cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22280884
title: Meyer et al. 2023. Cell Host & Microbe. Conspecific versus heterospecific transmission shapes host specialization of the phyllosphere microbiome. https://doi.org/10.1016/j.chom.2023.11.002

description: These are the data from Meyer et al. 2023. Cell Host & Microbe. Conspecific versus heterospecific transmission of bacteria between plants shapes host specialization of the phyllosphere microbiome. Please cite the paper when using these data. Article DOI: https://doi.org/10.1016/j.chom.2023.11.002There are four main experiments designed to test the effects of microbiome transmission between the same host species (conspecific) vs between different host species (heterospecific). These are 1) the main passaging experiment, in which microbiomes were passaged for 6 experimental month-long passages, 2) the specialization assay (aka follow-up 2) where microbiomes were competed using community coalescence, 3) the generalism common garden experiment (aka follow-up 1), where microbiomes were inoculated onto novel host plants, and 4) RNAseq of the specialization experiment, to test whether host specialization of microbiomes influences differential gene expression in the leaf tissue of the recipient host species.Included are raw genetic sequences of the V5-V7 region of the bacterial 16S rRNA gene derived from experimental leaf surfaces of tomato, Solanum pimpinellifolium, pepper, bean, canola, sorghum, and corn plants.Included in this archive are:Raw sequence data (RawFASTQ_PassagingFollow1.zip, RawFASTQ_PassagingFollow2.zip)Reproducible R script (MeyerEtAl2023.R)R objects corresponding to script MeyerEtAl2023.R (.RDS)Data for generating certain plots (PermanovaRValues_Passaging_edit_noT.txt)Sample metadata (SampleInfoPassagingAndFollowup1_edit.txt, MetaDataPassagingFollow2, RNAseqMetaData) corresponding to MeyerEtAl2023.RPhylogenetic Tree file for sample ASVs (PhyloTreePassaging.tre)Plant health and fitness data (FruitFlowerTimeSeriesFollow2.txt, PassagingFollow2TomatoData)ddPCR (microbial abundance) data (R_CFU_HarvestvInoculum.csv)R script for rarefication function (Rarefy_mean.R) and read tree function (read.newick.R)RNAseq concatanated gene counts (Raw RNAseq fastq files available at NCBI BioProject database, Project ID: PRJNA1012508)Individual ASV tables for differential ASV abundance analysis in MeyerEtAl2023.R (data-to-send.zip)
DOI: 10.6073/pasta/f7b91f19e0aa77534ac8e809196fde43
title: Heliconia invertebrate counts

description: Identification and number of invertebrates recovered from each Heliconia inflorescence sampled. Support for this work was provided by grants BSR-8811902, DEB-9411973, DEB-9705814 , DEB-0080538, DEB-0218039 , DEB-0620910 , DEB-1239764, DEB-1546686, and DEB-1831952 from the National Science Foundation to the University of Puerto Rico as part of the Luquillo Long-Term Ecological Research Program. Additional support provided by the University of Puerto Rico and the International Institute of Tropical Forestry, USDA Forest Service.
DOI: 10.6073/pasta/30971db3591bd258e91d3eba50472487
title: Bromeliad invertebrate counts at different elevations in the LEF

description: Identification and number of invertebrates recovered from each bromeliad sampled. Collection details of bromeliads collected for invertebrate community and diversity analysis from 3 localities in the Luquillo Experimental Forest. Dates, elevations and forest types, plant size, amounts, pH and temp. of contained water, weights of debris retained by the bromeliads, and counts of organisms, identified to species or morphospecies, collected from each plant. Support for this work was provided by grants BSR-8811902, DEB-9411973, DEB-9705814 , DEB-0080538, DEB-0218039 , DEB-0620910 , DEB-1239764, DEB-1546686, and DEB-1831952 from the National Science Foundation to the University of Puerto Rico as part of the Luquillo Long-Term Ecological Research Program. Additional support provided by the University of Puerto Rico and the International Institute of Tropical Forestry, USDA Forest Service.
DOI: 10.21227/9tr1-q453
title: Noise based in speckle

