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29,897 results for “activism”
Removal of Crystal Violet (CV) in aqueous solution by Activated Carbon- Equilibrium, kinetic and Thermodynamic
<p>The quantitative kinetic and equilibrium adsorption parameters for Crystal Violet (CV) removed by commercial activated carbon (AC) were studied by UV visible absorption spectroscopy. (AC) with a high specific surface area (1250.320m2 /g) was characterized by the Brunauer-Emmett-Teller (BET) method and the zero charge point (pzc).The adsorptive properties of (AC) with (CV) was conducted at variable stirring speed , adsorbent dose, solution pH, initial (CV) concentrations, contact time and temperature using batch mode operation to find the optimal conditions for a maximum adsorption. The adsorption mechanism of CV onto (AC) was studied using the first pseudo order, second pseudo order and Elovich kinetic models. The kinetic was found to follow a pseudo-second order kinetic model. The equilibrium adsorption data for CV on AC were analyzed by the Langmuir, Freundlich, Elovich and Temkin models. The results indicate that the Langmuir model provides the best correlation (qmax = 35.71, 90.91 mg/g at 25 °C and 40 °C respectively).The adsorption isotherms at different temperatures have been used for the determination of thermodynamic parameters i.e. the free energy (ΔGo = -2.30 to -5.34 kJ/mol), enthalpy (ΔHo = 36.966 kJ/mol), entropy (ΔSo = 0.131 kJ/mol K) and activation energy (Ea) 40.208 kJ/mol of adsorption. The negative ΔGo and positive ΔHo values indicate that the overall adsorption is spontaneous and endothermic in nature</p>
Cellular uptake of silica and gold nanoparticles induces early activation of nuclear receptor NR4A1
<p>The approval of new nanomedicines requires a deeper understanding of the interaction between cells and nanoparticles (NPs). Silica (SiO<sub>2</sub>) and gold (Au) NPs have shown great potential in biomedical applications, such as the delivery of therapeutic agents, diagnostics, and biosensors. NP-cell interaction and internalization can trigger several cellular responses, including gene expression regulation. The identification of differentially expressed genes in response to NP uptake contributes to a better understanding of the cellular processes involved, including potential side effects. We investigated gene regulation in human macrophages and lung epithelial cells after acute exposure to spherical 60 nm SiO<sub>2</sub> NPs. SiO<sub>2</sub> NPs uptake did not considerably affect gene expression in epithelial cells, whereas five genes were up-regulated in macrophages. These genes are principally related to inflammation, chemotaxis, and cell adhesion. NR4A1, an important modulator of inflammation in macrophages, was found to be up-regulated. The expression of this gene was increased upon 1 h of macrophage exposure to spherical 50 nm AuNPs and 200 nm spherical SiO<sub>2</sub> NPs. NR4A1 can thus be an important immediate regulator of inflammation provoked by NP uptake in macrophages.</p>
Single cell imaging of ERK and Akt activation dynamics and heterogeneity induced by G protein-coupled receptors - Scripts & Source data
<p>Source data and scripts to reproduce the figures that are part of the publication "Single cell imaging of ERK and Akt activation dynamics and heterogeneity induced by G protein-coupled receptors".</p> <p>Journal of Cell Science (2022) 135, jcs259685, DOI: 10.1242/jcs.259685</p> <p> </p> <p>An earlier version of this work is published as a preprint: "Heterogeneity and dynamics of ERK and Akt activation by G protein-coupled receptors depend on the activated heterotrimeric G proteins", DOI: <a href="https://doi.org/10.1101/2021.07.27.453948">10.1101/2021.07.27.453948</a></p>
Dataset of results for a copper switch for inducing CRISPR/Cas9-based transcriptional activation tightly regulates gene expression in Nicotiana benthamiana.
