bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protocol for semantic segmentation of spinal endoscopic instruments and anatomic structures : how far is robotic endoscopy surgery?
Authors: Fan Guoxin , Yue Guanghui , Hu Zhouyang , Xu Zhipeng , Zhang Jianjin , Wang Hong , Liao Xiang 
Published: April 2024

AbstractBackgroundAutomatic analysis of endoscopic images will played an important role in the future spine robotic surgery. The study is designed as a translational study to develop AI models of semantic segmentation for spinal endoscopic instruments and anatomic structures. The aim is to provide the visual understanding basis of endoscopic images for future intelligent robotic surgery.MethodsAn estimate of 500 cases of endoscopic video will be included in the study. More data may also be included from the internet for external validation. Video clip containing typical spinal endoscopic instruments and distinct anatomic structures will be extracted. Typical spinal endoscopic instruments will include forceps, bipolar electrocoagulation, drill and so on. Endoscopic anatomic structures will include ligament, upper lamina, lower lamina, nerve root, disc, adipofascia, etc. The ratio of training, validation and testing set of included samples is initially set as 8: 1: 1. State-of-art algorithm (namely UNet, Swin-UNet, DeepLab-V3, etc) and self-developed deep learning algorithm will be used to develop the semantic segmentation models. Dice coefficient (DC), Hausdorff distance (HD), and mean surface distance (MSD) will be used to assess the segmentation performance.DiscussionsThis protocol firstly proposed the research plans to develop deep learning models to achieve multi-task semantic segmentation of spinal endoscopy images. Automatically recognizing and simultaneously contouring the surgical instruments and anatomic structures will teach the robot understand the surgical procedures of human surgeons. The research results and the annotated data will be disclosed and published in the near future.MetadataThe authors did not receive any funding for this work yet.The authors have declared no competing interests.No data analyzed during the current study. All pertinent data from this study will be disclosed upon study completion.
Causal Relationship between Rheumatoid Arthritis and Atherosclerosis Risk: A Mendelian Randomized Study
Authors: Liu Qi-Pei , Du Hong-Cheng , Xie Ping-Jin , Zhang Lei-Xiao , Gao Hao-Ze , Luo Jie-Hua , Chai Sheng-Ting 
Published: April 2024

AbstractObjectivesPrevious observational studies have revealed an association between rheumatoid arthritis (RA) and atherosclerosis (AS). However, observational studies are prone to bias due to potential confounding factors and reverse causality. Therefore, this study investigates the causal relationship between RA and AS risk using Mendelian randomization (MR).MethodsGenetic data related to RA and AS were sourced from the Integrative Epidemiology Unit Open-Genome-Wide Association Studies database and the seventh edition of the FinnGen Biobank gene database, respectively. The initial analysis employed the inverse variance weighted (IVW) method for the MR analysis, with other methods utilized as supplementary methods. To ensure the robustness and reliability of the conclusions, various sensitivity analyses were conducted.ResultsThe MR results indicate a positive causal relationship between genetically determined RA and the risk of coronary atherosclerosis(OR = 1.026, 95% CI: 1.004, 1.049, p = 0.179), peripheral atherosclerosis(OR = 1.072, 95% CI: 1.035, 1.111, p < 0.001), and atherosclerosis excluding coronary atherosclerosis, cerebral atherosclerosis, and PAD (ASE) (OR = 1.046, 95% CI: 1.015, 1.079, p = 0.004), while no significant causal relationship with cerebral AS was observed. The MR-Egger regression did not reveal any significant horizontal pleiotropy.ConclusionThis study elucidates the causal relationship between RA and various AS risks, highlighting the importance of actively detecting and intervening in RA for AS risk.
A novel multi-omics mendelian randomization method for gene set enrichment and its application to psychiatric disorders
Authors: Gedik Huseyin , Peterson Roseann , Chatzinakos Christos , Dozmorov Mikhail G. , Vladimirov Vladimir , Riley Brien P. , Bacanu Silviu-Alin 
Published: April 2024

