bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association of aortic valve size with the degree of aortic valve calcification in severe high-gradient aortic stenosis
Authors: Mousavi Roya Anahita , Lamm Gudrun , Will Maximilian , Kammerlander Andreas A , Krackowizer Philip , Gunacker Petra Carmen , Höbart Philipp , Voith Nikolaus , Grüninger Marc Felix , Schwarz Konstantin , Vock Paul , Hoppe Uta C , Mascherbauer Julia 
Published: January 2025

Abstract

Aims
Less pronounced calcification of the aortic valve (AVC) was observed in women with aortic stenosis (AS) when compared with men. Since women have smaller aortic valves (AVs), this could explain a lower calcium load. We aimed to analyse the association of AV size with AVC independent from sex.

Methods and results
Consecutive patients with high-gradient AS, who underwent cardiac computed tomography (CT), were assessed. AV annulus area and AVC with the Agatston score were measured on CT. In total, 601 patients (mean age 80 ± 7 years, 45% female) were included. Women had smaller AV annulus areas (4.12 ± 0.67 vs. 5.15 ± 0.78 cm2, P &lt; 0.001) and lower Agatston scores [2018 (1456–3017) vs. 3394 (2562–4530), P &lt; 0.001] than men. We found a significant correlation (r = 0.594, P &lt; 0.001) and independent association (β = 926.20, P &lt; 0.001) of AV annulus area with AVC. On separate regression analyses for men and women, AVC was independently associated with AV annulus area in both sexes (βmen = 887.77; βwomen = 863.48, both P &lt; 0.001). When patients were stratified into AV size quartiles, patients in the lower quartiles were more likely to have AVC values below recommended sex-specific AVC thresholds. In the lowest quartile, 28% of female and 27% of male patients had Agatston scores below 1200 Agatston units (AU) (women) and 2000 AU (men), while this proportion decreased to 6 and 2%, respectively, in the quartiles with the largest annulus areas.

Conclusion
In high-gradient AS, AVC strongly depends on AV annulus area. This association is not dependent on sex. Thus, AVC should be indexed to AV size in addition to sex.
The prognostic value of global longitudinal strain in patients with myocardial infarction and preserved ejection fraction: a prespecified substudy of the REDUCE-AMI trial
Authors: Mars Katarina , Hofmann Robin , Jonsson Martin , Manouras Aristomenis , Engvall Jan , Yndigegn Troels , Jernberg Tomas , Shahgaldi Kambiz , Sundqvist Martin G 
Published: January 2025

Abstract

Aims
The REDUCE-AMI trial showed that beta-blockers in patients with preserved left ventricular ejection fraction (LVEF) after acute myocardial infarction (AMI) had no effect on mortality or cardiovascular outcomes. The aim of this substudy was to evaluate whether global longitudinal strain (GLS) is a better prognostic marker than LVEF, and if beta-blockers have a beneficial effect in patients with decreased GLS.

Methods and results
REDUCE-AMI was a registry-based randomized clinical trial. Conventional echocardiographic parameters and GLS were obtained and a likelihood ratio test between models adjusted for age, sex, hypertension, smoking, diabetes, previous AMI, and multi-vessel disease was used to compare LVEF and GLS as prognostic methods. A Cox regression model evaluated the impact of beta-blocker treatment on the composite endpoint of death from any cause or new AMI. A total of 1436 patients (28.6% of the total population) were included in this substudy. Due to poor image quality or incompatible equipment, 324 (22.6%) patients were excluded from the analysis of GLS. The median GLS was 17.3%. The likelihood ratio test resulted in no difference (P = 0.56) when comparing the combination of GLS to LVEF. The results were robust when adding beta-blocker randomization status as an independent variable.

Conclusion
In patients after AMI with preserved LVEF, GLS did not add prognostic value regarding death from any cause or new AMI. In addition, beta-blocker treatment did not alter the prognostic information obtained from GLS. Consequently, this study does not support an additive value of GLS compared with standard echocardiographic measurement in this patient population.
Strategies to optimize the engagement of culturally and linguistically diverse populations in cardiac research: a systematic review
Authors: Abou Chakra Melissa , L Jessup Rebecca , Beauchamp Alison , Azar Denise , Sharma Laveena , Gumanti Audrey , Šeman Michael , Talevski Jason 
Published: January 2025

Abstract

Aims
Culturally and linguistically diverse (CALD) populations remain underrepresented in cardiovascular disease (CVD) research despite their higher disease burden compared with non-CALD populations. The purpose of this review is to synthesize the available literature on strategies to engage CALD participants in CVD research.

