Find research datasets worth reusing

opencc-by-4.0Feb 2017View details →

Figure 6 in Neutron imaging investigation of fossil woods: non-destructive characterization of microstructure and detection of in situ changes as occurring in museum cabinets

Figure 6. Radiographic images of sample upon desorption experiments. The Angeac sample is on the top, while the Rivecourt sample is on the bottom. The scale represents 1 cm. The marked areas correspond to the zones used for measuring average grey levels. (For Rivecourt, it was done on another sample due to implosion of the sample.)

opencc-by-4.0Feb 2017View details →

Figure 4 in Neutron imaging investigation of fossil woods: non-destructive characterization of microstructure and detection of in situ changes as occurring in museum cabinets

Figure 4. Evolution of average grey levels in the wetting experiments plotted as a function of the square root of time. (a) Rivecourt and (b) Angeac.

opencc-by-4.0Dec 2019View details →

Fig. 4 in Molecular and physiological characterization of the chitin synthase B gene isolated from CUlex pipieNS palleNS (Diptera: Culicidae)

Fig. 4 RNA interference (RNAi) of CpCHSB in third-instar larvae (n = 200). a Expression levels of CpCHSB at 72 h after injecting siCHSB assessed by RT-qPCR. b siCHSB injection into third-instar reduces body length in fourth-instar larvae, as well as midgut length (c). d Percentage of pupation (x-axis) after egg-hatching. e Comparison of wing length in wild type (WT), negative control (NC) and siCHSB adults. f Number of follicles per ovary and the number of eggs per female mosquito (g) after injecting (n = 50) siCHSB. All surviving individuals were used for measurements, and results are shown as the mean ± SE (Student's t-tests: **P <0.01, ***P <0.001)

opencc-by-4.0Oct 2020View details →

Fig. 4 in Molecular characterization of the re-emerging West Nile virus in avian species and equids in Israel, 2018, and pathological description of the disease

Fig. 4 Replication of yellow-legged seagull-derived WNV in Vero and C6/36 cells. Cytopathic effect (left) was observed after one passage in both cell lines. The control cells (right) were grown under the same conditions. Scale-bars: 100 µM

opencc-by-4.0Oct 2020View details →

Fig. 5 in Molecular characterization of the re-emerging West Nile virus in avian species and equids in Israel, 2018, and pathological description of the disease

Fig. 5 Phylogenetic analysis of West Nile viruses (WNVs) from avian and equine hosts studied in Israel during 2016 and 2018. The analysis was conducted on a nucleotide sequence of the genes encoding the capsid, pre-membrane protein, and membrane protein, using the neighbor-joining method implemented in MEGA X software. The robustness of branching pattern was tested by 1000 bootstrap replications. The rates among sites algorithm used was gamma distribution with invariant sites (G+I). The bar denotes 0.02 nucleotide substitutions per site. Lineage 1 and 2 reference strains are present with country and year of isolation. The GenBank annotated sequences are underlined and the sequences obtained in this study (during 2016 and 2018) are marked with rectangles