AbstractGenome-wide association studies (GWAS) of psychiatric disorders (PD) yield numerous loci with significant signals, but often do not implicate specific genes. Because GWAS risk loci are enriched in expression/protein/methylation quantitative loci (e/p/mQTL, hereafter xQTL), transcriptome/proteome/methylome-wide association studies (T/P/MWAS, hereafter XWAS) that integrate xQTL and GWAS information, can link GWAS signals to effects on specific genes. To further increase detection power, gene signals are aggregated within relevant gene sets (GS) by performing gene set enrichment (GSE) analyses.Often GSE methods test for enrichment of “signal” genes in curated GS while overlooking their linkage disequilibrium (LD) structure, allowing for the possibility of increased false positive rates. Moreover, no GSE tool uses xQTL information to perform mendelian randomization (MR) analysis. To make causal inference on association between PD and GS, we develop a novel MR GSE (MR-GSE) procedure. First, we generate a “synthetic” GWAS for each MSigDB GS by aggregating summary statistics for x-level (mRNA, protein or DNA methylation (DNAm) levels) from the largest xQTL studies available) of genes in a GS. Second, we use synthetic GS GWAS as exposure in a generalized summary-data-based-MR analysis of complex trait outcomes.We applied MR-GSE to GWAS of nine important PD. When applied to the underpowered opioid use disorder GWAS, none of the four analyses yielded any signals, which suggests a good control of false positive rates. For other PD, MR-GSE greatly increased the detection of GO terms signals (2,594) when compared to the commonly used (non-MR) GSE method (286). Some of the findings might be easier to adapt for treatment, e.g., our analyses suggest modest positive effects for supplementation with certain vitamins and/or omega-3 for schizophrenia, bipolar and major depression disorder patients. Similar to other MR methods, when applying MR-GSE researchers should be mindful of the confounding effects of horizontal pleiotropy on statistical inference.
The microtubule regulator EFA-6 forms spatially restricted cortical foci dependent on its intrinsically disordered region and interactions with tubulins
Authors: Sandhu Anjali , Lyu Xiaohui , Wan Xinghaoyun , Meng Xuefeng , Tang Ngang Heok , Gonzalez Gilberto , Syed Ishana N. , Chen Lizhen , Jin Yishi , Chisholm Andrew D. 
Published: April 2024

ABSTRACTMicrotubules (MTs) are dynamic components of the cytoskeleton and play essential roles in morphogenesis and maintenance of tissue and cell integrity. Despite recent advances in understanding MT ultrastructure, organization, and growth control, how cells regulate MT organization at the cell cortex remains poorly understood. The EFA-6/EFA6 proteins are recently identified membrane-associated proteins that inhibit cortical MT dynamics. Here, combining visualization of endogenously taggedC. elegansEFA-6 with genetic screening, we uncovered tubulin-dependent regulation of EFA-6 patterning. In the mature epidermal epithelium, EFA-6 forms punctate foci in specific regions of the apical cortex, dependent on its intrinsically disordered region (IDR). We further show the EFA-6 IDR is sufficient to form biomolecular condensatesin vitro. In screens for mutants with altered GFP::EFA-6 localization, we identified a novel gain-of-function (gf) mutation in an α-tubulintba-1that induces ectopic EFA-6 foci in multiple cell types.tba-1(gf)animals exhibit temperature-sensitive embryonic lethality, which is partially suppressed byefa-6(lf), indicating the interaction between tubulins and EFA-6 is important for normal development. TBA-1(gf) shows reduced incorporation into filamentous MTs but has otherwise mild effects on cellular MT organization. The ability of TBA-1(gf) to trigger ectopic EFA-6 foci formation requires β-tubulin TBB-2 and the chaperon EVL-20/Arl2. Thetba-1(gf)-induced EFA-6 foci display slower turnover, contain the MT-associated protein TAC-1/TACC, and require the EFA-6 MTED. Our results reveal a novel crosstalk between cellular tubulins and cortical MT regulatorsin vivo.HighlightsThe MT regulator EFA-6 forms spatially restricted punctate cortical fociThe EFA-6 N-terminal intrinsically disordered region (IDR) is essential for the formation of cortical fociin vivoand is sufficient for droplet formationin vitroTubulins regulate formation of EFA-6 foci via the EFA-6 MT elimination domainEFA-6 foci induced by altered tubulin heterodimer function display reduced turnover and recruit TAC-1/TACC
Refined mechanism of promoter Nucleosome-Depleted Regions resetting after replication
Authors: Zencir Sevil , Gill Jatinder Kaur , Stutz Françoise , Soudet Julien 
Published: April 2024

