bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of machine learning and conventional criteria in detecting left ventricular hypertrophy and prognosis with electrocardiography
Authors: Huang Jui-Tzu , Tseng Chih-Hsueh , Huang Wei-Ming , Yu Wen-Chung , Cheng Hao-Min , Chao Hsi-Lu , Chiang Chern-En , Chen Chen-Huan , Yang Albert C , Sung Shih-Hsien 
Published: February 2025

Abstract

Aims
Left ventricular hypertrophy (LVH) is clinically important; current electrocardiography (ECG) diagnostic criteria are inadequate for early detection. This study aimed to develop an artificial intelligence (AI)-based algorithm to improve the accuracy and prognostic value of ECG criteria for LVH detection.

Methods and results
A total of 42 016 patients (64.3 ± 16.5 years, 55.3% male) were enrolled. LV mass index was calculated from echocardiographic measurements. Left ventricular hypertrophy screening utilized ECG criteria, including Sokolow–Lyon, Cornell product, Cornell/strain index, Framingham criterion, and Peguero–Lo Presti. An AI algorithm using CatBoost was developed and validated (training dataset 80% and testing dataset 20%). F1 scores, reflecting the harmonic mean of precision and recall, were calculated. Mortality data were obtained through linkage with the National Death Registry. The CatBoost-based AI algorithm outperformed conventional ECG criteria in detecting LVH, achieving superior sensitivity, specificity, positive predictive value, F1 score, and area under curve. Significant features to predict LVH involved QRS and P-wave morphology. During a median follow-up duration of 10.1 years, 1655 deaths occurred in the testing dataset. Cox regression analyses showed that LVH identified by AI algorithm (hazard ratio and 95% confidence interval: 1.587, 1.309–1.924), Sokolow–Lyon (1.19, 1.038–1.365), Cornell product (1.301, 1.124–1.505), Cornell/strain index (1.306, 1.185–1.439), Framingham criterion (1.174, 1.062–1.298), and echocardiography-confirmed LVH (1.124, 1.019–1.239) were all significantly associated with mortality. Notably, AI-diagnosed LVH was more predictive of mortality than echocardiography-confirmed LVH.

Conclusion
Artificial intelligence-based LVH diagnosis outperformed conventional ECG criteria and was a superior predictor of mortality compared to echocardiography-confirmed LVH.
A model of elastic softening and displacive phase transitions in anisotropic phases, with application to stishovite and post-stishovite
Authors: Myhill R 
Published: February 2025

Summary
This paper introduces a comprehensive framework for modelling both instantaneous and time-dependent elastic softening in anisotropic materials at high pressure and temperature. This framework employs Landau Theory, minimizing the Helmholtz energy by varying isochemical parameters (q) that capture structural changes, atomic ordering, and/or electronic spin states. This allows for internally consistent predictions of volume, unit cell parameters, the elastic tensor, and other thermodynamic properties, while allowing large symmetry-breaking strains. The formulation is validated using the stishovite-to-post-stishovite transition. It is demonstrated that, near this transition, both stishovite and post-stishovite exhibit auxetic behaviour in several directions, with post-stishovite also displaying negative linear compressibility along the long axis of its unit cell (either the a or b axis). The new formulation is implemented in the open-source BurnMan software package.
Reduced-order modelling for complex three-dimensional seismic wave propagation
Authors: Rekoske John M , May Dave A , Gabriel Alice-Agnes 
Published: February 2025

