bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preoperative prediction of diffuse glioma type and grade in adults: a gadolinium-free MRI-based decision tree
Authors: Azizova Aynur , Prysiazhniuk Yeva , Wamelink Ivar J. H. G. , Cakmak Marcus , Kaya Elif , Wesseling Pieter , de Witt Hamer Philip C. , Verburg Niels , Petr Jan , Barkhof Frederik , Keil Vera C. 
Published: October 2024

Abstract

Objectives
To develop a gadolinium-free MRI-based diagnosis prediction decision tree (DPDT) for adult-type diffuse gliomas and to assess the added value of gadolinium-based contrast agent (GBCA) enhanced images.

Materials and methods
This study included preoperative grade 2–4 adult-type diffuse gliomas (World Health Organization 2021) scanned between 2010 and 2021. The DPDT, incorporating eleven GBCA-free MRI features, was developed using 18% of the dataset based on consensus readings. Diagnosis predictions involved grade (grade 2 vs. grade 3/4) and molecular status (isocitrate dehydrogenase (IDH) and 1p/19q). GBCA-free diagnosis was predicted using DPDT, while GBCA-enhanced diagnosis included post-contrast images. The accuracy of these predictions was assessed by three raters with varying experience levels in neuroradiology using the test dataset. Agreement analyses were applied to evaluate the prediction performance/reproducibility.

Results
The test dataset included 303 patients (age (SD): 56.7 (14.2) years, female/male: 114/189, low-grade/high-grade: 54/249, IDH-mutant/wildtype: 82/221, 1p/19q-codeleted/intact: 34/269). Per-rater GBCA-free predictions achieved ≥ 0.85 (95%-CI: 0.80–0.88) accuracy for grade and ≥ 0.75 (95%-CI: 0.70–0.80) for molecular status, while GBCA-enhanced predictions reached ≥ 0.87 (95%-CI: 0.82–0.90) and ≥ 0.77 (95%–CI: 0.71–0.81), respectively. No accuracy difference was observed between GBCA-free and GBCA-enhanced predictions. Group inter-rater agreement was moderate for GBCA-free (0.56 (95%-CI: 0.46–0.66)) and substantial for GBCA-enhanced grade prediction (0.68 (95%-CI: 0.58–0.78), p = 0.008), while substantial for both GBCA-free (0.75 (95%-CI: 0.69–0.80) and GBCA-enhanced (0.77 (95%-CI: 0.71–0.82), p = 0.51) molecular status predictions.

Conclusion
The proposed GBCA-free diagnosis prediction decision tree performed well, with GBCA-enhanced images adding little to the preoperative diagnostic accuracy of adult-type diffuse gliomas.

Key Points

Question

Given health and environmental concerns, is there a gadolinium-free imaging protocol to preoperatively evaluate gliomas comparable to the gadolinium-enhanced standard practice?

Findings

The proposed gadolinium-free diagnosis prediction decision tree for adult-type diffuse gliomas performed well, and gadolinium-enhanced MRI demonstrated only limited improvement in diagnostic accuracy.

Clinical relevance

Even inexperienced raters effectively classified adult-type diffuse gliomas using the gadolinium-free diagnosis prediction decision tree, which, until further validation, can be used alongside gadolinium-enhanced images to respect standard practice, despite this study showing that gadolinium-enhanced images hardly improved diagnostic accuracy.

Graphical Abstract
multiRegionFoam: A Unified Multiphysics Framework for Multi-Region Coupled Continuum-Physical Problems
Authors: Alkafri Heba , Habes Constantin , Elwardi Fadeli Mohammed , Hess Steffen , Beale Steven B. , Zhang Shidong , Jasak Hrvoje , Marschall Holger 
Published: October 2024

