Digital Commons Network^™

Author Correction: Oncolytic Dnx-2401 Virotherapy Plus Pembrolizumab In Recurrent Glioblastoma: A Phase 1/2 Trial, Farshad Nassiri, Vikas Patil, Leeor S Yefet, Olivia Singh, Jeff Liu, Rachel M A Dang, Takafumi N Yamaguchi, Mariza Daras, Timothy F Cloughesy, Howard Colman, Priya U Kumthekar, Clark C Chen, Robert Aiken, Morris D Groves, Shirley S Ong, Rohan Ramakrishna, Michael A Vogelbaum, Simon Khagi, Thomas Kaley, Jason M Melear, David M Peereboom, Analiz Rodriguez, Maxim Yankelevich, Suresh G Nair, Vinay K Puduvalli, Kenneth Aldape, Andrew Gao, Álvaro López-Janeiro, Carlos E De Andrea, Marta M Alonso, Paul Boutros, Joan Robbins, Warren P Mason, Adam M Sonabend, Roger Stupp, Juan Fueyo, Candelaria Gomez-Manzano, Frederick F Lang, Gelareh Zadeh

Faculty, Staff and Student Publications

No abstract provided.

Correction: Imaging In Pelvic Exenteration-A Multidisciplinary Practice Guide From The Esgar-Sar-Esur-Pelvex Collaborative Group, Stephanie Nougaret, Doenja M J Lambregts, Geerard L Beets, Regina G H Beets-Tan, Lennart Blomqvist, David Burling, Quentin Denost, Maria A Gambacorta, Benedetta Gui, Ann Klopp, Yulia Lakhman, Kate E Maturen, Riccardo Manfredi, Iva Petkovska, Luca Russo, Atul B Shinagare, James A Stephenson, Damian Tolan, Aradhana M Venkatesan, Aaron J Quyn, Rosemarie Forstner

Faculty, Staff and Student Publications

No abstract provided.

Trop2 Expression In Salivary Gland Adenoidcystic Carcinoma (Acc) According To Histologic Subtype: Therapeutic Implications, Juliana Mota Siqueira, Yoshitsugu Mitani, Mario L Marques-Piubelli, Camilla Oliveira Hoff, Flavia Bonini, Luana Guimaraes De Sousa, Mutsumi Mitani, Giovanna Lopes Carvalho, Fabio Daumas Nunes, Leandro Luongo Matos, Shiaw-Yih Lin, Michael T Spiotto, Ehab Y Hanna, Daniel J Mcgrail, Adel K El-Naggar, Renata Ferrarotto

Faculty, Staff and Student Publications

Background: Adenoid cystic carcinoma (ACC) is a common salivary gland carcinoma with high recurrence and distant metastasis rates. Currently, there is no standard systemic treatment available. TROP2 is a transmembrane glycoprotein involved in the oncogenesis of several tumors that can be therapeutically targeted by a TROP2-antibody-drug conjugate (ADC). We aimed to characterize TROP2 expression in ACC and assess TROP2 as a potential therapeutic target.

Methods: TROP2 immunohistochemistry was performed in a tissue microarray including 165 ACC of salivary gland. The tumors were grouped according to the histological pattern as non-solid, solid + non-solid, or solid. TROP2 protein expression in ACC …

Mature And Migratory Dendritic Cells Promote Immune Infiltration And Response To Anti-Pd-1 Checkpoint Blockade In Metastatic Melanoma, Jiekun Yang, Cassia Wang, Doris Fu, Li-Lun Ho, Kyriakitsa Galani, Lee Chen, Jose Gonzalez, Jolene Fu, Amy Y Huang, Dennie T Frederick, Liang He, Mukta Asnani, Rahul Tacke, Emily J Robitschek, Sandeep K Yadav, Wentao Deng, Kelly P Burke, Tatyana Sharova, Ryan J Sullivan, Sarah Weiss, Kunal Rai, David Liu, Genevieve M Boland, Manolis Kellis

