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7,228 results for “Modules”
Pharmulator™ Module: Quantifying Functional Groups and Its Applications in Drug Design
<p><strong>MS-Excel-1.xlsx:</strong> It contains SMILES codes of the training and test sets along with their GHS classification </p> <p><strong>MS-Excel-2.xlsx: </strong>It contains<strong> </strong>SMILES codes of the 8993 chemicals and their experimental aqueous solubility parameters and FGs, Morgan and MACCS-based structural descriptor values</p> <p><strong>MS-Excel-3.xlsx: </strong>It contains the DrugBank IDs, SMILES codes and number of FG occurrences (binary string) of the 2356 drug molecules</p> <p><strong>MS-Excel-4.xlsx:</strong> It contains SMILES codes as well as FGs descriptors for the entire training sets, balanced training sets and final test sets</p> <p><strong>MS-Excel-5.xlsx:</strong> It contains SMILES codes as well as Morgan descriptors for the entire training sets, balanced training sets and final test sets</p> <p><strong>MS-Excel-6.xlsx:</strong> It contains SMILES codes as well as MACCS descriptors for the entire training sets, balanced training sets and final test sets</p>
Relatedness modulates reproductive competition among queens in ant societies with multiple queens
<p>Reproductive sharing in animal groups with multiple breeders, insects and vertebrates alike, contains elements of both conflict and cooperation, and depends on both relatedness between co-breeders, as well as their internal and external conditions. We studied how queens of the ant Formica fusca adjust their reproductive efforts in response to experimental manipulations of the kin competition regime in their nest, as well as their own reproductive status. Queens respond to the presence of competitors by increasing their egg laying efforts, but only if the competitors are highly fecund and distantly related. Furthermore, queens only engage in cannibalism of eggs when the risk of erroneously destroying own offspring is absent. We demonstrate that queens of Formica fusca fine-tune their behaviours in response to kinship and fecundity of others as well as their own physiological state in a manner that is unusually precise for any cooperative breeder.</p>
Modules for Experiments in Stellar Astrophysics (MESA): Time-Dependent Convection, Energy Conservation, Automatic Differentiation, and Infrastructure
<p>We update the capabilities of the open-knowledge software instrument Modules for Experiments in Stellar Astrophysics (MESA). The new auto_diff module implements automatic differentiation in MESA, an enabling capability that alleviates the need for hard-coded analytic expressions or finite difference approximations. We significantly enhance the treatment of the growth and decay of convection in MESA with a new model for time-dependent convection, which is particularly important during late-stage nuclear burning in massive stars and electron degenerate ignition events. We strengthen MESA's implementation of the equation of state, and we quantify continued improvements to energy accounting and solver accuracy through a discussion of different energy equation features and enhancements. To improve the modeling of stars in MESA we describe key updates to the treatment of stellar atmospheres, molecular opacities, Compton opacities, conductive opacities, element diffusion coefficients, and nuclear reaction rates. We introduce treatments of starspots, an important consideration for low-mass stars, and modifications for superadiabatic convection in radiation-dominated regions. We describe new approaches for increasing the efficiency of calculating monochromatic opacities and radiative levitation, and for increasing the efficiency of evolving the late stages of massive stars with a new operator split nuclear burning mode. We close by discussing major updates to MESA's software infrastructure that enhance source code development and community engagement.</p>
Allosteric modulation of the adenosine A2A receptor by cholesterol
<p>Cholesterol is a major component of the cell membrane and commonly regulates membrane protein function. Here, we investigate how cholesterol modulates the conformational equilibria and signaling of the adenosine A2A receptor (A2AR) in reconstituted phospholipid nanodiscs. This model system conveniently excludes possible effects arising from cholesterol-induced phase separation or receptor oligomerization and focuses on the question of allostery. GTP hydrolysis assays show that cholesterol weakly enhances the basal signaling of A2AR while decreasing the agonist EC50. Fluorine nuclear magnetic resonance (19F NMR) spectroscopy shows that this enhancement arises from an increase in the receptor's active state population and a G-protein-bound precoupled state. 19F NMR of fluorinated cholesterol analogs reveals transient interactions with A2AR, indicating a lack of high-affinity binding or direct allosteric modulation. The combined results suggest that the observed allosteric effects are largely indirect and originate from cholesterol-mediated changes in membrane properties, as shown by membrane fluidity measurements and high-pressure NMR.</p>
Intermediary and supplemental data for publication "Heterogenous circulating miRNA changes in ME/CFS converge on a unified cluster of target genes and may be a result of modulation by latent herpesviruses: A computational analysis"
<p>Intermediary and supplemental data for publication "Heterogenous circulating miRNA changes in ME/CFS converge on a unified cluster of target genes and may be a result of modulation by latent herpesviruses: A computational analysis"</p>
