bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mining functional gene modules by multi-view NMF of phenome-genome association
Authors: Jin Xu , He WenQian , Liu MingMing , Wang Lin , Zhang YaoGong , Xu YingJie , Ma Ling , Huang YaLou , Xie MaoQiang 
Published: January 2025

Abstract
Background
Mining functional gene modules from genomic data is an important step to detect gene members of pathways or other relations such as protein-protein interactions. This work explores the plausibility of detecting functional gene modules by factorizing gene-phenotype association matrix from the phenotype ontology data rather than the conventionally used gene expression data. Recently, the hierarchical structure of phenotype ontologies has not been sufficiently utilized in gene clustering while functionally related genes are consistently associated with phenotypes on the same path in phenotype ontologies.

Results
This work demonstrates a hierarchical Nonnegative Matrix Factorization (NMF) framework, called Consistent Multi-view Nonnegative Matrix Factorization (CMNMF), which factorizes genome-phenome association matrix at consecutive levels of the hierarchical structure in phenotype ontology to mine functional gene modules. CMNMF constrains the gene clusters from the association matrices at two consecutive levels to be consistent since the genes are annotated with both the child-level phenotypes and the parent-level phenotypes in two levels. CMNMF also restricts the identified gene clusters to be densely connected in the phenotype ontology hierarchy. In the experiments on mining functionally related genes from mouse phenotype ontology and human phenotype ontology, CMNMF effectively improves clustering performance over the baseline methods. Gene ontology enrichment analysis is also conducted to verify its practical effectiveness to reveal meaningful gene modules.

Conclusions
Utilizing the information in the hierarchical structure of phenotype ontology, CMNMF can identify functional gene modules with more biological significance than conventional methods. CMNMF can also be a better tool for predicting members of gene pathways and protein-protein interactions.
Management of acute myocardial infarction in chronic kidney disease in Germany: an observational study
Authors: Walendy Victor , Stang Andreas , Girndt Matthias 
Published: January 2025

Abstract
Background
Managing acute myocardial infarction (AMI) in patients with chronic kidney disease (CKD) or end-stage renal disease on dialysis (renal replacement therapy, RRT) presents challenges due to elevated complication risks. Concerns about contrast-related kidney damage may lead to the omission of guideline-directed therapies like percutaneous coronary intervention (PCI) or coronary artery bypass grafting (CABG) in this population.

Methods
We analysed German-DRG data of 2016 provided by the German Federal Bureau of Statistics (DESTATIS). We included cases with a primary diagnosis of AMI (ST-Elevation Myocardial Infarction (STEMI) or Non-ST-Elevation Myocardial Infarction (NSTEMI) ICD-10: I21 or I22) with and without CKD or RRT. We calculated crude- and age-standardized hospitalization rates (ASR, per 100,000 person years). Furthermore, we calculated log-binominal regression models adjusting for sex, CKD, RRT, comorbidities, and place of residence to estimate adjusted relative-risks (aRR) for receiving treatments of interest in AMI, such as PCI or CABG.

Results
We identified 217,514 AMI-cases (69,728 STEMI-cases and 147,786 NSTEMI-cases). AMI-cases without CKD had percutaneous coronary intervention (PCI) in 60.8%. In contrast, AMI-cases with CKD or RRT had PCI in 46.6% and 54.5%, respectively. The ASR for AMI-cases amounted to 184.7 (95%CI 183.5-185.8) per 100,000 person years. In regression analysis AMI-cases with CKD were less likely treated with PCI (aRR: 0.89 (95%CI 0.88–0.90)), compared to cases without CKD. AMI-Cases with RRT showed no difference in PCI rates (aRR: 1.0 (95%CI 0.97–1.03)) but were more frequently treated with CABG (aRR: 2.20 (95%CI 2.03–2.39)). Conversely, CKD was negatively associated with CABG (aRR: 0.71, 95%CI 0.67–0.75) when non-CKD cases were used as the reference group.

