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440 results for “Combined analysis”
Fig. 1 in Geometric morphometric on a new species of Trichodinidae. A tool to discriminate trichodinid species combined with traditional morphology and molecular analysis
Fig. 1. Microphotographs of Trichodina bellottii n. sp. from Austrolebias bellottii. (A–D) Adhesive disc after dry silver impregnation. E) Ciliature. (F) Macronucleus with methylene-blue staining. Scale bars: 20 μm.
Text-fig. 1. D&E tree of Endress and Doyle (2009), from the combined morphological and molecular analysis of Doyle and Endress (2000), with modifications based on more recent data, showing the inferred evolution of the reticulum grading character (39). Boxes under names of taxa indicate their character state; shading of branches indicates their reconstructed state based on parsimony optimization with MacClade (Maddison and Maddison 2003). Nymph = Nymphaeales, Aust = Austrobaileyales, Chlor = Chloranthaceae, Piper = Piperales, Ca = Canellales, Magnol = Magnoliales. in Early Cretaceous Monocots: A Phylogenetic Evaluation
Text-fig. 1. D&E tree of Endress and Doyle (2009), from the combined morphological and molecular analysis of Doyle and Endress (2000), with modifications based on more recent data, showing the inferred evolution of the reticulum grading character (39). Boxes under names of taxa indicate their character state; shading of branches indicates their reconstructed state based on parsimony optimization with MacClade (Maddison and Maddison 2003). Nymph = Nymphaeales, Aust = Austrobaileyales, Chlor = Chloranthaceae, Piper = Piperales, Ca = Canellales, Magnol = Magnoliales.
Figure 9 in Combined phylogenetic analysis of a new North American fossil species confirms widespread Eocene distribution for stem rollers (Aves, Coracii)
Figure 9. Strict consensus cladogram of 24 most parsimonious trees (length = 345; consistency index = 0.499; retention index = 0.474; rescaled consistency index = 0.237) from the analysis using the morphological data set. Bootstrap support values are presented above and Bremer support values are presented below the branch they refer to. Note that the crown clade Coracioidea (Coraciidae + Brachypteraciidae) is not labelled; the position of Geranopterus alatus with respect to this clade is unresolved. †, extinct taxa; NA, North American Coracii.
Figure 6 in Combined phylogenetic analysis of a new North American fossil species confirms widespread Eocene distribution for stem rollers (Aves, Coracii)
Figure 6. Distal wing elements of Paracoracias in dorsal view. Anatomical abbreviations: I:1, left manual phalanx I:1; II:1, manual phalanx II:1; II:2, manual phalanx II:2; cmc, carpometacarpus; r, radius; u, ulna; ul, ulnare.
Figure 4 in Combined phylogenetic analysis of a new North American fossil species confirms widespread Eocene distribution for stem rollers (Aves, Coracii)
Figure 4. Cervical series, thoracic region, and sacrum of Paracoracias. Anatomical abbreviations: c, coracoid; cev, cervical vertebrae; f, frontal; fe, femur; fu, furcula; h, humerus; i, ischium; k, keel; lp, lateral process of sternum; p, pubis; r, radius; s, scapulae; sa, sacrum; u, ulna; up, uncinate processes.
Figure 2 in Combined phylogenetic analysis of a new North American fossil species confirms widespread Eocene distribution for stem rollers (Aves, Coracii)
Figure 2. Holotype specimen of Paracoracias occidentalis (AMNH 30572). Anatomical abbreviations: II:1, manual phalanx II:1; cev, cervical vertebrae; cmc, carpometacarpus; cv, caudal vertebrae; f, frontal; fe, femur; h, humerus; k, keel; lp, lateral process of sternum; m, mandible; pe, pelvis; pmx, premaxilla; r, radius; s, scapulae; tbt, tibiotarsus; tmt, tarsometatarsus; u, ulna.
Figure 5 in Combined phylogenetic analysis of a new North American fossil species confirms widespread Eocene distribution for stem rollers (Aves, Coracii)
Figure 5. Pectoral girdle and limbs of Paracoracias. Anatomical abbreviations: I:1, manual phalanx I:1; II:1, manual phalanx II:1; II:2, manual phalanx II:2; c, coracoid; cmc, carpometacarpus; fu, furcula; h, humerus; lp, lateral process of sternum; r, radius; s, scapulae; t, tracheal ring; tbt, tibiotarsus; u, ulna; ul, ulnare.
Figure 3 in Combined phylogenetic analysis of a new North American fossil species confirms widespread Eocene distribution for stem rollers (Aves, Coracii)
Figure 3. Skull of Paracoracias. Anatomical abbreviations: cv, caudal vertebrae; f, frontal; hy, hyoid; j, jugal; l, lacrimal; m, mandible; na, naris; pal, palatine; pmx, premaxilla; por, postorbital process; pt, pterygoid; py, pygostyle; scl, sclerotic ring.
Figure 7 in Combined phylogenetic analysis of a new North American fossil species confirms widespread Eocene distribution for stem rollers (Aves, Coracii)
Figure 7. Pelvic limb of Paracoracias in lateral view. Anatomical abbreviations: I:1, pedal phalanx I:1; II:1, pedal phalanx II:1; fb, fibula; fe, femur; h, humerus; tbt, tibiotarsus; tmt, tarsometatarsus; u, ulna.
