cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10598900
title: NFDI4Ing Community Survey 2023

description: NFDI4Ing Community Survey 2023

Questionnaire and anonymised raw data (results)

Duration of the survey: 27.09.2023-22.12.2023

Topics: 



Research Data Management (RDM): Knowledge and application

Research Data Management (RDM): Need for services and support

Research Data Management (RDM): Data and Software

Research Data Management (RDM): Work Flow and Strategy

Research Data Management (RDM): Governance concepts in the Engineering Sciences

Socio-economic information
description: The authors would like to thank the Federal Government and the Heads of Government of the Länder, as well as the Joint Science Conference (GWK), for their initiative within the framework of the NFDI4Ing consortium (German Research Foundation (DFG) - project number 442146713)
DOI: 10.5281/zenodo.10598959
title: Fostering Open and Distributed Design in Early Design Education The Case of IPL - Dataset 1 - Anonimyzed Survey Responses - Abstracts and DD qual/quant Evaluation

description: "DatasetSurvey1ProjectsCollection.xlsx" is the anonymized data collected through a survey where students (81) were invited to analyze past and present projects, produce an abstract (1000 words max) about it and quantively score and qualitatively justify the alignment of the project with Distributed Design Values and Principles. (distributeddesign.eu/about);R-script generated files:"DatasetSurvey1ProjectsCollection.xlsx" is the first layer of automated analysis, counts keywords in EN abstracts scoring them for each DD value and Production Paradigm and for their overall score;"votesCuration.xlsx" presents second survey results where students voted for the projects in two categories DD and Exhibition impact;"Comprehensive_Projects_Analysis.txt" associates the highest scoring projects with the given PT justification so we can check the alignment. Also lists the second survey results, allowing quick reading and cross-checking information.
DOI: 10.5281/zenodo.10598960
title: Fostering Open and Distributed Design in Early Design Education The Case of IPL - Dataset 1 - Anonimyzed Survey Responses - Abstracts and DD qual/quant Evaluation

description: "DatasetSurvey1ProjectsCollection.xlsx" is the anonymized data collected through a survey where students (81) were invited to analyze past and present projects, produce an abstract (1000 words max) about it and quantively score and qualitatively justify the alignment of the project with Distributed Design Values and Principles. (distributeddesign.eu/about);R-script generated files:"DatasetSurvey1ProjectsCollection.xlsx" is the first layer of automated analysis, counts keywords in EN abstracts scoring them for each DD value and Production Paradigm and for their overall score;"votesCuration.xlsx" presents second survey results where students voted for the projects in two categories DD and Exhibition impact;"Comprehensive_Projects_Analysis.txt" associates the highest scoring projects with the given PT justification so we can check the alignment. Also lists the second survey results, allowing quick reading and cross-checking information.
DOI: 10.13140/rg.2.2.31392.56322
title: Implementación de actividades docentes virtuales en la facultad de Ciencias Médicas Miguel Enríquez
DOI: 10.5519/qd.qpbndmu5
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.5281/zenodo.7568726
title: ddRAD-seq  generated genomic SNP dataset of Central and Southeast European Turkey oak (Quercus cerris L.) populations

description: Turkey oak (Quercus cerris L.) is one of the most ecologically and economically significant deciduous tree species in the Central and Southeast European regions. The species has long been known to exhibit high levels of genetic and phenotypic variation. Recent climate response predictions for Turkey oak suggest a significant distribution extension in Europe under climate change. Since Turkey oak has relative drought-tolerant behavior, it is regarded as a potential alternative for other forest tree species during forestry climate adaptation efforts, not only in its native regions but also in Western Europe. For this reason, the survey of existing genetic variability, genetic resources, and adaptability of this species has great significance. Next-generation sequencing approaches, such as ddRAD-seq (Double digest restriction-site associated DNA sequencing), allow the attainment of high-resolution genome-wide simple nucleotide polymorphisms (SNPs). This study provides the first highly variable genome-wide SNP data for Turkey oak generated by ddRAD-seq. The dataset comprises 17 607 de novo and 26 059 reference-mapped SNPs for 88 individuals from eight populations, two from Bulgaria, one from Kosovo, and five from Hungary. Reference mapping was carried out by using cork oak’s reference genome. The obtained high-resolution genome-wide markers are suitable for investigating selection and local adaptation and inferring genetic diversity, differentiation, and population structure. The dataset is accessible at: https://doi.org/10.5281/zenodo.8091252
DOI: 10.5281/zenodo.7568727
title: ddRAD-seq generated genomic SNP dataset of Central and Southeast European Turkey oak (Quercus cerris L.) populations

