bluuebunny/crossref_metadata_2025_split huggingface dataset:
Developing a clinical decision support system software prototype that assists in the management of patients with self-harm in the emergency department: protocol of the PERMANENS project
Authors: Mortier Philippe , Amigo Franco , Bhargav Madhav , Conde Susana , Ferrer Montse , Flygare Oskar , Kizilaslan Busenur , Latorre Moreno Laura , Leis Angela , Mayer Miguel Angel , Pérez-Sola Víctor , Portillo-Van Diest Ana , Ramírez-Anguita Juan Manuel , Sanz Ferran , Vilagut Gemma , Alonso Jordi , Mehlum Lars , Arensman Ella , Bjureberg Johan , Pastor Manuel , Qin Ping 
Published: March 2024

Abstract
Background
Self-harm presents a significant public health challenge. Emergency departments (EDs) are crucial healthcare settings in managing self-harm, but clinician uncertainty in risk assessment may contribute to ineffective care. Clinical Decision Support Systems (CDSSs) show promise in enhancing care processes, but their effective implementation in self-harm management remains unexplored.

Methods
PERMANENS comprises a combination of methodologies and study designs aimed at developing a CDSS prototype that assists clinicians in the personalized assessment and management of ED patients presenting with self-harm. Ensemble prediction models will be constructed by applying machine learning techniques on electronic registry data from four sites, i.e., Catalonia (Spain), Ireland, Norway, and Sweden. These models will predict key adverse outcomes including self-harm repetition, suicide, premature death, and lack of post-discharge care. Available registry data include routinely collected electronic health record data, mortality data, and administrative data, and will be harmonized using the OMOP Common Data Model, ensuring consistency in terminologies, vocabularies and coding schemes. A clinical knowledge base of effective suicide prevention interventions will be developed rooted in a systematic review of clinical practice guidelines, including quality assessment of guidelines using the AGREE II tool. The CDSS software prototype will include a backend that integrates the prediction models and the clinical knowledge base to enable accurate patient risk stratification and subsequent intervention allocation. The CDSS frontend will enable personalized risk assessment and will provide tailored treatment plans, following a tiered evidence-based approach. Implementation research will ensure the CDSS’ practical functionality and feasibility, and will include periodic meetings with user-advisory groups, mixed-methods research to identify currently unmet needs in self-harm risk assessment, and small-scale usability testing of the CDSS prototype software.

Discussion
Through the development of the proposed CDSS software prototype, PERMANENS aims to standardize care, enhance clinician confidence, improve patient satisfaction, and increase treatment compliance. The routine integration of CDSS for self-harm risk assessment within healthcare systems holds significant potential in effectively reducing suicide mortality rates by facilitating personalized and timely delivery of effective interventions on a large scale for individuals at risk of suicide.
Distribution of internal medicine rotations among resident physicians in Japan: a nationwide, multicenter, cross-sectional study
Authors: Shikino Kiyoshi , Sekine Miwa , Nishizaki Yuji , Yamamoto Yu , Shimizu Taro , Fukui Sho , Nagasaki Kazuya , Yokokawa Daiki , Watari Takashi , Kobayashi Hiroyuki , Tokuda Yasuharu 
Published: March 2024

Abstract
Background
In Japan, postgraduate clinical training encompasses a 2-year residency program, including at least 24 weeks of internal medicine (IM) rotations. However, the fragmented structure of these rotations can compromise the training’s quality and depth. For example, a resident might spend only a few weeks in cardiology before moving to endocrinology, without sufficient time to deepen their understanding or have clinical experience. This study examined current patterns and lengths of IM rotations within the Japanese postgraduate medical system. It scrutinized the piecemeal approach—whereby residents may engage in multiple short-term stints across various subspecialties without an overarching, integrated experience—and explored potential consequences for their clinical education.

