the issues that must be faced. This study aims to discuss the aforementioned issue.Design/methodology/approachFrom a bibliometric perspective, 5,217 research papers in this field from CNKI from 2011 to 2021 are selected, and the title and abstract of each paper are subjected to subword processing and topic model analysis, and the extended labels are obtained by taking the merged set with the original keywords, so as to construct a conceptually expanded KLN. At the same time, appropriate time window slicing is performed to observe the temporal evolution of the network topology. Specifically, the basic network topological parameters and the complex modal structure are analyzed empirically to explore the evolution pattern and inner mechanism of the KLN in this domain. In addition, the ARIMA time series prediction model is used to further predict and compare the changing trend of network structure among different disciplines, so as to compare the differences among different disciplines.FindingsThe results show that the degree sequence distribution of the KLN is power-law distributed during the growth process, and it performs better in the mature stage of network development, and the network shows more stable scale-free characteristics. At the same time, the network has the characteristics of “short path and high clustering” throughout the time series, which is a typical small-world network. The KLN consists of a small number of hub nodes occupying the core position of the network, while a large number of label nodes are distributed at the periphery of the network and formed around these hub nodes, and its knowledge expansion pattern has a certain retrospective nature. More knowledge label nodes expand from the center to the periphery and have a gradual and stable trend. In addition, there are certain differences between different disciplines, and the research direction or topic of library and information science (LIS) is more refined and deeper than that of journalism and media and computer science. The LIS discipline has shown better development momentum in this field.Originality/valueKLN is constructed by using extended labels and empirically analyzed by using network frontier conceptual motifs, which reflects the innovation of the study to a certain extent. In future research, the influence of larger-scale network motifs on the structural features and evolutionary mechanisms of KLNs will be further explored.
Testing spillover-crossover effects of work-family conflict and family-work conflict on Indonesian spouses
Authors: Ratnaningsih Ika Zenita , Idris Mohd Awang , Yulita Yulita 
Published: October 2022

PurposeThis study aims to investigate the spillover–crossover effects on the work–family interface, with an emphasis on work–family conflict (WFC) and family–work conflict (FWC) on marital satisfaction and personal burnout.Design/methodology/approachData were collected from matched dyads by 300 teachers and their spouses (N = 600) in Indonesia. Multiple regression analysis served to test the hypotheses.FindingsThe results showed significant spillover–crossover effects of WFC on personal burnout amongst working wives to their spouses, but not working husbands to their spouses. Moreover, there was a spillover effect of FWC on personal burnout amongst working wives, and a crossover effect of FWC on spouses' personal burnout amongst working husbands to their spouses. However, there was no spillover–crossover effect of WFC and FWC on marital satisfaction for both working wives and husbands.Practical implicationsThe findings have implications for occupational stress management. Decision-makers have to create a positive atmosphere that reduces WFC in the workplace by providing support to the workers.Originality/valueThis study contributes to the literature by exploring the crossover effects of WFC and FWC amongst marital spouses in a country with inherent conservatism and traditional gender role perspectives.
Corporate social responsibility performance and its effects on climate for innovation and opportunism: evidence from Vietnamese architectural design firms
Authors: Nguyen Minh Van 
Published: October 2022

PurposeThe purpose of this research is to expand a better understanding of how corporate social responsibility (CSR) initiatives affect climate for innovation and opportunism within architectural design firms (ADFs).Design/methodology/approachThe literature review and discussions with industry practitioners identified an initial list of variables. A questionnaire survey was developed, validated and delivered to employees working in ADFs. 226 valid responses were collected. Then, the structural equation modeling (SEM) method was employed to empirically investigate the relationships between CSR performance, climate for innovation and opportunism in a single integrative model.FindingsThe results empirically support that CSR performance has a positive effect on climate for innovation and a negative effect on opportunism. In addition, climate for innovation shows a negative effect on opportunism.Research limitations/implicationsThis research highlights that CSR performance is essential for ADFs to better achieve sustainable development. By doing CSR activities, climate for innovation in ADFs is expected to be improved, and a sense of opportunism is mitigated. The findings of this paper are explicitly delivered in the context of Vietnamese ADFs and could not be straightforwardly generalized or translated to the construction industry or other sectors in different research contexts.Practical implicationsThe findings show that a climate for innovation is crucial in ADFs. Business managers are encouraged to employ CSR initiatives to foster an innovation climate and reduce a sense of opportunism within ADFs.Originality/valueThis study is one of the first attempts to investigate the relationships between CSR performance, climate for innovation, and opportunism within ADFs. While the findings highlight the critical role of CSR performance, the study argues that CSR should be carefully implemented because there are no “one-size-fits-all” CSR strategies for different business contexts.
Impact of institutional pressures and dynamic capabilities on sustainability performance of oil and gas sector
Authors: Jain Nikunj Kumar , Choudhary Piyush , Panda Abinash , Jain Sourabh , Dey Prasanta Kumar 
Published: October 2022

Purpose
Globally, the oil and gas (OG) industries are under pressure from numerous stakeholders for their sustainable operations against the backdrop of climate change, ecological damage and social challenges. Drawing on the twin theoretical frameworks of the institutional theory and dynamic capability perspective, this study aims to examine the impact of the institutional pressures and dynamic capabilities on the overall sustainability performance of OG industry.

