214 Works

Data from: The influence of depression on cognitive control: disambiguating approach and avoidance tendencies

He Huang, Javier Movellan, Martin P. Paulus & Katia M. Harlé
Dysfunctions of approach and avoidance motivation play an important role in depression, which in turn may affect cognitive control, i.e., the ability to regulate thoughts and action to achieve internal goals. We use a novel experimental paradigm, i.e. a computer simulated driving-task, to study the impact of depression on cognitive control by measuring approach and avoidance actions in continuous time. In this task, 39 subjects with minimal to severe depression symptoms were instructed to use...

Data from: Deep neural networks for accurate predictions of crystal stability

Weike Ye, Chi Chen, Zhenbin Wang, Iek-Heng Chu & Shyue Ping Ong
Predicting the stability of crystals is one of the central problems in materials science. Today, density functional theory (DFT) calculations remain comparatively expensive and scale poorly with system size. Here we show that deep neural networks utilizing just two descriptors—the Pauling electronegativity and ionic radii—can predict the DFT formation energies of C3A2D3O12 garnets and ABO3 perovskites with low mean absolute errors (MAEs) of 7–10 meV atom−1 and 20–34 meV atom−1, respectively, well within the limits...

Data from: Advancing Precambrian palaeomagnetism with the PALEOMAGIA and PINT(QPI) databases

Toni H. Veikkolainen, Andrew J. Biggin, Lauri J. Pesonen, David A. Evans & Nicholas A. Jarboe
State-of-the-art measurements of the direction and intensity of Earth’s ancient magnetic field have made important contributions to our understanding of the geology and palaeogeography of Precambrian Earth. The PALEOMAGIA and PINT(QPI) databases provide thorough public collections of important palaeomagnetic data of this kind. They comprise more than 4,100 observations in total and have been essential in supporting our international collaborative efforts to understand Earth's magnetic history on a timescale far longer than that of the...

Data from: The future of evolutionary diversity in reef corals

Danwei Huang & Kaustuv Roy
One-third of the world's reef-building corals are facing heightened extinction risk from climate change and other anthropogenic impacts. Previous studies have shown that such threats are not distributed randomly across the coral tree of life, and future extinctions have the potential to disproportionately reduce the phylogenetic diversity of this group on a global scale. However, the impact of such losses on a regional scale remains poorly known. In this study, we use phylogenetic metrics in...

Data from: Surface energies of elemental crystals

Richard Tran, Zihan Xu, Balachandran Radhakrishnan, Donald Winston, Wenhao Sun, Kristin A. Persson & Shyue Ping Ong
The surface energy is a fundamental property of the different facets of a crystal that is crucial to the understanding of various phenomena like surface segregation, roughening, catalytic activity, and the crystal’s equilibrium shape. Such surface phenomena are especially important at the nanoscale, where the large surface area to volume ratios leads to properties that are significantly different from the bulk. In this work, we present the largest database of the calculated surface energies of...

Data from: Multi-behavioral endpoint testing of an 87-chemical compound library in freshwater planarians

Siqi Zhang, Danielle Hagstrom, Patrick Hayes, Aaron Graham & Eva-Maria S. Collins
There is an increased recognition in the field of toxicology of the value of medium-to-high-throughput screening methods using in vitro and alternative animal models. We have previously introduced the asexual freshwater planarian Dugesia japonica as a new alternative animal model and proposed that it is particularly well-suited for the study of developmental neurotoxicology. In this paper, we discuss how we have expanded and automated our screening methodology to allow for fast screening of multiple behavioral...

Data from: Comparative dynamics of microglialand glioma cell motility at the infiltrative margin of brain tumours

Joseph Juliano, Orlando Gil, Andrea Hawkins-Daarud, Sonal Noticewala, Russell C. Rockne, Jill Gallaher, Susan C. Massey, Peter A. Sims, Alexander R. A. Anderson, Kristin R. Swanson & Peter Canoll
Microglia are a major cellular component of gliomas, and abundant in the centre of the tumour and at the infiltrative margins. While glioma is a notoriously infiltrative disease, the dynamics of microglia and glioma migratory patterns have not been well characterized. To investigate the migratory behaviour of microglia and glioma cells at the infiltrative edge, we performed two-colour time-lapse fluorescence microscopy of brain slices generated from a platelet-derived growth factor-B (PDGFB)-driven rat model of glioma,...

