bluuebunny/crossref_metadata_2025_split huggingface dataset:
MGcount: a total RNA-seq quantification tool to address multi-mapping and multi-overlapping alignments ambiguity in non-coding transcripts
Authors: Hita Andrea , Brocart Gilles , Fernandez Ana , Rehmsmeier Marc , Alemany Anna , Schvartzman Sol 
Published: January 2022

Abstract
Background
Total-RNA sequencing (total-RNA-seq) allows the simultaneous study of both the coding and the non-coding transcriptome. Yet, computational pipelines have traditionally focused on particular biotypes, making assumptions that are not fullfilled by total-RNA-seq datasets. Transcripts from distinct RNA biotypes vary in length, biogenesis, and function, can overlap in a genomic region, and may be present in the genome with a high copy number. Consequently, reads from total-RNA-seq libraries may cause ambiguous genomic alignments, demanding for flexible quantification approaches.

Results
Here we present Multi-Graph count (MGcount), a total-RNA-seq quantification tool combining two strategies for handling ambiguous alignments. First, MGcount assigns reads hierarchically to small-RNA and long-RNA features to account for length disparity when transcripts overlap in the same genomic position. Next, MGcount aggregates RNA products with similar sequences where reads systematically multi-map using a graph-based approach. MGcount outputs a transcriptomic count matrix compatible with RNA-sequencing downstream analysis pipelines, with both bulk and single-cell resolution, and the graphs that model repeated transcript structures for different biotypes. The software can be used as a python module or as a single-file executable program.

Conclusions
MGcount is a flexible total-RNA-seq quantification tool that successfully integrates reads that align to multiple genomic locations or that overlap with multiple gene features. Its approach is suitable for the simultaneous estimation of protein-coding, long non-coding and small non-coding transcript concentration, in both precursor and processed forms. Both source code and compiled software are available at https://github.com/hitaandrea/MGcount.
LuxRep: a technical replicate-aware method for bisulfite sequencing data analysis
Authors: Malonzo Maia H. , Halla-aho Viivi , Konki Mikko , Lund Riikka J. , Lähdesmäki Harri 
Published: January 2022

Abstract
Background
DNA methylation is commonly measured using bisulfite sequencing (BS-seq). The quality of a BS-seq library is measured by its bisulfite conversion efficiency. Libraries with low conversion rates are typically excluded from analysis resulting in reduced coverage and increased costs.

Results
We have developed a probabilistic method and software, LuxRep, that implements a general linear model and simultaneously accounts for technical replicates (libraries from the same biological sample) from different bisulfite-converted DNA libraries. Using simulations and actual DNA methylation data, we show that including technical replicates with low bisulfite conversion rates generates more accurate estimates of methylation levels and differentially methylated sites. Moreover, using variational inference speeds up computation time necessary for whole genome analysis.

Conclusions
In this work we show that taking into account technical replicates (i.e. libraries) of BS-seq data of varying bisulfite conversion rates, with their corresponding experimental parameters, improves methylation level estimation and differential methylation detection.
COVID-19 impact on mental health
Authors: Cui Jingyu , Lu Jingwei , Weng Yijia , Yi Grace Y. , He Wenqing 
Published: January 2022

AbstractBackgroundThe coronavirus disease 2019 (COVID-19) pandemic has posed a significant influence on public mental health. Current efforts focus on alleviating the impacts of the disease on public health and the economy, with the psychological effects due to COVID-19 relatively ignored. In this research, we are interested in exploring thequantitativecharacterization of the pandemic impact on public mental health by studying an online survey dataset of the United States.MethodsThe analyses are conducted based on a large scale of online mental health-related survey study in the United States, conducted over 12 consecutive weeks from April 23, 2020 to July 21, 2020. We are interested in examining the risk factors that have a significant impact on mental health as well as in their estimated effects over time. We employ the multiple imputation by chained equations (MICE) method to deal with missing values and take logistic regression with the least absolute shrinkage and selection operator (Lasso) method to identify risk factors for mental health.ResultsOur analysis shows that risk predictors for an individual to experience mental health issues include the pandemic situation of the State where the individual resides, age, gender, race, marital status, health conditions, the number of household members, employment status, the level of confidence of the future food affordability, availability of health insurance, mortgage status, and the information of kids enrolling in school. The effects of most of the predictors seem to change over time though the degree varies for different risk factors. The effects of risk factors, such as States and gender show noticeable change over time, whereas the factor age exhibits seemingly unchanged effects over time.ConclusionsThe analysis results unveil evidence-based findings to identify the groups who are psychologically vulnerable to the COVID-19 pandemic. This study provides helpful evidence for assisting healthcare providers and policymakers to take steps for mitigating the pandemic effects on public mental health, especially in boosting public health care, improving public confidence in future food conditions, and creating more job opportunities.Trial registrationThis article does not report the results of a health care intervention on human participants.
Prediction of acute appendicitis among patients with undifferentiated abdominal pain at emergency department
Authors: Su Dai , Li Qinmengge , Zhang Tao , Veliz Philip , Chen Yingchun , He Kevin , Mahajan Prashant , Zhang Xingyu 
Published: January 2022

