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8,537 results for “Openness”
Open Social Scholarship, In Real Terms
<p>4<sup>th</sup> Lecture</p>
How to find open access materia?
<p>A 4-minute video on how to find open access material (publications and datasets). Emphasis on Finland and University of Helsinki.</p>
Open data for publication: Deposition of Extended Ordered Ultrathin Films of Au38(SC2H4Ph)24 Nanocluster Using Langmuir-Blodgett Technique
<p>Open data for publication: Deposition of Extended Ordered Ultrathin Films of Au38(SC2H4Ph)24 Nanocluster Using Langmuir-Blodgett Technique</p>
Quantitative analysis of subcellular distributions with an open-source, object-based tool
<p>The subcellular localization of objects, such as organelles, proteins, or other molecules, instructs cellular form and function. Understanding the underlying spatial relationships between objects through colocalization analysis of microscopy images is a fundamental approach used to inform biological mechanisms. We generated an automated and customizable computational tool, the SubcellularDistribution pipeline, to facilitate object-based image analysis from 3D fluorescence microcopy images. To test the utility of the SubcellularDistribution pipeline, we examined the subcellular distribution of mRNA relative to centrosomes within <i>Drosophila</i> embryos. Centrosomes are microtubule-organizing centers, and RNA enrichments at centrosomes are of emerging importance. Our open-source and freely available software detected RNA distributions comparably to commercially available image analysis software. The SubcellularDistribution pipeline is designed to guide the user through the complete process of preparing image analysis data for publication, from image segmentation and data processing to visualization.</p>
Out in the open: behavior's effect on predation-risk and thermoregulation by aposematic caterpillars
Warning coloration should be under strong stabilizing selection but often displays considerable intraspecific variation. Opposing selection on color by predators and temperature is one potential explanation for this seeming paradox. Despite the importance of behavior for both predator avoidance and thermoregulation, its role in mediating selection by predators and temperature on warning coloration has received little attention. Wood tiger moth caterpillars, <i>Arctia plantaginis</i>, have aposematic coloration, an orange patch on the black body. The size of the orange patch varies considerably: individuals with larger patches are safer from predators, but having a small patch is beneficial in cool environments. We investigated microhabitat preference by these caterpillars and how it interacted with their coloration. We expected caterpillar behavior to reflect a balance between spending time exposed to maximize basking and spending time concealed to avoid detection by predators. Instead, we found that caterpillars preferred exposed locations regardless of their coloration. Whether caterpillars were exposed or concealed had a strong effect on both temperature and predation risk, but caterpillars in exposed locations were both much warmer and less likely to be attacked by a bird predator (great tits, <i>Parus major</i>). This shared optimum may explain why we observed so little variation in caterpillar behavior and demonstrates the important effects of behavior on multiple functions of coloration.