description: Turkey oak (<em>Quercus cerris</em> L.) is one of the ecologically and economically most important deciduous tree species in the Central and Southeast European regions. The species distribution range covers hundreds of thousands of hectares throughout the Apennine and Balkan Peninsula, the Carpathian Basin to Asia Minor. Turkey oak has long been known exhibit high levels of genetic and phenotypic variation. Recent predictions on climate responses of this species suggest a significant extension of its distribution in Europe under climate change. Since Turkey oak has relative drought-tolerant behavior, it is regarded as a potential alternative for other forest tree species during forestry climate adaptation efforts, not only in its native regions but in Western Europe as well. For this reason, the survey of existing genetic variability, genetic resources and adaptability of this species has great importance. Next-generation sequencing approaches, such as ddRAD-seq (Double digest restriction-site associated DNA sequencing), allow for obtaining high-resolution genome-wide simple nucleotide polymorphisms (SNPs). Based on thousands of SNP markers the genetic structure of populations and the genetic background of adaptation processes can be studied in far more depth than ever before. In this study, we provide highly variable genome-wide SNP data belonging to Turkey oak for the first time. This dataset comprises the SNP data of 88 individuals of eight populations, two from Bulgaria, one from Kosovo and five from Hungary, respectively. The high-resolution genome-wide markers are suitable to infer genetic diversity, differentiation, population structure and to investigate selection and local adaptation. The dataset accessible at: https://doi.org/10.5281/zenodo.7568727
DOI: 10.5281/zenodo.8091252
title: ddRAD-seq  generated genomic SNP dataset of Central and Southeast European Turkey oak (Quercus cerris L.) populations

description: Turkey oak (Quercus cerris L.) is one of the most ecologically and economically significant deciduous tree species in the Central and Southeast European regions. The species has long been known to exhibit high levels of genetic and phenotypic variation. Recent climate response predictions for Turkey oak suggest a significant distribution extension in Europe under climate change. Since Turkey oak has relative drought-tolerant behavior, it is regarded as a potential alternative for other forest tree species during forestry climate adaptation efforts, not only in its native regions but also in Western Europe. For this reason, the survey of existing genetic variability, genetic resources, and adaptability of this species has great significance. Next-generation sequencing approaches, such as ddRAD-seq (Double digest restriction-site associated DNA sequencing), allow the attainment of high-resolution genome-wide simple nucleotide polymorphisms (SNPs). This study provides the first highly variable genome-wide SNP data for Turkey oak generated by ddRAD-seq. The dataset comprises 17 607 de novo and 26 059 reference-mapped SNPs for 88 individuals from eight populations, two from Bulgaria, one from Kosovo, and five from Hungary. Reference mapping was carried out by using cork oak’s reference genome. The obtained high-resolution genome-wide markers are suitable for investigating selection and local adaptation and inferring genetic diversity, differentiation, and population structure. The dataset is accessible at: https://doi.org/10.5281/zenodo.8091252
DOI: 10.15131/shef.data.21830094.v3
title: Near-field Multislice Ptychography

description: This folder includes all near-field multi-slice ptychography data for both optical bench experiment and x-ray experiment appeared in this paper.
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An example ThreePIE* MATLAB code of the multislice ptychography for use with data collected in a near-field cone beam experiment is attached. 
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* academic license agreement attached for none-commercial use only.
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DOI: 10.15131/shef.data.21830094
title: Near-field Multislice Ptychography