Benchmark dataset for verification and validation of elPaSo Core module
<p>This dataset contain the set of vibroacoustic benchmark problems for verification and validation of the FEM research code "elPaSo Core".</p>
Constrained trait variation by water availability modulates radial growth in evergreen and deciduous Mediterranean oaks
<p>Data supporting the findings of the study "Constrained trait variation by water availability modulates radial growth in two coexisting Mediterranean oaks"</p>
Dataset for computational study of the ALS mutation G335D modulating the dimerization of TDP-43 amyloidogenic core peptide
<p>This dataset consist the following contents:</p> <p>1. The data used to generate MD/RSET2 trajectories for WT and G335D systems, including initial structures, parameter files and topology files;</p> <p>2. The final structures and representative conformations of intermediates for WT and G335D systems in MD simulations;</p> <p>3. Representative conformations of the top eight clusters for WT and G335D systems in REST2 simulations.</p>
Melanoma-derived soluble mediators modulate neutrophil plasticity and the release of Neutrophil Extracellular Traps
<p>Background: polymorphonuclear neutrophils (PMNs) are main effector cells in the inflammatory responses. The significance of PMN infiltration in tumor microenvironment remains to be clarified. Metastatic melanoma is the most lethal type of skin cancer with an increasing incidence over the last decades. Few studies investigated the role of PMNs in human melanoma. The aim of this study was to investigate the role of PMNs and their mediators in human melanoma; (2) Methods: highly purified human PMNs from healthy donors were stimulated, in vitro, with conditioned media derived from the melanoma cell lines SKMEL28 and A375 (melanoma-CM) as well as from primary melanocytes as control. PMN functions (chemotaxis, survival, activation, cell tracking, morphology and NETs release) were evaluated; (3) Results: we found that the A375 cell line produced soluble factors able to promote PMN chemotaxis, survival, activation, and to modify PMN morphological changes and kinetic properties. Furthermore, both melanoma cell lines CM induced activation and the release of neutrophil extracellular traps (NETs) from PMNs. By contrast, primary melanocytes CM did not modify any PMN biological behavior. In addition, serum levels of myeloperoxidase (MPO), matrix metalloprotease-9 (MMP-9), CXCL8/IL-8, granulocyte and monocyte colony stimulating factor (GM-CSF) and NETs components were significantly increased in advanced melanoma patients compared to healthy controls; (4) Conclusions: melanoma cell lines produce soluble factors able to ‘educate’ PMNs towards an activated functional state. Metastatic melanoma patients display increased circulating levels of neutrophil-related mediators and NETs, suggesting that a neutrophil-related signature exists in metastatic melanoma patients. Further investigations are needed to better understand the role of these “tumor-educated neutrophils” in modifying melanoma cell behavior.</p>
OMMT-Fibre: textile fibres acquired using OptoMechanical Modulation Tomography (OMMT)
<p><strong>Description</strong></p><p>This dataset contains compressed sensing images of fluorescent textile fibres acquired using OptoMechanical Modulation Tomography (OMMT).</p><p>The dataset was collected to illustrate a reconstruction algorithm for 3D fluorescence microscopy data that uses a 1+2D TV regularization to enforce volumetric coherence constraints while being efficient to compute.</p><p> </p><p><strong>Reference</strong></p><p>If you use this dataset, please cite the following publication:</p><p>François Marelli and Michael Liebling, "Efficient compressed sensing reconstruction for 3D fluorescence microscopy using OptoMechanical Modulation Tomography (OMMT) with a 1+2D regularization," Opt. Express 31, 31718-31733 (2023) <br><a href="https://doi.org/10.1364/OE.493611">https://doi.org/10.1364/OE.493611</a></p>
Data and code for 'Transient knickpoint migrating modulated by fault activities on the Northeastern Tibetan Plateau margin: A case from the Yellow River '
<p> </p> <p>Kindly feel free to reach out to me (<a href="mailto:lizhch@smail.nju.edu.cn">lizhch@smail.nju.edu.cn</a>) if you have any queries or encounter issues with the 'codes'.</p>
Data for: Divergence of alternative sugar preferences through modulation of the expression and activity of the Gal3 sensor in yeast
<p>Optimized nutrient utilization is crucial for the progression of microorganisms in competing communities. Here we investigate how different budding yeast species and ecological isolates have established divergent preferences for two alternative sugar substrates: Glucose, which is fermented preferentially by yeast, and galactose, which is alternatively used upon induction of the relevant <em>GAL</em> metabolic genes. We quantified the dose-dependent induction of the <em>GAL1</em> gene encoding the central galactokinase enzyme, and found that a very large diversification exists between different yeast ecotypes and species. The sensitivity of <em>GAL1</em> induction correlates with the growth performance of the respective yeasts with the alternative sugar. We further define some of the mechanisms, which have established different glucose/galactose consumption strategies in representative yeast strains by modulating the activity of the Gal3 inducer. (1) Optimal galactose consumers, such as <em>Saccharomyces uvarum</em>, contain a hyperactive <em>GAL3</em> promoter, sustaining highly sensitive <em>GAL1</em> expression, which is not further improved upon repetitive galactose encounters. (2) Desensitized galactose consumers, such as <em>S. cerevisiae </em>Y12, contain a less sensitive Gal3 sensor, causing a shift of the galactose response towards higher sugar concentrations even in galactose experienced cells. (3) Galactose insensitive sugar consumers, such as <em>S. cerevisiae</em> DBVPG6044, contain an interrupted <em>GAL3</em> gene, causing extremely reluctant galactose consumption, which however still is improved upon repeated galactose availability. In summary, different yeast strains and natural isolates have evolved galactose utilization strategies, which cover the whole range of possible sensitivities by modulating the expression and/or activity of the inducible galactose sensor Gal3.</p>
