cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/4jytx9s44j.1
title: Specific leaf area, biomass equations and leaf area equations for European tree species

description: The data set contains specific leaf area data, biomass equations and leaf area equations for 24 European tree species and 3 introduced species. This includes 868 equations from the literature and 105 raw data sets that were either from the literature or our own data. The number of biomass or leaf area measurements used to produce the equations or included as raw data was &gt; 60,000. The specific leaf area data was also obtained from the literature. The equations were used to produce pseudo-observations of mass or leaf area and were combined with the raw data sets to develop new “general” equations for each species and biomass component (foliage, branch, stem, root, aboveground) that can account for factors describing stand structure and age by including those factors as independent variables. These general equations are provided in separate worksheets of this dataset. The main findings and methodology are described in Forrester et al. (in review). Forrester, D. I., Tachauer, I. H. H., Annighoefer, P., Barbeito, I., Pretzsch, H., Ruiz-Peinado, R., Stark, H., Vacchiano, V., Zlatanov, T., Chakraborty, T., Saha, S., Sileshi, G. W. in review. Biomass and leaf area allometric equations for European tree species incorporating stand structure and tree age.
DOI: 10.17638/datacat.liverpool.ac.uk/211
title: Validation of chondrocyte and tenocyte gene expression by qPCR
DOI: 10.21227/h2204g
title: Test Zika Dataset June 2017
DOI: 10.5255/ukda-sn-8156-2
title: Millennium Cohort Study: Sixth Survey, 2015
DOI: 10.5517/ccdc.csd.cc1p9kp7
title: CCDC 1558329: Experimental Crystal Structure Determination

description: Related Article: Brian W. Skelton|2017|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.17632/34cnpysb7k.1
title: Inhibition Mechanism of an Anti-CRISPR Suppressor AcrIIA4 Targeting SpyCas9

description: Original data for SDS-PAGE, EMSA, cleavage assay
DOI: 10.17632/34cnpysb7k.2
title: Inhibition Mechanism of an Anti-CRISPR Suppressor AcrIIA4 Targeting SpyCas9

description: Original data for SDS-PAGE, EMSA, cleavage assay
DOI: 10.17632/34cnpysb7k.3
title: Inhibition Mechanism of an Anti-CRISPR Suppressor AcrIIA4 Targeting SpyCas9

description: Original data for SDS-PAGE, EMSA, cleavage assay
DOI: 10.17632/46v4njmrs3.1
title: Gu et al., Molecular Cell 2017 "mTORC2 regulates amino acid metabolism in cancer by phosphorylation of the cystine-glutamate antiporter xCT "

description: Mutations in cancer reprogram amino acid metabolism to drive tumor growth, but the molecular mechanisms are not well understood. Using an unbiased proteomic screen, we identified mTORC2 as a critical regulator of amino acid metabolism in cancer via phosphorylation of the cystine-glutamate antiporter xCT. mTORC2 phosphorylates serine 26 at the cytosolic N-terminus of xCT, inhibiting its activity. Genetic inhibition of mTORC2, or pharmacologic mTOR kinase inhibition, promotes glutamate secretion, cystine uptake and incorporation into glutathione linking growth factor receptor signaling with amino acid uptake and utilization. These results identify an unanticipated mechanism of amino acid metabolic reprogramming in cancer, enabling tumor cells to adapt to changing environmental conditions.
DOI: 10.17632/v4wp2mmztd.3
title: Argonaute CLIP defines a deregulated miR-122 bound transcriptome that correlates with patient survival in human liver cancer - Raw autoradiograms and Western Blots

