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23,351 results for “Comparative”
Fig. 1 in Comparative Analysis of Complete Mitogenomes of Two Gobies and Their Phylogenetic Implication.
Fig. 1. Gene map of Oxyurichthys ophthalmonema mitogenome.
Fig. 4 in Comparative Analysis of Complete Mitogenomes of Two Gobies and Their Phylogenetic Implication.
Fig. 4. Relative synonymous codon usage of Protein-coding genes in Oxyurichthys microlepis.
PlasEval: a framework for comparing and evaluating plasmid binning tools
<p>PlasEval is a tool aimed at evaluating the accuracy and at comparing methods for the problem of <strong>plasmid binning</strong>. It has two modes: <strong>evaluate</strong> and <strong>compare</strong>.</p> <p>In the <strong>evaluation</strong> mode of PlasEval, a given set of <em>predicted plasmid bins</em> resulting from a plasmid binning method is evaluated against a <em>ground truth</em> set of plasmid bins, yielding three statistics, the <em>precision</em>, the <em>recall</em> and the <em>F1-score</em>.</p> <p>In the <strong>comparison</strong> mode of PlasEval, given two sets of <em>predicted plasmid bins</em> (either resulting from two plasmid binning tools or from a plasmid binning tool and a ground truth), PlasEval computes a <em>dissimilarity measure</em> that indicates how much both sets of predicted plasmid bins are in agreement.</p> <p>The data shared consists of output files of PlasBin-flow as well as those of 3 other plasmid binning methods, namely, HyAsP, MOB-recon and gplas for 53 test samples. Details about each sample have been provided in the file <strong>Ecoli_samples.csv</strong>. It also includes the short read assembly files (fasta as well as gfa) and the hybrid assembly files. The mappings of short-read contigs to hybrid contigs for all 53 samples have been provided in the <strong>BLAST_output </strong>folder. The plasmid bins, including those representing the ground truth, used as input for PlasEval have been provided in the <strong>PlasEval_input</strong> folder.</p> <p> </p>
Fig. 8 in Megascolex (Perichaeta) diffringens Baird, 1869 and Pheretima pingi Stephenson, 1925 types compared to the Amynthas corticis (Kinberg, 1867) and A. carnosus (Goto & Hatai, 1899) species-groups (Oligochaeta: Megadrilacea: Megascolecidae)
Fig. 8. Amynthas diffringens copy of Baird's original fig. 1 (habitus and a seta).
Fig. 13 in Megascolex (Perichaeta) diffringens Baird, 1869 and Pheretima pingi Stephenson, 1925 types compared to the Amynthas corticis (Kinberg, 1867) and A. carnosus (Goto & Hatai, 1899) species-groups (Oligochaeta: Megadrilacea: Megascolecidae)
Fig. 13. Prior Amynthas hongkongensis after Michaelsen (1910: fig. 22), for comparison.
Fig. 9 in New earthworm species from NIBR's Jeju-do biosphere compared to historical and new Japanese types (Oligochaeta: Megadrilacea: Megascolecidae)
Fig. 9. Amynthas yamizoyamensis after Ohfuchi's (1935: figs. 6- 10) originals.
Fig. 8. A in New earthworm species from NIBR's Jeju-do biosphere compared to historical and new Japanese types (Oligochaeta: Megadrilacea: Megascolecidae)
Fig. 8. A. shimaensis Mt. Fuji specimen (YNU) [boxed Goto & Hatai's (1899: fig. 3)].
Fig. 4 in New earthworm species from NIBR's Jeju-do biosphere compared to historical and new Japanese types (Oligochaeta: Megadrilacea: Megascolecidae)
Fig. 4. Amynthas micronarius neotype NMST An446-lhs; specimen NMST An445 - rhs.