Data from: Maternal provisioning is structured by species’ competitive neighborhoods

Rachel M. Germain, Tess N. Grainger, Natalie T. Jones & Benjamin Gilbert
Differential maternal provisioning of offspring in response to environmental conditions has been argued as ‘the missing link’ in plant life histories. Although empirical evidence suggests that maternal provisioning responses to abiotic conditions are common, there is little understanding of how differences in maternal provisioning manifest in response to competition. Frequency manipulations are commonly employed in ecological studies to assess the strength of interspecific competition, relative to intraspecific competition, and we used frequency manipulations to test...

Data from: Targeted multiplex next-generation sequencing: Advances in techniques of mitochondrial and nuclear DNA sequencing for population genomics

Brittany Hancock-Hanser, Amy Frey, Matthew S. Leslie, Peter H. Dutton, Frederick I. Archer, Phillip A. Morin & Brittany L. Hancock-Hanser
Next-generation sequencing (NGS) is emerging as an efficient and cost-effective tool in population genomic analyses of nonmodel organisms, allowing simultaneous resequencing of many regions of multi-genomic DNA from multiplexed samples. Here, we detail our synthesis of protocols for targeted resequencing of mitochondrial and nuclear loci by generating indexed genomic libraries for multiplexing up to 100 individuals in a single sequencing pool, and then enriching the pooled library using custom DNA capture arrays. Our use of...

Data from: Differences in combinatorial calls among the 3 elephant species cannot be explained by phylogeny

Michael A. Pardo, Joyce H. Poole, Angela S. Stoeger, Peter H. Wrege, Caitlin E. O'Connell-Rodwell, Udaha Kapugedara Padmalal & Shermin De Silva
Understanding why related species combine calls in different ways could provide insight into the selection pressures on the evolution of combinatorial communication. African savannah elephants (Loxodonta africana), African forest elephants (Loxodonta cyclotis), and Asian elephants (Elephas maximus) all combine broadband calls (roars, barks, and cries) and low-frequency calls (rumbles) into single utterances known as “combination calls.” We investigated whether the structure of such calls differs among species and whether any differences are better explained by...

Data from: Physiological, morphological, and ecological tradeoffs influence vertical habitat use of deep-diving toothed-whales in the Bahamas

Trevor W. Joyce, John W. Durban, Diane E. Claridge, Charlotte A. Dunn, Holly Fearnbach, Kim M. Parsons, Russel D. Andrews & Lisa T. Ballance
Dive capacity among toothed whales (suborder: Odontoceti) has been shown to generally increase with body mass in a relationship closely linked to the allometric scaling of metabolic rates. However, two odontocete species tagged in this study, the Blainville’s beaked whale Mesoplodon densirostris and the Cuvier’s beaked whale Ziphius cavirostris, confounded expectations of a simple allometric relationship, with exceptionally long (mean: 46.1 min & 65.4 min) and deep dives (mean: 1129 m & 1179 m), and...

Social trematodes parasites increase standing army size in areas of greater invasion threat

Emlyn Resetarits, Mark Torchin & Ryan Hechinger
Organisms or societies are resource limited, causing important trade-offs between reproduction and defence. Given such trade-offs, optimal allocation theory predicts that, for animal societies with a soldier caste, allocation to soldiers should reflect local external threats. Although both threat intensity and soldier allocation can vary widely in nature, we currently lack strong evidence that spatial variation in threat can drive corresponding variation in soldier allocation. The diverse guild of trematode parasites of the California horn...

Data from: Validation of serum neurofilaments as prognostic & potential pharmacodynamic biomarkers for ALS

Michael Benatar, Lanyu Zhang, Lily Wang, Volkan Granit, Jeffrey Statland, Richard Barohn, Andrea Swenson, John Ravitz, Carlayne Jackson, Ted Burns, Jaya Trivedi, Erik Pioro, James Caress, Jonathan Katz, Jacob McCauley, Rosa Rademakers, Andrea Malaspina, Lyle Ostrow & Joanne Wuu
Objective. Identify preferred neurofilament assays, and clinically validate serum NfL and pNfH as prognostic and potential pharmacodynamic biomarkers relevant to ALS therapy development. Methods. Prospective, multi-center, longitudinal observational study of patients with ALS (n=229), primary lateral sclerosis (PLS, n=20) and progressive muscular atrophy (PMA, n=11). Biological specimens were collected, processed and stored according to strict standard operating procedures (SOPs) 1. Neurofilament assays were performed in a blinded manner by independent contract research organizations (CROs). Results....

