Digital Commons Network^™

Single Cell Analysis Of Short-Term Dry Eye Induced Changes In Cornea Immune Cell Populations, Jehan Alam, Ebru Yaman, Gerda Cristal Villalba Silva, Rui Chen, Cinita S De Paiva, Mary Ann Stepp, Stephen C Pflugfelder

Faculty, Staff and Students Publications

BACKGROUND: Dry eye causes corneal inflammation, epitheliopathy and sensorineural changes. This study evaluates the hypothesis that dry eye alters the percentages and transcriptional profiles of immune cell populations in the cornea.

METHODS: Desiccating stress (DS) induced dry eye was created by pharmacologic suppression of tear secretion and exposure to drafty low humidity environment. Expression profiling of corneal immune cells was performed by single-cell RNA sequencing (scRNA-seq). Cell differentiation trajectories and cell fate were modeled through RNA velocity analysis. Confocal microscopy was used to immunodetect corneal immune cells. Irritation response to topical neurostimulants was assessed.

RESULTS: Twelve corneal immune cell populations …

Ispad Clinical Practice Consensus Guidelines 2024: Screening, Staging, And Strategies To Preserve Beta-Cell Function In Children And Adolescents With Type 1 Diabetes, Michael J Haller, Kirstine J Bell, Rachel E J Besser, Kristina Casteels, Jenny J Couper, Maria E Craig, Helena Elding Larsson, Laura Jacobsen, Karin Lange, Tal Oron, Emily K Sims, Cate Speake, Mustafa Tosur, Francesca Ulivi, Anette-G Ziegler, Diane K Wherrett, M Loredana Marcovecchio

Faculty, Staff and Students Publications

The International Society for Pediatric and Adolescent Diabetes (ISPAD) guidelines represent a rich repository that serves as the only comprehensive set of clinical recommendations for children, adolescents, and young adults living with diabetes worldwide. This guideline serves as an update to the 2022 ISPAD consensus guideline on staging for type 1 diabetes (T1D). Key additions include an evidence-based summary of recommendations for screening for risk of T1D and monitoring those with early-stage T1D. In addition, a review of clinical trials designed to delay progression to Stage 3 T1D and efforts seeking to preserve beta-cell function in those with Stage 3 …

Etiology Of Hospital Mortality In Children Living In Low- And Middle-Income Countries: A Systematic Review And Meta-Analysis, Teresa B Kortz, Rishi P Mediratta, Audrey M Smith, Katie R Nielsen, Asya Agulnik, Stephanie Gordon Rivera, Hailey Reeves, Nicole F O'Brien, Jan Hau Lee, Qalab Abbas, Jonah E Attebery, Tigist Bacha, Emaan G Bhutta, Carter J Biewen, Jhon Camacho-Cruz, Alvaro Coronado Muñoz, Mary L Dealmeida, Larko Domeryo Owusu, Yudy Fonseca, Shubhada Hooli, Hunter Wynkoop, Mara Leimanis-Laurens, Deogratius Nicholaus Mally, Amanda M Mccarthy, Andrew Mutekanga, Carol Pineda, Kenneth E Remy, Sara C Sanders, Erica Tabor, Adriana Teixeira Rodrigues, Justin Qi Yuee Wang, Niranjan Kissoon, Yemisi Takwoingi, Matthew O Wiens, Adnan Bhutta

Faculty, Staff and Students Publications

In 2019, 80% of the 7.4 million global child deaths occurred in low- and middle-income countries (LMICs). Global and regional estimates of cause of hospital death and admission in LMIC children are needed to guide global and local priority setting and resource allocation but are currently lacking. The study objective was to estimate global and regional prevalence for common causes of pediatric hospital mortality and admission in LMICs. We performed a systematic review and meta-analysis to identify LMIC observational studies published January 1, 2005-February 26, 2021. Eligible studies included: a general pediatric admission population, a cause of admission or death, …

