bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing the performance of methods for cell clustering from single-cell DNA sequencing data
Authors: Khan Rituparna , Mallory Xian 
Published: October 2023

BackgroundMany cancer genomes have been known to contain more than one subclone inside one tumor, the phenomenon of which is called intra-tumor heterogeneity (ITH). Characterizing ITH is essential in designing treatment plans, prognosis as well as the study of cancer progression. Single-cell DNA sequencing (scDNAseq) has been proven effective in deciphering ITH. Cells corresponding to each subclone are supposed to carry a unique set of mutations such as single nucleotide variations (SNV). While there have been many studies on the cancer evolutionary tree reconstruction, not many have been proposed that simply characterize the subclonality without tree reconstruction. While tree reconstruction is important in the study of cancer evolutionary history, typically they are computationally expensive in terms of running time and memory consumption due to the huge search space of the tree structure. On the other hand, subclonality characterization of single cells can be converted into a cell clustering problem, the dimension of which is much smaller, and the turnaround time is much shorter. Despite the existence of a few state-of-the-art cell clustering computational tools for scDNAseq, there lacks a comprehensive and objective comparison under different settings.ResultsIn this paper, we evaluated six state-of-the-art cell clustering tools–SCG, BnpC, SCClone, RobustClone, SCITE and SBMClone–on simulated data sets given a variety of parameter settings and a real data set. We designed a simulator specifically for cell clustering, and compared these methods’ performances in terms of their clustering accuracy, specificity and sensitivity and running time. For SBMClone, we specifically designed an ultra-low coverage large data set to evaluate its performance in the face of an extremely high missing rate.ConclusionFrom the benchmark study, we conclude that BnpC and SCG’s clustering accuracy are the highest and comparable to each other. However, BnpC is more advantageous in terms of running time when cell number is high (> 1500). It also has a higher clustering accuracy than SCG when cluster number is high (> 16). SCClone’s accuracy in estimating the number of clusters is the highest. RobustClone and SCITE’s clustering accuracy are the lowest for all experiments. SCITE tends to over-estimate the cluster number and has a low specificity, whereas RobustClone tends to under-estimate the cluster number and has a much lower sensitivity than other methods. SBMClone produced reasonably good clustering (V-measure > 0.9) when coverage is > = 0.03 and thus is highly recommended for ultra-low coverage large scDNAseq data sets.
Clinical performance validation of the STANDARD G6PD test: A multi-country pooled analysis
Authors: Adissu Wondimagegn , Brito Marcelo , Garbin Eduardo , Macedo Marcela , Monteiro Wuelton , Mukherjee Sandip Kumar , Myburg Jane , Alam Mohammad Shafiul , Bancone Germana , Bansil Pooja , Pal Sampa , Sharma Abhijit , Zobrist Stephanie , Bryan Andrew , Chu Cindy S. , Das Santasabuj , Domingo Gonzalo J. , Hann Amanda , Kublin James , Lacerda Marcus V. G. , Layton Mark , Ley Benedikt , Murphy Sean C. , Nosten Francois , Pereira Dhélio , Price Ric N. , Talukdar Arunansu , Yilma Daniel , Gerth-Guyette Emily 
Published: October 2023

Introduction
Screening for G6PD deficiency can inform disease management including malaria. Treatment with the antimalarial drugs primaquine and tafenoquine can be guided by point-of-care testing for G6PD deficiency.

Methods and findings
Data from similar clinical studies evaluating the performance of the STANDARD G6PD Test (SD Biosensor, South Korea) conducted in Bangladesh, Brazil, Ethiopia, India, Thailand, the United Kingdom, and the United States were pooled. Test performance was assessed in a retrospective analysis on capillary and venous specimens. All study sites used spectrophotometry for reference G6PD testing, and either the HemoCue or complete blood count for reference hemoglobin measurement. The sensitivity of the STANDARD G6PD Test using the manufacturer thresholds for G6PD deficient and intermediate cases in capillary specimens from 4212 study participants was 100% (95% Confidence Interval (CI): 97.5%–100%) for G6PD deficient cases with <30% activity and 77% (95% CI 66.8%–85.4%) for females with intermediate activity between 30%–70%. Specificity was 98.1% (95% CI 97.6%–98.5%) and 92.8% (95% CI 91.6%–93.9%) for G6PD deficient individuals and intermediate females, respectively. Out of 20 G6PD intermediate females with false normal results, 12 had activity levels >60% on the reference assay. The negative predictive value for females with G6PD activity >60% was 99.6% (95% CI 99.1%–99.8%) on capillary specimens. Sensitivity among 396 P. vivax malaria cases was 100% (69.2%–100.0%) for both deficient and intermediate cases. Across the full dataset, 37% of those classified as G6PD deficient or intermediate resulted from true normal cases. Despite this, over 95% of cases would receive correct treatment with primaquine, over 87% of cases would receive correct treatment with tafenoquine, and no true G6PD deficient cases would be treated inappropriately based on the result of the STANDARD G6PD Test.

