bluuebunny/crossref_metadata_2025_split huggingface dataset:
Corticosteroids in severe alcohol-associated hepatitis? Not so fast: A systematic review of randomized controlled trials
Authors: Shi Michael A. , Pungwe Prisca , Comer Lauren LM. , Balakrishnan Maya , Lee Tzu-Hao , Cholankeril George , Patidar Kavish R. , Flores Avegail G. , Shah Vijay H. , Bataller Ramon , Asrani Sumeet K. , Arab Juan P. , Kanwal Fasiha , Hernaez Ruben 
Published: January 2025

Background:
Severe alcohol-associated hepatitis (AH) is rising in incidence with a high mortality burden. While corticosteroids are recommended for eligible patients with severe AH, no guidance exists for the timing of steroid initiation, tapering regimens, and surveillance of adverse events.

Objective:
We aim to systematically review these variables and provide evidence-based recommendations for the inpatient and outpatient management of severe AH.

Design:
We performed a literature search from inception to 5/30/2024 to include clinical trials published in full form and assessed the quality of evidence using the Cochrane Risk of Bias tool. Data were collected on the timing of initiation, rate, and complications following steroid therapy, and taper regimens in the setting of severe AH.

Results:
Of 28 studies that fulfilled our inclusion criteria, median time from admission to steroid initiation was 6.5 days. The most common steroid dosing regimen was prednisolone 40 mg daily for 28 days. Twenty-five studies containing 3,196 subjects reported adverse events, with exactly 50% in the steroid arm and the other half in the comparison arm. Infections, gastrointestinal bleeds, and renal impairment were the most frequently reported adverse events. Most infections occurred within the first month of the study. A two-week steroid taper was the most frequently reported regimen.

Conclusion:
We recommend taking up to a week to systematically and thoroughly evaluate patients before initiating steroids, and vigilant monitoring in the first month of treatment. We also recommend the lowest possible steroid exposure with a two-week steroid taper and close outpatient follow-up.
Neurobehavioral Symptoms Partially Mediate the Effects of Depression and PTSD on Participation for Veterans With Mild Traumatic Brain Injury: A Cross-Sectional Study
Authors: Wyrwa Jordan M. , Brenner Lisa A. , Yan Xiang-Dong , Schneider Alexandra L. , Burke Lindsay , King Samuel E. , Forster Jeri E. , Kinney Adam R. 
Published: January 2025

Objective:
To examine whether neurobehavioral symptoms mediate the relationship between comorbid mental health conditions (major depressive disorder [MDD] and/or posttraumatic stress disorder [PTSD]) and participation restriction among Veterans with mild traumatic brain injury (mTBI).

Setting:
Veterans Health Administration (VHA).

Participants:
National sample of Veterans with mTBI who received VHA outpatient care between 2012 and 2020.

Design:
Secondary data analysis of VHA clinical data. We specified a latent variable path model to estimate relationships between: (1) comorbid mental health conditions and 3 latent indicators of neurobehavioral symptoms (vestibular-sensory; mood-behavioral; cognitive); (2) latent indicators of neurobehavioral symptoms and 2 latent indicators of participation restriction (social and community participation; productivity); and (3) comorbid mental health conditions and participation restriction.

Main Measures:
International Classification of Diseases codes, Neurobehavioral Symptom Inventory, and Mayo-Portland Adaptability Inventory Participation Index to measure mental health conditions, neurobehavioral symptoms, and participation restrictions, respectively.

Results:
Indirect effect estimates indicated that comorbid MDD and/or PTSD was associated with greater social and community participation restrictions, as mediated by mood-behavioral (β = .22-.33; 99% CI 0.18-0.4; small to medium effect) and cognitive symptoms (β = .08-.13; 99% CI 0.05-0.18; small effect), and with greater productivity restrictions, as mediated by vestibular-sensory (β = .06-.11; 99% CI 0.04-0.15; small effect) and cognitive symptoms (β = .08-.13; 99% CI 0.05-0.18; small effect). Direct effect estimates indicated that comorbid MDD and/or PTSD was associated with greater challenges with both social and community participation (β = .19-.40; 99% CI 0.12-0.49; small to medium effect) and productivity (β = .08-.44; 99% CI −0.02 to 0.55; small to medium effect).

