Medicine and Health Sciences Commons^™

Increasing Metadata Coverage Of Sra Biosample Entries Using Deep Learning-Based Named Entity Recognition, Adam Klie, Brian Y Tsui, Shamim Mollah, Dylan Skola, Michelle Dow, Chun-Nan Hsu, Hannah Carter

2020-Current year OA Pubs

High-quality metadata annotations for data hosted in large public repositories are essential for research reproducibility and for conducting fast, powerful and scalable meta-analyses. Currently, a majority of sequencing samples in the National Center for Biotechnology Information's Sequence Read Archive (SRA) are missing metadata across several categories. In an effort to improve the metadata coverage of these samples, we leveraged almost 44 million attribute-value pairs from SRA BioSample to train a scalable, recurrent neural network that predicts missing metadata via named entity recognition (NER). The network was first trained to classify short text phrases according to 11 metadata categories and achieved …

Indole-3-Carbinol-Dependent Aryl Hydrocarbon Receptor Signaling Attenuates The Inflammatory Response In Experimental Necrotizing Enterocolitis, Lila S Nolan, Belgacem Mihi, Qingqing Gong, Jamie M Rimer, Shay S Bidani, Sarah E Gale, Martin Goree, Elise Hu, Wyatt E Lanik, Elizabeth Huang, Jennifer K Bando, Angela N Lewis, Marie L Laury, Misty Good, Et Al.

2020-Current year OA Pubs

Necrotizing enterocolitis (NEC) causes significant morbidity and mortality in premature infants; therefore, the identification of therapeutic and preventative strategies against NEC remains a high priority. The ligand-dependent transcription factor aryl hydrocarbon receptor (AhR) is well known to contribute to the regulation of intestinal microbial communities and amelioration of intestinal inflammation. However, the role of AhR signaling in NEC is unclear. Experimental NEC was induced in 4-d-old wild-type mice or mice lacking AhR expression in the intestinal epithelial cells or AhR expression in CD11c

A Retrospective Look At The Predictions And Recommendations From The 2009 Amia Policy Meeting: Did We See Ehr-Related Clinician Burnout Coming?, Justin B Starren, William M Tierney, Marc S Williams, Paul Tang, Charlene Weir, Ross Koppel, Philip Payne, George Hripcsak, Don E Detmer

2020-Current year OA Pubs

Clinicians often attribute much of their burnout experience to use of the electronic health record, the adoption of which was greatly accelerated by the Health Information Technology for Economic and Clinical Health Act of 2009. That same year, AMIA's Policy Meeting focused on possible unintended consequences associated with rapid implementation of electronic health records, generating 17 potential consequences and 15 recommendations to address them. At the 2020 annual meeting of the American College of Medical Informatics (ACMI), ACMI fellows participated in a modified Delphi process to assess the accuracy of the 2009 predictions and the response to the recommendations. Among …

Dorsal Anterior Cingulate Cortex Encodes The Integrated Incentive Motivational Value Of Cognitive Task Performance, Debbie M Yee, Jennifer L Crawford, Bidhan Lamichhane, Todd S Braver

2020-Current year OA Pubs

Humans can seamlessly combine value signals from diverse motivational incentives, yet it is not well understood how these signals are "bundled" in the brain to modulate cognitive control. The dorsal ACC (dACC) is theorized to integrate motivational value dimensions in the service of goal-directed action, although this hypothesis has yet to receive rigorous confirmation. In the present study, we examined the role of human dACC in motivational incentive integration. Healthy young adult men and women were scanned with fMRI while engaged in an experimental paradigm that quantifies the combined effects of liquid (e.g., juice, neutral, saltwater) and monetary incentives on …

Optimized Polyepitope Neoantigen Dna Vaccines Elicit Neoantigen-Specific Immune Responses In Preclinical Models And In Clinical Translation, Lijin Li, Xiuli Zhang, Xiaoli Wang, Samuel W Kim, John M Herndon, Michelle K Becker-Hapak, Beatriz M Carreno, Nancy B Myers, Mark A Sturmoski, Michael D Mclellan, Christopher A Miller, Tanner M Johanns, Benjamin R Tan, Gavin P Dunn, Timothy P Fleming, Ted H Hansen, S Peter Goedegebuure, William E Gillanders

2020-Current year OA Pubs

BACKGROUND: Preclinical studies and early clinical trials have shown that targeting cancer neoantigens is a promising approach towards the development of personalized cancer immunotherapies. DNA vaccines can be rapidly and efficiently manufactured and can integrate multiple neoantigens simultaneously. We therefore sought to optimize the design of polyepitope DNA vaccines and test optimized polyepitope neoantigen DNA vaccines in preclinical models and in clinical translation.

