bluuebunny/crossref_metadata_2025_split huggingface dataset:
Keepers of the Academic Mission: Calling All Faculty
Authors: Pellegrini Vincent D. , Babbott Stewart 
Published: February 2025

Abstract
Academic medical centers expand their patient care mission through mergers often with nonacademic health care organizations to create more clinical revenue and a larger financial margin with the intent of cross-subsidizing the academic mission. Ironically, an unintended consequence of governance changes implicit in such mergers is the marginalization of the academic mission. Historically, the education and research missions have been effectively cross-subsidized by the medical school dean from the margin derived from the faculty clinical practice plan. Yet, in many merged entities the faculty practice is subsumed under the health system, where its margin no longer directly accrues to the school. Concurrent shifts in health system governance have removed clinical enterprise oversight from the dean and chairs, effectively assigning financial support of education and research to the health system where it competes with a strong appetite to grow the clinical enterprise. Likewise, faculty are conscripted to more clinical service rather than encouraged to engage in academic endeavors. Consequently, the vigor of the education and research missions has been compromised in academic health system mergers. This circumstance invites critical review of the fundamental concept of academic medical center mergers and their resulting unintended consequences for the academic mission and faculty well-being to inform the wisdom of continuing this trend. A unified cadre of university leaders, deans, and faculty are needed to advocate for greater reinvestment of the margin in teaching and research efforts. Concurrently, academic medicine must develop more academic physicians committed to the academic mission as leaders of health systems. Taken together, these actions can reinforce that funding the academic mission must be an obligation rather than an option for academic health systems. Nothing less than the future of academic medicine, the well-being of faculty and learners, and the health of the nation depend on it.
Hypophosphatemia as a Predictor of Pancreatic Necrosis in Acute Alcohol Induced Pancreatitis
Authors: Nasir Syed Alishan , Pandya Deep , Chambers Ethan , Zubair Sarah , Kanneganti Sri Prathima , Hopkins Reid , Mangla Rakhee , Anand Naveen 
Published: February 2025

Objective:
Pancreatic necrosis is a catastrophic complication of acute pancreatitis and is associated with increased morbidity and mortality. While there is no objective means to predict pancreatic necrosis, recent studies have identified serum phosphate levels as a contributor in the disease process with worse outcomes noted in patients with low serum phosphates. We aimed to determine if there was a relationship between low serum phosphate levels and the risk of developing pancreatic necrosis in patients with acute alcoholic pancreatitis (AAP).

Methods:
Health care records from patients admitted between January 2017 to December 2022 for acute alcoholic pancreatitis were retrospectively reviewed. These patients were categorized based on their phosphate levels within 48 hours of admission: normal phosphate levels (2.8-4.5 mg/dL) and hypophosphatemia (<2.8 mg/dL). Imaging findings from hospital stays were examined to identify cases of pancreatic necrosis. These cases were then compared across patients with normal and low phosphate levels.

Results:
Among the 207 patients admitted for acute alcoholic pancreatitis, 67 met the inclusion and exclusion criteria. Of these, 37 patients exhibited serum phosphate levels below 2.8 mg/dL, while 30 maintained levels between 2.8 and 4.5 mg/dL within the first 48 hours of admission. Of the patients in the hypophosphatemia group 27.02% were noted to develop pancreatic necrosis during hospital stay compared to only 6.66% in the normal phosphate group (P-value: 0.029). Additionally, those that developed necrosis had an overall lower mean phosphate level of 2.13 mg/dL compared to the mean phosphate level of 2.60 mg/dL (P-value: 0.0521) in patients without necrosis. The median duration of hospital stay (P-value: 0.65) and rate of intensive care unit (ICU) admission (P-value: 0.41) were similar in both groups.

Conclusion:
Early hypophosphatemia during admission for AAP was associated with increased risk of developing pancreatic necrosis, however it may not affect overall length of hospital stay or rate of ICU admission.
Promoting Pre-Exposure Prophylaxis to Gay, Bisexual, and Other Men who Have Sex with Men in the US Deep South: A Qualitative Exploration of Promotion Perceptions and Preferences
Authors: Gravett Ronnie M. , Tucker Joseph D. , Matthews Lynn T. , Van Der Pol Barbara , McCollum Greer , Ong Jason J. , Marrazzo Jeanne , Elopre Latesha 
Published: February 2025

Abstract

Background
Effective HIV pre-exposure prophylaxis (PrEP) promotion is critical to mitigate PrEP disparities, yet there are gaps in understanding how gay, bisexual, and other men who have sex with men (GBM) respond to and prefer PrEP promotion. The Deep South of the United States, a region with high HIV rates and low PrEP uptake, has unique contextual factors that stifle effective PrEP provision and uptake, which could be overcome with effective PrEP promotional messaging.

