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920 results for “Functional analysis”
Macro-scale analysis of biodiversity-ecosystem functioning relationships in lakes (github repository)
<p>National Lakes Assessment biodiversity-ecosystem functioning relationships across the continental United States. This is an archived version of a github repository, containing data and R code. The repository can also be found online https://github.com/cont-limno/NLA-Diversity-.</p>
rfsed: Receiver function analysis and dealing with sediment effects
<h2>Receiver functions analysis and dealing with sediment effects in receiver functions</h2>
Supplementary material for "Quantitative morphological analysis of skulls of pterosaurs and early birds highlight a functional shift during the Mesozoic" by Gauweiler J. et al.
<p>This data repository contains additional information and supplemental material for the publication "Quantitative morphological analysis of skulls of pterosaurs and early birds highlight a functional shift during the Mesozoic". For information on the authors, see the original publication.</p> <p>The folder "Prehistoric_Ornithodira_BMPs.zip" contains outline images in .bmp format of all skulls used for the analysis.</p> <p>The file "Groups.csv" contains the grouping variables for all data points.</p> <p>The file "PC_Scores.csv" contaisn the principal component scores of the SHAPE analysis for all individuals used in the analysis.</p> <p>The file "Pterosaur_Avian_Script.R" contaisn the R code used for statistical analysis and plotting of the data.</p>
Tissue-engineered vocal fold replacement in swine: Methods for functional and structural analysis.
<p>S2 Data. 5534 pig squeal events investigated in this study, provided in a folder structure sorted by pigs, pre- / post-treatment and recording date as .wav files.</p>
Functional profiling and evolutionary analysis of a marine microalgal virus pangenome
<p>Phycodnaviridae are large double-stranded DNA viruses, which facilitate studies of host–virus interactions and co-evolution due to their prominence in algal infection and their role in the life cycle of algal blooms. However, the genomic interpretation of these viruses is hampered by a lack of functional information, stemming from the surprising number of hypothetical genes of unknown function. It is also unclear how many of these genes are widely shared within the clade. Using one of the most extensively characterized genera, <em>Coccolithovirus</em>, as a case study, we combined pangenome analysis, multiple functional annotation tools, AlphaFold structural modeling, and literature analysis to compare the core and accessory pangenome and assess support for novel functional predictions. We determined that the <em>Coccolithovirus</em> pangenome shares 30% of its genes with all 14 strains, making up the core. Notably, 34% of its genes were found in at most three strains. Core genes were enriched in early expression based on a transcriptomic dataset of <em>Coccolithovirus</em> EhV-201 algal infection, were more likely to be similar to host proteins than the non-core set, and were more likely to be involved in vital functions such as replication, recombination, and repair. In addition, we generated and collated annotations for the EhV representative EhV-86 from 12 different annotation sources, building up information for 142 previously hypothetical and putative membrane proteins. AlphaFold was further able to predict structures for 204 EhV-86 proteins with a modelling accuracy of good–high. These functional clues, combined with generated AlphaFold structures, provide a foundational framework for the future characterization of this model genus (and other giant viruses) and a further look into the evolution of the <em>Coccolithovirus</em> proteome.</p>
An analysis of the effects of prior drying and vertebrate colonization on ecological functioning and vertebrate fitness
<p>We investigated the legacy effects of drying and refilling of wetlands via mesocosms on growth and survival of recolonizing aquatic vertebrates and their subsequent effects on ecological function. Specifically, we tested the effects of prior drying on anuran and fish growth and survival (using Gompertz growth curves), and joint effects of vertebrates and drying on periphyton biomass, and whole-system gross primary productivity. Using 64 1,000-L hard plastic cattle tanks to create replicate aquatic mesocosms, four trophic treatments (no vertebrate control, larval anurans, fish, larval anurans and fish) were crossed with two drying treatments (undried and dried-refilled) to simulate different outcomes of colonization by two common vertebrate guilds and drying/refilling cycles. Mesocosms with anuran treatments received 50 <em>Lithobates</em> <em>blairi</em> tadpoles (1,600 total) and mesocosms with fish treatments received one <em>Lepomis</em> <em>cyanellus</em> juvenile (32 total). We recorded anuran growth rates, survival, and time/size at metamorphosis, fish growth, gross primary productivity, and periphyton biomass over 12 weeks from 9 May 2021 to 1 August 2021.