Faculty, Staff and Student Publications

Immune checkpoint inhibitors (ICIs) have revolutionized cancer therapy, yet most patients fail to achieve durable responses. To better understand the tumor microenvironment (TME), we analyze single-cell RNA-seq (~189 K cells) from 36 metastatic melanoma samples, defining 14 cell types, 55 subtypes, and 15 transcriptional hallmarks of malignant cells. Correlations between cell subtype proportions reveal six distinct clusters, with a mature dendritic cell subtype enriched in immunoregulatory molecules (mregDC) linked to naive T and B cells. Importantly, mregDC abundance predicts progression-free survival (PFS) with ICIs and other therapies, especially when combined with the TCF7 + /- CD8 T cell ratio. Analysis …

Spatial Colocalization And Molecular Crosstalk Of Myofibroblastic Cafs And Tumor Cells Shape Lymph Node Metastasis In Oral Squamous Cell Carcinoma, Ken Furudate, Shuya Kasai, Tadashi Yoshizawa, Yuya Sasaki, Kohei Fujikura, Shintaro Goto, Ryohei Ito, Koki Takagi, Tomoyuki Tanaka, Hiroshi Kijima, Kosei Kubota, Ken Itoh, Wataru Kobayashi, Koichi Takahashi

Faculty, Staff and Student Publications

Lymph node metastasis (LNM) is a critical prognostic factor for patients with oral squamous cell carcinoma (OSCC). Previous research has implicated the partial epithelial-to-mesenchymal transition of tumor cells and myofibroblastic cancer-associated fibroblasts (myCAFs) in the LNM process. However, the underlying molecular mechanisms remain poorly understood. Here, we conducted a comprehensive molecular analysis integrating original and publicly available OSCC data from bulk genome and transcriptome, single-cell transcriptome, and spatial transcriptome analyses. We found that myCAFs were quantitatively and functionally activated in LNM-positive samples and spatially colocalized with OSCC cells within the invasive tumor front (ITF), providing a niche that may facilitate …

The Brescia International Multidisciplinary Consensus Guidelines On The Optimal Pathology Assessment And Multidisciplinary Pathways Of Non-Pancreatic Neoplasms In And Around The Ampulla Of Vater (Peripan), Mohammad Abu Hilal, Bas A Uijterwijk, Daniël H L Lemmers, Boris V Janssen, Marc G Besselink, Denise Bianchi, Arantza Fariña, Noriyoshi Fukushima, Anthony J Gill, Seung-Mo Hong, Alyssa Krasinskas, Claudio Luchini, Laura Melocchi, Giulio Rossi, Aldo Scarpa, Olca Basturk, Deyali Chatterjee, Angela Chou, Irene Esposito, Roger Feakins, Bas Groot Koerkamp, Ralph H Hruban, Stefano La Rosa, Chanjuan Shi, Aatur Singhi, Joanne Verheij, Huamin Wang, Sergio Alfieri, Fabio Ausania, Adnan Alseidi, Marco J Bruno, Ugo Boggi, Claudio Bnà, Christos Dervenis, Massimo Falconi, Michele Ghidini, Jakob W Kist, Giovanni Marchegiani, Michele Milella, Roberto Salvia, Ajith Siriwardena, Hanneke Wilmink, Alberto Zaniboni, Shaimaa Al-Janabi, Maia Blomhoff Holm, Eva Roos, Naoki Sano, In Hye Song, Zeynep Tarcan, Gianpaolo Balzano, Isabella Frigerio, Alfredo Guglielmi, Giuseppe Malleo, Horacio Asbun, Volkan Adsay, Caroline Verbeke

Faculty, Staff and Student Publications

IMPORTANCE: The lack of multidisciplinary workflow guidelines and clear definitions and classifications for neoplasms in and around the ampulla of Vater results in inconsistencies affecting patient care and research.

OBJECTIVE: The PERIPAN international multidisciplinary consensus group aimed to standardize the multidisciplinary diagnostic workflow and achieve consensus on definitions and classifications in order to ensure proper classification and optimal diagnostic assessment and consequently to improve patient care and future research.