Methods
This nationwide, multicenter, cross-sectional study used data from self-reported questionnaires completed by participants in the 2022 General Medicine In-Training Examination (GM-ITE). Data of 1,393 postgraduate year (PGY) one and two resident physicians who participated in the GM-ITE were included. We examined the IM rotation duration and number of IM subspecialties chosen by resident physicians during a 2-year rotation.

Results
Approximately half of the participants chose IM rotation periods of 32–40 weeks. A significant proportion of participants rotated in 5–7 internal medicine departments throughout the observation period. Notable variations in the distribution of rotations were observed, characterized by a common pattern where resident physicians typically spend 4 weeks in each department before moving to the next. This 4-week rotation is incrementally repeated across different subspecialties without a longer, continuous period in any single area. Notably, 39.7% of participants did not undertake general internal medicine rotations. These results suggest a narrowed exposure to medical conditions and patient care practices.

Conclusions
Our study highlights the need to address the fragmented structure of IM rotations in Japan. We suggest that short, specialized learning periods may limit the opportunity to gain broad in-depth knowledge and practical experience. To improve the efficacy of postgraduate clinical education, we recommend fostering more sustained and comprehensive learning experiences.
Evaluation and associated factors of public health emergency management among medical college students in a city in Southwest China: a cross-sectional study
Authors: Chen Xinrui , Zhang Meng , Bu Qingqing , Tan Bo , Deng Dan 
Published: March 2024

Abstract
Background
Colleges and universities face an increased risk of public health emergencies. Among them, medical colleges and universities deserve more attention as they serve as the play a fundamental role in providing public health emergency services and in cultivating medical professionals. Effectively managing infectious disease prevention and control, as well as responding to public health emergencies in medical colleges and universities, is of great importance for enhancing the capacity of social emergency governance and improving the completeness of the public health system. This study aims to understand the management of public health emergencies in medical colleges in a city in southwest China, explore the factors associated with medical college students’ evaluations, and provide recommendations for emergency management mechanisms in colleges and universities.

Methods
In total, 781 medical college students were selected through stratified random sampling and surveyed using a questionnaire. The main factors affecting students’ evaluation of emergency management were analyzed using multiple linear regression and structural equation modeling.

Results
The overall emergency management situation in medical colleges was relatively complete, with satisfactory results. Medical college students’ satisfaction with the timeliness of prevention measures was the highest, while the publicity and education were the lowest. Multiple linear regression analysis showed that grades, emergency education, -simulation training, -information reporting, and dynamic adjustment measures were associated with the evaluation of emergency management by medical students.

Conclusions
Although the evaluation of emergency management in medical colleges was generally positive, certain limitations still existed. To improve the development of the public health system, colleges and universities should constantly reform and innovate emergency management mechanisms according to the important links in the prevention and control processes.
Knowledge, attitudes, and practices of the ethics in medical research among Moroccan interns and resident physicians
Authors: Harch Ibtissam El , Benmaamar Soumaya , Tachfouti Nabil , Hida Moustapha , Belahsen Mohammed Faouzi , Houssaini Tarik Sqalli , Rhazi Karima El 
Published: March 2024

Abstract
Background
In Morocco, medical research ethics training was integrated into the medical curriculum during the 2015 reform. In the same year, a law on medical research ethics was enacted to protect individuals participating in medical research. These improvements, whether in the reform or in the enactment of the law, could positively impact the knowledge of these researchers and, consequently, their attitudes and practices regarding medical research ethics. The main objective of this work is to assess Moroccan physicians’ knowledge, attitudes, and practices at the beginning of their careers (interns and residents) in medical research ethics.

Patients and methods
This is a multicenter cross-sectional study conducted in 2021 among Moroccan physicians. Three scores were created and validated to assess physicians’ level of knowledge, attitudes, and practices regarding research ethics. A descriptive analysis was carried out, followed by a univariate analysis and a multivariate analysis using multivariate binary logistic regression to study the factors associated with the different calculated scores.