METHODS: We developed and optimized a DNA vaccine platform to target multiple neoantigens. The polyepitope DNA vaccine platform was first optimized using model antigens in vitro and in vivo. We then identified neoantigens in preclinical breast cancer …

Solvent Exposed Occupations And Risk Of Parkinson Disease In Finland, Susan Searles Nielsen, Mark N Warden, Markku Sallmén, Markku Sainio, Sanni Uuksulainen, Harvey Checkoway, Christer Hublin, Brad A Racette

2020-Current year OA Pubs

INTRODUCTION: Epidemiologic and toxicology studies suggest that exposure to various solvents, especially chlorinated hydrocarbon solvents, might increase Parkinson disease (PD) risk.

METHODS: In a population-based case-control study in Finland, we examined whether occupations with potential for solvent exposures were associated with PD. We identified newly diagnosed cases age 45-84 from a nationwide medication reimbursement register in 1995-2014. From the population register, we randomly selected non-PD controls matched on sex, along with birth and diagnosis years (age). We included 11,757 cases and 23,236 controls with an occupation in the 1990 census, corresponding to age 40-60. We focused on 28 occupations with …

Risk Factors Associated With Physician Trainee Concern Over Missed Educational Opportunities During The Covid-19 Pandemic, Sunny S Lou, Charles W Goss, Bradley A Evanoff, Jennifer G Duncan, Thomas Kannampallil

2020-Current year OA Pubs

BACKGROUND: The COVID-19 pandemic resulted in a transformation of clinical care practices to protect both patients and providers. These changes led to a decrease in patient volume, impacting physician trainee education due to lost clinical and didactic opportunities. We measured the prevalence of trainee concern over missed educational opportunities and investigated the risk factors leading to such concerns.

METHODS: All residents and fellows at a large academic medical center were invited to participate in a web-based survey in May of 2020. Participants responded to questions regarding demographic characteristics, specialty, primary assigned responsibility during the previous 2 weeks (clinical, education, or …

Real-World Outcomes Of Patients With Locally Advanced Or Metastatic Epithelioid Sarcoma, Mrinal M Gounder, Brian A Van Tine, Et Al.

2020-Current year OA Pubs

BACKGROUND: Limited data are available on the real-world effectiveness and safety of systemic therapies for advanced (surgically unresectable and/or metastatic) epithelioid sarcoma (ES).

METHODS: A retrospective medical records review was conducted in patients with advanced ES who were initiating first-line or ≥2 lines of systemic therapy (2000-2017) at 5 US cancer centers. The real-world overall response rate (rwORR), the duration of response (rwDOR), the disease control rate (rwDCR) (defined as stable disease for ≥32 weeks or any duration of response), and progression-free survival (rwPFS) were assessed by radiology reports. Overall survival (OS), rwDOR, and rwPFS were estimated from the time …

The Antigenic Anatomy Of Sars-Cov-2 Receptor Binding Domain, Wanwisa Dejnirattisai, James Brett Case, Natasha M. Kafai, Adam L. Bailey, Rita E. Chen, Baoling Ying, Michael S. Diamond, Et Al.

2020-Current year OA Pubs

No abstract provided.

Implementation Strategies To Improve Statin Utilization In Individuals With Hypercholesterolemia: A Systematic Review And Meta-Analysis, Laney K Jones, Stephanie Tilberry, Christina Gregor, Lauren H Yaeger, Yirui Hu, Amy C Sturm, Terry L Seaton, Thomas J Waltz, Alanna K Rahm, Anne Goldberg, Ross C Brownson, Samuel S Gidding, Marc S Williams, Michael R Gionfriddo

2020-Current year OA Pubs

BACKGROUND: Numerous implementation strategies to improve utilization of statins in patients with hypercholesterolemia have been utilized, with varying degrees of success. The aim of this systematic review is to determine the state of evidence of implementation strategies on the uptake of statins.