description: JL0109 - Autoradiogram of 32P-labelled RNA crosslinked to IP purified AGO from five normal adjacent (left) or matched HCC tumor from from livers of human HCC patients (right) using the 2A8 anti-Ago antibody, exposed overnight after running on an 8% Novex NuPage gel. Irrelevant antibody control “IgG”, non-crosslinked control "-XL", and high “Hi” RNAse A control are shown. RNA-protein complexes from 110-150kDa were used for subsequent RNA sequencing library preparation. A weak band of ~110kDa is typically observed under non-crosslinked conditions. Protein size markers labeled with boxes at indicated molecular weights. Mass of sample (in milligrams) are indicated beneath each lane. JL0173 - Autoradiogram of 32P-labelled RNA crosslinked to IP purified AGO from four 122KO (top) or five WT floxed control livers (bottom) using the 2A8 anti-Ago antibody, exposed overnight after running on an 8% Novex NuPage gel. Irrelevant antibody control “IgG”, non-crosslinked control "-XL", and high “Hi” RNAse A control are shown. RNA-protein complexes from 110-150kDa were used for subsequent RNA sequencing library preparation. A weak band of ~110kDa was typically observed under non-crosslinked conditions. Protein size markers labeled with boxes at indicated molecular weights. Mass of sample (in milligrams) and sex of animal are indicated beneath each lane. Fig 7A - FLAG-tagged human BCL9 expression levels in 293T cells after transfection with 50nM control or miR-122 mimic. WT BCL9 is compared to a mutant where all 6 exonic miR-122 sites were mutated while preserving amino acid sequence. Blots were imaged on a LiCor with ImageStudio Software V5.2. Short exposure displays Flag BCL9 channel (800nm) and GAPDH channel (680nm). Long exposure shows only the flag-BCL9 channel signal (800nm). Fig 7B - FLAG-tagged human BCL9 expression levels in MHCC-LM3 cells after transfection with 50nM control or miR-122 mimic. WT BCL9 is compared to a mutant where all 6 exonic miR-122 sites were mutated while preserving amino acid sequence. Blots were imaged on a LiCor with ImageStudio Software V5.2. Short exposure used for GAPDH normalization (lower set of bands). Long exposure shows only the flag-BCL9 channel signal in the upper set of bands.
DOI: 10.17632/v9z4bs8y8x.2
title: PLOS ONE: PONE-D-16-50350R1 - [EMID:c5cb5e2f76a1fa09]

description: 3D US Measure and CT reference raw dataset
DOI: 10.5281/zenodo.819511
title: Imagesurf Moab2 Image Example

description: A set of 2000x2000 raw confocal fluorescence images of MOAB2-labelled cortex from APPswe/PS1dE9 mouse models of Alzheimer's disease, un-annotated intensity scaled 8-bit images, sparsely annotated pixel labels and reference segmentation examples. Pixels are annotated as signal (red 0xFFFF0000) and background (blue 0xFF0000FF).

Images were captured as stitched 12-bit greyscale single-plane images and cropped to size. Image acquisition was performed at 561nm excitation and  615nm emission wavelengths using a Perkin Elmer Ultraview VOX imaging system with Nikon Eclipse Ti inverted microscope, 20x objective lens, x-y motorised stage, Hamamatsu ORCA-R2 C10600-10B CCD camera and Volocity 6.3 software package.

These images are shared as examples for the ImageSURF segmentation plugin for ImageJ2/FIJI (https://doi.org/10.5281/zenodo.818109).
DOI: 10.17632/7rd29h4p3m.1
title: FormTracer. A Mathematica tracing package using FORM

description: We present FormTracer, a high-performance, general purpose, easy-to-use Mathematica tracing package which uses FORM. It supports arbitrary space and spinor dimensions as well as an arbitrary number of simple compact Lie groups. While keeping the usability of the Mathematica interface, it relies on the efficiency of FORM. An additional performance gain is achieved by a decomposition algorithm that avoids redundant traces in the product tensors spaces. FormTracer supports a wide range of syntaxes which endows it with a high flexibility. Mathematica notebooks that automatically install the package and guide the user through performing standard traces in space–time, spinor and gauge-group spaces are provided.
DOI: 10.17632/g73xtfyjc3.1
title: Moldova vineyards soil

