cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.1683162
title: Genome alignments for 'Machine-driven parameter-space exploration of biochemical reactions'

description: The development of complex, multi-step <em>omics</em> methods in molecular biology is a laborious, costly, iterative and often intuition-bound process where an optimum is sought in a parameter space through step-by-step optimisations. The the difficulty of miniaturising assays and the cost of the experiments limit the dynamic range and the number of parameters that can be explored. However, because of non-linearities of the response of biochemical systems to their reagent concentrations, a broad dynamic range is necessary. Here we demonstrate the use of a high-performance nanoliter handling platform (Labcyte Echo 525) and computer generation of liquid transfer programs to explore in quadruplicates more than 600 combination of 4 parameters of a biochemical reaction, which lead us to uncover non-linear responses, parameter interactions and novel mechanical insights. With the increased availability of « <em>cloud biology</em> » computer-driven laboratory platforms, our results participate in changing methods development for biotechnology towards reproducible, computer-aided exhaustive characterisation of biochemical systems. This dataset contains the sequence alignments and other processing files produced by running the raw data (10.5281/zenodo.1680999) through a processing pipeline using the MOIRAI workflow manager. The most important output is the "CAGEscan_fragments" directories and represent the alignment of single mRNA molecules, which can be further analysed using the "CAGEr" software package available from Bioconductor. Run IDs: 171227_M00528_0321_000000000-B4GLP, 180123_M00528_0325_000000000-B4PCK, 180326_M00528_0346_000000000-B4GJR, 180403_M00528_0348_000000000-B4GP8, 180411_M00528_0351_000000000-BN3BL, 180501_M00528_0359_000000000-B4PJY, 180517_M00528_0364_000000000-BRGK6 180606_M00528_0367_000000000-BN3FG, 180607_M00528_0368_000000000-BN9KM
DOI: 10.5281/zenodo.1494857
title: btw17 query auto completion - query suggestions for German politicians and parties before the federal election 2017

description: The dataset contains the query suggestions for 5 major German parties (terms: "afd", "csu", "dielinke", "fdp", "grüne", "spd") and ten popular politicians and party leaders (terms: "Alexander Gauland", "Alice Weidel", "Angela Merkel", "Cem Özdemir", "Christian Lindner", "Dietmar Bartsch", "Katrin Göring-Eckardt", "Martin Schulz", "Sahra Wagenknecht").

The data was crawled on (mostly) two times per day from Tue Aug 04, 2017 to Tue Oct 31, 2017. The dataset contains 20001 suggestions from Bing search (http://api.bing.net/osjson.aspx), 11935 suggestions from Duck-Duck-Go (https://duckduckgo.com/ac/) and 33521 suggestions from Google search (http://clients1.google.de/complete/search). Note, that for some terms and dates no suggestions were returned by some of the APIs.

German language settings were used for Google and Bing, English language setting was used for Duck-Duck-Go. The API requests were sent with an IP address from Cologne, Germany. 

The UTF-8 encoded comma separated text file contains the following columns:

&lt;source&gt;: google, bing or ddg

&lt;queryterm&gt;: the query term

&lt;date&gt;: the date and time of the API call formatted as ISO8601

&lt;suggestterm&gt;: the suggested query completion (the query term was removed from the suggestion)

&lt;position&gt;: the position of the query suggestion within the list returned by the API (ranges from 0 to 19)

 

 

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DOI: 10.5281/zenodo.1688739
title: Synthetic dataset used in "The maximum weighted submatrix coverage problem: A CP approach"

description: Synthetic dataset used in "The maximum weighted submatrix coverage problem: A CP approach". Includes both the generated datasets as a zip archive and the python script used to generate them. Each instance is composed of two files in the form XxY_K_O_0xN_AxB_Smatrix.tsv being the matrix to use. Each row on a separate line, with tab-separated cells. XxY_K_O_0xN_AxB_Ssolution.txt giving the implanted solution. One submatrix per line. Then two JSON arrays follow, separated by a tabulation. The first is the list of rows selected in the submatrix, the second the columns. With: X and Y the size of the matrix K the number of submatrices in the implanted solution O the (minimum) overlap percentage of each submatrix N the sigma used for the background noise A and B the size of the implanted submatrices (subject to noise)
DOI: 10.5281/zenodo.1654296
title: Modeling organic aerosol over Europe in summer conditions with the VBS-GECKO parameterization: sensitivity to secondary organic compound properties and IVOC emissions [Dataset]

