bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metaproteomics reveals age-specific alterations of gut microbiome in hamsters with SARS-CoV-2 infection
Authors: Creskey Marybeth , Angulo Fabiola Silva , Wu Qing , Tamming Levi , Fekete Emily E F , Cheng Kai , Ning Zhibin , Wang Angela , Rodrigues Patrícia Brito , Rodovalho Vinícius de Rezende , Vinolo Marco Aurélio Ramirez , Figeys Daniel , Li Xuguang , Trottein Francois , Zhang Xu 
Published: November 2024

AbstractThe gut microbiome’s pivotal role in health and disease is well-established. SARS-CoV-2 infection often causes gastrointestinal symptoms and is associated with changes of the microbiome in both human and animal studies. While hamsters serve as important animal models for coronavirus research, there exists a notable void in the functional characterization of their microbiomes with metaproteomics. In this study, we present a workflow for analyzing the hamster gut microbiome, including a metagenomics-derived hamster gut microbial protein database and a data-independent acquisition metaproteomics method. Using this workflow, we identified 32419 protein groups from the fecal microbiomes of young and old hamsters infected with SARS-CoV-2. We showed age-specific changes in the expressions of microbiome functions and host proteins associated with microbiomes, providing further functional insight into the dysbiosis and aberrant cross-talks between the microbiome and host in SARS-CoV-2 infection. Altogether this study established and demonstrated the capability of metaproteomics for the study of hamster microbiomes.
Improving Differentiation of Crohn’s Disease and Ulcerative Colitis Proteomes through Protein-Wide Association Study Feature Selection in Machine Learning
Authors: Gorelik Mark G. , Gorelik Aaron J. , Fishbein Skye R.S. , Fehlmann Tara , Deepak Parakkal , Bogdan Ryan , Dantas Gautam , Jain Umang ,   SPARC IBD Investigators
Published: November 2024

AbstractBackground and AimsDiagnostic differentiation between Crohn’s disease (CD) and ulcerative colitis (UC) is crucial for timely and suitable therapeutic measures. The current gold standard for differentiating between CD and UC involves endoscopy and histology, which are invasive and costly. We aimed to identify blood plasma proteomic signatures using a Protein-Wide Association Study (PWAS) approach to differentiate CD from UC and evaluate the efficacy of these signatures as features in machine learning (ML) classifiers.MethodsAmong participants (n=1,106; nCD=636; nUC=470) of the Study of a Prospective Adult Research Cohort with IBD (SPARC), plasma protein (n=2,920) levels were estimated using Olink proteomics. A PWAS with Bonferroni correction for multiple testing was used to identify proteins associated with disease states after controlling for age, sex, and disease severity. ML classifiers examined the diagnostic utility of these models. Feature importance was determined via SHapley Additive exPlanations (SHAP) analysis.ResultsThirteen proteins which were significantly differentially abundant in CD vs UC (all |β|s > 0.22, all adjusted p values < 8.42E-06). Random forest models of proteins differentiated between CD and UC with models trained only on PWAS identified proteins (Average ROC-AUC 0.73) outperforming models trained of the full proteome (Average ROC-AUC 0.62). SHAP analysis revealed that Granzyme B, insulin-like peptide 5 (INSL5), and interleukin-12 subunit beta (IL-12B) were the most important features.ConclusionsOur findings demonstrate that PWAS-based feature selection approaches are a powerful method to identify features in complex, noisy datasets. Importantly, we have identified novel peptide based biomarkers such as INSL5, that can be potentially used to complement existing strategies to differentiate between CD and UC.
Development and Validation of an Artificial Intelligence-based Pipeline for Predicting Oral Epithelial Dysplasia Malignant Transformation
Authors: Shephard Adam J , Mahmood Hanya , Raza Shan E Ahmed , Damaceno Araujo Anna Luiza , Santos-Silva Alan Roger , Lopes Marcio Ajudarte , Vargas Pablo Agustin , McCombe Kris D. , Craig Stephanie G. , James Jacqueline , Brooks Jill , Nankivell Paul , Mehanna Hisham , Khurram Syed Ali , Rajpoot Nasir M 
Published: November 2024