description: The elemental content of Na, Mg, Al, Ca, K, Mn and Fe as major elements as well as of the other 28 trace elements: Sc, Ti, V, Cr, Co, Ni, Zn, As, Br, Rb, Sr, Zr, Sb, Cs, Ba, La, Ce, Nd, Sm, Eu, Gd, Tb, Tm, Yb, Hf, Ta, Th and U (in mg/kg) in 17 samples of soil collected from two Moldavian vineyards (Romanesti 12 samples; Cricova - 5 samples) as determined by Epithermal Neutron Activation Analysis at the Frank Neutron Physics Laboratory of the Joint Institute for Nuclear Research (summer - autumn 2015). All data saved contained in a csv file.
DOI: 10.5281/zenodo.817856
title: Paralog Variant Classification And Scoring

description: <em>Para_zscore </em>data

Input data, annotation of all hg19 missense variants, score for every paralog gene

more details to follow

 

Information on the files, scripts to generate and use the <em>para_zscore</em> are available under

https://git-r3lab.uni.lu/genomeanalysis/paralogs.
DOI: 10.5281/zenodo.818234
title: Rotavirus Infection And Health Related Quality Of Life Of Hospitalized Children In Latvia

description: Data on Rotavirus infection and health related quality of life of hospitalized children in Latvia, 527 respondents, anonymous data, data collected: April 2013 to December 2015.
DOI: 10.5281/zenodo.818235
title: Rotavirus Infection And Health Related Quality Of Life Of Hospitalized Children In Latvia

description: Data on Rotavirus infection and health related quality of life of hospitalized children in Latvia, 527 respondents, anonymous data, data collected: April 2013 to December 2015.
DOI: 10.17632/4mhd4v4ssc.2
title: Striking pseudogenization in avian phylogenetics: numts are large and common in falcons

description: Original files containing all mitochondrial sequences used in this work. Genes present in numts are included.
DOI: 10.17632/gwtwc4ndpj.1
title: supporting data for Warfield et al 2017; MOLECULAR-CELL-D-17-00515

description: Western blot images of TFIID subunit depletion experiments
DOI: 10.17632/v4wp2mmztd.4
title: Argonaute CLIP defines a deregulated miR-122 bound transcriptome that correlates with patient survival in human liver cancer - Raw autoradiograms and Western Blots

description: JL0109 - Autoradiogram of 32P-labelled RNA crosslinked to IP purified AGO from five normal adjacent (left) or matched HCC tumor from from livers of human HCC patients (right) using the 2A8 anti-Ago antibody, exposed overnight after running on an 8% Novex NuPage gel. Irrelevant antibody control “IgG”, non-crosslinked control "-XL", and high “Hi” RNAse A control are shown. RNA-protein complexes from 110-150kDa were used for subsequent RNA sequencing library preparation. A weak band of ~110kDa is typically observed under non-crosslinked conditions. Protein size markers labeled with boxes at indicated molecular weights. Mass of sample (in milligrams) are indicated beneath each lane. JL0173 - Autoradiogram of 32P-labelled RNA crosslinked to IP purified AGO from four 122KO (top) or five WT floxed control livers (bottom) using the 2A8 anti-Ago antibody, exposed overnight after running on an 8% Novex NuPage gel. Irrelevant antibody control “IgG”, non-crosslinked control "-XL", and high “Hi” RNAse A control are shown. RNA-protein complexes from 110-150kDa were used for subsequent RNA sequencing library preparation. A weak band of ~110kDa was typically observed under non-crosslinked conditions. Protein size markers labeled with boxes at indicated molecular weights. Mass of sample (in milligrams) and sex of animal are indicated beneath each lane. Fig 7A - FLAG-tagged human BCL9 expression levels in 293T cells after transfection with 50nM control or miR-122 mimic. WT BCL9 is compared to a mutant where all 6 exonic miR-122 sites were mutated while preserving amino acid sequence. Blots were imaged on a LiCor with ImageStudio Software V5.2. Short exposure displays Flag BCL9 channel (800nm) and GAPDH channel (680nm). Long exposure shows only the flag-BCL9 channel signal (800nm). Fig 7B - FLAG-tagged human BCL9 expression levels in MHCC-LM3 cells after transfection with 50nM control or miR-122 mimic. WT BCL9 is compared to a mutant where all 6 exonic miR-122 sites were mutated while preserving amino acid sequence. Blots were imaged on a LiCor with ImageStudio Software V5.2. Short exposure used for GAPDH normalization (lower set of bands). Long exposure shows only the flag-BCL9 channel signal in the upper set of bands. Fig S7 - FLAG-tagged human BCL9 expression charcterization. Immunoblots of H293T cells transfected with empty vector (lane 1), FLAG-BCL9 expression vector (lane 2), or no vector (lane 3) and harvested after 48 hours. Blots were probed with anti-FLAG and anti-tubulin (red channel) and anti-BCL9 (green channel) antibodies. Merged channel is also shown.
DOI: 10.17632/x9wkrghz23.1
title: Brexit Tweets from the morning of it's annoucement

