bluuebunny/crossref_metadata_2025_split huggingface dataset:
CTCF binding landscape is established by the epigenetic status of the nucleosome, well-positioned relative to CTCF motif orientation
Authors: Tajmul Md , Bhatt Dharmendra Nath , Ruje Luminita , Price Emma , Ji Yon , Loukinov Dmitri , Teif Vladimir B. , Lobanenkov Victor V. , Pugacheva Elena M. 
Published: September 2024

AbstractCTCF binding sites serve as anchors for the 3D chromatin architecture in vertebrates. The functionality of these anchors is influenced by the residence time of CTCF on chromatin, which is determined by its binding affinity and its interactions with nucleosomes and other chromatin-associated factors. In this study, we demonstrate that CTCF occupancy is driven by CTCF motifs strategically positioned at the entry sites of a well-positioned nucleosome, such that, upon binding, the N-terminus of CTCF is oriented towards the nucleosome. We refer to this nucleosome as the CTCF priming nucleosome (CpN). CTCF recognizes its binding sites if they are not methylated. It can then displace the CpN, provided the nucleosome is not marked by CpG methylation or repressive histone modifications. Under these permissive conditions, the N-terminus of CTCF recruits SMARCA5 to reposition the CpN downstream, thereby creating nucleosome-free regions that enhance CTCF occupancy and cohesin stalling. In contrast, when CpNs carry repressive epigenetic marks, CTCF binding is transient, without nucleosome displacement or chromatin opening. In such cases, cohesin is not effectively retained at CTCF binding sites. We propose that the epigenetic status of CpNs governs cell-specific CTCF binding patterns, ensuring the maintenance of chromatin architecture throughout the cell cycle.Graphical Abstract
Low-affinity ligands of the epidermal growth factor receptor are long-range signal transmitters during collective cell migration of epithelial cells
Authors: Deguchi Eriko , Lin Shuhao , Hirayama Daiki , Matsuda Kimiya , Tanave Akira , Sumiyama Kenta , Tsukiji Shinya , Otani Tetsuhisa , Furuse Mikio , Sorkin Alexander , Matsuda Michiyuki , Terai Kenta 
Published: September 2024

SummaryEpidermal growth factor receptor ligands (EGFRLs) consist of seven proteins. In stark contrast to the amassed knowledge concerning the epidermal growth factor receptors themselves, the extracellular dynamics of individual EGFRLs remain elusive. Here, employing fluorescent probes and a tool for triggering ectodomain shedding of EGFRLs, we show that EREG, a low-affinity EGFRL, exhibits the most rapid and efficient activation of EGFR in confluent epithelial cells and mouse epidermis. In Madin-Darby canine kidney (MDCK) renal epithelial cells, EGFR- and ERK-activation waves propagate during collective cell migration in an ADAM17 sheddase- and EGFRL-dependent manner. Upon induction of EGFRL shedding, radial ERK activation waves were observed in the surrounding receiver cells. Notably, the low-affinity ligands EREG and AREG mediated faster and broader ERK waves than the high-affinity ligands. The integrity of tight/adherens junctions was essential for the propagation of ERK activation, implying that the tight intercellular spaces prefer the low-affinity EGFRL to the high-affinity ligands for efficient signal transmission. To validate this observationin vivo, we generated EREG-deficient mice expressing the ERK biosensor and found that ERK wave propagation and cell migration were impaired during skin wound repair. In conclusion, we have quantitatively demonstrated the distinctions among EGFRLs in shedding, diffusion, and target cell activation in physiological contexts. Our findings underscore the pivotal role of low-affinity EGFRLs in rapid intercellular signal transmission.
Molybdate application in the early stages of shrimp growth suppresses sulphide formation in a shrimp pond bottom model
Authors: Torun Funda , Matisli Feyzâ , Hostins Barbara , De Schryver Peter , Boon Nico , De Vrieze Jo 
Published: September 2024

