bluuebunny/crossref_metadata_2025_split huggingface dataset:
ScGOclust: leveraging gene ontology to compare cell types across distant species using scRNA-seq data
Authors: Song Yuyao , Hu Yanhui , Dow Julian , Perrimon Norbert , Papatheodorou Irene 
Published: January 2024

AbstractBasic biological processes are shared among animal species, yet their cellular mechanisms are profoundly diverse. Comparing cell type expression profiles across species reveals the conservation and divergence of cellular functions. With the increase of phylogenetic distance between species of interest, a gene-based comparison becomes limited. The Gene Ontology (GO) knowledgebase is the most comprehensive resource of gene functions, providing a bridge for comparing cell types between remote species. Here, we present scGOclust, a computational tool to construct cellular functional profiles using GO terms and facilitates systematic, robust comparisons within and across species. We use scGOclust to analyse and compare the heart, gut and kidney between mouse and fly. We show that scGOclust recapitulates the function spectrum of different cell types, characterises functional similarities between homologous cell types, and reveals functional convergence between unrelated cell types. Furthermore, we identify subpopulations in the fly crop by cross-species comparison of GO profiles. Finally, scGOclust resolved the analogy between Malpighian tubule and kidney segments.
Differences in Alu vs L1-rich chromosome bands underpin architectural reorganization of the inactive-X chromosome and SAHFs
Authors: Hall Lisa L. , Creamer Kevin M. , Byron Meg , Lawrence Jeanne B. 
Published: January 2024

ABSTRACTThe linear DNA sequence of mammalian chromosomes is organized in large blocks of DNA with similar sequence properties, producing a pattern of dark and light staining bands on mitotic chromosomes. Cytogenetic banding is essentially invariant between people and cell-types and thus may be assumed unrelated to genome regulation. We investigate whether large blocks of Alu-rich R-bands and L1-rich G-bands provide a framework upon which functional genome architecture is built. We examine two models of large-scale chromatin condensation: X-chromosome inactivation and formation of senescence-associated heterochromatin foci (SAHFs). XIST RNA triggers gene silencing but also formation of the condensed Barr Body (BB), thought to reflect cumulative gene silencing. However, we find Alu-rich regions are depleted from the L1-rich BB, supporting it is a dense core but not the entire chromosome. Alu-rich bands are also gene-rich, affirming our earlier findings that genes localize at the outer periphery of the BB. SAHFs similarly form within each territory by coalescence of syntenic L1 regions depleted for highly Alu-rich DNA. Analysis of senescent cell Hi-C data also shows large contiguous blocks of G-band and R-band DNA remodel as a segmental unit. Entire dark-bands gain distal intrachromosomal interactions as L1-rich regions form the SAHF. Most striking is that sharp Alu peaks within R-bands resist these changes in condensation. We further show that Chr19, which is exceptionally Alu rich, fails to form a SAHF. Collective results show regulation of genome architecture corresponding to large blocks of DNA and demonstrate resistance of segments with high Alu to chromosome condensation.Graphical Abstract
PathIntegrate: Multivariate modelling approaches for pathway-based multi-omics data integration
Authors: Wieder Cecilia , Cooke Juliette , Frainay Clement , Poupin Nathalie , Bowler Russell , Jourdan Fabien , Kechris Katerina J. , Lai Rachel PJ , Ebbels Timothy 
Published: January 2024

