69 Works

White matter damage in frontotemporal dementia and Alzheimer's disease measured by diffusion MRI

Yu Zhang, Norbert Schuff, An-Tao Du, Howard J. Rosen, Joel H. Kramer, Maria Luisa Gorno-Tempini, Bruce L. Miller, Michael W. Weiner & Memory And Aging Center
Frontotemporal dementia (FTD) and Alzheimer's disease are sometimes difficult to differentiate clinically because of overlapping symptoms. Using diffusion tensor imaging (DTI) measurements of fractional anisotropy (FA) can be useful in distinguishing the different patterns of white matter degradation between the two dementias. In this study, we performed MRI scans in a 4 Tesla MRI machine including T1-weighted structural images and diffusion tensor images in 18 patients with FTD, 18 patients with Alzheimer's disease and 19...

Gut Microbiota from Multiple Sclerosis patients triggers spontaneous autoimmune encephalomyelitis in mice --16S data--

Hartmut Wekerle, Kerstin Berer, Lisa Ann Gerdes, Egle Cekanaviciute, Sherman Jia, Liang Xiao, Zhongkui Xia, Chuan Liu, Luisa Klotz, Uta Stauffer, Sergio Baranzini, Tania Kümpfel, Reinhard Hohlfeld & Gurumoorthy Krishnamoorthy
The commensal microbiota has emerged as a key factor influencing human health and has been associated with several diseases, including those of the central nervous system (CNS). To investigate the role of the microbiome in multiple sclerosis (MS), a complex autoimmune disorder shaped by a multitude of genetic and environmental factors, we recruited a cohort of 34 monozygotic twin pairs discordant for MS, and compared their gut microbial composition by 16S ribosomal RNA sequencing of...

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...

Provider counseling and provision of female condom in South Africa and Zimbabwe

Cynthia Harper, Kelly Blanchard, Tsungai Chipato, Taazadza Nhemachena, Gita Ramjee & Maya Blum
Objectives: Female condoms are the only female-initiated HIV and pregnancy prevention technology currently available. We examined female condom counseling and provision among providers in South Africa and Zimbabwe, high HIV-prevalence countries. Design: Cross-sectional study using a nationally-representative survey. Setting: All facilities that provide family planning or HIV/STI services in the two countries. Participants: National probability sample of 1,444 nurses and physicians who provide family planning or HIV/STI services. Primary and secondary outcome measures: Female condom...

Postpartum Family Planning Preliminary DataSet

Pamela Williams
Strengthened efforts in postpartum family planning (PPFP) is a key priority to accelerate progress in reproductive, maternal, newborn, and child health outcomes. In Rwanda, approximately 62% of women have unmet family planning needs in their first year after childbirth. This mixed methods secondary data analysis explores factors associated with PPFP uptake. Women (n=68) were surveyed at two time points to glean insights to the antenatal and postnatal care (PNC) experience. Additionally, a total of 202...

10x Lacrimal Gland scRNA seq data matrix

Shengyang Yu, Aaron Tward & Sarah Knox
Isolated Lacrimal gland for Single Cell RNA sequence data from E16 and P4 mice. These are the raw read count matrices along side the barcode for the cells and genes that span the sparse matrix. These results are published in Development: Defining epithelial cell dynamics and lineage relationships in the developing lacrimal gland. Abstract: The tear producing lacrimal gland is a tubular organ that protects and lubricates the ocular surface. While the lacrimal gland possesses...

Survey Dataset: UDLI, LLRC. NLRC

Robert Rodriguez
ABSTRACT Statements about building walls, deportation and denying services to undocumented immigrants made by the US president may induce fear in Latino populations and create barriers to their health care access. To assess the impact of these statements on undocumented Latino immigrants’ (UDLI) and Latino legal residents/citizens’ (LLRC) perceptions of safety and their presentations for emergency care, we conducted surveys of adult patients at three county emergency departments (EDs) in California from June 2017 to...

