bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved quality metrics for association and reproducibility in chromatin accessibility data using mutual information
Authors: Roth Cullen , Venu Vrinda , Job Vanessa , Lubbers Nicholas , Sanbonmatsu Karissa Y. , Steadman Christina R. , Starkenburg Shawn R. 
Published: November 2023

AbstractBackgroundCorrelation metrics are widely utilized in genomics analysis and often implemented with little regard to assumptions of normality, homoscedasticity, and independence of values. This is especially true when comparing values between replicated sequencing experiments that probe chromatin accessibility, such as assays for transposase-accessible chromatin via sequencing (ATAC-seq). Such data can possess several regions across the human genome with little to no sequencing depth and are thus non-normal with a large portion of zero values. Despite distributed use in the epigenomics field, few studies have evaluated and benchmarked how correlation and association statistics behave across ATAC-seq experiments with known differences or the effects of removing specific outliers from the data. Here, we developed a computational simulation of ATAC-seq data to elucidate the behavior of correlation statistics and to compare their accuracy under set conditions of reproducibility.ResultsUsing these simulations, we monitored the behavior of several correlation statistics, including the Pearson’sRand Spearman’s$$\rho$$ρcoefficients as well as Kendall’s$$\tau$$τand Top–Down correlation. We also test the behavior of association measures, including the coefficient of determinationR$$^2$$2, Kendall’s W, and normalized mutual information. Our experiments reveal an insensitivity of most statistics, including Spearman’s$$\rho$$ρ, Kendall’s$$\tau$$τ, and Kendall’s W, to increasing differences between simulated ATAC-seq replicates. The removal of co-zeros (regions lacking mapped sequenced reads) between simulated experiments greatly improves the estimates of correlation and association. After removing co-zeros, theR$$^2$$2coefficient and normalized mutual information display the best performance, having a closer one-to-one relationship with the known portion of shared, enhanced loci between simulated replicates. When comparing values between experimental ATAC-seq data using a random forest model, mutual information best predicts ATAC-seq replicate relationships.ConclusionsCollectively, this study demonstrates how measures of correlation and association can behave in epigenomics experiments. We provide improved strategies for quantifying relationships in these increasingly prevalent and important chromatin accessibility assays.
MiREx: mRNA levels prediction from gene sequence and miRNA target knowledge
Authors: Pianfetti Elena , Lovino Marta , Ficarra Elisa , Martignetti Loredana 
Published: November 2023

AbstractMessenger RNA (mRNA) has an essential role in the protein production process. Predicting mRNA expression levels accurately is crucial for understanding gene regulation, and various models (statistical and neural network-based) have been developed for this purpose. A few models predict mRNA expression levels from the DNA sequence, exploiting the DNA sequence and gene features (e.g., number of exons/introns, gene length). Other models include information about long-range interaction molecules (i.e., enhancers/silencers) and transcriptional regulators as predictive features, such as transcription factors (TFs) and small RNAs (e.g., microRNAs - miRNAs). Recently, a convolutional neural network (CNN) model, called Xpresso, has been proposed for mRNA expression level prediction leveraging the promoter sequence and mRNAs’ half-life features (gene features). To push forward the mRNA level prediction, we present miREx, a CNN-based tool that includes information about miRNA targets and expression levels in the model. Indeed, each miRNA can target specific genes, and the model exploits this information to guide the learning process. In detail, not all miRNAs are included, only a selected subset with the highest impact on the model. MiREx has been evaluated on four cancer primary sites from the genomics data commons (GDC) database: lung, kidney, breast, and corpus uteri. Results show that mRNA level prediction benefits from selected miRNA targets and expression information. Future model developments could include other transcriptional regulators or be trained with proteomics data to infer protein levels.
Analysis of codon usage patterns in 48 Aconitum species
Authors: Yang Meihua , Liu Jiahao , Yang Wanqing , Li Zhen , Hai Yonglin , Duan Baozhong , Zhang Haizhu , Yang Xiaoli , Xia Conglong 
Published: November 2023

Abstract
Background
The Aconitum genus is a crucial member of the Ranunculaceae family. There are 350 Aconitum species worldwide, with about 170 species found in China. These species are known for their various pharmacological effects and are commonly used to treat joint pain, cold abdominal pain, and other ailments. Codon usage bias (CUB) analysis contributes to evolutionary relationships and phylogeny. Based on protein-coding sequences (PCGs), we selected 48 species of Aconitum for CUB analysis.

