bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mortality risk stratification based on comorbidity status among cervical cancer patients in Lagos, Nigeria
Authors: Ola Idris O , Okunowo Adeyemi A , Habeebu Muhammad Y 
Published: February 2025

Abstract

Background
Comorbidity amplifies mortality risk by approximately sixfold in cancer patients and affects about 26% of cervical cancer (CC) patients in Nigeria. However, its impact on CC outcomes has yet to be fully explored.

Methods
We analysed data from the Lagos University Teaching Hospital and the NSIA-LUTH Cancer Center in Lagos, Nigeria, between January 2015 and December 2021. Based on the hypertension-augmented Charlson comorbidity index (hCCI), the hazard ratios (HRs) associated with CC mortality were estimated using Cox proportional hazards model.

Results
Our results showed a mortality rate of 30.1/100 women-years with a mean age at death of 59.8 years. Women with hCCI 2–6 had a significant increase in mortality risk in unadjusted (HR 1.68 [95% confidence interval {CI} 1.10 to 2.57]) and age-adjusted models (adjusted HR 1.57 [95% CI 1.02 to 2.42]) compared with those with hCCI 0. When CC stage was considered, the mortality risk gradient by hCCI was pronounced for late-metastatic CC with hCCI 2–6 (HR 2.32 [95% CI 1.23 to 4.39], increasing to 4.15 (95% CI 1.69 to 10.18) in the adjusted model compared with hCCI 0.

Conclusions
Cervical cancer mortality risk increases with an increasing comorbidity score. Routine incorporation of comorbidity scoring in the clinical assessment of CC patients as well as the use of multidisciplinary cancer care teams may positively impact their clinical and psychosocial management.
Terrestrial-aquatic connectivity structures microbial communities during the formation of thermokarst lakes
Authors: Leroy Martial , Burnett Melanie S , Laurion Isabelle , Douglas Peter M J , Kallenbach Cynthia M , Comte Jérôme 
Published: February 2025

Abstract
Rising air temperatures and permafrost degradation drive the erosion of palsas (permafrost mounds mainly composed of frozen peat and ice layers) and lead to the formation of thermokarst ponds and lakes, known for their high greenhouse gas (GHG) emissions. This study investigates the impact of permafrost soil erosion during thermokarst lake formation on microbial community structure and its implications for GHG dynamics in a highly degraded permafrost valley (Nunavik, northern Quebec, Canada). Samples were collected from a palsa, an emerging lake connected to the palsa, surrounding peat and soil pore water, and two mature lakes which are older, stratified, and less connected to the palsa. Analysis of total and potentially active microbial communities, based on 16S rRNA gene amplicon sequence variants revealed significant changes in taxonomic and phylogenetic diversity during thermokarst lake formation. We found distinct assembly processes depending on the stage of formation. Firstly stochastics, they became more deterministic as lakes mature. Distinct methanogens/trophs communities in emerging lake led to lower CO2:CH4 ratio compared to the surface of mature lakes. Which presented a greater diversity of methanogens and distinct methanotrophic communities, with acetogenic, hydrogenotrophic and methylotrophic methanogens along anaerobic an aerobic methanotrophs. Multivariate analyses revealed that selection processes were primarily driven by concentrations of CH4, CO2, and NO3−. The interplay between the nitrogen and carbon cycles appears to be pivotal in these assemblages, with nitrogen playing key roles on community structure. These findings underscore the significance of terrestrial-aquatic connectivity in shaping microbial communities and GHG emissions in thermokarst lakes.
Strain identity effects contribute more to Pseudomonas community functioning than strain interactions
Authors: Kramer Jos , Maréchal Simon , Figueiredo Alexandre R T , Kümmerli Rolf 
Published: February 2025