SUMMARY
Elastodynamic Green’s functions are an essential ingredient in seismology as they form the connection between direct observations of seismic waves and the earthquake source. They are also fundamental to various seismological techniques including physics-based ground motion prediction and kinematic or dynamic source inversions. In regions with established 3-D models of the Earth’s elastic structure, such as southern California, 3-D Green’s functions can be computed using numerical simulations of seismic wave propagation. However, such simulations are computationally expensive, which poses challenges for real-time ground motion prediction and uncertainty quantification in source inversions. In this study, we address these challenges by using a reduced-order model (ROM) approach that enables the rapid evaluation of approximate Green’s functions. The ROM technique developed approximates three-component time-dependent surface velocity wavefields obtained from numerical simulations of seismic wave propagation. We apply our ROM approach to a 50 km $\times$ 40 km area in greater Los Angeles accounting for topography, site effects, 3-D subsurface velocity structure, and viscoelastic attenuation. The ROM constructed for this region enables rapid computation ($\approx 0.0001$ CPU hr) of complete, high-resolution (500 m spacing), 0.5 Hz surface velocity wavefields that are accurate for a shortest wavelength of 1.0 km for a single elementary moment tensor source. Using leave-one-out cross validation, we measure the accuracy of our Green’s functions for the CVM-S velocity model in both the time domain and frequency domain. Averaged across all sources, receivers, and time steps, the error in the rapid seismograms is less than 0.01 cm s−1. We demonstrate that the ROM can accurately and rapidly reproduce simulated seismograms for generalized moment tensor sources in our region, as well as kinematic sources by using a finite fault model of the 1987 $M_\mathrm{ W}$ 5.9 Whittier Narrows earthquake as an example. We envision that rapid, accurate Green’s functions from reduced-order modelling for complex 3-D seismic wave propagation simulations will be useful for constructing real-time ground motion synthetics and source inversions with high spatial resolution.
Cohen–Lenstra Distribution for Sparse Matrices with Determinantal Biasing
Authors: Mészáros András 
Published: February 2025

Abstract
Let us consider the following matrix $B_{n}$. The columns of $B_{n}$ are indexed with $[n]=\{1,2,\dots ,n\}$ and the rows are indexed with $[n]^{3}$. The row corresponding to $(x_{1},x_{2},x_{3})\in [n]^{3}$ is given by $\sum _{i=1}^{3} e_{x_{i}}$, where $e_{1},e_{2},\dots ,e_{n}$ is the standard basis of $\mathbb{R}^{[n]}$. Let $A_{n}$ be random $n\times n$ submatrix of $B_{n}$, where the probability that we choose a submatrix $C$ is proportional to $|\det (C)|^{2}$. Let $p\ge 5$ be a prime. We prove that the asymptotic distribution of the $p$-Sylow subgroup of the cokernel of $A_{n}$ is given by the Cohen–Lenstra heuristics. Our result is motivated by the conjecture that the first homology group of a random two dimensional hypertree is also Cohen–Lenstra distributed.
Receipt of fluoroquinolone prophylaxis is not associated with development of vancomycin-resistant Enterococcus colonization during pediatric hematopoietic cell transplantation
Authors: Murphy Catherine R , Liu Chunyan , Courter Joshua , Griffin Cameron , Scaggs Huang Felicia , Miller-Handley Hilary , Grimley Michael S , Danziger-Isakov Lara , Otto William R 
Published: February 2025

Abstract
Fluoroquinolones are used to prevent bloodstream infections in pediatric hematopoietic cell transplant (HCT) recipients. We performed a retrospective cohort study in 799 pediatric HCT patients to evaluate the association between fluoroquinolone prophylaxis and VRE colonization. Propensity score analyses were performed. Fluoroquinolone prophylaxis was not associated with VRE colonization.
Article 74: A General Overview
Authors: Zeller Bruno 
Published: February 2025

Abstract
This chapter focuses on Article 74 of the United Nations Convention on Contracts for the International Sale of Goods (CISG), which allows the aggrieved party to claim damages for any breach of a contract. Four general points need to be addressed to understand the consequences of a breach. The first point to note is that Article 74 does not specify what types of losses are included in a claim of damages except loss of profit. Second, damages can be claimed only if a promisee is not in breach of any of the rules of the Convention. Third, consideration must be given to the fact that Article 74 is in competition with other remedies pursuant to Article 45. The fourth point is that Article 74 contains what appears to be a simple formula for calculating damages. Under Article 74, the calculation of damages can ‘only be based on maintenance and performance of the contract’.
Tailoring explanations through conversation
Authors: Luo Jieting , Studer Thomas , Dastani Mehdi 
Published: February 2025

