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Dataset from "Matthieu Delescluse and Christophe Pouzat (2006) Efficient spike-sorting of multi-state neurons using inter-spike intervals information Journal of Neuroscience Methods 150: 16-29."
<p>The dataset (in HDF5 format) used in Delescluse and Pouzat (2006) Efficient spike-sorting of multi-state neurons using inter-spike intervals information Journal of Neuroscience Methods 150: 16-29. arXiv:q-bio/0505053. See this reference for recording details. Data collected by Matthieu Delescluse. Briefly, 4 channels (data sets Channel_0,1,2,3, organized in a group called 'ExtracellularData'; extracellular recordings along the Purkinje cell layer of a young rat cerebellar cortex slice) of a linear 'Michigan' (now Neuronexus) probe and a loose cell-attached recording (data set Reference, in group 'CellAttached') from one of the Purkinje cells that is also extracellularly recorded: a 'ground truth' for spike sorting algorithms. Each group has three attributes: SamplingRate, HighPass and LowPass. The last two are the filter settings used prior to A/D conversion. These attributes have identical values for the 5 traces (2 groups): the data were sampled at 15 kHz, high-passed at 300 Hz and low-passed at 5 kHz.</p>
GCMMA-MMA-Python: Python implementation of the Method of Moving Asymptotes
This record contains the Python implementation of the Method of Moving Asymptotes (MMA), originally developed and written in MATLAB by Krister Svanberg. The MMA algorithm is used for solving non-linear programming problems. Users of this code are encouraged to inform Krister Svanberg of their application and intentions via email, as provided on his website. When publishing work that uses this code, please cite Krister Svanberg's original academic work.
Climate Forcing due to Future Ozone Changes: An intercomparison of metrics and methods
<p>The data provided in this repository relates to a paper on ozone radiative forcing submitted for publication in Atmos. Chem. Phys., as part of the TOAR-II special issue (<a href="https://acp.copernicus.org/articles/special_issue1256.html">ACP – Special issue – Tropospheric Ozone Assessment Report Phase II (TOAR-II) Community Special Issue (ACP/AMT/BG/GMD inter-journal SI)</a>). The paper is entitled "<span>Climate Forcing due to Future Ozone Changes</span><span>: An intercomparison of metrics and methods" by authors <span><span>William J. Collins</span></span><span><span>,</span> <span>Fiona M. O’Connor</span></span><span><span>, </span><span>Connor R. Barker</span></span><span><span>, </span><span>Rachael E. Byrom</span></span><span><span>, </span><span>Sebastian D. Eastham</span></span><span><span>,</span> <span>Øivind Hodnebrog</span></span><span><span>, Patrick Jöckel</span></span><span><span>, </span><span>Eloise A. Marais</span></span><span><span>, </span><span>Mariano Mertens</span></span><span><span>, Gunnar Myhre</span></span><span><span>, Matthias Nützel</span></span><span><span>, Dirk Olivié</span></span><span><span>, Ragnhild </span><span>Bieltvedt</span><span> Skeie</span></span><span><span>5</span></span><span><span>, Laura Stecher</span></span><span><span>, Larry W. Horowitz</span></span><span><span>, Vaishali Naik</span></span><span><span>, Gregory Faluvegi</span></span><span><span>, Ulas Im</span></span><span><span>, Lee T. Murray</span></span><span><span>, Drew Shindell</span></span><span><span>, Kostas Tsigaridis</span></span><span><span>, Nathan Luke Abraham</span></span><span><span>, James Keeble.</span></span></span></p>
The role of injection method on residual trapping at the pore-scale in continuum-scale samples: segmented data
<p>The experiments in this work explore the role of a variable injection rate on gas saturation and residual trapping. There are 2 experiments in this work H2L (high to low injection rate) and L2H (low to high injection rate). The workflow for processing the micro-CT images to get the segmented images is described in [1]. </p><p>The following scans are included in this repository NB. all data for this repository is segmented micro-CT data.: </p><ol><li>Dry scan prior to experiment = merged_binning_2_38_1927</li><li>H2L during high flow = merged_segmented_flow_09_h2lh_merged</li><li>H2L during low flow = merged_segmented_flow_11_h2ll_2_merged</li><li>H2L at the end of drainage (no flow) =merged_segmented_flow_16_dra1_pd5_merged</li><li>H2L at the end of imbibition (no flow) =merged_segmented_flow_21_imb1_pi1_merged</li><li>L2H during low flow = merged_segmented_flow_29_2_l2hl_merged</li><li>L2H during high flow = merged_segmented_flow_30_l2hh_merged</li><li>L2H at the end of drainage (no flow) =merged_segmented_flow_31_dra2_pd1_merged</li><li>L2H at the end of imbibition (no flow) =merged_segmented_flow_33_imb2_pi1_merged</li></ol>
Statistical analysis and dataset for: A high-throughput and sensitive method for food preference assays in walking insects
