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ShareScore release 0.9.0
Dataset results
920 results for “Functional analysis”
Dissection of human fibroblast populations by lung regions: genomic differences and functional pathway analysis
GEO Series GSE19362. Homo sapiens. 6 samples. Type: Expression profiling by array.
Genome-wide mapping and functional analysis of DNA methylation in clonal invasive crayfish [RNA-seq]
GEO Series GSE112410. Procambarus fallax; Procambarus virginalis. 9 samples. Type: Expression profiling by high throughput sequencing.
High resolution methylome analysis reveals widespread functional hypomethylation during adult human erythropoiesis
GEO Series GSE44054. Homo sapiens. 12 samples. Type: Methylation profiling by genome tiling array.
A genome-wide analysis of open chromatin in human tracheal epithelial cells reveals novel candidate regulatory elements for lung function (DNase-hypersensitivity)
GEO Series GSE52179. Homo sapiens. 2 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Data from: Assessment of grain quality in terms of functional group response to elevated [CO2], water and nitrogen using a meta-analysis: Grain protein, zinc and iron under future climate
The increasing [CO2] in the atmosphere increases crop productivity. However, grain quality of cereals and pulses are substantially decreased and consequently compromise human health. Meta-analysis techniques were employed to investigate the effect of elevated [CO2] (e[CO2]) on protein, zinc (Zn) and iron (Fe) concentrations of major food crops (542 experimental observations from 135 studies) including wheat, rice, soybean, field peas and corn considering different levels of water and nitrogen (N). Each crop, except soybean, had decreased protein, Zn and Fe concentrations when grown at e[CO2] concentration ( ≥550 μmol mol-1) compared ambient [CO2] (a[CO2]) concentration (≤ 380 μmol mol-1). Grain protein, Zn and Fe concentrations were reduced under e[CO2], however, the responses of protein, Zn and Fe concentrations to e[CO2 ] were modified by water stress and N. There was an increase in Fe concentration in soybean under medium N and wet conditions but non-significant. The reductions in protein concentrations for wheat and rice were ~ 5-10%, and the reductions in Zn and Fe concentrations were ~ 3-12%. For soybean, there was a small and non-significant increase of 0.37% in its protein concentration under medium N and dry water, while Zn and Fe concentrations were reduced by ~ 2-5%. The protein concentration of field peas decreased by 1.7%, and the reductions in Zn and Fe concentrations were ~ 4-10%. The reductions in protein, Zn and Fe concentrations of corn were ~ 5-10%. Bias in the dataset was assessed using a regression test and rank correlation. The analysis indicated that there are medium levels of bias within published meta-analysis studies of crops responses to Free Air [CO2]Enrichment (FACE). However, the integration of the influence of reporting bias did not affect the significance or the direction of the [CO2] effects.
Orthopedic treatment for Class II malocclusion with functional appliances and its effect on upper airways: a systematic review with meta-analysis
<p>Dataset for all analyses in the paper.</p>
Data from: Integrated analysis and visualization of group differences in structural and functional brain connectivity: applications in typical ageing and schizophrenia
Structural and functional brain connectivity are increasingly used to identify and analyze group differences in studies of brain disease. This study presents methods to analyze uni- and bi-modal brain connectivity and evaluate their ability to identify differences. Novel visualizations of significantly different connections comparing multiple metrics are presented. On the global level, "bi-modal comparison plots" show the distribution of uni- and bi-modal group differences and the relationship between structure and function. Differences between brain lobes are visualized using "worm plots". Group differences in connections are examined with an existing visualization, the "connectogram". These visualizations were evaluated in two proof-of-concept studies: (1) middle-aged versus elderly subjects; and (2) patients with schizophrenia versus controls. Each included two measures derived from diffusion weighted images and two from functional magnetic resonance images. The structural measures were minimum cost path between two anatomical regions according to the "Statistical Analysis of Minimum cost path based Structural Connectivity" method and the average fractional anisotropy along the fiber. The functional measures were Pearson's correlation and partial correlation of mean regional time series. The relationship between structure and function was similar in both studies. Uni-modal group differences varied greatly between connectivity types. Group differences were identified in both studies globally, within brain lobes and between regions. In the aging study, minimum cost path was highly effective in identifying group differences on all levels; fractional anisotropy and mean correlation showed smaller differences on the brain lobe and regional levels. In the schizophrenia study, minimum cost path and fractional anisotropy showed differences on the global level and within brain lobes; mean correlation showed small differences on the lobe level. Only fractional anisotropy and mean correlation showed regional differences. The presented visualizations were helpful in comparing and evaluating connectivity measures on multiple levels in both studies.
