bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bridging Histopathology and Radiomics Toward Prognosis of Metastasis in Early Breast Cancer
Authors: Radulović Marko , Li Xingyu , Djuričić Goran J , Milovanović Jelena , Todorović Raković Nataša , Vujasinović Tijana , Banovac Dušan , Kanjer Ksenija 
Published: July 2024

Abstract
Tumor histomorphology is crucial for the prognostication of breast cancer outcomes because it contains histological, cellular, and molecular tumor heterogeneity related to metastatic potential. To enhance breast cancer prognosis, we aimed to apply radiomics analysis—traditionally used in 3D scans—to 2D histopathology slides. This study tested radiomics analysis in a cohort of 92 breast tumor specimens for outcome prognosis, addressing -omics dimensionality by comparing models with moderate and high feature counts, using least absolute shrinkage and selection operator for feature selection and machine learning for prognostic modeling. In the test folds, models with radiomics features [area under the curves (AUCs) range 0.799–0.823] significantly outperformed the benchmark model, which only included clinicopathological (CP) parameters (AUC = 0.584). The moderate-dimensionality model with 11 CP + 93 radiomics features matched the performance of the highly dimensional models with 1,208 radiomics or 11 CP + 1,208 radiomics features, showing average AUCs of 0.823, 0.799, and 0.807 and accuracies of 79.8, 79.3, and 76.6%, respectively. In conclusion, our application of deep texture radiomics analysis to 2D histopathology showed strong prognostic performance with a moderate-dimensionality model, surpassing a benchmark based on standard CP parameters, indicating that this deep texture histomics approach could potentially become a valuable prognostic tool.
The stability of deep learning for 21cm foreground removal across various sky models and frequency-dependent systematics
Authors: Chen T , Bianco M , Tolley E , Spinelli M , Forero-Sanchez D , Kneib J P 
Published: July 2024

ABSTRACT
Deep learning (DL) has recently been proposed as a novel approach for 21cm foreground removal. Before applying DL to real observations, it is essential to assess its consistency with established methods, its performance across various simulation models, and its robustness against instrumental systematics. This study develops a commonly used U-Net and evaluates its performance for post-reionization foreground removal across three distinct sky simulation models based on pure Gaussian realizations, the Lagrangian perturbation theory, and the Planck sky model. Consistent outcomes across the models are achieved provided that training and testing data align with the same model. On average, the residual foreground in the U-Net reconstructed data is $\sim 10~{{\ \rm per\ cent}}$ of the signal across angular scales at the considered redshift range. Comparable results are found with traditional approaches. However, blindly using a network trained on one model for data from another model yields inaccurate reconstructions, emphasizing the need for consistent training data. The study then introduces frequency-dependent Gaussian beams and bandpass fluctuations to the test data. The network struggles to denoise data affected by ‘unexpected’ systematics without prior information. However, after re-training consistently with systematics-contaminated data, the network effectively restores its reconstruction accuracy. Our results highlight the importance of incorporating prior knowledge during network training compared with established blind methods. Our work provides critical guidelines for using DL for 21cm foreground removal, tailored to specific data attributes. Notably, it is the first time that DL has been applied to the Planck sky model being most realistic foregrounds at present.
Effects of stratification on overshooting and waves atop the convective core of M⊙ main-sequence stars
Authors: Morison A , Le Saux A , Baraffe I , Morton J , Guillet T , Vlaykov D G , Goffrey T , Pratt J 
Published: July 2024

ABSTRACT
As a massive star evolves along the main sequence, its core contracts, leaving behind a stable stratification in helium. We simulate two-dimensional convection in the core at three different stages of evolution of a $5\,\mathrm{ M}_{\odot }$ star, with three different stratifications in helium atop the core. We study the propagation of internal gravity waves in the stably stratified envelope, along with the overshooting length of convective plumes above the convective boundary. We find that the stratification in helium in evolved stars hinders radial motions and effectively shields the radiative envelope against plume penetration. This prevents convective overshooting from being an efficient mixing process in the radiative envelope. In addition, internal gravity waves are less excited in evolved models compared to the zero-age-main-sequence model, and are also more damped in the stratified region above the core. As a result, the wave power is several orders of magnitude lower in mid- and terminal-main-sequence models compared to zero-age-main-sequence stars.
Systematic Review on the Impact of Salt-Reduction Initiatives by Socioeconomic Position to Address Health Inequalities in Adult Populations
Authors: Contreras Navarro Ana , Gallagher Kerrie , Griffin Sally , Leydon Clarissa L , Perry Ivan J , Harrington Janas M 
Published: July 2024

