bluuebunny/crossref_metadata_2025_split huggingface dataset:
Demographics and Clinical Characteristics of Patients With Cpue
Authors: Stathopoulos Anna G. , Hylind Linda M. , Giardiello Francis M. , Foda Zachariah H. 
Published: February 2025

Goals:
This study examines the demographic and clinical characteristics of patients with CPUE (colonic polyposis of unknown etiology) to determine who may benefit from increased surveillance.

Background:
CPUE refers to individuals with 10 or more colonic adenomas with no identifiable genetic mutation as determined by multigene panel testing. Unlike hereditary syndromes, such as familial adenomatous polyposis, CPUE lacks well-established guidelines for polyp and colorectal cancer surveillance, relying heavily on expert opinion.

Study:
This single-center retrospective study included 75 individuals over the age of 18. Data on demographics, medical history, social history, and endoscopic data were collected via chart review. Patients were stratified by total number of polyps (10 to 19, 20 to 29, and over 30). Data were analyzed using the Pearson χ2 test for categorical variables and ANOVA to compare means.

Results:
Among all CPUE patients, 58.7% were male, and 89.3% were white. Tobacco use was reported in 44.0% of patients. Nearly half had hypertension (49.3%) or hyperlipidemia (49.3%). The total prevalence of CRC was 10.7%. Of the 44 patients who underwent EGD, 25.0% had at least one gastric polyp. No statistically significant differences were found between the 3 groups.

Conclusions:
The NCCN recommends exercising clinical judgment for the management of those with 10 to 19 adenomas; however, these findings suggest that individuals in that group do not significantly differ from patients with 20 or more adenomas and may therefore benefit from similar management.
The use of simple tests to predict biopsy-proven steatohepatitis in people with type 2 diabetes
Authors: Machado-Silva Lilian , Terra Carlos , Campos Carlos Frederico , Lanzoni Valeria , Miguez Marcio , Perazzo Hugo , Gomes Marilia Brito , Perez Renata M. 
Published: February 2025

Background/aims
Metabolic-associated steatotic liver disease (MASLD) has become the most common chronic liver disease, especially in people with type 2 diabetes mellitus (T2DM). Liver biopsy remains the gold standard method for diagnosis of MASLD subtypes, but prevalences may be under or overestimated when biopsy is performed with selection bias. The aims of this study were to define prevalence of MASLD subtypes by liver biopsy in T2DM participants not selected by abnormal exams, determine variables associated with metabolic-associated steatohepatitis (MASH), and analyze performance of aminotransferases and abdominal ultrasound in diagnosis.

Methods
T2DM participants from 18 to 70 years were considered for enrollment. Of the 396 participants, 85 were included and submitted to clinical, laboratory examinations, and ultrasound. Eighty-three performed liver biopsy evaluated by two independent pathologists. Factors independently associated to MASH and significant fibrosis were assessed by hierarchical multivariate logistic regression.

Results
Prevalence of MASLD was 92% (50% simple steatosis, 42% MASH) and kappa = 0.78. Steatosis was mild in 76% of participants with simple steatosis and severe in 65% of MASH (P < 0.001). Presence of MASH or fibrosis was associated with BMI and alanine aminotransferase (ALT) [threshold of 33.5 mg/dl in predicting MASH (area under the curve = 0.82, P = 0.001)].

Conclusion
Prevalence of MASLD by liver biopsy in T2DM regardless of ultrasound or ALT elevation is almost 100%, with 42% of MASH. MASH was associated to severe steatosis on histology. BMI and ALT were independently associated with MASH and ALT close to the upper limit of normal gave the best cutoff point for MASH detection.
Reversal of Roe v. Wade and implications of legal restrictions for neonatal care
Authors: Bishop Christine E. , Manian Maya 
Published: February 2025

Purpose of review
This review examines the implications of the 2022 Dobbs v. Jackson Women's Health Organization decision on neonatal care and explores how legal restrictions on abortion are influencing medical practices for neonates and the broader healthcare landscape for neonates.

