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5,530 results for “informal”
Python Type Information
<p>Python type information of 1000 projects. </p>
Humans represent the precision and utility of information acquired across fixations dataset
<p>This dataset contrains the behavioural and eyetracking data for the paper:</p> <p>Stewart, E.E.M., Ludwig, C.J.H. & Schütz, A.C. Humans represent the precision and utility of information acquired across fixations. <em>Sci Rep</em> <strong>12, </strong>2411 (2022). https://doi.org/10.1038/s41598-022-06357-7</p> <p>For results of the supplementary online experiment for this paper, as well as analysis of the images in the Amsterdam Library of Object Images (ALOI) dataset, please see the separate dataset: <strong>https://doi.org/10.5281/zenodo.6068096 </strong></p> <p>This dataset also contrains a copy of the ALOI images used in the experiment, originally sourced from https://aloi.science.uva.nl/. </p>
Supporting Information for "First Observations of Large Scale Traveling Ionospheric Disturbances Using Automated Amateur Radio Receiving Networks"
<p><strong>Introduction</strong></p> <p>The supporting information for this paper consists of a movie version of Figure 2 in the main paper, comparing the high frequency (HF) amateur radio observations to differential Global Navigation Satellite System (GNSS) Total Electron Content (TEC) measurements. In this revised version of the repository, the TEC data has been reprocessed such that all GNSS data with elevation angles down to 10 degrees were kept when applying the Savitzky–Golay (SG) filter. After the SG filter was applied, data with elevation angles below 30 degrees were discarded. This was done to remove artifacts observed in the original movies.</p> <p> </p> <p><strong>Movie S1 (20171103 Ham and TEC LSTID.mp4)</strong></p> <p>(Top Panel) Time series showing the TX-RX distance for 14 MHz amateur radio spots in 2 min by 25 km bins from 1200 UT 3 Nov 2017 - 0000 UT 4 Nov 2017. (Bottom Panel) differential Global Navigation Satellite System (GNSS) Total Electron Content (TEC) measurements over the Continental United States corresponding to the times indicated by the moving white vertical line in the top panel.</p> <p> </p> <p><strong>Movie S2 (20171103 Ham and TEC LSTID – With Arrow.mp4)</strong></p> <p>Same as movie S1, but with a fiducial black arrow indicating an estimated LSTID horizontal wavelength of 1681 km and propagation azimuth of 163°.</p>
Data from: Genotyping-in-Thousands by sequencing panel development and application to inform kokanee salmon (Oncorhynchus nerka) fisheries management at multiple scales
<p>The ability to differentiate life history variants is vital for estimating fisheries management parameters, yet traditional survey methods can be inaccurate in mixed-stock fisheries. Such is the case for kokanee, the resident freshwater form of sockeye salmon (<i>Oncorhynchus nerka</i>), which exhibits various reproductive ecotypes (stream-, shore-, deep-spawning) that co-occur with each other and/or anadromous <i>O. nerka</i> in some systems across their pan-Pacific distribution. Here, we developed a multi-purpose Genotyping-in-Thousands by sequencing (GT-seq) panel of 288 targeted single nucleotide polymorphisms (SNPs) to enable accurate kokanee stock identification by geographic basin, migratory form, and reproductive ecotype across British Columbia, Canada. The GT-seq panel exhibited high self-assignment accuracy (93.3%) and perfect assignment of individuals not included in the baseline to their geographic basin, migratory form, and reproductive ecotype of origin. The GT-seq panel was subsequently applied to Wood Lake, a valuable mixed-stock fishery, revealing high concordance (>98%) with previous assignments to ecotype using microsatellites and TaqMan<span> </span>SNP genotyping assays, while improving resolution, extending a long-term time-series, and demonstrating the scalability of this approach for this system and others.</p>
Datasets for manuscript: The nature, representation and measure of genetic information
