bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of Photon-Counting CT for Spectral Imaging in Cardiovascular Applications: Impact of Lumen Size, Dose, and Patient Habitus
Authors: Rybertt Martin V. , Liu Leening P. , Mathew Manoj , Sahbaee Pooyan , Litt Harold I. , Noël Peter B. 
Published: January 2025

AbstractObjectivesThis study evaluates the performance of a clinical dual-source photon-counting computed tomography (PCCT) system in quantifying iodine within calcified vessels, using 3D- printed phantoms with vascular-like structures lined with calcium.MethodsParameters assessed include lumen diameters (4, 6, 8, 10, and 12 mm), phantom sizes (S: 20×20 cm, M: 25×25 cm, L: 30×40 cm, XL: 40×50 cm, representing the 99th percentile of US patient sizes), and iodine concentrations (2, 5, and 10 mg/mL). Scans were performed at radiation dose levels of 5, 10, 15, and 20 mGy to systematically evaluate iodine quantification accuracy and spectral imaging performance.ResultsThe results indicate that for lumen diameters ≥6 mm, iodine quantification remains stable across all dose levels and phantom sizes, with deviations consistently below 0.6 mg/mL. Whereas, for 4 mm lumens, stability is observed primarily in smaller to medium phantoms, highlighting the influence of patient size and radiation dose on quantification accuracy. Virtual Monoenergetic Imaging (VMI) at 70 keV showed stable performance for larger lumens (≥6 mm) with variations of 13 ± 2 HU across all conditions, while smaller lumens remained stable in medium to small phantoms.ConclusionsThese findings highlight the influence of lumen diameter, patient size, and radiation dose in optimizing PCCT protocols for spectral imaging. Importantly, the study demonstrates that PCCT delivers stable and highly accurate imaging across nearly the entire range of patient sizes in the U.S..Advances in knowledgeThis study demonstrates PCCT’s potential to enhance spectral imaging in vascular applications, surpassing conventional or Dual Energy CT.
Harnessing Mondo and the ILAE Classification for Curation and Analysis of 71,942 epilepsy patient variants
Authors: Ivaniuk Alina , Bruenger Tobias , Perez-Palma Eduardo , Xiao Junhui , St John Mark , Nascimento Fábio A. , Zhang Guo-Qiang , Lhatoo Samden , Lal Dennis 
Published: January 2025

AbstractMapping epilepsy variants in ClinVar to standard disease classifications remains challenging due to incomplete phenotype information. We integrated the Mondo Disease Ontology (Mondo) with the International League Against Epilepsy (ILAE) Classification to systematically identify, organize, and analyze age-dependent epilepsy-associated variants from the world’s largest public variant repository. Starting from over three million ClinVar entries, we filtered monogenic disorders tagged with 421 Mondo terms representing neonatal/infantile, childhood, or variable-onset epilepsy syndromes. Gene-disease validity was further refined using multiple expert-curated lists, resulting in 71,942 unique variant submissions in 171 genes. Approximately 70% of pathogenic and uncertain variants clustered in 50 genes, highlighting the concentration of clinically relevant findings in a relatively small subset of known epilepsy genes.SCN1A,GRIN2A, andDEPDC5stood out as top contributors to neonatal/infantile, childhood, and variable-onset syndromes, respectively. Notably, two-thirds of genes were specific to a single age group, but the remaining one-third spanned multiple syndromes, reflecting both phenotypic and genetic heterogeneity. We also observed substantial overlap with neurodevelopmental and autism-related genes, especially among early-onset epilepsies, emphasizing shared molecular pathways. Our Mondo-driven approach demonstrates the feasibility of large-scale, ontology-based curation of ClinVar for domain-specific analyses, offering greater clinical precision than traditional text-based queries. This resource can guide epilepsy-focused gene panel design, inform new classification updates, and pave the way for age-targeted therapeutics. By bridging the gap between extensive genomic repositories and detailed clinical ontologies, we provide a robust, standardized framework to accelerate progress in precision epilepsy genetics.
The Role ofde novoand Ultra-Rare Variants in Hirschsprung Disease (HSCR): Extended Gene Discovery for Risk Profiling of Patients
Authors: Fu Mingzhou , Berk-Rauch Hanna E , Chatterjee Sumantra , Chakravarti Aravinda 
Published: January 2025

