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328 results for “Analysis results”
Cryptic Diversity in Cladosporium cladosporioides Resulting from Species Delimitation Analysis
<p><strong>Concatenated loci alignment (.fasta), Maximum-Likelihood, Maximum-Parsimony and Bayesian reconstruction of <em>Cladosporium cladosporioides</em> phylogeny. </strong></p> <p>Files represent dataset of the study: "Cryptic Diversity in Cladosporium cladosporioides Resulting from Species Delimitation Analysis"</p> <p> </p> <p>ABSTRACT</p> <p>Establishing a stable taxonomy is particularly important for understanding fungal biodiversity, as well as the evolution of particular traits related to symbiotic interactions. <em>Cladosporium cladosporioides </em>is an extremely widespread fungus involved in associations ranging from mutualistic to pathogenic, and is the most represented <em>Cladosporium</em> species in genetic sequence databases, such as Genbank. Although the taxonomy of <em>Cladosporium</em> species is subjected to frequent revisions, which nowadays mostly rely on molecular data, few studies explored cryptic diversity of this genus using the recently developed species delimitation methods. Considering a previous study which reported several hypothetical species within <em>C. cladosporioides</em>, here we try to fill the gap of knowledge about phylogenetic relationships for this species and tested four different methods of species delimitation using the combined DNA barcodes ITS, <em>translation elongation factor 1</em> and <em>actin</em>. The analyses involved 105 isolates revealing that currently available sequences of <em>C. cladosporioides</em> in GenBank actually represent more than one species. Moreover, we reported the erroneous taxonomical assignment of several isolates that should be ascribed to <em>C. anthropophilum</em>. Our results revealed a certain degree of discordance among species delimitation methods, which can be efficiently treated using conservative approaches, in order to minimize the risk of considering false positives.</p>
Text-fig. 30. Scanning electron microscope (SEM) images of monocolpate pollen of Dejaxia brevicolpites gen. et sp. nov. from a pollen clump; Torres Vedras locality, Portugal. a) Holotype; pollen clump (possible single pollen sac) that yielded the pollen in this Textfigure; b, c) Group of almost spherical pollen grains showing the irregularly undulating psilate tectum and abundant orbicules; d–g) Pollen grains showing the short colpi with a granular aperture membrane (d, f) and the irregularly undulating psilate tectum with scattered small perforations; note abundant orbicules (g); h) Pollen grain in proximal view showing the irregularly undulating psilate tectum resulting from the depressions around the perforations in the pollen wall. Specimen, TV44-S137909 (holotype). Scale bars 300 Μm (a), 30 Μm (b), 12 Μm (c), 6 Μm (d–h). in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community
Text-fig. 30. Scanning electron microscope (SEM) images of monocolpate pollen of Dejaxia brevicolpites gen. et sp. nov. from a pollen clump; Torres Vedras locality, Portugal. a) Holotype; pollen clump (possible single pollen sac) that yielded the pollen in this Textfigure; b, c) Group of almost spherical pollen grains showing the irregularly undulating psilate tectum and abundant orbicules; d–g) Pollen grains showing the short colpi with a granular aperture membrane (d, f) and the irregularly undulating psilate tectum with scattered small perforations; note abundant orbicules (g); h) Pollen grain in proximal view showing the irregularly undulating psilate tectum resulting from the depressions around the perforations in the pollen wall. Specimen, TV44-S137909 (holotype). Scale bars 300 Μm (a), 30 Μm (b), 12 Μm (c), 6 Μm (d–h).
Text-fig. 3. Scanning electron microscope (SEM) images of a charalean oospore (a), and fragments of probable marchantialean liverwort thalli (b–d); Torres Vedras locality, Portugal. a) Apical view of oospore showing the pattern of spiral ridges and grooves resulting from the enclosing cells of the oogonium. b–d) Thallus fragments in probable ventral view showing two rows of imbricate scales and occasional branching of the thallus (d). Specimens, TV38-S174607 (a), TV43-S174655 (b), TV43-S174654 (c), TV43-S174661 (d). Scale bars 1 mm (b–d), 100 Μm (a). in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community
Text-fig. 3. Scanning electron microscope (SEM) images of a charalean oospore (a), and fragments of probable marchantialean liverwort thalli (b–d); Torres Vedras locality, Portugal. a) Apical view of oospore showing the pattern of spiral ridges and grooves resulting from the enclosing cells of the oogonium. b–d) Thallus fragments in probable ventral view showing two rows of imbricate scales and occasional branching of the thallus (d). Specimens, TV38-S174607 (a), TV43-S174655 (b), TV43-S174654 (c), TV43-S174661 (d). Scale bars 1 mm (b–d), 100 Μm (a).
Fig. 76. Results from exploratory phylogenetic analysis including Epidendrosaurus ningchengensis. A, reduced strict consensus cladogram. B in A Review Of Dromaeosaurid Systematics And Paravian Phylogeny
Fig. 76. Results from exploratory phylogenetic analysis including Epidendrosaurus ningchengensis. A, reduced strict consensus cladogram. B, detail of the base of Avialae showing the number of additional steps required to constrain Epidendrosaurus and Epidexipteryx are sister taxa.