</p> <p>This dataset contains 4 R script files (one for each of the 4 components of this study: Amphibians, fish, gross primary productivity, and periphyton) along with their corresponding Excel files. Survival for each tank was calculated as the total number of emerged frogs from weeks 1–12 divided by 50 (initial number of larvae per tank). Size at metamorphosis was determined by dry mass (g) measured after 72 hours in a drying oven at 60° C. Metamorph dry mass and wet mass were strongly correlated (grams dry mass = 0.1957*grams wet mass – 0.0398; R<sup>2</sup> = 0.9733) and we chose dry mass for size at metamorphosis to reduce variability caused by water weight. We measured the dry mass of metamorphosed frogs to the nearest 0.01g. Time to metamorphosis was measured as the days past the first day of the experiment (9 May 2021) to the day the frog reached Gosner stage 46 (Gosner, 1960). We calculated relative fish growth as the change in standard length (SL) over the duration of the experiment divided by the initial SL for each fish. Individual fish growth calculations used each of the single fish per tank as independent replicates. Relative fish growth measurements for fish within the same treatments (n = 8) were combined and analyzed together. Gross primary productivity values were collected by measuring dissolved oxygen (DO) values after sunset for maximum DO and before sunrise for minimum DO. DO measurements were collected using a YSI meter (ProQuatro XA00088 – 02; YSI Inc., Yellow Springs, OH, USA) as a percentage out of 500. </p> <p>Gompertz growth curves provided estimates of asymptotic larval body mass (W<sub>max</sub>), maximum growth rate (K), and the time at which growth rates reach K (xm). However, only W<sub>max</sub> and K were included in statistical analyses as they were the primary parameters of interest for our study. All statistical analyses were performed in RStudio version 4.1.1 (R Core Team, 2021). We constructed generalized linear models (GLMs; 'stats' package in R; R Core Team, 2021) for each of Wmax, K, number of emerged frogs (survival), size at metamorphosis, time to metamorphosis, range of metamorph sizes, and range of metamorphosis days as response variables with drying treatment as the predictor variable. We also constructed GLMs with fish growth as the response variable and a combination of drying treatment and anuran presence as predictor variables with interaction terms. We then used type II ANOVAs for models without significant interaction terms and type III ANOVAs for models with interaction terms via the 'car' package in R (Fox & Weisberg, 2019) to determine the treatment effects on above response variables. GLM model fit and assumptions were checked by a visual assessment of the plotted residuals of each GLM model.</p> <p>Since GPP varied nonlinearly over the duration of the experiment (Fig. 4), we investigated the effects of drying and refilling and trophic treatment on GPP using generalized additive mixed models (GAMMs) with the 'gam' function ('mgcv' package; Wood, 2015). The GAMM model included trophic treatment and drying treatment as parametric effects, trophic treatment over time, drying treatment over time, and time as cubic regression smoother terms, and individual mesocosm and individual mesocosm over time as random effects. The number of knots was set to -1 to utilize the generalized cross-validation method to automatically choose the number of knots for the model. GAMMs allow us to test hypotheses related to main effects (e.g., trophic treatment, drying treatment) within non-linear time series while accounting for random effects related to individual mesocosms and changes over time due to seasonality. We then used a subsequent ANOVA via the 'anova.gam' function within the 'gam' package to determine treatments effects. </p> <p>We investigated the effects of drying and refilling and trophic treatment on periphyton biomass using GAMMs constructed and analyzed identically to GPP except that they are only for experimental days 19–80. This is because periphyton sampling techniques were not standardized until after the second week of data collection. Because data for periphyton biomass was right-skewed and included some 0's that were not true zeros (periphyton was present but below measurement limits), we added 0.5 to each measurement (untransformed mean was 1.838 g) and then log-transformed them. Models run with the transformed data met the assumptions of GAMMs and subsequent ANOVAs.</p>
