46 Works

Supplemental Data: Low bone mineral density in early pubertal transgender/gender diverse youth: Findings from the Trans Youth Care Study

Janet Y. Lee, Courtney Finlayson, Johanna Olson-Kennedy, Robert Garofalo, Yee-Ming Chan, David V. Glidden & Stephen M. Rosenthal
Context. Transgender youth may initiate gonadotropin-releasing hormone agonists (GnRHa) to suppress puberty, a critical period for bone-mass accrual. Low bone mineral density (BMD) has been reported in late-pubertal transgender girls prior to gender-affirming therapy, but little is known about BMD in early-pubertal transgender youth. Objective. To describe BMD in early-pubertal transgender youth. Design. Cross-sectional analysis of the prospective, observational, longitudinal Trans Youth Care Study cohort. Setting. Four multi-disciplinary academic pediatric gender centers in the United...

Pregnancy outcomes in facility deliveries in Kenya and Uganda: A large cross-sectional analysis of maternity registers illuminating opportunities for mortality prevention

Peter Waiswa, Brennan V. Higgins, Paul Mubiri, Leah Kirumbi, Elizabeth Butrick, Rikita Merai, Nancy L. Sloan, Dilys Walker & Kenya
Introduction As facility-based deliveries increase globally, maternity registers offer a promising way of documenting pregnancy outcomes and understanding opportunities for perinatal mortality prevention. This study aims to contribute to global quality improvement efforts by characterizing facility-based pregnancy outcomes in Kenya and Uganda including maternal, neonatal, and fetal outcomes at the time of delivery and neonatal discharge outcomes using strengthened maternity registers. Methods Cross sectional data were collected from previously strengthened maternity registers at 23 facilities...

Apathy and risk of probable incident dementia among community-dwelling older adults

Meredith Bock, Amber Bahorik, Willa Brenowitz & Kristine Yaffe
Objective: To evaluate the association between baseline apathy and probable incident dementia in a population-based sample of community-dwelling older adults. Methods: We studied 2,018 white and black community-dwelling older adults from the Health, Aging, and Body Composition (Health ABC) study. We measured apathy at year 6 (our study baseline) with the modified Apathy Evaluation Scale and divided participants into tertiles based on low, moderate, or severe apathy symptoms. Incident dementia was ascertained over 9 years...

Data from: Identification of novel, clinically correlated autoantigens in the monogenic autoimmune syndrome APS1 by PhIP-Seq

Sara Vazquez, Elise Ferré, David Scheel, Sara Sunshine, Brenda Miao, Caleigh Mandel-Brehm, Zoe Quandt, Alice Chan, Mickie Cheng, Michael German, Mihalis Lionakis, Joseph DeRisi & Mark Anderson
The identification of autoantigens remains a critical challenge for understanding and treating autoimmune diseases. Autoimmune polyendocrine syndrome type 1 (APS1), a rare monogenic form of autoimmunity, presents as widespread autoimmunity with T and B cell responses to multiple organs. Importantly, autoantibody discovery in APS1 can illuminate fundamental disease pathogenesis, and many of the antigens found in APS1 extend to common autoimmune diseases. Here, we performed proteome-wide programmable phage-display (PhIP-Seq) on sera from an APS1 cohort...

Blood biomarkers of traumatic brain injury and cognitive impairment in older veterans

Carrie Peltz, Kimbra Kenney, Jessica Gill, Ramon Diaz-Arrastia, Raquel Gardner & Kristine Yaffe
Objective: To determine whether blood-based biomarkers can differentiate older veterans with and without traumatic brain injury (TBI) and cognitive impairment (CI). Methods: We enrolled 155 veterans from two veterans’ retirement homes: 90 without TBI and 65 with TBI history. Participants were further separated into CI groups: Controls (no TBI, no CI), n=60; no TBI with CI, n=30; TBI without CI, n=30; and TBI with CI, n=35. TBI was determined by the Ohio State University TBI...

