Digital Commons Network^™

When Probiotics Guidelines Differ: A Practical Guide For Clinicians And Researchers, Geoffrey A Preidis, Hania Szajewska, Marla Cunningham, Howard Bauchner, Daniel J Merenstein

Faculty, Staff and Students Publications

Many professional organizations publish clinical practice guidelines for the use of probiotics in gastrointestinal disorders. Generally, no two guidelines align perfectly, and some differ markedly. These discrepancies occur because clinical practice guidelines are not purely mechanical outputs of data synthesis. They are shaped by structured interpretation, value judgments, and predefined thresholds for uncertainty. These elements become particularly visible when effect sizes are small, heterogeneity is high, and outcomes vary in clinical relevance-as is the case with probiotic research. This article examines why discordance among probiotic guidelines is predictable and provides practical guidance for clinicians who must decide among conflicting recommendations …

Ambulatory Blood Pressure Variability In Prediction Of Target Organ Injury: The Ship Ahoy Study, Coral D Hanevold, Jang Dong Seo, Stephen R Daniels, Bonita E Falkner, Michael A Ferguson, Joseph T Flynn, Julie R Ingelfinger, Philip R Khoury, Marc B Lande, Kevin E Meyers, Mark Mitsnefes, Joshua Samuels, Elaine M Urbina

Faculty, Staff and Student Publications

Background: Ambulatory hypertension is associated with elevated left ventricular mass index (LVMI), cardiac dysfunction, and increased arterial stiffness in adolescents. Whether the addition of measures of BP variability improves the prediction of subclinical cardiovascular target organ damage (TOD) over mean BP measures is not known.

Methods: We assessed clinic and ambulatory BP (ABP), anthropometrics, and TOD in 397 adolescents. ABP means standard deviation (SD), BP, and heart rate (HR) dipping were calculated; coefficients of variability (CV) were calculated (SD/mean) to assess ABP variabilities. Measures of TOD included LVMI, left ventricular hypertrophy (LVH), LV systolic shortening, LV diastolic function (e'/a'), and …

Artificial Intelligence, Machine Learning, And Deep Learning Approaches For Attention-Deficit/Hyperactivity Disorder Diagnosis: Protocol For A Scoping Review, Benedict Onochie Ibe, Amir Aly, Shaymaa S Al-Juboori, Emmanuel Ifeachor, Rohit Shankar

School of Engineering, Computing and Mathematics

BACKGROUND: Attention-deficit/hyperactivity disorder (ADHD) affects over 366 million adults and 139 million children worldwide, yet diagnosis remains fundamentally subjective, relying on clinical interviews, behavioral observations, and rating scales that yield inconsistent results across practitioners and settings. Artificial intelligence (AI), machine learning (ML), and deep learning (DL) offer a paradigm shift toward objective, data-driven diagnosis by detecting complex patterns across neuroimaging, electrophysiology, and digital biomarkers that elude conventional assessment. Although AI-based ADHD research has grown exponentially, no comprehensive synthesis examines the full spectrum of data modalities, validation practices, and clinical translation readiness. This gap limits our understanding of which approaches are …

Study Of Blood Linear Rna Nominates Cd55 And Dld As Early-Stage Biomarkers For Parkinson's Disease, Aleksandra Beric, Sarp Sahin, Santiago Sanchez, Zining Yang, Ravindra Kumar, Isabel Alfradique-Dunham, Jessie Sanford, Daniel Western, Bridget Phillips, John P Budde, Richard J Perrin, Paul T Kotzbauer, Joel S Perlmutter, Scott A Norris, Carlos Cruchaga, Laura Ibanez

2020-Current year OA Pubs

Parkinson's disease (PD) is the second leading neurodegenerative disease, pathologically characterized by the accumulation of alpha-synuclein in the brain and the loss of dopaminergic neurons in the substantia nigra pars compacta. Despite the intensive efforts to identify diagnostic biomarkers for PD and nominating prospective candidates such as such as CSF α-synuclein seed amplification assay or α-/β-synuclein ratio, establishment of minimally invasive biomarkers remains the focus of PD research. We leveraged transcriptomic data from 4343 participants from four independent datasets to robustly identify PD-associated transcripts. Following the differential abundance analyses, we integrated our findings with several brain transcriptomic, CSF proteomic, plasma …