METHODS AND RESULTS: This systematic review identified and categorized implementation strategies, according to the Expert Recommendations for Implementing Change (ERIC) compilation, used in studies to improve statin use. We searched Ovid MEDLINE, Embase, Scopus, Cochrane Database of Systematic Reviews, Cochrane Central Register of Controlled Trials, and Clinicaltrials.gov from inception to October 2018. All included studies were reported in …

A Risk Assessment Tool For Resumption Of Research Activities During The Covid-19 Pandemic For Field Trials In Low Resource Settings, Suzanne M Simkovich, Victor G Davila-Roman, Lisa De Las Fuentes, Et Al.

2020-Current year OA Pubs

RATIONALE: The spread of severe acute respiratory syndrome coronavirus-2 has suspended many non-COVID-19 related research activities. Where restarting research activities is permitted, investigators need to evaluate the risks and benefits of resuming data collection and adapt procedures to minimize risk.

OBJECTIVES: In the context of the multicountry Household Air Pollution Intervention (HAPIN) trial conducted in rural, low-resource settings, we developed a framework to assess the risk of each trial activity and to guide protective measures. Our goal is to maximize the integrity of reseach aims while minimizing infection risk based on the latest scientific understanding of the virus.

METHODS: We …

Pfmfr3: A Multidrug-Resistant Modulator In Plasmodium Falciparum, Frances Rocamora, Purva Gupta, Eva S Istvan, Madeline R Luth, Emma F Carpenter, Krittikorn Kümpornsin, Erika Sasaki, Jaeson Calla, Nimisha Mittal, Krypton Carolino, Edward Owen, Manuel Llinás, Sabine Ottilie, Daniel E Goldberg, Marcus C S Lee, Elizabeth A Winzeler

2020-Current year OA Pubs

In malaria, chemical genetics is a powerful method for assigning function to uncharacterized genes. MMV085203 and GNF-Pf-3600 are two structurally related napthoquinone phenotypic screening hits that kill both blood- and sexual-stage

Periostin Loss-Of-Function Protects Mice From Post-Traumatic And Age-Related Osteoarthritis, Mukundan Attur, Xin Duan, Lei Cai, Tianzhen Han, Weili Zhang, Eric D Tycksen, Jonathan Samuels, Robert H Brophy, Steven B Abramson, Muhammad Farooq Rai

2020-Current year OA Pubs

BACKGROUND: Elevated levels of periostin (Postn) in the cartilage and bone are associated with osteoarthritis (OA). However, it remains unknown whether Postn loss-of-function can delay or prevent the development of OA. In this study, we sought to better understand the role of Postn in OA development and assessed the functional impact of Postn deficiency on post-traumatic and age-related OA in mice.

METHODS: The effects of Postn deficiency were studied in two murine experimental OA models using Postn

RESULTS: Postn

CONCLUSIONS: Postn deficiency protects against DMM-induced post-traumatic and age-related spontaneous OA. RNA-seq findings warrant further investigations to better understand the mechanistic …

Molecular Classification Of A Complex Structural Rearrangement Of The Rb1 Locus In An Infant With Sporadic, Isolated, Intracranial, Sellar Region Retinoblastoma, Kathleen M Schieffer, Margaret Shatara, Et Al.

2020-Current year OA Pubs

Retinoblastoma is a childhood cancer of the retina involving germline or somatic alterations of the RB Transcriptional Corepressor 1 gene, RB1. Rare cases of sellar-suprasellar region retinoblastoma without evidence of ocular or pineal tumors have been described. A nine-month-old male presented with a sellar-suprasellar region mass. Histopathology showed an embryonal tumor with focal Flexner-Wintersteiner-like rosettes and loss of retinoblastoma protein (RB1) expression by immunohistochemistry. DNA array-based methylation profiling confidently classified the tumor as pineoblastoma group A/intracranial retinoblastoma. The patient was subsequently enrolled on an institutional translational cancer research protocol and underwent comprehensive molecular profiling, including paired tumor/normal exome and genome …