<p><span>Current studies in genetics very often refer to notions from information science. The concept of genetic information is still disputed because it attributes semantic traits to what seem to be regular biochemical entities. Some researchers maintain that the use of information in biology is just metaphorical and maybe even misleading. In this paper, we offer an analysis of the nature and characteristics of the use of information in proteins, protein families, and their sequences. It is argued that the foundation of the metaphorical view is relatively weak given the current findings in bioinformatics, and it is shown that the present understanding of genetics fits well into the context of the modern philosophy of information. Here, we propose an extension of Floridi's conceptual model of information to include genetic information better. In addition, we discuss how to understand the qualitative aspects of genetic information and how to measure its quantitative aspects and present a joint statistical model including qualitative genetics, where the nominal genetic function is represented jointly with its metric self-information. The functional information of protein families in the <strong><em>Cath</em></strong> and <strong><em>Pfam</em></strong> databases are analysed. The paper concludes that scientific work may place information firmly as one of the fundamental components of molecular biology.</span></p> <p><span>The protein alignment files from the </span><strong><em>Cath</em></strong> and <strong><em>Pfam</em></strong> databases are in FASTA format.</p>
Replication Package (version 2) for "Information Constraints and Examination Quality in Patent Offices: The Effect of Initiation Lags" (International Journal of Industrial Organization, forthcoming)
<p>This replication package contains the datasets in Stata 16 format and the Stata do file to generate the results reported in "Information Constraints and Examination Quality in Patent Offices: The Effect of Initiation Lags" by Sadao Nagaoka and Isamu Yamauchi, to be published in International Journal of Industrial Organization.</p>
Information on marine management policies for invasive lionfish in the Western Atlantic Ocean and Mediterranean Sea
<p>The invasion of lionfish (<em>Pterois volitans</em> and <em>P. miles</em>) in the Western Atlantic is perhaps the best studied marine fish invasion to date; meanwhile another lionfish invasion is rapidly evolving in the Mediterranean. We reviewed lionfish management policies from several decades in the Western Atlantic to suggest policy recommendations for the Mediterranean. These strategic recommendations are synthesized in our corresponding manuscript titled: "Lessons from the Western Atlantic lionfish invasion can inform policy and management strategies for their expanding invasion in the Mediterranean." The policy information that we collected is included in full in this data repository. For this table, information was opportunistically gathered via online searches and discussion with professional and personal contacts for the affected jurisdictions in both the Western Atlantic and Mediterranean regions. Particular attention was devoted to collecting current information on policy changes that permitted directed control efforts for lionfish, as well as management efforts to develop commercial lionfish fisheries for food and other products. Broadly, we found that managers in the Western Atlantic often needed to adapt current conservation policies to enable lionfish removals in areas where spearfishing with scuba was otherwise prohibited for conservation purposes. The risk of fishers abusing these policies was mitigated through the use of gear restrictions and engagement of scuba divers and other stakeholders in lionfish monitoring, removals, and management. Currently, many policies in the Mediterranean generally do not permit lionfish removals given current policies that prohibit take of marine fishes with the use of scuba and spearfishing, even if these fishes are designated as invasive. We note that this data table does not represent an exhaustive review, and also that its information is a static snapshot of current policies (dated early 2022), and we expect these policies to change in the future. In fact, we encourage that any missing information or discrepancies noted be sent to lionfish@reef.org. With these limitations noted, this data table contains robust information regarding policy changes and outreach efforts regarding lionfish across broad geographic regions. Our goal is that this may serve as a resource for researchers, managers, and stakeholders. Coordinated information sharing can assist science-based decision making to better manage impacts by lionfish and the myriad of stressors on marine environments and fisheries resources.</p>
Supporting information for Plant migration under long-lasting hyperaridity – phylogenomics unravels recent biogeographic history in one of the oldest deserts on Earth