A Deep-Learning Based Biomarker Of Systemic Cellular Senescence Burden To Predict Mortality And Health Outcomes, Shangshu Zhao, Chia-Ling Kuo, Eric J Lenze, Julie L Wetherell, Laura Haynes, Perla El-Ahmad, Richard Fortinsky, George Kuchel, Trevor Harris, Breno S Diniz

2020-Current year OA Pubs

The accumulation of senescent cells is a recognized hallmark of biological aging and is associated with the onset of multiple chronic medical conditions. Senescent cells exhibit a distinct secretory profile, known as the senescence-associated secretory phenotype (SASP), which can propagate cellular senescence to neighboring and distant tissues. Measuring SASP factors in blood serves as a practical proxy for cellular senescence burden and may help track disease states and intervention outcomes. We developed and validated a composite SASP Score by integrating large-scale population proteomics data with a semi-supervised deep learning framework. The analytical workflow included: (1) selection of biologically curated SASP …

Burden Of Disease In Us Patients With Skeletal Versus Muscular Or Pain Manifestations Of Hypophosphatasia: An Analysis From The Global Hpp Registry., Priya S. Kishnani, Steven Ing, Julie Hoover-Fong, J Carl Pallais, Angie Voskopoja, Shona Fang, William R Mowrey, Eric Rush, Kathryn Dahir

Manuscripts, Articles, Book Chapters and Other Papers

BACKGROUND: Hypophosphatasia (HPP) is a metabolic disorder characterized by deficient alkaline phosphatase (ALP) activity, defective mineralization of bones and teeth, and non-skeletal manifestations. We compared disease burden between patients with skeletal and non-skeletal manifestations.

METHODS: Data from US adults enrolled in the Global HPP Registry through July 2024 were analyzed to compare baseline characteristics, genetic testing results, functional outcomes, and patient-reported outcomes between participants with and without overt skeletal manifestations. Patients who had only dental manifestations were excluded.

RESULTS: Of 283 participants, 234 (82.7%) had skeletal manifestations (79.1% female; 89.3% White; median age 48.7 years) and 49 (17.3%) had only …

A Rare Recurring Gain-Of-Function Variant In Bmpr2 Causes Neurodevelopmental Phenotypes In Humans And Flies, Jung-Wan Mok, Carrie L Welch, Haley A Dostalik, Zhi Tan, Ariel Brautbar, Maria Descartes, Erica T Gray, Alejandro Iglesias, Scott D Mclean, Morgan Nutter, Olivia Daugherty, Amber Begtrup, Ingrid M Wentzensen, Yufeng Shen, Damian W Young, Martin M Matzuk, Oguz Kanca, Michael F Wangler, Hugo J Bellen, Wendy K Chung, Shinya Yamamoto

Faculty, Staff and Students Publications

Bone morphogenetic protein receptor type 2 (BMPR2) encodes an evolutionarily conserved serine/threonine kinase that phosphorylates type-1 BMP receptors to mediate intercellular communication upon ligand binding. Loss-of-function variants in BMPR2 are known to cause pulmonary arterial hypertension and other cardiovascular disorders. Here, we report a rare recurrent missense variant in BMPR2 (c.1126G>A [GenBank: NM_001204] [p.Glu376Lys]) identified in six individuals, who all present with neurodevelopmental phenotypes including autism spectrum disorder and global developmental delay. Trio analysis demonstrates de novo occurrence of this variant in at least five of the individuals. Using the fruit fly Drosophila melanogaster, we show that this variant …

Clinical Presentations, Treatments, And Outcomes Of Pediatric Lupus Nephritis: A Prospective Cohort Study From The Pediatric Nephrology Research Consortium., Melonie Phillips, Mahmoud Kallash, Chloe Tang, Steve Rust, Kia Jubert-Bacon, Scott Wenderfer, Smriti Mohan, Neal Blatt, Don Batisky, Alejandro Quiroga, Tetyana L. Vasylyeva, Nilka Dejesus, Jerome C. Lane

Manuscripts, Articles, Book Chapters and Other Papers

BACKGROUND: There are few prospective studies of mycophenolate mofetil (MMF) versus cyclophosphamide (CYC) for pediatric lupus nephritis (pLN) and none evaluating rituximab (RTX).