AbstractAs terabytes of multi-omics data are being generated, there is an ever-increasing need for methods facilitating the integration and interpretation of such data. Current multi-omics integration methods typically output lists, clusters, or subnetworks of molecules related to an outcome. Even with expert domain knowledge, discerning the biological processes involved is a time-consuming activity. Here we propose PathIntegrate, a method for integrating multi-omics datasets based on pathways, designed to exploit knowledge of biological systems and thus provide interpretable models for such studies. PathIntegrate employs single-sample pathway analysis to transform multi-omics datasets from the molecular to the pathway-level, and applies a predictive single-view or multi-view model to integrate the data. Model outputs include multi-omics pathways ranked by their contribution to the outcome prediction, the contribution of each omics layer, and the importance of each molecule in a pathway. Using semi-synthetic data we demonstrate the benefit of grouping molecules into pathways to detect signals in low signal-to-noise scenarios, as well as the ability of PathIntegrate to precisely identify important pathways at low effect sizes. Finally, using COPD and COVID-19 data we showcase how PathIntegrate enables convenient integration and interpretation of complex high-dimensional multi-omics datasets. The PathIntegrate Python package is available athttps://github.com/cwieder/PathIntegrate.Author summaryOmics data, which provides a readout of the levels of molecules such as genes, proteins, and metabolites in a sample, is frequently generated to study biological processes and perturbations within an organism. Combining multiple omics data types can provide a more comprehensive understanding of the underlying biology, making it possible to piece together how different molecules interact. There exist many software packages designed to integrate multi-omics data, but interpreting the resulting outputs remains a challenge. Placing molecules into the context of biological pathways enables us to better understand their collective functions and understand how they may contribute to the condition under study. We have developed PathIntegrate, a pathway-based multi-omics integration tool which helps integrate and interpret multi-omics data in a single step using machine learning. By integrating data at the pathway rather than the molecular level, the relationships between molecules in pathways can be strengthened and more readily identified. PathIntegrate is demonstrated on Chronic Obstructive Pulmonary Disease and COVID-19 metabolomics, proteomics, and transcriptomics datasets, showcasing its ability to efficiently extract perturbed multi-omics pathways from large-scale datasets.
Peptidoglycan fragment release and NOD activation by commensalNeisseriaspecies from humans and other animals
Authors: Harris-Jones Tiffany N. , Chan Jia Mun , Hackett Kathleen T. , Weyand Nathan J. , Schaub Ryan E. , Dillard Joseph P. 
Published: January 2024

AbstractNeisseria gonorrhoeae, a human restricted pathogen, releases inflammatory peptidoglycan (PG) fragments that contribute to the pathophysiology of pelvic inflammatory disease. The genusNeisseriais also home to multiple species of human- or animal-associatedNeisseriathat form part of the normal microbiota. Here we characterized PG release from the human-associated nonpathogenic speciesN. lactamicaandN. mucosaand animal-associatedNeisseriafrom macaques and wild mice. AnN. mucosastrain and anN. lactamicastrain were found to release limited amounts of the pro-inflammatory monomeric PG fragments. However, a single amino acid difference in the PG fragment permease AmpG resulted in increased PG fragment release in a secondN. lactamicastrain examined.Neisseriaisolated from macaques also showed significant release of PG monomers. The mouse colonizerN. musculiexhibited PG fragment release similar to that seen inN. gonorrhoeaewith PG monomers being the predominant fragments released. All the human-associated species were able to stimulate NOD1 and NOD2 responses.N. musculiwas a poor inducer of mouse NOD1, butldcAmutation increased this response. The ability to genetically manipulateN. musculiand examine effects of different PG fragments or differing amounts of PG fragments during mouse colonization will lead to a better understanding of the roles of PG inNeisseriainfections. Overall, we found that only some nonpathogenicNeisseriahave diminished release of pro-inflammatory PG fragments, and there are differences even within a species as to types and amounts of PG fragments released.
A new role for IFRD1 in regulation of ER stress in bladder epithelial homeostasis
Authors: Fashemi Bisiayo E. , Rougeau Amala K. , Salazar Arnold M. , Bark Steven J. , Chappidi Rayvanth , Brown Jeffrey W. , Cho Charles J. , Mills Jason C. , Mysorekar Indira U. 
Published: January 2024

