bluuebunny/crossref_metadata_2025_split huggingface dataset:
Latent dirichlet allocation for double clustering (LDA-DC): discovering patients phenotypes and cell populations within a single Bayesian framework
Authors: El Hachem Elie-Julien , Sokolovska Nataliya , Soula Hedi 
Published: February 2023

Abstract
Background
Current clinical routines rely more and more on “omics” data such as flow cytometry data from host and microbiota. Cohorts variability in addition to patients’ heterogeneity and huge dimensions make it difficult to understand underlying structure of the data and decipher pathologies. Patients stratification and diagnostics from such complex data are extremely challenging. There is an acute need to develop novel statistical machine learning methods that are robust with respect to the data heterogeneity, efficient from the computational viewpoint, and can be understood by human experts.

Results
We propose a novel approach to stratify cell-based observations within a single probabilistic framework, i.e., to extract meaningful phenotypes from both patients and cells data simultaneously. We define this problem as a double clustering problem that we tackle with the proposed approach. Our method is a practical extension of the Latent Dirichlet Allocation and is used for the Double Clustering task (LDA-DC). We first validate the method on artificial datasets, then we apply our method to two real problems of patients stratification based on cytometry and microbiota data. We observe that the LDA-DC returns clusters of patients and also clusters of cells related to patients’ conditions. We also construct a graphical representation of the results that can be easily understood by humans and are, therefore, of a big help for experts involved in pre-clinical research.
PriPath: identifying dysregulated pathways from differential gene expression via grouping, scoring, and modeling with an embedded feature selection approach
Authors: Yousef Malik , Ozdemir Fatma , Jaber Amhar , Allmer Jens , Bakir-Gungor Burcu 
Published: February 2023

AbstractBackgroundCell homeostasis relies on the concerted actions of genes, and dysregulated genes can lead to diseases. In living organisms, genes or their products do not act alone but within networks. Subsets of these networks can be viewed as modules that provide specific functionality to an organism. The Kyoto encyclopedia of genes and genomes (KEGG) systematically analyzes gene functions, proteins, and molecules and combines them into pathways. Measurements of gene expression (e.g., RNA-seq data) can be mapped to KEGG pathways to determine which modules are affected or dysregulated in the disease. However, genes acting in multiple pathways and other inherent issues complicate such analyses. Many current approaches may only employ gene expression data and need to pay more attention to some of the existing knowledge stored in KEGG pathways for detecting dysregulated pathways. New methods that consider more precompiled information are required for a more holistic association between gene expression and diseases.ResultsPriPath is a novel approach that transfers the generic process of grouping and scoring, followed by modeling to analyze gene expression with KEGG pathways. In PriPath, KEGG pathways are utilized as the grouping function as part of a machine learning algorithm for selecting the most significant KEGG pathways. A machine learning model is trained to differentiate between diseases and controls using those groups. We have tested PriPath on 13 gene expression datasets of various cancers and other diseases. Our proposed approach successfully assigned biologically and clinically relevant KEGG terms to the samples based on the differentially expressed genes. We have comparatively evaluated the performance of PriPath against other tools, which are similar in their merit. For each dataset, we manually confirmed the top results of PriPath in the literature and found that most predictions can be supported by previous experimental research.ConclusionsPriPath can thus aid in determining dysregulated pathways, which applies to medical diagnostics. In the future, we aim to advance this approach so that it can perform patient stratification based on gene expression and identify druggable targets. Thereby, we cover two aspects of precision medicine.
Association between urinary biomarkers of polycyclic aromatic hydrocarbons and severe abdominal aortic calcification in adults: data from the National Health and Examination Nutrition Survey
Authors: Yang Xi , Zhou Haobin , Zhang Hao , Zhang Peijian , Zheng Zhikang , Xu Dingli , Zeng Qingchun 
Published: February 2023

Abstract
Objective
Recent studies have found that polycyclic aromatic hydrocarbons (PAHs) exposure may increase the risk of cardiovascular disease. The present study aimed to explore the association between PAHs exposure and severe abdominal aortic calcification (AAC) in adults.

