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3,696 results for “Reference”
Data from: De novo reference genome of a Geomyid rodent, Botta’s pocket gopher (Thomomys bottae)
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Estimated wetland vegetation cover comparing reference and muskrat disturbed areas
Biota that act as ecosystem engineers are increasingly recognized as effective components of habitat restoration as they can continuously alter and shape their environments without human intervention. Muskrats are considered ecosystem engineers and are relatively common in North American wetlands. While muskrat impacts to large areas have been documented, few studies have quantified the impact of muskrats on ecosystem biodiversity. We conducted a field study in wetlands along the Upper St. Lawrence River (New York, USA) to investigate the effects of muskrat herbivory and structure building on plant biodiversity in cattail-invaded wetlands. The data collected are separated into two main groups, i.e. “reference” vegetation surveys and “muskrat” vegetation surveys. “Reference” surveys were conducted for the partial grant fulfillment funded by the New York Department of Environmental Conservation [contract AM10165] and the National Fish and Wildlife Foundation special project administered by the United States Fish and Wildlife Service, Partners for Fish and Wildlife Program, New York Field Office, Cortland, NY [grant number #2005-0129-055/58859]. “Muskrat” surveys were conducted for the Masters project by Z.X. Kua. The five datasets include 1) Reference quadrat plant taxa estimated cover (n = 1912), 2) Reference quadrat cattail measurements (n = 737), 3) Muskrat-disturbed quadrat plant taxa estimated cover (n = 1886), 4) Muskrat-disturbed quadrat cattail measurements (n = 582), and 5) Wetland plant taxa lookup table for vegetation survey (n = 135).
Virgin Islands National Park: Coral Reef: Reference: Geography
This is a reference dataset containing the site locations, year established, and types of surveys.
Soil extracellular enzyme activities in plots dominated by trees that associate with arbuscular mycorrhizal or ectomycorrhizal fungi in the N fertilized and reference watershed at the Bear Brook Watershed in Maine, USA.
Our objective was to detect possible differences in N fertilization responses of soil extracellular enzymes in plots dominated by trees that associate with arbuscular mycorrhizal fungi (AM) or ectomycorrhizal fungi (ECM). To do this, we established a plot network of 6 AM and 6 ECM dominated (>65% diameter at breast height) 10 x 10 m plots in the lower elevation hardwood zone of both the reference and N fertilized watersheds (N=24 plots) at Bear Brook Watershed, in Maine USA. We assayed the potential activity of hydrolytic enzymes that release N (N-acetylglucosaminidase; NAG), phosphorus (acid phosphatase; AP), and simple carbon (ß-glucosidase; BG). In addition, we measured microbial allocation to complex C degrading oxidative enzymes phenol oxidase and peroxidase. The activities of these enzymes were measured separately in bulk mineral, rhizosphere, and organic horizon soils during the growing season in 2016.
Fine root morphology in plots dominated by trees that associate with arbuscular mycorrhizal or ectomycorrhizal fungi in the N fertilized and reference watershed at the Bear Brook Watershed in Maine, USA during the final year of N fertilization (2016) and during the year after N fertilization ceased (2017).
Our objective was to detect possible differences in N fertilization responses of fine root morphology in plots dominated by trees that associate with arbuscular mycorrhizal fungi (AM) or ectomycorrhizal fungi (ECM). To do this, we sampled fine roots in a plot network of 6 AM and 6 ECM dominated (>65% diameter at breast height) 10 x 10 m plots in the lower elevation hardwood zone of both the reference and N fertilized watersheds (N=24 plots) at Bear Brook Watershed, in Maine USA during final year of N fertilization at Bear Brook in 2016 and during the year after N fertilization ceased in 2017.