AbstractOxygen depletion and sulphide formation, resulting from the accumulation of organic waste, are common challenges in shrimp ponds that could result in complete harvest failure. The stage at which these circumstances occur during the shrimp growth period remains elusive, yet, knowledge of the timing of oxygen depletion and sulphide formation is essential to enable remediating actions. Here, we used an experimental shrimp pond model at different stages in the shrimp growth period to determine when oxygen depletion and sulphide production occur. Microscale depth measurements of oxygen and H2S were determined using microelectrodes to visualize their profiles at different depths of the water-sediment interface and the sediment. We evaluated the potential of different molybdate concentrations at different stages to determine the optimal conditions to suppress H2S formation. Oxygen depletion and sulphide production took place in the middle of the shrimp growth cycle in the simulated model of waste accumulation. The addition of molybdate was only effective in the early stages of the onset of oxygen depletion and H2S formation, and residual molybdate was required to ensure a continuous suppression of sulphide production. However, oxygen depletion could not be prevented and reintroduction of oxygen did not occur when molybdate was added. In conclusion, molybdate appeared to be an effective strategy to suppress H2S formation at the onset of its production in a shrimp pond bottom model.
Nasal microbionts differentially colonize and elicit cytokines in human nasal epithelial organoids
Authors: Boyd Andrea I. , Kafer Leah A. , Escapa Isabel F. , Kambal Amal , Tariq Hira , Hilsenbeck Susan G. , Nguyen-Phuc Hoa , Rajan Anubama , Lensmire Joshua M. , Patras Kathryn A. , Piedra Pedro A. , Blutt Sarah E. , Lemon Katherine P. 
Published: September 2024

SUMMARYNasal colonization byStaphylococcus aureusorStreptococcus pneumoniaeis associated with an increased risk of infection by these pathobionts, whereas nasal colonization byDolosigranulumspecies is associated with health.Humannasal epithelialorganoids (HNOs) physiologically recapitulate human nasal respiratory epithelium with a robust mucociliary blanket. We reproducibly monocolonized HNOs with these three bacteria for up to 48 hours with varying kinetics across species. HNOs tolerated bacterial monocolonization with localization of bacteria to the mucus layer and minimal cytotoxicity compared to uncolonized HNOs. Human nasal epithelium exhibited both species-specific and general cytokine responses, without induction of type I interferons, consistent with colonization rather than infection. Only liveS. aureuscolonization induced IL-1 family cytokines, suggestive of inflammasome signaling.D. pigrumand liveS. aureusdecreased CXCL10, whereasS. pneumoniaeincreased CXCL11, chemokines involved in antimicrobial responses. HNOs are a compelling model system to reveal host-microbe dynamics at the human nasal mucosa.
An atlas of RNA-dependent proteins in cell division reveals the riboregulation of mitotic protein-protein interactions
Authors: Rajagopal Varshni , Seiler Jeanette , Nasa Isha , Cantarella Simona , Theiss Jana , Herget Franziska , Kaifer Bianca , Schneider Martin , Helm Dominic , König Julian , Zarnack Kathi , Diederichs Sven , Kettenbach Arminja N. , Caudron-Herger Maïwen 
Published: September 2024