Results
A total of 924 physicians were included in the study, with an average age of 27.8 ± 2.2 years. 40.7% had a high medical research ethics knowledge score, and 68.8% had good attitudes. These two scores were positively associated with age and were statistically higher in residents and in physicians who had received training in medical research ethics during their medical curriculum. Only 29,9% of physicians who had participated in research studies had adequate practices with medical research ethics. This score was statistically higher in residents and in physicians who had heard about research ethics.

Conclusion
A genuine introduction to ethics in the medical curriculum is essential to enhance researchers’ knowledge, attitudes, and practices. This, in turn, can lead to an increase in both the quantity and quality of research conducted in Morocco.
Pharmacist-led medication reconciliation service for patients after discharge from tertiary hospitals to primary care in Singapore: a qualitative study
Authors: Griva Konstadina , Chua Zi Yang , Lai Lester Yousheng , Xu Sandra Jialun , Bek Esther Siew Joo , Lee Eng Sing 
Published: March 2024

Abstract
Background
Medication discrepancies commonly occur when patients are transferred between care settings. Despite the presence of medication reconciliation services (MRS), medication discrepancies are still prevalent, which has clinical costs and implications. This study aimed to explore the perspectives of various stakeholders on how the MRS can be optimized in Singapore.

Methods
This is a descriptive qualitative study. Semi-structured interviews with 30 participants from the National Healthcare Group, including family physicians (N = 10), pharmacists (N = 10), patients recently discharged from restructured hospitals (N = 7) and their caregivers (N = 3) were conducted. All transcribed interviews were coded independently by three coders and inductive thematic analysis approach was used.

Results
Five core themes were identified. (1) The MRS enhanced healthcare services in various aspects including efficiency and health literacy; (2) There were several challenges in delivering the MRS covering processes, technology and training; (3) Issues with suitable patient selection and follow-up; (4) Barriers to scaling up of MRS that involve various stakeholders, cross-sector integration and environmental restrictions; and finally (5) Role definition of the pharmacist to all the stakeholders.

Conclusion
This study identified the role of MRS in enhancing healthcare services and explored the challenges encountered in the provision of MRS from family physicians, pharmacists, patients and their caregivers. These findings supported the need for a shift of MRS towards a more comprehensive medication review model. Future improvement work to the MRS can be conducted based on the findings.
Adult dietary patterns with increased bean consumption are associated with greater overall shortfall nutrient intakes, lower added sugar, improved weight-related outcomes and better diet quality
Authors: Papanikolaou Yanni , Slavin Joanne , Fulgoni Victor L. 
Published: March 2024

Abstract
Background
Limited evidence is available that focuses on beans within American dietary patterns and health. The purpose of this study was to identify commonly consumed adult dietary patterns that included beans and compare shortfall nutrient intakes and diet quality, relative to adults whose typical dietary pattern did not include beans.

Methods
The analyses used data from the National Health and Nutrition Examination Survey, 2001–2018. Cluster analysis was used to identify bean patterns of consumption, while the USDA food coding system defined daily beans consumed. Five bean dietary patterns of consumption were identified, of which four patterns included both canned beans and dry beans, while one pattern had no bean consumption. Bean consumption was defined as those consuming kidney beans, black beans, chickpeas, and/or pinto beans.

Results
Adults consuming Bean Dietary Patterns 1, 2, 3 and 4 had significantly higher diet quality scores (as assessed by USDA’s Healthy Eating Index-2015) compared to the no-bean pattern (61.2 ± 0.5, 58.9 ± 0.5, 55.2 ± 0.4 and 56.5 ± 0.8 vs 48.8 ± 0.2 p’s < 0.0001). Bean consumers also had significantly higher intakes of several shortfall nutrients (choline, alpha-linolenic acid, folate, iron, magnesium and vitamin E) relative to non-consumers of beans. Similarly, intake of dietary fiber, potassium and calcium, all nutrients of public health concern were significantly higher in bean patterns compared to no-beans. Bean Dietary Pattern 1 (~ 13.5% of total daily kcal from beans or ~ 2 servings of beans/day) and 2 (~ 9.5% of total daily kcal from beans or ~ 1.7 servings of beans/day) were significantly associated with lower BMI, decreased body weight and improved waist circumference relative to no-beans.

