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Sustainable Development For Mobile Health Apps Using The Human-Centered Design Process, Qingfan An, Marjorie M Kelley, Audra Hanners, Po-Yin Yen Aug 2023

Sustainable Development For Mobile Health Apps Using The Human-Centered Design Process, Qingfan An, Marjorie M Kelley, Audra Hanners, Po-Yin Yen

2020-Current year OA Pubs

Well-documented scientific evidence indicates that mobile health (mHealth) apps can improve the quality of life, relieve symptoms, and restore health for patients. In addition to improving patients' health outcomes, mHealth apps reduce health care use and the cost burdens associated with disease management. Currently, patients and health care providers have a wide variety of choices among commercially available mHealth apps. However, due to the high resource costs and low user adoption of mHealth apps, the cost-benefit relationship remains controversial. When compared to traditional expert-driven approaches, applying human-centered design (HCD) may result in more useable, acceptable, and effective mHealth apps. In …


Microglial Rev-Erbα Regulates Inflammation And Lipid Droplet Formation To Drive Tauopathy In Male Mice, Jiyeon Lee, Julie M Dimitry, Jong Hee Song, Minsoo Son, Patrick W Sheehan, Melvin W King, G Travis Tabor, Young Ah Goo, Mitchell A Lazar, Leonard Petrucelli, Erik S Musiek Aug 2023

Microglial Rev-Erbα Regulates Inflammation And Lipid Droplet Formation To Drive Tauopathy In Male Mice, Jiyeon Lee, Julie M Dimitry, Jong Hee Song, Minsoo Son, Patrick W Sheehan, Melvin W King, G Travis Tabor, Young Ah Goo, Mitchell A Lazar, Leonard Petrucelli, Erik S Musiek

2020-Current year OA Pubs

Alzheimer's disease, the most common age-related neurodegenerative disease, is characterized by tau aggregation and associated with disrupted circadian rhythms and dampened clock gene expression. REV-ERBα is a core circadian clock protein which also serves as a nuclear receptor and transcriptional repressor involved in lipid metabolism and macrophage function. Global REV-ERBα deletion has been shown to promote microglial activation and mitigate amyloid plaque formation. However, the cell-autonomous effects of microglial REV-ERBα in healthy brain and in tauopathy are unexplored. Here, we show that microglial REV-ERBα deletion enhances inflammatory signaling, disrupts lipid metabolism, and causes lipid droplet (LD) accumulation specifically in male …


Design, Synthesis, And Evaluation Of Novel Δ2‑Thiazolino2‑Pyridone Derivatives That Potentiate Isoniazid Activity In An Isoniazid-Resistant Mycobacterium Tuberculosis Mutant, Souvik Sarkar, Anne E. Mayer Bridwell, Erin R. Wang, Samuel R. Mckee, Joy Valenta, Gregory A. Harrison, Kelly N. Flentie, Frederick L. Henry, Christina L. Stallings, Et Al. Aug 2023

Design, Synthesis, And Evaluation Of Novel Δ2‑Thiazolino2‑Pyridone Derivatives That Potentiate Isoniazid Activity In An Isoniazid-Resistant Mycobacterium Tuberculosis Mutant, Souvik Sarkar, Anne E. Mayer Bridwell, Erin R. Wang, Samuel R. Mckee, Joy Valenta, Gregory A. Harrison, Kelly N. Flentie, Frederick L. Henry, Christina L. Stallings, Et Al.

2020-Current year OA Pubs

No abstract provided.


The Proteome Of Extracellular Vesicles Of The Lung Fluke Paragonimus Kellicotti Produced In Vitro And In The Lung Cyst, Lucia S Di Maggio, Kerstin Fischer, Devyn Yates, Kurt C Curtis, Bruce A Rosa, John Martin, Petra Erdmann-Gilmore, Robert S W Sprung, Makedonka Mitreva, R Reid Townsend, Gary J Weil, Peter U Fischer Aug 2023

The Proteome Of Extracellular Vesicles Of The Lung Fluke Paragonimus Kellicotti Produced In Vitro And In The Lung Cyst, Lucia S Di Maggio, Kerstin Fischer, Devyn Yates, Kurt C Curtis, Bruce A Rosa, John Martin, Petra Erdmann-Gilmore, Robert S W Sprung, Makedonka Mitreva, R Reid Townsend, Gary J Weil, Peter U Fischer

2020-Current year OA Pubs

Paragonimiasis is a zoonotic, food-borne trematode infection that affects 21 million people globally. Trematodes interact with their hosts via extracellular vesicles (EV) that carry protein and RNA cargo. We analyzed EV in excretory-secretory products (ESP) released by Paragonimus kellicotti adult worms cultured in vitro (EV ESP) and EV isolated from lung cyst fluid (EV CFP) recovered from infected gerbils. The majority of EV were approximately 30-50 nm in diameter. We identified 548 P. kellicotti-derived proteins in EV ESP by mass spectrometry and 8 proteins in EV CFP of which 7 were also present in EV ESP. No parasite-derived proteins were …


