bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stigmas of holoparasitic Phelipanche arenaria (Orobanchaceae) – a suitable ephemeric flower habitat for development unique microbiome
Authors: Ruraż Karolina , Przemieniecki Sebastian Wojciech , Błaszak Magdalena , Czarnomska Sylwia Dagmara , Ochmian Ireneusz , Piwowarczyk Renata 
Published: October 2023

Abstract
Background
Microbial communities have occasionally been observed in part of the ephemeric reproductive structure of floral stigmas, but their prevalence, phylogenetic diversity and ecological roles are understudied. This report describes the first study of bacterial and fungal communities in immature and mature stigma tissue of the endangered holoparasitic plant Phelipanche arenaria. Culture-dependent methods coupled with next-generation sequencing indicated that a small surface of the flower stigma was an unexpectedly rich and diverse microhabitat for colonization of microbial. We also compared the enzymatic activity of the bacterial communities between immature and mature stigmas samples.

Results
Using high-throughput sequencing methods, we identified and classified 39 to over 51 OTUs per sample for bacterial OTUs represented by Pantoea agglomerans and P. ananatis, comprising 50.6%, followed by Pseudomonas, Luteibacter spp., Sphingomonas spp. with 17% of total frequency. The bacterial profile of immature stigmas of P. arenaria contained unique microorganisms (21 of the most numerous OTUs) that were not confirmed in mature stigmas. However, the enzymatic activity of bacteria in mature stigmas of P. arenaria showed more activity than observed in immature stigmas. In the fungal profile, we recorded even 80 OTUs in mature stigmas, consisting of Capnodiales 45.03% of the total abundance with 28.27% of frequency was created by Alternaria eichhorniae (10.55%), Mycosphaerella tassiana (9.69%), and Aureobasidium pullulans (8.03%). Additionally, numerous putative plant growth-promoting bacteria, fungal pathogens and pathogen-antagonistic yeasts were also detected.

Conclusions
Our study uncovered that P. arenaria stigmas host diverse bacterial and fungal communities. These microorganisms are well known and have been described as beneficial for biotechnological and environmental applications (e.g., production of different enzymes and antimicrobial compounds). This research provided valuable insight into the parasitic plant–microbe interactions.
Assembly and comparative analysis of the complete mitochondrial genome of Viburnum chinshanense
Authors: Zhu Haoxiang , Shan Yuanyu , Li Jingling , Zhang Xue , Yu Jie , Wang Haiyang 
Published: October 2023

Abstract
Background
Viburnum chinshanense is an endemic species found exclusively in the North-Central and South-Central regions of China. This species is a lush garden ornamental tree and is extensively utilized for vegetation restoration in rocky desertification areas.

Results
In this study, we obtained 13.96 Gb of Oxford Nanopore data for the whole genome, and subsequently, by combining Illumina short-reads, we successfully assembled the complete mitochondrial genome (mitogenome) of the V. chinshanense using a hybrid assembly strategy. The assembled genome can be described as a circular genome. The total length of the V. chinshanense mitogenome measures 643,971 bp, with a GC content of 46.18%. Our annotation efforts have revealed a total of 39 protein-coding genes (PCGs), 28 tRNA genes, and 3 rRNA genes within the V. chinshanense mitogenome. The analysis of repeated elements has identified 212 SSRs, 19 long tandem repeat elements, and 325 pairs of dispersed repeats in the V. chinshanense mitogenome. Additionally, we have investigated mitochondrial plastid DNAs (MTPTs) and identified 21 MTPTs within the mitogenome and plastidial genome. These MTPTs collectively span a length of 9,902 bp, accounting for 1.54% of the mitogenome. Moreover, employing Deepred-mt, we have confidently predicted 623 C to U RNA editing sites across the 39 protein-coding genes. Furthermore, extensive genomic rearrangements have been observed between V. chinshanense and the mitogenomes of related species. Interestingly, we have also identified a bacterial-derived tRNA gene (trnC-GCA) in the V. chinshanense mitogenome. Lastly, we have inferred the phylogenetic relationships of V. chinshanense with other angiosperms based on mitochondrial PCGs.

