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22,597 results for “Regulation”
The price of safety: Order picking in warehouses with in-house traffic regulations (Supplementary material)
<p>In what follows, you will find the code and results of the paper:</p> <p>"The price of safety: Order picking in warehouses with in-house traffic regulations" published in IISE Transactions.</p> <p> </p> <p>List of files:</p> <p>- Zip file: "Order Picking Problem with in-house traffic regulations" containing C# Code used to generate solutions for all safety policies</p> <p>- Result.csv containing all generated results</p> <p>- createPlots.py containing code to generate figures and tables from the paper</p> <p> </p> <p>The C# code is object-oriented and contains a Main function in the Program.cs file that converts the Example.OPP file with the InstanceReaders to an OPPInstance and uses the Solve function from either the DynamicProgrammic.cs or RuralPostman.cs file to solve the OPPInstance with all the TrafficRegulations as described in the paper.</p> <p> </p> <p>The Example.OPP defines the Depot location (0: decentral, 1: central), AisleLength, i.e. the number of pick positions within each aisle, and other dimensions of the warehouse. Finally, the items are defined by their picking aisle, shelf, position in the shelf, and region.</p> <p> </p> <p>The dynamic program (DP) described in the paper is implemented in DynamicProgrammic.cs. A HashSet of DPNode represents each layer of the DP. A DPNode basically consists of components, nodeDegrees, and a value. Depending on the TrafficRegulation the nodeDegrees are either NodeDegreeClassic, i.e. Null, Uneven, or Even, or NodeDegreeInAndOutDifference, i.e. the difference of the in- and out-degree. To construct the solution at the end, the inEdge is also saved for each DPNode and the additional member depotIsConnected ensures that the depot is visited. The DPNodes in the next layer of the DP are created by the functions MakeNextLayerVertical and MakeNextLayerHorizontal by determining all possibleTransitions per node in the current layer and combining them into a newNode. Products are stored with their position on the shelves in the item list within a PickingAisle. All vertical possibleTransitions are determined in a preprocessing step depending on the TrafficRegulations and are saved within the respective PickingAisle. All horizontal possibleTransitions are determined during the DP with specific functions depending on the TrafficRegulation in HorizontalTransition.cs. When the layers are created, the best feasible DPNode per layer is saved and the best one, i.e. the one with the lowest value, is returned at the end.</p> <p> </p> <p>The paper describes that certain safety policies cannot be solved with the DP. These OPPInstances are solved as a RuralPostman problem (RPP) by generating a Graph that adopts the rectangular structure of the warehouse. Within the Graph, requiredEdges are determined that correspond to PickingAisles containing items. The resulting RPP can be transformed into a traveling salesman problem (TSP) as described by applying an arc-oriented Dijkstra or, in certain cases, to a generalized TSP (GTSP) where one of the two directed edges must be visited. If necessary, the GTSP is transformed to an asymmetric TSP in GTSPInstance and then solved with TSPSolver using LKH-3.exe (Helsgaun 2017, http://webhotel4.ruc.dk/~keld/research/LKH-3/). To use LKH-3.exe, the TSP instance is saved in a TSPLIB format and a parameter file (.par) for LKH and a solution file (.sol) are created in the bin folder. These files are named according to the name specified in the instance.Solve function, where one can also choose to save or delete these files afterward.</p> <p> </p> <p>For more information on LKH-3 see: Keld Helsgaun: An Extension of the Lin-Kernighan-Helsgaun TSP Solver for Constrained Traveling Salesman and Vehicle Routing Problems (Technical Report, Roskilde University, 2017)</p> <p> </p> <p>Evaluation.py</p> <p>A Python script that generates figures 8, 9, and 10 and tables 6, 7 and 8 (in csv-format) of the paper by processing data from Results.csv.</p> <p>It requires Results.csv to be in the same directory as the code.</p> <p>It also requires the following Python packages:</p> <p>- matplotlib</p> <p>- pandas</p> <p>- seaborn</p>
