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3,696 results for “Reference”
Successful and timely uptake of artificial intelligence in science in the EU: references
<p>This reference list accompanies the SAPEA evidence review report on the same topic.</p>
RNA viral reference database
<p><span>The RNA viral reference database was composed of (1) 6,621 complete RNA viral genomes collected from the NCBI virus database (accessed on August 12<sup>th</sup>, 2022, [1]), (2) 378,253 RNA viral contigs from the RVMT database (v3)[2], and (3) 858 RNA viral genomes published in a terrestrial RNA viral study [3].</span></p> <p><span>[1] NCBI virus database, accessible at https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/</span></p> <p><span>[2] <span>Neri U, Wolf YI, Roux S, Camargo AP, Lee B, Kazlauskas D, Chen IM, Ivanova N, Allen LZ, Paez-Espino D.<strong><span> </span></strong>2022. Expansion of the global RNA virome reveals diverse clades of bacteriophages. Cell 185:4023-4037. e18.</span></span></p> <p><span>[3] <span>Chen Y-M, Sadiq S, Tian J-H, Chen X, Lin X-D, Shen J-J, Chen H, Hao Z-Y, Wille M, Zhou Z-C.<strong><span> </span></strong>2022. RNA viromes from terrestrial sites across China expand environmental viral diversity. Nature Microbiology 7:1312-1323.</span></span></p>
Reference files for MahaRank
<p>MahaRank uses the DNA sequence of the plasmid as input (query), searches the reference DB, and ranks hosts (bacteria) in the order in which they are likely to be entered by the plasmid.<br>These reference files are used as the reference DB, reference.tar.gz is the one actually used in MahaRank and reference_slim.tar.gz is the data to test the source-code of <a href="https://github.com/kokitsuyuzaki/MahaRank">MahaRank</a>.</p>
Reference Architecture for Autonomy and Adaptivity in the Space Domain
<p>File 1 - <strong>Protocol SLR - Reference Architecture for autonomous and adaptive space systems.xlsx</strong>: This data extraction worksheet presents the relevant data from the identified studies and provides the selection process in this systematic literature review. The main information reported in this worksheet summarizes the followed protocol, containing an identifier (id) for each returned study. This catalog helped us in the data extraction and synthesis procedures and may be used by potentially interested, for example, for updating or replication. </p> <p>File 2 - <strong>Interview_Guide_Questionnaire.pdf</strong>: The questionnaire was used to guide the interviews and also to ensure consistency between responses. It covers key aspects of the proposed reference architecture, such as general applicability, autonomy and adaptability, scalability, and standards compliance. There is also space for interviewers to add comments in each section and at the end of the form.</p> <p>File 3 - <strong>Filled_Questionnaire_Interviewee_1.pdf</strong>: The questionnaire answered by the interviewee 1, with the scores and comments.</p> <p>FIle 4 - <strong>Expert 1 Transcription.docx</strong>: The transcripts of the interviewee 1. The original language was not English, so we used OpenAI to generate the English version.</p> <p>File 5 - <strong>Filled_Questionnaire_Interviewee_2.pdf</strong>: The questionnaire answered by the interviewee 2, with the scores and comments.</p> <p>FIle 6 - <strong>Expert 2 Transcription.docx</strong>: The transcripts of the interviewee 2. The original language was not English, so we used OpenAI to generate the English version.</p> <p>File 7 - <strong>Filled_Questionnaire_Interviewee_3.pdf</strong>: The questionnaire answered by the interviewee 3, with the scores and comments.</p> <p><strong>Expert 3</strong> did not authorize us to release the interviews, so we are not sending the transcripts.</p>
Reference Architecture for Autonomy and Adaptivity in the Space Domain
<p>File 1 - <strong>Protocol SLR - Reference Architecture for autonomous and adaptive space systems.xlsx</strong>: This data extraction worksheet presents the relevant data from the identified studies and provides the selection process in this systematic literature review. The main information reported in this worksheet summarizes the followed protocol, containing an identifier (id) for each returned study. This catalog helped us in the data extraction and synthesis procedures and may be used by potentially interested, for example, for updating or replication. </p> <p>File 2 - <strong>Interview_Guide_Questionnaire.pdf</strong>: The questionnaire was used to guide the interviews and also to ensure consistency between responses. It covers key aspects of the proposed reference architecture, such as general applicability, autonomy and adaptability, scalability, and standards compliance. There is also space for interviewers to add comments in each section and at the end of the form.