description: To further our understanding of public reaction to political movement via social media, this dataset provides 17998 unfiltered tweets taken on the morning that Brexit was announced. This dataset contains metadata such as geolocation as an independent variable, to allow for rigorous qualitative investigation to be used. Additional tweets from trending topics were also taken at the same time provide context on trending themes at the time: - Scotland - Jeramy Corbyn - Nichola Sturgeon - David Cameron - EURefResults - Euromillions - Borris Data was captured with NCapture from QSR.
DOI: 10.17632/7sk82n38sh.1
title: Salmon Otolith Sonification Perceptual Survey Dataset

description: This is the data and survey materials from a perceptual survey testing participants ability to determine the location of transitions in sonified (data to sound) salmon otolith microchemical data. The sonified chemical data represents movement of fish into rivers with differing chemistry. The survey tested whether the sonification mappings allowed listeners to identify these movements as more fish were added to the sounds they heard. In addition it tested the ability of listeners to interpret these sound transitions using both sound and related visualizations.
DOI: 10.17632/448jdx7gcr.1
title: TabbyXL: Experiment Data

description: The data are designed to evaluate TabbyXL, a system for rule-based transformation spreadsheet data from arbitrary to relational tables that is freely available at GitHub (https://github.com/cellsrg/tabbyxl). Our data are based on the existing dataset of tables Troy_200 [1]. It contains 200 arbitrary tables as CSV files collected from 10 different government statistical websites. They were collected for the experiment on data extraction from tables that is presented in the paper [2]. We use its earlier version that stores the original tables with style features (fonts, alignment, and indentation) as Excel spreadsheets available at http://tango.byu.edu/data. We have put all of these tables with style features into the single spreadsheet file (data/TangoDataset.xlsx). Each of 200 tables is located in a separate sheet. The pair of tags $START and $END points out to its location inside the sheet. We initially used this file in our previous experiment described in the paper [3]. We have transformed automatically all tables of the single spreadsheet into the relational form, using TabbyXL and the ruleset (data/rules.dslr). The folder data/results contains the obtained results. The folder data/gt contains the ground-truth data for automated performance evaluation of TabbyXL in the role and structural stages of the table analysis. Each table of our data/results and data/gt dataset is accompanied with two recordsets: ENTRIES and LABELS. The first of them specifies entries. Each record presents an entry as a triple . In LABELS recordset each record presents a label as a triple . We also have stored the log files: results.log with the results of running and eval.log with the results of performance evaluation of TabbyXL. REFERENCES [1] Nagy G. TANGO-DocLab web tables from international statistical sites, (Troy_200), 1, ID: Troy_200_1. URL: http://tc11.cvc.uab.es/datasets/Troy_200_1. [2] Embley D., Krishnamoorthy M., Nagy G., & Seth S. (2016). Converting heterogeneous statistical tables on the web to searchable databases. Int. J. on Document Analysis and Recognition, 19(2), 119-138. URL: https://link.springer.com/article/10.1007/s10032-016-0259-1. [3] Shigarov A., Paramonov V., Belykh P., & Bondarev A. (2016) Rule-Based Canonicalization of Arbitrary Tables in Spreadsheets. Proc. 22nd Int. Conf. on Information and Software Technologies, pp. 78-91. URL: http://link.springer.com/chapter/10.1007/978-3-319-46254-7_7.
DOI: 10.17632/48fctynd77.4
title: Simulation Results for Multi-Class Multi-Server Queueing Systems with Cross-Training