AbstractBackgroundEarly screening and accurately identifying Acute Appendicitis (AA) among patients with undifferentiated symptoms associated with appendicitis during their emergency visit will improve patient safety and health care quality. The aim of the study was to compare models that predict AA among patients with undifferentiated symptoms at emergency visits using both structured data and free-text data from a national survey.MethodsWe performed a secondary data analysis on the 2005-2017 United States National Hospital Ambulatory Medical Care Survey (NHAMCS) data to estimate the association between emergency department (ED) patients with the diagnosis of AA, and the demographic and clinical factors present at ED visits during a patient’s ED stay. We used binary logistic regression (LR) and random forest (RF) models incorporating natural language processing (NLP) to predict AA diagnosis among patients with undifferentiated symptoms.ResultsAmong the 40,441 ED patients with assigned International Classification of Diseases (ICD) codes of AA and appendicitis-related symptoms between 2005 and 2017, 655 adults (2.3%) and 256 children (2.2%) had AA. For the LR model identifying AA diagnosis among adult ED patients, the c-statistic was 0.72 (95% CI: 0.69–0.75) for structured variables only, 0.72 (95% CI: 0.69–0.75) for unstructured variables only, and 0.78 (95% CI: 0.76–0.80) when including both structured and unstructured variables. For the LR model identifying AA diagnosis among pediatric ED patients, the c-statistic was 0.84 (95% CI: 0.79–0.89) for including structured variables only, 0.78 (95% CI: 0.72–0.84) for unstructured variables, and 0.87 (95% CI: 0.83–0.91) when including both structured and unstructured variables. The RF method showed similar c-statistic to the corresponding LR model.ConclusionsWe developed predictive models that can predict the AA diagnosis for adult and pediatric ED patients, and the predictive accuracy was improved with the inclusion of NLP elements and approaches.
Sample attrition analysis in a prospective cohort study of medical graduates in China
Authors: Li Mingyue , Wang Ziyue , Zhang Baisong , Wei Tiantian , Hu Dan , Liu Xiaoyun 
Published: January 2022

Abstract
Background
A major challenge of prospective cohort studies is attrition in follow-up surveys. This study investigated attrition in a prospective cohort comprised of medical graduates in China. We described status of attrition, identified participants with higher possibility of attrition, and examined if attrition affect the estimation of the key outcome measures.

Methods
The cohort study recruited 3,620 new medical graduates from four medical universities in central and western China between 2015 and 2019. Online follow-up surveys were conducted on an annual basis. Follow-up status was defined as complete (meaning that the participant completed all the follow-up surveys) and incomplete, while incomplete follow-up was further divided into ‘always-out’, ‘rejoin’ and ‘other’. Multivariable logistic and linear regressions were used to examine factors predicting attrition and the influence on the outcome measures of career development.

Results
2364 (65.3%) participants completed all follow-up surveys. For those with incomplete follow-up, 520 (14.4%) were ‘always-out’, 276 (7.6%) rejoined in the 2020 survey. Willingness to participate in residency training (OR=0.80, 95%CI[0.66 - 0.98]) and willingness to provide sensitive information in the baseline survey predicted a lower rate of attrition (providing scores for university entrance exam OR=0.82, 95%CI[0.69 - 0.97]]; providing contact information (OR=0.46, 95%CI[0.32 - 0.66]); providing household income (OR=0.60, 95%CI[0.43 - 0.84]). Participants with compulsory rural service (OR=1.52, 95%CI[1.05 - 2.19]) and those providing university entrance scores (OR=1.64, 95%CI[1.15-2.33)) were more likely to rejoin in the follow-up survey. These factors associated with follow-up status did not have significant impact on key outcome measures of career development.