description: This dataset is composed of simulation outputs of the CHIMERE model that were used to evaluate the VBS-GECKO SOA parameterization as described in the study : Lannuque, V., Couvidat, F., Camredon, M., Aumont, B., and Bessagnet, B. : Modelling organic aerosol over Europe in summer conditions with the VBS-GECKO parameterization: sensitivity to secondary organic compound properties and IVOC emissions, Atmos. Chem. Phys., <em>to be submitted soon</em>.<br> <br> <strong>Please cite the original ACP article when using these data in a publication.</strong> <br> The paper also contains more information about how these data were obtained. The dataset is composed of 34 netcdf files. The 17 "daily" files gather the daily averages and the 17 "profile" files present the average day profiles. Victor Lannuque
DOI: 10.14469/hpc/4820
title: YU14 SSSS conf4

description: Gaussian Calculation
DOI: 10.14469/hpc/4821
title: YU14 SSSS conf3

description: Gaussian Calculation
DOI: 10.14469/hpc/4822
title: YU14 SSSS conf2

description: Gaussian Calculation
DOI: 10.14469/hpc/4823
title: YU14 SSSS conf1

description: Gaussian Calculation
DOI: 10.14469/hpc/4824
title: YU14 SSRR conf4

description: Gaussian Calculation
DOI: 10.14469/hpc/4825
title: YU14 SSRR conf3

description: Gaussian Calculation
DOI: 10.14469/hpc/4826
title: YU14 SSRR conf2

description: Gaussian Calculation
DOI: 10.14469/hpc/4827
title: YU14 SSRR conf1

description: Gaussian Calculation
DOI: 10.14469/hpc/4828
title: Test3

description: Gaussian Calculation
DOI: 10.5066/p9g5k78f
title: Hawaii Volcanoes National Park Plant Reproductive and Rat Abundance Data 2016-2017

description: This data included data and metadata on 1) the number of open fruit of Hibiscidelphus giffardianus, 2) Mark recapture data for rats, 3) location data for rat traps within plots and 4) seedling count data for Hibiscidelphus giffardianus. All sites were within Hawaii Volcanoes National Park. This study aims to evaluate the effect of rat population control on the ability of Hibiscadelphus giffardianus to successfully establish seedlings. We compared H. giffardianus fruiting and recruitment in a stand treated for rats and a neighboring control stand. The study was conducted in two neighboring kipuka, Kipuka Puaulu and Kipuka Ki, which are patches of well-developed forest surrounded by more recent lava flows. These kipuka lie 2.5 km northwest of Kilauea Caldera in Hawaii Volcanoes National Park on the island of Hawaii. The 700 x 700 m rat-removal treatment area falls within Kipuka Ki, and Kipuka Puaulu served as a control. We monitored 181 mature, fruit-bearing individuals of this species, of which there exist 223 total.
DOI: 10.5281/zenodo.1692079
title: Example datasets generated with Stytra

description: Example datasets accompanying Stytra with: <strong>example_closed_loop_embedded.zip</strong> Behavioral data from a closed loop oculomotor response paradigm. The fish was swimming in response to backward-moving gratings controlled in closed loop. The code for the protocol is here. <strong>example_imaging.zip</strong> Behavioral and calcium imaging data from a closed loop oculomotor response paradigm in a transgenic Huc:GCaMP6f fish.<br> The fish was swimming in response to backward-moving gratings controlled in closed loop, while a plane of the fish brain was scanned with a two-photon microscope. The code for the protocol is here. <strong>replication_portugues2011.zip</strong> Dataset acquired with the experimental protocol described in Portugues and Engert, 2011, reproduced within Stytra. The code for the protocol is here. <strong>example_trace_cheap_setup.zip</strong> Behavioral data from a closed loop oculomotor response paradigm in the low-cost behavioral rig described in the article. The code for the protocol is here. <strong>example_eye_motion.zip</strong> eye motion in response to sinusoidal rotation of black and white windmill stimuli. The code for the protocol is here. <strong>phototaxis.zip</strong> Replication of the Huang et. al Current Biology. 2013 study. For 10 s, the right side of the visual field is illuminated, while the left side is kept dark. Then, for 10 s the full field is bright, which repeats 60-80 times. The code for the protocol is here. All datasets were acquired with 6-8dpf larvae of Danio Rerio. Notebooks demonstrating analysis of this data are avilable at github
description: {"references": ["Portugues, R., & Engert, F. (2011). Adaptive locomotor behavior in larval zebrafish. Frontiers in systems neuroscience, 5, 72.", "Huang, K. H., Ahrens, M. B., Dunn, T. W., & Engert, F. (2013). Spinal projection neurons control turning behaviors in zebrafish. Current Biology, 23(16), 1566-1573."]}
DOI: 10.5281/zenodo.1692080
title: Example datasets generated with Stytra