AbstractBackgroundHirschsprung disease (HSCR) is a rare neurodevelopmental disorder caused by disrupted migration and proliferation of enteric neural crest cells during enteric nervous system development. Genetic studies suggest a complex etiology involving both rare and common variants, but the contribution of ultra-rare pathogenic variants (PAs) remains poorly understood.MethodsWe perform whole-exome sequencing (WES) on 301 HSCR probands and 109 family trios, employing advanced statistical methods and gene prioritization strategies to identify genes carryingde novoand ultra-rare coding pathogenic variants. Multiple study designs, including case-control,de novomutation analysis and joint test, are used to detect associated genes. Candidate genes are further prioritized based on their biological and functional relevance to disease associated tissues and onset period (i.e., human embryonic colon).ResultsWe identify 19 risk genes enriched with ultra-rare coding pathogenic variants in HSCR probands, including four known genes (RET,EDNRB,ZEB2,SOX10) and 15 novel candidates (e.g.,COLQ,NES,FAT3) functioning in neural proliferation and neuromuscular synaptic development. These genes account for 17.5% of the population-attributable risk (PAR), with novel candidates contributing 6.5%. Notably, a positive correlation between pathogenic mutational burden and disease severity is observed. Female cases exhibit at least 42% higher ultra-rare pathogenic variant burden than males (P = 0.05).ConclusionsThis first-ever genome-wide screen of ultra-rare variants in a large, phenotypically diverse HSCR cohort highlights the substantial contribution of ultra-rare pathogenic variants to the disease risk and phenotypic variability. These findings enhance our understanding of the genetic architecture of HSCR and provide potential targets for genetic screening and personalized interventions.
Projecting neurons from lateral entorhinal cortex to basolateral amygdala mediate the encoding of incidental odor-taste associations
Authors: González-Parra Jose Antonio , Acciai Vittoria , Vidal-Palencia Laura , Canela Marc , Busquets-Garcia Arnau 
Published: January 2025

AbstractDaily choices are determined by prior direct or indirect associations between low-salience cues and reinforcers. In this study, we used a mouse odor-taste sensory preconditioning task combined with genetic, intersectional and chemogenetic approaches to identify a novel brain circuit involved in mediated learning. We found that neuronal projections from the lateral entorhinal cortex to the basolateral amygdala are engaged during low-salience stimuli associations, which is essential for mediated learning formation.
CENdetectHOR: a comprehensive tool for CENtromere profiling and HOR detection
Authors: Daponte Alessia , Pagliuca Paolo , Vila-Verde Carlos , Montinaro Francesco , Antonacci Francesca , Ventura Mario , Ceriani Miguel , Catacchio Claudia R 
Published: January 2025

AbstractCentromeres are essential for accurate chromosome segregation and are characterized by long arrays of repetitive satellite DNA, showing extensive variation in sequence, length, and organization across species. Despite extensive research, fully characterizing centromeric DNA has been challenging due to its repetitive nature and rapid evolution. Here, we present CENdetectHOR, a computational tool to identify and analyze higher-order repeat (HOR) arrays in centromeric regions across diverse organisms, requiring noa prioriinformation. We validate its efficacy using human and arabidopsis genomes, demonstrating its ability to reveal the complexity and diversity of centromeric architectures. CENdetectHOR also recognizes HOR variants, elucidating interindividual and interspecific variations in centromeric regions. These findings establish CENdetectHOR as a powerful, versatile, and rapid tool for advancing research on centromere structure, evolution, and function.
Nitrification in a Seagrass-Sponge Association
Authors: Berlinghof Johanna , Montilla Luis M. , Meador Travis B. , Gallucci Luigi , Giovannelli Donato , Gruber-Vodicka Harald , Maselli Maira , Margiotta Francesca , Wild Christian , Cardini Ulisse 
Published: January 2025

