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3,788 results for “indices”
Data from: Constrained optimization of landscape indices in conservation planning to support ecological restoration in New Caledonia
<p>1. Curbing habitat loss, reducing fragmentation, and restoring connectivity are frequent concerns of conservation planning. In this respect, the incorporation of spatial constraints, fragmentation, and connectivity indices into optimization procedures is an important challenge for improving decision support.</p> <p>2. Here we present a novel optimization approach developed to accurately represent a broad range of conservation planning questions with spatial constraints and landscape indices. Relying on constraint programming, a technique from artificial intelligence based on automatic reasoning, this approach provides both constraint satisfaction and optimality guarantees.</p> <p>3. We applied this approach in a real case study to support managers of the ``Côte Oubliée -- `Woen Vùù -- Pwa Pereeù'' provincial park project, in the biodiversity hotspot of New Caledonia. Under budget, accessibility, and equitable allocation constraints, we identified restorable areas optimal for reducing forest fragmentation and improving inter-patch structural connectivity, respectively measured with the effective mesh size and the integral index of connectivity.</p> <p>4. Synthesis and applications. Our work contributes to more effective and policy-relevant conservation planning by providing a spatially-explicit and problem-focused optimization approach. By allowing an exact representation of spatial constraints and landscape indices, it can address new questions and ensure whether the solutions will be socio-economically feasible, through optimality and satisfiability guarantees. Our approach is generic and flexible, thus applicable to a wide range of conservation planning problems such as ecological restoration planning, reserve or corridor design.</p>
Simulated time series and indicators for the Omo-Turkana Basin case study
<p>The archive includes:</p> <ul> <li>daily time series over 2021-2099 time horizon of different physical variables, simulated by the Water Energy Food Integrated Model on the Omo Turkana River Basin for the 6 interesting pathways identified in the Negotiation Simulation Lab meeting;</li> <li>a set of evaluation indicators, aggregated at different spatial and temporal scales, for the 6 interesting pathways.</li> </ul> <p>More details on physical variables and indicators included are available in the DAFNE Deliverable D7.3.</p> <p>Files are provided in the <em>csv </em>format, one per each physical variable or indicator: the first 13 rows contain metadata, while data starts at row 14 and use as many columns as the pathways considered. Metadata are the following:</p> <ul> <li><em>name</em>, time series or indicaror label</li> <li><em>author, </em>reference person or team for the specific time series</li> <li><em>created,</em> timestamp of the file creation</li> <li><em>description, </em>description of file content</li> <li><em>unit, </em>unit of measurement</li> <li><em>origin, </em>description of the simulation</li> <li><em>time_sampling,</em> whether the variable is sampled at a given point in time (instantaneous) or represents a time interval (interval)</li> <li><em>frequency, </em>time step of the time series</li> <li><em>scenario, </em>label of scenario</li> <li><em>marker_id, </em>label of the related model component</li> <li><em>id_type, </em>type of time series</li> <li><em>timestart,timeend,P1,P2,P3,P4,P5,P6 : </em>header row of the data, with time information (in the matlab datenum format) at the beginning and pathways on each column</li> </ul>
Data for: Susceptibility of domain experts to color manipula-tion indicate a need for design principles in data visualization (PLoS one)
<p>This data set accompanies the paper "<strong>Susceptibility of domain experts to color manipulation indicate a need for design principles in data visualization</strong>" by Markus Christen, Peter Brugger<span> </span>and Sara Irina Fabrikant, revision submitted to PLoS One. The paper will be open access, further information will be available there.</p>
Implementation of ATP and Microbial Indicator Testing for Hygiene Monitoring in a Tofu Production Facility Improves Product Quality and Hygienic Conditions of Food Contact Surfaces: A Case Study
