bluuebunny/crossref_metadata_2025_split huggingface dataset:
The efficacy and safety of a simple 14-day vonoprazan-minocycline dual therapy for Helicobacter pylori eradication: a retrospective pilot study
Authors: Wang Xiaolei , Teng Guigen , Dong Xinhong , Dai Yun , Wang Weihong 
Published: November 2024

Background: Current eradication regimens are not ideal for Helicobacter pylori infected patients who have difficulty choosing antibiotics due to penicillin allergy or antibiotic resistance. Objective: To explore the efficacy and safety of a simple vonoprazan-minocycline dual therapy (VM dual therapy) in H. pylori eradication. Design: Clinical data of patients who were prescribed 14-day VM dual therapy were retrospectively collected. The included patients were 18–70 years old and positive for 13C urea breath test (13C-UBT). They were allergic to penicillin or had a history of repeated antibiotic exposure or had failed eradication with multiple regimens containing amoxicillin. VM dual therapy consists of vonoprazan 20 mg twice daily and minocycline 100 mg twice daily. 13C-UBT was repeated 4–6 weeks after treatment to evaluate the therapeutic outcome. Results: Of the 88 enrolled patients, 54 were treatment naïve, 13 had one prior eradication failure, and 21 had multiple eradication failures. The overall intention to treat (ITT) and per-protocol (PP) eradication rates were 90.9% (95% CI: 82.4–95.7) and 95.2% (95% CI: 87.6–98.5). The ITT eradication rates were 90.7% (95% CI: 78.9–96.5) in treatment-naïve patients, 84.6% (95% CI: 53.7–97.3) in patients with one prior treatment failure, and 95.2% (95% CI: 74.1–99.8) in patients with multiple failures. The PP eradication rates were 94.2% (95% CI: 83.1–98.5), 91.7% (95% CI: 59.8–99.6), and 100%, respectively. The overall incidence of adverse events was 23.0%. The common adverse reactions were nausea and mild dizziness, which could be resolved without intervention. Conclusion: Simple VM dual therapy exhibited a good eradication rate, low incidence of adverse effects, and good adherence. It is a potential new regimen for both first-line and rescue therapy.
Liveborn children with trisomy 18: A scoping review
Authors: Schlosser Mary-Pat , MacPherson Melissa J , Castro-Codesal Maria , Mack Cheryl , Sue-Milne Kyle , Wren Tara , Shapka Larissa , Kung Janice Y , van Manen Michael 
Published: November 2024

Background There have been an increasing number of publications related to trisomy 18 associated with a shift in the philosophy of care. The objective of this review is to understand the scope of contemporary literature informing the care of children born alive with trisomy 18. Methods Included was peer-reviewed, primary literature in MEDLINE, Embase, CINAHL, Scopus, Web of Science, and Cochrane Library from 2012 to 2023 reporting outcomes of children born alive with trisomy 18. Data extraction involved descriptive statistics of the types of studies, and an inductive thematic analysis of the questions addressed by the studies. Results Of 4628 records identified, 229 met inclusion criteria. Key themes were organized around the domains: What is trisomy 18? What are the chances of survival with trisomy 18? What can be done to improve the chances of survival with trisomy 18? How do children with trisomy 18 die? Do surgical interventions provide a benefit? Are there non-surgical options? What knowledge is informing medical management? How is life described for children with trisomy 18? What are children with trisomy 18 like as babies and as they get older? What is life like for families caring for children with trisomy 18? Conclusions A sizeable number of publications grouped trisomy 18 with other syndromes. Relatively few showed the longitudinal evolution of medical issues associated with trisomy 18, nor did they unfold the clinical heterogeneity of this population. This review shows the limited knowledge base guiding decision-making and care for children born alive with trisomy 18.
Community opioid dispensing after rib fracture injuries: CODI study
Authors: Williamson Frances , Proper Melanie , Shibl Rania , Cramb Susanna , McCreanor Victoria , Warren Jacelle , Cameron Cate 
Published: November 2024