Methods
Data were collected from the 2013–2014 National Health and Nutrition Examination Survey. PAHs exposure was analyzed from urinary mono hydroxylated metabolites of PAHs. Logistic regression models and subgroup analysis were performed to explore the association of PAHs exposure with severe AAC prevalence.

Results
A total of 1,005 eligible individuals were recruited into the study. After adjusting for confounding factors, those with the highest quartiles of 1-hydroxynaphthalene (1-NAP: OR 2.19, 95% CI 1.03–4.68, Pfor trend < 0.001), 2-hydroxynaphthalene (2-NAP: OR 2.22, 95% CI 1.04–4.64, Pfor trend < 0.001) and 1-hydroxypyrene (1-PYR: OR 2.15, 95% CI 1.06–4.33, Pfor trend < 0.001) were associated with an increased prevalence of severe AAC in the adults compared to those who in the lowest quartile.

Conclusion
This study found that urinary 1-NAP, 2-NAP and 1-PYR were positively associated with severe AAC prevalence in adults.
Applying mathematical modelling to estimate the impact of COVID-19-related VMMC service disruptions on new HIV infections in Zimbabwe
Authors: Chagoma Newton , Kanyenda Tiwonge , Pindiwe Bothwell , Nyika Howard , Nyazema Lawrence , Stover John , Resar Danielle , Shoko Natsai , Jenkins Sarah , Katanda Yemurai , Xaba Sinokuthemba , Mugurungi Owen 
Published: February 2023

Abstract
Background
The COVID-19 pandemic has overwhelmed health systems with knock on effects on diagnosis, treatment, and care. To mitigate the impact, the government of Zimbabwe enforced a strict lockdown beginning 30 March 2020 which ran intermittently until early 2021. In this period, the Ministry of Health and Childcare strategically prioritized delivery of services leading to partial and full suspension of services considered non-essential, including HIV prevention. As a result, Voluntary Medical Male Circumcision (VMMC) services were disrupted leading to an 80% decline in circumcisions conducted in 2020. Given the efficacy of VMMC, we quantified the potential effects of VMMC service disruption on new HIV infections in Zimbabwe.

Methods
We applied the GOALS model to evaluate the impact of COVID-19-related disruptions on reducing new HIV infections over 30-years. GOALS is an HIV simulation model that estimates number of new HIV infections based on sexual behaviours of population groups. The model is parameterized based on national surveys and HIV program data. We hypothesized three coverage scenarios by 2030: scenario I - pre-COVID trajectory: 80% VMMC coverage; Scenario II - marginal COVID-19 impact: 60% VMMC coverage, and scenario III - severe COVID-19 impact: 45% VMMC coverage. VMMC coverage between 2020 and 2030 was linearly interpolated to attain the estimated coverage and then held constant from 2030 to 2050, and discounted outcomes at 3%.

Results
Compared to the baseline scenario I, in scenario II, we estimated that the disruption of VMMC services would generate an average of 200 (176–224) additional new infections per year and 7,200 new HIV infections over the next 30 years. For scenario III, we estimated an average of 413 (389–437) additional new HIV infections per year and 15,000 new HIV infections over the next 30 years. The disruption of VMMC services could generate additional future HIV treatment costs ranging from $27 million to $55 million dollars across scenarios II and III, respectively.

Conclusion
COVID-19 disruptions destabilized delivery of VMMC services which could contribute to an additional 7,200 new infections over the next 30 years. Unless mitigated, these disruptions could derail the national goals of reducing new infections by 2030.
A metabolome-wide case-control study of african american breast cancer patients
Authors: Luo Jiajun , Kibriya Muhammad G. , Chen Hui , Kim Karen , Ahsan Habibul , Olopade Olufunmilayo I. , Olopade Christopher S. , Aschebrook-Kilfoy Briseis , Huo Dezheng 
Published: February 2023

Abstract
Background
Breast cancer survivors face long-term sequelae compared to the general population, suggesting altered metabolic profiles after breast cancer. We used metabolomics approaches to investigate the metabolic differences between breast cancer patients and women in the general population, aiming to elaborate metabolic changes among breast cancer patients and identify potential targets for clinical interventions to mitigate long-term sequelae.

