Digital Commons Network^™

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 …

Indwelling Catheter Vs Intermittent Catheterization: Is There A Difference In Uti Susceptibility?, Vera Neumeier, Fabian P Stangl, Joëlle Borer, Collene E Anderson, Veronika Birkhäuser, Oksana Chemych, Oliver Gross, Miriam Koschorke, Jonas Marschall, Shawna Mccallin, Ulrich Mehnert, Helen Sadri, Lara Stächele, Thomas M Kessler, Lorenz Leitner

2020-Current year OA Pubs

BACKGROUND: Patients with neurogenic lower urinary tract dysfunction (NLUTD) often rely on some type of catheterization for bladder emptying. Intermittent catheterization (IC) is considered the gold standard and is preferred over continuous catheterization, since it is considered to cause fewer urinary tract infections (UTIs) than indwelling catheterization. The main objective of our study was to describe UTI prevalence (at visit) and incidence (within the last 12 months) and urine culture characteristics between patients using an indwelling catheter versus (vs) those performing IC.

METHODS: In this cross-sectional study, we prospectively evaluated from 02/2020 to 01/2021 patients with NLUTD undergoing urine cultures …

Exploring Caregiver Interest In And Preferences For Interventions For Children With Risk Of Asthma Exacerbation: Web-Based Survey, Gabrielle Pogge, David A Fedele, Erika A Waters, Julia Maki, Jean M Hunleth, Sreekala Prabhakaran, Deborah J Bowen, James A Shepperd

2020-Current year OA Pubs

BACKGROUND: Maintaining control of asthma symptoms is the cornerstone of asthma treatment guidelines in the United States. However, suboptimal asthma control and asthma exacerbations among young people are common and are associated with many negative outcomes. Interventions to improve asthma control are needed. For such interventions to be successful, it is necessary to understand the types of interventions that are appealing to caregivers of children with different levels of risk of exacerbation.

OBJECTIVE: This study aimed to evaluate whether caregivers of children with high (vs low) risk of asthma exacerbation show different levels of interest in and preferences for potential …

Impact Of Prior Therapies And Subsequent Transplantation On Outcomes In Adult Patients With Relapsed Or Refractory B-Cell Acute Lymphoblastic Leukemia Treated With Brexucabtagene Autoleucel In Zuma-3, Bijal D Shah, Armin Ghobadi, Et Al.

2020-Current year OA Pubs

BACKGROUND: Brexucabtagene autoleucel (brexu-cel) is an autologous anti-CD19 chimeric antigen receptor (CAR) T-cell therapy approved in the USA for adults with relapsed or refractory (R/R) B-cell acute lymphoblastic leukemia (B-ALL) and in the European Union for patients ≥26 years with R/R B-ALL. After 2 years of follow-up in ZUMA-3, the overall complete remission (CR) rate (CR+CR with incomplete hematological recovery (CRi)) was 73%, and the median overall survival (OS) was 25.4 months in 78 Phase 1 and 2 patients with R/R B-ALL who received the pivotal dose of brexu-cel. Outcomes by prior therapies and subsequent allogeneic stem cell transplantation (alloSCT) …

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). …

Use Of A Mixed Reality System For Navigational Mapping During Cardiac Electrophysiological Testing Does Not Prolong Case Duration: A Subanalysis From The Cardiac Augmented Reality Study, David Bloom, David Catherall, Nathan Miller, Michael K Southworth, Andrew C Glatz, Jonathan R Silva, Jennifer N Avari Silva

2020-Current year OA Pubs

BACKGROUND: CommandEP™ is a mixed reality (MXR) system for cardiac electrophysiological (EP) procedures that provides a real-time 3-dimensional digital image of cardiac geometry and catheter locations. In a previous study, physicians using the system demonstrated improved navigational accuracy. This study investigated the impact of the CommandEP system on EP procedural times compared to the standard-of-care electroanatomic mapping system (EAMS) display.

OBJECTIVE: The purpose of this retrospective case-controlled analysis was to evaluate the impact of a novel MXR interface on EP procedural times compared to a case-matched cohort.

METHODS: Cases from the Cardiac Augmented REality (CARE) study were matched for diagnosis …

Epigenetic Age Acceleration Mediates The Relationship Between Neighborhood Deprivation And Pain Severity In Adults With Or At Risk For Knee Osteoarthritis Pain, Pamela Jackson, Burel R Goodin, Et Al.