Conclusions
Graduates who were unwilling to participate in residency training or not providing sensitive information should be targeted early in the cohort study to reduce attrition. More information about the study should be provided to those graduates early to facilitate their understanding of the meaning in participation. On the contrary, medical graduates with compulsory rural service and those who provided university entrance scores were more likely to rejoin in the cohort. The research team should invest more effort in contacting those graduates and returned them to the cohort.
Misbeliefs about non-specific low back pain and attitudes towards treatment by primary care providers in Spain: a qualitative study
Authors: García-Martínez Ester , Soler-González Jorge , Blanco-Blanco Joan , Rubí-Carnacea Francesc , Masbernat-Almenara María , Valenzuela-Pascual Fran 
Published: January 2022

AbstractAimTo identify misbeliefs about the origin and meaning of non-specific chronic low back pain and to examine attitudes towards treatment by primary health care providers.DesignGeneric qualitative study.MethodsTen semi-structured interviews were conducted between October and November 2016 with physicians and nurses from primary health care centres in Lleida. The interviews were transcribed and analysed using inductive thematic analysis via Atlas.ti-8 software.ResultsFive themes were identified: i. beliefs about the origin and meaning of chronic low back pain, ii. psychosocial aspects of pain modulators, iii. Therapeutic exercise as a treatment for chronic low back pain, iv. biomedical attitudes of primary health care providers, and v. difficulties in the clinical approach to chronic low back pain.ConclusionPrimary health care providers have a unifactorial view of chronic low back pain and base their approach on the biomedical model. Professionals attribute chronic low back pain to structural alterations in the lumbar spine while psychosocial factors are only recognized as pain modulators. For professionals, therapeutic exercise represents a possible solution to chronic low back pain; however, they still do not prescribe it and continue to educate on postural hygiene and recommend limiting physical and/or occupational activities, as opposed to clinical practice guidelines. These findings suggest that to improve the adherence of primary health care providers to the biopsychosocial model, it may be necessary first to modify their misbeliefs about non-specific chronic low back pain by increasing their knowledge on pain neurophysiology.Trial registrationClinicalTrials.govIdentifier:NCT02962817. Date of registration: 11/11/2016.
“Even though they insult us, the delivery they give us is the greatest thing”: a qualitative study contextualizing women’s experiences with facility-based maternal health care in Ethiopia
Authors: Hagaman Ashley , Rodriguez Humberto Gonzalez , Barrington Clare , Singh Kavita , Estifanos Abiy Seifu , Keraga Dorka Woldesenbet , Alemayehu Abiyou Kiflie , Abate Mehiret , Bitewulign Befikadu , Barker Pierre , Magge Hema 
Published: January 2022

Abstract
Background
Globally, amidst increased utilization of facility-based maternal care services, there is continued need to better understand women’s experience of care in places of birth. Quantitative surveys may not sufficiently characterize satisfaction with maternal healthcare (MHC) in local context, limiting their interpretation and applicability. The purpose of this study is to untangle how contextual and cultural expectations shape women’s care experience and what women mean by satisfaction in two Ethiopian regions.

Methods
Health center and hospital childbirth care registries were used to identify and interview 41 women who had delivered a live newborn within a six-month period. We used a semi-structured interview guide informed by the Donabedian framework to elicit women’s experiences with MHC and delivery, any prior delivery experiences, and recommendations to improve MHC. We used an inductive analytical approach to compare and contrast MHC processes, experiences, and satisfaction.

Results
Maternal and newborn survival and safety were central to women’s descriptions of their MHC experiences. Women nearly exclusively described healthy and safe deliveries with healthy outcomes as ‘satisfactory’. The texture behind this ‘satisfaction’, however, was shaped by what mothers bring to their delivery experiences, creating expectations from events including past births, experiences with antenatal care, and social and community influences. Secondary to the absence of adverse outcomes, health provider’s interpersonal behaviors (e.g., supportive communication and behavioral demonstrations of commitment to their births) and the facility’s amenities (e.g., bathing, cleaning, water, coffee, etc) enhanced women’s experiences. Finally, at the social and community levels, we found that family support and material resources may significantly buffer against negative experiences and facilitate women’s overall satisfaction, even in the context of poor-quality facilities and limited resources.

