cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.4231/d5th-9d64
title: Data and code for Estimating statewide carrying capacity of bobcat (Lynx rufus) using improved maximum clique algorithms

description: &lt;p&gt;Maximum clique analysis (MCA) can approximate landscape carrying capacity (&lt;em&gt;N&lt;sub&gt;k&lt;/sub&gt;&lt;/em&gt;) for populations of territorial wildlife. However, MCA has not been widely adopted for wildlife applications, mainly due to computational constraints and software wildlife biologists may find difficult to use. Moreover, MCA does not incorporate uncertainty into estimates of &lt;em&gt;N&lt;sub&gt;k&lt;/sub&gt;&lt;/em&gt;. We extended MCA by applying a vertex cover algorithm to compute &lt;em&gt;N&lt;sub&gt;k&lt;/sub&gt;&lt;/em&gt; over a large (92,789 km&lt;sup&gt;2&lt;/sup&gt;), continuous spatial scale for female bobcats (&lt;em&gt;Lynx rufus&lt;/em&gt;) in Indiana, USA. We incorporated uncertainty by calculating confidence intervals for &lt;em&gt;N&lt;sub&gt;k&lt;/sub&gt;&lt;/em&gt; across five thresholds of habitat suitability using 10 replicate suitability maps from bootstrapped datasets. For portions of the landscape too large to be solved with the vertex cover algorithm, we compared predictions from a linear model and a &ldquo;greedy&rdquo; algorithm. Mean estimates of &lt;em&gt;N&lt;sub&gt;k&lt;/sub&gt;&lt;/em&gt; for female bobcats in Indiana across habitat suitability thresholds ranged from 539 (0.75 threshold) to 1200 territories (0.25 threshold). On average, each 12.5 percentile reduction in the suitability threshold increased estimates for &lt;em&gt;N&lt;sub&gt;k&lt;/sub&gt;&lt;/em&gt; by 1.2-fold. Both the predictive and greedy algorithm produced reasonable estimates of maximum cliques for areas that were too large to compute with the vertex cover algorithm. The greedy algorithm produced smaller confidence intervals compared to the predictive approach but underestimated maximum cliques by 1.2%. Our research demonstrates effective application of MCA to species occupying large landscapes while accounting for uncertainty. We provide sample data and scripts developed in R to conduct maximum clique analysis and calculate uncertainty estimates for bobcats in Indiana as an example for applications to other territorial animals and ecosystems.&lt;/p&gt;
description: Example data and code to run maximum clique analysis for female bobcat (Lynx rufus) territories in the state of Indiana, USA
DOI: 10.4231/amgq-0t59
title: A Machine Learning Approach to Design of Aperiodic, Clustered-Dot Halftone Screens via Direct Binary Search

description: &lt;p&gt;This dataset contains two parts: one has halftone patches that were used to predict the quality level and scale of halftone patterns using machine learning methods, and to allow others to perform their own ground truth assessment of halftone image quality. The second part contains full versions of the halftone images so viewers can zoom in to see the details since in the paper we only showed a crop due to the space limitation. &lt;/p&gt;

&lt;p&gt;Aperiodic, clustered-dot, halftone patterns have recently become popular for commercial printing of continuous- tone images with laser, electrophotographic presses, because of their inherent stability and resistance to moire ́ artifacts. Halftone screens designed using the multistage, multipass, clustered direct binary search (MS-MP-CLU-DBS) algorithm can yield halftone patterns with very high visual quality. But the characteristics of these halftone patterns depend on three input parameters for which there are no known formulas to choose their values to yield halftone patterns of a certain quality level and scale. Using machine learning methods, two predictors are developed that take as input these three parameters. One predicts the quality level of the halftone pattern. The other one predicts the scale of the halftone pattern. To provide ground truth information for training these predictors, human subjects viewed a large number of halftone patches generated from MS-MP-CLU-DBS designed screens and assigned each patch to one of four quality levels. For each patch, the location of the peak in the radially averaged power spectrum (RAPS) is calculated as a measure of the scale or effective line frequency of the pattern. Experimental results demonstrate the accuracy of the two predictors and the effectiveness of screen design procedures based on these predictors to generate both monochrome and color high quality halftone images.&lt;/p&gt;
description: This dataset contains two parts: one has halftone patches that were used to predicts the quality level and scale using machine learning methods. The second part contains full versions of halftone images so viewers can zoom in to see the details.
DOI: 10.15468/dl.x9sumh
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Pitar citrinus, Cytherea citrina, Dione ustulata, Meretrix citrina, Pitaria citrina, Pitarina citrina)",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Occurrence evidence)",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1950"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059524-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.4231/3pt4-gd65
title: Surface boundary layer turbulence on an 11% slope.