Optical liquid phantom characterization

This dataset contains the results of the characterisation of liquid phantoms compounds and recipes that will be used to test hyperspectral systems. We have characterize 4 compounds: Indian Ink, Protoporphyrin IX (PpIX), Blood (human and horse) and Yeast fluorescence. The files contained here are: <ul> <li>RawSpectraInk.zip: raw absorbance spectra of the Indian ink phantoms (Winsor & Newton, Black Indian 951) measured using a commercial spectrophotometer (PerkinElmer LAMBDA 950), between 400 and 900 nm with 0.5-nm resolution at 5 different concentrations (dilution in water) (0.2, 0.3, 0.4, 0.5 and 0.6 µl/ml).</li> <li>Spectrofluorometer_Yeast.zip. raw data of the fluorescence of baker’s yeast (Saccharomyces cerevisiae) diluted at a concentration of 20 mg/mL at different excitation wavelength measured using a commercial luminescence spectrometer (PerkinElmer LS 55). The illumination was sequential from 300 to 700 nm at 20-nm steps. Also contains the reference fluorescence spectra accounting from water and PS contribution without any yeast, illuminated from 300 to 400 nm at 20-nm steps</li> <li>SpectrophotometerSpectra.mat. Absorbance spectra of human blood, horse blood and PpIX.</li> </ul> The horse blood was defibrinated horse blood that can be easily purchased from a chemical supplier (https://uk.vwr.com/store/product/9131472/animal-blood-serum-products-for-microbiology) and the human blood was expired human red blood cells acquired from a blood bank. The data here are the absorption spectra measured using a commercial spectrophotometer (PerkinElmer Lambda 750 S). For the blood, solution of 5% blood in PBS for both blood type was prepared . Then the blood samples where fully oxygenated by bubbling O2, and by monitoring the level of dissolved oxygen (DO2) in these solutions. Once fully oxygenated, the absorbance of the solution was measured in the spectrophotometer.  A second sample of deoxygenated blood was measured in the same conditions. In order to induce the deoxygenation of the solution, a small quantity of sodium dithionite was added to the oxygenated solution, and the measurement was taken after the DO2 meter reading had fallen to 0%. The PpIX (solution of 1.2mM of PpIX in dimethyl sulfoxide (DMSO)) absorption spectra was measured with the same spectrophotometer. Variables in the file: Wavelength: the wavelength vector Spectra: the absorbance spectra of each compound Name: the name of each compound   The rest of the files report measurements performed in reflectance in a diffuse media. The setup used to test the different components was a metallic container, of dimensions 27 × 15 × 16 cm. The sides and bottom of the container were coated with a matt black absorbing paint to prevent any reflections from the boundaries. To ensure precise measurements of the volume, particularly for the large volumes of basal solution required, a gravimetric approach was used, as weighing liquids is a valid and accurate method for determining volume. DO2 levels within the solutions were monitored using a calibrated oxygen probe. Solution pH was concurrently monitored using a pH probe. The entire setup was placed on a hot stirring plate complete with a temperature probe, set to maintain a constant 37°C. Constant stirring at 700 RPM ensured that the solution remained homogeneous. The optical setup was composed of a broadband light (HL-2000 UV-Vis-NIR Halogen Light Source by Ocean Optics) for the source and of a USB4000 spectrometer (Ocean Optics) for the detection. Light was guided from the light source and to the spectrometer via optical fibres with s source detector distance of 1 cm. The compositions of the baseline solution for the two phantoms is of 1400g of PBS solution (at 50mM) and 75g of Intralipid 20%. The files contained here are: <ul> <li>SpectraPpIXalone.mat. Attenuation spectra of the PpIX (at 15uM concentration) in the baseline solution described above.</li> </ul> Variables in the file: Wavelength: the wavelength vector Spectra: Attenuation spectra of the PpIX in the diffusive media Name: the name of the spectra <ul> <li>DeltaA_Human_Horse_Blood.mat: Change in attenuation between oxygenated and deoxygenated blood for both horse and human blood. 5 mL of blood were added to the baseline solution. The blood was deoxygenated using N2.</li> </ul> Variables in the file: Wavelength: the wavelength vector Spectra: Change in attenuation between deoxygenated and oxygenated blood Name: the name of the spectrum <ul> <li>SpectraBloodPpIX.mat: Attenuation spectra of the blood with and without PpIX (same quantities as above) both for oxygenated and deoxygenated states.</li> </ul> Variables in the file: Wavelength: the wavelength vector Spectra: the attenuation spectra Name: the name of the spectra

Figure 3 in Isolation and characterization of bacteria associated with silkworm gut under antibiotic-treated larval feeding

Figure 3. Phylogenetic relationship of bacterial strains isolated in this study with each other based on 16S rRNA gene sequence through Neighbor-Joining method using 1000 bootstrap replicates.

Figure 1 in Isolation and characterization of bacteria associated with silkworm gut under antibiotic-treated larval feeding

Figure 1. Amplification of 16S rRNA gene (1500 bp) of isolated bacterial strains; lane 1 = HG1, lane 2 = HG2, lane 3 = HG3, lane 4 = DG1, lane 5 = DG2, lane 6 = DG3, -ve = negative control, +ve = positive control, M = 1kb DNA marker.