Supplemental data for "Intramolecular feedback regulation of the LRRK2 Roc G domain by a LRRK2 kinase dependent mechanism" (Gilsbach et al., eLife 2024, doi:10.7554/eLife.91083)
<p><strong>Supportive data for the eLife version of record.</strong></p> <p><strong>(1) Data used for the Michaelis Menten Kinetics.</strong></p> <p><strong>HPLC-based assay.</strong> Steady-state kinetic measurements of LRRK2-mediated GTP hydrolysis were performed as previously described (Ahmadian et al., 1997). Briefly, 0.1 µM of full-length LRRK2 was incubated with different amounts of GTP (0, 25, 75, 150, 250, 500, 1000, 2000, 3000 and 5000 µM) and production of GDP was monitored by reversed phase C18 HPLC. To this end, the samples (10 µl) were directly injected on a reversed-phase C18 column (pre-column: Hypersil Gold, 3µm particle size, 4.6x10mm; main column: Hypersil Gold, 5µm particle size, 4.6x250mm, Thermo Scientific) using an Ultimate 3000 HPLC system (Thermo Scientific, Waltham, MA, USA) in HPLC-buffer containing 50 mM KH<sub>2</sub>PO<sub>4</sub>/K<sub>2</sub>HPO<sub>4</sub> pH 6.0, 10 mM tetrabutylammonium bromide and 10-15% acetonitrile. Subsequently, samples were analyzed using the HPLC integrator (Chromeleon 7.2, Thermo Scientific, Waltham, MA, USA). Initial rates of GDP production were plotted against the GTP concentration using GraFit5 (v.5.0.13, Erithacus Software). The number of experiments is indicated in the graph and data point is the average (±s.e.m.) of indicated repetitions. The Michaelis-Menten equation was fitted to determine K<sub>M</sub> (±s.e.) and k<sub>cat</sub> (±s.e.). Excel sheets used for the calculation of means are provided. No values are reported if the HPLC separation failed (e.g. unstable baseline).</p> <p><strong>Charcoal GTP hydrolysis assay. </strong>The [γ-32P]GTP charcoal assay was performed as previously described (Bollag and McCormick, 1995). Briefly, 0.1 µM full-length LRRK2 or 0.5 µM 6xHIS-MBP-RocCOR was incubated with different GTP concentrations, ranging from 75 µM to 8 mM, in the presence of [γ-<sup>32</sup>P] GTP in GTPase assay buffer (30 mM Tris pH 8, 150 mM NaCl, 10 mM MgCl<sub>2</sub>, 5% (v/v) Glycerol and 3 mM DTT). Samples were taken at different time-points and immediately quenched with 5% activated charcoal in 20 mM phosphoric acid. All non-hydrolyzed GTP and proteins were stripped by the activated charcoal and sedimented by centrifugation. The radioactivity of the isolated inorganic phosphates was then measured by scintillation counting. The initial rates of γ-phosphate release and the Michaelis-Menten kinetics were calculated as described above.</p> <p><strong>(2) Profile plots (Raw data) obtained for the Mass photometry analysis for T1343A vs WT LRRK2.</strong></p> <p>MP was performed as described in (Guaitoli et al., 2023).<strong> </strong>Briefly, the dimer ratio of LRRK2 was determined on a Refeyn Two MP instrument (Refeyn). Prior to the experiment, a standard curve relating particle contrasts to molecular weight was established using a Native molecular weight standard (Invitrogen, 1:200 dilution in HEPES-based elution buffer: 50 mM HEPES [pH 8.0], 150 mM NaCl supplemented with 200 µM desthiobiotin). Prior to mass photometry, the proteins, either WT or T1343A LRRK2, were incubated with 0.5 mM ATP or buffer (control) for 30 min at 30 ℃. The LRRK2 protein was diluted to 2x of the final concentration (end concentrations: 75 nM and 100 nM) in elution buffer. The optical setup was focused in 10 μl elution buffer before adding 10 µl of the adjusted protein sample. Depending on the obtained count numbers, acquisition times were chosen between 20 s to 1 min. The dimer ratio in each measurement was normalize according to the equation. The measurement was perfomed in triplicates.</p> <p><strong>(3) AlphaFold3 model of LRRK2-pT1343 either bound to GDP/Mg or GTP/Mg.</strong></p> <p>Using AlphaFold3 (Abramson et al., 2024), we modeled and compared the GDP vs the GTP-state of phospho-T1343 LRRK2. Interestingly, the AlphaFold3 model suggests, that the phosphate group of the pT1343 residue is orientated inwards thereby substituting the gamma phosphate of the GTP in the GDP-bound state of LRRK2. This finding is in well agreement with MD simulations published recently (Stormer et al., 2023).