Interpreting The Mechanism Of Synergism For Drug Combinations Using Attention-Based Hierarchical Graph Pooling, Zehao Dong, Heming Zhang, Yixin Chen, Philip R O Payne, Fuhai Li Aug 2023

Interpreting The Mechanism Of Synergism For Drug Combinations Using Attention-Based Hierarchical Graph Pooling, Zehao Dong, Heming Zhang, Yixin Chen, Philip R O Payne, Fuhai Li

2020-Current year OA Pubs

Synergistic drug combinations provide huge potentials to enhance therapeutic efficacy and to reduce adverse reactions. However, effective and synergistic drug combination prediction remains an open question because of the unknown causal disease signaling pathways. Though various deep learning (AI) models have been proposed to quantitatively predict the synergism of drug combinations, the major limitation of existing deep learning methods is that they are inherently not interpretable, which makes the conclusions of AI models untransparent to human experts, henceforth limiting the robustness of the model conclusion and the implementation ability of these models in real-world human-AI healthcare. In this paper, we …


Chromophore Carbonyl Twisting In Fluorescent Biosensors Encodes Direct Readout Of Protein Conformations With Multicolor Switching, Malin J Allert, Shivesh Kumar, You Wang, Lorena S Beese, Homme W Hellinga Aug 2023

Chromophore Carbonyl Twisting In Fluorescent Biosensors Encodes Direct Readout Of Protein Conformations With Multicolor Switching, Malin J Allert, Shivesh Kumar, You Wang, Lorena S Beese, Homme W Hellinga

2020-Current year OA Pubs

Fluorescent labeling of proteins is a powerful tool for probing structure-function relationships with many biosensing applications. Structure-based rules for systematically designing fluorescent biosensors require understanding ligand-mediated fluorescent response mechanisms which can be challenging to establish. We installed thiol-reactive derivatives of the naphthalene-based fluorophore Prodan into bacterial periplasmic glucose-binding proteins. Glucose binding elicited paired color exchanges in the excited and ground states of these conjugates. X-ray structures and mutagenesis studies established that glucose-mediated color switching arises from steric interactions that couple protein conformational changes to twisting of the Prodan carbonyl relative to its naphthalene plane. Mutations of residues contacting the carbonyl …


Vegf-B Prevents Excessive Angiogenesis By Inhibiting Fgf2/Fgfr1 Pathway, Chunsik Lee, David M Ornitz, Et Al. Aug 2023

Vegf-B Prevents Excessive Angiogenesis By Inhibiting Fgf2/Fgfr1 Pathway, Chunsik Lee, David M Ornitz, Et Al.

2020-Current year OA Pubs

Although VEGF-B was discovered as a VEGF-A homolog a long time ago, the angiogenic effect of VEGF-B remains poorly understood with limited and diverse findings from different groups. Notwithstanding, drugs that inhibit VEGF-B together with other VEGF family members are being used to treat patients with various neovascular diseases. It is therefore critical to have a better understanding of the angiogenic effect of VEGF-B and the underlying mechanisms. Using comprehensive in vitro and in vivo methods and models, we reveal here for the first time an unexpected and surprising function of VEGF-B as an endogenous inhibitor of angiogenesis by inhibiting …


Defining The Roles Of Pyruvate Oxidation, Tca Cycle, And Mannitol Metabolism In Methicillin-Resistant Staphylococcus Aureus Catheter-Associated Urinary Tract Infection, Santosh Paudel, Sarah Guedry, Chloe L P Obernuefemann, Scott J. Hultgren, Jennifer N. Walker, Ritwij Kulkarni Aug 2023

Defining The Roles Of Pyruvate Oxidation, Tca Cycle, And Mannitol Metabolism In Methicillin-Resistant Staphylococcus Aureus Catheter-Associated Urinary Tract Infection, Santosh Paudel, Sarah Guedry, Chloe L P Obernuefemann, Scott J. Hultgren, Jennifer N. Walker, Ritwij Kulkarni

2020-Current year OA Pubs

Methicillin-resistant Staphylococcus aureus (MRSA) is an important cause of complicated urinary tract infection (UTI) associated with the use of indwelling urinary catheters. Previous reports have revealed host and pathogen effectors critical for MRSA uropathogenesis. Here, we sought to determine the significance of specific metabolic pathways during MRSA UTI. First, we identified four mutants from the Nebraska transposon mutant library in the MRSA JE2 background that grew normally in rich medium but displayed significantly reduced growth in pooled human urine (HU). This prompted us to transduce the uropathogenic MRSA 1369 strain with the transposon mutants in