Abstract
This paper presents a unified framework, called multiRegionFoam, for solving multiphysics problems of the multi-region coupling type within OpenFOAM (FOAM-extend). It is intended to supersede the existing solver with the same name. The design of the new framework is modular, allowing users to assemble a multiphysics problem region-by-region and coupling conditions interface-by-interface. The present approach allows users to choose between deploying either monolithic or partitioned interface coupling for each individual transport equation. The formulation of boundary conditions is generalised in the sense that their implementation is based on the mathematical jump/transmission conditions in the most general form for tensors of any rank. The present contribution focuses on the underlying mathematical model for interface coupled multiphysics problems, as well as on the software design and resulting code structure that enable a flexible and modular approach. Finally, deployment for different multi-region coupling cases is demonstrated, including conjugate heat, multiphase flows and fuel-cells. Source code: multiRegionFoam v1.1 [1], repository https://bitbucket.org/hmarschall/multiregionfoam/.

Article highlights

A novel multiphysics framework, called multiRegionFoam, has been developed for solving multi-region coupled problems in OpenFOAM.

The design of the framework allows for a modular multiphysics setup with freedom of choice on the coupling strategy (partitioned vs. monolithic).

Extension of the general transport equation by interface conditions enables a unified coupling approach.
An investigation of the relationship between long bone measurements and stature: Implications for estimating skeletal stature in subadults
Authors: Chu Elaine Y. , Stull Kyra E. 
Published: October 2024

Abstract
The present study introduces new regression formulae that address several challenges of current subadult stature estimation methods by 1) using a large, contemporary, cross-sectional sample of subadult skeletal remains; 2) generating regression models using both lengths and breadths; 3) utilizing both linear and nonlinear regression models to accommodate the nonlinear shape of long bone growth; and 4) providing usable prediction intervals for estimating stature. Eighteen long bone measurements, stature, and age were collected from computed tomography images for a sample of individuals (n = 990) between birth and 20 years from the United States. The bivariate relationship between long bone measurements and stature was modeled using linear and nonlinear methods on an 80% training sample and evaluated on a 20% testing sample. Equations were generated using pooled-sex samples. Goodness of fit was evaluated using Kolmogorov–Smirnov tests and mean absolute deviation (MAD). Accuracy and precision were quantified using percent testing accuracy and Bland–Altman plots. In total, 38 stature estimation equations were created and evaluated, all achieving testing accuracies greater than 90%. Nonlinear models generated better fits compared to linear counterparts and generally produced smaller MAD (3.65 – 15.90cm). Length models generally performed better than breadth models, and a mixture of linear and nonlinear methods resulted in highest testing accuracies. Model performance was not biased by sex, age, or measurement type. A freely available, online graphical user interface is provided for immediate use of the models by practitioners in forensic anthropology and will be expanded to include bioarchaeological contexts in the future.
Histological variants of pancreatic ductal adenocarcinoma: a survival analysis
Authors: Bengtsson Axel , Andersson Roland , Ansari Daniel 
Published: October 2024

Abstract
Purpose
Pancreatic ductal adenocarcinoma (PDAC) can be classified into distinct histological subtypes based on the WHO nomenclature. The aim of this study was to compare the prognosis of conventional PDAC (cPDAC) against the other histological variants at the population level.

Methods
The Surveillance, Epidemiology and End Results (SEER) database was used to identify patients with microscopically confirmed PDAC. These patients were divided into 9 histological subgroups. Overall survival was assessed using the Kaplan-Meier method and Cox regression models stratified by tumor histology.

Results
A total of 159,548 patients with PDAC were identified, of whom 95.9% had cPDAC, followed by colloid carcinoma (CC) (2.6%), adenosquamous carcinoma (ASqC) (0.8%), signet ring cell carcinoma (SRCC) (0.5%), undifferentiated carcinoma (UC) (0.1%), undifferentiated carcinoma with osteoclast-like giant cells (UCOGC) (0.1%), hepatoid carcinoma (HC) (0.01%), medullary carcinoma of the pancreas (MCP) (0.006%) and pancreatic undifferentiated carcinoma with rhabdoid phenotype (PUCR) (0.003%). Kaplan-Meier curves showed that PUCR had the worst prognosis (median survival: 2 months; 5-year survival: 0%), while MCP had the best prognosis (median survival: 41 months; 5-year survival: 33.3%). In a multivariable Cox model, several histological subtypes (i.e. CC, ASqC, SRCC, UCOGC) were identified as independent predictors of overall survival when compared to cPDAC.

