bluuebunny/crossref_metadata_2025 huggingface dataset:
Enhancing Inpatient Sleep Environments: A Design Thinking Case Study
Authors: Kennedy Oehlert Julie , Sheri Greeshma , Puerto Harold , Hill Kevin
Published: November 2024

Research shows how vital sleep is to total health, with poor sleep having a strong correlation with morbidity and mortality, yet fewer than half of top hospitals have sleep-friendly practices. This article describes a project motivated by the lived experiences of a nurse manager and a hospitalist who partnered to improve the sleep environments on two inpatient units. They used design thinking, empathizing with the patients’ experiences with the sleep environment, to design interventions to promote quality sleep. Results showed improvements in patient experience on the Hospital Consumer Assessment of Healthcare Providers & Systems question, “During your hospital stay how often was the area around your room quiet at night?” Patient measures on how well the hospital created conditions for sleep on the unit also showed improvements, as well as the patients’ perception of how well they slept. Care teams can use design thinking to replicate this project and listen to their patients to build and deploy interventions on their units to improve sleep environments.
Beyond Racial, Religious, and Political Binaries: Toward Antisemitism Literacy
Authors: Grayson Mara Lee
Published: November 2024

Literacy studies scholarship and pedagogy have not attended comprehensively to Jewish cultural literacies or the discursive operations of anti-Jewish hate. As a result, antisemitic rhetoric may be employed, strategically or accidentally, by people who do not see themselves as antisemitic—and who, regardless of their critical and cultural literacies, cannot accurately identify that rhetoric as such. In this article, I draw upon existing research, both mine and other scholars’, as I explore how histories of Jewishness and antisemitism disrupt binary understandings of race, power, and partisanship; explicate how these disruptions complicate efforts to recognize and understand antisemitic rhetoric; and identify strategies for moving forward with greater awareness of antisemitism as a rhetorical system and deeply situated cultural ideology. This article gestures toward the development of teachers’ and students’ antisemitism literacy.
Genetic Evidence of Obesity-Induced Chronic Wounds Mediated by Inflammatory Biomarkers
Authors: Xu Hai , Ding Sheyuan , Tong Yu , Zhang Qiong
Published: November 2024

Background: Obese patients are increasingly recognized as being at higher risk for skin diseases, particularly chronic wounds. While the exact mechanisms remain unclear, obesity is suspected to influence the development of chronic injuries via inflammatory biomarkers. Single nucleotide polymorphisms (SNPs) may further influence gene expression, protein function, and levels of inflammatory biomarkers through various mechanisms, thereby modulating inflammatory responses that contribute to wound pathogenesis. Methods: A two-sample two-step Mendelian Randomization (MR) was employed to explore the causal relationship between obesity and chronic wounds, focusing on the mediating role of inflammatory biomarkers. SNPs were used as instrumental variables (IVs) to infer causality. Obesity-related genetic data were sourced from the UK Biobank and GIANT consortium. Genome-wide association studies provided data on 92 inflammatory biomarkers, involving 14,824 and 575,531 individuals. Pressure injuries, lower limb venous ulcers, and diabetic foot ulcer data were obtained from FinnGen R10 and the Pan-UK Biobank. Results: Obesity significantly increased the risk of pressure injuries, lower limb venous ulcers, and diabetic foot ulcers. CCL19, hGDNF, IL-12B, and TNFRSF9 were identified as mediators in obesity-induced lower limb venous ulcers. Conclusion: This study provides genetic evidence that obesity leads to lower limb venous ulcers via inflammatory biomarkers, suggesting potential therapeutic targets for intervention.
Challenges, Health Risks and Recommendations on Meat Handling Practices in Africa: A Comprehensive Review
Authors: Adesola Ridwan Olamilekan , Hossain Delower , Ogundijo Oluwaseun Adeolu , Idris Ibrahim , Hamzat Abdulafees , Gulumbe Bashar Haruna , Bakre Adetolase Azizat , Banwo Olamilekan Gabriel , Lucero-Prisno Don Eliseo
Published: November 2024

Meat handling is a crucial aspect of public health as it forms complex interactions among humans, animals, and the environment. African meat handlers continue to face various challenges in slaughterhouses that significantly impact their lives and the general public during meat processing. This paper reviews the challenges meat handlers encounter and the associated risks of improper meat handling in various African slaughterhouses. A comprehensive literature search was performed on Science Direct, Web of Science, PubMed, Scopus and Google Scholar. Articles published to investigate the challenges and health risks of meat handling practices in Africa from 1961 to 2022 were included in this review. African meat handlers face socio-economic difficulties, including inadequate returns, unpredictable working environment, market, security, and limited healthcare access. Many meat handlers work informally in unregistered facilities and are not trained by experts on proper meat handling. This results in improper meat handling, raising the possibility of meat contamination by foodborne pathogens like Salmonella sp. and E. coli on slaughter and contact surfaces, hence posing a threat to meat safety and public health. We recommended that governmental, institutional and community-level actions should be used to address the health challenges associated with improper meat handling in Africa. Government and institutional bodies play an important role in supporting and upholding the laws that guide proper meat handling and processing. Meat handlers must be educated on meat safety, handling and storage to ensure meat is safe for consumption.
From the private to the public: Continuum of sexual–racial violence against migrant women
Authors: Contreras-Hernández Paola , Stuardo Ávila Valeria
Published: November 2024