<p>Linked to the journal article published in bioRxiv (https://doi.org/10.1101/2024.04.10.588882).</p> <p><em><strong>Abstract</strong></em></p> <p>Insects pose significant challenges in both pest management and ecological conservation. Often, the most effective strategy is employing toxicant-laced baits, which must also be designed to specifically attract and be preferred by the targeted species for optimal species-specific effectiveness. However, traditional methods for measuring bait preference are either non-comparative, meaning that most animals only ever taste one bait, or suffer from methodological or conceptual limitations. Here we demonstrate the value of direct comparison food preference assays using the invasive and pest ant <em>Linepithema humile </em>as a model. We compare the food preference sensitivity of non-comparative (one visit to a food source) and sequential comparative (visiting one type of food then another) assays at detecting low levels of aversive quinine in sucrose solution. We then introduce and test a novel dual-choice feeder method for simultaneous comparative evaluation of bait preferences, testing its effectiveness in discerning between foods with varying quinine or sucrose levels. While the non-sequential assay could not detect aversion to 1.25mM quinine in 1M sucrose, the sequential comparative approach detected aversion to quinine levels as low as 0.94mM. The novel dual feeder method approach could detect aversion to quinine levels as low as 0.31mM, and also preference for 1M sucrose over 0.75M sucrose. The dual-feeder method, combines the sensitivity of comparative evaluation with high throughput, ease of use, and avoidance of interpretational issues. This innovative approach offers a promising tool for rapid and effective testing of bait solutions, contributing to the development of targeted control strategies. Moreover, the method can be easily modified for application to a wide range of walking insects, such as cockroaches, crickets, and beetles.</p>
Analysis of two Methods for Aircraft Fuel Requirement Calculations in the Context of a novel Methodological Framework for LCA of Sustainable Aviation
<p>This Microsoft Excel file contains equations to compare different approaches to calculate fuel efficiency ("energy use" in [MJ/t*km]) of aircraft over a specific distance at a specific payload. </p> <p>Two approaches are compared: A novel approach by <a href="10.1016/j.scitotenv.2023.163881" target="_blank" rel="noopener">Su-ungkavatin et al.</a> and the more established approach well documented by eg. <a href="https://www.fzt.haw-hamburg.de/pers/Scholz/arbeiten/TextBurzlaff.pdf" target="_blank" rel="noopener">Burzlaff</a> or <a href="http://www.aircraftmonitor.com/uploads/1/5/9/9/15993320/aircraft_payload_range_analysis_for_financiers___v2.pdf" target="_blank" rel="noopener">Ackert</a>.</p> <p>This work augments a Letter to the Editor we submitted to the journal <a href="https://www.sciencedirect.com/journal/science-of-the-total-environment" target="_blank" rel="noopener">Science of the Total Environment</a>.</p>
A multi-method study of femtosecond laser modification and ablation of amorphous hydrogenated carbon coatings
<p>We report here the optical constants of ECR (MW) and RF generated a-C:H layers before and after laser irradiation. The work is described in the following publication:</p> <p><a title="A multi-method study of femtosecond laser modification and ablation of amorphous hydrogenated carbon coatings" href="https://doi.org/10.1007/s00339-024-07980-z" target="_blank" rel="noopener">https://doi.org/10.1007/s00339-024-07980-z</a></p> <p>The data uploaded are the optical constants (n and k) of the a-C:H layers before (base) and after (ROIx) laser irradiation. Please see the article for the nomenclature of the data and for the methods applied ot produce the layers, laser shots, and OK data.</p>
Data from Yellow Sigatoka monitoring methods in the subtropical climate of southern Brazil
<h2>Description of the data and file structure</h2> <p>In this study four methods of disease monitoring were tested under field conditions: Biological Pre Warning (BPW); Stage of Evolution (SE); youngest Leaf Spotted (YLS); Infection Index (II). The BPW system evaluates the youngest leaves (2, 3, and 4), assigning a value for each type of lesion present, as well as for intensity of the lesion on the leaves (BUREAU et al., 1992). In the dataset is cited as the variable gross sum (points).</p> <p>The SE evaluates more leaves (1, 2, 3, 4, and 5) and scores only the most advanced symptoms of leaf disease, but without considering lesion intensity (GANRY et al., 2008). The SE calculation also corrects the gross sum of the disease according to leaf emission. The leaf emission rate was calculated using the Brun scale, which evaluates cigar leaf growth in decimals from 0.0 to 0.8. In the dataset is cited as the variable corrected gross sum (points).