Abstract
Microbial communities can shape key ecological services, but the determinants of their functioning often remain little understood. While traditional research predominantly focuses on effects related to species identity (community composition and species richness), recent work increasingly explores the impact of species interactions on community functioning. Here, we conducted experiments with replicated small communities of Pseudomonas bacteria to quantify the relative importance of strain identity versus interaction effects on two important functions, community productivity and siderophore production. By combining supernatant and competition assays with an established linear model method, we show that both factors have significant effects on functioning, but identity effects generally outweigh strain interaction effects. These results hold irrespective of whether strain interactions are inferred statistically or approximated experimentally. Our results have implications for microbiome engineering, as the success of approaches aiming to induce beneficial (probiotic) strain interactions will be sensitive to strain identity effects in many communities.
Klebsiella spp. in healthy pigs: reservoirs of antimicrobial resistance and potential pathogenic threats
Authors: Rosa Jéssica Nogueira , da Silva Giarlã Cunha , Fontes Patrícia Pereira , Guidini Matheus Machado , Oliveira Rúzivia Pimentel , Bazzolli Denise Mara Soares 
Published: February 2025

Abstract

Aim
The aim of this study was to isolate Klebsiella spp. from clinically healthy animals fed diets with or without antimicrobial growth promoters (AGP). Additionally, the study evaluated whether the inclusion of growth promoters affected the recovery of multi-drug-resistant isolates.

Methods and results
A total of 144 isolates were obtained from rectal swabs on Simmons citrate agar supplemented with 1% inositol. Of these, 45 non-replicative isolates underwent extensive characterization, including molecular and phenotypic analyses. Sequencing identified that 77% were Klebsiella pneumoniae, 14.5% K. aerogenes, and 8.5% K. variicola. Isolates exhibiting the same polymorphic profiles were detected across different animals and treatments, with and without AGP. Seventy-one percent were multidrug-resistant, as determined by disk diffusion testing. The isolates harbored genes such as mcr-1, blaCTX-M-2, sul2, tetB, qnrS, and dfrA, among others. Additionally, genes encoding siderophores like enterobactin, aerobactin, and yersiniabactin were detected via Polymerase Chain Reaction (PCR). Thirty-nine isolates were strong biofilm producers, 45% moderate, and 16% weak in vitro tests. The predominant genetic profiles included single, double, or triple-locus variants of ST25, ST147, and ST4691. Two novel sequence types were identified: ST7694 (K. pneumoniae) and ST7699 (K. variicola). Survival and persistence analyses in Galleria mellonella showed that these isolates exhibited a virulent phenotype and an enhanced capacity for multiplication in the early hours of infection.

Conclusion
Clinically healthy swine act as reservoirs for multidrug-resistant Klebsiella spp. exhibiting significant virulence phenotypes. The identification of novel sequence types contributes to epidemiological surveillance and the One Health framework.
Inbreeding depression for litter size in two mice lines under divergent selection for environmental birth weight variability using genomic data
Authors: Ojeda-Marín Candela , Cervantes Isabel , Formoso-Rafferty Nora , Gutiérrez Juan Pablo , Rodríguez-Ramilo Silvia Teresa 
Published: February 2025

Abstract
Inbreeding depression (ID) is usually observed as reduced survival and fertility and may have a variable impact in different populations. The aim of this study was to estimate ID from genomic and pedigree data in the litter size (LS) of the high variability line (H-Line) and the low variability line (L-Line). Of these, the L-Line performed better on traits related to robustness. A total of 1587 females from 26 selection generations were genotyped with a high-density SNP array. LS data of 732 L-Line and 648 of H-Line animals were used. The following were calculated: pedigree inbreeding coefficient (FPED), genomic inbreeding derived from different genomic matrices (FNEJ, FL&H, FVR1, FVR2 and FYAN), from runs of homozygosity (FROH) and from homozygosity by descent probabilities (FHBD). FROH were calculated in the 19 autosomes (CHR). FROH and FHBD were divided into 9 lengths and age classes, respectively. All the inbreeding coefficients were standardized by the mean inbreeding coefficient of the 1st generation. Regression coefficients (b) obtained from genomic data were between -3.71 with FVR2 and -5.09 with FHBD in the H-Line, and that estimated from FPED was -5.67. In the L-Line the b obtained from genomic data were between -3.52 with FVR2 and -4.55 with FHBD, and that obtained with FPED was -4.08. Significant ID effects were detected in CHR13 in the H-Line and CHR1 and CHR9 in the L-Line. The b negative trended to be lower as the ROH length increased. The age of the homozygosity by descent segment performed differently in each line, for example FHBD raised 128 generations ago produced a significant positive effect only in the L-Line. The effect of global inbreeding coefficients on the LS was negative in both lines with a higher impact in the H-Line than in the L-Line, suggesting the L-Line having higher robustness. CHR 1, 9 and 13 were candidates for future gene search. In general, more recent FROH and FHBD presented negative effects on LS while older FROH and FHBD presented positive effects on LS in both selected lines.
Genetic Evaluation of Longevity in Australian Angus cattle Using Random Regression Models
Authors: Aliloo Hassan , van der Werf Julius H J , Clark Samuel A 
Published: February 2025