This article analyses the sexual–racial violence faced by migrant women in public spaces in the city of Barcelona. Based on a gendered perspective, this study conceptualises public space as an area where women’s rights to live a life free of violence are restricted and looks at sexism and racism as systems of oppression; further, the concept of a continuum of violence forms the theoretical basis of this article. Forty in-depth interviews were conducted with Latin American women living in the city of Barcelona. The study identified a continuum of violence that intensifies in the migratory context. Violence moves in a circular fashion from private to public spaces through a combination of sexism and racism perpetrated by (ex-)partners, strangers, and acquaintances. As a result, migrant women grapple with feelings of rejection and insecurity that hinder integration processes and condition their life in the city, experiences, and decisions regarding daily life.
The roles of self-compassion and social support on the maternal adjustment to a child’s hip dysplasia
Authors: Veloso Bruna , Palmeira Lara , Carvalhais Lénia , Marta-Simões Joana , Trindade Inês A
Published: November 2024

Parenthood can be challenging when facing a child’s chronic illness such as developmental dysplasia of the hip (DDH). Although social support is known as a protective factor for the caregiver’s mental health, the role of self-compassion is less explored. This study, conducted in Portugal, explored whether self-compassion and social support mediate the relationship between mothers’ psychological adjustment and perception of their child’s illness. Ninety-four mothers of children with DDH completed questionnaires on illness perception, self-compassion, perceived social support, and psychological distress. Results suggested that self-compassion and social support mediated the relationship between mothers’ overall negative perception of the children’s illness and psychological distress. The final model accounted for 50% of the variance of depressive symptoms, 40% of anxiety, and 63% of perceived stress. This study highlights the potential value of encouraging mothers to seek social support when facing their child’s DDH diagnosis. Promoting self-compassion may be important in clinical intervention.
Dancing on a tightrope: Uncertainty, risk perception and trust relationships in the live music industry
Authors: Mulder Martijn , Hitters Erik
Published: November 2024

In this study, we argue that organizers of live music have increasingly been confronted with uncertainty and risk in the pre-pandemic era and that the pandemic has clearly put them under further pressure. At the same time, live music venues and festivals have proven to be largely resilient to the extreme crisis of an ongoing industry lockdown. Also, the sector’s culture of carefully cultivated forms of active (emotive, interrelational) trust to counterbalance these risks has played an important role in the industry’s resilience and its response to both internal and external uncertainties. We base these conclusions on a framework of theories on uncertainty and risk from both business studies and sociology and in-depth interviews with directors of music festivals and venues in the Netherlands, both before the pandemic and after 16 months of lockdown. This study aims to (1) gain insight into how live music entrepreneurs perceived and experienced uncertainty and risk within the context of a rapidly changing music industry and a volatile and unpredictable market of concerts and festivals – both before the pandemic and at the eve of re-opening after a 16-month lockdown and (2) understand what strategies these entrepreneurs employ to manage these uncertainties and risks.
A scoping review of dementia education programs to assess for the inclusion of culture
Authors: Hulko Wendy , Mirza Noeman , Christianson Tracy , Nazemi Mahtab , Vicic Alicia , Bartle Emily
Published: November 2024

This scoping review examined literature on dementia education programs (DEPs) for healthcare providers and students. The search was conducted using the Discover! search engine that includes 63 databases. The review included a total of 25 articles that met the eligibility criteria. There were numerous DEPs that varied by frequency and duration, mode of delivery, content, target population, program evaluation measures, and outcomes. Most involved nursing staff and students and took place in Canada, the US, and the UK. The most common delivery mode was a one-time in-person session and a wide variety of topics were covered, both general (e.g., understanding dementia) and specific (e.g., driving, delirium). Twenty different tools were used to measure primarily changes in knowledge and attitudes, with little attention paid to performance and care provision. Only three studies on DEPs focused on culture in terms of race and ethnicity. The implications of this scoping review for education are that DEPs need to meaningfully address culture and culturally safe care in order to respond to the increasing diversity of older adults and care providers. In terms of future research on DEPs, program evaluation must attend to the importance of consistent measures, translation of knowledge to practice, and sustainability.
Co-designing a relational ethical decision-making framework with Aboriginal Elders and young people to address health inequities
Authors: Wright Michael , Webb Michelle , Davis Cheryl , Councillor Beverley , Ramirez-Watkins Ashton , Jones Tanya , Fielder John , Guima Chenin Tilsa , O’Connell Margaret
Published: November 2024

