39 Works

Amplitude modulations of cortical sensory responses in pulsatile evidence accumulation

Sue Ann Koay
Condensed neural and behavioral data, included secondary results from model fits and analyses. This dataset contains all information required to recreate figures from the paper.

Data from: Low-dimensional spatio-temporal dynamics underlie cortex-wide neural activity

Timothy Buschman & Camden MacDowell
Cognition arises from the dynamic flow of neural activity through the brain. To capture these dynamics, we used mesoscale calcium imaging to record neural activity across the dorsal cortex of awake mice. We found that the large majority of variance in cortex-wide activity (~75%) could be explained by a limited set of ~14 ‘motifs’ of neural activity. Each motif captured a unique spatio-temporal pattern of neural activity across the cortex. These motifs generalized across animals...

Data from: Social bonds do not mediate the relationship between early adversity and adult glucocorticoids in wild baboons

Stacy Rosenbaum, Shuxi Zeng, Fernando Campos, Laurence Gesquiere, Jeanne Altmann, Susan Alberts, Fan Li & Elizabeth Archie
In humans and other animals, harsh conditions in early life can have profound effects on adult physiology, including the stress response. This relationship may be mediated by a lack of supportive relationships in adulthood. That is, early life adversity may inhibit the formation of supportive social ties, and weak social support is itself often linked to dysregulated stress responses. Here we use prospective, longitudinal data from wild baboons in Kenya to test the links between...

LAMMPS simulations scripts for the manuscript \"A granular-physics-based view of fault friction experiments\"

Behrooz Ferdowsi & Allan M. Rubin
Rate- and State-dependent Friction (RSF) equations are commonly used to describe the time-dependent frictional response of fault gouge to perturbations in sliding velocity. Among the better-known versions are the Aging and Slip laws for the evolution of state. Although the Slip law is more successful, neither can predict all the robust features of lab data. RSF laws are also empirical, and their micromechanical origin is a matter of much debate. Here we use a granular-physics-based...

Supplemental Data for N management paper

Yixin Guo & Denise Mauzerall

Fluorescence Reconstruction Microscopy: Complete Testing Dataset

& Daniel Cohen
We provide all the test data and corresponding predictions for our paper, “Practical Fluorescence Reconstruction Microscopy for High-Content Imaging”. Please refer to the Methods section in this paper for experimental details. For each experimental condition, we provide the input transmitted-light images (either phase contrast or DIC), the ground truth fluorescence images, and the output predicted fluorescence images which should reconstruct the ground truth fluorescence images.

Shakespeare and Company Project Dataset: Lending Library Members

Joshua Kotin, Rebecca Sutton Koeser, Carl Adair, Serena Alagappan, Jean Bauer, Oliver J. Browne, Nick Budak, Harriet Calver, Jin Chow, Ian Davis, Gissoo Doroudian, Currie Engel, Elspeth Green, Benjamin Hicks, Madeleine E. Joelson, Carolyn Kelly, Sara Krolewski, Xinyi Li, Ellie Maag, Cate Mahoney, Jesse D. McCarthy, Mary Naydan, Isabel Ruehl, Sylvie Thode, Camey VanSant … & Clifford E. Wulfman
The Shakespeare and Company Project: Lending Library Members dataset includes information about approximately 5,700 members of Sylvia Beach's Shakespeare and Company lending library.

A dual-mechanism antibiotic kills Gram-negative bacteria and avoids drug resistance

James K. Martin, Joseph P. Sheehan, Benjamin Bratton, Gabriel M. Moore, André Mateus, Sophia Hsin-Jung Li, Hahn Kim, Joshua D. Rabinowitz, Athanasios Typas, Mikhail M. Savitski, Maxwell Z. Wilson & Zemer Gitai
The rise of antibiotic resistance and declining discovery of new antibiotics have created a global health crisis. Of particular concern, no new antibiotic classes have been approved for treating Gram-negative pathogens in decades. Here, we characterize a compound, SCH-79797, that kills both Gram-negative and Gram-positive bacteria through a unique dual-targeting mechanism of action (MoA) with undetectably-low resistance frequencies. To characterize its MoA, we combined quantitative imaging, proteomic, genetic, metabolomic, and cell-based assays. This pipeline demonstrates...

Eagle Ford Shale: Synchrotron-Based Element and Mineral Maps

Catherine Peters & Julie Kim
This project provides 2D synchrotron micro X-ray fluorescence (µXRF) and micro X-ray diffraction (µXRD) data, as well as generated mineral maps for a shale rock from the Eagle Ford formation. The Eagle Ford shale is an organic-rich laminate shale in southern Texas that is actively drilled for unconventional oil and gas operations. The Eagle Ford shale sample in this study is a calcareous mudstone consisting of ultra-fine-grained calcite and silicate minerals arranged in a foliated...

