UFGI Publication Round-Up: Week of 11/24/2025

Rodhouse C, Wang D, Tang H, Polcz VE, Hernández-Ríos M, Yu X, Balzano-Nogueira L, Rincon JC, Charles A, Fujishima S, Vo Q, Dirain ML, Ungaro R, Nacionales DC, Zeumer-Spataro L, Langhi Prata L, Larson SD, Casadesus G, Xiao F, Wallet SM, Brusko MA, Loftus TJ, Bible L, Mohr AM, Chakrabarty P, Kladde MP, Mathews CE, Moldawer LL, Maile R, Cai G, Efron PA.

bioRxiv [Preprint]. 2025 Oct 7:2025.10.06.680736. doi: 10.1101/2025.10.06.680736.

PMID: 41278644

Residual confounding in a study of acetaminophen risk: errors resulting from dichotomized variables.

Bubb MR.

Arthritis Care Res (Hoboken). 2025 Nov 28. doi: 10.1002/acr.70000. Online ahead of print.

PMID: 41312654

Microbial associations and viruses on the risk of celiac disease (MAVRiC): a longitudinal post-hoc case-cohort study.

Lynch KF, Triplett EW, Hyöty H, Ahrens AP, Laiho JE, Petrosino JF, Lloyd RE, Agardh D.

Sci Rep. 2025 Nov 28;15(1):42704. doi: 10.1038/s41598-025-26700-y.

PMID: 41315430

Machine Learning Algorithms for Predicting Injurious Fall Risk Among Older Adults With Depression: A Prognostic Modeling Study.

Wang GH, Lee YA, Goodin AJ, Reise RC, Shorr RI, Lo-Ciganic WH.

Pharmacotherapy. 2025 Nov 27. doi: 10.1002/phar.70087. Online ahead of print.

PMID: 41310296

One-Pot RT-LAMP CRISPR/Cas12b Platform for Rapid Detection of Tilapia Lake Virus.

Megarani DV, Yang L, Siler HJ, Quijano Cardé EM, Martyniuk CJ, Hick PM, Becker JA, Soto E, Surachetpong W, Yanong RPE, Subramaniam K.

J Fish Dis. 2025 Nov 28:e70087. doi: 10.1111/jfd.70087. Online ahead of print.

PMID: 41316685

Developmental PBDE exposure persistently impairs mast cell function in vivo and drives sex-specific morphological and transcriptional changes in bone marrow-derived mast cells.

Franges J, Malinowski L, De Alwis C, Doolittle T, Li Y, Dixon H, Tang Y, Watson H, Peace J, Jima D, Sombers L, McCarty G, Patisaul H, Stapleton HM, Duque-Wilckens N.

Environ Res. 2026 Jan 1;288(Pt 1):123250. doi: 10.1016/j.envres.2025.123250. Epub 2025 Oct 31.

PMID: 41177347

The chromatin regulator HELLS mediates SSB repair and responses to DNA alkylation damage.

Joseph JT, Wright CM, Peixoto E, Shibata E, Khan A, Li Y, Neidigk JSR, Chen BR, Tufail S, Mujawar AA, Decker O, Kadali KR, Imtiaz A, Jones BA, Zhang Y, Gradilone SA, Lewis ZA, Contreras-Galindo R, Sen A, Dutta A, Czaja W.

Nucleic Acids Res. 2025 Nov 26;53(22):gkaf1201. doi: 10.1093/nar/gkaf1201.

PMID: 41297801

Designing trials with multiple objectives with graphical approach for multiple scenarios.

Ding AA, Li Y, Wu SS.

Contemp Clin Trials Commun. 2025 Nov 10;48:101569. doi: 10.1016/j.conctc.2025.101569. eCollection 2025 Dec.

PMID: 41311868

Virome and Microbiome of Florida Bats Illuminate Viral Co-Infections, Dietary Viral Signals, and Gut Microbiome Shifts.

Paoli JE, Thongthum T, Bassett M, Beardsley J, Tagliamonte MS, Cash MN, Spertus Newman J, Smith LM, Anderson BD, Salemi M, Subramaniam K, von Fricken ME, Braun de Torrez E, Mathis V, Mavian CN.

