bluuebunny/crossref_metadata_2025_split huggingface dataset:
Considering social inequalities in health in large-scale testing for COVID-19 in Montréal: a qualitative case study
Authors: Gagnon-Dufresne Marie-Catherine , Gautier Lara , Beaujoin Camille , Lamothe Ashley Savard , Mikanagu Rachel , Cloos Patrick , Ridde Valéry , Zinszer Kate 
Published: April 2022

Abstract
Background
Evidence continues to demonstrate that certain marginalised populations are disproportionately affected by COVID-19. While many studies document the impacts of COVID-19 on social inequalities in health, none has examined how public health responses to the pandemic have unfolded to address these inequities in Canada. The purpose of our study was to assess how social inequalities in health were considered in the design and planning of large-scale COVID-19 testing programs in Montréal (Québec, Canada).

Methods
Part of the multicountry study HoSPiCOVID, this article reports on a qualitative case study of large-scale testing for COVID-19 in Montréal. We conducted semi-structured interviews with 19 stakeholders involved in planning large-scale testing or working with vulnerable populations during the pandemic. We developed interview guides and a codebook using existing literature on policy design and planning, and analysed data deductively and inductively using thematic analysis in NVivo.

Results
Our findings suggest that large-scale COVID-19 testing in Montréal did not initially consider social inequalities in health in its design and planning phases. Considering the sense of urgency brought by the pandemic, participants noted the challenges linked to the uptake of an intersectoral approach and of a unified vision of social inequalities in health. However, adaptations were gradually made to large-scale testing to improve its accessibility, acceptability, and availability. Actors from the community sector, among others, played an important role in supporting the health sector to address the needs of specific subgroups of the population.

Conclusions
These findings contribute to the reflections on the lessons learned from COVID-19, highlighting that public health programs must tackle structural barriers to accessing healthcare services during health crises. This will be necessary to ensure that pandemic preparedness and response, including large-scale testing, do not further increase social inequalities in health.
Relationship between depressive symptoms and self-reported menstrual irregularities during adolescence: evidence from UDAYA, 2016
Authors: Maurya Priya , Meher Trupti , Muhammad T. 
Published: April 2022

Abstract
Background
The study examined the prevalence of self-reported menstrual irregularities during adolescence and explored the association of depressive symptoms with self-reported menstrual irregularities in adolescents in two major states of Uttar Pradesh and Bihar in India.

Methods
This study is based on the data obtained from the first round of the "Understanding the lives of adolescents and young adults" (UDAYA, 2016) survey. The effective sample size for the study was 12,707 adolescent girls aged 10–19 years. A bivariate analysis with chi-square test was conducted to determine the self-reported menstrual irregularity by predictor variables. Multivariable logistic regression models were employed to examine the associations between self-reported menstrual irregularity, depressive symptoms and other explanatory variables.

Results
A proportion of 11.22% of adolescent girls reported menstrual irregularity and 11.40% of the participants had mild depressive symptoms. Adolescent girls with mild (AOR: 2.15, CI: 1.85–2.51), moderate (AOR: 2.64, CI: 2.03–3.42) and severe depressive symptoms (AOR: 2.99, CI: 2.19–4.10) were more likely to have menstrual irregularity as compared to those who had minimal depressive symptoms. Physically active adolescent girls were less likely to report menstrual irregularity (AOR: 0.82, CI: 0.73–0.93) than physically inactive girls. Adolescent girls who used piece of cloth for menstrual hygiene practices (AOR: 1.17; CI: 1.02–1.35) and those who used either napkin or cloth or other materials (AOR: 1.32; CI: 1.14–1.54) had higher likelihood of menstrual irregularity as compared to those who used only sanitary napkins.

Conclusion
A significant association of depressive symptoms with self-reported menstrual irregularity among adolescent girls was observed. Therefore, while treating females with irregular menstrual cycles, clinicians may need to pay greater attention to thir mental health peoblems.
Taking care to the patients: a qualitative evaluation of a community-based ART care program in northern Namibia
Authors: Katirayi Leila , Shoopala Naemi , Mitruka Kiren , Mengistu Assegid , Woelk Godfrey , Baughman Andrew L. , Mutandi Gram , Hong Steven Y. , Hamunime Ndapewa 
Published: April 2022

Abstract
Background
Namibia is a large sparsely populated country with a high prevalence of HIV. People living with HIV who reside in remote areas often travel long distances through tough desert terrain to access HIV care and treatment. To address this barrier, community-based antiretroviral therapy (C-BART) sites were established in Okongo (2007–2008) and Eenhana districts (2016) of northern Namibia with the goal of bringing HIV and other health services closer patients’ homes. We conducted a qualitative evaluation of the acceptability and challenges of C-BART to guide program improvement.