Conclusions
The STANDARD G6PD Test enables safe access to drugs which are contraindicated for individuals with G6PD deficiency. Operational considerations will inform test uptake in specific settings.
Outcome measures for assessing the effectiveness of physiotherapy interventions on equinus foot deformity in post-stroke patients with triceps surae spasticity: A scoping review
Authors: Campanini Isabella , Bò Maria Chiara , Bassi Maria Chiara , Damiano Benedetta , Scaltriti Sara , Lusuardi Mirco , Merlo Andrea 
Published: October 2023

Objective
Equinus foot deformity (EFD) is the most common deviation after stroke. Several physiotherapy interventions have been suggested to treat it. However, studies evaluating the efficacy of these treatments vary widely in terms of assessment modalities, type of data analysis, and nomenclature. This scoping review aimed to map current available evidence on outcome measures and the modalities employed to assess the effectiveness of physiotherapy programs for the reduction of triceps surae (TS) spasticity and EFD in patients with stroke.

Methods
Scoping review methodological frameworks have been used. Three databases were investigated. Primary literature addressing TS spasticity in adult patients with stroke using physiotherapy interventions was included. Findings were systematically summarized in tables according to the intervention used, intervention dosage, control group, clinical, and instrumental outcome measures.

Results
Of the 642 retrieved studies, 53 papers were included. TS spasticity was assessed by manual maneuvers performed by clinicians (mainly using the Ashworth Scale), functional tests, mechanical evaluation through robotic devices, or instrumental analysis and imaging (such as the torque-angle ratio, the H-reflex, and ultrasound images). A thorough critical appraisal of the construct validity of the scales and of the statistics employed was provided, particularly focusing on the choice of parametric and non-parametric approaches when using ordinal scales. Finally, the complexity surrounding the concept of “spasticity” and the possibility of assessing the several underlying active and passive causes of EFD, with a consequent bespoke treatment for each of them, was discussed.

Conclusion
This scoping review provides a comprehensive description of all outcome measures and assessment modalities used in literature to assess the effectiveness of physiotherapy treatments, when used for the reduction of TS spasticity and EFD in patients with stroke. Clinicians and researchers can find an easy-to-consult summary that can support both their clinical and research activities.
Prevalence of depression among students at Ethiopian universities and associated factors: A systematic review and meta-analysis
Authors: Anbesaw Tamrat , Zenebe Yosef , Necho Mogessie , Gebresellassie Moges , Segon Tesfaye , Kebede Fasikaw , Bete Tilahun 
Published: October 2023

Background
Depression is the most common cause of disability in the world, which affects 350 million people. University students struggle to cope with stressors that are typical of higher education institutions as well as anxiety related to education. Although evidence indicates that they have a high prevalence of depression, no reviews have been done to determine the prevalence of depression among students at Ethiopian universities comprehensively.

Methods
Without regard to time constraints, PubMed, Scopus, and EMBASE were investigated. A manual search for an article reference list was also conducted. The Meta XL software was used to extract relevant data, and the Stata-11 meta-prop package was used to analyze it. The Higgs I2 test was used to test for heterogeneity.

Results
A search of the electronic and manual systems resulted in 940 articles. Data were extracted from ten studies included in this review involving a total number of 5207 university students. The pooled prevalence of depression was 28.13% (95% CI: 22.67, 33.59). In the sub-group analysis, the average prevalence was higher in studies having a lower sample size (28.42%) than studies with a higher sample; 27.70%, and studies that utilized other (PHQ-9, HADS); 30.67% higher than studies that used BDI-II; 26.07%. Being female (pooled AOR = 5.56) (95% CI: 1.51, 9.61), being a first-year (pooled AOR = 4.78) (95% CI: 2.21, 7.36), chewing khat (pooled AOR = 2.83) (95% CI: 2.32, 3.33), alcohol use (pooled AOR = 3.12 (95% CI:3.12, 4.01) and family history of mental illness (pooled AOR = 2.57 (95% CI:2.00, 3.15) were factors significantly associated with depression.