Abstract

Context
International evidence shows that individuals from low socioeconomic positions (SEPs) consume a greater amount of salt than those from higher SEPs. This health inequality reflects a disproportionate effect of salt-reduction initiatives, and explains a higher prevalence of cardiovascular disease among the most vulnerable populations. Assessing this impact can help tailor implementation strategies in the future for the benefit of the whole population.

Objective
The aim was to systematically review the literature and assess the impact of salt-reduction initiatives on health and behavioral outcomes of adults by SEP.

Data Sources
The search strategy was conducted in 6 databases (CINAHL, Scopus, Embase, MEDLINE, PubMed, and Web of Science) using the terms sodium or salt, social class, policy, intervention or campaign. Peer-reviewed articles assessing salt-reduction interventions in adults reporting dietary or behavioral changes on salt consumption measurements by SEP were considered for inclusion. Articles in which salt intake data were not reported by SEP were excluded.

Data Extraction
Two reviewers collected data independently using a predesigned electronic form. The AXIS and RoB 2 tools were used for critical appraisal.

Data Analysis
Eight studies containing data from 111 548 adults were interpreted according to study design following a narrative synthesis approach.

Results
Salt-reduction initiatives are effective at reducing the intake of salt and sodium in adults. When reporting the impact of these initiatives, research outcomes are generally not evaluated by SEP, representing a question yet to be explored.

Conclusion
A small number of articles that focused on the impact of salt-reduction interventions reported salt consumption measurements by SEP, indicating a critical gap in research. The limited evidence suggests potentially greater health benefits to be gained from the implementation of population-wide initiatives in adults of low SEP.

Systematic Review Registration
PROSPERO registration no. CRD42021238055.
Diabetic Foot Osteomyelitis Undergoing Amputation: Epidemiology and Prognostic Factors for Treatment Failure
Authors: Baek Yae Jee , Lee Eunjung , Jung Jongtak , Won Sung Hun , An Chi Young , Kang Eun Myeong , Park Se Yoon , Baek Seung Lim , Chun Dong-il , Kim Tae Hyong 
Published: July 2024

Abstract

Background
When treating diabetic foot osteomyelitis (DFO), it remains difficult to determine the presence of residual infection and the optimal treatment after bone resection. In this study, we aimed to investigate the clinical characteristics of and prognostic factors in patients with DFO undergoing amputation.

Methods
This retrospective study involved 101 patients with DFO who underwent amputation. Data on their demographics, clinical characteristics, tissue culture, and surgery type were collected. Patients were grouped according to primary closure status and clinical outcome postamputation. A good outcome was defined as a successful complete remission, characterized by the maintenance of complete wound healing with no sign of infection at 6 months postamputation. Multivariate logistic regression analysis was performed. Outcomes according to surgery type were also analyzed.

Results
Staphylococcus aureus (17%) and Pseudomonas species (14%) were the most prevalent pathogens. Gram-negative bacteria were isolated from 62% of patients. In patients with primary closure, hemodialysis and ankle brachial index (ABI) &lt;0.6 were associated with poor outcomes. In patients with DFO, ABI &lt;0.6 was the only prognostic factor associated with treatment failure. Antimicrobial stewardship allows patients who underwent major amputation to reduce the duration of antibiotic therapy compared to those after minor amputation, although it did not contribute to reducing mortality.

