bluuebunny/crossref_metadata_2025_split huggingface dataset:
Finding high posterior density phylogenies by systematically extending a directed acyclic graph
Authors: Jennings-Shaffer Chris , Rich David H. , Macaulay Matthew , Karcher Michael D. , Ganapathy Tanvi , Kiami Shosuke , Kooperberg Anna , Zhang Cheng , Suchard Marc A. , Matsen Frederick A. 
Published: February 2025

Abstract
Bayesian phylogenetics typically estimates a posterior distribution, or aspects thereof, using Markov chain Monte Carlo methods. These methods integrate over tree space by applying local rearrangements to move a tree through its space as a random walk. Previous work explored the possibility of replacing this random walk with a systematic search, but was quickly overwhelmed by the large number of probable trees in the posterior distribution. In this paper we develop methods to sidestep this problem using a recently introduced structure called the subsplit directed acyclic graph (sDAG). This structure can represent many trees at once, and local rearrangements of trees translate to methods of enlarging the sDAG. Here we propose two methods of introducing, ranking, and selecting local rearrangements on sDAGs to produce a collection of trees with high posterior density. One of these methods successfully recovers the set of high posterior density trees across a range of data sets. However, we find that a simpler strategy of aggregating trees into an sDAG in fact is computationally faster and returns a higher fraction of probable trees.
Extinction of contextual fear memory is facilitated in TRPM2 knockout mice
Authors: Ko Seung Yeon , Kim Do Gyeong , Lee Huiju , Jung Sung Jun , Son Hyeon 
Published: February 2025

Abstract
Transient receptor potential melastatin type 2 (TRPM2) is a nonselective cation channel involved in synaptic plasticity. We investigated its role in contextual fear conditioning and extinction of conditioned fear using Trpm2-deficient (Trpm2

−/−
) mice. Trpm2

−/−
mice exhibited reduced acquisition of contextual fear memory during conditioning but had an intact freezing response to conditioning context 24 h after conditioning. They also showed a reduced freezing response to extinction training, indicating facilitated extinction. Consistent with this, infusion of flufenamic acid (FFA), a TRPM2 antagonist, into the dentate gyrus (DG) of the hippocampus in fear-conditioned mice facilitated extinction of contextual fear. The enhanced extinction in Trpm2

−/−
and FFA-treated mice was associated with down-regulation of immediate-early genes (IEGs) including Npas4, c-Fos, Arc and Egr1 in the hippocampus after extinction training. Our results indicate that TRPM2 plays a positive role in retention of contextual fear memory by modulating neuronal activity in the hippocampus, and suggest that TRPM2 activity could potentially be targeted to strengthen extinction-based exposure therapies for post-traumatic stress disorder (PTSD).
Clear-cell carcinoma of the soft palate: a case with atypical presentation and long-term follow-up: a case report
Authors: Qayyum Sardar Noman , Shah Sayyed Muddasir , Ullah Irfan , Khan Maleeka , Khan Gulmeena Aziz , Ullah Safi , Noori Samim , Hussain Mudassir 
Published: February 2025

Abstract

Background
Clear-cell carcinoma, a rare malignancy of the minor salivary gland of the soft palate, is diagnostically challenging neoplasm due to its rarity and overlapping features with other neoplasms. We report a case of atypical presentation, diagnostic challenges, and long-term follow-up post-surgical resection of the tumor, which adds valuable insights to literature on this rare malignancy.

Case presentation
A 34-years-old Pakistani female came to the hospital with a 2 × 2 cm ulcerative lesion of soft palate. The lesion had no active bleeding and any associated discharge. However, during history taking, she reported pain and occasional bleeding from the lesion.

Diagnosis and therapeutic interventions
Excisional biopsy was performed, and the specimen was sent for histopathological examination and immunohistochemistry, which confirmed the diagnosis of clear-cell carcinoma. Later on, radiological evaluation confirmed the diagnosis of hyalinizing variant of clear-cell carcinoma. Long-term follow-up revealed no recurrence and postoperative complications.