Strategies For Overcoming The Single-Molecule Concentration Barrier, David S White, Mackinsey A Smith, Baron Chanda, Randall H Goldsmith Aug 2023

Strategies For Overcoming The Single-Molecule Concentration Barrier, David S White, Mackinsey A Smith, Baron Chanda, Randall H Goldsmith

2020-Current year OA Pubs

Fluorescence-based single-molecule approaches have helped revolutionize our understanding of chemical and biological mechanisms. Unfortunately, these methods are only suitable at low concentrations of fluorescent molecules so that single fluorescent species of interest can be successfully resolved beyond background signal. The application of these techniques has therefore been limited to high-affinity interactions despite most biological and chemical processes occurring at much higher reactant concentrations. Fortunately, recent methodological advances have demonstrated that this concentration barrier can indeed be broken, with techniques reaching concentrations as high as 1 mM. The goal of this Review is to discuss the challenges in performing single-molecule fluorescence …


Kinase Inhibitor Pulldown Assay Identifies A Chemotherapy Response Signature In Triple-Negative Breast Cancer Based On Purine-Binding Proteins, Junkai Wang, Alexander B Saltzman, Eric J Jaehnig, Jonathan T Lei, Anna Malovannaya, Matthew V Holt, Meggie N Young, Mothaffar F Rimawi, Foluso O Ademuyiwa, Meenakshi Anurag, Beom-Jun Kim, Matthew J Ellis Aug 2023

Kinase Inhibitor Pulldown Assay Identifies A Chemotherapy Response Signature In Triple-Negative Breast Cancer Based On Purine-Binding Proteins, Junkai Wang, Alexander B Saltzman, Eric J Jaehnig, Jonathan T Lei, Anna Malovannaya, Matthew V Holt, Meggie N Young, Mothaffar F Rimawi, Foluso O Ademuyiwa, Meenakshi Anurag, Beom-Jun Kim, Matthew J Ellis

2020-Current year OA Pubs

UNLABELLED: Triple-negative breast cancer (TNBC) constitutes 10%-15% of all breast tumors. The current standard of care is multiagent chemotherapy, which is effective in only a subset of patients. The original objective of this study was to deploy a mass spectrometry (MS)-based kinase inhibitor pulldown assay (KIPA) to identify kinases elevated in non-pCR (pathologic complete response) cases for therapeutic targeting. Frozen optimal cutting temperature compound-embedded core needle biopsies were obtained from 43 patients with TNBC before docetaxel- and carboplatin-based neoadjuvant chemotherapy. KIPA was applied to the native tumor lysates that were extracted from samples with high tumor content. Seven percent of …


Discovery And Targeting Of A Noncanonical Mechanism Of Sarcoma Resistance To Adi-Peg20 Mediated By The Microenvironment, Leonard C Rogers, Jeff C Kremer, Caitlyn B Brashears, Zongtao Lin, Alliny C S Bastos, Adriana Baker, Nicole Fettig, Dong Zhou, Kooresh I Shoghi, Carina A Dehner, John S A Chrisinger, Benjamin A Garcia, Toshinao Oyama, Brian A Van Tine, Et Al. Aug 2023

Discovery And Targeting Of A Noncanonical Mechanism Of Sarcoma Resistance To Adi-Peg20 Mediated By The Microenvironment, Leonard C Rogers, Jeff C Kremer, Caitlyn B Brashears, Zongtao Lin, Alliny C S Bastos, Adriana Baker, Nicole Fettig, Dong Zhou, Kooresh I Shoghi, Carina A Dehner, John S A Chrisinger, Benjamin A Garcia, Toshinao Oyama, Brian A Van Tine, Et Al.

2020-Current year OA Pubs

PURPOSE: Many cancers lack argininosuccinate synthetase 1 (ASS1), the rate-limiting enzyme of arginine biosynthesis. This deficiency causes arginine auxotrophy, targetable by extracellular arginine-degrading enzymes such as ADI-PEG20. Long-term tumor resistance has thus far been attributed solely to ASS1 reexpression. This study examines the role of ASS1 silencing on tumor growth and initiation and identifies a noncanonical mechanism of resistance, aiming to improve clinical responses to ADI-PEG20.