ABSTRACTA healthy bladder requires the homeostatic maintenance of and rapid regeneration of urothelium upon stress/injury/infection. Several factors have been identified to play important roles in urothelial development, injury and disease response, however, little is known about urothelial regulation at homeostasis. Here, we identify a new role for IFRD1, a stress-induced gene that has recently been demonstrated to play a critical role in adult tissue proliferation and regeneration, in maintenance of urothelial function/ homeostasis in a mouse model. We show that the mouse bladder expresses IFRD1 at homeostasis and its loss alters the global transcriptome of the bladder with significant accumulation of cellular organelles including multivesicular bodies with undigested cargo, lysosomes and mitochondria. We demonstrate that IFRD1 interacts with several mRNA-translation-regulating factors in human urothelial cells and that the urothelium ofIfrd1−/−mice reveal decreased global translation and enhanced endoplasmic reticulum (ER) stress response.Ifrd1−/−bladders have activation of the unfolded protein response (UPR) pathway, specifically the PERK arm, with a concomitant increase in oxidative stress and spontaneous exfoliation of urothelial cells. Further, we show that such increase in cell shedding is associated with a compensatory proliferation of the basal cells but impaired regeneration of superficial cells. Finally, we show that upon loss of IFRD1, mice display aberrant voiding behavior. Thus, we propose that IFRD1 is at the center of many crucial cellular pathways that work together to maintain urothelial homeostasis, highlighting its importance as a target for diagnosis and/or therapy in bladder conditions.
MRI-Targeted Prostate Biopsy Introduces Grade Inflation and Overtreatment
Authors: Batouche Abderrahim Oussama , Czeizler Eugen , Lehto Timo-Pekka , Erickson Andrew , Shadbahr Tolou , Laajala Teemu Daniel , Pohjonen Joona , Vickers Andrew Julian , Mirtti Tuomas , Rannikko Antti Sakari 
Published: January 2024

AbstractPurposeThe use of MRI-targeted biopsies has led to lower detection of Gleason Grade Group 1 (GG1) prostate cancer and increased detection of GG2 disease. Although this finding is generally attributed to improved sensitivity and specificity of MRI for aggressive cancers, it might also be explained by grade inflation. Our objective was to determine the likelihood of definitive treatment and risk of post-treatment recurrence for patients with GG2 cancer diagnosed using targeted biopsies relative to men with GG1 cancer diagnosed using systematic biopsies.MethodsWe performed a retrospective study on a large tertiary centre registry (HUS Acamedic Datalake) to retrieve data on prostate cancer diagnosis, treatment, and cancer recurrence. We included patients with either GG1 with systematic biopsies (3317 men) or GG2 with targeted biopsies (554 men) from 1993 to 2019. We assessed the risk of curative treatment and recurrence after treatment. Kaplan-Meier survival curves were computed to assess treatment- and recurrence-free survival. Cox proportional hazards regression analysis was performed to assess the risk of posttreatment recurrence.ResultsPatients with systematic biopsy detected GG1 cancer had a significantly longer median time-to-treatment (31 months) than those with targeted biopsy detected GG2 cancer (4 months, p<0.0001). The risk of recurrence after curative treatment was similar between groups with the upper bound of 95% CI, excluding an important difference (HR: 0.94, 95% CI [0.71-1.25], p=0.7).ConclusionGG2 cancers detected by MRI-targeted biopsy are treated more aggressively than GG1 cancers detected by systematic biopsy, despite having similar oncologic risk. To prevent further overtreatment related to the MRI pathway, treatment guidelines from the pre-MRI era need to be updated to consider changes in the diagnostic pathway.
Risk and performance of Islamic and conventional banks under COVID-19 pandemic: Evidence from MENA region
Authors: Ghenimi Ameni , Chaibi Hasna , Omri Mohamed Ali 
Published: January 2024