Protein Biomarkers Gdf15 And Fgf21 To Differentiate Mitochondrial Hepatopathies From Other Pediatric Liver Diseases, Johan L K Van Hove, Marisa W Friederich, Dana K Strode, Roxanne A Van Hove, Kristen R Miller, Rohit Sharma, Hardik Shah, Jane Estrella, Linda Gabel, Simon Horslen, Rohit Kohli, Mark A Lovell, Alexander G Miethke, Jean P Molleston, Rene Romero, James E Squires, Estella M Alonso, Stephen L Guthery, Binita M Kamath, Kathleen M Loomes, Philip Rosenthal, Krupa R Mysore, Laurel A Cavallo, Pamela L Valentino, John C Magee, Shikha S Sundaram, Ronald J Sokol, Childhood Liver Disease Research Network (Children)

Faculty, Staff and Students Publications

BACKGROUND: Mitochondrial hepatopathies (MHs) are primary mitochondrial genetic disorders that can present as childhood liver disease. No recognized biomarkers discriminate MH from other childhood liver diseases. The protein biomarkers growth differentiation factor 15 (GDF15) and fibroblast growth factor 21 (FGF21) differentiate mitochondrial myopathies from other myopathies. We evaluated these biomarkers to determine if they discriminate MH from other liver diseases in children.

METHODS: Serum biomarkers were measured in 36 children with MH (17 had a genetic diagnosis); 38 each with biliary atresia, α1-antitrypsin deficiency, and Alagille syndrome; 20 with NASH; and 186 controls.

RESULTS: GDF15 levels compared to controls were …

The Impact Of Race On Pancreatic Cancer Treatment And Survival In The Nationwide Veterans Affairs Healthcare System, Natalia Khalaf, Ann Xu, Theresa Nguyen Wenker, Jennifer R Kramer, Yan Liu, Hardeep Singh, Hashem B El-Serag, Fasiha Kanwal

Faculty, Staff and Students Publications

OBJECTIVES: Among patients with pancreatic cancer, studies show racial disparities at multiple steps of the cancer care pathway. Access to healthcare is a frequently cited cause of these disparities. It remains unclear if racial disparities exist in an integrated, equal access public system such as the Veterans Affairs healthcare system.

METHODS: We identified all patients diagnosed with pancreatic adenocarcinoma in the national Veterans Affairs Central Cancer Registry from January 2010 to December 2018. We examined the independent association between race and 3 endpoints: stage at diagnosis, receipt of treatment, and survival while adjusting for sociodemographic factors and medical comorbidities.

RESULTS: …

Diagnosis And Management Of Shrimp Allergy, Bin Brenda Su, Warren Blackmon, Chun Xu, Christopher Holt, Nathaniel Boateng, Darren Wang, Vibha Szafron, Aikaterini Anagnostou, Sara Anvari, Carla M Davis

Faculty, Staff and Students Publications

Shrimp allergy, the most common food allergy in the United States, affects up to 2% of the population. Its etiology is multi-factorial with the combination of genetic predisposition and environmental exposures. This review summarizes the latest diagnosis and management strategies for shrimp allergy. Currently, the double-blind, placebo-controlled food challenge is the gold standard for diagnosis. Moreover, mainstream and experimental management strategies include food allergen avoidance, the FDA-approved omalizumab, and oral immunotherapy. Herein, we emphasize the urgent need to develop more effective diagnostic tools and therapies for shrimp allergy.

Applying Market Basket Analysis To Determine Complex Coassociations Among Food Allergens In Children With Food Protein-Induced Enterocolitis Syndrome (Fpies), Ankona Banerjee, Kenneth Nobleza, Cynthia Haddad, Joshua Eubanks, Ruchit Rana, Nicholas L Rider, Lisa Pompeii, Duc Nguyen, Sara Anvari

Faculty, Staff and Students Publications

BACKGROUND: Food protein-induced enterocolitis syndrome (FPIES) is a non-IgE-mediated food allergy, characterized by delayed onset of repetitive vomiting occurring 1 to 4 h following ingestion of a food allergen. Managing FPIES requires strict avoidance of the food trigger. The concern with FPIES is determining the risk of another FPIES food trigger reaction due to potential coassociations with other foods or food groups. An effective statistical approach for analyzing FPIES-related data is essential to identify common coallergens and their associations.