EXPERIMENTAL DESIGN: Tumor initiation and growth rates were measured for a spontaneous Ass1 knockout (KO) murine sarcoma model. Tumor cell lines were generated, and resistance to arginine deprivation therapy was studied in vitro and …


Pediatric Experience And Outcomes From The First Single-Vault Compact Proton Therapy Center, Stephanie M Perkins, Sabrina Prime, Michael Watts, Jiayi Huang, Tianyu Zhao Aug 2023

Pediatric Experience And Outcomes From The First Single-Vault Compact Proton Therapy Center, Stephanie M Perkins, Sabrina Prime, Michael Watts, Jiayi Huang, Tianyu Zhao

2020-Current year OA Pubs

The first single-vault compact proton therapy center opened in 2013, utilizing a gantry-mounted synchrocylotron. The center was placed within a large academic radiation oncology department with a high priority for pediatric cancer care. Here we performed a retrospective study of pediatric (≤21 years) patients treated with proton therapy at our institution between 2013-2022. Patient, tumor, and treatment characteristics were obtained including race, socioeconomic status, insurance type, distance travelled, need for anesthesia, and outside referrals for proton therapy. In total, 250 pediatric patients were treated with proton therapy comprising 18% of our proton patient volume. Median follow-up was 3.1 years, 38.4% …


A Comprehensive Report Of Intrinsically Disordered Regions In Inherited Retinal Diseases, Karen E Lee, Jose S Pulido, Mariana M Da Palma, Rebecca Procopio, Robert B Hufnagel, Margaret Reynolds Aug 2023

A Comprehensive Report Of Intrinsically Disordered Regions In Inherited Retinal Diseases, Karen E Lee, Jose S Pulido, Mariana M Da Palma, Rebecca Procopio, Robert B Hufnagel, Margaret Reynolds

2020-Current year OA Pubs

BACKGROUND/PURPOSE: A comprehensive review of the degree of disorder in all genes in the Retinal Information Network (RetNet) Database is implicated in inherited retinal diseases (IRDs). Their association with a missense variation was evaluated.

METHODS: IRD genes from RetNet were included in this study. Publicly available data on the genome aggregation database (gnomAD) were used to analyze the number of total and pathogenic missense variants. Metapredict, an accurate and high-performance predictor that reproduces consensus disorder scores, was used to calculate disorder.

MAIN OUTCOME MEASURES: The main outcome measures were percent disorder, percent pathogenicity, number of total missense variants, and percent …


Er-Mitochondria Contacts And Cholesterol Metabolism Are Disrupted By Disease-Associated Tau Protein, Leonora Szabo, Nadia Cummins, Paolo Paganetti, Alex Odermatt, Andreas Papassotiropoulos, Celeste Karch, Jürgen Götz, Anne Eckert, Amandine Grimm Aug 2023

Er-Mitochondria Contacts And Cholesterol Metabolism Are Disrupted By Disease-Associated Tau Protein, Leonora Szabo, Nadia Cummins, Paolo Paganetti, Alex Odermatt, Andreas Papassotiropoulos, Celeste Karch, Jürgen Götz, Anne Eckert, Amandine Grimm

2020-Current year OA Pubs

Abnormal tau protein impairs mitochondrial function, including transport, dynamics, and bioenergetics. Mitochondria interact with the endoplasmic reticulum (ER) via mitochondria-associated ER membranes (MAMs), which coordinate and modulate many cellular functions, including mitochondrial cholesterol metabolism. Here, we show that abnormal tau loosens the association between the ER and mitochondria in vivo and in vitro. Especially, ER-mitochondria interactions via vesicle-associated membrane protein-associated protein (VAPB)-protein tyrosine phosphatase-interacting protein 51 (PTPIP51) are decreased in the presence of abnormal tau. Disruption of MAMs in cells with abnormal tau alters the levels of mitochondrial cholesterol and pregnenolone, indicating that conversion of cholesterol into pregnenolone is impaired. …


Genetic Insights Into Resting Heart Rate And Its Role In Cardiovascular Disease, Yordi J Van De Vegte, Lihua Wang, Dabeeru C Rao, Et Al. Aug 2023

Genetic Insights Into Resting Heart Rate And Its Role In Cardiovascular Disease, Yordi J Van De Vegte, Lihua Wang, Dabeeru C Rao, Et Al.

2020-Current year OA Pubs

Resting heart rate is associated with cardiovascular diseases and mortality in observational and Mendelian randomization studies. The aims of this study are to extend the number of resting heart rate associated genetic variants and to obtain further insights in resting heart rate biology and its clinical consequences. A genome-wide meta-analysis of 100 studies in up to 835,465 individuals reveals 493 independent genetic variants in 352 loci, including 68 genetic variants outside previously identified resting heart rate associated loci. We prioritize 670 genes and in silico annotations point to their enrichment in cardiomyocytes and provide insights in their ECG signature. Two-sample …