DESIGN: An international team of 43 experts (pathologists, surgeons, radiologists, gastroenterologists, oncologists) from 12 countries identified knowledge gaps, reviewed 37061 articles, and proposed recommendations using the Scottish Intercollegiate Guidelines Network methodology …

Author Correction: Ppp2r1a Mutations Portend Improved Survival After Cancer Immunotherapy, Yibo Dai, Anne Knisely, Mitsutake Yano, Minghao Dang, Emily M Hinchcliff, Sanghoon Lee, Annalyn Welp, Manoj Chelvanambi, Matthew Lastrapes, Heng Liu, Zhe Yuan, Chen Wang, Hao Nie, Stephanie Jean, Luis J Montaner, Jiakai Hou, Ami Patel, Shrina Patel, Bryan Fellman, Ying Yuan, Baohua Sun, Renganayaki Krishna Pandurengan, Edwin Roger Parra Cuentas, Joseph Celestino, Yan Liu, Jinsong Liu, R Tyler Hillman, Shannon N Westin, Anil K Sood, Pamela T Soliman, Aaron Shafer, Larissa A Meyer, David M Gershenson, David Vining, Dhakshinamoorthy Ganeshan, Karen Lu, Jennifer A Wargo, Weiyi Peng, Rugang Zhang, Linghua Wang, Amir A Jazaeri

Faculty, Staff and Student Publications

No abstract provided.

Acute Loss Of Tactile Input Leads To General Compensatory Changes In Eye-Hand Coordination During Object Manipulation, Kevin Ung, John F Magnotti, Brandon Kim, Jeffrey M Yau, Per F Nordmark

Faculty, Staff and Students Publications

Current models of motor control emphasize the critical role of sensory feedback, as demonstrated by movement coordination deficits following sensory impairment. When both vision and touch are available for object-oriented manual behaviors, they serve distinct roles; vision guides the execution of planned movements, while touch provides more direct feedback on hand-object interactions. The impact of losing somatosensory feedback on eye-hand coordination during dexterous object manipulation tasks has not been thoroughly studied. Conceivably, vision is recruited to compensate for the feedback lost when touch is abolished based on the dexterity demands of the behavior. To investigate this, we tested healthy participants …

Treatment Of Cutaneous Collagenous Vasculopathy With Pulsed Dye Laser, Hannah L Hanania, Isabella Camacho-Hubbard, Zeena Y Nawas

Faculty, Staff and Students Publications

Objectives: Cutaneous collagenous vasculopathy (CCV) is a rare, idiopathic microangiopathy marked by widespread telangiectasias and histologic vessel wall thickening. Due to its rarity and clinical overlap with other vascular conditions, CCV poses diagnostic and therapeutic challenges. This report highlights the successful use of pulsed dye laser (PDL) therapy in treating a case of extensive CCV.

Methods: A 40-year-old woman with a decade-long history of progressive telangiectasias involving the extremities, trunk, and forearms underwent treatment with a 595-nm PDL. Six treatment sessions were conducted over 14 months.

Results: The patient experienced significant improvement in erythema, telangiectasias, and associated discomfort, with sustained …

High-Fidelity Finite Element Modeling Technique To Improve Sensitivity To Bone Tissue Changes Of Older Adults With Obesity Undergoing Intensive Lifestyle Intervention, Michael A K Liebschner, Daeseung Kim, Nina Klonis, Giulia Gregori, Reina Armamento-Villareal, Clifford Qualls, Dennis T Villareal

Faculty, Staff and Students Publications

Introduction: Obesity presents a significant health risk for the aging population. Research shows that weight loss and regular exercise can greatly improve the functional status of older adults who are obese. However, weight loss may also result in a decrease in bone mass. To properly assess changes in fracture risk due to lifestyle interventions, a direct biomechanical evaluation of bone strength and fracture risk at metabolically active sites is essential.

Methods: Computed tomography scans taken at two different time points of ten human volunteers provided the foundation for this study. A high-fidelity segmentation and modeling approach was taken to generate …

A Phase 2 Randomized Trial Of Nbi-1065846 (Tak-041) In Patients With Anhedonia Associated With Major Depressive Disorder: Results Of The Terpsis Study, Shannon R Benedetto, Adrian Ionescu, Tingting Ge, Maura Furey, Swan Lin, Manish K Jha, Andrew Krystal, Asim A Shah, David P Walling, Neel Shah, Sakina J Rizvi, Sidney Kennedy, Antonio Laurenza, Venkatesha Murthy, Eiry Roberts, Jaskaran B Singh

Faculty, Staff and Students Publications

Background: Anhedonia is a core symptom of major depressive disorder (MDD) that may result from aberrant lateral habenula hyperactivity. Targeting G-protein coupled receptor 139 (GPR139) may improve anhedonia by modulating lateral habenula activity. NBI-1065846 is an investigational GPR139 agonist that improved anhedonia, anxiety, and depression in rodent models.