The Clinical Course Of Coronavirus Disease 2019 In A Us Hospital System: A Multistate Analysis, Aaloke Mody, Patrick G Lyons, Cristina Vazquez Guillamet, Andrew Michelson, Sean Yu, Angella Sandra Namwase, Pratik Sinha, William G Powderly, Keith Woeltje, Elvin H Geng

2020-Current year OA Pubs

There are limited data on longitudinal outcomes for coronavirus disease 2019 (COVID-19) hospitalizations that account for transitions between clinical states over time. Using electronic health record data from a hospital network in the St. Louis, Missouri, region, we performed multistate analyses to examine longitudinal transitions and outcomes among hospitalized adults with laboratory-confirmed COVID-19 with respect to 15 mutually exclusive clinical states. Between March 15 and July 25, 2020, a total of 1,577 patients in the network were hospitalized with COVID-19 (49.9% male; median age, 63 years (interquartile range, 50-75); 58.8% Black). Overall, 34.1% (95% confidence interval (CI): 26.4, 41.8) had …

Uterine Contractions In Rodent Models And Humans, Manasi Malik, Michelle Roh, Sarah K England

2020-Current year OA Pubs

Aberrant uterine contractions can lead to preterm birth and other labour complications and are a significant cause of maternal morbidity and mortality. To investigate the mechanisms underlying dysfunctional uterine contractions, researchers have used experimentally tractable small animal models. However, biological differences between humans and rodents change how researchers select their animal model and interpret their results. Here, we provide a general review of studies of uterine excitation and contractions in mice, rats, guinea pigs, and humans, in an effort to introduce new researchers to the field and help in the design and interpretation of experiments in rodent models.

Thrombotic Microangiopathy Following Onasemnogene Abeparvovec For Spinal Muscular Atrophy: A Case Series, Deepa H Chand, Craig Zaidman, Kapil Arya, Rachel Millner, Michelle A Farrar, Fiona E Mackie, Natalie L Goedeker, Vikas R Dharnidharka, Raja Dandamudi, Sandra P Reyna

2020-Current year OA Pubs

Spinal muscular atrophy is treated with onasemnogene abeparvovec, which replaces the missing survival motor neuron 1 gene via an adeno-associated virus vector. As of July 1, 2020, we had identified 3 infants who developed thrombotic microangiopathy following onasemnogene abeparvovec. Early recognition and treatment of drug-induced thrombotic microangiopathy may lessen mortality and morbidity.

Modified Full-Face Snorkel Mask As Covid-19 Personal Protective Equipment: Quantitative Results, Kyle Nicholson, Ashley Henke-Adams, Daniel M Henke, Alexxai V Kravitz, Hiram A Gay

2020-Current year OA Pubs

The COVID-19 crisis has resulted in a shortage of personal protective equipment (PPE). Adapting commercially available full-faced snorkel masks has been proposed as an alternative to narrow the gap in PPE. An advantage of the full-faced snorkel mask design is that it serves two critical purposes: eye and face protection, and high quality air filtration to protect against SARS-CoV-2. We performed quantitative testing on various full-faced snorkel masks with 3D printed adapters that accept commercially available particulate filters, and report on a design that passed Occupational Safety and Health Administration (OSHA) full-facepiece respirator standards.

Momentum: Momelotinib Vs Danazol In Patients With Myelofibrosis Previously Treated With Jaki Who Are Symptomatic And Anemic, Srdan Verstovsek, Stephen T Oh, Et Al

2020-Current year OA Pubs

Hallmark features of myelofibrosis (MF) are cytopenias, constitutional symptoms and splenomegaly. Anemia and transfusion dependency are among the most important negative prognostic factors and are exacerbated by many JAK inhibitors (JAKi). Momelotinib (MMB) has been investigated in over 820 patients with MF and possesses a pharmacological and clinical profile differentiated from other JAKi by inhibition of JAK1, JAK2 and ACVR1. MMB is designed to address the complex drivers of iron-restricted anemia and chronic inflammation in MF and should improve constitutional symptoms and splenomegaly while maintaining or improving hemoglobin in JAKi-naive and previously JAKi-treated patients. The MOMENTUM Phase III study is …

Enteroscopy-Assisted Ercp With Needle-Knife Stricturoplasty Of A Strictured Hepaticojejunostomy, Michael J Weaver, Koushik K Das, Vladimir M Kushnir

2020-Current year OA Pubs

No abstract provided.

