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Figure 3 in Amylase in the hepatopancreas of a euryhaline burrowing crab: characteristics and modulation
Figure 3. Effect of temperature, NaCl concentrations, various ions, and Ca2+ on amylolytic activity of partially purified amylase from hepatopancreas of N. granulata. (a) Effect of temperature (4–70 °C). The activity was measured at pH 5.2 in the presence of 15 mg mL–1 of starch. The activity values are expressed in relation to the activity at 30 °C (100% = 4.3 mg maltose mg–1 protein min–1). (b) Effect of NaCl concentrations (0–4 M). The activity was measured at pH 5.2 and 30 °C in the presence of 15 mg mL–1 of starch. The activity values are expressed in relation to the activity in the absence of NaCl (100% = 6.16 mg maltose mg–1 protein min–1). (c) Effect of ions. The activity was measured in the presence of 15 mg mL–1 of starch at pH 5.2, 30 °C, in the absence (control) or the presence of the indicated ions (5 mM) (chloride or sulfate salts). The activity values are expressed in relation to the control (100% = 7.5 mg maltose mg–1 protein min–1). (d) Effect of Ca2+. The activity was determined in the presence of 15 mg mL–1 of starch at pH 5.2, 30 °C, in the absence or presence of 5 mM CaCl2, 5 mM EDTA, or both. The activity values are expressed in relation to the activity in the absence of CaCl2 or EDTA (100% = 3.3 mg maltose mg–1 protein min–1). The values are the average of triplicate assays.
Figure 4 in Amylase in the hepatopancreas of a euryhaline burrowing crab: characteristics and modulation
Figure 4. Lineweaver–Burk plot of activity of partially purified amylase from the hepatopancreas of N. granulata using starch or glycogen as substrates. The corresponding activities were measured at pH 5.2 and 30 °C. The values are the average of triplicate assays.
Figure 1 in Amylase in the hepatopancreas of a euryhaline burrowing crab: characteristics and modulation
Figure 1. (a) Zymogram of amylolytic activity from hepatopancreas extract of N. granulata acclimated to 35 psu. After electrophoresis, the gel was immersed in a starch solution (1%) at pH 6.0 for 90 min and then stained with an iodine/KI solution (10 mM). The gray arrow indicates the major active band (29 kDa). (b) Zymogram of amylolytic activity from the hepatopancreas extract of N. granulata acclimated to low (10 psu) and high (37 psu) salinity. After electrophoresis, the gel was immersed in a starch solution (1%) at pH 6.0 for 90 min and then stained with an iodine/KI solution (10 mM). The gray arrows indicate the bands of 29 and 30 kDa.
Dataset: Stimulus selection drives value-modulated somatosensory processing in superior colliculus
<p>Pluta Lab</p> <p>.mat data files used in the following paper</p> <p>Stimulus selection drives value-modulated somatosensory processing in superior colliculus </p> <p>Details can be found in readme.txt</p>
Dataset for the paper "Yield Performance of Standard Multicrystalline, Monocrystalline, and Cast-Mono Modules in Outdoor Conditions"
<p>Dataset for the paper "Yield Performance of Standard Multicrystalline, Monocrystalline, and Cast-Mono Modules in Outdoor Conditions", published at Energies.</p>
Dataset of "Identifying Active Oxygen and Copper Species in Cu/CeO2 Catalysts using Raman and UV-Vis Modulation Excitation Spectroscopy"
<p>This zip file contains the dataset of the publication "Identifying Active Oxygen and Copper Species in Cu/CeO2 Catalysts using Raman and UV-Vis Modulation Excitation Spectroscopy" (<span><a href="https://doi.org/10.1021/acs.jpcc.4c05826">https://doi.org/10.1021/acs.jpcc.4c05826</a></span>). The authors are Henrik Hoyer and Christan Hess*. The zip file includes the data for figures 2 and 3 in the manuscript and the data for figures S1-S12 in the SI. For more detailed information on the dataset, please refer to the description file. </p> <p>*email: christian.hess@tu-darmstadt.de</p>
Dataset for sea ice modulates air–sea methane flux in the Southern Ocean
<p>Air-sea methane (CH4) flux in marginal ice zone in the East Antarctic seas measurements on the icebreaker R/V Xuelong2 from December 2020 to January 2021</p>