State and National Government policies in Australia increasingly emphasise the need for partnerships and relationships to deliver positive outcomes for First Nations peoples. However, whether these partnerships embody First Nations relational ways of working, or meet the needs and priorities of communities, is not well known. An Aboriginal participatory action research project, grounded in an Aboriginal research methodology, Debakarn, Koorliny Wangkiny, brought together Elders, young people and service providers in Perth, Western Australia, to co-design an ethical decision-making framework. Applying the knowledge and wisdom of Elders, this framework was trialled with three community service organisations to assess the cultural safety of their service provision to Aboriginal people. The findings suggest that this co-designed ethical decision-making framework can be used to implement ethical standards and embed more authentic culturally safe practices and processes by developing meaningful relationships with First Nations People and Communities.
Mapping Cognition in Epilepsy: From the Lab to the Clinic
Authors: Bearden Donald Jay , Stasenko Alena , Prentice Freya , Benjamin Christopher , Hamberger Marla , Reppert Lauren , Jones Jana J. , Sepeta Leigh
Published: November 2024

In this article, we provide an overview of our panel presentation at the American Epilepsy Society meeting in December2023. Our presentation reviewed functional mapping methods for epilepsy surgery including well-established and newer methods, focusing mostly on language and memory. Dr Leigh Sepeta (Chair) and Dr Jana Jones (Chair) organized the presentation, which included 5 presenters. Dr Christopher Benjamin discussed the history and current and future mapping practices using functional magnetic resonance imaging; Ms. Freya Prentice reviewed functional mapping of language and memory in pediatric epilepsy; Dr Marla Hamberger compared pros and cons of functional mapping between subdural electrodes and stereoelectroencephalography (SEEG); Dr Donald J. Bearden presented a brief how-to guide on cognitive mapping using SEEG; and Dr Alena Stasenko discussed the complexities of functional mapping of bilingual patients. We have included references for more detailed information on the content of our presentation.
The impact of pathogenic BRCA1/2 tumor mutation status on high grade serous epithelial ovarian cancer survival outcome: A multicenter study from Indonesia
Authors: Sutrisno Sutrisno , Marlina Dina , Tjandraprawira Kevin Dominique , Adinda Adriansyah Putri Nadhira
Published: November 2024

Introduction:

Ovarian cancer is still a major health problem in Indonesia. development of breast cancer gene-related personalized medicine to increase the survival outcome of epithelial ovarian cancer patients in Indonesia is expected to be achieved. This research aims to evaluate the impact of pathogenic breast cancer gene 1 and breast cancer gene 2 tumor mutation on high-grade serous epithelial ovarian cancer survival outcome.

Methods:

This study is an observational analytic study, using a historical cohort study design. A total of 68 from 144 patients diagnosed with International Federation of Gynecology and Obstetrics 2014 stage IIB-IV high-grade serous epithelial ovarian cancer between January 1st, 2015 until March 31st, 2021, at three centers in Jakarta. Next-generation sequencing tumor breast cancer gene 1 and breast cancer gene 2 testing and were included in this cohort historical study. We compared patient’s overall survival outcomes, according to pathogenic breast cancer gene 1 and breast cancer gene 2 tumor mutational status. Clinicopathological characteristic factors that might affect patient’s survival outcomes were also investigated.

Results:

In the group of individuals with pathogenic breast cancer gene 1 and breast cancer gene 2 tumour mutations, the risk of death was significantly lower by 86% (adjusted RR 0.149; 95% CI: 0.046–0.475; p-value = 0.001), and the median survival time was significantly better (median 46 months; 95% CI: 34.009–57.991; p-value = 0.001) compared to the group without pathogenic breast cancer gene 1 and breast cancer gene 2 tumor mutations (median 23 months; 95% CI: 15.657–30.343; p-value = 0.001). The multivariate analysis revealed that the presence of a pathogenic breast cancer gene 1 and breast cancer gene 2 tumor mutation is an independent and positive prognostic factor for survival outcome. The adjusted relative risk was 0.149, with a 95% CI of 0.046–0.475, p-value = 0.001.

Conclusions:

In high-grade serous ovarian cancer patients, the pathogenic breast cancer gene 1 and breast cancer gene 2 tumor mutations group have a better prognosis with longer survival outcomes than those without pathogenic breast cancer gene 1 and breast cancer gene 2 tumor mutations.
High security and privacy protection model for STI/HIV risk prediction
Authors: Tang Zhaohui , Van Nguyen Thi Phuoc , Yang Wencheng , Xia Xiaoyu , Chen Huaming , Mullens Amy B. , Dean Judith A. , Osborne Sonya R , Li Yan
Published: November 2024

Introduction

Applying and leveraging artificial intelligence within the healthcare domain has emerged as a fundamental pursuit to advance health. Data-driven models rooted in deep learning have become powerful tools for use in healthcare informatics. Nevertheless, healthcare data are highly sensitive and must be safeguarded, particularly information related to sexually transmissible infections (STIs) and human immunodeficiency virus (HIV).

Methods

We employed federated learning (FL) in combination with homomorphic encryption (HE) for STI/HIV prediction to train deep learning models on decentralized data while upholding rigorous privacy. The dataset included 168,459 data entries collected from eight countries between 2013 and 2018. The data for each country was split into two groups, with 70% allocated for training and 30% for testing. Our strategy was based on two-step aggregation to enhance model performance and leverage the area under the curve (AUC) and accuracy metrics and involved a secondary aggregation at the local level before utilizing the global model for each client. We introduced a dropout approach as an effective client-side solution to mitigate computational costs.