Methods
For this qualitative descriptive study, research assistants collected data (August-December 2017) through in-depth interviews with 40 patients, seven health extension workers, and 11 policy/program managers, and through four focus group discussions with healthcare workers. Interviews were audio-recorded, translated, and coded using MAXQDA v.12. Data were analyzed using thematic analysis.

Results
The evaluation identified five themes: community ownership, acceptance of the C-BART sites, benefits of the C-BART program for the PLHIV community and their social networks, benefits of the C-BART program to the main health facility, and challenges with the C-BART program. The C-BART program was reported as life-changing by many patients who had previously struggled to afford four-wheel drive vehicles to access care. Patients and healthcare workers perceived that the community as a whole benefited from the C-BART sites not only due to the financial pressure lifted from friends and family members previously asked to help cover expensive transportation, but also due to the perception of diminished stigmatization of people living with HIV and improved health. The C-BART sites became a source of community and social support for those accessing the sites. Healthcare workers reported greater job satisfaction and decongestion of health facilities. The challenges that they reported included delays in authorization of vehicles for transportation to C-BART sites and lack of incentives to provide services in the community.

Conclusion
The C-BART program can serve as a model of care to expand access to HIV care and treatment and other health services to populations in remote settings, including rural and difficult-to-reach regions. The needs of healthcare workers should also be considered for the optimal delivery of such a model.
Prevalence of caffeine consumers, daily caffeine consumption, and factors associated with caffeine use among active duty United States military personnel
Authors: Knapik Joseph J. , Steelman Ryan A. , Trone Daniel W. , Farina Emily K. , Lieberman Harris R. 
Published: April 2022

Abstract
Background
Although representative data on caffeine intake in Americans are available, these data do not include US service members (SMs). The few previous investigations in military personnel largely involve convenience samples. This cross-sectional study examined prevalence of caffeine consumers, daily caffeine consumption, and factors associated with caffeine use among United States active duty military service members (SMs).

Methods
A stratified random sample of SMs were asked to complete an on-line questionnaire on their personal characteristics and consumption of caffeinated products (exclusive of dietary supplements). Eighteen percent (n = 26,680) of successfully contacted SMs (n = 146,365) completed the questionnaire.

Results
Overall, 87% reported consuming caffeinated products ≥1 time/week. Mean ± standard error per-capita consumption (all participants) was 218 ± 2 and 167 ± 3 mg/day for men and women, respectively. Caffeine consumers ingested 243 ± 2 mg/day (251 ± 2 mg/day men, 195 ± 3 mg/day women). On a body-weight basis, men and women consumed respectively similar caffeine amounts (2.93 vs 2.85 mg/day/kg; p = 0.12). Among individual caffeinated products, coffee had the highest use (68%), followed by sodas (42%), teas (29%), energy drinks (29%) and gums/candy/medications (4%). In multivariable logistic regression, characteristics independently associated with caffeine use (≥1 time/week) included female gender, older age, white race/ethnicity, higher body mass index, tobacco use or former use, greater alcohol intake, and higher enlisted or officer rank.

Conclusion
Compared to National Health and Nutrition Examination Survey data, daily caffeine consumption (mg/day) by SMs was higher, perhaps reflecting higher mental and physical occupational demands on SMs.
LinDA: linear models for differential abundance analysis of microbiome compositional data
Authors: Zhou Huijuan , He Kejun , Chen Jun , Zhang Xianyang 
Published: April 2022