Figure 2. A, Tree resulting from maximum likelihood analysis from the 12S in A molecular perspective on the evolutionary affinities of an enigmatic neotropical frog, Allophryne ruthveni
Figure 2. A, Tree resulting from maximum likelihood analysis from the 12S data set using the Hasegawa–Kishino–Yano two parameter model (Hasegawa et al., 1985). Included for comparative purposes are bootstrap support from NJ analyses. Below each resolved branch are indicated percentage bootstrap support in excess of 50% for: ML (100 pseudoreplicates), NJ (1000 pseudoreplicates; Kimura 2-parameter), NJ (1000 pseudoreplicates; Tamura–Nei). B, Strict consensus of three most parsimonious trees (all substitutions weighted equally; tree length = 164 steps). Below each branch are indicated percentage bootstrap support (1000 pseudreplicates) in excess of 50% for: MP (unweighted), MP (stems weighted twice loops), MP (transversions weighted four times transitions). Bremer decay indices (DI) are the final value shown below each resolved branch (for MP unweighted only). A dash indicates bootstrap support of less than 50%.
Annotation-based Modeling of Non-functional Requirements and Analysis Results in Domain-driven Design
<p>This repo contains all supplementary data sets that we have created and used throughout this thesis. In particular, it contains<br> - expert interview material (elicitation): consent form and question catalogue for requirements elicitation<br> - expert interview material (evaluation): consent form and task description for expert evaluation<br> - Diagrams related to our modeling concept and Dqualizer<br> - Screenshots of the Domain Story Modeler with our Modeling Concept</p>
Small-angle Scattering Data Analysis Round Robin: anonymized results, figures and Jupyter notebook
<p>The intent of this round robin was to find out how comparable results from different researchers are, who analyse exactly the same processed, corrected dataset.</p> <p>This zip file contains the anonymized results and the jupyter notebook used to do the data processing, analysis and visualisation. Additionally, TEM images of the samples are included. </p>
Example Data, Analysis and Results Files for MAUD-batch-analysis
<p>Example data, example analysis and example results files for using with the <a href="https://github.com/LightForm-group/MAUD-batch-analysis">MAUD-batch-analysis</a> package. The MAUD-batch analysis package can also be downloaded from Zenodo as <a href="https://doi.org/10.5281/zenodo.7603382">v1.0.0</a>.</p> <p>To run an example analysis with MAUD batch mode, download these data, analysis and results files and unzip them into the respective folders in the MAUD-batch-analysis package.</p>
Additional annotation, alignment, and results from Ka/Ks analysis for Chromosomal-level reference genome assembly of the African Spiny Mouse (Acomys cahirinus)
<p><strong>Annotation files, alignments, and results summaries from Chromosomal-level reference genome assembly of the African Spiny Mouse (Acomys cahirinus).</strong></p> <p>Pairwise genome alignments contain the .maf suffix</p> <p>FASTA alignments from stitched gene blocks contain the .fasta suffix</p> <p>CSV file containing the Ka/Ks results</p> <p>RepeatMasker .out file</p>
Swiss Dwellings: A large dataset of apartment models including aggregated geolocation-based simulation results covering viewshed, natural light, traffic noise, centrality and geometric analysis
<p><strong>Introduction</strong></p> <p>This dataset contains detailed data on over 45,000 apartments (370,000 rooms) in ~3,100 buildings including their geometries, room typology as well as their visual, acoustical, topological, and daylight characteristics. Additionally, we have included location-specific characteristics for the buildings, including climatic data and points of interest within walking distance.</p> <p><strong>Changelog</strong></p> <ul> <li><strong>v3.0.0 (2023-03-31):</strong> <ul> <li>Updated the dataset increasing the total number of apartments to 45176 and incorporating fixes to some of the sites. The update includes re-digitized apartments and thus alters some ID values.</li> </ul> </li> <li><strong>v2.2.1 (2023-03-10):</strong> <ul> <li>A file, <code>location_ratings.csv</code>, has been included to provide ratings of the locations in which the buildings are situated. The ratings, provided by <a href="https://en.fpre.ch/">Fahrländer Partner AG</a>, give insights into the living situation at the buildings' addresses. Details for the different dimensions are provided below.</li> <li>The file <code>location.csv</code> has been updated to include the minimum and maximum temperatures for the locations in which the buildings are situated.