Comparative Engagement: Political vs. Socio-humanitarian
<p>The war in Ukraine and the resulting flight of millions of people have once again put the reception of refugees at the centre of the public debate in Europe. Similar to 2015, volunteers are pitching in and organising support or politically campaigning for the rights of refugees. It is remarkable that many people are opening the doors of their houses and flats to those seeking protection. Private accommodation is currently making a significant contribution to ensuring the accommodation of arrivals from Ukraine. At the same time, there is a need for other forms of engagement for refugees, be it in accompanying them to the authorities, in language acquisition or in sponsorships.</p> <p>At the moment, however, we know little about what exactly engagement looks like in times of war in Ukraine. We don't know who is getting involved, for what reasons and with what attitude patterns. Are they the same people who were already active in 2015/2016, or is the Ukraine war activating other population groups? Similarly, we know little about the concrete practice of housing, such as the spatial conditions, the support and counselling needs of people hosting refugees, and the challenges. Has their engagement in general and private hosting in particular changed how they perceive refugees? By answering these questions, we can capture the current extent, shape, opportunities and challenges of refugee engagement. The findings will also enable us to better support engaged people and the government agencies, initial reception centres and charities that work with them.</p> <p>In order to close the research gap and address the acute lack of data, the project pursues an integrated research design that combines findings from different surveys with different sampling strategies, content-related foci and cooperation partners. This includes firstly a quantitative survey of private accommodation providers (including the extent, form and duration of accommodation, access to support services, practices and challenges of private accommodation (in short "private accommodation survey") and secondly a population survey of engaged people (in short "engagement survey"). Building on and inspired by previous surveys on refugee engagement (Volunteer Survey 2019, Allensbach Study on Refugee Engagement 2018), the survey allows for more differentiated insights into fields of activity, motivations, and experiences in engagement (including reasons for engagement termination). Finally, we supplement the quantitative surveys with qualitative background interviews to gain relevant contextual knowledge, an analysis of social media debates, and possibly, from 2023 onwards, discussion rounds on selected key questions with volunteers ("focus groups").</p> <p>The results of the project will enable us to formulate recommendations for action for politics and society on how to sustainably strengthen the engagement for refugees and improve the accommodation situation.</p>
A Comparative Analysis of Machine Learning Approaches to Gap Filling Meteorological Datasets (Results Only)
<p>This dataset contains the results from our evaluation of methodologies for filling gaps in meterological data. Variables were chosen to represent a standard set of measurements for purposes typically performed using Weather Stations installed in urban and rural areas. There are 4 dimensions by which we measure and validate each of the gap filling models across a large set of experimental configurations: meteorological variables <strong>TargetVar </strong>(dewpoint, humidity, leaf wetness, temp); <strong>feature_set</strong> (AWS, AWS-ERA5, ERA5, ERA5_Debias, Spatial); 3 types of machine learning algorithms <strong>ML</strong> (linear regression, random forests, LightGBM) combined with 2 non-ML algorithms; and <strong>gap_length</strong>: 1, 4, 36 and 288. A total of 1,720 experiments were conducted: 1,440 machine learning experiments; 160 using a spatial algorithm and 120 experiments using ERA5. For the 3 machine learning experiments, the average result was selected for each of 10 sites for 4 gap sizes (40 results) with the 3 ML models using 3 different feature sets (120 results).</p> <p>Data is provided in both CSV format and as a MySQL dump.</p> <p>Resultsets are accompanied with the SQL expression used to generate the result.</p>