METHODS: The Prospective Pediatric Lupus Nephritis Registry (ProPeL-R) enrolled patients <  21 years within 4 weeks of an initial kidney biopsy diagnostic of pLN. Demographic, clinical, and laboratory data were collected prospectively at enrollment, 3 months, 6 months, and then every 6 months thereafter for up to 5 years of follow-up. For this study, we compared patients receiving initial therapy with corticosteroids (CS) and either MMF (n = 33) vs. CYC (n = 18), and those treated with CS, either MMF or CYC, with RTX (n = 20) vs. without RTX (n = 51).

RESULTS: Histology consisted of 18% class III; 35% class IV; 25% mixed class; and 22% pure class V. Eighty-two percent were female. No significant differences in response or infection rates were identified between those receiving MMF or CYC. There was a significant increase in combined complete (CR) and partial response (PR) at 24 months with RTX use. Overall CR rates at 6 and 24 months were 35% …

Streamlining Diagnosis Of Bardet-Biedl Syndrome: New Diagnostic Algorithm With Updated Criteria., Jeremy J. Pomeroy, Jesse Richards, Brooke Sweeney, Seema Kumar, Katie E. Queen, Joshua Zaritsky, Carl H. Cramer, Elias I. Traboulsi, Brittni A. Scruggs, Erica E. Davis, Ekaterina Keifer, Emma Mcgibbon, Timothy Ogden, Bendert De Graaf, Tonia Hymers, Elizabeth Forsythe, Philip Beales

Manuscripts, Articles, Book Chapters and Other Papers

Considerable advances have been made in our understanding of Bardet-Biedl syndrome (BBS), particularly in its core clinical features and molecular genetics, warranting an update to the existing diagnostic criteria framework. Using a rigorous, evidence-based, and consensus-driven process, a multidisciplinary group of international experts and patient-led organizations developed an updated diagnostic algorithm. This algorithm provides practical, updated guidance for clinicians, including a pathway for accurately incorporating genetic findings into the diagnostic process. We recommend that a clinical diagnosis requires either 4 major criteria or 3 major and 2 minor criteria. Revised major criteria are retinal dystrophy, obesity (or overweight in individuals <  2 years old), congenital anomalies of the kidney and urinary tract or chronic kidney disease, hypogonadism/genital anomalies, neurodevelopmental/neurocognitive manifestations, and postaxial polydactyly. The diagnosis can also be established with a positive genetic testing result in patients exhibiting ≥ 1 major criterion, provided that genetic findings should be interpreted in the context of the patient's clinical presentation, age, family history, and overlap with related ciliopathies. These consensus criteria offer a simple algorithm incorporating updated definitions for major and minor criteria and genetic testing to support a timely and accurate diagnosis of patients with BBS, inform genetic counseling, and potentially facilitate earlier access to treatment. Trial Registration: CRIBBS Registry; ClinicalTrials.gov: NCT02329210.

Cytomegalovirus Immune Responses And Cognitive Impairment In People With Human Immunodeficiency Virus, Lakshmi Chauhan, Debashis Ghosh, Beau Ances, Katherine Tassiopoulos, Kunling Wu, Adriana Weinberg, Kristine M Erlandson

2020-Current year OA Pubs

People with human immunodeficiency virus (HIV) have an earlier occurrence of aging complications, including cognitive impairment (CI). Chronic immune activation from cytomegalovirus (CMV) may contribute to increased inflammation and CI. We explored this association using several measures of CMV immune response among people with HIV (PWH). In a case-control design, we compared CMV immunoglobulin G (IgG), enzyme-linked immunospot (ELISpot), and flow cytometry between cases (subsequent CI) and controls (no CI). Baseline CMV IgG, CMV ELISpot, or flow measures were not associated with subsequent CI. This exploratory analysis supports larger studies using more nuanced immunophenotyping to clarify relationship between CMV and …

Molecular And Structural Basis For Replication Initiation And Strand Separation By Human Mitochondrial Dna Polymerase Γ, Viktoriia Sokolova, Gina Buchel, S. Strock, Ashok R. Nayak, Dmitry Temiakov

Department of Biochemistry and Molecular Biology Faculty Papers

Defects in human mitochondrial DNA (mtDNA) replication can lead to somatic mutations associated with a range of devastating mitochondrial diseases. However, the molecular mechanisms governing the earliest steps of mtDNA replication and their fidelity remain poorly understood. Here, we found that DNA polymerase gamma (Polγ) forms stable complexes with RNA-DNA primer-template substrates, exhibiting greater stability and lower misincorporation than on DNA-primed substrates. Structural analysis revealed that Polγ interacts with the 2'-OH groups of ribose within the first four nucleotides of the primer, explaining the stability of complexes that utilize RNA primers. Although Polγ requires TWINKLE to extend RNA primers, its …