</li> </ul> </li> <li><strong>v2.1.0 (2022-12-23)</strong>: <ul> <li>A file, <code>locations.csv</code>, has been included to provide information on the climatic and infrastructural characteristics of the locations in which each building is situated</li> </ul> </li> <li><strong>v2.0.0 (2022-10-17):</strong> <ul> <li>Additional to the residential units, we also include the commercial and public parts (such as staircases) of the models. The field <code>unit_usage</code> describes whether an area belongs to a commercial, residential, janitor or public part of the building</li> <li>Added the fields <code>elevation</code> and <code>height</code> to <em>geometries.csv</em> to describe the elevation above the terrain surface and the height of objects.</li> <li>Added the field <code>plan_id</code> which allows identifying which floors are based on the same floor plan (in some cases multiple floors of a building share the same floor plan</li> <li>Improved the ordering of fields in the CSV files (instead of alphabetic order)</li> <li>Minor changes to individual sites</li> </ul> </li> </ul> <p><strong>Procurement</strong></p> <p>The data is sourced from commercial clients of <a href="https://www.archilyse.com/">Archilyse AG</a> specializing on the digitization and analysis of buildings. The existing building plans of clients are converted into a geo-referenced, semantically annotated representation and undergo a manual Q/A process to ensure the accuracy of the data and to ensure a maximum 5%-deviation in the apartments' areas (validated with a median deviation of 1.2%).</p> <p><strong>Geometries</strong></p> <p>The dataset contains a file <code>geometries.csv</code> which contains the geometries of all areas, walls, railings, columns, windows, doors and features (sinks, bathtubs, etc.) of an apartment.</p> <p>In total, the datasets contain the 2D geometry of ~1.7 million separators (walls, railings), ~715,000 openings (windows, doors), ca. 520,000 areas (rooms, bathrooms, kitchens, etc.), and ~315,000 features (sinks, toilets, bathtubs, etc.).</p> <p>Each row contains:</p> <ul> <li><code>apartment_id</code>: The ID of the apartment (for features, areas), <em>note</em>: an apartment id is only unique per site</li> <li><code>site_id</code>: The ID of the site</li> <li><code>building_id</code>: The ID of the building</li> <li><code>floor_id</code>: The ID of the floor</li> <li><code>plan_id</code>: The ID of the plan on which the floor is based, multiple floors of a building might be based on the same plan</li> <li><code>unit_id</code>: The ID of the unit in which the element is spatially contained (for features, areas)</li> <li><code>area_id</code>: The ID of the area in which the element is spatially contained (for features)</li> <li><code>unit_usage</code>: The usage of the unit, possible values are: RESIDENTIAL, COMMERCIAL, PUBLIC, JANITOR</li> <li><code>entity_type</code>: The entity type (<em>area, separator, opening, feature</em>)</li> <li><code>entity_subtype</code>: The entity’s sub-type (e.g. <em>WALL</em>)</li> <li><code>geometry</code>: The element’s geometry as a <a href="https://en.wikipedia.org/wiki/Well-known_text_representation_of_geometry">WKT</a> geometry in meters. The geometry is given in the site’s local coordinate system. I.e. the position between elements of the same site are correct in respect to each other. The +y direction points northwards, the +x direction points eastwards.</li> <li><code>elevation</code>: The object's elevation above the terrain surface in meters. We assume one terrain baseline per building, thus all walls in a given floor share the same elevation value. However, windows in particular might start at different elevations and have differing heights.</li> <li><code>height</code>: The height of the entity in meters, <em>note</em>: In many cases, a default height is assumed</li> </ul> <p>An example:</p> <table> <thead> <tr> <th scope="col">column</th> <th scope="col"> </th> </tr> </thead> <tbody> <tr> <td>apartment_id</td> <td> <p>d4438f2129b30290845ce7eef98a5ba7</p> </td> </tr> <tr> <td>site_id</td> <td>127</td> </tr> <tr> <td>building_id</td> <td>164</td> </tr> <tr> <td>plan_id</td> <td>492</td> </tr> <tr> <td>floor_id</td> <td>861</td> </tr> <tr> <td>unit_id</td> <td>63777</td> </tr> <tr> <td>area_id</td> <td>767676</td> </tr> <tr> <td>unit_usage</td> <td>RESIDENTIAL</td> </tr> <tr> <td>entity_type</td> <td>area</td> </tr> <tr> <td>entity_subtype</td> <td>LIVING_ROOM</td> </tr> <tr> <td>geometry</td> <td> <p>POLYGON ((-6.1501158933490139 -4.8490786654693...</p> </td> </tr> <tr> <td>elevation</td> <td>0</td> </tr> <tr> <td>height</td> <td>2.6</td> </tr> </tbody> </table> <p><strong>Simulations</strong></p> <p>Besides the geometrical model, we also provide simulation data on the visual, acoustic, solar, layout, and connectivity-related characteristics of the apartments. The file <code>simulations.csv</code> contains the simulation data aggregated on a per-area basis. Each row contains the identifier columns <code>area_id</code>, <code>unit_id</code>, <code>apartment_id</code>, <code>floor_id</code>, <code>building_id</code>, <code>site_id</code> as defined above as well as 367 simulation columns. Each simulation column is formatted as:</p> <pre><code><simulation_category>_<simulation_dimensions>_<aggregation_function></code></pre> <p>For instance. the column <code>view_buildings_median</code> describes the amount of building surface that can be seen from any point in a given room. The aggregation methods vary per simulation category and are described in detail below.