Figure 8 in Combined phylogenetic analysis of a new North American fossil species confirms widespread Eocene distribution for stem rollers (Aves, Coracii)
Figure 8. Strict consensus cladogram of two most parsimonious trees (length = 4882; consistency index = 0.424; retention index = 0.798; rescaled consistency index = 0.340) from the combined analysis using all morphological and sequence data (ND2, RAG-1, and c-myc). Bootstrap support values are presented above and Bremer support values are presented below the branch they refer to. Note that the crown clade Coracioidea (Coraciidae + Brachypteraciidae) is not labelled; the position of Geranopterus alatus with respect to this clade is unresolved. †, extinct taxa; NA, North American Coracii.
A niching particle swarm optimization strategy combined with cluster analysis for the multimodal inversion of surface waves
<p>The data include two study cases used for multimodal surface wave inversion.</p> <p>For case 1, the data present a combination of active and passive surface wave methods.</p> <p>For case 3, we use Rayleigh waves to detect a low-velocity soft interlayer underneath the road.</p> <p>Detailed description can be found in the data description document.</p>
Transcriptome Analysis of Cisplatin, Cannabidiol, and Intermittent Serum Starvation Alone and in Various Combinations on Colorectal Cancer Cells
<p>* See README file for the description of data files available in this repository</p> <p>1. Study Description:</p> <p>Platinum-derived chemotherapy medications are often combined with other conventional therapies for treating different tumours, including colorectal cancer. However, the development of drug resistance and multiple adverse effects remain common in clinical settings. Thus, there is a necessity to find novel treatments and drug combinations that could effectively target colorectal cancer cells and lower the probability of disease relapse. To find potential synergistic interaction, we designed multiple different combinations between cisplatin, cannabidiol, and intermittent serum starvation on colorectal cancer cell lines. Based on the cell viability assay, we found that combinations between cannabidiol and intermittent serum starvation, cisplatin, and intermittent serum starvation, as well as cisplatin, cannabidiol and intermittent serum starvation can work in a synergistic fashion on different colorectal cancer cell lines. Furthermore, we analyzed differentially expressed genes and affected pathways in colorectal cancer cell lines to understand further the potential molecular mechanisms behind the treatments and their interactions. We found that synergistic interaction between cannabidiol and intermittent serum starvation can be related to changes in the transcription of genes responsible for cell metabolism and cancer’s stress pathways. Moreover, when we added cisplatin to the treatments, there was a strong enrichment of genes taking part in G2/M cell cycle arrest and apoptosis.</p> <p> </p> <p>2. Bioinformatics workflow:</p> <p>Initial quality control was conducted using FastQC v0.11.9 https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. Sequencing reads were trimmed of adapter sequences and low-quality bases using Trimmomatic. Trimmed sequence files were examined with FastQC to verify the trimming results. Trimmed sequencing reads were mapped to Human genome (GRCh37, Ensembl) downloaded from Illumina iGenome website (<a href="https://support.illumina.com/sequencing/sequencing_software/igenome.html">https://support.illumina.com/sequencing/sequencing_software/igenome.html</a>). Mapping was done using splice aware aligner HISAT2 2.1.0. Alignment files in SAM format were converted to BAM, sorted and indexed with samtools v.1.3.1. Mapping quality and statistics were collected with QualiMap software package v.2.2.2 <a href="http://qualimap.conesalab.org/">http://qualimap.conesalab.org/</a> The counts if reads mapping to features (genes) were counted using FeatureCounts v.2.0.1 software.</p> <p>Data exploration, visualization and statistical comparisons were conducted using R language version 4.2.2. Pair-wise comparisons between experimental groups were done with DESeq2 v.2.1.36 as described in the package manual. To decrease computational time, only the genes with at least 5 reads across 3 samples were kept in the analysis. In addition to hard threshold filtering mentioned above, DESeq2 implements independent filtering based on mean of normalized count as a filter statistic.</p> <p>We used hierarchical clustering (HC) and principal components analysis (PCA) to investigate the relationship between samples and detect potential outliers. Prior to HC and PCA analysis, DESeq2 normalized values underwent variance stabilizing transformation with using vst() function from DESeq2. HC was done using hclust() function implemented in R, with the clustering method set as “complete” for the matrices of sample-to-sample distances, and “Ward.D2” in case of the sample and gene clustering based on top 500 most variable genes. The distance measure in HC analysis was set to “euclidean”. Principal components analysis (PCA), applied to top 500 highly variable genes, was conducted using prcomp() function implemented in R with default options.</p> <p>Differentially expressed genes (DEGs) were detected with DESeq2 function results() with default options. DESeq2 uses Wald test to determine significantly changed genes between groups. The independent filtering option was set to TRUE with alpha threshold (adjusted p-value) kept at 0.1. Multiple comparison adjustment was done using Bejamini-Hochberg procedure.</p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p>
Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion
Open the record for dataset details and reuse information.