Nemp1 Organizes The Meiotic Telomere-Linc Interface To Control Chromosome Movement And Telomere Integrity, Hui Zhang, Ling Zhang, Stephanie A Pangas, Andrea Jurisicova, Helen Mcneill

Faculty, Staff and Students Publications

Nuclear Envelope Membrane Protein 1 (NEMP1) is highly expressed in oocytes and required for fertility, yet its meiotic function remains poorly understood. Here, we identify NEMP1 as a critical organizer of meiotic telomere-nuclear envelope coupling and chromosome dynamics. Loss of NEMP1 causes telomere aggregation, loss of shelterin protection, telomere shortening, persistent DNA damage, aberrant non-homologous end joining, and chromosome end-to-end fusion, ultimately leading to aneuploidy in mouse oocyte. NEMP1 is required during early fetal meiotic prophase I for telomere-nuclear envelope attachment, bouquet formation, homolog pairing, and synapsis. Live-cell imaging revealed robust rapid prophase movements in wild-type meiocytes, which were nearly …

Interface Geometry Governs Probe Insertion Mechanics And Electrode Deviation In Layered Brain-Mimicking Phantoms For Deep Brain Stimulation, Siyu Chen, Chengyuan Wu, Ethan Anders, Rungun Nathan, Olivia M. Bailey, Qifu Wang, Curtis L. Johnson, Qianhong Wu

Department of Neurosurgery Faculty Papers

Parkinson's disease (PD) is a progressive neurological disorder often treated with Deep Brain Stimulation (DBS), a surgical procedure that involves implanting electrodes to improve motor function. Accurate electrode placement is critical for treatment efficacy but can be influenced by tissue deformation, insertion forces, and the mechanical properties of brain tissue. In this study, we investigated the role of layer interface angle as a controlled biomechanical factor affecting insertion forces and electrode deviation. A two-layer agar gel phantom was constructed to produce a prescribed stiffness transition between a lower-stiffness and a higher-stiffness gel layer, and its small-amplitude dynamic shear-stiffness contrast was …

Validation Of Next‑Generation Sequencing‑Derived Circulating Mrna Variants As Potential Diagnostic Tools In Hepatocellular Carcinoma And Cholangiocarcinoma, Daniel Zezulinski, Maarouf A. Hoteit, David E. Kaplan, Tingting Zhan, Cataldo Doria, Timothy M. Block, Aejaz Sayeed

Department of Pharmacology, Physiology, and Cancer Biology Faculty Papers

Liquid biopsy can transform oncology practice through early detection and real‑time monitoring of cancer progression and response to treatment. Circulating cell‑free tumor RNA offers promise as a novel and emerging alternative to circulating cell‑free tumor DNA for detecting the presence and understanding the biology of liver tumors. Both circulating DNA and RNA, which predominantly reside in extracellular vesicles, carry evidence of vital germline and somatic mutations. High impact single nucleotide changes, insertions and deletions in circulating RNA (ctRNA) serve a key role in cancer development and progression. Tumor cells exploit the RNA splicing machinery to induce structural and functional changes …

The C3-C3ar Axis Modulates Trained Immunity In Alveolar Macrophages, Alexander P Earhart, Rafael Aponte Alburquerque, Marick Starick, Lorena Garnica, Ayse Naz Ozanturk, Rahul Kumar Maurya, Xiaobo Wu, Jeffrey Haspel, Hrishikesh S Kulkarni, Et Al.