Methods
We conducted an exploratory qualitative study grounded in Andersen’s Behavioral Model for Healthcare Utilization. We recruited HIV-negative GBM, aged 18-39 years, from social media, dating apps, and community outreach to complete semi-structured interviews to explore perceptions of and preferences for PrEP promotion. Interview transcripts were inductively and deductively coded for thematic analysis.

Results
40 participants completed interviews (median age 28 years, 68% Black, 48% current PrEP users). Three themes emerged: 1) the role of different identities with sub-themes emphasizing diversity to reduce stigma and improve relatability, 2) interpersonal relationships, i.e., friends, partners, and family, affect PrEP promotion, and 3) reduced emphasis on HIV risk in promotions.

Conclusion
To see behavior change for seeking PrEP knowledge and PrEP uptake, PrEP promotions must evolve to improve diversity to foster relatability and reduce stigma, harness social networks to efficiently transmit messaging, and tactfully discuss risk behaviors without compounding stigma.
Machine-learning random forest algorithms predict post-cycloplegic myopic corrections from noncycloplegic clinical data
Authors: Hao Yansong , Wang Xianjiang , Sun Bin , Li Jinyu , Zhang Yuexin , Jiang Shanhao 
Published: February 2025

SIGNIFICANCE
Machine learning random forest algorithms were used to predict objective refractive outcomes after cycloplegic refraction using noncycloplegic clinical data. A classification model predicted post-cycloplegic myopia and could be useful in screening, and a second regression model predicted post-cycloplegic refractive and could provide a useful objective starting point in noncycloplegic subjective refractions.

PURPOSE
A classification model sought to predict post-cycloplegic myopia using noncycloplegic clinical data to enhance myopia screening accuracy, whereas the regression model looked to predict objective refraction outcomes after cycloplegia for use as a starting point for noncycloplegic subjective refraction.

METHODS
A cross-sectional study included data from 2483 eyes. Pre-refraction measurements, such as uncorrected visual acuity, axial length, and corneal curvature radius, were recorded. After cycloplegia, the spherical equivalent was measured. Random forest–based classification and regression models were established with input variables including age, gender, axial length, corneal curvature radius, axial length–to–corneal curvature radius ratio, spherical equivalent, and uncorrected visual acuity. Model performance was assessed using various metrics.

RESULTS
The random forest classification model achieved high out-of-bag validation accuracy (92%), cross-validation accuracy (93%), external validation accuracy (94%), and precision (95%). The external validation sensitivity was 93%, and specificity was 95%. The regression model internal validation showed an out-of-bag validation R
2 of 0.86, root mean square error (RMSE) of 0.66, and mean absolute error of 0.49. The 10-fold cross-validation R
2 was 0.87, the RMSE was 0.64, and the mean absolute error was 0.48. In the external validation, R
2 was 0.88, the RMSE was 0.63, and the mean absolute error was 0.48.

CONCLUSIONS
By analyzing noncycloplegic clinical data, the classification model enables earlier detection of myopia, supporting timely intervention and management. The regression model aims to accurately predict post-cycloplegia myopic corrections, providing reliable initial data for subjective refraction. This could help optometrists perform noncycloplegic subjective refraction more efficiently and is particularly relevant in China, where retinoscopy is not yet fully popularized and many school students decline cycloplegic refraction due to academic pressures and limited free time, primarily because it requires a follow-up the next day.
Social Impacts of Multi-City HIV Research Participation Among Sexual and Gender Expansive Individuals in Kazakhstan
Authors: Vinogradov Vitaliy , Lee Yong Gun , Zhakupova Gulnara , Mergenova Gaukhar , Davis Alissa , Paine Emily Allen , Reeder Kelsey G. , Laughney Caitlin I. , Sung Jimin , Primbetova Sholpan , Terlikbayeva Assel , Sugarman Jeremy , Wu Elwin 
Published: February 2025

Background:
Sexual and gender expansive (SGE) individuals in Kazakhstan are disproportionately affected by HIV yet stigma and discrimination pose ethical and practical challenges for HIV prevention research involving them. Although researchers are tasked with ensuring that risks of research participation are reasonable in relation to its benefits, participant-reported risks and benefits of research participation—including negative (NSIs) and positive social impacts (PSIs) on personal relationships, social status, health, and other life domains—among SGE populations have received little attention.