Recent Findings
The Dobbs decision has led to increased uncertainty and challenges in both maternal and neonatal healthcare. Restrictive abortion laws are associated with higher infant mortality rates, increased health disparity, and increased care provider ethical dilemmas and moral distress due to legal uncertainty surrounding the care of infants. However, current changes in federal and state law regarding abortion do not change the previously established standard of care for neonates. Other federal legal statutes potentially addressing the care of neonates have existed for over 20 years and have had minimal effect on the practice of neonatology, because there is no record of federal enforcement actions or federal case law to clarify how the law should be interpreted.

Summary
While restrictive abortion laws primarily affect women and pregnant people's health care, indirect effects on neonatal care are becoming more common. There are other laws and policies with greater potential to regulate care for infants at the federal and state level. Professional medical standards remain the guiding framework in neonatal care. Clinicians can mitigate legal concerns through knowledge and advocacy.
Deep Learning Reconstruction Combined With Conventional Acceleration Improves Image Quality of 3 T Brain MRI and Does Not Impact Quantitative Diffusion Metrics
Authors: Wilpert Caroline , Russe Maximilian Frederic , Weiss Jakob , Voss Christian , Rau Stephan , Strecker Ralph , Reisert Marco , Bedin Ricardo , Urbach Horst , Zaitsev Maxim , Bamberg Fabian , Rau Alexander 
Published: February 2025

Objectives
Deep learning reconstruction of magnetic resonance imaging (MRI) allows to either improve image quality of accelerated sequences or to generate high-resolution data. We evaluated the interaction of conventional acceleration and Deep Resolve Boost (DRB)–based reconstruction techniques of a single-shot echo-planar imaging (ssEPI) diffusion-weighted imaging (DWI) on image quality features in cerebral 3 T brain MRI and compared it with a state-of-the-art DWI sequence.

Materials and Methods
In this prospective study, 24 patients received a standard of care ssEPI DWI and 5 additional adapted ssEPI DWI sequences, 3 of those with DRB reconstruction. Qualitative analysis encompassed rating of image quality, noise, sharpness, and artifacts. Quantitative analysis compared apparent diffusion coefficient (ADC) values region-wise between the different DWI sequences. Intraclass correlations, paired sampled t test, Wilcoxon signed rank test, and weighted Cohen κ were used.

Results
Compared with the reference standard, the acquisition time was significantly improved in accelerated DWI from 75 seconds up to 50% (39 seconds; P < 0.001). All tested DRB-reconstructed sequences showed significantly improved image quality, sharpness, and reduced noise (P < 0.001). Highest image quality was observed for the combination of conventional acceleration and DL reconstruction. In singular slices, more artifacts were observed for DRB-reconstructed sequences (P < 0.001). While in general high consistency was found between ADC values, increasing differences in ADC values were noted with increasing acceleration and application of DRB. Falsely pathological ADCs were rarely observed near frontal poles and optic chiasm attributable to susceptibility-related artifacts due to adjacent sinuses.

Conclusions
In this comparative study, we found that the combination of conventional acceleration and DRB reconstruction improves image quality and enables faster acquisition of ssEPI DWI. Nevertheless, a tradeoff between increased acceleration with risk of stronger artifacts and high-resolution with longer acquisition time needs to be considered, especially for application in cerebral MRI.
68Ga-FAPI PET/CT in a Patient With Multiple Aneurysms Due to Idiopathic Hypereosinophilic Syndrome
Authors: Li Puhao , Liang Juan , Chen Yue , Ding Haoyuan 
Published: February 2025

Abstract
Idiopathic hypereosinophilic syndrome is a group of unexplained diseases characterized by a persistent increase in eosinophils with multiple organs damage. Herein, we describe the 68Ga-FAPI PET/CT findings of idiopathic hypereosinophilic syndrome in a 56-year-old woman. 68Ga-FAPI PET/CT showed multiple aneurysms with increased FAPI uptake. In addition, myocardial uptake of FAPI was observed.
Imaging Spectrum of Extrathyroidal Neck Masses
Authors: Patel Naiya , Gharai Sean , Brindle Kathleen A. , Khati Nadia J. 
Published: February 2025