Microorganisms. 2025 Nov 19;13(11):2625. doi: 10.3390/microorganisms13112625.

PMID: 41304309

Inhalation exposure to a tire-derived pollutant (6-PPD) triggers lung injury and mitochondrial dysfunction in mice.

Kim JH, Kim HJ, Suh HN, Kang MS, Kim IH, Park SW, Lee MH, Yoon HS, Han SM, Kim E, Meier J, Kim SH, Hyun M.

Ecotoxicol Environ Saf. 2025 Nov 24;307:119429. doi: 10.1016/j.ecoenv.2025.119429. Online ahead of print.

PMID: 41289760

Cryopreserved Tissue Biospecimens Offer Superior Quality for Whole-Genome Sequencing of Various Cancers Compared to Paired Formalin-Fixed Paraffin-Embedded Tissues.

Dixon K, Lee JH, Miller R, Booker D, Anderson D, Okojie J, Kirkham M, Lee EK, Bao C, Tuncay IO, Kim JA, Lee S, Barrott J.

Int J Mol Sci. 2025 Nov 14;26(22):11038. doi: 10.3390/ijms262211038.

PMID: 41303519

Interferon gamma stimulates coordinated changes in LRRK2, GCase, and cathepsin activities in idiopathic and genetic Parkinson’s disease monocytes.

Hughes LP, Wallings RL, Agin-Liebes J, Alcalay RN, Garrido A, Tansey MG, Dzamko N.

NPJ Parkinsons Dis. 2025 Nov 26;11(1):337. doi: 10.1038/s41531-025-01185-8.

PMID: 41298592

mop1 affects maize recombination landscapes by modulating methylation of MITEs near genes in open chromatin.

Hasan MM, Yin L, Wang M, Pawlowski WP, Zhao M.

Nat Commun. 2025 Nov 25;16(1):10476. doi: 10.1038/s41467-025-65469-6.

PMID: 41290628

GatorAffinity: Boosting Protein-Ligand Binding Affinity Prediction with Large-Scale Synthetic Structural Data.

Wei J, Zhang Y, Ramdhan PA, Huang Z, Seabra G, Jiang Z, Li C, Li Y.

bioRxiv [Preprint]. 2025 Oct 1:2025.09.29.679384. doi: 10.1101/2025.09.29.679384.

PMID: 41256614

Donor-dependent heterogeneity in therapeutic effects of adipose tissue extracellular vesicles.

Beetler DJ, Giresi P, Xu V, McCabe EJ, Fliess JJ, Puls AM, Auda ME, Watkins MM, Walker SA, Di Florio DN, Iannotta D, Whelan ER, Macomb LP, Keegan KC, Jain A, Balamurugan V, Khatib S, Weigel GJ, Gorelov DJ, Pham A, Edenfield BH, Cooper LT Jr, Farres H, Shapiro SA, Bruno KA, Wolfram J, Fairweather D.

Cell Commun Signal. 2025 Nov 26. doi: 10.1186/s12964-025-02563-8. Online ahead of print.

PMID: 41299530

The immune receptor XA21 causes semi-male sterility and grain loss in rice.

de Toledo Franceschi B, Vergish S, Singh Y, Li JL, Shamsunnaher, Ding GL, Chen S, Song WY.

Front Plant Sci. 2025 Nov 10;16:1673821. doi: 10.3389/fpls.2025.1673821. eCollection 2025.

PMID: 41293474

Inhibition of cell-mediated immunity in type 1 diabetes by beta cell-targeted PD-1 agonists in pancreas tissue slices.

Becker MW, Brown M, Wiseman K, Chiodetti AL, Huber MK, Cuaycal AE, Sintara P, Ferreira SM, Smurlick D, Barra JM, Ladd AM, Drotar DM, Atkinson MA, Weber P, Al-Mossawi H, Russ HA, Mahon TM, Brusko TM, Bossi G, Phelps EA.

bioRxiv [Preprint]. 2025 Oct 22:2025.10.21.683528. doi: 10.1101/2025.10.21.683528.