Methods:
We examined NSIs and PSIs of research participation among SGE individuals in a three-city HIV prevention study in Kazakhstan at the trial’s follow-up visits. We analyzed responses from 579 unique participants who completed a total of 2648 follow-up visits over the 36-month study period (2019–2022).

Results:
Overall, NSIs were rare: 9 (2%) participants reported NSIs during the study; nearly no NSIs (

=0.0037, SD=0.03) were reported at follow-up visits. These few NSIs included ‘trouble with friends, family, or acquaintances’ and ‘other’. By contrast, PSIs were extensive: 515 (89%) participants reported PSIs during the study; an average of almost five PSIs (

=4.8, SD=3.4) were reported at follow-up visits. The most frequently reported PSIs were ‘gained knowledge’, ‘improvement in HIV-related issues’, and ‘improvement in mental health’.

Conclusions:
Our findings demonstrate the potential for HIV prevention research to be associated with PSIs for SGE individuals experiencing stigmatization and discrimination. Future research should address NSIs, particularly confidentiality breaches and interpersonal challenges, within HIV prevention research to minimize risks and burdens of participation.
Clinical Application of 68Ga-Pentixafor PET/CT for the Detection of Thymoma: A Pilot Study
Authors: Wang Rongxi , Gao Xuehan , Peng Xingtong , Wang Jiarou , Xiang Jialin , Li Linlin , Jia Chenhao , Chen Jingci , Du Xin , Guo Chao , Zhou Xiaoyun , Zheng Yumin , Zhu Zhaohui , Chen Yeye , Li Shanqing 
Published: February 2025

Purpose:
This study was designed to evaluate 68Ga-pentixafor, which targets C-X-C chemokine receptor 4 (CXCR4), in the noninvasive diagnosis of thymomas.

Patients and Methods:
With institutional review board approval and signed informed consent, 32 patients with thymic masses were enrolled in this study, and all patients underwent 68Ga-pentixafor PET/CT scans.

Results:
Among the 28 patients included in the analysis, 13 patients were diagnosed with thymomas, 9 patients with cysts, and 6 patients with other anterior mediastinal masses. 68Ga-pentixafor identified all patients with thymomas (13/13, 100%), and the mean SUVmax in all 13 thymomas lesions was 13.96±8.20, which was significantly higher than that in patients with cysts (1.54±0.88) and other anterior mediastinal masses (2.59±1.68), respectively (P<0.001).

Conclusions:
The preliminary study indicates the diagnostic utility of 68Ga-pentixafor in thymomas and the differential diagnostic ability of 68Ga-pentixafor in thymomas, thymic cysts and other benign anterior mediastinal masses.
ScatTR: Estimating the Size of Long Tandem Repeat Expansions from Short-Reads
Authors: Al-Abri Rashid , Gürsoy Gamze 
Published: February 2025

AbstractTandem repeats (TRs) are sequences of DNA where two or more base pairs are repeated back-to-back at specific locations in the genome. The expansions of TRs are implicated in over 50 conditions, including Friedreich’s ataxia, autism, and cancer. However, accurately measuring the copy number of TRs is challenging, especially when their expansions are larger than the fragment sizes used in standard short-read genome sequencing. Here we introduce ScatTR, a novel computational method that leverages a maximum likelihood framework to estimate the copy number of large TR expansions from short-read sequencing data. ScatTR calculates the likelihood of different alignments between sequencing reads and reference sequences that represent various TR lengths and employs a Monte Carlo technique to find the best match. In simulated data, ScatTR outperforms state-of-the-art methods, particularly for TRs with longer motifs and those with lengths that greatly exceed typical sequencing fragment sizes. When applied to data from the 1000 Genomes Project, ScatTR detected potential large TR expansions that other methods missed, highlighting its ability to better identify genome-wide characterization of TR variation. ScatTR can be accessed via:https://github.com/g2lab/scattr.
Clinical properties of the Short Mood and Feelings Questionnaire: Development of a free calculator based on a Brazilian High-Risk Cohort Study
Authors: Jobim Gabriele dos Santos , do Amaral João Villanova , Gonçalves Pacheco João Pedro , Gadelha Ary , Miguel Euripedes Constantino , Affonseca Bressan Rodrigo , Pan Pedro Mario , Rohde Luis Augusto , Salum Giovanni Abrahão , Scopel Hoffmann Mauricio 
Published: February 2025