Aldosterone and dexamethasone activate African lungfish mineralocorticoid receptor: Increased activation after removal of the amino-terminal domain

Michael Baker
Aldosterone, the main physiological mineralocorticoid in humans and other terrestrial vertebrates, first appears in lungfish, which are lobe-finned fish that are forerunners of terrestrial vertebrates. Aldosterone activation of the MR regulates internal homeostasis of water, sodium and potassium, which was critical in the conquest of land by vertebrates. We studied transcriptional activation of the slender African lungfish MR by aldosterone, other corticosteroids and progesterone and find that aldosterone, 11-deoxycorticosterone, 11-deoxycortisol and progesterone have half-maximal responses...

Gorilla herpes simplexvirus phylogenetic analysis

Joel Wertheim
Viruses closely related to human pathogens can reveal the origins of human infectious diseases. Human herpes simplexvirus type 1 (HSV-1) and type 2 (HSV-2) are hypothesized to have arisen via host-virus co-divergence and cross-species transmission. We report the discovery of novel herpes simplexviruses during a large-scale screening of fecal samples from wild gorillas, bonobos, and chimpanzees. Phylogenetic analysis indicates that, contrary to expectation, simplexviruses from these African apes are all more closely related to HSV-2...

Triennial migration and philopatry in the critically endangered soupfin shark (Galeorhinus galeus)

Andrew Nosal, Daniel Cartamil, Arnold Ammann, Lyall Bellquist, Noah Ben-Aderet, Kayla Blincow, Echelle Burns, Eric Chapman, Ryan Freedman, Peter Klimley, Ryan Logan, Christopher Lowe, Brice Semmens, Connor White & Philip Hastings
Globally, one-quarter of shark and ray species is threatened with extinction due to overfishing. Effective conservation and management can facilitate population recoveries; however, these efforts depend on robust data on movement patterns and stock structure, which are lacking for many threatened species, including the Critically Endangered soupfin shark (Galeorhinus galeus), a circumglobal coastal-pelagic species. Using passive acoustic telemetry, we continuously tracked 34 mature female soupfin sharks, surgically implanted with coded acoustic transmitters, for seven years...

Analysis of independent cohorts of outbred CFW mice reveals novel loci for behavioral and physiological traits and identifies factors determining reproducibility

Jennifer Zou, Shyam Gopalakrishnan, Clarissa Parker, Jerome Nicod, Richard Mott, Na Cai, Arimantas Lionikas, Robert Davies, Abraham Palmer & Jonathan Flint
Combining samples for genetic association is standard practice in human genetic analysis of complex traits, but is rarely undertaken in rodent genetics. Here, using 23 phenotypes and genotypes from two independent laboratories, we obtained a sample size of 3,076 commercially available outbred mice and identified 70 loci, more than double the number of loci identified in the component studies. Fine-mapping in the combined sample reduced the number of likely causal variants, with a median reduction...

Adaptation of the Texas Christian University Organisational Readiness for Change Short Form (TCU-ORC-SF) for use in primary health facilities in South Africa

Carrie Brooke-Sumner, Petal Petersen-Williams, Emma Wagener, Katherine Sorsdahl, Gregory Aarons & Bronwyn Meyers
Objectives: The Texas Christian University Organisational Readiness for Change Scale (TCU-ORC) assesses factors influencing adoption of evidence-based practices. It has not been validated in low- and middle-income countries (LMIC). This study assessed its psychometric properties in a South African setting with the aim of adapting it into a shorter measure. Methods: This study was conducted in 24 South African primary health care clinics in the Western Cape Province. The TCU-ORC and two other measures, the...

Legacy effects of fish but not elevation influence lake ecosystem response to environmental change

Celia Symons, Marika Schulhof, Hamanda Cavalheri & Jonathan Shurin
How communities reorganize during climate change depends on the distribution of diversity within ecosystems and across landscapes. Understanding how environmental and evolutionary history constrain community resilience is critical to predicting shifts in future ecosystem function. The goal of our study was to understand how communities with different histories respond to environmental change with regard to shifts in elevation (temperature, nutrients) and introduced predators. We hypothesized that community responses to the environment would differ in ways...

