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621 results for “methodologies”
Methodological approaches to assessing the genetic predisposition of Osteochondrosis of the tarsocrural joint in the Pura Raza Española horses
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Data on methodology_paper_CapSa_project
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Impact of Methodological Choices on the Analysis of Code Metrics and Maintenance
<p>The repo-data folder contains 53 <code>.json</code> files, each corresponding to one of the 53 Java open-source projects. Each file contains various metrics for methods in the project.</p> <p> </p> <pre><code> { "hawtio-3976.json": { "Age": 794, "sloc": [11,11,11], "slocAsItIs": [11,14,14], "slocNoCommentPretty": [11,11,11], "diffSizes": [0,7,0 ], "bodychanges": [0,1,0], "newAdditions": [0,5,0], "isGetter": [false,false,false], "isSetter": [false,false,false], "changeDates": [0,3,794], "isEssentialChange": [false,true,false], "isBuggy": [false,false,false], "changeTypes": ["Yintroduced","Ybodychange","Yfilerename"], "filename": "hawtio-3976.json", "authors": ["X","Y","Z"], "editDistance": [0, 68, 0], "repo": "hawtio" }, "method_id": {...}, "method_id": {...} } </code></pre> <p> </p> <p>The above method with id <code>hawtio-3976.json</code> has total 3 revisions which is why the array of values for a particular metric (e.g., sloc: <code>[11,11,11]</code>) are of length 3. <code>Index 0</code> of the array represents the introduction value of a particular metric for the above method.</p> <div> <h3>Description of the metrics</h3> </div> <ul> <li><code>Age</code>: Age of the method in days</li> <li><code>sloc</code>: Source line of code of a method without comment and blank lines</li> <li><code>slocAsItIs</code>: Source line of code of a method with comment and blank lines</li> <li><code>slocNoCommentPretty</code>: Source line of code pretty printed without comment and blank lines</li> <li><code>diffSizes</code>: Total number of lines added + removed in git <code>diff</code></li> <li><code>bodychanges</code>: Contains value 0 or 1; where 1 implies occurrence of body change</li> <li><code>newAdditions</code>: Total number of lines added in git <code>diff</code></li> <li><code>isGetter</code>: Contains <code>true</code> or <code>false</code>; where <code>true</code> indicates it is a <code>get</code> method</li> <li><code>isSetter</code>: Contains <code>true</code> or <code>false</code>; where <code>true</code> indicates it is a <code>set</code> method</li> <li><code>changeDates</code>: Contains the date difference in days from when the method was introduced. Index <code>0</code> is always 0 which indicates the introduction date</li> <li><code>isEssentialChange</code>: Contains <code>true</code> or <code>false</code>; where <code>true</code> indicates it is an essential change. Essential change includes: <code>Ybodychange</code>, <code>Ymodifierchange</code>, <code>Yexceptionschange</code>, <code>Yrename</code>, <code>Yparameterchange</code>, <code>Yreturntypechange</code> and <code>Yparametermetachange</code> detected by <code>CodeShovel</code></li> <li><code>isBuggy</code>: Contains <code>true</code> or <code>false</code>; where <code>true</code> indicates the method bug was fixed at a particular revision</li> <li><code>changeTypes</code>: All transformations applied to the method at each revision. The full list of transformation that is detected by <code>CodeShovel</code> are: <code>Ybodychange</code>, <code>Ymodifierchange</code>, <code>Yexceptionschange</code>, <code>Yrename</code>, <code>Yparameterchange</code>, <code>Yreturntypechange</code>, <code>Yparametermetachange</code>, <code>Yannotationchange</code>, <code>Ydocchange</code>, <code>Yformatchange</code>, <code>Yfilerename</code> and <code>Ymovefromfile</code></li> <li><code>filename</code>: It is the method <code>id<br></code> <p><strong>bugData</strong> folder contains 53 .json files with bug information, each belonging to one of the 53 Java open-source projects. The sample JSON schema of a file is given below:</p> <pre><code>{ "hawtio-3976.json":{ "exactBug0Match": [false, false, false], "exactBug1Match": [false, false, false], "exactBug2Match": [false, false, false], "exactBug3Match": [false, false, false], "regExBug0": [false, false, false], "regExBug1": [false, false, false], "regExBug2": [false, false, false], "regExBug3": [false, false, false] }, "method_id": {...