CLDF dataset derived from Blum et al.'s (2024) "A Comparative Wordlist for Investigating Distant Relations Among Languages in Lowland South America"
<p>Cite the source of the dataset as:</p> <blockquote> <p>Blum, Frederic and Barrientos, Carlos and Zariquiey, Roberto and List, Johann-Mattis. 2024. A Comparative Wordlist for Investigating Distant Relations Among Languages in Lowland South America. *Scientific Data* 11(92). https://doi.org/10.1038/s41597-024-02928-7</p> </blockquote>
Supplementary material - Comparative genitalic morphology in ten genera of thread-legged bugs of the tribe Metapterini, and its phylogenetic importance (Hemiptera: Heteroptera: Reduviidae)
<p><strong>Supplementary information of the paper entitled: Comparative genitalic morphology in ten genera of thread-legged bugs of the tribe Metapterini, and its phylogenetic importance (Hemiptera: Heteroptera: Reduviidae), original images and data matrix in nexus format.</strong></p>
Comparing developer-provided to user-provided tests for fault localization and automated program repair: Artifacts
<p>Artifacts for the paper <em>Comparing developer-provided to user-provided tests for fault localization and automated program repair.</em></p> <p>Note that the artifacts are maintained in the following repositories:</p> <ul> <li>https://github.com/rjust/defects4j</li> <li>https://bitbucket.org/rjust/tests-tested-data</li> <li>https://bitbucket.org/rjust/fault-localization-data</li> </ul>
Comparing laser patterning of submicron structures into metal
<p>Within the EU funded project Laser4Surf European researchers are exploring how using laser structuring can alter and improve the properties or performance of metals. This graphic compares the patterning of metal surfaces with the help of Direct Laser Interference or Direct Laser Ablation (DLA) with Laser Induced Periodic Surface Structures (LIPSS).</p>
Detection of genetic alterations in gastric cancer patients from Saudi Arabia using comparative genomic hybridization (CGH)
<p>Abstract</p> <p>Background: The present study was conducted to discover genetic imbalances such as DNA copy number variations (CNVs) associated with gastric cancer (GC) and to examine their association with different genes involved in the process of gastric carcinogenesis in Saudi population. </p> <p>Methods: Formalin-fixed paraffin-embedded (FFPE) tissues samples from 33 gastric cancer patients and 15 normal gastric samples were collected. Early and late stages GC samples were genotyped and CNVs were assessed by using Illumina HumanOmni1-Quad v.1.0 BeadChip. </p> <p>Results: Copy number gains were more frequent than losses throughout all GC samples compared to normal tissue samples. The mean number of the altered chromosome per case was 64 for gains and 40 for losses, and the median aberration length was 679115bp for gains and 375889bp for losses. We identified 7 high copy gain, 52 gains, 14 losses, 32 homozygous losses, and 10 copy neutral LOHs (loss of heterozygosities). Copy number gains were frequently detected at 1p36.32, 1q12, 1q22, 2p11.1, 4q23-q25, 5p12-p11, 6p21.33, 9q12-q21.11, 12q11-q12, 14q32.33, 16p13.3, 17p13.1, 17q25.3, 19q13.32, and losses at 1p36.23, 1p36.32, 1p32.1, 1q44, 3q25.2, 6p22.1, 6p21.33, 8p11.22, 10q22.1, 12p11.22, 14q32.12 and 16q24.2. We also identified 2 monosomy at chromosome 14 and 22, 52 partially trisomy and 22 whole chromosome 4 neutral loss of heterozygosities at 13q14.2-q21.33, 5p15.2-p15.1, 5q11.2-q13.2, 5q33.1-q34 and 3p14.2-q13.12. Furthermore, 11 gains and 2 losses at 1p36.32 were detected for 11 different GC samples and this region has not been reported before in other populations. Statistical analysis confirms significant association of H. pylori infection with T4 stage of GC as compare to control and other stages.</p>
Comparative analysis of huntingtin interaction partner database searches with Dr. Maiuri's work - 2018/08/31
<p><strong>Project </strong>- Huntingtin structure-function open lab notebook. </p> <p><strong>Rationale</strong> - To compare the ROS-specific huntingtin interaction partners identified by Dr. Tamara Maiuri with those detailed in existing databases. </p> <p><strong>Overview</strong> - Previously, different online databases which detail protein interaction partners were searched for huntingtin protein interaction partners. Following completion of this initial analysis, Dr. Tamara Maiuri posted in her open notebook a detailed list of high and medium confidence ROS-specific huntingtin interacting proteins: <a href="https://zenodo.org/record/1319540">https://zenodo.org/record/1319540</a>. A comparison of these interactors with those identified in the previously mined databases is briefly detailed. </p>
