192 Works

Data for: Can language representation models think in bets?

Mayank Kejriwal
The dataset contains three files: *Item_Sets.xlsx*, *Value_Questions.xlsx*, and *Bet_Questions.xlsx*. Each of the three files corresponds to each of the three benchmarks in the manuscript currently under submission to Royal Society Open Science and is also available as a preprint: https://arxiv.org/abs/2210.07519. The items in Item_Sets.xlsx is used to create the other two files. Value_Questions.xlsx is used in RQ1, and Bet_Questions.xlsx is used in both RQ2 and RQ3.

Piezo1 as a force-through-membrane sensor in red blood cells

George Vaisey, Priyam Banerjee, Alison J North, Christoph A Haselwandter & Roderick MacKinnon
Piezo1 is the stretch-activated Ca2+ channel in red blood cells that mediates homeostatic volume control. Here we study the organization of Piezo1 in red blood cells using a combination of super-resolution microscopy techniques and electron microscopy. Piezo1 adopts a nonuniform distribution on the red blood cell surface, with a bias towards the biconcave "dimple". Trajectories of diffusing Piezo1 molecules, which exhibit confined Brownian diffusion on short timescales and hopping on long timescales, also reflect a...

Data from: Genetic and phenotypic influences on copulatory plug survival in mice

Rachel Mangels, Brent Young, Sara Keeble, Reza Ardekani, Camille Meslin, Zelia Ferreira, Nathan L. Clark, Jeffrey M. Good & Matthew D. Dean
Across a diversity of animals, male seminal fluid coagulates upon ejaculation to form a hardened structure known as a copulatory plug. Previous studies suggest that copulatory plugs evolved as a mechanism for males to impede remating by females, but detailed investigations into the time course over which plugs survive in the female’s reproductive tract are lacking. Here, we cross males from eight inbred strains to females from two inbred strains of house mice (Mus musculus...

Data from: Do convergent ecomorphs evolve through convergent morphological pathways? Cranial shape evolution in fossil hyaenids and borophagine canids (Carnivora, Mammalia)

Zhijie Jack Tseng & Xiaoming Wang
Cases of convergent evolution, particularly within ecomorphological contexts, are instructive in identifying universally adaptive morphological features across clades. Tracing of evolutionary pathways by which ecomorphological convergence takes place can further reveal mechanisms of adaptation, which may be strongly influenced by phylogeny. Ecomorphologies of carnivorous mammals represent some of the most outstanding cases of convergent evolution in the Cenozoic radiation of mammals. This study examined patterns of cranial shape change in the dog (Canidae) and hyena...

San Jacinto Fault Zone Experiment

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The San Jacinto fault is one of the most active branches of the San Andreas system in southern CA, and it consists of multiple segments that exhibit considerably different properties and behaviors both at the surface and at depth. As such, it provides an excellent natural laboratory for studying the mechanics, architecture and evolutionary behavior of a young evolving plate boundary. The goal of this project is to provide improved quantitative understanding of brittle and...

Data from: The genetic architecture of freezing tolerance varies across the range of Arabidopsis thaliana

Matthew W. Horton, Glenda Willems, Eriko Sasaki, Maarten Koornneef & Magnus Nordborg
The capacity to tolerate freezing temperatures limits the geographical distribution of many plants, including several species of agricultural importance. However, the genes involved in freezing tolerance remain largely unknown. Here, we describe the variation in constitutive freezing tolerance that occurs among worldwide accessions of Arabidopsis thaliana. We found that although plants from high latitudes tend to be more freezing tolerant than plants from low latitudes, the environmental factors that shape cold adaptation differ across the...

Data from: The wings before the bird: an evaluation of flapping-based locomotory hypotheses in bird antecedents

T. Alexander Dececchi, Hans C.E. Larsson & Michael B. Habib
Background. Powered flight is implicated as a major driver for the success of birds. Here we examine the effectiveness of three hypothesized pathways for the evolution of the flight stroke, the forelimb motion that powers aerial locomotion, in a terrestrial setting across a range of stem and basal avians: flap running, Wing Assisted Incline Running (WAIR), and wing-assisted leaping. Methods. Using biomechanical mathematical models based on known aerodynamic principals and in vivo experiments and ground...