AbstractOral epithelial dysplasia (OED) is a potentially malignant histopathological diagnosis given to lesions of the oral cavity that are at risk of progression to malignancy. Manual grading of OED is subject to substantial variability and does not reliably predict prognosis, potentially resulting in sub-optimal treatment decisions. We developed a Transformer-based artificial intelligence (AI) pipeline for the prediction of malignant transformation from whole-slide images (WSIs) of Haematoxylin and Eosin (H&E) stained OED tissue slides, named ODYN (Oral Dysplasia Network). ODYN can simultaneously classify OED and assign a predictive score (ODYN-score) to quantify the risk of malignant transformation. The model was trained on a large cohort using three different scanners (Sheffield, 358 OED WSIs, 105 control WSIs) and externally validated on cases from three independent centres (Birmingham and Belfast, UK, and Piracicaba, Brazil; 108 OED WSIs). Model testing yielded an F1-score of 0.96 for classification of dysplastic vs non-dysplastic slides, and an AUROC of 0.73 for malignancy prediction, gaining comparable results to clinical grading systems. With further large-scale prospective validation, ODYN promises to offer an objective and reliable solution for assessing OED cases, ultimately improving early detection and treatment of oral cancer.
Investigating the potential role of intimin/invasin in Aeromonas hydrophila virulence in Labeo rohita: a host-microbe interaction study
Authors: Bhattacharyya Agradip , Banerjee Goutam , Chattopadhyay Pritam 
Published: November 2024

AbstractAeromonas hydrophilais a primary bacterial pathogen affecting freshwater fish, includingLabeo rohita(rohu), leading to significant losses in aquaculture. This study investigates the probable role of intimin/invasin, known virulence factors in several bacterial pathogens, in the pathogenesis ofA. hydrophilainL. rohita. Using an in-silico approach, we explore the genetic and structural features of these proteins to predict their potential function in facilitating infection. We analysed the distribution of invasin and intimin across 53A. hydrophilagenomes and examined their physicochemical properties, including molecular weight and stability. Additionally, we evaluated the secondary structures to understand their functional roles in host-pathogen interactions. Using homology-based modelling, we generated 3D (tertiary) structures of invasin and intimin and selected the most suitable models for in silico docking experiments with all eight Rohu (Labeo rohita) β-integrins-a crucial step in understanding their interactions with the fish (Rohu) host cells. Due to the unavailability of the crystal structure of Rohu β-integrins, we performed homology-based modelling prior to the docking experiments. Our findings reveal that invasin and intimin are present in only 6 of the 53A. hydrophilastrains examined, primarily in highly virulent strains previously reported. Notably, invasin lacks disulfide bonds and beta turns. 3D modelling indicates a significant binding affinity of invasin with all human β-integrins, suggesting a critical role in host-pathogen interactions.
Optimisation of single-nuclei isolation and RNA sequencing of parasitic nematodes
Authors: Buddenborg Sarah K , Morrison Alison A , Fletcher Anna C , Kieninger Manuela R , Ng Bee Ling , Maitland Kirsty , Hart Emily , Bartley Dave J , Duque-Correa Maria A , Doyle Stephen R 
Published: November 2024

AbstractSingle-cell/nuclei transcriptomics has revolutionised our understanding of cell, tissue, and organismal biology during health and disease of humans and model organisms. However, for non-model species, reassessment and refinement of conventional methods to address novel technical and biological challenges are needed. Here, we evaluate three established nuclei isolation protocols and, building on experiences, optimised single nuclei isolation for parasitic nematodes (SNIP). We test the versatility of SNIP across diverse species and life stages, validating it with snRNA-seq to reveal sex, stage, and tissue-specific gene expression. Optimised protocols will advance the understanding of parasitic nematodes, from fundamental biology to infection and disease.
Discovery of lydiamycin A biosynthetic gene cluster in the plant pathogenRhodococcus fasciansguides structural revision and identification of molecular target
Authors: Ford Jonathan J. , Santos-Aberturas Javier , Hems Edward S. , Sallmen Joseph W. , Bögeholz Lena A. K. , Polturak Guy , Osbourn Anne , Wright Joseph A. , Rodnina Marina V. , Vereecke Danny , Francis Isolde M. , Truman Andrew W. 
Published: November 2024