</p> <p><strong>Layout</strong></p> <p>The <em>layout</em> features represent simple features based on the geometry and composition of a room, the dataset provides the following information in an unaggregated form.</p> <p>Area Basics / Geometry</p> <table> <thead> <tr> <th>dimension</th> <th>description</th> </tr> </thead> <tbody> <tr> <td>layout_area_type</td> <td>The area’s area type</td> </tr> <tr> <td>layout_net_area</td> <td>The area’s share of the apartment’s net area (e.g. 0 for a balcony)</td> </tr> <tr> <td>layout_area</td> <td>The area’s actual area</td> </tr> <tr> <td>layout_perimeter</td> <td>The area’s perimeter</td> </tr> <tr> <td>layout_compactness</td> <td>The area’s compactness (the Polsby–Popper score)</td> </tr> <tr> <td>layout_room_count</td> <td>The area’s share to the apartment’s room count</td> </tr> <tr> <td>layout_is_navigable</td> <td>True if the area is navigable by a wheelchair</td> </tr> </tbody> </table> <p>Area Features</p> <table> <thead> <tr> <th>dimension</th> <th>description</th> </tr> </thead> <tbody> <tr> <td>layout_has_sink</td> <td>True if the area has a sink</td> </tr> <tr> <td>layout_has_shower</td> <td>True if the area has a shower</td> </tr> <tr> <td>layout_has_bathtub</td> <td>True if the area has a bathtub</td> </tr> <tr> <td>layout_has_toilet</td> <td>True if the area has a toilet</td> </tr> <tr> <td>layout_has_stairs</td> <td>True if the area has stairs</td> </tr> <tr> <td>layout_has_entrance_door</td> <td>True if the area is directly leading to an exit of the apartment</td> </tr> </tbody> </table> <p>Area Windows / Doors</p> <table> <thead> <tr> <th>dimension</th> <th>description</th> </tr> </thead> <tbody> <tr> <td>layout_number_of_doors</td> <td>The number of doors directly leading to the area</td> </tr> <tr> <td>layout_number_of_windows</td> <td>The number of windows of the area</td> </tr> <tr> <td>layout_door_perimeter</td> <td>The sum of all door lengths directly leading to the area</td> </tr> <tr> <td>layout_window_perimeter</td> <td>The sum of all window lengths of the area</td> </tr> </tbody> </table> <p>Area Walls / Railings</p> <table> <thead> <tr> <th>dimension</th> <th>description</th> </tr> </thead> <tbody> <tr> <td>layout_open_perimeter</td> <td>The sum of all of the boundaries of the area that are neither walls nor railings</td> </tr> <tr> <td>layout_railing_perimeter</td> <td>The sum of all of the boundaries of the area that are railings</td> </tr> <tr> <td>layout_mean_walllengths</td> <td>The mean length of the area’s sides</td> </tr> <tr> <td>layout_std_walllengths</td> <td>The standard deviation of the lengths of the area’s sides</td> </tr> </tbody> </table> <p>Area Adjacency</p> <table> <thead> <tr> <th>dimension</th> <th>description</th> </tr> </thead> <tbody> <tr> <td>layout_connects_to_bathroom</td> <td>True if the area connects to a bathroom</td> </tr> <tr> <td>layout_connects_to_private_outdoor</td> <td>True if the area connects to an outside area that is private to the apartment</td> </tr> </tbody> </table> <p><strong>View</strong></p> <p>The views from an object help to understand the impact of the surroundings on the object. The view simulation calculates the visible amount of buildings, greenery, water, etc. on each individual hexagon from the analyzed object. The values are expressed in steradians (sr) and represent the amount a particular object category occupies in the spherical field of view.</p> <p>Each of the following dimensions is provided using the room-wise aggregations' <em>min</em>, <em>max</em>, <em>mean</em>, <em>std</em>, <em>median</em>, <em>p20,</em> and <em>p80</em>. For instance, the column <code>view_greenery_p20</code> describes the amount of greenery that can be seen from at least 20% of the positions in the area.</p> <table> <thead> <tr> <th>dimension</th> <th>description</th> </tr> </thead> <tbody> <tr> <td>view_buildings</td> <td>The amount of visible buildings</td> </tr> <tr> <td>view_greenery</td> <td>The amount of visible greenery</td> </tr> <tr> <td>view_ground</td> <td>The amount of visible ground</td> </tr> <tr> <td>view_isovist</td> <td>The amount of visible isovist</td> </tr> <tr> <td>view_mountains_class_2</td> <td>The amount of visible mountains of UN mountain class 2</td> </tr> <tr> <td>view_mountains_class_3</td> <td>The amount of visible mountains of UN mountain class 3</td> </tr> <tr> <td>view_mountains_class_4</td> <td>The amount of visible mountains of UN mountain class 4</td> </tr> <tr> <td>view_mountains_class_5</td> <td>The amount of visible