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7,228 results for “Modules”
Transmission of optical analog signals with 16QAM modulation scheme using a 5GHz RF carrier signal
<p>The specific data sets correspond to the transmission experiments carried out in laboratory settings to assess the performance of an analog optical link. The optical link is based on a commercial InP Mach-Zehnder modulator (MZM) with approximately 25GHz 3-dB bandwidth, which modulates the CW signal of a DFB laser diode at 1560 nm. The electrical signals driving the modulator were generated using a arbitrary waveform generator (AWG) with 20GHz analog bandwidth and 65GSa/s sampling rate (Keysight M8195A). Electrical 16QAM signals at 1GBaud having a 5GHz RF carrier and utilizing Raised Cosine pulse shaping filters were used to feed the MZM. The detection of the back-to-back signals was realized by means of a single 40GHz photodiode. The signals were acquired, sampled and stored using Agilent Infinium DSO-X93304Q 33GHz, 80GSa/s real time oscilloscope.</p> <p>The data sets have the name format of "ModulatorType_ModulationFormat_RFcarierFrequency_SignalBandwidth_FIlterType_Roll-offFactor_OpticalReceivedPower_#of run.bin" . As an example "MZM_16QAM_5GHz_1Gbaud_RC_035_-3dbm_run0.bin".</p> <p>For each experimental set two instances were captured "run0, run1" in a slightly different time.</p>
Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α-Fig. 2def
<p>smTIRF-FRET Data for Fig 2, for "Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α"</p>
Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α-Fig. 7cde
<p>smTIRF-FRET Data for Fig 7, for "Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α"</p>
Antibiotic resistant pathogen outbreak investigation: an interdisciplinary module to teach fundamentals of evolutionary biology
<p>The evolution of resistance to antibiotics provides a timely and relevant topic for teaching undergraduate students evolutionary biology. Here, we present a module incorporating modified sequencing data from eight antibiotic resistant pathogen outbreaks in hospital settings with bioinformatics and phylogenetic analyses. This module uses whole genome sequencing data from hospital outbreaks investigated by the Centers for Disease Control and Prevention to provide examples of antibiotic resistance spread. Students work in groups to analyze outbreak data to identify the bacterial species and antibiotic resistance genes, to infer a phylogenetic tree examining relatedness among isolates, and to determine a possible source of the outbreak. Students then compile their results in individual reports and provide recommendations for preventing the further spread of antibiotic resistant organisms. In addition to providing genomic outbreak data, we include a teaching concepts guide discussing three integral components of the module: how evolutionary biology concepts of natural selection and competition impact antibiotic resistance; outbreak investigation information to aid in phylogenetic analysis and creation of recommendations; and instructions for the bioinformatics protocol. Completion of this module provides students an opportunity to think critically about the evolution of resistance, practice bioinformatics techniques, and relate evolutionary biology to current events.</p>
Data layers for FORCOAST service module A3 Limfjorden 2009-2017
<p>The environmental bottom data layers behind the FORCOAST service module A3 is generated by the 3D FlexSem model consisting of a hydrodynamic model coupled to the biogeochemical model ERGOM. The original data is on an unstructured grid (varying size of polygons), but for this purpose the data was interpolated to a structured grid and converted to netcdf files. The data layers are:</p> <p>1) bottom temperature</p> <p>2) bottom salinity</p> <p>3) bottom Chl a</p> <p>4) resuspension of detritus</p> <p>5) bottom oxygen</p> <p>6) bottom detritus</p>
Bioinformatics for public health microbiologists: Module 1 dataset (South African Salmonella)
<p>Module 1 (WGS) dataset (paired-end Illumina reads of <em>Salmonella enterica </em>strains isolated from animals and animal products in South Africa)</p> <ul> <li> <p>module1_dataset_ZAsalmonella.tar.gz: raw Illumina paired-end reads</p> </li> <li> <p>trimmed_reads.tar.gz: trimmed Illumina paired-end reads (i.e., trimmed via fastp v0.23.4)</p> </li> <li> <p>contigs.tar.gz: assembled genomes (i.e., trimmed reads assembled into contigs using SKESA v2.5.1)</p> </li> <li> <p>prokka.tar.gz: whole-genome annotation results (i.e., produced via Prokka v1.14.6)</p> </li> <li> <p>enterobase_salmonella.tar.gz: publicly available assembled genomes (downloaded via Enterobase; https://enterobase.warwick.ac.uk/, accessed 1 June 2024)</p> </li> <li> <p>snippy_input.tsv: input file used for Snippy (https://github.com/tseemann/snippy)</p> </li> <li> <p><span>snippy_final.tar.gz: output files produced by Snippy (https://github.com/tseemann/snippy), Gubbins (https://github.com/nickjcroucher/gubbins), and SNP-sites (https://github.com/sanger-pathogens/snp-sites)</span></p> </li> </ul>