ABSTRACTThe natural products actinonin and matlystatin feature anN-hydroxy-2-pentyl-succinamyl (HPS) chemophore that facilitates metal chelation and confers their metalloproteinase inhibitory activity. Actinonin is the most potent natural inhibitor of peptide deformylase (PDF) and exerts antimicrobial and herbicidal bioactivity by disrupting protein synthesis. Here, we used a genomics-led approach to identify candidate biosynthetic gene clusters (BGCs) hypothesised to produce novel HPS-containing natural products. We show that one of these BGCs is on the pathogenicity megaplasmid of the plant pathogenRhodococcus fasciansand produces lydiamycin A, a macrocyclic pentapeptide. The presence of genes predicted to make a HPS-like chemophore informed the structural recharacterisation of lydiamycin via NMR and crystallography to show it features a rare 2-pentyl-succinyl chemophore. We demonstrate that lydiamycin A inhibits bacterial PDF in vitro and show that a cluster-situated PDF gene confers resistance to lydiamycin A, representing a novel self-immunity mechanism associated with the production of a PDF inhibitor.In plantacompetition assays showed that lydiamycin enhances the fitness ofR. fasciansduring plant colonisation. This study highlights how a BGC can inform the structure, biochemical target and ecological function of a natural product.
Magnetic structure and crystal-field states of antiferromagnetic
CeNiGe3
: Neutron scattering and
μSR
investigations
Authors: Kataria A. , Kumar R. , Adroja D. T. , Ritter C. , Anand V. K. , Hillier A. D. , Huddart B. M. , Lancaster T. , Rols S. , Koza M. M. , Langridge Sean , Sundaresan A. 
Published: November 2024

We present the results of microscopic investigations of antiferromagnetic CeNiGe3 using neutron powder diffraction (NPD), inelastic neutron scattering (INS), and muon spin relaxation (μSR) measurements. CeNiGe3 crystallizes in a centrosymmetric orthorhombic crystal structure (space group Cmmm) and undergoes antiferromagnetic (AFM) ordering. The occurrence of long-range AFM ordering at TN≃5.2K is confirmed by magnetic susceptibility, heat capacity, neutron diffraction, and μSR measurements. The NPD data characterize the AFM state with an incommensurate helical magnetic structure having a propagation vector = (0, 0.41, 1/2). In addition, INS measurements at 10 K identified two crystal electric field (CEF) excitations at 9.17 meV and 18.42 meV. We analyzed the INS data using a CEF model for an orthorhombic environment of Ce3+ (J=5/2) and determined the CEF parameters and ground state wave functions of CeNiGe3. Moreover, zero-field μSR data for CeNiGe3 at T<TN show long-range AFM ordering with three distinct oscillation frequencies corresponding to three different internal fields at the muon sites. The internal fields at the muon-stopping sites have been further investigated using density functional theory calculations.

Published by the American Physical Society
2024
The nonlinear relationship between CEO stock options and strategic risk taking: the moderating role of CEO characteristics
Authors: Zaiane Sedki 
Published: November 2024

Purpose
The purpose of this study is to examine the nonlinear relationship between executive stock options and strategic risk taking and to investigate the moderating effect of CEO characteristics (CEO age and tenure). This study aims to analyze whether the impact of executive stock options on strategic risk-taking is moderated by CEO compensation and characteristics.