}, "method_id": {...}, }</code></pre> <p>The above method can be mapped to its metrics dataset using the method_id. For e.g., the above method with id hawtio-3976.json in bugData/hawtio.jsonthat has 3 revision can be found in the metric dataset using the same id hawtio-3976.json in the file repo-data/hawtio.json.<br>Description of bug dataset</p> <p>Each key in the above example contains value true or false indicating if a method was buggy or not at each revision. The "hawtio-3976.json method has 3 revisions (including method's introduction) which is why the array length is 3. The keys in the above json output represent bug-fix classification based on buggy keywords adopted from prior work.</p> <p>We identified bug-fix commit using two approaches:</p> <p> Exact case insensitive match of buggy keywords from the commit message (keys prefix wih exact represent this)<br> Partial case insensitive substring match (using regular expression) excluding words that ends with fix or bug. (keys prefix with regEx represent this)</p> <p> Bug0: This is the approach that we have used for classifying bug-fix commit. Buggy keyword list: <strong>["error", "bug", "fixes", "fixing", "fix", "fixed", "mistake", "incorrect", "fault", "defect", "flaw"]</strong><br> Bug1: Same keyword list as exactBug0Match with the addition of keyword issues<br> Bug2: Buggy keyword list from prior work: <strong>["bug", "fix", "error", "issue", "crash", "problem", "fail", "defect", "patch"]</strong><br> Bug3: Buggy keyword list from prior work: <strong>["error", "bug", "fix", "issue", "mistake", "incorrect", "fault", "defect", "flaw", "type"]</strong></p> </li> </ul>
Supplementary material 5 from: Schmidt M, Lischeid G, Nendel C (2018) Data on and methodology for measurements of microclimate and matter dynamics in transition zones between forest and adjacent arable land. One Ecosystem 3: e24295. https://doi.org/10.3897/oneeco.3.e24295
Explanation of header and data: Dist is the distance to the zero line (edge) into the forest in m; Month is the period of time before litterfall was sampled (see "Litterfall" for details); DryMass is the weight of the dried litter in g, Site is either west-facing or east-facing (see "Measurement site" for details).
Supplementary material 3 from: Schmidt M, Lischeid G, Nendel C (2018) Data on and methodology for measurements of microclimate and matter dynamics in transition zones between forest and adjacent arable land. One Ecosystem 3: e24295. https://doi.org/10.3897/oneeco.3.e24295
Explanation of header and data: Dist is the distance from the zero line (edge) into the arable land in m, 0 is the zero line; Crop refers to the species (see "Biomass of crops" for more details); DryMass is given in g per m2.
Supplementary material 4 from: Schmidt M, Lischeid G, Nendel C (2018) Data on and methodology for measurements of microclimate and matter dynamics in transition zones between forest and adjacent arable land. One Ecosystem 3: e24295. https://doi.org/10.3897/oneeco.3.e24295
Explanation of header and data: Site is either west-facing or east-facing site (see "Measurement site"); Dist is the distance from the zero line (edge) to the forest interior in m, 0 is the zero line; Tree number refers to a unique tree (number) in the plot (letter); Perimeter is measured at 1.30 m from the ground and is given in cm; BHD is derived from the perimeter and given in cm; Height is the measured height of the trees in m.
Supplementary material 6 from: Schmidt M, Lischeid G, Nendel C (2018) Data on and methodology for measurements of microclimate and matter dynamics in transition zones between forest and adjacent arable land. One Ecosystem 3: e24295. https://doi.org/10.3897/oneeco.3.e24295
Explanation of header and data: Site is either west-facing or east-facing (see "Measurement site"); DistToEdge is the distance to the zero line (edge) in m, negative values are in the forest, positive values are in the arable land, zero is the edge; Repetition is the number of repetitions in the lab; Depth is measured in cm and is the depth of soil sampling ±3 cm; Ctot is the percentage (%) of total soil carbon content in the tested soil sample; Ntot is the percentage (%) of total soil nitrogen content in the tested soil sample and pH is the numeric scale to specify the acidity or basicity of the soil sample in solution.