Code and data of "Uncovering disease-related multicellular pathway modules on large-scale single-cell transcriptomes with scPAFA"
<p>Code and data to reproduce the analyses and figures presented in "Uncovering disease-related multicellular pathway modules on large-scale single-cell transcriptomes with scPAFA"</p>
Intra-specific variation in metal tolerance modulate competition between two marine diatoms
<p><span><span><span><span><span><span><span><span><span><span><span>This project contains data for the manuscript<i> </i><em>Intra-specific variation in metal tolerance modulate competition between two marine diatoms</em>. The experiments tests how different toxic concentrations of heavy metals modulates competition between an artificially assembled community of Baltic Sea diatoms (four clonal strains each of the two diatom species <i>Skeletonema marinoi</i> (SM) and <i>Thalassiosira baltica</i> (TB). Briefly we use toxic Dose Response curves (DRC) to model how inter and intra specific selection between strains is expected to be modulated under Cadmium, Copper and Silver stress. The stress level was set at the average 50% inhibition concentration (EC50) between all eight strains. Strains were mixed at even biomass based on Relative Chl a Fluorescence Units (RFU) and cultivated semi-continuously to maintain exponential growth. The growth of individual species was measured through microscopy observations and the photosynthetic capacity was monitored using Pulse Amplitude Modulation (PAM) fluorometry. A experimental design flow figure is included as a supplement.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span>The complete functional set of scripts, statistical analysis, and graphical illustrations in R can be found on github: https://github.com/Bearstar85/Selection_Competition_2021 </span></span></span></span></span></span></span></span></span></span></span></p>
Raw data and figures for "Increasing Sensitivity and Versatility in NMR Supersequences with New HSQC-based Modules"
<p>Datasets, pulse programmes, processing scripts, and figures for the publication "Increasing Sensitivity and Versatility in NMR Supersequences with New HSQC-based Modules" (J. Magn. Reson., accepted, 2021).</p> <p>Please see the README.txt file for more information.</p> <p>If you are only interested in pulse programmes and processing scripts, then this dataset will likely be too big for your liking (it is ca. 9 GB because there is a lot of 2D data). You can download the pulse programmes and processing scripts from the Bruker User Library https://www.bruker.com/en/services/bruker-user-library.html.</p> <p><strong>Changelog</strong></p> <p>v1.0.1: some quality of life improvements to the Python NUS script to stop it from being accidentally used on old pulse programmes.</p> <p>v1.0.2: fixed a bug in the v1.0.1 Python script. It now also resets FnTYPE in case the user has changed it.</p>
Dataset for "Diets supplemented with Saccharina latissima influence the expression of genes related to lipid metabolism and oxidative stress modulating rainbow trout (Oncorhynchus mykiss) fillet composition" (doi.org/10.1016/j.fct.2020.111332)
<p>Dataset corresponding to the following article:</p> <p>Ferreira, M., Larsen, B.K., Granby, K., Cunha, S.C., Monteiro, C., Fernandes, J.O., Nunes, M.L., Marques, A., Dias, J., Cunha, I., Castro, L.F.C., Valente, L.M.P., 2020. Diets supplemented with <em>Saccharina latissima </em>influence the expression of genes related to lipid metabolism and oxidative stress modulating rainbow trout (<em>Oncorhynchus mykiss</em>) fillet composition. Food Chem. Toxicol. 140, 111332. <a href="https://doi.org/10.1016/j.fct.2020.111332">https://doi.org/10.1016/j.fct.2020.111332</a></p>
Forest resilience to global warming is strongly modulated by local-scale topographic, microclimatic and biotic conditions