AbstractIn the Mediterranean Sea, the demospongeChondrilla nuculacan occur in close association with the native seagrassPosidonia oceanica.C. nuculaharbors a diverse and abundant microbial community, including potential nitrifiers. Thus, the sponge may contribute to the nitrogen (N) demand of the seagrass holobiont. In this study, we investigated potential nitrification rates (PNR) and inorganic N fluxes within this association at a site whereC. nuculacovered 18 ± 3 % of the seagrass meadow area, during plant growth (spring) and senescence (autumn). Using incubation experiments with15N-labeled ammonium, we measured PNR and inorganic N of the seagrass-sponge association, and of sponge and seagrass independently, under light and dark conditions. We supplemented these experiments with 16s rRNA gene amplicon sequencing to characterize the microbial community of the sponge. PNR was exclusively measured when the sponge was present (alone or in association with the seagrass). PNR was highest in the dark and whenC. nuculawas associated with the seagrass, ranging from 21 ± 7 to 267 ± 33 nmol N g DW-1h-1in spring and autumn, respectively. Sponge-mediated PNR can support 8% of the N demand of theP. oceanicaholobiont during growth and 47 % during senescence. We identified key nitrifying bacterial and archaeal groups as members of the sponge’s microbial community. WhileC. nuculareleased inorganic N, potentially sustaining the seagrass, it benefitted from dissolved organic carbon released byP. oceanica. These results suggest that the interaction betweenC. nuculaandP. oceanicais mutually beneficial, ultimately supporting and stabilizing the seagrass ecosystem.
Cancer associated fibroblasts drive epithelial to mesenchymal transition and classical to basal change in pancreatic ductal adenocarcinoma cells with loss of IL-8 expression
Authors: Guinn Samantha , Perez Brayan , Tandurella Joseph A. , Ramani Mili , Lee Jae W. , Zabransky Daniel J. , Kartalia Emma , Patel Jignasha , Zlomke Haley , Nicolson Norman , Shin Sarah , Barrett Benjamin , Sun Nicholas , Hernandez Alexei , Coyne Erin , Cannon Courtney , Gross Nicole E. , Charmsaz Soren , Cho Yeonju , Leatherman James , Lyman Melissa , Mitchell Jacob , Kagohara Luciane T. , Goggins Michael G. , Lafaro Kelly J. , He Jin , Shubert Christopher , Burns William , Zheng Lei , Fertig Elana J. , Jaffee Elizabeth M. , Burkhart Richard A. , Ho Won Jin , Zimmerman Jacquelyn W. 
Published: January 2025

AbstractPancreatic ductal adenocarcinoma (PDAC) carries an extremely poor prognosis, in part resulting from cellular heterogeneity that supports overall tumorigenicity. Cancer associated fibroblasts (CAF) are key determinants of PDAC biology and response to systemic therapy. While CAF subtypes have been defined, the effects of patient-specific CAF heterogeneity and plasticity on tumor cell behavior remain unclear. Here, multi-omics was used to characterize the tumor microenvironment (TME) in tumors from patients undergoing curative-intent surgery for PDAC. In these same patients, matched tumor organoid and CAF lines were established to functionally validate the impact of CAFs on the tumor cells. CAFs were found to drive epithelial-mesenchymal transition (EMT) and a switch in tumor cell classificiaton from classical to basal subtype. Furthermore, we identified CAF-specific interleukin 8 (IL-8) as an important modulator of tumor cell subtype. Finally, we defined neighborhood relationships between tumor cell and T cell subsets.Statement of SignificanceThis multidimensional analysis highlights the diverse role CAFs have in influencing other cell types in the TME, including epithelial-derived tumor and infiltrating immune cells. Our methods provide a platform for evaluating emerging therapeutic approaches and for studying mechanisms that dictate tumor behavior in a manner that reflects patient-specific heterogeneity.
Variant effects depend on polygenic background: experimental, clinical, and evolutionary implications
Authors: Chapel Madison , Dennis Jessica , de Boer Carl G. 
Published: January 2025

AbstractBoth rare and common genetic variants contribute to human disease, and emerging evidence suggests that they combine additively to influence disease liability. However, due to the non-linear relationship between disease liability and disease prevalence, risk variants have more severe phenotypic consequences in high-risk polygenic backgrounds. Consequently, selecting individuals with appropriate polygenic backgrounds may improve variant characterization experiments, as disease-relevant phenotypes may be masked or revealed in different genomic contexts. Simultaneously, selection has limited power to eliminate risk variants because they have minimal impact in low polygenic risk backgrounds, yet is more powerful with higher polygenicity because more individuals achieve genetic and phenotypic extremes. This dependence on polygenic background means that selection acting on an allele should be modeled as a distribution that differs across populations, time, environments, and individuals rather than as a single value. Overall, considering polygenic backgrounds will be critical when investigating the origins of complex traits.
Prognostic and Diagnostic Utility of Heart Rate Variability to Predict and Understand Change in Cancer and Chemotherapy Related Fatigue, Pain, and Neuropathic Symptoms: A Systematic Review
Authors: Bolanos Jessica , Hneiny Layal , Gonzalez Juan , O’Malley Max , Wong Marlon L 
Published: January 2025