</p> <p>File 3 - <strong>Filled_Questionnaire_Interviewee_1.pdf</strong>: The questionnaire answered by the interviewee 1, with the scores and comments.</p> <p>FIle 4 - <strong>Expert 1 Transcription.docx</strong>: The transcripts of the interviewee 1. The original language was not English, so we used OpenAI to generate the English version.</p> <p>File 5 - <strong>Filled_Questionnaire_Interviewee_2.pdf</strong>: The questionnaire answered by the interviewee 2, with the scores and comments.</p> <p>FIle 6 - <strong>Expert 2 Transcription.docx</strong>: The transcripts of the interviewee 2. The original language was not English, so we used OpenAI to generate the English version.</p> <p>File 7 - <strong>Filled_Questionnaire_Interviewee_3.pdf</strong>: The questionnaire answered by the interviewee 3, with the scores and comments.</p> <p><strong>Expert 3</strong> did not authorize us to release the interviews, so we are not sending the transcripts.</p>
LD reference for HDL-L
<p>Update date according to new loci definition file</p>
Finnish referative constructions and subordinate että clauses in the Bible translations 1548-2020, coded verses
<p>Aineisto sisältää tiedot vuoden 1548 Uudesta testamentista haettujen referatiivirakenteiden ja <em>että</em>-lauseiden paikoista, jakaumasta ja matriisilauseiden verbeistä sekä vastineista uudemmissa raamatunkäännöksissä.</p> <p>Lähteet:</p> <p>Biblia. 1642. <em>Biblia</em>. <em>Se on: coco pyhä Ramattu, suomexi</em>. Stockholm: Henrich Keyser.</p> <p>Biblia. 1776. <em>Biblia</em>. <em>Se on: coco pyhä Ramattu, suomexi</em>. Turku: Johan Christopher Frenckell.</p> <p>Raamattu. 1938. <em>Pyhä Raamattu</em>. Sortavala: Suomen kirkon sisälähetysseura.</p> <p>Raamattu. 1992. <em>Pyhä Raamattu</em>. Helsinki: Suomen Pipliaseura.</p> <p><em>Se Wsi Testamenti</em> = The Morpho-Syntactic Database of Mikael Agricola's Works version 1.1, Korp. The database is available through the Korp Interface at <a href="http://korp.csc.fi/">http://korp.csc.fi/</a>. Access location: <a href="http://urn.fi/urn:nbn:fi:lb-2019121803">http://urn.fi/urn:nbn:fi:lb-2019121803</a>.</p> <p><em> </em><em>Uusi </em><em>testamentti 2020</em> – <em>Raamattu mobiilikäyttäjille</em>. 2020. Helsinki: Suomen Pipliaseura. </p>
Figures referring to the paper "Radii, masses, and transit-timing variations of the three-planet system orbiting the naked-eye star TOI-396" (Bonfanti et al.) accepted for publication in A&A on 20/11/2024
<p>Fig. A.1: ttv_pla1_2.pdf</p> <p>TTV amplitudes obtained for TOI-396 b (black markers) and TOI-396 c (red markers). This is a superposition of the first two panels of Figure 4 in the paper emphasising the anti-correlation pattern.</p> <p> </p> <p>Fig. A.2: lcGLS*.pdf</p> <p>First column: Generalised Lomb-Scargle periodograms of TESS Sector 3 (lcGLS_3.pdf), 4 (lcGLS_4RawFluxrm.pdf), 30 (lcGLS_30RawFlux.pdf), and 31 (lcGLS_31RawFlux.pdf) raw photometry. Second column: Generalised Lomb-Scargle periodograms of the residuals (lcGLSRaw_3noSine.pdf, lcGLSRaw_4noSinerm.pdf, lcGLSRaw_30noSine.pdf, lcGLSRaw_31noSine.pdf) after removing the best fitting sinusoidal signals at the most significant frequency identified in the periodograms of the corresponding TESS time series. The long dashed red line marks the FAP at 0.1\%. Significant peaks are detected in the 6---8 day range, which we attribute to the presence of active regions co-rotating with the star.</p>
Chinese Reference Population: open-source age-dependent computational phantoms of reference Chinese population
<p>The<strong> Chinese Reference Population (CRP)</strong> phantoms dataset encompass <strong>30 phantoms</strong> available in both voxel and NURBS formats, with age in 0, 1, 2, 3, 4, 5, 6, 8, 10, 12, 15, 18 years and adult male and female, as well as 4 pregnant women and fetus in early pregnancy, first trimester, second trimester and third trimester.</p> <ul> <li><strong>Voxelized phantoms</strong> are accessible in NII format :<strong> <em>"XXX.nii", which could be opened in AMIDE software.</em></strong></li> <li>Excel file<strong> </strong>containing<strong> organ masses and other descriptive information </strong>:<strong> <em>"CRP_descriptive_Info.xlsx"</em></strong></li> <li>In the application of F18−FDG dose calculation, <strong>organ absorbed doses per unit activity administered </strong>is provided in an Excel file :<strong> <em>"Application_F18-FDG.xlsx"</em></strong></li> </ul> <p>All data are stored on Zenodo and can be publicly accessed.</p>