Methods: TERPSIS was a phase 2, proof-of-concept clinical study. Adults with MDD experiencing a major depressive episode with anhedonia were randomized 1:1 to NBI-1065846 or placebo for 8 weeks. The primary endpoint was the change in the Dimensional Anhedonia Rating Scale (DARS) score. Secondary endpoints were change in total Montgomery Åsberg Depression …

Validation Of An Assay For Ngal In A Pediatric Population, Nazmin Bithi, Ridwan B Ibrahim, Estella L Tam, Radwa Almamoun, Annette C Frenk Oquendo, Ayse Akcan-Arikan, Sridevi Devaraj

Faculty, Staff and Students Publications

Background and objectives: Acute kidney injury (AKI) poses a serious clinical challenge, particularly in high-risk environments, due to its association with increased morbidity and mortality. Traditional diagnostic markers, such as serum creatinine, often detect AKI only after significant kidney damage has occurred, limiting opportunities for early intervention. Neutrophil gelatinase-associated lipocalin (NGAL) has emerged as a promising early biomarker due to its rapid upregulation following kidney ischemia. NGAL supports renal recovery by reducing toxicity and promoting tubular regeneration via heme oxygenase-1 activity. This study aimed to validate the BioPorto ProNephro AKI™ turbidimetric immunoassay for urinary NGAL on the Ortho Vitros XT7600 …

The Role Of Serum Phosphate Control In Supporting Transplant Readiness In Patients On Dialysis, Laura A Williams, Stephen Z Fadem

Faculty, Staff and Students Publications

Chronic kidney disease affects over 36 million Americans, with more than 800,000 progressing to end-stage kidney disease (ESKD). Treatment with kidney transplantation offers superior survival, quality of life, and cost-effectiveness compared with dialysis, yet access remains limited. Hyperphosphatemia is a highly prevalent and modifiable complication of ESKD that contributes to cardiovascular disease, mineral bone disorder, and potential pulmonary dysfunction. Additionally, elevated serum phosphate has been linked to transplant graft failure and adverse post-transplant outcomes. Although normal phosphate levels are not formally required for transplant eligibility, they are frequently considered as part of transplant readiness assessments. Persistent gaps between clinical guideline …

Moderate Coffee And Tea Consumption Is Associated With Slower Cognitive Decline, Stephanie R. Rainey-Smith, Kelsey R. Sewell, Belinda M. Brown, Hamid R. Sohrabi, Ralph N. Martins, Samantha L. Gardener

Research outputs 2022 to 2026

Background: Globally, coffee and tea are consumed extensively, potentially providing neuroprotection through anti-inflammatory and antioxidative stress effects. Objective: This study aimed to investigate associations between coffee and tea intake and cognitive function. Methods: In a longitudinal prospective cohort study, dementia-free (n = 8715; age range 60.0–85.2 years) older adults from the UK Biobank self-reported coffee and tea intake over the previous year; ‘never’, ‘moderate’ (1–3 cups/day), or ‘high’ (≥4 cups/day). Participants completed cognitive assessments at ≥2 timepoints (mean of 9.11 years). Results: Those ‘never’ consuming coffee and ‘moderate’ coffee consumers (β = 0.06, p = 0.005; β = 0.07, p <  0.001, respectively), as well as ‘moderate’ tea consumers and ‘high’ tea consumers (β = 0.06, p = 0.009; β = 0.06, p = 0.003, respectively) had slower fluid intelligence decline. Additionally, those ‘never’ consuming coffee and ‘moderate’ coffee consumers had a slower increase in pairs matching errors (β = −0.05, p = 0.022; β = 0.05, p = 0.013) compared to ‘high’ consumers. Conclusions: ‘Moderate’ coffee, and ‘moderate’ and ‘high’ tea intake may be a protective factor against cognitive decline. Randomized controlled trials are required to establish causal relationships leading to evidence-based recommendations regarding benefits of coffee and tea intake.