Methods
Serum samples were retrieved from 125 breast cancer cases recruited from the Chicago Multiethnic Epidemiologic Breast Cancer Cohort (ChiMEC), and 125 healthy controls selected from Chicago Multiethnic Prevention and Surveillance Study (COMPASS). We used liquid chromatography-high resolution mass spectrometry to obtain untargeted metabolic profiles and partial least squares discriminant analysis (PLS-DA) combined with fold change to select metabolic features associated with breast cancer. Pathway analyses were conducted using Mummichog to identify differentially enriched metabolic pathways among cancer patients. As potential confounders we included age, marital status, tobacco smoking, alcohol drinking, type 2 diabetes, and area deprivation index in our model. Random effects of residence for intercept was also included in the model. We further conducted subgroup analysis by treatment timing (chemotherapy/radiotherapy/surgery), lymph node status, and cancer stages.

Results
The entire study participants were African American. The average ages were 57.1 for cases and 58.0 for controls. We extracted 15,829 features in total, among which 507 features were eventually selected by our criteria. Pathway enrichment analysis of these 507 features identified three differentially enriched metabolic pathways related to prostaglandin, leukotriene, and glycerophospholipid. The three pathways demonstrated inconsistent patterns. Metabolic features in the prostaglandin and leukotriene pathways exhibited increased abundances among cancer patients. In contrast, metabolic intensity in the glycerolphospholipid pathway was deregulated among cancer patients. Subgroup analysis yielded consistent results. However, changes in these pathways were strengthened when only using cases with positive lymph nodes, and attenuated when only using cases with stage I disease.

Conclusion
Breast cancer in African American women is associated with increase in serum metabolites involved in prostaglandin and leukotriene pathways, but with decrease in serum metabolites in glycerolphospholipid pathway. Positive lymph nodes and advanced cancer stage may strengthen changes in these pathways.
When primary healthcare meets queerstory: community-based system dynamics influencing regional/rural LGBTQ + people’s access to quality primary healthcare in Australia
Authors: Lucas James J. , Afrouz Rojan , Brown Andrew D. , Epstein Sarah , Ryan Joleen , Hayward Joshua , Brennan-Olsen Sharon L. 
Published: February 2023

Abstract
Background
Lesbian, gay, bisexual, transgender, Queer, and people of any other minority sexuality or gender identity (LGBTQ + or “Queer”) are often marginalised from accessing quality primary healthcare (PHC) in their local community. This is largely due to Queerphobic, cis-heteronormative/sexist systems pathologising Queer life and identities. The study aims were to: (1) identify key priorities for increasing Queer people’s access to quality PHC as told by Queer people themselves, (2) identify the feedback loops that reduce or support Queer people’s access to quality PHC in non-metropolitan, regional/rural communities, and (3) identify potential action areas to improve system structures to increase Queer people’s access to quality PHC.

Methods
Group Model Building (GMB) workshops were held with a small group (n = 8) of LGBTQ + people in regional Victoria with lived experience of using PHC services. This participatory approach permits exploration and visual mapping of local structures causing behaviour patterns of community concern over time – in this case, Queer people’s ability to access quality PHC in the Geelong-Barwon region. This is the first study that specially applies GMB in Queer PHC in the non-metropolitan regional/rural context.

Results
Key community identified PHC priorities were: (a) providers’ level of Queer Literacy, (b) the responsibility of Queer Advocacy (at individual, systemic, and collective levels), (c) support from safe Queer Spaces, (d) strength from a Queer Presence, and (e) power from Intersectional Queer Life. These priorities interconnected, creating system-level feedback loops reinforcing barriers and enablers to Queer people’s access to quality PHC in the Geelong-Barwon region; with potential action areas identified.