METHODS: This study employed Market Basket Analysis, a data-mining technique, to examine correlations and patterns among allergens in FPIES patients at …

Development Of A Mini Pig Model Of Peanut Allergy, Akhilesh Kumar Shakya, Brittany Backus, Lazar D Nesovic, Malini Mallick, Olivia Banister, Carla M Davis, Sara Anvari, Harvinder Singh Gill

Faculty, Staff and Students Publications

INTRODUCTION: The prevalence of peanut allergies is increasing, emphasizing the need for an animal model to enhance our understanding of peanut allergy pathogenesis and to advance diagnostic tools and therapeutic interventions. While mice are frequently used as model organisms, their allergic responses do not fully mirror those observed in humans, warranting the exploration of a higher animal model. The porcine gastrointestinal system closely resembles that of humans, and exhibits allergy symptoms akin to human responses, making pigs a promising model for peanut allergy research.

METHODS: In this study we compared two allergen sensitization protocols involving either topical allergen application after …

Autophagy Determines Distinct Cell Fates In Human Amnion And Chorion Cells, Mary Elise L Severino, Lauren Richardson, Ananth Kumar Kammala, Enkhtuya Radnaa, Kamil Khanipov, Leslie Michelle M Dalmacio, Indira U Mysorekar, Marian Kacerovsky, Ramkumar Menon

Faculty, Staff and Students Publications

Human fetal membranes (amniochorion) that line the intrauterine cavity consist of two distinct cell layers; single-layer amnion epithelial cells (AEC) and multilayer chorion trophoblast cells (CTC). These layers are connected through a collagen-rich extracellular matrix. Cellular remodeling helps support membrane growth and integrity during gestation and helps to maintain pregnancy. Preterm prelabor rupture of the human amniochorionic (fetal) membrane (pPROM) is antecedent to 40% of all spontaneous preterm birth. Oxidative stress (OS) induced activation of the p38 MAPK due to various maternal risk exposures and the amniochorion cells' senescence are reported pathological features of pPROM. Our transcriptomics analysis implicated dysregulated …

Harnessing Speech-Derived Digital Biomarkers To Detect And Quantify Cognitive Decline Severity In Older Adults, Gozde Cay, Valeria A Pfeifer, Myeounggon Lee, Mohammad Dehghan Rouzi, Adonay S Nunes, Nesreen El-Refaei, Anmol Salim Momin, Md Moin Uddin Atique, Matthias R Mehl, Ashkan Vaziri, Bijan Najafi

Center on Aging Staff Publications

Introduction: Current cognitive assessments suffer from floor/ceiling and practice effects, poor psychometric performance in mild cases, and repeated assessment effects. This study explores the use of digital speech analysis as an alternative tool for determining cognitive impairment. The study specifically focuses on identifying the digital speech biomarkers associated with cognitive impairment and its severity.

Methods: We recruited older adults with varying cognitive health. Their speech data, recorded via a wearable microphone during the reading aloud of a standard passage, were processed to derive digital biomarkers such as timing, pitch, and loudness. Cohen's d effect size highlighted group differences, and correlations …

Differences In Prediagnostic Serum Metabolomic And Lipidomic Profiles Between Cirrhosis Patients With And Without Incident Hepatocellular Carcinoma, Hannah Powell, Cristian Coarfa, Elisa Ruiz-Echartea, Sandra L Grimm, Omar Najjar, Bing Yu, Luis Olivares, Michael E Scheurer, Christie Ballantyne, Abeer Alsarraj, Emad Mohamed Salem, Aaron P Thrift, Hashem B El Serag, Salma Kaochar

Faculty, Staff and Students Publications

BACKGROUND: Early detection of hepatocellular carcinoma (HCC) is crucial for improving patient outcomes, but we lack robust clinical biomarkers. This study aimed to identify a metabolite and/or lipid panel for early HCC detection.

METHODS: We developed a high-resolution liquid chromatography mass spectrometry (LC-MS)-based profiling platform and evaluated differences in the global metabolome and lipidome between 28 pre-diagnostic serum samples from patients with cirrhosis who subsequently developed HCC (cases) and 30 samples from patients with cirrhosis and no HCC (controls). We linked differentially expressed metabolites and lipids to their associated genes, proteins, and transcriptomic signatures in publicly available datasets. We used …