Conclusion
This systematic review and meta-analysis revealed that more than one-fourth of students at Ethiopian universities had depression. More efforts need to be done to provide better mental healthcare to university students in Ethiopia.
The prevalence of infertility and factors associated with infertility in Ethiopia: Analysis of Ethiopian Demographic and Health Survey (EDHS)
Authors: Legese Nanati , Tura Abera Kenay , Roba Kedir Teji , Demeke Henok 
Published: October 2023

Background
Despite having a high fertility rate, low-resource countries are also home to couples with infertility problems. Although many couples are suffering from the psychological impacts of infertility, its level and determinants are not adequately known. The main objective of this study is to assess the prevalence and factors associated with infertility among couples in Ethiopia using the 2016 Ethiopian Demographic and Health Survey (EDHS) data.

Method
The study employed a cross-sectional study design extracting variables from the 2016 EDHS. The study included all married or cohabitating women aged 15 to 49 years in the Couples Recode (CR) file data set. Weighted samples of 6141 respondents were analyzed. We used Stata 14 software for analyzing the data. The association of selected independent variables with primary, secondary, and total infertility was analyzed using a logistic regression model. We presented the results using an adjusted odds ratio (AOR) with a 95% confidence interval (CI) and a p-value <0.05 as a cut-off point for declaring statistical significance.

Results
The prevalence of infertility in the past 12 months was 24.2% (95% CI: 23.1–25.3%), of which the majority (90.7%) was secondary infertility. Greater than 35 years of age (AOR = 2.45, 95% CI (1.58–3.79)), rural residence (AOR = 1.06, 95% CI (1.01–1.39)), smoking (AOR = 2.29, 95% CI (1.39–3.77)), and <18.5 Body Mass Index (BMI) (AOR = 1.71, 95% CI (1.43–2.04)) were significantly associated with infertility. Conversely, infertility was less likely among women with formal education and better wealth index. Primary infertility was significantly higher among women whose partners drink alcohol (AOR = 1.55; 95% CI 1.06–2.28)) and chew khat (AOR = 1.62; 95% CI (1.12–2.36)). Secondary infertility was significantly higher among women with <18.5 BMI (AOR = 1.59, 95% CI (1.37–1.84)), >30 BMI (AOR = 1.54; 95% CI 1.01–2.35)), and <15 years of age at first birth (AOR = 1.40; 95% CI 1.15–1.69)).

Conclusion
More than one in five couples in Ethiopia has an infertility problem. Both male and female-related factors are associated with infertility. Primary infertility was significantly higher among women whose partner chews khat and drinks alcohol. Secondary infertility was significantly associated with being underweight, obese, smoking, and young age at first birth. Hence, taking action on preventable factors is the most critical treatment approach and will improve the health status of the couples in other ways.
On the utilization of the induced pluripotent stem cell (iPSC) model to study substance use disorders: A scoping review protocol
Authors: Niemis Wasiri , Peterson Shenita R. , Javier Chrisabella , Nguyen Amy , Subiah Sanchi , Palmer Rohan H. C. 
Published: October 2023

Introduction
Induced pluripotent stem cells (iPSCs) are cells derived from somatic cells via reprogramming techniques. The iPSC approach has been increasingly used in neuropsychiatric research in the last decade. Though substance use disorders (SUDs) are a commonly occurring psychiatric disorder, the application of iPSC model in addiction research has been limited. No comprehensive review has been reported. We conducted a scoping review to collate existing evidence on the iPSC technologies applied to SUD research. We aim to identify current knowledge gaps and limitations in order to advance the use of iPSCs in the SUD field.