Conclusions
Improving Queer people’s access to quality PHC in the Geelong-Barwon region requires embedding principles of Queer Literacy, Queer Advocacy, Queer Space, Queer Presence, and Intersectional Queer Life within practices and service systems. The study findings were distilled into a novel, preliminary set of Queer Equity Principles. These need to be taken back to regional Queer communities for further co-design and planning for translation across PHC practices and systems, with potential applicability in other areas of the healthcare spectrum.
Resettlement, mental health, and coping: a mixed methods survey with recently resettled refugee parents in Canada
Authors: Sim Amanda , Puffer Eve , Ahmad Afreen , Hammad Lina , Georgiades Katholiki 
Published: February 2023

Abstract
Background
Resettlement experiences of refugee parents are under-researched despite evidence indicating higher risk of poor mental health. The current study integrates family systems and social determinants of refugee mental health frameworks to examine: (1) Refugee parents’ experiences of resettlement stressors and mental health; (2) Perceived impacts of resettlement stressors on individual and family indicators of well-being; and (3) Refugee parents’ coping strategies and resources.

Methods
The study draws on data from a mixed methods survey conducted with 40 Government-Assisted Refugee parents who had resettled to Hamilton, Canada within the past 4 years. Quantitative and qualitative data were analyzed separately and then integrated at the results stage using a weaving approach.

Results
Results indicate significant exposure to economic and social stressors across multiple domains of daily life, as well as high levels of parental psychological distress. Parents drew linkages between resettlement stressors and negative mental health impacts that were compounded by intersecting risk factors of ill health, caregiving burden, single parenthood, and low levels of education and literacy. Most parents rated themselves as coping well or very well and described various coping strategies such as positive reframing, problem solving, planning, and turning to religion. Quantitative and qualitative findings indicate high frequency of positive parent-child interaction and low frequency of family conflict, and highlight the importance of family as a protective resource for coping with adversity. Exploratory regression analyses suggest that longer stay in Canada, poorer self-rated health, higher levels of resettlement stressors, and more conflict between adults in the household may be associated with greater psychological distress.

Conclusion
Study findings highlight both the resilience of refugee parents and the psychological toll of navigating their families through a new and challenging environment. Policies and programs to provide comprehensive social and economic supports to refugees beyond the first one to two years after arrival are necessary to mitigate the mental health impacts of displacement over time and strengthen individual and family resilience. Such programs should include culturally responsive and family-based models of mental health care that acknowledge collective experiences and impacts of adversity, as well as harness family resources to overcome past and present challenges.
Shoes for self-managing chronic hip Pain: the SCHIPP randomized clinical trial protocol
Authors: Paterson Kade L. , Bennell Kim L. , Metcalf Ben R. , Jones Sarah E. , Campbell Penny K. , McManus Fiona , Lamb Karen E. , Hinman Rana S. 
Published: February 2023

Abstract
Background
Chronic hip pain is common and disabling and is largely due to osteoarthritis (OA). Self-management is recommended by international OA clinical guidelines yet there are few effective treatment options. Footwear has been suggested as a self-management approach, given that foot motion influences hip forces. Currently, guidelines advocate ‘stable supportive’ shoes for people with OA, however this is based solely on expert opinion given no research has investigated whether these shoes are effective at reducing symptoms in people with OA-related chronic hip pain. Therefore, this randomized controlled trial (RCT) aims to determine if stable supportive footwear reduces hip pain during walking compared to flat flexible footwear in people with chronic hip pain consistent with OA.