Design/methodology/approach
This study is based on a sample of 90 French firms for the period extending from 2008 to 2021. To deal with the nonlinear relationship, the author adopts a dynamic threshold model.

Findings
The results reveal that the impact of CEO stock options on firm strategic risk-taking is nonlinear and moderated by CEO age and tenure. Using research and development (R&D) as a measure of risk taking, the author show a positive relationship between executive stock option and R&D below the threshold value of stock option, CEO age and tenure and it becomes negative above.

Research limitations/implications
Stock options, CEO age and tenure shows that CEO characteristics and compensation structure are major determinants in defining the direction of the nonlinear relationship between CEO stock options and firm strategic risk-taking.

Originality/value
The author extends through this paper the existing research on executive stock option, strategic risk-taking and CEO characteristics using a nonlinear dynamic estimator that caters to the problems of endogeneity. Insights from the findings provide boards and regulators with a better understanding of structuring CEO compensation.
Performance analysis of various wall treatments of RANS models for prediction of near-wall turbulence transport characteristics of plane wall jet
Authors: Patari Animesh , Pramanik Shantanu , Mondal Tanmoy 
Published: November 2024

PurposeThe present study scrutinizes the relative performance of various near-wall treatments coupled with two-equation RANS models to explore the turbulence transport mechanism in terms of the kinetic energy budget in a plane wall jet and the significance of the near-wall molecular and turbulent shear, to select the best combination among the models which reveals wall jet characteristics most efficiently.Design/methodology/approachA two-dimensional steady incompressible plane wall jet in a quiescent surrounding is simulated using ANSYS-Fluent solver. Three near-wall treatments, namely the Standard Wall Function (SWF), Enhanced Wall Treatment (EWT) and Menter-Lechner (ML) treatment coupled with Realisable, RNG and Standard k-e models and also the Standard and Shear-Stress Transport (SST) k-ω models are employed for this investigation.FindingsThe ML treatment slightly overestimated the budget components on an outer scale, whereas the k-ω models strikingly underestimated them. In the buffer layer at the inner scale, the SWF highly over-predicts turbulent production and dissipation and k-ω models over-predict dissipation. Appreciably accurate inner and outer scale k-budgets are observed with the EWT schemes. With a sufficiently resolved near-wall mesh, the Realisable model with EWT exhibits the mean flow, turbulence characteristics and turbulence energy transport even better than the SST k-ω model.Originality/valueThree distinct near-wall strategies are chosen for comparative performance analysis, focusing not only on the mean flow and turbulence characteristics but the turbulence energy budget as well, for finding the best combination, having potential as a viable and low-cost alternative to LES and DNS for wall jet simulation in industrial application.
Exploring online information sharing patterns among beekeepers: a thematic analysis of user-generated content
Authors: Mansourian Yazdan 
Published: November 2024

Purpose
This paper aims to report findings from a qualitative study about the information sharing patterns of beekeepers on online platforms.

Design/methodology/approach
The required data were collected from the publicly available user-generated content on popular beekeeping YouTube videos. Videos with high traffic were defined by the number of views, subscribers and comments. The sample includes 2,000 post-video comments, with the highest contribution in the discussions. The data were categorised through a deductive thematic analysis into ten categories, including information, advice, impression, opinion, responses, expression of personal feelings, general conversations, site processes, video content description and non-response comments.

Findings
The findings show that beekeepers are keen to share their experiences through public online platforms like YouTube and interact with fellow beekeepers and beekeeping enthusiasts. They share a range of beekeeping tips and techniques, varying from hive management and honey production to seasonal hive care and bee feeding. Sharing these practical hints helps them enhance their skills and learn from each other through tutorial videos or community engagement. Their willingness to share information generates a sense of support through online discussions and the formation of communities of practice.

Practical implications
The findings have practical implications for the stakeholders, including amateur beekeepers, beekeeping content creators and information professionals. Understanding the diverse engagement patterns can help YouTubers improve the quality of their videos and engage their audience. Also, information professionals can play various roles, such as curating special collections or local guides for beekeepers, facilitating workshops and promoting citizen science initiatives to help hobbyist beekeepers contribute relevant data to scientific research.