Results

Model performance was progressively enhanced from an AUC of 0.78 and an accuracy of 74.4% using the local model to an AUC of 0.94 and an accuracy of 90.7% using the more advanced model.

Conclusion

Our proposed model for STI/HIV risk prediction surpasses those achieved by local models and those constructed from centralized data sources, highlighting the potential of our approach to improve healthcare outcomes while safeguarding sensitive patient information.
Managing Diversity and Multi-Cultural Collaboration: A Systematic Review
Authors: Ketemaw Adissu , Ayenew Zerihun , Zewde Shimels
Published: November 2024

In this competitive business world, competent employees in terms of knowledge, skill, experience, and abilities are highly required for enhancing creativity and innovation within the organization. The main purpose of this study was to examine how best practices for managing diversity, multicultural collaboration, and employee engagement are applied in organizations across a range of industries. As a research design, this study used a systematic review method. A comprehensive, unbiased search approach was applied in this paper. The descriptive and narrative data analysis methods were used in this study. Effective diversity management and multicultural collaboration have a significant role in the development of ethnic groups’ cultural values, enhancing organizational performance, minimizing misunderstandings, and maximizing the potential for strong cross-cultural relationships. This research was limited to a review of managing diversity and multicultural collaboration in the workplace. However, the study didn’t show what the existing problems look like in different companies and how organizations face different challenges and what is the effect of managing diversity and multicultural collaboration therefore future researchers can fill this gap by conducting scientific research and collecting the primary data from different case companies. The researcher understands that updated and relevant data are critical for the expansion of multicultural collaboration and diversity management. Because culture encourages entrepreneurial values, norms, and beliefs that support the capacity of the organization to detect, interpret, and translate signals from the environment into new behavior responses and can play an important role in creating an organizational climate that enables learning and innovative response to challenges, competitive threats, or new opportunities.
Clonal hematopoiesis of indeterminate potential: a risk factor for future exacerbation in patients with COPD
Authors: Lee Jung-Kyu , An Hongyul , Koh Youngil , Lee Chang-Hoon
Published: November 2024

Background

There is limited data regarding the clinical significance of clonal hematopoiesis of indeterminate potential (CHIP) in patients with COPD. We aimed to evaluate whether CHIP could serve as a biomarker for the long-term prognosis of patients with COPD.

Methods

Next-generation sequencing was used to detect CHIP in peripheral blood mononuclear cell samples. Participants with COPD were enrolled in a prospective observational cohort between January 2013 and December 2023. We investigated the association of CHIP status with the risk of subsequent acute exacerbation and longitudinal changes in lung function, by using negative binomial regression and linear mixed regression models, respectively.

Results

Among 125 patients with COPD, the CHIP-positive group was 32 (25.6%). Higher smoking intensity and CAT score were significantly associated with increased risk of positive CHIP status, especially in current smokers. Positive CHIP of specific genes was significantly associated with a higher risk of subsequent mild and total acute exacerbation. Positive CHIP of ASXL transcriptional regulator 1 (ASXL1) had a lower risk of subsequent total acute exacerbation (aOR, 0.19; 95% CI, 0.04–0.95). The CHIP status did not show a statistically significant association with longitudinal changes in lung function.

Conclusions

In patients with COPD, CHIP positivity was significantly associated with an increased risk of subsequent acute exacerbations, but not with longitudinal changes in lung function.
Magnesium degradation-induced variable fixation plates promote bone healing in rabbits
Authors: Wen Jian , Zeng Yu , Su Shenghui , Song Meiling , Wang Zhe , Chen Xiaofan , Dong Xieping
Published: November 2024

Background

Both initial mechanical stability and subsequent axial interfragmentary micromotion at fracture ends play crucial roles in fracture healing. However, the conversion timing of variable fixation and its effect on and mechanism of fracture healing remain inadequately explored.

Methods

A magnesium degradation-induced variable fixation plate (MVFP) for femurs was designed, and its conversion timing was investigated both in vitro and in vivo. Then, locking plates and MVFPs with and without a magnesium shim were implanted in rabbit femur fracture models. X-ray photography and micro computed tomography (micro-CT) were performed to observe the healing of the fracture. Toluidine blue and Masson’s trichrome staining were performed to observe new bone formation. The torsion test was used to determine the strength of the bone after healing. Finally, reverse transcription-polymerase chain reaction (RT-PCR) and western blotting were used to detect the expression of osteogenesis-related genes in the three groups.

Results

The MVFP with sample 3 magnesium shim showed greater axial displacement within 15 days in vitro, and its variable capability was likewise confirmed in vivo. X-ray photography and micro-CT indicated increased callus formation in the variable fixation group. Toluidine blue and Masson’s trichrome staining revealed less callus formation on the rigid fixation side of the locking plate, whereas the variable fixation group presented more callus formation, more symmetrical intraosseous calli, and greater maturity. The torsion test indicated greater torsional resistance of the healed bone in the variable fixation group. RT-PCR and western blotting revealed that the expression levels of BMP2 and OPG increased during early fracture stages but decreased in late fracture stages, whereas RANKL expression showed the opposite trend in the variable fixation group.