AbstractAdvances in early cancer detection and treatment have significantly improved survival rates, resulting in over 18.1 million cancer survivors in the United States. Many of these survivors experience chronic pain, fatigue, and neuropathic symptoms related to cancer or its treatments. Emerging evidence suggests that autonomic nervous system dysfunction plays a crucial role in these symptoms. Heart rate variability (HRV), a measure of autonomic function, has shown potential in predicting the onset of somatic symptoms in cancer patients. This systematic review aimed to assess the association of HRV with pain, fatigue, and neuropathy in cancer patients and survivors.A comprehensive search was conducted across multiple databases, yielding 19 studies that met inclusion criteria. These studies varied in cancer types, stages, and HRV measurement methods. Most studies focused on breast cancer and reported a predominant female population. Fatigue was the most studied symptom, followed by pain. HRV measures included both time and frequency domain variables, with significant variability in measurement duration and control for confounding factors.Findings suggest that decreased HRV is associated with increased fatigue and pain, providing potential support for a bidirectional relationship between autonomic dysfunction and these symptoms. However, the heterogeneity in HRV measurement methods and the high risk of bias in many studies highlight the need for standardized HRV protocols in cancer research. Further large-scale studies with low risk of bias are necessary to validate HRV as a reliable tool for phenotyping and managing cancer-related symptoms.
The Characteristic Timescales of the Arabidopsis thaliana Metabolism and the Phenotypic Effects of Forcing Them
Authors: Santoro Giovanni , Rolli Enrico , Ricci Ada , Cademartiri Ludovico 
Published: January 2025

Response mechanisms preserve steady states in complex systems (including living systems). These mechanisms respond with characteristic timescales. Therefore, they can be identified and probed with oscillatory forcing. This approach is rarely used in plant biology.Sub-circadian intermittent illumination (i.e., square waves of light/dark periods of equal duration) ofArabidopsis thalianaplants cause remarkable phenotypical effects. We show these effects are highly dependent on the duration of the light-dark cycle, identifying characteristic timescales in three distinct windows (10.5-42 s, 168-336 s, and 1350-5400 s). Among these effects is an extension of the life cycle by 60%, a 2-fold increase in flower setting, and a near complete elimination of lateral root development.This oscillatory light forcing is compatible with vertical farming where it could reduce energy and chemical inputs and highlights the methodological value of temporal-forcing of environmental parameters on sub-circadian timescales in plant systems.
Long-term Monte Carlo-based neutrino-radiation hydrodynamics simulations for a black hole-torus system
Authors: Kawaguchi Kyohei , Fujibayashi Sho , Shibata Masaru 
Published: January 2025

We present our new general relativistic Monte Carlo (MC)-based neutrino radiation hydrodynamics code designed to solve axisymmetric systems with several improvements. The main improvements are as follows: (i) the development of an extended version of the implicit MC method for multispecies radiation fields; (ii) modeling of neutrino pair process rates based on a new numerically efficient and asymptotically correct fitting function for the kernel function; (iii) the implementation of new numerical limiters on the radiation-matter interaction to ensure a stable and physically correct evolution of the system. We apply our code to a black hole (BH)-torus system with a BH mass of 3M⊙, BH dimensionless spin of 0.8, and a torus mass of 0.1M⊙, which mimics a postmerger remnant of a binary neutron star merger in the case that the massive neutron star collapses to a BH within a short timescale (∼10  ms). We follow the evolution of the BH-torus system up to more than 1 s with our MC-based radiation viscous-hydrodynamics code that dynamically takes into account nonthermal pair annihilation. We find that the system evolution and the various key quantities, such as neutrino luminosity, ejecta mass, torus Ye, and pair annihilation luminosity, are broadly in agreement with the results of the previous studies. We also find that the νeν¯e pair annihilation can launch a relativistic outflow for a timescale of ∼0.1  s, and it can be energetic enough to explain some of short-hard gamma-ray bursts and the precursors. Finally, we calculate the indicators of the fast flavor instability directly from the obtained neutrino distribution functions, which indicate that the instability can occur particularly near the equatorial region of the torus.