Data from: The function(s) of the bone ornamentation in the crocodylomorph osteoderms: a biomechanical model based on a finite element analysis
This paper aims at assessing the influence of the bone ornamentation and, specifically, of the associated loss of bone mass on the mechanical response of the crocodylomorph osteoderms. To this aim, we have performed three dimensional modeling and finite element analyses on a sample which includes both extant dry bones and well-preserved fossils tracing back to the Late Triassic. We simulated an external attack under variable angles on the apical surface of each osteoderm and further repeated the simulation on an equivalent set of smoothed 3D-modeled osteoderms. The comparative results evidenced that the presence of an apical sculpture has no significant influence on the von Mises stress distribution in the osteoderm volume although it involves a slight increase in its numerical score. Moreover, performing parametric analyses, we evidenced that the Young's modulus in the osteoderm which may vary depending on the bone porosity, the collagen fiber orientation or the calcification density has no impact on the von Mises stress distribution inside the osteoderm volume. As the crocodylomorph bone ornamentation is continuously remodeled by pit resorption and secondary bone deposit, we assume that the apical sculpture may be the outcome of a "trade-off" between the bone mechanical resistance and the implication in physiological functions. These physiological functions are indeed based on the set-up of a bone superficial vessel network and/or on the recurrent release of mineral elements into the plasma: heat transfers when basking and respiratory acidosis buffering during prolonged apnea in neosuchians and teleosaurids; compensatory homeostasis in response to general calcium deficiencies. On a general morphological aspect, the osteoderm geometrical variability within our sample lead us to assess that the global osteoderm geometry (whether square or rectangular) does not influence the von Mises stress whereas the presence of a dorsal keel would rather reduce the stress along the vertical axis.
Data from: Mutational analysis of Rab3 function for controlling active zone protein composition at the Drosophila neuromuscular junction
At synapses, the release of neurotransmitter is regulated by molecular machinery that aggregates at specialized presynaptic release sites termed active zones. The complement of active zone proteins at each site is a determinant of release efficacy and can be remodeled to alter synapse function. The small GTPase Rab3 was previously identified as playing a novel role that controls the distribution of active zone proteins to individual release sites at the Drosophila neuromuscular junction. Rab3 has been extensively studied for its role in the synaptic vesicle cycle; however, the mechanism by which Rab3 controls active zone development remains unknown. To explore this mechanism, we conducted a mutational analysis to determine the molecular and structural requirements of Rab3 function at Drosophila synapses. We find that GTP-binding is required for Rab3 to traffick to synapses and distribute active zone components across release sites. Conversely, the hydrolytic activity of Rab3 is unnecessary for this function. Through a structure-function analysis we identify specific residues within the effector-binding switch regions that are required for Rab3 function and determine that membrane attachment is essential. Our findings suggest that Rab3 controls the distribution of active zone components via a vesicle docking mechanism that is consistent with standard Rab protein function.