Wandering Spleen In A Pediatric Lung Transplant Patient With Filamin A Deficiency: An Incidental Finding, Savannah Ellis Knight, Mayel Yepez Donado, Maria Carolina Gazzaneo

Faculty, Staff and Students Publications

Background: Filamin A (FLNA) deficiency is a known cause of progressive lung disease and need for pediatric lung transplant; however, what may be less well known to lung transplant providers are the extrapulmonary complications of FLNA deficiencies, such as wandering spleen. We present a patient who underwent a lung transplant for FLNA deficiency and later developed posttransplant abdominal pain.

Case presentation: An 11-year-old female who had previously undergone a bilateral lung transplant due to FLNA deficiency, causing progressive lung disease, presented with abdominal pain and diarrhea. The patient's stool was tested for causes of gastroenteritis using a gastrointestinal pathogen panel …

A Fascination With Gastrointestinal Viruses, Mary Kolb Estes

Faculty, Staff and Students Publications

My arrival into this world came quickly, according to my mother, and it feels like my life has mirrored that rapid beginning. I have enjoyed a rich, varied, and stimulating life and career that have gone through several phases. I credit genetics, my family, technological advances, and many environmental factors for shaping my career. Being a virologist allowed me to be curious and creative and to make several unexpected discoveries. This has been a fun and rewarding journey, but it wasn't always easy. I am not accustomed to talking about myself, but I am happy to share some scientific achievements …

Cognitive Performance In Early Neuronal Synuclein Disease With Hyposmia But Without Motor Disability: Association With Dopamine Deficiency And Isolated Rapid Eye Movement Sleep Behavior Disorder, Daniel Weintraub, Anuprita R Nair, Ryan Kurth, Michael C Brumm, Christine Kohnen, Michele K York, Roseanne D Dobkin, Kenneth Marek, Caroline Tanner, Tanya Simuni, Andrew Siderowf, Douglas Galasko, Lana M Chahine, Christopher Coffey, Kalpana Merchant, Kathleen L Poston, Tatiana Foroud, Brit Mollenhauer, Ethan G Brown, Karl Kieburtz, Mark Frasier, Sohini Chowdhury, Roy N Alcalay, Aleksandar Videnovic, Parkinson's Progression Markers Initiative

Faculty, Staff and Students Publications

Objective: To determine the impact of dopamine deficiency and isolated rapid eye movement (REM) sleep behavior disorder (iRBD) on cognitive performance in early neuronal α-synuclein disease (NSD) with hyposmia but without motor disability.

Methods: Using Parkinson's Progression Markers Initiative baseline data, cognitive performance was assessed with a cognitive summary score (CSS) derived from robust healthy control (HC) norms. Performance was examined for participants with hyposmia in early NSD-Integrated Staging System (NSD-ISS), either stage 2A (cerebrospinal fluid α-synuclein seed amplification assay [SAA]+, dopamine transporter scan [DaTscan]-) or 2B (SAA+, DaTscan+).

Results: Participants were stage 2A (n = 101), stage 2B (N …

A Consensus Guide To Preclinical Indirect Calorimetry Experiments, Alexander S Banks, David B Allison, Thierry Alquier, Ansarullah, Steven N Austad, Johan Auwerx, Julio E Ayala, Joseph A Baur, Stefania Carobbio, Gary A Churchill, Morten Dall, Rafael De Cabo, Jose Donato, Nathalia R V Dragano, Carol F Elias, Anthony W Ferrante, Brian N Finck, Jose E Galgani, Zachary Gerhart-Hines, Laurie J Goodyear, Justin L Grobe, Rana K Gupta, Kirk M Habegger, Sean M Hartig, Andrea L Hevener, Steven B Heymsfield, Corey D Holman, Martin Hrabě De Angelis, David E James, Lawrence Kazak, Jae Bum Kim, Martin Klingenspor, Xingxing Kong, Sander Kooijman, Louise Lantier, K C Kent Lloyd, James C Lo, Irfan J Lodhi, Paul S Maclean, Owen P Mcguinness, Gema Medina-Gómez, Raghavendra G Mirmira, Christopher D Morrison, Gregory J Morton, Timo D Müller, Yoshihiro Ogawa, David Pajuelo-Reguera, Matthew J Potthoff, Nathan Qi, Marc L Reitman, Patrick C N Rensen, Jan Rozman, Jennifer M Rutkowsky, Kei Sakamoto, Philipp E Scherer, Gary J Schwartz, Radislav Sedlacek, Mohammed Selloum, Saame Raza Shaikh, Shuai Chen, Gerald I Shulman, Vojtěch Škop, Alexander A Soukas, John R Speakman, Bruce M Spiegelman, Gregory R Steinberg, Katrin J Svensson, John P Thyfault, Tony Tiganis, Paul M Titchenell, Nigel Turner, Licio A Velloso, Antonio Vidal-Puig, Christopher S Ward, Ashley S Williams, Christian Wolfrum, Allison W Xu, Ying Xu, Juleen R Zierath, International Indirect Calorimetry Consensus Committee (Iiccc)