Plant invasion and fertilizer addition alter soil biota and their functions: A global meta-analysis
<p>Datasets used for meta-analysis on plant invasion and fertilizer addition effects on soil biota and their functions.</p>
Immune Landscape and Gene Function Analysis of Uveal Melanoma Based on Focal Adhesion-Related Gene Typing
<p><strong>Figure legend</strong><strong>s</strong></p> <p><strong>Figure 1 Identification of focal adhesion gene clusters and immune analysis</strong></p> <p>(A) Relative changes in the area under the CDF curve. (B) Consensus clustering results, K=3. (C) Survival curves of different clusters. (D) ssGSEA heatmap showing differences in immune infiltration between clusters. (E) Expression levels of immune checkpoints in different clusters. (F) Violin plots of immune scores, stromal scores, ESTIMATE scores, and tumor purity scores.</p> <p> </p> <p><strong>Figure 2 GSEA pathway enrichment analysis</strong></p> <p> </p> <p><strong>Figure 3 PPI network related to DEGs between cluster 2 and clusters 1 and 3 and HUB gene selection</strong></p> <p>(A) Selection of DEGs between cluster 2 and clusters 1 and 3. (B) PPI network of DEGs between clusters. (C) Intersection analysis of the top 20 HUB genes in the PPI network using five algorithms.</p> <p> </p> <p><strong>Figure 4 Functional analysis of HUB genes in the interaction network and construction of co-expression network</strong></p> <p>(A) Heatmap showing the expression of HUB genes in cluster 2 and clusters 1 and 3. (B) GO functional enrichment analysis of HUB genes. (C) KEGG pathway enrichment analysis of HUB genes. (D) Construction of the co-expression network of HUB genes and their co-expressed genes.</p> <p> </p> <p><strong>Figure 5 Survival curves of patients corresponding to HUB genes at high and low expression levels</strong></p> <p> </p> <p><strong>Figure 6 Exploration of the correlation between HUB genes and drug sensitivity through CellMiner database</strong></p> <p> </p>
Aspirin Resistance and Stroke Risk: Platelet Function Analysis in Patients With Ischemic Events
ClinicalTrials.gov study NCT01586975. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Anesthesia and Functional Connectivity: An Analysis of fMRI Changes
ClinicalTrials.gov study NCT02196259. IPD Sharing: UNDECIDED. Countries: 1. Publications: 12.
fNIRS-based Analysis and Evaluation of the Effect of Schroth Rehabilitation on Motor Functions in Adolescent Idiopathic Scoliosis (AIS)
ClinicalTrials.gov study NCT06884150. IPD Sharing: YES. Countries: 1. Publications: 1.
Dysregulation of FSH in Obesity: Functional and Statistical Analysis
ClinicalTrials.gov study NCT02478775. IPD Sharing: NO. Countries: 1. Publications: 1.
Genetic and functional analysis of Raynaud’s syndrome implicates loci in vasculature and immunity
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Theoretical analysis of superadiabatic combustion for non-stationary filtration combustion by excess enthalpy function
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Building functional and sustainable pharmacovigilance systems - an analysis of pharmacovigilance development across high-, middle- and low-income countries
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Data from: Evidence of functional divergence in MSP7 paralogous proteins: a molecular-evolutionary and phylogenetic analysis
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Knee function through finite element analysis and the role of Miocene hominoids in our understanding of the origin of antipronograde behaviours: the Pierolapithecus catalaunicus patella as a case study
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Finding functionality: Rasch analysis of the Functionality Appreciation Scale in community-dwelling adults in the US
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Genetic analysis of SnRK1β3 subunit of peach and the functional identification of overexpression transformed tomato
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Raw data: Association and functional analysis of angiotensin-converting enzyme 2 gene genetic variants with the pathogenesis of pre-eclampsia
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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.