Abstract
Extrathyroidal masses in the anterolateral neck are frequently encountered in the adult population and may represent a diagnostic dilemma. These neck masses can result from a diverse array of pathologies including congenital, inflammatory, infectious, and neoplastic causes. Relevant medical history and physical examination are essential to complement the imaging findings. Ultrasound (US) plays an important role in the initial evaluation of neck masses due to its reliability, availability, safety and cost-effectiveness. It can confirm or exclude the presence of a mass and initially characterize it as solid or cystic. Sonographically assessing the relationship of a mass to adjacent cervical anatomy can facilitate a more targeted differential diagnosis. US also effectively guides fine needle aspirations and/or biopsies of accessible lesions. Multimodality imaging is reserved for problem-solving complex cases and presurgical planning. The anterolateral neck masses are categorized into midline/paramedian lesions, salivary gland pathologies, and other soft tissue lesions. Midline and paramedian lesions include thyroglossal duct pathologies, ectopic thyroid tissue, and parathyroid adenomas. Salivary gland pathologies include obstructive/inflammatory processes, benign and malignant neoplasms, and systemic diseases. This pictorial essay presents clinical features and sonographic characteristics of extrathyroidal masses in the anterolateral neck with a brief discussion of other imaging modalities.
ACS NSQIP Surgical Risk Calculator Accuracy When Operative Risk is Represented by the Principal CPT® code Versus Many Codes
Authors: Cohen Mark E. , Liu Yaoming , Hall Bruce L. , Ko Clifford Y. 
Published: February 2025

Objective:
To determine whether ACS NSQIP risk calculator (RC) accuracy can be improved by incorporating CPT codes beyond the principal code.

Background:
Because of technical limitations, past and current RC algorithms have relied only on the principal CPT code, represented as a logit score, to adjust for procedure-related risk. RC performance was evaluated when using a new machine learning (ML) algorithm capable of incorporating an indeterminate number of high cardinality categorical variables (in this case, multiple CPT codes).

Methods:
ACS-NSQIP data from 5,020,713 patients from 2016-2020 were used. Predictive accuracy, for 13 outcomes, was assessed when the RC relied on, in addition to standard predictors, a logit score associated with the principal CPT code (extreme gradient boosting ML, XGB), or up to 21 codes in native categorical form (CatBoost ML, CATB). 80% of cases were used for training and 20% for validation. Discrimination (area under the receiver operator characteristic curve and area under the precision recall curve) and calibration (Hosmer-Lemeshow statistics) were assessed on the entire validation dataset and on a subset of that data that included only patients who had at least 1 CPT code recorded beyond the principal code.

Results:
There was no consistent accuracy advantage of CATB over XGB with respect to discrimination. XGB tended to have slightly better calibration than CATB when evaluated on the complete validation dataset but tended to have slightly worse calibration compared to CATB when the validation dataset was limited to the subset of 34.8% of cases where there was at least one code in addition to the principal CPT code. However, there was a subset of patients with 4 or more CPTs (about 8% of all patients) where CATB provided meaningfully more accurate estimates than XGB.

Conclusions:
While the current RC, relying on XGB and the principal CPT code, remains a viable approach to routine surgical risk assessment, an advanced version of the RC, based on the CATB algorithm and accommodating multiple CPT codes, may provide more accurate estimates.
The Utility of Follow-up Transthoracic Echocardiogram to Screen for Severe Portopulmonary Hypertension (POPH) in Patients Granted POPH Model for End-stage Liver Disease (MELD) Exceptions
Authors: del Valle Kathryn T. , Kay Dana , Krowka Michael J. , Runo James R. , Sadd Corey , Heimbach Julie K. , Cartin-Ceba Rodrigo , Cajigas Hector R. , Burger Charles D. , Moss John E. , DuBrock Hilary M. 
Published: February 2025

Background.
The current model for end-stage liver disease (MELD) exception policies for portopulmonary hypertension (POPH) require serial right heart catheterizations (RHCs) every 3 mo to maintain exception points. RHC is necessary for the initial diagnosis of POPH, but the utility of serial catheterizations has not been studied. In patients with POPH MELD exceptions, we sought to compare noninvasive and invasive hemodynamics and determine the sensitivity of echocardiography for the detection of hemodynamically severe POPH that would preclude liver transplant.

Methods.
We performed a single-center retrospective cohort study of patients with POPH MELD exceptions who underwent liver transplant from December 2008 to January 2024. Results were validated at an external center. Echocardiograms and RHCs performed within 1 mo were compared. Pearson correlation coefficient and Bland-Altman plots assessed the association between echocardiogram and RHC variables. We examined varied echocardiographic parameters to optimize sensitivity for the detection of hemodynamically severe POPH.

