46 Works

Altered hippocampal-prefrontal communication during anxiety-related avoidance in mice deficient for the autism-associated gene PogZ

Margaret Cunniff & Vikaas Sohal
Many genes have been linked to autism. However, it remains unclear what long-term changes in neural circuitry result from disruptions in these genes, and how these circuit changes might contribute to abnormal behaviors. To address these questions, we studied behavior and physiology in mice heterozygous for Pogz, a high confidence autism gene. Pogz+/- mice exhibit reduced anxiety-related avoidance in the elevated plus maze (EPM). Theta-frequency communication between the ventral hippocampus (vHPC) and medial prefrontal cortex...

Data from: Testing models of reciprocal relations between social influence and integration in STEM across the college years

Paul Hernandez, V. Bede Agocha, Lauren Carney, Mica Estrada, Sharon Lee, David Loomis, Michelle Williams & Crystal Park
The present study tests predictions from the Tripartite Integration Model of Social Influences (TIMSI) concerning processes linking social interactions to social integration into science, technology, engineering, and mathematics (STEM) communities and careers. Students from historically overrepresented groups in STEM were followed from their senior year of high school through their senior year in college. Based on TIMSI, we hypothesized that interactions with social influence agents (operationalized as mentor network diversity, faculty mentor support, and research...

Anatomy, ontogeny, and evolution of the archosaurian respiratory system: a case study on Alligator mississippiensis and Struthio camelus

Emma Schachner, Brandon Hedrick, Heather Richbourg, John Hutchinson & CG Farmer
The avian lung is highly specialized and is both functionally and morphologically distinct from that of their closest extant relatives, the crocodilians. It is highly partitioned, with a unidirectionally ventilated and immobilized gas-exchanging lung, and fully decoupled, compliant, poorly vascularized ventilatory air-sacs. To understand the evolutionary history of the archosaurian (birds, crocodilians and their common ancestors) respiratory system, it is essential to determine which anatomical characteristics are shared between birds and crocodilians and the role...

Data from: Distinct association between APOE ε2 and Aβ in Alzheimer- and vascular-type cognitive impairment

Jin San Lee, Hyejoo Lee, Seongbeom Park, Yeongsim Choe, Yu Hyun Park, Bo Kyoung Cheon, Alice Hahn, Rik Ossenkoppele, Hee Jin Kim, Seonwoo Kim, Heejin Yoo, Hyemin Jang, Soo Hyun Cho, Seung Joo Kim, Jun Pyo Kim, Young Hee Jung, Key-Chung Park, Charles DeCarli, Michael Weiner, Duk L. Na & Sang Won Seo
Objective: To investigate the association between apolipoprotein E (APOE) genotype and amyloid-β (Aβ) burden, as measured by PET in patients with subcortical vascular cognitive impairment (SVCI) and those with Alzheimer’s disease-related cognitive impairment (ADCI). Methods: This was a cross-sectional study of 310 patients with SVCI and 999 with ADCI. To evaluate the effects of APOE genotype or diagnostic group on Aβ-positivity, we performed multivariate logistic regression analyses. Further distinctive underlying features of latent subgroups were...

DNA scaffolds enable efficient and tunable functionalization of biomaterials for immune cell modulation

Xiao Huang, Jasper Z. Williams, Ryan Chang, Zhongbo Li, Cassandra E. Burnett, Rogelio Hernandez-Lopez, Initha Setiady, Eric Gai, David M. Patterson, Wei Yu, Kole T. Roybal, Wendell A. Lim & Tejal A. Desai
Biomaterials can improve the safety and presentation of therapeutic agents for effective immunotherapy, and a high level of control over surface functionalization is essential for immune cell modulation. Here, we developed biocompatible immune cell engaging particles (ICEp) that use synthetic short DNA as scaffolds for efficient and tunable protein loading. To improve the safety of chimeric antigen receptor (CAR) T cell therapies, micron-sized ICEp were injected intratumorally to present a priming signal for systemically administered...

The onset and offset of noxious stimuli robustly modulate perceived pain intensity

Irina Strigo, Benedict Alter & Howard Fields
Reported pain intensity depends not only on stimulus intensity but also on previously experienced pain. A painfully hot temperature applied to the skin evokes a lower subjective pain intensity if immediately preceded by a higher temperature, a phenomenon called offset analgesia. Previous work indicated that prior pain experience can also increase subsequent perceived pain intensity. Therefore, we examined whether a given noxious stimulus is experienced as more intense when it is preceded by an increase...