</p> <p><strong>(4) Western blot RAW files for the cell-based phospho Rab asssay (RAW data for Figure 6 supplement 2/ Supplemental Figure 4 in the preprint version, Gilsbach et al, 2024)</strong></p> <p>Cell-based LRRK2 activity assays were performed as previously described (Singh et al., 2022). Briefly,<strong> </strong>HEK293T cells were cultured in DMEM (supplemented with 10% Fetal Bovine Serum and 0.5% Pen/Strep). For the assay, the cells were seeded onto six-well plates and transfected at a confluency of 50-70% with SF-tagged LRRK2 variants using PEI-based lipofection. After 48 hours cells were lysed in lysis buffer [30 mM Tris-HCl (pH7.4), 150 mM NaCl, 1% NonidentP-40 substitute, complete protease inhibitor cocktail, PhosStop phosphatase inhibitors (Roche)]. Lysates were cleared by centrifugation at 10,000 x g and adjusted to a protein concentration of 1 µg/µl in 1x Laemmli Buffer. Samples were subsequently subjected to SDS PAGE and Western Blot analysis to determine LRRK2 pS935 and Rab10 T73 phosphorylation levels, as described below. Total LRRK2 and Rab10 levels were determined as a reference for normalization. For Western blot analysis, protein samples were separated by SDS–PAGE using NuPAGE 10% Bis-Tris gels (Invitrogen) and transferred onto PVDF membranes (Thermo Fisher). To allow simultaneous probing for LRRK2 on the one hand and Rab10 on the other hand, membranes were cut horizontally at the 140 kDa MW marker band. After blocking non-specific binding sites with 5% non-fat dry milk in TBST (1 h, RT) (25 mM Tris, pH 7.4, 150 mM NaCl, 0.1% Tween-20), membranes were incubated overnight at 4°C with primary antibodies at dilutions specified below. Phospho-specific antibodies were diluted in TBST/ 5% BSA (Roth GmbH). Non-phospho-specific antibodies were diluted in TBST/ 5% non-fat dry milk powder (BioRad). Phospho-Rab10 levels were determined by the site-specific rabbit monoclonal antibody anti-pRAB10(pT73) (Abcam, ab230261) and LRRK2 pS935 was determined by the site-specific rabbit monoclonal antibody UDD2 (Abcam, ab133450), both at a dilution of 1:2,000. Total LRRK2 levels were determined by the in-house rat monoclonal antibody anti-pan-LRRK2 (clone 24D8; 1:10,000) (Carrion et al., 2017). Total Rab10 levels were determined by the rabbit monoclonal antibody anti-RAB10/ERP13424 (Abcam, ab181367) at a dilution of 1:5,000. For detection, goat anti-rat IgG or anti-rabbit IgG HRP-coupled secondary antibodies (Jackson ImmunoResearch) were used at a dilution of 1:15,000 in TBST/ 5% non-fat dry milk powder. Antibody–antigen complexes were visualized using the ECL plus chemiluminescence detection system (GE Healthcare) using the Stella imaging system (Raytest) for detection and quantification.</p> <p><strong>Figure 6 Source Data 1:</strong> <span>Images generated by the Stella system are shown which were used for quantification. The annotation file equals Figure6-figure supplement 2 (Gilsbach et al., eLife 2024, doi:10.7554/eLife.91083). The lines corresponding to </span>LRRK2 pS935, total LRRK2, Rab10 pT73 and total Rab10 were <span>used for the quantification shown in Figure 6.</span></p>
The gut microbiota of environmentally enriched mice regulates visual cortical plasticity
<p>ABSTRACT</p> <p>The complexity of brain circuits is sculpted both by innate genetic programs and environmental stimuli. Since the 1960s scientists have noticed that raising rodents in an enriched environment (EE) is able to improve all aspects of brain plasticity, from learning and memory to visual plasticity in adult and developing animals. Importantly, EE has also been shown to have beneficial effects on a variety of preclinical models of central nervous system diseases: Alzheimer’s and Parkinson’s disease, Rett syndrome, epilepsy etc, prompting intervention protocols in humans. However, the “enrichment derived key signals” through which this special environment performs its broad positive effects on brain health have not been completely elucidated yet. Here, we focused on signals coming from the body periphery and in particular on the gut microbiota. We found that the intestinal microbiota composition of EE mice is significantly different from the one of standard raised (ST) animals. Treatment of EE mice with an antibiotic cocktail completely prevented the EE-driven enhancement of OD plasticity. Strikingly, the fecal microbiota transplant from EE donors to adult ST mice was able to re-activate OD plasticity in the ST recipients. Thus, taken together our data suggest that experience-dependent changes in gut microbiota regulate brain plasticity.