Methods and results
Four electronic databases (MEDLINE, EMBASE, CINAHL, and PsycINFO) were searched for literature up until May 2024. Qualitative, quantitative, or mixed-methods studies were included if they focused on CVD research, included participants who identified as coming from a CALD background, and the study included a description of their recruitment strategies. The methodological quality of the included studies was assessed using the Mixed Methods Appraisal Tool, and findings were analysed through a narrative synthesis. A total of 34 studies were included in this review, with the largest proportion conducted in the USA. The African American population was the most common CALD group. The most commonly used strategies to recruit CALD participants were strategically undertaking recruitment from places frequented by CALD communities; using CALD-specific promotional and advertisement material; offering monetary incentives; creating translated and jargon-free material; and improving staff diversity and cultural competency. The success of recruitment strategies was assessed in seven studies showing mostly positive results.

Conclusion
The findings of this review highlight cultural- and language-specific strategies that can be used to improve recruitment of CALD participants in CVD research. CALD communities must be included in CVD research to ensure cultural barriers are addressed when developing evidence-based CVD prevention guidelines.

Registration
PROSPERO: CRD42023473688.
Maintenance of long-term transposable element activity through regulation by nonautonomous elements
Authors: Omole Adekanmi Daniel , Czuppon Peter 
Published: January 2025

Abstract
Transposable elements are DNA sequences that can move and replicate within genomes. Broadly, there are 2 types: autonomous elements, which encode the necessary enzymes for transposition, and nonautonomous elements, which rely on the enzymes produced by autonomous elements for their transposition. Nonautonomous elements have been proposed to regulate the numbers of transposable elements, which is a possible explanation for the persistence of transposition activity over long evolutionary times. However, previous modeling studies indicate that interactions between autonomous and nonautonomous elements usually result in the extinction of one type. Here, we study a stochastic model that allows for the stable coexistence of autonomous and nonautonomous retrotransposons. We determine the conditions for this coexistence and derive an analytical expression for the stationary distribution of their copy numbers, showing that nonautonomous elements regulate stochastic fluctuations and the number of autonomous elements in stationarity. We find that the stationary variances of each element can be expressed as a function of the average copy numbers and their covariance, enabling data comparison and model validation. These results suggest that continued transposition activity of transposable elements, regulated by nonautonomous elements, is a possible evolutionary outcome that could for example explain the long coevolutionary history of autonomous LINE1 and nonautonomous Alu element transposition in the human ancestry.
Seismic and ultrasonic frequency measurements on partially saturated rocks under X-ray
Authors: Mews K S , Lozovyi S 
Published: January 2025