2020-Current year OA Pubs

An estimated 250 million people worldwide suffer from knee osteoarthritis (KOA), with older adults having greater risk. Like other age-related diseases, residents of high-deprivation neighborhoods experience worse KOA pain outcomes compared to their more affluent neighbors. The purpose of this study was to examine the relationship between neighborhood deprivation and pain severity in KOA and the influence of epigenetic age acceleration (EpAA) on that relationship. The sample of 128 participants was mostly female (60.9%), approximately half non-Hispanic Black (49.2%), and had a mean age of 58 years. Spearman bivariate correlations revealed that pain severity positively correlated with EpAA (ρ = …

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 …

Pact: A Pipeline For Analysis Of Circulating Tumor Dna, Jace Webster, Ha X Dang, Pradeep S Chauhan, Wenjia Feng, Alex Shiang, Peter K Harris, Russell K Pachynski, Aadel A Chaudhuri, Christopher A Maher

2020-Current year OA Pubs

MOTIVATION: Detection of genomic alterations in circulating tumor DNA (ctDNA) is currently used for active clinical monitoring of cancer progression and treatment response. While methods for analysis of small mutations are more developed, strategies for detecting structural variants (SVs) in ctDNA are limited. Additionally, reproducibly calling small-scale mutations, copy number alterations, and SVs in ctDNA is challenging due to the lack to unified tools for these different classes of variants.

RESULTS: We developed a unified pipeline for the analysis of ctDNA [Pipeline for the Analysis of ctDNA (PACT)] that accurately detects SVs and consistently outperformed similar tools when applied to …

Harm Reduction: A Missing Piece To The Holistic Care Of Patients Who Inject Drugs, Nathanial S Nolan, Sarah M Fracasso Francis, Laura R Marks, Susan E Beekmann, Philip M Polgreen, Stephen Y Liang, Michael J Durkin

2020-Current year OA Pubs

BACKGROUND: The rise in injection drug use (IDU) has led to an increase in drug-related infections. Harm reduction is an important strategy for preventing infections among people who inject drugs (PWID). We attempted to evaluate the harm reduction counseling that infectious diseases physicians provide to PWID presenting with infections.

METHODS: An electronic survey was distributed to physician members of the Emerging Infections Network to inquire about practices used when caring for patients with IDU-related infections.

RESULTS: In total, 534 ID physicians responded to the survey. Of those, 375 (70%) reported routinely caring for PWID. Most respondents report screening for human …

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 …

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.

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; …

Pharmacokinetics Of Moxidectin Combined With Albendazole Or Albendazole Plus Diethylcarbamazine For Bancroftian Filariasis, Yashpal S. Chhonker, Catherine Bjerum, Veenu Bala, Allassane F. Ouattara, Benjamin G. Koudou, Toki P. Gabo, Abdullah Alshehri, Abdoulaye Meïté, Peter U. Fischer, Gary J. Weil, Christopher L. King, Philip J. Budge, Daryl J. Murry

2020-Current year OA Pubs

Moxidectin (MOX) is a milbemycin endectocide recently approved by the U.S. FDA for the treatment of onchocerciasis in persons at least 12 years of age. MOX has been shown to have a good safety profile in recent clinical trials. The efficacy of MOX for the treatment of lymphatic filariasis (LF) and its potential use in mass drug administration protocols for the elimination of LF is currently under evaluation. In the context of a clinical trial, we investigated the pharmacokinetics and drug interactions of a combination of MOX plus albendazole (ALB) with or without diethylcarbamazine (DEC) compared to ivermectin (IVM) plus …

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 …

Csf Mtbr-Tau243 Is A Specific Biomarker Of Tau Tangle Pathology In Alzheimer's Disease, Kanta Horie, Nicolas R Barthélemy, Yan Li, Yingxin He, Benjamin Saef, Charles D Chen, Hong Jiang, Chihiro Sato, Brian A Gordon, Tammie L S Benzinger, David M Holtzman, John C Morris, Suzanne E Schindler, Randall J Bateman, Et Al.

2020-Current year OA Pubs

Aggregated insoluble tau is one of two defining features of Alzheimer's disease. Because clinical symptoms are strongly correlated with tau aggregates, drug development and clinical diagnosis need cost-effective and accessible specific fluid biomarkers of tau aggregates; however, recent studies suggest that the fluid biomarkers currently available cannot specifically track tau aggregates. We show that the microtubule-binding region (MTBR) of tau containing the residue 243 (MTBR-tau243) is a new cerebrospinal fluid (CSF) biomarker specific for insoluble tau aggregates and compared it to multiple other phosphorylated tau measures (p-tau181, p-tau205, p-tau217 and p-tau231) in two independent cohorts (BioFINDER-2, n = 448; and …