Conclusions

MVFP promoted faster and stronger bone healing in rabbits, potentially by accelerating the expression of BMP2 and modulating the OPG/RANKL/RANK signaling axis. This study offers valuable insights for the clinical application of variable fixation technology in bone plates and contributes to the advancement of both internal fixation technology and theory.

Level of evidence: level V.

Graphical Abstract
A computationally efficient algorithm to leverage average information REML for (co)variance component estimation in the genomic era
Authors: Strandén Ismo , Mäntysaari Esa A. , Lidauer Martin H. , Thompson Robin , Gao Hongding
Published: November 2024

Background

Methods for estimating variance components (VC) using restricted maximum likelihood (REML) typically require elements from the inverse of the coefficient matrix of the mixed model equations (MME). As genomic information becomes more prevalent, the coefficient matrix of the MME becomes denser, presenting a challenge for analyzing large datasets. Thus, computational algorithms based on iterative solving and Monte Carlo approximation of the inverse of the coefficient matrix become appealing. While the standard average information REML (AI-REML) is known for its rapid convergence, its computational intensity imposes limitations. In particular, the standard AI-REML requires solving the MME for each VC, which can be computationally demanding, especially when dealing with complex models with many VC. To bridge this gap, here we (1) present a computationally efficient and tractable algorithm, named the augmented AI-REML, which facilitates the AI-REML by solving an augmented MME only once within each REML iteration; and (2) implement this approach for VC estimation in a general framework of a multi-trait GBLUP model. VC estimation was investigated based on the number of VC in the model, including a two-trait, three-trait, four-trait, and five-trait GBLUP model. We compared the augmented AI-REML with the standard AI-REML in terms of computing time per REML iteration. Direct and iterative solving methods were used to assess the advances of the augmented AI-REML.

Results

When using the direct solving method, the augmented AI-REML and the standard AI-REML required similar computing times for models with a small number of VC (the two- and three-trait GBLUP model), while the augmented AI-REML demonstrated more notable reductions in computing time as the number of VC in the model increased. When using the iterative solving method, the augmented AI-REML demonstrated substantial improvements in computational efficiency compared to the standard AI-REML. The elapsed time of each REML iteration was reduced by 75%, 84%, and 86% for the two-, three-, and four-trait GBLUP models, respectively.

Conclusions

The augmented AI-REML can considerably reduce the computing time within each REML iteration, particularly when using an iterative solver. Our results demonstrate the potential of the augmented AI-REML as an appealing approach for large-scale VC estimation in the genomic era.
ClassifieR 2.0: expanding interactive gene expression-based stratification to prostate and high-grade serous ovarian cancer
Authors: McCabe Aideen , Quinn Gerard P. , Jain Suneil , Ó Dálaigh Micheál , Dean Kellie , Murphy Ross G. , McDade Simon S.
Published: November 2024

Background

Advances in transcriptional profiling methods have enabled the discovery of molecular subtypes within and across traditional tissue-based cancer classifications. Such molecular subgroups hold potential for improving patient outcomes by guiding treatment decisions and revealing physiological distinctions and targetable pathways. Computational methods for stratifying transcriptomic data into molecular subgroups are increasingly abundant. However, assigning samples to these subtypes and other transcriptionally inferred predictions is time-consuming and requires significant bioinformatics expertise. To address this need, we recently reported “ClassifieR,” a flexible, interactive cloud application for the functional annotation of colorectal and breast cancer transcriptomes. Here, we report “ClassifieR 2.0” which introduces additional modules for the molecular subtyping of prostate and high-grade serous ovarian cancer (HGSOC).

Results

ClassifieR 2.0 introduces ClassifieRp and ClassifieRov, two specialised modules specifically designed to address the challenges of prostate and HGSOC molecular classification. ClassifieRp includes sigInfer, a method we developed to infer commercial prognostic prostate gene expression signatures from publicly available gene-lists or indeed any user-uploaded gene-list. ClassifieRov utilizes consensus molecular subtyping methods for HGSOC, including tools like consensusOV, for accurate ovarian cancer stratification. Both modules include functionalities present in the original ClassifieR framework for estimating cellular composition, predicting transcription factor (TF) activity and single sample gene set enrichment analysis (ssGSEA).

Conclusions

ClassifieR 2.0 combines molecular subtyping of prostate cancer and HGSOC with commonly used sample annotation tools in a single, user-friendly platform, allowing scientists without bioinformatics training to explore prostate and HGSOC transcriptional data without the need for extensive bioinformatics knowledge or manual data handling to operate various packages. Our sigInfer method within ClassifieRp enables the inference of commercially available gene signatures for prostate cancer, while ClassifieRov incorporates consensus molecular subtyping for HGSOC. Overall, ClassifieR 2.0 aims to make molecular subtyping more accessible to the wider research community. This is crucial for increased understanding of the molecular heterogeneity of these cancers and developing personalised treatment strategies.
The gut microbiota of three avian species living in sympatry
Authors: Pereira Hugo , Chakarov Nayden , Caspers Barbara A. , Gilles Marc , Jones William , Mijoro Tafitasoa , Zefania Sama , Székely Tamás , Krüger Oliver , Hoffman Joseph I.
Published: November 2024

Background

Evolutionary divergence and genetic variation are often linked to differences in microbial community structure and diversity. While environmental factors and diet heavily influence gut microbial communities, host species contributions are harder to quantify. Closely related species living in sympatry provide a unique opportunity to investigate species differences without the confounding effects of habitat and dietary variation. We therefore compared and contrasted the gut microbiota of three sympatric plover species: the widespread Kittlitz’s and white-fronted plovers (Anarhynchus pecuarius and A. marginatus) and the endemic and vulnerable Madagascar plover (A. thoracicus).