Published by the American Physical Society
2025
Local quantum detection of the cosmological expansion: Unruh-DeWitt detectors in spatially compact Milne cosmology
Authors: Wilkinson Adam S. , Louko Jorma 
Published: January 2025

We analyze the excitations and deexcitations of an inertial Unruh-DeWitt detector in the (1+1)-dimensional expanding Milne cosmology with compact spatial sections, coupled to a real massless scalar field with either untwisted or twisted boundary conditions, prepared in the conformal vacuum. We find the detector’s response as a function of the energy gap, the Milne spatial circumference parameter, the interaction duration, the age of the Universe at the switch-on moment, the detector’s peculiar velocity at the switch-on moment, and, for the untwisted field, the state of the zero mode. Asymptotic analytic results are obtained at large energy gap and at large circumference parameter, in each case recovering the Minkowski vacuum response in the leading order, and in the double limit of small circumference parameter and late cosmological time, recovering the response in a static Minkowski cylinder. Numerical results are given in the interpolating regimes. The results confirm the detector’s sensitivity to both classical and quantum properties of its environment.

Published by the American Physical Society
2025
Perceived service quality and electronic word-of-mouth on food delivery services: extended theory of planned behaviour
Authors: Liao Shu-Hsien , Hu Da-Chian , Chen Cai-Jun 
Published: January 2025

PurposeThis study proposed an extended theory of planned behaviour (TPB), that is, considering that behavioural beliefs, normative beliefs and control beliefs (beliefs) will influence perceived service quality (PSQ) on food delivery services. PSQ (behavioural intention) will influence electronic word-of-mouth (EWOM) (behaviour). In addition, exogenous variables including information from online ratings and consumer groups will affect the strength of the relationship between received service quality and EWOM on food delivery service.Design/methodology/approachThis study aimed to investigate the mediation (PSQ) and moderation (Online ratings and consumer groups) effects on the extended TPB for Taiwanese consumers (n = 823).FindingsThis study first found a positive relationship between different beliefs and PSQ (behavioural intention). In addition, there is a positive relationship between PSQ and EWOM. Online rating has a moderating effect between PSQ and EWOM. Consumer group has a moderating relationship between PSQ and EWOM.Originality/valueThis study first found that the three stages of beliefs-intention-behaviour for consumers on food delivery service are reciprocal with two paths, starting with offline-to-online in terms of generating the positive relationship between individual belies and PSQ. Next, it can generate positive power to return online with a behaviour of EWOM. In addition, online ratings can enhance and strengthen the positive effect between PSQ and EWOM.
Benchmarking analysis of cyber-physical system-based lean tools using grey approaches
Authors: Rohit  , Vinodh S. , Vigneshvaran R. 
Published: January 2025

PurposeThis study aims to provide an analysis of cyber-physical system (CPS)-based lean tools. This study focuses on the identification of lean tools for integration with CPS and analyzes those tools using MCDM (multi-criteria decision-making) approaches.Design/methodology/approachThere exists a need to integrate lean manufacturing with Industry 4.0 technologies. According to literature analysis, CPS is the first stage to implement Industry 4.0 technologies. Based on the extensive study, six CPS-based lean tools, i.e. CPS-based Jidoka system, CPS-based Kanban, CPS-based Andon support system, CPS-based Just-in-time delivery system, CPS-based poka-yoke cell and CPS-based value stream mapping have been considered; then Grey TOPSIS (Technique for Order Preference by Similarity to Ideal Solution) MCDM technique has been applied to rank those tools. These CPS-based lean tools are ranked based on seven performance measures as recognized by academic and industry experts.FindingsThe top three CPS-based lean tools are CPS-based Kanban 4.0, CPS-based value stream mapping and CPS-based Just-in-time delivery system have been selected based on the above ranking. The study results have been validated using grey-based approach.Practical implicationsAppropriate criteria to evaluate significant lean tools for integration with CPS are identified, which facilitates managers to assess their current tools and technologies that could be integrated with I4.0, and the implementation of CPS-based lean tools would improve organizational performance.Originality/valueIn the emerging Industry 4.0, integration with advanced technologies provides high degrees of optimization. But there exist challenges for industries to integrate CPS with lean tools; hence, this study attempts to identify and analyze CPS-based lean tools. The lean tools are ranked for integration with CPS, the problem is modeled as MCDM problem, and the obtained results are again validated using grey approach. Prioritizing lean tools for integration with CPS is the original contribution of this study.