mountains of UN mountain class 5</td> </tr> <tr> <td>view_mountains_class_6</td> <td>The amount of visible mountains of UN mountain class 6</td> </tr> <tr> <td>view_railway_tracks</td> <td>The amount of visible railway_tracks</td> </tr> <tr> <td>view_site</td> <td>The amount of visible site</td> </tr> <tr> <td>view_sky</td> <td>The amount of visible sky</td> </tr> <tr> <td>view_tertiary_streets</td> <td>The amount of visible tertiary_streets</td> </tr> <tr> <td>view_secondary_streets</td> <td>The amount of visible secondary_streets</td> </tr> <tr> <td>view_primary_streets</td> <td>The amount of visible primary_streets</td> </tr> <tr> <td>view_pedestrians</td> <td>The amount of visible pedestrians</td> </tr> <tr> <td>view_highways</td> <td>The amount of visible highways</td> </tr> <tr> <td>view_water</td> <td>The amount of visible water</td> </tr> </tbody> </table> <p><strong>Sun</strong></p> <p>Sun simulations help to understand the impact of solar radiation on the object. The outcome of the sun simulations helps to identify surfaces that have great solar potential. Sun simulations are defined by the amount of solar radiation on each individual hexagon from the analyzed object. The sun simulation not only includes direct sun but also considers scattered light. The sun simulation values are given in Kilolux (klx). Simulations are performed for the days of the summer solstice, winter solstice, and the vernal equinox.</p> <p>Each of the following dimensions is provided using the room-wise aggregations' <em>min</em>, <em>max</em>, <em>mean</em>, <em>std</em>, <em>median</em>, <em>p20,</em> and <em>p80</em>. For instance, column <code>sun_201806211200_median</code> describes the median amount of direct daylight received on the positions in the area.</p> <p>Vernal Equinox</p> <table> <thead> <tr> <th>dimension</th> <th>description</th> </tr> </thead> <tbody> <tr> <td>sun_201803210800</td> <td>Daylight at 08:00 on 21st of March</td> </tr> <tr> <td>sun_201803211000</td> <td>Daylight at 10:00 on 21st of March</td> </tr> <tr> <td>sun_201803211200</td> <td>Daylight at 12:00 on 21st of March</td> </tr> <tr> <td>sun_201803211400</td> <td>Daylight at 14:00 on 21st of March</td> </tr> <tr> <td>sun_201803211600</td> <td>Daylight at 16:00 on 21st of March</td> </tr> <tr> <td>sun_201803211800</td> <td>Daylight at 18:00 on 21st of March</td> </tr> </tbody> </table> <p>Summer Solstice</p> <table> <thead> <tr> <th>dimension</th> <th>description</th> </tr> </thead> <tbody> <tr> <td>sun_201806210600</td> <td>Daylight at 06:00 on 21st of June</td> </tr> <tr> <td>sun_201806210800</td> <td>Daylight at 08:00 on 21st of June</td> </tr> <tr> <td>sun_201806211000</td> <td>Daylight at 10:00 on 21st of June</td> </tr> <tr> <td>sun_201806211200</td> <td>Daylight at 12:00 on 21st of June</td> </tr> <tr> <td>sun_201806211400</td> <td>Daylight at 14:00 on 21st of June</td> </tr> <tr> <td>sun_201806211600</td> <td>Daylight at 16:00 on 21st of June</td> </tr> <tr> <td>sun_201806211800</td> <td>Daylight at 18:00 on 21st of June</td> </tr> <tr> <td>sun_201806212000</td> <td>Daylight at 20:00 on 21st of June</td> </tr> </tbody> </table> <p>Winter Solstice</p> <table> <thead> <tr> <th>dimension</th> <th>description</th> </tr> </thead> <tbody> <tr> <td>sun_201812211000</td> <td>Daylight at 10:00 on 21st of December</td> </tr> <tr> <td>sun_201812211200</td> <td>Daylight at 12:00 on 21st of December</td> </tr> <tr> <td>sun_201812211400</td> <td>Daylight at 14:00 on 21st of December</td> </tr> <tr> <td>sun_201812211600</td> <td>Daylight at 16:00 on 21st of December</td> </tr> </tbody> </table> <p><strong>Noise / Window Noise</strong></p> <p>Noise level and the distribution of elements from an area help to understand how an object is exposed to the acoustics of this area. The acoustic simulation calculates the noise intensity on each individual hexagon from the analyzed object considering traffic and train noise datasets. Adjacent buildings are considered noise-blocking elements. The values are expressed in dBA (decibels).</p> <p>Window Noise</p> <p>The noise per window of a given area is aggregated via <code>min</code> and <code>max</code>. For instance, <code>window_noise_train_day_max</code> represents the maximum amount of noise received on any window of the area.</p> <table> <thead> <tr> <th>dimension</th> <th>description</th> </tr> </thead> <tbody> <tr> <td>window_noise_traffic_day</td> <td>The amount of noise received on the area’s windows from daytime car traffic</td> </tr> <tr> <td>window_noise_traffic_night</td> <td>The amount of noise received on the area’s windows from night-time car traffic</td> </tr> <tr> <td>window_noise_train_day</td> <td>The amount of noise received on the area’s windows from daytime train traffic</td> </tr> <tr> <td>window_noise_train_night</td> <td>The amount of noise received on the area’s windows from night-time train traffic</td> </tr> </tbody> </table> <p>Area-Wise Noise</p> <p>The area-wise noise describes the amount of noise received from a noise source aggregated over the whole area in an unaggregated form. For instance, <code>noise_traffic_night</code> describes the dBA of noise received in the area from car traffic at night when propagating noise from all windows.