bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial transcriptomics unveils thein situcellular and molecular hallmarks of the lung in fatal COVID-19
Authors: Garcia-Prieto Carlos A. , Musulen Eva , Davalos Veronica , Ferrer Gerardo , Grases Daniela , Porta Eduard , Pérez-Miés Belén , Caniego-Casas Tamara , Palacios José , Saenz-Sardà Xavier , Englund Elisabet , Esteller Manel 
Published: July 2024

ABSTRACTSevere Coronavirus disease 2019 (COVID-19) induces heterogeneous and progressive diffuse alveolar damage (DAD) highly disrupting lung tissue architecture and homeostasis, hampering disease management leading to fatal outcomes. Characterizing DAD pathophysiology across disease progression is of ultimate importance to better understand the molecular and cellular features driving different DAD patterns and to optimize treatment strategies. To contextualize the interplay between cell types and assess their distribution, spatial transcriptomics (ST) techniques have emerged, allowing unprecedented resolution to investigate spatial architecture of tissues. To this end, post-mortem lung tissue provides valuable insights into cellular composition and their spatial relationships at the time of death. Here, we have leveraged VisumST technology in post-mortem COVID-19 induced acute and proliferative DAD lungs including control samples with normal morphological appearance, to unravel the immunopathological mechanisms underlying DAD, providing novel insights into cellular and molecular communication events driving DAD progression in fatal COVID-19. We report a progressive loss of endothelial cell types, pneumocytes type I and natural killer cells coupled with a continuous increase of myeloid and stromal cells, mostly peribronchial fibroblasts, over disease progression. Spatial organization analysis identified variable cellular compartments, ranging from major compartments defined by cell type lineages in control lungs to increased and more specific compartmentalization including immune-specific clusters across DAD spectrum. Importantly, spatially informed ligand-receptor interaction (LRI) analysis revealed an intercellular communication signature defining COVID-19 induced DAD lungs. Transcription factor (TF) activity enrichment analysis identified TGF-B pathway as DAD driver, highlighting SMAD3 and SMAD7 TFs activity role during lung fibrosis. Integration of deregulated LRIs and TFs activity allowed us to propose a downstream intracellular signaling pathway in peribronchial fibroblasts, suggesting potential novel therapeutic targets. Finally, spatio-temporal trajectories analysis provided insights into the alveolar epithelium regeneration program, characterizing markers of pneumocytes type II differentiation towards pneumocytes type I. In conclusion, we provide a spatial characterization of lung tissue architecture upon COVID-19 induced DAD progression, identifying molecular and cellular hallmarks that may help optimize treatment and patient management.
Computational modelling identifies key determinants of subregion-specific dopamine dynamics in the striatum
Authors: Ejdrup Aske L. , Dreyer Jakob K. , Lycas Matthew D. , Jørgensen Søren H. , Robbins Trevor W. , Dalley Jeffrey W. , Herborg Freja , Gether Ulrik 
Published: July 2024

AbstractStriatal dopamine (DA) release regulates reward-related learning and behavioural activation and is believed to consist of a short-livedphasicand continuoustoniccomponent. Here, we build a three-dimensional model of extracellular DA dynamics in dorsal (DS) and ventral striatum (VS) that include tens of thousands of DA release sites. The model predicts rapid dynamics in DS with little-to-no basal DA, and much slower dynamics in the VS enabling build-up of atonicDA level. These regional differences do not primarily reflect different release phenomena but rather arise from differential dopamine transporter (DAT) activity. Interestingly, our simulations posit prevalent nanoclustering of DAT as a possible regulator of this activity. Receptor binding simulations show that D1 receptor occupancy follows extracellular DA concentration with millisecond delay, while D2 receptors integrate DA signal over seconds. Summarized, our model distills recent experimental observations into a computational framework that challenge prevailing paradigms of striatal DA signalling.
Fine-tuning of a CRISPRi screen in the seventh pandemicVibrio cholerae
Authors: Debatisse Kevin , Niault Théophile , Peeters Sarah , Maire Amandine , Darracq Baptiste , Baharoglu Zeynep , Bikard David , Mazel Didier , Loot Céline 
Published: July 2024