Supplementary material 2 from: Schmidt M, Lischeid G, Nendel C (2018) Data on and methodology for measurements of microclimate and matter dynamics in transition zones between forest and adjacent arable land. One Ecosystem 3: e24295. https://doi.org/10.3897/oneeco.3.e24295
Measured values are indicated in the header by the variable (e.g. "SoilMoist") followed by the distance to the zero line (e.g. 30, indicated by XX in the description below). Date.Time is given as YYYY-MM-DD HH:MM:SS; SoilMoistXX is the soil moisture given in cm3 cm-3; SoilTempXX is the soil temperature given in °C; RelHumXX is the relative humidity given as dimensionless number; AirTempXX is the air temperature in °C; AirPressXX is the barometric air pressure given in kPa; SolarRadXX is the solar radiation given in W m-2; WindAvgXX is the average wind speed given in m s-1; WindMaxXX is the maximum wind speed given in m s-1; WindDirXX is the direction of the wind given in °; PrecXX is the precipitation given in mm; DistXX is the distance to the zero line (edge), positive values are in the arable land, negative values are in the forest, zero is the edge. For more details see "Microclimate". The data was edited according to "Data converting". Timezone: Central European Time (CET).
Supplementary material 1 from: Schmidt M, Lischeid G, Nendel C (2018) Data on and methodology for measurements of microclimate and matter dynamics in transition zones between forest and adjacent arable land. One Ecosystem 3: e24295. https://doi.org/10.3897/oneeco.3.e24295
Measured values are indicated in the header by the variable (e.g. "SoilMoist") followed by the distance to the zero line (e.g. 30, indicated by XX in the description below). Date.Time is given as YYYY-MM-DD HH:MM:SS; SoilMoistXX is the soil moisture given in cm3 cm-3; SoilTempXX is the soil temperature given in °C; RelHumXX is the relative humidity given as dimensionless number; AirTempXX is the air temperature in °C; AirPressXX is the barometric air pressure given in kPa; SolarRadXX is the solar radiation given in W m-2; WindAvgXX is the average wind speed given in m s-1; WindMaxXX is the maximum wind speed given in m s-1; WindDirXX is the direction of the wind given in °; PrecXX is the precipitation given in mm; DistXX is the distance to the zero line (edge), positive values are in the arable land, negative values are in the forest, zero is the edge. For more details see "Microclimate". The data was edited according to "Data converting". Timezone: Central European Time (CET).
Optimizing methodology for the detection of H3K27me3 levels using flow cytometry
<p>Optimizing methods to detect H3K27m3 levels using flow cytometry in patient AML cells.</p>
Supplementary material 2 from: Vačkář D, Grammatikopoulou I, Daněk J, Lorencová E (2018) Methodological aspects of ecosystem service valuation at the national level. One Ecosystem 3: e25508. https://doi.org/10.3897/oneeco.3.e25508
Results of systematic review of ecosystem service valuation studies in Europe (2000 – 2017) for benefit transfer at the national level .
Supplementary material 1 from: Vačkář D, Grammatikopoulou I, Daněk J, Lorencová E (2018) Methodological aspects of ecosystem service valuation at the national level. One Ecosystem 3: e25508. https://doi.org/10.3897/oneeco.3.e25508
Classification of ecosystems based on CORINE Land Cover and Consolidated Layer of Ecosystems for the Czech Republic.