ABSTRACTRibonucleoprotein complexes are dynamic assemblies of RNA with RNA-binding proteins (RBPs), which can modulate the fate of the RNA molecules from transcription to degradation. Vice versa, RNA can regulate the interactions and functions of the associated proteins. Dysregulation of RBPs is linked to diseases such as cancer and neurological disorders. RNA and RBPs are present in mitotic structures like the centrosomes and spindle microtubules, but their influence on mitotic spindle integrity remains unknown. Thus, we applied the R-DeeP strategy for the proteome-wide identification of RNA-dependent proteins and complexes to cells synchronized in mitosis versus interphase. The resulting atlas of RNA-dependent proteins in cell division can be accessed through the R-DeeP 3.0 database (R-DeeP3.dkfz.de). It revealed key mitotic factors as RNA-dependent such as AURKA, KIFC1 and TPX2 that were linked to RNA despite their lack of canonical RNA-binding domains. KIFC1 was identified as a new interaction partner and phosphorylation substrate of AURKA at S349and T359. In addition, KIFC1 interacted with both, AURKA and TPX2, in an RNA-dependent manner. Our data suggest a riboregulation of mitotic protein-protein interactions during spindle assembly, offering new perspectives on the control of cell division processes by RNA-protein complexes.HighlightsDifferential R-DeeP screens in mitosis and interphase are provided as a resource in a user-friendly database at R-DeeP3.dkfz.deAn atlas of RNA-dependent proteins in cell division identifies a substantial number of unconventional RNA-binding proteins among mitotic factorsInvestigation of protein-protein interactions reveals KIFC1 as a new AURKA and TPX2 interaction partner during spindle assemblyKIFC1, AURKA and TPX2 interact with each other in an RNA-dependent manner and directly bind to RNAAURKA phosphorylates KIFC1 at residues S349and T359
Signal sequences target enzymes and structural proteins to bacterial microcompartments and are critical for microcompartment formation
Authors: Johnson Elizabeth R. , Kennedy Nolan W. , Mills Carolyn. E. , Liang Shiqi , Chandrasekar Swetha , Nichols Taylor M. , Rybnicky Grant A. , Tullman-Ercek Danielle 
Published: September 2024

AbstractSpatial organization of pathway enzymes has emerged as a promising tool to address several challenges in metabolic engineering, such as flux imbalances and off-target product formation. Bacterial microcompartments (MCPs) are a spatial organization strategy used natively by many bacteria to encapsulate metabolic pathways that produce toxic, volatile intermediates. Several recent studies have focused on engineering MCPs to encapsulate heterologous pathways of interest, but how this engineering affects MCP assembly and function is poorly understood. In this study, we investigated the role of signal sequences, short domains that target proteins to the MCP core, in the assembly of 1,2-propanediol utilization (Pdu) MCPs. We characterized two novel Pdu signal sequences on the structural proteins PduM and PduB, which constitutes the first report of metabolosome signal sequences on structural proteins rather than enzymes. We then explored the role of enzymatic and structural Pdu signal sequences on MCP assembly by deleting their encoding sequences from the genome alone and in combination. Deleting enzymatic signal sequences decreased MCP formation, but this defect could be recovered in some cases by overexpressing genes encoding the knocked-out signal sequence fused to a heterologous protein. By contrast, deleting structural signal sequences caused similar defects to knocking out the genes encoding the full length PduM and PduB proteins. Our results contribute to a growing understanding of how MCPs form and function in bacteria and provide strategies to mitigate assembly disruption when encapsulating heterologous pathways in MCPs.
First crystal structure of the DUF2436 domain of virulence proteins from Porphyromonas gingivalis
Authors: Kim Bogeun , Hwang Jisub , Im Sehyeok , Do Hackwon , Shim Youn-Soo , Lee Jun Hyuck 
Published: September 2024

Porphyromonas gingivalis is a major pathogenic oral bacterium that is responsible for periodontal disease. It is linked to chronic periodontitis, gingivitis and aggressive periodontitis. P. gingivalis exerts its pathogenic effects through mechanisms such as immune evasion and tissue destruction, primarily by secreting various factors, including cysteine proteases such as gingipain K (Kgp), gingipain R (RgpA and RgpB) and PrtH (UniProtKB ID P46071). Virulence proteins comprise multiple domains, including the pro-peptide region, catalytic domain, K domain, R domain and DUF2436 domain. While there is a growing database of knowledge on virulence proteins and domains, there was no prior evidence or information regarding the structure and biological function of the well conserved DUF2436 domain. In this study, the DUF2436 domain of PrtH from P. gingivalis (PgDUF2436) was determined at 2.21 Å resolution, revealing a noncanonical β-jelly-roll sandwich topology with two antiparallel β-sheets and one short α-helix. Although the structure of PgDUF2436 was determined by the molecular-replacement method using an AlphaFold model structure as a template, there were significant differences in the positions of β1 between the AlphaFold model and the experimentally determined PgDUF2436 structure. The Basic Local Alignment Search Tool sequence-similarity search program showed no sequentially similar proteins in the Protein Data Bank. However, DaliLite search results using structure-based alignment revealed that the PgDUF2436 structure has structural similarity Z-scores of 5.9–5.4 with the C-terminal domain of AlgF, the D4 domain of cytolysin, IglE and the extracellular domain structure of PepT2. This study has elucidated the structure of the DUF2436 domain for the first time and a comparative analysis with similar structures has been performed.
Adapting human resources management to global health crises: lessons from the COVID-19 pandemic in Saudi Arabia
Authors: Asfahani Ahmed 
Published: September 2024

