98 Works

Data from: 7 Tesla MRI of the ex vivo human brain at 100 micron resolution

Brian L. Edlow, Azma Mareyam, Andreas Horn, Jonathan R. Polimeni, Thomas Witzel, M. Dylan Tisdall, Jean Augustinack, Jason P. Stockmann, Bram R. Diamond, Allison Stevens, Lee S. Tirrell, Rebecca D. Folkerth, Lawrence L. Wald, Bruce Fischl & Andre Van Der Kouwe
We present an ultra-high resolution MRI dataset of an ex vivo human brain specimen. The brain specimen was donated by a 58-year-old woman who had no history of neurological disease and died of non-neurological causes. After fixation in 10% formalin, the specimen was imaged on a 7 Tesla MRI scanner at 100 µm isotropic resolution using a custom-built 31-channel receive array coil. Single-echo multi-flip Fast Low-Angle SHot (FLASH) data were acquired over 100 hours of...

Urinary suPAR: a non-invasive biomarker of infection and tissue inflammation for use in studies of large free-ranging mammals

James Higham, Christiane Stahl-Hennig & Michael Heistermann
Studies of large free-ranging mammals incorporating physiological measurements typically require the collection of urine or faecal samples, due to ethical and practical concerns over trapping or darting animals. However, there is a dearth of validated biomarkers of immune activation and inflammation that can be measured non-invasively. We here evaluate the utility of urinary measurements of the soluble form of the urokinase plasminogen activator receptor (suPAR), for use as a health marker in studies of wild...

Cortical encoding of melodic expectations in human temporal cortex

Giovanni Di Liberto, Claire Pelofi, Roberta Bianco, Prachi Patel, Ashesh D Mehta, Jose L Herrero, Alain De Cheveigné, Shihab A Shamme & Nima Mesgarani
Humans engagement in music rests on underlying elements such as the listeners’ cultural background and interest in music. These factors modulate how listeners anticipate musical events, a process inducing instantaneous neural responses as the music confronts these expectations. Measuring such neural correlates would represent a direct window into high-level brain processing. Here we recorded cortical signals as participants listened to Bach melodies. We assessed the relative contributions of acoustic versus melodic components of the music...

Data from: From refugia to rookeries: phylogeography of Atlantic green turtles

Eugenia Naro-Maciel, Brendan N. Reid, S. Elizabeth Alter, George Amato, Karen A. Bjorndal, Alan B. Bolten, Meredith Martin, Campbell J. Nairn, Brian Shamblin & Oscar Pineda-Catalan
Investigating species’ distribution and abundance over time is central to evolutionary biology, and provides important context for conservation and management. With respect to population genetic structure in green sea turtles (Chelonia mydas), certain processes such as female philopatry to natal rookeries are well understood, while others, such as male philopatry and historical changes in distribution and abundance, remain relatively understudied. Further, although inferences from mitochondrial DNA and nuclear microsatellites have both been critical in identifying...

Data from: Transcriptome dynamics of the stomatal lineage: birth, amplification, and termination of a self-renewing population

Jessika Adrian, Jessica Chang, Catherine E. Ballenger, Bastiaan O. R. Bargmann, Julien Alassimone, Kelli A. Davies, On Sun Lau, Juliana L. Matos, Charles Hachez, Amy Lanctot, Anne Vatén, Kenneth D. Birnbaum & Dominique C. Bergmann
Developmental transitions can be described in terms of morphology and the roles of individual genes, but also in terms of global transcriptional and epigenetic changes. Temporal dissections of transcriptome changes, however, are rare for intact, developing tissues. We used RNA sequencing and microarray platforms to quantify gene expression from labeled cells isolated by fluorescence-activated cell sorting to generate cell-type-specific transcriptomes during development of an adult stem-cell lineage in the Arabidopsis leaf. We show that regulatory...

Data from: Acclimatization of symbiotic corals to mesophotic light environments through wavelength transformation by fluorescent protein pigments

Edward G. Smith, Cecilia D'Angelo, Yoni Sharon, Dan Tchernov & Joerg Wiedenmann
The depth distribution of reef-building corals exposes their photosynthetic symbionts of the genus Symbiodinium to extreme gradients in the intensity and spectral quality of the ambient light environment. Characterizing the mechanisms used by the coral holobiont to respond to the low intensity and reduced spectral composition of the light environment in deeper reefs (greater than 20 m) is fundamental to our understanding of the functioning and structure of reefs across depth gradients. Here, we demonstrate...