Characterization Data for the Manuscript: "Unraveling Metal Effects on CO2 Uptake in Pyrene-based Metal-Organic Frameworks through Integrated Lab and Computer Experiments"

This entry contains characterization data for the manuscript "Unraveling Metal Effects on CO2 Uptake in Pyrene-based Metal-Organic Frameworks through Integrated Lab and Computer Experiments".

Data for "Characterizing the chemical potential disorder in the topological insulator (Bi1−xSbx)2Te3 thin films"

Here, the data underlying all figures of the paper "Characterizing the chemical potential disorder in the topological insulator (Bi$_{1−x}$Sb$_x$)$_2$Te$_3$ thin films" is given in .csv or .txt file format. Furthermore, raw data files are provided. The STM/STS data was recorded and stored with the Nanonis SPM Control Software Version Generic 5 in the Nanonis file format (.sxm) for scan images, binary file format (.3ds) for STSgrids and ASCII file format for simple point STS.

Coordinated Reply Attacks in Influence Campaigns: Characterization and Detection

We release the datasets to replicate the results of `Coordinated Reply Attacks in Influence Operations: Characterization and Detection'. See https://github.com/osome-iu/io-coordinated-replies for details.

The official dataset of the paper "Valorisation of Blackcurrant Pomace by Extraction of Pectin-Rich Fractions: Structural Characterization and Evaluation as Multifunctional Cosmetic Ingredient"

This is the official repository of the paper "Valorisation of Blackcurrant Pomace by Extraction of Pectin-Rich Fractions: Structural Characterization and Evaluation as Multifunctional Cosmetic Ingredient" (<a href="https://doi.org/10.3390/polym16192779">https://doi.org/10.3390/polym16192779</a>). DISCLAIMER The repository contains experimental data and is published for the sole purpose of giving additional background details on the respective publication, "Valorisation of Blackcurrant Pomace by Extraction of Pectin-Rich Fractions: Structural Characterization and Evaluation as Multifunctional Cosmetic Ingredient" (<a href="https://doi.org/10.3390/polym16192779">https://doi.org/10.3390/polym16192779</a>). See the README.txt file for more details.

CHARACTERIZATION OF BREAST LESIONS BY PROCESSING DIGITAL BREAST IMAGES

This Rendering to the World Health Organization, women in both developed and developing nations are most likely to develop breast cancer. This illness causes breast cells to grow and multiply out of control. According to research institutes and international organizations, there are various screening methods available based on age, and breast cancer can be cured if detected in time. The Breast Imaging Reporting and Data System (BIRADS) is a standardized system that is commonly used in these techniques to report results and findings. Results are sorted by BIRADS into six categories, numbered 0 through 6. Furthermore, mammography is the most widely utilized screening technique. This study suggests using mammography data processing to identify breast lesions. Adaptive filters are used for image cropping and contrast enhancement during the pre-processing phase. The pectoral muscle is then segmented using segmentation techniques that consider morphological and area growth factors. The lesion is then divided into sections at the muscle and breast levels using the Discrete Wavelet Transform (DWT), which finds any micro calcifications. Furthermore, to distinguish between dense lesions and other kinds of lesions, an area cultivation approach combined with multiple thresholding techniques is employed. Lastly, the obtained segmentation is used to extract textural and morphological features. When expert-segmented and automatically segmented images were compared, the Sorensen Decade similarity index was 0.73, indicating the effectiveness of the suggested method. Considering that the lesion area on a mammogram can only be roughly delineated by hand or automatically, this is a promising outcome.

Supplementary data for manuscript: "Characterizing dynamic heterogeneities during nanogel degradation"

Contains data files and code (python Jupyter notebook) to reconstruct plots for manuscript: "Characterizing dynamic heterogeneities during nanogel degradation" Contact: zmira@g.clemson.edu This work is supported by the National Science Foundation under NSF Award No. 2110309.

Data used in analyses of Danaher et al. 2024 "Childhood-onset lupus nephritis is characterized by complex interactions between kidney stroma and infiltrating immune cells"

CosMx 1000-plex data and R code from childhood-onset lupus nephris samples, generated for the article Danaher et al. 2024 "Childhood-onset lupus nephritis is characterized by complex interactions between kidney stroma and infiltrating immune cells".

