63 Works

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...

Data from: Non-random latitudinal gradients in range size and niche breadth predicted by spatial patterns of climate

Erin E. Saupe, Corinne E. Myers, A. Townsend Peterson, Jorge Soberón, Joy Singarayer, Paul Valdes & Huijie Qiao
Aim. Tropical species are thought to experience and be adapted to narrow ranges of abiotic conditions. This idea has been invoked to explain a broad array of biological phenomena, including the latitudinal diversity gradient and differential rates of speciation and extinction. However, debate continues regarding the broad-scale applicability of this pattern and potential processes responsible. Here, we use a simulation approach to test two propositions: (1) strong geographic patterns of variation in realized niche breadth...

Data from: Control of entropy in neural models of environmental state

Timothy H. Muller, Rogier B. Mars, Timothy E. Behrens & Jill X. O'Reilly
Humans and animals construct internal models of their environment in order to select appropriate courses of action. The representation of uncertainty about the current state of the environment is a key feature of these models that controls the rate of learning as well as directly affecting choice behaviour. To maintain flexibility, given that uncertainty naturally decreases over time, most theoretical inference models include a dedicated mechanism to drive up model uncertainty. Here we probe the...

Data from: Revised Airlie House consensus guidelines for design and implementation of ALS clinical trials

Leonard H Van Den Berg, Eric Sorenson, Gary Gronseth, Eric A. Macklin, Jinsy Andrews, Robert H. Baloh, Michael Benatar, James D. Berry, Adriano Chio, Philippe Corcia, Angela Genge, Amelie K. Gubitz, Catherine Lomen-Hoerth, Christopher J. McDermott, Erik P. Pioro, Jeffrey Rosenfeld, Vincenzo Silani, Martin R. Turner, Markus Weber, Benjamin Rix Brooks, Robert G. Miller & Hiroshi Mitsumoto
Objective: To revise the 1999 Airlie House consensus guidelines for the design and implementation of preclinical therapeutic studies and clinical trials in amyotrophic lateral sclerosis (ALS). Methods: A consensus committee comprising 140 key members of the international ALS community (ALS researchers, clinicians, patient representatives, research funding representatives, industry and regulatory agencies) addressed nine areas of need within ALS research: 1. Pre-clinical studies; 2. Biological and phenotypic heterogeneity; 3. Outcome measures; 4. Disease-modifying and symptomatic interventions;...

Data from: Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis

Oliver Ratmann, M. Kate Grabowski, Matthew Hall, Tanya Golubchik, Chris Wymant, Lucie Abeler-Dörner, David Bonsall, Anne Hoppe, Andrew Leigh Brown, Tulio De Oliveira, Astrid Gall, Paul Kellam, Deenan Pillay, Joseph Kagaayi, Godfrey Kigozi, Thomas C. Quinn, Maria J. Wawer, Oliver Laeyendecker, David Serwadda, Ronald H. Gray, Christophe Fraser, &
To prevent new infections with human immunodeficiency virus type 1 (HIV-1) in sub-Saharan Africa, UNAIDS recommends targeting interventions to populations that are at high risk of acquiring and passing on the virus. Yet it is often unclear who and where these ‘source’ populations are. Here we demonstrate how viral deep-sequencing can be used to reconstruct HIV-1 transmission networks and to infer the direction of transmission in these networks. We are able to deep-sequence virus from...

Data from: Range-wide spatial mapping reveals convergent character displacement of bird song

Alexander Kirschel, Nathalie Seddon & Joseph Tobias
A long-held view in evolutionary biology is that character displacement generates divergent phenotypes in closely related coexisting species to avoid the costs of hybridisation or ecological competition, whereas an alternative possibility is that signals of dominance or aggression may instead converge to facilitate coexistence among ecological competitors. Although this counter-intuitive process⎯termed convergent agonistic character displacement⎯is supported by recent theoretical and empirical studies, the extent to which it drives spatial patterns of trait evolution at continental...