AbstractBackgroundThe Short Mood and Feelings Questionnaire (SMFQ) is a validated tool for assessing depressive symptoms in youth, though no specific cut-point exists for the Brazilian population. Item response theory (IRT) and interval likelihood ratios (ILRs) offer refined methods to monitor symptoms but involve complex calculations that hinder clinical implementation.MethodsCross-sectional data were drawn from an urban school-based sample (Brazilian High-Risk Cohort Study in 2018-2019, n=1,905, aged 14-23, 46.6% females). Diagnoses were based on Development and Well-Being Assessment (DAWBA) clinical ratings. SMFQ factor scores were estimated using IRT and transformed into T-scores. ROC curves evaluated diagnostic properties for internalizing- and externalizing-spectrum disorders. A calculator was developed to estimate post-test probabilities from T-scores using ILRs. Sensitivity analysis excluded MDD as a comorbid diagnosis.ResultsROC curve analyses suggested a sum score cut-off of >6 and a T-score of >55 for detecting MDD. The SMFQ showed good accuracy for internalizing conditions (AUC > 0.8) but low for attention and externalizing disorders (AUC < 0.7). ILRs for internalizing conditions ranged from 0.12 (95% CI: 0.07–0.19) to 29.98 (95% CI: 11.99–75), with post-test probabilities exceeding pre-test probabilities for scores above the cut-off. Sensitivity analysis confirmed findings when excluding MDD. Including ILRs significantly improved predictive models over dichotomous cut-offs.ConclusionThe application of ILRs based on IRT T-scores improved SMFQ’s predictive ability for internalizing-spectrum conditions, regardless of comorbidity. A calculator can integrate these methods into clinical practice, supporting real-time data-driven decisions.
Role of the ETV5/p38 signaling axis in aggressive thyroid cancer cells
Authors: Houl Jerry H , Bagheri-Yarmand Rozita , Kunnimalaiyaan Muthusamy , Miranda Mendez Paola , Kidd Joseph L , Dadbin Ali , Jurado-Ruiz Andrea , Parekh Parag A , Henderson Ying C , Chari Nikhil S , Thennavan Aatish , Powell Reid T , Stephan Clifford C , Zhao Xiao , Maniakas Anastasios , Nurieva Roza , Busaidy Naifa L , Cabanillas Maria E , Dadu Ramona , Zafereo Mark , Wang Jennifer R , Lai Stephen Y , Hofmann Marie-Claude 
Published: February 2025

AbstractPoorly differentiated thyroid cancer (PDTC) and anaplastic thyroid cancer (ATC) patients face a much poorer prognosis compared to those with differentiated thyroid cancers. Around 25% of PDTCs and 35% of ATCs carry theBRAFV600Emutation, which constitutively activates the MAPK pathway, a key driver of cell growth. While combining BRAF and MEK inhibitors can shrink tumors, resistance often develops. The exact cause of this resistance remains unclear.We previously found that in PDTC and ATC cells theBRAFV600Emutation is strongly linked to the expression of ETV5, a transcription factor that is downstream of the MAPK pathway. In the current study, we observed a significant association between ETV5 expression and the activation of p38, a central component of the MAPK14 pathway. Upon reduction of ETV5 levels, p38 expression and activation also decreased, along with its upstream regulators MKK3/MKK6. This suggests that the MAPK and p38/MAPK14 pathways are interconnected and that p38 has oncogenic properties in these cancers.Using high-throughput screening, we established that combining p38 inhibitors with the BRAF inhibitor dabrafenib showed strong synergyin vitro, including in cells resistant to dabrafenib and trametinib that had acquired a secondaryTP53mutation. We then tested this combination in a genetically engineered mouse model (GEMM) of ATC.Overall, our findings suggest an oncogenic link between the MAPK and p38/MAPK14 pathways and that combining p38 pathway inhibitors with dabrafenib targeted therapy could improve treatment outcomes for aggressive thyroid cancers. However, more specific and effective p38 inhibitors are needed to fully harness this potential.
Corticospinal, reticulospinal, and motoneuronal contributions to fatigability during a sustained contraction of the elbow flexors
Authors: Hayman Oliver , Brownson-Smith Rosiered , Atkinson Elliott I , Spillane Padraig , Baker Stuart , Goodall Stuart , Howatson Glyn , Thomas Kevin , Ansdell Paul 
Published: February 2025