Background Pain from rib fractures often requires inpatient management with opioid medication. The need for ongoing opioid prescriptions following hospital discharge is poorly understood. Harms associated with long-term opioid use are generally accepted. However, a deeper understanding of current prescribing patterns in this population at-risk is required. Methods A retrospective cohort of adult patients hospitalised in Queensland, Australia between 2014 and 2015 with rib fractures (ICD-10-AM: S22.3, S22.4, S22.5), was obtained from the Community Opioid Dispensing after Injury (CODI) study, which includes person-linked hospitalisation, mortality and community opioid dispensing data. Data were extracted 90-days prior to the index-hospitalisation and 720-days after discharge. Factors associated with long-duration (>90 days cumulatively) and increased end-dose were examined using multivariable logistic regressions, odds ratios (OR), and 95% confidence intervals (95% CI). Results In total, 4306 patients met the inclusion criteria, and 58.8% had opioids dispensed in the community within 30 days of hospital discharge. 23.6% had long-duration dispensing and 13.7% increased opioid end-doses. Pre-injury opioid use was most associated with long-duration (OR = 12.00, 95% CI 8.99–16.01) and increased end-dose (OR = 9.00, 95% CI 6.75–12.00). Females and older persons had higher odds of long-duration dispensing (Females OR = 1.75, 95% CI 1.38–2.22; Age 65+ OR = 1.86, 95% CI 1.32–2.61). Injury severity and presence of concurrent injuries were not statistically significantly associated with duration or dose ( p > .05). Subsequent hospitalisations and death during the follow-up period had statistically significant associations with long-duration and increased end-dose ( p < .001). Conclusion Opiate prescribing following rib fractures is prolonged in older, and female patients, beyond the traditionally reported recovery time frames requiring analgesia. Previous opioid use (without dependence) is associated with long-duration opioid use and increased end-dose in rib fracture patients. These results support the need for a collaborative health system approach and individualised strategies for high-risk patients with rib fractures to reduce long-term opiate use. Level of Evidence Level III, Prognostic/Epidemiological.
PAHFKB: A knowledge base to support personalized exercise prescription recommendations in prevention and intervention of heart failure
Authors: Zhang Ke , Ren Shumin , Bao Ting , Wu Rongrong , Wu Erman , Liu Xingyun , Zhan Chaoying , Wei Jinhong , Shen Li , Li Danting , Shen Bairong 
Published: November 2024

Background and Aims Guidelines for exercise recommendations are typically designed for the population as a whole and do not account for individual differences, making it challenging to provide personalized exercise training for individuals with complex conditions. To address this issue, this study aimed to develop PAHFKB (Physical Activity-Heart Failure Knowledge Base), a knowledge-based system for personalized exercise prescription (EP) for heart failure (HF), by mining, analyzing, and organizing existing literature and data on the relationship between physical activity (PA) and HF. Methods Firstly, 3186 citations on PAHF were gathered from PubMed. Then, the data standards for personalized PAHF were defined with the entity-relationship model. Following data collection in accordance with these standards, PAHFKB was developed using MySQL and ASP.NET, integrating elaborate and diverse PAHF evidence, knowledge-based EP and visualization tools. Results PAHFKB (pahfkb.sysbio.org.cn) incorporated 357 studies published between 1989 and 2021, involving over 900,000 subjects from 43 countries. And 1010 PAHF items were extracted, encompassing 357 exercise training protocols, 333 outcomes, and 42 risk factors for HF prevention and intervention. Among all protocols, the most frequently employed regimen consisted of three 60-minute sessions of moderate-intensity aerobic exercise training on a weekly basis. Conclusion PAHFKB is an online system designed to support personalized EP in HF management. It incorporates diverse tools and visualization and will promote personalized decision support, establish data standards, and advance interpretable artificial intelligence in digital health. Ultimately, it will enhance clinical practice and digital therapy in the prevention and intervention of HF.
Methylation sequencing enhances interpretation of clonal hematopoiesis dynamics
Authors: Parker Alyssa C. , Van Amburg Joseph C. , Heimlich J. Brett , Pershad Yash , Mickels Nicole A. , Mack Taralynn M. , Ferrell P. Brent , Savona Michael R. , Jones Angela L. , Bick Alexander G. 
Published: November 2024

