Contributors: Elena Zudilova-Seinstra

Date: 2019-09-13

... In the selection task, participants had to select the region of interest (a specified vessel segment) as explained in the "Experiment_description.pdf" file. They were asked to manipulate (i.e., translate, rotate and scale) a 3D box widget, initially positioned such that the region of interest covered all vessel structures displayed on the screen. Three 3D model files ("level1.vtk", "level2.vtk" and "level.3 vtk") were used to define three complexity levels of the selection task: Level 1 (simple) — one vessel; Level 2 (average) — two closely located vessels; Level 3 (complex) — three vessels, where two vessels are located close to each other. This project was funded by the University of Amsterdam and NWO. This is version 8 of the dataset to test RDM implementations

Contributors: Nadzeya Marozkina

Date: 2019-09-10

... Method 1: L-CSNO binding to proteins after native-PAGE separation The mouse brain membrane fraction (above) was resuspended in HEPES buffer. A BCA (Pierce) protein assay was performed and 50 µg protein was run on two native-PAGE gels (TGX, Bio Rad). One gel was incubated for 30 min in the dark with 50 µM L-CSNO in S-nitrosothiol buffer (10 mM Tris-HCl, pH 6.0, 150 mM NaCl). The second gel was incubated for 30 min in the dark with 50 µM L-CSNO and 100 µM each S-phenyl-cysteine (L-CSφ) and S-methyl-cysteine (L-CSMe) in S-nitrosothiol buffer. Each gel was then rinsed with water and incubated in the dark with 40 µM diaminofluoroscein (DAF) 2 (Cayman Chemicals) for 10 min in the dark (RT) (24). Gels were then imaged on Chemidoc (Bio Rad; Hercules, CA) using the fluorescein setting and bands cut out for mass spectrometry proteomics (see below) that were seen without, but not with, the S-methyl and S-phenyl substituted cysteine co-incubations (21). Method 2: L-CSNO affinity chromatography L-CSNO affinity columns were prepared as follows. L-Cysteine was coupled to AminoLink Plus (Pierce/ThermoFisher; Waltham, MA) resin according to the manufacturer’s protocol. In control experiments, aminoLink Plus was used without reaction with L-cysteine. Briefly, L-cysteine was dissolved in coupling buffer A (0.1 M sodium citrate, 0.05 M sodium carbonate, pH 10) at a concentration of 100 mM and incubated with 0.4 ml, previously washed, AminoLink resin in a small (0.5 ml) column for 4 hours at room temperature. The resin was then washed with coupling buffer B (0.1 M phosphate. 0.15 M sodium chloride, pH 7.2) and incubated for 4 hours at room temperature with 100 mM cyanoborohydride in coupling buffer B. Active sites were then blocked with quenching buffer (1 M Tris-HCl, pH 7.4). Resin was then washed with 1 M NaCl and then incubated for 10 min with 30% ethyl nitrite (EtONO) in ethanol at room temperature in the dark (25). It was then washed with 100% ethanol followed by 1M NaCl. Excised mouse brain homogenate was briefly centrifuged and the supernatants were then incubated with prepared Aminolink columns for 30 min at room temperature. The columns were then washed with wash buffer and bound protein eluted with Laemmli buffer and elution buffer (0.1 M Glycine, pH 3.5). Eluate was concentrated and used for SDS-PAGE gel (TGX, BioRad; Hercules, CA) followed by Coomassie staining. Bands found in samples from + L- Cysteine columns but not in – L-cysteine columns were excised and analyzed further by MS proteomics. Biotin substitution analysis for NO-substituted cysteine’s in Kv proteins CHO cells expressing all three Kv proteins were plated on in 6 wells of a six well plate. Once confluent, cells were incubated with no treatment, 500 µM L-CSNO, or 500 µM L-CSNO plus 10mM leucine for two minutes. Wells were then washed with cold PBS and lysed in HEN buffer (250mM HEPES pH7.7, 1mM EDTA, 0.1mM Neocuproine). After biotin switch, samples went to LC-MS.