Abstract
The increasing applications of AI systems require personalized explanations for their behaviors to various stakeholders since the stakeholders may have various backgrounds. In general, a conversation between explainers and explainees not only allows explainers to obtain explainees’ background, but also allows explainers to tailor their explanations so that explainees can better understand the explanations. In this paper, we propose an approach for an explainer to tailor and communicate personalized explanations to an explainee through having consecutive conversations with the explainee. We prove that the conversation terminates due to the explainee’s justification of the initial claim as long as there exists an explanation for the initial claim that the explainee understands and the explainer is aware of.
Genome Assembly of a Living Fossil, the Atlantic Horseshoe Crab Limulus polyphemus, Reveals Lineage-Specific Whole-Genome Duplications, Transposable Element-Based Centromeres, and a ZW Sex Chromosome System
Authors: Castellano Kate R , Neitzey Michelle L , Starovoitov Andrew , Barrett Gabriel A , Reid Noah M , Vuruputoor Vidya S , Webster Cynthia N , Storer Jessica M , Pauloski Nicole R , Ameral Natalie J , McEvoy Susan L , McManus M Conor , Puritz Jonathan B , Wegrzyn Jill L , O’Neill Rachel J 
Published: February 2025

Abstract
Horseshoe crabs, considered living fossils with a stable morphotype spanning ∼445 million years, are evolutionarily, ecologically, and biomedically important species experiencing rapid population decline. Of the four extant species of horseshoe crabs, the Atlantic horseshoe crab, Limulus polyphemus, has become an essential component of the modern medicine toolkit. Here, we present the first chromosome-level genome assembly, and the most contiguous and complete assembly to date, for L. polyphemus using nanopore long-read sequencing and chromatin conformation analysis. We find support for three horseshoe crab-specific whole-genome duplications, but none shared with Arachnopulmonata (spiders and scorpions). Moreover, we discovered tandem duplicates of endotoxin detection pathway components Factors C and G, identify candidate centromeres consisting of Gypsy retroelements, and classify the ZW sex chromosome system for this species and a sister taxon, Carcinoscorpius rotundicauda. Finally, we revealed this species has been experiencing a steep population decline over the last 5 million years, highlighting the need for international conservation interventions and fisheries-based management for this critical species.
LoVis4u: a locus visualization tool for comparative genomics and coverage profiles
Authors: Egorov Artyom A , Atkinson Gemma C 
Published: February 2025

Abstract
Comparative genomic analysis often involves visualization of alignments of genomic loci. While several software tools are available for this task, ranging from Python and R libraries to stand-alone graphical user interfaces, a tool is lacking that offers fast, automated usage and the production of publication-ready vector images. Here we present LoVis4u, a command-line tool and Python API designed for highly customizable and fast visualization of multiple genomic loci. LoVis4u generates vector images in PDF format based on annotation data from GenBank or GFF files. It is capable of visualizing entire genomes of bacteriophages as well as plasmids and user-defined regions of longer prokaryotic genomes. Additionally, LoVis4u offers optional data processing steps to identify and highlight accessory and core genes in input sequences. Finally, LoVis4u supports the visualization of genomic signal track profiles from sequencing experiments. LoVis4u is implemented in Python3 and runs on Linux and MacOS. The command-line interface covers most practical use cases, while the provided Python API allows usage within a Python program, integration into external tools, and additional customization. The source code is available at the GitHub page: github.com/art-egorov/lovis4u. Detailed documentation that includes an example-driven guide is available from the software home page: art-egorov.github.io/lovis4u.
Genetically predicted basal metabolic rate and infectious diseases: a Mendelian randomization study
Authors: Li Zhanbin , Ma Yicheng , Xuan Qiuhui , Yao Zhenyu , Liu Qiaoran 
Published: February 2025

Abstract

Background
The causal relationship between basal metabolic rate (BMR) and infectious diseases remains elusive. This study aims to clarify this association.