PurposeThe aim of this study is to conduct a comparative analysis between Islamic and conventional banks in terms of whether Islamic banks was more or less resilient/risky than conventional counterparts to the pandemic shock. It also examines the role of capital in improving the performance and stability within the two banking systems.Design/methodology/approachThis study uses 82 banks from MENA (Middle East and North Africa) region for periods across 2011–2020, and employs a dynamic panel data approach to examine the resilience within both banking systems during the Covid-19 pandemic.FindingsThe results show that the Covid-19 pandemic has a negative impact on conventional banks' stability. However, Islamic banks performed better and were less risky than conventional ones. Banks with high-quality capital are more effective at controlling their risks and improving their performance during the pandemic.Practical implicationsThe results offer important financial observations and policy implications to many stakeholders engaging with banks. Actually, the findings of this study facilitate to the stakeholders and bankers to have an alluded picture about determinants of risk and performance. The results can be used by bankers’ policy decision-makers to improve and enhance their consideration for risk management, taking into consideration the type of banking systems.Originality/valueCompared to the various studies on the stability of Islamic and conventional banks, researchers have not sufficiently addressed the effect of the Covid-19 pandemic on risk and performance. Moreover, none of these studies has examined if Islamic banks was more or less resilient/risky than conventional counterparts to the pandemic shock. This leads the authors to identify the similarities and differences between two types of banks in the MENA region in a pandemic shock context.
What facilitates the emergence of shared leadership? The predictive role of team personality composition
Authors: Ge Xiaolin , Liu Siyuan , Zhang Qing , Yu Haibo , Du Xiaoyu , Song Shanghao , Shi Yunsheng 
Published: January 2024

Purpose
This study aims to investigate the predictive role of team personality composition in facilitating shared leadership through team member exchange (TMX), while also to examine the moderating effect of organizational culture.

Design/methodology/approach
The authors conducted a two-stage online survey and selected the customer service teams, claims teams and financial teams of 26 Chinese insurance companies as the research samples. The authors finally obtained validated questionnaires from 107 teams with 457 members. The hypothesized relationships were tested using SPSS 25.0 and Mplus.

Findings
The results indicate that both team relationship-oriented and task-oriented personality composition have significant positive effects on shared leadership with team-member exchange serving as a full mediator for both paths. As a boundary condition, organizational culture (i.e. including internal integration values and external adaptation values) has a moderating effect on the influence of TMX on shared leadership.

Originality/value
The study investigates the predictive role of team personality composition on shared leadership, which complements the empirical studies of shared leadership antecedents in the literature. Drawing on social exchange perspective, the authors find out that TMX serves as a mediator between team personality composition and shared leadership. The authors also identify the moderating effect of organizational culture on the emergence of shared leadership. The research emphasizes the contextual boundary condition in this process.
Delineating wine tourism experiences in Ningxia, China: a supply–demand perspective
Authors: Zhan Xiaohai , Shi Xiaolin (Crystal) 
Published: January 2024

Purpose
The purpose of this paper is to examine the relationship between wine tourism experiences (i.e. winescape, winery service quality, winery brand differentiation and tourist motivation) and tourist behavioral intentions (satisfaction, loyalty and revisit intention) from both demand and supply perspectives in Ningxia, China, by using the SERVQUAL model and the self-determination theory.

Design/methodology/approach
The research comprises two studies with an exploratory sequential mixed-methods approach. Study 1 adopted semi-structured interviews with winery owners and managers to explore the factors related to wine tourism experiences that influence tourists’ tourism experience. The results from the Study 1 leads to Study 2, which used a survey to explore wine tourist experiences and their behavioral intentions

Findings
This study provided important information regarding the factors that influence wine tourists experience in Ningxia wine region from the perspectives of supply and demands sides. Frist, this study confirmed the various factors influence wine tourism experiences in Ningxia based on the results from Study 1 (supply perspectives). Second, by further investigation in the Study 1, this study integrates the SERVQUAL model and the self-determination theory as fundamental theoretical frameworks in Study 2 to analysis the tourist perspectives. Third, as results, the authors finally confirmed the theoretical frameworks of wine tourism in Ningxia based on dual supply-demand perspectives.

Originality/value
The integration of multiple research approaches enriches the research findings and provides a more robust understanding of the wine tourism experiences in Ningxia.
Improving the picking efficiency of a cold warehouse to avoid temperature abuse
Authors: Benaglia Marco Fabio , Chen Mei-Hui , Lu Shih-Hao , Tsai Kune-Muh , Hung Shih-Han 
Published: January 2024