Results
The results revealed that Aconitum species had less than 50% GC content. Furthermore, the distribution of GC content was irregular and followed a trend of GC1 > GC2 > GC3, indicating a bias towards A/T bases. The relative synonymous codon usage (RSCU) heat map revealed the presence of conservative codons with slight variations within the genus. The effective number of codons (ENC)-Plot and the parity rule 2 (PR2)-bias plot analysis indicate that natural selection is the primary factor influencing the variation in codon usage. As a result, we screened various optimal codons and found that A/T bases were preferred as the last codon. Furthermore, our Maximum Likelihood (ML) analysis based on PCGs among 48 Aconitum species yielded results consistent with those obtained from complete chloroplast (cp.) genome data. This suggests that analyzing mutation in PCGs is an efficient method for demonstrating the phylogeny of species at the genus level.

Conclusions
The CUB analysis of 48 species of Aconitum was mainly influenced by natural selection. This study reveals the CUB pattern of Aconitum and lays the foundation for future genetic modification and phylogenetic analyses.
Aesthetics of everyday life and its related factors among older adults in Kashan (2021–2022)
Authors: Zamani Nafise , Izadi-Avanji Fatemeh Sadat , Safa Azade , Azizi-Fini Ismail , Mohammadnejad Esmaeil 
Published: November 2023

Abstract
Background
Aesthetics of everyday life are associated with the physical, mental, and social health of older adults, leading them to experience a successful old age. This study aimed to examine the aesthetics of everyday life and its related factors among older adults in Kashan from 2021 to 2022.

Methods
This cross-sectional study consisted of 350 older adults who were referred to Urban Comprehensive Health Service Centers (UCHSC) in Kashan. Sampling was done by a two-stage method (cluster, random). The data collection was performed with a background information questionnaire and the Elderly’s Perception of Everyday Aesthetics scale (EPEA-S). Data were analyzed using an independent t-test, analysis of variance, Pearson’s correlation coefficient, and multiple linear regression tests in the SPSS software.

Results
The mean age of the participants was 69.56 ± 6.63 years. The mean score of aesthetics of everyday life in older adults was 133.02 ± 14.73, with the family and others subscale receiving the highest score. The univariate test indicated a statistically significant correlation between age, employment status, education, income, smoking, social activities, physical activities, interest in artistic works, and the aesthetics of everyday life in older adults (P < 0.01). Multivariate linear analysis showed that age, employment status, smoking, income, social activities, physical activities, and interest in artistic works predicted and explained 28% of the variance of life aesthetics in older adults (R2 = 0.28).

Conclusions
The aesthetics of everyday life of the Iranian older adults were in a good range. Healthcare providers and families of older adults can use this concept to enhance the elderly’s physical, mental, and social health.
Phenotypic and genotypic characterization of multidrug resistant and extended-spectrum β-lactamase-producing Enterobacterales isolated from clinical samples in the western region in Cameroon
Authors: Nkengkana Omer Aurelle , Founou Raspail Carrel , Founou Luria Leslie , Dimani Brice Davy , Koudoum Patrice Landry , Zemtsa Jessica Ravalona , Mbossi Aurelia , Mawout Cyrielle Signe , Tegang Larissa Tchakounte , Noubom Michel 
Published: November 2023

Abstract
Background
The 2017 World Health Organization (WHO) report has listed extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E) as critical pathogens for public health and requiring urgently new antibiotics. The aim of this study was to characterize phenotypically and genotypically ESBL-E isolated among clinical samples in Dschang, Cameroon.

Methods
A cross-sectional study was conducted during a four-month periods from February to May 2022 in the two biggest hospitals of Dschang. Clinical samples were collected and cultured on Eosin Methylene Blue agar. Suspected growing colonies were biochemically identified using the Enterosystem Kit 18R. Antimicrobial susceptibility testing (AST) was done using the Kirby Bauer disc diffusion method and interpretated according to the CA-SFM recommendations. ESBL phenotypes were double screened using CHROMagar™ ESBL and double disk synergy test (DDST). The detection of resistance genes was performed using conventional and multiplex PCR methods. Results were analyzed with SPSS (version 21) and a p-value < 0.05 was considered statistically significant.

Results
A total of 152 Enterobacterales were isolated among 597 clinical samples including urine, blood, cervico-vaginal, urethral swabs and wound samples. The overall prevalence of ESBL-Enterobacterales was 29.61% (45/152). The most represented ESBL species were Escherichia coli (n = 23; 51.11%), Klebsiella pneumoniae (n = 8; 17.78%) and Citrobacter freundii (n = 6; 13.33%).

