cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.3945936
title: Volcano plot of Sigma B-dependent differential gene expression of Clostridioides difficile

description: A customized whole-genome DNA microarray of <em>Clostridioides difficile </em>630∆<em>erm</em> was used (8x15K format, Agilent). Quadruplicate samples were analysed for the DNA microarray. Using the ULS fluorescent labelling kit for Agilent arrays (Kreatech), 1 µg of total RNA was used for labelling with either Cy3 (P<sub>tet</sub>-<em>sigB</em>) or Cy5 (P<sub>tet</sub>-<em>sLuc<sup>opt</sup></em>). After pooling and fragmentation, 300 ng of labelled RNA per sample was hybridized according to the two-color microarray protocol from Agilent. DNA microarrays were scanned with an Agilent C scanner and analysed. CDS_ID=GenBank identifier, gene_name=annotated gene name (when available), locus_tag= locus tag, protein=annotation of protein function (when available), log2FC= log 2 of the fold change (sigB overproduction/control), adj_Pvalue = adjusted P-value, significance = -10log(adj_Pvalue).
DOI: 10.5281/zenodo.3945935
title: Volcano plot of Sigma B-dependent differential gene expression of Clostridioides difficile

description: A customized whole-genome DNA microarray of <em>Clostridioides difficile </em>630∆<em>erm</em> was used (8x15K format, Agilent). Quadruplicate samples were analysed for the DNA microarray. Using the ULS fluorescent labelling kit for Agilent arrays (Kreatech), 1 µg of total RNA was used for labelling with either Cy3 (P<sub>tet</sub>-<em>sigB</em>) or Cy5 (P<sub>tet</sub>-<em>sLuc<sup>opt</sup></em>). After pooling and fragmentation, 300 ng of labelled RNA per sample was hybridized according to the two-color microarray protocol from Agilent. DNA microarrays were scanned with an Agilent C scanner and analysed. CDS_ID=GenBank identifier, gene_name=annotated gene name (when available), locus_tag= locus tag, protein=annotation of protein function (when available), log2FC= log 2 of the fold change (sigB overproduction/control), adj_Pvalue = adjusted P-value, significance = -10log(adj_Pvalue).
DOI: 10.5281/zenodo.3945962
title: JGR atmosphere deposit

description: The data is used in the JGR Atmosphere paper.
DOI: 10.5281/zenodo.3945961
title: JGR atmosphere deposit

description: The data is used in the JGR Atmosphere paper.
DOI: 10.5281/zenodo.3945525
title: Low resolution scanned text dataset for optical character recognition

description: A collection of scanned pages of English text designed for testing low resolution OCR systems. There are 11 different pieces of text, each of which contains 5 pages of text. Each of these 55 pages is typeset in 18 different fonts and then scanned at 300 dpi, producing a total of 990 pages of scanned text. Downsampled 60 dpi and 75 dpi versions are included.
DOI: 10.5281/zenodo.3945524
title: Low resolution scanned text dataset for optical character recognition

description: A collection of scanned pages of English text designed for testing low resolution OCR systems. There are 11 different pieces of text, each of which contains 5 pages of text. Each of these 55 pages is typeset in 18 different fonts and then scanned at 300 dpi, producing a total of 990 pages of scanned text. Downsampled 60 dpi and 75 dpi versions are included.
DOI: 10.5281/zenodo.3945990
title: Data for "Cold surge pathways in East Asia and their tropical impacts"

description: This repository archives codes for analysis and plot presented in a manuscript submitted to Journal of Climate: "Cold surge pathways in East Asia and their tropical impacts". The codes are written in GrADS and Octave format. The repository also includes a Fortran package for isentropic polar cold air mass diagnosis as in Iwasaki et al. (2014). The package was specifically created by Dr. Y. Kanno.
DOI: 10.5281/zenodo.3945989
title: Data for "Cold surge pathways in East Asia and their tropical impacts"