Conclusions
Peripheral artery disease and hemodialysis were associated with poor outcomes despite radical resection of the infected bone. Vigilant monitoring after amputation and antimicrobial stewardship implemented based on microbiological epidemiology, prognostic factors, and the type of surgery are important. A multidisciplinary team could assist in these activities to ensure treatment success.
Cardiometabolic Characteristics of Obesity Phenotypes in Persons With HIV
Authors: Swartz Alison Z , Robles Michelle E , Park Seungweon , Esfandiari Helia , Bradshaw Marques , Koethe John R , Silver Heidi J 
Published: July 2024

Abstract

Background
In the general population, it is established that adipose tissue depots pose various risks for cardiometabolic diseases. The interaction among obesity, HIV, and antiretroviral treatment promotes even greater risk for persons with HIV (PWH). As obesity is a heterogeneous condition, determining the specific obesity phenotypes present and their characteristics is critical to personalize care in PWH.

Methods
Visceral, sarcopenic, myosteatotic, hepatosteatotic, and metabolically healthy obesity phenotypes were determined by pre-established cut points after segmentation of computed tomography scans at the L3 vertebra. Multivariable linear regression modeling included anthropometrics, clinical biomarkers, and inflammatory factors while controlling for age, sex, race, and body mass index (BMI).

Results
Of 187 PWH, 86% were male, and the mean ± SD age and BMI were 51.2 ± 12.3 years and 32.6 ± 6.3 kg/m2. Overall, 59% had visceral obesity, 11% sarcopenic obesity, 25% myosteatotic obesity, 9% hepatosteatotic obesity, and 32% metabolically healthy obesity. The strongest predictor of visceral obesity was an elevated triglyceride:high-density lipoprotein (HDL) ratio. Increased subcutaneous fat, waist circumference, and HDL cholesterol were predictors of sarcopenic obesity. Diabetes status and elevated interleukin 6, waist circumference, and HDL cholesterol predicted myosteatotic obesity. An increased CD4+ count and a decreased visceral:subcutaneous adipose tissue ratio predicted hepatosteatotic obesity, though accounting for only 28% of its variability. Participants with metabolically healthy obesity were on average 10 years younger, had higher HDL, lower triglyceride:HDL ratio, and reduced CD4+ counts.

Conclusions
These findings show that discrete obesity phenotypes are highly prevalent in PWH and convey specific risk factors that measuring BMI alone does not capture. These clinically relevant findings can be used in risk stratification and optimization of personalized treatment regimens. This study is registered at ClinicalTrials.gov (NCT04451980).
Clinical and Biochemical Characteristics of Hemophagocytic Lymphohistiocytosis in People Living With HIV and Disseminated Histoplasmosis at a Tertiary Hospital in Mexico
Authors: Cruz-Quezada Arlen , Moreno Joaquín , Solís-Bravo Miguel Ángel , López Chávez Claudia Andrea , Santos Tiburcio , Fonseca-Mata Juan José , Araiza Javier , Bonifaz Alexandro 
Published: July 2024

AbstractBackgroundHemophagocytic lymphohistiocytosis (HLH) is considered a rare disease with high morbidity and mortality risks. Most research on this disease is conducted in pediatric settings. Therefore, this study aimed to describe the clinical characteristics, laboratory findings, and outcomes related to HLH in people living with human immunodeficiency virus (HIV)/AIDS) and disseminated histoplasmosis.MethodsA retrospective and descriptive study was conducted in a tertiary hospital in México City from January 2018 to December 2022, including people living with HIV who had disseminated histoplasmosis confirmed through direct microbiological or immunological methods with an HScore ≥169 or who met 5 of the 8 HLH-2004 criteria.ResultsHLH occurred in 36.1% (n = 26) of patients with HIV and disseminated histoplasmosis; the majority were men (84.9%), and their mean age (standard deviation) was 30.19 (5.6) years. The most frequent clinical manifestations were hepatomegaly (100%), fever (96.2%), and dyspnea (84.6%). The most common biochemical changes were hyperferritinemia (100%), elevated lactate dehydrogenase (100%), and bicytopenia (61.5%). Partial thromboplastin time (P = .012) and prothrombin time (P = .004) were associated with the 30-day mortality rate, and the 30-day survival rate was 65.4%.ConclusionsWe detected a high frequency of HLH; therefore, we encourage physicians to use diagnostic prediction tools (HLH-2004 and HScore criteria) in each reassessment for timely detection.
Heparin-Binding Protein Stratifies Mortality Risk Among Ugandan Children Hospitalized With Respiratory Distress
Authors: Mishra Hridesh , Balanza Núria , Francis Caroline , Zhong Kathleen , Wright Julie , Conroy Andrea L , Opoka Robert O , Bassat Quique , Namasopo Sophie , Kain Kevin C , Hawkes Michael T 
Published: July 2024

