647 Works

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...

Mark-Release-Recapture data showing moth and dung beetle movements in riparian reserves within the SAFE project landscape, Malaysian Borneo, 2016-17

R.E.J. Gray, E.M. Slade, A.Y.C. Chung & O.T. Lewis
This dataset consists of moth and dung beetle recapture, movement, and trait data from a mark-release-recapture experiment conducted within riparian forest reserves, in an oil palm landscape in Sabah, Malaysian Borneo conducted as part of the SAFE project (Stability of Altered Forest Ecosystems). This resource includes information regarding the recapture frequency and movement behaviour of both moths and dung beetles with respect to three habitat types: riparian forest reserve, continuous forest, and oil palm plantation....

Geochemical and petrological data pertaining to the eruptive deposits of 1883 caldera-forming eruption of Krakatau

Amber Madden-Nadeau
Geochemical data has been collected on samples from new exposures of the 1883 deposits, revealed by the 2018 tsunamigenic flank collapse of Anak Krakatau, which provides improved stratigraphic context. Whole-rock data taken by X-ray Florescence shows no systematic stratigraphic correlation. Chemical data for transects across, and spot points on, plagioclase phenocrysts, including some trace element data, all obtained using Electron Probe Microanalysis (EPMA), with Backscatter electron (BSE) images of crystals, obtained using Scanning Electron Microscope,...

High-resolution global topographic index values

T.R. Marthews, S.J. Dadson, B. Lehner, S. Abele & N. Gedney
The topographic index is a hydrological quantity describing the propensity of the soil at landscape points to become saturated with water as a result of topographic position (i.e. not accounting for other factors such as climate that also affect soil moisture but are accounted for separately). Modern land surface models require a characterisation of the land surface hydrological regime and this parameter allows the use of the TOPMODEL hydrological model to achieve this .This Geographic...

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....

Thinner bark increases sensitivity of wetter Amazonian tropical forests to fire

Ann Carla Staver, Paulo M. Brando, Jos Barlow, Douglas C. Morton, C.E. Timothy Paine, Yadvinder Malhi, Alejandro Araujo Murakami & Jhon Pasquel
Understory fires represent an accelerating threat to Amazonian tropical forests and can, during drought, affect larger areas than deforestation itself. These fires kill trees at rates varying from < 10 to c. 90% depending on fire intensity, forest disturbance history and tree functional traits. Here, we examine variation in bark thickness across the Amazon. Bark can protect trees from fires, but it is often assumed to be consistently thin across tropical forests. Here, we show...

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)...

Insights from empirical analyses and simulations on using multiple fossil calibrations with relaxed clocks to estimate divergence times

Tom Carruthers & Robert Scotland
Relaxed clock methods account for among-branch-rate-variation when estimating divergence times by inferring different rates for individual branches. In order to infer different rates for individual branches, important assumptions are required. This is because molecular sequence data does not provide direct information about rates, but instead provides direct information about the total number of substitutions along any branch, which is a product of the rate and time for that branch. Often, the assumptions required for estimating...

Data from: Large-bodied sabre-toothed anchovies reveal unanticipated ecological diversity in early Palaeogene teleosts

Alessio Capobianco, Hermione Beckett, Etienne Steurbaut, Philip Gingerich, Giorgio Carnevale & Matthew Friedman
Many modern groups of marine fishes first appear in the fossil record during the early Palaeogene (66–40 million years ago), including iconic predatory lineages of spiny-rayed fishes that appear to have originated in response to ecological roles left empty after the Cretaceous/Palaeogene extinction. The hypothesis of extinction-mediated ecological release likewise predicts that other fish groups have adopted novel predatory ecologies. Here we report remarkable trophic innovation in early Palaeogene clupeiforms (herrings and allies), a group...