Abstract
Cow longevity is an economically important trait for beef breeders directly impacting profitability and sustainability of beef cattle production systems. Despite its great importance, early selection for longevity is complex because the true longevity of a cow is not known until the end of her life. In this study we aimed to estimate variance components and genetic parameters for two binary measures of cow longevity in Australian Angus cattle population. Traditional longevity (TL) represented the cow’s ability to avoid culling after the first calving while functional longevity (FL) also accounted for calving events while the cow was present in the herd. Five datasets consisting of animals culled because of different reasons were created and evaluated separately to compare the estimates of variance components and genetic parameters. We also investigated the impact of censored data on estimated breeding values of bulls with different proportions of active daughters. A single-trait random regression model using a Bayesian Gibbs sampler was applied to both longevity traits and all 5 culling reason groups between age 2 to 11 yr. The heritabilites were generally low and ranged between 0.02 to 0.19 for TL and between 0.02 to 0.20 for FL traits. The peak of heritabilites were found between ages 4 to 6 yr for both longevity measures. The low estimates of genetic correlations between ages at the beginning and end of the trajectory in all culling reason groups indicated that longevity evaluated at early and late stages of life are not genetically the same traits. The estimated breeding values of sires with active daughters were underestimated when the censored data was excluded from the analysis. The negative impact of censoring was larger for younger sires who had larger proportion of active daughters. Our results indicate the additive genetic component has a sizeable contribution to the variability of longevity in Australian Angus cattle and therefore, the genetic improvement of longevity can be achieved if longevity is considered as a long-term breeding objective.
Pedagogical virtues from the situationist insight: virtuous scaffolding and sensitivity to non-epistemic situational factors to learning
Authors: Clemente Noel L 
Published: February 2025

Abstract
This article explores two pedagogical virtues (intellectual virtues of a teacher) that arise from the insight that non-epistemic situational factors can affect students’ epistemic judgements and behaviour. First, a virtuous teacher must be sensitive enough to these factors in order to take advantage of how they boost student learning. However, while cultivating a situationally and epistemically favourable environment for learning sounds sensible, teachers should not spoil their students by making them too dependent on these beneficial external factors. The virtuous teacher must also realize that these are only scaffolds; they do help students initially, but must eventually be removed to promote the students’ intellectual autonomy. This characterizes a second pedagogical virtue: the competence to facilitate students’ growth so that they become more capable in future opportunities for knowledge acquisition.
PyLMT: A transient detection pipeline for the 4-m International Liquid Mirror Telescope
Authors: Pranshu Kumar , Misra Kuntal , Ailawadhi Bhavya , Dubey Monalisa , Dukiya Naveen , Filali Sara , Hickson Paul , Kumar Brajesh , Negi Vibhore , Surdej Jean 
Published: February 2025