<p>This is the code and associated data that was used to generate conclusions for the following manuscript published in Applied and Environmental Microbiology:</p> <p>DOI: 10.1128/AEM.02278-20</p> <p>Implementation of ATP and Microbial Indicator Testing for Hygiene Monitoring in a Tofu Production Facility Improves Product Quality and Hygienic Conditions of Food Contact Surfaces: A Case Study</p> <p>Authors: Jonathan H. Sogin(a), Gabriela Lopez Velasco(b), Burcu Yordem(b), Cari K. Lingle(b), John M. David(b), Mario Cobo(a), Randy W. Worobo(a)</p> <p>(a)Department of Food Science, Cornell University, Ithaca, NY, USA</p> <p>(b)3M Company, St. Paul, MN, USA</p> <p>Address correspondence to Jonathan H. Sogin, jhs397@cornell.edu</p>
Automated classification of avian vocal activity using acoustic indices in regional and heterogeneous datasets
<p>Acoustic indices combined with clustering and classification approaches have been increasingly used to automate identification of the presence of vocalizing taxa or acoustic events of interest. While most studies using this approach standardize data collection and study design parameters at the project or study level, recent trends in ecological research are to investigate patterns at regional or continental scales. Large-scale studies often require collaboration between research groups and integration of data from multiple sources to fulfill objectives, which can lead to variation in recording equipment and data collection protocols.</p> <p>Our objectives were to determine how analytical approaches and variation in data collection and processing that is typical of regional acoustic monitoring programs influences accuracy when identifying vocal activity in migratory breeding birds. We used data from three regional datasets in Northern Alberta, Northern British Columbia, and Southern and Central Yukon, Canada to investigate the effect of analytical framework, sample size, local species richness, and data collection variables on classification accuracy.</p> <p>We found supervised classification approaches to be the most effective, with boosted regression trees identifying vocal activity with a 92.0% accuracy and easily able to accommodate variation in data collection and processing parameters. We also provide recommendations on effectively processing large and heterogeneous datasets including sufficient sample size, accommodating nuisance variables, and selecting suitable model training data.</p> <p>The results presented in this study can help inform decisions in data collection, data processing, and study design and analysis, maximize performance and accuracy during analysis, and efficiently process large, heterogeneous datasets to answer questions at scales previously difficult to investigate.</p>
Buildings indicating the multicultural character of Balat on the Pervitich Maps
<p>Buildings indicating the multicultural character of Balat on the Pervitich Maps</p> <p>includes: (i) geo-referenced tiff images of the base maps (Pervititch Maps), tiff images of the 1946-aerial photos, a shapefile data on monuments and attributes, and a readme.txt file which explains the attributes.</p>
Applying RGB- and Thermal-Based Vegetation Indices from UAVs for High-Throughput Field Phenotyping of Drought Tolerance in Forage Grasses
<p>Basic data from publication <a href="https://doi.org/10.3390/rs13010147">https://doi.org/10.3390/rs13010147</a></p> <p><strong>All_TDRdata.csv</strong> contains the data from 48 TDR sensors (30 cm) installed in the three rainout shelters.</p> <ul> <li>Sensors 1 - 18 were installed vertically to obtain soil moisture content averaged over the 10 - 40 cm profile, on 6 locations per shelter</li> <li>Sensors 19-21 were installed diagonally to obtain soil moisture content averaged over the 20 - 40 cm profile on one location per shelter</li> <li>Sensors 22-24 were installed diagonally to obtain soil moisture content averaged over the 40 - 60 cm profile on one location per shelter</li> <li>Sensors 25-27 were installed horizontally to obtain soil moisture content at 10 cm depth on one location per shelter</li> <li>Sensors 28-30 were installed horizontally to obtain soil moisture content at 20 cm depth on one location per shelter</li> <li>Sensors 31-33 were installed horizontally to obtain soil moisture content at 30 cm depth on one location per shelter</li> <li>Sensors 34-36 were installed