Abstract
We have developed a cost-effective DNA methylation sequencing assay to improve monitoring of clonal hematopoiesis. By inferring cell-type proportions, this method enhances interpretation of clonal trajectories compared with interpretation based on variant allele fraction only.
Mucus plugging, disease severity, and sputum myeloperoxidase concentration in bronchiectasis
Authors: Kim Sun-Hyung , Man Lee Ki , Yoo Jin Young , Chae Kum Ju , Kim Geun-Hyeong , Cho Jun Yeun , The Nguyen Minh , Kim Eung-Gook , Choi Joong-Kook , Choe Kang Hyeon , Lee Hyun , Yang Bumhee 
Published: November 2024

BackgroundBronchiectasis is characterized by impaired mucociliary clearance, leading to persistent mucus accumulation, known as mucus plugging (MP). Myeloperoxidase (MPO) is a key molecule that activates neutrophilic inflammation during bronchiectasis, leading to disease progression. However, whether sputum MPO concentration is an independent factor associated with MP remains unclear.MethodsWe retrospectively evaluated 78 patients with bronchiectasis at Chungbuk National University Hospital between June 2022 and April 2023. According to the extent of MP in computed tomography of the chest, participants were divided into high MP (MP in ≥ 10 bronchopulmonary segments) and low MP (MP in ≤ 9 bronchopulmonary segments) groups. We evaluated whether sputum MPO concentration is independently associated with MP using multivariable adjusted logistic regression analyses.ResultsThere were 59 (75.6%) and 19 (24.4%) participants in the low and high MP groups, respectively. Compared with the low MP group, the high MP group had significantly higher disease severity, as measured by the modified Reiff score (p<0.001) and FACED score (p=0.003). Sputum MPO concentration was significantly correlated with the extent of MP (r=0.313, p=0.009). In addition, sputum MPO concentration (adjusted odds ratio=1.60, 95% confidence interval: 1.06–2.42) was independently associated with a high extent of MP even after adjusting for potential confounders.ConclusionsSputum MPO concentration was associated with a high degree of MP, suggesting a potential role of MPO in the pathogenesis of mucus plugging.
Elabela alleviates cuproptosis and vascular calcification in vitaminD3- overloaded mice via regulation of the PPAR-γ /FDX1 signaling
Authors: Qi Rui-Qiang , Chen Yu-Fei , Cheng Jing , Song Jia-Wei , Chen Yi-Hang , Wang Si-Yuan , Liu Ying , Yan Kai-Xin , Liu Xiao-Yan , Li Jing , Zhong Jiu-Chang 
Published: November 2024

Abstract
Background
Vascular calcification is a crucial pathophysiological process associated with age-related cardiovascular diseases. Elabela, a recently identified peptide, has emerged as a significant player in the regulation of cardiovascular function and homeostasis. However, the effects and underlying mechanisms of Elabela on age-related vascular calcification remain largely unexplored.

Methods
In-vivo vascular calcifications of C57BL/6J mice (8-week-old) and young (8-week-old) or aged (72-week-old) SD rats were injected with vitamin D3 (VitD3) or saline, respectively. Furthermore, the VitD3-overloaded mice received Elabela (1 mg/kg/d), peroxisome proliferators-activated receptor-γ (PPAR-γ) activator Rosiglitazone (5 mg/kg/d) or copper-ionophore Elesclomol (20 mg/kg/d), respectively. As for in-vitro studies, primary rat vascular smooth muscle cells (VSMCs) were isolated from aortas and cultured for explore the role and underlying mechanism of Elabela in vascular calcification.