Kelp forests at the end of the earth: 45 years later

Alan Friedlander, Enric Ballesteros, Tom Bell, Jennifer Caselle, Claudio Campagna, Mathias Hune, Alex Munoz, Pelayo Salinas-De-Leon, Enric Sala & Paul Dayton
The kelp forests of southern South America are some of the least disturbed on the planet. The remoteness of this region has, until recently, spared it from many of the direct anthropogenic stressors that have negatively affected these ecosystems elsewhere. Re-surveys of 11 locations at the easternmost extent of Tierra del Fuego originally conducted in 1973 showed no significant differences in the densities of adult and juvenile Macrocystis pyrifera kelp or kelp holdfast diameter between...

Data from: Phytoplankton growth and stoichiometric responses to warming, nutrient addition and grazing depend on lake productivity and cell size

Dedmer Van De Waal, Marika A. Schulhof, Jonathan B. Shurin & Steven A. J. Declerck
Global change involves shifts in multiple environmental factors that act in concert to shape ecological systems in ways that depend on local biotic and abiotic conditions. Little is known about the effects of combined global change stressors on phytoplankton communities, and particularly how these are mediated by distinct community properties such as productivity, grazing pressure and size distribution. Here, we tested for the effects of warming and eutrophication on phytoplankton net growth rate and C:N:P...

Impact of Helicoverpa zea salivary GOX on stomatal conductance and volatile emission of host plants

Po-An Lin, Yintong Chen, Duverney Chaverra-Rodriguez, Chan Chin Heu, Nursyafiqi Bin Zainuddin, Jagdeep Singh Sidhu, Michelle Peiffer, Ching-Wen Tan, Anjel Helms, Donghun Kim, Jared Ali, Jason Rasgon, Jonathan Lynch, Charles Anderson & Gary Felton
This data set contain raw data associated with the manuscript titled "Silencing the alarm: An insect salivary enzyme closes plant stomata and inhibits volatile release". Herbivore-induced plant volatiles (HIPVs) are widely recognized as ecologically important to plant. While the majority of studies focused on the induction of this “cry for help”, little is known about whether insect herbivores have evolved mechanisms to reduce the release of HIPVs. Here we show that a caterpillar (Helicoverpa zea)...

Mitonuclear mismatch alters performance and reproductive success in naturally-introgressed populations of a montane leaf beetle

Nathan Rank, Nathan E Rank, Patrick Mardulyn, Sarah J Heidl, Kevin T Roberts, Nicolas A Zavala, John T Smiley & Elizabeth P Dahlhoff
Coordination between nuclear and mitochondrial genomes is critical to metabolic processes underlying animals' ability to adapt to local environments, yet consequences of mitonuclear interactions have rarely been investigated in populations where individuals with divergent mitochondrial and nuclear genomes naturally interbreed. Genetic variation in the leaf beetle Chrysomela aeneicollis was assessed along a latitudinal thermal gradient in California's Sierra Nevada. Variation at mitochondrial cytochrome oxidase II (COII) and the nuclear gene phosphoglucose isomerase (PGI) shows concordance...

Data from: Anticholinergic medications: A potentially modifiable risk factor for development of MCI

Alexandra Weigand, Mark W. Bondi, Kelsey R. Thomas, Noll L Campbell, Douglas Galasko, David P. Salmon, Daniel Sewell, James B. Brewer, Howard H Feldman & Lisa Delano-Wood
Objective: To determine the cognitive consequences of anticholinergic medications (aCH) in cognitively normal older adults as well as interactive effects of genetic and cerebrospinal fluid (CSF) Alzheimer’s disease (AD) risk factors. Methods: 688 cognitively normal participants from the Alzheimer’s Disease Neuroimaging Initiative were evaluated (mean age = 73.5, 49.6% female). Cox regression examined risk of progression to mild cognitive impairment (MCI) over a 10-year period, and linear mixed effects models examined 3-year rates of decline...

Data from: Allocation of gene products to daughter cells is determined by the age of the mother in single Escherichia coli cells

Ulla Rang, Chao Shi, Lin Chao, Audrey Proenca, Andrew Qiu & Jasper Chao
Gene expression and growth rate are highly stochastic in E. coli. Some of the growth rate variations result from the deterministic and asymmetric partitioning of damage by the mother to its daughters. One daughter, denoted the old daughter, receives more damage, grows more slowly, and ages. To determine if expressed gene products are also allocated asymmetrically, we compared the levels of expressed green fluorescence protein in growing daughters descending from the same mother. Our results...

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