description: &lt;p&gt;Surface Boundary layer turbulence during mesoscale slope flows on a north-facing 11% slope off the Missouri Flats descending to the Yakima River in Eastern Washington State, USA. Measurements were made in support of a micrometeorological gas exchange research project during the months of March, May, June, August, and September over 2 years (2008-2009).&lt;/p&gt;

&lt;p&gt;Meteorological measurement records (WA_Met_2008-2009.csv) consist of valid &frac12; hourly averages of air temperature, relative humidity, barometric pressure, surface wetness, solar radiation, and wind speed, wind direction, Monin Obukov length, friction velocity, roughness length, dissipation rate, characteristic temperature, as well as turbulence stationarity and homogeneity statistics for the sonic anemometer measurements:  &lt;/p&gt;

&lt;ul&gt;
 &lt;li&gt;Air temperature and humidity measurements made using Vasiala HMP45C hygrothermometer at&lt;/li&gt;
 &lt;li&gt;Barometric pressure measurements made using Setra 278 aneroid barometer&lt;/li&gt;
 &lt;li&gt;Surface wetness measurements made using VAC resistance grid&lt;/li&gt;
 &lt;li&gt;Solar radiation measurements made using LiCOR 190SB silicon pyranometer&lt;/li&gt;
 &lt;li&gt;Wind and turbulence measurements were made using RM Young 91000 3 dimensional sonic anemometers sampling the wind at 16Hz at 2.5 m (sonic 1), 4 m (sonic 2) and 17 m (sonic 3) above ground level.&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;Turbulence measurement records consist of turbulence statistics (variances and covariances of 3 orthogonal wind components and sonic temperature) at 100s intervals.  Turbulence statistics are provided for (1) valid data, (2) invalid data due to spike values (greater than 3 standard deviations of the 100s mean), and (3) invalid data due to more than 10% of the measurements in the 100s period missing due to optical path obstruction. 3 files, one for each sonic anemometer are provided:&lt;/p&gt;

&lt;ul&gt;
 &lt;li&gt;Sonic 1 measurements: WA_Slope_son1_2008-2009.csv&lt;/li&gt;
 &lt;li&gt;Sonic 2 measurements: WA_Slope_son2_2008-2009.csv&lt;/li&gt;
 &lt;li&gt;Sonic 3 measurements: WA_Slope_son3_2008-2009.csv&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;NOTE: Temporal gaps in measurements exist due to instrument and communications failures as well as gaps due to no experimental need for the measurements.  Note that missing measurement periods do not have Date/Time record placeholders in the dataset.&lt;/p&gt;

&lt;p&gt;Additional files included:&lt;/p&gt;

&lt;p&gt;The sonic anemometer Standard Operating Procedure for the measurements is included: &quot;SOP Ultrasonic Anemometer (Revision 1.0) 2-20-08.pdf&#39;&quot;&lt;/p&gt;

&lt;p&gt;The Data Dictionary for the &frac12; hourly meteorological measurements is &#39;SlopeMet_Data Dictionary.pdf&#39;&lt;/p&gt;