AbstractDifferential abundance analysis is at the core of statistical analysis of microbiome data. The compositional nature of microbiome sequencing data makes false positive control challenging. Here, we show that the compositional effects can be addressed by a simple, yet highly flexible and scalable, approach. The proposed method, LinDA, only requires fitting linear regression models on the centered log-ratio transformed data, and correcting the bias due to compositional effects. We show that LinDA enjoys asymptotic FDR control and can be extended to mixed-effect models for correlated microbiome data. Using simulations and real examples, we demonstrate the effectiveness of LinDA.
mbDenoise: microbiome data denoising using zero-inflated probabilistic principal components analysis
Authors: Zeng Yanyan , Li Jing , Wei Chaochun , Zhao Hongyu , Wang Tao 
Published: April 2022

AbstractThe analysis of microbiome data has several technical challenges. In particular, count matrices contain a large proportion of zeros, some of which are biological, whereas others are technical. Furthermore, the measurements suffer from unequal sequencing depth, overdispersion, and data redundancy. These nuisance factors introduce substantial noise. We propose an accurate and robust method, mbDenoise, for denoising microbiome data. Assuming a zero-inflated probabilistic PCA (ZIPPCA) model, mbDenoise uses variational approximation to learn the latent structure and recovers the true abundance levels using the posterior, borrowing information across samples and taxa. mbDenoise outperforms state-of-the-art methods to extract the signal for downstream analyses.
N6-methyladenosine modification of CENPK mRNA by ZC3H13 promotes cervical cancer stemness and chemoresistance
Authors: Lin Xian , Wang Feng , Chen Jian , Liu Jing , Lin Yi-Bin , Li Li , Chen Chuan-Ben , Xu Qin 
Published: April 2022

Abstract
Background
Stemness and chemoresistance contribute to cervical cancer recurrence and metastasis. In the current study, we determined the relevant players and role of N6-methyladenine (m6A) RNA methylation in cervical cancer progression.

Methods
The roles of m6A RNA methylation and centromere protein K (CENPK) in cervical cancer were analyzed using bioinformatics analysis. Methylated RNA immunoprecipitation was adopted to detect m6A modification of CENPK mRNA. Human cervical cancer clinical samples, cell lines, and xenografts were used for analyzing gene expression and function. Immunofluorescence staining and the tumorsphere formation, clonogenic, MTT, and EdU assays were performed to determine cell stemness, chemoresistance, migration, invasion, and proliferation in HeLa and SiHa cells, respectively. Western blot analysis, co-immunoprecipitation, chromatin immunoprecipitation, and luciferase reporter, cycloheximide chase, and cell fractionation assays were performed to elucidate the underlying mechanism.

Results
Bioinformatics analysis of public cancer datasets revealed firm links between m6A modification patterns and cervical cancer prognosis, especially through ZC3H13-mediated m6A modification of CENPK mRNA. CENPK expression was elevated in cervical cancer, associated with cancer recurrence, and independently predicts poor patient prognosis [hazard ratio = 1.413, 95% confidence interval = 1.078 − 1.853, P = 0.012]. Silencing of CENPK prolonged the overall survival time of cervical cancer-bearing mice and improved the response of cervical cancer tumors to chemotherapy in vivo (P < 0.001). We also showed that CENPK was directly bound to SOX6 and disrupted the interactions of CENPK with β-catenin, which promoted β-catenin expression and nuclear translocation, facilitated p53 ubiquitination, and led to activation of Wnt/β-catenin signaling, but suppression of the p53 pathway. This dysregulation ultimately enhanced the tumorigenic pathways required for cell stemness, DNA damage repair pathways necessary for cisplatin/carboplatin resistance, epithelial-mesenchymal transition involved in metastasis, and DNA replication that drove tumor cell proliferation.

Conclusions
CENPK was shown to have an oncogenic role in cervical cancer and can thus serve as a prognostic indicator and novel target for cervical cancer treatment.
Association of FTO gene variant rs9939609 with hyperandrogenemia and fasting glucose levels in South Indian women with polycystic ovarian syndrome
Authors: Naghshband Zeinab , Malini Suttur S. 
Published: April 2022

Abstract
Background
Polycystic ovary syndrome (PCOS) is a common endocrine–metabolic disorder due to genetic and environmental factors. Genetic variants located in intron 1 of Fat mass and obesity-associated (FTO) gene are associated with increased risk of obesity and metabolic disorders. This study aims to investigate the association of common FTO polymorphism rs9939609 in South Indian women with PCOS to assess its association with metabolic and endocrine parameters. FTO genotyping was done on 100 PCOS patients and 70 controls by Sanger sequencing.