A Data-Driven Epigenetic Characterization of Morning Fatigue Severity in Oncology Patients Receiving Chemotherapy: Associations with Epigenetic Age Acceleration, Blood Cell Types, and Expression-Associated Methylation

This dataset contains supplementary materials including the eCpG mapping analysis results and annotation. The manuscript has been accepted for publication at Cancer Medicine. Please cite both the paper as well as the DOI of this dataset if you make use of the data.

Deep learning model for characterizing protein-RNA interactions from sequence at single-base resolution

<a href="https://zenodo.org/api/records/14021440/draft/files/encode_eclip.h5/content" target="_blank" rel="noopener noreferrer">encode_eclip.h5</a> - This file contains the training, validation, and test data for the Reformer model. <a href="https://zenodo.org/api/records/14021440/draft/files/encode_eclip_bc.h5/content" target="_blank" rel="noopener noreferrer">encode_eclip_bc.h5</a> - This file contains the training, validation, and test data for the Reformer-BC model. <a href="https://zenodo.org/api/records/14027315/draft/files/Reformer-code.zip/content" target="_blank" rel="noopener">Reformer-code.zip</a> - This file contains the training code of Reformer.

opencc-by-4.0Nov 2024View details →

AlphaFold2-Based Characterization of Apo and Holo Protein Structures and Conformational Ensembles Using Randomized Alanine Sequence Scanning Adaptation: Capturing Shared Signature Dynamics and Ligand-Induced Conformational Changes

Proteins often exist in multiple conformational states, influenced by the binding of ligands or substrates. The study of these states, particularly the apo (unbound) and holo (ligand-bound) forms, is crucial for understanding protein function, dynamics, and interactions. In the current study, we use AlphaFold2 that combines randomized  alanine  sequence masking  with shallow multiple sequence alignment  subsampling to expand the conformational diversity of the predicted structural  ensembles and   capture conformational changes between apo and holo protein forms. Using several well-established datasets of  structurally diverse apo-holo protein pairs, the proposed approach enables  robust predictions of apo and holo structures and conformational ensembles, while also displaying notably similar dynamics distributions. These observations are consistent with  the view  that the intrinsic dynamics of allosteric proteins is defined by the structural topology of the fold and favors conserved conformational motions driven by soft modes among orthologs. We also found  a significant correlation between conformational flexibility and  AlphaFold2 metric of statistical significance pLDDT for the apo-holo pairs in which ligand binding induced local moderate conformational changes. For apo-holo pairs exhibiting larger structural changes, this relationship  becomes nonlinear, reflecting inability of AlphaFold2 confidence metrics to identify high energy functional conformations. Our findings support the notion that AlphaFold2 approaches can yield reasonable accuracy in predicting minor conformational adjustments between apo and holo states, especially for proteins with  moderate localized changes upon ligand binding. However, for large, hinge-like domain movements, AF2 tends to predict the most stable domain orientation which is typically the apo form rather than the full range of functional conformations characteristic of the holo ensemble. These results indicate that modeling of multiple functional states of proteins may require more accurate detection of flexible region conformations and cannot solely rely on the pLDDT metric as the major determinant of the prediction accuracy in reproducing functional conformational ensembles.

opencc-by-4.0Jun 2021View details →

Characterizing ferromagnetic domains in ring structures using in-situ magnetic Fresnel imaging

This deposit contains supplementary datasets and data processing scripts used in a Specialization Project by Rajith Aravinth at the Norwegian University of Science and Technology (NTNU). Dataset: 2021_03_26_FA721_A6.5_in_situ_stack.hspy Sample FA721, window W1, ring A6.5um, objective lens 0768. Tilting range [-2.0, 2.0] deg. in X and [-2.0, 2.0] deg. in Y, step size 1.0 deg. Python files: processing.py utils.py p001_make_hyperspy.py Running processing.py produces the domains and areas as numpy files, that can be used for visualisation and quantifications. Looping through the whole dataset takes quite some time, hence the results are also to be found in the .npy files. # Numpy files areas.npy domains.npy Notebook: Jupyter_notebook.ipynb More detail overlook of the algorithm, with visualizations and result