&lt;p&gt;The Data Dictionary for the 100s turbulence measurements is &#39;SlopeTurb_Data Dictionary.pdf&#39;&lt;/p&gt;
description: Surface Boundary Layer Turbulence measurements in presence of mesoscale slope flow of 11% slope.
DOI: 10.4231/0bqq-dv64
title: A genetic labeling system to study dendritic spine development in zebrafish

description: &lt;p&gt;Dendritic spines are the principal site of excitatory synapse formation in the human brain. Several neurodevelopmental disorders cause spines to develop abnormally, resulting in altered spine number and morphology. While spine development has been thoroughly characterized in the mammalian brain, spines are not unique to mammals. We have developed a genetic system in zebrafish to enable high resolution &lt;em&gt;in vivo &lt;/em&gt;imaging of spine dynamics during larval development. Although spiny neurons are rare in the larval zebrafish, pyramidal neurons (PyrNs) of the zebrafish tectum form an apical dendrite containing a dense array of dendritic spines. To characterize dendritic spine development, we performed mosaic genetic labeling of individual PyrNs labeled by an &lt;em&gt;id2b:gal4&lt;/em&gt; transgene. Our findings identify a developmental period when PyrN dendrite growth is concurrent with spine formation. Throughout this period, motile, transient filopodia gradually transform into stable spines containing postsynaptic specializations. The utility of this system to study neurodevelopmental disorders was validated by examining spine development in &lt;em&gt;fmr1 &lt;/em&gt;mutant zebrafish, a model of Fragile X syndrome. PyrNs in &lt;em&gt;fmr1 &lt;/em&gt;mutants exhibit pronounced defects in dendrite growth and spine stabilization. Together, these findings establish a genetic labeling system to study dendritic spine development in larval zebrafish. In the future, this system could be combined with high throughput screening approaches to identify genes and drug targets that regulate spine formation.&lt;/p&gt;
description: We have developed a genetic labeling system in zebrafish to enable high resolution in vivo imaging of dendritic spine dynamics during larval development.
DOI: 10.4231/a2ww-ef74
title: Preference of dhurrin-free sorghum by ewes

description: &lt;p&gt;The dhurrin-free sorghum presents a valuable solution for mitigating cyanide poisoning risks in livestock.  This study focused on understanding both its nutritive value and livestock preference. Ewes&#39; preferences were evaluated through a free-choice grazing trial comparing a dhurrin-free hybrid to three commercial hybrids, and a comparison between a set of near isogenic lines varying in dhurrin production. The study also included an assessment of the nutritive value and nitrate levels in the hybrids. The results showed that ewes favored both the dhurrin-free hybrid and dhurrin-free near isogenic lines, while nutritional values were similar across the hybrids. These findings demonstrated ewes preferentially grazed the dhurrin-free sorghum lines and there was no reduction in nutritive value. &lt;/p&gt;
description: The preference of dhurrin-free sorghum was evaluated using ewes in a free choice grazing trial comparing a dhurrin-free hybrid to commercial hyrbids, and a set of near isogenic lines varying in dhurrin production.
DOI: 10.4231/cz4p-d448
title: Code for tropical cyclone wind profile model of Chavas et al (2015, JAS)

description: &lt;p&gt;MATLAB code (+ python version, courtesy of Chia-Ying Lee) to produce the tropical cyclone radial profile of the near-surface rotating wind, defined in Chavas et al (2015, JAS). The model&#39;s representation of wind field variability is described in Chavas and Lin (2016, JAS). The code is fast (runs in &lt;0.1s) and written in a robust manner to handle a very wide range of parameters. The code numerically merges a solution for the inner convecting wind field from Emanuel and Rotunno (2011) with a solution for the outer wind field from Emanuel (2004); each individual solution also require a fast numerical integration as neither is fully analytic.&lt;/p&gt;

&lt;p&gt;Chavas, D. R, N. Lin, and K. A. Emanuel (2015). A complete tropical cyclone radial wind structure model. Part I: Comparison with observed structure. J. Atmos. Sci., 72(9): 3647-3662. doi:10.1175/JAS-D-15-0014.1.&lt;/p&gt;