<p>Resilience of endangered rear edge populations of cold-adapted forests in the Mediterranean basin is increasingly altered by extreme heatwave and drought pressures. It remains unknown, however, whether microclimatic variation in these isolated forests could ultimately result in large intra-population variability in the demographic responses, allowing the coexistence of contrasting declining and resilient trends across small topographic gradients. Multiple key drivers promoting spatial variability in the resilience of rear edge forests remain largely unassessed, including amplified and buffered thermal exposure induced by heat waves along topographic gradients, and increased herbivory pressure on tree saplings in defaunated areas lacking efficient apex predators. Here we analysed whether indicators of forest resilience to global warming are strongly modulated by local-scale topographic, microclimatic and biotic conditions.</p> <p>We studied a protected rear edge forest of sessile oak (<em>Q. petraea</em>), applying a suite of 20 indicators of resilience of tree secondary growth, including multidecadal and short-term indices. We also analysed sapling recruitment success, recruit/adult ratios and sapling thermal exposure across topographic gradients. We found large within population variation in secondary growth resilience, in recruitment success and in thermal exposure of tree saplings to heatwaves, and this variability was spatially structured along small-scale topographical gradients. Multidecadal resilience indices and curves provide useful descriptors of forest vulnerability to climate warming, complementing assessments based in the analysis of short-term resilience indicators. Species-specific associations of trees with microclimatic variability are reported.</p> <p>Biotic factors are key in determining long-term resilience in climatically-stressed rear edge forests, with strong limitation of sapling recruitment by increased roe deer and wild boar herbivory. Our results also support non-stationary effects of climate determining forest growth responses and resilience, showing increased negative effects of warming and drought over the last decades in declining stands.</p> <p>Our findings do not support scenarios predicting spatially homogeneous distributional shifts and limited resilience in rear-edge populations, and are more supportive of scenarios including spatially heterogeneous responses, characterised with contrasting intra-population trends of forest resilience. We conclude that forest resilience responses to climate warming are strongly modulated by local-scale microclimatic, topographic and biotic factors. Accurate predictions of forest responses to changes in climate would therefore largely benefit from the integration of local-scale abiotic and biotic factors.</p>
Discrete regulatory modules instruct hematopoietic lineage commitment and differentiation
<p>bioRxiv preprint: https://www.biorxiv.org/content/10.1101/2020.04.02.022566v4</p> <p><strong>Contact:</strong> Grigorios Georgolopoulos (<a href="mailto:ggeorgol@altius.org">ggeorgol@altius.org</a>); Jeff Vierstra (<a href="mailto:jvierstra@altius.org?subject=Consensus%20DNase%20I%20footprints">jvierstra@altius.org</a>)</p> <p>Lineage commitment and differentiation is driven by the concerted action of master transcriptional regulators at their target chromatin sites. Multiple efforts have characterized the key transcription factors (TFs) that determine the various hematopoietic lineages. However, the temporal interactions between individual TFs and their chromatin targets during differentiation and how these interactions dictate lineage commitment remains poorly understood. Here we delineate the temporal interplay between the <em>cis</em>- and the <em>trans</em>-regulatory landscape in establishing lineage commitment and differentiation in human hematopoiesis by performing a dense timecourse of chromatin accessibility (DNase I-seq), and gene expression (total and single cell RNA-seq).</p> <p>All data uploaded correspond to human genome build version GRCh38.