2020-Current year OA Pubs

Complement protein C3 is crucial for immune responses in mucosal sites such as the lung, where it aids in microbe elimination, and enhances inflammation. While trained immunity - enhanced secondary responses of innate immune cells after prior exposure - is well-studied, the role of the complement system in trained immune responses remains unclear. We investigated the role of C3 in trained immunity and found that alveolar macrophage (AM)

Distinct Mutational Landscapes For Germline And Somatic Cancer Variants In Forty Tumor Suppressor Genes, Suhasini D Lulla, Deborah I Ritter, Chimene Kesserwan, Sharon E Plon

Faculty, Staff and Students Publications

Germline and somatic cancer variants in tumor suppressor genes (TSGs) share loss-of-function mechanisms, but studies of a few genes (DICER1 and CEBPA) have demonstrated differences in variant consequence and location. To systematically assess whether TSGs display distinct mutational patterns, we leveraged large public genetic databases and compared 32,941 high-quality pathogenic/likely pathogenic (P/LP) germline variants in ClinVar, with 12,907 oncogenic/likely oncogenic (O/LO) somatic tumor variants from cBioPortal across 40 TSGs. Only 3,863 (9.2%) variants were shared. Eighteen TSGs showed significantly different distributions of variant occurrences by molecular consequence, replicated with non-overlapping somatic data from the COSMIC database (chi-squared tests, false discovery …

Androgens Mediate Sexual Dimorphism In Pilarowski-Bjornsson Syndrome., Kimberley Jade Anderson, Eirny Tholl Thorolfsdottir, Ilana M. Nodelman, Sara Tholl Halldorsdottir, Stefania Benonisdottir, Malak A. Alghamdi, Naif A M Almontashiri, Brenda J. Barry, Matthias Begemann, Jacquelyn F. Britton, Sarah Burke, Benjamin Cogne, Ana S A Cohen, Carles De Diego Boguñá, Evan E. Eichler, Elizabeth C. Engle, Jill A. Fahrner, Laurence Faivre, Mélanie Fradin, Nico Fuhrmann, Christine W. Gao, Gunjan Garg, Dagmar Grečmalová, Mina Grippa, Jacqueline R. Harris, Kendra Hoekzema, Tova Hershkovitz, Sydney Hubbard, Katrien Janssens, Julie A. Jurgens, Stanislav Kmoch, Cordula Knopp, Meral Aktas Koptagel, Farah A. Ladha, Pablo Lapunzina, Tobias Lindau, Marije Meuwissen, Andreina Minicucci, Emily Neuhaus, Mathilde Nizon, Lenka Nosková, Kristen Park, Chirag Patel, Rolph Pfundt, Pankaj Prasun, Nils Rahner, Nathaniel H. Robin, Carey Ronspies, Jasmin Roohi, Jill Rosenfeld, Margarita Saenz, Carol J. Saunders, Zornitza Stark, Isabelle Thiffault, Sarah Thull, Danita Velasco, Clara Velmans, Jolijn Verseput, Antonio Vitobello, Tianyun Wang, Karin Weiss, Ingrid M. Wentzensen, Genay Pilarowski, Thor Eysteinsson, Madelyn Gillentine, Kári Stefánsson, Agnar Helgason, Gregory D. Bowman, Hans Tomas Bjornsson

Manuscripts, Articles, Book Chapters and Other Papers

Sex-specific penetrance in autosomal-dominant Mendelian conditions is largely understudied. The neurodevelopmental disorder Pilarowski-Bjornsson syndrome (PILBOS) was initially described in females. Here, we describe the clinical and genetic characteristics of the largest PILBOS cohort to date, showing that both sexes can exhibit PILBOS features, although males are overrepresented. A mouse model carrying a human-derived Chd1 missense variant (Chd1^R616Q/+) displays female-restricted phenotypes, including growth deficiency, anxiety, and hypotonia. Orchiectomy unmasks a growth-deficiency phenotype in male Chd1^R616Q/+ mice, while testosterone rescues the phenotype in females, implicating androgens in phenotype modulation. In the gnomAD and UK Biobank databases, rare missense variants …

Artificial Intelligence Models For Automated And Semiautomated Analysis And Interpretation Of Clinical Electroencephalography, Sándor Beniczky, Birgit Frauscher, Fábio Nascimento, Shobi Sivathamboo, Catalina Rojas, Michael Sperling, Samden Lhatoo, Philippe Ryvlin, Levin Kuhlmann

Department of Neurology Faculty Papers

Electroencephalography is the most commonly used diagnostic tool for epilepsy. However, interpreting electroencephalograms (EEGs) requires expertise that is not widely available. Advances in digital technology and wearables have enabled large-scale EEG recording, generating vast amounts of data that cannot be managed through traditional visual interpretation by experts. Artificial intelligence (AI) has the potential to augment human expertise and reduce workloads. The application of artificial neural networks in analysing clinical EEG recordings has led to major breakthroughs, bringing AI-based EEG interpretation closer to clinical implementation. In this Review, we summarise the most important research and development results in this field from …

