20 Works

Gibbon genome (Nleu3.0) custom gene annotation file

Mariam Okhovat, Kimberly A. Nevonen, Brett A. Davis, Pryce Michener, Samantha Ward, Mark Milhaven, Lana Harshman, Ajuni Sohota, Jason D. Fernandes, Sofie R. Salama, Rachel J. O'Neill, Nadav Ahituv, Krishna R. Veeramah & Lucia Carbone
Co-option of transposable elements (TEs) to become part of existing or new enhancers is an important mechanism for evolution of gene regulation. However, contributions of lineage-specific TE insertions to recent regulatory adaptations remain poorly understood. Gibbons present a suitable model to study these contributions as they have evolved a lineage-specific TE called LAVA, which is still active in the gibbon genome. The LAVA retrotransposon is thought to have played a role in the emergence of...

SATURN: an inexpensive, freely-available, and fully self-administered cognitive screening test

David Bissig, Deniz Erten-Lyons, Helmi Lutsep & Jeffrey Kaye
Cognitive screening tests improve detection of dementia in the outpatient setting, and are helpful in select inpatient settings. Barriers to widespread screening include provider time investment and variability in test administration and scoring. We therefore developed Self-Administered Tasks Uncovering Risk of Neurodegeneration (SATURN) for inexpensive (<$100) computer tablets. This submission to Dryad accompanies an abstract for the 2020 American Academy of Neurology conference, and is likely to referenced in a later manuscript. This Dryad data...

The Thr92Ala-DIO2 polymorphism affects outcomes in LT4-treated women

Sarah Peterson, Tatiana Fonseca, Kathryn Schuff, Elizabeth McAninch, Antonio Bianco & Mary Samuels
Context: The Thr92Ala-DIO2 polymorphism may affect hypothyroid patients’ responses to levothyroxine (LT4) treatment. Objective: To study whether the Thr92Ala-DIO2 polymorphism affects hypothyroid patients’ responses to levothyroxine (LT4) treatment. Design: Secondary analysis of a randomized intervention study. Setting: Primary care center. Patients or Other Participants: 109 hypothyroid women aged 21-70 years with normal TSH levels grouped in homozygous Thr92-DIO2 (THR; n=39) and homozygous Ala92-DIO2 plus heterozygous (ALA; n=70) groups. Intervention: Change in LT4 dose. Main Outcome...

Data from: Quantification of sensitivity and resistance of breast cancer cell lines to anti-cancer drugs using GR metrics

Marc Hafner, Laura M. Heiser, Elizabeth H. Williams, Mario Niepel, Nicholas J. Wang, James E. Korkola, Joe W. Gray & Peter K. Sorger
Traditional means for scoring the effects of anti-cancer drugs on the growth and survival of cell lines is based on relative cell number in drug-treated and control samples and is seriously confounded by unequal division rates arising from natural biological variation and differences in culture conditions. This problem can be overcome by computing drug sensitivity on a per-division basis. The normalized growth rate inhibition (GR) approach yields per-division metrics for drug potency (GR50) and efficacy...

Feasibility and preliminary efficacy for morning bright light therapy to improve sleep and plasma biomarkers in US Veterans with TBI. A prospective, open-label, single-arm trial

Jonathan Elliott, Alisha McBride, Nadir Balba, Stanley Thomas, Cassandra Pattinson, Benjamin Morasco, Andrea Wilkerson, Jessica Gill & Miranda Lim
Mild traumatic brain injury (TBI) is associated with persistent sleep-wake dysfunction, including insomnia and circadian rhythm disruption, which can exacerbate functional outcomes including mood, pain, and quality of life. Present therapies to treat sleep-wake disturbances in those with TBI (e.g., cognitive behavioral therapy for insomnia) are limited by marginal efficacy, poor patient acceptability, and/or high patient/provider burden. Thus, this study aimed to assess the feasibility and preliminary efficacy of morning bright light therapy, to improve...