</p> <p><strong>Contents</strong></p> <ol> <li><strong>DNase I Hotspot (DHS) metadata: </strong>Supplementary_Data_1.txt</li> <li><strong>DNase I Hotspot quantile-normalized counts:</strong> A tab-separated matrix with quantile-normalized DNase I density counts from 79,085 FDR 5% hotspots, across 12 erythroid differentiation timepoints from 3 donors, present in at least n=2 samples. Rows correspond to DHS information in Supplementary_Data_1.txt (hotspots.fdr.0.05.qnorm.counts.tsv.gz)</li> <li><strong>Column information for DNase I Hotspot quantile-normalized counts: </strong>hotspots.fdr.0.05.qnorm.counts.info.tsv</li> <li><strong>Developmentally regulated gene metadata (erythroid): </strong>Supplementary_Data_2.csv</li> <li><strong>Gene matrix of quantile-normalized FPKM values (erythroid): </strong>A tab-separated matrix with the quantile-normalized FPKM values of all detected genes, across 13 erythroid differentiation timepoints from 3 donors. (fpkm_erythroid_qnorm.tsv.gz)</li> <li><strong>Column information for the quantile-normalized FPKM gene matrix (erythroid): </strong>A tab-separated table (fpkm_erythroid_qnorm.info.tsv)</li> <li><strong>CD34+ HSPC TADs at 10kb resolution: </strong>Supplementary_Data_3.bed</li> <li><strong>Day 11 <em>ex vivo</em> erythroid progenitor TADs at 10kb resolution: </strong>Supplementary_Data_4.bed</li> <li><strong>Transcription factor motif enrichment per DHS cluster: </strong>Supplementary_Data_5.csv</li> <li><strong>Correlation information (links) between developmentally regulated DHS and target genes: </strong>Supplementary_Data_6.csv</li> <li><strong>Chromatin anchor loops called from 10kb resolution Hi-C data: </strong>Supplementary_Data_7.bedgraph</li> <li><strong>Developmentally regulated gene metadata (megakaryocytic): </strong>Supplementary_Data_8.csv</li> <li><strong>Gene matrix of quantile-normalized FPKM values (megakaryocytic): </strong>A tab-separated matrix with the quantile-normalized FPKM values of all detected genes, across 13 megakaryocytic differentiation timepoints from 3 donors. (fpkm_megakaryocyte_qnorm.tsv.gz)</li> <li><strong>Column information for the quantile-normalized FPKM gene matrix (megakaryocytic): </strong>A tab-separated table (fpkm_megakaryocyte_qnorm.info.tsv)</li> <li><strong>Marker (differentially expressed) genes per single cell population: </strong>Supplementary_Data_9.csv</li> <li><strong>A SCANPY h5ad Annotated DataFrame object: </strong>Annotated Data frame `anndata` in h5ad format including the gene-by-cell count matrix, Velocyto splicing kinetics (RNA velocity) information layer, along with obs, obsm, var, varm, and uns layers. (SCANPY_anndata_object.h5ad)</li> </ol>
Modulation of the tumour promoting functions of cancer associated fibroblasts by phosphodiesterase type 5 inhibition increases the efficacy of chemotherapy in human preclinical models of esophageal adenocarcinoma
<p>These are whole-slide digital pathology images of esophageal adenocarcinoma (EAC) patient-derived xenograft models. EAC biopsy specimens were cultured <em>in vitro</em> before implanting into immuno-deficient mice. Mice were then divided into the following treatment groups and treated with combinations of chemotherapy and PDE5 inhibitors as follows:</p> <ol> <li>Untreated</li> <li>Epirubicin + Cisplatin + Capecitabine (ECX)</li> <li>ECX + Vardenafil</li> <li>ECX + Tadalafil</li> </ol> <p>All whole slide images are in Olympus .vsi format and can be opened using the BioFormats library in QuPath. We have also included classifiers and scripts for performing the digital pathology analysis in QuPath, and information to link each mouse with treatment groups and corresponding whole slide images.</p> <p>File metadata:</p> <p>classifiers.zip - Folder containing pixel classifiers used for segmentation of IHC stains. These classifiers are to be important into QuPath for the respective analysis of Periostin (POSTN) and alpha Smooth Muscle Actin (SMA) staining using the included Groovy scripts in the scripts folder.</p> <p>SMA.zip - Folder containing whole slide images of mouse patient-derived xenograft tumours in .vsi format (Olympus VS110). Immunohistochemistry with anti-alpha Smooth Muscle Actin antibody.<br> POSTN.zip - Folder containing whole slide images of mouse patient-derived xenograft tumours in .vsi format (Olympus VS110). Immunohistochemistry with anti-Periostin antibody.</p> <p>scripts.zip - Folder containing all groovy scripts used in QuPath for tissue detection (Whole Section Tissue Detection.groovy), and segmentation of POSTN (POSTN Quantification Mice.groovy) and SMA staining tissue areas (SMA Quantification Mice.groovy).