Faslpr Gene Dosage Tunes The Extent Of Lymphoproliferation And T Cell Differentiation In Lupus, Ritu Bohat, Xiaofang Liang, Yanping Chen, Chunyu Xu, Ningbo Zheng, Ashley Guerrero, Jiakai Hou, Roshni Jaffery, Nicholas A Egan, Yaxi Li, Yitao Tang, Esra Unsal, Adolfo Robles, Si Chen, Angela M Major, Hadil Elldakli, Sang-Hyuk Chung, Han Liang, M John Hicks, Yong Du, Jamie S Lin, Xiqun Chen, Chandra Mohan, Weiyi Peng

Faculty, Staff and Student Publications

Sle1 and Fas^lpr are two lupus susceptibility loci that lead to manifestations of systemic lupus erythematosus. To evaluate the dosage effects of Fas^lpr in determining cellular and serological phenotypes associated with lupus, we developed a new C57BL/6 (B6) congenic lupus strain, B6.Sle1/Sle1.Fas^lpr/+ (Sle1homo.lprhet) and compared it with B6.Fas^lpr/lpr (lprhomo), B6.Sle1/Sle1 (Sle1homo), and B6.Sle1/Sle1.Fas^lpr/lpr (Sle1homo.lprhomo) strains. Whereas Sle1homo.lprhomo mice exhibited profound lymphoproliferation and early mortality, Sle1homo.lprhet mice had a lifespan comparable to B6 mice, with no evidence of splenomegaly or lymphadenopathy. Compared to B6 monogenic lupus strains, Sle1homo.lprhet mice exhibited significantly …

Effects Of Bioprosthetic Valve Fracturing On Valve-In-Valve Transcatheter Aortic Valve Implantation Transvalvular Gradients, Osama Hallak, Karley Fischer, Shaina Ailawadi, Damian Valencia, Yan Yatsynovich, Raja Nazir, Brian Schwartz

The Texas Heart Institute Journal

BACKGROUND: Valve-in-valve (ViV) transcatheter aortic valve implantation (TAVI) is quickly becoming a routine and effective means by which to treat degenerated bioprosthetic valves. A known complication of ViV-TAVI is patient-prosthesis mismatch, which substantially affects survival. Bioprosthetic valve fracture is a method by which to reduce the risk of patient-prosthesis mismatch and post-ViV-TAVI transvalvular gradients. This study sought to determine the safety and efficacy of post-ViV-TAVI bioprosthetic valve fracture.

METHODS: Patients with a history of surgical aortic valve replacement undergoing ViV-TAVI bioprosthetic valve fracture (N = 25) at the corresponding institution from 2015 to 2022 were cataloged for a retrospective analysis. …

Detection Of Invasive Bartonella Infections With Next-Generation Sequencing Of Microbial Cell-Free Dna, Fernando H Centeno, Ahmed M Hamdi, Todd M Lasco, Mayar Al Mohajer

Faculty, Staff and Students Publications

We report 9 patients with invasive Bartonella infections, including 5 with endocarditis, who were diagnosed with microbial cell-free DNA next-generation sequencing and Bartonella serology studies. Diagnosis with plasma mcfDNA NGS enabled a faster clinical and laboratory diagnosis in 8 patients. Prompt diagnosis impacted antibiotic management in all 9 patients.

Age-Associated Temporal Decline In Butyrate-Producing Bacteria Plays A Key Pathogenic Role In The Onset And Progression Of Neuropathology And Memory Deficits In 3×Tg-Ad Mice, Paula M Chilton, Smita S Ghare, Benjamin T Charpentier, Scott A Myers, Aakarsha V Rao, Joseph F Petrosino, Kristi L Hoffman, John C Greenwell, Neetu Tyagi, Jyotirmaya Behera, Yali Wang, Lucy J Sloan, Jingwen Zhang, Christopher B Shields, Gregory E Cooper, Leila Gobejishvili, Scott R Whittemore, Craig J Mcclain, Shirish S Barve

Faculty, Staff and Students Publications

Alterations in the gut-microbiome-brain axis are increasingly being recognized to be involved in Alzheimer's disease (AD) pathogenesis. However, the functional consequences of enteric dysbiosis linking gut microbiota and brain pathology in AD progression remain largely undetermined. The present work investigated the causal role of age-associated temporal decline in butyrate-producing bacteria and butyrate in the etiopathogenesis of AD. Longitudinal metagenomics, neuropathological, and memory analyses were performed in the 3×Tg-AD mouse model. Metataxonomic analyses showed a significant temporal decline in the alpha diversity marked by a decrease in butyrate-producing bacterial communities and a concurrent reduction in cecal butyrate production. Inferred metagenomics analysis …