description: This synthetic dataset or phantom consists of 3 jpg format databases, in the two-dimensional (2-D) domain, which are identified as follows: DB1: Ground Truth DB2: Speckle noise with zero mean and 0.005 standard deviation DB3: Speckle noise with zero mean and 0.05 standard deviation Considering a real cardiac CT database, images with information about both the left ventricular cavity (LVC) and the left ventricle wall (LVW) were selected. Then, the gray levels from these images were used to construct each of the aforementioned databases. This real database was acquired with a GE Bright Speed Elite 16-slice scanner and was donated by the Laboratory of Traitement signal et de l’image, belonging to Rennes I University, France.Thus, to generate all synthetic DBs, specific gray levels were considered, and the myocardium and LV wall was simulated by an inner cone and an outer cone, respectively. The spatial resolution of both cones was 256 × 256 × 50 voxels. The value 256 is equivalent to 50% of the spatial dimension of a typical cardiac tomography layer, whereas the value 50 corresponds to approximately 20% of the number of layers of the actual data analyzed.All the databases were built in a set of concentric circular circles or layers, which were conditioned to contain densitometric information obtained by considering the average gray levels (GL) exhibited by a real cardiac computed tomography database (CT_DB). To introduce in the databases the information related to the GLs, each of the generated circular layers was processed with a filling technique based on a region growing algorithm
DOI: 10.34740/kaggle/ds/4013785
title: eBay iPhone📱 Pricing Trends 2023
DOI: 10.6073/pasta/3b5b7ce66065538db9a5aa9ae5977e89
title: Recovery of a tropical stream after a harvest-related chlorine poisoning event

description: 1. Harvest-related poisoning events are common in tropical streams, yet research on stream recovery has largely been limited to temperate streams and generally does not include any measures of ecosystem function, such as leaf breakdown. 2. We assessed recovery of a second-order, high-gradient stream draining the Luquillo Experimental Forest, Puerto Rico, three months after a chlorine-bleach poisoning event. The illegal poisoning of freshwater shrimps for harvest caused massive mortality of shrimps and dramatic changes in those ecosystem properties influenced by shrimps. We determined recovery potential using an established recovery index and assessed actual recovery by examining whether the poisoned reach returned to conditions resembling an undisturbed upstream reference reach.3. Recovery potential was excellent (score=729 out of a possible 729) and can be attributed to nearby sources of organisms for colonization, the mobility of dominant organisms, unimpaired habitat, rapid flushing and processing of chlorine, and location within a national forest.4. Actual recovery was substantial. Comparison of the reference reach with the formerly poisoned reach indicated: (1) complete recovery of xiphocaridid and palaemonid shrimp population abundances, shrimp size distributions, leaf breakdown rates, and abundances of oligochaetes and mayflies on leaves, and (2) only small differences in atyid shrimp abundance and community and ecosystem properties influenced by atyid shrimps (standing stocks of epilithic fine inorganic and organic matter, chlorophyll a, and abundances of chironomids and copepods on leaves). 5. There was no detectable pattern between any measured variables and distance downstream from the poisoning. However, shrimp size-distributions indicated that the observed recovery may represent a source-sink dynamic, in which the poisoned reach acts as a sink which depletes adult shrimp populations from surrounding undisturbed habitats. Thus, the rapid recovery observed in this study is consistent with results from other field studies of pulse chlorine disturbances, harvest-related fish poisonings, and recovery of freshwater biotic interactions, but it is unlikely to be sustainable if multiple poisonings deplete adult populations to the extent that juvenile recruitment does not offset adult shrimp mortality.
DOI: 10.5517/ccdc.csd.cc2c930t
title: CCDC 2183485: Experimental Crystal Structure Determination