Children’s Nutrition Research Center Staff Publications

Understanding the complex factors influencing mammalian metabolism and body weight homeostasis is a long-standing challenge requiring knowledge of energy intake, absorption and expenditure. Using measurements of respiratory gas exchange, indirect calorimetry can provide non-invasive estimates of whole-body energy expenditure. However, inconsistent measurement units and flawed data normalization methods have slowed progress in this field. This guide aims to establish consensus standards to unify indirect calorimetry experiments and their analysis for more consistent, meaningful and reproducible results. By establishing community-driven standards, we hope to facilitate data comparison across research datasets. This advance will allow the creation of an in-depth, machine-readable data …

Corrigendum To "Validation Of An Assay For Ngal In A Pediatric Population" [Practical Laboratory Medicine, Plabm 486, E00486], Nazmin Bithi, Ridwan B Ibrahim, Estella Tam, Radwa Almamoun, Annett C Frenk Oquendo, Ayse Akcan-Arikan, Sridevi Devaraj

Faculty, Staff and Students Publications

This corrects the article "Validation of an assay for NGAL in a pediatric population", e00486.

Fluid Assessment Scoring Tool (Fast): Development Of A Novel Fluid Assessment Scoring Tool For Critically Ill Pediatric Patients-A Pilot Study, Mohammed Salameh, Pranali Awadhare, Jennifer Joiner, Michael Scheurer, Utpal Bhalala

Faculty, Staff and Students Publications

Introduction: Monitoring fluid balance (FB) is important yet challenging in the pediatric intensive care unit (PICU). Currently used, conventional methods of fluid assessment are either not feasible or unreliable. Also, there is a lack of composite scores or clinical algorithms that use different parameters of fluid status. We aim to develop a fluid assessment scoring tool (FAST) to clinically assess the fluid status of children in the PICU.

Methods: In this pilot study, we included critically ill patients aged 0-21 years who presented to our PICU between December 2020 and March 2021 and required invasive or non-invasive mechanical ventilation, inotropes, …

Eugenics And Polygenic Embryo Screening: Public, Clinician, And Patient Perceptions Of Conditions Versus Traits, Dorit Barlevy, Rémy A Furrer, Asha Kalapatapu, Abigail Martinez, Todd Lencz, Shai Carmi, Gabriel Lázaro-Muñoz, Stacey Pereira

Center for Medical Ethics and Health Policy Staff Publications

Purpose: Polygenic embryo screening (PES) estimates an embryo's genetic chances of developing complex conditions (eg, cancer) and traits (eg, height). Stakeholders have raised concerns that PES promotes eugenic practices and ideology.

Methods: We surveyed a nationally representative sample of the US public on approval of screening embryos for 12 conditions and 12 traits and examined the association between disapproval and concern about eugenics. We also conducted semistructured interviews with US-based reproductive endocrinology and infertility specialists and patients undergoing in vitro fertilization on their perspectives toward PES.

Results: Among the US public (n = 1423), disapproval of screening embryos for traits …

Deepmvp: Deep Learning Models Trained On High-Quality Data Accurately Predict Ptm Sites And Variant-Induced Alterations, Bo Wen, Chenwei Wang, Kai Li, Ping Han, Matthew V Holt, Sara R Savage, Jonathan T Lei, Yongchao Dou, Zhiao Shi, Yi Li, Bing Zhang

