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107 results for “differentiation process”
Age, sex, length (mm), weight (g), and plasma sex steroid concentrations (ng/ml) of greater amberjack Seriola dumerili reared in sea cages during the process of sex differentiation
<p>The dataset contains an excel file with the age, sex, total length (mm), wet weight (g) and plasma concentrations (ng/ml) of the following sex steroids, measured with the use of liquid chromatography/tandem mass spectrometry (LC-MS/MS): adrenosterone (Ad), androstenedione (Δ4), 11-ketotestosterone (11ΚΤ), testosterone (Τ), estradiol (Ε2), progesterone (P4) and 17,20β-dihydroxy-4-pregnen-3-one (17,20βP).</p>
Data from: Double-strand break repair pathways differentially affect processing and transduction by dual AAV vectors
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Processed datasets and codes for differential expression analysis on polulation-level RNA-seq data
<p>This version includes codes and data necessary to reproduce all results in our response to the correspondences ("Response to 'Neglecting normalization impact in semi‑synthetic RNA‑seq data simulation generates artificial false positives' and 'Winsorization greatly reduces false positives by popular differential expression methods when analyzing human population samples'") (<a href="https://doi.org/10.1186/s13059-024-03232-8">https://doi.org/10.1186/s13059-024-03232-8</a>).</p> <p>It also includes a README file to guide the reproduction of the results in our original publication and resources for the goodness of fit test in the original publication, "Exaggerated False Positives by Popular Differential Expression Methods When Analyzing Human Population Samples" (<a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02648-4">https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02648-4</a>).</p>
Simulation for "Asymptotic Behavior for a Time-Inhomogeneous Stochastic Differential Equation Driven by an α-Stable Lévy Process"
<p>The code and the video are related to the article G.Mihai, and E. Luirard. « Asymptotic Behavior for a Time-Inhomogeneous Stochastic Differential Equation Driven by an α-Stable Lévy Process », available on http://arxiv.org/abs/2112.07287.</p>
A comparative phylogenomic analysis of birds reveals heterogeneous differentiation processes among Neotropical Savannas
<p>The main objective of this study is to evaluate biogeographic hypotheses of diversification and connection between isolated savannas north (Amazonian savannas) and south (Cerrado core) of the Amazon River. To achieve our goal, we employed genomic markers (genotyping by sequencing) to evaluate the genetic structure, population phylogenetic relationships, and historical range shifts of four Neotropical passerines with peri-Atlantic distributions: the Narrow-billed Woodcreeper (<em>Lepidocolaptes angustirostris</em>), the Plain-crested Elaenia (<em>Elaenia cristata</em>), the Grassland Sparrow (<em>Ammodramus humeralis</em>), and the White-banded Tanager (<em>Neothraupis fasciata</em>). The population genetic analyses indicated that landscape (e.g., geographic distance, landscape resistance, and percentage of tree cover) and climate metrics explained divergence among populations in most species, but without indicating a differential role between current and historical factors. Our results did not fully support the hypothesis that isolated populations at Amazonian savannas have been recently derived from the Cerrado core domain. Intraspecific phylogenies and gene flow analyses supported multiple routes of connection between the Cerrado and Amazonian savannas, rejecting the hypothesis that the Atlantic corridor explains the peri-Atlantic distribution. Our results reveal that the biogeographic history of the region is complex and cannot be explained by simple vicariant models.</p>
A comparative phylogenomic analysis of birds reveals heterogeneous differentiation processes among Neotropical Savannas
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Data from: Niche divergence versus neutral processes: combined environmental and genetic analyses identify contrasting patterns of differentiation in recently diverged pine species
Background and Aims: Solving relationships of recently diverged taxa, poses a challenge due to shared polymorphism and weak reproductive barriers. Multiple lines of evidence are needed to identify independently evolving lineages. This is especially true of long-lived species with large effective population sizes, and slow rates of lineage sorting. North American pines are an interesting group to test this multiple approach. Our aim is to combine cytoplasmic genetic markers with environmental information to clarify species boundaries and relationships of the species complex of Pinus flexilis, Pinus ayacahuite, and Pinus strobiformis. Methods: Mitochondrial and chloroplast sequences were combined with previously obtained microsatellite data and contrasted with environmental information to reconstruct phylogenetic relationships of the species complex. Ecological niche models were compared to test if ecological divergence is significant among species. Key Results and Conclusion: Separately, both genetic and ecological evidence support a clear differentiation of all three species but with different topology, but also reveal an ancestral contact zone between P. strobiformis and P. ayacahuite. The marked ecological differentiation of P. flexilis suggests that ecological speciation has occurred in this lineage, but this is not reflected in neutral markers. The inclusion of environmental traits in phylogenetic reconstruction improved the resolution of internal branches. We suggest that combining environmental and genetic information would be useful for species delimitation and phylogenetic studies in other recently diverged species complexes.