PurposeThis study investigates the impact of the COVID-19 pandemic on human resource management (HRM) within Saudi Arabia's distinct socio-legal landscape, which is shaped by Islamic cultural norms, stringent labor laws and a diversifying economy. This context necessitates innovative HR strategies during crises.Design/methodology/approachGrounded in the resource-based view, this qualitative study employs semi-structured interviews with 18 HR professionals across various sectors. This approach enables an in-depth exploration of HRM practice adaptations during the pandemic, using purposive sampling to ensure the collection of rich and relevant data.FindingsSignificant shifts towards remote work, the digitalization of HR operations and prioritizing employee health and safety were identified. The analysis revealed key themes, including HR policy changes, resilience strategies, encountered challenges, the importance of communication in employee engagement and strategic learnings. These findings highlight the criticality of adaptability, clear communication and digital transformation in effective crisis management.Originality/valueThis research contributes novel insights into the resilience of HRM practices in Saudi Arabia’s unique socio-legal environment during health crises. It fills a gap in our understanding of how specific regional contexts influence HRM strategies during emergencies, offering valuable contributions to both theory and practice. The study provides practical guidance for HR professionals and policymakers on crafting effective HRM strategies tailored to organizational needs in crisis conditions, thereby enhancing the field’s knowledge on navigating HRM challenges in future health crises.
Drivers of social media use among SMEs and its impact on brand awareness and customer engagement
Authors: Alkhasoneh Osama Mohammad , Jamaludin Hamiza , Bin Zahar Abdul Rahman i , Al-Sharafi Mohammed A. 
Published: September 2024

PurposeDespite the widespread use of social media globally, SMEs exhibit a below-average adoption rate. This raises critical questions about the reasons behind SMEs' limited engagement with this ubiquitous platform. The primary objective of this research is to explore the factors influencing the utilization of social media by small and medium-sized enterprises (SMEs) and assess its influence on brand awareness and customer engagement in the Jordanian context.Design/methodology/approachThis study utilizes a quantitative research approach to examine SMEs' adoption of social media. Data are collected from 290 SMEs in Jordan through paper-based and online surveys employing purposive sampling. The validity of the proposed model is confirmed using a partial least squares (PLS) approach, specifically employing SmartPLS 4 for analysis.FindingsThe results reveal that the examined model successfully captures the dynamics of social media usage among SMEs, shedding light on the significant drivers influencing their decision to use social media in their activities. The findings also underscore the pivotal role of social media usage in SMEs, particularly in enhancing brand awareness and fostering customer engagement within the Jordanian business landscape.Originality/valueThis study significantly contributes to the existing literature by highlighting the practical implications of social media activity, specifically in the context of SMEs. Using the UTAUT2 model to examine the drivers of social media use among SMEs and extend it to assess the broader impact of social media usage on brand awareness and customer engagement adds uniqueness to the study, providing a more nuanced view of social media usage in the SME sector.
Strategic justification of integrated resource planning tools in organizations
Authors: Mahmoodi Armin , Hashemi Leila 
Published: September 2024

