bluuebunny/crossref_metadata_2025_split huggingface dataset:
The impact of applying various de novo assembly and correction tools on the identification of genome characterization, drug resistance, and virulence factors of clinical isolates using ONT sequencing
Authors: Safar Hussain A. , Alatar Fatemah , Nasser Kother , Al-Ajmi Rehab , Alfouzan Wadha , Mustafa Abu Salim 
Published: July 2023

AbstractOxford Nanopore sequencing technology (ONT) is currently widely used due to its affordability, simplicity, and reliability. Despite the advantage ONT has over next-generation sequencing in detecting resistance genes in mobile genetic elements, its relatively high error rate (10–15%) is still a deterrent. Several bioinformatic tools are freely available for raw data processing and obtaining complete and more accurate genome assemblies. In this study, we evaluated the impact of using mix-and-matched read assembly (Flye, Canu, Wtdbg2, and NECAT) and read correction (Medaka, NextPolish, and Racon) tools in generating complete and accurate genome assemblies, and downstream genomic analysis of nine clinical Escherichia coli isolates. Flye and Canu assemblers were the most robust in genome assembly, and Medaka and Racon correction tools significantly improved assembly parameters. Flye functioned well in pan-genome analysis, while Medaka increased the number of core genes detected. Flye, Canu, and NECAT assembler functioned well in detecting antimicrobial resistance genes (AMR), while Wtdbg2 required correction tools for better detection. Flye was the best assembler for detecting and locating both virulence and AMR genes (i.e., chromosomal vs. plasmid). This study provides insight into the performance of several read assembly and read correction tools for analyzing ONT sequencing reads for clinical isolates.
The need for digital health education among next-generation health workers in China: a cross-sectional survey on digital health education
Authors: Ma Mingxue , Li Yuanheng , Gao Lei , Xie Yuzhuo , Zhang Yuwei , Wang Yazhou , Zhao Lu , Liu Xinyan , Jiang Deyou , Fan Chao , Wang Yushu , Demuyakor Isaac , Jiao Mingli , Li Ye 
Published: July 2023

Abstract
Background
Digital health is important for sustainable health systems and universal health coverage. Since the outbreak of COVID-19, many countries, including China, have promoted the introduction of digital health in their medical services. Developing the next generation of physicians with digital health knowledge and skills is a prerequisite for maximizing the potential of digital health.

Objective
We aimed to understand the perception of digital health among Chinese medical students, the current implementation of digital health education in China, and the urgent need of medical students.

Methods
Our cross-sectional survey was conducted online and anonymously among current medical students in China. We used descriptive statistical analysis to examine participant demographic characteristics and the demand for digital health education. Additional analysis was conducted by grouping responses by current participation in a digital health course.

Results
A total of 2122 valid responses were received from 467 medical schools. Most medical students had positive expectations that digital health will change the future of medicine. Compared with wearable devices (85.53%), telemedicine (84.16%), and medical big data (86.38%), fewer respondents believed in the benefits of clinical decision support systems (CDSS) (63.81%). Most respondents said they urgently needed digital health knowledge and skills, and the teaching method of practical training and internship (78.02%) was more popular than the traditional lecture (10.54%). However, only 41.45% wanted to learn about the ethical and legal issues surrounding digital health.

Conclusions
Our study shows that the current needs of Chinese medical students for digital health education remain unmet. A national initiative on digital health education, is necessary and attention should be paid to digital health equity and education globally, focusing on CDSS and artificial intelligence. Ethics knowledge must also be included in medical curriculum. Students as Partners (SAP) is a promising approach for designing digital health courses.
Requirements analysis for an AI-based clinical decision support system for general practitioners: a user-centered design process
Authors: Schütze Dania , Holtz Svea , Neff Michaela C. , Köhler Susanne M. , Schaaf Jannik , Frischen Lena S. , Sedlmayr Brita , Müller Beate S. 
Published: July 2023

Abstract
Background
As the first point of contact for patients with health issues, general practitioners (GPs) are frequently confronted with patients presenting with non-specific symptoms of unclear origin. This can result in delayed, prolonged or false diagnoses. To accelerate and improve the diagnosis of diseases, clinical decision support systems would appear to be an appropriate tool. The objective of the project ‘Smart physician portal for patients with unclear disease’ (SATURN) is to employ a user-centered design process based on the requirements analysis presented in this paper to develop an artificial Intelligence (AI)-based diagnosis support system that specifically addresses the needs of German GPs.