Conclusion
This study reveals the high burden of ESBL-E among clinical samples in the regional hospital in Dschang with the most common species being E. coli and K. pneumoniae. It confirmed the high occurrence of blaCTX−M and blaTEM among ESBL-E. The study suggests that implementing antimicrobial stewardship program and real-time surveillance of antimicrobial resistance are needed in the Western region of Cameroon. Moreover, the implementation of infection prevention and control measures (IPC) is essential to curb the dissemination of these bacteria from community to hospital settings. Implementation of national action plan to fight against antimicrobial resistance at the local levels is urgently needed.
Evaluation of a method to identify midwives in national provider identifier data
Authors: Vanderlaan Jennifer , Jefferson Karen 
Published: November 2023

Abstract
Objectives
Comparison of national midwife workforce data from the National Provider Identifier file determined it undercounted midwives compared to national data available from the American Midwifery Certification Board. This undercount may be due to the existence of three taxonomy categories for midwives when registering for the National Provider Identifier. The objective of this study was to obtain an accurate count of advanced practice midwives using the National Provider Identifier Data.

Methods
A recode strategy was created using the NPPES Data Dissemination File for November 7, 2021. The strategy identified advanced practice midwives using education and certification information provided in the “credentials” field. The strategy was validated using the NPPES Data Dissemination File for August 7, 2022 and the gold standard was the American Midwifery Certification Board count of midwives by state for August, 2022. Validation compared the accuracy and precision of the recode to the accuracy and precision of using the advanced practice midwife taxonomy category.

Results
The recode strategy improved the accuracy and precision of the count of advanced practice midwives compared to the identification of advanced practice midwives using the advanced practice midwife taxonomy category.

Conclusions for practice
Recoding the NPPES Data Dissemination File provides a more accurate and precise count of advanced practice midwives than relying on the existing advanced practice midwife taxonomy classification. Researchers can use the NPPES Data Dissemination File when studying the midwifery workforce.
Prevalence and pattern of retinopathy of prematurity at two national referral hospitals in Uganda: a cross-sectional study
Authors: Ndyabawe Iddi , Namiiro Flavia , Muhumuza Anita Tumwebaze , Nakibuka Jesca , Otiti Juliet , Ampaire Anne , Kasadhakawo Moses , Msonge Fransisco , Mohamed Siyad , Nyanzi Mary , Tumukunde Victor Spector , Semulimi Andrew Weil , Mukunya David , Bwonya Dan , Magala Primrose , Gilbert Clare , Dietrich Nancy Maria Douat , Cagliari Patricia Zanotelli , Hedstrom Anna , Blair Mike , Jones Becca , Nyonyintono James , Doka Aisha Muhamad , Nakitende Bariirah Bushirah , Graham Hamish R. , Carden Susan Mary , Subhi Rami , Nsibirwa Grace Ssali 
Published: November 2023

Abstract
Background
Retinopathy of prematurity (ROP) is a leading cause of blindness in children and an ROP epidemic is predicted this decade in sub-Saharan Africa. With the increasing survival rate of preterm babies in Uganda, and no data on ROP prevalence, there is a need to assess the burden of ROP to inform preventive strategies and targeted screening.

Methods
We conducted a two-center cross-sectional study of preterm (< 37 weeks gestational age) infants from the neonatal units of Kawempe National Referral Hospital (KNRH) and Mulago Specialised Women and Neonatal Hospital (MSWNH) from August 2022 to October 2022. An ophthalmologist examined all participants using an indirect ophthalmoscope with a + 20D convex lens and captured digital images using a Volk iNview™ Fundus Camera. The collected data were entered into Epidata 4.2 and exported to Stata 14.0 for analysis.

Results
331 preterm infants enrolled in this study. The oxygen received was unblended. The mean gestational age was 30.4 ± 2.7 weeks, and the mean birth weight was 1597 ± 509 g. 18/101 (17.8%) were found to have any ROP amongst the preterm infants recruited from MSWNH, 1/230 (0.4%) from KNRH [95% CI] had any stage of ROP (i.e. stage 5). Of these, 8 (42.1%) had stage 2 ROP. Infants with a birth weight below 1500 g were 10 times more likely to have ROP than those among infants with a birth weight more than 1500 g [AOR: 10.07 (2.71–37.44)]. Infants who were not fed exclusively on breast milk had higher odds of having ROP than those exclusively fed on breast milk [AOR: 7.82(1.92–31.82)].