Methods
This trial is a 6-month, participant- and assessor-blinded, pragmatic, comparative effectiveness, superiority RCT conducted in Melbourne, Australia. We are recruiting 120 participants aged over 45 years with chronic hip pain consistent with OA from the community. Following baseline assessment, participants are randomized to receive either i) stable supportive shoes or ii) flat flexible shoes. Participants are permitted to choose two different pairs of shoes in their allocated group from a range of options that match prespecified shoe classification criteria. They are advised to wear either pair of study shoes daily for a minimum of 6 hours each day for 6 months. The primary outcome is the 6-month change in average hip pain on walking in the last week. Secondary outcomes include changes in other measures of hip pain, symptoms, function in daily living and sports and recreation, hip-related quality of life, pain at other sites, adverse events, and physical activity. Other measures include co-intervention use, adherence, shoe comfort, descriptive characteristics, footwear characteristics, and objective foot measures.

Discussion
This RCT will determine whether stable supportive shoes reduce hip pain during walking more than flat flexible shoes in people with chronic hip pain. Outcomes will help to inform footwear recommendations in international clinical guidelines for OA-related chronic hip pain, which to date have been based solely on expert opinion because of an absence of RCTs.

Trial registration
Australian New Zealand Clinical Trials Registry reference: ACTRN12621001532897.
Were surgical outcomes for acute appendicitis impacted by the COVID-19 pandemic?
Authors: Waldman Rachel , Kaplan Harrison , Leitman I. Michael 
Published: February 2023

Abstract
Background
The COVID-19 pandemic disrupted healthcare systems throughout the world. We examine whether appendectomy outcomes in 2020 and 2021 were affected by the pandemic.

Methods
We conducted a retrospective cohort study of 30-day appendectomy outcomes using the ACS-NSQIP database from 2019 through 2021. Logistic regression and linear regression analyses were performed to create models of post-operative outcomes.

Results
There were no associations between the time period of surgery and death, readmission, reoperation, deep incisional SSI, organ space SSI, sepsis, septic shock, rate of complicated appendicitis, failure to wean from the ventilator, or days from admission to operation. During the first 21 months of the pandemic (April 2020 through December 2021), there was a decreased length of hospital stay (p = 0.016), increased operative time (p < 0.001), and increased likelihood of laparoscopic versus open surgery (p < 0.001) in compared to 2019.

Conclusions
There were minimal differences in emergent appendectomy outcomes during the first 21 months of the pandemic when compared to 2019. Surgical systems in the US successfully adapted to the challenges presented by the COVID-19 pandemic.
Factors associated with the extent of nurses’ involvement in promotion of the nursing profession: a cross-sectional study among nurses working in diverse healthcare settings
Authors: Rozani Violetta , Kagan Ilya 
Published: February 2023

Abstract
Aims and objectives
To examine factors associated with promotion of the nursing profession, to the nursing community, other healthcare professionals and the general public, by nurses employed in diverse healthcare settings.

Background
Little is known about the factors that contribute to nurses’ involvement in the promotion of the nursing profession.

Methods
This cross-sectional study comprises a convenience sample of registered nurses (n = 526) with ≥ 3 months’ experience in nursing, who are employed in internal and surgical units, pediatric wards, psychiatric wards or in the community across Israel. Participants completed a self-administered questionnaire addressing socio-demographic, occupational and organizational factors relating to the nursing work environment and to the extent of nurses’ involvement in promotion of the nursing profession. Descriptive statistics, one-way analysis of variance, Pearson’s correlation analysis, and multivariate linear regression were performed.

Results
Nurses in all the surveyed healthcare settings reported relatively low levels of involvement in promotion of the profession, either to the nursing community or to other healthcare professionals and the public. Being a female-nurse was significantly negatively associated with nurses’ involvement in promotion of the nursing profession. In contrast, holding a master’s degree in nursing, having a managerial role, and working in a supportive organizational nursing work environment were the principal factors associated with positive promotion of the nursing profession.

Conclusion
The extent of nurses’ involvement in promotion of the nursing profession mainly depends on occupational factors and a supportive organizational nursing work environment.

Clinical relevance
Healthcare managers may advance nurses’ involvement in promotion of the profession by modifying the organizational nursing work environment. Specifically, we recommend nurse leaders to dedicate efforts to make professional promotion an integral part of a nurse’s role.