bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative population genomics of island birds reveal contrasting signals of ancient and recent population structure and panmixia
Authors: HA-SHAN Marine , Thébaud Christophe , Tournebize Rémi , Gabrielli Maëva , Arredondo Armando , Mila Borja , Chikhi Lounès 
Published: November 2024

Abstract

The evolutionary history of insular species is linked to the ecology genetic diversity and structure of the founder population as well as the ancestral population that served as a source. Population genetic studies of insular species have focused on single species and their recent post-colonisation history, ignoring the genetic characteristics of ancestral populations. Here we analysed population genomic data from three closely related island birds (Zosterops) with varying levels of structure to investigate their recent history and past population structure. The demographic history of each species was investigated using the Structured Non-Stationary Inferential Framework (SNIF). We inferred a number of demes with high and variable estimates for two of the three species, possibly reflecting structure in the ancestral population before colonisation. To explore this possibility, we simulated genomic data under different colonisation models where an ancestral structured population colonised an island once and formed either a panmictic or a structured population. We tested the influence of the colonisation time and the level of structure in both the ancestral and founding populations on SNIF inference. We observed that SNIF correctly inferred the ancient population structure when the colonisation event was recent. When the colonisation time was old enough, SNIF inferred the recent island structure. Lastly, when the population has always been panmictic, SNIF tended to infer high numbers of demes. Altogether our results suggest that none of the simple scenarios studied here can fully explain the complex signatures of population structure and panmixia which we found in our study species.
Clinical Integration of Germline Findings from a Tumor Testing Precision Medicine Program
Authors: Sanabria-Salas Maria Carolina , Anggala Nina C. , Gillies Brittany , Farncombe Kirsten M. , Hofstedter Renee , Peck Larissa , Purnaghshband Helia , Redondo Laura , Thain Emily , Xu Wei , Sabatini Peter , Bedard Philippe L. , Kim Raymond H. 
Published: November 2024

Abstract

Background:
Integrating germline genetic testing (GGT) recommendations from tumor testing into hereditary cancer clinics and precision oncology trials presents challenges that require multidisciplinary expertise and infrastructure. While there have been advancements in standardizing molecular tumor boards, the implementation of tumor profiling for germline-focused assessments has only recently gained momentum. However, this progress remains inconsistent across institutions, largely owing to a lack of systematic approaches for managing these findings. This study outlines the development of a clinical pathway for identifying potential germline variants from an institutional tumor-sequencing research program at Princess Margaret Cancer Centre.
Methods:
Between August 2022 and August 2023, a clinical pathway led by a germline Molecular Tumor Board (gMTB) was established to review tumor genetic variants (TGVs) flagged as potential germline findings in patients with advanced cancer via a multigene panel. Eligibility for hereditary cancer syndrome investigation (‘germline criteria’) followed Cancer Care Ontario’s Hereditary Cancer Testing Criteria and clinical judgment. Germline-focused analysis of TGVs followed the European Society of Medical Oncology guidelines and similar published criteria (‘tumor-only criteria’).
Results:
Of 243 tumor profiles, 83 (34.2%) had ≥1 flagged TGV and were referred to the gMTB. Among them, 47 (56.6%) met ‘germline criteria’ for GGT. Of 127 TGVs, 44 (34.6%) were considered germline relevant. Tier I TGVs, interpreted as pathogenic/likely pathogenic (P/LP) and in most- or standard-actionable genes with high germline conversion rates (GCRs) in any context, were more likely to be considered germline relevant (p-value < 0.05). One confirmed germline variant was identified in nine patients meeting solely ‘tumor-only criteria’. The rate of true germline P/LP variants was 10.8% (9/83), with a GCR of 33% (9/27).
Conclusions:
Incorporating genetic counselors into gMTBs enhanced the integration of research findings into clinical care and improved the detection of disease-causing variants in patients outside traditional testing criteria.
Triglyceride Glucose (TyG) Index Is Associated With Heart Failure With Recovered Ejection Fraction in Patients With Diabetes
Authors: Jiao Siqi , Sun Yihong 
Published: November 2024