Compositional variation in early life parenting structures alters oxytocin and vasopressin 1a receptor development in prairie voles (Microtus ochrogaster)

Forrest Rogers, Sara Freeman, Marina Anderson, Michelle Palumbo & Karen Bales
Paternal absence can significantly alter bio-behavioral development in many biparental species. This effect has generally been demonstrated by comparing the development of offspring reared under biparental care with those reared after removal of the father. However, studies employing this design conflate two significant modifications to early life experience: removal of father-specific qualities and the general reduction of offspring-directed care. In the socially monogamous prairie vole (Microtus ochrogaster), the experience of paternal absence without substitution during...

Data from: Telemedicine in neurology: telemedicine work group of the American Academy of Neurology update

Jaime M. Hatcher-Martin, Jamie Lynn Adams, Eric R Anderson, Riley Bove, Tamika M. Burrus, Mahan Chehrenama, Mary Dolan O'Brien, Dawn S. Eliashiv, Deniz Erten-Lyons, Barbara S. Giesser, Lauren Moo, Pushpa Narayanaswami, Marvin A. Rossi, Madhu Soni, Nauman Tariq, Jack W. Tsao, Bert Vargas, Scott Vota, Scott Wessels, Hannah Planalp & Raghav Govindarajan
ABSTRACT Purpose: While there is strong evidence supporting the importance of telemedicine in stroke, its role in other areas of neurology is not as clear. The goal of this review is to provide an overview of evidence-based data regarding the role of teleneurology in the care of patients with neurologic disorders other than stroke. Recent findings: Studies across multiple specialties report noninferiority of evaluations by telemedicine compared with traditional, in-person evaluations in terms of patient...

Identification of an inhibitory neuron subtype, the L-stellate cells of the cochlear nucleus

Tenzin Ngodup, Gabriel Romero & Laurence Trussell
Auditory processing depends upon inhibitory signaling by interneurons, even at its earliest stages in the ventral cochlear nucleus (VCN). Remarkably, to date only a single subtype of inhibitory neuron has been documented in the VCN, a projection neuron termed the D-stellate cell. With the use of a transgenic mouse line, optical clearing and imaging techniques, combined with electrophysiological tools, we revealed a population of glycinergic cells in the VCN distinct from the D-stellate cell. These...

Data from: Leptin increases sympathetic nerve activity via induction of its own receptor in the paraventricular nucleus

Virginia Brooks, Zhigang Shi, Nicole Pelletier, Jennifer Wong, Baoxin Li, Andrei Sdrulla, Christopher Madden & Daniel Marks
Whether leptin acts in the paraventricular nucleus (PVN) to increase sympathetic nerve activity (SNA) is unclear, since PVN leptin receptors (LepR) are sparse. We show in rats that PVN leptin slowly increases SNA to muscle and brown adipose tissue, because it induces the expression of its own receptor and synergizes with local glutamatergic neurons. PVN LepR are not expressed in astroglia and rarely in microglia; instead, glutamatergic neurons express LepR, some of which project to...

Data from: Loss of murine Paneth cell function alters the immature intestinal microbiome and mimics changes seen in neonatal necrotizing enterocolitis

Shiloh R. Lueschow, Jessica Stumphy, Huiyu Gong, Stacy L. Kern, Timothy G. Elgin, Mark A. Underwood, Karen M. Kalanetra, David A. Mills, Melissa H. Wong, David K. Meyerholz, Misty Good & Steven J. McElroy
Necrotizing enterocolitis (NEC) remains the leading cause of gastrointestinal morbidity and mortality in premature infants. Human and animal studies suggest a role for Paneth cells in NEC pathogenesis. Paneth cells play critical roles in host-microbial interactions and epithelial homeostasis. The ramifications of eliminating Paneth cell function on the immature host-microbial axis remains incomplete. Paneth cell function was depleted in the immature murine intestine using chemical and genetic models, which resulted in intestinal injury consistent with...