</p> <table> <thead> <tr> <th>dimension</th> <th>description</th> </tr> </thead> <tbody> <tr> <td>noise_traffic_day</td> <td>The amount of noise received in the area from daytime car traffic</td> </tr> <tr> <td>noise_traffic_night</td> <td>The amount of noise received in the area from night-time car traffic</td> </tr> <tr> <td>noise_train_day</td> <td>The amount of noise received in the area from daytime train traffic</td> </tr> <tr> <td>noise_train_night</td> <td>The amount of noise received in the area from night-time train traffic</td> </tr> </tbody> </table> <p><br> <strong>Connectivity</strong></p> <p>Centrality simulations help to analyze a floor plan, whether it’s a shopping mall and you want to identify prominent areas in order to select the most prominent spot or it’s an interior design circulation path and you want to determine open floor plan areas. Centrality simulations are done using topological measures that score grid cells by their importance as a part of a grid cell network.</p> <p>The distances and centralities are aggregated via <em>min</em>, <em>max</em>, <em>mean</em>, <em>std</em>, <em>median</em>, <em>p20,</em> and <em>p80</em>. For instance, <code>connectivity_balcony_distance_min</code> describes the shortest distance to the next balcony from the point closest to the balcony in the area.</p> <p>Distances</p> <table> <thead> <tr> <th>dimension</th> <th>description</th> </tr> </thead> <tbody> <tr> <td>connectivity_room_distance</td> <td>Distance to the next area of type ROOM</td> </tr> <tr> <td>connectivity_living_dining_distance</td> <td>Distance to the next area of type LIVING_DINING</td> </tr> <tr> <td>connectivity_bathroom_distance</td> <td>Distance to the next area of type BATHROOM</td> </tr> <tr> <td>connectivity_kitchen_distance</td> <td>Distance to the next area of type KITCHEN</td> </tr> <tr> <td>connectivity_balcony_distance</td> <td>Distance to the next area of type BALCONY</td> </tr> <tr> <td>connectivity_loggia_distance</td> <td>Distance to the next area of type LOGGIA</td> </tr> <tr> <td>connectivity_entrance_door_distance</td> <td>Distance to the next apartment exit</td> </tr> </tbody> </table> <p>Centralities</p> <table> <thead> <tr> <th>dimension</th> <th>description</th> </tr> </thead> <tbody> <tr> <td>connectivity_eigen_centrality</td> <td>The Eigen-Centrality value</td> </tr> <tr> <td>connectivity_betweenness_centrality</td> <td>The Betweenness-Centrality value</td> </tr> <tr> <td>connectivity_closeness_centrality</td> <td>The Closeness-Centrality value</td> </tr> </tbody> </table> <p><strong>Location Properties</strong></p> <p>In addition to the apartment-related data, we also provide simulation data on the climatic, and infrastructural characteristics of the locations. The file <code>locations.csv</code> contains the simulation data aggregated on a per-building basis. Each row contains the identifier <code>building_id</code> corresponding to the building ids referenced in <code>geometries.csv</code> and <code>simulations.csv</code>.</p> <p><strong>Climate</strong></p> <p>The climate features represent 39 simple features based on the spatial climate analysis of Meteo Swiss as derived from <a href="https://www.meteoswiss.admin.ch/climate/the-climate-of-switzerland/spatial-climate-analyses.html.">MeteoSwiss</a>. Each column is formatted as <code>climate_<category>_<period>. </code>For instance, the column <code>climate_tnorm_january</code> describes the monthly mean temperature in degrees Celsius (from the norm period of 1991-2020) at the location of the building. The aggregation methods vary per simulation category and are described in detail below.</p> <p>Temperature Normals</p> <table> <thead> <tr> <th>dimension</th> <th>description</th> </tr> </thead> <tbody> <tr> <td>climate_tnorm_year</td> <td>The yearly mean temperature in degrees Celsius of the current norm period from 1991 to 2020 (TnormY9120)</td> </tr> <tr> <td>climate_tnorm_january</td> <td>The monthly mean temperature in January in degrees Celsius of the current norm period from 1991 to 2020 (TnormM9120)</td> </tr> <tr> <td>climate_tnorm_februry</td> <td>The monthly mean temperature in February in degrees Celsius of the current norm period from 1991 to 2020 (TnormM9120)</td> </tr> <tr> <td>...</td> <td>...</td> </tr> <tr> <td>climate_tnorm_december</td> <td>The monthly mean temperature in December in degrees Celsius of the current norm period from 1991 to 2020 (TnormM9120)</td> </tr> <tr> <td>climate_tminnorm_january</td> <td>The monthly minimum temperature in January in degrees Celsius of the current norm period from 1991 to 2020 (TminnormM9120)</td> </tr> <tr> <td>...