Methods and analysis
We employed a scoping review using the methodological framework first created by Arksey and O’Malley and further updated by Levac et al. and the Joanna Briggs Institute (JBI). We adopted the Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Protocols (PRISMA-P) to report items for the protocol. We searched evidence from four electronic databases: PubMed®, Embase®, Web of Science™, and Scopus®. Primary research, systematic reviews, and meta-analyses were included and limited to studies published in English, at the time from 2007 to March 2022. This is an “ongoing” scoping review. Searched studies will be independently screened, selected, and extracted by two reviewers. Disagreement will be solved by the third reviewer and discussion. Extracted data will be analyzed in descriptive and quantitative approaches, then summarized and presented in appropriate formats. Results will be reported following the Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR) guideline and disseminated through a peer-reviewed publication and conference presentations.

Conclusion
To our best knowledge, this is the first comprehensive scoping review of iPSC methods specifically applied to a broad range of addictive drugs/substances that lead to SUDs or misuse behavior.

Registration
This protocol is registered on Zenodo repository (https://zenodo.org/) with doi:10.5281/zenodo.7915252.
Public health risk communication through the lens of a quarantined community: Insights from a coronavirus hotspot in Germany
Authors: Licht Annika , Wetzker Wibke , Scholz Juliane , Scherag André , Weis Sebastian , Pletz Mathias W. , Bauer Michael , Dickmann Petra ,   the CoNAN study group
Published: October 2023

Background
Quarantine is one of the most effective interventions to contain an infectious disease outbreak, yet it is one of the most disruptive. We investigated the quarantine of an entire village to better understand risk communication requirements for groups.

Methods
We conducted a cross-sectional, mixed-methods survey study on a single cohort of adult residents in Neustadt am Rennsteig, Germany, six weeks after the removal of a 14-day mandatory community quarantine. The survey response rate was 33% (289/883 residents).

Findings
Survey participants reported a lack of information on the quarantine implementation process. What authorities communicated was not necessarily what residents desired to know. While inhabitants used social media and telephones to communicate with each other, the official information sources were regional radio, television, newspapers and official websites. Public health authorities did not employ social media communication to engage with their communities. Despite a lack of information, the majority of respondents stated that they had complied with the quarantine and they expressed little sympathy for those who violated the quarantine. After lifting the quarantine, many respondents continued to avoid places where they suspected a significant risk of infection, such as family and friends’ homes, doctor’s offices and grocery stores.

Interpretation
The survey participants utilised existing social networks to disseminate vital information and stabilise its group identity and behaviour (quarantine compliance). The authorities communicated sparsely in a unidirectional, top-down manner, without engaging the community. Despite the lack of official information, the social coherency of the group contributed to considerate and compliant conduct, but participants expressed dissatisfaction with official leadership and asked for more attention.

Conclusion
Public health risk communication must engage with communities more effectively. This necessitates a deeper comprehension of groups, their modes of communication and their social needs.
Understanding the influence of ethnicity on adherence to antidiabetic medication: Meta-ethnography and systematic review
Authors: Asiri Rayah , Robinson-Barella Anna , Iqbal Anum , Todd Adam , Husband Andy 
Published: October 2023

Introduction
A high prevalence of diabetes and diabetes-related complications in people from minority ethnic communities in high income countries is of significant concern. Several studies have indicated low adherence rates to antidiabetic medication in ethnic minority groups. Poor adherence to antidiabetic medication leads to a higher risk of complications and potential mortality. This review aims to qualitatively explore the barriers to and facilitators of adherence to antidiabetic medication among ethnic minority groups in high-income countries.

Methods
A comprehensive search of MEDLINE, Embase, CINAHL, PsycINFO, and Global Health databases for qualitative studies exploring the barriers to or facilitators of adherence to antidiabetic medication in minority ethnic groups was conducted from database inception to March 2023 (PROSPERO CRD42022320681). A quality assessment of the included studies was conducted using the Critical Appraisal Skills Programme (CASP) tool. Key concepts and themes from relevant studies were synthesised using a meta-ethnographic approach. The Grading of Recommendations Assessment, Development and Evaluation Confidence in the Evidence from Reviews of Qualitative research (GRADE-CERQual) approach was used to assess the Confidence in the review findings.

Result
Of 13,994 citations screened, 21 studies that included primary qualitative studies were selected, each of which involved people from minority ethnic communities from eight high income countries. This qualitative evidence synthesis has identified three overarching themes around the barriers to and facilitators of adherence to antidiabetic medication among ethnic minority groups.: 1) cultural underpinnings, 2) communication and building relationships, and 3) managing diabetes during visiting home countries. Based on the GRADE-CERQual assessment, we had mainly moderate- and high-confidence findings.

