bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNA-clique: a method for computing genetic distances from RNA-seq data
Authors: Tapia Andrew C. , Jaromczyk Jerzy W. , Moore Neil , Schardl Christopher L. 
Published: June 2024

Abstract
Background
Although RNA-seq data are traditionally used for quantifying gene expression levels, the same data could be useful in an integrated approach to compute genetic distances as well. Challenges to using mRNA sequences for computing genetic distances include the relatively high conservation of coding sequences and the presence of paralogous and, in some species, homeologous genes.

Results
We developed a new computational method, RNA-clique, for calculating genetic distances using assembled RNA-seq data and assessed the efficacy of the method using biological and simulated data. The method employs reciprocal BLASTn followed by graph-based filtering to ensure that only orthologous genes are compared. Each vertex in the graph constructed for filtering represents a gene in a specific sample under comparison, and an edge connects a pair of vertices if the genes they represent are best matches for each other in their respective samples. The distance computation is a function of the BLAST alignment statistics and the constructed graph and incorporates only those genes that are present in some complete connected component of this graph. As a biological testbed we used RNA-seq data of tall fescue (Lolium arundinaceum), an allohexaploid plant ($$2n = 14\text { Gb}$$

2
n
=
14

Gb

), and bluehead wrasse (Thalassoma bifasciatum), a teleost fish. RNA-clique reliably distinguished individual tall fescue plants by genotype and distinguished bluehead wrasse RNA-seq samples by individual. In tests with simulated RNA-seq data, the ground truth phylogeny was accurately recovered from the computed distances. Moreover, tests of the algorithm parameters indicated that, even with stringent filtering for orthologs, sufficient sequence data were retained for the distance computations. Although comparisons with an alternative method revealed that RNA-clique has relatively high time and memory requirements, the comparisons also showed that RNA-clique’s results were at least as reliable as the alternative’s for tall fescue data and were much more reliable for the bluehead wrasse data.

Conclusion
Results of this work indicate that RNA-clique works well as a way of deriving genetic distances from RNA-seq data, thus providing a methodological integration of functional and genetic diversity studies.
miR-486-5p predicted adverse outcomes of SCAP and regulated K. pneumonia infection via FOXO1
Authors: Jin Qianqi , Liu Chuanlan , Cao Yan , Wang Feiyan 
Published: June 2024

Abstract
Purpose
Severe community-acquired pneumonia (SCAP) is a common respiratory system disease with rapid development and high mortality. Exploring effective biomarkers for early detection and development prediction of SCAP is of urgent need. The function of miR-486-5p in SCAP diagnosis and prognosis was evaluated to identify a promising biomarker for SCAP.

Patients and methods
The serum miR-486-5p in 83 patients with SCAP, 52 healthy individuals, and 68 patients with mild CAP (MCAP) patients were analyzed by PCR. ROC analysis estimated miR-486-5p in screening SCAP, and the Kaplan-Meier and Cox regression analyses evaluated the predictive value of miR-486-5p. The risk factors for MCAP patients developing SCAP were assessed by logistic analysis. The alveolar epithelial cell was treated with Klebsiella pneumonia to mimic the occurrence of SCAP. The targeting mechanism underlying miR-486-5p was evaluated by luciferase reporter assay.

Results
Upregulated serum miR-486-5p screened SCAP from healthy individuals and MCAP patients with high sensitivity and specificity. Increasing serum miR-486-5p predicted the poor outcomes of SCAP and served as a risk factor for MCAP developing into SCAP. K. pneumonia induced suppressed proliferation, significant inflammation and oxidative stress in alveolar epithelial cells, and silencing miR-486-5p attenuated it. miR-486-5p negatively regulated FOXO1, and the knockdown of FOXO1 reversed the effect of miR-486-5p in K. pneumonia-treated alveolar epithelial cells.