Supplemental datasets for 'A near telomere-to-telomere phased reference assembly for the male mountain gorilla (Gorilla beringei beringei)'
<p>The endangered mountain gorilla <em>Gorilla beringei beringei</em> faces numerous threats to its survival, highlighting the urgent need for genomic resources to aid conservation efforts. Here, we present a near telomere-to-telomere, haplotype-phased reference genome assembly for a male mountain gorilla generated using Pacbio HiFi and Oxford Nanopore Ultralong data. The resulting assembly exhibits exceptional contiguity, with contig N50 of ~ 95 Mbps for the combined pseudohaplotype (3,540,458,497 bps, and 56.5 Mbps (3.1 Gbps) and 51.0 Mbps (3.2 Gbps) for the maternal and paternal haplotypes and an average QV of 65.15 (error rate = 3.1 x 10-7). These represent substantial improvements over most other available primate genomes. This high-quality reference genome provides an invaluable resource for future studies on gorilla evolution, adaptation, and conservation, ultimately contributing to the long-term survival of this iconic species.</p> <p>A preprint for this work is available at bioRXiv, doi: https://doi.org/10.1101/2024.10.28.620258</p>
CM2 Reference Database Uniref100/KO
<p>CM2 DIAMOND reference database - Version 3. Compatible with DIAMOND version 2.1.11 specifically. </p>
Supplementary files for 'Adding 'flavour' to past cuisines: first steps towards a phytolith reference collection of modern Mediterranean herbs'
<p><strong>ESM1</strong>. Supplementary tables:</p> <ul> <li> <p><strong><span>Table S1</span></strong><span>. List of samples analysed in this study. </span><span>Phytolith concentration per gram of original plant tissue. BBG: Barcelona Botanical Garden. BGPC: Botanical Park & Gardens of Crete. PPFF: Park for the Preservation of Fauna and Flora of the Technical University of Crete. Aerial parts: mix of leaves and flowers/inflorescences.</span></p> </li> <li> <p><strong>Table S2</strong>. <span>Protocol for extracting phytoliths from modern plants.</span></p> </li> <li> <p><strong><span>Table S3</span></strong><span>. Weight (in grams) of the original dry plant tissue and the ash left after processing the samples, number of phytoliths observed in each sample and phytolith concentration per gram of original dry plant tissue.</span></p> </li> <li> <p><strong><span>Table S4</span></strong><span>. Code used for describing phytolith morphotypes and sub-morphotypes according to the ICPN 2.0 (ICPT 2019).</span></p> </li> <li><strong><span>Table S5</span></strong><span>. Results of the microscopic analysis of phytolith samples from modern Mediterranean herbs.</span></li> </ul> <p><span><strong>ESM2</strong>. Reference atlas of phytoliths observed in modern Mediterranean herbs.</span></p>
Reference Manager Data Citation Analysis
<p>DESCRIPTION:</p> <p>This package contains data used to analyze citation metadata completeness and correctness for several common reference managers used in scholarly research and several common repositories in the Earth, space, and environmental sciences.</p> <p>METHODS:</p> <p>Metadata fields for import and export methods and for 8 metadata fields (authors/creators, publisher, DOI, dataset title, version, access date, publication date, and resource type) were collected from reference managers via all import methods available (app or wizard and plugin) during summer 2024 from most recent software versions of all. To encode data, citation information for each dataset as imported by Reference Manager was compared to that registered for the DOI with DataCite. Correct metadata for each of 8 fields for both import and export was encoded as 0, incorrect as 1, and missing as '' or nan. See publication and software package for more information.</p> <p>FILES:</p> <p>FOLDER 'coded-data' contains files that include information (DOIs) about the data examined in this study, preserved copies of exported data citations used in the data interpretation and processing, and the processed data itself encoded in columns.</p> <p>FOLDER 'datacite-metadata-profiles' includes the raw metadata from each dataset DOI at the time of analysis, included for reproducibility purposes. </p> <p>FOLDER 'bibtex-files' includes the downloaded .bib files, where available, for each dataset DOI examined.</p> <p>See README file for more information.</p>
How to cite & reference using OSCOLA
<p>This video shows how to cite and reference using OSCOLA and style guide Cite Them Right.</p>
STRetch reference data
<p>STRetch reference data</p>
PalaeoChip Arctic v1.0 reference and bait sequences.