Conclusions
This study marks the first report of a mitogenome from the Viburnum genus, offering a valuable genomic resource for exploring the evolution of mitogenomes within the Dipsacales order.
Exploring the perspectives of selectors and collecters of trial outcome data: an international qualitative study
Authors: Green Heidi R. , Dawson Annabel , Elfeky Adel , Pickles David , Treweek Shaun , Gillies Katie 
Published: October 2023

Abstract
Introduction
Selecting and collecting data to support appropriate primary and secondary outcomes is a critical step in designing trials that can change clinical practice. In this study, we aimed to investigate who contributes to the process of selecting and collecting trial outcomes, and how these people are involved. This work serves two main purposes: (1) it provides the trials community with evidence to demonstrate how outcomes are currently selected and collected, and (2) it allows people involved in trial design and conduct to pick apart these processes to consider how efficiencies and improvements can be made.

Methods
One-with-one semi-structured interviews, supported by a topic guide to ensure coverage of key content. The Framework approach was used for thematic analysis of data, and themes were linked through constant comparison of data both within and across participant groups. Interviews took place between July 2020 and January 2021. Participants were twenty-nine international trialists from various contributor groups, working primarily on designing and/or delivering phase III pragmatic effectiveness trials. Their experience spanned various funders, trial settings, clinical specialties, intervention types, and participant populations.

Results
We identified three descriptive themes encompassing the process of primary and secondary outcome selection, collection, and the publication of outcome data. Within these themes, participants raised issues around the following: 1) Outcome selection: clarity of the research question; confidence in selecting trial outcomes and how confidence decreases with increased experience; interplay between different interested parties; how patients and the public are involved in outcome selection; perceived impact of poor outcome selection including poor recruitment and/or retention; and use of core outcome sets. 2) Outcome collection: disconnect between decisions made by outcome selectors and the practical work done by outcome collectors; potential impact of outcome measures on trial participants; potential impact on trial staff workload; and use of routinely collected data. 3) Publication of outcome data: difficulties in finding time to write and revise manuscripts for publication due to time and funding constraints. Participants overwhelmingly focused on the process of outcome selection, a topic they talked about unprompted. When prompted, participants do discuss outcome collection, but poor communication between selectors and collectors at the trial design stage means that outcome selection is rarely linked with the data collection workload it generates.

Discussion
People involved in the design and conduct of trials fail to connect decisions around outcome selection with data collection workload. Publication of outcome data and effective dissemination of trial results are hindered due to the project-based culture of some academic clinical trial research.
An improved multiply robust estimator for the average treatment effect
Authors: Wang Ce , Wei Kecheng , Huang Chen , Yu Yongfu , Qin Guoyou 
Published: October 2023

AbstractBackgroundIn observational studies, double robust or multiply robust (MR) approaches provide more protection from model misspecification than the inverse probability weighting and g-computation for estimating the average treatment effect (ATE). However, the approaches are based on parametric models, leading to biased estimates when all models are incorrectly specified. Nonparametric methods, such as machine learning or nonparametric double robust approaches, are robust to model misspecification, but the efficiency of nonparametric methods is low.MethodIn the study, we proposed an improved MR method combining parametric and nonparametric models based on the previous MR method (Han, JASA 109(507):1159-73, 2014) to improve the robustness to model misspecification and the efficiency. We performed comprehensive simulations to evaluate the performance of the proposed method.ResultsOur simulation study showed that the MR estimators with only outcome regression (OR) models, where one of the models was a nonparametric model, were the most recommended because of the robustness to model misspecification and the lowest root mean square error (RMSE) when including a correct parametric OR model. And the performance of the recommended estimators was comparative, even if all parametric models were misspecified. As an application, the proposed method was used to estimate the effect of social activity on depression levels in the China Health and Retirement Longitudinal Study dataset.ConclusionsThe proposed estimator with nonparametric and parametric models is more robust to model misspecification.
Causal inference and observational data
Authors: Olier Ivan , Zhan Yiqiang , Liang Xiaoyu , Volovici Victor 
Published: October 2023

