bluuebunny/crossref_metadata_2025_split huggingface dataset:
Machine learning based study for the classification of Type 2 diabetes mellitus subtypes
Authors: Ordoñez-Guillen Nelson E. , Gonzalez-Compean Jose Luis , Lopez-Arevalo Ivan , Contreras-Murillo Miguel , Aldana-Bobadilla Edwin 
Published: August 2023

Abstract
Purpose
Data-driven diabetes research has increased its interest in exploring the heterogeneity of the disease, aiming to support in the development of more specific prognoses and treatments within the so-called precision medicine. Recently, one of these studies found five diabetes subgroups with varying risks of complications and treatment responses. Here, we tackle the development and assessment of different models for classifying Type 2 Diabetes (T2DM) subtypes through machine learning approaches, with the aim of providing a performance comparison and new insights on the matter.

Methods
We developed a three-stage methodology starting with the preprocessing of public databases NHANES (USA) and ENSANUT (Mexico) to construct a dataset with N = 10,077 adult diabetes patient records. We used N = 2,768 records for training/validation of models and left the remaining (N = 7,309) for testing. In the second stage, groups of observations –each one representing a T2DM subtype– were identified. We tested different clustering techniques and strategies and validated them by using internal and external clustering indices; obtaining two annotated datasets Dset A and Dset B. In the third stage, we developed different classification models assaying four algorithms, seven input-data schemes, and two validation settings on each annotated dataset. We also tested the obtained models using a majority-vote approach for classifying unseen patient records in the hold-out dataset.

Results
From the independently obtained bootstrap validation for Dset A and Dset B, mean accuracies across all seven data schemes were $$85.3\%$$

85.3
%

($$\pm 9.2\%$$

±
9.2
%

) and $$97.1\%$$

97.1
%

($$\pm 3.4\%$$

±
3.4
%

), respectively. Best accuracies were $$98.8\%$$

98.8
%

and $$98.9\%$$

98.9
%

. Both validation setting results were consistent. For the hold-out dataset, results were consonant with most of those obtained in the literature in terms of class proportions.

Conclusion
The development of machine learning systems for the classification of diabetes subtypes constitutes an important task to support physicians for fast and timely decision-making. We expect to deploy this methodology in a data analysis platform to conduct studies for identifying T2DM subtypes in patient records from hospitals.
How does the clinical practice of Aotearoa New Zealand podiatrists align with international guidelines for the prevention of diabetes‐related foot disease? A cross‐sectional survey
Authors: Jepson Hannah , Lazzarini Peter A , Garrett Michele , Carroll Matthew R 
Published: August 2023

AbstractBackgroundGiven the importance of preventive care for the lower limb in people with diabetes, and the absence of local guidelines in Aotearoa New Zealand (NZ), the aim of this study was to determine the alignment of assessment and management used in the prevention of diabetes‐related foot disease by NZ podiatrists to the international prevention guideline recommendations.
MethodsA 37‐item web‐based survey was developed using a 5‐point Likert scale (0 = always; 5 = never) based on the International Working Group of the Diabetic Foot (IWGDF) 2019 prevention guidelines and included domains on participant demographics, sector, caseloads, guidelines, screening, management, education, and referral. The survey was distributed to NZ podiatrists through the NZ podiatry association and social media. Participants completing > 50% of items were included. The Mann‐Whitney U test was used to examine differences between sector subgroups.ResultsSeventy‐seven responses (16.3% of the NZ podiatry workforce) were received, of which 52 completed > 50% of items and were included. Of those 52 podiatrists, 73% were from the private sector. Public sector podiatrists reported higher weekly caseloads of patients with diabetes (p = 0.03) and foot ulcers (p < 0.001). The New Zealand Society for the Study of Diabetes (NZSSD) risk stratification pathway and IWGDF guidelines were the two most frequently utilised guidance documents. Participants reported median scores of at least “often” (< 2) for all items in the assessment and management, inspection, examination, and education provision domains for people with a high‐risk foot. More than 50% of respondents reported screening more frequently than guideline recommendations for people with a very low to moderate risk foot. Structured education program was only used by 4 (5%) participants. Public sector podiatrists reported greater provision of custom‐made footwear (p = 0.04) and multi‐disciplinary team care (p = 0.03).
ConclusionNZ podiatrists generally follow international guideline recommendations with respect to screening, self‐care education, appropriate footwear, and treatment of risk factors for people at‐risk of diabetes‐related foot disease. However there may be over‐screening of people with very low to medium risk occurring in clinical practice. Increasing access to integrated healthcare, custom‐made footwear and structured educational programmes appear to be areas of practice that could be developed in future to help prevent diabetes‐related foot disease in NZ.
A randomized control trial to support smoke-free policy compliance in public housing
Authors: Hernandez Diana , Khan Farzana , Albert David , Giovenco Daniel , Branas Charles , Valeri Linda , Navas-Acien Ana 
Published: August 2023