Conclusion
We show that AMI-cases with CKD underwent PCI less frequently, while RRT has no discernible impact on PCI utilization in AMI. Furthermore, AMI-cases with RRT exhibited a higher CABG rate.
Cancer-related health behaviors during the COVID 19 pandemic in geographically diverse samples across the US
Authors: Greteman Breanna B. , Cole Allison , Charlton Mary E. , Shannon Jackilen , Kepka Deanna , Paskett Electra D. , Borrayo Evelinn A. , Studts Jamie L. , Thompson Hayley S. , Scarinci Isabel , Hinton Lynn Chollet , Chrischilles Elizabeth A. , Garcia-Auguste Crystal J. , Christini Kaila , Aker Heather , Plascak Jesse J. , Harper Felicity W. K. , Baskin Monica L. , Bae Sejong , Pandya Vishruti , Kim Young-il , Faseru Babalola , Befort Christie , Kuo Hanluen , Dignan Mark , Canedo Juan , Champion Victoria , Drake Bettina F. , Davis Kia L. , Friedman Debra L. , Elsaid Mohamed I. , Mama Scherezade K. , Cohn Wendy F. 
Published: January 2025

Abstract
Background
The COVID-19 pandemic involved business closures (e.g., gyms), social distancing policies, and prolonged stressful situations that may have impacted engagement in health behaviors. Our study assessed changes in cancer-related health behaviors during the pandemic, specifically physical activity, fruit/vegetable intake, smoking/tobacco use, and alcohol consumption.

Methods
Eight cancer centers administered mailed/web-based/telephone surveys between June 2020 and March 2021. Surveys assessed demographics, perceptions on social distancing, and self-reported changes of behaviors (less/same/more) associated with cancer prevention or risk, e.g., physical activity, fruit/vegetable intake, tobacco/smoking use, and alcohol consumption. Descriptive analyses and logistic regression models assessed association of variables with behavior change.

Results
Most of the 21,911 respondents reported adhering to at least 4(of 5) social distancing measures (72%) and indicated social distancing was very/somewhat important to prevent the spread of COVID-19 (91%). 35% of respondents reported less physical activity, 11% reported less fruit/vegetable intake, 27% reported more smoking/tobacco use (among those who used tobacco/smoking products in past 30 days), and 23% reported more alcohol consumption (among those who reported at least 1 drink in past 30 days) than before the pandemic. Urban residence, younger age, female gender, and worse general health were associated with less physical activity, less fruit/vegetable intake, more smoking/tobacco use, and more alcohol intake. Higher educational attainment was associated with less physical activity and fruit/vegetable intake and more alcohol consumption. Reporting social distancing as important and adhering to more COVID-19 safety practices were associated with less physical activity and more alcohol consumption.

Conclusion
Our findings suggest that certain demographics and those who adhered to social distancing measures were more likely to self-report unfavorable changes in health behaviors during the pandemic. Future studies should examine if the behaviors returned to baseline following relief from pandemic restrictions, and if these behavior changes are associated with increased cancer incidence and mortality.
Effects of the MyBFF@school program on anthropometry and body composition among overweight and obese adolescent schoolchildren
Authors: Kamil Nur Zati Iwani Ahmad , Mokhtar Abdul Halim , Yahya Abqariyah , Zain Fuziah Md. , Selamat Rusidah , Ishak Zahari , Jalaludin Muhammad Yazid 
Published: January 2025

Abstract
Background
Effective and feasible large-scale interventions are urgently needed to reverse the current rise in childhood obesity. The objective of this study was to evaluate the efficacy of a multicomponent intervention program, MyBFF@school, on anthropometric indices and body composition metrics among overweight and obese adolescent schoolchildren in Malaysia.

Methods
This is a cluster randomized controlled trial which involved schoolchildren aged 13, 14 and 16 years old from 15 out of 415 government secondary schools in central Peninsular Malaysia which were randomly assigned into six intervention (N = 579 schoolchildren) and nine control (N = 462 schoolchildren).The intervention group followed MyBFF@school program carried out by trained personnel for 6 month while the control group only followed the existing school curriculum by the Ministry of Education. The primary outcomes presented in this study were body mass index adjusted for age (BMI z-score), waist circumference (WC), percentage body fat (PBF) and skeletal muscle mass (SMM), measured at baseline, three and six months. Analyses of all outcomes except for the baseline characteristics were conducted according to the intention-to-treat principle. Mixed linear models adjusted for baseline outcome value and gender were used to evaluate the effectiveness after three and six months of intervention.

Results
Overall, there was no significant difference in the mean difference (MD) of BMI z-score (MD = 0.05, Confident Interval (95%CI: -0.077 to 0.194), WC (MD = 0.437, (95%CI:-3.64 to 0.892), PBF (MD = 0.977,95%CI:-1.04 to 3.0) and SMM (MD = 0.615,95%CI:-2.14,0.91) between the intervention and control group after 6 months of intervention after controlling for outcomes measured at baseline and gender.