description: This repository archives codes for analysis and plot presented in a manuscript submitted to Journal of Climate: "Cold surge pathways in East Asia and their tropical impacts". The codes are written in GrADS and Octave format. The repository also includes a Fortran package for isentropic polar cold air mass diagnosis as in Iwasaki et al. (2014). The package was specifically created by Dr. Y. Kanno.
DOI: 10.25345/c58b3k
title: MassIVE MSV000085757 - Mammalian telomeres reforged with non-telomeric sequences
title: Telomere is a highly refined system for maintaining the stability of linear chromosomes. Most telomeres rely on simple repetitive sequences and telomerase enzymes, but in some species or telomerase-defective situations, alternative telomere lengthening (ALT) mechanism is utilized to protect chromosomal ends. Telomere loss can induce telomere recombination by which specific sequences can be recruited into telomeres. However, canonical telomeric repeat-based telomeres have been found in mammals. Here, we show that mammalian telomeres can also be completely reconstituted using a non-telomeric unique sequence. We found that a specific subtelomeric element, named as mouse template for ALT (mTALT), is utilized for repairing telomeric DNA damage and composing new telomeric sequences in mouse embryonic stem cells. We found a high-level of non-coding mTALT transcript despite the heterochromatic nature of mTALT-based telomere. After ALT activation, the increased HMGN1, a non-histone chromosomal protein, contributed to maintaining telomere stability by regulating telomeric transcriptions. Our findings reveal novel molecular features of potential telomeric sequences which can reconstitute telomeres during cancer formation and evolution.
DOI: 10.5281/zenodo.3945949
title: Trained tesseract networks for low-resolution optical character recognition

description: Tesseract eng.traineddata files for low-resolution optical character recognition (English).
DOI: 10.5281/zenodo.3945948
title: Trained tesseract networks for low-resolution optical character recognition

description: Tesseract eng.traineddata files for low-resolution optical character recognition (English).
DOI: 10.5281/zenodo.3946044
title: ChemDBPublic

description: Data and scripts necessary to run the GUI of the reactor code
DOI: 10.5281/zenodo.3946043
title: ChemDBPublic

description: Data and scripts necessary to run the GUI of the reactor code
DOI: 10.21227/mrgx-rh96
title: Malaria dataset (thin blood smear, updated)

description: Malaria thin smear images. Five groups: parasitized, uninfected, bad segmentation, unsure, weird.nbsp;
DOI: 10.21227/77p0-d633
title: Malaria dataset (thin blood smear, updated)

description: Malaria thin smear images. Five groups: parasitized, uninfected, bad segmentation, unsure, weird.nbsp;
DOI: 10.5281/zenodo.3534568
title: Visual perception of liquids: insights from deep neural networks

description: Datasets and analysis code of the following publication: Van Assen, J.J.R., Nishida, S. & Fleming, R. W. (2020). Visual perception of liquids: insights from deep neural networks. <em>PLOS Computational Biology. </em>DOI: 10.1371/journal.pcbi.1008018 For any questions please contact the first author at mail [at] janjaap [dot] info <strong>Contents:</strong> 1. DataAnalysis<br> - Jupyter Notebook to run the full analysis in R<br> - For installation details see: https://irkernel.github.io/requirements/ 2. FullStimulusSet<br> - 2 million liquid images with 16 viscosities, 10 scenes, 625 variations, and 20 frames<br> - Matlab script that merges the images horizontally for network input 3. NeuralActivations<br> - Matlab files containing the neural activations if you cannot read out the networks 4. TrainedNetworks<br> - 100 Trained networks referred to in the paper using Matlab and the Deep Learning Toolbox<br> - One custom layer file “switchLayerAdvanced.m” 5. ValidationSet<br> - 800 experimental stimuli that were used for validation 16 viscosities, 10 scenes, 5 variations (1,6,11,16,21)<br> - Matlab script that merges the images horizontally for network input
DOI: 10.5281/zenodo.3534567
title: Visual perception of liquids: insights from deep neural networks

description: Datasets and analysis code of the following publication: Van Assen, J.J.R., Nishida, S. & Fleming, R. W. (2020). Visual perception of liquids: insights from deep neural networks. <em>PLOS Computational Biology. </em>DOI: 10.1371/journal.pcbi.1008018 For any questions please contact the first author at mail [at] janjaap [dot] info <strong>Contents:</strong> 1. DataAnalysis<br> - Jupyter Notebook to run the full analysis in R<br> - For installation details see: https://irkernel.github.io/requirements/ 2. FullStimulusSet<br> - 2 million liquid images with 16 viscosities, 10 scenes, 625 variations, and 20 frames<br> - Matlab script that merges the images horizontally for network input 3. NeuralActivations<br> - Matlab files containing the neural activations if you cannot read out the networks 4. TrainedNetworks<br> - 100 Trained networks referred to in the paper using Matlab and the Deep Learning Toolbox<br> - One custom layer file “switchLayerAdvanced.m” 5. ValidationSet<br> - 800 experimental stimuli that were used for validation 16 viscosities, 10 scenes, 5 variations (1,6,11,16,21)<br> - Matlab script that merges the images horizontally for network input
DOI: 10.15161/oar.it/30560
title: CovidStat project data