Conclusion
PDAC is a heterogenous disease and accurate identification of variant histology is important for risk stratification, as these variants may have different biological behavior.
Gender matters, especially if you are a Polish teenager being examined by a doctor or a doctor examining a teenager
Authors: Henzler Michał , Henzler Ania Stella , Jacewicz Jan , Nitsch-Osuch Aneta , Kuchar Ernest , Rybicka-Kramarz Anika , Kucharski Bartłomiej , Bogdan Magdalena 
Published: October 2024

AbstractTo analyse how the specific gender configurations of the adolescent patient and the doctor affect the performance of intimate areas examinations during adolescent well-care visits and the emotions that accompany these examinations, the use of comfort measures, and the subsequent willingness of adolescents to visit the doctor in the future. An anonymous questionnaire was completed by adolescents (n = 1072) and their parents (n = 685) recruited from 80 randomly selected secondary schools in Poland. Genital examination and puberty assessment were performed more often in boys than in girls (OR = 14.1, p < .0001 and OR = 5.5, p < .0001, respectively). Female doctors performed intimate examinations more frequently than male doctors (OR = 2.2, p = .0059). Male doctors were more likely to ask for consent than female doctors, 66.7% vs. 40.2% (p = .0556), and use the screen more often than female doctors, 46.7% vs. 21.7% (p = .0393). Intimate examinations significantly discouraged adolescents from revisiting the doctor, especially when performed by a physician of the opposite sex. The majority of Polish adolescents and their parents believe that routine prophylactic genital region examinations are illegal, especially if girls’ genitals are to be examined by male physicians.Conclusion: The implementation of preventive genital region examinations in adolescents depends largely on non-medical factors—the gender of the patient, the physician, and the mutual configuration of these genders. The level of public non-acceptance of these procedures should not be underestimated by experts setting standards of well-care for adolescents.

What is known:• Although the assessment of sexual maturity is an integral part of the preventive examination of adolescents (both girls and boys) these examinations are often overlooked.What is new:• The gender of the physician and the congruence of his/her gender with the gender of the adolescent patient influence whether a puberty assessment will be performed, as well as the social acceptance of such procedures.• Examinations of the intimate area are a significant factor discouraging both adolescent girls and adolescent boys from seeing the doctor again.
Methodologies underpinning polygenic risk scores estimation: a comprehensive overview
Authors: Ndong Sima Carene Anne Alene , Step Kathryn , Swart Yolandi , Schurz Haiko , Uren Caitlin , Möller Marlo 
Published: October 2024

AbstractPolygenic risk scores (PRS) have emerged as a promising tool for predicting disease risk and treatment outcomes using genomic data. Thousands of genome-wide association studies (GWAS), primarily involving populations of European ancestry, have supported the development of PRS models. However, these models have not been adequately evaluated in non-European populations, raising concerns about their clinical validity and predictive power across diverse groups. Addressing this issue requires developing novel risk prediction frameworks that leverage genetic characteristics across diverse populations, considering host-microbiome interactions and a broad range of health measures. One of the key aspects in evaluating PRS is understanding the strengths and limitations of various methods for constructing them. In this review, we analyze strengths and limitations of different methods for constructing PRS, including traditional weighted approaches and new methods such as Bayesian and Frequentist penalized regression approaches. Finally, we summarize recent advances in PRS calculation methods development, and highlight key areas for future research, including development of models robust across diverse populations by underlining the complex interplay between genetic variants across diverse ancestral backgrounds in disease risk as well as treatment response prediction. PRS hold great promise for improving disease risk prediction and personalized medicine; therefore, their implementation must be guided by careful consideration of their limitations, biases, and ethical implications to ensure that they are used in a fair, equitable, and responsible manner.
Deep attention for enhanced OCT image analysis in clinical retinal diagnosis
Authors: Talaat Fatma M. , Ali Ahmed Ali Ahmed , ElGendy Raghda , ELShafie Mohamed A. 
Published: October 2024