<p>R Scripts, input and parameter files as well as analysis results are provided for the publication: Böhnert et la. (2022) Plant migration under long-lasting hyperaridity – phylogenomics unravels recent biogeographic history in one of the oldest deserts on Earth. New Phyotologist.</p>
Supporting Information - An experimental assessment of competitive interactions between sexual and apomictic fern gametophytes using Easy Leaf Area
<p>Supporting Information for the paper titled <strong>An experimental assessment of competitive interactions between sexual and apomictic fern gametophytes using Easy Leaf Area</strong> published in Applications in Plant Sciences.</p>
List of benthic macroinvertebrate taxa from the upper Paraná River floodplain: summarizing information from a literature search
<p>We created a checklist of benthic macroinvertebrates taxa found in the environments of the upper Parana River floodplain according to the information found in published articles. The checklist data presents the taxa list, the substrate type, the environment type, and the year that each taxon was initially recorded for the region. We searched for data on aquatic macroinvertebrates recorded in the upper Paraná River floodplain by reviewing published articles and reports (grey literature). We took data from an extensive literature search at the ISI Web of Knowledge, SciELO, and Scopus websites, using the keyword combination “upper Paraná River” or “Paraná River” and “floodplain” or “wetland” and “macroinvertebrate*” for the search. We selected articles published between 1990 and 2020. We selected the articles following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) model (Liberati et al., 2009) and considered the selection in four steps: (1) the country of the study, (2) the title, (3) the abstract, and (4) the full text. The selection of papers followed some eligible parameters such as type of organisms, study area, and the presence of taxa data. During the selection, we excluded macroinvertebrates recorded as parasites or those found in studies of vertebrate feeding habits. Articles that contained these two criteria were excluded from the analyses. The articles that remained were analysed regarding the type of substrate where the macroinvertebrates were recorded (i.e., sediment, macrophytes, or artificial substrates), type of environment where each taxon was found (i.e., lentic or lotic environment), and the year in which each taxon was recorded for the first time in the upper Paraná River floodplain.</p>
Phylogenomics and fossil data inform the systematics and geographic range evolution of a diverse Neotropical ant lineage
<p>Recent advances in phylogenomics allow for the use of large amounts of genetic information in phylogenetic inference. Ideally, the increased resolution and accuracy of such inferences facilitate improved understanding of macroevolutionary processes. Here, we integrate ultraconserved elements (UCEs) with fossil and biogeographic range data to explore diversification and geographic range evolution in the diverse turtle ant genus <em>Cephalotes</em>. We focus on the potential role of the uplift of the Panamanian land bridge and the putative ephemeral GAARlandia land bridge linking South America and the Antilles in shaping the evolution in this group. Our phylogenetic analyses provide new resolution to the backbone of the turtle ant phylogeny. We further found that a majority of geographic range shifts between the South America and Central America regions were temporally consistent with the development of the Panamanian land bridge, while we did not find support for the GAARlandia land bridge. Additionally, we did not infer any shifts in diversification rates associated with our focal land bridges, or any other historical events (we inferred a single diversification rate regime across the genus). Our findings highlight the impact of the Panamanian land bridge for <em>Cephalotes</em> geographic range evolution as well as the influence of taxonomic sampling on macroevolutionary inferences. Keywords: Formicidae, Hymenoptera, Biogeography, Biology, Evolution, Phylogeny, Systematics</p>
SynPhoRest - Synthetic Photorealistic Forest Dataset with Depth Information for Machine Learning Model Training