Positron Emission Tomography And Magnetic Resonance Imaging Methods And Datasets Within The Dominantly Inherited Alzheimer Network (Dian), Nicole S Mckay, Brian A Gordon, Russ C Hornbeck, Aylin Dincer, Shaney Flores, Sarah J Keefe, Nelly Joseph-Mathurin, Peter R Millar, Beau M Ances, Charles D Chen, Alisha Daniels, Diana A Hobbs, Kelley Jackson, Deborah Koudelis, Parinaz Massoumzadeh, Austin Mccullough, Michael L Nickels, Farzaneh Rahmani, Laura Swisher, Qing Wang, Carlos Cruchaga, Jason Hassenstab, Celeste Karch, Eric Mcdade, Richard J Perrin, Chengjie Xiong, John C Morris, Randall J Bateman, Tammie L S Benzinger, Et Al. Aug 2023

Positron Emission Tomography And Magnetic Resonance Imaging Methods And Datasets Within The Dominantly Inherited Alzheimer Network (Dian), Nicole S Mckay, Brian A Gordon, Russ C Hornbeck, Aylin Dincer, Shaney Flores, Sarah J Keefe, Nelly Joseph-Mathurin, Peter R Millar, Beau M Ances, Charles D Chen, Alisha Daniels, Diana A Hobbs, Kelley Jackson, Deborah Koudelis, Parinaz Massoumzadeh, Austin Mccullough, Michael L Nickels, Farzaneh Rahmani, Laura Swisher, Qing Wang, Carlos Cruchaga, Jason Hassenstab, Celeste Karch, Eric Mcdade, Richard J Perrin, Chengjie Xiong, John C Morris, Randall J Bateman, Tammie L S Benzinger, Et Al.

2020-Current year OA Pubs

The Dominantly Inherited Alzheimer Network (DIAN) is an international collaboration studying autosomal dominant Alzheimer disease (ADAD). ADAD arises from mutations occurring in three genes. Offspring from ADAD families have a 50% chance of inheriting their familial mutation, so non-carrier siblings can be recruited for comparisons in case-control studies. The age of onset in ADAD is highly predictable within families, allowing researchers to estimate an individual's point in the disease trajectory. These characteristics allow candidate AD biomarker measurements to be reliably mapped during the preclinical phase. Although ADAD represents a small proportion of AD cases, understanding neuroimaging-based changes that occur during …


Association Of Soluble Markers Of Inflammation With Peri-Coronary Artery Inflammation In People With And Without Hiv Infection And Without Cardiovascular Disease, Michael L Freeman, Mian B Hossain, Shana A B Burrowes, Jean Jeudy, Ryan Bui, Daniela Moisi, Sarah E Mitchell, Mariam Khambaty, Robert G Weiss, Michael M Lederman, Shashwatee Bagchi Aug 2023

Association Of Soluble Markers Of Inflammation With Peri-Coronary Artery Inflammation In People With And Without Hiv Infection And Without Cardiovascular Disease, Michael L Freeman, Mian B Hossain, Shana A B Burrowes, Jean Jeudy, Ryan Bui, Daniela Moisi, Sarah E Mitchell, Mariam Khambaty, Robert G Weiss, Michael M Lederman, Shashwatee Bagchi

2020-Current year OA Pubs

BACKGROUND: Inflammation is linked to elevated cardiovascular disease (CVD) risk in people with HIV (PWH) on antiretroviral therapy (ART). Fat attenuation index (FAI) is a measure of peri-coronary inflammation that independently predicts CVD risk in HIV-uninfected persons. Whether FAI is associated with soluble inflammatory markers is unknown.

METHODS: Plasma levels of inflammatory markers were measured in 58 PWH and 16 controls without current symptoms or prior known CVD who underwent coronary computed tomography angiography and had FAI measurements. A cross-sectional analysis was performed, and associations of markers with FAI values of the right coronary artery (RCA) and left anterior descending …


Symbiotic Bacteria, Immune-Like Sentinel Cells, And The Response To Pathogens In A Social Amoeba, Trey J. Scott, Tyler J. Larsen, Debra A. Brock, So Yeon Stacey Uhm, David C. Queller, Joan E. Strassmann Aug 2023

Symbiotic Bacteria, Immune-Like Sentinel Cells, And The Response To Pathogens In A Social Amoeba, Trey J. Scott, Tyler J. Larsen, Debra A. Brock, So Yeon Stacey Uhm, David C. Queller, Joan E. Strassmann

2020-Current year OA Pubs

Some endosymbionts living within a host must modulate their hosts' immune systems in order to infect and persist. We studied the effect of a bacterial endosymbiont on a facultatively multicellular social amoeba host. Aggregates of the amoeba


Effect Of Fecal Microbiota, Live-Jslm (Rebyota [Rbl]) On Health-Related Quality Of Life In Patients With Recurrent Clostridioides Difficile Infection: Results From The Punch Cd3 Clinical Trial, Kevin W Garey, Erik R Dubberke, Amy Guo, Adam Harvey, Min Yang, Viviana García-Horton, Mirko Fillbrunn, Hongjue Wang, Glenn S Tillotson, Lindy L Bancke, Paul Feuerstadt Aug 2023