FIGURE 10 in New species of Pseudonereis Kinberg, 1865 (Polychaeta: Nereididae) from the Atlantic Ocean, and a review of paragnath morphology and methodology
FIGURE 10. Pseudonereis variegata (Grube & Kröyer in Grube, 1858). Topotype A–B, I–J (USNM 176578); topotype C– H (USNM 176579). A, anterior end, dorsal view. B, posterior end, dorsal view. C, anterior end, dorsal view (insert: close-up of chaetigers 20–22). D, pharynx, dorsal view. E, same, ventral view. F, chaetiger 1, right parapodium. G, chaetiger 13, right parapodium. H, chaetiger 41, right parapodium. I, chaetiger 56, right parapodium. J, sub-acicular heterogomph falciger, chaetiger 56. Scale bars: A–C, 1 mm; D, E, 0.5 mm; F–I, 0.1 mm; J, 10 µm.
FIGURE 9. Pseudonereis gallapagensis Kinberg, 1865. Non-types A–B, E–K in New species of Pseudonereis Kinberg, 1865 (Polychaeta: Nereididae) from the Atlantic Ocean, and a review of paragnath morphology and methodology
FIGURE 9. Pseudonereis gallapagensis Kinberg, 1865. Non-types A–B, E–K (USNM 24265), non-type C–D (USNM 24266). A, anterior end, dorsal view. B, posterior end, dorsal view. C, pharynx, dorsal view. D, same, ventral view. E, subacicular heterogomph falcigers, chaetiger 12. F, supra-acicular heterogomph falciger, chaetiger 40. G, sub-acicular heterogomph falciger, chaetiger 40. H, chaetiger 2, right parapodium. I, chaetiger 12, right parapodium. J, chaetiger 30, right parapodium. K, chaetiger 73, right parapodium. Scale bars: A–D, 1 mm; E–G, 10 µm; H–K, 0.2 mm.
FIGURE 6 in New species of Pseudonereis Kinberg, 1865 (Polychaeta: Nereididae) from the Atlantic Ocean, and a review of paragnath morphology and methodology
FIGURE 6. Pseudonereis brunnea sp. n. Holotype A–H (ECOSUR 0191); paratypes I–O (ECOSUR 0192). A, anterior end, dorsal view. B, posterior end, dorsal view. C, chaetiger 2, right parapodium. D, chaetiger 10, right parapodium. E, Chaetiger 26, right parapodium. F, chaetiger 46, right parapodium. G, chaetiger 65, right parapodium. H, close up of anterior end. I, maxillary ring, frontal view. J, oral ring, frontal view. K, supra-acicular heterogomph falciger, chaetiger 55. L, sub-acicular heterogomph falciger, chaetiger 55. M, sub-acicular heterogomph spiniger, chaetiger 55. N, notopodial homogomph spiniger, chaetiger 55. O, sub-acicular heterogomph spiniger, chaetiger 55. Black triangles= points used for length measurement. Scale bars: A, B, 1 mm; C–G, 0.2 mm; H–J, 0.5 mm; K–M, 10 µm; N, O, 30 µm.
FIGURE 5 in New species of Pseudonereis Kinberg, 1865 (Polychaeta: Nereididae) from the Atlantic Ocean, and a review of paragnath morphology and methodology
FIGURE 5. Classification of some rectangular-base paragnaths. A, shield-shaped bars. B, crescent-shaped bars. C and D, pointed bars (P-bars). Drawings show the tip (dark brown) and base (light brown) of paragnaths, in both anterior and superior views; each drawing is accompanied with a picture of the same paragnath and at the same view. Green arrowheads point toward the anterior end of the body, showing the relative position of the paragnaths in relation to the pharynx axis. Blue vertical triangles point to the distal tip of the paragnaths; red triangles point the midpoint of the bases, and white dotted lines represent the bases' altitude lines. A, D, Pseudonereis brunnea sp. n. (ECOSUR P2926); B, Perinereis floridana (ECOSUR P1100); C, Nereis garwoodi (ECOSUR P2831).
