16 Works

Isolating human monoclonal antibodies against adeno-associated virus from donors with pre-existing immunity

James Wilson, April R. Giles, Roberto Calcedo & Anna P. Tretiakova
With the advent of single B-cell cloning technology, we can isolate antibodies against virtually any antigen to study the interaction of a given pathogen with the immune system and develop novel therapeutic strategies. Antibodies directed against the capsid of adeno-associated viruses (AAV) are a significant obstacle to effectively leveraging AAV as a gene-delivery vector in seropositive individuals. In order to design next-generation vectors that can evade neutralization by these antibodies, studies have mapped the epitopes...

The soil microbiome increases plant survival and modifies interactions with root endosymbionts in the field

Corlett Wood, Shaniya Markalanda, Connor McFadden & Steven Cassidy
Evidence is accumulating that the soil microbiome—the community of microorganisms living in soils—has a major effect on plant traits and fitness. However, most work to date has taken place under controlled laboratory conditions and has not experimentally disentangled the effect of the soil microbiome on plant performance from the effects of key endosymbiotic constituents. As a result, it is difficult to extrapolate from existing data to understand the role of the soil microbiome in natural...

Data from: Broad geographic sampling reveals predictable, pervasive, and strong seasonal adaptation in Drosophila

Heather E. Machado, Alan O. Bergland, Ryan Taylor, Susanne Tilk, Emily Behrman, Kelly Dyer, Daniel K. Fabian, Thomas Flatt, Josefa González, Talia L. Karasov, Iryna Kozeretska, Brian P. Lazzaro, Thomas JS Merritt, John E. Pool, Katherine O’Brien, Subhash Rajpurohit, Paula R. Roy, Stephen W. Schaeffer, Svitlana Serga, Paul Schmidt, Dmitri Petrov & Bernard Kim
To advance our understanding of adaptation to temporally varying selection pressures, we identified signatures of seasonal adaptation occurring in parallel among Drosophila melanogaster populations. Specifically, we estimated allele frequencies genome-wide from flies sampled early and late in the growing season from 20 widely dispersed populations. We identified parallel seasonal allele frequency shifts across North America and Europe, demonstrating that seasonal adaptation is a general phenomenon of temperate fly populations. Seasonally fluctuating polymorphisms are enriched at...

Did shell-crushing predators drive the evolution of ammonoid septal shape?

Erynn Johnson, Briana DiMarco, David Peterman, Aja Carter & Warren Allmon
For centuries, paleontologists have sought functional explanations for the uniquely complex internal walls (septa) of ammonoids, extinct shelled cephalopods. Ammonoid septa developed increasingly complex fractal margins, unlike any modern shell morphologies, throughout more than 300 million years of evolution. Some have suggested these morphologies provided increased resistance to shell-crushing predators. We perform the first physical compression experiments on model ammonoid septa using controlled, theoretical morphologies generated by computer-aided design and 3D printing. These biomechanical experiments...

Cellular dataset for: The anterior Hox gene ceh-13 and elt-1/GATA activate the posterior Hox genes nob-1 and php-3 to specify posterior lineages in the C. elegans embryo

Amanda Zacharias, John Isaac Murray, Elicia Preston, Jeremy Crawford, Jonathan Rumley, Prativa Amom, Breana Anderson, Priya Sivaramakrishnan, Shaili Patel, Barrington Bennett, Teddy Lavon & Felicia Peng
Hox transcription factors play a conserved role in specifying positional identity during animal development, with posterior Hox genes typically repressing the expression of more anterior Hox genes. Here, we dissect the regulation of the posterior Hox genes nob-1 and php-3 in the nematode C. elegans. We show that nob-1 and php-3 are co-expressed in gastrulation-stage embryos in cells that previously expressed the anterior Hox gene ceh-13. This expression is controlled by several partially redundant transcriptional...

Phenotypic data for clinal populations, foxo genotypes

Paul Schmidt
The insulin/insulin-like growth factor signaling pathway has been hypothesized as a major determinant of life-history profiles that vary adaptively in natural populations. In Drosophila melanogaster, multiple components of this pathway vary predictably with latitude; this includes foxo, a conserved gene that regulates insulin signaling and has pleiotropic effects on a variety of fitness-associated traits. We hypothesized that allelic variation at foxo contributes to genetic variance for size-related traits that vary adaptively with latitude. We first...

Data From: Fear conditioning potentiates the Hippocampal CA1 commissural pathway In vivo and increases awake phase sleep

Manivannan Subramaniyan, Sumithrra Manivannan, Vikas Chelur, Theodoros Tsetsenis, Evan Jiang & John Dani
The hippocampus is essential for spatial learning and memory. To assess learning we used contextual fear conditioning (cFC), where animals learn to associate a place with aversive events like foot-shocks. Candidate memory mechanisms for cFC are long-term potentiation and long-term depression, but there is little direct evidence of them operating in the hippocampus in vivo following cFC. Also, little is known about the behavioral state changes induced by cFC. To address these issues, we recorded...