Conclusion
miR-486-5p acted as a biomarker for the screening and monitoring of SCAP and predicting the malignancy of MCAP. Silencing miR-486-5p alleviated inflammation and oxidative stress induced by K. pneumonia via negatively modulating FOXO1.
Comparison of Bayesian approaches for developing prediction models in rare disease: application to the identification of patients with Maturity-Onset Diabetes of the Young
Authors: Cardoso Pedro , McDonald Timothy J. , Patel Kashyap A. , Pearson Ewan R. , Hattersley Andrew T. , Shields Beverley M. , McKinley Trevelyan J. 
Published: June 2024

Abstract
Background
Clinical prediction models can help identify high-risk patients and facilitate timely interventions. However, developing such models for rare diseases presents challenges due to the scarcity of affected patients for developing and calibrating models. Methods that pool information from multiple sources can help with these challenges.

Methods
We compared three approaches for developing clinical prediction models for population screening based on an example of discriminating a rare form of diabetes (Maturity-Onset Diabetes of the Young - MODY) in insulin-treated patients from the more common Type 1 diabetes (T1D). Two datasets were used: a case-control dataset (278 T1D, 177 MODY) and a population-representative dataset (1418 patients, 96 MODY tested with biomarker testing, 7 MODY positive). To build a population-level prediction model, we compared three methods for recalibrating models developed in case-control data. These were prevalence adjustment (“offset”), shrinkage recalibration in the population-level dataset (“recalibration”), and a refitting of the model to the population-level dataset (“re-estimation”). We then developed a Bayesian hierarchical mixture model combining shrinkage recalibration with additional informative biomarker information only available in the population-representative dataset. We developed a method for dealing with missing biomarker and outcome information using prior information from the literature and other data sources to ensure the clinical validity of predictions for certain biomarker combinations.

Results
The offset, re-estimation, and recalibration methods showed good calibration in the population-representative dataset. The offset and recalibration methods displayed the lowest predictive uncertainty due to borrowing information from the fitted case-control model. We demonstrate the potential of a mixture model for incorporating informative biomarkers, which significantly enhanced the model’s predictive accuracy, reduced uncertainty, and showed higher stability in all ranges of predictive outcome probabilities.

Conclusion
We have compared several approaches that could be used to develop prediction models for rare diseases. Our findings highlight the recalibration mixture model as the optimal strategy if a population-level dataset is available. This approach offers the flexibility to incorporate additional predictors and informed prior probabilities, contributing to enhanced prediction accuracy for rare diseases. It also allows predictions without these additional tests, providing additional information on whether a patient should undergo further biomarker testing before genetic testing.
Group-based exercise for Parkinson’s: a qualitative study of participants and partners’ perceptions of an exercise class delivered through a community-university collaboration
Authors: Ferrusola-Pastrana Anna , Fullerton Christopher L , Meadows Stephen N 
Published: June 2024

AbstractBackgroundCommunity-based exercise programmes (CBEPs) offer a practical and viable approach to providing people with Parkinson’s disease (PwP) the opportunity to exercise as an ancillary therapeutic benefit to pharmacological management. This study explores the perceptions of exercising participants (PwP) and non-participating partners involved in an exercise class delivered through a community-university partnership.MethodsTwo separate focus group discussions were conducted: one with class participants (PwP:n = 7, H&Y scale I to III), and the other with non-participating partners of PwP (n = 4).ResultsThematic analysis of the data identified that a range of physical, psychological and social factors were perceived to influence engagement: (1) actively taking control, (2) exercise is medicine for the mind and body, and (3) a community working together to promote exercise for parkinson’s. Participants and partners felt that the support from the group, including the instructors and student volunteers, empowered and supported PwP to proactively self-manage their health, enjoy exercise in an inclusive group setting, and develop strong social connections with others in the local Parkinson’s community. Support to exercise from healthcare professionals was identified as both an enabler and barrier to participation.ConclusionsThis study underscores the significance of a community-university partnership as a complementary therapeutic approach for PwP. It also provides critical reflections on its sustainability, including implications for how exercise is considered as medicine for PwP. Additionally, it offers practical recommendations to galvanise community participation and provide inclusive and viable exercise opportunities for PwP.
Relationship between hukou conversion and psychological integration of rural older migrants: the mediating effect of accessibility to health resources
Authors: Cai Tianxin , Ma Shilong , Zhong Renyao , Lou Vivian W. Q. 
Published: June 2024

Abstract
Objective
This study investigates the relationship between hukou conversion and the psychological integration of rural older migrants, exploring the mediating role of accessibility to health resources.