Abstract
Retinal illnesses such as age-related macular degeneration (AMD) and diabetic maculopathy pose serious risks to vision in the developed world. The diagnosis and assessment of these disorders have undergone revolutionary change with the development of optical coherence tomography (OCT). This study proposes a novel method for improving clinical precision in retinal disease diagnosis by utilizing the strength of Attention-Based DenseNet, a deep learning architecture with attention processes. For model building and evaluation, a dataset of 84495 high-resolution OCT images divided into NORMAL, CNV, DME, and DRUSEN classes was used. Data augmentation techniques were employed to enhance the model's robustness. The Attention-Based DenseNet model achieved a validation accuracy of 0.9167 with a batch size of 32 and 50 training epochs. This discovery presents a promising route for more precise and speedy identification of retinal illnesses, ultimately enhancing patient care and outcomes in clinical settings by integrating cutting-edge technology with powerful neural network architectures.
Organic geochemical and compound specific stable carbon isotope analyses of n-alkanes and saturated carboxylic acids extracted from late Paleozoic coals
Authors: Weniger Philipp , Schwarzbauer Jan 
Published: October 2024

AbstractIsotopic studies of coal organic matter are often conducted to gain information about past ecosystems and plant communities e.g. under changing climate conditions. While many studies focused on isotope analysis of bulk coal organic matter or extractable aliphatic hydrocarbons, the polar fraction and compounds that are bound to kerogen and not freely extractable have received less attention. The aim of this study was to provide a systematic comparison and evaluation of information gained from different molecular compounds (n-alkanes, n-carboxylic acids) extracted from Paleozoic coals before and after alkaline hydrolysis. Stable carbon isotope analysis of these compounds were used to evaluate a possible application of extractable and ‘bound’ lipids for paleoenvironmental analyses. Coal samples of different stratigraphic age, low thermal maturity (VRr < 1.02%, mostly VRr < 0.8%) and from different paleogeographic locations were selected to investigate organic matter deposited under different paleoenvironmental and paleoclimatic conditions. Molecular distributions show prominent carbon preference suggesting preservation of biologic signatures in coal organic matter. Permian Gondwana coals show similar n-alkane and n-carboxylic acid distribution which may be related to Glossopteris flora. Molecular distributions of Carboniferous coal from Europe are more variable with unimodal or bimodal patterns and maxima in the short- or long-chain range, reflecting higher diversity of paleovegetation and different contribution from algae or bacteria in limnic and paralic environments. The isotope signals of free as well as bound fatty acids show closer response for different depositional environments, whereas signals of paraffins and bulk organic matter are less variable. However, averaged fatty acid isotope signals in coals from different paleovegetational realms, e.g. Euramerica and Gondwana differed only marginally.
Graphical abstract
Isolation and characterization of Yersinia phage fMtkYen3-01
Authors: Goladze Sophia , Patpatia Sheetal , Tuomala Henni , Ylänne Matti , Gachechiladze Nino , de Oliveira Patricio Daniel , Skurnik Mikael , Sundberg Lotta-Riina 
Published: October 2024

AbstractYersinia enterocolitica causes yersiniosis, the third most common gastrointestinal infection in humans throughout Europe. The emergence of multidrug resistance and the lack of effective new antibiotics have drawn attention to phage therapy as a treatment option. Here, we report the complete genome sequence of phage fMtkYen3-01, which infects Y. enterocolitica serotype O:3 strains. This phage has a genome 40,415 bp in length with 45.1% GC content and 49 predicted genes. fMtkYen3-01 infected 9.5% of the 42 Y. enterocolitica strains tested and showed stability at 25–40 °C, as well as pH 5.0–10.0. These results suggest the therapeutic potential of this phage.
‘Argumentative Disobedience’ as a Strategy to Confront Hate Speech
Authors: Domínguez-Armas Álvaro 
Published: October 2024

