162 Works

A Patient-specific heterogeneous Radiobiological Model for Glioblastoma Multiforme

Christopher McGuinness

The Art of Evidence and the Morality of Medical Decisions

Brian Dolan

Anatomy Through History

Brian Dolan

Monroe Monroe Group Videos

Lauren Haack

Retinofugal projections from melanopsin-expressing retinal ganglion cells revealed by intraocular injections of Cre-dependent virus

David R Copenhagen & Anton Delwig
To understand visual functions mediated by intrinsically photosensitive melanopsin-expressing retinal ganglion cells (mRGCs), it is important to elucidate axonal projections from these cells into the brain. Initial studies reported that melanopsin is expressed only in retinal ganglion cells within the eye. However, recent studies in Opn4-Cre mice revealed Cre-mediated marker expression in multiple brain areas. These discoveries complicate the use of melanopsin-driven genetic labeling techniques to identify retinofugal projections specifically from mRGCs. To restrict labeling...

Alpha-1A Adrenergic Receptor in Rabbit Heart

Paul C. Simpson
The alpha-1A-adrenergic receptor (AR) subtype is associated with cardioprotective signaling in the mouse and human heart. The rabbit is useful for cardiac disease modeling, but data on the alpha-1A in the rabbit heart are limited. Our objective was to test for expression and function of the alpha-1A in rabbit heart. By quantitative real-time reverse transcription PCR (qPCR) on mRNA from left ventricular myocardium of adult male New Zealand White rabbits, the alpha-1B was 99% of...

Mentor Assessment Instrument validation study

Michi Yukawa, Stuart Gansky, Patricia O'Sullivan, Mitchell Feldman, Holly Nishimura & Arianne Teherani
Prospective survey study

SIVD (Subcortical Ischemic Vascular Dementia)

Michael W. Weiner & Helena Chui
The overall goal of this project was to determine the extent to which subcortical ischemia and infaraction, and Alzheimer's disease, contribute to dementia. This project aimed to provide a greater understanding of the pathogenesis of dementia in patients with SIVD and AD.

Frontotemporal Lobar Degeneration (FTLD)

Michael W. Weiner
This data set was acquired with the aim of determining the structural and chemical changes that occur in the brain as a result of frontotemporal lobar degeneration (FTLD). The data includes proton density, T1, and T2-weighted neuroimages from subjects suffering from FTLD and Alzheimer's Disease, as well as a population of matched controls.

Progression of white matter degeneration in amyotrophic lateral sclerosis: A diffusion tensor imaging study

Yu Zhang, Norbert Schuff, Susan Woolley, Gloria Chiang, Lauren Boreta, Joel Laxamana, Jonathon Katz & Michael W. Weiner
Whether longitudinal diffusion tensor MRI imaging (DTI) can capture disease progression in patients with amyotrophic lateral sclerosis (ALS) is unclear. The primary goal of this study was to determine if DTI detects progression of the corticospinal tracts (CST) degeneration in ALS. Seventeen ALS patients and 19 ageand gender-matched healthy controls were scanned with DTI at baseline for cross-sectional analyses. For longitudinal analyses, the ALS patients had repeat DTI scans after eight months. Tractography of the...

A Systems Biology approach to determine cell-specific gene regulatory effects of genetic associations in multiple sclerosis

Lohith Madireddy, Kicheol Kim & Sergio Baranzini
We have conducted a cell-specific pathway analysis of the latest GWAS in multiple sclerosis (MS); which analyzed a total of 47,351 cases and 68,284 healthy controls and found more than 200 non-MHC genome-wide associations. Our approach makes extensive use of gene regulatory data generated by the ENCODE and REP projects to build data-driven models of the predicted regulatory effects (PRE) of each associated variant and their flanking correlated variation over a wide range of linkage...

Map PAINS substructures according to PAINS class and find the highest PAINS violation

Julia Davies
Many scientists are unaware that PAINS substructures are classified by hit frequency; this has led to a tendency to irresponsibly use PAINS filters during compound triage by filtering out potential leads based on the presence of a PAINS substructure instead of the presence of a type of PAINS substructure. Baell suggested in his review, Seven Year Itch: Pan-Assay Interference Compounds (PAINS) in 2017 - Utility and Limitations, that scientists should focus on class A, maybe...