Abstract

Background
Due to advances in medical treatments, a substantial proportion of patients with heart failure with reduced ejection fraction (HFrEF) have experienced partial or complete recovery of ejection fraction (EF), termed Heart failure with recovered ejection fraction (HFrecEF). The triglyceride-glucose index (TyG index) has been regarded as a reliable alternative marker of insulin resistance (IR) and an effective predictor of the development and adverse prognosis of heart failure (HF). This study aims to explore the correlation between the TyG index and the recovery of ejection fraction in HF patients with diabetes.
Methods
A total of 245 hospitalized HFrEF patients with diabetes from January 2019 to December 2023 were included in this retrospective study. Left ventricular ejection fraction (LVEF) was measured using echocardiography, and patients were divided into the persistent HFrEF group and the HFrecEF group. Multivariate logistic regression analysis was used to analyze the correlation between the TyG index and the occurrence of HFrecEF, and a receiver operating characteristic curve (ROC) was constructed to determine the predictive value of the TyG index for HFrecEF.
Results
During a median follow-up time of 12 ± 1.6 months, 118 patients (48.1%) belonged to the HFrecEF group, and 127 patients (51.9%) belonged to the persistent HFrEF group. Compared with patients with persistent HFrEF, patients with HFrecEF were younger, less likely to have atrial fibrillation, had higher systolic blood pressure, lower HbA1c, and lower TyG index levels. The TyG index was an independent predictor of the incidence of HFrecEF (OR = 0.573, 95%CI: 0.388–0.867, P = 0.001). The area under the ROC curve for predicting the occurrence of HFrecEF using the TyG index was 0.701.
Conclusions
In HFrEF patients with diabetes, an elevated TyG index is associated with a decreased incidence of HFrecEF.
Establishing a Preoperative Predictive Model for Gallbladder Adenoma and Cholesterol Polyps Based on Machine Learning: A Multicentre Retrospective Study
Authors: Wang Yubing , Qu Chao , Zeng Jiange , Jiang Yumin , Sun Ruitao , Li Changlei , Li Jian , Xing Chengzhi , Tan Bin , Liu Kui , Liu Qing , Zhao Dianpeng , Cao Jingyu , Hu Weiyu 
Published: November 2024

Abstract

Background
With the rising diagnostic rate of gallbladder polypoid lesions (GPLs), differentiating benign cholesterol polyps from gallbladder adenomas with a higher preoperative malignancy risk is crucial. This study aimed to establish a preoperative prediction model capable of accurately distinguishing between gallbladder adenomas and cholesterol polyps using machine learning algorithms.
Materials and Methods
We retrospectively analysed the patients' clinical baseline data, serological indicators, and ultrasound imaging data. Using 12 machine learning algorithms, 110 combination predictive models were constructed. The models were evaluated using internal and external cohort validation, receiver operating characteristic curves, area under the curve (AUC) values, calibration curves, and clinical decision curves to determine the best predictive model.
Results
Among the 110 combination predictive models, the Support Vector Machine + Random Forest (SVM + RF) model demonstrated the highest AUC values of 0.972 and 0.922 in the training and internal validation sets, respectively, indicating an optimal predictive performance. The model-selected features included gallbladder wall thickness, polyp size, polyp echo, and pedicle. Evaluation through external cohort validation, calibration curves, and clinical decision curves further confirmed its excellent predictive ability for distinguishing gallbladder adenomas from cholesterol polyps. Additionally, this study identified age, adenosine deaminase level, and metabolic syndrome as potential predictive factors for gallbladder adenomas.
Conclusion
This study employed the latest machine learning combination algorithms and preoperative ultrasound imaging data to construct an SVM + RF predictive model, enabling effective preoperative differentiation of gallbladder adenomas and cholesterol polyps. These findings will assist clinicians in accurately assessing the risk of GPLs and providing personalised treatment strategies.
Ondasetron in Premedication During Unsedated Upper Digestive Endoscopy: Evaluation of Tolerance and Acceptability
Authors: Shindano Tony Akilimali , Murhi Espoir Batumike , Boroto Raissa Iranga , Lembembu Corneille 
Published: November 2024