PurposeThis research investigates how to optimize storage location assignment to decrease the order picking time and the waiting time of orders in the staging area of low-temperature logistics centers, with the goal of reducing food loss caused by temperature abuse.Design/methodology/approachThe authors applied ABC clustering to the products in a simulated database of historical orders modeled after the actual order pattern of a large cold logistics company; then, the authors mined the association rules and calculated the sales volume correlation indices of the ordered products. Finally, the authors generated three different simulated order databases to compare order picking time and waiting time of orders in the staging area under eight different storage location assignment strategies.FindingsAll the eight proposed storage location assignment strategies significantly improve the order picking time (by up to 8%) and the waiting time of orders in the staging area (by up to 22%) compared with random placement.Research limitations/implicationsThe results of this research are based on a case study and simulated data, which implies that, if the best performing strategies are applied to different environments, the extent of the improvements may vary. Additionally, the authors only considered specific settings in terms of order picker routing, zoning and batching: other settings may lead to different results.Practical implicationsA storage location assignment strategy that adopts dispersion and takes into consideration ABC clustering and shipping frequency provides the best performance in minimizing order picker's travel distance, order picking time, and waiting time of orders in the staging area. Other strategies may be a better fit if the company's objectives differ.Originality/valuePrevious research on optimal storage location assignment rarely considered item association rules based on sales volume correlation. This study combines such rules with several storage planning strategies, ABC clustering, and two warehouse layouts; then, it evaluates their performance compared to the random placement, to find which one minimizes the order picking time and the order waiting time in the staging area, with a 30-min time limit to preserve the integrity of the cold chain. Order picking under these conditions was rarely studied before, because they may be irrelevant when dealing with temperature-insensitive items but become critical in cold warehouses to prevent temperature abuse.
Experimental analysis of vibration and noise characteristics of helical gears with nano-lubricant additives
Authors: Xu Kai , Xiao Ying , Cheng Xudong 
Published: January 2024

Purpose
The purpose of this study is to investigate the effects of nanoadditive lubricants on the vibration and noise characteristics of helical gears compared with conventional lubricants. The experiment aims to analyze whether nanoadditive lubricants can effectively reduce gear vibration and noise under different speeds and loads. It also analyzes the sensitivity of the vibration reduction to load and speed changes. In addition, it compares the axial and radial vibration reduction effects. The goal is to explore the application of nanolubricants for vibration damping and noise reduction in gear transmissions. The results provide a basis for further research on nanolubricant effects under high-speed conditions.

Design/methodology/approach
Helical gears of 20CrMnTi were lubricated with conventional oil and nanoadditive oils. An open helical gearbox with spray lubrication was tested under different speeds (200–500 rpm) and loads (20–100 N·m). Gear noise was measured by a sound level meter. Axial and radial vibrations were detected using an M+P VibRunner system and fast Fourier transform analysis. Vibration spectrums under conventional and nanolubrication were compared. Gear tooth surfaces were observed after testing. The experiment aimed to analyze the noise and vibration reduction effects of nanoadditive lubricants on helical gears and the sensitivity to load and speed.

Findings
The key findings are that nanoadditive lubricants significantly reduce the axial and radial vibrations of helical gears under low-speed conditions compared with conventional lubricants, with a more pronounced effect on axial vibrations. The vibration reduction is more sensitive to rotational speed than load. At the same load and speed, nanolubrication reduces noise by 2%–5% versus conventional lubrication. Nanoparticles change the friction from sliding to rolling and compensate for meshing errors, leading to smoother vibrations. The nanolubricants alter the gear tooth surfaces and optimize the microtopography. The results provide a basis for exploring nanolubricant effects under high speeds.

Originality/value
The originality and value of this work is the experimental analysis of the effects of nanoadditive lubricants on the vibration and noise characteristics of hard tooth surface helical gears, which has rarely been studied before. The comparative results under different speeds and loads provide new insights into the vibration damping capabilities of nanolubricants in gear transmissions. The findings reveal the higher sensitivity to rotational speed versus load and the differences in axial and radial vibration reduction. The exploration of nanolubricant effects on gear tribological performance and surface interactions provides a valuable reference for further research, especially under higher speed conditions closer to real applications.

Peer review
The peer review history for this article is available at: https://publons.com/publon/10.1108/ILT-07-2023-0220/