AbstractSynaptic input to the motoneuron pool is altered during fatiguing muscle contractions. In humans, the corticospinal tract is often studied, with equivocal findings regarding its role in the reduction of force. To date, the involvement of the reticulospinal tract during states of fatigue has not been explored.Fourteen participants (28±6 years, nine males) visited the laboratory twice, first for a familiarisation, then an experimental trial. Participants completed a 5-min sustained elbow flexor contraction at an intensity eliciting 40% of the EMG recorded during a maximal isometric voluntary contraction (MVC). Before, during, and after the contraction, transcranial magnetic stimulation and electrical cervicomedullary stimulation were used to elicit motor evoked potentials (MEPs) and cervicomedullary evoked potentials during the silent period (SP-CMEPs) respectively, with CMEPs also being evoked in combination with a startling acoustic sound (CMEPcon). Electrical stimulation of the brachial plexus was used to evoke maximal compound action potentials of the elbow flexors (Mmax).The 5-min contraction induced a 53% loss of force (p<0.001), with no change in background EMG (∼4% Mmax,p=0.293). Neither MEP amplitude (p=0.246) nor CMEPcon ratio (p=0.489) were altered during the contraction. Whereas CMEP and SP-CMEP amplitudes were reduced by ∼20 and 50%, respectively (p<0.001) and remained depressed post-task.The results suggest that neither corticospinal nor reticulospinal tract excitability was altered during a 5-min constant-EMG task at 40% maximal EMG. Instead, the aetiology of the neural contribution to fatigability appeared to be primarily related to the loss of motoneuron excitability.
Synergistic RAS-MAPK and AKT Activation in MYC-Driven Tumors via Adjacent PVT1 Rearrangements
Authors: Tiwari Ashutosh , Paithane Utkarsha , Friedlein Jordan , Tashiro Kojiro , Saulnier Olivier , Barbosa Karina , Trinh Quang , Hall Bryan , Saha Shrawantee , Soni Aditi , Nakashima Takuma , Bobkov Andrey , Fujimoto Lynn Miya , Murad Rabi , Maurya Svetlana , Saraswat Mayank , Sarmashghi Shahab , Lange Joshua T. , Wu Sihan , Masihi Meher Beigi , Ghosh Srija , Hemmati Gazal , Chapman Owen , Hendrikse Liam , James Brian , Luebeck Jens , Eisemann Tanja , Tzaridis Theophilos , Rohila Deepak , Leary Robyn , Varshney Jyotika , Konety Badrinath , Dehm Scott M. , Kawakami Yasuhiko , Beroukhim Rameen , Largaespada David A , Stein Lincoln , Chavez Lukas , Suzuki Hiromichi , Weiss William A , Zhao Jianhua , Deshpande Aniruddha , Wechsler-Reya Robert J. , Taylor Michael D. , Bagchi Anindya 
Published: February 2025

ABSTRACTMYC-driven (MYC+) cancers are aggressive and often fatal. MYC dysregulation is a key event in these cancers, but overexpression of MYC alone is not always enough to cause cancer.Plasmocytoma Variant Translocation 1(PVT1), a long non-coding RNA (lncRNA) adjacent to MYC on chromosome 8 is a rearrangement hotspot in many MYC+ cancers. In addition to being co-amplified with MYC, the genomic rearrangement at PVT1 involves translocation, which has had obscure functional consequences. We report that translocation at the PVT1 locus cause asymmetric enrichment of 5’-PVT1 and loss of 3’-PVT1. Despite being classified as a non-coding RNA, the retained 5’ region of PVT1 generates a circular RNA (CircPVT1) that codes for the novel peptide we call Firefox (FFX). FFX augments AKT signaling and synergistically activates MYC and mTORC1 in these cells. Further, the 3’ end of PVT1, which is lost during the translocation, codes for a tumor-suppressing micropeptide we named as Honeybadger (HNB). We demonstrate that HNB interacts with KRAS and disrupts the activation of KRAS effectors. Loss of HNB leads to activation of RAS/MAPK signaling pathway, and enhances MYC stability by promoting phosphorylation of MYC at Ser62. These findings identify PVT1 as a critical node that synchronizes MYC, AKT, and RAS-MAPK activities in cancer. Our study thus identifies a key mechanism by which rearrangements at the PVT1 locus activate additional oncogenic pathways that synergize with MYC to exacerbate the aggressiveness of MYC+ cancers. This newfound understanding explains the poor prognosis associated with MYC+ cancers and offers potential therapeutic targets that could be leveraged in treatment strategies for these cancers.