Evaluating QualiCO: An ontology to facilitate qualitative methods sharing to support open science
<p>This dataset includes the quantitative analysis we did in our paper. It includes the time on task the participants needed as well as the scores they obtained in the task</p>
A Large Open Dataset from the Parler Social Network
<p>There are two main zip files in this dataset. Each zip file contains multiple <a href="http://ndjson.org/">newline delimited JSON files</a>. The JSON objects in each file contain all the key/value pairs returned from their respective Parler API endpoints.</p> <p><strong>NOTE:</strong> All identifying data has been redacted by removing the "name" field from posts, comments and user profiles.</p> <p><a href="https://arxiv.org/abs/2101.03820">Current paper</a> for more details and preferred citation information.</p> <p> </p> <p><strong>Parler Users (parler_user.zip)</strong></p> <p>Returned by the <em>/v1/profile</em> endpoint. Each line consists of an individual user profile object.</p> <p><strong>Parler Posts and Comments (parlerpostcomments.zip)</strong></p> <p>Returned by the <em>/v1/post[comment] </em>endpoints. Each line consists of an individual post or comment object.</p> <p><strong>How to extract the data:</strong></p> <p>The data provided is compressed in zip format. See the instructions below on how to extract it:</p> <ul> <li><strong>Linux and Mac</strong></li> </ul> <p>Navigate to the file in a terminal window or file browser.</p> <p>Run the following command (or typically you can double click if you are in a file browser):</p> <p>User profiles:</p> <pre><code>unzip parler_users.zip</code></pre> <p>Posts and comments:</p> <pre><code>unzip parler_data.zip</code></pre> <p>The unzipped version contains multiple files for each data type.</p> <ul> <li><strong>Windows</strong></li> </ul> <p>Microsoft provides instructions on to extract a zip file. The authors cannot recommend a particular method or software.</p>
Multidimensional framework for furthering open access
<p>The spreadsheet provides a multidimensional framework for furthering open access to research output. Combining three dimensions (i.e. aspects of open access, actors involved and the levels at which actions can be taken) results in a multidimensional framework that can inform future developments. Vertically, the different aspects of open access are projected. Horizontally, the five “levels of engagement” are presented for each of the different actors relevant for open access in the Dutch context. The framework can be used in various ways. For instance one could fill it with current actions/policies. But one could also use it to prioritize or plan future actions. This file set contains both the template and the versions filled with current actions relevant for researchers in the Nederlands in PDF format, in spreadsheet format and as presentation slides.</p>
Quality Evaluation Models or Frameworks for Open Source Software: A Systematic Literature Review (Article Pool)
<p>This pdf includes all of the articles that analyzed in the study: "Quality Evaluation Models or Frameworks for Open Source Software: A Systematic Literature Review".</p>
Data from: Nineteenth-century collapse of a benthic marine ecosystem on the open continental shelf
The soft-sediment seafloor of the open continental shelf is among the least-known biomes on Earth, despite its high diversity and importance to fisheries and biogeochemical cycling. Abundant dead shells of epifaunal suspension-feeding terebratulid brachiopods (Laqueus) and scallops on the now-muddy mainland continental shelf of southern California reveal the recent, previously unsuspected extirpation of an extensive offshore shell-gravel ecosystem, evidently driven by anthropogenic siltation. Living populations of attached epifauna, which formerly existed in a middle- and outer-shelf mosaic with patches of trophically diverse muds, are restricted today to rocky seafloor along the shelf edge and to the sandier shelves of offshore islands. Geological age-dating of 190 dead brachiopod shells shows that (i) no shells have been produced on the mainland shelf within the last 100 years, (ii) their shell production declined steeply during the nineteenth century, and (iii) they had formerly been present continuously for at least 4 kyr. This loss, sufficiently rapid (less than or equal to 100 years) and thorough to represent an ecosystem collapse, coincides with intensification of alluvial-plain land use in the nineteenth century, particularly livestock grazing. Extirpation was complete by the start of twentieth-century urbanization, warming, bottom fishing and scientific surveys. The loss of this filter-feeding fauna and the new spatial homogeneity and dominance of deposit- and detritus-feeders would have altered ecosystem functioning by reducing habitat heterogeneity and seawater filtering. This discovery, attesting to the power of this geological approach to recent ecological transitions, also strongly increases the spatial scope attributable to the negative effects of siltation, and suggests that it has been under-recognized on continental shelves elsewhere as a legacy of coastal land use.
Data from: Does warming by open-top chambers induce change in the root-associated fungal community of the arctic dwarf shrub Cassiope tetragona (Ericaceae)?