Clinical Trial Transparency and Data-Sharing Among Bio-Pharmaceutical Companies and the Role of Company Size, Location, and Product Type: A Cross-Sectional Descriptive Analysis

Sydney Axson, Michelle Mello, Deborah Lincow, Catherine Yang, Cary Gross, Joseph Ross & Jennifer Miller
Objective: To examine company characteristics associated with better transparency and to apply a tool used to measure and improve clinical trial transparency among large companies and drugs, to smaller companies and biologics. Design: Cross-sectional descriptive analysis. Setting and participants. Novel drugs and biologics FDA approved in 2016 and 2017, and their company sponsors. Using established Good Pharma Scorecard (GPS) measures, companies and products were evaluated on their clinical trial registration, results dissemination, and FDA Amendments...

Pinpointing the neural signatures of single-exposure visual recognition memory

Vahid Mehrpour, Travis Meyer, Eero P. Simoncelli & Nicole C. Rust
Memories of the images that we have seen are thought to be reflected in the reduction of neural responses in high-level visual areas such as inferotemporal (IT) cortex, a phenomenon known as repetition suppression (RS). We challenged this hypothesis with a task that required rhesus monkeys to report whether images were novel or repeated while ignoring variations in contrast, a stimulus attribute that is also known to modulate the overall IT response. The monkeys’ behavior...

Retinotopic organization of visual cortex in human infants

Cameron Ellis, Tristan Yates, Lena Skalaban, Vikranth Bejjanki, Michael Arcaro & Nicholas Turk-Browne
Vision develops rapidly during infancy, yet how visual cortex is organized during this period is unclear. In particular, it is unknown whether functional maps that organize the mature adult visual cortex are present in the infant striate and extrastriate cortex. Here we test the functional maturity of infant visual cortex by performing retinotopic mapping with fMRI. Infants aged 5–23 months had retinotopic maps, with alternating preferences for vertical and horizontal meridians indicative of area boundaries...

Collective detection based on visual information in animal groups

Jacob D. Davidson, Matthew M. G. Sosna, Colin R. Twomey, Vivek H. Sridhar, Simon P. Leblanc & Iain D. Couzin
We investigate key principles underlying individual, and collective, visual detection of stimuli, and how this relates to the internal structure of groups. While the individual and collective detection principles are generally applicable, we employ a model experimental system of schooling golden shiner fish ( Notemigonus crysoleucas ) to relate theory directly to empirical data, using computational reconstruction of the visual fields of all individuals. This reveals how the external visual information available to each group...

Data from: Competitive history shapes rapid evolution in a seasonal climate

Tess Grainger, Seth Rudman, Paul Schmidt & Jonathan Levine
Eco-evolutionary dynamics will play a critical role in determining species’ fates as climatic conditions change. Unfortunately, we have little understanding of how rapid evolutionary responses to climate play out when species are embedded in the competitive communities that they inhabit in nature. We tested the effects of rapid evolution in response to interspecific competition on subsequent ecological and evolutionary trajectories in a seasonally changing climate using a field-based evolution experiment with Drosophila melanogaster. Populations of...

Ex Vivo MRI in Frontotemporal Lobar Degeneration

Dylan Tisdall
Ex vivo MRI of 7 human hemispheres, acquired at 7 T using multi-echo gradient recalled echo imaging. Details of these samples are presented in the associated manuscript.

Phase response analyses support a relaxation oscillator model of locomotor rhythm generation in Caenorhabditis elegans

Hongfei Ji, Anthony Fouad, Shelly Teng, Alice Liu, Pilar Alvarez-Illera, Bowen Yao, Zihao Li & Christopher Fang-Yen
This dataset contains all data and codes that are used in the manuscript entitled "Phase response analyses support a relaxation oscillator model of locomotor rhythm generation in Caenorhabditis elegans". The data include raw videos and intermediate data for optogenetic experiments of all strains, experimental conditions (illumination duration, illuminated region, fluid viscosity and date). Within the parent folder 'Videos', each subfolder represents data of a group of experiments using the same strain under the same condition,...

Load-Bearing Entanglements in Polymer Glasses

Cynthia Bukowski, Tianren Zheng, Robert Riggleman & Alfred Crosby

Data from: Prevalence of disability associated with head injury with loss of consciousness: a population-based study

Andrea Lauren Christman Schneider
Objective: To provide nationally representative prevalence estimates of disability associated with prior head injury with loss of consciousness in the U.S. and to examine associations between prior head injury and disability. Methods: Cross-sectional analysis of 7,390 participants aged ³40 years in the 2011-2014 National Health and Nutrition Examination Surveys (NHANES). Head injury with loss of consciousness was assessed by self-report. Domains of disability were assessed using a standardized structured questionnaire and measured grip strength. Logistic...

Registration Year

  • 2021
    16

Resource Types

  • Dataset
    16

Affiliations

  • University of Pennsylvania
    16
  • Stanford University
    2
  • Princeton University
    2
  • Yale University
    2
  • Cornell University
    2
  • University of Kansas
    1
  • Howard Hughes Medical Institute
    1
  • University of Massachusetts Amherst
    1
  • University of Georgia
    1
  • University of Virginia
    1