Data from: Hierarchical structure of ecological and non-ecological processes of differentiation shaped ongoing gastropod radiation in the Malawi Basin
Ecological processes, non-ecological processes or a combination of both may cause reproductive isolation and speciation, but their specific roles and potentially complex interactions in evolutionary radiations remain poorly understood, which defines a central knowledge gap at the interface of microevolution and macroevolution. Here I examine genome scans in combination with phenotypic and environmental data to disentangle how ecological and non-ecological processes contributed to population differentiation and speciation in an ongoing radiation of Lanistes gastropods from the Malawi Basin. I found a remarkable hierarchical structure of differentiation mechanisms in space and time: neutral and mutation-order processes are older and occur mainly between regions, whereas more recent adaptive processes are the main driver of genetic differentiation and reproductive isolation within regions. The strongest differentiation occurs between habitats and between regions, i.e. when ecological and non-ecological processes act synergistically. The structured occurrence of these processes based on the specific geographic setting and ecological opportunities strongly influenced the potential for evolutionary radiation. The results highlight the importance of interactions between various mechanisms of differentiation in evolutionary radiations, and suggest that non-ecological processes are important in adaptive radiations, including those of cichlids. Insight into such interactions is critical to understanding large-scale patterns of organismal diversity.
Data from: Zebrafish differentially process colour across visual space to match natural scenes
Animal eyes have evolved to process behaviorally important visual information, but how retinas deal with statistical asymmetries in visual space remains poorly understood. Using hyperspectral imaging in the field, in vivo 2-photon imaging of retinal neurons, and anatomy, here we show that larval zebrafish use a highly anisotropic retina to asymmetrically survey their natural visual world. First, different neurons dominate different parts of the eye and are linked to a systematic shift in inner retinal function: above the animal, there is little color in nature, and retinal circuits are largely achromatic. Conversely, the lower visual field and horizon are color rich and are predominately surveyed by chromatic and color-opponent circuits that are spectrally matched to the dominant chromatic axes in nature. Second, in the horizontal and lower visual field, bipolar cell terminals encoding achromatic and color-opponent visual features are systematically arranged into distinct layers of the inner retina. Third, above the frontal horizon, a high-gain UV system piggybacks onto retinal circuits, likely to support prey capture.
Data from: Comparison of spatial and temporal genetic differentiation in a harmful dinoflagellate species emphasises impact of local processes
Population genetic studies provide insights into intraspecific diversity and dispersal patterns of microorganisms such as protists, which help understanding invasions, harmful algal bloom development and occurrence of seafood poisoning. Genetic differentiation across geography has been reported in many microbial species indicating significant dispersal barriers among different habitats. Temporal differentiation has been less studied and its frequency, drivers and magnitude are poorly understood due to a lack of integral studies. The toxic dinoflagellate species /Gambierdiscus caribaeus/ was sampled during two years in the Florida Keys, and repeatedly from 2006 to 2016 at St. Thomas, US Virgin Islands (USVI), including a three-year period with monthly sampling, to compare spatial and temporal genetic differentiation. Samples from the USVI site showed high temporal variability in local population structure, which correlated with changes in salinity and benthic habitat cover. In some cases, temporal variability exceeded spatial differentiation, despite apparent lack of connectivity and dispersal across the Greater Caribbean Region based on the spatial genetic data. Thus, local processes such as selection might have a stronger influence on population structure in microorganisms than geographic distance. The observed high temporal genetic diversity challenges the prediction of harmful algal blooms and toxin concentrations, but illustrates also the evolutionary potential of microalgae to respond to environmental change.
Differentially Private Release of Event Logs for Process Mining
<p>The anonymized event logs of the experiments in the paper "Differentially Private Release of Event Logs for Process Mining"</p>
Utilization of Crude Coconut Oil as an Oil Base Mud to Overcome Differential Pipe Sticking in Drilling Processes when Penetrating Shale Formation
<p>This material has presented on 2nd International Conference on Advanced Research in Engineering and Technology in October 25, 2023.</p>
Data from: Niche divergence versus neutral processes: combined environmental and genetic analyses identify contrasting patterns of differentiation in recently diverged pine species
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Data from: Zebrafish differentially process colour across visual space to match natural scenes
Open the record for dataset details and reuse information.
Data from: Correlations between broad-scale taxonomic and genetic differentiations suggest a dominant imprint of historical processes on beta diversities
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Data from: Hierarchical structure of ecological and non-ecological processes of differentiation shaped ongoing gastropod radiation in the Malawi Basin
Open the record for dataset details and reuse information.