<p>CRISPR-based programmable transcriptional activators (PTAs) are used in plants for rewiring gene networks. Better tuning of their activity in a time and dose-dependent manner should allow precise control of gene expression. Here, we report the optimization of a Copper Inducible system called CI-switch for conditional gene activation in Nicotiana benthamiana. In the presence of copper, the copper-responsive factor CUP2 undergoes a conformational change and binds a DNA motif named copper-binding site (CBS). In this study, we tested several activation domains fused to CUP2 and found that the non-viral Gal4 domain results in strong activation of a reporter gene equipped with a minimal promoter, offering advantages over previous designs. To connect copper regulation with downstream programmable elements, several copper-dependent configurations of the strong dCasEV2.1 PTA were assayed, aiming at maximizing activation range, while minimizing undesired background expression. The best configuration involved a dual copper regulation of the two protein components of the PTA, namely dCas9:EDLL and MS2:VPR, and a constitutive RNA pol III-driven expression of the third component, a guide RNA with anchoring sites for the MS2 RNA-binding domain. With these optimizations, the CI/dCasEV2.1 system resulted in copper-dependent activation rates of 2,600-fold and 245-fold for the endogenous N. benthamiana DFR and PAL2 genes, respectively, with negligible expression in the absence of the trigger. The tight regulation of copper over CI/dCasEV2.1 makes this system ideal for the conditional production of plant-derived metabolites and recombinant proteins in the field.</p>
Raw data for "Effect of MRgFUS treatment on cortical activity in Parkinson's disease: a fNIRS study"
<p>In this paper, a new combined approach, based on Magnetic Resonance-guided Focused Ultrasound Surgery (MRgFUS) technique and functional Near Infrared Spectroscopy (fNIRS), was applied for treatment and monitoring of patients affected by bilateral Parkinson’s disease (PD). On one side, MRgFUS enables non-invasive thalamotomy by combining FUS for tissue ablation and MR for targeting and monitoring. On the other side, fNIRS allows to monitor, non-invasively and without strict motion restriction even in a daily life environment, cortical neural activity related dynamics of both oxygenated and deoxygenated haemoglobin (HbO and HbR, respectively). In particular, the changes of cortical activation pattern in PD patients, with respect to age matched healthy control subjects, were analysed, while performing left and right hand finger tapping (LFT and RFT, respectively), before MRgFUS treatment, and at two different time intervals after the treatment. By comparison with the pre-treatment session, significant activations were predominantly observed one week after the treatment, with patterns recalling those of control group, and partially lost one month later, likely because of the neurodegenerative nature of PD. In addition, activations were more marked for LFT task, being the treatment performed on the right hemisphere. These results appear promising in view of the application of fNIRS for neurorehabilitation, especially in those clinical settings where traditional neuroimaging techniques cannot be applied.</p>
Raw Data for the article: Extracellular Vesicle-Derived microRNAs of Human Wharton's Jelly Mesenchymal Stromal Cells May Activate Endogenous VEGF-A to Promote Angiogenesis
<p>Despite low levels of vascular endothelial growth factor (VEGF)-A, the secretome of human Wharton's jelly (WJ) mesenchymal stromal cells (MSCs) effectively promoted proangiogenic responses in vitro, which were impaired upon the depletion of small (~140 nm) extracellular vesicles (EVs). The isolated EVs shared the low VEGF-A profile of the secretome and expressed five microRNAs, which were upregulated compared to fetal dermal MSC-derived EVs. These upregulated microRNAs exclusively targeted the <em>VEGF-A</em> gene within 54 Gene Ontology (GO) biological processes, 18 of which are associated with angiogenesis. Moreover, 15 microRNAs of WJ-MSC-derived EVs were highly expressed (Ct value ≤ 26) and exclusively targeted the thrombospondin 1 (<em>THBS1</em>) gene within 75 GO biological processes, 30 of which are associated with the regulation of tissue repair. The relationship between predicted microRNA target genes and WJ-MSC-derived EVs was shown by treating human umbilical-vein endothelial cells (HUVECs) with appropriate doses of EVs. The exposure of HUVECs to EVs for 72 h significantly enhanced the release of VEGF-A and THBS1 protein expression compared to untreated control cells. Finally, WJ-MSC-derived EVs stimulated in vitro tube formation along with the migration and proliferation of HUVECs. Our findings can contribute to a better understanding of the molecular mechanisms underlying the proangiogenic responses induced by human umbilical cord-derived MSCs, suggesting a key regulatory role for microRNAs delivered by EVs.</p>
Panmixia and active colonisation of the invasive palm Trachycarpus fortunei (Arecaceae) in Southern Switzerland and Northern Italy as inferred by microsatellites and SNP markers
<p>Dataset for the paper named "Panmixia and active colonisation of the invasive palm Trachycarpus fortunei (Arecaceae) in Southern Switzerland and Northern Italy as inferred by microsatellites and SNP markers"</p> <p>GBS analysis:</p> <p>- variants.vcf.gz : compressed non filtered VCF file with 208 samples and 73685 markers on 36195 loci</p> <p>- variants.filt.vcf.gz: Filtered Variant call file (compressed) - Samples with > 50% missing genotypes, and variants with genotype calls in less than 80% of samples are removed; variants with maf < 1% are removed -207 samples and 31312 markers on 19301 loci - 1 samples removed 6CL</p> <p>Microsatellites:</p> <p>TFT.fortunei_Microsatellites_FSTATFINAL_Pop.dat</p> <p>Samples file</p> <p>-Trachycarpus_Samples_sheet.xlsx : list of samples used (lab extractions) </p> <p> </p> <p> </p>