description: Related Article: Chenglong Feng|2023|CSD Communication|||
description: Related Article: Chenglong Feng, Xin Liu, Yuanbin She, Zhenlu Shen, Meichao Li|2023|Chin.Chem.Lett.|34|107935|doi:10.1016/j.cclet.2022.107935
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: 10.5517/ccdc.csd.cc2cp069
title: CCDC 2194930: Experimental Crystal Structure Determination

description: Related Article: Weidong Zhang, Juanfang Zhou, Chao Zhang, Xinliang Liu|2023|New J.Chem.|47|20510|doi:10.1039/D3NJ04283A
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: 10.5517/ccdc.csd.cc2cmg2k
title: CCDC 2193438: Experimental Crystal Structure Determination

description: Related Article: Mahsa Pooyan, Zahra Shariatinia, Fahimeh Mohammadpanah, Khodayar Gholivand, Michal Dusek, Vaclav Eigner, Mohammad Satari, Ali Asghar Ebrahimi Valmoozi|2023|J.Mol.Liq.|391|123442|doi:10.1016/j.molliq.2023.123442
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: 10.5517/ccdc.csd.cc2cp98n
title: CCDC 2195211: Experimental Crystal Structure Determination

description: Related Article: Weidong Zhang, Juanfang Zhou, Chao Zhang, Xinliang Liu|2023|New J.Chem.|47|20510|doi:10.1039/D3NJ04283A
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: 10.6084/m9.figshare.24114597
title: Supplemental materials for a set of yellow mustard (<i>Sinapis alba</i> L.) germplasm with polycotyledony

description: This is the supplemental materials Table S1 for the paper "a set of yellow mustard (<i>Sinapis alba</i> L.) germplasm with polycotyledony" published in Plants
DOI: 10.6084/m9.figshare.24114597.v1
title: Supplemental materials for a set of yellow mustard (<i>Sinapis alba</i> L.) germplasm with polycotyledony

description: This is the supplemental materials Table S1 for the paper "a set of yellow mustard (<i>Sinapis alba</i> L.) germplasm with polycotyledony" published in Plants
DOI: 10.6073/pasta/882f11da081f5d49be3d5876c4e48aeb
title: Bisley Watershed 3 and Quebrada Prieta Algae Monitoring

description: The LTER is conducting annual monitoring of Algae, Chlorophyll a, benthic organic matter, and benthic inorganic matter in order to document baseline stream characteristics. These data may be used to examine effects of disturbances such as hurricanes on stream ecosystems. Support for this work was provided by grants BSR-8811902, DEB-9411973, DEB-9705814 , DEB-0080538, DEB-0218039 , DEB-0620910 , DEB-1239764, DEB-1546686, and DEB-1831952 from the National Science Foundation to the University of Puerto Rico as part of the Luquillo Long-Term Ecological Research Program. Additional support provided by the University of Puerto Rico and the International Institute of Tropical Forestry, USDA Forest Service.
DOI: 10.18434/mds2-1859
title: Data from "High-temperature tensile constitutive data and models for structural steels in fire (NIST Technical Note 1714)"
DOI: 10.5281/zenodo.10144174
title: Supporting Data for: A Multimer Embedding Approach for Molecular Crystals up to Harmonic Vibrational Properties

description: Accurate calculations of molecular crystals are crucial for drug design and crystal engineering. However, periodic high-level density functional calculations using hybrid functionals are often prohibitively expensive for relevant systems. These expensive periodic calculations can be circumvented by the usage of embedding methods in which for instance the periodic calculation is only performed at a lower-cost level and then monomer energies and dimer interactions are replaced by those of the higher-level method. Herein, we extend upon such a multimer embedding approach to enable energy corrections for trimer interactions and the calculation of harmonic vibrational properties up to the dimer level. We evaluate this approach for the X23 benchmark set of molecular crystals by approximating a periodic hybrid density functional (PBE0+MBD) by embedding multimers into less expensive calculations using a generalized-gradient approximation (GGA) functional (PBE+MBD). We show that trimer interactions are crucial for accurately approximating lattice energies within 1 kJ/mol and might also be needed for further improvement of lattice constants and hence cell volumes. Finally, vibrational properties are already very well captured at the monomer and dimer level, making it possible to approximate vibrational free energies at room temperature within 1 kJ/mol.
This supporting dataset includes results of PBE0+MBD, PBE+MBD, and multimer embedding calculations for the X23 set of molecular crystals. See the included README.md file for more details. The related preprint can be found at https://doi.org/10.48550/arXiv.2209.02687.
DOI: 10.5281/zenodo.7098570
title: Supporting Data for: A Multimer Embedding Approach for Molecular Crystals up to Harmonic Vibrational Properties