Sexual harassment in the library: understanding experiences and taking action

Jill Barr-Walker, Denise Caramagno, Iesha Nevels, Dylan Romero & Peggy Tahir
Sexual harassment in libraries exists, but it has not been comprehensively studied. In the wake of the #MeToo movement and shared anecdotal experiences, library staff members at the University of California, San Francisco were empowered to address this issue in our library. This paper will present the results of our survey of sexual harassment experiences of our staff and, in an effort to encourage other academic library workers to spearhead similar efforts in their own...

Program to Reduce Incontinence through Diet and Exercise (PRIDE)

Jennifer Creasman
Background Obesity is an established and modifiable risk factor for urinary incontinence, but conclusive evidence for a beneficial effect of weight loss on urinary incontinence is lacking. Methods We randomly assigned 338 overweight and obese women with at least 10 urinary incontinence episodes per week to an intensive 6-month weight-loss program that included diet, exercise, and behavior modification (226 patients) or to a structured education program (112 patients). Results The mean (±SD) age of the...

Remineralization of dentin, Effect of Protease Inhibitors

Stefan Habelitz, Grayson Marshall & Hamid Nurrohman
Mineralized and sound dentin matrices contain inactive preforms of proteolytic enzymes that may be activated during the demineralization cycle. In this study, we tested the hypothesis that protease inhibitors (PI) preserve demineralized collagen fibrils and other constituents of the dentin matrix and thereby affect the potential for remineralization. Artificial carious lesions with lesion depths of 140 µm were created with acetate buffer (pH=5.0, 66 hours), and remineralized using a polymer-induced-liquid-precursor (PILP) process (pH=7.4, 14 days)...

Voxel-wise co-analysis of macro- and microstructural brain alteration in Mild Cognitive Impairment and Alzheimer's disease using anatomical and diffusion MRI

Valerie Cardenas, Duygu Tosun, Linda Chao, P. Thomas Fletcher, Sarang Joshi, Michael W. Weiner & Norbert Schuff
Structural and diffusion data from cognitively normal elderly and those with mild cognitive impairment. Background and Purpose: To determine if a voxel-wise "co-analysis" of structural and diffusion tensor magnetic resonance imaging (MRI) together reveals additional brain regions affected in mild cognitive impairment (MCI) and Alzheimer's Disease (AD) than voxel-wise analysis of the individual MRI modalities alone. Conclusion: These results suggest that in corpus callosum and temporal regions macroand microstructural variations in MCI can be congruent,...

Pooled metagenomic sequence from human stool

Alexander Greninger & Joseph DeRisi
This dataset corresponds to the data presented in "The complete genome of klassevirus – a novel picornavirus in pediatric stool" by Greninger et al (http://www.ncbi.nlm.nih.gov/pubmed/19538752).

Preterm Birth Initiative-Rwanda antenatal care and postnatal care providers survey

Tiffany Lundeen, Elizabeth Butrick, Dilys Walker, Hana Azman, Sabine Musange, David Nzeyimana & Nathalie Murindahabi
Background: The East Africa Preterm Birth Initiative-Rwanda began a cluster randomized controlled trial of group antenatal care (ANC) and postnatal care (PNC) in Rwanda in 2017. That trial will report its primary outcome, gestational length at birth, after data collection concludes in 2019. This nested study includes providers of ANC and/or PNC at the 18 health centers randomized to provide the group model of ANC/PNC and the 18 health centers randomized to continue providing ANC/PNC...

Data from: Influence of periaqueductal gray on other salience network nodes predicts social sensitivity

Myrthe Rijpma, Winson Yang, Gianina Toller, Giovanni Battistella, Arseny Sokolov, Virginia Sturm, William Seeley, Joel Kramer, Bruce Miller & Katherine Rankin
The intrinsic connectivity of the salience network (SN) plays an important role in social behavior, however the directional influence that individual nodes have on each other has not yet been fully determined. In this study, we used spectral Dynamic Causal Modeling to characterize the effective connectivity patterns in the SN for 44 healthy older adults and for 44 patients with behavioral variant frontotemporal dementia (bvFTD) who have focal SN dysfunction. We examined the relationship of...