Methods
The 3,963 valid samples of rural older migrants included in the study were sourced from the 2017 China Migrants Dynamic Survey (CMDS). The study established a multiple linear regression model for estimation and utilized inverse probability-weighted regression adjustment (IPWRA) method to correct for the selection bias of hukou conversion.

Results
Compared to older migrants with rural hukou, merit-based (β = 0.384, 95% CI: 0.265 to 0.504), family-based (β = 0.371, 95% CI: 0.178 to 0.565) and policy-based (β = 0.306, 95% CI: 0.124 to 0.487) converters have significantly higher psychological integration. These findings remain robust even after addressing the potential issue of endogenous selection bias using the IPWRA method. Bootstrap mediating effect tests indicate that hukou conversion can indirectly affect psychological integration through the mediator role of health resources accessibility.

Conclusion
Accessibility of health resources mediates the association between hukou conversion and psychological integration. Policymakers should enhance the implementation of hukou conversion, strengthen the health resource guarantee system, and achieve a deeper psychological integration among rural older migrants.
Access to urban green spaces and use of social services and institutional long-term care among older people in Malmö, Sweden: a longitudinal register study
Authors: Axmon Anna , Mattisson Kristoffer , Lethin Connie , Fänge Agneta Malmgren , Carlsson Gunilla , Stroh Emilie 
Published: June 2024

Abstract
Background
Finding ways to prolong independence in daily life among older people would be beneficial for both individuals and society. Urban green spaces have been found to improve health, but only a few studies have evaluated the association between urban green spaces and independence in daily life. The aim of this study was to assess the long-term effect of urban green spaces on independence in daily life, using social services and support, mobility aids, and relocation to institutional long-term care as proxies, among community dwelling people 65 + years.

Methods
We identified 40 357 people 65 + years living in the city of Malmö, Sweden in 2010. Using geographical information systems (GIS), we determined the amount of urban green spaces (total, public, and quiet) within 300 m of each person’s residence. All three measures were categorized based on their respective percentiles, so that the first quartile represented the 25% with the least access and the fourth quartile the 25% with the most access. In 2015 and 2019, we assessed the outcomes minor assistance (non-personal support), major assistance (personal support), and relocation into institutional long-term care. These three outcome measures were used as proxies for independence in daily life. The effect of amount of urban green spaces in 2010 on the three outcomes in 2015 and 2019, respectively, was assessed by pairwise comparing the three highest quartiles to the lowest.

Results
Compared to the lowest quartile, those in the highest quartile of quiet green spaces in 2010 were less likely to receive minor assistance in both 2015 and 2019. Besides this, there were no indications that any of the measures of urban green space affected independence in daily life at the five- and nine-year follow-up, respectively.

Conclusion
Although urban green spaces are known to have positive impact on health, physical activity, and social cohesion among older people, we found no effect of total, public, or quiet green spaces on independence in daily life. This could possibly be a result of the choice of measures of urban green spaces, including spatial and temporal aspects, an inability to capture important qualitative aspects of the green spaces, or the proxy measures used to assess independence in daily life.
Risk of cervical high-grade squamous intraepithelial neoplasia in cytologic negative and persistently high-risk human papillomavirus positive patients according to genotypes: a retrospective single center analysis
Authors: Kipp Barbara , Ulrich Elena , van Meegen Carmen , Schwenzer Thomas 
Published: June 2024