Conclusion:
Neurobehavioral symptoms partially mediated the impact of MDD and/or PTSD on participation restrictions among Veterans with mTBI. These findings advance the understanding of explanatory mechanisms underlying participation challenges among Veterans with comorbid mTBI and mental health challenges, thereby informing the development of tailored intervention strategies.
Assessing Traumatic Brain Injury in Refugees: Feasibility, Usability, and Prevalence Insights From a US-Based Clinical Sample
Authors: Sherman Rosa Sofia , Nadal Rodrigo , Saadi Altaf 
Published: January 2025

Objective:
This study assessed (1) the feasibility and usability of traumatic brain injury (TBI) assessment using the Ohio State University TBI Identification Method (OSU-TBI-ID) in a sample of English and Spanish-speaking refugees and asylum seekers (hereafter refugees), and (2) the prevalence and characteristics of TBI in this population.

Setting and Participants:
Refugees seeking care from Massachusetts General Hospital (MGH) Asylum Clinic, the MGH Chelsea HealthCare Center, and other asylum programs in the Greater Boston Area.

Design and Main Measures:
Bilingual clinical research coordinators screened 158 English and Spanish-speaking refugees using the OSU-TBI-ID. A “positive” screen for TBI was made if a participant reported loss of consciousness (LOC) or being dazed or confused following a head injury, with determinations of mild, moderate, and severe TBI based on established metrics of TBI severity using duration of LOC. We conducted descriptive statistics of the sample demographics and screening outcomes, including group comparisons between those with and without TBI and associated demographic characteristics.

Results:
The mean age was 36.8 years (SD: 9.1), with participants predominantly from Latin America and the Caribbean (51%), followed by Sub-Saharan Africa (35%). Less than half (43%) identified as men. The majority (59%) screened positive for having experienced at least 1 TBI in their lifetime. Among those with a TBI history, nearly three-quarters (73%) had a mild TBI, and about a third (38%) had sustained a moderate-to-severe TBI. A majority (56%) had more than 1 TBI and about 40% had sustained a childhood TBI. The most common mechanisms of injury were interpersonal assault (55%) and blunt trauma by an object (46%). There were no significant statistical differences in demographics and TBI characteristics.

Conclusion:
Our findings demonstrate the feasibility and usability of the OSU-TBI-ID in a sample of refugees. We call for greater and improved detection of TBI among refugees to ensure they receive the optimal care they need.
Removal of band keratopathy involving a LASIK flap with Amoils brush and ethylenediaminetetraacetic acid chelation
Authors: Khambati Alisha , Shean-Young Lee Patrick , Khambati Shabbir , McDermott Mark 
Published: January 2025

Introduction:
To report a new method for ethylenediaminetetraacetic acid (EDTA) chelation with the use of an Amoils brush to debride calcium band keratopathy involving a laser-assisted in situ keratomileusis (LASIK) flap.

Patient and Clinical Findings:
A 77-year-old man with a history of bilateral LASIK presented with visually significant band keratopathy involving the flap.

Diagnosis, Intervention, and Outcomes:
We report the successful removal of the band keratopathy using EDTA chelation and debridement with an Amoils brush to prevent flap dislodgment. 1 month postoperatively, the patient experienced an improvement in corrected distance visual acuity with resolution of the band keratopathy.

Conclusions:
Debridement using an Amoils brush, in conjunction with EDTA chelation, is an effective and safe treatment for visually significant band keratopathy involving a LASIK flap.
Antiretroviral therapy in people with HIV and end-stage kidney disease
Authors: Spencer Matthew , Pieri Christopher , Hamzah Lisa , Popoola Joyce , Shah Sapna , Jones Rachael , Levy Jeremy , Murphy Maurice , Booth John , Post Frank A. 
Published: January 2025

Objective:
To summarize antiretroviral therapy (ART) use in the setting of end-stage kidney disease (ESKD).

Design:
Cross-sectional analysis.

Methods:
Descriptive analysis of ART regimens and dose of nucleoside/nucleotide reverse-transcriptase inhibitors (NRTI) in people with HIV and ESKD (dialysis, kidney transplantation, or estimated glomerular filtration rate (eGFR) <15 mL/min/1.73m2) receiving HIV and renal care at five London centres. Exposures of interest were use of dual/unboosted ART regimens and higher than recommended doses of renally-cleared NRTI.