Inter And Intra-Host Diversity Of Rsv In Hematopoietic Stem Cell Transplant Adults With Normal And Delayed Viral Clearance, Vasanthi Avadhanula, Daniel Paiva Agustinho, Vipin Kumar Menon, Roy F Chemaly, Dimpy P Shah, Xiang Qin, Anil Surathu, Harshavardhan Doddapaneni, Donna M Muzny, Ginger A Metcalf, Sara Javornik Cregeen, Richard A Gibbs, Joseph F Petrosino, Fritz J Sedlazeck, Pedro A Piedra

Faculty, Staff and Students Publications

Respiratory syncytial virus (RSV) infection in immunocompromised individuals often leads to prolonged illness, progression to severe lower respiratory tract infection, and even death. How the host immune environment of the hematopoietic stem cell transplant (HCT) adults can affect viral genetic variation during an acute infection is not understood well. In the present study, we performed whole genome sequencing of RSV/A or RSV/B from samples collected longitudinally from HCT adults with normal (<14 >days) and delayed (≥14 days) RSV clearance who were enrolled in a ribavirin trial. We determined the inter-host and intra-host genetic variation of RSV and the effect of …

Prospective Associations Of Psychedelic Treatment For Co-Occurring Alcohol Misuse And Posttraumatic Stress Symptoms Among United States Special Operations Forces Veterans, Stacey B Armstrong, Yitong Xin, Nathan D Sepeda, Martín Polanco, Lynnette A Averill, Alan K Davis

Faculty, Staff and Students Publications

This study evaluated prospective associations of ibogaine and 5-MeO-DMT treatment for risky alcohol use and post-traumatic stress disorder (PTSD) symptoms among United States (US) Special Operations Forces Veterans (SOFV). Data were collected during standard clinical operations at pre-treatment and 1-month (1 m), 3-months (3 m), and 6-months (6 m) post-treatment in an ibogaine and 5-MeO-DMT treatment program in Mexico. Of the 86 SOFV that completed treatment, 45 met criteria for risky alcohol use at pre-treatment (mean age = 44; male = 100%; White = 91%). There was a significant reduction in alcohol use from pre-treatment (M = 7.2, SD = …

Metabolink Is A Novel Algorithm For Unveiling Cell-Specific Metabolic Pathways In Longitudinal Datasets, Jared Lichtarge, Gerarda Cappuccio, Soumya Pati, Alfred Kwabena Dei-Ampeh, Senghong Sing, Lihua Ma, Zhandong Liu, Mirjana Maletic-Savatic

Duncan NRI Faculty and Staff Publications

Introduction: In the rapidly advancing field of 'omics research, there is an increasing demand for sophisticated bioinformatic tools to enable efficient and consistent data analysis. As biological datasets, particularly metabolomics, become larger and more complex, innovative strategies are essential for deciphering the intricate molecular and cellular networks.

Methods: We introduce a pioneering analytical approach that combines Principal Component Analysis (PCA) with Graphical Lasso (GLASSO). This method is designed to reduce the dimensionality of large datasets while preserving significant variance. For the first time, we applied the PCA-GLASSO algorithm (i.e., MetaboLINK) to metabolomics data derived from Nuclear Magnetic Resonance (NMR) spectroscopy …

The Next-Generation Dna Vaccine Platforms And Delivery Systems: Advances, Challenges And Prospects, Bowen Lu, Jing Ming Lim, Boyue Yu, Siyuan Song, Praveen Neeli, Navid Sobhani, Pavithra K, Srinivasa Reddy Bonam, Rajendra Kurapati, Junnian Zheng, Dafei Chai

Faculty, Staff and Students Publications

Vaccines have proven effective in the treatment and prevention of numerous diseases. However, traditional attenuated and inactivated vaccines suffer from certain drawbacks such as complex preparation, limited efficacy, potential risks and others. These limitations restrict their widespread use, especially in the face of an increasingly diverse range of diseases. With the ongoing advancements in genetic engineering vaccines, DNA vaccines have emerged as a highly promising approach in the treatment of both genetic diseases and acquired diseases. While several DNA vaccines have demonstrated substantial success in animal models of diseases, certain challenges need to be addressed before application in human subjects. …