Deep Potential training data for crystalline and disordered TiO2 phases

Marcos Felipe Calegari Andrade & Annabella Selloni
Data set used to train a Deep Potential (DP) model for crystalline and disordered TiO2 phases. Training data contain atomic forces, potential energy, atomic coordinates and cell tensor. Energy and forces were evaluated with the density functional SCAN, as implemented in Quantum-ESPRESSO. Atomic configurations of crystalline systems were generated by random perturbation of atomic positions (0-0.3 A) and cell tensor (1-10%). Amorphous TiO2 was explored by DP molecular dynamics (DPMD) at temperatures in the range...

Chinese overseas development financing of electric power generation: A comparative analysis

Xu Chen, Kevin P. Gallagher & Denise Mauzerall
Global power generation must rapidly decarbonize by mid-century to meet the goal of stabilizing global warming below 2 degree Celsius. To meet this objective, multilateral development banks (MDBs) have gradually reduced fossil fuel and increased renewable energy financing. Meanwhile, globally active national development finance institutions (DFIs) from Japan and South Korea have continued to finance overseas coal plants. Less is known about the increasingly active Chinese DFIs. Here we construct a new dataset of China’s...

Domestication phenotype linked to vocal behavior in marmoset monkeys

Asif Ghazanfar, Lauren Kelly, Daniel Takahashi, Sandra Winters, Rebecca Terrett & James Higham
The domestication syndrome refers to a set of traits that are the incidental by-products of artificial selection for increased tolerance towards humans. One hypothesis is that some species like humans and bonobos “self domesticated”, that they have been under selection for that same suite of domesticated phenotypes. However, the evidence for this has been largely circumstantial. Here, we provide evidence that in marmoset monkeys, the size of a domestication phenotype—a white facial fur patch—is linked...

Data from: Upper tidal flats are disproportionately important for the conservation of migratory shorebirds

Tong Mu & David S. Wilcove
Migratory animals are crucial for global ecosystems, yet many species are threatened by human activities. Coastal shorebirds along the East Asian-Australasian Flyway have experienced precipitous declines over the past three decades, primarily due to the rapid development of the tidal flats, their major stopover habitat. However, populations of several species have declined must faster than the rate of habitat loss. To explain this discrepancy, we quantified the foraging distribution of 17 migratory shorebirds throughout the...

Shakespeare and Company Project Dataset: Lending Library Members, Books, Events

Joshua Kotin, Rebecca Sutton Koeser, Carl Adair, Serena Alagappan, Jean Bauer, Oliver J. Browne, Nick Budak, Harriet Calver, Jin Chow, Ian Davis, Gissoo Doroudian, Currie Engel, Elspeth Green, Benjamin Hicks, Madeleine E. Joelson, Carolyn Kelly, Sara Krolewski, Xinyi Li, Ellie Maag, Cate Mahoney, Jesse D. McCarthy, Mary Naydan, Isabel Ruehl, Sylvie Thode, Camey VanSant … & Clifford E. Wulfman
The Shakespeare and Company Project makes three datasets available to download in CSV and JSON formats. The datasets provide information about lending library members; the books that circulated in the lending library; and lending library events, including borrows, purchases, memberships, and renewals. The datasets may be used individually or in combination site URLs are consistent identifiers across all three. The DOIs for each dataset are as follows: Members (https://doi.org/10.34770/ht30-g395); Books (https://doi.org/10.34770/g467-3w07); Events (https://doi.org/10.34770/2r93-0t85).

Agincourt Integrated Family Survey 2004

Anne Case

Agincourt Integrated Family Survey 2002

Anne Case

Fluorescence Reconstruction Microscopy Data: Keratinocyte (10x) Phase to Nuclei (DAPI)

Julienne LaChance & Daniel Cohen
The data provided in this DataSpace consists of sample training data to be used for Fluorescence Reconstruction Microscopy (FRM) testing. We provide a subset of the keratinocyte (10x magnification) dataset used in our paper, in which interested parties may find more complete information about our data collection methods. Matched pairs of phase contrast and fluorescent images are given. The nuclei were stained using Hoechst 33342 and imaged using a standard DAPI filter set.

Multiple dimensions of dietary diversity in large mammalian herbivores

Tyler Kartzinel & Robert Pringle
Theory predicts that trophic specialization (i.e., low dietary diversity) should make consumer populations sensitive to environmental disturbances, yet diagnosing specialists is complicated both by the difficulty of precisely quantifying diet composition and by definitional ambiguity—what makes a diet ‘diverse’? We sought to characterize the relationship between taxonomic dietary diversity (TDD) and phylogenetic dietary diversity (PDD) in a species-rich community of large mammalian herbivores in semi-arid East African savanna. We hypothesized that TDD and PDD would...