Abstract
The International Liquid Mirror Telescope (ILMT) is a 4-m aperture, zenith-pointing telescope with a field-of-view of 22′, situated in the foothills of the Himalayas. The telescope operates in continuous survey mode, making it a useful instrument for time-domain astronomy, particularly for detecting transients, variable stars, active galactic nuclei variability, and asteroids. This paper presents the PyLMT transient detection pipeline to detect such transient/varying sources in the ILMT images. The pipeline utilises the image subtraction technique to compare a pair of images from the same field, identifying such sources in subtracted images with the help of convolutional neural networks (CNN) based real/bogus classifiers. The test accuracies determined for the real/bogus classifiers ranged from 94 % to 98 %. The resulting precision of the pipeline calculated over candidate alerts in the ILMT frames is 0.91. It also houses a CNN-aided transient candidate classifier that classifies the transient/variable candidates based on host morphology. The test accuracy of the candidate classifier is 98.6 %. It has the provision to identify catalogued asteroids and other solar system objects using public databases. The median execution time of the pipeline is approximately 29 minutes per image of 17 minutes exposure. Relevant CNNs have been trained on data acquired with the ILMT during the cycle of October–November 2022. Subsequent tests on those images have confirmed the detection of numerous catalogued asteroids, variable stars, and other uncatalogued sources. The pipeline has been operational and has detected 12 extragalactic transients, including 2 new discoveries in the November 2023–May 2024 observation cycle.
A self-consistent framework to study magnetic fields with strong gravitational lensing and polarised radio sources
Authors: Ndiritu S W , Vegetti S , Powell D M , McKean J P 
Published: February 2025

Abstract
We introduce a unified approach that, given a strong gravitationally lensed polarised source, self-consistently infers its complex surface brightness distribution and the lens galaxy mass-density profile, magnetic field and electron density from interferometric data. The method is fully Bayesian, pixellated and three-dimensional: the source light is reconstructed in each frequency channel on a Delaunay tessellation with a magnification-adaptive resolution. We tested this technique using simulated interferometric observations with a realistic model of the lens, for two different levels of source polarisation and two different lensing configurations. For all data sets, the presence of a Faraday rotating screen in the lens is supported by the data with strong statistical significance. In the region probed by the lensed images, we can recover the Rotation Measure and the parallel component of the magnetic field with an average error between 0.6 and 11 rad m−2 and 0.3 and 3 nG, respectively. Given our choice of model, we find the electron density is the least well-constrained component due to a degeneracy with the magnetic field and disk inclination. The background source total intensity, polarisation fraction, and polarisation angle are inferred with an error between 4 and 10percnt, 15 and 50percnt, and 1 to 12 degrees, respectively. Our analysis shows that both the lensing configuration and the intrinsic model degeneracies play a role in the quality of the constraints that can be obtained.
Subcellular Enrichment Patterns of New Genes in Drosophila Evolution
Authors: Dong Chuan , Xia Shengqian , Zhang Li , Arsala Deanna , Fang Chengchi , Tan Shengjun , Clark Andrew G , Long Manyuan 
Published: February 2025

Abstract
The evolutionary patterns of proteins within subcellular compartments underlie the innovation and diversification foundation of the living eukaryotic organism. The location of proteins in subcellular compartments promotes the formation of network interaction modules, which in turn reshape the architecture of higher-level protein–protein interaction networks. Here, we conducted the most up-to-date gene age dating of Drosophila melanogaster by employing recently available long-read sequencing genomes as references. We found that an elevated gene fixation in the most recent common ancestor of Drosophila genus predated the divergence between two Drosophila subgenera, and a significant tendency of these genes in D. melanogaster encode proteins that localize to the extracellular matrix, accompanying the adaptive radiation of Drosophila species. Proteins encoded by genes located in the extracellular space exhibit higher sequence divergence, suggesting a rapid evolutionary process. We also observed that proteins encoded by genes originating from the same evolutionary branches tend to co-localize in the same subcellular compartments, and proteins in the same subcellular compartment tend to interact with each other. The proteins encoded by genes that have persisted through deeper branches exhibit broader localization across multiple subcellular compartments, enhancing the likelihood of their integration into various protein or gene regulatory networks, thereby increasing functional diversity. These evolutionary patterns not only contribute to understanding the evolution of subcellular localization in proteins encoded by genes originating from different branches, but also provide insights into the evolution of protein–protein networks driven by the emergence of new genes.
Insufficient Evidence for a Severe Bottleneck in Humans During the Early to Middle Pleistocene Transition
Authors: Cousins Trevor , Durvasula Arun 
Published: February 2025