Center on Aging Staff Publications

Post-translational modifications (PTMs) are critical regulators of protein function, and their disruption is a key mechanism by which missense variants contribute to disease. Accurate PTM site prediction using deep learning can help identify PTM-altering variants, but progress has been limited by the lack of large, high-quality training datasets. Here, we introduce PTMAtlas, a curated compendium of 397,524 PTM sites generated through systematic reprocessing of 241 public mass-spectrometry datasets, and DeepMVP, a deep learning framework trained on PTMAtlas to predict PTM sites for phosphorylation, acetylation, methylation, sumoylation, ubiquitination and N-glycosylation. DeepMVP substantially outperforms existing tools across all six PTM types. Its …

Author Correction: Clonal Evolution Of Hematopoietic Stem Cells After Autologous Stem Cell Transplantation, Hidetaka Uryu, Koichi Saeki, Hiroshi Haeno, Chiraag Deepak Kapadia, Ken Furudate, Jyoti Nangalia, Michael Spencer Chapman, Linda Zhang, Jennifer Padilla, Li Zhao, Joanne I Hsu, Chong Zhao, Shujuan Chen, Tomoyuki Tanaka, Zongrui Li, Satoko Ogata, Sarah Hanache, Hui Yang, Courtney Dinardo, Naval Daver, Naveen Pemmaraju, Nitin Jain, Farhad Ravandi, Jianhua Zhang, Xingzhi Song, Erika Thompson, Hongli Tang, Latasha Little, Curtis Gumbs, Robert Z Orlowski, Muzaffar Qazilbash, Kapil Bhalla, Simona Colla, Hagop Kantarjian, Rashmi Kanagal-Shamanna, Carlos Bueso-Ramos, Daisuke Nakada, Gheath Al-Atrash, Jeffery Molldrem, P Andrew Futreal, Elizabeth Shpall, Margaret Goodell, Guillermo Garcia-Manero, Koichi Takahashi

Faculty, Staff and Student Publications

No abstract provided.

Spatial Omics Enters The Microscopic Realm: Opportunities And Challenges, Yichen Si, Joo Sang Lee, Goo Jun, Hyun Min Kang, Jun Hee Lee

Faculty, Staff and Students Publications

Spatial transcriptomics (ST) enables systematic profiling of whole-transcriptome gene expression in tissues while preserving spatial context. Recent advances in sequencing- and imaging-based ST technologies have ushered in the era of microscopic-resolution ST (μST), allowing transcriptome mapping at cellular and even subcellular scales with unprecedented precision. Despite these advances, μST faces substantial challenges, including sparse transcript discovery per submicron (or micron)-sized spatial units and data fragmentation across platforms, hindering integration and analysis. There is also a growing demand for scalable, segmentation-free, and universally applicable analysis methods, as well as strategies for 3D mapping, multi-omics integration, and artificial intelligence (AI)-driven spatial analysis. …

Prenatal Obsessive Beliefs Predict Postpartum Obsessive-Compulsive Symptoms: A Prospective Study, Jonathan S Abramowitz, Samantha N Hellberg, Janice Krasnow, Joseph B Friedman, Nicholas S Myers, Paul S Nestadt, Heidi J Ojalehto, Emily K Juel, Jack Samuels, Mary E Kimmel, Lauren M Osborne, Eric A Storch, Gerald Nestadt, Rashelle J Musci

Faculty, Staff and Students Publications

This longitudinal study examined whether specific cognitive patterns during pregnancy predict postpartum obsessive-compulsive (OC) symptoms. A diverse sample of 256 women was assessed at 20 weeks of pregnancy (Time 1), 6 weeks postpartum (Time 2; n = 233), and 6 months postpartum (Time 3; n = 231). At each point, participants completed interview and/or self-report measures of OC symptoms, psychological distress, and obsessive beliefs (i.e., cognitive patterns related to OC symptoms). Postpartum OC symptoms were common, reported by 87.1 % at Time 2 and 74.5 % at Time 3. Stronger prenatal obsessive beliefs during pregnancy predicted greater postpartum OC symptom …

Auprc: A Metric For Evaluating The Performance Of In-Silico Perturbation Methods In Identifying Differentially Expressed Genes, Hongxu Zhu, Amir Asiaee, Leila Azinfar, Jun Li, Han Liang, Ehsan Irajizad, Kim-Anh Do, James P Long