Data from: MR1-restricted mucosal-associated invariant T (MAIT) cells respond to mycobacterial vaccination and infection in nonhuman primates

Justin M. Greene, Pradyot Dash, Sobhan Roy, Curtis McMurtrey, Walid Awad, Jason S. Reed, Katherine B. Hammond, Shaheed Abdulhaqq, Helen L. Wu, Benjamin J. Burwitz, Benjamin F. Roth, David W. Morrow, Julia C. Ford, Guangwu Xu, Joseph Y. Bae, Hugh Crank, Alfred W. Legasse, Thurston H. Dang, Hui Yee Greenaway, Monica Kurniawan, Marielle C. Gold, Melanie J. Harriff, Deborah A. Lewinsohn, Byung S. Park, Michael K. Axthelm … & Jonah B. Sacha
Studies on mucosal-associated invariant T cells (MAITs) in nonhuman primates (NHP), a physiologically relevant model of human immunity, are handicapped due to a lack of macaque MAIT-specific reagents. Here we show that while MR1 ligand-contact residues are conserved between human and multiple NHP species, three T-cell receptor contact-residue mutations in NHP MR1 diminish binding of human MR1 tetramers to macaque MAITs. Construction of naturally loaded macaque MR1 tetramers facilitated identification and characterization of macaque MR1-binding...

Data from: Characteristics of the healthcare information technology workforce in the HITECH era: underestimated in size, still growing, and adapting to advanced uses

William R. Hersh, Keith W. Boone & Annette M. Totten
Objective: There is little readily available data about the size and characteristics of the healthcare information technology workforce. We sought to update a previous description of the size, growth, and characteristics of this workforce based on the Healthcare Information Management Systems Society (HIMSS) Analytics® Database, a resource that includes hospital size, number of beds, amount of staffing, and an eight-stage model of electronic health record adoption (Electronic Medical Record Adoption Model, EMRAM℠). Materials and Methods:...

Data from: Brief in-hospital cognitive screening anticipates complex admissions and may detect dementia

David P. Bissig & Charles S. DeCarli
Objective: With the long-term goal of improving community health by screening for dementia, we tested the utility of integrating the Six-Item Screener (SIS) into our emergency department neurology consultations. Methods: In this cross-sectional observational study, we measured SIS performance within 24 hours of hospital arrival in 100 consecutive English-speaking patients aged ≥ 45 years. Performance was compared to patient age, previously charted cognitive impairment, and proxies for in-hospital complexity: whether or not a patient was...

A practical approach to functional optical coherence tomography shows abnormal retinal responses in Alzheimer’s disease

David Bissig, Clarice Zhou, Vy Le & Jacqueline Bernard
Spectral-domain optical coherence tomography (SD-OCT) is an accessible clinical tool for measuring structural changes to the retina, and increasingly as a biomarker for brain-predominant neurodegenerative diseases like Alzheimer’s. Information about retinal function can also be extracted from OCT images, but is under-studied, with literature examples often employing challenging protocols or requiring specialized hardware. The first goal of this study was to verify that functional retinal imaging was feasible with a commercially-available SD-OCT device and a...

OHSU 2019-2020 utilization of ambulatory telehealth and office visits by patient demographics

Jonathan Sachs, Peter Graven, Jeffrey Gold & Steven Kassakian
The COVID-19 pandemic and subsequent expansion of telehealth may be exacerbating inequities in ambulatory care access due to institutional and structural barriers. We conduct a repeat cross-sectional analysis of ambulatory patients to evaluate for demographic disparities in the utilization of telehealth modalities. The ambulatory patient population at Oregon Health & Science University (Portland, OR) is examined from June 1 through September 30, in 2019 (reference period) and in 2020 (study period). We first assess for...

Data from: The Teleost Anatomy Ontology: anatomical representation for the genomics age

Wasila M. Dahdul, John G. Lundberg, Peter E. Midford, James P. Balhoff, Hilmar Lapp, Todd J. Vision, Melissa A. Haendel, Monte Westerfield & Paula M. Mabee
The rich knowledge of morphological variation among organisms reported in the systematic literature has remained in free-text format, impractical for use in large-scale synthetic phylogenetic work. This noncomputable format has also precluded linkage to the large knowledgebase of genomic, genetic, developmental, and phenotype data in model organism databases. We have undertaken an effort to prototype a curated, ontology-based evolutionary morphology database that maps to these genetic databases (http://kb.phenoscape.org) to facilitate investigation into the mechanistic basis...