Abstract

Introduction: The practice of gastroduodenal endoscopy under conscious sedation is still limited in many low-income countries due to additional costs generated as well as concerns related to the management of many constraints and other adverse effects. The aim of this study is to evaluate the practice of this act without any sedation but with addition of a potent antinauseant in premedication.
Methodology: This was a prospective single center study conducted from 2020 to 2022 in Bukavu, East of the Democratic Republic of the Congo. Endoscopies were performed without sedation, but by additionally associating a protocol using a sublingual spray of ondasetron. Clinical data, data related to the endoscopic procedure and those related to patients’ opinions before and after the procedure were respectively analyzed.
Results: The study enrolled 145 patients, of whom 76 (52.4%) were men. Only 12 patients (8.28%) reported a poor tolerance during the procedure. The patients (91.72%) who have well tolerated the procedure were those who followed instructions well and in whom the introduction of the endoscope was easy (p < 0.001). In multivariate analysis, only the easy introduction of the endoscope appeared to be the main determinant of tolerance (adjusted OR 44.34 [2.78; 708.22] , p=0.007).
Conclusion: Unsedated upper digestive endoscopy using ondansetron in premedication seems to be well tolerated but this tolerance also depends on good conditions of patients’ preparation as well as good mastering of first stages of the exploration.
The effect of reducing markers of ageing under Metabolic Bariatric Surgery is weight-indipendent.
Authors: Dudek Alicja , Zapała Barbara , Kawa Ilona , Ciszek Karol , Tylec Piotr , Cyranka Katarzyna , Wysocki Michał , Major Piotr 
Published: November 2024

Abstract

Introduction
Obesity, a chronic disease linked to premature aging, is increasingly managed through metabolic bariatric surgery (MBS). This study aims to evaluate whether changes in biological age markers are related to the success of bariatric surgery, as measured by weight loss rates.
Methods
In this prospective observational study, 100 obese patients scheduled for bariatric surgery from July 2020 to May 2021 underwent a 24-month postoperative follow-up. The telomere length (TL) using qPCR, DNA damage, C-reactive protein (CRP), Interleukin-6 (IL-6), tumor necrosis factor alpha (TNFalpha), total oxidant status (TOS) and metabolic age were assessed. The analysis whether percentage excess weight loss (%EWL) and percentage excess BMI loss (%EBMIL) correlated with changes in aging markers post-surgery was established.
Results
Forty patients completed follow-up, with 22 achieving optimal (%EWL, %EBMIL ≥ 50%) and 18 suboptimal (%EWL, %EBMIL < 50%) surgical outcomes. Both groups showed significant prolongation of TL and reduction of DNA damage, CRP, IL-6, TNFalpha, TOS, metabolic age, but only metabolic age showed a greater change in the optimal outcome group. The delta of change in other ageing markers did not differ between groups.
Conclusion
Improvements in aging markers such as telomere length, DNA damage, inflammation, and oxidative stress occur independently of weight loss rates after metabolic bariatric surgery, suggesting that weight loss indices alone do not fully capture the therapeutic success of the procedure.
Comparative Effectiveness of Immunotherapies for Untreated Advanced Non-Small Cell Lung Cancer in Real-World Clinical Practice: a Japanese Cancer Registry Cohort Study
Authors: Miyazaki Akito , Kunimasa Kei , Morishima Toshitaka , Tamiya Motohiro , Inoue Takako , Kawamura Takahisa , Tanaka Tsunehiro , Komuta Kiyohide , Futamura Shun , Nishino Kazumi , Miyashiro Isao 
Published: November 2024

Abstract

Objectives
No direct comparative study has evaluated first-line immunomonotherapy and immunochemotherapy regimens for advanced non–small cell lung cancer (NSCLC). To compare the effectiveness of them, focusing on time to treatment failure (TTF) and overall survival (OS).
Materials and Methods
This retrospective, multicenter cohort study at 68 hospitals in Osaka Prefecture, Japan, included patients with advanced NSCLC who received immunomonotherapy or immunochemotherapy as initial treatment between January 2019 and December 2021. Data were collected from cancer registry and administrative databases. The median follow-up was 267 days (IQR, 143–247 days). The endpoints were OS and TTF comparisons among regimens, further comparing atezolizumab-chemotherapy (ATZ-chemo), pembrolizumab-chemotherapy (Pembro-chemo), and nivolumab–ipilimumab-chemotherapy (NIV + IPI-chemo) regimens. Baseline characteristics were obtained, and propensity score-matched analyses were performed.
Results
We identified 2,101 patients with Stage IV NSCLC treated with ATZ, Pembro, or NIV + IPI. After propensity score matching, comparing immunomonotherapy and immunochemotherapy showed no significant difference in TTF (median: 247 vs. 233 days; P = 0.74), but immunochemotherapy significantly improved OS (median: 653 vs. 492 days; P < 0.05). Among chemotherapy combinations, the Pembro-chemo group had significantly longer TTF (287 vs. 211 days; P < 0.05) and OS (not reached vs. 609 days; P = 0.03) compared to the ATZ-chemo group. Comparing Pembro-chemo and NIV + IPI-chemo showed no significant difference in TTF (239 vs. 217 days; P = 0.53) or OS (814 days vs. not reached; P = 0.26).
Conclusions
This study suggests that immunochemotherapy regimens and pembrolizumab-containing regimens may contribute more to prolonged survival.
Phenotyping to predict 12-month health outcomes of older general medicine patients
Authors: Woodman Richard John , Bryant Kimberly , Sorich Michael J , Thompson Campbell H , Russell Patrick , Pilotto Alberto , Mangoni Aleksander A 
Published: November 2024