description: This record contains the daily updated data of the CovidStat project. CovidStat is a project carried out by the CovidStat Working Group at INFN, whose creation was promoted within the Italian National Institute of Nuclear Physics with the aim of making a statistical analysis of the data provided daily by the Civil Protection on the spread of the pandemic in Italy. CovidStat data can interactively be browsed at https://covid19.infn.it.
description: The software to process this Root TTree is in the related identifier. Be sure to use the right corresponding version, based on the data in which Root TTree was generated.
DOI: 10.5281/zenodo.3946057
title: The POLUSA Dataset: 0.9M Political News Articles Balanced by Time and Outlet Popularity

description: The POLUSA dataset, as presented at the ACM/IEEE Joint Conference on Digital Libraries in August 2020 (JCDL '20)
DOI: 10.5281/zenodo.3813663
title: The POLUSA Dataset: 0.9M Political News Articles Balanced by Time and Outlet Popularity

description: The POLUSA dataset, as presented at the ACM/IEEE Joint Conference on Digital Libraries in August 2020 (JCDL '20)
DOI: 10.5281/zenodo.3760480
title: Multiharmonic resonance control data

description: Data files presented in the paper: Alexander D. Shaw, Thomas L. Hill, Simon A. Neild, Michael I. Friswell, “Multi-harmonic Resonance Control Testing of an Internally Resonant Structure”, <em>Vibration</em>, MDPI, 2020.
DOI: 10.17898/adp_dv_pn4ntf/sgonyz
title: license.txt

description: :unav
DOI: 10.17898/adp_dv_pn4ntf
title: Test dataset

description: Test
DOI: 10.5281/zenodo.1432921
title: Verlage und Open Access. Ergebnisse einer Umfrage unter wissenschaftlichen Verlagen in Deutschland, Österreich und der Schweiz.

description: Im Rahmen einer Umfrage zum Thema „Verlage und Open Access“ kontaktierten wir im Mai/Juni 2018 82 wissenschaftliche Verlage in Deutschland, Österreich und der Schweiz, um einen Überblick über deren Einschätzungen bezüglich Open Access, über Erfahrungen, Angebote und Überlegungen zu erhalten. Ziel war es, die Positionen wissenschaftlicher Verlage besser kennen zu lernen und damit einen Beitrag zu einem besseren Austausch zwischen Verlagen, Bibliotheken und anderen Stakeholdern zu leisten. Dazu wurden in 33 Fragen die Nachfrage von AutorInnen bezüglich Open-Access-Angeboten, Herausforderungen und Chancen durch Open Access aus Verlagssicht und der Investitionsbedarf für eine Umstellung auf Open Access ebenso erhoben wie die Einstellung der Verlage zur Zweitveröffentlichung wissenschaftlicher Publikationen, Einschätzungen zu Entwicklungen im Bereich des wissenschaftlichen Publizierens und die mögliche zukünftige Rolle von Verlagen. In May and June 2018 we contacted 82 scholarly publishers in Germany, Austria and Switzerland for a survey on the subject of "Publishers and Open Access" in order to obtain an overview of their opionins on Open Access, their experiences, offers and considerations. Our aim was to find out more about the positions of scholarly publishers and thus contribute to a better exchange between publishers, libraries and other stakeholders. To this end, we asked 33 questions on the demand of authors for Open Access offers, the challenges and opportunities related to Open Access from the publishers' point of view and the investment requirements for a Transition to Open Access, as well as on the attitude of publishers to the self-archiving of scholarly publications, assessments of developments in the field of scholarly publishing and the possible future role of publishers.
DOI: 10.5281/zenodo.1432920
title: Verlage und Open Access. Ergebnisse einer Umfrage unter wissenschaftlichen Verlagen in Deutschland, Österreich und der Schweiz.