Conclusion
This case report highlights the importance of thorough diagnostic evaluation and long-term follow-up in management of a rare oral malignancy. Histopathological examination and immunohistochemistry are crucial in differentiating clear-cell carcinoma from other malignancies with overlapping features. Surgical excision remains the primary treatment modality, with a favorable prognosis if diagnosed and managed adequately.
Improving route development using convergent retrosynthesis planning
Authors: Torren-Peraire Paula , Verhoeven Jonas , Herman Dorota , Ceulemans Hugo , Tetko Igor V. , Wegner Jörg K. 
Published: February 2025

Abstract
Retrosynthesis consists of recursively breaking down a target molecule to produce a synthesis route composed of readily accessible building blocks. In recent years, computer-aided synthesis planning methods have allowed a greater exploration of potential synthesis routes, combining state-of-the-art machine-learning methods with chemical knowledge. However, these methods are generally developed to produce individual routes from a singular product to a set of proposed building blocks and are not designed to leverage potential shared paths between targets. These methods do not necessarily encompass real-world use cases in medicinal chemistry, where one seeks to synthesize sets of target compounds in a library mode, looking for maximal convergence into a shared retrosynthetic path going via advanced key intermediate compounds. Using a graph-based processing pipeline, we explore Johnson & Johnson Electronic Laboratory Notebooks (J&J ELN) and publicly available datasets to identify complex routes with multiple target molecules sharing common intermediates, producing convergent synthesis routes. We find that over 70% of all reactions are involved in convergent synthesis, covering over 80% of all projects in the case of J&J ELN data.

Scientific contribution

We introduce a novel planning approach to develop convergent synthesis routes, which can search multiple products and intermediates simultaneously guided by state-of-the-art machine learning single-step retrosynthesis models, enhancing the overall efficiency and practical applicability of retrosynthetic planning. We evaluate the multi-step synthesis planning approach using the extracted convergent routes and observe that solvability is generally high across those routes, being able to identify a convergent route for over 80% of the test routes and showing an individual compound solvability of over 90%. We find that by using a convergent search approach, we can synthesize almost 30% more compounds simultaneously for J&J ELN as compared to using an individual search, while providing an increased use of common intermediates.
Machine learning-based prediction of elliptical double steel columns under compression loading
Authors: Ren Yang , Isleem Haytham F. , Almoghaye Walaa J. K. , Hamed Abdelrahman Kamal , Jangir Pradeep , Arpita  , Tejani Ghanshyam G. , Ezugwu Absalom E. , Soliman Ahmed A. 
Published: February 2025

Abstract
This paper presents a comprehensive investigation into the prediction of axial load capacity (P) for elliptical double steel columns (EDSCs) using a diverse set of machine learning models (MLMs). These include Artificial Neural Network (ANN), Gene Expression Programming (GEP), Support Vector Regression (SVR), Random Forest (RF), and AdaBoost. Among the models, AdaBoost demonstrated superior performance, achieving an R2 of 0.996 and a MAPE of 0.013 during training, outperforming other models under identical conditions. Using a dataset of 119 finite element models derived from prior experimental research, the study validates the proposed solution through k-fold cross-validation, feature importance analysis, and detailed comparisons with experimental data. A Graphical User Interface (GUI) was developed specifically for the AdaBoost model due to its superior accuracy and efficiency, offering engineers a practical and accessible tool for axial load prediction in EDSC design. This research highlights the significance of using advanced machine learning techniques for structural engineering applications, providing valuable insights for the optimization of EDSC performance and design under varying conditions.
Snakebites and resource utilization in pediatric urban and rural populations in the United States: 2016–2023
Authors: Jeffries Kristyn , Sanders Sara C. , Ekdahl Rachel , Williford Dustin E. , Taylor Maxwell , Fisher Charalene , Filipek Jacob , Slagle Brittany , Birisci Esma , Cantu Rebecca M. 
Published: February 2025

Abstract

Background
Nearly 7,000 snakebite injuries are reported yearly in the United States, with almost one quarter of those in the pediatric population. Due to increased exposure to snakes, rural children may experience different clinical outcomes for snakebite injuries. The goal of this study was to examine differences in resource utilization of rural and urban pediatric patients with snakebite injuries.