</p> <p>METHODS</p> <p>In the first dataset (Dataset1, files called zr2423) we report the raw data (.fastq) obtained from the sequencing of the fecal samples from C57BL/6J mice raised in EE or in ST from birth and collected at different time points during their lives.</p> <p>To analyze the composition of the microbiota of ST and EE mice at different ages, fresh faeces were collected longitudinally in the same subject at postnatal day (P)20 (n=6), P25 (n=6) and P90 (n=6). </p> <p>In the second dataset (Dataset2, files called zr2747) we report the raw data (.fastq) obtained from the sequencing of the fecal samples from C57BL/6J: adult donor mice living in EE (EE, n=8), adult recipient mice living in ST condition before the fecal transplantation (preFT, n=8) and 4 weeks after the fecal transplantation (postFT, n=8).</p> <p>For further details about the sample names see the “Explanation Table”.</p> <p>Bacterial DNA was extracted using a specific kit (QIAamp Powerfecal DNA kit, Qiagen) following the manufacturer's protocol. The 16S rRNA sequencing and analysis was performed by a service offered by Zymo Research (Irvine, CA, USA). </p> <p><em>Targeted Library Preparation</em>: The DNA samples were prepared for targeted sequencing with the Quick-16S™ NGS Library Prep Kit (Zymo Research). The primer sets used were Quick-16S™ Primer Set V3-V4 (Zymo Research). The sequencing library was prepared using an innovative library preparation process in which PCR reactions were performed in real-time PCR machines to control cycles and therefore limit PCR chimera formation. The final PCR products were quantified with qPCR fluorescence readings and pooled together based on equal molarity. The final pooled library was cleaned up with the Select-a-Size DNA Clean & Concentrator™, then quantified with TapeStation® (Agilent Technologies, Santa Clara, CA) and Qubit® (Thermo Fisher Scientific, Waltham, WA). </p> <p><em>Sequencing:</em> The final library was sequenced on Illumina® MiSeq™ with a v3 reagent kit (600 cycles). The sequencing was performed with >10% PhiX spike-in.</p> <p> </p>
Genome-wide association analyses identify novel Brugada syndrome risk loci and highlight a new mechanism of sodium channel regulation in disease susceptibility
<p>The Brugada syndrome GWAS summary statistics</p> <p>Brugada syndrome is a cardiac arrhythmia disorder associated with sudden death in young adults. With the exception of <em>SCN5A</em>, encoding the cardiac sodium channel Na<sub>V</sub>1.5, susceptibility genes remain largely unknown. We performed a genome-wide association meta-analysis comprising 2,820 unrelated cases with Brugada syndrome and 10,001 controls.</p> <p> </p>
S86 | TATTOOINK | TATTOOINK as per EU regulation 2020/2081
<p>This is the collection associated with list S86 TATTOOINK as per EU regulation 2020/2081 on the NORMAN Suspect List Exchange.</p> <p><a href="https://www.norman-network.com/nds/SLE/">https://www.norman-network.com/nds/SLE/</a></p> <p>A list of regulated ingredients for tattoo ink and permanent make up, <a href="https://eur-lex.europa.eu/legal-content/EN/TXT/HTML/?uri=CELEX:32020R2081">Appendix 13 added to Commission Regulation (EU) 2020/2081</a>, 14 December 2020 amending Annex XVII of REACH.</p> <p>Individual Polycyclic-aromatic Hydrocarbons (PAH) compounds from <a href="https://eur-lex.europa.eu/eli/reg/2008/1272/oj">Regulation (EC) No 1272/2008 of the European Parliament and of the Council of 16 December 2008 </a> manually updated in master list as follows:</p> <ul> <li>PAH list (72 compounds) obtained from <a href="https://comptox.epa.gov/dashboard/chemical_lists">CompTox chemical list </a>search</li> <li> InChIKeys of the compounds in the form of Entrez history from <a href="https://pubchem.ncbi.nlm.nih.gov/idexchange/idexchange.cgi">PubChem Identifier Exchange</a> input into <a href="https://pubchem.ncbi.nlm.nih.gov/classification/#hid=72">PubChem TOC</a></li> <li>resulted in 12 compounds with information source corresponding to EU REGULATION (EC) No 1272/2008 (Data source of the TATTOOINK list) </li> <li>After cross verification, 9/12 compounds which passed the check added to master list.</li> </ul> <p>We gratefully acknowledge the JRC at the European Commission for permission to add this dataset to the NORMAN Suspect List Exchange.</p> <p>Change log: v0.1.1: concentrations adjusted to remove %. v0.1.2 removed duplicate BaP, added missing CIDs.</p>