horizontally to obtain soil moisture content at 40 cm depth on one location per shelter</li> <li>Sensors 37-39 were installed horizontally to obtain soil moisture content at 50 cm depth on one location per shelter</li> <li>Sensors 40-42 were installed horizontally to obtain soil moisture content at 60 cm depth on one location per shelter</li> <li>Sensors 43-45 were installed horizontally to obtain soil moisture content at 70 cm depth on one location per shelter</li> <li>Sensors 46-48 were installed horizontally to obtain soil moisture content at 80 cm depth on one location per shelter</li> </ul> <p>Climate.txt contains the daily averaged microclimatic data</p> <p>PhenotypingData.csv contains the phenotypic data from the UAV flights and the breeder scores</p> <p> </p>
Data in the analysis of Comparative Study of the Impact of Dummy Variables on Regression Coefficients and Canonical Correlation Indices: an Empirical perspective
<p>This data is used in the analysis related to the article Comparative Study of the Impact of Dummy Variables on Regression Coefficients and Canonical Correlation Indices: an Empirical perspective. The data contain Crude Oil Prices, Exchange Rates, and Dummy variables coded 1 for the era before the Covid-19 outbreak and 0 for the era of Covid-19.</p> <p> </p>
Short-Tandem-Repeat (STR) marker set for Eurasian lynx for article: Genetic analysis indicates spatial-dependent patterns of sex-biased dispersal in Eurasian lynx in Finland
<p>Conservation and management of large carnivores requires knowledge of female and male dispersal. Such information is crucial to evaluate the population's status and thus management actions. This knowledge is challenging to obtain, often incomplete and contradictory at times. The size of the target population and the methods applied can bias the results. Also, population history and biological or environmental influences can affect dispersal on different scales within a study area. We have genotyped Eurasian lynx (180 males and 102 females, collected 2003-2017) continuously distributed in southern Finland (~23,000 km<sup>2</sup>) using 21 short tandem repeats (STR) loci and compared statistical genetic tests to infer local and sex-specific dispersal patterns within and across genetic clusters as well as geographic regions. We tested for sex-specific substructure with individual-based Bayesian assignment tests and spatial autocorrelation analyses. Differences between the sexes in genetic differentiation, relatedness, inbreeding, and diversity were analysed using population-based AMOVA, F-statistics, and assignment indices. Our results showed two different genetic clusters that were spatially structured for females but admixed for males. Similarly, spatial autocorrelation and relatedness was significantly higher in females than males. However, we found weaker sex-specific patterns for the Eurasian lynx when the data were separated in three geographical regions than when divided in the two genetic clusters. Overall, our results suggest male-biased dispersal and female philopatry for the Eurasian lynx in Southern Finland. The female genetic structuring increased from west to east within our study area. In addition, detection of male-biased dispersal was dependent on analytical methods utilized, on whether subtle underlying genetic structuring was considered or not, and the choice of population delineation. Conclusively, we suggest using multiple genetic approaches to study sex-biased dispersal in a continuously distributed species in which population delineation is difficult.</p>
Data used in the paper entitled: Damaged Speleothems and Collapsed Karst Chambers Indicate Paleoseismicity of the NE Bohemian Massif (Niedźwiedzia Cave, Poland), published in TECTONICS