Comparative genomics of ten new Caenorhabditis species
<p><strong>Phylogenomic analysis</strong></p> <p><code>ASTRAL_species_tree.ASTRAL_branch_lengths.nwk</code>: Species tree generated by ASTRAL-III with branch lengths in coalescent units</p> <p><code>ASTRAL_species_tree.RAxML_branch_lengths.nwk</code>: Species tree generated by ASTRAL-III with branch lengths in substitutions per site as estimated by RAxML (GTR+Γ)</p> <p><code>Caenorhabditis_33species_1988loci_supermatrix.fas</code>: Supermatrix composed of 1988 single-copy loci 27 of 33 species analysed</p> <p><code>Orthogroups.txt</code>: Original orthology clustering file</p> <p><code>PhyloBayes_species_tree.nwk</code>: Species tree generated by PhyloBayes MPI (CAT-GTR+Γ)</p> <p><code>RAxML_species_tree.nwk</code>: Species tree generated by RAxML (GTR+Γ)</p> <p><code>singlecopy_orthologues_redundantseqs_removed.txt</code>: Orthogroups used in analysis, after removing redundant sequences</p> <p><strong>Intron analysis</strong></p> <p><code>Orthogroups_990_0missing_5hetero_paraloguesremoved_withCDSalignments.txt</code>: Single copy orthogroups.txt file (note: this is after removing redundant sequences arising from uncollapsed heterozygosity and removing orthogroups containing paralogues)</p> <p><code>genome_gene_structure_stats.tsv</code>: File containing gene structure and genome size statistics</p> <p><strong>Notch-like receptor analysis</strong></p> <p><code>OG0000658.below700removed.fa</code>: FASTA file of all sequences in orthogroup that were 700 amino acids or longer.</p> <p><code>OG0000658.below700removed.fa.aln</code>: alignment of the above FASTA file</p> <p><code>OG0000658.below700removed.fa_ProSiteProfiles.tsv</code>: InterProScan search results of the above FASTA file using the ProSiteProfiles database (release 2017_09)</p> <p><code>OG0000658.txt</code>: Line from orthology clustering with all (including those below 700 amino acid) sequence IDs</p> <p><code>RAxML_bipartitions.OG0000658.below700removed.nwk</code>: RAxML ML tree of the above alignment file with bootstrap support values</p> <p><code>extract_branch_lengths.py</code>: Python script used to extract branch lengths</p>
Comparative genome analysis of Lactococcus lactis indicates niche adaptation and resolves genotype/phenotype disparity
<p>This publication describes the comparative genome analysis of 43 L. lactis strains</p> <p>The data stored here are individual alignments (alignments.zip) and the output files from gene trait matching (GTM_output.zip) used in this study.</p>
FreeCiv games for the experiment on comparing Knowledge-Based Reinforcement Learning and Neural Networks in Strategic Games
<p>Dataset provides played FreeCiv games. The Tournament subset of them was played fully by two Artificial Intelligence (AI) agents against each other and one more computer player. The Human games subset was played by humans for demonstration/teaching purposes. The rest of the games were played 120 turns and stopped.</p>
Evolution of neocortical folding: A phylogenetic comparative analysis of MRI from 34 primate species
<p>Dorsal view of the reconstructed cerebral hemispheres of 34 different primate species.</p> <p>This figure is from our open access paper:</p> <p>Heuer, K., Gulban, O. F., Bazin, P.-L., Osoianu, A., Valabregue, R., Santin, M., Herbin, M., & Toro, R. (2018). Evolution of neocortical folding: A phylogenetic comparative analysis of MRI from 33 primate species. bioRxiv. <a href="https://doi.org/10.1101/379750">https://doi.org/10.1101/379750</a>. </p> <p>Abstract</p> <p>We present a comparative analysis of cerebral size and neocortical folding. Magnetic resonance imaging data was collected from 66 individuals belonging to 34 different primate species. We measured several neocortical folding parameters and studied their evolution using phylogenetic comparative methods. Our results suggest that the most likely model is one where phenotypical differences vary randomly through evolution (the Brownian Motion model). We present estimations of the ancestral primate phenotypes as well as estimations of the rates of phenotypic change.</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.