Xiao et al, Oligodendrocyte Precursor Cells Sculpt the Visual System by Regulating Axonal Remodeling [Dataset]
<p>Raw data from the behavior and imaging experiments of Xiao et al., Nature Neuroscience 2022. For additional details about the acquisition of each part of the dataset, refer to the methods section of the paper. From this dataset, using the published code, all the figures relative to the imaging in the optic tectum can be generated and all the cumulative statistics for the behavioural assays run with Stytra recomputed.</p> <p> </p> <p><strong>Organisation of the dataset</strong></p> <p>This dataset is organised in the following subdirectories:<br> - <em>freely_swimming</em>: contains the data for the freely swimming experiments quantifying motor activity in the various ablated groups. It contains subfolders of groups, each of which contains the Stytra raw data directories for all fish of that group. Refer to `Stytra` and `bouter` documentation for further details about the files.<br> - <em>OMR</em>: contains the data for the quantification of OMR reflex across different spatial frequencies. It contains subfolders for the control and ablated group, each of which contains the Stytra raw data directories for all fish of that group.<br> - <em>receptive_field_imaging</em>: contains the imaging data for the receptive field estimation. Subfolders contains, for each individual fish (both ablated and controls are pooled in the same directory):<br> - stytra raw output from the experiment<br> - data_from_suite2p_unfiltered.h5: `flammkuchen`-loadable `.h5` file that contains the raw fluorescent trace<br> - anatomy.mask: `flammkuchen`-loadable mask file saved by the `pypra` tool that was used for segmenting the tectum, delimiting the region of the tectum<br> The folder contains an additional file, `manual_alignment_offsets.h5`, where the offsets of the manual morphing across fish were saved.</p>
Insider trading regulation and shorting constraints. Evaluating the joint effects of two market interventions.
<p>This dataset contains the raw experimental data and the analysis script for the paper Merl, R., Stöckl, T., Palan, S., 2022. "Insider trading regulation and shorting constraints. Evaluating the joint effects of two market interventions", Journal of Banking and Finance 106490, https://doi.org/10.1016/j.jbankfin.2022.106490.</p> <p>Instructions:</p> <p>1. Unpack all files into one folder.<br> 2. Open R version 4.1.2 and set the working directory to the folder with all the files.<br> 3. Run Script.R.</p> <p>In case the SPTools package is not available from GitHub anymore, you can also find it included in this dataset so you can install it from here.</p>
Multi-omic analysis of the Arabidopsis clock activator mutant rve 4 6 8 reveals connections to carbohydrate metabolism and proteasome regulation
<p>Plants are able to sense changes in their light environments, such as the onset of day and night, as well as anticipate these changes in order to adapt and survive. Central to this ability is the plant circadian clock, a molecular circuit that precisely orchestrates plant cell processes over the course of a day. REVEILLE proteins (RVEs) are recently discovered members of the plant circadian circuitry that activate the evening complex and PRR genes to maintain regular circadian oscillation. The RVE 8 protein and its two homologs, RVE 4 and 6, have been shown to limit the length of the circadian period, with rve 4 6 8 triple-knockout plants possessing an elongated period along with increased leaf surface area, biomass, cell size and delayed flowering relative to wild-type Col-0 plants. Here, using a multi-omics approach consisting of phenomics, transcriptomics, proteomics, and metabolomics we draw novel connections between RVE8-like proteins and a number of core plant cell processes. In particular, we reveal that loss of RVE8-like proteins results in altered carbohydrate, organic acid and lipid metabolism, including a starch excess phenotype at dawn. We further demonstrate that rve 4 6 8 plants have lower levels of 20S proteasome subunits and possess significantly reduced proteasome activity, potentially explaining the increase in cell-size observed in RVE8-like mutants. Overall, this robust, multi-omic dataset, provides substantial new insights into the far reaching impact RVE8-like proteins have on the diel plant cell environment.<br> <br> This dataset has the raw search outputs for the mass-spec analysis for this manuscript. </p>
