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4,090 results for “Protocol”
Experimental Protocol on Creative Engagement and Meaning Creation in Interactive Experiences for Cultural Heritage. Tabular Data
<p>The following document contains the material produced for the testing of the "caring prototype" <em>MyTISSE</em>, an interactive user experience on Matisse's painting <em>Bathers by a rive</em>r (Art Institute of Chicago). Focusing on the change of the pigments made by the artist during the gestation of this canvas, the UX exploits creative engagement to catalyze meaning creation processes.</p> <p>This pubblication contains the data collected through the form. All the participants agreed to the reuse and sharing of these data for academic purposes, filling in an <em>ad hoc </em>privacy form.</p>
Reads-per-UMI tables across single-cell RNA sequencing protocols
<p>Data analyzed in <a href="https://www.biorxiv.org/content/10.1101/2023.08.02.551637v1">Lause, Ziegenhain et al. (2023)</a>.</p> <p>Code to obtain these tables from public data sources is available on <a href="https://github.com/berenslab/read-normalization">github</a>.</p> <p> </p> <p>Each row in the table is a UMI-tag detected in a certain cell (column RG) attached to a molecule from a specific gene (column GE) with a certain barcode (column UB). Column N gives the number of times the UMI was detected for that gene and cell.</p> <p>Data sources and protocols are given with the respective file names below.</p> <p><strong>Johnsson2022_Smartseq3_PE.hd1.txt.gz</strong>: Mouse fibroblasts profiled with <strong>Smart-seq3</strong> paired-end; accession E-MTAB-10148, sample plate2,<br> <a href="https://doi.org/10.1038/s41588-022-01014-1">Paper</a><br> <br> <strong>Hagemann-Jensen2020_Smartseq3_SE.hd1.txt.gz: </strong>Mouse fibroblasts profiled with <strong>Smart-seq3</strong> single-end; accession E-MTAB-8735, sample Smartseq3.Fibroblasts.smFISH<br> <a href="https://doi.org/10.1038/s41587-020-0497-0">Paper</a><br> <br> <strong>Hagemann-Jensen2022_Smartseq3xpress.hd1.txt.gz: </strong>HEK293 cells profiled with <strong>Smart-seq3Xpress</strong>; accession E-MTAB-11467.<br> <a href="https://www.biorxiv.org/content/10.1101/2021.07.10.451889v1">Paper</a><br> <br> <strong>Ziegenhain2017.hd1.txt.gz: </strong>Mouse embryonic stem cells profiled by <strong>CEL-seq2, Drop-seq, MARS-seq, </strong>and<strong> SCRB-seq</strong>; GEO accession GSE75790<br> <a href="https://doi.org/10.1016/j.molcel.2017.01.023">Paper</a></p>
Data deposit accompanying Accurate Energy Barriers for Catalytic Reaction Pathways: An Automatic Training Protocol for Machine Learning Force Fields
<p>Dataset accompanying the paper: <em>"Accurate Energy Barriers for Catalytic Reaction Pathways: An Automatic Training Protocol for Machine Learning Force Fields"</em>. Contains the training sets curated during active learning as well as .xyz files used for creating the Figures. <br> <br> The paper highlights that the computational efficiency of ML force fields not only results in decreased computational costs for routine catalytic investigations but also facilitates more comprehensive exploration of catalytic pathways.</p> <p><strong>Published in NPJ Computational Materials</strong>: <a href="https://www.nature.com/articles/s41524-023-01124-2">https://www.nature.com/articles/s41524-023-01124-2</a><br> Formerly on Arxiv: <a href="https://arxiv.org/abs/2301.09931">https://arxiv.org/abs/2301.09931</a></p>
Accuracy of EFP/AAP 2018 and CDC/AAP 2012 in partial periodontitis diagnostic protocols with 11-12 & 13-14 NHANES periodontal data
<p>Accuracy of EFP/AAP 2018 and CDC/AAP 2012 in partial periodontitis diagnostic protocols with 11-12 & 13-14 NHANES periodontal data</p>
Fig. 3 in Defining the reproductive period of freshwater fish species using the Gonadosomatic Index: a proposed protocol applied to ten species of the Patos Lagoon basin
Fig. 3. Monthly variation of Cyphocharax voga GSI values (adult females only) in Guaíba Lake (white) and Casamento Lake (dark gray), Rio Grande do Sul, Brazil (median, 25- 75% quartiles and lower-upper GSI limits by month and site). Three GSI cut-off values were tested with respect to the maximum GSI recorded for each species, for delimitation of reproductive months: 20% (G20), 30% (G30) and 40% (G40).