Aberrant oligodendroglial-vascular interactions disrupt the Blood Brain Barrier triggering CNS inflammation

Jianqin Niu, Kicheol Kim, Stephen Fancy & Sergio Baranzini
Disruption of the blood brain barrier (BBB) is critical to initiation and perpetuation of disease in Multiple Sclerosis (MS). We report here an interaction between oligodendroglia and vasculature in MS that distinguishes human white matter injury from normal rodent remyelination. We find perivascular clustering of oligodendrocyte precursor cells (OPCs) in active MS lesions, representing an inability to properly detach from vessels following perivascular migration. These perivascular OPCs can themselves disrupt the BBB, interfering with astrocyte...

Associations between vascular risk factors, carotid atherosclerosis and cortical volume and thickness in older adults

Valerie Cardenas, Bruce Reed, Linda Chao, Helena Chui, Nerses Sanossian, Charles DeCarli, Wendy Mack, Joel Kramer, Howard Hodis, Mingzhu Yan, Michael Buonocore, Owen Carmichael, William J. Jagust & Michael W. Weiner
Data from healthy and cognitively impaired elderly, enriched for cerebrovascular disease. Background and Purpose: To investigate whether the Framingham Cardiovascular Risk Profile (FCRP) and carotid artery intima-media thickness (CIMT) are associated with cortical volume and thickness. Results: 152 subjects (82 men) were aged 78 (±7) years old, 94 had a CDR of 0, 58 had a clinical dementia rating (CDR) of 0.5 and the mean mini-mental status examination (MMSE) was 28 ±2. FCRP score was...

Tobacco-free retailers project

Patricia A McDaniel & Ruth E Malone
This dataset contains the transcripts of 15 focus groups conducted in California, New York state, and Ohio from 2009-2013 concerning retailers that had voluntarily discontinued tobacco sales. Transcripts are grouped by state: FG1-8 are the California groups, FG9-13 are the New York groups, and FG14-15 are the Ohio groups.

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...

Comparison of Outcomes before and after Ohio's Law Mandating Use of the FDAApproved Protocol for Medication Abortion: A Retrospective Cohort Study

Ushma D. Upadhyay, Nicole E. Johns, Sarah L. Combellick, Julia E. Kohn, Lisa M. Keder & Sarah C.M. Roberts
Background: In February 2011, an Ohio law took effect mandating use of the United States Food and Drug Administration (FDA)-approved protocol for mifepristone, which is used with misoprostol for medication abortion. Other state legislatures have passed or enacted similar laws requiring use of the FDA-approved protocol for medication abortion. The objective of this study is to examine the association of this legal change with medication abortion outcomes and utilization. Methods and Findings: We used a...

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...

Industry payments to physician journal editors

Victoria S. S. Wong, Laurel N. Avalos & Michael L. Callaham
Background: Open Paymentsis a United States federal program mandating reporting of medical industry payments to physicians, increasing transparency of physician conflicts of interest (COI).Study objectives were to assess industry payments to physician-editors, and compare their financial COI rate to all physicians within the specialty. Methods and Findings: We performed a retrospective analysis of prospectively collected data, reviewing Open Paymentsfrom August 1, 2013 to December 31, 2016. We reviewed general payments (“… not made in connection...

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...

Score compounds using 275 frequent hitter rules published in the Lilly-Medchem-Rules

Julia Davies
Robert Bruns and Ian Watson published 275 rules to identify frequent hitters based on 18-years of experiments at Eli-Lilly. This protocol requires the Lilly-Medchem-Rules to be installed on the server and accessible to Pipeline Pilot. Reference: Rules for Identifying Potentially Reactive or Promiscuous Compounds GitHub Repository: Lilly-Medchem-Rules This protocol is being made available in conjunction with an upcoming publication.