Conclusion
Our findings highlight the importance of understanding contextual factors including past experiences, expectations, and social support that influence perceived quality of MHC and the agency a woman has to negotiate her care experience. Our finding that newborn and maternal survival primarily drove women’s satisfaction suggests that quantitative assessments conducted shortly following delivery may be overly influenced by these outcomes and not fully capture the complexity of women’s care experience.
Effect of peripheral iridectomy on VEGF-A and TGF-β levels in rabbit aqueous humour
Authors: Chew Annabel C. Y. , Seet Li-Fong , Chu Stephanie W. L. , Lwin Nyein C. , Wong Tina T. 
Published: January 2022

Abstract
Background
Peripheral iridectomy (PI), routinely performed during glaucoma filtration surgery, may contribute to scarring. This study aims to determine whether PI alters the concentrations of VEGF-A and TGF-β isoforms in the rabbit aqueous humour.

Methods
Anterior chamber paracentesis (ACP) was performed in both eyes of six New Zealand white rabbits, with additional surgical PI performed in the right eyes. Eyes were examined on postoperative days (PODs) 1, 7, 30 and 60 by means of the tonopen, slit-lamp biomicroscopy, and bead-based cytokine assays for TGF-β and VEGF-A concentrations in the aqueous humor.

Results
ACP caused a significant reduction in intraocular pressure (IOP) from mean preoperative 11.47 ± 1.01 mmHg to 5.67 ± 1.63 mmHg on POD 1 while PI did not cause further IOP reduction. Limbal conjunctival vasculature appeared slightly increased on POD 1 in both ACP and PI eyes with PI also causing mild bleeding from damaged iris vessels. Two PI eyes developed fibrinous anterior chamber reaction and/ or peripheral anterior synechiae. Aqueous VEGF-A levels were not significantly different between eyes treated with ACP and PI. Aqueous TGF-β concentrations distributed in the ratio of 4:800:1 for TGF-β1:TGF-β2:TGF-β3 respectively. While aqueous TGF-β2 was not significantly induced by either procedure at any time point, TGF-β1 and TGF-β3 were significantly induced above baseline levels by PI on POD 1.

Conclusion
PI increases the risk of inflammation. The combined induction of aqueous TGF-β1 and TGF-β3 by PI in glaucoma surgery may impact surgery success in glaucoma subtypes sensitive to these isoforms.
Arterial health during early childhood following abnormal fetal growth
Authors: Olander Rasmus F.W. , Sundholm Johnny K.M. , Suonsyrjä Sanna , Sarkola Taisto 
Published: January 2022

Abstract
Background
Abnormal fetal growth is associated with increased cardiovascular risk in adulthood. We investigated the effect of fetal programming on arterial health and morphology during early childhood.

Methods
We examined 90 children (median age 5.81 years, interquartile range: 5.67; 5.95), born small for gestational age with fetal growth restriction, large or appropriate for gestational age (SGA, N = 23, LGA, N = 19, AGA N = 48). We measured body composition, anthropometrics, blood pressure, pulse wave velocity (PWV), lipids, glucose and inflammatory markers, and assessed carotid, brachial, radial and femoral arterial morphology and stiffness using very-high resolution ultrasound (46–71 MHz).

Results
LGA showed increased anthropometry, lean body mass and body mass index. SGA displayed decreased anthropometry and lean body mass. Blood pressure, PWV, carotid artery stiffness and blood work did not differ groupwise. Differences in lumen diameters, intima-media thicknesses (IMT) and adventitia thicknesses disappeared when adjusted for lean body mass and sex. In multiple regression models arterial dimensions were mainly predicted by lean body mass, with birth weight remaining associated only with carotid and brachial lumen dimensions, and not with IMTs. Carotid-femoral PWV was predicted by height and blood pressure only. No independent effect of adiposity was observed.