Data and code for the publication "DNA methylation underpins the epigenomic landscape regulating genome transcription in Arabidopsis"
<p>The zipped file of this repository contains code and data to reproduce the results of the publication:</p> <p>Zhao et al, DNA methylation underpins the epigenomic landscape regulating genome transcription in Arabidopsis. Genome Biology (2022). </p> <p>All sequence data have been deposited in NCBI GEO accession codes GSE183987 and GSE169497.</p> <p> </p> <p>Please see the README document for detailed:</p> <p>- Descriptions of the code and data provided</p> <p>- Lists of the required dependencies</p>
MERRIN: MEtabolic Regulation Rule INference from time series data (Docker image and notebooks)
<p>This record contains notebooks and Docker image for reproducing the results of the paper "MERRIN: MEtabolic Regulation Rule INference from time series data" published as part of the ECCB 2022 conference.</p> <p>Notebooks can be executed interactively within the Docker image <code>bioasp/merrin:v1</code> which extends the <a href="http://colomoto.org/notebook">CoLoMoTo Docker</a> version <code>2021-02-01.</code></p> <p>Also see <a href="https://github.com/bioasp/merrin-covert">https://github.com/bioasp/merrin-covert</a></p> <p>The Docker image can be executed as follows:</p> <pre><code class="language-bash">docker pull bioasp/merrin:v1 docker run -it --rm -p 8888:8888 bioasp/merrin:v1 </code></pre> <p>then point your browser to <a href="http://127.0.0.1:8888">http://127.0.0.1:8888</a>.</p> <p>The image can be imported using the command <code>docker load</code> with the image file provided in this record:</p> <pre><code>docker load -i image.tar.gz</code></pre> <p>or with the <code>donodo</code> command available at <a href="https://github.com/pauleve/donodo">https://github.com/pauleve/donodo</a>:</p> <pre><code>pip install -U donodo donodo pull 10.5281/zenodo.6670165</code></pre>
Data repository for the publication "Economic Interests Cloud Hazard Reductions in the European Regulation of Substances of Very High Concern"
<p>This repository contains the data and scripts associated with the article “Economic Interests Cloud Hazard Reductions in the European Regulation of Substances of Very High Concern“, written by Jessica Coria, Erik Kristiansson and Mikael Gustavsson.</p>
Data from: Cross-scale regulation of seasonal microclimate by vegetation and snow in the Arctic tundra
<p>The zip file contains data and code from the analyses for von Oppen et al. (2022) <em>Global Change Biology</em> (<a href="https://doi.org/10.1111/gcb.16426">https://doi.org/10.1111/gcb.16426</a>). Access through the provided R project file (e.g. with RStudio) is recommended for seamless running of the code. Please see the paper (link below) for methodological details, results and discussion, and the ReadMe included in the archive for further detail and usage policy.</p>
"The pathway of hyaluronic acid (HA) and its receptors (CD44, RHAMM) in the regulation of Rho GTPases and their effectors in an in vitro colorectal cancer model" ("Szlak kwasu hialuronowego (HA) i jego receptorów (CD44, RHAMM) w regulacji GTPaz Rho i ich efektorów w modelu raka jelita grubego in vitro"); NCN Miniatura 2022/06/X/NZ3/00848
<p>Results from Screening for "The pathway of hyaluronic acid (HA) and its receptors (CD44, RHAMM) in the regulation of Rho GTPases and their effectors in an in vitro colorectal cancer model" the project <strong>Miniatura</strong> (<strong>2022/06/X/NZ3/00848</strong>) funded by Polish <strong>National Science Centre (NCN)</strong></p> <p>Wyniki skriningu w projekcie "Szlak kwasu hialuronowego (HA) i jego receptorów (CD44, RHAMM) w regulacji GTPaz Rho i ich efektorów w modelu raka jelita grubego in vitro", <strong>Miniatura</strong> (<strong>2022/06/X/NZ3/00848</strong>) finansowanym przez <strong>Narodowe Centrum Nauki (NCN)</strong></p>
Data from A functional transcriptomics analysis in the relict marsupial Dromiciops gliroides reveals adaptive regulation of protective functions during hibernation
<p>This dataset contains files with the differentially expressed genes, raw counts, DESeq2 analyses and assembled transcriptome of D. gliroides. This information is linked to the manuscript published in Molecular Ecology.</p>
The LAVA mutants defective in auxin-regulated primary or lateral root development.