Effect Of Fecal Microbiota, Live-Jslm (Rebyota [Rbl]) On Health-Related Quality Of Life In Patients With Recurrent Clostridioides Difficile Infection: Results From The Punch Cd3 Clinical Trial, Kevin W Garey, Erik R Dubberke, Amy Guo, Adam Harvey, Min Yang, Viviana García-Horton, Mirko Fillbrunn, Hongjue Wang, Glenn S Tillotson, Lindy L Bancke, Paul Feuerstadt

2020-Current year OA Pubs

BACKGROUND: Recurrence of

METHODS: This was a secondary analysis of a randomized, double-blind, placebo-controlled phase 3 study (PUNCH CD3). The disease-specific

RESULTS: Findings were analyzed in a total of 185 patients (RBL, n = 128 [69.2%]; placebo, n = 57 [30.8%]) with available Cdiff32 data. Patients from both arms showed significant improvements in Cdiff32 scores relative to baseline across all outcomes and at all time points (all

CONCLUSIONS: In a phase 3 double-blinded clinical trial, RBL-treated patients reported more substantial and sustained disease-specific HRQL improvements than placebo-treated patients.

CLINICAL TRIALS REGISTRATION: ClinicalTrials.gov NCT03244644 (https://clinicaltrials.gov/ct2/show/NCT03244644).


Demographics And Baseline Disease Characteristics Of Black And Hispanic Patients With Multiple Sclerosis In The Open-Label, Single-Arm, Multicenter, Phase Iv Chimes Trial, Mitzi J Williams, Anne H Cross, Gregory F Wu, Et Al. Aug 2023

Demographics And Baseline Disease Characteristics Of Black And Hispanic Patients With Multiple Sclerosis In The Open-Label, Single-Arm, Multicenter, Phase Iv Chimes Trial, Mitzi J Williams, Anne H Cross, Gregory F Wu, Et Al.

2020-Current year OA Pubs

BACKGROUND: Black/African American patients with multiple sclerosis (BpwMS) and Hispanic/Latino patients with multiple sclerosis (HpwMS), who historically have been underrepresented in multiple sclerosis (MS) clinical trials, exhibit greater disease severity and more rapid disease progression than White patients with MS (WpwMS). The lack of diversity and inclusion in clinical trials, which may be due to barriers at the system, patient and study levels, impacts the ability to effectively assess risks, benefits and treatment responses in a generalized patient population.

METHODS: CHIMES (Characterization of Ocrelizumab in Minorities With Multiple Sclerosis), an open-label, single-arm, multicenter, phase IV study of self-identified BpwMS and …


Shephard: A Modular And Extensible Software Architecture For Analyzing And Annotating Large Protein Datasets, Garrett M Ginell, Aidan J Flynn, Alex S Holehouse Aug 2023

Shephard: A Modular And Extensible Software Architecture For Analyzing And Annotating Large Protein Datasets, Garrett M Ginell, Aidan J Flynn, Alex S Holehouse

2020-Current year OA Pubs

MOTIVATION: The emergence of high-throughput experiments and high-resolution computational predictions has led to an explosion in the quality and volume of protein sequence annotations at proteomic scales. Unfortunately, sanity checking, integrating, and analyzing complex sequence annotations remains logistically challenging and introduces a major barrier to entry for even superficial integrative bioinformatics.

RESULTS: To address this technical burden, we have developed SHEPHARD, a Python framework that trivializes large-scale integrative protein bioinformatics. SHEPHARD combines an object-oriented hierarchical data structure with database-like features, enabling programmatic annotation, integration, and analysis of complex datatypes. Importantly SHEPHARD is easy to use and enables a Pythonic interrogation …


Increased Incidence And Risk Of Septicemia And Urinary Tract Infection After Clostridioides Difficile Infection, Margaret A Olsen, Matthew R Keller, Dustin Stwalley, Holly Yu, Erik R Dubberke Aug 2023

Increased Incidence And Risk Of Septicemia And Urinary Tract Infection After Clostridioides Difficile Infection, Margaret A Olsen, Matthew R Keller, Dustin Stwalley, Holly Yu, Erik R Dubberke

2020-Current year OA Pubs

BACKGROUND: Although increased occurrence of septicemia in persons with

METHODS: The first episode of CDI was identified using 2011-2017 MarketScan and CMS Medicare data and CDI cases categorized by standard surveillance definitions. Uninfected persons were frequency matched 4:1 to cases by the CDI case surveillance definition. Multivariable Cox proportional hazards models were used to identify risk factors for septicemia and UTI within 90 days of CDI onset, accounting for the competing risk of death in the Medicare population.