Climate change may alter mycorrhizal communities, which impact ecosystem characteristics such as carbon sequestration processes. These impacts occur at a greater magnitude in Arctic ecosystems, where the climate is warming faster than in lower latitudes. Cassiope tetragona (L.) D. Don is an Arctic plant species in the Ericaceae family with a circumpolar range. C. tetragona has been reported to form ericoid mycorrhizal (ErM) as well as ectomycorrhizal (ECM) symbioses. In this study, the fungal taxa present within roots of C. tetragona plants collected from Svalbard were investigated using DNA metabarcoding. In light of ongoing climate change in the Arctic, the effects of artificial warming by open-top chambers (OTCs) on the fungal root community of C. tetragona were evaluated. We detected only a weak effect of warming by OTCs on the root-associated fungal communities that was masked by the spatial variation between sampling sites. The root fungal community of C. tetragona was dominated by fungal groups in the Basidiomycota traditionally classified as either saprotrophic or ECM symbionts, including the orders Sebacinales and Agaricales and the genera Clavaria, Cortinarius, and Mycena. Only a minor proportion of the operational taxonomic units (OTUs) could be annotated as ErM-forming fungi. This indicates that C. tetragona may be forming mycorrhizal symbioses with typically ECM-forming fungi, although no characteristic ECM root tips were observed. Previous studies have indicated that some saprophytic fungi may also be involved in biotrophic associations, but whether the saprotrophic fungi in the roots of C. tetragona are involved in biotrophic associations remains unclear. The need for more experimental and microscopy-based studies to reveal the nature of the fungal associations in C. tetragona roots is emphasized.
Data from: Safety of single low-dose primaquine in glucose-6-phosphate dehydrogenase deficient falciparum-infected African males: two open-label, randomized, safety trials
Background: Primaquine (PQ) actively clears mature Plasmodium falciparum gametocytes but in glucose-6-phosphate dehydrogenase deficient (G6PDd) individuals can cause hemolysis. We assessed the safety of low-dose PQ in combination with artemether-lumefantrine (AL) or dihydroartemisinin-piperaquine (DP) in G6PDd African males with asymptomatic P. falciparum malaria. Methods and findings: In Burkina Faso, G6PDd adult males were randomized to treatment with AL alone (n = 10) or with PQ at 0.25 (n = 20) or 0.40 mg/kg (n = 20) dosage; G6PD-normal males received AL plus 0.25 (n = 10) or 0.40 mg/kg (n = 10) PQ. In The Gambia, G6PDd adult males and boys received DP alone (n = 10) or with 0.25 mg/kg PQ (n = 20); G6PD-normal males received DP plus 0.25 (n = 10) or 0.40 mg/kg (n = 10) PQ. The primary study endpoint was change in hemoglobin concentration during the 28-day follow-up. Cytochrome P-450 isoenzyme 2D6 (CYP2D6) metabolizer status, gametocyte carriage, haptoglobin, lactate dehydrogenase levels and reticulocyte counts were also determined. In Burkina Faso, the mean maximum absolute change in hemoglobin was -2.13 g/dL (95% confidence interval [CI], -2.78, -1.49) in G6PDd individuals randomized to 0.25 PQ mg/kg and -2.29 g/dL (95% CI, -2.79, -1.79) in those receiving 0.40 PQ mg/kg. In The Gambia, the mean maximum absolute change in hemoglobin concentration was -1.83 g/dL (95% CI, -2.19, -1.47) in G6PDd individuals receiving 0.25 PQ mg/kg. After adjustment for baseline concentrations, hemoglobin reductions in G6PDd individuals in Burkina Faso were more pronounced compared to those in G6PD-normal individuals receiving the same PQ doses (P = 0.062 and P = 0.022, respectively). Hemoglobin levels normalized during follow-up. Abnormal haptoglobin and lactate dehydrogenase levels provided additional evidence of mild transient hemolysis post-PQ. Conclusions: Single low-dose PQ in combination with AL and DP was associated with mild and transient reductions in hemoglobin. None of the study participants developed moderate or severe anemia; there were no severe adverse events. This indicates that single low-dose PQ is safe in G6PDd African males when used with artemisinin-based combination therapy.