<p>Multiphase speleothem damage and passage collapse in Niedźwiedzia Cave (E: 16°50′36,65″, N: 50°14′04,26″) NE Bohemian Massif, Poland, were studied with an integrative approach to decipher the cause of damage during the last 320 ka. Since the most likely trigger of damage in the cave was an earthquake, we support our interpretation with a probable seismic intensity prediction to define a seismogenic source and to calculate the expected macroseismic intensity and peak ground acceleration (PGA) at the research site. Finally, we evaluate probable seismic effects in the cave with the elastic properties of speleothems to ascertain a threshold value of failure.<br> The relative range of earthquake hazards for a particular site depends significantly on the decrease in the ground motion amplitude (or intensity) with distance from all surrounding potential seismic sources, event size, and type of acting mechanism. The ground motion relation generally depends on the depth of focus, earthquake mechanism, and geological conditions along the path (Schenková et al., 1981). Therefore, to discuss probable seismic effects in Niedźwiedzia caves and their vicinities, we used the attenuation curves presented previously for the research area (Schenková et al., 1981; <a href="https://doi.org/10.1007/BF00878971;">https://doi.org/10.1007/BF00878971;</a> see the coefficient for the 13th zone). Dataset 2020TC006459_ds_to fig.5 contains a calculation of the attenuation curves, i.e., decrees of the intensity (on the MSK scale) and PGA (m/s2) with distance from the epicenter. We used these data to estimate (or to predict) the expected values of intensities ranging with distance from the seismogenic source region. This approach is a steady-state approximation because we assumed that isoseismal spread is regularly distributed around the epicenter and that the local influence of discontinuities is omitted.<br> The failure criteria resulting in speleothem damage were evaluated on a prismatic cantilever beam supported at one end. The parameters describing these criteria are the speleothem natural frequency and the corresponding critical horizontal ground acceleration (m/s2), which depend on elastic properties of the speleothem and the following geometric dimensions: height, H, and diameter, D, measured in situ (we acquired geometric measurements for 50 broken speleothems in Niedźwiedzia Cave). The horizontal ground acceleration is the limit value when at which speleothems breaks. The natural frequency (Hz) indicates that the failure process is more likely to occur if the natural frequency (or resonance frequency) is in accordance with the seismic wave frequency affecting the speleothem. If both frequencies match, the speleothem resonates, enhancing the oscillation effect, which may lead to damage. Dataset 2020TC006459_ds_to fig.6 contains H and D measurements of 50 broke speleothems and calculated natural frequency and critical horizontal ground acceleration for each measured speleothem. The values of both failure parameters depend on elastic properties that can be assessed in laboratory tests in which the following parameters are estimated: P- and S-wave velocities, Vp and Vs, respectively, using an acoustic measurement system, density, ρ, (from the measured mass and volume), Young’s modulus, E, and tensile stress, σt. The AMS tests were carried out at the Institute of Earth Sciences, University of Silesia, Sosnowiec, Poland. The failure stress was estimated based on the uniaxial compressive stress test carried out in the external laboratory of AP GEOTECHNIKA, Katowice, Poland, using a universal testing machine. The strength tests were conducted for two 0.05x0.05 m (height/dimension, h/d = 1) speleothems samples.</p>
List of specimens, collection numbers, localities, and GenBank accessions of sequences. The neotype of Scinax x‑signatus is underlined. New sequences produced for this study are in bold. Abbreviations are as follow. Countries: ARG = Argentina, BOL = Bolivia, BRA = Brazil, GUF = French Guiana, GUY = Guyana, MTQ = Martinique, PER = Peru, SUR = Suriname; Brazilian states: AP = Amapá, BA = Bahia, CE = Ceará, ES = Espírito Santo, MA = Maranhão, MG = Minas Gerais, PE = Pernambuco, RJ = Rio de Janeiro, RS = Rio Grande do Sul, SP = São Paulo. An asterisk (*) indicates approximate coordinates taken from Google Earth. in A neotype for Hyla x-signata Spix, 1824 (Amphibia, Anura, Hylidae)
List of specimens, collection numbers, localities, and GenBank accessions of sequences. The neotype of Scinax x‑signatus is underlined. New sequences produced for this study are in bold. Abbreviations are as follow. Countries: ARG = Argentina, BOL = Bolivia, BRA = Brazil, GUF = French Guiana, GUY = Guyana, MTQ = Martinique, PER = Peru, SUR = Suriname; Brazilian states: AP = Amapá, BA = Bahia, CE = Ceará, ES = Espírito Santo, MA = Maranhão, MG = Minas Gerais, PE = Pernambuco, RJ = Rio de Janeiro, RS = Rio Grande do Sul, SP = São Paulo. An asterisk (*) indicates approximate coordinates taken from Google Earth.