AbstractObservational studies using causal inference frameworks can provide a feasible alternative to randomized controlled trials. Advances in statistics, machine learning, and access to big data facilitate unraveling complex causal relationships from observational data across healthcare, social sciences, and other fields. However, challenges like evaluating models and bias amplification remain.
“The measures taken by the government overburdened the daily practice” – insights of the PRICOV-19 study on German general practitioners in times of COVID-19
Authors: Stark Stefanie , Schaubroeck Emmily , Kluge Marie , Burggraf Larissa , Roos Marco , Borowski Eve , Van Poel Esther , Willems Sara , Kühlein Thomas , Hueber Susann , Werner Felix 
Published: October 2023

Abstract
Background
The international study PRICOV-19 aims to assess the impact of the COVID-19 pandemic on the organisation of primary health care. The German part focuses on German general practitioners during the second wave of the COVID-19 pandemic. This paper addresses the following research questions: (1) How were changes in tasks on primary care and patient treatment perceived by GPs?, (2) What was the role of GPs during the pandemic, and how was their wellbeing?, (3) How did GPs perceive health policy measures?, and, (4) What influenced the attitudes of GPs on health policy measures?

Methods
This study pursues a multi-country cross-sectional design. Data collection took place throughout Germany from 01.02. to 28.02.2021 with a quantitative online questionnaire consisting of 53 items. The questionnaire was analysed through descriptive and inferential analyses using correlation and multiple regression models.

Results
The response rate was 20.4% (n = 349). The respondents were mainly GPs (59.6%) in single practices (62.5%) with a mean work experience of 15 to 20 years. GPs experienced a change in their work and practice organisation (80.3%). They felt a high responsibility (70.6%) and found their work has become more meaningful to them (76%). They also saw a lack of political support (75.2%) and that the measures taken by the government overburdened the daily practice (66.4%). Not many GPs were at risk of being distressed (53.4%) but rated the health policies rather negatively (60%). The multiple regression showed, the more GPs were exposed to risk of distress, the worse they assessed the government's measures.

Conclusion
GPs perceived their work as relevant and felt confident they could fulfil their tasks, but noticed that health policy initially hardly supported the outpatient sector. Health policies should increase their competence in relation to primary care, ensure its needs and consider an active inclusion of GPs in preparedness plans.
Lower serum Klotho level and higher systemic immune-inflammation index: an inverse correlation
Authors: Chen Ping , Tang Yafen , Luo Liang , Chen Haotian , He Xingkang 
Published: October 2023

Abstract
Objectives
Klotho, an anti-aging protein, has been identified to control tissue inflammatory responses. The objective of this research is to determine the linkage between soluble Klotho (S-Klotho) level and systemic immune-inflammation index (SII).

Methods
Eligible participants with complete information of S-Klotho level and SII were selected from the National Health and Nutrition Examination Surveys (NHANES). Subsequently, weighted multivariate linear regression and subgroup analysis were carried out to evaluate the association.

Results
Totally, 11,108 adults with complete data on S-Klotho level, SII and other important covariates were included in final analysis. Multivariate liner regression revealed that high level of S-Klotho was associated with low level of SII after multivariate adjustments (β=-0.08, 95%CI:-0.10- -0.05, P < 0.01). When classifying S-Klotho into tertiles, participants in S-Klotho tertile 3 (Q3) showed a decrease in SII level compared with those in the lowest tertile (Q1) (β=-45.44, 95%CI:-64.41- -26.47, P < 0.01 ). The negative associations remained significant regardless of age and gender, and varied depending on smoking status and BMI subgroups.

Conclusion
S-Klotho level was negatively related to SII after controlling for covariates. Further studies need to validate current findings and explore the fundamental mechanisms.
Dietary amino acid intake and sleep duration are additively involved in future cognitive decline in Japanese adults aged 60 years or over: a community-based longitudinal study
Authors: Kinoshita Kaori , Otsuka Rei , Takada Michihiro , Nishita Yukiko , Tange Chikako , Jinzu Hiroko , Suzuki Katsuya , Shimokata Hiroshi , Imaizumi Akira , Arai Hidenori 
Published: October 2023

Abstract
Background
Sleep duration and amino acid intake are independently associated with cognitive decline. This study aimed to determine the longitudinal association between sleep duration and cognitive impairment incidence and to examine the involvement of diet, particularly amino acid intake, in these associations in community dwellers.