Data from: Estimating abundance of an open population with an N-mixture model using auxiliary data on animal movements
Accurate assessment of abundance forms a central challenge in population ecology and wildlife management. Many statistical techniques have been developed to estimate population sizes because populations change over time and space, and to correct for the bias resulting from animals that are present in a study area but not observed. The mobility of individuals makes it difficult to design sampling procedures that account for movement into and out of areas with fixed jurisdictional boundaries. Aerial surveys are the gold standard used to obtain data of large mobile species in geographic regions with harsh terrain, but these surveys can be prohibitively expensive and dangerous. Estimating abundance with ground based census methods have practical advantages, but it can be difficult to simultaneously account for temporary emigration and observer error to avoid biased results. Contemporary research in population ecology increasingly relies on telemetry observations of the states and locations of individuals to gain insight on vital rates, animal movements, and population abundance. Analytical models that use observations of movements to improve estimates of abundance have not been developed. Here we build upon existing multi-state mark recapture methods using a hierarchical N-mixture model with multiple sources of data, including telemetry data on locations of individuals, to improve estimates of population sizes. We used a state-space approach to model animal movements to approximate the number of marked animals present within the study area at any observation period, thereby accounting for a frequently changing number of marked individuals. We illustrate the approach using data on a population of elk (Cervus elaphus nelsoni) in Northern Colorado, USA. We demonstrate substantial improvement compared to existing abundance estimation methods and corroborate our results from the ground based surveys with estimates from aerial surveys during the same seasons. We develop a hierarchical Bayesian N-mixture model using multiple sources of data on abundance, movement and survival to estimate the population size of a mobile species that uses remote conservation areas. The model improves accuracy of inference relative to previous methods for estimating abundance of open populations.
Data from: Functional traits, not productivity, predict openness to seedling recruitment in alpine plant communities under climatic warming
Understanding the degree to which plant communities are open to seedling recruitment is key to predicting how they will be impacted by climate change. We experimentally assessed whether communities assembled under colder climates were inherently more open to recruitment than warmer-climate communities, after controlling for differences in the current climate under which the communities were growing. We then tested whether variation in openness to recruitment could be explained by community biomass or by the plant functional traits of the community. The study was conducted in a climate grid of twelve grassland sites across southern Norway, differing systematically in temperature and precipitation. Along a 2000 mm precipitation gradient, we transplanted turfs with intact plant communities from alpine and sub-alpine sites into 2℃ warmer sites, and measured natural seedling emergence in these transplanted turfs vs. locally replanted control turfs at the transplant destination sites. Mixed effect models were used to assess the effect of origin (cold vs warm climate), biomass, and functional trait composition of the communities on seedling emergence. We further assessed variation in these effects across different climatic contexts (the temperature and precipitation gradients). Communities originating from colder climates were consistently more open to recruitment, with on average 44% more seedlings emerging, than the locally replanted control communities. The higher rates of seedling emergence in colder-climate communities were attributable to systematic differences in plant functional traits, but not in biomass. The colder-climate communities were composed of species with smaller leaves and lower maximum plant heights; traits that may make these communities less effective at excluding new recruits. These trait-related responses were not significant in the warmest sites and did not very across the precipitation gradient. Our results suggest that alpine species lack the competitive effect traits required to make their communities resistant to invasion by novel competitors under climate change.