Chemical-genetic interrogation of RNA polymerase mutants reveals structure-function relationships and physiological tradeoffs

Anthony Shiver, Hendrik Osadnik, Jason Peters, Rachel Mooney, Peter Wu, Kemardo Henry, Hannes Braberg, Carol Gross, Kerwyn Huang, Robert Landick, Nevan Krogan & James Hu
The multi-subunit bacterial RNA polymerase (RNAP) and its associated regulators carry out transcription and integrate myriad regulatory signals. Numerous studies have interrogated the inner workings of RNAP, and mutations in genes encoding RNAP drive adaptation of Escherichia coli to many health- and industry-relevant environments, yet a paucity of systematic analyses has hampered our understanding of the fitness benefits and trade-offs from altering RNAP function. Here, we conduct a chemical-genetic analysis of a library of RNAP...

Single center series of boys with recurrent strokes and rotational vertebral arteriopathy: Supplemental Table

Christine Fox, Heather Fullerton, Steven Hetts, Van Halbach, Kurtis Auguste, Michael Lawton & Nalin Gupta
Objective: To describe a pediatric stroke syndrome with chronic focal vertebral arteriopathy adjacent to cervical abnormalities. Methods: At a single pediatric stroke center, we identified consecutive children with stroke and vertebral arteriopathy of the V3 segment with adjacent cervical bony or soft tissue abnormalities. We abstracted clinical presentation, treatment and follow-up data from medical charts. Results: From 2005-2016, ten children (all boys, ages 6 – 16 years) presented with posterior circulation strokes and vertebral arteriopathy...

East Africa preterm birth initiative birth register data (March 2016 - October 2016)

Lara Miller
Abstract Objective: Preterm birth is the primary driver of neonatal mortality worldwide, but it is defined by gestational age (GA) which is challenging to accurately assess in low-resource settings. In a commitment to reducing preterm birth while reinforcing and strengthening facility, routine data sources, the East Africa Preterm Birth Initiative (PTBi-EA) chose eligibility criteria that combined GA and birth weight. This analysis evaluated the quality of the GA data as recorded in maternity registers in...

Parallel molecular mechanisms for enzyme temperature adaptation

Margaux M. Pinney, Daniel A. Mokhtari, Eyal Akiva, Filip Yabukarski, David M. Sanchez, Ruibin Liang, Tzanko Doukov, Todd J. Martinez, Patricia C. Babbitt & Daniel Herschlag
The mechanisms that underly the adaptation enzyme activities and stabilities to temperature are fundamental to our understanding of molecular evolution and how enzymes work. Herein, we investigate the molecular and evolutionary mechanisms of enzyme temperature adaption, combining deep mechanistic studies with comprehensive sequence analyses of thousands of enzymes. We show that temperature adaptation in ketosteroid isomerase (KSI) arises primarily from one residue change with limited, local epistasis and we establish the underlying physical mechanisms. This...

Altered cerebellar white matter in sensory processing dysfunction is associated with impaired multisensory integration and attention

Anisha Narayan, Mikaela Rowe, Eva Palacios, Jamie Wren-Jarvis, Ioanna Bourla, Molly Gerdes, Annie Brandes-Aitken, Shivani Desai, Elysa Marco & Pratik Mukherjee
Sensory processing dysfunction (SPD) is characterized by a behaviorally observed difference in the response to sensory information from the environment. While the cerebellum is involved in normal sensory processing, it has not yet been examined in SPD. Diffusion tensor imaging scans of children with SPD (n=42) and typically developing controls (TDC; n=39) were compared for fractional anisotropy (FA), mean diffusivity (MD), radial diffusivity (RD) and axial diffusivity (AD) across the following cerebellar tracts: the middle...