Data from: Effect of IV glyburide on adjudicated edema endpoints in the GAMES-RP Trial

W. Taylor Kimberly, Matthew B. Bevers, Rüdiger Von Kummer, Andrew M. Demchuk, Javier M. Romero, Jordan J. Elm, Holly E. Hinson, Bradley J. Molyneaux, J. Marc Simard & Kevin Navin Sheth
Objective: In this secondary analysis of the GAMES-RP trial, we report the effect of IV glyburide on adjudicated, edema-related endpoints. Methods: Blinded adjudicators assigned designations for hemorrhagic transformation, neurological deterioration, malignant edema and edema-related death to patients from the GAMES-RP Phase II randomized controlled trial of IV glyburide for large hemispheric infarct. Rates of these endpoints were compared between treatment arms in the per-protocol sample. In those participants with malignant edema, the effects of treatment...

Data from: Genetic differentiation among isolates of Teredinibacter turnerae, a widely occurring intracellular endosymbiont of shipworms

Marvin A. Altamia, Nicole Wood, Jennifer M. Fung, Sandra Dedrick, Eric W. Linton, Gisela P. Concepcion, Margo G. Haygood & Daniel L. Distel
Teredinibacter turnerae is a cultivable intracellular endosymbiont of xylotrophic (wood-feeding) bivalves of the Family Teredinidae (shipworms). Although T. turnerae has been isolated from many shipworm taxa collected in many locations, no systematic effort has been made to explore genetic diversity within this symbiont species across the taxonomic and geographical range of its hosts. The mode of symbiont transmission is unknown. Here, we examine sequence diversity in fragments of six genes (16S rRNA, gyrB, sseA, recA,...

Data from: A unified anatomy ontology of the vertebrate skeletal system

Wasila M. Dahdul, James P. Balhoff, David C. Blackburn, Alexander D. Diehl, Melissa A. Haendel, Brian K. Hall, Hilmar Lapp, John G. Lundberg, Christopher J. Mungall, Martin Ringwald, Erik Segerdell, Ceri E. Van Slyke, Matthew K. Vickaryous, Monte Westerfield & Paula M. Mabee
The skeleton is of fundamental importance in research in comparative vertebrate morphology, paleontology, biomechanics, developmental biology, and systematics. Motivated by research questions that require computational access to and comparative reasoning across the diverse skeletal phenotypes of vertebrates, we developed a module of anatomical concepts for the skeletal system, the Vertebrate Skeletal Anatomy Ontology (VSAO), to accommodate and unify the existing skeletal terminologies for the species-specific (mouse, the frog Xenopus, zebrafish) and multispecies (teleost, amphibian) vertebrate...

Data from: Test collections for EHR-based clinical information retrieval

Yanshan Wang, Andrew Wen, Sijia Liu, William Hersh, Steven Bedrick & Hongfang Liu
Objectives: To create test collections for evaluating clinical Information Retrieval (IR) systems and advancing clinical IR research. Materials and Methods: Electronic Health Records (EHR) data, including structured and free text data, from 45,000 patients who are a part of the Mayo Clinic Biobank cohort was retrieved from the clinical data warehouse. The clinical IR system indexed 42 million free-text EHR documents. The search queries consisted of 56 topics developed through a collaboration between Mayo Clinic...

Registration Year

  • 2022
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  • 2012

Resource Types

  • Dataset


  • Oregon Health & Science University
  • University of California, Davis
  • National Evolutionary Synthesis Center
  • Massachusetts General Hospital
  • University of South Dakota
  • University of North Carolina
  • Rush University Medical Center
  • University of Oregon
  • University of Tennessee Health Science Center
  • University of Kansas