Supporting Information for "An empirical modification of the force field approach to describe the modulation of galactic cosmic rays close to Earth in a broad range of rigidities"
<p>This supporting information provides the Data Set S1 used to produce Fig. 6 in <strong>"An empirical modification of the force field approach to describe the modulation of galactic cosmic rays close to Earth in a broad range of rigidities"</strong> (Gieseler et al., 2017). It can be used to calculate the rigidity-dependent solar modulation potential <span class="math-tex">\(\phi(P)\)</span> for monthly intervals from 1973-2017 following Eq. 10 in Gieseler et al. (2017).</p> <p>If you use this data, please refer to and cite <strong>BOTH</strong> following publications:</p> <ul> <li>Gieseler, J., B. Heber, and K. Herbst, <em>An empirical modification of the force field approach to describe the modulation of galactic cosmic rays close to Earth in a broad range of rigidities</em>, J. Geophys. Res., 2017 (doi:10.1002/2017JA024763).</li> <li>Usoskin, I. G., G. A. Bazilevskaya, and G. A. Kovaltsov, <em>Solar modulation parameter for cosmic rays since 1936 reconstructed from ground-based neutron monitors and ionization chambers</em>, J. Geophys. Res., 2011 (doi:10.1029/2010JA016105).</li> </ul> <p>This data set contains the solar modulation potential values in MV for monthly intervals from 1973-2017 derived from the proton proxies IMP-8 He and ACE/CRIS C (Phi_pp), and from Usoskin et al. (2011) as provided by http://cosmicrays.oulu.fi/phi/phi.html (Phi_Uso11). The uncertainties of Phi_pp are given in column 4, those of Phi_Uso11 are 26 MV for the observed period. The LIS used to calculate the modulation potentials is that from Burger et al. (2000) as given by Usoskin et al. (2005).</p> <p>Column 1: Fractional year (start of interval)<br> Column 2: Month<br> Column 3: Phi_pp /MV<br> Column 4: Uncertainty of Phi_pp /MV<br> Column 5: Phi_Uso11 /MV</p> <p>Data also available at http://www.ieap.uni-kiel.de/et/ag-heber/cosmicrays</p>
Elevation modulates the phenotypic responses to light of four co-occurring Pyrenean forest tree species
<p>Data on plant water potential for seedlings of four Pyrenean tree species planted along an elevation gradient. The dataset contains three files:</p> <ol> <li><strong>Biomass.txt: </strong>Data on plant biomass per fraction (leaf, stem and roots) 4 years after plantation. Included variables:<br> - Piso (factor): elevational stage at which the seedling was planted. Two levels: montane (M) or subalpine (S)<br> - Luz (factor): whether the seedling was plantes at a gap or in the understory. Two levels: gap (O) or understroy (T)<br> - N (numeric): number of plant in that plot<br> - Sp (factor): species. Four levels: BEPE (Betula pendula) / PISY (Pinus sylvestris) / PIUN (Pinus uncinata) / ABAL (Abies alba)<br> - Planta (factor): code to identify uniquely each plant<br> - File (factor): code to identify uniquely each plant<br> - GLI (num): Global Light Index, the amount of irradiance that receives each seedling<br> - Code (factor): code to identify uniquely each plant<br> - PLB (numeric): total plant biomass (g)<br> - LFB (numeric): leaf biomass (g)<br> - STB (numeric): stem biomass (g)<br> - RTB (numeric): root biomass (g)<br> - LMF (numeric): leaf mass fraction (LFB/PLB)<br> - SMF (numeric): stem mass fraction (STB/PLB)<br> - RMF (numeric): root mass fraction (RTB/PLB)<br> - SLA (numeric): specific leaf area<br> - H (numeric): plant height (mm)<br> - D (numeric): plant diameter at root collar (mm)<br> - PB2 (numeric): total plant biomass without considering leaves (g)<br> - SF2 (numeric): stem mass fraction without considering leaves (STB/PB2)<br> - RF2 (numeric): root mass fraction without considering leaves (RTB/PB2)</li> <li><strong>init_biomass.txt:</strong> for biomass at the moment of plantation<br> - Piso (factor): elevational stage at which the seedling was planted. Two levels: montane (M) or subalpine (S)<br> - N (numeric): number of plant<br> - Sp (factor): species. Four levels: BEPE (Betula pendula) / PISY (Pinus sylvestris) / PIUN (Pinus uncinata) / ABAL (Abies alba)<br> - Planta (factor): code to identify uniquely each plant<br> - File (numeric): code to identify uniquely each plant<br> - PB (numeric): total plant biomass (g)<br> - LB (numeric): leaf biomass (g)<br> - SB (numeric): stem biomass (g)<br> - RB (numeric): root biomass (g)</li> <li><strong>WaterPot.txt</strong>: data on plant water potential for seedlings of four Pyrenean tree species planted along an elevation gradient during a period of intense drought<br> - Piso (factor): elevational stage at which the seedling was planted. Two levels: montane (M) or subalpine (S)<br> - Luz (factor): whether the seedling was plantes at a gap or in the understory. Two levels: gap (O) or understroy (T)<br> - N (numeric): number of plant <br> - Parcela (factor): identifier ofthe plot<br> - Sp (factor): species. Four levels: BEPE (Betula pendula) / PISY (Pinus sylvestris) / PIUN (Pinus uncinata) / ABAL (Abies alba)<br> - Estacion (factor): the moment for the measurement. One level: September<br> - GLI (numeric): global light index, the ration of total irradiance received by the plant at the moment of plantation<br> - WPt (numeric): water potential (bars)</li> </ol>
Supporting transcriptomic data and code for: "Rapid and dose-dependent Natural Killer (NK) cell modulation and cytokine correlations after human rVSV-ZEBOV Ebolavirus vaccination"
<p>The counts_NK.csv file contains gene expression data (counts) for genes in the Ion Ampliseq human Gene expression kit panel. Data were obtained from whole blood RNA. Subjects were vaccinated with a high dose of the rVSV-ZEBOV vaccine against Ebola virus disease in the Geneva clinical trial.</p> <p>The Descriptive_Table_NK_2.csv contains descriptive data of the subjects for differential expression analysis.</p> <p>The NK_analysis_code.R file contains the code used for analysis.</p>
Three-dimensional subnanoscale imaging of unit cell doubling due to octahedral tilting and cation modulation in strained perovskite thin films
<p>Transmission electron microscopy data used in the journal publication <a href="https://doi.org/10.1103/PhysRevMaterials.3.063605">"Three-dimensional subnanoscale imaging of unit cell doubling due to octahedraltilting and cation modulation in strained perovskite thin films"</a></p> <p><strong>Data files</strong></p> <p>There are two data types:</p> <ul> <li>Scanning TEM (STEM) diffraction patterns acquired with a Medipix3 detector (Merlin): m004_LSMO_LFO_STO_medipix.hdf5 <ul> <li>Acquired on a probe corrected Jeol ARM200CF</li> <li>Acceleration voltage: 200 kV</li> <li>Convergence semi-angle: 20.4 mrad (calibrated using the SrTiO<sub>3</sub> substrate HOLZ ring)</li> <li>Detector calibration: 1.357 mrad per pixel (calibrated using the SrTiO<sub>3</sub> substrate HOLZ ring)</li> </ul> </li> <li>Atomic resolution STEM data, both annular dark field (ADF) and annular bright field (ABF), which were acquired simultaneously: s007_ADF.hdf5, s007_ABF.hdf5</li> </ul> <p>The data can be loaded in python using h5py.</p> <p>For the Medipix3 data:</p> <pre><code class="language-python">import h5py f = h5py.File('m004_LSMO_LFO_STO_medipix.hdf5', mode='r') data = f['fpd_expt/fpd_data/data'] data_subset = data[0:16, 0:16, :, :]</code></pre> <p>For the STEM-ADF or STEM-ABF data:</p> <pre><code class="language-python">import h5py f = h5py.File('s007_ADF.hdf5', mode='r') data = f['Experiments/__unnamed__/data']</code></pre> <p>Exploring the Medipix3 dataset lazily, i.e. without loading the whole dataset into memory at the same time. Using pixStem:</p> <pre><code class="language-python">import pixstem.api as ps s = ps.load_ps_signal("003_stripe1.hdf5", lazy=True) s.plot()</code></pre> <p>Loading the STEM-ADF or STEM-ABF data using HyperSpy, which automatically loads the probe scaling:</p> <pre><code class="language-python">import hyperspy.api as hs s = hs.load("s007_ADF.hdf5") s.plot()</code></pre> <p><br> <strong>Processing files</strong></p> <p>All the TEM data has been processed using python scripts, which is named based on the type of processing:</p> <ul> <li>d00N_...: Medipix3 data processing</li> <li>a00N_...: Atomic resolution STEM-ADF and STEM-ABF processing using Atomap</li> </ul> <p>The scripts generate intermediate files, which are saved in folders with the same prefix as the scripts. So the d001_... script makes a folder named d001_... . These intermediate files are included here as zip-files, since Zenodo doesn't support folder structures.</p> <p>The python libraries required to run the scripts are listed in requirements.txt. Newer versions of the libraries will most likely also work.</p> <p>To setup the python environment with the required libraries, and run all the scripts:</p> <pre><code class="language-bash">pip3 install -r requirements.txt python3 run_all_scripts.py</code></pre> <p> </p>