Data from: The African ape-like foot of Ardipithecus ramidus and its implications for the origin of bipedalism

Thomas Cody Prang
The ancestral condition from which humans evolved is critical for understanding the adaptive origin of bipedal locomotion. The 4.4 million-year-old hominin partial skeleton attributed to Ardipithecus ramidus preserves a foot that purportedly shares morphometric affinities with monkeys, but this interpretation remains controversial. Here I show that the foot of Ar. ramidus is most similar to living chimpanzee and gorilla species among a large sample of anthropoid primates. The foot morphology of Ar. ramidus suggests that...

Data from: Extreme QTL mapping of germination speed in Arabidopsis thaliana

Wei Yuan, Jonathan M. Flowers, Dustin J. Sahraie, Ian M. Ehrenreich & Michael D. Purugganan
Seed germination is a key life history transition for annual plants and partly determines lifetime performance and fitness. Germination speed, the elapsed time for a nondormant seed to germinate, is a poorly understood trait important for plants’ competitiveness and fitness in fluctuating environments. Germination speed varied by 30% among 18 Arabidopsis thaliana populations measured, and exhibited weak negative correlation with flowering time and seed weight, with significant genotype effect (P < 0.005). To dissect the...

Data from: The evolutionary relationships and age of Homo naledi: an assessment using dated Bayesian phylogenetic methods

Mana Dembo, Davorka Radovčić, Heather M. Garvin, Myra F. Laird, Lauren Schroeder, Jill E. Scott, Juliet Brophy, Rebecca R. Ackermann, Charles M. Musiba, Darryl J. De Ruiter, Arne Ø. Mooers, Mark Collard & Chares M. Musiba
Homo naledi is a recently discovered species of fossil hominin from South Africa. A considerable amount is already known about H. naledi but some important questions remain unanswered. Here we report a study that addressed two of them: “Where does H. naledi fit in the hominin evolutionary tree?” and “How old is it?” We used a large supermatrix of craniodental characters for both early and late hominin species and Bayesian phylogenetic techniques to carry out...

Data from: Assessment of plasma proteomics biomarker’s ability to distinguish benign from malignant lung nodules

Gerard A. Silvestri, Nichole T. Tanner, Paul Kearney, Anil Vachani, Pierre P. Massion, Alexander Porter, Steven C. Springmeyer, Kenneth C. Fang, David Midthun, Peter J. Mazzone, D. Madtes, J. Landis, A. Levesque, K. Rothe, M. Balaan, B. Dimitt, B. Fortin, N. Ettinger, A. Pierre, L. Yarmus, K. Oakjones-Burgess, N. Desai, Z. Hammoud, A. Sorenson, R. Murali … & F. Allison
Background: Lung nodules are a diagnostic challenge, with an estimated yearly incidence of 1.6 million in the United States. This study evaluated the accuracy of an integrated proteomic classifier in identifying benign nodules in patients with a pretest probability of cancer (pCA) ≤ 50%. Methods: A prospective, multicenter observational trial of 685 patients with 8- to 30-mm lung nodules was conducted. Multiple reaction monitoring mass spectrometry was used to measure the relative abundance of two...

Data from: Concurrent temporal channels for auditory processing: oscillatory neural entrainment reveals segregation of function at different scales

Xiangbin Teng, Xing Tian, Jess Rowland & David Poeppel
Natural sounds convey perceptually relevant information over multiple timescales, and the necessary extraction of multi-timescale information requires the auditory system to work over distinct ranges. The simplest hypothesis suggests that temporal modulations are encoded in an equivalent manner within a reasonable intermediate range. We show that the human auditory system selectively and preferentially tracks acoustic dynamics concurrently at 2 timescales corresponding to the neurophysiological theta band (4–7 Hz) and gamma band ranges (31–45 Hz) but,...