Conclusions
Although the MyBFF@school programme appeared promising in engaging children and promoting awareness of healthy behaviors, it did not lead to significant improvements in the anthropometric outcomes. Possible reasons for the lack of effectiveness could include the need for more intensive or targeted interventions, parental involvement, or challenges in sustaining behavior changes outside of school settings.

Trial registration
Clinical trial number: NCT04155255, November 7, 2019 (Retrospective registered). National Medical Research Register: NMRR-13-439-16,563. Registered July 23, 2013. The intervention program was approved by the Medical Research and Ethics Committee (MREC), Ministry of Health Malaysia and Educational Planning and Research Division (EPRD), Ministry of Education Malaysia. It was funded by the Ministry of Health Malaysia.
Engineering Saccharomyces cerevisiae for medical applications
Authors: Maneira Carla , Chamas Alexandre , Lackner Gerald 
Published: January 2025

Abstract
Background
During the last decades, the advancements in synthetic biology opened the doors for a profusion of cost-effective, fast, and ecologically friendly medical applications priorly unimaginable. Following the trend, the genetic engineering of the baker’s yeast, Saccharomyces cerevisiae, propelled its status from an instrumental ally in the food industry to a therapy and prophylaxis aid.

Main text
In this review, we scrutinize the main applications of engineered S. cerevisiae in the medical field focusing on its use as a cell factory for pharmaceuticals and vaccines, a biosensor for diagnostic and biomimetic assays, and as a live biotherapeutic product for the smart in situ treatment of intestinal ailments. An extensive view of these fields' academic and commercial developments as well as main hindrances is presented.

Conclusion
Although the field still faces challenges, the development of yeast-based medical applications is often considered a success story. The rapid advances in synthetic biology strongly support the case for a future where engineered yeasts play an important role in medicine.
Optimizing vaccine uptake in sub-Saharan Africa: a collaborative COVID-19 vaccination campaign in Madagascar using an adaptive approach
Authors: Pavoncello Viola , Kislaya Irina , Andrianarimanana Diavolana Koecher , Marchese Valentina , Rakotomalala Rivo , Rasamoelina Tahinamandranto , Veilleux Simon , Guth Ariane , Zafinimampera Alexina Olivasoa Tsiky , Ratefiarisoa Sonya , Totofotsy Olivette , Doumbia Cheick Oumar , Rakotonavalona Rivomalala , Ramananjanahary Holinirina , Randriamanantany Zely Arivelo , May Jürgen , Rakotoarivelo Rivo Andry , Puradiredja Dewi Ismajani , Fusco Daniela 
Published: January 2025

Abstract
Background
The COVID-19 pandemic has highlighted the need for more effective immunization programs, including in limited resource settings. This paper presents outcomes and lessons learnt from a COVID-19 vaccination campaign (VC), which used a tailored adaptive strategy to optimise vaccine uptake in the Boeny region of Madagascar.

Methods
Guided by the Dynamic Sustainability Framework (DSF), the VC implementation was regularly reviewed through multi-sectoral stakeholder feedback, key informant interviews, problem-solving meetings, and weekly monitoring of outcome indicators to identify and apply key adaptations. Qualitative data on processes were collected and analysed using a rapid assessment approach. Outcome indicators, including pre- and post-VC vaccine hesitancy and trends in vaccine doses administered, were analysed using generalized linear models. Additionally, vaccination coverage, geographic reach, and target population characteristics, and sustainability indicators, such as staff trained, facilities equipped, and degree of integration of operational and educational materials were also tracked.

Results
Key strategy adaptations included using a proactive campaign approach, community-led awareness and outreach, particularly in remote areas, and addressing cold chain, waste management, vaccine transport, and information technology (IT) equipment gaps. Over six months, 24,888 COVID-19 vaccines were administered. The adapted strategy led to an 8% increase in doses administered weekly (RR = 1.08, CI 95%: 1.01-1.15). However, vaccine hesitancy among the unvaccinated population remained unchanged (∆ = 0.02, CI 95%: -0.04-0.08). In terms of sustainability, 340 staff were trained, and 10 primary healthcare facilities were equipped and refurbished.