Human decisions about when to act originate within a basal forebrain-nigral circuit

Nima Khalighinejad, Luke Priestley, Saad Jbabdi & Matthew Rushworth
Decisions about when to act are critical for survival in humans as in animals but how a desire is translated into the decision that an action is worth taking at any particular point in time is incompletely understood. Here we show that a simple model developed to explain when animals decide it is worth taking an action also explains a significant portion of the variance in timing observed when humans take voluntary actions. The model...

Distal and proximal hypoxia response elements cooperate to regulate organ-specific erythropoietin gene expression

Roland Wenger, Ilaria M.C. Orlando, Véronique N. Lafleur, Federica Storti, Patrick Spielmann, Lisa Crowther, Sara Santambrogio, Johannes Schödel, David Hoogewijs & David R. Mole
While it is well-established that distal hypoxia response elements (HREs) regulate hypoxia-inducible factor (HIF) target genes such as erythropoietin (Epo), an interplay between multiple distal and proximal (promoter) HREs has not been described so far. Hepatic Epo expression is regulated by a HRE located downstream of the EPO gene, but this 3' HRE is dispensable for renal EPO gene expression. We previously identified a 5' HRE and could show that both HREs direct exogenous reporter...

Data from: Prey colonization in freshwater landscapes can be stimulated or inhibited by the proximity of remote predators

Beth Turner, Hendrik Trekels, Mathil Vandromme & Bram Vanschoenwinkel
1. Recent findings suggest that the colonization of habitat patches may be affected by the quality of surrounding patches. For instance, patches that lack predators may be avoided when located near others with predators, a pattern known as risk contagion. Alternatively, predator avoidance might also redirect dispersal towards nearby predator-free patches resulting in so-called habitat compression. However, it is largely unknown how predators continue to influence these habitat selection behaviors at increasing distances from outside...

Data from: It takes two: heritable male effects on reproductive timing but not clutch size in a wild bird population

Simon R. Evans, Erik Postma & Ben C. Sheldon
Within-population variation in the traits underpinning reproductive output has long been of central interest to biologists. Since they are strongly linked to lifetime reproductive success, these traits are expected to be subject to strong selection and, if heritable, to evolve. Despite the formation of durable pair bonds in many animal taxa, reproductive traits are often regarded as female-specific, and estimates of quantitative genetic variation seldom consider a potential role for heritable male effects. Yet reliable...

Oldest fossil ciliates from the Cryogenian glacial interlude reinterpreted as possible red algal spores

Phoebe Cohen, Maoli Vizcaino & Ross Anderson
The Cryogenian Period experienced two long lived global glaciations known as Snowball Earths. While these events were dramatic, eukaryotic life persisted through them, and fossil evidence shows that eukaryotes thrived during the ca. 30-million-year interlude between the glaciations. Carbonate successions have become an important taphonomic window for this interval. One of the most notable examples is the ca. 662–635 Ma Taishir Formation (Tsagaan Olom Group, Zavkhan Terrane, Mongolia) which has yielded a number of eukaryotic...

Data from: Evolutionary origin of the Scombridae (tunas and mackerels): members of a Paleogene adaptive radiation with 14 other pelagic fish families

Masaki Miya, Matt Friedman, Takashi P. Satoh, Hirohiko Takeshima, Tetsuya Sado, Wataru Iwasaki, Yusuke Yamanoue, Masanori Nakatani, Kohji Mabuchi, Jun G. Inoue, Jan Yde Poulsen, Tsukasa Fukunaga, Yukuto Sato & Mutsumi Nishida
Uncertainties surrounding the evolutionary origin of the epipelagic fish family Scombridae (tunas and mackerels) are symptomatic of the difficulties in resolving suprafamilial relationships within Percomorpha, a hyperdiverse teleost radiation that contains approximately 17,000 species placed in 13 ill-defined orders and 269 families. Here we find that scombrids share a common ancestry with 14 families based on (i) bioinformatic analyses using partial mitochondrial and nuclear gene sequences from all percomorphs deposited in GenBank (10,733 sequences) and...