FIGURE 3 in New species of Pseudonereis Kinberg, 1865 (Polychaeta: Nereididae) from the Atlantic Ocean, and a review of paragnath morphology and methodology
FIGURE 3. Transversal distribution of paragnaths in the furrow and ridge regions. A, Alitta succinea (ECOSUR P2729), five rows in two bands. B, distances among rows in region A of A. succinea, showing the gap between the bands. C, Nereis garwoodi (ECOSUR P2831), two rows in two bands. D, distances among rows in region A of N. garwoodi, showing the gap between the bands. E, Hediste cf. diversicolor (USNM 58131), three rows in two bands. F, distances among rows in region Br of H. cf. diversicolor, showing the gap between the bands. G, Perinereis floridana (ECOSUR P1100), three rows in two bands. H, distances among rows in region A of P. floridana, showing the gap between the bands. I, Pseudonereis gallapagensis (USNM 24266), two rows and one band. J. Platynereis magalhaensis (ECOSUR P2935), two rows and one band.
FIGURE 8 in New species of Pseudonereis Kinberg, 1865 (Polychaeta: Nereididae) from the Atlantic Ocean, and a review of paragnath morphology and methodology
FIGURE 8. Pseudonereis fauveli sp. n. Holotype A–M (USNM 1494007). A, anterior end, dorsal view. B, posterior end, dorsal view. C, chaetiger 2, right parapodium. D, chaetiger 13, right parapodium. E, chaetiger 32, right parapodium. F, chaetiger 50, right parapodium. G, chaetiger 67, right parapodium. H, right jaw in lateral (left) and dorsal (right) view. I, supraacicular homogomph spiniger, chaetiger 13. J, supra-acicular heterogomph falciger, chaetiger 13. K, sub-acicular heterogomph falciger, chaetiger 13. L, supra-acicular heterogomph falciger, chaetiger 67. M, sub-acicular heterogomph falciger, chaetiger 67. Scale bars: A, 1 mm; B–H, 0.2 mm; I–M, 10 µm.
FIGURE 2 in New species of Pseudonereis Kinberg, 1865 (Polychaeta: Nereididae) from the Atlantic Ocean, and a review of paragnath morphology and methodology
FIGURE 2. The midventral pharynx area in some nereidid genera. A, midventral area in Alitta succinea (ECOSUR P2729). B, midventral area in Pseudonereis gallapagensis (USNM 24266). C, midventral area in Nereis garwoodi (ECOSUR P2831). D, midventral area in Perinereis floridana (ECOSUR P1100). E, midventral area in Hediste cf. diversicolor (USNM 58131). F, midventral area in Kainonereis polaris (USNM 55514). G, midventral area in Platynereis magalhaensis (ECOSUR P2935). A– B and E–F show pharynges fully everted; C–D show pharynges partially everted; G shows a pharynx dorsally dissected. The midventral area in all drawings is highlighted in white.
FIGURE 7 in New species of Pseudonereis Kinberg, 1865 (Polychaeta: Nereididae) from the Atlantic Ocean, and a review of paragnath morphology and methodology
FIGURE 7. Pseudonereis citrina sp. n. Holotype A–C, F–P (ECOSUR 0194); paratypes D (ECOSUR 0195) and E (ECOSUR 0196). A, anterior end, dorsal view. B, posterior end, dorsal view (insert: close-up of glandular masses in notopodial ligules). C, left jaw, dorsal view. D and E, pharynx areas V and VI. F, chaetiger 2, right parapodium. G, chaetiger 10, right parapodium. H, chaetiger 24, right parapodium. I, chaetiger 38, right parapodium. J, chaetiger 56, right parapodium. K, sub-acicular heterogomph spiniger, chaetiger 56. L, supra-acicular heterogomph falciger, chaetiger 56. M, sub-acicular heterogomph falciger, chaetiger 56. N, sub-acicular heterogomph falciger, chaetiger 38. O, notopodial homogomph spiniger, chaetiger 38. P, sub-acicular heterogomph spiniger, chaetiger 56. Scale bars: A, B, 1 mm; C, 0.3mm; D, E, 0.1 mm; F–J, 0.2 mm; K–N, 10 µm; O, P, 30 µm.
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
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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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.