Hydroxyethyl Starch And Perioperative Complications: A Systematic Review And Meta-Analysis, Daniel I Sessler, Lorenzo Pradelli, Massimiliano Povero, Daniel Chappell, E Wang

Faculty, Staff and Student Publications

Background: Based on renal injury reported in critically ill and septic patients, the U.S. Food and Drug Administration issued a black box warning regarding hydroxyethyl starch (HES 130/0.4) use in 2013 and expanded the warning to surgical and trauma patients in 2021. Similarly, the European Medicines Agency initiated withdrawal of hydroxyethyl starch in 2022. This study was a new meta-analysis focused on renal injury designed to complement a 2021 meta-analysis of perioperative hydroxyethyl starch use, adding 45 trials and 6,895 patients. The focus was acute kidney injury and preoperative-to-postoperative change in creatinine concentration in surgical patients.

Methods: This study searched …

The Who Classification Of Genetic Tumour Syndromes: Considerations For Genetics, Ian A Cree, Mark J Arends, Joseph D Khoury, Erika R E Denton, Anthony J Gill, Alexander J Lazar, Ian M Frayling, Stefan M Pfister, Mark A Rubin, Katia R M Leite, Raymond Dalgleish, Elspeth A Bruford, Sharon E Plon, Ada Hamosh, Michael Francis Walsh, Gabrielle Goldman-Lévy, Harshima Wijesinghe, William D Foulkes, Dilani Lokuhetty

Faculty, Staff and Students Publications

The WHO Classification of Tumours is used widely by histopathologists and other disciplines as it provides an internationally agreed taxonomy of neoplastic disorders. Now published online and in print, it has often included genetic tumour syndromes (GTS) relevant to particular organs, as suggested by the editorial board. This highlighted the lack of a systematic classification of GTS, providing international standards for their diagnosis and a basis for research. The need for this was established by a series of meetings, leading to the adoption of a hierarchical classification of GTS based on the cellular mechanism affected, the molecular pathway involved, the …

Non-Vigorous Physical Activity Associated With Reduced Hospitalization Risk With Or Without Diabetes Or Peripheral Artery Disease: Study Of Latinos., Sarah K. Alver, Carmen C. Cuthbertson, Kelly R. Evenson, Jennifer A. Schrack, Daniela Sotres-Alvarez, Natasha Z. Anita, Yasmin Mossavar-Rahmani, Linda C. Gallo, Jordan A. Carlson, Matthew Allison, Martha L. Daviglus, Olga Garcia-Bedoya, Christina Cordero, Xiaonan Xue, Jianwen Cai, Kunihiro Matsushita, Robert C. Kaplan

Manuscripts, Articles, Book Chapters and Other Papers

PURPOSE: This study assessed whether greater physical activity (PA) and lesser sedentary behavior (SB) reduce hospitalization risk equally among those with and without prediabetes, diabetes, or peripheral artery disease (PAD).

METHODS: We studied PA, SB and hospitalizations in 12,734 adults from the Hispanic Community Health Study/Study of Latinos, who were 52.2% female with mean (standard deviation) age 41.1 (14.9) yr at baseline. Participants reported 10,025 nonpregnancy-related hospitalizations (excluding emergency room only) over 13 yr. We modeled the association between accelerometer-measured activity (SB; light intensity physical activity [LPA]; moderate physical activity [MPA]; vigorous physical activity [VPA]) and hospitalization, using Andersen-Gill proportional …

Irs: Iterative Reference Selection Improves Normalization Of Microbiome Sequencing Data, Yiming Shi, Lili Liu, Jun Chen, Kristine M Wylie, Todd N Wylie, Sung Hee Park, Ruiwen Zhou, Yin Cao, Stephanie A Fritz, Molly J Stout, Maria Cristina Vazquez Guillamet, Lei Liu

2020-Current year OA Pubs

Microbiome studies often seek to determine how the absolute abundances of individual taxa change across biological conditions, yet sequencing read counts are sample-specific scaled representations of those abundances. Because sampling depth can differ across samples, fold changes calculated directly from sequencing read counts do not generally represent absolute-abundance fold changes. Normalization methods attempt to account for these between-sample differences in sampling depth, but their accuracy depends on the reference used. In particular, total-sum scaling uses all taxa as the reference and can introduce compositional bias. Reference-based methods instead rely on taxa that are stable across conditions, but contamination of the …