Open-source software collaboration network mining dataset
<p>The resulting dataset of the <a href="https://github.com/gotec/git2net">git2net </a>and <a href="https://github.com/wschuell/repo_tools">repo_tools </a>mining process for randomly selected large open-source repositories.</p>
Data from: Exploratory and confirmatory research in the open science era
<p>1. Applied ecological research is increasingly inspired by the Open Science movement. However, new challenges about how we define our science when biodiversity data is being shared and re-used are not solved. Among these challenges is the risk associated with blurring the distinction between research that mainly seeks to explore patterns with no a-priori articulated hypotheses (exploratory research), and research that explicitly tests a-priori formulated hypotheses (confirmatory research).</p> <p>2. A rapid screening of a random selection of peer-reviewed articles suggests that neither experimental protocols nor hypothesis-testing sensu stricto are common in applied ecological research. In addition, most experiments are carried out on small spatial scales, which contrast with current global policy needs and research trends towards addressing large spatial and temporal scales. This latter trend make it unfeasible for policy to rely mainly on insights gained from experimental research.</p> <p>3. To solve fundamental local, regional and global societal challenges, we need both exploratory and confirmatory research, and the fundamental (but different) role that hypothesis-testing and prediction play in applied ecological research should be revaluated.</p> <p>4. A clearer distinction between exploratory and confirmatory research could be facilitated by allocating journal sections to different types of research; embracing new tools offered by the open science era, such as pre-registration of hypothesis; establishing new systems where post-hoc hypotheses emerging through exploration can also be registered for later testing; and more broad adoption of causal inference methods that foster more structured testing of hypotheses about causal mechanisms from observational biodiversity data.</p> <p>5. Synthesis and applications. To gain the full benefits from the open science era, researchers, funding bodies and journal editors should explicitly consider incentives that encourage openness about methods and approaches, as well as value the full plurality of scientific approaches needed to address questions in conservation science.</p>
Listening and watching: do camera traps or acoustic sensors more efficiently detect wild chimpanzees in an open habitat?
<p>1. With one million animal species at risk of extinction, there is an urgent need to regularly monitor threatened species. However, in practice this is challenging, especially with wide-ranging, elusive and cryptic species or those that occur at low density.<br> 2. Here we compare two non-invasive methods, passive acoustic monitoring (n=12) and camera trapping (n=53), to detect chimpanzees (Pan troglodytes) in a savanna-woodland mosaic habitat at the Issa Valley, Tanzania. With occupancy modelling we evaluate the efficacy of each method, using the estimated number of sampling days needed to establish chimpanzee absence with 95% probability, as our measure of efficacy.<br> 3. Passive acoustic monitoring was more efficient than camera trapping in detecting wild chimpanzees. Detectability varied over seasons, likely due to social and ecological factors that influence party size and vocalization rate. The acoustic method can infer chimpanzee absence with less than ten days of recordings in the field during the late dry season, the period of highest detectability, which was five times faster than the visual method.<br> 4. Synthesis and applications: Despite some technical limitations, we demonstrate that passive acoustic monitoring is a powerful tool for species monitoring. Its applicability in evaluating presence/absence, especially but not exclusively for loud call species, such as cetaceans, elephants, gibbons or chimpanzees provides a more efficient way of monitoring populations and inform conservation plans to mediate species-loss.</p>
Star Wars New Hope Opening Crawl (Animation)
Each of the eight episodic Star Wars films begin with nearly identical openings, in which the text "A long time ago in a galaxy far, far away...." is displayed, followed by the Star Wars logo over a field of stars. A subsequent downward tilt reveals the film's episode number, the subtitle in all-capital letters, and a three-paragraph summary of events immediately prior to the events of the film. I have a Patreon Join now! :https://www.patreon.com/user?u=14434838 I have a Patreon Join now! :https://www.patreon.com/user?u=14434838 Source: Objaverse 1.0 / Sketchfab
Sol Lewitt - Incomplete Open Cube 6/8 (1974)
Painted aluminum, 106.7 x 106.7 x 106.7 cm Solomon R. Guggenheim Foundation, Hannelore B. and Rudolph B. Schulhof Collection, bequest of Hannelore B. Schulhof, 2012 © Sol LeWitt, by SIAE 2012 Source: Objaverse 1.0 / Sketchfab
Wood stack - open-air museum at Kolbuszowa
A photogrammetry model created in Kolbuszowa's open-air museum showcasing an old, XIX-century village in subcarpathian region. Source: Objaverse 1.0 / Sketchfab
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.