description: This folder includes all near-field multi-slice ptychography data for both optical bench experiment and x-ray experiment which appeared in this paper.
<br>
An example ThreePIE MATLAB code of the multislice ptychography for use with data collected in a near-field cone beam experiment is attached. 
[note non-commercial licence]
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Ptychography is a form of lens-free coherent diffractive imaging now used extensively in electron and synchrotron-based X-ray microscopy. In its near-field implementation, it offers a route to quantitative phase imaging at an accuracy and resolution competitive with holography, with the added advantages of extended field of view and blind deconvolution of the illumination beam profile from the sample image. In this paper we show how near-field ptychography can be combined with a multi-slice model, adding to this list of advantages the unique ability to recover high-resolution phase images of larger samples, whose thickness places them beyond the depth of field of alternative methods.
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DOI: 10.15131/shef.data.21830094.v4
title: Near-field Multislice Ptychography

description: This folder includes all near-field multi-slice ptychography data for both optical bench experiment and x-ray experiment which appeared in this paper.
<br>
An example ThreePIE MATLAB code of the multislice ptychography for use with data collected in a near-field cone beam experiment is attached. 
[note non-commercial licence]
<br>
Ptychography is a form of lens-free coherent diffractive imaging now used extensively in electron and synchrotron-based X-ray microscopy. In its near-field implementation, it offers a route to quantitative phase imaging at an accuracy and resolution competitive with holography, with the added advantages of extended field of view and blind deconvolution of the illumination beam profile from the sample image. In this paper we show how near-field ptychography can be combined with a multi-slice model, adding to this list of advantages the unique ability to recover high-resolution phase images of larger samples, whose thickness places them beyond the depth of field of alternative methods.
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DOI: 10.5281/zenodo.10599102
title: Connectivity matrix of the internal connectivity of an earlier version of an SSCX model

description: This is a simplified view of the internal synaptic connectivity of the model described in Reconstruction and Simulation of Neocortical Microcircuitry.

While in this view a lot of data is lost compared to the detailed representation in the raw model (such as the pre- and postsynaptic locations of synaptic contacts and their physiology), it can still be used for structural connectomics analyses.

Note that this is the connectivity of the model described in the 2015 publication linked above. The connectivity of the new, improved model described in our preprint Modeling and Simulation of Rat Non-Barrel Somatosensory Cortex. Part I: Modeling Anatomy can be found here.

The data is in a format that can be loaded using our Connectome_Utilities package.
DOI: 10.6084/m9.figshare.25117844
title: Supplementary Material for: The incidence of necrotizing enterocolitis and late-onset sepsis during the COVID-19 pandemic in Sweden: A population-based cohort study

description: Introduction: The effect of the pandemic restrictions in the NICUs is not well studied. Necrotizing enterocolitis (NEC) is characterized by intestinal inflammation and bacterial invasion. This study aimed to investigate whether the incidence of NEC has changed during the COVID-19 pandemic in Sweden and whether it was associated with a change in the frequency of extremely preterm births.
Methods: Data were retrieved from the Swedish Neonatal Quality Register (SNQ) for infants registered between January 2017 and December 2021 born below a gestational age of 35 weeks. The registry completeness is 98-99%. The diagnosis of NEC was the primary outcome. Generalized linear model analysis was used to calculate the risk ratio for NEC.
Results: Totally 13239 infants were included. 235 (1.8%) infants developed NEC, out of which 91 required surgical treatment. 8967 infants were born before COVID-19 pandemic and 4272 during. Median gestational age at birth was 32.8 weeks in both periods. The incidence of NEC was significantly lower during COVID-19 pandemic compared to the prior period (1.43% vs 1.94% p 0.037), but not the incidence of surgical NEC. The crude Risk ratio of developing NEC during COVID-19 pandemic was 0.74 (95% CI(0.55-0.98)). The incidence of Late onset sepsis with positive culture was also declined during COVID-19 (3.21% vs 4.15%, p value 0.008).
Conclusion: While we found significant reduction in the incidence of NEC and culture-positive late-onset sepsis during the COVID-19 pandemic, the number of extremely preterm births was unchanged.
DOI: 10.6084/m9.figshare.24312292.v4
title: feature-representation-for-LLMs