Results

We found no significant differences in the beta diversity (composition) of the gut microbiota of the three species. However, A. thoracicus exhibited higher intraspecific compositional similarity (i.e. lower pairwise distances) than the other two species; this pattern was especially pronounced among juveniles. By contrast, microbial alpha diversity varied significantly among the species, being highest in A. pecuarius, intermediate in A. marginatus and lowest in A. thoracicus. This pattern was again stronger among juveniles. Geographical distance did not significantly affect the composition of the gut microbiota, but genetic relatedness did.

Conclusion

While patterns of microbial diversity varied across species, the lack of compositional differences suggests that habitat and diet likely exert a strong influence on the gut microbiota of plovers. This may be enhanced by their precocial, ground-dwelling nature, which could facilitate the horizontal transmission of microbes from the environment. We hypothesise that gut microbiota diversity in plovers primarily reflects the ecological pool of microbiota, which is subsequently modified by host-specific factors including genetics. The reduced microbial and genetic diversity of the endemic A. thoracicus may hinder its ability to adapt to environmental changes, highlighting the need for increased conservation efforts for this vulnerable species.
Chemical quantification of N-acyl alanine methyl ester (NAME) production and impact on temporal gene expression patterns in Roseovarius tolerans EL-164
Authors: Leinberger Janina , Koteska Diana , Boldt Judith , Petersen Jörn , Shivaramu Sahana , Tomasch Jürgen , Schulz Stefan , Brinkhoff Thorsten
Published: November 2024

Background

Previous studies have identified structurally diverse N-acyl amino acid methyl esters (NAMEs) in culture extracts of Roseovarius tolerans EL-164 (Roseobacteraceae). NAMEs are structural analogues of the common signaling compounds N-acyl homoserine lactones (AHLs), but do not participate in AHL-mediated signaling. NAMEs show minor antialgal and antimicrobial activity, but whether this activity serves as the primary ecological role remains unclear.

Results

To enable dose-dependent bioactivity-testing, we have established a chromatographic method for quantification of NAMEs in bacterial culture extracts. The concentrations determined for the two major NAMEs produced by EL-164, C16:1-NAME and C17:1-NAME, ranged between 0.685 and 5.731 mg L− 1 (2.0-16.9 µM) and 5.3–86.4 µg L− 1 (15.0-244.3 nM), respectively. Co-quantification of the C14:1-AHL showed concentrations ranging between 17.5 and 58.7 mg L− 1 (56.6-189.7 µM). We observed distinct production patterns for NAMEs and AHLs, with a continuous NAME production during the entire incubation period. We conducted a spike-in experiment, using the determined metabolite concentrations. By comparing the transcriptomes of pre- and post-metabolite-spikes, we identified three clusters of differentially expressed genes with distinct temporal expression patterns. Expression levels of stress response genes differed between NAME- and AHL-spiked EL-164 cultures in the stationary phase.

Conclusions

Our findings support previous studies suggesting an ecological role for C16:1-NAME as antibiotic, by proving that NAME concentrations in batch cultures were higher than the minimal inhibitory concentrations against Maribacter sp. 62 − 1 (Flavobacteriia) and Skeletonema costatum CCMP 1332 (Coscinodiscophyceae) reported in the literature. Our study further exemplified the broad application range of dose-dependent testing and highlighted the different biological activities of NAMEs and AHLs.
Characterization of non-O157 enterohemorrhagic Escherichia coli isolated from different sources in Egypt
Authors: Bahgat Omnia T. , Rizk Dina E. , Kenawy Hany I. , Barwa Rasha
Published: November 2024

Background

Enterohemorrhagic Escherichia coli (EHEC) O157 is implicated in serious food and water-borne diseases as hemorrhagic colitis (HC), and the potentially fatal hemolytic uremic syndrome (HUS). However, new players of non-O157 EHEC have been implicated in serious infections worldwide. This work aims at analyzing serotype and genotypic-based virulence profile of EHEC local isolates.

Methods

A total of 335 samples were collected from different sources in Egypt. E. coli was isolated and subjected to serotyping. Non-O157 EHEC isolates were tested for virulence genes using PCR, phenotypic examination, phylogenetic typing, and molecular investigation by ERIC typing and MLST to disclose genetic relatedness of isolates. A heat map was used to identify potential associations between the origin of the isolates, their phenotypic and genotypic characteristics.