Data from: Disentangling the genetic effects of refugial isolation and range expansion in a trans-continentally distributed species

Brendan N. Reid, Jamie M. Kass, Seth Wollney, Evelyn L. Jensen, Michael A. Russello, Ella M. Viola, Jenna Pantophlet, John B. Iverson, Marcus Z. Peery, Christopher J. Raxworthy & Eugenia Naro-Maciel
In wide-ranging taxa with historically dynamic ranges, past allopatric isolation and range expansion can both influence the current structure of genetic diversity. Considering alternate historical scenarios involving expansion from either a single refugium or from multiple refugia can be useful in differentiating the effects of isolation and expansion. Here, we examined patterns of genetic variability in the trans-continentally distributed painted turtle (Chrysemys picta). We utilized an existing phylogeographic dataset for the mitochondrial control region and...

Data from: Intrinsically regulated learning is modulated by synaptic dopamine signaling

Pablo Ripollés, Laura Ferreri, Ernest Mas-Herrero, Helena Alicart, Alba Gómez-Andrés, Josep Marco-Pallares, Rosa Maria Antonijoan, Toemme Noesselt, Marta Valle, Jordi Riba & Antoni Rodriguez-Fornells
We recently provided evidence that an intrinsic reward-related signal-triggered by successful learning in absence of any external feedback-modulated the entrance of new information into long-term memory via the activation of the dopaminergic midbrain, hippocampus, and ventral striatum (the SN/VTA-Hippocampal loop; Ripollés et al., 2016). Here, we used a double-blind, within-subject randomized pharmacological intervention to test whether this learning process is indeed dopamine-dependent. A group of healthy individuals completed three behavioral sessions of a language-learning task...

Data from: Ancient mechanisms for the evolution of the bicoid homeodomain's function in fly development

Qinwen Liu, Pinar Onal, Rhea R. Datta, Julia M. Rogers, Urs Schmidt-Ott, Martha L. Bulyk, Stephen Small & Joseph W. Thornton
The ancient mechanisms that caused developmental gene regulatory networks to diversify among distantly related taxa are not well understood. Here we use ancestral protein reconstruction, biochemical experiments, and developmental assays of transgenic animals carrying reconstructed ancestral genes to investigate how the transcription factor Bicoid (Bcd) evolved its central role in anterior-posterior patterning in flies. We show that most of Bcd's derived functions are attributable to evolutionary changes within its homeodomain (HD) during a phylogenetic interval...

Data from: Postconvulsive central apnea as a biomarker for sudden unexpected death in epilepsy (SUDEP)

Laura Vilella, Nuria Lacuey, Johnson P. Hampson, M.R. Sandhya Rani, Rup K. Sanju, Daniel Friedman, Maromi Nei, Kingman Strohl, Catherine Scott, Brian K. Gehlbach, Bilal Zony, Norma J. Hupp, Anita Zaremba, Nassim Shafiabadi, Xihue Zhao, Victoria Reick-Mitrisin, Stephan Schuele, Jennifer Ogren, Ronald M. Harper, Beate Diehl, Lisa Bateman, Orrin Devinsky, George B. Richerson, Philippe Ryvlin & Samden D. Lhatoo
Objective: To characterize peri-ictal apnea and post-ictal asystole in generalized convulsive seizures (GCS) of intractable epilepsy. Methods: Prospective, multi-center epilepsy monitoring study of autonomic and breathing biomarkers of SUDEP in patient’s ≥18 years old with intractable epilepsy and monitored GCS. Video EEG, thoraco-abdominal excursions, nasal airflow, capillary oxygen saturation and electrocardiography were analyzed. Results: We studied 148 GCS in 87 patients. Nineteen patients had generalized epilepsy, 65 had focal, one had both and in two,...

Data from: A resource-rational theory of set size effects in human visual working memory

Ronald Van Den Berg & Wei Ji Ma
Encoding precision in visual working memory decreases with the number of encoded items. Here, we propose a normative theory for such set size effects: the brain minimizes a weighted sum of an error-based behavioral cost and a neural encoding cost. We construct a model from this theory and find that it predicts set size effects. Notably, these effects are mediated by probing probability, which aligns with previous empirical findings. The model accounts well for effects...