Fig. 5 in Defining the reproductive period of freshwater fish species using the Gonadosomatic Index: a proposed protocol applied to ten species of the Patos Lagoon basin
Fig. 5. Monthly variation of Oligosarcus jenynsii GSI values (adult females only) in Guaíba Lake (white) and Casamento Lake (dark gray), Rio Grande do Sul, Brazil (median, 25- 75% quartiles and lower-upper GSI limits by month and site). Three GSI cut-off values were tested with respect to the maximum GSI recorded for each species, for delimitation of reproductive months: 20% (G20), 30% (G30) and 40% (G40).
Fig. 2 in Defining the reproductive period of freshwater fish species using the Gonadosomatic Index: a proposed protocol applied to ten species of the Patos Lagoon basin
Fig. 2. Monthly variation of Astyanax fasciatus GSI values (adult females only) in Guaíba Lake (white) and Casamento Lake (dark gray), Rio Grande do Sul, Brazil (median, 25- 75% quartiles and lower-upper GSI limits by month and site). Three GSI cut-off values were tested with respect to the maximum GSI recorded for each species, for delimitation of reproductive months: 20% (G20), 30% (G30) and 40% (G40).
H2020 BuildHeat - Retrofit protocols
<p>The high share of energy consumption of the residential sector and the low renovation rate of existing buildings move through the need of finding solutions that facilitate the retrofit process. In this context, a set of retrofit solutions packages are studied for different multi-family house typologies located through Europe. Intervention on the envelope follows the actual national minimum requirements for energy efficiency, different efficient heating and cooling systems are recommended for the different building typologies and renewable energies technologies are considered for contributing to the reduction of energy consumption. Energy performance of the retrofit packages, energy savings and running costs are assessed through dynamic simulations for all the studied cases.</p> <p>The available documents are:</p> <p>- <strong>BuildHeat_T4.3_Database_ONLINE.xlsx</strong>: dataset of the simulation-based results. The studied retrofit packages applied to the building typologies in different locations are modelled in the TRNSYS environment and dynamic simulations through one year are run. The file collects energy performance of the reference case, energy performance of the retrofit case, divided by energy use (space heating, space cooling, Domestic Hot Water use, mechanical ventilation), and energy cost.</p> <p>- <strong>D4.4_BuildHeat_Report on systemic retrofit packages.pdf</strong>: document where the modelling of the project case studies is described in detail. The report includes energy performance, energy savings and energy costs. These case studies are used as reference case for the retrofit protocols definition.</p> <p>- <strong>D4.5_BuildHeat_Retrofit_protocols.pdf</strong>: Description of the studied building typologies, locations, retrofit packages including intervention on the envelope, replacement of the HVAC system and adoption of renewable energy technologies. This document contains the results reported in the dataset.</p>
A protocol to assess the risk of dementia among patients with coronary artery diseases using CAIDE score-Extended Data
<p>The contents of this extended data file are-<br> 01. Consent form (English & Bengali Version)<br> 02. Interview Questionnaire (English & Bengali Version)<br> These contents will help to address the objectives of the study that attempted to identify the risk of long-term dementia among coronary artery disease patients in Bangladesh.</p>
Performance measurements for in-depth energy analysis of security algorithms and protocols for the Internet of Things