Identification Of Constrained Sequence Elements Across 239 Primate Genomes, Lukas F K Kuderna, Jacob C Ulirsch, Sabrina Rashid, Mohamed Ameen, Laksshman Sundaram, Glenn Hickey, Anthony J Cox, Hong Gao, Arvind Kumar, Francois Aguet, Matthew J Christmas, Hiram Clawson, Maximilian Haeussler, Mareike C Janiak, Martin Kuhlwilm, Joseph D Orkin, Thomas Bataillon, Shivakumara Manu, Alejandro Valenzuela, Juraj Bergman, Marjolaine Rouselle, Felipe Ennes Silva, Lidia Agueda, Julie Blanc, Marta Gut, Dorien De Vries, Ian Goodhead, R Alan Harris, Muthuswamy Raveendran, Axel Jensen, Idriss S Chuma, Julie E Horvath, Christina Hvilsom, David Juan, Peter Frandsen, Joshua G Schraiber, Fabiano R De Melo, Fabrício Bertuol, Hazel Byrne, Iracilda Sampaio, Izeni Farias, João Valsecchi, Malu Messias, Maria N F Da Silva, Mihir Trivedi, Rogerio Rossi, Tomas Hrbek, Nicole Andriaholinirina, Clément J Rabarivola, Alphonse Zaramody, Clifford J Jolly, Jane Phillips-Conroy, Gregory Wilkerson, Christian Abee, Joe H Simmons, Eduardo Fernandez-Duque, Sree Kanthaswamy, Fekadu Shiferaw, Dongdong Wu, Long Zhou, Yong Shao, Guojie Zhang, Julius D Keyyu, Sascha Knauf, Minh D Le, Esther Lizano, Stefan Merker, Arcadi Navarro, Tilo Nadler, Chiea Chuen Khor, Jessica Lee, Patrick Tan, Weng Khong Lim, Andrew C Kitchener, Dietmar Zinner, Ivo Gut, Amanda D Melin, Katerina Guschanski, Mikkel Heide Schierup, Robin M D Beck, Ioannis Karakikes, Kevin C Wang, Govindhaswamy Umapathy, Christian Roos, Jean P Boubli, Adam Siepel, Anshul Kundaje, Benedict Paten, Kerstin Lindblad-Toh, Jeffrey Rogers, Tomas Marques Bonet, Kyle Kai-How Farh

Faculty, Staff and Students Publications

Noncoding DNA is central to our understanding of human gene regulation and complex diseases1,2, and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in the human genome3–9. Identifying the genomic elements that have become constrained specifically in primates has been hampered by the faster evolution of noncoding DNA compared to protein-coding DNA10, the relatively short timescales separating primate species11, and the previously limited availability of whole-genome sequences12. Here we construct a whole-genome alignment of 239 species, representing nearly half of …

Improved Sequence Mapping Using A Complete Reference Genome And Lift-Over, Nae-Chyun Chen, Luis F Paulin, Fritz J Sedlazeck, Sergey Koren, Adam M Phillippy, Ben Langmead

Faculty, Staff and Students Publications

Complete, telomere-to-telomere genome assemblies promise improved analyses and the discovery of new variants, but many essential genomic resources remain associated with older reference genomes. Thus, there is a need to translate genomic features and read alignments between references. Here we describe a new method called levioSAM2 that accounts for reference changes and performs fast and accurate lift-over between assemblies using a whole-genome map. In addition to enabling the use of multiple references, we demonstrate that aligning reads to a high-quality reference (e.g. T2T-CHM13) and lifting to an older reference (e.g. GRCh38) actually improves the accuracy of the resulting variant calls …

Inference Of Phylogenetic Trees Directly From Raw Sequencing Reads Using Read2tree, David Dylus, Adrian Altenhoff, Sina Majidian, Fritz J Sedlazeck, Christophe Dessimoz

Faculty, Staff and Students Publications

Current methods for inference of phylogenetic trees require running complex pipelines at substantial computational and labor costs, with additional constraints in sequencing coverage, assembly and annotation quality, especially for large datasets. To overcome these challenges, we present Read2Tree, which directly processes raw sequencing reads into groups of corresponding genes and bypasses traditional steps in phylogeny inference, such as genome assembly, annotation and all-versus-all sequence comparisons, while retaining accuracy. In a benchmark encompassing a broad variety of datasets, Read2Tree is 10-100 times faster than assembly-based approaches and in most cases more accurate-the exception being when sequencing coverage is high and reference …