ABSTRACTVibrio cholerae O1 El Tor, the etiological agent responsible for the last cholera pandemic, has become a well-established model organism for which some genetic tools exist. While CRISPRi has been applied inV. cholerae, improvements were necessary to upscale it and enable pooled screening by high-throughput sequencing in this bacterium. In this study, we introduce a pooled genome wide CRISPRi library construction specifically optimized for thisV. choleraestrain, characterized by minimal cytotoxicity and streamlined experimental setup. This library allows the depletion of 3, 674 (98.9%) annotated genes from theV. choleraegenome. To confirm its effectiveness, we screened for essential genes during exponential growth in rich medium and identified 368 genes for which guides were significantly depleted from the library (log2FC < - 2). Remarkably, 82% of these genes had previously been described as hypothetical essential genes inV. choleraeor in a closely related bacterium,V. natriegens. We thus validated the robustness and accuracy of our CRISPRi-based approach for assessing gene fitness in a given condition. Our findings highlight the efficacy of the developed CRISPRi platform as a powerful tool for high-throughput functional genomics studies ofV. cholerae.GRAPHICAL ABSTRACT
Effects of temperature and salinity on microbial degradation of bacterial necromass in urban river sediments in outdoor mesocosm experiments
Authors: Hadžiomerović Una , Baikova Daria , Madge Pimentel Iris , Buchner Dominik , Vermiert Anna-Maria , Rehsen Philipp M. , Brauer Verena S. , Meckenstock Rainer U. 
Published: July 2024

AbstractMicroorganisms play a key role in the functioning of healthy river ecosystems because they consume carbon and nutrients from dead biomass derived from algae and other higher organisms, or “necromass”, to feed it back into the food web. This so-called microbial loop is known to be substantial in aquatic systems, but it is so far unknown to which extent microorganisms perform self-recycling, i.e. recycling of necromass derived from microorganisms, and how this process is affected by multiple stressors such as increased temperature and salinity. In this study, we investigated microbial self-recycling in the sediment of the urban river Boye within a food-web context before, during, and after a period of increased temperature and salinity using the outdoor flow-through mesocosm system “ExStream”. Rates of self-recycling were measured in additional microcosms with sediment and water from ExStream as an increase in13CO2-concentration over time resulting from the microbial degradation of13C-labelled microbial necromass, which was offered either in the form of intact but deadEscherichia colicells, or lysedE. colicells. The results showed that microbial self-recycling was highest in the first days of incubation suggesting that microbial necromass is an easily biodegradable carbon source. Increased salinity had no effect, but increased temperature or temperature and salinity strongly increased the rate of whole cell-necromass recycling compared to the unstressed control, while it had no effect on lysed cell-necromass recycling. After stressor removal, rates of self-recycling were not distinguishable from the unstressed control, showing the resilience of this community function. The compositions of the necromass-degrading communities were highly similar and little affected by stressor increase or release but changed during the course of the experiment. This indicated that both necromass types stimulated growth of the same organisms and that stressor levels were rather low for microorganisms and dominated by the effects of the seasonal variation in the Boye. The study suggests that microbial communities in urban rivers exposed to moderate levels of multiple anthropogenic stressors will be rather stressor-resistant and show fast recovery of community functioning.
Cooperativity among clustered κB sites within promoters and enhancers dictates transcriptional specificity of NF-κB-RelA along with specific cofactors
Authors: Shahabi Shandy , Biswas Tapan , Shen Yuting , Sanahmadi Rose , Zou Yaya , Ghosh Gourisankar 
Published: July 2024