Abstract

Background
Current prognostic tools do not reliably and objectively identify children with pneumonia at risk of a severe or life-threatening episode. Heparin-binding protein (HBP) is a host immune protein that is released in response to infection. We hypothesized that measuring HBP concentrations at hospital admission could help risk-stratify children with pneumonia and identify those at higher risk of an adverse prognosis.

Methods
We evaluated the prognostic accuracy of HBP for predicting in-hospital mortality among children with respiratory distress, and whether HBP could improve the accuracy of validated composite clinical severity scores.

Results
Of 778 Ugandan children under 5 years of age and presenting with clinically defined pneumonia, 60 (7.7%) died during hospital admission. HBP concentrations at presentation were significantly higher in children with fatal outcomes (median, 76 ng/mL [interquartile range {IQR}, 41–150]) compared to children who survived (median, 31 ng/mL [IQR, 18–57]) (P &lt; .001). Children with HBP &gt;41 ng/mL on admission had an elevated risk of death (hazard ratio, 5.3 [95% confidence interval {CI}, 2.9–9.5]; P &lt; .0001). In receiver operating characteristic (ROC) curve analysis, HBP concentrations distinguished between fatal and nonfatal outcomes (area under the ROC curve, 0.75 [95% CI, .66–.84]) and significantly improved the prediction provided by the Respiratory Index of Severity in Children, a composite clinical severity score (P = .0026).

Conclusions
Measuring HBP at presentation could help identify children at risk of severe and fatal pneumonia. Adding HBP to clinical scores could improve the recognition and triage of children with pneumonia at risk of death.
Cell wall integrity modulates HOOKLESS1 and PHYTOCHROME INTERACTING FACTOR4 expression controlling apical hook formation
Authors: Lorrai Riccardo , Erguvan Özer , Raggi Sara , Jonsson Kristoffer , Široká Jitka , Tarkowská Danuše , Novák Ondřej , Griffiths Jayne , Jones Alexander M , Verger Stéphane , Robert Stéphanie , Ferrari Simone 
Published: July 2024

Abstract
Formation of the apical hook in etiolated dicot seedlings results from differential growth in the hypocotyl apex and is tightly controlled by environmental cues and hormones, among which auxin and gibberellins (GAs) play an important role. Cell expansion is tightly regulated by the cell wall, but whether and how feedback from this structure contributes to hook development are still unclear. Here, we show that etiolated seedlings of the Arabidopsis (Arabidopsis thaliana) quasimodo2-1 (qua2) mutant, defective in pectin biosynthesis, display severe defects in apical hook formation and maintenance, accompanied by loss of asymmetric auxin maxima and differential cell expansion. Moreover, qua2 seedlings show reduced expression of HOOKLESS1 (HLS1) and PHYTOCHROME INTERACTING FACTOR4 (PIF4), which are positive regulators of hook formation. Treatment of wild-type seedlings with the cellulose inhibitor isoxaben (isx) also prevents hook development and represses HLS1 and PIF4 expression. Exogenous GAs, loss of DELLA proteins, or HLS1 overexpression partially restore hook development in qua2 and isx-treated seedlings. Interestingly, increased agar concentration in the medium restores, both in qua2 and isx-treated seedlings, hook formation, asymmetric auxin maxima, and PIF4 and HLS1 expression. Analyses of plants expressing a Förster resonance energy transfer-based GA sensor indicate that isx reduces accumulation of GAs in the apical hook region in a turgor-dependent manner. Lack of the cell wall integrity sensor THESEUS 1, which modulates turgor loss point, restores hook formation in qua2 and isx-treated seedlings. We propose that turgor-dependent signals link changes in cell wall integrity to the PIF4-HLS1 signaling module to control differential cell elongation during hook formation.
Attraction by pairwise coherence explains the emergence of ideological sorting
Authors: Zimmerman Federico , Pedraza Lucía , Navajas Joaquín , Balenzuela Pablo 
Published: July 2024