Detailed emergency medical services midazolam administration by dose and route

Elan Guterman
This is a table describing the use of midazolam in the treatment of out-of-hospital status epilepticus at a local EMS agency. Specifically, it calculates the frequency of cases where intramuscular, intranasal, intraosseous, or intravenous midazolam is administered and stratifies these frequencies by dose.

ZipSeq : barcoding for real-time mapping of single cell transcriptomes

Kenneth Hu
Spatial transcriptomics seeks to integrate single-cell transcriptomic data within the 3-dimensional space of multicellular biology. Current methods use glass substrates pre-seeded with matrices of barcodes or fluorescence hybridization of a limited number of probes. We developed an alternative approach, called ‘ZipSeq’, that uses patterned illumination and photocaged oligonucleotides to serially print barcodes (Zipcodes) onto live cells within intact tissues, in real-time and with on-the-fly selection of patterns. Using ZipSeq, we mapped gene expression in three...

Data from: Integrative genomic analysis in African American children with asthma finds 3 novel loci associated with lung function

Pagé Goddard, Kevin Keys, Angel Mak, Eunice Lee, Amy Liu, Lesly-Anne Samedy-Bates, Oona Risse-Adams, Maria Contreras, Jennifer Elhawary, Donglei Hu, Sam Oh, Sandra Salazar, Celeste Eng, Blanca Himes, Marquitta White & Esteban Burchard
Bronchodilator drugs are commonly prescribed for treatment and management of obstructive lung function present with diseases such as asthma. Administration of bronchodilator medication can partially or fully restore lung function as measured by pulmonary function tests. The genetics of baseline lung function measures taken prior to bronchodilator medication has been extensively studied, and the genetics of the bronchodilator response itself has received some attention. However, few studies have focused on the genetics of post-bronchodilator lung...

Data for: Cytoprotection by a naturally occurring variant of ATP5G1 in Arctic ground squirrel neural progenitor cells

Neel Singhal & Dengke Ma
Many organisms in nature have evolved mechanisms to tolerate severe hypoxia or ischemia, including the hibernation-capable Arctic ground squirrel (AGS). Although hypoxic or ischemia tolerance in AGS involves physiological adaptations, little is known about the critical cellular mechanisms underlying intrinsic AGS cell resilience to metabolic stress. Through cell survival-based cDNA expression screens in neural progenitor cells, we identify a genetic variant of AGS Atp5g1 that confers cell resilience to metabolic stress. Atp5g1 encodes a subunit...

Functionally heterogeneous human satellite cells identified by single cell RNA sequencing

Jason Pomerantz & Emilie Barruet
Although heterogeneity is recognized within the murine satellite cell pool, a comprehensive understanding of distinct subpopulations and their functional relevance in human satellite cell population is lacking. We used a combination of single cell RNA sequencing and flow cytometry to identify, distinguish, and physically separate novel subpopulations of human PAX7+ satellite cells (HuSCs) from normal muscles. We found that, although relatively homogeneous compared to activated satellite cells and committed progenitors, the HuSC pool contains clusters...

Data from: Knowledge, provision of information and barriers to high quality medication abortion provision by pharmacists in Uttar Pradesh, India

Nadia Diamond-Smith, Joanna Percher, Malvika Saxena, Pravesh Dwivedi & Aradhana Srivastava
Background: Almost three quarters of the 16 millions abortions in India were medication abortion (MA) purchased outside of facilities. Past research has shown low quality of care given to clients seeking MA from pharmacists in this setting. Most purchasers of MA from pharmacies in India are men, further complicating the pathway to high quality information for women taking MA. Developing interventions that can improve the information and quality of interactions for women obtaining MA through...

Data from: Delineating the early transcriptional specification of the mammalian trachea and esophagus

Akela Kuwahara & Jeffrey Bush
The genome-scale transcriptional programs that specify the mammalian trachea and esophagus are unknown. Though NKX2.1 and SOX2 are hypothesized to be co-repressive master regulators of tracheal and esophageal fates, this is untested at a whole transcriptomic scale and their downstream networks remain unidentified. By combining single cell RNA-sequencing with bulk RNA-sequencing of Nkx2.1 mutants and NKX2.1 ChIP-sequencing in mouse embryos, we delineate the NKX2.1 transcriptional program in trachea and esophagus specification, and reveal a previously...