SiEUGreen - Dataset for Baseline study including key indicators and development of a typology
<p>Dataset used for the report (D1.2) presenting the baseline study including key indicators and development of a typology. develops a theoretical and methodological framework that sustains a coherent Urban Agriculture (UA) typology that covers the specificities of the different SiEUGreen showcases. Data contains qualitative and quantitative data in an excel sheet and docx files. The purpose of the dataset is to be used to create a comprehensive conceptual framework about UA including a comparative perspective across different institutional settings and cultures. The data collection was conducted by SiEUGreen partners at Nordregio, International Research Centre for Regional Development and Planning.</p>
Data from: Worldwide exploration of the microbiome harbored by the cnidarian model, Exaiptasia pallida (Agassiz in Verrill, 1864) indicates a lack of bacterial association specificity at a lower taxonomic rank
Examination of host-microbe interactions in early diverging metazoans, such as cnidarians, is of great interest from an evolutionary perspective to understand how host-microbial consortia have evolved. To address this problem, we analyzed whether the bacterial community associated with the cosmopolitan and model sea anemone Exaiptasia pallida shows specific patterns across worldwide populations ranging from the Caribbean Sea, and the Atlantic and Pacific oceans. By comparing sequences of the V1–V3 hypervariable regions of the bacterial 16S rRNA gene, we revealed that anemones host a complex and diverse microbial community. When examined at the phylum level, bacterial diversity and abundance associated with E. pallida are broadly conserved across geographic space with samples, containing largely Proteobacteria and Bacteroides. However, the species-level makeup within these phyla differs drastically across space suggesting a high-level core microbiome with local adaptation of the constituents. Indeed, no bacterial OTU was ubiquitously found in all anemones samples. We also revealed changes in the microbial community structure after rearing anemone specimens in captivity within a period of four months. Furthermore, the variation in bacterial community assemblages across geographical locations did not correlate with the composition of microalgal Symbiodinium symbionts. Our findings contrast with the postulation that cnidarian hosts might actively select and maintain species-specific microbial communities that could have resulted from an intimate co-evolution process. The fact that E. pallida is likely an introduced species in most sampled localities suggests that this microbial turnover is a relatively rapid process. Our findings suggest that environmental settings, not host specificity, seem to dictate bacterial community structure associated with this sea anemone. More than maintaining a specific composition of bacterial species some cnidarians associate with a wide range of bacterial species as long as they provide the same physiological benefits towards the maintenance of a healthy host. The examination of the previously uncharacterized bacterial community associated with the cnidarian sea anemone model E. pallida is the first global-scale study of its kind.
Data from: A ketocarotenoid-based color polymorphism in the Sira poison frog Ranitomeya sirensis indicates novel gene interactions underlying aposematic signal variation
<p>The accumulation of red ketocarotenoids is an important component of coloration in many organisms, but the underlying mechanisms are poorly understood. In some organisms, ketocarotenoids are sequestered from the diet and can accumulate when enzymes responsible for carotenoid breakdown are disrupted. In other organisms, ketocarotenoids are formed endogenously from dietary precursors via oxidation reactions carried out by carotenoid ketolase enzymes. Here, we study the genetic basis of carotenoid coloration in an amphibian. We demonstrate that a red/yellow polymorphism in the dendrobatid poison frog <em>Ranitomeya sirensis</em> is due to the presence/absence of ketocarotenoids. Using whole-transcriptome sequencing of skins and livers, we found that a transcript encoding a cytochrome P450 enzyme (CYP3A80) is expressed 3.4-fold higher in livers of red frogs versus yellow. As CYP3A enzymes are known carotenoid ketolases in other organisms, our results point to CYP3A80 as a strong candidate for a carotenoid ketolase in amphibians. Furthermore, in red frogs, the transcript encoding the carotenoid cleavage enzyme BCO2 is expressed at a low level or as a splice variant lacking key catalytic amino acids. This suggests that BCO2 function may be disrupted in red frogs, providing a mechanism whereby the accumulation of ketocarotenoids and their dietary precursors may be enhanced.</p>
Initial Set of Open Digital Science indicators