Conclusions
Implementing collaborative, multi-sectoral vaccination strategies that integrate healthcare services with proactive outreach and community-driven campaigns are effective in increasing vaccine coverage in resource-limited settings. It demonstrates how theory-based adaptive strategies can enhance vaccination rates, even if they do not significantly impact COVID-19 vaccine hesitancy within the community. More generally, this initiative has important implications for adult vaccination programmes other than those related to COVID-19.
Study protocol for a hybrid type 3 effectiveness-implementation trial of a team-based implementation strategy to support educators’ use of a social engagement intervention
Authors: Locke Jill , Sridhar Aksheya , Shih Wendy , Shire Stephanie , Eisman Andria B. , Kim Emily , Du Adora , Espeland Christine , Kasari Connie 
Published: January 2025

Abstract
Background
Remaking Recess (RR) is a school-based evidence-based peer social engagement intervention for autistic students. RR involves direct training and coaching with educators; however, educators face several barriers to implementation at both the individual- and organizational-levels. This protocol paper describes a multi-site study that will test whether an educator-level implementation strategy, coaching, with or without a school-level implementation strategy, school-based teams, will maximize educators’ use (fidelity and sustainment) of RR for autistic students and their peers who are socially-isolated, rejected, or peripheral and may need additional support during recess.

Methods
This study will employ a hybrid type-3 effectiveness-implementation trial. Fifty-five elementary schools will be recruited as well as 121 educators (e.g., classroom assistants, aides), 55 general and special educator teachers, and 83–138 other school personnel (e.g., administrators). Additionally, at least 118 autistic students and allistic or non-autistic classmates will be recruited as RR recipients. Participants will complete baseline assessments at the beginning of the year, and all schools will be provided RR training. Schools will be randomized to coaching with or without school-based teams. This study will measure RR fidelity (primary outcome), RR sustainment, as well as peer engagement, social network inclusion, and social skills (secondary outcomes). It is expected that coaching with school-based teams will improve both RR fidelity and social network inclusion, while coaching with and without school-based teams will result in improved peer engagement and social skills.

Discussion
Previous research has documented barriers to RR implementation at both the individual- (provider) and organization-level (school). Using multi-level implementation strategies such as coaching with school-based teams may address these barriers and support RR implementation in schools. Findings from this study may guide future efforts to scale up tailored implementation strategies for use in public school districts, with the ultimate goal of increasing intervention access and improving student outcomes.

Trial registration
Name of the Registry: clinicaltrials.gov.
Trial Registration: Clinical Trials ID: NCT06559267.
Date of Registration: August 15, 2024. Prospectively registered.
Eco-sustainable chromatographic method for the determination of favipiravir and nitazoxanide for COVID-19: application to human plasma
Authors: Ahmed Amal B. , Abdelrahman Maha M. , Edrees Fadwa H. 
Published: January 2025

AbstractCoronavirus disease 2019 (COVID-19), an extremely contagious illness, has posed enormous challenges to healthcare systems around the world. Although the evidence on COVID-19 management is growing, antiviral medication is still the first line of treatment. Therefore, it is critical that effective, safe, and tolerable antivirals be available to treat early COVID-19 and stop its progression. Recently, favipiravir (FAV) has received FDA approval as safe and effective antiviral medication for COVID-19 management. Nitazoxanide (NTZ) also possesses antiviral and immunomodulating activities. Moreover, FAV and NTZ in combination are clinically used in COVID-19 treatment with reported safety, synergistic antiviral and immunomodulating effects. Despite the availability of various clinical studies on both FAV and NTZ, no existing analytical application for the simultaneous estimation of FAV and NTZ exists. As a result, the current work goal is to establish a green HPLC method for their analysis and implementation to human plasma. The developed method utilizes isocratic elution with 0.1% aqueous formic acid: ethanol (55:45, v/v) and dantrolene as internal standard. The bioanalytical validation parameters passed the FDA acceptance criteria. NEMI, eco scale, AGREE and ComplexGAPI approaches were used for qualitative and quantitative evaluation of the method’s greenness.
Integrating CT-based radiomics and clinical features to better predict the prognosis of acute pancreatitis
Authors: Chen Hang , Wen Yao , Li Xinya , Li Xia , Su Liping , Wang Xinglan , Wang Fang , Liu Dan 
Published: January 2025

Abstract
Objectives
To develop and validate the performance of CT-based radiomics models for predicting the prognosis of acute pancreatitis.