AbstractIn January 2020, a different cervical cancer screening program started in Germany. Women above the age of 35 are recommended to have a combined HPV and cytology swab every three years. Showing persistent high-risk human papillomavirus (hrHPV), cytologic negative cervical samples at baseline and after 12 months, patients are referred to colposcopy. Entailing considerable additional workload due to the required colposcopies, we analyzed the risk of high-grade cervical intraepithelial neoplasia (CIN 3) in cytologic negative and persistent hrHPV women according to their hrHPV genotypes.Methods In this single center retrospective study, patients with persistent hrHPV, cytology negative cervical samples from our certified Colposcopy Unit in 2020 and 2021 were analyzed. Patient demographics, hrHPV types, biopsy rates and histological reports were collected.Results During the study, 69 patients were enrolled. Most frequent hrHPV genotypes were: hrHPV other 72.5%; HPV 16, 20.3% and HPV 18, 7.2%. Colposcopy showed no or minor changes in 92.7% and major changes in 7.2%. CIN 3 was found in 7 patients (10.1%). Prevalence of CIN 3 by hrHPV genotypes was 27.3% for HPV16, 20.0% for HPV18 and 7.1% for HPVO. A statistically significant dependency between hrHPV and cervical intraepithelial neoplasia was demonstrated (p = 0.048).Conclusion Within this single center study of persistent hrHPV, cytologic negative samples, patients with HPV 16 were more likely to have high-grade disease compared to other hrHPV subtypes. Larger prospective randomized trials are needed to substantiate our results and obtain adjusted cervical cancer screening time intervals according to the hrHPV genotypes.
Empathy in undergraduate medical students: a multi-center cross-sectional study in China
Authors: Huang Runzhi , Zhou Zhitong , Liu Yifan , Lin Min , Gong Meiqiong , Xian Shuyuan , Yin Huabin , Meng Tong , Wang Xiaonan , Wang Yue , Chen Wenfang , Zhang Chongyou , Du Erbin , Liu Xin , Lin Qing , Wu Hongbin , Huang Zongqiang , Zhang Jie , Zhang Guoyang , Ji Shizhao 
Published: June 2024

Abstract
Background
Fostering empathy has been continuously emphasized in the global medical education. Empathy is crucial to enhance patient-physician relationships, and is associated with medical students’ academic and clinical performance. However, empathy level of medical students in China and related influencing factors are not clear.

Methods
This was a cross-sectional study among medical students in 11 universities. We used the Jefferson Scale of Empathy Student-version of Chinese version to measure empathy level of medical students. Factors associated with empathy were identified by the univariate and multivariate logistic regression analyses. Based on the variables identified above, the nomogram was established to predict high empathy probability of medical students. Receiver operating characteristic curve, calibration plot and decision curve analysis were used to evaluate the discrimination, calibration and educational utility of the model.

Results
We received 10,901 samples, but a total of 10,576 samples could be used for further analysis (effective response rate of 97.02%). The mean empathy score of undergraduate medical students was 67.38 (standard deviation = 9.39). Six variables including gender, university category, only child or not, self-perception doctor-patient relationship in hospitals, interest of medicine, Kolb learning style showed statistical significance with empathy of medical students (P < 0.05). Then, the nomogram was established based on six variables. The validation suggested the nomogram model was well calibrated and had good utility in education, as well as area under the curve of model prediction was 0.65.

Conclusions
We identify factors influencing empathy of undergraduate medical students. Moreover, increasing manifest and hidden curriculums on cultivating empathy of medical students may be needed among medical universities or schools in China.
Assessment of the appropriate cutoff points for anthropometric indices and their relationship with cardio-metabolic indices to predict the risk of metabolic associated fatty liver disease
Authors: Hosseini Seyed Ahmad , Alipour Meysam , Sarvandian Sara , Haghighat Neda , Bazyar Hadi , Aghakhani Ladan 
Published: June 2024

Abstract
Background
Research on Metabolic Associated Fatty Liver Disease (MAFLD) is still in its early stages, with few studies available to identify and predict effective indicators of this disease. On the other hand, early diagnosis and intervention are crucial to reduce the burden of MAFLD. Therefore, the aim of this research was to investigate the effectiveness of eleven anthropometric indices and their appropriate cut-off values as a non-invasive method to predict and diagnose MAFLD in the Iranian population.