Quantitative Endophenotypes As An Alternative Approach To Understanding Genetic Risk In Neurodegenerative Diseases, Fabiana H G Farias, Bruno A Benitez, Carlos Cruchaga

2020-Current year OA Pubs

Endophenotypes, as measurable intermediate features of human diseases, reflect underlying molecular mechanisms. The use of quantitative endophenotypes in genetic studies has improved our understanding of pathophysiological changes associated with diseases. The main advantage of the quantitative endophenotypes approach to study human diseases over a classic case-control study design is the inferred biological context that can enable the development of effective disease-modifying treatments. Here, we summarize recent progress on biomarkers for neurodegenerative diseases, including cerebrospinal fluid and blood-based, neuroimaging, neuropathological, and clinical studies. This review focuses on how endophenotypic studies have successfully linked genetic modifiers to disease risk, disease onset, or …

Signet-Ring Cutaneous Metastasis Presenting With Massive Anasarca, Neel Raval, Leonid Shmuylovich, John Strickley, Tiffany Y Chen, Ilana S Rosman, Amy Musiek

2020-Current year OA Pubs

No abstract provided.

Effect Of Ketamine On Cardiovascular Function During Procedural Sedation Of Adults, Kara Goddard, Christopher Sampson, Starr-Mar'ee Bedy, Rugheed Ghadban, Julie Stilley

2020-Current year OA Pubs

INTRODUCTION: Ketamine is commonly used in emergency department procedural sedation. Mild to moderate transient increases in blood pressure, heart rate, and cardiac output are common due to ketamine causing an increase in sympathetic activity. There is a concern that these physiological changes could result in an increased myocardial oxygen demand that may exacerbate underlying cardiac disease.

METHODS: Convenience sample of patients older than 50 years receiving ketamine for procedural sedation in the emergency department was used (n = 31). Patients were selected to receive ketamine based on provider discretion. Primary outcome was incidence of new myocardial ischemia apparent on an …

Progression Of Pediatric Celiac Disease From Potential Celiac Disease To Celiac Disease: A Retrospective Cohort Study, Shruti Sakhuja, Lori R Holtz

2020-Current year OA Pubs

BACKGROUND: A subset of patients with serology suggesting celiac disease have an initially negative biopsy but subsequently develop histopathologic celiac disease. Here we characterize patients with potential celiac disease who progress to celiac disease.

METHODS: We performed a retrospective analysis of children (0-18 years of age) with biopsy-confirmed celiac disease seen at St. Louis Children's Hospital between 2013 and 2018.

RESULTS: Three hundred sixteen of 327 (96%) children with biopsy-confirmed celiac disease were diagnosed on initial biopsy. The 11 children with potential celiac disease who progressed to celiac disease had lower anti-tissue transglutaminase (anti-TTG IgA) concentrations (2.4 (1.6-5) X upper …

Functional Connectivity Within Glioblastoma Impacts Overall Survival, Andy G S Daniel, Ki Yun Park, Jarod L Roland, Donna Dierker, James Gross, Joseph B Humphries, Carl D Hacker, Abraham Z Snyder, Joshua S Shimony, Eric C Leuthardt

2020-Current year OA Pubs

BACKGROUND: Glioblastoma (GBM; World Health Organization grade IV) assumes a variable appearance on MRI owing to heterogeneous proliferation and infiltration of its cells. As a result, the neurovascular units responsible for functional connectivity (FC) may exist within gross tumor boundaries, albeit with altered magnitude. Therefore, we hypothesize that the strength of FC within GBMs is predictive of overall survival.

METHODS: We used predefined FC regions of interest (ROIs) in de novo GBM patients to characterize the presence of within-tumor FC observable via resting-state functional MRI and its relationship to survival outcomes.