Daily United States COVID-19 data for select cities and counties, May 29, 2020 to October 21, 2020

The COVID Tracking Project At The Atlantic
This dataset by The COVID Tracking Project at The Atlantic captures the virus’s transmission in 65 cities and counties across the country. Many of these metropolitan areas only report the current day’s totals and remove older data from their public health dashboards so that no historical archive is available. As a result, it’s often impossible to see the impact of the virus on a particular geography over time. Our dataset captures this historical information. It...

HIV efficiently infects T cells from the endometrium and remodels them to promote systemic viral spread

Tongcui Ma, Xiaoyu Luo, Ashley George, Gourab Mukherjee, Nandini Sen, Trimble Spitzer, Linda Giudice, Warner Greene & Nadia Roan
The female reproductive tract (FRT) is the most common site of infection during HIV transmission to women, but viral remodeling complicates characterization of cells targeted for infection. Here, we report extensive phenotypic analyses of HIV-infected endometrial cells by CyTOF, and use a "nearest neighbor" bioinformatics approach to trace cells to their original pre-infection phenotypes. Like in blood, HIV preferentially targets memory CD4+ T cells in the endometrium, but these cells exhibit unique phenotypes and sustain...

Sex, Race, and Risk of Dementia after Traumatic Brain Injury among Older Veterans

Erica Kornblith, Carrie Peltz, Feng Xia, Brenda Plassman, Tatjana Novakovic-Apopain & Kristine Yaffe
Objective: To investigate whether sex and race differences exist in dementia risk associated with TBI among older Veterans. Materials and Methods: Using Fine-Gray regression models, we investigated incident dementia risk with TBI exposure by sex and race. Results: After excluding baseline prevalent dementia, the final sample (all Veterans 55+ diagnosed with TBI during the 2001-2015 study period and a random sample of all Veterans receiving Veterans Health Administration care) included nearly one million Veterans (4.3%...

Data from: Quantitative global studies reveal differential translational control by start codon context across the fungal kingdom

Jade Sales-Lee
Chapter 1: Eukaryotic protein synthesis generally initiates at a start codon defined by an AUG and its surrounding Kozak sequence context, but the quantitative importance of this context in different species is unclear. We tested this concept in two pathogenic Cryptococcus yeast species by genome-wide mapping of translation and of mRNA 5’ and 3’ ends. We observed thousands of AUG-initiated upstream open reading frames (uORFs) that are a major contributor to translation repression. uORF use...

Cortical astrocytes independently regulate sleep depth and duration via separate GPCR pathways

Kira Poskanzer & Trisha Vaidyanathan
Non-rapid eye movement (NREM) sleep, characterized by slow-wave electrophysiological activity, underlies several critical functions, including learning and memory. However, NREM sleep is heterogeneous, varying in duration, depth, and spatially across the cortex. While these NREM sleep features are thought to be largely independently regulated, there is also evidence that they are mechanistically coupled. To investigate how cortical NREM sleep features are controlled, we examined the astrocytic network, comprising a cortex-wide syncytium that influences population-level neuronal...

mRNA vaccine-induced T cells respond identically to SARS-CoV-2 variants of concern but differ in longevity and homing properties depending on prior infection status

Nadia Roan
While mRNA vaccines are proving highly efficacious against SARS-CoV-2, it is important to determine how booster doses and prior infection influence the immune defense they elicit, and whether they protect against variants. Focusing on the T cell response, we conducted a longitudinal study of infection-naïve and COVID-19 convalescent donors before vaccination and after their first and second vaccine doses, using a high-parameter CyTOF analysis to phenotype their SARS-CoV-2-specific T cells. Vaccine-elicited spike-specific T cells responded...

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  • University of California, San Francisco
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