Conclusions
Dietary patterns that are rich in canned and dry beans were associated with significantly higher diet quality scores and greater intake of shortfall nutrients, including nutrients of public health concern. Bean dietary patterns were also associated with improved weight-related outcomes. Dietary guidance should consider the nutrient and health benefits associated with the promotion of increased canned and dry bean consumption in American dietary patterns.
Liraglutide improved the reproductive function of obese mice by upregulating the testicular AC3/cAMP/PKA pathway
Authors: Qi Ruibing , Liang Yuzhen , Yu Jinming , Chen Bing , Jiang Jiaqin , Wu Xingye , Lu Wensheng , Li Zhengming 
Published: March 2024

Abstract
Background
The incidence of male reproductive dysfunction is increasing annually, and many studies have shown that obesity can cause severe harm to male reproductive function. The mechanism of male reproductive dysfunction caused by obesity is unclear, and there is no ideal treatment. Identification of effective therapeutic drugs and elucidation of the molecular mechanism involved in male reproductive health are meaningful. In this study, we investigated the effects of the GLP-1 receptor agonist liraglutide on sex hormones, semen quality, and testicular AC3/cAMP/PKA levels in high-fat-diet-induced obese mice.

Methods
Obese mice and their lean littermates were treated with liraglutide or saline for 12 weeks. Body weight was measured weekly. Fasting blood glucose (FBG) was measured using a blood glucose test strip. The serum levels of insulin (INS), luteinizing hormone (LH), follicle stimulating hormone (FSH), testosterone (T), free testosterone (F-TESTO), estradiol (E2), and sex hormone binding globulin (SHBG) were detected using ELISA. The sperm morphology and sperm count were observed after Pap staining. The mRNA and protein expression levels of testicular GLP-1R and AC3 were measured by RT-qPCR and Western blot, respectively. Testicular cAMP levels and PKA activity were detected using ELISA.

Results
Liraglutide treatment can decrease body weight, FBG, INS, HOMA-IR, E2 and SHBG levels; increase LH, FSH, T, and F-TESTO levels; increase sperm count; decrease the sperm abnormality rate; and increase GLP-1R and AC3 expression levels and cAMP levels and PKA activity in testicular tissue.

Conclusions
Liraglutide can improve the sex hormone levels and semen quality of obese male mice. In addition to its weight loss effect, liraglutide can improve the reproductive function of obese male mice, which may also be related to the upregulation of AC3/cAMP/PKA pathway in the testis. This work lays the groundwork for future clinical studies.
A computational approach to design a multiepitope vaccine against H5N1 virus
Authors: Dashti Fatemeh , Raisi Arash , Pourali Ghazaleh , Razavi Zahra Sadat , Ravaei Fatemeh , Sadri Nahand Javid , Kourkinejad-Gharaei Fatemeh , Mirazimi Seyed Mohammad Ali , Zamani Javad , Tarrahimofrad Hossein , Hashemian Seyed Mohammad Reza , Mirzaei Hamed 
Published: March 2024