Results

A total of 105 out of 335 isolates were identified as E. coli. Surprisingly, 49.5% of these isolates were EHEC, where O111, O91, O26 and O55 were the most prevalent serotypes including 38.46% from stool, 21.15% urine, 23.1% cheese, 9.62% meat products, 3.85% from both yogurt and sewage water. Screening 15 different virulence genes revealed that sheA, stx2 and eae were the most prevalent with abundance rates of 85%, 75% and 36%, respectively. Fifteen profiles of virulence gene association were identified, where the most abundant one was stx2/sheA (19%) followed by stx2/stx2g/sheA/eae (11.5%). Both stx2/sheA/eae and stx2/stx2g/sheA were equally distributed in 9.6% of total isolates. Phylogenetic typing revealed that pathogenic phylogroups B2 and D were detected among clinical isolates only. Forty-six different patterns were detected by ERIC genotyping. MLST resolved three sequence types of ST70, ST120 and ST394. The heat map showed that 21 isolates were of 70% similarity, 9 groups were of 100% clonality.

Conclusions

The prevalence of non-O157 EHEC pathotype was marginally higher among the food isolates compared to the clinical ones. The endemic ST120 was detected in cheese, necessitating crucial measures to prevent the spread of this clone. Clinical EHEC isolates exhibited a higher score, and combination of virulence genes compared to food and sewage water isolates, thereby posing a significant public health concern.
Communicating treatment options to older patients with advanced kidney disease: a conversation analysis study
Authors: Selman Lucy E. , Shaw Chloe B. , Sowden Ryann , Murtagh Fliss E. M. , Tulsky James A. , Parry Ruth , Caskey Fergus J. , Barnes Rebecca K.
Published: November 2024

Background

Choosing to have dialysis or conservative kidney management is often challenging for older people with advanced kidney disease. While we know that clinical communication has a major impact on patients’ treatment decision-making, little is known about how this occurs in practice. The OSCAR study (Optimising Staff-Patient Communication in Advanced Renal disease) aimed to identify how clinicians present kidney failure treatment options in consultations with older patients and the implications of this for patient engagement.

Methods

An observational, multi-method study design was adopted. Outpatient consultations at four UK renal units were video-recorded, and patients completed a post-consultation measure of shared decision-making (SDM-Q-9). Units were sampled according to variable rates of conservative management. Eligible patients were ≥ 65 years old with an eGFR of ≤ 20 mls/min/1.73m2 within the last 6 months. Video-recordings were screened to identify instances where clinicians presented both dialysis and conservative management. These instances were transcribed in fine-grained detail and recurrent practices identified using conversation-analytic methods, an empirical, observational approach to studying language and social interaction.

Results

110 outpatient consultations were recorded (105 video, 5 audio only), involving 38 clinicians (doctors and nurses) and 94 patients: mean age 77 (65–97); 61 males/33 females; mean eGFR 15 (range 4–23). There were 21 instances where clinicians presented both dialysis and conservative management. Two main practices were identified: (1) Conservative management and dialysis both presented as the main treatment options; (2) Conservative management presented as a subordinate option to dialysis. The first practice was less commonly used (6 vs. 15 cases), but associated with more opportunities in the conversation for patients to ask questions and share their perspective, through which they tended to evaluate conservative management as an option that was potentially personally relevant. This practice was also associated with significantly higher post-consultation ratings of shared decision-making among patients (SDM-Q-9 median total score 24 vs. 37, p = 0.041).

Conclusions

Presenting conservative management and dialysis as on an equal footing enables patient to take a more active role in decision-making. Findings should inform clinical communication skills training and education.

Clinical trial number

No trial number as this is not a clinical trial.
Barriers and facilitators to high-volume evidence-based innovation and implementation in a large, community-based learning health system
Authors: Durojaiye Cimone , Prausnitz Stephanie , Schneider Jennifer L. , Lieu Tracy A. , Schmittdiel Julie A. , Rouillard Smita , Chen Yi-Fen , Lee Kristine , Corley Douglas A.
Published: November 2024

Background

Broad-scale, rapid health care change is critically needed to improve value-based, effective health care. Health care providers and systems need to address common barriers and facilitators across the evidence to implementation pathway, across diverse specialties. However, most evidence translation / implementation research evaluates single topic areas, and may be of limited value for informing comprehensive efforts. This project’s objective was to identify, characterize, and illustrate common trans-topic facilitators and barriers of translating new health care evidence results to clinical implementation across multiple medical specialties.

Methods

This study was an evaluation of all evidence-based innovation projects completed during 2019–2021. Each project was created with medical group clinical leaders and was intended to inform clinical care. The evaluation took place in a large community-based integrated health care system, and an embedded delivery science and applied research program. Clinical investigators, scientific investigators, and clinical operational leaders received structured questionnaires regarding barriers and facilitators for the operational implementation of new research findings for each project. Responses were mapped to the Consolidated Framework for Implementation Research to identify perceived implementation barriers and facilitators.