</p> <p>YLS is evaluated as the first leaf that has 10 spots with gray centers (CARLIER et al., 2003). In the dataset is cited as the variable YLS, which means the leaf position counted from the top to the botton of the plant (leaf number 3, leaf number 4...).</p> <p>Sigatoka Infection Index is quantified by assessing the severity of banana leaf disease using the Stover scale, with indexes from 0 to 50%, by means of the following formula: Infection Index =% (IF): [Σn × b / (N- 1) × T] × 100, in which: n = the number of leaves at each Stover scale level; b = degree according to the scale; N = the number of degrees employed in the scale (6); T = the total number of leaves evaluated (CARLIER et al., 2003). In the dataset is cited as the variable Infection index that should be understood like the severity of this leaf disease.</p> <p>In the second phase of the study, two monitoring methods were applied in commercial orchards in order to compare the standard model (Biological Pre-Warning – BPW) with the alternative method selected in the experimental phase (Youngest Leaf Spotted – YLS). The methods were applied, as described before in three sites in Criciúma (site 1) and Siderópolis (sites 2 e 3), municipalities in the southern coast of the state of Santa Catarina, from March 2016 to November 2018. During this period, 37 disease evaluations were performed at each location.</p> <p>Disease data of the experimental area were submitted to descriptive analysis and Pearson correlation at 5% probability of error. Disease progress curves were also plotted. The disease development data in commercial orchards were analyzed by plotting disease progress curves for BPW and by frequency distribution (%) for the YLS variable during all period of the experiment.</p>
Synthetic cryo electron subtomograms containing biomolecular complexes with continuous conformational variability, used for validating TomoFlow method
<p>Two datasets used for validating TomoFlow method, an optical-flow based approach for analyzing continuous conformational variability of biomolecular complexes in cryo electron subtomograms. The TomoFlow method and the methods used to synthesize the two test datasets have been fully described in the following article: "M. Harastani, M. Eltsov, A. Leforestier, S. Jonic, TomoFlow: Analysis of continuous conformational variability of macromolecules in cryogenic subtomograms based on 3D dense optical flow, Journal of Molecular Biology (2021), doi: https://doi.org/10.1016/j.jmb.2021.167381". Additionally, this article describes a test of TomoFlow using one experimental cryo electron tomography dataset (available in EMPIAR and EMDB databases under the accession codes EMPIAR-10679 and EMD-12699). </p>
Annotations to direct and indirect image rotation estimation methods of orthopedic X-ray images
<p>The annotation file contains labels for AP wrist images of the MURA dataset on the center line of the radius bone. The annotations are stored in json format. For each annotated image file of the MURA dataset an entry is provided with the coordinates of the start and end point of the radius' center line.</p>
Dataset for "Numerical methods for the detection of phase defect structures in excitable media"
<p>This archive contains the numerical methods presented in the publication "Numerical methods for the detection of phase defect structures in excitable media" as well as the data sets these methods have been applied on. The Python module for Ithildin (py_ithildin.zip) contains the actual Python source code of those methods. Additional Python scripts have been used to generate the figures in the paper (scripts-pdl-detection.zip). The optical voltage mapping data (optical_*) has been slightly pre-processed (noise reduction, re-scaling, etc). The second variable for the optical data (optical_20200204114234_v.npy) is a delayed version of the first variable. The other files contain simulation results from several finite differences simulations of the mono-domain model. For details, see our paper.</p> <p><a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0271351"><strong>Numerical methods for the detection of phase defect structures in excitable media</strong></a><br> Kabus D, Arno L, Leenknegt L, Panfilov AV, Dierckx H (2022) Numerical methods for the detection of phase defect structures in excitable media. PLOS ONE 17(7): e0271351. <a href="https://doi.org/10.1371/journal.pone.0271351">https://doi.org/10.1371/journal.pone.0271351</a></p>
Regional Estimates of Chemical Composition of Fine Particulate Matter Using a Combined Geoscience-Statistical Method with Information from Satellites, Models, and Monitors: V4.NA.02.MAPLE