Methods
In this cross-sectional study, we analyzed baseline data from the Hoveyzeh Cohort Study, a prospective population-based study conducted in Iran that enrolled a total of 7836 subjects aged 35 to 70 years from May 2016 through August 2018.

Results
The optimal cut-off values of anthropometric indices for predicting MAFLD risk were determined for waist circumference(WC) (102.25 cm for males and 101.45 cm for females), body mass index (BMI) (27.80 kg/m2 for males and 28.75 kg/m2 for females), waist-to-hip ratio (WHR) (0.96 for both males and females), waist-to-height ratio (WHtR) (0.56 for males and 0.63 for females), body adiposity index (BAI) (23.24 for males and 32.97 for females), visceral adiposity index (VAI) (1.64 for males and 1.88 for females), weight-adjusted waist index (WWI) (10.63 for males and 11.71 for females), conicity index (CI) (1.29 for males and 1.36 for females), body roundness index (BRI) (4.52 for males and 6.45 for females), relative fat mass (RFM) (28.18 for males and 44.91 for females) and abdominal volume index (AVI) (18.85 for males and for 21.37 females). VAI in males (sensitivity: 77%, specificity: 60%, Youden’s Index: 0.37) and RFM in females (sensitivity: 76%, specificity: 59%, Youden’s Index: 0.35) were found to have higher sensitivity and specificity compared to other anthropometric indices. Furthermore, anthropometric indices demonstrated statistically significant correlations with various hepatic and cardiometabolic indices. Among these, the strongest positive correlations were observed between WC, BMI, BAI, BRI, and AVI with the Hepatic Steatosis Index (HSI), TyG-BMI, and TyG-WC, as well as between VAI and the Atherogenic Index of Plasma (AIP), Lipid Accumulation Product (LAP), Cardiometabolic Index (CMI), and the Triglyceride and Glucose (TyG) Index.

Conclusion
Anthropometric indices are effective in predicting MAFLD risk among Iranian adults, with WWI, VAI, and RFM identified as the strongest predictors. The proposed cutoff values could serve as a straightforward and non-invasive methods for the early diagnosis of MAFLD.
The relationships of inflammatory blood markers with maternal periodontal and dental states and their effects on preterm membrane rupture development
Authors: Temur Isa , Temur Katibe Tugce , Donertas Safak Necati , Dönertas Aycan Dal 
Published: June 2024

Abstract
Background
The influence of maternal oral and dental health on the occurrence of Preterm Premature Rupture of Membranes (P-PROM) and its underlying mechanisms remain uncertain. This research seeks to investigate the impact of maternal oral and dental health on the incidence of P-PROM and its association with inflammatory markers in the blood.

Methods
This study adopts a prospective case-control design methodology. The study involved 70 women diagnosed with P-PROM and delivered by an obstetrician and 79 women who had healthy deliveries with no prenatal complications. The values for DMFT (Number of decayed, missing and filled teeth) index, Gingival Index (GI), Plaque index (PI), Pocket depth (PD), Clinical attachment loss (CAL) and medical history were recorded. Mann-Whitney U test and hierarchical binomial logistic regression analysis were applied. It was considered statistically significant at p < 0.05.

Results
The case group’s DMFT, PI, GI, PD values were statistically significantly higher than the control group (p < 0.001). There was no relationship between DMFT, GI, PD, CAL and inflammatory blood markers (p > 0.05). In the regression analysis for possible risk factors that may be effective in P-PROM, oral and dental health parameters were the most effective.

Conclusions
Oral and dental health of women with P-PROM was found to be worse than that of the control group. Oral and dental health may be a potential risk factor that may contribute to adverse pregnancy outcomes associated with P-PROM.