White oak and red maple foliar chemistry of urban and reference forests of the eastern US
Foliar chemistry values were obtained from two important native tree species (white oak (Quercus alba L.) and red maple (Acer rubrum L.)) across urban and reference forest sites of three major cities in the eastern United States during summer 2015 (New York, NY (NYC); Philadelphia, PA; and Baltimore, MD). Trees were selected from secondary growth oak-hickory forests found in New York, NY; Philadelphia, PA; and Baltimore, MD, as well as at reference forest sites outside each metropolitan area. In all three metropolitan areas, urban forest patches and references forest sites were selected based on the presence of red maple and white oak canopy dominant trees in patches of at least 1.5 hectares with slopes less than 25%, and well-drained soils of similar soil series within each metropolitan area. Within each city, several forest patches were selected to capture the variation in forest patch site conditions across an individual city. All reference sites were located in protected areas outside of the city and within intermix wildland-urban interface landscapes, in order to target similar contexts of surrounding land use and population density (Martinuzzi et al. 2015). Several reference sites were selected for each city, located within the same protected area considered representative of rural forests of the region. White oaks were at least 38.1 cm diameter at breast height (DBH), red maples were at least 25.4 cm DBH, and all trees were dominant or co-dominant canopy trees. The trees had no major trunk cavities and had crown vigor scores of 1 or 2 (less than 25% overall canopy damage; Pontius & Hallett 2014). From early July to early August 2015, sun leaves were collected from the periphery of the crown of each tree with either a shotgun or slingshot for subsequent analysis to determine differences in foliar chemistry across cities and urban vs. reference forest site types. The data were used to invstigate whether differences in native tree physiology occur between urban
Spatial reference data for the Central Arizona-Phoenix area: change in elevation
This dataset has been created to support the research activities of Arizona State University researchers. The slope grid identifies the rate of maximum change in elevation value from each grid cell and is calculated in degrees. The data are derived from the 30 meter Digital Elevation Model created for the Central Arizona-Phoenix Long Term Ecological Research program (dem30_utm).
Coweeta Hydrologic Laboratory and Basin Reference GIS data
Coweeta Basin reference GIS data that were either commissioned or produced by the USDA Forest Service Coweeta Hydrologic Laboratory or the Coweeta LTER starting in the late 1980s.
Fertilized and reference tidal creek sediment chlorophyll a and pheophytin concentrations following whole core incubations, Ipswich and Rowley, MA
Salt marsh ecosystems serve as critical nutrient filters by removing reactive nitrogen (N) through denitrification. We examined the influence of long-term fertilization on N transformation and removal in a salt marsh tidal creek ecosystem fringing the Plum Island Sound estuary in northern Massachusetts, USA. Sediment oxygen demand was within the range of other marsh systems (1271.9 to 7855.0 µmol m-2 h-1) and was not significantly different between the fertilized and reference creek. Net N2 fluxes ranged from net N fixation of -402.7 µmol N2-N m-2 h-1 in the reference creek to net denitrification of 524.9 µmol N2-N m-2 h-1 in the fertilized creek. Net N2 flux and nitrate uptake were significantly higher in the fertilized creek, and in both creeks, net denitrification appeared to be nitrate limited. We calculated rates of dissimilatory nitrate reduction to ammonium (DNRA) and found it to be significantly higher in the fertilized creek, representing 45 and 11% of the total nitrate uptake in the fertilized and reference creeks, respectively. Additionally, there was a strong relationship between ammonium and nitrite fluxes in both creeks. These results suggest that DNRA may outcompete denitrification at high nitrate concentrations. Increased anthropogenic nutrient loading may therefore have a detrimental effect on the N removal capacity of salt marsh ecosystems. (From: Vieillard and Fulweiler (2012) Marine Ecology Progress Series 147: 11-22. DOI:10.3354/meps10013).
Sediment oxygen, di-nitrogen (gas), nitrate, nitrite, ammonium, phosphate, and silicate flux from sealed, whole sediment core incubations from a fertilized (Sweeney) and reference (West) creek in the Plum Island Estuary, Massachusetts.
Salt marsh ecosystems serve as critical nutrient filters by removing reactive nitrogen (N) through denitrification. We examined the influence of long-term fertilization on N transformation and removal in a salt marsh tidal creek ecosystem fringing the Plum Island Sound estuary in northern Massachusetts, USA. Sediment oxygen demand was within the range of other marsh systems (1271.9 to 7855.0 µmol m-2 h-1) and was not significantly different between the fertilized and reference creek. Net N2 fluxes ranged from net N fixation of -402.7 µmol N2-N m-2 h-1 in the reference creek to net denitrification of 524.9 µmol N2-N m-2 h-1 in the fertilized creek. Net N2 flux and nitrate uptake were significantly higher in the fertilized creek, and in both creeks, net denitrification appeared to be nitrate limited. We calculated rates of dissimilatory nitrate reduction to ammonium (DNRA) and found it to be significantly higher in the fertilized creek, representing 45 and 11% of the total nitrate uptake in the fertilized and reference creeks, respectively. Additionally, there was a strong relationship between ammonium and nitrite fluxes in both creeks. These results suggest that DNRA may outcompete denitrification at high nitrate concentrations. Increased anthropogenic nutrient loading may therefore have a detrimental effect on the N removal capacity of salt marsh ecosystems. (From: Vieillard and Fulweiler (2012) Marine Ecology Progress Series 147: 11-22. DOI:10.3354/meps10013).