ABSTRACTThe functional role of weak DNA binding sites for transcription factor (TF) recruitment and gene expression remains largely unknown. Our study reveals that the weak NF-κB DNA binding sites, which are abundant in gene promoters and enhancers, appear in clusters and exhibit minimal to undetectable NF-κB binding activity in isolation in vitro, yet they play prominent roles in gene regulation within native context in cells. We found nuclear concentration of RelA/p65, the predominant NF-κB, is approximately 0.2 µM in stimulated cells, challenging the idea that these weak κB sites operate through mass action-dependent binding mechanisms. Through proteomic analysis, we identified a range of nuclear factors, including various other TFs, interacting with RelA at these κB-sites. ChIP-seq, RNA-seq and phase-separated condensation analyses suggest these additional TFs, referred to as the cofactors of NF-κB, facilitate dynamic recruitment of NF-κB to clustered κB sites of specific target genes. Overall, our findings demonstrate the collective contribution of both strong and weak κB sites in occupancy of NF-κB at the promoters and enhancers, with the recruitment facilitated by a variety of cofactors. This congregation of multiple factors forming larger dynamic complexes appearing as a transcription condensate is likely to be common to all transcriptional programs.
Women, sustainable development and heritage regeneration in Qatar and Bahrain
Authors: Grichting Solder Anna , Alfaraidy Maryam 
Published: July 2024

PurposeThis research examines the role of women in shaping sustainable urban development in Gulf cities. It focuses on heritage preservation and urban regeneration, examining projects commissioned by women in Qatar and Bahrain, which are revitalizing heritage, creating gender-sensitive public spaces and implementing sustainable development. Furthermore, it questions the role of these projects to inspire the next generation of female designers and cultural influencers, while also introducing innovative approaches to sustainable design and heritage regeneration.Design/methodology/approachPresented at the Gulf Research Meeting in Cambridge as part of a workshop entitled “Women in the GCC Socio-economic Contributions to the Urbanisation of Gulf Countries” the paper proposes the framework of SDG11 (sustainable cities and communities) and the SDG5 (equity integration of women into the workforce) to discuss the status, challenges and aspirations for integrated future urbanization of desert cultures in the GCC and to achieve the desired net-zero urbanization in deserts and drylands that are part of Gulf countries’ strategic development plans. The methodology uses case studies in Qatar and Bahrain and examines them through the lens of the Sustainable Development Goals indicators (SDG 5–SDG 11). It begins by looking at the National context to examine how the SDGs 5 and 11 are being achieved, what indicators are being used and how both countries are scoring.FindingsThe preliminary research findings reveal that both Qatar and Bahrain are reporting on these SDGs that relate to Women and Urbanization, and that the two cases studies demonstrate that certain indicators on women’s empowerment and sustainability can be fulfilled and highlighted through these female led urban projects – Msheireb Downtown and the Muharraq Pearling Path. The projects also contribute to the education and training of young female architects through commissions, internships and seminars.Originality/valueThis is an exploratory research in an emerging field and can lead to further and deeper enquiries into how the SDGs 5 and 11 are being implemented and reported on in Gulf countries, as well as how women in leadership, urban policy and design can contribute to more sustainable, inclusive and female friendly cities, as well to gender mainstreaming in urban design.
Integrating three pillars of sustainability for evaluating the modular construction building
Authors: Tighnavard Balasbaneh Ali , Ramadan Bimastyaji Surya 
Published: July 2024

Purpose
The purpose of this study is to evaluate the sustainability performance of modular construction from a life cycle perspective. So far, the sustainability performance of modular buildings has been explored from a life cycle viewpoint. There is no comprehensive study showing which material is the best choice for modular construction considering all three sustainable pillars. Therefore, a life cycle sustainability performance framework, including the three-pillar evaluation framework, was developed for different modular buildings. The materials are concrete, steel and timber constructed as a modular construction method.

Design/methodology/approach
Transitioning the built environment to a circular economy is vital to achieving sustainability goals. Modular construction is perceived as the future of the construction industry, and in combination with objective sustainability, it is still in the evaluation phase. A life cycle sustainability assessment, which includes life cycle assessment, life cycle cost and social life cycle assessment, has been selected to evaluate alternative materials for constructing a case study building using modular strategies. Subsequently, the multi-criteria decision-making (MCDM) method was used to compute the outranking scores for each modular component.