description: The JSON file contains a number of cases for multi-class multi-server systems with partial class-server assignments (cross-training). For each recorded systems all possible (feasible) class-server assignments were generated, and simulation results were recorded. The simulation results (for each assignment) include: (i) marginal probabilities that each class has the corresponding number of items in the system, (ii) class-server utilizations (utilization of server time capacity), (iii) class server distribution with percentages of class flows assigned to each server. Maximum numbers of servers and classes were limited to 6. Please note that NOT ALL possible combinations for numbers of servers and classes were generated, due to the exponential growth of possible class-server assignments. However, for each presented case (with certain numbers of servers, classes, and certain arrival/service rates), ALL possible class-server assignments were generated and simulated. The presented results allow easy analysis and optimization of systems where such queue occurs (call-centers, production facilities, maintenance systems) and benchmarking with possible optimization algorithms for class-server assignments.
DOI: 10.17632/7kckhkp4yh.1
title: Edisto Forage Bull Test Data Set Years 2013 - 2016

description: Data collected
DOI: 10.17632/ssmgdvbyg6.1
title: Edisto Forage Bull Test Data 1983 - 2011

description: Dr. Olsons Data for the EFBT
DOI: 10.17632/hnc25t5y5v.1
title: (Guo et al.) Regulation of hetDNA length during mitotic double-strand break in yeast

description: Unprocessed PacBio sequencing data files and barcode pairs used for each strain.
DOI: 10.5281/zenodo.818276
title: Sketches And Diagrams In Practice  — Supplementary Material

description: Sketches and diagrams play an important role in the daily work of software developers. In our paper "Sketches and Diagrams in Practice" we present the results of our <strong>research on the usage of sketches and diagrams in software engineering practice</strong>. We focused especially on their relation to the core elements of a software project, the source code artifacts. Furthermore, we wanted to assess how helpful sketches are for understanding the related source code. We intended to find out if, how, and why sketches and diagrams are archived and are thereby available for future use. Software is created with and for a wide range of stakeholders. Since sketches are often a means for communicating between these stakeholders, we were not only interested in sketches and diagrams created by software developers, but by all software practitioners, including testers, architects, project managers, as well as researchers and consultants. In a <strong>survey with 394 software ‘practitioners’</strong>, we mainly asked questions about the the last sketch or diagram that they had created. Contrary to our expectations and previous work, the majority of sketches and diagrams contained at least some UML elements. However, most of them were informal. The most common purposes for creating sketches and diagrams were designing, explaining, and understanding, but analyzing requirements was also named often. More than half of the sketches and diagrams were created on analog media like paper or whiteboards and have been revised after creation. Most of them were used for more than a week and were archived. About half of the sketches were rated as helpful to understand the related source code artifact(s) in the future. Our study complements a number of existing studies on the use of sketches and diagrams in software development, which analyzed the above aspects only in parts and often focused on an academic environment, a single company, open source projects, or were limited to a small group of participants.

The questionnaire for the online survey was online from August 28, 2013 until December 31, 2013. Further information on our research design and research questions can be found in the referenced paper. This dataset contains the questionnaire, the data we collected during this survey, and a basic R script that can be used as a starting point for validating our results and further exploring the data. This data set has been reviewed and accepted by the Artifact Evaluation Committee of FSE 2014. Since we assured our participants that their data is handled confidentially, only the quantitative data is directly available here. If you are also interested in the qualitative data from our survey, don’t hesitate to contact the authors.
description: {"references": ["Baltes and Diehl - Sketches and Diagrams in Practice (FSE 2014 ): https://doi.org/10.1145/2635868.2635891", "Baltes and Diehl - Sketches and Diagrams in Practice (FSE 2014 ): https://sbaltes.github.io/assets/pdf/fse14-sketches.pdf"]}