Methods
Requirements analysis for a GP-specific diagnosis support system was conducted in an iterative process with five GPs. First, interviews were conducted to analyze current workflows and the use of digital applications in cases of diagnostic uncertainty (as-is situation). Second, we focused on collecting and prioritizing tasks to be performed by an ideal smart physician portal (to-be situation) in a workshop. We then developed a task model with corresponding user requirements.

Results
Numerous GP-specific user requirements were identified concerning the tasks and subtasks: performing data entry (open system, enter patient data), reviewing results (receiving and evaluating results), discussing results (with patients and colleagues), scheduling further diagnostic procedures, referring to specialists (select, contact, make appointments), and case closure. Suggested features particularly concerned the process of screening and assessing results: e.g., the system should focus more on atypical patterns of common diseases than on rare diseases only, display probabilities of differential diagnoses, ensure sources and results are transparent, and mark diagnoses that have already been ruled out. Moreover, establishing a means of using the platform to communicate with colleagues and transferring patient data directly from electronic patient records to the system was strongly recommended.

Conclusions
Essential user requirements to be considered in the development and design of a diagnosis system for primary care could be derived from the analysis. They form the basis for mockup-development and system engineering.
Modes and models of care delivery in municipal long-term care services: a cross-sectional study from Norway
Authors: Rostad Hanne Marie , Skinner Marianne Sundlisæter , Wentzel-Larsen Tore , Hellesø Ragnhild , Sogstad Maren Kristine Raknes 
Published: July 2023

Abstract
Background
Numerous forces drive the evolution and need for transformation of long-term care services. Decision-makers across the globe are searching for models to redesign long-term care to become more responsive to changing health and care needs. Yet, knowledge of different care models unfolding in the long-term care service landscape is limited. The objective of this article is twofold: 1) to identify and characterise models of care in Norwegian municipal long-term care services based on four different modes of service delivery: Specialised municipal services, Assistive technology, Planning and coordination, and Health Promotion and Activity, and 2) to analyse whether the identified care models vary with regard to municipal characteristics, more specifically ‘population size’ and ‘income’.

Methods
We adopted a cross-sectional approach and used data from a web-based survey conducted in 2019 to identify and characterize models of care in Norwegian long-term care services, based on four modes of service delivery. The questionnaire was developed through a comprehensive review of national healthcare policy documents and previous research and amended in collaboration with a user panel. A set of questions from the questionnaire were used to create four modes of service delivery. Hierarchical cluster analysis was used to cluster the municipalities based on the mean scores of the modes to identify care models.

Results
In total, 277 municipalities (response rate 66%) completed the survey. The four modes made it possible to identify four care models that differ on the level of Specialised municipal services, Assistive technology, Planning and coordination, and Health Promotion and Activity. Additionally, the models differed regarding municipal population size (p < 0.001) and income (p = 0.006).

Conclusions
We put forward a theoretical description of the variety of ways long-term care services are provided, offering a way of simplifying complex information which can assist care providers and policymakers in analysing and monitoring their own service provision and making informed decisions. This is important to the development of services for current and future care needs.
Economic analysis of a new four-panel rapid screening test in antenatal care in Kenya, Rwanda, and Uganda
Authors: Shepard Donald S , Halasa-Rappel Yara A , Rowlands Katharine R , Kulchyckyj Maria , Basaza Robert K , Otieno Emmanuel D , Mutatina Boniface , Kariuki Simon , Musange Sabine F 
Published: July 2023

Abstract
Background
We performed an economic analysis of a new technology used in antenatal care (ANC) clinics, the ANC panel. Introduced in 2019–2020 in five Rwandan districts, the ANC panel screens for four infections [hepatitis B virus (HBV), human immunodeficiency virus (HIV), malaria, and syphilis] using blood from a single fingerstick. It increases the scope and sensitivity of screening over conventional testing.

Methods
We developed and applied an Excel-based economic and epidemiologic model to perform cost-effectiveness and cost-benefit analyses of this technology in Kenya, Rwanda, and Uganda. Costs include the ANC panel itself, its administration, and follow-up treatment. Effectiveness models predicted impacts on maternal and infant mortality and other outcomes. Key parameters are the baseline prevalence of each infection and the effectiveness of early treatment using observations from the Rwanda pilot, national and international literature, and expert opinion. For each parameter, we found the best estimate (with 95% confidence bound).