Roles of irrigation and reservoir operations in modulating terrestrial water and energy budgets in the Indian sub-continental river basins
<p>We have simulated water budget and energy budget over Indian subcontinental basins, using three scenarios from the Variable Infiltration Capacity (VIC) model by including irrigation and reservoir practices in it:</p> <p>1). No irrigation and reservoir (VIC-NATURAL)<br> 2). Free irrigation and no reservoir (VIC-FREE)<br> 3). Reservoir and restricted irrigation (VIC-MANAGED)</p> <p>Here, we have shared results in below folders.</p> <p>Fig1: Annual precipitation (P) and reservoir locations used in study.<br> Fig2: Satellite (MODIS and GLEAM) based annual evapotranspiration (ET) and VIC-MANAGED simulated annual ET.<br> Fig3: Annual land surface temperature (LST) from MODIS, AATSR and VIC-MANAGED.<br> Fig4: Mean monthly observed and simulated reservoir storage.<br> Fig5: P, ET, total runoff (TR) and LST from one grid.<br> Fig6: Annual ET change between VIC-NATURAL and VIC-MANAGED run.<br> Fig7: Same as Fig6 but for TR.<br> Fig8: Same as Fig6 but for LST.<br> Fig9: Annual ET change between VIC-FREE and VIC-MANAGED run.<br> Fig10: Annual latent heat flux and sensible heat flux change between VIC-NATURAL and VIC-MANAGED run.</p> <p>More detail is available in "Roles of irrigation and reservoir operations in modulating terrestrial water and energy budgets in the Indian sub-continental river basins" paper in JGR-Atmosphere. Or contact at harsh.lovekumar.shah@iitgn.ac.in</p> <p>Harsh Shah</p>
Conventional therapy induces tumor immunoediting and modulates the immune contexture in colorectal cancer
<p>Cancer immunotherapies for patients with colorectal cancer (CRC) continue to lag behind other solid cancer types with the exception of 4% of patients with microsatellite-instable tumors. Thus, there is an urgent need to broaden the clinical benefit of checkpoint blockers to CRC by combining conventional therapies to sensitize tumors to immunotherapy. However, the impact of conventional drugs on immunoediting and hence, imposing positive selection towards less immunogenic variants, and on the tumor immune contexture in CRC remains elusive.</p> <p>In this study, we performed comprehensive multimodal profiling using longitudinal samples from metastatic CRC patients undergoing neoadjuvant therapy with mFOLFOX6 and Bevacizumab. Exome-sequencing, RNA-sequencing and multiplexed immunofluorescence imaging was carried out on tumor samples obtained before and after therapy and the data was analyzed using established methods. The results of the analysis were extrapolated to publicly available datasets (TCGA and CPTAC). In order to identify a surrogate marker, an explainable artificial intelligence method was developed using a transformer-based analytical pipeline for the identification of features in H&E images associated with specific biological processes, followed by manual evaluation of highly informative tiles by a pathologist.</p> <p>We expect that the results of this project will provide a deeper understanding of the tumor-immune interactions and will allow the development of more robust combinatorial therapeutic strategies for MSS CRC.</p>
Guest-Mediated Modulation of Photophysical Pathways in a Coronene Bisimide Cyclophane
<p>Additional data to report <a href="https://doi.org/10.1021/jacs.4c08479">https://doi.org/10.1021/jacs.4c08479</a>: </p> <p>The properties and functions of chromophores utilized by nature are strongly affected by the environment formed by the protein structure in the cells surrounding them. This concept is transferred here to host−guest complexes with the encapsulated guests acting as an environmental stimulus. A new cyclophane host based on coronene bisimide is presented that can encapsulate a wide variety of planar guest molecules with binding constants up to (4.29 ± 0.32) × 10<sup>10</sup> M<sup>−1</sup> in chloroform. Depending on the properties of the chosen guest, the excited state deactivation of the coronene bisimide chromophore can be tuned by the formation of host−guest complexes toward fluorescence, exciplex formation, charge separation, room-temperature phosphorescence (RTP), or thermally activated delayed fluorescence (TADF). The photophysical processes were investigated by absorption, emission, and femto- and nanosecond transient absorption spectroscopy. To enhance the TADF, two different strategies were used by employing suitable guests: the reduction of the singlet−triplet gap by exciplex formation and the external heavy atom effect. Altogether, by using supramolecular host−guest complexation, a versatile multimodal chromophore system is achieved with the coronene bisimide cyclophane.</p>