cimr references
<p>Reference panels used in cimr processing. The original files were downloaded and parsed from the dir links in the format of</p> <p>'ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_' + [snp build and genome reference build ids] + '/database/organism_data/'</p> <p> </p>
Paper Repository and References for "Early software defect prediction: A systematic map and review"
<p>Context: Software defect prediction is a trending research topic, and a wide variety of the published papers focus on coding phase or after. A limited number of papers, however, includes the prior (early) phases of the software development lifecycle (SDLC).<br> Objective: The goal of this study is to obtain a general view of the characteristics and usefulness of Early Software Defect Prediction (ESDP) models reported in scientific literature. <br> Method: A systematic mapping and systematic literature review study has been conducted. We searched for the studies reported between 2000 and 2016. We reviewed 52 studies and analyzed the trend and demographics, maturity of state-of-research, in-depth characteristics, success and benefits of ESDP models. <br> Results: We found that categorical models that rely on requirement and design phase metrics, and few continuous models including metrics from requirements phase are very successful. We also found that most studies reported qualitative benefits of using ESDP models.<br> Conclusion: We have highlighted the most preferred prediction methods, metrics, datasets and performance evaluation methods, as well as the addressed SDLC phases. We expect the results will be useful for software teams by guiding them to use early predictors effectively in practice, and for researchers in directing their future efforts.</p>
Software Variability Tools SMS and Survey: List of References and Tools
<p>Software Variability Tools SMS and Survey: List of References and Tools</p>
Updated functional annotation of the Mycobacterium bovis AF2122/97 reference genome - datasets
<p>This is an archive of the repository held under https://github.com/dmnfarrell/gordon-group/tree/master/mbovis_annotation</p> <p>It contains a notebook and required input files for updating the MTB/Mbovis AF2122/97 genomes with new protein product annotations from literature.</p> <p>D Farrell UCD February 2020</p> <p>Updates to M.bovis genome (Aug 2019):<br> added 611 product annotations<br> added 689 gene names<br> added 5 manually edited entries from pdb hits<br> removed locus_tags for repeat_region features<br> added prefix to tRNA and mobile_element features for consistency</p> <p><br> References<br> Updated functional annotation of the Mycobacterium bovis AF2122/97 reference genome (https://www.biorxiv.org/content/10.1101/757823v1)</p>
Dataset for publication "Setup and Characterisation of Reference Current-to-Voltage Transformers for Wideband Current Transformers Calibration up to 2 kA"
<p>This is dataset related to paper published in AMPS 2019:</p> <p>Y. Chen, E. Mohns, H. Badura, P. Räther and M. Luiso: Setup and Characterisation of Reference Current-to-Voltage Transformers for Wideband Current Transformers Calibration up to 2 kA, <a href="https://doi.org/10.7795/EMPIR.17NRM01.CA.20190411">https://doi.org/10.7795/EMPIR.17NRM01.CA.20190411</a></p> <p>Excel file contains the data for Figures 7, 8, 9 and 10.</p>
Chaetoceros decipiens (UNC1416) reference transcriptome
<p>Reference transcriptome and associated annotations for <em>Chaetoceros decipiens </em>(UNC1416). </p> <p>A culture was grown into late exponential phase for filtration. Total RNA was extracted using the RNAqueous-4PCR Total RNA Isolation Kit (Ambion, Foster City, CA, USA) according to the manufacturer’s protocol with an initial bead beating step to disrupt cells. RNA libraries were created with either the Illumina TruSeq Stranded mRNA Library Preparation Kit. The library was sequenced on an Illumina MiSeq (300 bp, paired-end reads) and an Illumina HiSeq 2500 with one lane in high output mode (100 bp, paired-end reads) and another lane in rapid run mode (150 bp, paired-end reads).</p> <p>Raw reads were trimmed for quality with Trimmomatic v0.36 then assembled <em>de novo </em>with Trinity v2.5.1 with the default parameters for paired-reads and a minimum contig length of 90 bp. Contigs were clustered based on 99% similarity using CD-HIT-EST v4.7 and then protein sequences were predicted with GeneMark S-T. Protein sequences were annotated by best-homology (lowest E-value) with the KEGG (Release 86.0), UniProt (Release 2018_03), and PhyloDB (v1.076) databases via BLASTP v2.7.1 (E-value ≤ 10<sup>-5</sup>) and with Pfam 31.0 via HMMER v3.1b2 (Dataset S2). KEGG Ortholog (KO) annotations were assigned from the top hit with a KO annotation from the top 10 hits (<a href="https://github.com/ctberthiaume/keggannot">https://github.com/ctberthiaume/keggannot</a>).</p> <p>Provided here are predicted proteins as nucleotides and peptides. Raw reads are deposited in SRA (SRP234548).</p>