SARS-CoV-2-specific T cells exhibit phenotypic features reflecting helper function, lack of terminal differentiation, and high proliferation potential

Nadia Roan
Convalescing COVID-19 patients mount robust T cell responses against SARS-CoV-2, suggesting an important role for T cells in viral clearance. To date, the phenotypes of SARS-CoV-2-specific T cells remain poorly defined. Using 38-parameter CyTOF, we phenotyped longitudinal specimens of SARS-CoV-2-specific CD4+ and CD8+ T cells from nine individuals who recovered from mild COVID-19. SARS-CoV-2-specific CD4+ T cells were exclusively Th1 cells, and predominantly Tcm with phenotypic features of robust helper function. SARS-CoV-2-specific CD8+ T cells...

Results of a Person-Centered Maternal Health Quality Improvement intervention in Uttar Pradesh, India

Dominic Montagu, May Sudhinaraset & Nadia Diamond-Smith
This data is from a larger 5 year project on person-centered quality for delivery, family planning, and abortion in both India and Kenya. We conducted a quality improvement collaborative to improve person-centered quality for maternal health services in Uttar Pradesh, India. Data was collected pre and post intervention. The aim was to evaluate if quality improvement cycles were effective at improving women's experiences while seeking care and if the changes made during this intervention could...

Evaluation of Person Centered-Care During Family Planning Services at Public Facilities in India

Dominic Montagu, May Sudhinaraset & Nadia Diamond-Smith
This data is from a larger 5 year project on person-centered quality for delivery, family planning, and abortion in both India and Kenya. This is the baseline data evaluating Person Centered Care during Family Planning services at Public Facilities in Uttar Pradesh, India.

CovidCounties is an interactive real time tracker of the COVID19 pandemic at the level of US counties

Douglas Arneson, Matthew Elliot, Arman Mosenia, Boris Oskotsky, Vivek Rudrapatna, Rohit Vashisht, Travis Zack, Paul Bleicher & Atul Butte
Management of the COVID-19 pandemic has proven to be a significant challenge to policy makers. This is in large part due to uneven reporting and the absence of open-access visualization tools to present and analyze local trends as well as infer healthcare needs. Here we report the development of CovidCounties.org, an interactive web application that depicts daily disease trends at the level of US counties using time series plots and maps. This application is accompanied...

Data from: They are likely to be there: using a family-centered index-testing approach to identify HIV-positive children in Kenya

Jayne Lewis-Kulzer, Nicollate Okoko, Kirsten Ohe, Margaret Mburu, Hellen Muttai, Lisa Abuogi, Elizabeth Bukusi, Craig Cohen & Jeremy Penner
In Kenya, only half of children with an HIV-positive parent have been tested for HIV. The effectiveness of a family-centred index-testing approach to identify children (0-14 years) living with HIV was examined. A retrospective clinical record review was conducted among adult index patients newly enrolled in HIV care between May–July 2015 and family outcomes were followed through May 2016 at 60 high-volume clinics in western Kenya. HIV testing uptake and results, health facility level, enrollment...

Dynamic post-translational modification profiling of M. tuberculosis-infected primary macrophages

Jonathan M Budzik, Danielle L Swaney, David Jimenez-Morales, Jeffrey R Johnson, Nicholas E Garelis, Teresa Repasy, Allison W Roberts, Lauren M Popov, Trevor J Parry, Dexter Pratt, Trey Ideker, Nevan J Krogan & Jeffery S Cox
Macrophages are highly plastic cells with critical roles in immunity, cancer, and tissue homeostasis, but how these distinct cellular fates are triggered by environmental cues is poorly understood. To uncover how primary murine macrophages respond to bacterial pathogens, we globally assessed changes in post-translational modifications of proteins during infection with Mycobacterium tuberculosis, a notorious intracellular pathogen. We identified hundreds of dynamically regulated phosphorylation and ubiquitylation sites, indicating that dramatic remodeling of multiple host pathways, both...