Contributors: Boda Liu

Date: 2019-09-04

... We provide the original data and visualization scripts associated with "Importance of the size and distribution of chemical heterogeneities in the mantle source to the variations of isotope ratios and trace element abundances in mid-ocean ridge basalts" GCA2019

Contributors: Huajun Ming

Date: 2019-09-04

... The Fredlund-Xing (FX) model was chosen to develop the proposed equation. 1. SWR data sets were recoreded from other published papers. Related references can be found in Table 3. 2. Tables and Figures are shown in the paper. 3. Original datum of figures can be found in the folder "OriginPro and pictures related to Figures", and original pictures of figures can also be found in the jpg type.

Contributors: Bruno Luís Hönigmann Cereser

Date: 2019-09-03

... Tests, Results and Codes of the paper "A Mathematical Model for the Berth Allocation Problem with Variable Service Time and Continuous Time Horizon".

Contributors: Bruno Luís Hönigmann Cereser

Date: 2019-09-03

... Intances, codes and results.

Contributors: Constance Schmidt, Stephen Schmidt, Kara Wilson

Date: 2019-09-02

... Word Lists for Experiments 1 through 3. SPSS data files for Experiments 1 through 3. T-test data file for Experiment 3. SPSS files include recall as a function of condition in each experiment.

Contributors: Enrique Garcia-Macias, Alejandro E. Martínez-Castro

Date: 2019-09-02

... All the data relating the case studies used to validate the HTSA approach. These include: simply supported beam, continuous three-span bridge, the viaduct of Rodenillo, and the viaduct of Santa Ana. Along with the data files, MATLAB scripts are also provided to post-process the results.

Contributors: Peter Hojrup, Sanne Grundvad Boelt

Date: 2019-09-01

... Description of raw-files: FUS04612: Orbitrap Fusion analysis of heat-treated and BS3 cross-linked dimeric calreiticulin where the dimer is a combination of human recombinant 15N-labelled calreticulin expressed in P. pastoris mixed with native human placental calreticulin. FUS04614: Duplicate of FUS04612 QHF1883: Q Exactive HF analysis of heat-treated and BS3 cross-linked dimeric calreiticulin where the dimer is a combination of human recombinant 15N-labelled calreticulin expressed in P. pastoris mixed with native human placental calreticulin. QHF1884: Duplicate of QHF1883 Obvb08125: Orbitrap Velos Pro analysis of heat-treated and BS3 cross-linked dimeric calreiticulin where the dimer is a combination of human recombinant 15N-labelled calreticulin expressed in P. pastoris mixed with native human placental calreticulin. Obvb08126, Obvb08127, Obvb08128: Three replicates of Obvb08125.

Contributors: Joshua Soderholm

Date: 2019-09-01

... The following collection is used to demonstrate the HailPixel survey technique as part of an AGU GRL publication. The following is an abstract for this paper: A new technique, named "HailPixel," is introduced for measuring the maximum dimension and intermediate dimension of hailstones from aerial imagery. The photogrammetry procedure applies a convolutional neural network for robust detection of hailstones against complex backgrounds and an edge detection method for measuring the shape of identified hailstones. This semi-automated technique is capable of measuring many thousands of hailstones within a single survey, which is several orders of magnitude larger than population sizes from existing sensors (e.g., a hail pad). Comparison with a co-located hail pad for an Argentinan hailstorm event demonstrates the larger population size of the HailPixel survey significantly improves the shape and tails of the observed hail size distribution. When hailfall is sparse, such as during large and giant hail events, the large survey area of this technique is especially advantageous for resolving the hail size distribution. The dataset contains the DEM and orthomosaic imagery, processing reports, final location of hail centroids, final measurements of hail major and minor axis, subset offsets and hail pad data. For more information applying the subset offsets to calculate the true position of the hail centroids please see the paper.