Cardiovascular risk factors and accelerated cognitive decline in midlife

Kristine Yaffe, Amber L. Bahorik, Tina D. Hoang, Sarah Forrester, David R. Jacobs, Cora E. Lewis, Donald M. Lloyd-Jones, Stephen Sidney & Jared P. Reis
ObjectiveIncreasing evidence supports an association between midlife cardiovascular risk factors (CVRFs) and risk of dementia, but less is known about whether CVRFs influence cognition in midlife. We examined the relationship between CVRFs and midlife cognitive decline.MethodsIn 2,675 black and white middle-aged adults (mean age 50.2 ± 3.6 years, 57% female, 45% black), we measured CVRFs at baseline: hypertension (31%), diabetes mellitus (11%), obesity (43%), high cholesterol (9%), and current cigarette smoking (15%). We administered cognitive...

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%...

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...

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...

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...

Differentiation of parathyroid hormone expressing cells from human pluripotent stem cells

Diane Krause, Betty R Lawton, Corine Martineau, Julie Ann Sosa, Sanziana Roman, Courtney E Gibson, Michael A Levine & Diane S Krause
Abstract Differentiation of pluripotent stem cells into functional parathyroid-like cells would accelerate development of important therapeutic options for subjects with parathyroid-related disorders, from the design and screening of novel pharmaceutical agents to the development of durable cellular therapies. We have established a highly reproducible directed differentiation approach leading to parathyroid hormone (PTH) expressing cells from human embryonic stem cells (hESC) and induced pluripotent stem cells (iPSC). We accomplished this through the comparison of multiple different...

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...

Data from: Natural language processing systems for pathology parsing in limited data environments with uncertainty estimation

Anobel Odisho, Briton Park, Nicholas Altieri, John DeNero, Matthew Cooperberg, Peter Carroll & Bin Yu
Objective: Cancer is a leading cause of death, but much of the diagnostic information is stored as unstructured data in pathology reports. We aim to improve uncertainty estimates of machine-learning based pathology parsers and evaluate performance in low data settings. Materials and Methods: Our data comes from the Urologic Outcomes Database at UCSF which includes 3,232 annotated prostate cancer pathology reports from 2001-2018. We approach 17 separate information extraction tasks, involving a wide range of...

Prehospital midazolam use and outcomes among patients with out-of-hospital status epilepticus

Elan Guterman, Elan L. Guterman, Joseph K Sanford, John Betjemann, Li Zhang, James F Burke, Daniel H. Lowenstein, S. Andrew Josephson & Karl A. Sporer
Objective: To examine the use of benzodiazepines and the association between low benzodiazepine dose, breakthrough seizures, and respiratory support in patients with status epilepticus. Methods: Cross-sectional analysis of adult patients with status epilepticus treated by an emergency medical services (EMS) agency from 2013 to 2018. The primary outcome was treatment with a second benzodiazepine dose, an indicator for breakthrough seizure. The secondary outcome was receiving respiratory support. Midazolam was the only benzodiazepine administered. Results: Among...

Qualitative survey instruments for a study on equity from a large-scale private-sector healthcare intervention in Ghana and Kenya: the African Health Markets for Equity (AHME) study

Dominic Montagu & Lauren Suchman
The African Health Markets for Equity (AHME) Initiative took place in Ghana and Kenya for seven years beginning in 2012. AHME applied four linked interventions to increase access and use of quality healthcare for common childhood and adult illnesses, working with private providers in peri-urban areas. The four interventions included social franchsing, quality accreditation, business loans and training, and support for empanellment with the national health insurance scheme in each country. The qualitative study of...

Impaired therapeutic efficacy of bone marrow cells from post-myocardial infarction patients in the TIME and lateTIME clinical trials

Xiaoyin Wang
Implantation of bone marrow-derived cells (BMCs) into mouse hearts post-myocardial infarction (MI) limits cardiac functional decline. However, clinical trials of post-MI BMC therapy have yielded conflicting results. While most laboratory experiments use healthy BMC donor mice, clinical trials use post-MI autologous BMCs. Post-MI mouse BMCs are therapeutically impaired, due to inflammatory changes in BMC composition. Thus, therapeutic efficacy of the BMCs progressively worsens after MI but recovers as donor inflammatory response resolves. The availability of...

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