<p><strong>SynPhoRest </strong>is a synthetic dataset collected on virtual forests. It features RGB images, semantic segmentation maps, depth maps and the projection of LIDAR point clouds on the RGB FOV for two different LIDAR scanning patterns. The dataset has a total of 3154 frames.<br> <br> A description of the available data follows:</p> <p><strong>RGB images</strong></p> <ul> <li>Resolution: 848 x 480 pixels.</li> <li>PNG files with 8 bits encoding per channel.</li> </ul> <p><strong>Segmentation Maps</strong></p> <ul> <li>Resolution: 848 x 480 pixels.</li> <li>PNG files with a single 8 bit channel.</li> <li>Classes are encoded as follows:</li> <li> <table> <thead> <tr> <th scope="col"><strong>Value</strong></th> <th scope="col"><strong>Class</strong></th> </tr> </thead> <tbody> <tr> <td>0</td> <td>Background</td> </tr> <tr> <td>1</td> <td>Soil</td> </tr> <tr> <td>2</td> <td>Traversable</td> </tr> <tr> <td>3</td> <td>Canopy</td> </tr> <tr> <td>4</td> <td>Fuel</td> </tr> <tr> <td>5</td> <td>Trunks</td> </tr> </tbody> </table> <p>Fuel represents flammable material such as shrubbery and grass.</p> </li> </ul> <p><strong>Depth Maps</strong></p> <ul> <li>Resolution: 848 x 480 pixels.</li> <li>PNG files with a single 16 bit channel</li> <li>The depth value is encoded in the unsigned integer format.</li> <li>Infinite depth is represented by the value 65535.</li> <li>To obtain the depth values in meters, the original values must by divided by 256.</li> <li>The FOV of the virtual depth camera was the same as the FOV of the RGB camera.</li> </ul> <p><strong>LIDAR Point Cloud Projections on the RGB Camera FOV</strong></p> <ul> <li>Resolution: 848 x 480 pixels.</li> <li>PNG files with a single 16 bit channel.</li> <li>The distance values are encoded in the unsigned integer format.</li> <li>To obtain the distance values in meters the original values must by divided by 256.</li> <li>On average, the projection images have a point density of 5.5%. In practice, this means that 5.5% of the pixels in the projection image have distance information.</li> <li>Two LIDAR Point Cloud Projections were made available. One for a LIDAR with a repeating line pattern and other resembling the commercially available Livox Horizon LIDAR scanner.</li> </ul>
Using seabird and whale distribution models to estimate spatial consumption of krill to inform fishery management
<p>Ecosystem dynamics at the north-west Antarctic Peninsula are driven by interactions between physical and biological processes. For example, baleen whale populations are recovering from commercial harvesting against the backdrop of rapid climate change, including reduced sea-ice extent and changing ecosystem composition. Concurrently, the commercial harvesting of Antarctic krill is increasing, with the potential to increase the likelihood for competition with and between krill predators and the fishery. However, understanding the ecology, abundance, and spatial distribution of krill predators is often limited, outdated, or at spatial scales that do not match those desired for effective fisheries management. We update current knowledge of predator dependence on krill by integrating telemetry-based data, at-sea observational surveys, estimates of predator abundance, and physiological data to estimate the spatial distribution of krill consumption during the austral summer by three species of Pygoscelis penguin, 11 species of flying seabirds, one species of pinniped and two species of baleen whale. Our models show that the majority of important areas for krill-predator foraging are close to penguin breeding colonies in nearshore areas where humpback whales also regularly feed, and along the shelf-break, though we caution that not all known krill predators are included in these analyses. We show that krill consumption is highly variable across the region, and often concentrated at fine spatial scales, emphasising the need for management of the local krill fishery at relevant temporal and spatial scales. We also note that krill consumption by recovering populations of krill predators provides further evidence in support of the krill surplus hypothesis, and highlight that despite less than comprehensive data, cetaceans are likely to consume a significant proportion of the krill consumed by natural predators but are not currently considered directly in the management of the krill fishery. If management of the krill fishery is to be precautionary and operate in a way that minimises the risks to krill predator populations, it will be necessary in future analyses, to include up-to-date and precise abundance and consumption estimates for pack-ice seals, finfish, squid, and other baleen whale species not currently considered.</p>
Distribution. Unknown; according to type locality, it occurs in South America, but this information is dubious. in Vespertilionidae
Distribution. Unknown; according to type locality, it occurs in South America, but this information is dubious.