Design/methodology/approach
This study uses survey method to analyze the responses from 275 middle management professionals of OG industry in India using partial least squares structural equation modeling. Further, focused group discussions with the select industry leaders validate the empirical findings of this study.

Findings
The research reveals that both institutional pressures and firm’s dynamic capabilities have significant positive impact on its economic and environmental performances in OG sector in India. However, they do not have any impact on social performance, unlike earlier findings.

Research limitations/implications
The main limitation of the study is generalizability of the findings, given the cross-sectional design of the study.

Practical implications
Insights of this study will help regulators and policymakers in formulating effective regulatory and policy frameworks, besides creating awareness amongst the organizations to simultaneously focus on all the three aspects of sustainability performance.

Originality/value
The research has bearing on policy formulation and creating a regulatory ecosystem to ensure overall sustainability performance of OG industry in India.
Public diplomacy in an age of perpetual crisis: assessing the EU's strategic narratives through six crises
Authors: Manfredi-Sánchez Juan-Luis , Smith Nicholas Ross 
Published: October 2022

PurposeThe purpose of this research is to identify the strengths and weaknesses of the EU's public diplomacy – towards both domestic and external audiences – during times of crisis. The EU's public diplomacy is examined across six major crises: the Eurozone crisis (2008), the Ukrainian crisis (2014), the migrant crisis (2015), the Brexit referendum (2016), the new transatlantic relationship (2017) and the COVID-19 pandemic (2020). The goal of examining these crises in conjunction is to derive policy-relevant insights.Design/methodology/approachThis article adopts a problem-driven approach – the problem being how successful is the EU at public diplomacy during times of crisis – that draws theoretical and empirical insights from Communication Studies, International Relations and EU studies via a “strategic narratives” framework. It situates the EU as a unique public diplomacy actor, one which is becoming more prominent due to the mediatisation of diplomacy, especially driven by the advent of cyberspace.FindingsThe article finds that the EU has been experiencing a cycle of crises that have affected the political, economic, symbolic and social foundations of the common project. The EU has had some notable success – such as restoring confidence at the height of the Eurozone crisis – and some notable challenges – such as effectively combatting disinformation. Regardless, the EU has the potential to better manage these and future crises by engaging in an effective public diplomacy strategy that tells a shared European story that informs and inspires people, both domestically and externally.Originality/valueThe article offers an original examination of the EU's public diplomacy response to six different crises. It looks at different types of crises and utilises concepts from different social science perspectives. It offers novel strategic and policy recommendations.
A bibliometric analysis of work engagement in the hospitality and tourism industry
Authors: Han Yao , Yang Ying , Mohamed Rosmah 
Published: October 2022

PurposeFor the past two decades, researchers have been exploring knowledge of work engagement in the hospitality and tourism industry (HTI). This study aims to provide a comprehensive analysis of global research trends in the field through a bibliometric analysis.Design/methodology/approachA total of 335 papers from 2005 to 2021 were searched using the Scopus database. The analysis focused on the temporal distribution, most productive journals, countries/territories, institutions, authors, international and authors' collaboration, the most cited publications and author keywords. The VOS viewer and R software were used to visualise the scientific landscapes.FindingsThe results indicated a rapidly increasing trend of studies on work engagement in the HTI. The journal with the most published articles was the International Journal of Hospitality Management. The USA ranked first in production, and Karatepe, O.M., from Turkey was the leading author. The first and most cited article was from Salanova et al. (2005). Other themes were identified, mainly related to job resources and outcomes associated with work engagement.Practical implicationsThe study provides a more comprehensive understanding of the progress of work engagement in HTI studies and offers clues for further investigation in this field.Originality/valueThis is the first paper to explore work engagement in the HTI using quantitative and visualised bibliometric analysis.
Leader humor and newcomer adjustment: The mediating role of role breadth self-efficacy
Authors: Kang Fei , Li Jiyu , Zhang Han , Zhang Ying 
Published: October 2022

PurposeDespite the increasingly growing empirical research on leader humor, the critical issue of how and when leader humor affects newcomer adjustment was largely overlooked. The purpose of this study is to examine the relationship between leader humor and newcomer adjustment. Based on social information processing theory, the authors identify newcomers' role breadth self-efficacy (RBSE) as the mediator and suggest that newcomers' cognitive flexibility moderates the effects.Design/methodology/approachData were obtained from a 2-wave sample of 195 newcomers. The authors utilized the PROCESS procedure developed by Hayes to assess the hypothesized moderated mediation model.FindingsThe findings showed that leader humor could boost newcomers' RBSE which, in turn, was beneficial to newcomer adjustment. Besides, newcomers' cognitive flexibility plays a moderating role in the relationship between leader humor and newcomers' RBSE.Research limitations/implicationsThis study utilized a cross-sectional research design, making the design difficult to obtain causal conclusions. Moreover, the data were all based on self-reports from newcomers, which may raise a concern of common method bias.Originality/valueThis paper extends the literature on leader humor and newcomer adjustment by treating RBSE as the mediator and newcomers' cognitive flexibility as the moderator. This study is one of several empirical studies to test the link between leader humor and newcomer adjustment.