description: This is a database for feature representation of ESM2, which includes Swiss data, Swiss normalized data, original TrEMBL data, original TrEMBL normalized data, non-homology TrEMBL data and Table S10.Non-homologous TrEMBL normalized data can be created by extracting Entry ID from the non-homologous TrEMBL data and then extracting the corresponding feature representation from the original TrEMBL normalized data.Figure S4 (eos) and Figure S5 (eos) are supplement for the Histogram plots and Scatter plots of feature eos in corresponding Figure S4 and Figure S5.Figure S6 and Figure S8 are the results of GO annotation enrichment. The GO gene set is a grouped protein dataset used for GO annotation enrichment.Figure S7 is a silhouette score plot.For specific usage of the dataset, please refer to Github.
DOI: 10.5281/zenodo.10514299
title: Data and code for "Nominally identical microplastic models differ greatly in their particle-cell interactions"

description: This dataset provides the data and code for the study “Nominally identical microplastic models differ greatly in their particle-cell interactions”. Due to the size of the raw data, they were deposited only for one particle type (PX). With these files, it is possible to run all code and follow the evaluation procedure. The complete set of raw data, which is about 575 GB in size (compressed), can be obtained from the corresponding authors upon request. Holger Kress: holger.kress@uni-bayreuth.de, Christian Laforsch: christian.laforsch@uni-bayreuth.de.
DOI: 10.5281/zenodo.10514300
title: Data and code for "Nominally identical microplastic models differ greatly in their particle-cell interactions"

description: This dataset provides the data and code for the study “Nominally identical microplastic models differ greatly in their particle-cell interactions”. Due to the size of the raw data, they were deposited only for one particle type (PX). With these files, it is possible to run all code and follow the evaluation procedure. The complete set of raw data, which is about 575 GB in size (compressed), can be obtained from the corresponding authors upon request. Holger Kress: holger.kress@uni-bayreuth.de, Christian Laforsch: christian.laforsch@uni-bayreuth.de.
DOI: 10.4121/26980373-90c2-4388-b475-40eb5c0a6072
title: Testimonies of Experiences with AAC technologies and empathy

description: This dataset contains a summary of collected testimonies of experiences of AAC technology users related to empathy, as part of Caroline Bollen’s PhD thesis project. It is being made public to act as supplementary data for publications and the PhD thesis "Empathy 2.0: What it means to be empathetic in a diverse and digital world".
DOI: 10.4121/26980373-90c2-4388-b475-40eb5c0a6072.v1
title: Testimonies of Experiences with AAC technologies and empathy

description: This dataset contains a summary of collected testimonies of experiences of AAC technology users related to empathy, as part of Caroline Bollen’s PhD thesis project. It is being made public to act as supplementary data for publications and the PhD thesis "Empathy 2.0: What it means to be empathetic in a diverse and digital world".
DOI: 10.34740/kaggle/dsv/7520430
title: Global Genomic Neurofibromatosis Neoplasia
DOI: 10.6084/m9.figshare.25117862
title: DeSide_model

description: A pre-trained deep learning model for cellular deconvolution.whole_workflow_20231110_12ds_subtypes/DeSide_03_new_ds_subtypes_all_range/Mixed_N100K_segment_filtered-Mixed_N100K_segment_without_filtering
DOI: 10.6084/m9.figshare.25117862.v1
title: DeSide_model

description: A pre-trained deep learning model for cellular deconvolution.whole_workflow_20231110_12ds_subtypes/DeSide_03_new_ds_subtypes_all_range/Mixed_N100K_segment_filtered-Mixed_N100K_segment_without_filtering
DOI: 10.6084/m9.figshare.24500212
title: Data and models for Plant mixture models

description: testing_dataset.zip: the testing dataset.training_dataset.zip: the training dataset.QPlant.mix.zip: the new proposed QPlant.mix mixture models.nQPlant.mix.zip: the new proposed nQPlant.mix mixture models.script_QPlant.mix.zip: the script to estimate reversible mixture model QPlant.mixscript_nQPlant.mix.zip: the script to estimate non reversible mixture model nQPlant.mix
DOI: 10.6084/m9.figshare.24500212.v4
title: Data and models for Plant mixture models

description: testing_dataset.zip: the testing dataset.training_dataset.zip: the training dataset.QPlant.mix.zip: the new proposed QPlant.mix mixture models.nQPlant.mix.zip: the new proposed nQPlant.mix mixture models.script_QPlant.mix.zip: the script to estimate reversible mixture model QPlant.mixscript_nQPlant.mix.zip: the script to estimate non reversible mixture model nQPlant.mix
DOI: 10.6084/m9.figshare.24500212.v3
title: Data and models for Plant mixture models