<p>Organelle reference sequences of Holarctic fauna and flora from GenBank NCBI, as well as the sequences of the individual baits designed to target those referneces in the PalaeoChip Arctic v1.0 bait-set.</p>
LungMAP Azimuth Reference - Human Adult Lung scRNA-Seq
<p>The LungMAP scRNA-Seq reference associated with the Lung CellCards resource. The initial reference integrated 259k cells from 72 donors from five published (PMIDs: 32726565, 32427931, 30554520, 32832599, 32832598) and one unpublished single cell RNA-seq cohort. Non-diseased adult and pediatric healthy lung single-cell 10x Genomics captures (3’ v2 and v3). Cells from different donors were integrated using Batchlor. Preliminary cell types were called based on Leiden clustering analysis and expression patterns of LungMAP cell card markers. UMAP embeddings were generated using monocle3. This reference, along with a corresponding single-nucleus specific version of this atlas, is under active construction. We expect to release the beta version of the reference in November 2021. Conforms to<strong> </strong>Azimuth reference data structure described at <a href="https://github.com/satijalab/azimuth/wiki/Azimuth-Reference-Format">https://github.com/satijalab/azimuth/wiki/Azimuth-Reference-Format</a>.</p>
SingleM reference database
<p>DEPRECATED: See <a href="https://aus01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fzenodo.org%2Frecord%2F5739612&data=05%7C01%7Crossen.zhao%40hdr.qut.edu.au%7Cc3c9e94152b54b06e14008dbc868dcfa%7Cdc0b52a368c544f7881d9383d8850b96%7C0%7C0%7C638324124934642739%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=wycEGojHU4c%2B6B3b7Ds9BwJ9IPUGfy%2BDmlXLOHn%2F3dY%3D&reserved=0">https://zenodo.org/record/5739612</a></p> <p>SingleM reference database. Metapackage containing packages for 59 broad-spectrum single-copy marker genes. Associated sequences and taxonomy based on GTDB r202 release.</p>
The accuracy and efficiency of a reference-based adaptive selection algorithm for comparative judgement
<p>Data and R code with article for Frontiers in Education special issue Validity, Reliability and Efficiency of Comparative Judgement to Assess Student Work. [Submitted]</p> <p>Abstract:</p> <p>Several studies have proven that comparative judgement (CJ) is a reliable and valid assessment method for a variety of competences, expert assessment and peer assessment, and CJ is emerging as a possible approach to help maintain standards over time. For consecutive pairs of student works (representations) assessors are asked to judge which representation is better. It has been shown that random construction of pairs leads to very inefficient assessments, requiring a lot of pairwise comparisons to reach reliable results. Some adaptive selection algorithms using information from previous comparisons were proposed to increase the efficiency of CJ. These adaptive algorithms appear however to artificially inflate the reliability of CJ results through increasing the spread of the results. The current article proposes a new adaptive selection algorithm using a previously calibrated reference set. Using a reference set should eliminate the reliability inflation. In a real assessment, using reference sets of different reliability, and in a simulation study it is proven that this adaptive selection algorithm is more efficient without reducing the accuracy of the results and without increasing the standard deviation of the assessment results. As a consequence, a reference-based adaptive selection algorithm produces high and correct reliability values in an efficient manner.</p>
Hybridization dynamics and extensive introgression in the Daphnia longispina species complex: new insights from a high-quality Daphnia galeata reference genome
<p>Supplementary data for the Genome Biology and Evolution paper <a href="http://dx.doi.org/10.1093/gbe/evab267">10.1093/gbe/evab267</a></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.