Eco-evolutionary significance of 'loners'

Corina Tarnita, Fernando Rossine, Ricardo Martinez-Garcia, Allyson Sgro & Thomas Gregor
Loners, individuals out-of-sync with a coordinated majority, occur frequently in nature. Are loners incidental byproducts of large-scale coordination attempts or are they part of a mosaic of life-history strategies? Here, we provide empirical evidence of naturally occurring heritable variation in loner behavior in the model social amoeba Dictyostelium discoideum. We propose that Dictyostelium loners—cells that do not join the multicellular life-stage—arise from a dynamic population-partitioning process, the result of each cell making a stochastic, signal-based...

Data from: Strong effects of lab-to-field environmental transitions on the bacterial intestinal microbiota of Mus musculus are modulated by Trichuris muris infection

Julian Bär, Jacqueline Leung, Christina Hansen, P'ng Loke, Alex Hall, Laura Conour & Andrea Graham
Studies of controlled lab animals and natural populations represent two insightful extremes of microbiota research. We bridged these two approaches by transferring lab-bred female C57BL/6 mice from a conventional mouse facility to an acclimation room and then to an outdoor enclosure, to investigate how the gut microbiota changes with environment. Mice residing under constant conditions served as controls. Using 16S rRNA sequencing of fecal samples, we found that the shift in temperature and humidity, as...

Data associated with 'Metformin rescues Parkinson’s disease phenotypes caused by hyperactive mitochondria'

Danielle Mor, Salman Sohrabi, Rachel Kaletsky, William Keyes, Alp Tartici, Vrinda Kalia, Gary Miller & Coleen Murphy
Metabolic dysfunction occurs in many age-related neurodegenerative diseases, yet its role in disease etiology remains poorly understood. We recently discovered a potential causal link between the branched-chain amino acid transferase, BCAT-1, and the neurodegenerative movement disorder, Parkinson’s disease (PD). RNAi-mediated knockdown of C. elegans bcat-1 recapitulates PD-like features, including progressive motor deficits and neurodegeneration with age, yet the underlying mechanisms have remained unknown. Using transcriptomic, metabolomic, and imaging approaches, we show here that bcat-1 knockdown...

Cardio-metabolic biomarkers measured across a lifestyle gradient

Amanda Lea
The “mismatch” between evolved human physiology and Western lifestyles is thought to explain the current epidemic of cardiovascular disease (CVD) in industrialized societies. However, this hypothesis has been difficult to test because few populations concurrently span ancestral and modern lifestyles. To address this gap, we collected interview and biomarker data from individuals of Turkana ancestry who practice subsistence-level, nomadic pastoralism (the ancestral way of life for this group), as well as individuals who no longer...

An updated life history scheme for marine fishes predicts recruitment variability and sensitivity to exploitation

Colleen Petrik, Fernando González Taboada, Charles Stock & Jorge Sarmiento
Aim: Patterns of population renewal in marine fishes are often irregular and lead to volatile fluctuations in abundance that challenge management and conservation efforts. Here, we examine the relationship between life history strategies and recruitment variability in exploited marine fish species using a macroecological approach. Location: Global ocean. Time period: 1950-2018. Major taxa studied: Bony and cartilaginous fish. Methods: Based on trait data for 244 marine fish species, we objectively extend the established Equilibrium-Periodic-Opportunistic (E-P-O)...

Dataset for 'Auditory Activity is Diverse and Widespread Throughout the Central Brain of Drosophila'

DIEGO PACHECO PINEDO, Stephan Thiberge, Eftychios Pnevmatikakis & Mala Murthy
Sensory pathways are typically studied starting at receptor neurons and following postsynaptic neurons into the brain. However, this leads to a bias in analysis of activity towards the earliest layers of processing. Here, we present new methods for volumetric neural imaging with precise across-brain registration, to characterize auditory activity throughout the entire central brain of Drosophila and make comparisons across trials, individuals, and sexes. We discover that auditory activity is present in most central brain...

Shakespeare and Company Project Dataset: Lending Library Books

Joshua Kotin, Rebecca Sutton Koeser, Carl Adair, Serena Alagappan, Jean Bauer, Oliver J. Browne, Nick Budak, Harriet Calver, Jin Chow, Ian Davis, Gissoo Doroudian, Currie Engel, Elspeth Green, Benjamin Hicks, Madeleine E. Joelson, Carolyn Kelly, Sara Krolewski, Xinyi Li, Ellie Maag, Cate Mahoney, Jesse D. McCarthy, Mary Naydan, Isabel Ruehl, Sylvie Thode, Camey VanSant … & Clifford E. Wulfman
This dataset includes information about approximately 6,000 books and other items with bibliographic data as well as summary information about when the item circulated in the Shakespeare and Company lending library and the number of times an item was borrowed or purchased.

Registration Year

  • 2020

Resource Types

  • Dataset


  • Princeton University
  • Columbia University
  • Massachusetts General Hospital
  • Stanford University
  • University of Notre Dame
  • Duke University
  • New York University
  • University of Edinburgh
  • Icahn School of Medicine at Mount Sinai
  • Boston University