Data from: Influence of Check Dams on the Activity Pattern and Morphometric Traits of Overwintering Tadpoles in the Western Himalaya
<p>Dataset for the paper: Influence of Check Dams on the Activity Pattern and Morphometric Traits of Overwintering Tadpoles in the Western Himalaya. See readme.txt for details.</p>
Characterization of Salix nigra floral insect community and activity of three native Andrena bees
<i>Salix nigra</i> (black willow) is a widespread tree that hosts many species of polylectic hymenopterans and oligolectic bees of the genus <i>Andrena</i>. The early flowering of <i>S. nigra</i> makes it an important nutritive resource for insects emerging from hibernation. However, since <i>S. nigra</i> is dioecious, not all insect visits will lead to successful pollination. Using both visual observation and pan-trapping we characterized the community of insects that visited <i>S. nigra</i> flowers and assessed differences among male and female trees as well as the chemical and visual drivers that influenced community composition across three years. We found that male trees consistently supported higher diversity of insects than female trees and only three insect species, all <i>Andrena spp.</i>, consistently visited both sexes. Additionally, <i>A. nigrae</i>, which was the only insect that occurred more on female than male flowers, correlated strongly to volatile cues. This suggests that cross-pollinators cue into specific aspects of floral scent, but diversity of floral visitors is driven strongly by visual cues of yellow male pollen. Through time the floral activity of two <i>Andrena</i> species remained stable, but <i>A. nigrae</i> visited less in 2017 when flowers bloomed earlier than other years. When native bee emergence does not synchronize with bloom, activity appears to be diminished which could threaten species that subsist on a single host. Despite the community diversity of <i>S. nigra</i> flowers, its productivity depends on a small fraction of species that are not threatened by competition, but rather by rapidly changing conditions that lead to host-insect asynchrony.
Compound activity data sets for 15 biological targets compiled from the ChEMBL and PubChem databases.
<p>Compound activity data sets for the 15 biological targets are deposited, along with structure-activity relationship matrices IDs. Active compounds were extracted from the ChEMBL database and inactive were from the PubChem database. Details of the data sets are described in the original publication. and the summary of the data sets is given in the readme.txt file. </p>
Experimental data from Dietler et al. (2022) "Signal Transduction in Light-Oxygen-Voltage Receptors Lacking the Active-Site Glutamine"
<p>This .xlsx file contains the experimental data underpinning the research reported in Dietler et al. (2022) "Signal Transduction in Light-Oxygen-Voltage Receptors Lacking the Active-Site Glutamine"</p>
Breaking photoswitch activation depth limit using ionising radiation stimuli adapted to clinical application
<p>This deposit gathers the main raw data and custom codes related to the manuscript "Breaking photoswitch activation depth limit using ionising radiation stimuli adapted to clinical application".</p>
Processed and additional data for our publication titled "Endoplasmic reticulum stress activates human IRE1α through reversible assembly of inactive dimers into small oligomers"
<p>This is an updated version of our original data archive (which can be found under the doi 10.5281/zenodo.5513025) that reflects changes we've made to the manuscript over the course of the review process and incorporates the new data we've collected since the time of the initial bioRxiv submission.</p> <p>This data archive contains all raw data EXCEPT for single-particle microscopy movies (which are deposited separately due to their size) for our paper titled "Endoplasmic reticulum stress activates human IRE1a through reversible assembly of inactive dimers into small oligomers". These raw data are stored in "non_SPT_data_final_v2.zip". Additionally, full plasmid sequences for all plasmids used in this paper are stored in GenBank format in the file "plasmid_sequences_v2.zip". Finally, this repository contains processed single-particle movies in the form of dual-color tracks from the TrackMate ImageJ plugin in XML format (file: "SPT_processed_data_and_settings_final_v2.zip").</p> <p>The processed XML tracks are organized in the same way as the raw data files in the separate repository. They are sorted into subfolders by date of acquisition first, followed by experimental conditions. To recreate the figures from the paper, follow instructions in the README.md file included with the source code repository and use the JSON settings files saved here under "analysis_settings".</p>
Peroxy intermediate drives carbon bond activation in the dioxygenase AsqJ
<p>QM/MM structures and trajectories for <br> Dirk Auman, Felix Ecker, Sophie L. Mader, Kevin M. Dorst, Alois Bräuer, Göran Widmalm, Michael Groll, & Ville R. I. Kaila<br> Peroxy intermediate drives carbon bond activation in the dioxygenase AsqJ (2022)</p>
Datasets for: The HIV-1 viral protease is activated during assembly and budding prior to particle release