Results
The ANC panel averted 92 (69–115) disability-adjusted life years (DALYs) per 1,000 pregnant women in ANC in Kenya, 54 (52–57) in Rwanda, and 258 (156–360) in Uganda. Net healthcare costs per woman ranged from $0.53 ($0.02-$4.21) in Kenya, $1.77 ($1.23-$5.60) in Rwanda, and negative $5.01 (-$6.45 to $0.48) in Uganda. Incremental cost-effectiveness ratios (ICERs) in dollars per DALY averted were $5.76 (-$3.50-$11.13) in Kenya, $32.62 ($17.54-$46.70) in Rwanda, and negative $19.40 (-$24.18 to -$15.42) in Uganda. Benefit-cost ratios were $17.48 ($15.90-$23.71) in Kenya, $6.20 ($5.91-$6.45) in Rwanda, and $25.36 ($16.88-$33.14) in Uganda. All results appear very favorable and cost-saving in Uganda.

Conclusion
Though subject to uncertainty, even our lowest estimates were still favorable. By combining field data and literature, the ANC model could be applied to other countries.
Rehabilitation models that support transitions from hospital to home for people with acquired brain injury (ABI): a scoping review
Authors: Eliassen Marianne , Arntzen Cathrine , Nikolaisen Morten , Gramstad Astrid 
Published: July 2023

Abstract
Background
Research shows a lack of continuity in service provision during the transition from hospital to home for people with acquired brain injuries (ABI). There is a need to gather and synthesize knowledge about services that can support strategies for more standardized referral and services supporting this critical transition phase for patients with ABI. We aimed to identify how rehabilitation models that support the transition phase from hospital to home for these patients are described in the research literature and to discuss the content of these models.

Methods
We based our review on the “Arksey and O`Malley framework” for scoping reviews. The review considered all study designs, including qualitative and quantitative methodologies. We extracted data of service model descriptions and presented the results in a narrative summary.

Results
A total of 3975 studies were reviewed, and 73 were included. Five categories were identified: (1) multidisciplinary home-based teams, (2) key coordinators, (3) trained family caregivers or lay health workers, (4) predischarge planning, and (5) self-management programs. In general, the studies lack in-depth professional and contextual descriptions.

Conclusions
There is a wide variety of rehabilitation models that support the transition phase from hospital to home for people with ABI. The variety may indicate a lack of consensus of best practices. However, it may also reflect contextual adaptations. This study indicates that health care service research lacks robust and thorough descriptions of contextual features, which may limit the feasibility and transferability to diverse contexts.
Supervised smoking facility access, harm reduction practices, and substance use changes during the COVID-19 pandemic: a community-engaged cross-sectional study
Authors: van Draanen Jenna , Hamilton Jonah , Morgan Jeffrey , Maxwell Scott , Taylor Tara , Richardson Lindsey , Nolan Seonaid 
Published: July 2023

Abstract
Background
The potential public health benefits of supervised smoking facilities (SSFs) are considerable, and yet implementation of SSFs in North America has been slow. We conducted this study to respond to significant knowledge gaps surrounding SSF utilization and to characterize substance use, harm reduction practices, and service utilization following the onset of the COVID-19 pandemic.

Methods
A questionnaire was self-administered at a single site by 175 clients using an outdoor SSF in Vancouver, Canada, between October–December 2020. Questionnaire responses were summarized using descriptive statistics. Multinomial logistic regression techniques were used to examine factors associated with increased SSF utilization.

Results
Almost all respondents reported daily substance use (93% daily use of opioids; 74% stimulants). Most used opioids (85%) and/or methamphetamine (66%) on the day of their visit to the SSF. Respondents reported drug use practice changes at the onset of COVID-19 to reduce harm, including using supervised consumption sites, not sharing equipment, accessing medically prescribed alternatives, cleaning supplies and surfaces, and stocking up on harm reduction supplies. Importantly, 45% of SSF clients reported using the SSF more often since the start of COVID-19 with 65.2% reporting daily use of the site. Increased substance use was associated with increased use of the SSF, after controlling for covariates.

Conclusions
Clients of the SSF reported increasing not only their substance use, but also their SSF utilization and harm reduction practices following the onset of COVID-19. Increased scope and scale of SSF services to meet these needs are necessary.
A topology-marginal composite likelihood via a generalized phylogenetic pruning algorithm
Authors: Jun Seong-Hwan , Nasif Hassan , Jennings-Shaffer Chris , Rich David H , Kooperberg Anna , Fourment Mathieu , Zhang Cheng , Suchard Marc A , Matsen Frederick A 
Published: July 2023