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

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

Spatial Epidemiologic Analysis And Risk Factors For Nontuberculous Mycobacteria Infections, Missouri, Usa, 2008-2019, Carlos Mejia-Chew, Miguel A Chavez, Min Lian, Angela Mckee, Leighton Garrett, Thomas C Bailey, Andrej Spec, Mansi Agarwal, George Turabelidze

2020-Current year OA Pubs

Nontuberculous mycobacteria (NTM) infections are caused by environmental exposure. We describe spatial distribution of NTM infections and associations with sociodemographic factors and flooding in Missouri, USA. Our retrospective analysis of mycobacterial cultures reported to the Missouri Department of Health and Social Services surveillance system during January 1, 2008-December 31, 2019, detected geographic clusters of infection. Multilevel Poisson regression quantified small-area geographic variations and identified characteristics associated with risk for infection. Median county-level NTM infection rate was 66.33 (interquartile range 51-91)/100,000 persons. Risk of clustering was significantly higher in rural areas (rate ratio 2.82, 95% CI 1.90-4.19) and in counties with …

Anesthesia Clinical Workload Estimated From Electronic Health Record Documentation Vs Billed Relative Value Units, Sunny S Lou, Laura R Baratta, Daphne Lew, Derek Harford, Michael S Avidan, Thomas Kannampallil

2020-Current year OA Pubs

IMPORTANCE: Accurate measurements of clinical workload are needed to inform health care policy. Existing methods for measuring clinical workload rely on surveys or time-motion studies, which are labor-intensive to collect and subject to biases.

OBJECTIVE: To compare anesthesia clinical workload estimated from electronic health record (EHR) audit log data vs billed relative value units.

DESIGN, SETTING, AND PARTICIPANTS: This cross-sectional study of anesthetic encounters occurring between August 26, 2019, and February 9, 2020, used data from 8 academic hospitals, community hospitals, and surgical centers across Missouri and Illinois. Clinicians who provided anesthetic services for at least 1 surgical encounter were …

Engaging Adolescents In Using Online Patient Portals, Bryan A Sisk, Alison L Antes, Christine Bereitschaft, Madi Enloe, Sunny Lin, Meghana Srinivas, Fabienne Bourgeois, James M Dubois

2020-Current year OA Pubs

IMPORTANCE: Many health care systems offer adolescents access to health information through online patient portals, but few studies have explored how to engage adolescents in using and benefiting from online portals.

OBJECTIVE: To determine how US children's hospitals have attempted to encourage adolescent portal use, barriers to engaging adolescents, and ideal future goals for engagement.

DESIGN, SETTING, AND PARTICIPANTS: This qualitative study performed structured qualitative interviews with informatics administrators from children's hospitals across the US between February and July 2022. Informatics administrators were employed by US health care systems that managed a children's hospital with at least 50 dedicated pediatrics …

Induction Of Cancer Neoantigens Facilitates Development Of Clinically Relevant Models For The Study Of Pancreatic Cancer Immunobiology, Usman Y Panni, Michael Y Chen, Felicia Zhang, Darren R Cullinan, Lijin Li, C Alston James, Xiuli Zhang, S Rogers, A Alarcon, John M Baer, Daoxiang Zhang, Feng Gao, Christopher A Miller, Qingqing Gong, Kian-Huat Lim, David G Denardo, S Peter Goedegebuure, William E Gillanders, William G Hawkins

2020-Current year OA Pubs

Neoantigen burden and CD8 T cell infiltrate are associated with clinical outcome in pancreatic ductal adenocarcinoma (PDAC). A shortcoming of many genetic models of PDAC is the lack of neoantigen burden and limited T cell infiltrate. The goal of the present study was to develop clinically relevant models of PDAC by inducing cancer neoantigens in KP2, a cell line derived from the KPC model of PDAC. KP2 was treated with oxaliplatin and olaparib (OXPARPi), and a resistant cell line was subsequently cloned to generate multiple genetically distinct cell lines (KP2-OXPARPi clones). Clones A and E are sensitive to immune checkpoint …

Genomic Risk For Post-Traumatic Stress Disorder In Families Densely Affected With Alcohol Use Disorders, Stacey Saenz De Viteri, Emma C Johnson, Vivia V Mccutcheon, Kathleen K Bucholz, Et Al.