<p>We estimate ground-level fine particulate matter (PM<sub>2.5</sub>) total and compositional mass concentrations over North America by combining Aerosol Optical Depth (AOD) retrievals from the NASA MODIS, MISR, and SeaWIFS instruments with the GEOS-Chem chemical transport model, and subsequently calibrated to regional ground-based observations of both total and compositional mass using Geographically Weighted Regression (GWR) as detailed in the provided reference for V4.NA.02. V4.NA.02.MAPLE further modified the V4.NA.02 GWR method with additional developments as part of the MAPLE (Mortality–Air Pollution Associations in Low-Exposure Environments) project. This adjustment was of particular value over low concentrations. The GWR method of individual components remains unchanged from V4.NA.02, but are provided are percentages to ensure mass closure and recommended to be applied to the V4.NA.02.MAPLE total PM<sub>2.5</sub>.</p> <p>Annual datasets are provided in NetCDF [.nc]. Gridded files use the WGS84 projection. Compositional estimates are provided for sulfate (SO4), nitrate (NO3), ammonium (NH4), organic matter (OM), black carbon (BC), mineral dust (DUST), and sea-salt (SS). Percentages are denoted with a ‘p’ after component identifiers within filenames. A slight change in file name has been included for 2017, corresponding to minor internal changes compared to earlier years. Overall, however, the dataset is consistent throughout its entire time period and can be appropriately used for trend analysis.</p> <p><strong>Reference:</strong><br> van Donkelaar, A., R. V. Martin, et al. (2019). <strong>Regional Estimates of Chemical Composition of Fine Particulate Matter using a Combined Geoscience-Statistical Method with Information from Satellites, Models, and Monitors.</strong> Environmental Science & Technology, 2019, doi:10.1021/acs.est.8b06392.</p>
A Novel Crop Shortlisting Method for Sustainable Agricultural Diversification Across EU (Italy)
<p>In order to shortlist possible options from a pool of 2700 crops, a crop-climate-soil matching ex-ercise was performed across Italian territory and crops with more than 70% suitability where chosen for further analysis. In the second phase, a multicriteria ranking index was employed to assign ranks to chosen crops of 4 main types; (i) cereals and pseudocereals, (ii) legumes, (iii) starchy roots/ tubers and (iv) vegetables. In order to provide a comprehensive analysis, major crops that are grown in the region where also included in the analysis. The results of evaluation of 4 major criteria (a) calorie and nutrition demand b) functions and uses c) availability and acces-sibility to their genomic material d) possession of adaptive traits, and e) physiological traits) re-vealed the potential for teff, faba bean, cowpea, green arrow arum, Jerusalem artichoke, Fig-leaved Gourd and Watercress. </p>
Characterization of TiO2/Fe2O3 nanocomposites prepared via impregnation-calcination method
<p>The link contains XRD, SEM-EDX, UV-DRS, PL, Electrochemical measurements of the prepared TiO<sub>2</sub>/Fe<sub>2</sub>O<sub>3</sub> photocatalyst</p>
Marine plastics alter the organic matter composition of the air-sea boundary layer, with influences on CO2 exchange: a large-scale analysis method to explore future ocean scenarios
<p>Microplastics are substrates for microbial activity and can influence biomass production. This has potentially important implications in the sea-surface microlayer, the marine boundary layer that controls gas exchange with the atmosphere and where biologically produced organic compounds can accumulate. In the present study, we used six large scale mesocosms to simulate future ocean scenarios of high plastic concentration. Each mesocosm was filled with 3 m3 of seawater from the oligotrophic Sea of Crete, in the Eastern Mediterranean Sea. A known amount of standard polystyrene microbeads of 30 μm diameter was added to three replicate mesocosms, while maintaining the remaining three as plastic-free controls. Over the course of a 12-day experiment, we explored microbial organic matter dynamics in the sea-surface microlayer in the presence and absence of microplastic contamination of the underlying water. Our study shows that microplastics increased both biomass production and enrichment of carbohydrate-like and proteinaceous marine gel compounds in the sea-surface microlayer. Importantly, this resulted in a 3 % reduction in the concentration of dissolved CO2 in the underlying water. This reduction was associated to both direct and indirect impacts of microplastic pollution on the uptake of CO2 within the marine carbon cycle, by modifying the biogenic composition of the sea's boundary layer with the atmosphere.</p>
Data for: Impact of SO2 injection profiles on simulated volcanic forcing for the Sarychev 2009 eruptions - investigating the importance of using high vertical resolution methods when compiling SO2 data