PMID: 41278996

Short-Course Antibiotic Agent Therapy for Early Ventilator-Associated Pneumonia in Patients with Trauma.

Shoulders BR, Fassler AM, Maguigan KL, Loftus TJ, Efron PA, Mohr AM, Vanzant E.

Surg Infect (Larchmt). 2025 Dec;26(10):725-731. doi: 10.1177/10962964251376956. Epub 2025 Sep 10.

PMID: 40931784

The Rapid Autism Assessment: Reducing Barriers to Behavioral Intervention Services.

Kovic Y, Dallas GD, Andrade JL, Lloveras LA, Peters KP, Soda T.

J Am Acad Child Adolesc Psychiatry. 2025 Dec;64(12):1380-1385. doi: 10.1016/j.jaac.2025.03.001. Epub 2025 Mar 10.

PMID: 40074072

Haplotype-resolved Chromatin Conformation Data reveals relationship between Transposable Elements and Chromosomal Pairing.

Genutis LK, Villanueva P, Graze RM, AlHaj Abed J, McIntyre LM, Nuzhdin SV.

Genome Biol Evol. 2025 Nov 26:evaf222. doi: 10.1093/gbe/evaf222. Online ahead of print.

PMID: 41293827

Multiparent Recombinant Inbred lines crossed to a tester provide novel insights into sources of cis and trans regulation of gene expression.

Marroni F, Morse AM, Nanni AV, Nolte N, Williams-Simon P, Leon-Novelo L, Graze RM, Schmidt P, King E, McIntyre LM.

Genetics. 2025 Nov 27:iyaf257. doi: 10.1093/genetics/iyaf257. Online ahead of print.

PMID: 41308074

The Role of Artificial Intelligence in Deep Brain Stimulation.

Mehta T, Lavu V, Gao H, Banerjee T, Hu R, Fang R, Wong J.

Semin Neurol. 2025 Nov 25. doi: 10.1055/a-2753-6166. Online ahead of print.

PMID: 41290209

Biosynthesis, Chemical Synthesis, and Pharmacological Evaluation of Lyngbyapeptin A as a GPCR Antagonist of Motilin, Cannabinoid, and Amylin Receptors.

Pham THD, Chen M, Liu J, Chen QY, Seabra G, Paul VJ, Donia MS, Bruner SD, Ding Y, Luesch H.

J Nat Prod. 2025 Nov 28;88(11):2610-2624. doi: 10.1021/acs.jnatprod.5c00963. Epub 2025 Oct 17.

PMID: 41105455

Integrative Epigenomic and Targeted Protein Analysis in MRONJ: Correlating DNA Methylation with Bone Biomarkers.

Alshammari RA, Tantawy M, Wang D, Castro-Hall E, Abreu M, Villa A, Katz J, Holliday LS, Gong Y.

Int J Mol Sci. 2025 Nov 20;26(22):11208. doi: 10.3390/ijms262211208.

PMID: 41303691

Defective HIV DNA genomes provide ancestral relevance critical for phylogenetic inference of reservoir dynamics.

Droske LE, Ramirez-Mata AS, Cash MN, Estrada J, Shank SD, Browning A, Rafiei F, Pond SLK, Salemi M, Magalis BR.

bioRxiv [Preprint]. 2025 Nov 14:2025.10.03.680205. doi: 10.1101/2025.10.03.680205.

PMID: 41256621

Virome and Microbiome of Florida Bats Illuminate Viral Co-Infections, Dietary Viral Signals, and Gut Microbiome Shifts.

Paoli JE, Thongthum T, Bassett M, Beardsley J, Tagliamonte MS, Cash MN, Spertus Newman J, Smith LM, Anderson BD, Salemi M, Subramaniam K, von Fricken ME, Braun de Torrez E, Mathis V, Mavian CN.

Microorganisms. 2025 Nov 19;13(11):2625. doi: 10.3390/microorganisms13112625.

PMID: 41304309