Methods
This study analyzed genome-wide association studies (GWASs) data from the UK Biobank and FinnGen cohorts to investigate the association between BMR and infectious diseases in European populations. Mendelian randomization (MR) analysis was initially employed, followed by multivariable Mendelian randomization (MVMR) to account for potential confounders. Mediation analysis further confirmed significant relationships. Sensitivity analyses were conducted to validate the study findings.

Results
Using two sample MR, genetically predicted BMR was positively linked to skin and soft tissue infections (SSTIs) (OR: 1.31, 95% CI: 1.18–1.47, P &lt; .001), osteomyelitis (OR: 1.95, 95% CI: 1.36–2.80, P &lt; .001) (1.36 ± 2.80), all-cause infections (OR: 1.36, 95% CI: 1.26–1.48, P &lt; .001) and sepsis (OR: 1.36, 95% CI: 1.23–1.51, P &lt; .001). MVMR analysis confirmed BMR's direct causal effect on SSTIs, osteomyelitis, all-cause infections, and sepsis, except for BMI and other factors affecting osteomyelitis. Mediation analysis revealed VAT as a mediator in the linkage between BMR and SSTIs and all-cause infections. HbA1c mediated the path from BMR to osteomyelitis, while CRP and BMI exhibited mediation effects in the BMR-all-cause infections relationship.

Conclusion
The study revealed a significant link between increased BMR and elevated risks of SSTIs, osteomyelitis, and bacterial infections, highlighting the intricate BMR-immune connection and its implications for disease control.
Key message What is already known on this topic: High BMR is positively correlated with COVID-19 and associated with proinflammatory and immunological activation, but the relationship between BMR and other infectious diseases remains largely unexplored. What this study adds: Higher BMR significantly raises the risk of SSTIs, osteomyelitis, all-cause infections, and sepsis. VAT, HbA1c, CRP, and BMI may mediate the BMR-infection relationship. How this study might affect research, practice, or policy: A higher BMR may be a valuable indicator associated with an increased risk for SSTIs, osteomyelitis, and sepsis. Modulating BMR might hold promise as a clinically relevant intervention to prevent specific infectious diseases.
Genetic diversity, phylogeography, and sexual dimorphism in the extinct giant short-faced bear (Arctodus simus)
Authors: Salis Alexander T , Schubert Blaine W , Bray Sarah C E , Heiniger Holly , Meachen Julie , Cooper Alan , Mitchell Kieren J 
Published: February 2025

Abstract
Giant short-faced bears (Arctodus simus) were the largest carnivoran of Pleistocene North America and are one of the most extensively studied extinct megafaunal species from the continent. Smaller and larger forms of A. simus have previously been recognized and are sometimes considered subspecies (A. s. simus and A. s. yukonensis, respectively). However, researchers have also proposed that this size variation is primarily the result of sexual dimorphism. We sequenced 31 mitogenomes of A. simus from locations ranging from Alaska to New Mexico. Our results revealed a lack of phylogeographic structure in A. simus, as well as low genetic diversity and relatively recent mitochondrial diversification. These observations may either represent population bottlenecks during the Late Pleistocene or simply a naturally low effective population size resulting from a dispersed population and low population density. We found no evidence for genetic differences among our samples, which were compatible with the previously proposed A. simus subspecies. In contrast, all large specimens to which we could assign a sex using genetic data were male, whereas the small specimens in our dataset were all female, supporting the hypothesis that A. simus size variation can be explained by sexual dimorphism.
Test-Retest Reliability of a Timeline Follow-back Method to Assess Opioid Use and Treatment
Authors: McCann Nicole C. , Yan Shapei , McMahan Vanessa M. , Pope Emily , Rolles Andrew , Brennan Sarah , Marti Xochitl Luna , Kosakowski Sarah , Coffin Phillip O. , Walley Alexander Y. 
Published: February 2025

Background
Calendar-based timeline follow-back (TLFB) instruments have been used to assess alcohol use, smoking, and other behaviors. We assessed test-retest reliability of an adapted TLFB addressing opioid-related outcomes over 120 days among opioid overdose survivors using nonprescribed opioids.