Results:
A total of 157 participants were included (median age 55 years, 66% male, 84% black ethnicity, median CD4 cell count 382 cells/mm3, 99% HIV RNA <200 copies/mL). Fifty-eight (37%) were on dual/unboosted ART regimens, mainly dolutegravir/lamivudine. Participants on dual/unboosted ART had similar rates of HIV suppression as those on triple-ART. Two participants currently virologically controlled on triple-ART had previously failed to suppress on dual/unboosted ART (dolutegravir/rilpivirine and dolutegravir/lamivudine [50 mg]). Lamivudine doses were higher than recommended in 75 (77%) and lower than recommended in 8 (8%) participants. Full dose lamivudine (300 mg daily) was used by 24 (32%) participants with eGFR <30 mL/min/1.73m2. None of those currently on reduced-dose lamivudine had required dose reductions for previous toxicity concerns.

Conclusions:
Dual/unboosted ART regimens such as dolutegravir/lamivudine provide robust viral efficacy in the setting of ESKD, and higher than recommended, including full-dose, lamivudine was well tolerated. The dolutegravir/lamivudine (300 mg) fixed-dose combination provides a single-tablet regimen for use across the eGFR spectrum, avoids under-exposure to lamivudine, and merits further evaluation in this population.
Assessing Readability of Patient Education Materials on Adult-Acquired Buried Penis
Authors: Thornton Sarah M. , Orgun Doruk , Bay Caroline C. , Seitz Allison J. , Poore Samuel O. 
Published: January 2025

Introduction
Adult-acquired buried penis (AABP) is an increasingly prevalent condition characterized by the penis “buried” in prepubic/suprapubic tissue. AABP affects urinary and sexual function, hygiene, and psychosocial well-being. Because many affected individuals are unfamiliar with the condition or hesitant to seek medical help, accessible, high-quality patient education materials (PEMs) are necessary. The American Medical Association recommends that PEMs be written at or below a 6th-grade reading level. This study aimed to assess the readability of the most easily accessible AABP PEMs.

Methods
After disabling user account information, the top 10 results for “buried penis treatment” from 3 search engines were collected. Academic journal articles, advertisements, and pediatric PEMs were excluded. Plain texts without graphics and extraneous information were copied to the Readability Test Tool (WebFX, Harrisburg, PA) to generate readability scores. Descriptive statistics were used to analyze the data.

Results
The top 10 results for each search engine, excluding duplicates, resulted in 12 unique articles. Of 5 readability tests used by the Readability Test Tool, the mean grade level necessary to comprehend resource content was 12.3, or about a 12th-grade level. The mean age estimated for understanding was 17.7, or an age range of 17–18 years old. Complex words comprised on average, 16.6% of a resource's material.

Conclusions
This study emphasizes the inadequate readability of current PEMs for AABP. The readability for most accessible materials exceeds the recommended reading level of at or below 6th grade. Providers should aim to publish easily comprehensible online PEMs to promote patient awareness and comprehension.
Protein profile of the Escherichia coli strain, BW25113, exposed to two novel iron-halide compounds: Fe(Hampy)2Cl4 and Fe(Hampy)2Br4
Authors: Abedin Nusrat , Wagner Sarah , Khalkar Yukta Sanjay , Johnson Zulekha , Egbowon Biola F. , Hargreaves Alan J. , Fitzpatrick Anthony J. , Miles Amanda K. , Dafhnis-Calas Felix 
Published: January 2025

Graphical abstract
Characterizing the proteomic profile of the Escherichia coli strain, BW2513, exposed to two novel iron-halide complexes: iron tetrachloride and iron tetrabromide.
Biosynthetic plasticity enables CD8+ T cell functional resilience under nutrient stress
Authors: Scaglione Michael , Knight Montana , Trihemasava Krittin , Rome Kelly , Archambault Anne-Sophie , Oh Juhee , Tanaka Erin , Hall Elise , Van Le Tran Ngoc , Lines Caleb L. , Goldspiel Brian , Fazelinia Hossein , Queriault Clemence , Turner Lucien , Parnaik Tanay , Xu Jimmy , Spruce Lynn A. , Bartman Caroline , Mesaros Clementina , Klein Geltink Ramon I. , Conn Crystal S. , Bailis Will 
Published: January 2025