Research Participants' Perspectives On Precision Diagnostics For Alzheimer's Disease, Hadley Stevens Smith, Jill O Robinson, Ariel Levchenko, Stacey Pereira, Belen Pascual, Kathleen Bradbury, Victoria Arbones, Jamie Fong, Joshua M Shulman, Amy L Mcguire, Joseph Masdeu

Faculty, Staff and Students Publications

BACKGROUND: Understanding research participants' responses to learning Alzheimer's disease (AD) risk information is important to inform clinical implementation of precision diagnostics given rapid advances in disease modifying therapies.

OBJECTIVE: We assessed participants' perspectives on the meaning of their amyloid positron emission tomography (PET) imaging results for their health, self-efficacy to understand their results, psychological impact of learning their results, experience receiving their results from the clinical team, and interest in genetic testing for AD risk.

METHODS: We surveyed individuals who were being clinically evaluated for AD and received PET imaging six weeks after the return of results. We analyzed responses …

Scientific Impact Of The National Birth Defects Prevention Network Multistate Collaborative Publications, Jacqueline T Bascom, Sara B Stephens, Philip J Lupo, Mark A Canfield, Russell S Kirby, Eirini Nestoridi, Jason L Salemi, Cara T Mai, Wendy N Nembhard, Nina E Forestieri, Paul A Romitti, Amanda M St Louis, A J Agopian

Faculty, Staff and Students Publications

BACKGROUND: Given the lack of a national, population-based birth defects surveillance program in the United States, the National Birth Defects Prevention Network (NBDPN) has facilitated important studies on surveillance, research, and prevention of major birth defects. We sought to summarize NBDPN peer-reviewed publications and their impact.

METHODS: We obtained and reviewed a curated list of 49 NBDPN multistate collaborative publications during 2000-2022, as of December 31, 2022. Each publication was reviewed and classified by type (e.g., risk factor association analysis). Key characteristics of study populations and analytic approaches used, along with publication impact (e.g., number of citations), were tabulated.

RESULTS: …

Combined Bioinformatic And Splicing Analysis Of Likely Benign Intronic And Synonymous Variants Reveals Evidence For Pathogenicity, Owen R Hirschi, Stephanie A Felker, Surya P Rednam, Kelly L Vallance, D Williams Parsons, Angshumoy Roy, Gregory M Cooper, Sharon E Plon

Faculty, Staff and Students Publications

PURPOSE: Clinical variant analysis pipelines likely have poor sensitivity to the effects on splicing from variants beyond 10 to 20 bases of exon-intron boundaries. Here, we demonstrate the value of SpliceAI to inform curation of rare variants previously classified as benign/likely benign (B/LB) under current guidelines.

METHODS: Exome sequencing data from 576 pediatric cancer patients enrolled in the Texas KidsCanSeq study were filtered for intronic or synonymous variants absent from population databases, predicted to alter splicing via SpliceAI (>0.20), and scored >10 by combined annotation-dependent depletion. Rare synonymous or intronic B/LB variants in 61 genes submitted to ClinVar were …

Bi-Allelic Variants In Cep295 Cause Seckel-Like Syndrome Presenting With Primary Microcephaly, Developmental Delay, Intellectual Disability, Short Stature, Craniofacial And Digital Abnormalities, Niu Li, Yufei Xu, Hongzhu Chen, Jingqi Lin, Lama Alabdi, Mir Reza Bekheirnia, Guoqiang Li, Yoel Gofin, Nasim Bekheirnia, Eissa Faqeih, Lina Chen, Guoying Chang, Jie Tang, Ruen Yao, Tingting Yu, Xiumin Wang, Wei Fu, Qihua Fu, Yiping Shen, Fowzan S Alkuraya, Keren Machol, Jian Wang

Faculty, Staff and Students Publications

BACKGROUND: Pathogenic variants in the centrosome protein (CEP) family have been implicated in primary microcephaly, Seckel syndrome, and classical ciliopathies. However, most CEP genes remain unlinked to specific Mendelian genetic diseases in humans. We sought to explore the roles of CEP295 in human pathology.