Online Appendix and Cetacean Datasets for: The Occurrence Birth-Death Process for combined-evidence analysis in macroevolution and epidemiology
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Path analysis reveals combined winter climate and pollution effects on the survival of a marine top predator
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Fig. 5 in Generic status of Winitia (Annonaceae, Miliuseae) reaffirmed by molecular phylogenetic analysis, including a new species and a new combination from Thailand
Fig. 5. Holotype of Winitia thailandana Chaowasku & Aongyong sp. nov. at CMUB.
A Combined approach of MALDI-TOF Mass Spectrometry and multivariate analysis as a potential tool for the detection of SARS-CoV-2 virus in nasopharyngeal swabs.
<p>The spectra were provided as unprocessed raw data in the manufacturers data format (Bruker), as labelled two zip archives with SARS CoV 2 positives and negative, according to the reviewer's recommendation.</p> <p>This information belongs to the publication (in review in <em>Journal of Virological Methods</em>)<br> "A Combined approach of MALDI-TOF Mass Spectrometry and multivariate analysis as a potential tool for the detection of SARS-CoV-2 virus in nasopharyngeal swabs"<br> All the information belongs to the National Reference Institute, INEI-ANLIS DR CARLOS G MALBRAN, BUENOS AIRES, ARGENTINA.</p>
Data for: The Clam Before the Storm: A Meta Analysis Showing the Effect of Combined Climate Change Stressors on Bivalves
<p>These data were used to conduct a meta-analysis (as descirbed in the pre-print; The Clam Before the Storm: A Meta Analysis Showing the Effect of Combined Climate Change Stressors on Bivalves). These data can be used to reproduce our analysis.</p>
Minimal dataset for the manuscript "Better together against genetic heterogeneity: a sex-combined joint main and interaction analysis of 290 quantitative traits in the UK Biobank".
<p>Dataset "lin2024-sex_combined_interaction-association_signifincant_in_one_or_more_tests-summary.txt" is a minimal dataset to reproduce the figures and tables in the manuscript "Better together against genetic heterogeneity: a sex-combined joint main and interaction analysis of 290 quantitative traits in the UK Biobank". </p> <p><br>To generate this dataset, see "https://github.com/BoxiLin/t2meta" Steps 0, 1.</p> <p>This dataset is the input for Steps 2, 3, 4, 5 to generate Figures 1-3 and Table 2-3.</p> <p> </p> <p>##### Column information ########################</p> <p>The following columns are annotations on each variant in the GWAS, calculated across the analysis subset of 361,194 samples by the Neale lab:</p> <p>code: Phenotype identifier in the form of "[UKB Data field]_raw"<br>variant: Unique variant identifier in the form "chr:pos:ref:alt", where "ref" is aligned to the forward strand.<br>chr: Chromosome of the variant.<br>pos: Position of the variant in GRCh37 coordinates.<br>rsid: rs ID<br>ref: Reference allele on the forward strand.<br>alt: Alternate allele (not necessarily minor allele).<br>p_hwe: Hardy-Weinberg p-value.<br>info: Imputation INFO score as provided by UK Biobank.</p> <p> </p> <p>The following columns are sex-stratified test statistics calculated by the Neale lab:</p> <p>minor_allele.x: Minor allele (AF < 0.5) in the female GWAS <br>minor_AF.x: Minor allele frequency in the female GWAS <br>beta.x: Estimated effect size of alt allele in the female GWAS <br>se.x: Estimated standard error of beta in the female GWAS<br>tstat.x: t-statistic of beta estimate (= beta/se) in the female GWAS <br>pval.x: p-value of beta significance test in the female GWAS </p> <p>minor_allele.y: Minor allele (AF < 0.5) in the male GWAS <br>minor_AF.y: Minor allele frequency in the male GWAS <br>beta.y: Estimated effect size of alt allele in the male GWAS <br>se.y: Estimated standard error of beta in the male GWAS <br>tstat.y: t-statistic of beta estimate (= beta/se) in the male GWAS <br>pval.y: p-value of beta significance test in the male GWAS </p> <p> </p> <p><br>The following columns are sex-combined test statistics calculated in our analysis:</p> <p>T.I: test statsitic for interaction effect-only <br>p.T.I: p-value of the interaction effect-only test <br>TSG.L: test statsitic for inverse variance weighted meta-analysis<br>p.TSG.L: p-value of the inverse variance weighted meta-analysis<br>TSG.Q: test statsitic for the omnibus meta-analysis<br>p.TSG.Q: p-value for the omnibus meta-analysis</p>
Data from: Combined analysis of micro RNA and proteomic profiles and interactions in patients with primary lung adenocarcinoma and lung adenocarcinoma brain metastases
<p>We carried out an analysis of miRNAs expression profiles and protein spectrums of non-metastatic primary lung adenocarcinoma (LP) and patients with brain metastases (BM) to better explore the molecular basis of BM. Files containing raw data of miRNA expression and proteomic profiles in the manuscript "Combined analysis of micro RNA and proteomic profiles and interactions in patients with primary lung adenocarcinoma and lung adenocarcinoma brain metastases".</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.