Abstract
Background
Smoke-free housing policies in multiunit housing are increasingly widespread interventions to reduce smoking and secondhand smoke exposure. Little research has identified factors that impede compliance with smoke-free housing policies in low-income multiunit housing and test corresponding solutions.

Methods
We are using an experimental design to test two compliance support interventions: (A) a “compliance through reduction (via relocation and reduction in personal smoking) and cessation” intervention targets households with smokers and involves support to shift smoking practices to areas beyond the apartment or building setting, reduce personal smoking, and deliver in-residence smoking cessation support services via trained peer educators and (B) a “compliance through resident endorsement” intervention involving voluntary adoption of smoke-free living environments through personal pledges, visible door markers, and/or via social media. We will compare randomly sampled participants in buildings that receive A or B or A plus B to the NYCHA standard approach.

Discussion
This RCT addresses key gaps in knowledge and capitalizes on key scientific opportunities by (1) leveraging the federal mandate to ban smoking in a public housing system of more than sufficient size to conduct an adequately powered RCT; (2) expanding our understanding of smoke-free policy compliance beyond policy implementation by testing two novel treatments: (a) in-residence smoking cessation and (b) resident endorsement, while (3) addressing population and location-specific tobacco-related disparities. At the conclusion of the study, this RCT will have leveraged a monumental policy shift affecting nearly half a million NYC public housing residents, many of whom disproportionately experience chronic illness and are more likely to smoke and be exposed to secondhand smoke than other city residents. This first-ever RCT will test the effects of much-needed compliance strategies on resident smoking behavior and secondhand smoke exposure in multiunit housing.

Trial registration
Clinical Trials Registered, NCT05016505. Registered on August 23, 2021.
Community-based integrated care for patients with diabetes and depression (CIC-PDD): study protocol for a cluster randomized controlled trial
Authors: Wang Yanshang , Guo Dan , Wang Ming , Hu Mingzheng , Zhu Dawei , Yu Qianqian , Li Zhansheng , Zhang Xiaoyi , Ding Ruoxi , Zhao Miaomiao , He Ping 
Published: August 2023

Abstract
Background
Managing the multimorbidity of diabetes and depression remains a clinical challenge for patients and healthcare professionals due to the fragmented healthcare delivery system. To effectively cope with multimorbidity, there is an urgent need for the health system to transform into people-centered integrated care (PCIC) system globally. Therefore, this paper describes the protocol of community-based integrated care for patients with diabetes and depression (CIC-PDD) project, an integrated and shared-care intervention project.

Methods/design
CIC-PDD project is conducted in two phases, namely “care model development” and “implementation and evaluation.” In the first phase, CIC-PDD model was designed and developed based on the four criteria of collaborative care model (CCM) and was subsequently adjusted to align with the context of China. The second phase entails a pragmatic, two-arm, cluster randomized controlled implementation trial, accompanied by parallel mixed-methods process evaluation and cost-effectiveness analysis.

Discussion
We anticipate CIC-PDD project will facilitate the development and innovation of PCIC model and related theories worldwide, particularly in low- and middle-income countries (LMICs). In addition, CIC-PDD project will contribute to the exploration of primary health care (PHC) in addressing the multimorbidity of physical and mental health issues.