Methods
The Repeated-dose Behavioral intervention to reduce Opioid Overdose Trial utilized a TLFB that collected data over the preceding 120 days. A subset of participants was administered a retest TLFB 3–21 days after their TLFB assessment. The test and retest assessed days of opioid and medication for opioid use disorder (MOUD) use, hospitalization, residential substance use disorder (SUD) treatment, incarceration, and overdose during overlapping time periods. For outcomes reported by ≥15% of the sample, intraclass correlation coefficients (ICC) were calculated between test and retest. ICC > 0.9 was considered “very high” reliability. For outcomes reported by <15%, frequencies were described; statistical tests were not conducted.

Results
Seventy-seven participants completed a retest. On the test/retest, most participants reported opioid (87%/83%) and MOUD (58%/60%) use. Median (IQR) number of days of opioid and MOUD use on the test/retest was 71 (25–117)/86 (23–108) and 4 (0–72)/5 (0–79) days. ICC between test and retest was >0.9 for both opioid and MOUD use. On test/retest, few participants reported hospitalization (8%/9%), residential SUD treatment (3%/3%), incarceration (5%/7%), or overdose (4%/3%).

Discussion
The adapted TLFB had very high reliability for self-reported opioid and MOUD use over 120 days. For less frequent outcomes, including overdose, a higher frequency or larger sample size is needed to assess reliability.
Impact of Sensitive Circulating Tumor DNA Monitoring on CT Scan Intervals During Postoperative Colorectal Cancer Surveillance
Authors: Sasaki Tomoko , Iwaya Takeshi , Yaegashi Mizunori , Idogawa Masashi , Hiraki Hayato , Abe Masakazu , Koizumi Yuka , Sasaki Noriyuki , Yashima-Abo Akiko , Fujisawa Ryosuke , Endo Fumitaka , Tange Shoichiro , Otsuka Koki , Sasaki Akira , Masuda Mari , Fujita Masashi , Nakagawa Hidewaki , Takahashi Fumiaki , Sasaki Yasushi , Tokino Takashi , Nishizuka Satoshi S. 
Published: February 2025

Objective:
This study investigated whether digital polymerase chain reaction (dPCR)-based circulating tumor DNA (ctDNA) monitoring can allow longer intervals between computed tomography (CT) scans during postoperative surveillance of colorectal cancer (CRC).

Background:
Practical guidelines still recommend intensive postoperative surveillance of CRC using periodical CT scans and serum carcinoembryonic antigen testing.

Methods:
The longitudinal dynamics of ctDNA for 52 patients with CRC as measured by dPCR using probes targeting 87 individual tumor-specific mutations (1–5 per patient) were compared with results from conventional (ie, clinical) surveillance using serum tumor markers and CT.

Results:
A total of 382 CT procedures were carried out for the patient cohort (3.3/year per patient) and the median lead time from ctDNA relapse to clinical relapse was 182 days (range, 0–376 days). If the CT interval was annual, potential delays in the detection of clinical relapse would have occurred for 7 of the 10 patients who experienced clinical relapse (9 of 13 events), with a median delay of 164 days (range, 0–267 days). If annual CT surveillance was performed together with ctDNA monitoring, 218 (57.1%) CTs would not have been needed to detect the first clinical relapse. In addition, the ctDNA monitoring would have provided a lead time of 339 days for detection of clinical relapse (range, 42–533 days).

Conclusions:
Our findings suggest that the ctDNA monitoring as part of postoperative surveillance and clinical relapse detection for patients with CRC could allow the CT interval to be lengthened.

Trial Registration:
This trial was registered with University Hospital Medical Information Network Clinical Trial Registry (UMIN000045114).