<p><span>Regulation of PIN activity, polarity as well as auxin gradient generation and its canalisation remain crucial topics in plant developmental biology especially in the context of organogenesis like the formation new lateral roots. Here, we are presenting the LAVA (LR Alterations Visualised after Auxin) collection of 278 mutants, defective in auxin-induced lateral root (LR) morphogenesis. Those mutants were obtained from a forward genetic screen in which synthetic auxin 1-Naphtyl Acetic Acid (1-NAA) was used to induce LR formation in the mutagenized PIN3::PIN3-GFP population. Our database contains mutant root phenotyping and for a subset of the collection, we recorded PIN polarity and subcellular trafficking, cotyledon vasculature development, primary and LR gravitropism as well as aerial phenotypes with some reminiscent to auxin-regulated organogenesis aberrations. We are convinced that our dataset can serve as a unique tool to identify novel components of auxin signalling, transport, and cell polarity but also be of interest to the broader plant research community interested in the roots system architecture that is vital for plant survival, growth and adaptation to environmental conditions.</span></p> <p><span>The phenotype analysis of the mutant collection is summarized and organised in an Excel spreadsheet (2024-08-07_mutant_database_Table S1). The photographic material is organised in folder form (see Supporting Data S1 in this repository), where each folder number corresponds to a particular mutant and entry in the excel table.</span></p> <p><span> Mutant seeds will be available in the European Arabidopsis Stock Centre (NASC). The seed sending to the repository is in progress. </span></p> <p><span>The manuscript describing this work is currently being submitted to the research journal. Its version will be available on the open access Masaryk University repository.</span></p>
Improvement of regulations interpretation and formalisation for information need definition - Municipality of Ascoli Piceno, Italy
<p>CHEK Digital Building Permit Maturity Model (CDBPMM) as developed within the HORIZON EUROPE project 'Change toolkit for Digital Building Permit'.</p> <p>(CHEK) https://chekdbp.eu </p> <p>It is described in the CHEK project deliverable D2.1.</p> <p>This project has received funding from the European Union's Horizon Europe program under Grant Agreement No.101058559.</p> <p>The aim of CHEK is to remove barriers preventing municipalities from adopting digital building permit processes by developing, connecting, and aligning scalable solutions in the regulatory and policy context, in open standards and interoperability (geospatial and BIM), in closing knowledge gaps through education, in renewing municipal processes, and in deploying technology. </p>
Stimulating Wnt signaling reveals context-dependent genetic effects on gene regulation in primary human neural progenitors
<p>Summary statistics for chromatin accessibility and gene expression quantitative trait loci (ca/eQTLs) from Matoba, N., Le, B.D., Valone, J.M. <em>et al.</em> Stimulating Wnt signaling reveals context-dependent genetic effects on gene regulation in primary human neural progenitors. <em>Nat Neurosci</em> (2024). https://doi.org/10.1038/s41593-024-01773-6</p>
Ternary π–π Stacking Complexes by Allosteric Regulation in Multilayer Nanographenes