SUMMARY
Low-frequency laboratory measurements provide direct access to the elastic properties of samples within the seismic frequency band, offering calibration data for seismic survey analysis. Additionally, µCT imaging can quantify actual saturations and provides insights into phase distributions at the pore scale. To conduct laboratory triaxial measurements at seismic frequencies while simultaneously imaging the rock interior, we developed an X-ray transparent low-frequency apparatus. Our apparatus determines rock mechanical properties at seismic frequencies (0.5–150 Hz) and strain amplitudes (10$\mathrm{^{-7}}$–10$\mathrm{^{-5}}$), measuring Young’s modulus, Poisson’s ratio and attenuation. In addition P- and S-wave velocities at ultrasonic frequencies are measured. We conducted imbibition-drainage experiments to assess the effect of saturation and patch size on seismic and ultrasonic elastic properties in sandstone. Additional tests with liquid and gaseous $\mathrm{CO_2}$ reveal the impact of partial $\mathrm{CO_2}$-gas saturation. The imbibition-drainage experiment demonstrated that P-wave velocity at ultrasonic frequencies was elevated during drainage and reduced during imbibition. Drainage caused patchy saturation, while imbibition resulted in uniform saturation. This implies that ultrasonic measurements, with wavelengths comparable to the pore fluid patch size, are likely influenced by scattering. In contrast, low-frequency measurements, where the wavelength surpasses the patch size, capture effective medium properties and therefore are not affected by scattering effects. The results of the $\mathrm{CO_2}$ test suggest that low-frequency measurements can detect even low gas saturations (4 per cent gaseous $\mathrm{CO_2}$). In contrast, ultrasonic velocity measurements primarily reflect the response of the fully saturated sample at low gas saturations and do not indicate a reduction in velocity. Identifying fluid–solid interactions and estimating saturation via µCT imaging is crucial, especially with minimal gas presence. Our combined approach allows precise determination of elastic properties at seismic frequencies and shows the importance of low-frequency over ultrasonic measurements.
Resistome and plasmidome genomic features of mcr-1.1-harboring Escherichia coli: a One Health approach
Authors: Simões de Oliveira Gabriela , Lentz Silvia Adriana Mayer , Müller Camila Zanfelice , Guerra Rafaela Ramalho , Dalmolin Tanise Vendruscolo , Volpato Fabiana Caroline Zempulski , de Lima-Morales Daiana , Lamb Wink Priscila , Barth Afonso Luís , Rabinowitz Peter , Martins Andreza Francisco 
Published: January 2025

Abstract

Aims
This study evaluated the phenotypic and genotypic traits of mcr-1.1-harboring Escherichia coli isolates from chickens, pigs, humans, and farm environments. The resistome and the mobile genetic elements associated with the spread of mcr-1.1 in Southern Brazil were also characterized.

Methods and results
The 22 mcr-1.1-harboring E. coli isolates from different origins were selected for antimicrobial susceptibility testing and whole genome sequencing for characterization of the resistome, plasmids, and sequence types. All isolates presented several resistance genes and harbored the mcr-1.1 gene in a highly similar IncX4 plasmid. Furthermore, the mcr-1.1 gene co-occurred with the mcr-3.12 gene in a multidrug-resistant isolate from the farm environment.

Conclusions
These findings demonstrate that the mcr-1.1 gene in E. coli isolates from Brazil is spreading mainly by horizontal transfer of the IncX4 plasmid. The co-occurrence of mcr-1.1 and mcr-3.12 highlights pig farming as an important reservoir of colistin resistance.
Development and evaluation of a 4M taxonomy from nursing home staff text messages using a fine-tuned generative language model
Authors: Farmer Matthew Steven , Popescu Mihail , Powell Kimberly 
Published: January 2025

Abstract

Objective
This study aimed to explore the utilization of a fine-tuned language model to extract expressions related to the Age-Friendly Health Systems 4M Framework (What Matters, Medication, Mentation, and Mobility) from nursing home worker text messages, deploy automated mapping of these expressions to a taxonomy, and explore the created expressions and relationships.

Materials and Methods
The dataset included 21 357 text messages from healthcare workers in 12 Missouri nursing homes. A sample of 860 messages was annotated by clinical experts to form a “Gold Standard” dataset. Model performance was evaluated using classification metrics including Cohen’s Kappa (κ), with κ ≥ 0.60 as the performance threshold. The selected model was fine-tuned. Extractions were clustered, labeled, and arranged into a structured taxonomy for exploration.

Results
The fine-tuned model demonstrated improved extraction of 4M content (κ = 0.73). Extractions were clustered and labeled, revealing large groups of expressions related to care preferences, medication adjustments, cognitive changes, and mobility issues.

Discussion
The preliminary development of the 4M model and 4M taxonomy enables knowledge extraction from clinical text messages and aids future development of a 4M ontology. Results compliment themes and findings in other 4M research.