Trial registration
ClinicalTrials.gov registration ChiCTR2200065608 (China Clinical Trials Registry https://www.chictr.org.cn). Registered on November 9, 2022.
Quantification of transcriptome changes to investigate the role of glucocorticoid receptor-RNA binding during dexamethasone treatment
Authors: Lammer Nickolaus C. , Allen Mary A. , Batey Robert T. , Wuttke Deborah S. 
Published: August 2023

Abstract
Objectives
The glucocorticoid receptor (GR) is a well-studied, ligand-activated transcription factor and a common target of anti-inflammatory treatments. Recently, several studies have drawn attention the effects of binding of GR to RNA rather than DNA and the potential implications of this activity for GR function. The objective of our study was to further characterize the relationship between GR function and RNA binding by measuring changes in the glucocorticoid-driven transcriptome in the presence of a GR mutant that exhibited reduced RNA affinity.

Data description
GR was activated in three cell lines containing GR constructs (GR-HaloTag). One of the cell lines contained a wild-type GR-HaloTag. Another contained GR-HaloTag with a mutation that reduced RNA affinity and slightly reduced DNA affinity. The third cell line contained GR-HaloTag with a mutation that only slightly reduced DNA affinity. All three cell lines were treated with dexamethasone, a GR agonist. RNA-seq samples were collected every hour for 3 h. Moreover, transcriptome quantification was accomplished via labeling of RNAs transcribed in the final hour of dexamethasone treatment using 4-thiouridine. These labeled RNAs were then purified and sequenced. This data set is the first of its kind for GR and contains valuable insights into the function of RNA binding by GR.
Weissella confusa F213 ameliorated inflammation and maintained intestinal mucosa integrity in chemically induced colitis rats
Authors: Sujaya I Nengah , Dharmika Ida Ayu Gde Wahyudevi , Suwardana Gede Ngurah Rsi , Mariadi I Ketut , Arijana I Gusti Kamasan Nyoman , Winaya Ida Bagus Oka , Nocianitri Komang Ayu , Ramona Yan , Fatmawati Ni Nengah Dwi 
Published: August 2023

Abstract
Objective
This study was performed to investigate the potential effects of Weissella confusa F213 (WCF213) on chemically-induced colitis rats. Twelve male Wistar rats were divided into three groups: T1 (saline sterile), T2 (2.5% dextran sulfate sodium (DSS)- for 7 days), and T3 (WCF213 for 14 days, continued with 2.5% DSS for 7 days). The disease activity index (DAI) was monitored. After sacrificing the rats, the colon was collected for length measurement, local TNF-α level, HE staining for histology, and ZO-1 expression by using immunohistochemistry.

Results
WCF213 administration prevented weight loss and haematochezia, maintained average colon length and alleviated the clinical symptom of colitis, such as diarrhoea, albeit statistically non-significant (p < 0.05) compared with the T2 group. The histopathology of WCF213-treated colitis rats showed better architecture and less inflammatory cell infiltration into colon tissue. WCF213 significantly maintained the expression of ZO-1 in the mucosa (p < 0.001) and markedly reduced mucosal TNF-α concentration (p < 0.001) compared with the DSS group. Hence, these findings suggested that WCF213 attenuated clinical symptoms and inflammation and maintained mucosal integrity in DSS-induced colitis in vivo.
A metagenomic study of gut viral markers in amyloid-positive Alzheimer’s disease patients
Authors: Ghorbani Mahin , Ferreira Daniel , Maioli Silvia 
Published: August 2023

Abstract
Background
Mounting evidence suggests the involvement of viruses in the development and treatment of Alzheimer’s disease (AD). However, there remains a significant research gap in metagenomic studies investigating the gut virome of AD patients, leaving gut viral dysbiosis in AD unexplored. This study aimed to fill this gap by conducting a metagenomics analysis of the gut virome in both amyloid-positive AD patients (Aβ + ADs) and healthy controls (HCs), with the objective of identifying viral signatures linked with AD.

Method
Whole-genome sequence (WGS) data from 65 human participants, including 30 Aβ + ADs and 35 HCs, was obtained from the database NCBI SRA (Bio Project: PRJEB47976). The Metaphlan3 pipeline and linear discriminant analysis effect size (LEfSe) analysis were utilized for the bioinformatics process and the detection of viral signatures, respectively. In addition, the Benjamini–Hochberg method was applied with a significance cutoff of 0.05 to evaluate the false discovery rate for all biomarkers identified by LEfSe. The CombiROC model was employed to determine the discriminatory power of the viral signatures identified by LEfSe.