<p>The files are data assosicated with the study High-resolution stratospheric volcanic SO2 injections in WACCM. The files are associated with four differnt simulaions described in the paper: M16, S21-1D, S21-3D and No-Volc. The files with "input" in the name are the SO2 input files used in the WACCM (Whole Atmosphere Community Climate Model) simulations in the paper. The files with "monthly_averages" in the filenames are monthly averages of model output data the variables used in the paper. </p> <p>The CALIOP_monthly_averages.nc file is monthly average of the CALIOP (Cloud-Aerosol Lidar with Orthogonal Polarization) satellite data used in the study to evaluate the WACCM simulations. </p> <p> </p>
Dataset of the paper entitled methods for high-throughput screening of novel agents against the maize pest, Diabrotica virgifera virgifera (Coleoptera: Chrysomelidae)
<p>Title: Methods for high-throughput screening of novel agents against the maize pest, Diabrotica virgifera virgifera (Coleoptera: Chrysomelidae) </p> <p>Authors: Sri Ita Tarigan, Gyorgy Turoczi, Jozsef Kiss, Stefan Toepfer</p> <p>Abstract: <br>The western corn rootworm, <em>Diabrotica virgifera virgifera</em> (Coleoptera: Chrysomelidae), poses a significant threat to maize crops in North America and Europe, necessitating development of novel, effective, and less disruptive crop protection agents. With recent bans on key insecticides and concerns about overuse of remaining options, there is an urgent need for accessible and comparable screening methods. We propose comparative high-throughput screening methods against the eggs, larvae and adults of this pest, emphasizing the importance of suitable positive controls tailored to the specific bioassay types. We evaluated seven common insecticides (imidacloprid, clothianidin, acetamiprid, novaluron, cypermethrin, chlorpyrifos-methyl, spinosad) against eggs, larvae, and adults as potential positive controls for each of the proposed assay methods. Dipping assays with ready-to-hatch eggs revealed several ingredients to cause mortality; but imidacloprid might be most suitable as a positive control due to its robust dose-response in reducing egg hatching and causing mortality of hatching neonates. Larval bioassays using artificial diet overlay assays revealed mortality caused by all insecticides, with imidacloprid and acetamiprid exhibiting best dose-mortality response curves as well as sublethal effects. Adult bioassays using artificial diet-core overlay assays revealed mortality caused by all insecticides, with cypermethrin or acetamiprid exhibiting best dose-mortality response curves. The provided ED <sub>50</sub>, ED <sub>80</sub> values, and dose-response equations offer valuable insight for researchers in selecting appropriate positive controls for screening new crop protection agents or assessing resistance levels against different life stages of this pest.</p> <p>Data:</p> <p>The data file is related to the screening of commercial insecticides against eggs, first instar larvae (L1) and adults of the maize pest, <em>Diabrotica virgifera virgifera</em> using standard bioassays. We are proposing comparative high-throughput screening methods against the eggs, larvae and adults of this maize pest. This includes the crucial aspect of suitable positive controls tailored to the specific bioassay type. We evaluated seven common insecticides (imidacloprid, clothianidin, acetamiprid, novaluron, cypermethrin, chlorpyrifos-methyl, spinosad) against eggs, larvae, and adults as potential positive controls for each of the proposed assay method. To access effects and dose-responses of commonly used insecticides on eggs, we applied standard screening methods under controlled semi-sterile conditions.</p> <p>For egg bioassays, eggs were transferred to the 200 ml of treatments in the eppendorf tubes and then soaked for 1 hour. Then 20µl with 10 to 20 eggs were pipetted onto a filter paper in a petri dish (150 mm×25 mm). Then 100 µl of sterilized tap water was added for moisture. The pipette tip was replaced between treatments. The eggs been transferred were counted per filter paper and dish (15± 8). The eggs were then incubated in the dishes at 23-25<sup>0</sup>C for 7 days, when the experiment was terminated. Egg hatching, mortality of newly hatching larvae, and days until start of egg hatching were observed under stereo microscope and recorded. Data were collected at 1,3, 5 and 7 days after treatments.