RESULTS: Fifty-seven GBM patients (mean age, 57.8 ± 13.9 …

Longitudinal Accumulation Of Cerebral Microhemorrhages In Dominantly Inherited Alzheimer Disease, Nelly Joseph-Mathurin, Guoqiao Wang, Eric Mcdade, Jason Hassenstab, Tyler M Blazey, Brian A Gordon, Gengsheng Chen, Parinaz Massoumzadeh, Russ C Hornbeck, Beau M Ances, Carlos Cruchaga, Celeste M Karch, Richard J Perrin, Chengjie Xiong, John C Morris, Randall J Bateman, Tammie L S Benzinger, Et Al

2020-Current year OA Pubs

OBJECTIVE: To investigate the inherent clinical risks associated with the presence of cerebral microhemorrhages (CMHs) or cerebral microbleeds and characterize individuals at high risk for developing hemorrhagic amyloid-related imaging abnormality (ARIA-H), we longitudinally evaluated families with dominantly inherited Alzheimer disease (DIAD).

METHODS: Mutation carriers (n = 310) and noncarriers (n = 201) underwent neuroimaging, including gradient echo MRI sequences to detect CMHs, and neuropsychological and clinical assessments. Cross-sectional and longitudinal analyses evaluated relationships between CMHs and neuroimaging and clinical markers of disease.

RESULTS: Three percent of noncarriers and 8% of carriers developed CMHs primarily located in lobar areas. Carriers with …

Beyond Somatosensation: Mrgprs In Mucosal Tissues, Juan M Inclan-Rico, Brian S Kim, Ishmail Abdus-Saboor

2020-Current year OA Pubs

Mas-related G coupled receptors (Mrgprs) are a superfamily of receptors expressed in sensory neurons that are known to transmit somatic sensations from the skin to the central nervous system. Interestingly, Mrgprs have recently been implicated in sensory and motor functions of mucosal-associated neuronal circuits. The gastrointestinal and pulmonary tracts are constantly exposed to noxious stimuli. Therefore, it is likely that neuronal Mrgpr signaling pathways in mucosal tissues, akin to their family members expressed in the skin, might relay messages that alert the host when mucosal tissues are affected by damaging signals. Further, Mrgprs have been proposed to mediate the cross-talk …

In-Laboratory Breast Specimen Radiography Reduces Tissue Block Utilization And Improves Turnaround Time Of Pathologic Examination, Sri Krishna Chaitanya Arudra, Laura C Garvey, Ian S Hagemann

2020-Current year OA Pubs

BACKGROUND: This study was performed to determine whether in-laboratory specimen radiography reduces turnaround time or block utilization in surgical pathology.

METHODS: Specimens processed during a 48-day trial of an in-lab cabinet radiography device (Faxitron) were compared to a control group of specimens imaged in the mammography suite during a prior 1-year period, and to a second group of specimens not undergoing imaging of any type.

RESULTS: Cases imaged in the mammography suite had longer turnaround time than cases not requiring imaging (by 1.15 days for core biopsies, and 1.73 days for mastectomies; p < 0.0001). In contrast, cases imaged in-lab had turnaround time that was no longer than unimaged cases (p > 0.05 for core biopsies, lumpectomies and mastectomies). …

Shared Developmental Gait Disruptions Across Two Mouse Models Of Neurodevelopmental Disorders, Rachel M Rahn, Claire T Weichselbaum, David H Gutmann, Joseph D Dougherty, Susan E Maloney

2020-Current year OA Pubs

BACKGROUND: Motor deficits such as abnormal gait are an underappreciated yet characteristic phenotype of many neurodevelopmental disorders (NDDs), including Williams Syndrome (WS) and Neurofibromatosis Type 1 (NF1). Compared to cognitive phenotypes, gait phenotypes are readily and comparably assessed in both humans and model organisms and are controlled by well-defined CNS circuits. Discovery of a common gait phenotype between NDDs might suggest shared cellular and molecular deficits and highlight simple outcome variables to potentially quantify longitudinal treatment efficacy in NDDs.

METHODS: We characterized gait using the DigiGait assay in two different murine NDD models: the complete deletion (CD) mouse, which models …

Affective Temperaments, Panic Disorder And Their Bipolar Connections, Zsuzsanna Belteczki, Zoltan Rihmer, Sandor Rozsa, Julia Ujvari, Maurizio Pompili, Xenia Gonda, Péter Dome

2020-Current year OA Pubs

No abstract provided.