Conclusion
6% of preterm infants born in two tertiary hospitals in Uganda were found to have ROP. Lack of exclusive feeding on breast milk and birth weight of less than 1500 g were strong predictors of ROP. The higher prevalence of ROP in MSWNH calls for cautious use of oxygen among preterms. We recommend targeted ROP screening for those at risk.
Echocardiographic measurements of left ventricular dimensions and function in newborns with omphalocele and pulmonary
Authors: Yang Si-Si , Huang Wen-Chang , Wang Peng , Gong Fang-Qi , Liu Tai-Xiang , Tou Jin-Fa , Lai Deng-Ming 
Published: November 2023

Abstract
Purpose
The purpose of this study was to explore echocardiographic parameters of the left ventricle (LV) in relation to the outcomes of omphalocele neonates with pulmonary hypertension (PH).

Methods
This retrospective study was conducted among omphalocele patients with PH born from 2019 to 2020. Patients in this study did not have additional severe malformations or chromosomal aberrations. Patients who died under palliative care were excluded. The echocardiographic parameters of LV were obtained within 24 h after birth. Clinical and outcomes data were recorded, echocardiograms evaluated for left ventricular internal dimension in end-diastole (LVIDd), end-diastolic volume (EDV), stroke volume (SV) and cardiac output index (CI), among others.

Results
There were 18 omphalocele newborns with PH, of whom 14 survived and 4 died. Both groups were comparable in the baseline characteristics. Non-survival was associated with a smaller LV [LVIDd (12.2 mm versus15.7 mm, p < 0.05), EDV (3.5 ml versus 6.8 ml, p < 0.05)] and with worse systolic function [SV (2.3 ml versus 4.2 ml, p < 0.05), and CI (1.7 L/min/m2 versus 2.9 L/min/m2, p < 0.01)].

Conclusion
In the cohort of omphalocele patients with PH, lower LVIDd, EDV, SV and CI were associated with mortality.

Level of evidence
Level III.
Association between mitochondrial DNA levels and depression: a systematic review and meta-analysis
Authors: Li Wenhui , Zhu Lingqun , Chen Yi , Zhuo Yudi , Wan Shurun , Guo Rongjuan 
Published: November 2023

Abstract
Background
Mitochondrial dysfunction leading to disturbances in energy metabolism has emerged as one of the risk factors in the pathogenesis of depression. Numerous studies have identified alterations in the content of mitochondrial DNA (mtDNA) in peripheral blood and cerebrospinal fluid of individuals with depression. Researchers have sought to establish a clear association between mtDNA and depression. Consequently, we conducted a comprehensive meta-analysis to assess the existing evidence regarding the impact of mtDNA on depression.

Methods
This study conducted a thorough search of the following databases up to March 13, 2023: PubMed, Embase, the Cochrane Library, the Web of Science, Wanfang Database, SINOMED, the China Science and Technology Journal Database, and China National Knowledge Infrastructure. The meta-analysis was carried out using RevMan (version 5.4) and Stata (version 16.0) software. In addition, publication bias was assessed with funnel plots, Begg’s test and Egger’s test.

Results
Our analysis included data from 10 articles, including 12 studies for further examination. A total of 1400 participants were included in this study, comprising 709 (including 300 males and 409 females) patients with depression and 691 (including 303 males and 388 females) healthy controls. The average age of depressed patients was (42.98 ± 2.55) years, and the average age of healthy people was (41.71 ± 2.6) years. The scales used to assess outcomes are Hamilton-rating scale for Depression(4 articles), Montgomery-Asberg Depression Rating Scale(3 articles), and Mini-Internatioal Neuropsychiatric Interview (1 articles). The meta-analysis revealed significantly higher levels of mtDNA in circulating blood samples and skin fibroblasts of individuals with depression in comparison to healthy controls [standardized mean difference(SMD) = 0.42, 95% confidence intervals(CI): 0.16, 0.67].

Conclusions
Our study concludes that there is a significant (p < 0.05) increase in mtDNA levels in serum, plasma, and cerebrospinal fluid in individuals with depression. These findings suggest that mtDNA could serve as a potential biomarker for diagnosing depression.