description: Example datasets accompanying Stytra with: <strong>example_closed_loop_embedded.zip</strong> Behavioral data from a closed loop oculomotor response paradigm. The fish was swimming in response to backward-moving gratings controlled in closed loop. The code for the protocol is here. <strong>example_imaging.zip</strong> Behavioral and calcium imaging data from a closed loop oculomotor response paradigm in a transgenic Huc:GCaMP6f fish.<br> The fish was swimming in response to backward-moving gratings controlled in closed loop, while a plane of the fish brain was scanned with a two-photon microscope. The code for the protocol is here. <strong>replication_portugues2011.zip</strong> Dataset acquired with the experimental protocol described in Portugues and Engert, 2011, reproduced within Stytra. The code for the protocol is here. <strong>example_trace_cheap_setup.zip</strong> Behavioral data from a closed loop oculomotor response paradigm in the low-cost behavioral rig described in the article. The code for the protocol is here. <strong>example_eye_motion.zip</strong> eye motion in response to sinusoidal rotation of black and white windmill stimuli. The code for the protocol is here. <strong>phototaxis.zip</strong> Replication of the Huang et. al Current Biology. 2013 study. For 10 s, the right side of the visual field is illuminated, while the left side is kept dark. Then, for 10 s the full field is bright, which repeats 60-80 times. The code for the protocol is here. All datasets were acquired with 6-8dpf larvae of Danio Rerio. Notebooks demonstrating analysis of this data are avilable at github
description: {"references": ["Portugues, R., & Engert, F. (2011). Adaptive locomotor behavior in larval zebrafish. Frontiers in systems neuroscience, 5, 72.", "Huang, K. H., Ahrens, M. B., Dunn, T. W., & Engert, F. (2013). Spinal projection neurons control turning behaviors in zebrafish. Current Biology, 23(16), 1566-1573."]}
DOI: 10.5281/zenodo.1705343
title: Epigenetic and genetic variability of Hordeum murinum subsp. leporinum

description: Binary array from MSAP analysis for epigenetic variability studies in Hordeum murinum subsp. leporinum in response to climatic treatments. Also, a binary array from AFLP analysis provides basis of genetic diversity in this species.
DOI: 10.7910/dvn/xsofhd/kow6bh
title: stateoffices2016.tab

description: :unav
DOI: 10.7910/dvn/yfrsxw/3dii0b
title: data_release_documentation.pdf

description: :unav
DOI: 10.7910/dvn/yfrsxw/hdefvy
title: self_reports.tab

description: :unav
DOI: 10.20350/digitalcsic/8582
title: Dataset of the publication "Myelinated axons and functional blood vessels populate mechanically compliant rGO foams in chronic cervical hemisected rats"

description: The copyright of the content of this dataset belongs to the authors of the article indicated above. Permission must be requested to the authors for the reproduction and/or use of any parts of this dataset. Access to this dataset has been made public through the use of the public repository of CSIC (DIGITAL.CSIC). For any further questions, please contact the corresponding author of the article at mc.terradas@csic.es
description: Spinal cord injury (SCI) remain a therapeutic challenge. In this work, we have explored the regenerative ability of reduced graphene oxide (rGO) scaffolds to support pivotal features of neural repair at 4 months after SCI. 3D randomly porous foams have been prepared in mechanical compliance with neural cells and tissues. After 4 months, these scaffolds are fully vascularized and populated with neurites, some of them identified as myelinated excitatory axons. Magnetic resonance imaging studies demonstrate reduce perilesional damage in the presence of the scaffolds. In summary, these 3D porous rGO scaffolds are able to induce a compilation of positive effects that have been rarely described before, if ever, for any other material implanted in the injured spinal cord. The techniques used in this study include: immunofluorescence, scanning electron microscopy, atomic force microscopy, transmission electron microscopy, confocal laser scanning microscopy, histology, behavioral tests, magnetic resonance imaging, and X-ray photoelectron spectroscopy.
DOI: 10.5281/zenodo.1744988
title: AYNEC-Datasets