PurposeThis paper presents a novel multi-objective optimization model aimed at enhancing the success rate of resource planning (RP) implementation. The model optimization is developed based on the organizational structure types, fit-gap contingency analysis reports, uncertainty optimization problems on implementation schedule time and relative time and budget constraints.Design/methodology/approachTwo pivotal strategies are employed: RP tools redesign through customization and organizational redesign. The synergistic integration of these strategies is essential, recognizing that RP tools implementation success hinges not only on technical aspects but also on aligning the system with organizational structure, culture and practices. In the analysis phase, a committee of experts identifies the initial gaps, which are evaluated through three conflicting objective functions: cost, time and penalty and running by the e-constraint method. In case of uncertainty nature time of RP tools implementation, the Activity-on-Arrow (A-O-A) method has been utilized.FindingsThe e-constraint method is utilized to derive the Pareto-optimal front, representing solutions effectively addressing identified gaps. A compromised solution is then proposed using the LP-metric method to strike a balance between conflicting objectives, ultimately improving RP tool implementation by reducing misfits.Originality/valueTo demonstrate and validate the model, a controlled case study is initially presented, illustrating its effectiveness. Subsequently, a real industry case study is provided, further validating the model’s applicability and practical relevance. This comprehensive approach offers valuable insights to optimize RP tool implementation outcomes, a critical concern for organizations undergoing technological transitions.
Generation of adaptive refinement tetrahedral meshes over domains of multi-chamber partition
Authors: Huang Haoyu , Shan Julin , Lo S.H. , Yu Fei , Cao Jie , Chang Jihai , Guan Z.Q. 
Published: September 2024

PurposeIn this study, we propose a tetrahedral mesh generation and adaptive refinement method for multi-chamber, multi-facet, multiscale and surface-solid mesh coupling with extremely thin layers, solving the two challenges of mesh generation and refinement in current electromagnetic simulation models.Design/methodology/approachUtilizing innovative topology transformation techniques, high-precision intersection judgment algorithms and highly reliable boundary recovery algorithms to reduce the number of Steiner locking points. The feasible space for the reposition of Steiner points is determined by using the linear programming. During mesh refinement, an edge-split method based on geometric center and boundary facets node size is devised. Solving the problem of difficult insertion of nodes in narrow geometric spaces, capable of filtering the longest and boundary edges of tetrahedrons, refining the mesh layer by layer through multiple iterations, and achieving collaborative optimization of surface and tetrahedral mesh. Simultaneously, utilizing a surface-facet preserving mesh topology optimization algorithm to improve the fit degree between the mesh and geometry.FindingsInitial mesh generation for electromagnetic models, compared to commercial software, the method proposed in this paper has a higher pass rate and better mesh quality. For the adaptive refinement performance of high-frequency computing, this method can generate an average of 50% fewer meshes compared to commercial software while meeting simulation accuracy.Originality/valueThis paper proposes a complete set of mesh generation and adaptive refinement theories and methods designed for the structural characteristics of electromagnetic simulation models, which meet the needs of real-world industrial applications.
Financial technology’s role in advancing social responsibility: a bibliometric review of research progress and future opportunities
Authors: AlQudah Mohammad Zakaria , Samara Husni , Qudah Hanan , Nazzal Reem , Yousef Bani Hani Laith , Radwan Razan Adil , Alrahamneh Samer 
Published: September 2024

Purpose
The primary aim is to identify and examine the critical success factors (CSFs) in FinTech that influence social responsibility (SR). This study aims to differentiate between internal factors (e.g. risk management, innovation, regulatory compliance, technology integration) and external factors (e.g. market conditions and regulatory changes) and offer insights into effective FinTech practices that enhance SR performance.

Design/methodology/approach
A comprehensive literature review using the Web of Science database analyzed 143 relevant articles. This review categorizes CSFs and assesses how FinTech practices impact SR.

Findings
The findings indicate that strategic FinTech practices, such as innovation in financial services, effective data management and stakeholder collaboration, are crucial for enhancing operational efficiency, fostering sustainability and improving responsiveness to social and environmental needs. This study also highlights current trends in FinTech and SR, emphasizing the integration of FinTech into broader SR strategies.

Practical implications
This study provides valuable insights for practitioners on how to leverage FinTech to enhance SR, including strategies for integrating innovative technologies and improving stakeholder engagement.

Social implications
By advancing the understanding of how FinTech can contribute to SR, this research highlights the potential for FinTech to drive positive social and environmental outcomes, fostering greater corporate responsibility and sustainability.

Originality/value
This research provides a novel bibliometric analysis of FinTech’s role in advancing SR, offering a comprehensive overview of the CSFs and emerging trends in this field.