<p>HIV-1 encodes a viral protease that is essential for the maturation of infectious viral particles. While protease inhibitors are effective antiretroviral agents, recent studies have shown that prematurely activating – rather than inhibiting – protease function leads to the pyroptotic death of infected cells, with exciting implications for efforts to eradicate viral reservoirs. Despite 40 years of research into the kinetics of protease activation, it remains unclear exactly when protease becomes activated. Recent reports have estimated that protease activation occurs minutes to hours after viral release, suggesting that premature protease activation may be challenging to induce efficiently. Here, combining a powerful FRET-based assay to monitor viral protease activity with sensitive techniques including nanoscale flow cytometry and instant structured illumination microscopy, we demonstrate that the viral protease is activated within cells prior to the release of free virions. Using genetic mutants that lock protease into a 'precursor' conformation, we further show that both the precursor and mature protease have rapid activation kinetics and that the activity of the precursor protease is sufficient for viral fusion with target cells. Our finding that HIV-1 protease is activated within producer cells prior to release of free virions helps resolve a long-standing question of when protease is activated and suggests that only a modest acceleration of protease activation kinetics may be required to induce potent and specific elimination of HIV-infected cells.</p>
Potent activity of high concentration ozone therapy against an-tibiotic-resistant bacteria
<p><strong>Figure S1. </strong>SANITECH O3-80-Sanitization equipment ozone generator coupled to two containers of approximately 1m<sup>3</sup> each, used for exposing samples to ozone.</p>
Data from: Even low light pollution levels affect the spatial distribution and timing of activity of a "light tolerant" bat species
<p>Abstract of the related publication :</p> <p>By disrupting nocturnal landscapes worldwide, light pollution caused by Artificial Light At Night (ALAN) is recognised as a major threat to biodiversity. As even low light intensities might affect some taxa, concerns are arising about biological responses to widespread low light levels. We used data from a French citizen science bat monitoring program (1,894 full-nights monitored on 1,055 sites) to explore the landscape-scale effects of light on an open-space-foraging bat species, the Serotine bat (<em>Eptesicus serotinus</em>). We assessed this species' abundance and timing of night-time activity (median time of activity) at foraging sites. ALAN, and to a lesser extent moonlight, reduced <em>E. serotinus</em> abundance. ALAN delayed activity, and this delay was amplified during overcast nights. On the contrary, where there was no ALAN, the higher the cloud cover, the earlier the activity occurred. Cloud cover likely darkened the night sky in rural locations, whereas it amplified skyglow in light-polluted places, increasing ALAN effects on bats. Interestingly, moonlight also delayed activity but this effect was weakened where there was ALAN. Our study shows that even fine variations of light levels could affect the spatiotemporal distribution of a common species usually considered to be “light tolerant”, with potential cascading effects on individual fitness and population dynamics. It stresses how urgent it is to preserve and restore dark areas to protect biodiversity from light pollution while working on light intensity and directivity where ALAN is needed.</p>
Towards bio-inspired polymer adhesives: Activation assisted via HOBt for grafting of dopamine onto poly(acrylic acid)
<p>The design of bio-inspired polymers has long been an area of intense study, however applications to the design of concrete admixtures for improved materials performance have been relatively unexplored. In this work we functionalized poly(acrylic acid) (PAA), a simple analogue to polycarboxylate ether admixtures in concrete, with dopamine to form a catechol-bearing polymer (PAA-g-DA). Synthetic routes utilizing hydroxybenzotriazole (HOBt) as an activating agent were examined for their ability in grafting dopamine to the PAA backbone. Previous literature using the traditional coupling reagent 1-Ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC) to graft dopamine to PAA were found to be inconsistent and the sensitivity of EDC coupling reactions necessitated a search for an alternative. Additionally, HOBt allowed for greater control over percent functionalization of the backbone, is a simple, robust reaction, and showed potential for scalability. This finding also represents a novel synthetic pathway for amide bond formation between dopamine and PAA. Finally, we performed preliminary adhesion studies of our polymer on rose granite specimens and demonstrated a 56% improvement in the median adhesion strength over unfunctionalized PAA. These results demonstrate an early study on the potential of PAA-g-DA to be utilized for improving the bonds within concrete.</p>
Investigation the cytotoxicity of newly synthesized quinazo-line–sulfonamide derivatives in human leukemia cell lines and hematopoietic activity in zebrafish embryos.
<p>These videos contain the time lapse imaging of the wild type zebrafish embryos showing the circulation, control (mock 0.5% V/V DMSO) and compound 4a treated embryos at 72 hours post fertilization. The compound 4a specifically blocked the formation of blood and no circulation was seen in these embryos. </p>
Supplementary Material for Mapping Active Site Geometry to Activity in Immobilized Frustrated Lewis Pair Catalysts
<p>Supplementary Material for "Mapping Active Site Geometry to Activity in Immobilized Frustrated Lewis Pair Catalysts".</p>
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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.