Abstract
A recently proposed model suggests a severe bottleneck in the panmictic ancestral population of modern humans during the Early to Middle Pleistocene transition. Here, we show this model provides a worse fit to the data than a panmictic model without the bottleneck.
Identifying appropriate external control datasets in support of future glioblastoma clinical trials leveraging external data
Authors: Rahman Rifaquat , Ventz Steffen , Redd Robert , Fell Geoffrey , Tan Yujue , Orio Peter , Tanner Kirk , Wen Patrick Y , Trippa Lorenzo 
Published: February 2025

Abstract

Background
Recent interest in leveraging external data for clinical trial design and analysis in glioblastoma has raised questions on the identification of appropriate data to use as external controls for future trials. We perform a comprehensive analysis assessing candidate sources of external data and comparing clinical trial and real-world datasets in newly diagnosed glioblastoma.

Methods
Individual patient-level data (PLD) from several clinical trials, a large academic institutional database and a registry (National Cancer Database) were used for analysis of patients receiving standard of care radiation with concurrent and adjuvant temozolomide. Data summaries from randomized trials 2012-2022 were analyzed to account for trials without available PLD. Multivariable modeling was employed to compare survival across datasets.

Results
In total, 8 datasets with PLD for 3061 patients with newly diagnosed glioblastoma treated with standard chemoradiation were analyzed. Patients on trials were younger (age&lt;60:64% vs. 48%,p&lt;0.001) and had higher KPS (KPS&gt;90:58% vs. 48%,p&lt;0.001) compared to non-trial patients. Patients in clinical trials exhibited inferior survival relative to non-trial patients (HR 1.30,95%CI 1.13-1.48,p&lt;0.001) after adjustment for age, sex, KPS, extent of resection and MGMT methylation status. In assessment of data summaries of 19 randomized trials, there was no detectable time-trend toward improved outcomes 2012-2022.

Conclusions
In newly diagnosed glioblastoma patients treated with standard of care chemoradiation, there were significant differences between trial datasets and real-world datasets but no evidence of a trial effect benefit from trial participation. After adjustment of relevant covariates, there was no evidence of temporal drift of improved survival over the last decade.
Association between heated tobacco product use and quitting combustible cigarette smoking among Korean adults
Authors: Kim Seung Hee , Lee Jung Ah , Cho Hong-Jun 
Published: February 2025

Abstract

Introduction
Combustible cigarette (CC) smokers often use heated tobacco products (HTPs) to quit CC smoking; however, the role of HTPs in quitting CC smoking is uncertain. We evaluated the link between HTP use and quitting CC smoking considering the intensity of HTP use among a large nationally representative sample of Korean adults.

Methods
We performed a cross-sectional study using data from the 2019 Community Health Survey in Korea. A total of 46,781 adult participants (current CC smokers and former CC smokers’ &lt; 5 years) were included and Poisson regression analysis was performed to evaluate the association between HTP use and quitting CC smoking among ever CC smokers.

Results
In ever CC smokers, compared with never HTP use, current daily HTP use was positively associated with quitting CC smoking (&lt; 1-year; prevalence ratio (PR) = 1.63, 95% confidence interval (CI) = 1.36–1.96, 1–5 years; PR = 1.47, 95% CI = 1.36–1.60), whereas current non-daily HTP use showed an inverse association with quitting CC smoking (&lt; 1-year; PR = 0.18, 95% CI = 0.12–0.29, 1–5 years; PR = 0.23, 95% CI = 0.17–0.31). Former HTP use was positively associated with short-term quitting CC smoking (PR = 1.38, 95% CI = 1.18–1.63), but negatively related to quit CC smoking after 1 year (PR = 0.81, 95% CI = 0.74–0.88).

Conclusions
Daily use of HTPs appeared to be related to the increase in quitting CC smoking, but discontinuation of HTP use was significantly associated with the recurrence of CC smoking among former HTP users of 1–5 years.

Implications
Among ever CC smokers, daily use of HTPs was positively associated with quitting CC smoking, but non-daily use of HTPs was inversely associated with quitting CC smoking. Former HTP use was linked to an increased likelihood of short-term quitting CC smoking but was significantly associated with CC smoking relapse after 1 year.