Methods
This is a retrospective cross-sectional study of patients aged 21 years and under presenting with venomous snakebites in the United States from January 1, 2016, through March 31, 2023, using the Pediatric Hospital Information System database and ICD-10 codes indicating snakebites. Comparisons were conducted to evaluate demographic and clinical characteristics in association with resource utilization and complications between patients living in rural areas and patients living in urban areas.

Results
The study included 2,633 patients from 23 states. The median age was 9 years; 61% of patients were male. Most patients were in the South and over 70% resided in urban areas. 82% of the population was admitted to a hospital, with median length of stay 1.59 days. Compared to urban patients, rural patients were more likely to be admitted and receive antivenom but were less likely to have an intensive care unit admission and have abnormal coagulation studies.

Conclusions
Rural pediatric patients with snakebites had different resource utilization and clinical complications than urban patients.
The influence of heatwaves on traffic safety in five cities across Québec with different thermal landscapes
Authors: Nazif-Munoz José Ignacio , Gilani Vahid Najafi Moghaddam , Rana Juwel , Choma Ernani , Spengler John D. , Cedeno-Laurent José Guillermo 
Published: February 2025

Abstract

Background
This study assesses the impact of heatwaves on road safety in five Québec cities (Montréal, Québec City, Laval, Longueuil, and Sherbrooke) from June to September 2015–2022. Using Urban Heat Island (UHI), 90th and 95th percentile thresholds for heatwaves, we analyze their effects on collisions, traffic injuries, and killed and seriously injured (KSI) cases.

Methods
Traffic data were analyzed across two heatwave definitions, utilizing a time-stratified case-crossover design. UHI was approximated using the annual maximum of mean warm-season land surface temperatures (LST) derived from Landsat 8 (30 m resolution) over three consecutive years, identifying areas that stay hotter during the day and radiate excess heat at night. Heatwaves were defined as periods of at least two consecutive days with mean temperatures exceeding the historical 90th or 95th percentile of mean temperatures. Negative Binomial regression models were used to examine associations between UHI, heatwave events and traffic incidents. Models controlled for time varying variables such as rainfall, seasonality, and COVID-19 impacts.

Results
Heatwaves, particularly at the 95th percentile threshold, significantly increased traffic incidents in Montréal and Longueuil. In Sherbrooke, the 90th percentile threshold showed significant effects on collisions and injuries, while Québec City and Laval exhibit no significant associations. UHIs show a modest overall increase in collisions (IRR: 1.07) but limited effects on traffic injuries and KSI. Differences across cities highlight Montréal's higher IRR for collisions under heatwaves and lower IRR for KSI compared to Québec and Longueuil respectively.

Discussion and conclusion
The results indicate that cities like Montréal and Longueuil, with slightly stronger UHI and higher susceptibility to heatwaves, face increased road safety risks. However, UHI levels in Montréal were not significantly different from those in other cities, and heatwaves at the 95th percentile showed variability across regions. These findings highlight the need for targeted climate-adaptive strategies, such as green spaces and heat-reflective materials, to mitigate risks. Integrating climate resilience into urban planning remains critical as extreme weather events grow more frequent.
Medicare in Treacherous Markets: From Community Bake Sales to Private Equity
Authors: Morone James A. 
Published: February 2025

Abstract
Medicare's 60th birthday marks a shocking milestone for social democrats: More than half of all beneficiaries are signed up with private insurance plans that routinely deny payments. This paper flips the focus from the government program itself to the broader health care markets in which Medicare operates. I show how Medicare has lived through four very different health market eras. Each involves new kinds of medical institutions, new financial logics, and new thinking about what markets are and what role they ought to play in the program. First, during the long battle over Medicare, government programs and markets were (quite mistakenly) viewed as simple opposites. Second, in the 1970s, a new view emerged: Competition between HMOs would provide enrollees choice of providers, enhancing quality and lowering costs. Third, in the 1980s, Republicans pressed market choices into Medicare – drawing on rhetorical images from a bygone era; as conservatives were imagining medical markets, corporations arrived, asserted vast controls over medicine, and redirected consumer choice itself -- from selecting health providers to picking between insurance plans. Finally, beginning in the 2000s, private equity poured into health care and, once again, transformed the market. By Medicare's 60th birthday, enrollees found themselves in turbulent new era as health care in America was growing increasingly monetized.
Improving bench-to-bedside translation for acute graft-versus-host disease models
Authors: McDaniel Mims Brianyell , Furr Kathryn L. , Enriquez Josue , Grisham Matthew B. 
Published: February 2025