<p>Additional data to report <a href="https://doi.org/10.1021/jacs.4c11119">https://doi.org/10.1021/jacs.4c11119</a>:</p> <p>Construction of π–π stacking supramolecular complexes with more than two components is challenging due to the weak and directionless nature of dispersion interactions. Here we report ternary complexes of a ditopic nanographene tetraimide (<strong>1</strong>), α-substituted phthalocyanine (<strong>Pc</strong>) and polyaromatic hydrocarbons (PAHs) in solution and crystalline state via allosteric regulation. Binding of one <strong>Pc</strong> give rise to significant distortion and conformational changes in <strong>1</strong> that in turn lead to the inhibition of the second binding of <strong>Pc</strong>. The conformational changes associated with first binding allowed an allosteric binding of a third component (PAHs) to form ternary complexes in solution. <sup>1</sup>H NMR titration revealed a moderately high thermodynamic stability for the ternary complexes in CDCl<sub>3</sub>. Competition between allosterically regulated ternary complexes ([<strong>Pc·1</strong>·PAH]) and 1:2 stoichiometric binary complexes of <strong>1</strong> with PAHs ([PAH·<strong>1</strong>·PAH]) were elucidated. Further, selective formation of ternary complexes in solution led to the generation of ternary cocrystals from a 1:1:1 mixture of three components in solution. Our work shows that large π-conjugated nanographenes designed with allosteric recognition sites allow the construction of multilayer ternary complexes in solution and solid-state even with dispersive π–π interactions.</p>
SERENA EJP Soil: Green House Gas Regulation Application Emilia-Romagna, Italy (Summer)
<p>The internal EJP SOIL project SERENA contributed to the evaluation of soil multifunctionality aiming at providing assessment tools for land planning and soil policies at different scales. By co-working with relevant stakeholders, the project provided co-developed indicators and associated cookbooks to assess and map them, to report both on soil degradation, soil-based ecosystem services and their bundles, under actual conditions and for climate and land-use changes, at the regional, national, and European scales.</p>
Stacks of microCT Scans, Cell size, weight, volume and thallus size data supporting the paper 'Mechanical regulation of tissue flatness in Marchantia'
<div> <div> <div> <p>These data are the supporting elements to the following paper: 'Mechanical regulation of tissue flatness in Marchantia'</p> </div> </div> </div> <p> .tif files contain MicroCT (MCT) scans of 16-day-old <em>Marchantia polymorpha</em> thalli. Three genotypes were analysed here: <strong><em>fer-2</em></strong> mutant (from Mecchia et al., 2022), <strong>FER-OE #9</strong> (proMpEF1::MpFERONIA-mCitrine trangenic line 9)<strong> </strong>from Mecchia et al., 2022), and Tak-1 (WT line). These plants were grown in 3 different media: Gamborgh B5 + vitamins and 0.6, 1.2 and 2.5% agar, and one stress condition consisting of the adjunction of a thin PDMS film at 4, to mimich external mechanical stimulus (only performed on thalli grown on 1.2% agar).</p> <p>MicroCT scans were performed at the faculity of odontology of Université Paris-Cité (Plateform imagerie du vivant) with the technical support of Lotfi Slimani and Baptiste Casel. https://piv.u-paris.fr/micro-ct-haute-resolution/ </p> <p>All files already have embeded scales.</p> <p>Each file name consists of a unique ID number in the following form:</p> <p>P+<LETTER>+<NUMBER>-<CONDITION></p> <p>-LETTER: One letter = one imaging session</p> <p>-NUMBER: Individual and Genotype: 33-40 -> Tak1; 200-207-><em>fer-2</em>; 41-49 -> FER-OE</p> <p>-CONDITION : AGAR0.6/AGAR2.5/PDMS. Absence of condition indicates growth on standard medium (1.2% agar). PDMS indicated growth on standard medium and supplementation of a topping PDMS film at day 4)</p> <p> </p> <p>-Volume data were calculated from MicroCT scans</p> <p>-thallus projected surfaces were calculated from MicroCT scans</p> <p><a href="https://zenodo.org/api/records/13981438/draft/files/Lambda%20curvature%20calculation.ipynb/content" target="_blank" rel="noopener noreferrer">-Lambda curvature calculation.ipynb</a> is suited for MorphographX mesh exported .txt files.</p> <p> </p> <p> </p> <p> </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.