AbstractIn this paper, I examine argumentative strategies that social movements can follow to counter hate speech. I begin by reconstructing the disagreement space of the abortion debate in Argentina as a polylogue, identifying the protests of the social movement Pañuelos verdes as argumentative contributions. I then describe two different forms of hate speech used in response to the movement’s protests. I argue that hate speech discredits the position of Pañuelos verdes in the abortion debate and depicts their protests as social threats. Subsequently, I discuss three argumentative strategies that social movements can implement to address hate speech: arguing with hate speakers; advocating for a dialogue with restrictions; and opting for argumentative disobedience. Arguing with hate speakers aims to make hate speakers retract hate speech by exposing the undesirability of using hateful messages in argumentative exchanges. Advocating for a dialogue with restrictions aims to impose limited bans on public speech in order to ensure equal participation of arguers in argumentation. Finally, I propose the notion of argumentative disobedience to describe communicative responses to hate speech that aim to bring bystanders in line with the position of social movements in public debates.
Prompt gamma rays of lanthanum and praseodymium produced by inelastic scattering of fission neutrons
Authors: Ophoven Niklas , Mauerhofer Eric , Ilic Zeljko , Stieghorst Christian , Révay Zsolt , Meleshenkovskii Iaroslav , Randriamalala Tsitohaina H. 
Published: October 2024

AbstractEmission of prompt gamma rays in lanthanum and praseodymium nuclei triggered by (n,n’γ) inelastic scattering reactions of fission neutrons was investigated with the instrument FaNGaS (Fast Neutron-induced Gamma-ray Spectrometry) at Heinz Maier-Leibnitz Zentrum (MLZ). We identified 125 gamma lines (54 for lanthanum and 71 for praseodymium), for which we give the relative intensities and production cross sections. Presence of oxygen and chlorine in the samples was exploited to verify previous measurements. Our results are consistent with available literature data but also enhance it as we detect new lines and recognize a few false assignments. In addition, for a counting time of 12 h we estimated the detection limits of lanthanum and praseodymium as 0.6 and 0.4 mg, respectively.
Widening the frequency bandgap and reducing thermal conductivity in phononic crystals by tuning structural parameters using a novel computational simulation method
Authors: Bun Khemrith , Pathak Saurabh , Wang Xu 
Published: October 2024

AbstractThis paper introduces and models a phononic structure based on single-crystal silicon, aiming to investigate the width of its frequency bandgap and the impact of key parameters on thermal conductivity. The modeled phononic crystal structure features a periodic arrangement of cylindrical holes in a silicon matrix. This research holds the potential to enhance thermal management performance of thermal metamaterials. Utilizing a 3D finite element method (FEM) model in COMSOL, we have computed phonon dispersion to estimate thermal conductivity. The study systematically has explored the influence of phononic crystal parameters—specifically, porosity, lattice constant, and thickness—along with their interactions on both thermal conductivity and frequency bandgap width.A comprehensive investigation of these parameters has been conducted for their optimization to achieve the maximum frequency bandgap width and minimum thermal conductivity using the response surface method model. Eigenfrequencies and wave vector parameters are extracted from the finite element model using a MATLAB script. Subsequently, thermal conductivity is calculated through the Callaway–Holland model, a simplification of the Boltzmann transport equation (BTE).Our results indicate that the frequency bandgap begins to form at approximately 43% porosity for a lattice constant and thickness of 100 nm each. Furthermore, adjusting the parameters led to a significant reduction in thermal conductivity, decreasing from 43.89 W m−1 K−1 to 0.39 W m−1 K−1. The novelty of our research lies in thermal conductivity control of phononic crystal metamaterials through their parameter variations, or a predictive method of thermal conductivity and its parameter sensitivity. This study advances the state of the art in phononic crystal metamaterial research, contributing to improved thermal management performance by enlarging frequency bandgaps.Overall, our findings deepen the understanding of how porosity, lattice constant, and thickness influence thermal conductivity and frequency bandgap width. They offer valuable insights into optimizing phononic crystal parameters, enhancing thermal management performance, and designing more efficient and effective phononic crystal structures.