ABSTRACT
The transplantation of allogeneic hematopoietic stem cells is a potentially curative treatment for hematological malignancies, inherited blood disorders and immune deficiencies. Unfortunately, 30-50% of patients receiving allogeneic hematopoietic stem cells will develop a potentially life-threatening inflammatory disease called acute graft-versus-host disease (aGVHD). In patients with aGVHD, graft-associated T cells, which typically target the skin, intestinal tract and liver, can also damage the lungs and lymphoid tissue. Damage to lymphoid tissue creates prolonged immunodeficiency that markedly increases the risk of infections and bleeding, resulting in considerable morbidity and mortality. Although mouse models of aGVHD have been instrumental to our understanding of this condition's pathogenesis, translation of preclinical data into new and more effective treatments for human disease has been limited for reasons that remain to be fully understood. However, evidence suggests that factors associated with mouse models of aGVHD likely contribute to these unsatisfactory results. In this Review, we identify and discuss the specific factors inherent to mouse models of aGVHD that may limit the translation of preclinical data to patient treatment, and suggest how to improve the translatability of these models.
Impact of COVID-19 on In-Patient and Out-Patient services in Bangladesh
Authors: Manna Ridwana Maher , Rahman Md Hafizur , Ara Tasnu , Usmani Nasimul Ghani , Tanvir K. M. , Haider M. Sabbir , Akter Ema , Shomik Mohammad Sohel , Hossain Aniqa Tasnim 
Published: February 2025

Introduction
The global Coronavirus disease (COVID-19) pandemic disrupted healthcare systems, reducing access to medical services. In Bangladesh, strict lockdowns, healthcare worker shortages, and resource diversion further strained the system. Despite these challenges, the impact on inpatient and outpatient service utilisation in Bangladesh remains unaddressed. This study explored the levels of inpatient admissions and outpatient visits in public healthcare facilities before and during COVID-19 pandemic in Bangladesh.

Methods
We conducted a cross-sectional secondary analysis of inpatient and outpatient data from all public hospitals collected via District Health Information System, version 2 (DHIS2) from January 2017 to June 2021. Using 2017-2019 as the baseline, we analysed healthcare utilisation indicators (outpatient visits and inpatient admissions) with descriptive and segmented Poisson regression to assess the impact of COVID-19 in 2020 and 2021.

Results
In 2020, outpatient visits and inpatient admissions significantly declined to 34.1 million and 37.5 million, respectively, from 47.6 million and 56.2 million in 2019. Segmented regression analysis confirmed these drops, especially in Dhaka (IRR =  0.62, p < 0.001) and Barisal (IRR =  0.69, p < 0.002) for outpatient visits, and in Dhaka (IRR =  0.64, p < 0.000) and Khulna (IRR =  0.70, p < 0.000) for inpatient admissions. In 2021, most divisions saw an increase in outpatient visit and inpatient admission numbers, with the lowest rebound in Sylhet.

Conclusion
The COVID-19 pandemic significantly reduced Outpatient Department (OPD) visits and Inpatient Department (IPD) admissions in Bangladesh in 2020, with partial recovery in 2021. To ensure sustained access to care, it is crucial to strengthen healthcare facilities and equip healthcare providers to be prepared for future pandemics or emergencies.
Effects of cochlear implantation on gait performance in adults with hearing impairment: A systematic review
Authors: Rafoul Bahaa , Tzemah-Shahar Roy , Lubetzky Anat V. , Cohen-Vaizer Mauricio , Karawani Hanin , Agmon Maayan 
Published: February 2025

Background
Previous systematic reviews evaluated the effect of hearing interventions on static and dynamic stability and found several positive effects of hearing interventions. Despite numerous reviews on hearing interventions and balance, the impact of cochlear implantation on gait and fall risk remains unclear.