Crosstalk Between Upr And Mitochondria: The Triad Of Er-Mitochondria Contacts, Ca²⁺, And Ros, Ester Zito, György Hajnóczky

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

Endoplasmic reticulum (ER) stress is triggered by several cellular perturbations causing protein misfolding, and activates the unfolded protein response (UPR), an initially adaptive signaling network that aims to restore ER and cellular homeostasis. Growing evidence indicates that UPR signaling extends beyond ER proteostasis, influencing mitochondrial function and bioenergetics through ER-mitochondria contact sites (ERMCs). The CHOP-ERO1A-IP3R axis has a primary role in recruiting mitochondria to adaptive UPR. However, its sustained activation renders UPR signaling maladaptive, leading to mitochondrial dysfunction through both outer mitochondrial membrane permeabilization (OMMP) and mitochondrial permeability transition pore (mPTP) opening, ultimately contributing to irreversible cell injury and disease …

Valvular Heart Failure Is A Distinct Heart Transplant Phenotype With Comparable Adjusted Survival To Other Heart Failure Etiologies, Devon Kelley, Varun Kathawate, Joyce Ho, Andrew Belec, Takahiro Tashima, Kazuhiro Ueno, Jessica Dominic, Pavan Atluri

Division of Cardiology Faculty Papers

PURPOSE: Valvular heart failure (VHF) accounts for 1-5% of heart transplant listings. Comparative outcomes relative to other heart failure etiologies remain poorly characterized. This study defines the VHF phenotype and compares waitlist and transplant outcomes to other heart failure recipients.

METHODS: This retrospective cohort study uses the UNOS thoracic transplant database to analyze adult, first-time, heart-only listings with a diagnosis of heart disease. Patients were grouped by diagnosis as VHF or non-VHF. The primary outcome was waitlist events; post-transplant survival and outcomes were secondary analyses. Subgroup analysis was performed in the post-2018 allocation era.

RESULTS: VHF recipients were older (55.3 …

Cells And Networks In Flux: Rethinking Ontogenesis And Pathogenesis, Mark L. Tykocinski

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

Organ and tissue functions emerge from the coordinated activity of cell networks. Therapeutics that act on pathogenic cell networks, modulating their cellular interplay, follow naturally. Over several decades, our laboratory has developed a series of approaches for rewiring cell networks, culminating in a class of cell surface-directed signal converter proteins (SCPs) that do so by modulating juxtacrine and autocrine signaling in and among their nodal cells. A first such SCP has now produced encouraging clinical data for cancer immunotherapy. Yet, these early network-directed fusion proteins rest on a deliberately simplified picture: discrete end-cell types plugged into graphically tractable networks. That …

Malt1 Protease Inhibition Restrains Glioblastoma Progression By Reversing Tumor-Associated Macrophage-Dependent Immunosuppression In Mice, Juliana Hofstätter Azambuja, Saigopalakrishna Yerneni, Lisa Maurer, Hannah Crentsil, Gabriela Debom, Linda Klei, Mei Smyers, Chaim Sneiderman, Kristina Schwab, Rajesh Acharya, Aivi Nguyen, Josie Emery, John Little, Jeffrey Meridew, Yijen Lin Wu, Prasanna Ekambaram, Dong Hu, Pete Gough, John Bertin, Ari Melnick, Gary Kohanbash, Riyue Bao, Peter Lucas, Linda Mcallister-Lucas

College of Life Sciences Faculty Papers

MALT1 protease is an intracellular signaling molecule that promotes tumor progression via cancer cell-intrinsic and cancer cell-extrinsic mechanisms. MALT1 has been mostly studied in lymphocytes, and little is known about its role in tumor-associated macrophages. We show that MALT1 is expressed in glioblastoma (GBM)-associated macrophages. Mechanistically, GBM tumor cells induce a MALT1-NF-κB signaling axis in macrophages, leading to enhanced macrophage migration and polarization toward an immunosuppressive ('M2-like') phenotype. Inactivation of MALT1 protease promotes transcriptional reprogramming that reduces migration and restores a macrophage anti-tumor 'M1-like' phenotype. Preclinical in vivo analysis shows that MALT1 inhibitor treatment results in immuno-reactivity of GBM-associated macrophages …

Premarket Clinical Evidence Strength And Recalls Of High-Risk Therapeutic Medical Devices, Maryam Mooghali, Faaizah Arshad, Vinay K Rathi, Kushal T Kadakia, Alexander O Everhart, Joseph S Ross, Sanket S Dhruva

2020-Current year OA Pubs

IMPORTANCE: High-risk medical devices approved through the US Food and Drug Administration (FDA) premarket approval (PMA) pathway may be supported by limited premarket clinical evidence, leaving uncertainties about safety. Whether device, premarket clinical evidence, or regulatory characteristics are associated with subsequent device recalls is unknown.