<p>Performance dataset of cryptographic algorithms running on the following embedded devices (results in ms):</p> <p><strong>nuc </strong>The NUCLEO-L073RZ is a STM32 Nucleo-64 Development Board of STMicroelectronics. It features the STM32L073RZT6 32~MHz ARM Cortex-M0+ microcontroller with 192~KB flash memory and 20~KB RAM.<br> <strong>msp </strong>The TI SimpleLink MSP-EXP432P401R development kit uses the MSP432P401R 48~MHz ARM Cortex-M4F microcontroller with 256~KB flash and 64~KB RAM.<br> <strong>max </strong>The MAXREFDES\#100 health sensor platform features the MAX32620 96~MHz ARM Cortex-M4F microcontroller with 2~MB flash and 256~KB RAM. It has a wide range of sensors, like a human body temperature sensor and a heart rate sensor.</p> <p>The measured cryptographic operations:</p> <ul> <li><strong>The basic arithmetic operations for elliptic curve cryptography </strong>(point addition~(PA), point doubling~(PD), point multiplication~(PM), and fixed-point multiplication~(PMG))</li> <li><strong>The AES symmetric-key cipher in five modes of operations</strong> (Electronic Codebook (ECB), Cipher Block Chaining (CBC), Counter (CTR), Counter with CBC-MAC (CCM), and Galois/Counter Mode (GCM))</li> <li><strong>Hash functions </strong>(SHA256 and SHA3-256)</li> </ul> <p>The performance of all identified basic operations is measured on the three platforms. 50 time measurements are done for each basic operation using the platforms' available timer. Moreover, the AES cipher operation is an encryption on 256 Bytes of data. We have chosen a multiple of the AES block size, because, longer time periods ensure less influence of potential timing inaccuracies like an early start and late end. For the hash function, the maximum input size of the respective algorithm for one round is chosen as follows: 55~B for SHA256 and 135~B for SHA3-256. The total available internal state size is not used for SHA256 and SHA3-256, as we take into account the minimal padding or suffix that is required for the last block of input data. Note that the most optimal scenario, i.e. the maximum amount of input data to fill up the internal state completely, is used for each of the operations.</p> <p>All basic operations are implemented using software libraries and cross-compiled with the GNU Tools for ARM Embedded Processors version 6-2017-q2-update. Furthermore, the compiler is configured to optimise for size (-Os). The RELIC-toolkit library is used to implement the EC arithmetic and the SHA256 hash function. We use the SECG K-256 prime elliptic curve, BASIC;COMBA;COMBA;MONTY;MONTY;SLIDE configuration for the prime field arithmetic, and PROJC;LWNAF;COMBS;INTER}} configuration for the prime elliptic curve arithmetic. For more information on how to configure RELIC and other examples that use it, we refer to the relic-toolkit wiki. The AES ciphers are implemented using Mbed TLS and SHA3 using wolfCrypt. We use the SHA3-256 hash function as specified in FIPS PUB 202.</p>
Data accompanying the manuscript "Protocol Discovery for the Quantum Control of Majoranas by Differentiable Programming and Natural Evolution Strategies"
<p>Dataset for figures 2, A6 and A8 for the manuscript: "Protocol Discovery for the Quantum Control of Majoranas by Differentiable Programming and Natural Evolution Strategies." The dataset contains the optimal protocols for Majorana transport in both the Kitaev Chain model as well as the Proximity Coupled Semiconduncting Nanowire model obtained with Differentiable Programming and Natural Evolution Strategies. Also the Simulated Annealing (SA) optimal protocols for the Kitaev chain are included.</p>
FIG. 9 in Overview of Mitaraka survey: research frame, study site and field protocols
FIG. 9. — Sample size and sorting process according to the sampling type and impact on the quantity and availability of specimens for taxonomic study. Process for broad-spectrum traps: A, automatic light trap with blue LED; B, yield of the trap after one week; C, conditioning of the sample in the field laboratory, and storage in WhirlPack bags with alcohol; D-F, sorting specimens by order and family at the SEAG laboratory (Montjoly, French Guiana); G, preparing packages with glassine envelopes and Eppendorf vials for dissemination among coordinators and/or taxonomic experts; H, typical output of this kind of broad-spectrum trap samples: about 50% fraction may finally be studied (arbitrary estimate). Photos: Julien Touroult.
FIG. 10 in Overview of Mitaraka survey: research frame, study site and field protocols
FIG. 10. — Process for active collecting: A, active collection of cricket (Orthoptera); B, photography of live specimens, important part of the process in some groups; C, preparation and management of the specimens for short term storage in the field laboratory; D, output of the active or selective methods: lower yields than broad-spectrum traps but a larger proportion is effectively studied. Photos: A, C, Xavier Desmier; B, Julien Touroult.