ABSTRACTReplication disrupts chromatin organization. Thus, the rapid resetting of nucleosome positioning is essential to maintain faithful gene expression. The initial step of this reconfiguration occurs at Nucleosome-Depleted Regions (NDRs). While studies have elucidated the role of Transcription Factors (TFs) and Chromatin Remodelers (CRs)in vitroor in maintaining NDRsin vivo, none has addressed theirin vivofunction shortly after replication. Through purification of nascent chromatin in yeast, we dissected the choreography of events governing the proper positioning of the −1/+1 nucleosomes flanking promoter NDRs. Our findings reveal that CRs are the primary contributors of −1/+1 repositioning post-replication, with RSC acting upstream of INO80. Surprisingly, while Reb1 and Abf1 TFs are not essential for NDR resetting, they are required for NDR maintenanceviathe promotion of H3 acetylations. Altogether, we propose a two-step model for NDR resetting inS. cerevisiae: first, CRs alone reset promoter NDRs after replication, while a combination of TFs and CRs is required for subsequent maintenance.TeaserRSC acts upstream of INO80 for NDR re-establishment after replication followed by a combined action of CRs and TFs for NDR maintenance.
Tick-borne flavivirus exoribonuclease-resistant RNAs contain a ‘double loop’ structure
Authors: Langeberg Conner J. , Szucs Matthew J. , Sherlock Madeline E. , Vicens Quentin , Kieft Jeffrey S. 
Published: April 2024

ABSTRACTFlaviviridaeviruses are human pathogens that generate subgenomic noncoding RNAs during infection using structured exoribonuclease resistant RNAs (xrRNAs) that block progression of host cell’s exoribonucleases. The structures of several xrRNAs from mosquito-borne and insect-specific flaviviruses have been solved, revealing a conserved fold in which a ring-like motif encircles the end of the xrRNA. However, the xrRNAs found in tick-borne and no known vector flaviviruses have distinct characteristics and their 3-D fold was unsolved. To address this, we identified subgenomic flaviviral RNA formation in the encephalitis-causing tick-borne Powassan Virus. We characterized their secondary structure using chemical probing and solved the structure of one of its xrRNAs using cryo-EM. This structure reveals a novel double loop ring element leading to a model in which the ring is remodeled upon encountering the exoribonuclease. Using bioinformatic analyses we showed that this structure is representative of a broad class of xrRNAs and defined key structural and sequence determinants of function. These discoveries reveal a conserved strategy of structure-based exoribonuclease resistance achieved through a unique topology across a viral family of key importance to global health.
Properties of theUreaplasma parvumSMC protein related to its interaction with DNA
Authors: Rumyantseva Natalya A. , Shutov Vladimir M. , Belenkaia Dina G. , Alekseev Aleksandr A. , Morozova Natalia E. , Vedyaykin Alexey D. 
Published: April 2024

AbstractSMC (Structural Maintenance of Chromosomes) ATPase proteins are integral components of complexes bearing the same name, crucial for the spatial organization of DNA across diverse life forms, spanning bacteria, archaea, and eukaryotes. It is proposed that in bacteria, SMC complexes facilitate DNA compaction through loop extrusion and aid in the segregation of daughter nucleoids. In this paper the properties of the SMC ATPase protein fromUreaplasma parvumwere investigated by using a spectrum of methods, including conventional biochemical methods as well as advanced single-molecule techniques. Our findings reveal distinctive properties of this protein compared to its extensively studied homologue fromBacillus subtilis. Notably, our results suggest thatU. parvumSMC ATPase facilitates DNA compaction even in the absence of ATP.
ARHGEF17/TEM4 regulates the cell cycle through control of G1 progression
Authors: Prifti Diogjena Katerina , Calvo Eva , Lauzier Annie , Garand Chantal , Devillers Romain , Roy Suparba , Santos Alexsandro Dos , Descombes Laurence , Bordeleau François , Elowe Sabine 
Published: April 2024