Data from: Comparison of spatial and temporal genetic differentiation in a harmful dinoflagellate species emphasises impact of local processes
Open the record for dataset details and reuse information.
Data from: Differential temperature sensitivity of synaptic and firing processes in a neural mass model of epileptic discharges explains heterogeneous response of experimental epilepsy to focal brain cooling
Experiments with drug-induced epilepsy in rat brains and epileptic human brain region reveal that focal cooling can suppress epileptic discharges without affecting the brain's normal neurological function. Findings suggest a viable treatment for intractable epilepsy cases via an implantable cooling device. However, precise mechanisms by which cooling suppresses epileptic discharges are still not clearly understood. Cooling experiments in vitro presented evidence of reduction in neurotransmitter release from presynaptic terminals and loss of dendritic spines at post-synaptic terminals offering a possible synaptic mechanism. We show that termination of epileptic discharges is possible by introducing a homogeneous temperature factor in a neural mass model which attenuates the post-synaptic impulse responses of the neuronal populations. This result however may be expected since such attenuation leads to reduced post-synaptic potential and when the effect on inhibitory interneurons is less than on excitatory interneurons, frequency of firing of pyramidal cells is consequently reduced. While this is observed in cooling experiments in vitro, experiments in vivo exhibit persistent discharges during cooling but suppressed in magnitude. This leads us to conjecture that reduction in the frequency of discharges may be compensated through intrinsic excitability mechanisms. Such compensatory mechanism is modelled using a reciprocal temperature factor in the firing response function in the neural mass model. We demonstrate that the complete model can reproduce attenuation of both magnitude and frequency of epileptic discharges during cooling. The compensatory mechanism suggests that cooling lowers the average and the variance of the distribution of threshold potential of firing across the population. Bifurcation study with respect to the temperature parameters of the model reveals how heterogeneous response of epileptic discharges to cooling (termination or suppression only) is exhibited. Possibility of differential temperature effects on post-synaptic potential generation of different populations is also explored.
Data from: Neutral and selective processes drive population differentiation for Iris hexagona
Gene flow among widespread populations can be reduced by geographical distance or by divergent selection resulting from local adaptation. In this study, we tested for the divergence of phenotypes and genotypes among 8 populations of Iris hexagona. Using a genotyping-by-sequencing approach, we generated a panel of 750 single nucleotide polymorphisms (SNPs) and used population genetic analyses to determine what may affect patterns of divergence across I. hexagona populations. Specifically, genetic differentiation was compared between populations at neutral and nonneutral SNPs and detected significant differences between the 2 types of markers. We then asked whether loci with the strongest degree of population genetic differentiation were also the loci with the strongest association to morphology or climate differences, allowing us to test if pollinators or climate drive population differentiation or some combination of both. We found 2 markers that were associated with morphology and 1 marker associated with 2 of the environmental variables, which were also identified in the outlier analysis. We then show that the SNPs putatively under selection were positively correlated with both geographic distance and phenotypic distance, albeit weakly to phenotypic distance. Moreover, neutral SNPs were only correlated with geographic distance and thus isolation-by-distance was observed for neutral SNPs. Our data suggest that both deterministic and neutral processes have contributed to the evolutionary trajectory of I. hexagona populations.
Data from: Differential neural processing during motor imagery of daily activities in chronic low back pain patients
Chronic low back pain (chronic LBP) is both debilitating for patients but also a major burden on the health care system. Previous studies reported various maladaptive structural and functional changes among chronic LBP patients on spine- and supraspinal levels including behavioral alterations. However, evidence for cortical reorganization in the sensorimotor system of chronic LBP patients is scarce. Motor Imagery (MI) is suitable for investigating the cortical sensorimotor network as it serves as a proxy for motor execution. Our aim was to investigate differential MI-driven cortical processing in chronic LBP compared to healthy controls (HC) by means of functional magnetic resonance imaging (fMRI). Twenty-nine subjects (15 chronic LBP patients, 14 HC) were included in the current study. MI stimuli consisted of randomly presented video clips showing every-day activities involving different whole-body movements as well as walking on even ground and walking downstairs and upstairs. Guided by the video clips, subjects had to perform MI of these activities, subsequently rating the vividness of their MI performance. Brain activity analysis revealed that chronic LBP patients exhibited significantly reduced activity compared to HC subjects in MI-related brain regions, namely the left supplementary motor area and right superior temporal sulcus. Furthermore, psycho-physiological-interaction analysis yielded significantly enhanced functional connectivity (FC) between various MI-associated brain regions in chronic LBP patients indicating diffuse and non-specific changes in FC. Current results demonstrate initial findings about differences in MI-driven cortical processing in chronic LBP pointing towards reorganization processes in the sensorimotor network.
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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.