Findings
The calculated embodied impacts and global warming potential (GWP) showed that material production is the most critical phase (65%–88% of embodied energy and 64%–86% of GWP). The result of embodied energy and GWP shows timber as an ideal choice. Timber modular has a 21% and 11% lower GWP than concrete and steel, respectively. The timber structure also has 19% and 13% lower embodied energy than concrete and steel. However, the result of the economic analysis revealed that concrete is the most economical choice. The cost calculations indicate that concrete exhibits a lower total cost by 4% compared to timber and 11% higher than steel structures. However, the social assessment suggests that steel emerges as the optimal material when contrasted with timber and concrete. Consequently, determining the best single material for constructing modular buildings becomes challenging. To address this, the MCDM technique is used to identify the optimal choice. Through MCDM analysis, steel demonstrates the best overall performance.

Originality/value
This research is valuable for construction professionals as it gives a deliberate framework for modular buildings’ life cycle sustainability performance and assists with sustainable construction materials.
Role of collective organizational engagement in the emergence of innovation: a microfoundations perspective
Authors: Ganesh Pavithra , Srivastava Kailash B.L. 
Published: July 2024

PurposeThe present study uses dynamic capabilities and micro foundations theory to unearth the emergence of multilevel innovation in service sector organizations. Transformational leadership (TL) and corporate social responsibility (CSR) are proposed as human resource (HR) based antecedents. The study also aims to reveal the role of collective organizational engagement (COE) as a mediator in developing dynamic capabilities and contingent pay policy (CPP) as a moderator.Design/methodology/approachThe research is a multilevel study where employees are nested within organizations. We used multilevel modeling in Mplus V. 8.7 to perform the analyses.FindingsResults of multilevel structural equation modeling revealed that TL, CSR, and COE are vital microfoundations through which innovation emerges in an organization. COE acts as a partial mediator in the relationship between CSR and innovation. The level of CPP in organizations moderates these relationships at the employee level rather than at the firm level.Originality/valueThis research is one of the few multilevel and multisource studies to empirically test the impact of HR-based antecedents on innovative work behavior and firm innovativeness simultaneously. It also contributes to engagement literature by furthering an understanding of the nascent concept of COE.
Neoliberalism and the changing direction of schools: an edupreneurial leadership approach
Authors: Larey Desireé Pearl 
Published: July 2024

PurposeThis qualitative study discusses the importance of effective leadership practices in connecting the macro-, meso-, and micro-contexts in which school leaders operate, considering the colonial and apartheid history of South Africa and the current era of neoliberal philosophies by exploring the degree to which school leaders in historically disadvantaged schools in Western Cape Province use an edupreneurial approach to steer their schools in new directions. The school leaders, especially in historically disadvantaged Colored schools, are expected to be more autonomous and accountable for making the school environment conducive to performance standards and improved learning results. The study uses an edupreneurial leadership approach as a theoretical lens to explore entrepreneurial agency, together with the educational leadership approach of school principals as a consequence of neoliberal policies.Design/methodology/approachThis study focuses on secondary schools in historically Colored communities in Western Cape Province through semi-structured interviews with four purposively selected school principals and four teachers from four different schools in the Western Cape Province.FindingsEducation and training programs should focus on cultural values and practices to enhance the efficacy of these schools. Furthermore, an entrepreneurial mindset and spirit are aspects that can be encouraged in a culturally sensitive manner. The edupreneurial leadership approach in developing countries has a distinctive nature.Originality/valueThis study contributes to forging an understanding of how neoliberal trends influence school leadership practices in developing countries, especially the leadership work of school principals across public schools in the Western Cape Province in South Africa.
Responsible leadership and organizational sustainability performance: investigating the mediating role of sustainable HRM
Authors: Nakra Neelam , Kashyap Vaneet 
Published: July 2024