OBJECTIVE: To examine the association between device, premarket clinical evidence, and regulatory characteristics and serious recalls among high-risk therapeutic devices.

DESIGN AND SETTING: This cross-sectional study reviewed 193 high-risk therapeutic medical devices approved through the FDA's PMA pathway between January 1, 2014, and December 31, 2023. Data were analyzed between August 2025 and December 2025. …

Childhood Cancer Predisposition Study: A Prospective Registry And Biorepository Protocol, Melissa R Perrino, Suzanne P Macfarland, Luke Maese, Jennie Vagher, Junne Kamihara, Surya Rednam, Philip J Lupo, Garrett M Brodeur, Joshua Schiffman, Lisa Diller, Lauren Desrosiers-Battu, Sharon E Plon, Kim E Nichols, Samuel L Volchenboum, David Malkin, Anita Villani, Christopher C Porter

Faculty, Staff and Students Publications

Introduction: Cancer is the most common cause of disease-related mortality in children, highlighting the urgent need for improved care in this population. It is estimated that >15% of children diagnosed with cancer harbour a germline pathogenic variant in a cancer predisposition gene which confers an increased risk to develop cancer. There are over 100 genes associated with cancer predisposition syndromes (CPSs) and greater availability and acceptability of genetic testing in the last decade has facilitated their recognition in childhood. However, individually, each of these CPSs is rare, impeding robust research and advancement of clinical care. Once a specific CPS is …

Unfolded Protein Response As A Therapeutic Target: 4-(Heptyloxy)Phenol Induces Programmed Cell Death In Ewing Sarcoma, Nenggang Zhang, Mary Perez, Gaye N Jenkins, Terzah M Horton, Scott R Gilbertson, Debananda Pati

Faculty, Staff and Students Publications

Ewing sarcoma is a rare and aggressive pediatric malignancy with limited therapeutic options, particularly for relapsed or refractory cases, highlighting the urgent need for innovative treatment strategies. In this study, we identify endoplasmic reticulum stress (ERS) and the unfolded protein response (UPR) as critical therapeutic vulnerabilities in Ewing sarcoma and introduce 4-(heptyloxy)phenol (AC-45594) as a novel small-molecule agent that exploits these stress pathways. AC-45594 selectively inhibited the growth of Ewing sarcoma cells among 13 cancer and 6 noncancerous cell lines, demonstrating marked tumor specificity. Structure-activity relationship studies revealed that both the phenolic hydroxyl group and an optimal alkoxy chain length …

Mir155, Triplicated In Down Syndrome, Regulates The Development Of Neural Stem Cells And Gabaergic Interneurons In Alzheimer's Disease Mouse And Human Ipsc Models., Xiaodong Zhu, Jean-Vianney Haure-Mirande, Mesude Bicak, Pengfei Dong, Ilya Kruglikov, Aiqun Li, Aisha Al-Subaie, Valentina Fossati, Scott Noggle, Sam Gandy, Michelle E Ehrlich

Faculty Research 2026

INTRODUCTION: Dysfunctional microRNAs and GABAergic interneurons are features of Alzheimer's disease (AD). The role of neuronal microRNA155 (miR155), elevated in both AD and Down syndrome (DS), remains unknown.

METHODS: We utilized in silico analyses of published databases, MIR155-deleted and -overexpressing human induced pluripotent stem cell (hiPSC)-derived cells, cortical organoids, and amyloid beta precursor protein (APP)/PS1-miR155 knockout mouse.

RESULTS: MIR155HG (miR155 host gene) colocalizes with APP in a neuron-specific, topologically associated domain (TAD) in chromosome 21. In human neural stem cells (NSCs), neurons, and cortical organoids, MIR155 deletion enhanced NSC proliferation and GABAergic interneuron generation. MIR155 overexpression inhibited NSC marker expression …