RESULTS: The incidence of septicemia was highest after hospital-onset CDI in the Medicare, younger commercial, and younger Medicaid populations (25.5%, 15.7%, and …


Proteomics Of Adjacent-To-Tumor Samples Uncovers Clinically Relevant Biological Events In Hepatocellular Carcinoma, Hongwen Zhu, Li Ding, Et Al. Aug 2023

Proteomics Of Adjacent-To-Tumor Samples Uncovers Clinically Relevant Biological Events In Hepatocellular Carcinoma, Hongwen Zhu, Li Ding, Et Al.

2020-Current year OA Pubs

Normal adjacent tissues (NATs) of hepatocellular carcinoma (HCC) differ from healthy liver tissues and their heterogeneity may contain biological information associated with disease occurrence and clinical outcome that has yet to be fully evaluated at the proteomic level. This study provides a detailed description of the heterogeneity of NATs and the differences between NATs and healthy livers and revealed that molecular features of tumor subgroups in HCC were partially reflected in their respective NATs. Proteomic data classified HCC NATs into two subtypes (Subtypes 1 and 2), and Subtype 2 was associated with poor prognosis and high-risk recurrence. The pathway and …


Impact Of Donor Age And Relationship On Outcomes Of Peripheral Blood Haploidentical Hematopoietic Cell Transplantation, Aaron Pruitt, Feng Gao, Elisa De Togni, Hunter Cochran, Sonia Godbole, Michael Slade, Ramzi Abboud Aug 2023

Impact Of Donor Age And Relationship On Outcomes Of Peripheral Blood Haploidentical Hematopoietic Cell Transplantation, Aaron Pruitt, Feng Gao, Elisa De Togni, Hunter Cochran, Sonia Godbole, Michael Slade, Ramzi Abboud

2020-Current year OA Pubs

Here we describe a retrospective analysis of outcomes in 299 patients who underwent peripheral blood haplo-HCT with PTCy from July 2009 through May 2021 and their association with donor characteristics. Patients had mostly acute leukemias and high or very high DRI. Multivariate analyses were conducted examining OS, NRM, relapse, cytokine release syndrome, acute and chronic GVHD. Donor characteristics included age, sex, relationship, ABO status, CMV status, and HLA match grade. Our analysis revealed increasing donor age was associated with higher NRM (compared to age <30; age 30-44 HR, 1.65; P = 0.110, age >44 HR, 1.80; P = 0.056) but lower relapse risk (compared to age <30; age 30-44 HR, 0.61; P = 0.034, age > 44 HR, 0.71; …


Music Can Be Reconstructed From Human Auditory Cortex Activity Using Nonlinear Decoding Models, Ludovic Bellier, Anaïs Llorens, Déborah Marciano, Aysegul Gunduz, Gerwin Schalk, Peter Brunner, Robert T. Knight Aug 2023

Music Can Be Reconstructed From Human Auditory Cortex Activity Using Nonlinear Decoding Models, Ludovic Bellier, Anaïs Llorens, Déborah Marciano, Aysegul Gunduz, Gerwin Schalk, Peter Brunner, Robert T. Knight

2020-Current year OA Pubs

Music is core to human experience, yet the precise neural dynamics underlying music perception remain unknown. We analyzed a unique intracranial electroencephalography (iEEG) dataset of 29 patients who listened to a Pink Floyd song and applied a stimulus reconstruction approach previously used in the speech domain. We successfully reconstructed a recognizable song from direct neural recordings and quantified the impact of different factors on decoding accuracy. Combining encoding and decoding analyses, we found a right-hemisphere dominance for music perception with a primary role of the superior temporal gyrus (STG), evidenced a new STG subregion tuned to musical rhythm, and defined …


Perceived Utility Of Intracranial Pressure Monitoring In Traumatic Brain Injury: A Seattle International Brain Injury Consensus Conference Consensus-Based Analysis And Recommendations, Randall M. Chesnut, Michael Diringer, Et Al. Aug 2023

Perceived Utility Of Intracranial Pressure Monitoring In Traumatic Brain Injury: A Seattle International Brain Injury Consensus Conference Consensus-Based Analysis And Recommendations, Randall M. Chesnut, Michael Diringer, Et Al.

2020-Current year OA Pubs

BACKGROUND: Intracranial pressure (ICP) monitoring is widely practiced, but the indications are incompletely developed, and guidelines are poorly followed.

OBJECTIVE: To study the monitoring practices of an established expert panel (the clinical working group from the Seattle International Brain Injury Consensus Conference effort) to examine the match between monitoring guidelines and their clinical decision-making and offer guidance for clinicians considering monitor insertion.