Conclusion
This research underscores the need for consensus building in ontology creation and the role of language models in developing ontologies, while acknowledging their limitations in logical reasoning and ontological commitments. Further development and context expansion with expert involvement of a 4M ontology are necessary.
Estimation of Finite Population Proportions for Small Areas—A Statistical Data Integration Approach
Authors: Sen Aditi , Lahiri Partha 
Published: January 2025

Abstract
Empirical best prediction (EBP) is a well-known method for producing reliable proportion estimates when the primary data source provides only small or no sample from finite populations. There are potential challenges in implementing existing EBP methodology, such as limited auxiliary variables in the frame (not adequate for building a reasonable working predictive model), or unable to accurately link the sample to the finite population frame, due to the absence of identifiers. In this paper, we propose a new data linkage approach, where the finite population frame is replaced by a big probability sample, having a large set of auxiliary variables, but not the outcome binary variable of interest. We fit an assumed model on the small probability sample and then impute the outcome variable for all units of the big sample to obtain standard weighted proportions. We develop a new adjusted maximum likelihood (ML) method so that the estimate of model variance does not fall on the boundary, which is otherwise encountered in the commonly used ML method. We also propose an estimator of the mean squared prediction error using a parametric bootstrap method and address computational issues by developing an efficient Expectation Maximization algorithm. The proposed methodology is illustrated in the context of election projection for small areas.
Modeling plant phenotypic plasticity and its underlying genetic architecture: a comparative study
Authors: Arenas Sebastian , Djabali Yacine , Rincent Renaud , Cubry Philippe , Martin Marie-Laure , Blein-Nicolas Mélisande , Laplaze Laurent , Schneider Hannah , Grondin Alexandre 
Published: January 2025

Abstract
Phenotypic plasticity can contribute to crop adaptation to challenging environments. Plasticity indices are potentially useful to identify the genetic basis of crop phenotypic plasticity. Numerous methods exist to measure phenotypic plasticity, but their ability to capture quantitative trait loci with environmental effects remains elusive. Here, we analysed a published multi-trial maize phenotyping dataset that examined the water stress response of leaf area, shoot biomass, and water use efficiency, calculating phenotypic plasticity for these traits using seven different plasticity indices. A comprehensive genetic analysis of phenotypic plasticity for these traits was further performed and the ability of methods to detect genetic regions capturing variance due to genotype-by-environment interaction was evaluated. Our results suggest that not all plasticity indices are amenable to identifying genomic regions associated with phenotypic plasticity. We observed that plasticity indices based on calculation of a ratio between environments or the slope of the Finlay–Wilkinson model were particularly useful in uncovering the genetic architecture underlying phenotypic plasticity when studying responses to treatments within and across trials. Ultimately, a deeper understanding of phenotypic plasticity should provide opportunities for breeding plants better able to adapt to climate uncertainty.
Rapid Parallel Adaptation in Distinct Invasions of Ambrosia Artemisiifolia Is Driven by Large-Effect Structural Variants
Authors: Battlay Paul , Craig Samuel , Putra Andhika R , Monro Keyne , De Silva Nissanka P , Wilson Jonathan , Bieker Vanessa C , Kabir Saila , Shamaya Nawar , van Boheemen Lotte , Rieseberg Loren H , Stinchcombe John R , Fournier-Level Alexandre , Martin Michael D , Hodgins Kathryn A 
Published: January 2025

Abstract
When introduced to multiple distinct ranges, invasive species provide a compelling natural experiment for understanding the repeatability of adaptation. Ambrosia artemisiifolia is an invasive, noxious weed, and chief cause of hay fever. Leveraging over 400 whole-genome sequences spanning the native-range in North America and 2 invasions in Europe and Australia, we inferred demographically distinct invasion histories on each continent. Despite substantial differences in genetic source and effective population size changes during introduction, scans of both local climate adaptation and divergence from the native-range revealed genomic signatures of parallel adaptation between invasions. Disproportionately represented among these parallel signatures are 37 large haploblocks—indicators of structural variation—that cover almost 20% of the genome and exist as standing genetic variation in the native-range. Many of these haploblocks are associated with traits important for adaptation to local climate, like size and the timing of flowering, and have rapidly reformed native-range clines in invaded ranges. Others show extreme frequency divergence between ranges, consistent with a response to divergent selection on different continents. Our results demonstrate the key role of large-effect standing variants in rapid adaptation during range expansion, a pattern that is robust to diverse invasion histories.
The iMab antibody selectively binds to intramolecular and intermolecular i-motif structures
Authors: Ruggiero Emanuela , Marušič Maja , Zanin Irene , Peña Martinez Cristian David , Christ Daniel , Plavec Janez , Richter Sara N 
Published: January 2025