Data from: The W100 pocket on HIV-1 gp120 penetrated by b12 is not a target for other CD4bs monoclonal antibodies

Maria J. Duenas-Decamp, Olivia J. O'Connell, Davide Corti, Susan Zolla-Pazner & Paul R. Clapham
BACKGROUND: The conserved CD4 binding site (CD4bs) on HIV-1 gp120 is a major target for vaccines. It is a priority to determine sites and structures within the CD4bs that are important for inclusion in vaccines. We studied a gp120 pocket penetrated by W100 of the potent CD4bs monoclonal antibody (mab), b12. We compared HIV-1 envelopes and corresponding mutants that carried blocked W100 pockets to evaluate whether other CD4bs mabs target this site. FINDINGS: All CD4bs...

Dynamic expression of MMP28 during cranial morphogenesis

Nadege Gouignard
Matrix metalloproteinases (MMP) are a large family of proteases comprising 24 members in vertebrates. They are well known for their extracellular matrix remodelling activity. MMP28 is the last member of the family to be discovered. It is a secreted MMP involved in wound healing, immune system maturation, cell survival and migration. MMP28 is also expressed during embryogenesis in human and mouse. Here we describe the detailed expression profile of MMP28 in Xenopus laevis embryos. We...

2013 Machine Learning Data Set for NASA's Solar Dynamics Observatory - Atmospheric Imaging Assembly

David Fouhey, Meng Jin, Mark Cheung, Abndres Munoz-Jaramillo, Richard Galvez, Rajat Thomas, Paul Wright, Alexander Szenicer, Monica G. Bobra, Yang Liu & James Mason
We present a curated dataset from the NASA Solar Dynamics Observatory (SDO) mission in a format suitable for machine learning research. Beginning from level 1 scientific products we have processed various instrumental corrections, downsampled to manageable spatial and temporal resolutions, and synchronized observations spatially and temporally. We anticipate this curated dataset will facilitate machine learning research in heliophysics and the physical sciences generally, increasing the scientific return of the SDO mission. This work is a...

Movement Tracing of Patients Recovering from COVID in New York City, 2020

Debra Laefer
This shapefile layer and associated datasets represent the movements of patients after they had been released from various healthcare facilities in New York during the onset of the COVID-19 outbreak in New York City during late-March and early-April, 2020. A team of field researchers recorded movements and observations, which have been aggregated to a shapefile layer for analysis. This data is released with an Attribution 4.0 International (CC BY 4.0) license. Please consult the documentation...

Female fertile phase synchrony, and male mating and reproductive skew, in the crested macaque

James Higham, Michael Heistermann, Muhammad Agil, Dyah Perwitasari-Farajallah, Anja Widdig & Antje Engelhardt
High social status is the primary determinant of reproductive success among group-living male mammals. Primates living in multimale–multifemale groups show the greatest variation in the strength of this link, with marked variation in reproductive skew by male dominance among species, dependent on the degree of female fertile phase synchrony, and the number of competing males. Here, we present data on two groups of wild crested macaques (Macaca nigra), living in the Tangkoko Reserve, Sulawesi, Indonesia....

Effects of tidal influence on the structure and function of prokaryotic communities in the sediments of a pristine Brazilian mangrove

Pieter Spealman, Carolina Santana, David Gresham, Vânia Maria Maciel Melo, Taíse Bomfim De Jesus & Fabio Alexandre Chinalia
Mangrove forests are ecosystems that constitute a large portion of the world’s coastline and span tidal zones below, between, and above the waterline, while the ecosystem as a whole is defined by the health of these tidal microhabitats. However, we are only beginning to understand tidal zone microbial biodiversity and the role of these microbiomes in nutrient cycling. While extensive research has characterized microbiomes in pristine versus anthropogenically impacted mangroves these have, largely, overlooked differences...

Dataset from: Ardipithecus hand provides evidence that humans and chimpanzees evolved from an ancestor with suspensory adaptations

Thomas Cody Prang, Kristen Ramirez, Mark Grabowski & Scott Williams
The morphology and positional behavior of the last common ancestor of humans and chimpanzees are critical for understanding the evolution of bipedalism. Early 20th century anatomical research supported the view that humans evolved from a suspensory ancestor bearing some resemblance to apes. However, the hand of the 4.4 million-year-old hominin Ardipithecus ramidus, purportedly provides evidence that the hominin hand was derived from a more generalized form. Here we use morphometric and phylogenetic comparative methods to...

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