AbstractThe Ras homolog (Rho) small GTPases, via their role in regulating the actin cytoskeleton, coordinate diverse cellular functions including cell morphology, adhesion and motility, as well as cell cycle progression, survival and apoptosis. The upstream Rho regulators for many of these functions are unknown. ARHGEF17 (also known as TEM4) is a Rho family guanine nucleotide exchange factor (GEF) that been implicated in cell migration, cell-cell junction formation and the mitotic checkpoint. In this study we characterize the regulation of the cell cycle by TEM4. We demonstrate that TEM4 depleted cells exhibit multiple defects in mitotic entry and duration, spindle morphology, and spindle orientation. In addition, we find that TEM4 insufficiency leads to excessive cortical actin polymerization and cell rounding defects. Mechanistically, we demonstrate that TEM4 depleted cells delay in G1 as a consequence of elevated levels of the G1/S inhibitor p21waf1/cip1and that TEM4 depleted cells that progress through to mitosis, do so with decreased transcription ofCCNB1and thus attenuated levels of cyclin B. Importantly, cyclin B overexpression in TEM4-depleted cells largely rescues mitotic progression and chromosome segregation defects in anaphase. Our study thus illustrates the consequences of Rho signalling imbalance on cell cycle progression and identifies TEM4 as the first GEF governing Rho GTPase-mediated regulation of G1/S.
No “cookie cutter rules”: best practice for social care staff in supporting autistic adults with relationships and sexuality
Authors: Bates Claire , Matthews Rose 
Published: April 2024

Purpose
The purpose of this study is to explore the support needs surrounding intimate relationships and sexuality of autistic adults accessing funded social care in England.

Design/methodology/approach
Semi-structured interviews with 15 autistic adults who were accessing funded social care examined their support needs surrounding intimate relationships and sexuality, with subsequent data analysis using reflexive thematic analysis.

Findings
Four themes were generated: Help at hand, but not too close for comfort, No “cookie-cutter rules”: personalised, inclusive approaches, Playing it safe, not leaving it too late, and Autism-informed education and support.

Practical implications
The authors produced an online learning module for social care staff in England on best practice in supporting autistic adults without learning disabilities with relationships and sexuality.

Originality/value
To the best of the authors' knowledge, there has been no other UK-based research published to date on the social care support needs of autistic adults without learning disabilities surrounding relationships, gender and sexuality.
Human capital and financial performance of Islamic banks: a meta-analysis
Authors: Zafar Muhammad Bilal 
Published: April 2024

Purpose
This paper aims to meta-analyze the results of the prior studies related to the relationship of human capital and financial performance in Islamic banking.

Design/methodology/approach
To examine the relationship between human capital and financial of Islamic banks, 23 empirical studies having sample of 15,607 are considered for the meta-analysis. Moreover, different measures related to financial performance including return on assets (ROA), return of equity (ROE) and Tobin’s Q have been taken as moderating for further subgroup analysis.

Findings
The results of meta-analysis reveal a positive correlation between human capital and financial performance with an effect size of 0.268. The subgroup analyses showed significant positive associations of human capital with ROA and ROE, insignificant with Tobin’s Q.