Data from: Systolic blood pressure postural changes variability is associated with greater dementia risk

Laure ROUCH, Jean-Sébastien VIDAL, Tina HOANG, Philippe CESTAC, Olivier HANON & Kristine YAFFE
Objective: To determine whether orthostatic hypotension (OHYPO) and visit-to-visit blood pressure (BP) postural changes variability are associated with incident dementia. Methods: We studied 2,131 older adults from the Health, Aging, Body Composition cohort study. Orthostatic BP was repeatedly assessed over a 5-year baseline period. OHYPO was defined as a fall ≥ 15 mmHg in systolic or ≥ 7 mmHg in diastolic BP after standing from a sitting position for ≥ 1/3 of visits. Systolic and...

Data from: Evaluation of a person-centered quality improvement intervention for maternal health and family planning in Kenya

Nadia Diamond-Smith
This data is from a 5 year project on person-centered quality for delivery, family planning, and abortion in both India and Kenya. We conducted a quality improvement collaborative to improve person-centered quality for maternal health and family planning services in Nairobi and Kiambu County, Kenya. Data was collected pre and post intervention. The aim was to evaluate if quality improvement cycles were effective at improving women's experiences while seeking care

On the cross-population generalizability of gene expression prediction models

Kevin L. Keys, Angel C.Y. Mak, Marquitta J. White, Walter L. Eckalbar, Andrew W. Dahl, Joel Mefford, Anna V. Mikhaylova, María G. Contreras, Jennifer R. Elhawary, Celeste Eng, Donglei Hu, Scott Huntsman, Sam S. Oh, Sandra Salazar, Michael A. Lenoir, Jimmie Chun Ye, Timothy A. Thornton, Noah Zaitlen, Esteban G. Burchard & Christopher R. Gignoux
The genetic control of gene expression is a core component of human physiology. For the past several years, transcriptome-wide association studies have leveraged large datasets of linked genotype and RNA sequencing information to create a powerful gene-based test of association that has been used in dozens of studies. While numerous discoveries have been made, the populations in the training data are overwhelmingly of European descent, and little is known about the generalizability of these models...

Schistosoma mansoni IgG antibody response and Kato-Katz infection among pre-school aged children in Mbita, Western Kenya 2012-2014

Benjamin Arnold, Henry Kanyi, Sammy Njenga, Fredrick Rawago, Jeffrey Priest, W. Evan Secor, Patrick Lammie, Kimberly Won & Maurice Odiere
We compared serological measures of transmission based on antibody response to S. mansoni soluble egg antigen (SEA) with stool-based measures of infection among 3,663 preschool-age children in an area endemic for S. mansoni in western Kenya. We estimated force of infection among children using the seroconversion rate examined how it varied geographically and by age.

Phenotypic analysis of the unstimulated in vivo HIV CD4 T cell reservoir

Jason Neidleman, Xiaoyu Luo, Julie Frouard, Guorui Xie, Feng Hsiao, Tongcui Ma, Vincent Morcilla, Ashley Lee, Sushama Telwatte, Reuben Thomas, Whitney Tamaki, Benjamin Wheeler, Rebecca Hoh, Ma Somsouk, Poonam Vohra, Jeffrey Milush, Katherine Sholtis James, Nancie Archin, Peter Hunt, Steven Deeks, Steven Yukl, Sarah Palmer, Warner Greene & Nadia Roan
The latent reservoir is a main barrier for curing HIV. But because latently-infected cells cannot be phenotyped directly, the features of the in vivo reservoir have remained elusive. Here, we describe a method that leverages high-dimensional phenotyping using CyTOF to trace latently-infected cells reactivated ex vivo to their original pre-activation states. Our results suggest that contrary to common assumptions, the reservoir is not randomly distributed among cell subsets, and is remarkably conserved between individuals. However,...

Registration Year

  • 2020

Resource Types

  • Dataset


  • University of California, San Francisco
  • Kenya Medical Research Institute
  • University of California, Berkeley
  • University of California Los Angeles
  • University of Pennsylvania
  • Stanford University
  • Duke University
  • University of Connecticut
  • University of Colorado Denver
  • University of California, Santa Cruz