Abstract
i-Motifs (iMs) are quadruplex nucleic acid conformations that form in cytosine-rich regions. Because of their acidic pH dependence, iMs were thought to form only in vitro. The recent development of an iM-selective antibody, iMab, has allowed iM detection in cells, which revealed their presence at gene promoters and their cell cycle dependence. However, recent evidence emerged which appeared to suggest that iMab recognizes C-rich sequences regardless of their iM conformation. To further investigate the selectivity of iMab, we examined the binding of iMab to C-rich sequences, using a combination of pull-down and western blot assays. Here, we observe that the composition of buffers used during binding and washing steps strongly influences the selectivity of antibody binding. In addition, we demonstrate by nuclear magnetic resonance that several of the previously reported C-rich sequences, which were not expected to form iMs, actually form intermolecular iMs which are selectively recognized by iMab. Our results highlight the specificity of the iMab antibody, emphasize the importance of avoiding in vitro artifacts by optimizing DNA concentrations, blocking and washing conditions, and confirm that iMab is selective not only for intramolecular iMs but also for intermolecular iMs, while not affecting the iM conformation.
Energy Expenditure in Chronic Kidney Disease: Affecting Factors and Evaluation Methods
Authors: Şahin Kezban , Acar Tek Nilüfer 
Published: January 2025

Abstract
Chronic kidney disease (CKD) is a chronic health problem whose prevalence is increasing. Nutrition and nutrition-related factors, one of the modifiable risk factors for CKD, are of primary importance. The key to planning optimal nutritional therapy is accurately determining energy requirements and total energy expenditure. Many health problems can accompany CKD, such as protein-energy malnutrition, sarcopenia, etc, and increase the mortality rate. This study aims to present the specific factors affecting energy expenditure specific to CKD in line with the current literature, to discuss the methods used to determine energy expenditure, and to examine these methods according to groups receiving and not receiving renal replacement therapy (hemodialysis, peritoneal dialysis, and renal transplantation).
Ablation of satellite cell‐specific clock gene, Bmal1, alters force production, muscle damage, and repair following contractile‐induced injury
Authors: Kahn Ryan E. , Zhu Pei , Roy Ishan , Peek Clara , Hawley John A. , Dayanidhi Sudarshan 
Published: January 2025

AbstractFollowing injury, skeletal muscle undergoes repair via satellite cell (SC)‐mediated myogenic progression. In SCs, the circadian molecular clock gene, Bmal1, is necessary for appropriate myogenic progression and repair with evidence that muscle molecular clocks can also affect force production. Utilizing a mouse model allowing for inducible depletion of Bmal1 within SCs, we determined contractile function, SC myogenic progression and muscle damage and repair following eccentric contractile‐induced injury. At baseline, SC‐Bmal1iKO animals exhibited a ~20–25% reduction in normalized force production (ex vivo and in vivo) versus control SC‐Bmal1Cntrl and SC‐Bmal1iKO untreated littermates (p < .05). Following contractile injury, SC‐Bmal1iKO animals displayed reduced muscle damage and subsequent repair post‐injury (Dystrophinnegative fibers 24 h: SC‐Bmal1Cntrl 199 ± 41; SC‐Bmal1iKO 36 ± 13, p < .05) (eMHC+ fibers 7 day: SC‐Bmal1Cntrl 217.8 ± 115.5; SC‐Bmal1iKO 27.8 ± 17.3; Centralized nuclei 7 day: SC‐Bmal1Cntrl 160.7 ± 70.5; SC‐Bmal1iKO 46.2 ± 15.7). SC‐Bmal1iKO animals also showed reduced neutrophil infiltration, consistent with less injury (Neutrophil content 24 h: SC‐Bmal1Cntrl 2.4 ± 0.4; SC‐Bmal1iKO 0.4 ± 0.2, % area fraction, p < .05). SC‐Bmal1iKO animals had greater SC activation/proliferation at an earlier timepoint (p < .05) and an unexplained increase in activation 7 days post injury. Collectively, these data suggest SC‐Bmal1 plays a regulatory role in force production, influencing the magnitude of muscle damage/repair, with an altered SC myogenic progression following contractile‐induced muscle injury.