</p> <p>To assess the effect and dose-responses of commonly used insecticides on neonates of <em>D. v. virgifera</em>, we applied artificial diet-overlay bioassays under controlled semi-sterile conditions. Each insecticide was prepared in at least six concentrations. Each bioassay consisted of 3 to 6 polystyrene plates of 96 wells each (07-6096 of Biologix Ltd., USA, or Costar 3917 of Corning Inc., USA). Each well had a volume of 330 µl, with a diameter of 5 mm, a height of 10 mm, and a surface area of 0.34 cm². 190 µl of the diet were pipetted into each 330 µl well, filling each to approximately 2/3<sup>rd </sup>of its capacity. Plates containing the diet were left to dry in a laminar flow cabinet for 45 minutes and then stored overnight at temperatures ranging from 3 to 5°C. The following day, treatments were applied. This is, 17 µl of a treatment was applied to the 0.34 cm<sup>2</sup> diet surface reaching good coverage and therefore forcing the after-placed larvae to feed through (10 to 100 µl pipette Biohit TM Proline). Each treatment was applied to 8 wells per plate. Following application, the plates were allowed to dry for a duration of 1 to 1.5 hours and were subsequently cooled for 1 hour in a refrigerator set at temperatures between 23 to 25°C. Each well received one neonate larva, carefully placed on the diet surface using a fine artist brush. A vigorous and visibly healthy larva was selected, lifted from the end of the abdomen with the brush, maneuvered towards a well surface, and allowed to crawl off the brush onto the diet. To avoid systematic errors, larvae were not arranged in treatment column order but rather in a rectangular pattern. After every 12 individual larvae, the brush was cleaned using 70% ethanol followed by sterile tap water. The filled plate was sealed with an optically clear adhesive qPCR seal sheet (#AB-1170, Termo Scientific, USA, or #BS3017000, Bioleader, USA), enabling data assessments without the need to open the plate. Four to five holes were carefully made with fine 00-insect pins into the seal per well to facilitate aeration. The plates, housing the larvae, were then incubated in a dark, ventilated incubator at a temperature of 23-25 °C and a relative humidity of 50 to 90% for a period of 5 days. We assessed mortality and stunting larvae within 3 and 5 days. </p> <p>To access the effect and dose-responses of common insecticides on <em>D.v.virgifera</em> adults, artificial diet-overlay bioassays with different doses were performed under controlled, semi-sterile conditions. Each insecticide was prepared in at least six concentrations. Active ingredients as specified on the product labels underwent serial dilutions using sterile tap water. Sterilized tap water was used as untreated control. In detail, each bioassay consisted of 6 polystyrene plates of 6 wells each (Eppendorf® 0030720016). Each treatment was applied to 3 wells of each plate per bioassay. The adult diet for a bioassay had been prepared 1-7days before treatment and adult infestation. The diet was prepared under semi-sterile conditions. The diet was poured out to 5-6 sterile 11 mm Petri dishes. The plates with diet were allowed to dry for up to 15 minutes under laminar flow cabinet then stored at 3 to 5°C overnight.The following day, a core of the diet was initially transferred to each well using flamed iron core-cutter (1 cm diameter) under a laminar flow. A core diet was placed each of the 6 wells of the plates. Approximately 40 µl of the treatments were then applied across the surface of diet core (0.34 cm<sup>3</sup>). The following day, a core of the diet was initially transferred to each well using flamed iron core-cutter (1 cm diameter) under a laminar flow. A core diet was placed each of the 6 wells of the plates. Approximately 40 µl of the treatments were then applied across the surface of diet core (0.34 cm<sup>3</sup>). Adult were subsequently transferred from the rearing cage into the wells of the 6-well plates containing the diet and treatments using a tube aspirator. For ease of transfer, the adults were cooled in a fridge for 4 to 7 minutes. Each well plate received 3 to 4 adults. Plates were sealed and incubated at 23-25<sup>0</sup>C, 50–90% r.h, L: D 12:12. Adult mortality were recorded on days 1,3, 5, 7 of experiment. </p> <p>To allow comparisons between experiments, data were standardized to the data of the corresponding negative control, usually sterilized tap water, as follows: standardized data = 100 × (data in negative control - data in treatment)/maximum (data in control or in treatment). The distributions of the data were investigated using histograms and QQ normal and detrended normal probability. Skewness and kurtosis of residuals was also observed for normality of influences of treatments on eggs, neonates, or adults. Equality of variances was assessed using Levene’s test. Multiple comparisons were performed using the Tukey HSD post hoc test for data with equal variances and the Games-Howell post hoc test for data with unequal variances. For each tested insecticide, linear and logarithmic regression models were fit to the dose-response data. In case of significant linear or logartimic relathionships, doses leading to 50% or 80% of relative effects (ED <sub>50,80</sub>) were calculated. </p> <p>The raw data as well as the standardised data are available as a csv file on zenodo. </p> <p> </p> <p> </p>
Dataset for: Evaluating phylogenetic methods for quantifying risks and opportunities presented by forks in open source software (master dissertation).