Supporting information for "Amorphous Mn2SiO4: A potential manganese phase in the stagnant slab"
<p>This is the supplementary file for the article "Amorphous Mn2SiO4: A potential manganese phase in the stagnant slab". It includes 5 supplementary texts, 7 figures, and 6 tables.</p> <p>Supplementary texts describe experimental methods, single-crystal X-ray diffraction results, and high-pressure Raman spectra results.</p> <p>Figures show the experimental PT path, crystal structure of tephroite, normalized unit-cell parameters as a function of pressure, pressure independence of polyhedron volume and averaged bond length, pressure dependence of the Raman-active modes for tephroite, amorphous transformation pressure of end-member olivine.</p> <p>Tables describe chemical compositions of tephroite, lattice parameters and unit-cell volumes of tephroite, structure refinement details, best-fit volumetric and linear BM3 parameters, frequency of Raman modes of tephroite.</p>
Suplementary Information Lapuente et al. BIOMEDICINES
<p>Tables S1, S2, S3 and S4</p>
Supplementary Information of Amplicon-based nanopore sequencing of patients with COVID-19 omicron (B.1.1.529) variant from India
<p><strong>We report sequencing of omicron variants from SARS-CoV-2 in 75 patients, using Nanopore long-read sequencing chemistry. We highlight the nature of mutations in spike glycoprotein that are unique and common to other populations.</strong></p> <p> </p>
Distribution. Known from two localities in SW Ecuador (El Oro Province); more recently, it has been recorded in the Pacific coast of Colombia (Choco and Valle del Cauca departments), and NW Peru (Tumbes Department). Known distribution is changing as existing specimens from NW South America (listed as S. Lilium parvidens) are reidentified as this species; new geographic and ecological information is being gathered in the process, and it could be locally common at some specific habitats. in Phyllostomidae
Distribution. Known from two localities in SW Ecuador (El Oro Province); more recently, it has been recorded in the Pacific coast of Colombia (Choco and Valle del Cauca departments), and NW Peru (Tumbes Department). Known distribution is changing as existing specimens from NW South America (listed as S. Lilium parvidens) are reidentified as this species; new geographic and ecological information is being gathered in the process, and it could be locally common at some specific habitats.
Bringing Back the Manchester Argus Coenonympha tullia ssp. davus (Fabricius 1777): Quantifying the habitat resource requirements to inform the successful reintroduction of a specialist peatland butterfly
<p>2021-30 has been designated the UN decade of ecosystem restoration. A landscape scale peatland restoration project is being undertaken on Chat Moss, Greater Manchester, UK, with conservation translocations an important component of this work. The Manchester Argus Coenonympha tullia ssp. davus, a specialist butterfly of lowland raised bogs in the northwest of England, UK is under threat due to severe habitat loss and degradation. A species reintroduction was planned for spring 2020. </p> <p>This study aimed to quantify the resource thresholds for C. tullia, in order to assess potential risks for the project. Thirteen peatland habitat patches with either recent historic or current C. tullia populations were surveyed for biotic and abiotic factors based on previous qualitative research on the species' requirements. </p> <p>Percentage cover of two habitat resources were found to be the strongest predictors in models of C. tullia presence: cross-leaved heath Erica tetralix and hair's-tail cotton-sedge Eriophorum vaginatum. </p> <p>Critical inflection points on logistic regression curves were used to make quantitative estimates of the minimum requirement of each resource for population survival and the near-optimum abundance of each resource. </p> <p>The results of this study improve our understanding of C. tullia's ecology and the restoration of peatlands for its reintroduction. Additionally, the method has wider utility for the quantitative assessment of habitat readiness before attempting species reintroductions.</p>
Supporting information for "Global trade-drivers in emissions of polycyclic aromatic hydrocarbons and associated health impacts"
<p>Emissions: PAH emission inventory for 17 sectors in 189 regions, input-output tables of emissions from the perspectives of primary input, final sale and final consumption, net flow patterns of emissions, the contributions of different drivers to the changes in PAH emissions (Gg) in 13 worldwide regions from 2012 to 2015.</p> <p>Health impacts: Lung cancer rates, Concentrations of BaP, lifetime lung cancer deaths in worldwide regions, input-output tables of deaths from the perspectives of primary input, final sale and final consumption, net flow patterns of deaths, the contributions of different drivers to the changes in the lifetime lung cancer deaths in 13 worldwide regions from 2012 to 2015.</p>
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.