</p> <p>POSTN.xlsx - Data on the mice for which anti-POSTN IHC is available. Column names as follows:<br> Image: file name (corresponding to .vsi file).<br> Mouse_ID: Mouse identifier.<br> Treatment: Treatment administered. ECX - Epirubicin, Cisplatin and Capecitabine.<br> POSTN_Area: Total measured area of POSTN+ tissue in the tissue section (in um^2).<br> Total_Area: Total area of the tissue section (in um^2).<br> percentage_POSTN: Percentage of total tissue area that is stained with POSTN (%).</p> <p>SMA.xlsx - Data on the mice for which anti-SMA IHC is available. Column names as follows:<br> Image: file name (corresponding to .vsi file).<br> Mouse_ID: Mouse identifier.<br> Treatment: Treatment administered. ECX - Epirubicin, Cisplatin and Capecitabine.<br> SMA_Area: Total measured area of SMA+ tissue in the tissue section (in um^2).<br> Total_Area: Total area of the tissue section (in um^2).<br> percentage_SMA: Percentage of total tissue area that is stained with SMA (%).</p>
MOBSTER: Identifying Candidate Magnetic O Stars through Rotational Modulation of TESS Photometry
<p>O-type stars display rotational modulation of their photometric brightness due to surface features induced by fossil magnetic fields, and possibly through dynamos driven by subsurface convection. These features introduce wind perturbations that may drive large-scale structures and flows, including magnetospheres and corotating interaction regions. Until recently there has been a lack of high-precision, high-cadence photometry of O stars capable of detecting this variability. The wealth of new observations provided by the Transiting Exoplanet Survey Satellite (TESS) offers an unparalleled opportunity to conduct comprehensive studies of O-star variability at the sub-mmag level. Using the Galactic O-Stars Catalogue (GOSC) we have identified a sample of confirmed Galactic O stars observed by TESS with existing high-resolution spectroscopy from the IACOB and OWN surveys. Frequency analysis of the photometry is preceded by a careful examination of potential blending sources. Existing spectroscopy of each candidate is employed to test the rotational modulation hypothesis. In this presentation we describe the preliminary results of our study and outline plans for future analysis.</p>
Data supporting "Changes in human dorsal root ganglion neuron excitability from modulating Nav 1.8 conductance are non-linear and depend on the conductances of the delayed rectifier and M-type potassium currents: a simulation study"
<p>Data and code supporting the article "Changes in human dorsal root ganglion neuron excitability from modulating Nav 1.8 conductance are non-linear and depend on the conductances of the delayed rectifier and M-type potassium currents: a simulation study".</p> <p> </p>
Experimental data of "Novel flow modulation method for R744 two-phase ejectors – Proof of concept, optimization and first experimental results"
<p>Experimental data of "Novel flow modulation method for R744 two-phase ejectors – Proof of concept, optimization and first experimental results"</p>
Top-down modulation of shape and roughness discrimination in active touch by covert attention
<p>Due to limitations in perceptual processing, information relevant to momentary task goals is selected from the vast amount of available sensory information by top-down mechanisms (e.g. attention) that can increase perceptual performance. We investigated how covert attention affects perception of 3D objects in active touch. In our experiment, participants simultaneously explored the shape and roughness of two objects in sequence, and were told afterwards to compare the two objects with regard to one of the two features. To direct the focus of covert attention to the different features we manipulated the expectation of a shape or roughness judgment by varying the frequency of trials for each task (20%, 50%, 80%), then we measured discrimination thresholds. We found higher discrimination thresholds for both shape and roughness perception when the task was unexpected, compared to the conditions in which the task was expected (or both tasks were expected equally). Our results suggest that active touch perception is modulated by expectations about the task. This implies that despite fundamental differences, active and passive touch are affected by feature selective covert attention in a similar way.