Results.
Twenty-two individuals underwent 60 follow-up RHCs with paired echocardiograms. Right ventricular systolic pressure (RVSP) and cardiac index estimated with echocardiogram were not strongly correlated with RHC measurements at follow-up (RVSP and RHC pulmonary artery systolic pressure: R = 0.30, P = 0.02; cardiac index: R = 0.17, P = 0.21). However, echocardiograms with RVSP ≥48 mm Hg had 100% sensitivity for detecting hemodynamically severe POPH, with 100% negative predictive value. In external validation of 13 paired echocardiograms and RHCs, our algorithm had 64% specificity and 100% negative predictive value.

Conclusions.
Although echocardiogram and RHC hemodynamic estimates were not strongly correlated, these results could potentially negate the current requirement for repeat RHC every 3 mo to maintain POPH MELD exception.
State-of-the-art gene therapy in epilepsy
Authors: Walker Matthew C. 
Published: February 2025

Purpose of review
Gene therapy in epilepsy has undergone a rapid expansion in recent years. This has largely been driven by both advances in our understanding of epilepsy genetics and mechanisms, and also significant advances in gene therapy tools, in particular safe and effective viral vectors. Epilepsy remains an ideal target disease for gene therapy and this review highlights recent developments in this area.

Recent findings
There have been continued advances in the development of antisense oligonucleotide therapies to knock down genes in the treatment of monogenic epilepsies with some now entering clinical trial. However, the greatest recent advances have been in vector gene therapy, which offers a more permanent solution by delivering therapeutic genes directly to the brain as a one-off therapy. In particular, there has been a growth in methods that target focal epilepsy. Such promising approaches close to or in clinical trial include expressing NPY and its Y2 receptor, knocking-down GluK5, a kainate receptor subunit, and the over-expression of Kv1.1, an endogenous potassium channel.
In the future, it is likely that we will take advantage of approaches of regulating more precisely network excitability by using methods such as optogenetics, designer receptors exclusively activated by designer drugs (DREADDs), ‘inhibitory’ glutamate receptors activated by excessive glutamate spill-over, and activity-dependent promoters, which target gene expression to the ‘hyperactive’ neurons.

Summary
Gene therapies offer a novel approach to the treatment of not just genetic epilepsies but any form of epilepsy and may in the future offer an alternative to drug and surgical therapies, allowing more precise, permanent and targeted treatment with fewer adverse effects.
Interim Effectiveness of the Influenza Vaccine for the 2024-2025 Respiratory Viral Season
Authors: Shrestha Nabin K. , Burke Patrick C. , Nowacki Amy S. , Gordon Steven M. 
Published: February 2025

ABSTRACTBackgroundThe purpose of this study was to evaluate the effectiveness of the influenza vaccine during the 2024-2025 viral respiratory season.MethodsEmployees of Cleveland Clinic in employment in Ohio on October 1, 2024, were included. The cumulative incidence of influenza among those in the vaccinated and unvaccinated states was compared over the following weeks. Protection provided by vaccination (analyzed as a time-dependent covariate) was evaluated using Cox proportional hazards regression. The analysis was adjusted for age, sex, job type, employment location, and eagerness to get vaccinated.ResultsAmong 53321 employees, 43771 (82.1%) had received the influenza vaccine by the end of the study. Influenza occurred in 324 (0.6%) during the study. In an analysis adjusted for age, sex, job type, employment location, and eagerness to get vaccinated, the risk of influenza was not significantly different between the vaccinated and unvaccinated states (HR, 1.10; 95% C.I., .77 - 1.57;P= 0.59), yielding a calculated vaccine effectiveness of −10.1% (95% C.I. −57.0 - 22.7%).ConclusionsThis study has been unable to find that the influenza vaccine given to working-aged adults has provided protection overall against influenza during the 2024-2025 respiratory viral season thus far.SummaryAmong 53321 working-aged Cleveland Clinic employees, we were unable to find that the influenza vaccine has been effective in preventing infection during the 2024-2025 respiratory viral season thus far.
xOmicsShiny: an R shiny application for cross-omics data analysis and pathway mapping
Authors: Gao Benbo , Sun Yu H. , Zhang Xinmin , Lin Tinchi , Li Wei , Admanit Romi , Zhang Baohong 
Published: February 2025