</td> <td> </td> </tr> <tr> <td>climate_tminnorm_december</td> <td>The monthly minimum temperature in December in degrees Celsius of the current norm period from 1991 to 2020 (TnormM9120)</td> </tr> <tr> <td>climate_tmaxnorm_january</td> <td>The monthly maximum temperature in January in degrees Celcius of the current norm period from 1991 to 2020 (TnormM9120)</td> </tr> <tr> <td>...</td> <td> </td> </tr> <tr> <td>climate_tmaxnorm_december</td> <td>The monthly maximum temperature in December in degrees Celcius of the current norm period from 1991 to 2020 (TnormM9120)</td> </tr> </tbody> </table> <p>Sunshine Duration Normals</p> <table> <thead> <tr> <th>dimension</th> <th>description</th> </tr> </thead> <tbody> <tr> <td>climate_snorm_year</td> <td>The yearly mean relative sunshine duration in percent of the current norm period from 1991 to 2020 (SnormY9120). Relative sunshine duration (RSD) is the ratio between the effective sunshine duration and the duration maximally possible if no clouds were covering the sun. A period with sunshine is defined as a period when the direct solar irradiance exceeds 200 W/m²</td> </tr> <tr> <td>climate_snorm_january</td> <td>The monthly mean relative sunshine duration for January in percent of the current norm period</td> </tr> <tr> <td>climate_snorm_februry</td> <td>The monthly mean relative sunshine duration for February in percent of the current norm period</td> </tr> <tr> <td>...</td> <td>...</td> </tr> <tr> <td>climate_snorm_december</td> <td>The monthly mean relative sunshine duration for December in percent of the current norm period</td> </tr> </tbody> </table> <p>Precipitation Normals</p> <table> <thead> <tr> <th>dimension</th> <th>description</th> </tr> </thead> <tbody> <tr> <td>climate_rnorm_year</td> <td>The yearly mean precipitation in mm of the current norm period (RnormY9120)</td> </tr> <tr> <td>climate_rnorm_january</td> <td>The monthly mean precipitation for January in mm of the current norm period (RnormM9120)</td> </tr> <tr> <td>climate_rnorm_februry</td> <td>The monthly mean precipitation for February in mm of the current norm period (RnormM9120)</td> </tr> <tr> <td>...</td> <td>...</td> </tr> <tr> <td>climate_rnorm_december</td> <td>The monthly mean precipitation for December mm of the current norm period (RnormM9120)</td> </tr> </tbody> </table> <p><strong>10-Minute Walkshed Infrastructure</strong></p> <p>Based on OpenStreetMap data and its tagging system we counted all 465 tags (key and value tuples as listed here: https://wiki.openstreetmap.org/wiki/Map_features) which can be reached within a 10-minute walk from the location of the building. Each column is formatted as <code>walkshed_<poi_category>_<poi_type>. </code>For instance, the column <code>walkshed_shop_coffee</code> describes the number of coffee shops located within 10 minutes of walking from the building.</p> <p>The following is an excerpt of support categories and their corresponding types.</p> <ul> <li><code>shop: antique, art, ...</code></li> <li><code>amenity: art, atm, ...</code></li> <li><code>tourism: alpine, attraction, ...</code></li> <li><code>leisure: amusement, beach, ...</code></li> <li><code>healthcare: clinic, dentist, ...</code></li> <li><code>historic: archaeological, battlefield, ...</code></li> <li><code>ariaelway: station</code></li> </ul> <p><strong>Location Ratings</strong></p> <p>The location ratings, provided by <a href="https://en.fpre.ch/">Fahrländer Partner AG</a>, give insights into the living situation at locations in which the buildings are situated. The file location_ratings.csv provides the following information:</p> <table> <thead> <tr> <th>dimension</th> <th>description</th> </tr> </thead> <tbody> <tr> <td>location_rating_MIKRAT_W</td> <td>Living situation - Overall (1.0=worst, 5.0=best)</td> </tr> <tr> <td>location_rating_IMAGE_W</td> <td>Living situation - Image (1.0=worst, 5.0=best)</td> </tr> <tr> <td>location_rating_DL_W</td> <td>Living situation - Service Quality (1.0=worst, 5.0=best)</td> </tr> <tr> <td>location_rating_FZ_W</td> <td> <p>Living situation - Leisure Quality (1.0=worst, 5.0=best)</p> </td> </tr> <tr> <td>location_rating_NASE_W_DOM</td> <td>The most dominant segment of demand:<br> <br> 1 Rural-traditional<br> 2 Modern worker<br> 3 Transitional-alternative<br> 4 Traditional middle class<br> 5 Liberal middle class<br> 6 Established alternative<br> 7 Upper middle class<br> 8 Professional elite<br> 9 Urban elite<br> 10 Unknown<br> <br> <a href="https://en.fpre.ch/marktdaten/nachfragersegmente/nachfragersegmente-im-wohnungsmarkt/">More Information</a></td> </tr> <tr> <td>location_rating_FGFRQZ</td> <td> <p>The mean number of pedestrians per hour throughout a day between 7 am and 8 pm of an average working day.<br> <br> 1 <50<br> 2 50-100<br> 3 100-200<br> 4 200-500<br> 5 >500</p> </td> </tr> </tbody> </table>
Clinical trials analysis results. Rising pharmaceutical innovation in the Global South.