Results
The distribution of rs9939609 was observed between groups (28% TT, 57% TA, and 15% AA for PCOS and 37.1% TT, 51.4% TA, and 11.4% AA for the controls). In the PCOS group, across the carriers of different genotypes, a significant association was found between body mass index (BMI), fasting glucose levels, and testosterone with the presence of at least one risk allele of FTO rs9939609. Logistic regression analysis showed the association of fasting glucose levels and testosterone (OR 1.30 [1.03–1.63] and OR 5.83 [1.61–21.11], respectively) with FTO rs9939609.

Conclusions
Our findings indicated that FTO SNP rs9939609 was not associated with PCOS, but suggested a significant association of rs9939609 with hyperandrogenemia, fasting glucose levels, and BMI in South Indian women with PCOS.
Comparison of the antibacterial properties of phycocyanin and its SNPs and their effects on rat blood cells and liver enzymes
Authors: Izadi Mahdieh , Latifi Elaheh 
Published: April 2022

Abstract
Background
Phycocyanin is an important protein in cyanobacteria that has many medical and therapeutic properties. The aim of the present study was to compare the antibacterial properties of phycocyanin and its SNPs and to evaluate their effects on rat blood cells and liver enzymes.

Results
The UV absorption in phycocyanin was 620 nm but in phycocyanin nanoparticles was 420 nm. For fluorometry, the maximum emission peak of phycocyanin was 660 nm and that of phycocyanin-AgNO3 nanoparticles was 580 nm. PC-AgNp showed greater antibacterial effects than phycocyanin. In animal studies, it was found that the platelet count in both groups was higher than the control group. Red blood cells and white blood cells had changes. AST and ALT levels increased in both phycocyanin and nanoparticle groups and ALK levels decreased in both groups compared to the control group.

Conclusions
Examination of antibacterial activity showed that PC-AgNp showed more antibacterial effects than PC. Also, in the study of the effect of PC and NP-PC, accumulation of PC and C-Np in mice also altered blood cells and liver enzymes in rats.
Isolated bone marrow sarcoidosis presenting as fever of unknown origin in a case of chronic myeloid leukemia
Authors: Grover Ashok , Puri Saurabh , Chabra Smriti , Mehta Meenal , Mishra Pravas Chand 
Published: April 2022

Abstract
Background
Isolated involvement of bone marrow in sarcoidosis has not been reported commonly. Sarcoidosis is a systemic granulomatous disease of unknown origin, characterized by the presence of non-caseating granulomatous lesions. There should be high index of suspicion in patients having underlying lymphoproliferative malignancies.

Case presentation
We present a 27-year-old male, known case of chronic myeloid leukemia, presenting as fever of unknown origin diagnosed with isolated bone marrow sarcoidosis.
Validity and cardio-metabolic risk profiles of DNA methylation clocks among adults in south-central Côte d’Ivoire
Authors: Sanchez Dafne , Jeong Ayoung , Essé Clemence , Bassa Fidèle K. , Koné Siaka , Acka Félix , Laubhouet-Koffi Véronique , Kouassi Dinard , Utzinger Jürg , N’Goran Eliézer K. , Bonfoh Bassirou , Imboden Medea , Holloway John W. , Eze Ikenna C. 
Published: April 2022

Abstract
Background
Aging populations in Africa face a growing burden of non-communicable diseases (NCDs), contextualized in broad external exposome and weak health systems. These could accelerate aging and shorten lifespan. DNA methylation (DNAm) epigenetic clocks allow investigation of biological aging, and perform well in high-income countries. However, their validity has rarely been tested in low- and middle-income countries. We investigated the performance of epigenetic clocks (as aging biomarkers), and their cardio-metabolic risk profiles among adults in south-central Côte d’Ivoire.