Summary / AbstractTo maintain lineage-specific functions, cells must acquire and allocate nutrients across diverse cellular processes, even in metabolically-dysregulated environments. The mechanisms allowing CD8+ T cells to maintain immune function in perturbed environments are poorly understood. We find that CD8+ T cells adapt to nutrient stresses over time, reconfiguring gene-regulatory and metabolic networks to license functional recovery. Under acute stress, T cells reorient translational programming, limiting nutrient demand while prioritizing stress-sensitive metabolic and transcriptional responses. Within these responses, the transcription factors ATF4 and CEBPG jointly establish an adaptive metabolic program, promoting amino acid synthesis and uptake while maintaining mitochondrial anaplerosis. Despite diminished energetic capacity under environmental stress, this program prevents failure of central carbon metabolism, mitigating stress amplification and cellular dysfunction to potentiate anti-tumor immunity. Altogether, we demonstrate that biosynthetic plasticity via translational and metabolic reprioritization confers functional resilience to immune cells in unfavorable environments, offering novel strategies to enhance immunotherapies.
Acoustic pH sensor for dynamic ultrasound imaging of cellular acidification
Authors: Terwiel Dion , Park Byung Min , Heiles Baptiste , Waasdorp Rick , Muñoz-Ibarra Eleonora , Ara Tarannum , Gazzola Valeria , Maresca David 
Published: January 2025

AbstractGenetically encoded pH sensors based on fluorescent proteins enable dynamic optical imaging of cellular processes such as endocytosis and exocytosis. To date, light scattering in thick tissue as well as photobleaching of fluorescent proteins prevent deep cellular imaging over sustained periods of time. To visualize intracellular pH variations across opaque organs, we introduce a genetically encoded acoustic pH sensor dubbed ‘pHonon’. We modified the outer gas vesicle protein (GvpC) of echogenic protein nanostructures via histidine point mutations. At low pH, engineered gas vesicles exhibit an increased shell stiffness which switched their acoustic response from nonlinear to linear. By combining pHonons with nonlinear ultrasound imaging, we captured dynamic deep tissue images of lysosomal acidification by macrophages in murine liver. The combination of pHonon with nonlinear ultrasound creates the possibility for basic studies of endo- and exocytic activity in deep tissue of living opaque organisms.
Deconvolution and Phylogeny Inference of Diverse Variant Types Integrating Bulk DNA-seq with Single-cell RNA-seq
Authors: Bristy Nishat Anjum , Schwartz Russell 
Published: January 2025

AbstractMotivationReconstructing clonal lineage trees (“tumor phylogenetics”) has become a core tool of cancer genomics. Earlier approaches based on bulk DNA sequencing (DNA-seq) have largely given way to single-cell DNA-seq (scDNA-seq), which offers far greater resolution for clonal substructure. Available data has lagged behind computational theory, though. While single-cell RNA-seq (scRNA-seq) has become widely available, scDNA-seq is still sufficiently costly and technically challenging to preclude routine use on large cohorts. This forces difficult tradeoffs between the limited genome coverage of scRNA-seq, limited availability of scDNA-seq, and limited clonal resolution of bulk DNA-seq. These limitations are especially problematic for studying structural variations and focal copy number variations that are crucial to cancer progression but difficult to observe in RNA-seq.ResultsWe develop a method, TUSV-int, combining advantages of these various genomic technologies by integrating bulk DNA-seq and scRNA-seq data into a single deconvolution and phylogenetic inference computation while allowing for single nucleotide variant (SNV), copy number alteration (CNA) and structural variant (SV) data. We accomplish this by using integer linear programming (ILP) to deconvolve heterogeneous variant types and resolve them into a clonal lineage tree. We demonstrate improved deconvolution performance over comparative methods lacking scRNA-seq data or using more limited variant types. We further demonstrate the power of the method to better resolve clonal structure and mutational histories through application to a previously published DNA-seq/scRNA-seq breast cancer data set.AvailabilityThe source code for TUSV-int is available athttps://github.com/CMUSchwartzLab/TUSV-INT.git
Class-agnostic annotation of small RNAs balances sensitivity and specificity in diverse organisms
Authors: Johnson Nathan R. , Gonzalez-Toro Fabian , Bernal Gomez Barbara 
Published: January 2025