Data from: Using GPS collars to investigate the frequency and behavioural outcomes of intraspecific interactions among carnivores: a case study of male cheetahs in the Maasai Mara, Kenya

Femke Broekhuis, Emily Madsen, Kosiom Keiwua & David Macdonald
Intraspecific interactions between individuals or groups of individuals of the same species are an important component of population dynamics. Interactions can be static, such as spatial overlap, or dynamic based on the interactions of movements, and can be mediated through communication, such as the deployment of scent marks. Interactions and their behavioural outcomes can be difficult to determine, especially for species that live at low densities. With the use of GPS collars we quantify both...

Data from: Multidimensional ecological analyses demonstrate how interactions between functional traits shape fitness and life history strategies

Nuria Pistón Caballero, Francesco De Bello, André T. C. Dias, Lars Götzenberger, Bruno Henrique P. Rosado, Eduardo A. De Mattos, Roberto Salguero-Gómez & Carlos Perez Carmona
1.Traditionally, trait‐based studies have explored single‐trait‐fitness relationships. However, this approximation in the study of fitness components is often too simplistic, given that fitness is determined by the interplay of multiple traits, which could even lead to multiple functional strategies with comparable fitness (i.e. alternative designs). 2.Here we suggest that an analytical framework using boosted regression trees (BRT) can prove more informative to test hypotheses on trait combinations compared to standard linear models. We use two...

Tree trait, insect herbivore abundance and powdery mildew infection data (2018) from a tree diversity experiment in south-west France

E. Field, B. Castagneyrol, M. Gibbs, H. Jactel, N. Barsoum, K. Schonrogge & A. Hector
This data set consists of data collected from one field season (2018) from the ORPHEE tree diversity experiment run by INRA Bordeaux in SW France. Data was collected on tree traits (tree height, shoot length), abundance of leaf miners, damage by leaf chewers, and leaf damage by oak powdery mildew, a foliar fungal pathogen. Data was collected from plots differing in tree species richness and drought treatment.

Life history evolution, species differences and phenotypic plasticity in hemiparasitic eyebrights (Euphrasia)

Max Brown, Natacha Frachon, Edgar Wong & Alex Twyford
Premise of the study: Species delimitation in parasitic organisms is challenging as traits used in the identification of species are often plastic and vary depending on the host. Here, we use species from a recent radiation of generalist hemiparasitic Euphrasia to investigate trait variation and trait plasticity. We test whether Euphrasia species show reliable trait differences, investigate whether these differences correspond to life history trade-offs between growth and reproduction, and quantify plasticity in response to...

Data from: Space and rank: infants expect agents in higher position to be socially dominant

Xianwei Meng, Yo Nakawake, Hiroshi Nitta, Yusuke Moriguchi & Kazuhide Hashiya
Social hierarchies exist throughout the animal kingdom, including among humans. Our daily interactions inevitably reflect social dominance relationships between individuals. How do we mentally represent such concepts? Studies show that social dominance is represented as vertical space (i.e., high=dominant) by adults and preschool children, suggesting a space-dominance representational link in social cognition. However, little is known about its early development. Here, we present experimental evidence that 12- to 16-month-old infants expect agents presented in a...

Consistent patterns of distractor effects during decision making

Bolton K H Chau, Chun-Kit Law, Alizée Lopez-Persem, Miriam C Klein-Flügge, Matthew F S Rushworth, Bolton KH Chau & Matthew FS Rushworth
The value of a third potential option or distractor can alter the way in which decisions are made between two other options. Two hypotheses have received empirical support: that a high value distractor improves the accuracy with which decisions between two other options are made and that it impairs accuracy. Recently, however, it has been argued that neither observation is replicable. Inspired by neuroimaging data showing that high value distractors have different impacts on prefrontal...

Beyond Buddhism and animism: A psychometric test of the structure of Burmese Theravada Buddhism

Mark Stanford & Jonathan Jong
Anthropologists and religious scholars have long debated the relationship between doctrinal Theravada Buddhism, so-called ‘animism’, and other folk practices in southeast Asian societies. A variety of models of this relationship have been proposed on the basis of ethnographic evidence. We provide the first psychometric and quantitative evaluation of these competing models, using a new scale developed for this purpose, the Burmese Buddhist Religiosity Scale. Having tested existing hypotheses in our first study (n = 2285)...

2014 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...