description: These datasets are presented in the article "AYNEC: All You Need for Evaluating Completion Techniques in Knowledge Graphs", sent for the ESWC19. Please, cite it in your work if you make use of them. The following datasets are included: WN18-AF, generated from WN18. WN18-AR, generated from WN18, removing inverses. WN11-AF, generated from WN11. WN11-AR, generated from WN11, removing inverses. FB13-A, generated from FB13. FB15K-AF, generated from FB15K. FB15K-AR, generated from FB15K, keeping relations that cover 95% of the graph and removing inverses. NELL-AF, generated from NELL. NELL-AR, generated from NELL, keeping relations that cover 95% of the graph and removing inverses. In all datasets, we removed relations with only one instance, used 20% of each relation in the graph for test, generated one negative for each positive in both training and testing by replacing the target of the positive with a random entity. In WN11 and WN18 all entities are potential candidates. In the rest of datasets, only entities that have appeared as targets of the relation are candidates.<br> <br> Two relations were considered inverses when there was a 90% overlap between them. That is, relationc A and B are inverses if for 90% of instances of A there is an instance of B with inversed source and target, and vice-versa. When removing inverses, the smallest of each pair of inverses was removed. Each zip file contains the following files about a dataset: train.txt - triples used for training. Each line contains the source, the relation, the target, and the label (1 for positives and -1 for negatives). test.txt - triples used for testing, following the same format. relations.txt - a list of the relations in the dataset, each with its frequency. entities.txt - a list of the entities in the dataset, eac with its total degree, inwards degree, and output degree. inverses.txt - a list of the inverses in the original graph, whether or not they were removed. Each inverse relationship is represented by a pair of relations. summary.html - the visual summary of the relation frequencies and entity degrees (without removed inverses). dataset.gexf - the entire dataset in the open graph format "gexf", which can be opened by applications such as Gephi.
description: {"references": ["Ayala, D., Borrego, A., Hern\u00e1ndez, I., Rivero, C. R., & Ruiz, D. (2019, June). AYNEC: All You Need for Evaluating Completion Techniques in Knowledge Graphs. In European Semantic Web Conference (pp. 397-411). Springer, Cham."]}
DOI: 10.5066/f7tt4pws
title: Inputs and Selected Predictions of the CBTN_v5 and CBTP_v5 SPARROW Models for the Chesapeake Bay Watershed

description: The CBTN_v5 and CBTP_v5 SPARROW models were developed to support inferences about causes of observed changes in nitrogen and phosphorus (respectively) fluxes in Chesapeake Bay tributaries between 1992 and 2012. Model inputs and outputs are included in three files, which are described below. Detailed documentation of the SPARROW modeling technique is available at https://pubs.er.usgs.gov/publication/tm6B3.
DOI: 10.5281/zenodo.1744798
title: Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk (sequence model release)

description: (This is the updated version that has been converted a standard pytorch model format) This is the deep learning sequence model used in Jian Zhou, Chandra L. Theesfeld, Kevin Yao, Kathleen M. Chen, Aaron K. Wong, and Olga G. Troyanskaya, Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk, Nature Genetics, 2018. Note the full software is available from https://github.com/FunctionLab/ExPecto and this release is created for the convenience of use and under the same non-commercial license. The model weights can be loaded with pytorch load_state_dict function (for an example please find https://github.com/FunctionLab/ExPecto/blob/master/chromatin.py). We also provide a web server for browsing mutations with strong predicted effects at https://hb.flatironinstitute.org/expecto/, which are currently limited to mutations within 1kb to TSS or are 1000 Genomes variants. Trivia: we code-named our models with whale names. This model has an unofficial codename DeepSEA "Beluga".
DOI: 10.15482/usda.adc/1484022
title: Cephus cinctus Official Gene Set OGSv1.0 and OGSv1.1

description: The Official Gene Set cepcin_OGSv1.0 is an integration (NCBI Cephus cinctus Annotation Release 101) from NCBI's eukaryotic annotation pipeline v8.0 with manual annotations by the research community (done via the Apollo manual annotation software). QC and Merge of the dataset was performed using the GFF3toolkit software (https://github.com/NAL-i5K/GFF3toolkit). The Official Gene Set cepcin_OGSv1.1 is an update from Cephus cinctus Official Gene Set 1.0 (cepcin_OGSv1.0). Updates were performed to the feature metadata, including cross-references and identifiers from NCBI-derived models. Protein-coding genes predicted by NCBI on mitochondrial DNA were added, and all tRNAs and rRNAs removed (these are still available from NCBI and at the i5k Workspace).
DOI: 10.5066/p9vrv6us
title: Compilation of data not available in the National Water Information System for domestic wells sampled by the U.S. Geological Survey in Bradford County, Pennsylvania, May-August 2016

description: This dataset contains the lithologic class and topographic position index information and quality-assurance and quality-control data not available in the online National Water Information System for 72 domestic wells sampled by the U.S. Geological Survey in Bradford County, Pennsylvania, May-August 2016. The topographic position index (TPI) for each well location was computed on the basis of a 25-meter digital elevation model (U.S. Geological Survey, 2009) using criteria reported by Llewellyn (2014) to indicate potential classes for topographic setting. The bedrock geologic unit and primary lithology were determined for each well location on the basis of the digital bedrock geologic map of Pennsylvania (Miles and Whitfield, 2001). The quality-assurance and quality-control data (such as blanks or replicates) were collected at a subset of sites to ensure that the data met specific data-quality objectives outlined for the study.
DOI: 10.6073/pasta/90006cec899f2388062f5786bc12bf5c
title: Climate data for Saddle chart recorder, 1982 - 1988.