Originality/value
This study suggests Islamic banking should prioritize human capital development, maintain consistency and adopt a long-term perspective. Future research should consider context-specific factors and harmonize human capital and financial performance measurements for consensus.
Research needs for enhancing pre-occupancy evaluation of buildings
Authors: Nazeer Fathima Sabrina , Kamardeen Imriyas , Hasan Abid 
Published: April 2024

PurposeMany buildings fail to meet user expectations, causing a performance gap. Pre-occupancy evaluation (PrOE) is believed to have the potential to close the gap. It enables designers to obtain end-user feedback in the design phase and improve the design for better performance. However, PrOE implementation faces challenges due to still maturing knowledgebase. This study aims to understand the state-of-the-art knowledge of PrOE, thereby identifying future research needs to advance the domain.Design/methodology/approachA systematic literature review following the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) framework was conducted. A thorough search in five databases and Google Scholar retrieved 90 articles, with 30 selected for systematic review after eliminating duplicates and irrelevant articles. Bibliometric analyses were performed using VOSviewer and Biblioshiny on the article metadata, and thematic analyses were conducted on their contents.FindingsPrOE is a vehicle for engaging building end-users in the design phase to address the credibility gap caused by the discrepancies between the expected and actual performance of buildings. PrOE has gained limited applications in healthcare, residential, office and educational building design for two broad purposes: design management and marketing. Using virtual reality technologies for PrOE has demonstrated significant benefits. Yet, the PrOE domain needs to mature in multiple perspectives to serve its intended purpose effectively.Originality/valueThis study identifies four knowledge gaps for future research to advance the PrOE domain: (1) developing a holistic PrOE framework, integrating comprehensive performance evaluation criteria, useable at different stages of the design phase and multi-criteria decision algorithms, (2) developing a mixed reality tool, embodying the holistic PrOE framework, (3) formulating a PrOE framework for adaptive reuse of buildings and (4) managing uncertainties in user requirements during the lifecycle in PrOE decisions.
Breaking with the seductive promises of internal social media: a critical appraisal
Authors: Høvring Christiane Marie , Ballantyne Anne Gammelgaard 
Published: April 2024

PurposeThe purpose of this article is to critically analyze the existing literature on internal social media (ISM) within the context of internal communication, aiming to provide a more nuanced understanding of the roles of ISM and its potential implications for communicative practices.Design/methodology/approachDrawing on a problematizing review methodology, the article conducts a critical analysis of a selected body of literature with the aim of problematizing assumptions that form the foundation of existing theories and constructs in the literature on ISM communication.FindingsThe article points out two interrelated critical issues that might constrain our understanding, scholarly conversation and theoretical development of the roles of ISM communication in organizations: (1) Philosophical inexplicitness; (2) Ontological inconsistency.Originality/valueAssuming a communication perspective, the article contributes suggestions for future research on ISM in the context of internal communication, calling for research to: (1) explicitly consider the epistemological implications of philosophical positions, including the view of technology; and (2) foreground meaning creation processes as the analytical point of interest.
Deliberative ideals and hegemonic practices – political CSR in extractive industries
Authors: Persson Sara 
Published: April 2024

Purpose
Political Corporate Social Responsibility (CSR), based on ideas about deliberative democracy, have been criticised for increasing corporate power and democratic deficits. Yet, deliberative ideals are flourishing in the corporate world in the form of dialogues with a broad set of stakeholders and engagement in wider societal issues. Extractive industry areas, with extensive corporate interventions in weak regulatory environments, are particularly vulnerable to asymmetrical power relations when businesses engage with society. This paper aims to illustrate in what way deliberative CSR practices in such contexts risk enhancing corporate power at the expense of community interests.

Design/methodology/approach
This paper is based on a retrospective qualitative study of a Canadian oil company, operating in an Albanian oilfield between 2009 and 2016. Through a study of three different deliberative CSR practices – market-based land acquisition, a grievance redress mechanism and dialogue groups – it highlights how these practices in various ways enforced corporate interests and prevented further community mobilisation.

Findings
By applying Laclau and Mouffe’s theory of hegemony, the analysis highlights how deliberative CSR activities isolated and silenced community demands, moved some community members into the corporate alliance and prevented alternative visions of the area to be articulated. In particular, the close connection between deliberative practices and monetary compensation flows is underlined in this dynamic.

Originality/value
The paper contributes to critical scholarship on political CSR by highlighting in what way deliberative practices, linked to monetary compensation schemes, enforce corporate hegemony by moving community members over to the corporate alliance.