description: Im Rahmen einer Umfrage zum Thema „Verlage und Open Access“ kontaktierten wir im Mai/Juni 2018 82 wissenschaftliche Verlage in Deutschland, Österreich und der Schweiz, um einen Überblick über deren Einschätzungen bezüglich Open Access, über Erfahrungen, Angebote und Überlegungen zu erhalten. Ziel war es, die Positionen wissenschaftlicher Verlage besser kennen zu lernen und damit einen Beitrag zu einem besseren Austausch zwischen Verlagen, Bibliotheken und anderen Stakeholdern zu leisten. Dazu wurden in 33 Fragen die Nachfrage von AutorInnen bezüglich Open-Access-Angeboten, Herausforderungen und Chancen durch Open Access aus Verlagssicht und der Investitionsbedarf für eine Umstellung auf Open Access ebenso erhoben wie die Einstellung der Verlage zur Zweitveröffentlichung wissenschaftlicher Publikationen, Einschätzungen zu Entwicklungen im Bereich des wissenschaftlichen Publizierens und die mögliche zukünftige Rolle von Verlagen. In May and June 2018 we contacted 82 scholarly publishers in Germany, Austria and Switzerland for a survey on the subject of "Publishers and Open Access" in order to obtain an overview of their opionins on Open Access, their experiences, offers and considerations. Our aim was to find out more about the positions of scholarly publishers and thus contribute to a better exchange between publishers, libraries and other stakeholders. To this end, we asked 33 questions on the demand of authors for Open Access offers, the challenges and opportunities related to Open Access from the publishers' point of view and the investment requirements for a Transition to Open Access, as well as on the attitude of publishers to the self-archiving of scholarly publications, assessments of developments in the field of scholarly publishing and the possible future role of publishers.
DOI: 10.5281/zenodo.3837625
title: Integrative modeling results of in-cell architecture of an actively transcribing-translating expressome

description: Repository containing good-scoring models, input files, modeling and analysis protocols for the integrative modeling of the M. pneumoniae expressome from in-cell cryo-electron tomography and crosslinking mass spectrometry using IMP.
DOI: 10.5281/zenodo.3829334
title: Integrative modeling results of in-cell architecture of an actively transcribing-translating expressome

description: Repository containing good-scoring models, input files, modeling and analysis protocols for the integrative modeling of the M. pneumoniae expressome from in-cell cryo-electron tomography and crosslinking mass spectrometry using IMP.
DOI: 10.14469/hpc/3261
title: NH4 radical, Wiberg bond index on N 2.8198, on H 0.8365. Rydberg population 0.36421.

description: Gaussian Calculation
DOI: 10.18739/a26g4c
title: Effect of grazing, trampling, and fecal deposition on vegetation and soil nutrients
DOI: 10.3886/icpsr36815.v1
title: Newly Licensed Registered Nurse Survey, 2013
title: Version 1

description: This is the fifth wave of a multi wave panel survey that studied newly licensed registered nurses who obtained their first license to practice between September 1, 2004 and August 31, 2005. It was conducted as part of the RN Work Project, a national study of new nurses funded by the Robert Wood Johnson Foundation. The survey interviewed the nurses about their jobs, turnover, intentions and attitudes--including intent, satisfaction, organizational commitment, and preferences about work.
description: ICPSR data undergo a confidentiality review and are altered when necessary to limit the risk of disclosure. ICPSR also routinely creates ready-to-go data files along with setups in the major statistical software formats as well as standard codebooks to accompany the data. In addition to these procedures, ICPSR performed the following processing steps for this data collection: Checked for undocumented or out-of-range codes..
description: Response Rates: 67 percent of nurses contacted for wave 5 returned a completed survey.
description: Datasets: DS1: Dataset
description: Newly Licensed Registered Nurse Survey Series
description: mail questionnaire
description: Nurses who responded to the third wave of the study.
description: The wave 5 survey attempted to interview all of the nurses who responded to the wave 3 survey: Newly Licensed Registered Nurse Survey, 2009 (ICPSR 36813).
DOI: 10.5063/f1639mvd
title: The National Eutrophication Survey: lake characteristics and historical nutrient concentrations