&lt;p&gt;Chavas, D. R. and Lin, N. (2016). A model for the complete radial structure of the tropical cyclone wind field. Part II: Wind field variability. J. Atmos. Sci., 73(8): 3093-3113. doi:10.1175/JAS-D-15-0185.1.&lt;/p&gt;
description: This code will output a tropical cyclone near-surface wind profile as defined in Chavas et al (2015, JAS); MATLAB or python version
DOI: 10.4231/rtaw-jw77
title: BreakOut Automatic Picking From Image Logs (BOAPFIL)

description: &lt;p&gt;This is a Matlab-based program to automate borehole breakout (BO) interpretation from ultrasonic image logs. Using a peak-detection-based method, BO azimuth and width are automatically determined at each depth slice from a combination of the amplitude and pulse reflection times. The program is composed of a main algorithm file &ldquo;BOAPFIL.m&rdquo; and four subroutines. &lt;/p&gt;

&lt;p&gt;This easily-access program will help researchers quantitatively complement the manual examination of ultrasonic images. Besides researchers who are specialized in oil and gas exploration, the program is also likely to be an interest to researchers in mining and tunneling as well where the stability of subsurface applications needs to be ensured.&lt;/p&gt;

&lt;p&gt;This program is referred to the manuscript entitled &ldquo;Automated Borehole Breakout Interpretation from Ultrasonic Imaging: Application to a Deep Borehole Drilled into the Crystalline Crust&rdquo;, by Wenjing Wang and Douglas R. Schmitt published in 54th US Rock Mechanics/Geomechanics Symposium, OnePetro (2020).&lt;/p&gt;
description: A Matlab-based algorithm that picks breakout azimuth and width from ultrasonic image logs automatically
DOI: 10.15468/dl.n4hzpy
title: Occurrence Download

description: A dataset containing 17150 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Thunbergia alata",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 17150 records from 312 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059522-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.4231/c2wh-y183
title: Spring and autumn phenology data from a northern red oak (Quercus rubra) common garden in West Lafayette, IN from 2013-2020.

description: &lt;p&gt;The provenance test was established in 1962-1964, with 16 trees from each of 32 seed sources. By the time of this study (2013-2020), only 28 seed sources had sufficient remaining trees for accurate assessment of spring and autumn phenology. Phenology observations were made from autumn 2013 to spring 2020. This dataset also includes information about the seed sources, including 19 bioclimatic variables from the Worldclim database (https://www.worldclim.org/data/bioclim.html), and diameter at breast height (DBH) measurements of individual trees in 2013 and 2020.&lt;br /&gt;
 &lt;/p&gt;
description: The files in this repository contain autumn and spring phenology data from a northern red oak (Quercus rubra) common garden at Martell Forest, West Lafayette, IN.
DOI: 10.4231/mmj2-nh88
title: River Obstacle Segmentation En-route By USV Dataset (ROSEBUD)

description: &lt;p dir="auto"&gt;Supervised Semantic Image Segmentation has proven to be a robust and effective method to obtain dense feature and location information from RGB images. Such methods rely on neural network architectures being trained on ground truth data to obtain network weights and biases that accurately provide feature information for RGB input images. Many datasets exist of ground and aerial scenes that can be used for training of neural networks built to aid in navigation of unmanned aerial and ground vehicles. Fewer datasets that aid in the recognition of water for the determination of navigable areas for Unmanned Surface Vehicles (USV) exist and fewer yet exist that can aid in the segmentation of fluvial (river) scenes. Such datasets are needed to train segmentation agents in properly interpreting visual data from complex fluvial scenes to allow for efficient autonomous navigation of  USVs (boats) down rivers and creeks.&lt;/p&gt;