Data from: Feeding and water temperature modulate the activity of gut microbiota in greater amberjack juveniles (Seriola dumerili)
<p>Illumina (MiSeq v3) sequencing data for gut microbiota profiling in greater amberjack (<em>Seriola dumerili</em>) juveniles reared at three different water temperatures and sampled along a day cycle. </p>
Matlab code for " Prior expectation enhances sensorimotor behavior by modulating population tuning and subspace activity in sensory cortex"
<p>Here are the data and code supporting the findings of the paper, 'Prior expectation enhances sensorimotor behavior by modulating population tuning and subspace activity in sensory cortex.'</p>
Receptor cavity-based screening reveals potential allosteric modulators of gonadotropin receptors in carp (Cyprinus carpio)
<p>The dataset include phase database consisting of prepared ligand used in screening of potential allosteric modulators for carp FSHR and LHR. the original dataset were sourced from The compound libraries from <a href="https://enamine.net/compound-libraries">https://enamine.net/compound-libraries</a> and are free to access and downloaded and used as per the mentioned sites terms and conditions the Datasets given here are processed databases constructed using the Phase module (Phase, Schrödinger, LLC, New York, NY, 2021.).</p>
Data from: Theta-phase-specific modulation of dentate gyrus memory neurons
<p>The theta rhythm, a quasi-periodic 4-10 Hz oscillation, is observed during memory processing in the hippocampus, with different phases of theta hypothesized to separate independent streams of information related to the encoding and recall of memories. At the cellular level, the discovery of hippocampal memory cells (engram neurons), as well as the modulation of memory recall through optogenetic activation of these cells, has provided evidence that certain memories are stored, in part, in a sparse ensemble of neurons in the hippocampus. In previous research, however, engram reactivation has been carried out using open loop stimulation at fixed frequencies; the relationship between engram neuron reactivation and ongoing network oscillations has not been taken into consideration. To address this concern, we implemented a closed-loop reactivation of engram neurons that enabled phase-specific stimulation relative to theta oscillations in the local field potential. Using this real-time approach, we tested the impact of activating engram neurons during the peak (encoding phase) and trough (recall phase) of theta oscillations. Consistent with previously hypothesized functions of theta oscillations in memory function, we show that stimulating engram neurons at the trough of theta is more effective in eliciting behavioral recall than either fixed frequency stimulation or stimulation at the peak of theta. Moreover, phase-specific trough stimulation is accompanied by an increase in the coupling between gamma and theta oscillations in CA1 hippocampus. Oure results provide a causal link between phasespecific activation of engram cells and the behavioral expression of memory.</p>
Fig. 5 in Unique guanidine-conjugated catechins from the leaves of Alchornea rugosa and their autophagy modulating activity
Fig. 5. (A) The level of autophagy marker protein expression in cells treated with compounds 4–7. LC3B was determined using the LC3B II/I ratio, which was then standardized against the control group (nontreated group). The p62 protein level was detected, and the expression level was normalized by dividing by the protein level in the control group. (CQ: chloroquine treatment group at 25 μM, Rapa: rapamycin treatment group at 0.25 μM). (B) GFP-mRFP-tagged LC3 puncta after treatment with the test compounds. HEK293 cells were treated with autophagy-regulating compounds 4–7, and LC3 puncta were detected by using confocal microscopy.
Fig. 4 in Unique guanidine-conjugated catechins from the leaves of Alchornea rugosa and their autophagy modulating activity
Fig. 4. Screening for autophagy regulation by compounds (1–9) isolated from A. rugosa in HEK293 cells. HEK293 cells stably expressing GFP-LC3 were treated with 20 μM compounds for 24 h, and confocal imaging was used to examine the production of LC3-GFP puncta.
Dynamic corticothalamic modulation of the somatosensory thalamocortical circuit during wakefulness
<p>Data and code to accompany "Dynamic corticothalamic modulation of the somatosensory thalamocortical circuit during wakefulness" by Dimwamwa, E. D., Pala, A., Chundru, V., Wright, N. C., Stanley, G. B., under review.</p>
Fig. 7. A in MAPKK2/4/5/7-MAPK3-JAZs modulate phenolic acid biosynthesis in Salvia miltiorrhiza
Fig. 7. A proposed model for the roles of SmMAPK3 in S. miltiorrhiza phenolic acid biosynthesis. Model illustrating the roles of SmMAPK3 in S. miltiorrhiza phenolic acid biosynthesis.
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.