Methods
In this longitudinal study in a community-based setting, we analyzed data from 623 adults aged 60–83 years without cognitive impairment at baseline. Sleep duration was assessed using a self-report questionnaire. Amino acid intake was assessed using 3-day dietary records. Cognitive impairment was defined as a Mini-Mental State Examination score ≤ 27. Participants were classified into short-, moderate-, and long-sleep groups according to baseline sleep duration (≤ 6, 7–8, and > 8 h, respectively). Using moderate sleep as a reference, odds ratios (ORs) and 95% confidence intervals (CIs) of short- and long-sleep for cognitive-impairment incidence were estimated using the generalized estimating equation. Participants were classified according to sex-stratified quartiles (Q) of 19 amino acid intake: Q1 and Q2–Q4 were low- and middle to high-intake groups, respectively. Using middle- to high-intake as a reference, ORs and 95% CIs of low intake for cognitive impairment incidence were estimated using the generalized estimating equation in each sleep-duration group. Follow-up period, sex, age, body mass index, depressive symptoms, education, smoking status, employment status, sleep aids use, physical activity, medical history, and Mini-Mental State Examination score at baseline were covariates.

Results
Mean follow-up period was 6.9 ± 2.1 years. Adjusted ORs (95% CIs) for cognitive impairment in short- and long-sleep groups were 0.81 (0.49–1.35, P = 0.423) and 1.41 (1.05–1.87, P = 0.020), respectively. Particularly in long sleepers (i.e., > 8 h), cognitive impairment was significantly associated with low cystine, proline, and serine intake [adjusted ORs (95% CIs) for cognitive impairment were 2.17 (1.15–4.11, P = 0.017), 1.86 (1.07–3.23, P = 0.027), and 2.21 (1.14–4.29, P = 0.019), respectively].

Conclusions
Community-dwelling adults aged ≥ 60 years who sleep longer are more likely to have cognitive decline, and attention should be paid to the low cystine, proline, and serine intake.
Association between elevated serum uric acid levels and high estimated glomerular filtration rate with reduced risk of low muscle strength in older people: a retrospective cohort study
Authors: Huang Yu Cheng , Chen Si Liang , Dong Ying , Shi Ying 
Published: October 2023

Abstract
Background
We aimed to investigate the interaction between serum uric acid (SUA) levels with estimated glomerular filtration rate (eGFR) to low muscle strength (LMS) among older people in China.

Methods
Cohort data were obtained from China Health and Retirement Longitudinal Study (CHARLS) in 2011 and 2015. A total of 2,822 community-dwelling adults aged 60 and above were enrolled for the follow-up. Serum uric acid was collected after 8 h of fasting, and handgrip strength was measured with a dynamometer. eGFR was calculated with an equation based on the Chinese population. A generalized additive model was employed for interaction analysis and progressively adjusted confounders.

Results
During the follow-up, a total of 659 individuals were excluded due to the lack of grip strength data, leaving 2,163 participants for analysis. Despite the protective effect of high uric acid against low muscle strength, especially in older females, it is not statistically significant (OR = 0.69, 95%CI = 0.45–1.04, P = 0.075). Following the progressive adjustment of covariates, the association between higher eGFR and elevated SUA levels remained statistically significant in females, showing a reduced odds ratio with low muscle strength (OR = 0.82, 95%CI = 0.70–0.97, P = 0.021). However, this trend was not observed in male participants.