Abstract

Background: A variety of unsupervised learning algorithms have been used to phenotype older patients, enabling directed care and personalised treatment plans. However, the ability of the clusters to accurately discriminate for the risk of older patients, may vary depending on the methods employed.
Aims: To compare seven clustering algorithms in their ability to develop patient phenotypes that accurately predict health outcomes.
Methods: Data was collected for N=737 older medical inpatients for five different types of medical data (ICD-10 codes, ATC drug codes, laboratory, clinic and frailty data). We trialled five unsupervised learning algorithms (K-means, K-modes, hierarchical clustering, latent class analysis (LCA), and DBSCAN) and two graph-based approaches to create separate clusters for each method and datatype. These were used as input for a random forest classifier to predict eleven health outcomes: mortality at one, three, six and 12 months, in-hospital falls and delirium, length-of-stay, outpatient visits, and readmissions at one, three and six months.
Results: The overall area-under-the-curve (AUC) across the eleven outcomes for the seven methods were (from highest to lowest) 0.758 (hierarchical), 0.739 (K-means), 0.722 (KG-Louvain), 0.718 (KNN-Louvain), 0.698 (LCA), 0.694 (DBSCAN) and 0.656 (K-modes). Overall, frailty data was most important data type for predicting mortality, ICD-10 disease codes for predicting readmissions, and laboratory data the most important for predicting falls.
Conclusions: Clusters created using hierarchical, K-means and Louvain community detection algorithms identified well-separated patient phenotypes that were consistently associated with age-related adverse health outcomes. Frailty data was the most valuable data type for predicting most health outcomes.
Application of GIS for Spatio-Temporal Modeling of Land Use Change and Environmental Degradation in Dhaka, Narayanganj, and Gazipur: A 24-Year Study (1999–2023)
Authors: Mahmud Abdullah al , Sultana Niger , Habib Muhammad Enamul 
Published: November 2024

Abstract

The rapid transformation of land use and land cover (LULC) in Bangladesh, particularly in the central economic hubs of Dhaka, Narayanganj, and Gazipur, poses critical challenges for environmental sustainability. This study examines LULC changes between 1999 and 2023, revealing significant increases in built-up and newly developed areas, while natural environments, including vegetation, wetlands, and barren land, have diminished. Gazipur experienced the most dramatic increase in development (5162.82% for new developments and 1148.89% for built-up areas), followed by Narayanganj and Dhaka. Land Surface Temperature (LST) consistently increased across all districts, with strong correlations between built-up areas and LST (r = 0.91). Additionally, LULC changes were linked to environmental variables, including air quality (PM10, PM2.5) and water quality (pH, BOD, COD), with Gazipur showing the highest number of significant correlations. The findings underscore the environmental impact of rapid urbanization and provide critical data for land management and policy interventions to mitigate further environmental degradation. These results can serve as a baseline for future studies on the environmental vulnerability caused by LULC changes in rapidly urbanizing regions.
Evaluation of the Efficacy and Safety of Adjuvant Chemotherapy Regimens after Pancreatic Cancer Surgery: A Single-Center Real-World Study
Authors: Zhang Xinyue , Deng Yaya , Lai Jiahui , Zhang Haibo , Song Tao , Hong Yupeng , Hu Renzhi , Yang Liu 
Published: November 2024