<p>This is a supplementary document of the research reports from the "Research Collaboration on Technology, Equity, and the Right to Health", between the Global Health Centre (GHC) at the Geneva Graduate Institute in Switzerland, the James P. Grant School of Public Health at BRAC University in Bangladesh, and the Universidad de los Andes (ANDES) in Colombia, supported by the Open Society University Network (OSUN). For more information please refer to: Knowledge Portal on Innovation and Access to Medicines - <a href="https://www.knowledgeportalia.org/">https://www.knowledgeportalia.org/</a></p>
Image dataset for cow identification, including code to train deep learning model, as well as analysis of results (SmARtview, 51088)
<p>This dataset and code was a result of the UKRI project "SmARtview: An AI-powered Augmented Reality Tool for Animal Health and Productivity", linked here: <a href="https://gtr.ukri.org/projects?ref=51088">https://gtr.ukri.org/projects?ref=51088</a></p> <p>These files are intended to be used for an accompanying publication in an academic journal.</p> <p>Anyone is free to use the contents for research and teaching purposes.</p>
Result of COJO analysis on 7 chronic pain types
<p>JMA files were obtained from COJO analysis ran across 7 chronic pain types: neck, back, hip, knee, abdominal, and facial and headaches. I used the GCTA-COJO tool along with the summary statistics uploaded in this repository and a reference panel produced using our bgen files from UKB. There are only 6 files uploaded as there were no SNPs returned from the COJO analysis for the chronic facial pain phenotype.</p>
Results of the differential gene expression analysis in SIV infection in Chlorocebus sabaeus and Macaca mulatta
<p>Results of differential gene expression analysis in SIV infection in Chlorocebus sabaeus and Macaca mulatta.</p> <p>From the transcriptome data repository MACE (http://mace.ihes.fr)</p>
The raw microarray data and the differential expression analysis results from "Manipulating the growth environment through co-culture to enhance stress tolerance and viability of probiotic strains in the gastrointestinal tract".
<p>The signal data for each spot were subsequently quantified by using Feature Extraction software (Agilent Technologies).M1.txt to M5.txt: monoculture; C1.txt to C5.txt: co-culture; P1.txt to P5.txt: pH-controlled monoculture. The differential expression analysis results were obtained by using limma.</p>
Plastid-nuclear ERCnet analysis results
Open the record for dataset details and reuse information.
Data from: Single cell RNA-seq analysis reveals that prenatal arsenic exposure results in long-term, adverse effects on immune gene expression in response to Influenza A infection
<p>Arsenic exposure via drinking water is a serious environmental health concern. Epidemiological studies suggest a strong association between prenatal<i> </i>arsenic exposure and subsequent childhood respiratory infections, as well as morbidity from respiratory diseases in adulthood, long after systemic clearance of arsenic.<i> </i>We investigated the impact of exclusive prenatal arsenic exposure on the inflammatory immune response and respiratory health after an adult influenza A (IAV) lung infection. C57BL/6J mice were exposed to 100 ppb sodium arsenite<i> in utero,</i> and subsequently infected with IAV (H1N1) after maturation to adulthood. Assessment of lung tissue and bronchoalveolar lavage fluid (BALF) at various time points post IAV infection reveals greater lung damage and inflammation in arsenic exposed mice versus control mice. Single-cell RNA sequencing analysis of immune cells harvested from IAV infected lungs suggests that the enhanced inflammatory response is mediated by dysregulation of innate immune function of monocyte derived macrophages, neutrophils, NK cells, and alveolar macrophages. Our results suggest that prenatal arsenic exposure results in lasting effects on the adult host innate immune response to IAV infection, long after exposure to arsenic, leading to greater immunopathology. This study provides the first direct evidence that exclusive prenatal exposure to arsenic in drinking water causes predisposition to a hyperinflammatory response to IAV infection in adult mice, which is associated with significant lung damage.</p>
Thesis DRIS leaf nutrient analysis results
<p>The data file contains results from leaf nutrient analysis that have been analyzed with the Florida citrus DRIS program, created by Arnold Schumann (UF IFAS Citrus Research and Education Center, Soil and Precision Agricultura Lab). This data was used to train an AI model to recognize nutrient deficiencies of citrus. </p>
Weight loss, insulin resistance, and study design confound results in a meta-analysis of animal models of fatty liver
The classical drug development pipeline necessitates studies using animal models of human disease to gauge future efficacy in humans, however there is a low conversion rate from success in animals to humans. Non-alcoholic fatty liver disease (NAFLD) is a complex chronic disease without any established therapies and a major field of animal research. We performed a meta-analysis with meta-regression of 603 interventional rodent studies (10,364 animals) in NAFLD to assess which variables influenced treatment response. Weight loss and alleviation of insulin resistance were consistently associated with improvement in NAFLD. Multiple drug classes that do not affect weight in humans caused weight loss in animals. Other study design variables, such as age of animals and dietary composition, influenced the magnitude of treatment effect. Publication bias may have increased effect estimates by 37-79%. These findings help to explain the challenge of reproducibility and translation within the field of metabolism.
Raw data and analysis results in paper by Cho and Iwata published in JGR
<p>Thirty-two microtremor arrays were analyzed in Cho and Iwata (2021) (Cho, I., & Iwata, T., 2021, Limits and benefits of the spatial autocorrelation microtremor array method due to the incoherent noise, with special reference to the analysis of long wavelength ranges. Journal of Geophysical Research: Solid Earth, 126, e2020JB019850. https://doi.org/10.1029/2020JB019850). This archive includes the raw digital data of microtremors and analysis results, plots of the processing results of individual arrays, and script files to plot some graphs.</p> <p> </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.