Results
There were marked increases in FDX1 and Slc31a1 levels in both aortas and VSMCs during vascular calcification, coinciding with a rise in copper levels and a decrease in Elabela levels. Alizarin red and von-Kossa staining indicated that the administration of Elabela effectively hindered the progression of vascular cuproptosis and arterial calcification in VitD3-overloaded mice and rat arterial rings models. Moreover, Elabela significantly suppressed osteogenic differentiation and calcium deposition in VSMCs and strikingly reversed high phosphate-induced augmentation of FDX1 expression, DLAT aggregation as well as intracellular copper ion levels. More importantly, Elabela exhibited remarkable abilities to prevent mitochondrial dysfunctions in primary rat VSMCs by maintaining mitochondrial membrane potential, inhibiting mitochondrial division, reducing mitochondrial ROS production and increasing ATP levels. Interestingly, Elabela mitigated cellular senescence and production of pro-inflammatory cytokines including IL-1α, IL-1β, IL-6, IL-18 and TNF-α, respectively. Furthermore, Elabela upregulated the protein levels of PPAR-γ in VitD3-overloaded mice. Administrating PPAR-γ inhibitor GW9662 or blocking the efflux of intracellular copper abolished the protective effect of Elabela on vascular calcification by enhancing levels of FDX1, Slc31a1, Runx2, and BMP2.

Conclusion
Elabela plays a crucial role in protecting against vascular cuproptosis and arterial calcification by activating the PPAR-γ /FDX1 signaling. Elabela supplementation and cuproptosis suppression serve as effective therapeutic approaches for managing vascular calcification and related cardiovascular disorders.
Calculating the effect of intensive use of urban organic waste on soil concentrations of potentially toxic elements in a peri-urban agriculture context in Norway
Authors: Løes Anne-Kristin , Eiter Sebastian , Rittl Tatiana 
Published: November 2024

Abstract
Background
Recycling nutrients and organic matter available as waste in urban areas may close nutrient gaps and improve soil quality, but the concentrations of potentially toxic elements (PTEs) are commonly higher than in mineral fertilisers. How quickly may the limits for soil quality be exceeded, and for which elements, if such materials are applied intensively? For a rough answer to this question, we used soil data from ten case farms near Oslo and Bergen (Norway) to estimate how PTE concentrations increased when the demand for nitrogen (N), phosphorus (P) and potassium (K) in a theoretical carrot crop produced every year was covered by compost or digestate from source-separated food waste, or composted garden waste, compared with manure from horses and poultry which are often kept in peri-urban areas.

Results
With the intensive fertilisation assumed here, the Norwegian soil quality limits for PTEs were reached within 20–85 years, and faster for soil with more organic matter since regulatory limits set by weight discriminate soils with low bulk density. The limits were reached first for Cu and Zn, which are both essential micronutrients for crop plants. The concentrations of macronutrients in the urban waste-based fertilisers were not well balanced. Rates covering the K demand would lead to high surpluses of P and N. In peri-urban vegetable growing, high applications of compost are not unusual, but more balanced fertilisation is required.

Conclusions
The Norwegian regulations for PTEs in organic soil amendments and agricultural soil are stricter than in the EU, and do not support recycling of organic matter and nutrients from urban waste. Many materials which can only be applied with restricted amounts to Norwegian agricultural soil, may be applied according to crop demand in the EU. Growers utilising urban waste-based fertilisers intensively should monitor the soil regularly, including PTE analyses. Soil sampling should occur on fixed sampling points to reveal changes in concentrations over time. Norwegian authorities should consider a revision of the organic fertiliser regulation to support recycling of valuable organic materials. There is a need for more data on the PTE concentrations in agricultural soil and organic fertiliser materials.
Scoping review and thematic analysis of informed consent in humanitarian emergencies
Authors: Thomson Benjamin , Mehta S. , Robinson C. 
Published: November 2024

Abstract
Background
To identify and to summarize challenges related to the informed consent process for research completed during humanitarian emergencies.

Methods
Using relevant search terms, a search of 5 databases was completed, without language, date, or study type restriction. Studies were screened for inclusion, with eligible studies being those that were relevant to the informed consent process for research studies completed in humanitarian emergencies. A Grounded Theory Analysis was completed to identify themes and subthemes.