Data from: A qualitative study exploring the health literacy issues in the care of Chinese American immigrants with diabetes

Angela Yee Man Leung, Ai Bo, Hsin-Yi Hsiao, Song Song Wang & Iris Chi
Objectives: To investigate why first-generation Chinese immigrants with diabetes have difficulty obtaining, processing and understanding diabetes related information despite the existence of translated materials and translators. Design: This qualitative study employed purposive sampling. Six focus groups and two individual interviews were conducted. Each group discussion lasted approximately 90 min and was guided by semistructured and open-ended questions. Setting: Data were collected in two community health centres and one elderly retirement village in Los Angeles, California....

Data from: Connecting thermal performance curve variation to the genotype: a multivariate QTL approach

Camille A. L. Latimer, Brad Foley, Stephen F. Chenoweth & B. R. Foley
Thermal performance curves (TPCs) are continuous reaction norms that describe the relationship between organismal performance and temperature and are useful for understanding trade-offs involved in thermal adaptation. While thermal trade-offs such as those between generalists and specialists or between hot- and cold-adapted phenotypes are known to be genetically variable and evolve during thermal adaptation, little is known of the genetic basis to TPCs – specifically, the loci involved and the directionality of their effects across...

Data from: Whole genome sequencing of two North American Drosophila melanogaster populations reveals genetic differentiation and positive selection

Daniel Campo, Kjong Lehmann, Courtney Fjeldsted, Tade Souaiaia, Joyce Kao & Sergey V. Nuzhdin
The prevailing demographic model for Drosophila melanogaster suggests that the colonization of North America occurred very recently from a subset of European flies that rapidly expanded across the continent. This model implies a sudden population growth and range expansion consistent with very low or no population subdivision. As flies adapt to new environments, local adaptation events may be expected. To describe demographic and selective events during North American colonization, we have generated a data set...

Data from: Environmental stress increases selection against and dominance of deleterious mutations in inbred families of the Pacific oyster Crassostrea gigas

Louis V. Plough
The deleterious effects of inbreeding are well documented and of major concern in conservation biology. Stressful environments have generally been shown to increase inbreeding depression; however, little is known about the underlying genetic mechanisms of the inbreeding-by-stress interaction and to what extent the fitness of individual deleterious mutations is altered under stress. Using microsatellite marker segregation data and quantitative trait locus (QTL) mapping methods, I performed a genome scan for deleterious mutations affecting viability (viability...

Data from: Nonadditive indirect effects of group genetic diversity on larval viability in Drosophila melanogaster imply key role of maternal decision-making

Julia B. Saltz, Evan T. Alicuben, Jessica Grubman, Matthew Harkenrider, Nichelle Megowan & Sergey V. Nuzhdin
Genetic variation can have important consequences for populations: high population genetic diversity is typically associated with ecological success. Some mechanisms that account for these benefits assume that local social groups with high genetic diversity are more successful than low-diversity groups. At the same time, active decision-making by individuals can influence group genetic diversity, a behavioral process not generally incorporated into discussions of population-level diversity effects. Here, we examine how maternal decisions that determine group genetic...

Data from: A parapithecid stem anthropoid of African origin in the Paleogene of South America

Erik Seiffert, Marcelo Tejedor, John Fleagle, Nelson Novo, Fanny Cornejo, Mariano Bond, Dorien De Vries & Kenneth Campbell
Phylogenetic evidence suggests that platyrrhine (or New World) monkeys and caviomorph rodents of the Western Hemisphere derive from source groups from the Eocene of Afro-Arabia, a landmass that was ~1500 to 2000 kilometers east of South America during the late Paleogene. Here, we report evidence for a third mammalian lineage of African origin in the Paleogene of South America—a newly discovered genus and species of parapithecid anthropoid primate from Santa Rosa in Amazonian Perú. Bayesian...