Registration number
PROSPERO CRD42023414285.
Association of bone turnover markers and cognitive function in Chinese chronic schizophrenia patients with or without vitamin D insufficiency
Authors: Ling Chen , Sun Liling , Luo Bei , Yu Haiyun , Li Wei , Yang Yating , Liu Huanzhong 
Published: November 2023

Abstract
Background
Increasing evidence shows that bone turnover markers (BTMs) and vitamin D can affect human cognitive function. However, there are few studies that have investigated the association between BTMs and cognitive function in chronic schizophrenia patients. The aim of this study was to investigate the relationship between BTMs and cognitive function in chronic schizophrenia patients with or without vitamin D insufficiency (VDI).

Methods
In all, 118 chronic schizophrenia patients were enrolled in this cross-sectional study. Repeatable Battery for the Assessment of Neuropsychological Status (RBANS) was applied to evaluate the cognitive function of the subjects. Blood analysis included bone turnover markers, vitamin D levels, and glycolipid levels.

Results
Relative to 72 vitamin D-sufficient (VDS) patients, 46 VDI patients had higher bone resorption markers levels and lower bone formation markers levels. Regression analysis showed that, in the total sample, CTX and language function exhibited independent positive correlation (p = 0.027, R2 change = 0.042), and in the VDS group, procollagen type I N-terminal propeptide (PINP) was independently negatively correlated with language function (p = 0.031, R2 change = 0.065), while the positive correlation between osteopontin (OPN) and delayed memory remained in the VDI group (p = 0.036, R2 change = 0.083).

Conclusion
Our study showed an association between the levels of BTMs and cognitive function among chronic schizophrenia patients. This correlation may have different mechanisms of action at different vitamin D levels.
Application of exponential smoothing method and SARIMA model in predicting the number of admissions in a third-class hospital in Zhejiang Province
Authors: Yang Wanjun , Su Aonan , Ding Liping 
Published: November 2023

AbstractObjectiveTo establish the exponential smoothing prediction model and SARIMA model to predict the number of inpatients in a third-class hospital in Zhejiang Province, and evaluate the prediction effect of the two models, and select the best number prediction model.MethodsThe data of hospital admissions from January 2019 to September 2022 were selected to establish the exponential smoothing prediction model and the SARIMA model respectively. Then compare the fitting parameters of different models: R2_adjusted, R2, Root Mean Square Error (RMSE)、Mean Absolute Percentage Error (MAPE)、Mean Absolute Error(MAE) and standardized BIC to select the best model. Finally, the established model was used to predict the number of hospital admissions from October to December 2022, and the prediction effect of the average relative error judgment model was compared.ResultsThe best fitting exponential smoothing prediction model was Winters Addition model, whose R2_adjusted was 0.533, R2was 0.817, MAPE was 6.133, MAE was 447.341. The best SARIMA model is SARIMA(2,2,2)(0,1,1)12model, whose R2_adjusted is 0.449, R2is 0.199, MAPE is 8.240, MAE is 718.965. The Winters addition model and SARIMA(2,2,2)(0,1,1)12model were used to predict the number of hospital admissions in October-December 2022, respectively. The results showed that the average relative error was 0.038 and 0.015, respectively. The SARIMA(2,2,2)(0,1,1)12model had a good prediction effect.ConclusionBoth models can better fit the number of admissions, and SARIMA model has better prediction effect.
Coexistent Sjogren’s syndrome and Birt-Hogg-Dube´ syndrome: a case report
Authors: Lin Yongkang , Guo Ting , Lei Cheng , Yang Binyi , Yang Danhui , Luo Hong , Peng Hong 
Published: November 2023

AbstractWe report a rare case of Sjogren’s syndrome complicated with Birt-Hogg-Dubé syndrome (BHDS) not previously mentioned in the literature. Further, there is insufficient evidence linking the two diseases. Here, we review existing diagnostic algorithms for diagnosing diffuse cystic lung disease and provide new insights. The patient initially complained of thirst and dry eyes for ten years, and gradually developed shortness of breath. After admission, physical examination showed five missing teeth, decreased respiratory sounds in both lower lungs, and Velcro rales. Computed tomography showed multiple thin-walled cystic lesions in both lungs. Initial xerophthalmia and labial gland biopsy seemed to reveal a pulmonary cystic change associated with Sjogren’s syndrome. Before discharge, a rash suspected to indicate a fibrofollicular tumor in the neck was observed, and then FLCN variant has been found. The challenges how to clarify the diagnosis of DCLD causes are discussed.