description: Climatological data were collected from a Niwot Ridge climate station (Saddle at 3525 m) throughout the year. Parameters measured were temperature, relative humidity, solar radiation, wind speed, and run of wind. The station was instrumented with a thermohygrograph (regularly calibrated and checked with maximum and minimum thermometers and psychrometers), which was equipped with a Bourdon tube (to measure temperature) and a banjo-spread hair element (to measure relative humidity). The thermohygrograph was situated in a white, all wood, louvered Stevenson screen which was oriented with the door facing north. Solar radiation was recorded on a bimetalic strip mechanical actinometer. Ninety percent of solar radiation from 360 to 2000 nm was transmitted through the instrument's glass dome. Wind speed (peak gust) was measured near T-Van (3440 m), at a location approximately 400 m south of the Saddle climate station, with a 3-cup, AC-generating anemometer that continuously recorded onto an Esterline Angus strip chart recorder. Run of wind was measured with a Belford totalizing cup anenometer with a counter (at a height of approximately 3 meters above ground) and was located near T-Van as well. Average wind speed was calculated from the peak gust trace. The thermohygrograph, and actinometer both used wind-up or battery-driven clock drives that rotated the recording chart on a right cylindrical drum with a fixed period between 24 h and 861 h depending on the gears used. These clock mechanisms were virtually identical and therefore completely interchangeable among the instruments.
DOI: 10.14469/hpc/4829
title: 5Br2 + 2,4,6-tributylbenzene in CCl4, Wheland GD3BJ Def2-TZVPP freq -26445.903711

description: Gaussian Calculation
DOI: 10.14469/hpc/4830
title: 5Br2 + 2,4,6-tributylbenzene in CCl4, Reactant GD3BJ Def2-TZVPP

description: Gaussian Calculation
DOI: 10.5281/zenodo.1461710
title: The fatigue damage evolution in the load-carrying composite laminates of wind turbine blades

description: Video and data-set behind the figures used in the book chapter: Mikkelsen, LP, The fatigue Damage evolution in the load-carrying composite laminates of wind turbine blades, chapter 16 in “Fatigue life prediction of composites and composite structures”, Edited by A.P. Vassilopoulos, Second edition, Elsevier Ltd, To be published in 2019. https://doi.org/10.1016/B978-0-08-102575-8.00016-4. The files are organised based on the first characters in the filename with fist two numbers and than a "a" for video and "b,c.." for data behind that video. The video have the following link to the figures in the book chapter: Figure 16.19: 03a-Eps05-2-Zoom.mp4 , https://youtu.be/PynQ0IEyne8<br> Figure 16.21A: 01a-2Dprojection.avi , https://youtu.be/sr1J_5oc2EE<br> Figure 16.21B: 02a-Video 3D 360.mpg , https://youtu.be/riqtI6fARko<br> Figure 16.25: 11a-Eps05-2.mp4 , https://youtu.be/RJwfpiiLws0<br> Figure 16.28A: 21a-LFoVexsitu.mp4 , https://youtu.be/PmUWAI9qfMQ<br> Figure 16.28B: 22a-SFoV1G.mp4 , https://youtu.be/sFBgVyF1Bfw<br> Figure 16.29: 23a-SFoVGreen.mp4 , https://youtu.be/wJMV9bP5ntw<br> Figure 16.30: 24a-SFoVRed.mp4 , https://youtu.be/9m1Q0MrzJrY<br> Figure 16.31: 25a-RotatingSegmentedDamage.mpg , https://youtu.be/OHPkwwaTUSM<br> Figure 16.34: 31a-Stained.mpg , https://youtu.be/Sddg0sbzw6w<br> Figure 16.35: 41a-RLmovie.mpg , https://youtu.be/H7aZrIYjKeQ<br> Figure 16.36A: 51a-SFoV-Tension-Compression-T.mpg , https://youtu.be/AdsjDkq8QE8<br> Figure 16.36B: 52a-SFoV-Tension-Compression-W.mpg , https://youtu.be/ddSqQnW8jMo