NEMO Reference configurations inputs
<p>This page refers to input archives for running the configurations included in NEMO 4.2 (beta version) and earlier. Subsequent releases have been served from an alternative site: <a href="https://gws-access.jasmin.ac.uk/public/nemo/sette_inputs">SETTE input files delivered through JASMIN</a>. Users are advised to download from that site for versions 4.2.0 onwards. The <a href="https://sites.nemo-ocean.io/user-guide/sette.html#obtaining-configuration-input-files">NEMO User Guide</a> contains a detailed section on running SETTE, including further information on obtaining the input files. </p> <p>This site is retained to provide a DOI for citing these datasets but remember to state clearly the exact version used.</p> <p>Input archives for running the configurations included in <strong>NEMO 4.2 (beta version) -not suitable for releases 4.2.0 and later</strong>:</p> <ul> <li>AGRIF_DEMO: <em>AGRIF_DEMO_v4.0.tar</em> and <em>ORCA2_ICE_v4.0.tar</em></li> <li>AMM12: <em>AMM12_v4.0.tar</em></li> <li>C1D_PAPA: <em>INPUTS_C1D_PAPA_v4.0.tar</em></li> <li>ISOMIP+: ISOMIP+_v4.0.tar, input for the new ISOMIP+ test case on ice shelf module and the coupling with an ice sheet model</li> <li>ORCA2_ICE_PISCES: <em>ORCA2_ICE_v4.2.tar</em>, <em>INPUTS_PISCES_v4.2.tar and ORCA2_ABL_4.2.tar</em></li> <li>ORCA2_OFF_PISCES: <em>ORCA2_OFF_v4.0.tar</em> and <em>INPUTS_PISCES_v4.0.tar</em></li> <li>ORCA2_OFF_TRC: <em>ORCA2_OFF_v4.0.tar</em></li> <li>ORCA2_SAS_ICE: <em>ORCA2_ICE_v4.0.tar</em> and <em>INPUTS_SAS_v4.0.tar</em></li> <li>SPITZ12: <em>SPITZ12_v4.0.tar</em></li> <li>WED025: WED025_v4.2.tar, input for the new WED025 reference configuration, now replacing SPITZ12 to demonstrate ice shelf module, SI3, bdy with tide and sea ice capabilities<br> </li> </ul>
Kenyan reference values for chemistry and immunoassay tests
<p>This data set contains reference values for several chemistry and immunoassay tests. The samples tha were analysed were from healthy adults aged 18-65 years recruited from selected counties in Kenya as part of a reference interval study carried out by the International Federation of Clinical Chemistry committee on reference intervals and decision limits. </p>
Namibian reference ochres description and geochemical data
<p>The datasets present the macroscopic description and ICP-OES and ICP-MS geochemical data of Namibian reference ochres. </p>
Maps of reference evapotranspiration for the irrigation project in Brazil
<p>The maximum daily evapotranspiration data set for a project (ETproject) for Brazil. It has a spatial resolution of <strong>30 seconds (~ 1 km²)</strong>. The data set grid is in <strong>GeoTIFF format</strong> and corresponds perfectly to WorldClim. It uses the <strong>geographic coordinate</strong> reference system, with <strong>WGS84 projection (EPSG: 4326)</strong>.</p> <p>The objective study is to estimate and provide evapotranspiration values of monthly reference and the maximum of twelve months, for dimensioning irrigation systems throughout the Brazilian territory. With the meteorological data of two hundred and fifty-nine conventional INMET stations, the daily reference evapotranspiration (ETo) for 15 years was calculated. For each weather station, the data was grouped by month and the ETo for the irrigation project (ETproject) was determined to meet the eighty percent probability of occurrence, following the recommendations of FAO24. In parallel, monthly images of 15 years of ETo were acquired for Brazil, and the climatic variables of WorldClim. Using the ET values of the stations design, it was modeled for the rest of Brazil, using machine learning algorithms and the covariates. After modeling, the following performances were achieved: mean square error of 0.306 mm / d, mean bias error of -0.004 mm / d, mean absolute error of 0.227 mm / d, determination coefficient of 0.938 and efficiency of Nash-Sutcliffe 0.937. ETo values for irrigation projects were similar to several others reported in the literature when compared at a given point. With this research it was possible to determine the monthly and annual ETo for irrigation projects throughout the Brazilian territory.</p> <p>The article has been submitted for publication.</p>
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.