Results

All 48 projects completed between 2019 and 2021 were evaluated; responses were received for 45 (94%) and 34 had comments mappable to framework domains. Potential barriers and facilitators to clinical implementation of new research results were identified across all five framework domains and, within these, the 38 constructs or sub-constructs. Among 245 total comments, the most commonly cited facilitators were how the new research evidence generated, compelled change (n = 29), specialty communication networks for disseminating results and initiating change (n = 20), leadership engagement in the project (n = 19), and the innovation’s relative advantage over existing practices (n = 11). The most commonly cited barriers were inadequate resource commitment for next-step implementation (n = 15), insufficient learning/implementation culture (n = 5), and insufficient individual-level willingness/ability for change (n = 5).

Conclusions

A novel large-scale evaluation of barriers and facilitators across the evidence to implementation pathway identified common factors across multiple topic areas and specialties. These common potentially replicable facilitators and modifiable barriers can focus health systems and leaders pursuing large-volume evidence-to-implementation initiatives on those areas with the likely greatest benefit-for-effort, for accelerating health care change.
Prognostic efficacy of lymph node parameters in resected ampullary adenocarcinoma based on long-term follow-up data after adjuvant treatment
Authors: Park Namyoung , Cho In Rae , Lee Sang Hyub , Kim Joo Seong , Choi Jin Ho , Lee Min Woo , Paik Woo Hyun , Joo Kwang Ro , Ryu Ji Kon , Kim Yong-Tae
Published: November 2024

Background

Lymph node (LN) metastasis is an important prognostic factor in the ampulla of Vater (AoV) adenocarcinoma. Various LN parameters have been proposed, but their prognostic efficacy has not been compared in the same population. We aimed to evaluate the prognostic values of LN parameters in AoV adenocarcinoma patients who underwent surgical resection and adjuvant treatment based on the long-term follow-up data.

Methods

A total of 86 patients with surgically resected AoV adenocarcinoma followed by adjuvant treatment were analyzed. We evaluated the prognostic values of various LN parameters such as pathologic N stage, number of metastatic regional LN (LNN), LN ratio (LNR), and log odds of positive LNs (LODDS). Each LN parameter was separately analyzed using Cox regression models with the same confounders.

Results

The median follow-up period was 69.4 months, and the median overall survival (OS) was 114 months. The median number of dissected LNs is 15, with an interquartile range of 8 to 25. In the univariable analyses, all LN parameters showed significant prognostic efficacy for OS, disease-free survival (DFS), and distant metastasis-free survival (DMFS). In the multivariable Cox regression analyses, LNN ≥ 2 was a statistically significant prognostic factor for OS (hazard ratio (HR) 2.10, 95% confidence interval (CI), 1.11–3.97; p = 0.022), DFS (HR 2.51, 95% CI 1.28–4.93; p = 0.007), and DMFS (HR 2.74, 95% CI 1.39–5.41; p = 0.004). LNR showed significant prognostic performance for DFS (HR 2.35, 95% CI 1.23–4.50; p = 0.010), and DMFS (HR 2.26, 95% CI 1.17–4.35; p = 0.015). N stage showed significant prognostic performance in DFS (HR 1.55 for pN1; p = 0.243 and HR 4.31 for pN2; p = 0.003), DMFS (HR 1.46 for pN1; p = 0.323 and 4.59 for pN2; p = 0.002). LODDS and the presence of LN metastasis, did not demonstrate significant prognostic value across survival outcomes.

Conclusions

LN parameters showed good long-term predictive performance in AoV adenocarcinoma patients treated with curative resection and adjuvant treatments. Among LN parameters, LNN ≥ 2 showed better prognostic value than others. Further large-scale studies are needed to validate the clinical usefulness of various LN parameters.
A study on the design of a universal signage system for the Ruijin Soviet cultural heritage site
Authors: Shizhu Lu , Qiuyu Huang , Ziyi Min , Pengjiang Jia
Published: November 2024

Ruijin, the birthplace of China’s first red regime, has always been the core of the central revolutionary base. Integrating the design of cultural heritage sites with universal signage systems is an effective way to protect and pass on red cultural heritage while promoting the continued dissemination of the national image. In heritage site tourism, the signage system is crucial in guiding, indicating, and explaining, serving as a critical component of essential public infrastructure. Given Ruijin’s rich and historic red cultural resources, the design of the signage system must consider the diverse needs of visitors from different nationalities, cultural backgrounds, and age groups. This study adopts a universal design perspective, using the red cultural heritage of the Ruijin Soviet period as a case study. It constructs universal metadata from three key aspects: Cultural Type, Data Attribute, and Data Type. These elements are then visually represented through digital technology. The study also incorporates theoretical support from semiotics, Gestalt psychology, cognitive psychology, and semantics. Through surveys, in-depth interviews, and a “structure-humanity” composite evaluation method, we thoroughly explores the relationships between perception, comprehensibility, visual cognition, and the design of universal signage systems. Additionally, the study analyzes the key factors affecting the universality of the signage system. The results indicate that visual cognition positively impacts the design of universal signage systems. Key factors influencing the universality of signage systems include symbolic element modeling, the familiarity of graphics, the semantic distance of graphics, and the rationality of graphic usage. These findings offer a strategy for creating a universal signage system guided by the heritage routes and based on the dimensions of perception, comprehensibility, and visual cognition. It provides new methods and perspectives for cultural education and heritage preservation in Ruijin and other red cultural heritage sites.