AbstractSmall RNAs (sRNAs) are important regulatory elements in eukaryotic organisms and comprise the functional elements of RNAi. Numerous classes of sRNAs have been annotated, however they vary greatly in their ease of annotation and compatibility with most annotators. Significant challenges exist for the annotation process, including variation in sRNA library quality, alignment depth, and poorly defined loci, collectively making this process difficult. Additionally, few annotators are fully agnostic to sRNA classes and may struggle identifying loci in less explored organisms (exceptional organisms, fungi). To address these problems, we present an integrated sRNA annotation suite, YASMA, which is specifically suited to finding reliable thresholds for locus annotation which balance sensitivity with specificity. By comparing YASMA with other annotators, we show that pipelines based on coverage-normalization methods have great advantages in balancing many metrics to produce a more reproducible annotation. We also demonstrate that YASMA produces more contiguous and representative loci, through the aggressive merging of similar adjacent expressed regions. Finally, we also show that the tool produces much more descriptive locus dimensions, a major advantage in species where sRNAs may be distinct or unique. Overall, we demonstrate substantial improvements in annotation accuracy, reproducibility, and description, particularly in non-model organisms and less-explored clades.
Resident Tissue Macrophages Govern Intraocular Pressure Homeostasis
Authors: Liu Katy C. , Grimsrud Aleksander O. , Suarez Maria Fernanda , Schuman Darren , De Ieso Michael L. , Kuhn Megan , Kelly Ruth A. , Mathew Rose , Kalnitsky Joan , Mack Matthias , Ginhoux Florent , Bupp-Chickering Violet , Balasubramanian Revathi , John Simon W. M. , Stamer W. Daniel , Saban Daniel R. 
Published: January 2025

SUMMARYIntraocular pressure is tightly regulated by the conventional outflow tissues, preventing ocular hypertension that leads to neurodegeneration of the optic nerve, or glaucoma. Although macrophages reside throughout the conventional outflow tract, their role in regulating intraocular pressure remains unknown. Using macrophage lineage tracing approaches, we uncovered a dual macrophage ontogeny with distinct spatial organizations across the mouse lifespan. Long-lived, resident tissue macrophages concentrated in the trabecular meshwork and Schlemm’s canal, whereas short-lived monocyte-derived macrophages, instead, were abundant around distal vessels. Specific depletion of resident tissue macrophages triggered elevated intraocular pressure and outflow resistance, linked to aberrant extracellular matrix turnover in the resistance-generating tissues of the trabecular meshwork. This dysregulated physiology and tissue remodeling were not observed when we depleted monocyte-derived macrophages. Results show ontogeny and tissue-specific macrophage function within the outflow tract, uncovering the integral homeostatic role of resident tissue macrophages in resistance-generating tissues whose dysfunction is responsible for glaucoma.
mzLearn, a data-driven LC/MS signal detection algorithm, enables pre-trained generative models for untargeted metabolomics
Authors: Pirhaji Leila , Eaton Jonah , Jeewajee Adarsh K. , Zhang Min , Morris Matthew , Karasarides Maria 
Published: January 2025

AbstractMetabolite alterations are linked to diseases, yet large-scale untargeted metabolomics remains constrained by challenges in signal detection and integration of diverse datasets for developing pre-trained metabolic models. Here, we introduce mzLearn, a data-driven algorithm for untargeted metabolomic signal detection that requires no input parameters or metabolomics expertise. mzLearn outperforms existing methods in both signal quantity and quality, effectively correcting instrument drifts across large cohorts without experimental QC samples. mzLearn detected robust metabolite signals from 20,548 blood samples from diverse studies, enabling the development of first-in-class pre-trained generative models for untargeted metabolomics. Learned metabolite representations reflected demographic data and when fine-tuned on unseen renal cell carcinoma data, improved downstream clinical and survival tasks. Metabolite representation further facilitated joint and adversarial learning for prognostic and predictive patient stratification, outperforming clinical-grade risk criteria in survival prediction. mzLearn democratizes untargeted metabolomics data and paves the way for developing foundation models for untargeted metabolomics.
MOSHPIT: accessible, reproducible metagenome data science on the QIIME 2 framework
Authors: Ziemski Michal , Gehret Liz , Simard Anthony , Castro Dau Santiago , Risch Vinzent , Grabocka Doriela , Matzoros Christos , Wood Colin , Momo Cabrera Paula , Hernández-Velázquez Rodrigo , Herman Chloe , Evans Keegan , Robeson Michael S. , Bolyen Evan , Caporaso J. Gregory , Bokulich Nicholas A. 
Published: January 2025

AbstractMetagenome sequencing has revolutionized functional microbiome analysis across diverse ecosystems, but is fraught with technical hurdles. We introduce MOSHPIT (https://moshpit.readthedocs.io), software built on the QIIME 2 framework (Q2F) that integrates best-in-class CAMI2-validated metagenome tools with robust provenance tracking and multiple user interfaces, enabling streamlined, reproducible metagenome analysis for all expertise levels. By building on Q2F, MOSHPIT enhances scalability, interoperability, and reproducibility in complex workflows, democratizing and accelerating discovery at the frontiers of metagenomics.