Dataset for "Scaling of ultrashort-pulsed laser structuring processes for electromobility applications using a spatial light modulator"
<p>The dataset represents the experimental data for publication "<span>Scaling of ultrashort-pulsed laser structuring processes for electromobility applications using a spatial light modulator</span>"</p>
Genetic Modulation of Protein Expression in Rat Brain
<p><span>Genetic variations in protein expression are implicated in a broad spectrum of common diseases and complex traits. However, the fundamental genetic architecture and variation of protein expression have received comparatively less attention than either mRNA or classical phenotypes. In this study, we systematically quantified proteins in the brains of a large family of rats using tandem mass tag (TMT)-based quantitative mass-spectrometry (MS) technology. We identified and quantified a comprehensive proteome of 8,119 proteins from Spontaneously Hypertensive (SHR/Olalpcv), Brown Norway with polydactyly-luxate (BN-Lx/Cub), and 29 of their fully inbred HXB/BXH progeny. Differential expression (DE) analysis identified 597 proteins with significant differences in expression between the parental strains (fold change > 2 and FDR < 0.01). We characterized 95 variant peptides by proteogenomics approach and discovered 464 proteins linked to strong <em>cis</em>-acting quantitative trait loci (pQTLs, FDR < 0.05). We also explored the linkage of pQTLs with behavioral phenotypes in rats and examined the sex-specific pQTLs to reveal both distinct and shared <em>cis</em>-pQTLs between sexes. Furthermore, by creating a novel view of the rat pangenome, we improved the ability to pinpoint candidate genes underlying pQTL. Finally, we explored the connection between the pQTLs in rat and human disorders, underscoring the translational potential of our findings. Collectively, this work demonstrates the value of large and systematic proteo-genetic datasets in understanding protein modulation in the brain and its functional linkage to complex central nervous system (CNS) traits.</span><span> </span></p>
Overview: Simulation Module + Optimisation Algorithm + LCA Support Tool
<p>Overview of the Model2Bio elements: Simulation Module + Optimisation Algorithm + LCA Support Tool</p> <p>Platforms showing all the processes of the Model2Bio project. From the beginning of the Simulation Module, the variables for the production line models (agriculture and food production industries) to bio-products created from the residues.</p>
Measurement and prediction of bottom boundary layer hydrodynamics under modulated oscillatory flows
<p>Experimental and numerical model data pertaining to the manuscript "Measurement and prediction of bottom boundary layer<br> hydrodynamics under modulated oscillatory flows" accepted for publication in Coastal Engineering (<a href="https://doi.org/10.1016/j.coastaleng.2021.103954">https://doi.org/10.1016/j.coastaleng.2021.103954</a>)</p> <p>Please read the README.txt file for more information.</p>
Peripheral MC1R activation modulates immune responses and confers neuroprotection in a mouse model of Parkinson's disease
<p>Raw data sets for the manuscripts</p> <p>This work was supported by NIH grants R01NS102735 and R01NS110879, the Farmer Family Foundation Initiative for Parkinson’s Disease Research and the MJFF and ASAP [ASAP-000312].</p>
Framework for Assessing Changes To Sea-level (FACTS) Module Data - Part 2
<p>Additional input module data sets from the Framework for Assessing Changes To Sea-level. These files should be installed in the modules-data/ directory. See https://github.com/radical-collaboration/facts for more information.</p>
Stability of the Modulator in a Plasma-Modulated Plasma Accelerator
<p>Input decks for the particle-in-cell code WarpX used in a new study to simulate the modulator stage of a recently proposed laser-plasma accelerator scheme [Phys. Rev. Lett. <strong>127</strong>, 184801 (2021)], dubbed the Plasma-Modulated Plasma Accelerator (P-MoPA). </p>
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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.