Data from: Payoff-based learning explains the decline in cooperation in public goods games

Maxwell N. Burton-Chellew, Heinrich H. Nax & Stuart A. West
Economic games such as the public goods game are increasingly being used to measure social behaviours in humans and non-human primates. The results of such games have been used to argue that people are pro-social, and that humans are uniquely altruistic, willingly sacrificing their own welfare in order to benefit others. However, an alternative explanation for the empirical observations is that individuals are mistaken, but learn, during the game, how to improve their personal payoff....

Data from: Efficient inference of recombination hot regions in bacterial genomes

Koji Yahara, Xavier Didelot, M Azim. Ansari, Samuel K. Sheppard & Daniel Falush
In eukaryotes, detailed surveys of recombination rates have shown variation at multiple genomic scales and the presence of “hotspots” of highly elevated recombination. In bacteria, studies of recombination rate variation are less developed, in part because there are few analysis methods that take into account the clonal context within which bacterial evolution occurs. Here we focus in particular on identifying “hot regions” of the genome where DNA is transferred frequently between isolates. We present a...

Data from: Range-wide multilocus phylogeography of the red fox reveals ancient continental divergence, minimal genomic exchange, and distinct demographic histories

Mark J. Statham, Zhenghuan Wang, Carl D. Soulsbury, Jan Janecka, Benjamin N. Sacks, Keith B. Aubry, Oliver Berry, Ceiridwen J. Edwards & James Murdoch
Widely distributed taxa provide an opportunity to compare biogeographic responses to climatic fluctuations on multiple continents and to investigate speciation. We conducted the most geographically and genomically comprehensive study to date of the red fox (Vulpes vulpes), the world's most widely distributed wild terrestrial carnivore. Analyses of 697 bp of mitochondrial sequence in ~1000 individuals suggested an ancient Middle Eastern origin for all extant red foxes and a 400 kya (SD = 139 kya) origin...

Data from: Cost, risk, and avoidance of inbreeding in a cooperatively breeding bird

Amy Leedale, Michelle Simeoni, Stuart Sharp, Jonathan Green, Jon Slate, Robert Lachlan, Ben Hatchwell & Elva Robinson
Inbreeding is often avoided in natural populations by passive processes such as sex-biased dispersal. But, in many social animals, opposite-sexed adult relatives are spatially clustered, generating a risk of incest and hence selection for active inbreeding avoidance. Here we show that, in long-tailed tits (Aegithalos caudatus), a cooperative breeder that risks inbreeding by living alongside opposite-sex relatives, inbreeding carries fitness costs and is avoided by active kin discrimination during mate choice. First, we identified a...

Data from: Longevity, body dimension and reproductive mode drive differences in aquatic versus terrestrial life history strategies

Pol Capdevila, Maria Beger, Simone Blomberg, Bernat Hereu, Cristina Linares & Roberto Salguero-Gómez
1. Aquatic and terrestrial environments display stark differences in key environmental factors and phylogenetic composition but their consequences for the evolution of species’ life history strategies remain poorly understood. 2. Here, we examine whether and how life history strategies vary between terrestrial and aquatic species. We use demographic information for 685 terrestrial and 122 aquatic animal and plant species to estimate key life history traits. We then use phylogenetically corrected least squares regression to explore...

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: Temporal transcriptomics suggest that twin-peaking genes reset the clock

William G. Pembroke, Arran Babbs, Kay E. Davies, Chris P. Ponting & Peter L. Oliver
The mammalian suprachiasmatic nucleus (SCN) drives daily rhythmic behavior and physiology, yet a detailed understanding of its coordinated transcriptional programmes is lacking. To reveal the finer details of circadian variation in the mammalian SCN transcriptome we combined laser-capture microdissection and RNA-seq over a 24-hour light/dark cycle. We show that 7-times more genes exhibited a classic sinusoidal expression signature than previously observed in the SCN. Another group of 766 genes unexpectedly peaked twice, near 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...

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