METHODS: Whole-exome sequencing was performed to screen for pathogenic variants in patients with severe microcephaly. Patient-derived fibroblasts and CEP295-depleted U2OS and RPE1 cells were used to clarify the underlying pathomechanisms, including centriole/centrosome development, cell cycle and proliferation changes, and ciliogenesis. Complementary experiments using CEP295 mRNA were performed to determine the pathogenicity of the identified missense variant. …

Tremor In Cervical Dystonia, Sinem Balta Beylergil, Krishna Nikhil Mukunda, Mohamed Elkasaby, Joel S Perlmutter, Stewart Factor, Tobias Bäumer, Jeanne Feurestein, Erika Shelton, Steven Bellows, Joseph Jankovic, Abhimanyu Mahajan, Tila Wamer-Rosen, Stephen G Reich, Aparna Wagle Shukla, Irene Malaty, Alberto Espay, Kevin Duque, Mark S Ledoux, Rachel Saunders-Pullman, Katherine Leaver, Samuel Frank, Alexander Pantelyat, Victor Fung, Sarah Pirio Richardson, Brian Berman, Natividad Stover, Andres Deik, William Ondo, Christopher Groth, Hyder A Jinnah, Aasef G Shaikh

Faculty, Staff and Students Publications

BACKGROUND: Cervical dystonia (CD) is the most common form of focal dystonia encountered in the clinic. Approximately one-third of CD patients have co-existing tremor in the head and hands. Assessment of tremor as regular or irregular in context of its oscillation trajectory, frequency, and amplitude is a major clinical challenge and can confound the diagnosis of CD. The misdiagnosis may lead to therapeutic failures, poor quality of life, and poor utilization of medical and financial resources.

METHODS: We analyzed the largest cohort of CD patients (

RESULTS: Out of 3,117 CD patients, 1,367 had neck tremor. The neck tremor was …

Use Of Botulinum Toxin In The Management Of Dystonia In Parkinson’S Disease, Charenya Anandan, Joseph Jankovic

Faculty, Staff and Students Publications

Botulinum toxin is one of the most potent neurotoxins, but when injected into an overactive muscle, it can transiently alleviate an involuntary movement, such as dystonia. The primary aim of this article is to provide a comprehensive review of the various forms of dystonia observed in patients with Parkinson's disease who can benefit from a therapeutic trial of botulinum toxin. Although most of these indications are not supported by randomized controlled clinical trials and, therefore, not approved by the Food and Drug Administration, there are many open-label trials supporting a large body of empirical experience testifying to the benefits of …

Screening For Adhd In Adult Patients With Epilepsy: Prevalence Of Symptoms And Challenges To Diagnosis, Trung Nguyen, Emily Xiao, Allison Clark, Afroz Shamim, Atul Maheshwari

Faculty, Staff and Students Publications

OBJECTIVE: Given the complex nature of seizure disorders and their treatments, ADHD may be underdiagnosed in this population. We hypothesized that a higher percentage of patients presenting to a seizure clinic would endorse ADHD symptoms compared to rates reported in the general population and that formal screening for ADHD symptoms would identify patients with previously undiagnosed comorbid ADHD.

METHODS: In this study, we surveyed 312 adults in a seizure clinic using the Adult ADHD Self-Report Scale (ASRS-v1.1).

RESULTS: We found that 90 patients (28.8%) screened positive with the ASRS-v1.1, but only nine of these patients were able to complete neuropsychological …

Nutritional Importance Of Animal-Sourced Foods In A Healthy Diet, Sydney Sheffield, Marta L Fiorotto, Teresa A Davis

Faculty, Staff and Students Publications

Animal-sourced foods, such as meats, poultry, eggs, milk, and fish are nutrient-dense foods that are rich sources of protein, essential amino acids, and micronutrients that can be challenging to obtain solely through plant-based foods. Animal-sourced protein foods provide crucial nutrients that support the growth and development in children, maintenance of muscle mass and function in adults, gain in muscle mass and strength in exercising individuals, and mitigation of sarcopenia in the elderly. The 2020–2025 Dietary Guidelines for Americans have identified the important role of animal-sourced foods in the diet at every stage of life. Animal-sourced foods are consumed worldwide and …