AbstractBayesian phylogenetics is a computationally challenging inferential problem. Classical methods are based on random-walk Markov chain Monte Carlo (MCMC), where random proposals are made on the tree parameter and the continuous parameters simultaneously. Variational phylogenetics is a promising alternative to MCMC, in which one fits an approximating distribution to the unnormalized phylogenetic posterior. Previous work fit this variational approximation using stochastic gradient descent, which is the canonical way of fitting general variational approximations. However, phylogenetic trees are special structures, giving opportunities for efficient computation. In this paper we describe a new algorithm that directly generalizes the Felsenstein pruning algorithm (a.k.a. sum-product algorithm) to compute a composite-like likelihood by marginalizing out ancestral states and subtrees simultaneously. We show the utility of this algorithm by rapidly making point estimates for branch lengths of a multi-tree phylogenetic model. These estimates accord with a long MCMC run and with estimates obtained using a variational method, but are much faster to obtain. Thus, although generalized pruning does not lead to a variational algorithm as such, we believe that it will form a useful starting point for variational inference.
Changes in proprioception at different time points following anterior cruciate ligament injury or reconstruction
Authors: Zhao Yixuan , Chen Ze , Li Longfei , Wu Xipeng , Li Wei 
Published: July 2023

Abstract
Purpose
To investigate the changes in 30° and 60° position sense in patients with anterior cruciate ligament (ACL) injury at different time points after injury and reconstruction.

Methods
Patients were divided into six groups according to time after ACL injury and reconstruction: group A (ACL injury 1.5–6 months), group B (ACL injury 6–12 months), group C (ACL injury > 12 months), group D (postoperative ACL reconstruction 1–6 months), group E (postoperative ACL reconstruction > 6 months), and group F consisting of 14 healthy adults (control group). The ability of the affected leg to reproduce the same joint position during knee flexion was tested using active joint position sense assays to assess proprioception in both the lower extremities of the patient or between groups.

Results
Proprioception decreased rapidly during the early stages of ACL injury. Significant difference in the affected side at 30° compared to the healthy side (Group A: 4.70 (4.78, 9.00) vs 4.15 (3.35, 6.13), P = 0.03; Group B: 2.90 (0.48, 4.56) vs 8.30 (4.18, 10.43), P = 0.001; Group E: 6.25 (2.55, 11.60) vs 9.60 (3.90, 12.73), P = 0.009). However, no significant differences were detected for a double lower limb contrast of 60° (Group A: 5.1 (1.00, 8.00) vs 3.00 (0.75, 3.55), P = 0.044). Finally, the affected side of patients in groups C, D and E had significant differences in position perception at 30° compared with healthy subjects (P < 0.01), and the affected side of patients in groups C and E had significant differences in position sense at 60° compared with healthy subjects (P < 0.01).

Conclusion
ACL injury had a greater impact on the patient's 30° position sense, with only a small impact for 60°. Further, the early and middle proprioception recovery stages after ACL injury were the best before surgery. Finally, proprioception recovery training should be performed soon after injury.
MicroRNA-185-5p targets tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta to regulate non-small cell lung cancer progression
Authors: Ma Jiangang , Bai Yan , Chen Fangyuan , Zhou Feng , Zhang Liyuan , Xue Peini , Wang Dong 
Published: July 2023

Abstract
Background
Lung cancer (LC) is one of the most frequent cancers worldwide, as well as the leading cause of cancer-related death. Non-small cell lung cancer (NSCLC, which accounts for 85% of occurrences) is the main type of LC. MiRNAs appear to play a role in the occurrence and progression of many malignancies, according to mounting data. The underlying mechanism of miRNAs in regulating NSCLC cell biological activity and progression, on the other hand, is still being investigated.

Methods
QRT-PCR were used to detect miR-185-5p expression and YWHAZ mRNA in NSCLC. The CCK-8 assay was used to determine the tumor cells’ ability to proliferate. Transwall assay was used to test the migratory and invasive properties of cells. Cell apoptosis was detected using flow cytometry. Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta (YWHAZ), E-Cadherin, N-Cadherin and cleaved-caspase3 protein expression were assessed using Western Blot. The bioinformatics analysis software StarBase2.0 predicted miR-185-5p downstream targets. To confirm the target association between miR-185-5p and YWHAZ, a luciferase experiment was used. In addition, an NCl-H1299 xenograft model was created to assess the anti-tumor impact of miR-185-5p in vivo. The expression level of YWHAZ in tumor tissues of small xenograft tumor model was detected by immunohistochemistry assay.

Results
Decreased miR-185-5p expression levels were observed in NSCLC. In vitro, over-expressed miR-185-5p decreased cell viability, proliferation, invasion/migration, and induced cell apoptosis, while inhibiting tumor growth in vivo. Dual-luciferase gene experiments confirmed that YWHAZ binds to miR-185-5p. Overexpression of YWHAZ partially restored the inhibitory effects of miR-185-5p on cell behaviors.

Conclusion
MiR-185-5p was down-regulated in NSCLC, and that overexpressed miR-185-5p inhibited malignant behaviors of cells and tumor growth by negatively regulating YWHAZ.