<p>This is the data for my master dissertation [1]. If you wish to get a copy, download it from Zenodo and open docs/master.pdf.</p> <p>Data acquisition and encoding techniques are described in paragraph 3.1.1 (table 3.1).</p> <p>The data is described in more detail in paragraph 4.1 (table 4.2).</p> <p>* fork1_all.csv: MySQL server / MariaDB server<br> * fork2_all.csv: Linux kernel / Android kernel<br> * fork3_all.csv: Apache OpenOffice / LibreOffice</p> <p>==Cite==<br> [1] A. Ortiz-Troncoso. Evaluating phylogenetic methods for quantifying risks and opportunities presented<br> by forks in open source software (master dissertation). Zenodo, 2018. doi: http://doi.org/10.5281/zenodo.1158292</p>
Bayesian Methods for Ancestral State Reconstruction in Morphosyntax
<p>Supplementary files to accompany journal submission.</p> <p>Files are:</p> <p> </p> <p>tree.pdf - pdf consensus tree, for illustration</p> <p>data.txt - coding file</p> <p>TREE_Set.t - nexus format sample of trees.</p> <p>sources.pdf - source materials used for languages</p>
Dataset Comparison of MRI-based automated segmentation methods and functional neurosurgery targeting with direct visualization of the Ventro-intermediate thalamic nucleus at 7T
<p>Scientific Reports - Nature - DOI : 10.1038/s41598-018-37825-8</p> <p>##################################<br> "Comparison of MRI-based automated segmentation methods and functional neurosurgery targeting with direct visualization of the Ventro-intermediate thalamic nucleus at 7T"<br> ##################################</p> <p>E. Najdenovska*, C. Tuleasca*, J. Jorge, P. Maeder, J.P. Marques, T. Roine, D. Gallichan, J.-P. Thiran, M. Levivier, and M. Bach Cuadra</p> <p>*Equally contributed authors</p> <p><br> Copyright (c) - All rights reserved. University of Lausanne. 2018.</p> <p><br> To reproduce the analyses presented in the referred study, in this repository you could find the MR images acquired from nine young healthy subjects (YS1-YS5), four elderly healthy subject (ES1-ES4) and two drug-resistant tremor patients treated treated with Vim radiosurgery by Gamma Knife (P1 and P2).</p> <p>The provided dataset includes the following NifTI files:</p> <p>- MPRRAGE @3T<br> - DWI @3T (together with the corresponding bvals and bvecs)<br> - MP2RAGE @7T<br> - SWI @7T<br> - binary masks of the manual delineation of both left and right Vim respectively that were done on the SWI (as NifTI files as well).</p> <p>Additionally, for the young cohort (YS1-YS5) we include as well the images used for building the quadrilateral of Guiot:<br> - T2-w @3T<br> - T2 CISS @3T</p> <p>For the patients (P1 and P2), a follow-up MPRAGE (acquired at 3T) with Gadolinium enhancement is also provided.</p> <p>——————————————<br> Notes:<br> 1. For YS3 MP2RAGE at 7T is missing, instead MPRAGE at 3T was used</p> <p>2. The code performing the thalamic nuclei clustering could be found in Zenodo (DOI: 10.5281/zenodo.123768)</p>
ScienceDex guides
Understand access before you commit
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.