Data from: Diversity dynamics of Phanerozoic terrestrial tetrapods at the local-community scale

Roger A. Close, Roger B. J. Benson, John Alroy, Anna K. Behrensmeyer, Juan Benito, Matthew T. Carrano, Terri J. Cleary, Emma M. Dunne, Philip D. Mannion, Mark D. Uhen & Richard J. Butler
The fossil record provides one of the strongest tests of the hypothesis that diversity within local communities is constrained over geological timescales. Constraints to diversity are particularly controversial in modern terrestrial ecosystems, yet long-term patterns are poorly understood. Here we document patterns of local richness in Phanerozoic terrestrial tetrapods using a global data set comprising 145,332 taxon occurrences from 27,531 collections. We show that the local richness of non-flying terrestrial tetrapods has risen asymptotically since...

Data from: Robust design for coalescent model inference

Kris V Parag & Oliver G Pybus
The coalescent process describes how changes in the size or structure of a population influence the genealogical patterns of sequences sampled from that population. The estimation of (effective) population size changes from genealogies that are reconstructed from these sampled sequences is an important problem in many biological fields. Often, population size is characterized by a piecewise-constant function, with each piece serving as a population size parameter to be estimated. Estimation quality depends on both the...

Data from: Palaeoproteomics resolves sloth phylogeny

Samantha Presslee, Graham J. Slater, Francois Pujos, Analia M. Forasiepi, Roman Fischer, Kelly Molloy, Meaghan Mackie, Jesper V. Olsen, Alejandro Kramarz, Matias Taglioretti, Fernando Scaglia, Maximiliano Lezcano, José Luis Lanata, John Southon, Robert Feranec, Jonathan Bloch, Adam Hajduk, Fabiana M. Martin, Rodolfo Salas Gismondi, Marcelo Reguero, Christian De Muizon, Alex Greenwood, Brian T. Chait, Kirsty Penkman, Matthew Collins … & Ross D. E. MacPhee
The living tree sloths Choloepus and Bradypus are the only remaining members of Folivora, a major xenarthran radiation that occupied a wide range of habitats in many parts of the western hemisphere during the Cenozoic, including both continents and the West Indies. Ancient DNA evidence has played only a minor role in folivoran systematics, as most sloths lived in places not conducive to genomic preservation. Here we utilize collagen sequence information, both separately and in...

Data from: Adding ecological and evolutionary processes to restoration biodiversity offset models using neutral theory

Falko T. Buschke & Samuel P. Sinclair
Aim: Biodiversity offsets are being implemented or planned across all continents and biogeographical realms. Due to their popularity, new offset projects have developed faster than empirical evidence of their ecological effectiveness, so policy has been informed by quantitative models. However, these models have yet to incorporate ecological and evolutionary processes, which vary globally. Here we use the unified neutral theory of biodiversity to integrate speciation and dispersal into models of restoration biodiversity offsets. Location: A...

Data from: Data gaps and opportunities for comparative and conservation biology

Dalia A. Conde, Johanna Staerk, Fernando Colchero, Rita Da Silva, Jonas Schöley, H. Maria Baden, Lionel Jouvet, John E. Fa, Hassan Syed, Eelke Jongejans, Shai Meiri, Jean-Michel Gaillard, Scott Chamberlain, Jonathan Wilcken, Owen R. Jones, Johan P. Dahlgren, Ulrich K. Steiner, Lucie M. Bland, Ivan Gomez-Mestre, Jean-Dominique Lebreton, Jaime González Vargas, Nate Flesness, Vladimir Canudas-Romo, Roberto Salguero-Gómez, Onnie Byers … & James W. Vaupel
Biodiversity loss is a major challenge. Over the past century, the average rate of vertebrate extinction has been about 100-fold higher than the estimated background rate and population declines continue to increase globally. Birth and death rates determine the pace of population increase or decline, thus driving the expansion or extinction of a species. Design of species conservation policies hence depends on demographic data (e.g., for extinction risk assessments or estimation of harvesting quotas). However,...