Conclusion
Multiple barriers and facilitators of adherence to antidiabetic medication among people from minority ethnic communities in high-income countries have been identified. A medication adherence intervention focusing on identified barriers to adherence to antidiabetic medication in these communities may help in improving diabetes outcomes in these groups.
Knowledge of prevention of mother-to-child transmission of HIV among reproductive age women in high HIV/AIDS prevalent countries: A multilevel analysis of recent Demographic and Health Surveys
Authors: Eshetu Habitu Birhan , Kebede Natnael , Bogale Eyob Ketema , Zewdie Amare , kassie Tadele Derbew , Anagaw Tadele Fentabil , Mazengia Elyas Melaku , Gelaw Sintayehu Shiferaw , Fenta Eneyew Talie 
Published: October 2023

Background
A lack of enough knowledge about the mother-to-child transmission (MTCT) of the human immunodeficiency virus (HIV) among reproductive-age women is thought to be a key contributor to new pediatric HIV infections worldwide, and rising HIV-related infant mortality, particularly in resource-limited countries. Knowledge of MTCT of HIV is key to halt the progression of HIV/AIDS. Therefore, this study aimed to assess knowledge of MTCT of HIV and its associated factors among reproductive-age women in high HIV/AIDS prevalent countries.

Methods
A secondary data analysis was performed using 8 HIV/AIDS prevalent countries’ Demographic and Health Surveys. A total weighted sample of 97,130 respondents was included in this study. Stata 17 was used for data extraction, coding, and analysis. A multilevel binary logistic regression model was fitted. The odds ratios along with the 95% confidence interval were generated to determine the factors of good knowledge of MTCT of HIV among reproductive-age women. A 95% confidence interval and a p-value of less than 0.05 were used to declare statistical significance.

Results
The prevalence of good knowledge of MTCT HIV was 57.89% (95% CI: 57.67,58.29). Mothers aged 25–34 (AOR  =  1.37, 95% CI = 1.32, 1.42), 35 and above(AOR  =  2.46,95% CI = 1.41, 1.52), mothers’ primary education (AOR  = 1.32, 95% CI = 1.26, 1.38),), secondary education (AOR  = 1.65,95% CI = 1.56, 1.74), higher education (AOR  = 1.72,95% CI = 1.58,1.86), exposed to mass media (AOR  = 1.12, 95% CI = 1.08,1.16) rich wealth status (AOR  = 1.11 (95% CI = 1.06,1.15), talked about MTCT (AOR  = 1.70,95% CI = 1.64, 1.76), visited by field worker (AOR  = 1.09, 95% CI = 1.03,1.14), health facility visit (AOR  = 1.15, 95% CI = 1.11, 1.18), urban dwellers (AOR = 1.09, 95% CI = 1.04,1.14), ever tested for HIV(AOR = 2.18 (95% CI = 2.10,2.27), currently working status (AOR = 1.15, 95% CI = 1.12,1.19) were factors associated with good knowledge of MTCT of HIV/AIDS among reproductive age women.

Conclusions
Overall, the prevalence of good knowledge of MTCT was low in high HIV/AIDS prevalent countries. Maternal age, primary education and above, exposed to media, having higher wealth status, talked about MTCT during ANC visits, being visited by a field worker, visited a health facility, currently working, living in the urban area, and ever been tested for HIV were positively associated with knowledge of MTCT. Health policy and programs should focus on educating mothers, encouraging women to contact health facilities and a well-targeted communications program is required to enhance knowledge of MTCT of HIV.
Aktualność Oświecenia według Stevena Pinkera (ze szczególnym uwzględnieniem idei postępu)
Authors: Kopciuch Leszek 
Published: October 2023

In this article, I begin by sketching Steven Pinker’s understanding of main ideas of the Enlightenment, and then discuss in detail his understanding of the idea of progress. In the reconstruction section, I mainly refer to Pinker’s 2018 work Enlightenment Now: the Case for Science, Reason, Humanism, and Progress. Then I consider the issue of the relationship between Pinker’s concept of progress and the strictly philosophical understanding of this idea, clarified both in the texts of its defenders and critics.