Objective
This systematic review examines the effects of cochlear implantation on gait performance in adults with hearing loss.

Methods
A comprehensive literature search was conducted in PubMed, Web of Science, and Scopus, using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The PEDro scale assessed the methodological quality, risk of bias, and study design of included articles.

Results
Seven studies met the inclusion criteria. Five focused solely on cochlear implantation, while two included both cochlear implants (CIs) and hearing aids. Methodological inconsistencies were evident in measurement approaches and follow-up durations, leading to variable outcomes. Short-term follow-up post-implantation showed no improvement or even worsened gait outcomes. However, a longer follow-up of three months post-implantation indicated partial improvements in specific gait measures like Tandem Walk speed, though not in comfortable walking speed. Cross-sectional studies comparing on-off CI conditions revealed no significant differences in gait outcomes.

Conclusions
Improvements in gait due to cochlear implantation require at least three months to manifest. The variability in study methodologies complicates understanding the full impact of cochlear implantation on gait. Given that only seven, methodologically inconsistent articles were found, it is necessary to conduct additional research to understand the relationship between hearing, gait and fall risk and to specifically include longer post-CI monitoring periods.
Estimasi Dampak Penyalahgunaan Narkoba pada Produktivitas Kerja: Studi Corss Sectional Pada Pekerja di Indonesia
Authors: Sudaryo Mondastri Korib , Antasari Erma 
Published: February 2025

Background: Prevalence of drugs abuse among workers is still high. Drug use among workers has a negative impact on the health and safety of both workers and the community. This study was aimed to examine the relationship between impaired work productivity and drug behaviour among workers in Indonesia.Methods: This study used secondary data from the national survey on drug abuse among workers in 2017. The total sample size was 34,397 persons. We used cox regression model to estimates the Prevalence Ratios (PR) and its 95% confidence intervals for associations between drug abuse and impaired work productivityResults: Drug abuse, marijuana and methamphetamine, used by workers were associated with impaired work productivity. Drug abuse in workers increased the likelihood of impaired work productivity by 2.3 times (p-value: <0.001; 95% CI: 1.97-2.73). Meanwhile, the use of marijuana types increased the probability of impaired work productivity by 1.6 times (p-value <0.001; 95% CI: 1.32-2.00). Workers using methamphetamine drugs were 1.29 times more likely to experience impaired work productivity than workers who did not use methamphetamine (p-value: 0.03; 95% CI: 1.03-1.62).Conclusion: impaired work productivity among workers was significantly associated with drug abuse
Keputusan untuk Melahirkan dengan Tenaga Kesehatan Terlatih pada Persalinan di Rumah (Analisis Data Survei Demografi dan Kesehatan Indonesia 2017)
Authors: Choirunisa Septyana , Adisasmita Asri 
Published: February 2025

Background: IDHS 2017 reported that there are 20.5% of births occur at home. Among births at home, the presence of a skilled health provider as a birth attendant is critical to ensure safe birth care, especially for mothers who could not access health facilities. However, the presence of skilled birth attendants has not been accessible during home births.Methods: This study used a cross-sectional study design using the 2017 IDHS data. The sample of this study was all women of childbearing age who gave birth at home in 2012-2017. The variables analyzed included maternal education, ownership index, region, place of residence, insurance, pregnancy complications, delivery complications, ANC visits, parity, maternal age at delivery, and delivery assistants. Predictive model analysis was performed using Cox regression.Results: 59.5% of home deliveries were attended by skilled birth attendants, while 40.5% were attended by traditional birth attendants/relatives. Higher wealth index/socioeconomic status (PR=1.35; 95% CI 1.23-1.48), >4 ANC visits (PR=1.28; 95% 1.18-1.40), and higher education (PR=1.21; 95% CI 1.10-1.32) were the most dominant characteristics affecting the odds of delivery by a skilled birth attendant. Conclusion: Increasing coverage of skilled birth attendants can be pursued by increasing the coverage of recommended ANC visits (>4 times), improving socio-economic status, and increasing maternal education levels.