Originality/value
There is little research about the information behaviour patterns among beekeepers, and this paper contributes to this area by providing some empirical findings and attempts to fill the gap to some extent.
Intention to donate in green waqf among Muslim community: Indonesian case
Authors: Huda Nurul , Trianto Budi , Masrizal Masrizal , Maskuroh Nihayatul 
Published: November 2024

Purpose
The Indonesian Waqf Board and United Nation Development Program are developing green waqf in Indonesia. Development of green waqf in Indonesia as a response to save the earth from environmental damage and other social impacts. This paper aims to measure public perceptions about willingness to participate in making donations to the green waqf program in Indonesia.

Design/methodology/approach
Modifying the Theory of Reasoned Action framework, questionnaire data were collected from 311 Muslims in Indonesia. Data were analyzed using the partial least squares structural equation modeling method.

Findings
The findings show that attitude, subjective norm, product knowledge and trust influence the Muslims in Indonesia to donate to green waqf. In contrast, Islamic religiosity harms the intention to donate in green waqf but is insignificant.

Research limitations/implications
This research was conducted using a quantitative approach with a limited sample of several communities, so the results cannot be generalized. Further investigation needs to be carried out by involving a more diverse sample to get better results. However, the results of this study can be used as an illustration of how Muslims behave in donating green waqf.

Practical implications
These results imply that to develop green waqf in Indonesia, especially in attracting waqf candidates willing to make donations, waqf institutions must carry out engineering to shape the attitude of prospective donors through various activities such as socialization and education of the green waqf program. Waqf institutions must also build public trust by involving public figures to campaign for the green waqf program. This will likely increase prospective donors’ active participation in donating their money to develop green waqf in Indonesia.

Originality/value
Waqf is a severe concern for the Indonesian Government, including waqf for the environment. To the bets of the authors’ knowledge, this paper is the first attempt to look at the behavior of the green waqf model in Indonesia. Thus, the acceleration of waqf development can be realized and is expected to impact the community significantly.
Climate change, conflict and gender nexus: evidence from Bor County, South Sudan
Authors: Mohammed Umar , Laki Kiden 
Published: November 2024

PurposeThis study aims to explore the nexus between gender, conflict and climate change in Bor County, highlighting the negative feedback cycle between climate change and conflict and assuming gender as a framework through which individuals see and interpret climate change and instances of conflict.Design/methodology/approachThe research employs a qualitative method utilizing carefully designed semi-structured interviews and focus group discussions conducted in Bor, Jonglei State. Data were collected from a diverse sample of 35 interviews and one focus group discussion (FGD) involving various stakeholders. The research study encompassed a total of 70 participants. The study employs reflexive thematic methods in the data analysis.FindingsThis research reveals Bor County’s enduring climate challenges: extreme temperatures, erratic rainfall and shifting seasonal patterns have led to droughts and severe floods. These disruptions affect livelihoods, trigger displacement and escalate community conflicts. Similarly, conflict exacerbates environmental degradation and undermines economic activities. In effect, climate change and conflict are self-perpetuating cycles. However, while climate change may contribute to conflicts in Bor, Jonglei state underlying causes predate current climate changes and would likely persist. The study further shows that gendered perceptions of climate change and conflict reveal distinct concerns among women and men, with women more attuned to resource implications while men prioritize immediate security. Moreover, women are disproportionately affected by both climate change and conflict, exacerbating their vulnerability due to structural inequalities.Practical implicationsThis study provides policymakers and stakeholders valuable insights into climate change-conflict and Gender Nexus in Bor. Incorporating a gender-sensitive and inclusive perspective into developing justice procedures involving national consultations, bills and enforcement procedures is imperative.Originality/valueThis is the first work to examine climate, conflict and gender nexus in Bor County, South Sudan.