Faculty, Staff and Student Publications

In silico perturbation models, computational methods that can predict cellular responses to perturbations, present an opportunity to reduce the need for costly and time-intensive in vitro experiments. Many recently proposed models predict high-dimensional cellular responses, such as gene or protein expression to perturbations such as gene knockout or drugs. However, evaluating in silico performance has largely relied on metrics such as $R^{2}$, which assess overall prediction accuracy but fail to capture biologically significant outcomes like the identification of differentially expressed (DE) genes. In this study, we present a novel evaluation framework that introduces the AUPRC metric to assess the precision …

Whole-Genome Sequence-Based Association Analysis Of African American Individuals With Bipolar Disorder And Schizophrenia, Runjia Li, Sarah A Gagliano Taliun, Kevin Liao, Matthew Flickinger, Janet L Sobell, Giulio Genovese, Adam E Locke, Rebeca Rothwell Chiu, Jonathon Lefaive, Jiongming Wang, Taylor Martins, Sinéad Chapman, Anna Neumann, Robert E Handsaker, Donna K Arnett, Kathleen C Barnes, Eric Boerwinkle, David Braff, Brian E Cade, Myriam Fornage, Richard A Gibbs, Karin F Hoth, Lifang Hou, Charles Kooperberg, Ruth J F Loos, Ginger A Metcalf, Courtney G Montgomery, Alanna C Morrison, Zhaohui S Qin, Susan Redline, Alexander P Reiner, Stephen S Rich, Jerome I Rotter, Kent D Taylor, Karine A Viaud-Martinez, Tim B Bigdeli, Stacey Gabriel, Sebastian Zollner, Albert V Smith, Goncalo Abecasis, Steve A Mccarroll, Michele T Pato, Carlos N Pato, Michael Boehnke, James Knowles, Hyun Min Kang, Roel A Ophoff, Jason Ernst, Laura J Scott

Faculty, Staff and Student Publications

In studies of individuals of primarily European genetic ancestry, common and low-frequency variants and rare coding variants have been found to be associated with the risk of bipolar disorder (BD) and schizophrenia (SZ). However, less is known for individuals of other genetic ancestries or the role of rare non-coding variants in BD and SZ risk. We performed whole-genome sequencing (∼27X) of African American individuals: 1,598 with BD, 3,295 with SZ, and 2,651 unaffected controls (InPSYght study). We increased power by incorporating 14,812 jointly called psychiatrically unscreened ancestry-matched controls from the Trans-Omics for Precision Medicine (TOPMed) Program for a total of …

Endoscopic Management Of Ureteric Stenosis And Calculi In Bilateral Incomplete Renal Duplication: A Case Study, Hafeez Sohaib Ahmad Warraich, Zirwa Younis, Jawairia Warraich, Khizra Warraich

BioMedicine

Renal duplication anomalies are one of the most frequent congenital urological conditions in the general population all over the world. Bilateral incomplete duplication, however, is exceedingly rare. We present a case of a 29-year-old female with bilateral incomplete duplex kidneys complicated by mid-ureteric stenosis on the right side and calculi in the left ureter and upper moiety of the left duplex kidney. Diagnostic imaging, including ultrasound, computed tomography (CT), and intravenous urography (IVU) confirmed these findings. The patient underwent successful bilateral ureteroscopy (URS) and left-sided retrograde intra-renal surgery (RIRS) for management of the above mentioned complications related to the duplex …

Metabolomics In Cancer Detection: A Review Of Techniques, Biomarkers, And Clinical Utility, Kavitha Liegelin Bernhardt, Janita R. T. Pinto

BioMedicine

Cancer poses a significant burden on global public health, contributing to high mortality rates worldwide. Ongoing diagnostic strategies have predominantly relied on imaging techniques, histopathological examination and molecular analyses which have limitations in sensitivity, and specificity. Early cancer detection is a pivotal determinant of successful treatment and patient survival rates. Metabolomic applications involve the comprehensive analysis of metabolites to understand the metabolic profile of an organism, tissue, or cell under different conditions such as lack of oxygen in tumors. The aim of this review is to provide an extensive approach of metabolomic applications in early cancer detection and to provide …

The Immunophenotypic And Genetic Characterization Of Pediatric T -L Ymphoblastic Leukemia With A Mature Immunophenotype, Mahsa Khanlari, Wei Wang, Parastou Tizro, Mohammad K Eldomery

Faculty, Staff and Student Publications

Not available.