Abstract
Political polarization has become a growing concern in democratic societies, as it drives tribal alignments and erodes civic deliberation among citizens. Given its prevalence across different countries, previous research has sought to understand under which conditions people tend to endorse extreme opinions. However, in polarized contexts, citizens not only adopt more extreme views but also become correlated across issues that are, a priori, seemingly unrelated. This phenomenon, known as “ideological sorting”, has been receiving greater attention in recent years but the micro-level mechanisms underlying its emergence remain poorly understood. Here, we study the conditions under which a social dynamic system is expected to become ideologically sorted as a function of the mechanisms of interaction between its individuals. To this end, we developed and analyzed a multidimensional agent-based model that incorporates two mechanisms: homophily (where people tend to interact with those holding similar opinions) and pairwise-coherence favoritism (where people tend to interact with ingroups holding politically coherent opinions). We numerically integrated the model's master equations that perfectly describe the system's dynamics and found that ideological sorting only emerges in models that include pairwise-coherence favoritism. We then compared the model's outcomes with empirical data from 24,035 opinions across 67 topics and found that pairwise-coherence favoritism is significantly present in datasets that measure political attitudes but absent across topics not considered related to politics. Overall, this work combines theoretical approaches from system dynamics with model-based analyses of empirical data to uncover a potential mechanism underlying the pervasiveness of ideological sorting.
What is creativity?
Authors: Brainard Lindsay 
Published: July 2024

Abstract
I argue for an account of creativity that unifies creative achievements in the arts, sciences, and other domains and identifies its characteristic value. This account draws upon case studies of creative work in both the arts and sciences to identify creativity as a kind of successful exploration. I argue that if creativity is properly understood in this way, then it is fundamentally a property of processes, something only agents can achieve, something that comes in degrees, subjectively novel, and non-formulaic. As I develop the account, I show how it avoids challenges faced by other accounts of creativity, especially concerning creativity's value. Hills and Bird have together argued that creativity is not necessarily valuable. My account challenges this view. If I am right that creativity is a kind of successful exploration, then creativity does have a characteristic value, specifically epistemic value.
Equitable Grading Practices in Physical Therapist Education: A Case Report
Authors: Richardson Shannon , Dial Monica , Kneiss Janet , Somyoo Nipaporn , Varnado Kimberly 
Published: July 2024

Abstract

Objective
To optimize learning in physical therapist education, learners need opportunities to grow from their unique starting points. Traditional grading practices like A to F grades, zero grades, and grading on timeliness and professionalism hinder content mastery and accurate competency assessment. Grading should focus on mastery of skill and content, using summative assessments for final grades, a no-zero policy, and actionable feedback. Equitable grading supports learners from all backgrounds and identities and promotes academic success. This case study provides guidance and recommendations for implementing equitable grading practices in academic physical therapist programs.

Methods
Over a 2-year period, a doctor of physical therapy program began implementing 5 strategies to create more equitable grading practices: (1) eliminating zero grades, (2) allowing late assignment submissions without penalty, (3) using low-stakes formative assessments throughout the semester, (4) weighing end-of-course assessments more heavily than initial ones, and (5) offering a no-stakes anatomy prep course before matriculation.

Results
Outcomes from implementing equitable grading practices varied. Some learners felt increased stress from fewer points opportunities, while others appreciated the reduced anxiety from low-stakes assessments. Some saw multiple attempts for peers as unfair. Faculty faced higher workloads due to detailed feedback and remediation but believed it benefited learners. Median final grades improved in some courses, remained stable in others, and slightly decreased in one. Overall, the changes had minimal impact on most learners’ grades but significantly improved outcomes and retention for struggling learners.

Conclusion
This case report documents the implementation of equitable grading practices in a Doctor of Physical Therapy program, offering valuable insights and recommendations for other institutions aiming to adopt similar practices.

Impact
Inequity in assessment widens the gap between learners entering professional programs. Equitable assessment practices level the playing field, enabling learners from diverse backgrounds and identities to succeed. Increased diversity benefits everyone, especially patients, by reducing health disparities for historically marginalized groups.