<p>Initial set of indicators developed in the Open Digital Science Study. Since the indicators proposed differed considerably in terms of their scope, granularity, specificity, and measurability, it was stated in the introductory part of the assessment that they should be considered a starting point for further development rather than a mature set of indicators</p> <p> </p> <p> </p>
Microblogging violent attacks on medical staff: A case study of the Longmen County People’s Hospital incident, an indication of a health care crisis in China
<p>A violent attack on medical staff in Guangdong Province, in which a female doctor at Longmen County People’s Hospital (LCPH) was severely injured by a knife-wielding patient, has drawn significant public attention to the phenomenon of hospital violence and initiated discussions on how to resolve violence in hospitals. Social networking sites, such as Sina Weibo, a Chinese version of Twitter, have played a role in this public debate. The incident at LCPH provides an opportunity to examine how Weibo has been used in the debate about violence against medical staff in China. Using the Sina Weibo’s built-in search tool, we established a dataset of 661 Chinese-language micro-blogs containing the search terms: Longmen (“龙门”), doctor (“医生”), and slash (“砍”) that were posted between July 15, 2015, the date of the violent incident at LCPH, and August 15, 2015. We performed a content analysis of the micro-blogs to examine: users’ demographics, attitudes toward the injured doctor and the attacker, possible reasons for the hospital violence, and proposed measures for preventing doctors from violent incidents. </p>
A voltage-dependent fluorescent indicator for optogenetic applications, archaerhodopsin-3: Structure and optical properties from in silico modeling
<p>seq.fasta and P96787_1UAZ.fasta are the input files for I-TASSER suite.</p> <p>The command of running I-TASSER suite:<br> path-to-I-TASSER-dir/I-TASSERmod/runI-TASSER.pl -pkgdir path-to-I-TASSER-dir -libdir path-to-I-TASSER-lib-dir -seqname P96787 -datadir path-to-workdir -outdir path-to-outdir -java_home /usr/ -restraint2 P96787_1UAZ.fasta</p> <p>For detailed data please refer to I-TASSER documentation.</p> <p>The P96787_1UAZ_IT.zip is an archieve with I-TASSER output for the best achaerhodopsin-3 prediciton.</p> <p>SCRIPTS_GENERAL.zip contains all the scripts for the structure postprocessing: addition of hydrogen atoms,<br> chromophore insertion and equilibration, internal waters addition.</p> <p>P96787_wi.pdb is a final prepared structure.</p> <p>Input files for spectra calculations are rhodopsin_gaussian.inp and rhodopsin_orca.inp.</p> <p> </p>
Supplementary information for: "A voltage-dependent fluorescent indicator for optogenetic applications, archaerhodopsin-3: Structure and optical properties from in silico modeling".
<p>This is supplementary data for F1000Research article: A voltage-dependent fluorescent indicator for optogenetic applications, archaerhodopsin-3: Structure and optical properties from in silico modeling.</p> <p>Here are files for modeling archaerhodopsin-3 with I-TASSER, Medeller and RosettaCM algorithms, structure postprocessing and spectra calculations.</p>
Figure 2. - Phylogenetic relationships among Dicronocephalus species reconstructed with Bayesian inference using COI sequences. Numbers above branches indicate ML bootstrap values and Bayesian posterior probabilities. Numbers below branches are bootstrap, symmetric resampling, and jacknife support from parsimony searches, respectively. Scale bar represents 10% nucleotide mutation rate.
Figure 2. - Phylogenetic relationships among Dicronocephalus species reconstructed with Bayesian inference using COI sequences. Numbers above branches indicate ML bootstrap values and Bayesian posterior probabilities. Numbers below branches are bootstrap, symmetric resampling, and jacknife support from parsimony searches, respectively. Scale bar represents 10% nucleotide mutation rate.
Figure 1. - Nesting habitat of Xylocopanasalis; A nesting habitat of Xylocopanasalis on a makeshift roof of a restaurant in Suan Pheung district, Ratch Buri province, Thailand. The red arrows indicate locations where the bamboo culms were arranged ca. 2.50 m above the ground (1a and 1b). At the nest entrance, the female of Xylocopanasalis was dehydrating the nectar previously foraged (1c).
Figure 1. - Nesting habitat of Xylocopanasalis; A nesting habitat of Xylocopanasalis on a makeshift roof of a restaurant in Suan Pheung district, Ratch Buri province, Thailand. The red arrows indicate locations where the bamboo culms were arranged ca. 2.50 m above the ground (1a and 1b). At the nest entrance, the female of Xylocopanasalis was dehydrating the nectar previously foraged (1c).
ScienceDex guides
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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.