description: Historical ecological surveys are an important source of baseline information to provide context for contemporary research, yet many of these records are not preserved in a way to ensure their long-term usability. The National Eutrophication Survey database is currently only available as portable document files (PDF) scanned from printed records with no embedded character information. This limits its searchability and the ability of current and future scientists to systematically evaluate its contents. The data was collected by the United States Environmental Protection Agency between 1972 and 1975, as part of an effort to investigate eutrophication in freshwater lakes and reservoirs. Although several studies have hand-transcribed portions of the database in support of specific studies, there have been no systematic attempts to transcribe and preserve the database in its entirety. Here we use a combination of automated optical character recognition and manual quality assurance to make this data available for analysis. The performance of the optical character recognition procedure was highly variable depending on scan quality. For each of the four archival pdf files, we found an error rate of between 5.9 and 17%. The goal of our approach was to strike a balance efficiency and data quality by combining hand-entry of data with digital transcription technologies. The finished database contains information on the physical characteristics, hydrology, and water quality of about 800 lakes in the continental United States. This database could be combined with more recent data to generate meta analyses of water quality trends and spatial variation across the continental United States.
DOI: 10.5066/f7ng4nvx
title: Water Quality Data for Bushy Park Reservoir, South Carolina 2013-2015

description: Water-quality data for the Bushy Park Reservoir near Goose Creek, South Carolina, from September 2013 to May 2015. Data includes the chemical, physical, and biological properties that influence (1) geosmin and 2-methyisobornel (MIB) occurrence in this source-water reservoir, (2) cyanobacterial biovolumes, and (3) geosmin-producing and toxin-producing genera of cyanobacteria. Data Release for USGS SIR entitled "Characterization of the Water Quality of Bushy Park Reservoir, South Carolina 2013-2015".
DOI: 10.18739/a2b54h
title: Forage quality and community composition of a slightly brackish wet sedge meadow, Yukon-Kuskokwim, Delta, Alaska, 2015-2016
DOI: 10.5063/f12b8w5j
title: Projected loss of maritime forest in North Carolina, 2010 - 2050

description: These data represent the projected loss of maritime forest in North Carolina based on state-transition models for decadal time steps from 2010 - 2050.
DOI: 10.5281/zenodo.1048268
title: Database for mi-faser: Functional sequencing read annotation for high precision microbiome analysis

description: <strong>[Database for mi-faser]</strong> <strong>mi-faser: </strong><em>microbiome - functional annotation of sequencing reads</em> A super-fast ( &lt; 20min/10GB of reads ) and accurate ( &gt; 90% precision ) method for annotation of molecular functionality encoded in sequencing read data without the need for assembly or gene finding. Web Service: http://services.bromberglab.org/mifaser/|<br> Repository: https://bitbucket.org/bromberglab/mifaser_base/
DOI: 10.5281/zenodo.1049136
title: Mars surface image (Curiosity rover) labeled data set

description: This data set consists of 6691 images spanning 24 classes that were collected by the Mars Science Laboratory (MSL, Curosity) rover by three instruments (Mastcam Right eye, Mastcam Left eye, and MAHLI). These images are the "browse" version of each original data product, not full resolution. They are roughly 256x256 pixels each. We divided the MSL images into train, validation, and test data sets according to their sol (Martian day) of acquisition. This strategy was chosen to model how the system will be used operationally with an image archive that grows over time. The images were collected from sols 3 to 1060 (August 2012 to July 2015). The exact train/validation/test splits are given in individual files. Full-size images can be obtained from the PDS at https://pds-imaging.jpl.nasa.gov/search/ . <strong>Contents</strong>: calibrated/: Directory containing calibrated MSL images train-calibrated-shuffled.txt: Training labels (images in shuffled order) val-calibrated-shuffled.txt: Validation labels test-calibrated-shuffled.txt: Test labels msl_synset_words-indexed.txt: Mapping from class IDs to class names <strong>Attribution</strong>: If you use this data set in your own work, please cite this DOI: 10.5281/zenodo.1049137 Please also cite this paper, which provides additional details about the data set. Kiri L. Wagstaff, You Lu, Alice Stanboli, Kevin Grimes, Thamme Gowda, and Jordan Padams. "Deep Mars: CNN Classification of Mars Imagery for the PDS Imaging Atlas." <em>Proceedings of the Thirtieth Annual Conference on Innovative Applications of Artificial Intelligence</em>, 2018.
description: {"references": ["Kiri L. Wagstaff, You Lu, Alice Stanboli, Kevin Grimes, Thamme Gowda, and Jordan Padams. \"Deep Mars: CNN Classification of Mars Imagery for the PDS Imaging Atlas.\" Proceedings of the Thirtieth Annual Conference on Innovative Applications of Artificial Intelligence, 2018."]}