&lt;p dir="auto"&gt;To help solve the data sparsity issue this repository contains images and ground truth masks of the River Obstacle Segmentation En-route By USV Dataset (ROSEBUD) Fluvial Dataset. The dataset contains annotated images for training supervised networks on the task of recognizing and segmenting fluvial scnenes as well as water. In total there are 549 images in the data obtained on Sugar Creek and the Wabash River in the US state of Indiana during July and September of 2021 respectively. Annotated sematic masks are provided as both binary (water and non-water) as well as multi-class (water, sky, foliage, boats/people, debrise/obstacles, river bank/shore, and bridge) problems. The masks are also provided as RGB (3-channel) as well as greyscale (1-channel) in both standard and high definition formats. Mask descriptions, a structure of the files, and class RGB/greyscale values are recorded in the readme.&lt;/p&gt;
description: This dataset contains stills from video taken on Sugar Creek and the Wabash River in the US state of Indiana. Images are hand annotated to provide training and testing data for semantic segmentation networks.
DOI: 10.4231/e3v1-gt04
title: Ecological correlates of extinction risk and persistence of direct-developing stream-dwelling frogs in Mesoamerica

description: &lt;p&gt;Understanding the threats to wildlife across space and time is essential for developing effective conservation strategies. In Mesoamerica (i.e., the region that extends from Central Mexico to the most southern point in Panama) at least 40% of amphibian species declined between the late 1970s and the early 2000s. Most of these declines have been linked with the destruction of suitable habitats for amphibians as well as the introduction and spread of the fungal pathogen &lt;i&gt;Batrachochytrium dendrobatidis&lt;/i&gt;, the causal agent of the disease known as chytridiomycosis. In this study, we quantified geographic and elevational ranges for &lt;a name="_Hlk99385152"&gt;direct-developing, stream-dwelling frog species (DSFS)&lt;/a&gt; in Mesoamerica. Within the range of each DSFS, we estimated the extent of suitable area for the occurrence of &lt;i&gt;Batrachochytrium dendrobatidis&lt;/i&gt; and the types of land use to quantify habitat deterioration. To date, 33% of DSFS remain undetected since 2005 or before. At the regional level (i.e., Mesoamerica), as in previous studies, we found that narrow geographic and elevational ranges increased vulnerability to extinction. Nevertheless, the ranges of 83% of DSFS were composed of 50% or more high-quality habitats between the 1980s and 2005, when most species declined. We also found that on average, 80% of the range of each species currently overlaps with predicted suitable areas for the occurrence of &lt;i&gt;Batrachochytrium dendrobatidis&lt;/i&gt;. At the local and site level (i.e., focusing on two species ranges where extensive monitoring has been conducted even before decline occurred), we found that the present suitable habitat for &lt;i&gt;Batrachochytrium dendrobatidis&lt;/i&gt; corresponded with the reduction in predicted habitat suitability and climatic niche of DSFS. We also found that the location of remnant populations &lt;a name="_Hlk104991990"&gt;can be predicted by environmental factors, which can help identify regions where remnant populations of these declined species and others with similar ecology may occur&lt;/a&gt;. Combined, results from our regional and local analyses support the idea that &lt;i&gt;Batrachochytrium dendrobatidis&lt;/i&gt; was the main driver of DSFS declines and of the current lack of recent observations of fifteen DSFS. We used our results to propose specific actions for all DSFS included in this study. This study highlights the importance of considering multiple threats and spatial scales when assessing the status of declined and threatened species.&lt;/p&gt;
description: List of CSV files used to produce the models
DOI: 10.4231/12hs-8g97
title: Highly Transportation Disadvantaged Areas Indianapolis

description: &lt;p&gt;This file contains areas designated as highly transportation disadvantaged (HTDA) in Indianapolis which were outlined using a combination of three measures: accessibility, mobility, and outcome-based measures. This data can be used in combination with other publicly available data to identify if new projects are benefiting HTDA. This file only contains two polygons as it was the result of our analysis. They are in CSV and shapefile format. &lt;/p&gt;
description: This file contains areas designated as highly transportation disadvantaged in Indianapolis. These two areas were outlined using three different measures and publicly available data. The methodology is replicable and can be used in other cities.