AbstractSummaryWe developed xOmicsShiny, a feature-rich R Shiny-powered application that enables biologists to fully explore omics datasets across experiments and data types, with an emphasis on uncovering biological insights at the pathway level. The data merging feature ensures flexible exploration of cross-omics data, such as transcriptomics, proteomics, metabolomics, and lipidomics. The pathway mapping function covers a broad range of databases, including WikiPathways, Reactome, and KEGG pathways. In addition, xOmicsShiny offers several visualization options and analytical tasks for everyday omics data analysis, namely, PCA, Volcano plot, Venn Diagram, Heatmap, WGCNA, and advanced clustering analyses. The application employs customizable modules to perform various tasks, generating both interactive plots and publication-ready figures. This dynamic, modular design overcomes the issue of slow loading in R Shiny tools and allows it to be readily expanded by the research and developer community.Availability and implementationThe R Shiny application is publicly available at:http://xOmicsShiny.bxgenomics.com. Researchers can upload their own data to the server or use the pre-loaded demo dataset. The source code, under MIT license is provided athttps://github.com/interactivereport/xOmicsShinyfor local installation. A full tutorial of the application is available athttps://interactivereport.github.io/xOmicsShiny/tutorial/docs/index.html.Contactyuhenry.sun@biogen.comorbaohong.zhang@biogen.comSupplementary dataSupplementary data are available atbioRxivonline.
Model predictive game control for personalized and targeted interactive assistance
Authors: Hafs Abdelwaheb , Farr Anaïs , Verdel Dorian , Bruneau Olivier , Burdet Etienne , Berret Bastien 
Published: February 2025

AbstractContact robots are increasingly used to assist humans in physical training and manufacturing tasks. However, the effectiveness of current systems is limited as their control focuses on the system performance without explicitly considering the upcoming human user’s control. Here we present a differential game-based controller for contact robots that ensures optimal interaction with the human user by predicting their control during movement while considering their inherently finite planning horizon. Using this model-predictive game (MPG) controller, we systematically investigated human-robot co-adaptation in experiments, demonstrating that: (a) interaction with MPG remains stable for all participants while effectively reducing human effort; (b) the robot adapts to human behavior, identifying and characterizing individual motor control strategies that remain consistent over time and may be used as control biomarkers; (c) the human adapts to the robot’s behavior, and their interaction behavior can be modulated through an assistance meta-parameter. These findings indicate that humans can understand and adapt to a partner’s control strategy during movement, thereby exhibiting behavior consistent with game theory principles. Furthermore, the ability of the assistance meta-parameter to guide human users toward specific interaction behaviors can be used to develop versatile robot-assisted learning systems for physical training and rehabilitation.
Learning single-cell spatial context through integrated spatial multiomics with CORAL
Authors: He Siyu , Bieniosek Matthew , Song Dongyuan , Zhou Jingtian , Chidester Benjamin , Wu Zhenqin , Boen Joseph , Sharma Padmanee , Trevino Alexandro E. , Zou James 
Published: February 2025

AbstractCellular organization is central to tissue function and homeostasis, influencing development, disease progression, and therapeutic outcomes. The emergence of spatial omics technologies, including spatial transcriptomics and proteomics, has enabled the integration of molecular and histological features within tissues. Analyzing these multimodal data presents unique challenges, including variable resolutions, imperfect tissue alignment, and limited or variable spatial coverage. To address these issues, we introduce CORAL, a probabilistic deep generative model that leverages graph attention mechanisms to learn expressive, integrated representations of multimodal spatial omics data. CORAL deconvolves low-resolution spatial data into high-resolution single-cell profiles and detects functional spatial domains. It also characterizes cell-cell interactions and elucidates disease-relevant spatial features. Validated on synthetic data and experimental datasets, including Stero-CITE-seq data from mouse thymus, and paired CODEX and Visium data from hepatocellular carcinoma, CORAL demonstrates robustness and versatility. In hepatocellular carcinoma, CORAL uncovered key immune cell subsets that drive the failure of response to immunotherapy, highlighting its potential to advance spatial single-cell analyses and accelerate translational research.