</p> <p> </p> <p>There are zip files for the main experiment and the two pilot experiments, which contain all data relative to the publication. The data of each participant is contained in a separate folder. This folder contains a *.raw file with the participant's answers for each session of the experiment and a "data" folder, which contains movement trajectories (*.trj files) for each session in separate folders.</p> <p>Variables of the main experiment are described in the file VARIABLE_CODES_MainExp.txt and the variables of the pilot experiments are described in the files VARIABLE_CODES_PilotRoughness.txt and VARIABLE_CODES_PilotShape.txt.</p>
Input data for performing a model evaluation of the sectional aerosol module SALSA embedded to PALM model system 6.0
<p>This dataset includes the input information applied to perform a model evaluation study of the PALM model system together with the sectional aerosol module SALSA. </p> <p>The content:</p> <ul> <li>PIDS_STATIC: building height and leaf area density data</li> <li>PIDS_AERO_<simulation time>_<number of aerosol size bins>: aerosol emission data as size bin specific surface emissions (level of detail 2) and aerosol background concentrations</li> <li>PIDS_CHEM_<simulation time>: emission data and background concentrations of gaseous compounds</li> </ul> <p>PIDS_STATIC contains static data and is therefore the same for all simulations.</p> <p>See the model documentation https://palm.muk.uni-hannover.de/trac/wiki/doc for further details.</p>
Data from: Fertiliser application modulates the impact of interannual climate fluctuations and plant-to-plant interactions on the dynamics of annual species in a Mediterranean grassland
<p><span><strong><span>Background:</span></strong><span> Climate and land-use changes, which include the application of various types of organic and inorganic fertilisers, have been reducing the species diversity of Mediterranean grasslands and threatening their conservation. Annual plants are one of the most diverse functional groups of species in these grasslands, despite suffering competitive pressure from perennial herbaceous and woody species, and they are essential for ecosystem functioning and stability. </span></span></p> <p><span><strong><span>Aims:</span></strong><span> To quantify how fertilisation modulates the impact of plant-to-plant interactions and climate fluctuations on the dynamics of annuals in Mediterranean grasslands. We hypothesised that the application of sewage sludge would increase competition between functional groups, reducing the abundance of annuals in the long-term, but would buffer the negative impacts of drought on the year-to-year fluctuation of the diversity of annuals.</span></span></p> <p><span><strong><span>Methods:</span></strong><span> In a semi-natural species-rich Mediterranean grassland in northern Spain, we analysed the changes in the taxonomical and functional composition and diversity of annuals over 14 years in response to variations in the abundance of perennial herbaceous and woody species, climate fluctuations, and fertilisation with sewage sludge. We quantified separately the patterns of year-to-year fluctuations and long-term trends. </span></span></p> <p><span><strong><span>Results:</span></strong><span> The frequency and diversity of annuals decreased with a higher abundance of perennial herbaceous species, drought in June, and cold winters. The addition of sewage sludge decreased the abundance of annuals in the long-term, seemed to promote competition between annuals and other functional groups at an interannual scale, and mitigated the negative effects of drought and cold.</span></span></p> <p><span><span><strong>Conclusions:</strong> Fertilisation influences differently the temporal response of annuals to climate fluctuations and plant-to-plant interactions.</span></span></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.