Conclusions
This Chinese population-based cohort study suggests that among older females, a higher serum uric acid level combined with a higher estimated glomerular filtration rate is linked to a reduced risk of low muscle strength. This implies that the relationship between high serum uric acid levels and the risk of low grip strength might differ by gender.
A nomogram based on the expression level of angiopoietin-like 4 to predict the severity of community-acquired pneumonia
Authors: Chen Siqin , Jiang Jia , Su Minhong , Chen Ping , Liu Xiang , Lei Wei , Zhang Shaofeng , Wu Qiang , Rong Fu , Li Xi , Zheng Xiaobin , Xiao Qiang 
Published: October 2023

Abstract
Background
The morbidity and mortality of community-acquired pneumonia (CAP) remain high among infectious diseases. It was reported that angiopoietin-like 4 (ANGPTL4) could be a diagnostic biomarker and a therapeutic target for pneumonia. This study aimed to develop a more objective, specific, accurate, and individualized scoring system to predict the severity of CAP.

Methods
Totally, 31 non-severe community-acquired pneumonia (nsCAP) patients and 14 severe community-acquired pneumonia (sCAP) patients were enrolled in this study. The CURB-65 and pneumonia severity index (PSI) scores were calculated from the clinical data. Serum ANGPTL4 level was measured by enzyme-linked immunosorbent assay (ELISA). After screening factors by univariate analysis and receiver operating characteristic (ROC) curve analysis, multivariate logistic regression analysis of ANGPTL4 expression level and other risk factors was performed, and a nomogram was developed to predict the severity of CAP. This nomogram was further internally validated by bootstrap resampling with 1000 replications through the area under the ROC curve (AUC), the calibration curve, and the decision curve analysis (DCA). Finally, the prediction performance of the new nomogram model, CURB-65 score, and PSI score was compared by AUC, net reclassification index (NRI), and integrated discrimination improvement (IDI).

Results
A nomogram for predicting the severity of CAP was developed using three factors (C-reactive protein (CRP), procalcitonin (PCT), and ANGPTL4). According to the internal validation, the nomogram showed a great discrimination capability with an AUC of 0.910. The Hosmer–Lemeshow test and the approximately fitting calibration curve suggested a satisfactory accuracy of prediction. The results of DCA exhibited a great net benefit. The AUC values of CURB-65 score, PSI score, and the new prediction model were 0.857, 0.912, and 0.940, respectively. NRI comparing the new model with CURB-65 score was found to be statistically significant (NRI = 0.834, P < 0.05).

Conclusion
A robust model for predicting the severity of CAP was developed based on the serum ANGPTL4 level. This may provide new insights into accurate assessment of the severity of CAP and its targeted therapy, particularly in the early-stage of the disease.
Preoperative prediction of cervical cancer survival using a high-resolution MRI-based radiomics nomogram
Authors: Li Jia , Zhou Hao , Lu Xiaofei , Wang Yiren , Pang Haowen , Cesar Daniel , Liu Aiai , Zhou Ping 
Published: October 2023

AbstractBackgroundCervical cancer patients receiving radiotherapy and chemotherapy require accurate survival prediction methods. The objective of this study was to develop a prognostic analysis model based on a radiomics score to predict overall survival (OS) in cervical cancer patients.MethodsPredictive models were developed using data from 62 cervical cancer patients who underwent radical hysterectomy between June 2020 and June 2021. Radiological features were extracted from T2-weighted (T2W), T1-weighted (T1W), and diffusion-weighted (DW) magnetic resonance images prior to treatment. We obtained the radiomics score (rad-score) using least absolute shrinkage and selection operator (LASSO) regression and Cox’s proportional hazard model. We divided the patients into low- and high-risk groups according to the critical rad-score value, and generated a nomogram incorporating radiological features. We evaluated the model’s prediction performance using area under the receiver operating characteristic (ROC) curve (AUC) and classified the participants into high- and low-risk groups based on radiological characteristics.ResultsThe 62 patients were divided into high-risk (n = 43) and low-risk (n = 19) groups based on the rad-score. Four feature parameters were selected via dimensionality reduction, and the scores were calculated after modeling. The AUC values of ROC curves for prediction of 3- and 5-year OS using the model were 0.84 and 0.93, respectively.ConclusionOur nomogram incorporating a combination of radiological features demonstrated good performance in predicting cervical cancer OS. This study highlights the potential of radiomics analysis in improving survival prediction for cervical cancer patients. However, further studies on a larger scale and external validation cohorts are necessary to validate its potential clinical utility.