Results
We derived four measures of epigenetic clocks (i.e., HorvathAge, HannumAge, PhenoAge and GrimAge) and their corresponding epigenetic age acceleration (EAA; Intrinsic, Extrinsic, PhenoAA and GrimAA) using genome-wide DNAm data from 393 participants of the Côte d’Ivoire dual burden of disease study, aged 18–79 years. Epigenetic age exhibited strong correlations (0.83 ≤ Pearson’s r ≤ 0.93) but weaker concordance (0.73 ≤ Lin’s rC ≤ 0.85) with chronological age. Epigenetic clocks optimally predicted chronological age at 32 (HannumAge), 62 (HorvathAge) and 78 (GrimAge) years. Multivariable linear EAA models identified male sex (IEAA, EEAA and GrimAA), lower household wealth (EEAA and PhenoAA), high-risk alcohol intake (PhenoAA and GrimAA), smoking (GrimAA), physical activity (IEAA and GrimAA) and body mass index [BMI] (GrimAA) as independent determinants. Physical activity and BMI exhibited quadratic associations with GrimAA. Illustratively, GrimAge was accelerated in underweight and obese participants. Risk associations of GrimAA were largely driven by age-adjusted DNAm surrogate plasminogen activator inhibitor-1 (DNAmPAI-1) and pack years. Multivariable logistic models of cardio-metabolic phenotypes identified EEAA, PhenoAA and DNAmPAI-1 as determinants of high blood pressure, fasting glucose, triglycerides and metabolic syndrome severity.

Conclusions
We provide evidence validating the applicability of epigenetic clocks as aging biomarkers and potential link between sociodemographic and lifestyle-related factors, and cardio-metabolic health in the underrepresented African population. Future longitudinal studies incorporating broad environmental aspects and age-related clinical outcomes should allow to pinpoint the clinical and public health utility of DNAm clocks as mediators in NCD trajectory, in low- and middle-income countries.
Planar cell polarity-dependent asymmetric organization of microtubules for polarized positioning of the basal body in node cells
Authors: Sai Xiaorei , Ikawa Yayoi , Nishimura Hiromi , Mizuno Katsutoshi , Kajikawa Eriko , Katoh Takanobu A. , Kimura Toshiya , Shiratori Hidetaka , Takaoka Katsuyoshi , Hamada Hiroshi , Minegishi Katsura 
Published: April 2022

ABSTRACT
For left-right symmetry breaking in the mouse embryo, the basal body must become positioned at the posterior side of node cells, but the precise mechanism for this has remained unknown. Here, we examined the role of microtubules (MTs) and actomyosin in this basal body positioning. Exposure of mouse embryos to agents that stabilize or destabilize MTs or F-actin impaired such positioning. Active myosin II was detected at the anterior side of node cells before the posterior shift of the basal body, and this asymmetric activation was lost in Prickle and dachsous mutant embryos. The organization of basal-body associated MTs (baMTs) was asymmetric between the anterior and posterior sides of node cells, with anterior baMTs extending horizontally and posterior baMTs extending vertically. This asymmetry became evident after polarization of the PCP core protein Vangl1 and before the posterior positioning of the basal body, and it also required the PCP core proteins Prickle and dachsous. Our results suggest that the asymmetry in baMT organization may play a role in correct positioning of the basal body for left-right symmetry breaking.
Suppression of microRNA 124-3p and microRNA 340-5p ameliorates retinoic acid-induced cleft palate in mice
Authors: Yoshioka Hiroki , Suzuki Akiko , Iwaya Chihiro , Iwata Junichi 
Published: April 2022

ABSTRACT
The etiology of cleft lip with or without cleft palate (CL/P), a common congenital birth defect, is complex, with genetic and epigenetic, as well as environmental, contributing factors. Recent studies suggest that fetal development is affected by maternal conditions through microRNAs (miRNAs), a group of short noncoding RNAs. Here, we show that miR-129-5p and miR-340-5p suppress cell proliferation in both primary mouse embryonic palatal mesenchymal cells and O9-1 cells, a neural crest cell line, through the regulation of Sox5 and Trp53 by miR-129-5p, and the regulation of Chd7, Fign and Tgfbr1 by miR-340-5p. Notably, miR-340-5p, but not miR-129-5p, was upregulated following all-trans retinoic acid (atRA; tretinoin) administration, and a miR-340-5p inhibitor rescued the cleft palate (CP) phenotype in 47% of atRA-induced CP mice. We have previously reported that a miR-124-3p inhibitor can also partially rescue the CP phenotype in atRA-induced CP mouse model. In this study, we found that a cocktail of miR-124-3p and miR-340-5p inhibitors rescued atRA-induced CP with almost complete penetrance. Taken together, our results suggest that normalization of pathological miRNA expression can be a preventive intervention for CP.