OpenEye PAINS Mapping Python Script

Julia Davies
OpenEye advertises an additional 170 PAINS rules (versus the original 480) to accomodate data loss when converting the substructure patterns from SLN to SMARTS format. However, it was found that many of these additional rules mapped to rules that had been blocked out by Baell as part of an expanded set. These rules have not necessarily been validated as PAINS substructures. The naming pattern for the OpenEye PAINS classification is: "pains_{PAINS class}_{PAINS registration ID}". If...

Media coverage of nonsmoker only hiring policies

Ruth E. Malone & Patricia A. McDaniel
This SPSS dataset contains 1,159 records (from 1995-2013) representing the content of media items published in the US concerning employers who chose to hire only nonsmokers. The Excel spreadsheet contains a list of the titles, authors, publication sources, and publication dates of all the media items in the SPSS database.

North-Central Namibia: RACD around index cases and controls 2013-2014

Jennifer Smith & Hugh Sturrock
Data from a prospective case-control study conducted between January 2013 and August 2014 in Ohangwena and Omusati regions in north central Namibia. Patients attending health facilities who tested positive by malaria rapid diagnostic test (RDT) (index cases) were traced back to their home. All occupants of index case households (n = 116 households) and surrounding households (n = 225) were screened for Plasmodium infection with a rapid diagnostic test (RDT) and loop mediated isothermal amplification...

Evaluating the Impact of a Mandatory Pre-Abortion Ultrasound Viewing Law: A Mixed Methods Study

Ushma Upadhyay, Katrina Kimport, Elise Belusa, Nicole Johns, Douglas Laube & Sarah Roberts
Background Since mid-2013, Wisconsin abortion providers have been legally required to display and describe pre-abortion ultrasound images. We aimed to understand the impact of this law. Methods We used a mixed-methods study design at an abortion facility in Wisconsin. We abstracted data from medical charts one year before the law to one year after and used multivariable models, mediation/moderation analysis, and interrupted time series to assess the impact of the law, viewing, and decision certainty...

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, 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,...

Monroe Monroe Group Videos

Lauren Haack

Gut Microbiota from Multiple Sclerosis patients triggers spontaneous autoimmune encephalomyelitis in mice --shotgun data--

Hartmut Wekerle, Kerstin Berer, Lisa Ann Gerdes, Egle Cekanaviciute, Sherman Jia, Liang Xiao, Zhongkui Xia, Chuan Liu, Luisa Klotz, Uta Stauffer, Sergio Baranzini, Tania Kümpfel, Reinhard Hohlfeld & Gurumoorthy Krishnamoorthy
There is emerging evidence that the commensal microbiota has a role in the pathogenesis of multiple sclerosis (MS), a putative autoimmune disease of the central nervous system. Here, we compared the gut microbial composition of 34 monozygotic twin pairs discordant for MS. While there were no major differences in the overall microbial profiles, we found a significant increase in some taxa such as Akkermansia in untreated MS twins. Furthermore, most notably, when transplanted to a...

Re-analysis of microarray data from rapamycin resistant DLBCL cell lines

Megan Laurance
This dataset contains a re-analysis of the raw microarray data originally published by Petrich AM et al in 2012 (citation details are provided through the link to the GEO record). We were interested in re-analyzing the data because the list of differentially expressed genes that were identified when comparing rapamycin resistant DLBCL cell lines to rapamycin sensitive cell lines was not included in the original article or supplemental materials. We were interested in validating and...

Patterns of age-related water diffusion changes in human brain by concordance and discordance analysis.

Yu Zhang, An-Tao Du, Satoru Hayasaka, Geon-Ho Jahng, Jennifer Hlavin, Wang Zhan, Michael W. Weiner, Norbert Schuff & Memory And Aging Center
In diffusion tensor imaging (DTI), interpreting changes in terms of fractional anisotropy (FA) and mean diffusivity or axial (D(||)) and radial (D(?)) diffusivity can be ambiguous. The main objective of this study was to gain insight into the heterogeneity of age-related diffusion changes in human brain white matter by analyzing relationships between the diffusion measures in terms of concordance and discordance instead of evaluating them separately, which is difficult to interpret. Fifty-one cognitively normal subjects...

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