Methods
All 344 patients (51 ± 15 years, 171 men) in a first episode of acute pancreatitis (AP) were retrospectively enrolled and randomly divided into training (n = 206), validation (n = 69), and test (n = 69) sets with the ratio of 6:2:2. The patients were dichotomized into good and poor prognosis subgroups based on follow-up CT and clinical data. The radiomics features were extracted from contrast-enhanced CT. Logistic regression analysis was applied to analyze clinical-radiological features for developing clinical and radiomics-derived models. The predictive performance of each model was evaluated using the area under the receiver operating characteristic curve (AUC), calibration curve, and decision curve analysis (DCA).

Results
Eight pancreatic and six peripancreatic radiomics features were identified after reduction and selection. In the training set, the AUCs of clinical, pancreatic, peripancreatic, radiomics, and combined models were 0.859, 0.800, 0.823, 0.852, and 0.899, respectively. In the validation set, the AUCs were 0.848, 0.720, 0.746, 0.773, and 0.877, respectively. The combined model exhibited the highest AUC among radiomics-based models (pancreatic, peripancreatic, and radiomics models) in both the training (0.899) and validation (0.877) sets (all p < 0.05). Further, the AUC of the combined model was 0.735 in the test set. The calibration curve and DCA indicated the combined model had favorable predictive performance.

Conclusions
CT-based radiomics incorporating clinical features was superior to other models in predicting AP prognosis, which may offer additional information for AP patients at higher risk of developing poor prognosis.

Critical relevance statement
Integrating CT radiomics-based analysis of pancreatic and peripancreatic features with clinical risk factors enhances the assessment of AP prognosis, allowing for optimal clinical decision-making in individuals at risk of severe AP.

Key Points

Radiomics analysis provides help to accurately assess acute pancreatitis (AP).

CT radiomics-based models are superior to the clinical model in the prediction of AP prognosis.

A CT radiomics-based nomogram integrated with clinical features allows a more comprehensive assessment of AP prognosis.

Graphical Abstract
The prognostic role of cardiac and inflammatory biomarkers in extubation failure in patients with COVID-19 acute respiratory distress syndrome
Authors: Groenland Carline N. L. , Siemers Adinde H. , Dubois Eric A. , Gommers Diederik , Heunks Leo , Wils Evert-Jan , Baggen Vivan J. M. , Endeman Henrik 
Published: January 2025

Abstract
Background
Extubation failure is associated with an increased morbidity, emphasizing the need to identify factors to further optimize extubation practices. The role of biomarkers in the prediction of extubation failure is currently limited. The aim of this study was to investigate the prognostic value of cardiac (N-terminal pro–B-type natriuretic peptide (NT-proBNP), High-sensitivity Troponin T (Hs-TnT)) and inflammatory biomarkers (Interleukin-6 (IL-6) and Procalcitonin (PCT)) for extubation failure in patients with COVID-19 Acute Respiratory Distress Syndrome (C-ARDS).

Materials and methods
In this single-center retrospective cohort study, patient characteristics and laboratory measurements were extracted from electronic medical records. Patients were eligible for inclusion if they were extubated after mechanical ventilation. The primary endpoint was extubation failure, defined as the need for reintubation or death within the next seven days after extubation, regardless of whether post-extubation respiratory support was used. Uni- and multivariable logistic regression was performed to investigate the association between biomarkers and extubation failure. Biomarkers were log2 transformed.

Results
Of the 297 patients included, 21.5% experienced extubation failure. In univariable analysis, NT-proBNP (OR 1.24, 95% CI 1.06–1.47), Hs-TnT (OR 1.72, 95% CI 1.37–2.19) and PCT (OR 1.38, 95% CI 1.16–1.65) measured on the day of extubation were significantly associated with extubation failure. After multivariable adjustment for clinical variables (age, duration of mechanical ventilation, SOFA score), Hs-TnT was the only biomarker that was independently associated with extubation failure (adjusted OR 1.38, 95% CI 1.02–1.90). Patients with both elevated Hs-TnT (≥ 14 ng/mL) and elevated PCT (≥ 0.25 ng/mL) carried the highest risk of extubation failure (46%), while in patients with normal Hs-TnT and PCT values, only 13% experienced extubation failure.

Conclusions
Hs-TnT, NT-proBNP and PCT measured on the day of extubation are associated with extubation failure in mechanically ventilated patients with C-ARDS. Since Hs-TnT is the only biomarker that is independently associated with extubation failure, Hs-TnT could offer additional objective measures for assessing readiness for extubation. Future studies should focus on an integrative approach of biomarkers combined with relevant clinical factors to predict extubation failure.