Contributors: Joshua French
... This archive provides data and code related to "A sandwich smoother for spatio-temporal functional data" by Joshua P. French and Piotr S. Kokoszka. The archive includes data from the North American Regional Climate Change Assessment Program (NARCCAP) and the North American Coordinated Regional Downscaling Experiment (NA-CORDEX). Mearns, L., et al., 2007, updated 2014. The North American regional climate change assessment program dataset, National Center for Atmospheric Research Earth System Grid data portal, Boulder, CO. doi:10.5065/D6RN35ST. Mearns, L., et al., 2017. The NA-CORDEX dataset, version 1.0. doi:10. 5065/D6SJ1JCH. NCAR Climate Data Gateway, Boulder CO. Accessed October 12, 2019. Mearns, L.O., Arritt, R., Biner, S., Bukovsky, M.S., McGinnis, S., Sain, S., Caya, D., Correia Jr, J., Flory, D., Gutowski, W., et al., 2012. The North American regional climate change assessment program: overview of phase I results. Bulletin of the American Meteorological Society 93, 1337–1362. Mearns, L.O., Gutowski, W., Jones, R., Leung, R., McGinnis, S., Nunes, A., Qian, Y., 2009. A regional climate change assessment program for North America. EOS, Transactions American Geophysical Union 90, 311–311.
Data for: New spectroscopic method for true color determination in natural water with high agreement with visual methods”
Contributors: Mikhail Zobkov
... The program is dedicated to true water color (TWC) calculation by light absorption in visual range from 390 up to 830 nm. Calculation is based on mathematical model of color perception by standard observer using spectral data, contained in text files. It allows: 1 – To load standard solutions and samples spectra with spectrum conversion into absorption when required; 2 – To save and upload calculation of graduation curve and graduation data; 3 – To calculate true water color and export data to Microsoft (MS) Excel table; Surce code and data examples are also attached.
Contributors: Ronald Machaka, Trevor Derry, Iakovos Sigalas
... B6O Nanoindentation Dataset - 24 indentations
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Contributors: BURHAN SHAMURAD
... Mineral wastes utilised for pretreatment of OFMSW, followed by anaerobic digestion at mesophilic temperature of 37oC in lab scale continuous stirred reactor systems (CSTR). Genomic DNA of samples of digestate from these reactors were used for Illumina Hiseq 16S rRNA analysis.
Contributors: thanh Pham Dinh, thang ta bao, Hoang Ngo Viet, Long Nguyen Binh
... + The tested data for Inter-Domain Path Computation under Domain Uniqueness constraint (IDPCDU). + On account of no instances were available for IDPC-DU, we made up our minds to generate a set for test instances to evaluate the proposed algorithms. To generate an instance, we first passed three parameter: number of nodes, number of domains and number of edges. After that, we created an array of distinct nodes and an array of distinct domains that satisfied the number of nodes is greater than the length of domain array. Source nodes and terminal node are the first and the last nodes of the nodes array, respectively. With the above arrays, we merged them to make a valid solution called P. Each edge of P was set to the weight one, except the out-edge of the source node is set to the weight two. To add noise to the test instance, for every single node in P, we added some edges to random nodes not in P. Moreover, we created some one-weighed-edges between the the nodes not in P. These traps would make simple greedy algorithms get it harder to find optimal solution. Eventually, we randomly generated edges that have greater values of weight than the value of the length of P. This method guaranteed that P is the optimal solution of the instance. There were two set of instances created, a small set and a large set. + Filename idpc_xx.idpc First line of a file constains two intergers N and D, which are number of nodes and number of domains, respectively. Second line contains two integers s and t, which are the source node and terminal node. Every next line contains four integers u, v, w, d, represents an edge (u,v) has weight w and belong to domain d.
Contributors: Guangwei Zhang
... Data for "Medial Preoptic Area Antagonistically Mediates Stress-induced Anxiety and Parental Behavior"
Contributors: Olayinka Abegunde
... The planar morphology and topography of TiC thin films coated on commercially pure Titanium (CpTi) grown by RF magnetron sputtering were investigated using Field emission scanning electron microscope (FESEM) and Atomic force microscope (AFM). The mechanical properties such as Hardness and Young Modulus of the thin film coating was studied using Nanohardness. Furthermore, grazing incidence X-ray diffractometer (GIXRD) and Raman spectroscopy were used to analyse the structural and composition of the TiC thin film coating
Contributors: Gerard Baquer, pere Ràfols Soler
... Mass Spectrometry Imaging dataset of mouse pancreatic tissue to be used as sample dataset to demonstrate the functionality of rMSIcleanup (https://github.com/gbaquer/rMSIcleanup). Acquired with silver-assisted LDI using MALDI TOF/TOF ultrafleXtreme. It is referred to as Dataset 2 in the accompanying publication (https://doi.org/10.1101/2019.12.20.884957).
Contributors: Junha Shin, Harald Marx, Alicia Richards, Dries Vaneechoutte, Dhileepkumar Jayaraman, Junko Maeda, Klaas Vandepoele, Jean-Michel Ané, Joshua Coon, Sushmita Roy
... Proteome: MS data was searched with the MaxQuant software (version 18.104.22.168). Searches were performed against the following UniProt protein sequence databases (v20150827): Medicago truncatula, Arabidopsis thaliana, Solanum tuberosum, Oryza sativa, Physcomitrella patens, and Zea mays. Searches used the default precursor mass tolerances (20 ppm first search and 4.5 ppm main search) and a product mass tolerance of 0.35 Da. The in silico digest was set to specific tryptic cleavage and a maximum of two missed cleavages. The fixed modification specified were carbamidomethylation of cysteine residues, and variable modifications were oxidation of methionine and acetylation of protein N-terminus. Peptides and proteins groups were both filtered to a 1% FDR. Label-free quantification was performed within MaxQuant using MaxLFQ. Protein groups were screened for "Reverse" and "Contaminant" identifications. The final protein levels are the LFQ intensity values. Transcriptome: The compendia of transcriptomic datasets for 6 plant species were created using publicly available RNA-seq dataset from Sequence Read Archive. We used the Curse and Prose suite (http://bioinformatics.psb.ugent.be/webtools/Curse/) to construct these expression compendia. First, we searched for datasets corresponding to "RNA-seq" and "Transcriptome analysis" for each species, and manually excluded the experiments which contained mutant, knock-out, and transgenic lines by curating the metadata in the Curse interface. We passed the chosen experiments and genomic sequence files to the Prose tool, which downloads data, performs quality control, and quantifies transcript expression to normalized TPM values. To change the transcript level expression to gene level, we summed up the multiple values of transcript expression for one gene. Co-expression network: We defined a species-specific graph as a fully-connected weighted graph, where the weight corresponds to the Gaussian kernel-based similarity between two gene expression profiles. First, we collected genes that are defined in the orthogroups of 6 species in the previous step (see method in the paper). Then we generated a distance matrix by calculating the pairwise Euclidean distance between two genes of the transcriptome compendium, and finally we transformed it to the similarity matrix using the Gaussian kernel to map the nearer distance to higher similarity.
Contributors: Ahinoam Pollack
... This dataset includes data relevant to a research project investigating the cause of surface expression in a section of the Midway Sunset Oil Field. The data includes earth models of the Midway Sunset Oil Field (well data, core data, surfaces, property models), a presentation on this topic, and surface expression data. The surface expression excel sheet provides the presence/absence of surface expressions in relation to other parameters (such as concentration of plugged wells, seal thickness, etc.).