description: testing_dataset.zip: the testing dataset.training_dataset.zip: the training dataset.matrices_pca.zip: the matrices for PCA.rev_plant.tar.gz: the script to estimate reversible mixture modelnrev_plant.tar.gz: the scripts to estimate non-reversible mixture model
DOI: 10.5281/zenodo.10598846
title: Sverdlovsk UFSIN News Crawl Pt.2

description: WARC files produced by a webcrawl of Sverdlovsk UFSIN news online resource. WARC reader is necessary to view files.
DOI: 10.5281/zenodo.10598847
title: Sverdlovsk UFSIN News Crawl Pt.2

description: WARC files produced by a webcrawl of Sverdlovsk UFSIN news online resource. WARC reader is necessary to view files.
DOI: 10.25625/ngg0q7
title: Radiometric Dates from the South American Andes and Adjacent Areas: A Compilation

description: A compilation of published radiometric dates for igneous, metamorphic, and sedimentary rocks from the South American Andes and adjacent parts of South America have been tabulated for access by researchers via GEOROC. The compilations exist as three distinct spreadsheets for access via MS Excel, Google Sheets, and other spreadsheet applications. Initial igneous compilations were utilized in two publications by the author, Pilger (1981, 1984), The compilations have been added to in subsequent years with the metamorphic and sedimentary compilations separated in the last few years. Locations in latitude and longitude are largely taken from the original source, if provided, with UTM locations maintained and converted; in some cases, sample locations were digitized from electronic maps if coordinates were otherwise not available. Analytical results are not included to prevent the files from becoming too large. The existing compilation incorporates compilations by other workers in smaller regions of the Andes. References to original and compilation sources are included. While I am updating reconstructions of the South American and Nazca/Farallon plates, incorporating recent studies in the three oceans, for comparison with the igneous dates for the past 80 m. y., it is hoped that the spreadsheets will be of value to other workers.
DOI: 10.6084/m9.figshare.25117520.v1
title: Annotated results of <i>Pampus argenteus</i> genome Item

description: we provide the annotation results of gene structure, functional prediction for the de novo assembled genome of Pampus argenteus.
DOI: 10.5281/zenodo.10589796
title: Selfish herd effects in aggregated caterpillars and their interaction with warning signals

description: Dataset and R script used to analyse data.
DOI: 10.5281/zenodo.10589797
title: Selfish herd effects in aggregated caterpillars and their interaction with warning signals

description: Dataset and R script used to analyse data.
DOI: 10.5281/zenodo.10599414
title: Selfish herd effects in aggregated caterpillars and their interaction with warning signals

description: Dataset and R script used to analyse data.
DOI: 10.5281/zenodo.10555908
title: Data from: Evaluation of depth perception in crowded volumes
DOI: 10.5281/zenodo.10555909
title: Data from: Evaluation of depth perception in crowded volumes
DOI: 10.6084/m9.figshare.25111610
title: GDP per capita levels for regions and countries in Europe and North America, 1300-2000

description: We publish our out-of-sample estimates on historical GDP per capita levels between the years 1300 and 2000 together with the collected source data on countries and regions in a comprehensive dataset comprising 5,690 observations (1,313 source data observations, and 4,377 out-of-sample estimates). All references to the source data are provided in the manuscript.Locations refer to NUTS-2 regions in Europe (2021 edition), metro- and micropolitan statistical areas for the United States, metropolitan areas for Canada, and regions of similar size for other countries, e.g. oblasts in Russia. For countries, we use ISO 3166-1 alpha-3 country codes.The column <i>GDPpc</i> is denoted in 2011 USD PPP, matching the unit provided in the Maddison project. The column <i>flag</i> describes whether the value in column <i>GDPpc</i> is taken from source data (see manuscript for references) or an out-of-sample estimate. If it is an out-of-sample estimate, the columns <i>GDPpc_lower</i> and <i>GDPpc_upper</i> provide 90 percent confidence intervals obtained by bootstrapping.The code to generate all estimates will be published soon to ensure reproducibility of results.