Results
Review identified 30 relevant studies. We identified 11 challenges (lack of trust, therapeutic misconception, reduced capacity, security and privacy concerns, harmful research, power differential, literacy, language/local and cultural context, researcher burden and re-evaluation of ongoing trials) and 7 strategies (engage local research communities, use alternative to standard written consent process, modify traditional process of research ethics board review, dynamic consent, training of research staff, mandating transparency of commercial interests, and mandating reporting of informed consent process in all publications) to confront the challenges. These challenges and strategies were unique to the informed consent process in research conducted during humanitarian emergencies.

Conclusions
This scoping review identified an evidence-based guide for researchers and research ethics boards to perform ethical informed consent procedures in humanitarian emergencies.

Trial Registration
This trial was not registered as scoping reviews can not be registered as per updated PROSPERO guidelines.
Systemic and transcriptional response to intermittent fasting and fasting-mimicking diet in mice
Authors: Michenthaler Helene , Duszka Kalina , Reinisch Isabel , Galhuber Markus , Moyschewitz Elisabeth , Stryeck Sarah , Madl Tobias , Prokesch Andreas , Krstic Jelena 
Published: November 2024

Abstract
Background
Dietary restriction (DR) has multiple beneficial effects on health and longevity and can also improve the efficacy of certain therapies. Diets used to instigate DR are diverse and the corresponding response is not uniformly measured. We compared the systemic and liver-specific transcriptional response to intermittent fasting (IF) and commercially available fasting-mimicking diet (FMD) after short- and long-term use in C57BL/6 J mice.

Results
We show that neither DR regimen causes observable adverse effects in mice. The weight loss was limited to 20% and was quickly compensated during refeeding days. The slightly higher weight loss upon FMD versus IF correlated with stronger fasting response assessed by lower glucose levels and higher ketone body, free fatty acids and especially FGF21 concentrations in blood. RNA sequencing demonstrated similar transcriptional programs in the liver after both regimens, with PPARα signalling as top enriched pathway, while on individual gene level FMD more potently increased gluconeogenesis-related, and PPARα and p53 target gene expression compared to IF. Repeated IF induced similar transcriptional responses as acute IF. However, repeated cycles of FMD resulted in blunted expression of genes involved in ketogenesis and fatty acid oxidation.

Conclusions
Short-term FMD causes more pronounced changes in blood parameters and slightly higher weight loss than IF, while both activate similar pathways (particularly PPARα signalling) in the liver. On individual gene level FMD induces a stronger transcriptional response, whereas cyclic application blunts transcriptional upregulation of fatty acid oxidation and ketogenesis only in FMD. Hence, our comparative characterization of IF and FMD protocols renders both as effective DR regimens and serves as resource in the fasting research field.
The embedded research model: an answer to the research and evaluation needs of community service organizations?
Authors: Kavanagh Bianca E. , Versace Vincent L. , Mc Namara Kevin P. 
Published: November 2024

AbstractThere is an increasing need to provide evidence of outcomes within the community services sector. However, funding challenges, workforce pressures, and the complex social contexts in which community service organizations operate limit their potential for organizational capacity building. This has flow on effects on the ability to conduct impactful and strategic research. The embedded research model (i.e., when a researcher is embedded into a “host” organisation) may aid in building research and evaluation capacity. This may be particularly useful for the purposes of routine outcome monitoring and continuous quality improvement, which may in turn lead to opportunities for local research and evaluation through the embedded research model. Previous research on the embedded research model across various settings has suggested a number of lessons for implementation. However, to date, nil research has focused on community service organizations. Additional considerations need to be made within this context due to resource limitations, ethical issues, and diverse reporting requirements. Such considerations include the need to take a ‘slow science’ approach to research and evaluation outputs, consideration of the organisation’s readiness for change, and the need to report activities in a transparent, thorough, and consistent manner. The endorsement of embedded research in community service organisations may aid in providing evidence of outcomes for clients, and simultaneously, increase the ability for policymakers to evidence-informed decisions on how to improve outcomes for the local population.