METHODS: We polled the 42 Seattle International Brain Injury Consensus Conference panel members' ICP monitoring decisions for virtual patients, using matrices of presenting signs (Glasgow Coma Scale [GCS] total or GCS motor, pupillary examination, and computed tomography diagnosis). …


Scca1/Serpinb3 Suppresses Antitumor Immunity And Blunts Therapy-Induced T Cell Responses Via Stat-Dependent Chemokine Production, Liyun Chen, Victoria Shi, Songyan Wang, Lulu Sun, Rebecca Freeman, Jasmine Yang, Matthew J. Inkman, Subhajit Ghosh, Fiona Ruiz, Kay Jayachandran, Yi Huang, Jingqin Luo, Jin Zhang, Pippa Cosper, Clifford J Luke, Perry W. Grigsby, Julie K. Schwarz, Stephanie Markovina, Et Al. Aug 2023

Scca1/Serpinb3 Suppresses Antitumor Immunity And Blunts Therapy-Induced T Cell Responses Via Stat-Dependent Chemokine Production, Liyun Chen, Victoria Shi, Songyan Wang, Lulu Sun, Rebecca Freeman, Jasmine Yang, Matthew J. Inkman, Subhajit Ghosh, Fiona Ruiz, Kay Jayachandran, Yi Huang, Jingqin Luo, Jin Zhang, Pippa Cosper, Clifford J Luke, Perry W. Grigsby, Julie K. Schwarz, Stephanie Markovina, Et Al.

2020-Current year OA Pubs

Patients with cancer who have high serum levels of squamous cell carcinoma antigen 1 (SCCA1, now referred to as SERPINB3) commonly experience treatment resistance and have a poor prognosis. Despite being a clinical biomarker, the modulation of SERPINB3 in tumor immunity is poorly understood. We found positive correlations of SERPINB3 with CXCL1, CXCL8 (CXCL8/9), S100A8, and S100A9 (S100A8/A9) myeloid cell infiltration through RNA-Seq analysis of human primary cervical tumors. Induction of SERPINB3 resulted in increased CXCL1/8 and S100A8/A9 expression, which promoted monocyte and myeloid-derived suppressor cell (MDSC) migration in vitro. In mouse models, Serpinb3a tumors showed increased MDSC and tumor-associated …


Courage-Als: A Randomized, Double-Blind Phase 3 Study Designed To Improve Participant Experience And Increase The Probability Of Success, Jeremy M Shefner, Timothy M Miller, Et Al. Aug 2023

Courage-Als: A Randomized, Double-Blind Phase 3 Study Designed To Improve Participant Experience And Increase The Probability Of Success, Jeremy M Shefner, Timothy M Miller, Et Al.

2020-Current year OA Pubs

No abstract provided.


Cerebrospinal Fluid Proteomics Define The Natural History Of Autosomal Dominant Alzheimer's Disease, Erik C B Johnson, Brian A Gordon, Eric Mcdade, Nicolas R Barthélemy, Celeste M Karch, Chengjie Xiong, Carlos Cruchaga, Richard J Perrin, John C Morris, Tammie L S Benzinger, Randall J Bateman, Anne M Fagan, Et Al. Aug 2023

Cerebrospinal Fluid Proteomics Define The Natural History Of Autosomal Dominant Alzheimer's Disease, Erik C B Johnson, Brian A Gordon, Eric Mcdade, Nicolas R Barthélemy, Celeste M Karch, Chengjie Xiong, Carlos Cruchaga, Richard J Perrin, John C Morris, Tammie L S Benzinger, Randall J Bateman, Anne M Fagan, Et Al.

2020-Current year OA Pubs

Alzheimer's disease (AD) pathology develops many years before the onset of cognitive symptoms. Two pathological processes-aggregation of the amyloid-β (Aβ) peptide into plaques and the microtubule protein tau into neurofibrillary tangles (NFTs)-are hallmarks of the disease. However, other pathological brain processes are thought to be key disease mediators of Aβ plaque and NFT pathology. How these additional pathologies evolve over the course of the disease is currently unknown. Here we show that proteomic measurements in autosomal dominant AD cerebrospinal fluid (CSF) linked to brain protein coexpression can be used to characterize the evolution of AD pathology over a timescale spanning …


A High-Performance Speech Neuroprosthesis, Francis R Willett, Erin M Kunz, Chaofei Fan, Donald T Avansino, Guy H Wilson, Eun Young Choi, Foram Kamdar, Matthew F Glasser, Leigh R Hochberg, Shaul Druckmann, Krishna V Shenoy, Jaimie M Henderson Aug 2023

A High-Performance Speech Neuroprosthesis, Francis R Willett, Erin M Kunz, Chaofei Fan, Donald T Avansino, Guy H Wilson, Eun Young Choi, Foram Kamdar, Matthew F Glasser, Leigh R Hochberg, Shaul Druckmann, Krishna V Shenoy, Jaimie M Henderson

2020-Current year OA Pubs

Speech brain-computer interfaces (BCIs) have the potential to restore rapid communication to people with paralysis by decoding neural activity evoked by attempted speech into text