Conclusions
Arterial dimensions in childhood associate with current anthropometrics, especially lean body mass, and sex, explaining differences in arterial layer thickness. We found no signs of fetal programming of cardiovascular risk or arterial health in early childhood.
Time to develop severe acute malnutrition and its predictors among children living with HIV in the era of test and treat strategies at South Gondar hospitals, northwest, Ethiopia, 2021: a multicentre retrospective cohort study
Authors: Chanie Ermias Sisay , Legas Getasew , Zewude Shimeles Biru , Mekie Maru , Sewyew Dagne Addisu , Yehuala Enyew Dagnew , Melkie Abenezer , Ambie Minale Bezie , Assefa Mengesha , Admasu Fitalew Tadele , Yitbarek Getachew Yideg , Asnakew Sintayehu , Mersha Mekuant , Feleke Dejen Getaneh 
Published: January 2022

Abstract
Background
Although severe acute malnutrition is a major public issue among HIV infected children, there is no prior evidence in Ethiopia. Hence, this study aims to assess the time to develop severe acute malnutrition and its predictors among children living with human immunodeficiency virus in Ethiopia, 2012.

Methods
An institution based retrospective cohort study was conducted in South Gondar hospitals among 363 HIV infected children from February 10, 2014, to January 7, 2021. Epi-data version 3.1 was used to enter data, which was then exported to STATA version 14 for analysis. Besides, WHO (World Health Organization) Anthro Plus software was used to assess the nutritional status of the children. A standardized data extraction tool was used to collect the data. The Kaplan Meier survival curve was used to estimate the median survival time. The Cox-proportional hazard model assumption was checked via the Schoenfeld residual ph test and a stph plot. Bivariable and multivariable Cox proportional hazard models were employed at 95% confidence intervals (CI). A variable having a p-value < 0.05 was considered a statistically significant predictor of severe acute malnutrition.

Results
A total of 363 children living with HIV, 97 (26.72%) developed severe acute malnutrition during the follow-up period. The overall incidence rate was 5.4 (95% CI: 4.7–5.9) person per year with a total of 21, 492 months or 1791 years of observation. Moreover, the median survival time was 126 months. Treatment failure [AHR =3.4 (95% CI: 2.05–5.75)], CD4 count below threshold [AHR =2.5 (95% CI: 1.64–3.95)], and WHO stage III & IV [AHR =2.9 (95% CI: 1.74–4.73)] were all significant predictors of severe acute malnutrition.

Conclusion
The time to develop severe acute malnutrition was found to be very low. Treatment failure, CD4 count below threshold, and WHO stage III were all significant predictors of severe acute malnutrition. Hence, emphasizing those predictor variables is essential for preventing and controlling the occurrence of severe acute malnutrition among HIV infected children.
Maternal advanced age, single parenthood, and ART increase the risk of child morbidity up to five years of age
Authors: Pettersson Malin Lindell , Bladh Marie , Nedstrand Elizabeth , Svanberg Agneta Skoog , Lampic Claudia , Sydsjö Gunilla 
Published: January 2022

Abstract
Background
Advanced maternal age, single status and use of assisted reproductive technology (ART) are increasing in mothers in high-income countries, and all are known risk factors for negative obstetric outcomes. Less is known about their long-term consequences for childhood morbidity. Thus, the aim of this study was to investigate morbidity up to five years of age, in the children of older, single, and/or ART-treated mothers.

Methods
A cross-sectional using Swedish registers was performed comprising 23 772 children. The prevalence of diagnosis and the number of hospital visits for specialist care, were compared and analyzed in relation to maternal age at childbirth, maternal civil status, and mode of conception. The odds ratio for specialized care within each ICD-chapter were estimated using single and multiple logistic regression.

Results
Children born to single mothers and children conceived using ART had significantly more outpatient visits for specialist care and significantly more diagnoses compared to children with married/cohabiting mothers, and spontaneously conceived children. Children born to mothers of advanced maternal age (≥40) had fewer in- and outpatient visits. However, they were significantly more often diagnosed within ICD-chapters XVI, XVII i.e., they experienced more morbidity in the neonatal period.

Conclusion
The results indicate that children born to single mothers and children of ART-treated mothers have a higher morbidity and consume more specialist care than children of married/cohabiting and spontaneously pregnant mothers. We conclude that the use of ART, maternal single status and advanced maternal age are risk factors of importance to consider in pediatric care and when counseling women who are considering ART treatment.