Abstract

Background: This study evaluated the efficacy and safety of dual-drug and multidrug adjuvant chemotherapy regimens for the treatment of pancreatic cancer, with a focus on key prognostic factors influencing patient outcomes.
Methods: This single-center retrospective analysis was conducted at Zhejiang Provincial People's Hospital from 2017--2022 and involved 97 patients with radical pancreatic cancer treated postoperatively. Patients were classified into dual-drug (86 patients) and multidrug (11 patients) regimen groups. The data collected included preoperative and postoperative blood tests, biochemical parameters, and tumor markers (CEA, CA199, CA125). Statistical analyses were used to assess overall survival (OS), disease-free survival (DFS), and adverse events (AEs). Kaplan‒Meier survival curves, Lasso‒Cox regression models, and univariate/multivariate Cox regression analyses were used to identify prognostic factors, with internal validation via the bootstrap method.
Results: 1. Neoadjuvant chemotherapy, age, the postoperative platelet-to-lymphocyte ratio (PLR), and the choice of adjuvant regimen were significantly associated with survival (p<0.05). Patients over 55.5 years of age or with a PLR >188.3 favored dual-drug regimens.
2. The median DFS was 12.4 months for the dual-drug group and 11.5 months for the multidrug group (p=0.520); the median OS was 22.5 and 18.5 months, respectively (p=0.570). Diarrhea was more common in the multidrug group (p=0.001).
3. Independent DFS factors included preoperative CA125 levels, the neutrophil-to-lymphocyte ratio (NLR), low-density lipoprotein (LDL), and alanine aminotransferase (ALT) levels. The factors associated with OS were abdominal pain, tumor location, number of chemotherapy cycles, CA125, NLR, LDL, aspartate aminotransferase (AST), and postoperative cholesterol (TC) (p<0.05).
4. In the dual-drug regimens, the significant factors associated with DFS were preoperative HDL, postoperative ALB, postoperative CA125, and neoadjuvant chemotherapy. The significant OS determinants included tumor location, number of chemotherapy cycles, and postoperative serum ALB concentration (p<0.05).
5. The DFS of patients receiving multidrug regimens was influenced by preoperative CA125, total cholesterol (TC), and postoperative CRP/ALB levels.
6. The initiation timing of adjuvant chemotherapy significantly influences OS, with midterm and very late starts correlating with increased mortality risk.
Conclusions: No significant differences in efficacy or safety were found between dual-drug and multidrug regimens for postoperative pancreatic cancer patients. High adverse event rates and prognostic marker significance highlight the need for personalized strategies and prompt chemotherapy initiation.
Seagrass organic carbon stocks are not correlated with seagrass abundance at local scale, but loss of seagrasses does lead to decrease in surficial sediment organic carbon at the seascape scale in Bermuda
Authors: Fourqurean James , Krause Johannes R. , manuel Sarah A. , Coates Katherine A. , Worboys Philip E , Gonzales-Corredor Juan David , Zuill Treiana , Roden Ana , Campbell Justin E. 
Published: November 2024

Abstract

Seagrass ecosystems are recognized as important carbon sinks that accumulate organic carbon (Corg) in their biomass and underlying soils. In Bermuda, seagrass meadows have declined precipitously over the last two decades, potentially leading to loss of those Corg stocks. This study found 45% lower Corg stocks in Bermuda (ca. 32.3°N) compared to lower-latitude tropical Atlantic seagrass meadows. We also report 2–3 orders of magnitude lower long-term carbon burial rates (0.10 Mg Corgha−1y− 1 over the last 1830 years) compared to global estimates, determined via 14C dating of mangrove peats buried 1m below the modern sediment-water interface. Historical data from 2008, relatively early in the decline of Bermuda’s seagrasses, showed that neither seagrass abundance nor life history strategy (persistent vs. ephemeral) were associated with Corg content of surficial sediments or the relative contribution of seagrass-derived organic matter to the soil Corg. Following the collapse of most of Bermuda’s seagrasses, Corg content of surficial sediments declined by 15% over the period 2008–2024, although this decline was not a function of seagrass loss at the site scale. This suggests that seagrass-derived Corg is deposited across the Bermuda Platform, regardless of seagrass presence or abundance, and that the regional loss in seagrasses has led to a regional-scale decline in Corg content of the surficial soils. We conclude that seagrass loss can have landscape-scale effects on sediment Corg stocks even without site-specific relationships, and that caution should be exercised when applying regional or global literature values for average Corg stocks to estimate carbon market valuations.