Results
Compared to HCs, the gut virome profiles of Aβ + ADs showed lower alpha diversity, indicating a lower bacteriophage richness. The Siphoviridae family was decreased in Aβ + ADs. Significant decreases of Lactococcus phages were found in Aβ + ADs, including bIL285, Lactococcus phage bIL286, Lactococcus phage bIL309, and Lactococcus phage BK5 T, Lactococcus phage BM13, Lactococcus phage P335 sensu lato, Lactococcus phage phiLC3, Lactococcus phage r1t, Lactococcus phage Tuc2009, Lactococcus phage ul36, and Lactococcus virus bIL67. The predictive combined model of these viral signatures obtained an area under the curve of 0.958 when discriminating Aβ + ADs from HCs.

Conclusion
This is the first study to identify distinct viral signatures in the intestine that can be used to effectively distinguish individuals with AD from HCs.
Diagnostic performance of prediction models for extraprostatic extension in prostate cancer: a systematic review and meta-analysis
Authors: Zhu MeiLin , Gao JiaHao , Han Fang , Yin LongLin , Zhang LuShun , Yang Yong , Zhang JiaWen 
Published: August 2023

Abstract
Purpose
In recent decades, diverse nomograms have been proposed to predict extraprostatic extension (EPE) in prostate cancer (PCa). We aimed to systematically evaluate the accuracy of MRI-inclusive nomograms and traditional clinical nomograms in predicting EPE in PCa. The purpose of this meta-analysis is to provide baseline summative and comparative estimates for future study designs.

Materials and methods
The PubMed, Embase, and Cochrane databases were searched up to May 17, 2023, to identify studies on prediction nomograms for EPE of PCa. The risk of bias in studies was assessed by using the Prediction model Risk Of Bias ASsessment Tool (PROBAST). Summary estimates of sensitivity and specificity were obtained with bivariate random-effects model. Heterogeneity was investigated through meta-regression and subgroup analysis.

Results
Forty-eight studies with a total of 57 contingency tables and 20,395 patients were included. No significant publication bias was observed for either the MRI-inclusive nomograms or clinical nomograms. For MRI-inclusive nomograms predicting EPE, the pooled AUC of validation cohorts was 0.80 (95% CI: 0.76, 0.83). For traditional clinical nomograms predicting EPE, the pooled AUCs of the Partin table and Memorial Sloan Kettering Cancer Center (MSKCC) nomogram were 0.72 (95% CI: 0.68, 0.76) and 0.79 (95% CI: 0.75, 0.82), respectively.

Conclusion
Preoperative risk stratification is essential for PCa patients; both MRI-inclusive nomograms and traditional clinical nomograms had moderate diagnostic performance for predicting EPE in PCa. This study provides baseline comparative values for EPE prediction for future studies which is useful for evaluating preoperative risk stratification in PCa patients.

Critical relevance statement
This meta-analysis firstly evaluated the diagnostic performance of preoperative MRI-inclusive nomograms and clinical nomograms for predicting extraprostatic extension (EPE) in prostate cancer (PCa) (moderate AUCs: 0.72–0.80). We provide baseline estimates for EPE prediction, these findings will be useful in assessing preoperative risk stratification of PCa patients.

Key points
• MRI-inclusive nomograms and traditional clinical nomograms had moderate AUCs (0.72–0.80) for predicting EPE.
• MRI combined clinical nomogram may improve diagnostic accuracy of MRI alone for EPE prediction.
• MSKCC nomogram had a higher specificity than Partin table for predicting EPE.
• This meta-analysis provided baseline and comparative estimates of nomograms for EPE prediction for future studies.

Graphical Abstract
Unhealthy food availability, prominence and promotion in a representative sample of supermarkets in Flanders (Belgium): a detailed assessment
Authors: Vandevijvere Stefanie , Van Dam Iris , Inaç Yasemin , Smets Vincent 
Published: August 2023

Abstract
Introduction
The supermarket food environment is a key setting for potential public health interventions. This study assessed food availability, prominence and promotion in a representative sample of supermarkets in Flanders (Belgium).

Methods
A sample of 55 supermarkets across five chains and 16 Flemish municipalities was selected in 2022, about 64% in the most deprived socioeconomic areas. Healthiness indicators related to food availability (ratio of cumulative linear shelf length for healthy versus unhealthy foods), prominence (proportion of unhealthy foods at check-outs and end-of-aisle endcaps), and promotion (food marketing on food packages) were measured.