AbstractSince 1997, highly pathogenic avian influenza viruses, such as H5N1, have been recognized as a possible pandemic hazard to men and the poultry business. The rapid rate of mutation of H5N1 viruses makes the whole process of designing vaccines extremely challenging. Here, we used an in silico approach to design a multi-epitope vaccine against H5N1 influenza A virus using hemagglutinin (HA) and neuraminidase (NA) antigens. B-cell epitopes, Cytotoxic T lymphocyte (CTL) and Helper T lymphocyte (HTL) were predicted via IEDB, NetMHC-4 and NetMHCII-2.3 respectively. Two adjuvants consisting of Human β-defensin-3 (HβD-3) along with pan HLA DR-binding epitope (PADRE) have been chosen to induce more immune response. Linkers including KK, AAY, HEYGAEALERAG, GPGPGPG and double EAAAK were utilized to link epitopes and adjuvants. This construct encodes a protein having 350 amino acids and 38.46 kDa molecular weight. Antigenicity of ~ 1, the allergenicity of non-allergen, toxicity of negative and solubility of appropriate were confirmed through Vaxigen, AllerTOP, ToxDL and DeepSoluE, respectively. The 3D structure of H5N1 was refined and validated with a Z-Score of − 0.87 and an overall Ramachandran of 99.7%. Docking analysis showed H5N1 could interact with TLR7 (docking score of − 374.08 and by 4 hydrogen bonds) and TLR8 (docking score of − 414.39 and by 3 hydrogen bonds). Molecular dynamics simulations results showed RMSD and RMSF of 0.25 nm and 0.2 for H5N1-TLR7 as well as RMSD and RMSF of 0.45 nm and 0.4 for H5N1-TLR8 complexes, respectively. Molecular Mechanics Poisson-Boltzmann Surface Area (MM/PBSA) confirmed stability and continuity of interaction between H5N1-TLR7 with the total binding energy of − 29.97 kJ/mol and H5N1-TLR8 with the total binding energy of − 23.9 kJ/mol. Investigating immune response simulation predicted evidence of the ability to stimulate T and B cells of the immunity system that shows the merits of this H5N1 vaccine proposed candidate for clinical trials.
MR compatible detectors assessment for a 0.35 T MR-linac commissioning
Authors: Chea Michel , Croisé Mathilde , Huet Christelle , Bassinet Céline , Benadjaoud Mohamed-Amine , Jenny Catherine 
Published: March 2024

Abstract
Purpose
To assess a large panel of MR compatible detectors on the full range of measurements required for a 0.35 T MR-linac commissioning by using a specific statistical method represented as a continuum of comparison with the Monte Carlo (MC) TPS calculations. This study also describes the commissioning tests and the secondary MC dose calculation validation.

Material and methods
Plans were created on the Viewray TPS to generate MC reference data. Absolute dose points, PDD, profiles and output factors were extracted and compared to measurements performed with ten different detectors: PTW 31010, 31021, 31022, Markus 34045 and Exradin A28 MR ionization chambers, SN Edge shielded diode, PTW 60019 microdiamond, PTW 60023 unshielded diode, EBT3 radiochromic films and LiF µcubes. Three commissioning steps consisted in comparison between calculated and measured dose: the beam model validation, the output calibration verification in four different phantoms and the commissioning tests recommended by the IAEA-TECDOC-1583.

Main results
The symmetry for the high resolution detectors was higher than the TPS data of about 1%. The angular responses of the PTW 60023 and the SN Edge were − 6.6 and − 11.9% compared to the PTW 31010 at 60°. The X/Y-left and the Y-right penumbras measured by the high resolution detectors were in good agreement with the TPS values except for the PTW 60023 for large field sizes. For the 0.84 × 0.83 cm2 field size, the mean deviation to the TPS of the uncorrected OF was − 1.7 ± 1.6% against − 4.0 ± 0.6% for the corrected OF whereas we found − 4.8 ± 0.8% for passive dosimeters. The mean absolute dose deviations to the TPS in different phantoms were 0 ± 0.4%, − 1.2 ± 0.6% and 0.5 ± 1.1% for the PTW 31010, PTW 31021 and Exradin A28 MR respectively.

Conclusions
The magnetic field effects on the measurements are considerably reduced at low magnetic field. The PTW 31010 ionization chamber can be used with confidence in different phantoms for commissioning and QA tests requiring absolute dose verifications. For relative measurements, the PTW 60019 presented the best agreement for the full range of field size. For the profile assessment, shielded diodes had a behaviour similar to the PTW 60019 and 60023 while the ionization chambers were the most suitable detectors for the symmetry. The output correction factors published by the IAEA TRS 483 seem to be applicable at low magnetic field pending the publication of new MR specific values.