Speleothem chronology in Ledyanaya Lenskaya and Botovskaya caves used in publication \"Paleoclimate evidence of vulnerable permafrost during times of low sea-ice\" By Vaks, A. et al.(2020)

A Vaks, A.J. Mason, S. F. M. Breitenbach, A. M. Kononov, A. V. Osinzev, M. Rosensaft, A. Borshevsky, O. S. Gutareva & G. M. Henderson
The tables describe U-series chronology of speleothems in Ledyanaya Lenskaya and Botovskaya caves used in the manuscript "Paleoclimate evidence of vulnerable permafrost during times of low sea ice" by Vaks et al. 2020, Nature 577, 7789, 221–225. The information included in the tables is listed as following: Table 1: Table 1a includes U–Pb data from Ledyanaya Lenskaya and Botovskaya caves; Table 1b includes common Pb estimates for Ledyanaya Lenskaya and Botovskaya caves. Table 2: U–Th...

Interprofessional education in geriatric medicine: towards best practice. A controlled before-after study of medical and nursing student attitudes

Sanja Thompson, Kiloran Metcalfe, Katy Boncey, Clair Merriman, Lorna Flynn, Gaggandeep Singh Alg, Harriet Bothwell, Carol Forde-Forde-Johnston, Elizabeth Puffett, Caroline Hardy, Liz Wright & James Beale
Objectives To investigate nursing and medical students’ readiness for interprofessional learning before and after implementing geriatric Interprofessional education (IPE), based on interactive case scenarios Problem Based Learning (PBL). To determine optimal number of geriatric IPE sessions, the size and the ratio of participants in the learner groups, the outcomes related to the Kirkpatrick four-level typology of learning evaluation, students’ concerns about joint learning, perception of roles of the “other” profession and students choice of topic....

Data from: Weak spatiotemporal response of prey to predation risk in a freely interacting system

Jeremy J. Cusack, Michel T. Kohl, Matthew C. Metz, Tim Coulson, Daniel R. Stahler, Douglas W. Smith & Daniel R. MacNulty
1.The extent to which prey space use actively minimises predation risk continues to ignite controversy. Methodological reasons that have hindered consensus include inconsistent measurements of predation risk, biased spatiotemporal scales at which responses are measured, and lack of robust null expectations. 2.We addressed all three challenges in a comprehensive analysis of the spatiotemporal responses of adult female elk (Cervus elaphus) to the risk of predation by grey wolves (Canis lupus) during winter in northern Yellowstone,...

Dung beetle abundance data from a before-and-after El Niño experiment in the Brazilian Amazon

F.M. França, V.H. Oliveira, J.N.C. Louzada, F.Z. Vaz-De-Mello, J.N Ferreira, E. Berenguer, T. Gardner, A. Lees & J. Barlow
This data set includes longitudinal abundance of dung beetles at dung-baited pitfall traps, recorded in 2010, 2016 and 2017 (around six years before, six months after and 18 months after the 2015-16 El Niño event, respectively) in the Brazilian Amazon region. Dung beetles were collected during the collaborative projects AFIRE (Assessing ENSO-induced Fire Impacts in tropical Rainforest Ecosystems) and ECOFOR (Biodiversity and Ecosystem Functioning in degraded and recovering Amazonian and Atlantic Forests), which are part...

Data from: Match and mismatch between dietary switches and microbial partners in plant sap-feeding insects

Louis Bell-Roberts, Angela E. Douglas & Gijsbert D.A. Werner
Some animal groups associate with the same vertically-transmitted microbial symbionts over extended periods of evolutionary time, punctuated by occasional symbiont switches to different microbial taxa. Here we test the oft-repeated suggestion that symbiont switches are linked with host diet changes, focusing on hemipteran insects of the suborder Auchenorrhyncha. These insects include the only animals that feed on plant xylem sap through the life cycle, as well as taxa that feed on phloem sap and plant...

2010 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...

Registration Year

  • 2019
    63

Resource Types

  • Dataset
    63

Affiliations

  • University of Oxford
    54
  • Hansen Experimental Physics Laboratory, Stanford University
    9
  • Electrical Engineering and Computer Science Department, University of Michigan
    9
  • SUPA School of Physics and Astronomy, University of Glasgow
    9
  • NASA Goddard Space Flight Center
    9
  • Center for Data Science, New York University
    9
  • Lockheed Martin Solar & Astrophysics Laboratory
    9
  • SETI Institute
    9
  • Southwest Research Institute
    7
  • Department of Psychiatry, University of Amsterdam
    7