FIG. 12 in Overview of Mitaraka survey: research frame, study site and field protocols
FIG. 12. —Database and portals for entry, consultation and access to data, illustrated by means of a newly described Mitaraka species, Eupromera pascali Dalens, 2016 (Coleoptera, Cerambycidae): A, CardObs database entry interface (https://cardobs.mnhn.fr). The morphospecies name was initially entered as "Eupromera n. sp." in April 2015 and after publication (Feb. 2016), the morphospecies name was replaced by the species name, and the record was completed with publication reference and the collection deposit number; B, INPN French Natural Heritage consultation portal, displaying this species from the Mitaraka dataset (https://inpn.mnhn.fr/espece/cd_nom/814643/tab/rep/GUF); C, public interface to database of the Coleoptera collection (EC) of the MNHN illustrating the holotype and its labels, with full traceability (http://coldb.mnhn.fr/catalognumber/mnhn/ ec/ec7591); D, International GBIF Data Portal displaying the Coleoptera collection (EC) dataset of the MNHN (https://www.gbif.org/occurrence/1413051340).
FIG. 8 in Overview of Mitaraka survey: research frame, study site and field protocols
FIG. 8. — Active and passive substrate sampling: A, B, collection of dead branches infested with saproxylic larvae for "rearing" in emergence chambers (EXL); C, sampling soil litter for invertebrates with Winkler sieve (WS); D, spraying trunks with insecticide to collect small bark-dwelling arthropods that fall on the white sheet at the bottom of the trunk; E, searching for Annelida in soil samples collected with a spade; F, fish sampling in a small stream using rotenone. Photos: A, B, Stéphane Brûlé; C, Benoît Fontaine; D, Jürgen Schmidl; E, F, Xavier Desmier.
FIG. 7 in Overview of Mitaraka survey: research frame, study site and field protocols
FIG. 7. — Active collecting techniques: A, collecting butterflies with a net; B, sweeping vegetation (NS or SW) with a rugged sweep net; C, beating tray (BS), the vegetation is hit with a stick, which causes the arthropods to fall on the white nape mounted on a frame; D, searching for aquatic larvae with a rugged aquatic net; E, looking for butterfly caterpillars (Riodinidae and Lycaenidae) on liana flowers; F, visual search for reptiles, here with a Lachesis muta (Linnaeus, 1766) snake. Photos: A, B, C, E, Stéphane Brûlé; D, Nicolas Moulin; F, Xavier Desmier.
FIG. 3 in Overview of Mitaraka survey: research frame, study site and field protocols
FIG. 3. — Illustration of the landscape and main habitat types found in the Mitaraka study area: A, general landscape of the study area, with the drop zone visible in the foreground; B, inselberg "Sommet-en-Cloche" with bare rocks and transition forest; C, mosaic of forests and cambrouses; D, forest interior; E, swamp forest (bas-fond) with Euterpe oleracea Mart palm. Photos: Xavier Desmier, except B, Stéphane Brûlé.
FIG. 5 in Overview of Mitaraka survey: research frame, study site and field protocols
FIG. 5. — Passive interception traps: A, windowpane flight intercept trap (FIT) suspended over a fallen tree crown; B, 6 meter Malaise trap (MT) set up over a fallen tree near the Alama river; C, SLAM traps on an inselberg forest edge; D, a buprestid beetle (Buprestidae) trapped in artificial spider web (ASW). Photos: A, B, D, Julien Touroult; C, Stéphane Brûlé.
FIG. 4 in Overview of Mitaraka survey: research frame, study site and field protocols
FIG. 4. — Some of the collecting sites and techniques: A, drop zone forest clearing, with a high amount a freshly cut trees, and scattered SLAM traps; B, clearing, equiped with SLAM traps, automatic light trap and artificial spider web (ASW); C, active net collecting of butterflies on the "Sommet-en-Cloche" inselberg. Photos: A, B, Julien Touroult, C, Stéphane Brûlé.
FIG. 2 in Overview of Mitaraka survey: research frame, study site and field protocols
FIG. 2. — Mitaraka study area map with the four trails indicated (map by Maël Dewynter, map base by IGN and Parc amazonien de Guyane).
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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.