2020-Current year OA Pubs

Recent genome-wide association studies (GWAS) have identified genetic markers of post-traumatic stress disorder (PTSD) in civilian and military populations. However, studies have yet to examine the genetics of PTSD while factoring in risk for alcohol dependence, which commonly co-occur. We examined genome-wide associations for DSM-IV PTSD among 4,978 trauma-exposed participants (31% with alcohol dependence, 50% female, 30% African ancestry) from the Collaborative Study on the Genetics of Alcoholism (COGA). We also examined associations of polygenic risk scores (PRS) derived from the Psychiatric Genomics Consortium (PGC)-PTSD Freeze 2 (N = 3533) and Million Veterans Program GWAS of PTSD (N = 5200) …

Prescribing Patterns For Sodium-Glucose Cotransporter 2 Inhibitors: A Survey Of Nephrologists, Tripti Singh, Tingting Li, Didier Mandelbrot, Brad C Astor, Ali Poyan Mehr

2020-Current year OA Pubs

No abstract provided.

Loop-And-Let-Go Technique For The Management Of Symptomatic Large Colonic Lipoma, Syedreza Haider, Matthew Peller, Vladimir Lamm, Ahmad Najdat Bazarbashi

2020-Current year OA Pubs

Video 1We depict (1) identification of a large lipoma in the sigmoid colon; (2) radial echo endoscopy confirming diagnosis; (3) removal with the loop-and-let-go technique; (4) ex vivo demonstration of the technique; and (5) an interval follow-up demonstrating healing of the lesion.

Radiofrequency-Based Chondroplasty Creates A Precise Area Of Targeted Chondrocyte Death With Minimal Necrosis Outside The Target Zone: A Systematic Review, Garrett R Jackson, Luis M Salazar, Johnathon R Mccormick, Varun Gopinatth, Alex Hodakowski, Colton C Mowers, Suhas Dasari, Luc M Fortier, Daniel J Kaplan, Zeeshan A Khan, Enzo S Mameri, Derrick M Knapik, Jorge Chahla, Nikhil N Verma

2020-Current year OA Pubs

PURPOSE: To systematically examine the effects of radiofrequency (RF) ablation or coblation (controlled ablation) on chondrocyte viability following knee chondroplasty in preclinical literature to determine the effectiveness and safety of RF-based techniques.

METHODS: A literature search was performed in September 2022 using PubMed and Scopus using the following search terms combined with Boolean operators: "chondroplasty," "radiofrequency," "thermal," "knee," "chondral defect," "articular cartilage," and "cartilage." The inclusion criteria consisted of preclinical studies examining the effect of RF ablation or coblation on chondrocytes during knee chondroplasty. Exclusion criteria consisted of studies reporting chondroplasty in joints other than the knee, clinical studies, in …

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 …

Cation Leak Through The Atp1a3 Pump Causes Spasticity And Intellectual Disability, Daniel G Calame, Marwan Shinawi, Et Al.

2020-Current year OA Pubs

ATP1A3 encodes the α3 subunit of the sodium-potassium ATPase, one of two isoforms responsible for powering electrochemical gradients in neurons. Heterozygous pathogenic ATP1A3 variants produce several distinct neurological syndromes, yet the molecular basis for phenotypic variability is unclear. We report a novel recurrent variant, ATP1A3(NM_152296.5):c.2324C>T; p.(Pro775Leu), in nine individuals associated with the primary clinical features of progressive or non-progressive spasticity and developmental delay/intellectual disability. No patients fulfil diagnostic criteria for ATP1A3-associated syndromes, including alternating hemiplegia of childhood, rapid-onset dystonia-parkinsonism or cerebellar ataxia-areflexia-pes cavus-optic atrophy-sensorineural hearing loss (CAPOS), and none were suspected of having an ATP1A3-related disorder. Uniquely among known …

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 …

Standardized Radiomics Analysis Of Clinical Myocardial Perfusion Stress Spect Images To Identify Coronary Artery Calcification, Saeed Ashrafinia, Pejman Dalaie, Thomas H. Schindler, Martin G. Pomper, Arman Rahmim

2020-Current year OA Pubs

PURPOSE: Myocardial perfusion (MP) stress single-photon emission computed tomography (SPECT) is an established diagnostic test for patients suspected of coronary artery disease (CAD). Meanwhile, coronary artery calcification (CAC) scoring obtained from diagnostic CT is a highly sensitive test, offering incremental diagnostic information in identifying patients with significant CAD yet normal MP stress SPECT (MPSS) scans. However, after decades of wide utilization of MPSS, CAC is not commonly reimbursed (e.g. by the CMS), nor widely deployed in community settings. We studied the potential of complementary information deduced from the radiomics analysis of normal MPSS scans in predicting the CAC score.

METHODS: …