PurposeThe purpose of the present study is to investigate the role of responsible leadership in impacting organizational sustainability performance grounded in the stakeholder theory. Further, it delves into the underlying mechanism that accentuates the link between responsible leadership and organizational sustainability performance via mediating role of sustainable HRM practices within the organization.Design/methodology/approachThe study follows a cross-sectional research design using data collected via questionnaire-based survey from employees working in top 100 NSE listed organizations in India. The proposed hypotheses of the research were tested using SPSS Process Macro.FindingsResults depicted that there is a direct relationship between responsible leadership and organizational sustainability performance. However, the relationship is better explained with a mediating role of sustainable HRM practices within the organization.Practical implicationsThe study is helpful for the practitioners to understand the instrumentality of responsible leadership and sustainable HRM practices within Indian organizations. Moreover, the study promotes the relevance of achieving sustainability-oriented goals of the organizations.Originality/valueThe study fosters the limited research on the integration of leadership style and HRM function. The results further add to literature on sustainable HRM by studying its antecedents and consequences.
Mobility during COVID-19 recovery: role of media and culture as social amplifiers
Authors: Rana Arunima , Mukherjee Tuheena , Adak Souradip 
Published: July 2024

PurposeThe COVID-19 pandemic has resulted in countries reacting differently to an ongoing crisis. Latent to this reaction mechanism is the inherent cultural characteristics of each society resulting in differential responses to the epidemic spread. In this study, the moderated moderation role of culture, on information dissemination by media during epidemic recovery-phase has been investigated.Design/methodology/approachHofstede’s cultural factors are hypothesized to moderate the moderating effect of free-liberal media on the relationship of COVID-19 recovery rate and human mobility. Panel regression model, using mobility data and recovery rate across 95 countries for a period of 170 days has been preferred to test the hypotheses. The results are further substantiated using factor wise interaction plots and slope difference analysis.FindingsThe findings suggest that societies with high power distance and masculinity scores strengthen the impact of media on the relationship between COVID-19 recovery rate and mobility whereas, high individualistic and long-term orientation societies weaken the same effect. However, similar conclusions were not confirmed for uncertainty avoidance. Cross-cultural impact, as elucidated by this study, forms a crucial element in policy formulation on epidemic control by indigenous Governing bodies.Originality/valueWhile most of the studies emphasizing on cultural characteristics of a society in an epidemic situation covers the growth phase of infection, This research talks about the recovery-phase of the epidemic and the effect of culture.Peer reviewThe peer review history for this article is available at: https://publons.com/publon/10.1108/IJSE-04-2023-0314
Affordance of conciliation: increasing the social impact of hybrid organizations
Authors: Norato Hélida , Pozzebon Marlei 
Published: July 2024

PurposeHybrid organizations offer an innovative approach to promote social impact. However, hybrids face the challenge of reconciling the dual mission (social/financial). The purpose is to understand how hybrids and information and communication technologies (ICT) interact, unveiling opportunities ICT offers for hybrids regarding the dual mission.Design/methodology/approachWe used affordance theory and adopted a predominantly inductive approach inspired by the so-called “Gioia template.” The research design was based on semi-structured interviews with entrepreneurs, specialists, and people working in institutes, foundations, and accelerators, i.e. social actors operating in the hybrid organizational ecosystem in Brazil.FindingsOur findings suggest that the affordances of the relationship between organizational and ICT resources act as facilitators. A theoretical contribution is conceptualizing “affordance of conciliation,” indicating how ICT resources might facilitate achieving social/financial goals, thus minimizing efforts to reconcile mission duality. Furthermore, we list categories and aggregate dimensions and elucidate how results aligned with goals are generated through the process-based model. We show that ICT has a significant role in helping hybrids overcome challenges.Originality/valueOur results extend affordance theory with theoretical and practical implications. We highlight fundamental components that contribute to proposing the new concept of “affordance of conciliation.” We contribute to information systems literature by better understanding the social interactions between ICT and hybrids. Finally, we help hybrids understand the support of ICT resources to fulfill their dual mission.