Results
Overall, the average ratio of healthy/unhealthy foods in supermarkets in Flanders was 0.36, meaning that for every 10m of shelf length of unhealthy foods there was 3.6m of healthy foods. There was a large variation in ratio’s across supermarket chains. Of all foods available, 97.5% were ultra-processed at the check outs, while 72.2% and 58.5% were ultra-processed at the front and back end-of-aisle end-caps, respectively. Confectionery and sweet biscuits were the food categories with on average the highest number of marketing messages on pack per 10m of shelf length.

Conclusion
Supermarket in-store food environments in Flanders were found generally unhealthy, with those located in low income areas having unhealthier in-store food environments than supermarkets located in medium and high income areas. Despite commitments of all large supermarket chains in Flanders to promote and create healthier in-store food environments, our findings indicate that currently consumers are incentivized to buy unhealthy rather than healthy food products.
Hospital cleaning: past, present, and future
Authors: Dancer Stephanie J. 
Published: August 2023

Abstract
Introduction
The importance of hospital cleaning for controlling healthcare-associated infection (HAI) has taken years to acknowledge. This is mainly because the removal of dirt is inextricably entwined with gender and social status, along with lack of evidence and confusion over HAI definitions. Reducing so-called endogenous infection due to human carriage entails patient screening, decolonisation and/or prophylaxis, whereas adequate ventilation, plumbing and cleaning are needed to reduce exogenous infection. These infection types remain difficult to separate and quantitate. Patients themselves demonstrate wide-ranging vulnerability to infection, which further complicates attempted ranking of control interventions, including cleaning. There has been disproportionate attention towards endogenous infection with less interest in managing environmental reservoirs.

Quantifying cleaning and cleanliness
Finding evidence for cleaning is compromised by the fact that modelling HAI rates against arbitrary measurements of cleaning/cleanliness requires universal standards and these are not yet established. Furthermore, the distinction between cleaning (soil removal) and cleanliness (soil remaining) is usually overlooked. Tangible bench marking for both cleaning methods and all surface types within different units, with modification according to patient status, would be invaluable for domestic planning, monitoring and specification.

Aims and objectives
This narrative review will focus on recent history and current status of cleaning in hospitals. While its importance is now generally accepted, cleaning practices still need attention in order to determine how, when and where to clean. Renewed interest in removal and monitoring of surface bioburden would help to embed risk-based practice in hospitals across the world.
Antifungal effects of seven plant essential oils against Penicillium digitatum
Authors: Zulu Lovemore , Gao Hongshan , Zhu Yijing , Wu Huiming , Xie Yongjian , Liu Xunyue , Yao Haifeng , Rao Qiong 
Published: August 2023

Abstract
Background
Research interest in plant essential oils has increased significantly due to their natural properties and consumer demand for safer methods of food preservation. Plants produce large amounts of secondary metabolites, which have potential activity against fungal pathogens. This study aimed at screening essential oils for their antifungal effects on citrus against Penicillium digitatum, morphological effect and finally determine which essential oils are the most effective.

Results
The EC50 of seven selected cinnamon (0.424 μL/mL), patchouli (0.513 μL/mL), vetiver (0.612 μL/mL), dill (1.597 μL/mL), origanum (1.971 μL/mL) and ylang (2.214 μL/mL) was determined. In addition, cinnamon substantially reduced sporulation (100%) followed by patchouli (86.02%), vetiver (82.73%), and chamomile (79.04%), respectively. Our GC–MS result determined variance in concentration of essential oils compound composition. The total compound composition in all seven essential oils > 1% was found to be 3 in cinnamon, 5 in dill, 10 in origanum, 13 in ylang, 11 in patchouli, 9 in chamomile and 16 in vetiver. Addition of essential oils significantly altered fungal morphology by scanning electron cryomicroscopy. Patchouli and origanum showed broken hyphae while there was an indication of severe deformation and collapse of spores in cinnamon and chamomile.

Conclusion
Based on our findings, we report that these essential oils could potentially be applicable in controlling P. digitatum with reduced concern for human health, environmental contamination and possibly replacement of synthetic treatments.

Graphical abstract