Fluorescence image time series for pair correlation function analysis
<p>Data files for the tutorial "<a href="https://github.com/cgohlke/ipcf.ipynb">Pair Correlation Function Analysis of Fluorescence Fluctuations in Big Image Time Series using Python</a>", presented at the Big Data Image Processing & Analysis BigDIPA workshops 2016, 2017, and 2018.<br><br>The <strong>Simulation_Channel.bin</strong> file contains the result of a simulation of fluorescent particles diffusing on a 64x64 grid. The grid contains a diagonal, 300 nm wide channel, which restricts free diffusion. The file was produced using the Globals for Images, SimFCS software. The array shape is (32000, 64, 64), the data type is uint16.<br><br>The <strong>Simulation_Channel.ipcf.bin</strong> file contains the expected results of an ipCF analysis with 32 points at radius 6, and 32 bins. The array shape is (52, 52, 32, 30), the data type is float32.<br><br>The <strong>nih3t3-egfp_2.zip</strong> dataset contains a time series of SPIM images of a biological cell. It consists 35,000 TIFF files of 1024x512 16-bit grayscale samples each, 34.5 GB total.</p>
Identification of Potential Functional Modules and Diagnostic Genes for Crohn's Disease Based on Weighted Gene Co-expression Network Analysis and LASSO Algorithm
<p>Table S1 651 DEGs between CD and control samples</p> <p>Table S2 381 ME turquoise module genes</p> <p>Table S3 Coefficients of the eight module genes analyzed by LASSO regression</p>
What effect does functional appliance treatment have on the temporomandibular joint? A systematic review with meta-analysis
<p>Data for all analyses done in the paper.</p>
Alkyne-functionalized cyclooctyne on Si(001) – reactivity studies and surface bonding from an energy decomposition analysis perspective
<p>The reactivity and bonding of an ethinyl-functionalized cyclooctyne on Si(001) is studied by means of density functional theory. This system is promising for the organic functionalization of semiconductors. Singly bonded adsorption structures are obtained by [2+2] cycloaddition reactions of the cyclooctyne or ethinyl group with the Si(001) surface. A thermodynamic preference for an adsorption with the cyclooctyne group in on-top position is found and traced back to minimal structural deformation of adsorbate and surface with the help of the energy decomposition analysis for extended systems (pEDA). Starting from singly bonded structures a plethora of reaction paths describing conformer changes and consecutive reactions with the surface are discussed. Strongly exothermic and exergonic reactions to doubly bonded structures are presented, while small reaction barriers highlight the high reactivity of the studied organic molecule on the Si(001) surface. Dynamic aspects of the competitive bonding of the functional groups are addressed by ab initio molecular dynamics calculations. Several trajectories to doubly bonded structures are obtained in agreement to calculations using the nudged-elastic band approach. However, our findings are in disagreement with experimental observations of a selective adsorption by the cyclooctyne moiety, which is critically discussed.</p>
3D Analysis of the Effects of tDCS (Transcranial Direct Current Stimulation) on a Functional Task in High Level Athletes
ClinicalTrials.gov study NCT03901222. IPD Sharing: NO. Countries: 1. Publications: 0.
Left Atrial Function Analysis for Patients With Persistent Atrial Fibrillation Undergoing Pulmonary Vein Isolation
ClinicalTrials.gov study NCT03242694. IPD Sharing: NO. Countries: 1. Publications: 0.
Evaluation of Architectural Changes in Mandibular Bone Pattern After Functional Treatment by Fractal Dimension Analysis
ClinicalTrials.gov study NCT04730115. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Three-dimensional Analysis of Obliquus Capitis Inferior Muscle Function in the Rotatory Form of Cervical Dystonia
ClinicalTrials.gov study NCT05327985. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Functional Movement Analysis (FMS) of Diaphragmatic Breathing-Immediate Effect on Shoulder Mobility
ClinicalTrials.gov study NCT05748522. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Analysis of the Pathophysiological and Functional State of the Knee Joint
ClinicalTrials.gov study NCT06490770. IPD Sharing: Not stated. Countries: 1. Publications: 0.
A Comparative Analysis of Prognostic Factors for Functional Outcomes in Patients With Acute Subdural Hematoma
ClinicalTrials.gov study NCT06364059. IPD Sharing: NO. Countries: 1. Publications: 0.
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.