Classification of Type 2 Diabetes Genetic Variants and a Novel Genetic Risk Score Association with Insulin Clearance

Mark Goodarzi, Nicholette D Palmer, Jinrui Cui, Xiuqing Guo, Yii-Der I Chen, Kent D Taylor, Leslie J Raffel, Lynne E Wagenknecht, Thomas A Buchanan, Willa A Hsueh & Jerome I Rotter
Abstract Context Genome-wide association studies have identified >450 single nucleotide polymorphisms (SNPs) for type 2 diabetes (T2D). Objective To facilitate use of these SNPs in future genetic risk score (GRS)-based analyses, we aimed to classify the SNPs based on physiology. We also sought to validate GRS associations with insulin-related traits in deeply-phenotyped Mexican Americans. Design, Setting, and Participants 457 T2D SNPs from the literature were assigned physiologic function based on association studies and cluster analyses....

Data from: Elovanoids counteract oligomeric β-Amyloid-induced gene expression and protect photoreceptors

Nicolas Bazan, Khanh Do, Marie-Audrey Kautzmann, Bokkyoo Jun, William Gordon, Robert Nshimiyimana, Rong Yang & Nicos Petasis
The onset of neurodegenerative diseases activates inflammation that leads to progressive neuronal cell death and impairments in cognition (Alzheimer’s disease, AD) and sight (age-related macular degeneration, AMD). How neuroinflammation can be counteracted is not known. In AMD, amyloid β-peptide (Aβ) accumulates in subretinal drusen. In the 5xFAD retina, we found early functional deficiencies (ERG) without photoreceptor cell (PRC) death and identified early insufficiency in biosynthetic pathways of pro-homeostatic/neuroprotective mediators, neuroprotectin D1 (NPD1) and elovanoids (ELVs)....

Ecological niche models for American black bear, Rafinesque's big-eared bat, and timber rattlesnake

James Watling, Jennifer Costanza, Ron Sutherland, Curtis Belyea, Bistra Dilkina, Heather Cayton, David Bucklin, Stephanie Romañach & Nick Haddad
This data set contains rasters that are predictive environmental suitability maps for three wildlife species: the American black bear (Ursus americanus), Rafinesque's big-eared bat (Corynorhinus rafinesquii), and Timber rattlesnake (Crotalus horridus). Rasters for each species include: individual prediction maps for each of 5 ENMs (GBM: generalized boosting model, GLM: generalized linear model, MARS: multivariate adaptive regression spline, MX: maximum entropy, and RF: random forest), as well as the ensemble prediction map from all five ecological...

Subducted lithospheric boundary tomographically imaged beneath arc-continent collision in Eastern Indonesia

Cooper Harris
We use travel-times from a temporary seismic deployment of 30 broadband seismometers and a national catalog of arrival times to construct a finite frequency teleseismic P-wave tomographic model of the upper mantle beneath astern Indonesia, where subduction of the Indo-Australian plate beneath the Banda Arc transitions to arc-continent collision. The change in tectonics is due to a change from oceanic to continental lithosphere in the lower plate as inferred from geologic mapping and geophysical, geochemical,...

Data from: Functional genomic analysis of corals from natural CO2-seeps reveals core molecular responses involved in acclimatization to ocean acidification

Carly D. Kenkel, Aurelie Moya, Julia Strahl, Craig Humphrey & Line K. Bay
Little is known about the potential for acclimatization or adaptation of corals to ocean acidification and even less about the molecular mechanisms underpinning these processes. Here we examine global gene expression patterns in corals and their intracellular algal symbionts from two replicate population pairs in Papua New Guinea that have undergone long-term acclimatization to natural variation in pCO2. In the coral host, only 61 genes were differentially expressed in response to pCO2 environment, but the...

Intentional Control of Type I Error Over Unconscious Data Distortion: A Neyman–Pearson Approach to Text Classification

Lucy Xia, Richard Zhao, Yanhui Wu & Xin Tong
This article addresses the challenges in classifying textual data obtained from open online platforms, which are vulnerable to distortion. Most existing classification methods minimize the overall classification error and may yield an undesirably large Type I error (relevant textual messages are classified as irrelevant), particularly when available data exhibit an asymmetry between relevant and irrelevant information. Data distortion exacerbates this situation and often leads to fallacious prediction. To deal with inestimable data distortion, we propose...

Data from: Fossil lemurs from Egypt and Kenya suggest an African origin for Madagascar’s aye-aye

Gregg F. Gunnell, Doug M. Boyer, Anthony F. Friscia, Steven Heritage, Fredrick K. Manthi, Ellen R. Miller, Hesham M. Sallam, Nancy B. Simmons, Nancy J. Stevens & Erik R. Seiffert
In 1967 G.G. Simpson described three partial mandibles from early Miocene deposits in Kenya that he interpreted as belonging to a new strepsirrhine primate, Propotto. This interpretation was quickly challenged, with the assertion that Propotto was not a primate, but rather a pteropodid fruit bat. The latter interpretation has not been questioned for almost half a century. Here we re-evaluate the affinities of Propotto, drawing upon diverse lines of evidence to establish that this strange...

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,...

nkx3.2 mutant zebrafish accommodate jaw joint loss through a phenocopy of the head shapes of Paleozoic jawless fish

Ted Allison, Tetsuto Miyashita, Pranidhi Baddam, Joanna Smeeton, Adam Phillip Oel, Natasha Natarajan, Brogan Gordon, A. Richard Palmer, Gage Crump, Daniel Graf & W. Ted Allison
The vertebrate jaw is a versatile feeding apparatus. To function, it requires a joint between the upper and lower jaws, so jaw joint defects are often highly disruptive and difficult to study. To describe the consequences of jaw-joint dysfunction, we engineered two independent null alleles of a single jaw-joint marker gene, nkx3.2, in zebrafish. These mutations caused zebrafish to become functionally jawless via fusion of the upper and lower jaw cartilages (ankylosis). Despite lacking jaw...

Data from: Differential responses to ocean acidification between populations of Balanophyllia elegans corals from high and low upwelling environments

Joanna S. Griffiths, Francis T. Pan & Morgan W. Kelly
Ocean acidification (OA), the global decrease in surface water pH from absorption of anthropogenic CO2, may put many marine taxa at risk. However, populations that experience extreme localized conditions, and are adapted to these conditions predicted in the global ocean in 2100, may be more tolerant to future OA. By identifying locally adapted populations, researchers can examine the mechanisms used to cope with decreasing pH. One oceanographic process that influences pH, is wind driven upwelling....

Genomic population structure of Helicobacter pylori Shanghai isolates and identification of genomic features uniquely linked with pathogenicity

Feng Yang, Jinghao Zhang, Su Wang, Zhaoyang Sun, Jun Zhou, Feng Li, Yue Liu, Li Ding, Yixin Liu, Wenjing Chi, Tao Liu, Yongqun He, Ping Xiang, Zhijun Bao, Michal A. Olszewski, Hu Zhao & Yanmei Zhang
Severe Helicobacter pylori-linked gastric disorders are especially prevalent in the East Asia region. The ability of H. pylori to cause different clinical outcomes is thought to be associated with unique sets of its genetic features. However, only few genetic features have been definitively linked to specific gastrointestinal pathologies. Genome heterogeneity of clinical H. pylori strains from patients with four different gastric disorders was studied to explore the population structure and molecular genomic features and their...

Detrital magnetite grains scanned to detect inclusions for cosmogenic 3He exposure dating

Florian Hofmann & Emily Cooperdock
More than 3000 individual detrital magnetite grains from a fanglomerate near Whitewater (California, USA) were scanned using microCT. These data were used to detect mineral inclusion in these magnetite grains, which can contribute significant amounts of 3He. Grains without inclusions were then picked from these analyzed grains and used to calibrate the cosmogenic 3He production rate in magnetite (manuscript submitted to GChron).

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