description: Accurate calculations of molecular crystals are crucial for drug design and crystal engineering. However, periodic high-level density functional calculations using hybrid functionals are often prohibitively expensive for relevant systems. These expensive periodic calculations can be circumvented by the usage of embedding methods in which for instance the periodic calculation is only performed at a lower-cost level and then monomer energies and dimer interactions are replaced by those of the higher-level method. Herein, we extend upon such a multimer embedding approach to enable energy corrections for trimer interactions and the calculation of harmonic vibrational properties up to the dimer level. We evaluate this approach for the X23 benchmark set of molecular crystals by approximating a periodic hybrid density functional (PBE0+MBD) by embedding multimers into less expensive calculations using a generalized-gradient approximation (GGA) functional (PBE+MBD). We show that trimer interactions are crucial for accurately approximating lattice energies within 1 kJ/mol and might also be needed for further improvement of lattice constants and hence cell volumes. Finally, vibrational properties are already very well captured at the monomer and dimer level, making it possible to approximate vibrational free energies at room temperature within 1 kJ/mol.
This supporting dataset includes results of PBE0+MBD, PBE+MBD, and multimer embedding calculations for the X23 set of molecular crystals. See the included README.md file for more details. The related preprint can be found at https://doi.org/10.48550/arXiv.2209.02687.
DOI: 10.5281/zenodo.7098571
title: Supporting Data for: A Multimer Embedding Approach for Molecular Crystals up to Harmonic Vibrational Properties

description: Accurate calculations of molecular crystals would be crucial for drug design and crystal engineering. However, periodic high-level density functional calculations using hybrid functionals are often prohibitively expensive for relevant systems. Therefore, these expensive periodic calculations are sometimes circumvented by the usage of quantum-mechanical embedding methods, in which for instance the periodic calculation is only performed at a lower-cost level and then monomer energies and dimer interactions are replaced by those of the higher-level method. Herein, we extend upon such a multimer embedding approach to enable energy corrections for trimer interactions and the calculation of harmonic vibrational properties up to the dimer level. We show that trimer interactions are crucial for accurately approximating lattice energies and might also be needed for a better description of lattice constants. Finally, vibrational properties are already very well captured at the dimer level.<br> This supporting dataset includes results of PBE0+MBD/light, PBE+MBD/light, and multimer embedding calculations for the X23 set of molecular crystals. See the included README.md file for more details. The related preprint can be found at https://doi.org/10.48550/arXiv.2209.02687.
DOI: 10.5281/zenodo.8379098
title: Supporting Data for: A Multimer Embedding Approach for Molecular Crystals up to Harmonic Vibrational Properties

description: Accurate calculations of molecular crystals are crucial for drug design and crystal engineering. However, periodic high-level density functional calculations using hybrid functionals are often prohibitively expensive for relevant systems. These expensive periodic calculations can be circumvented by the usage of embedding methods in which for instance the periodic calculation is only performed at a lower-cost level and then monomer energies and dimer interactions are replaced by those of the higher-level method. <br> Herein, we extend upon such a multimer embedding approach to enable energy corrections for trimer interactions and the calculation of harmonic vibrational properties up to the dimer level. We evaluate this approach for the X23 benchmark set of molecular crystals by approximating a periodic hybrid density functional (PBE0+MBD) by embedding multimers into less expensive calculations using a generalized-gradient approximation (GGA) functional (PBE+MBD). We show that trimer interactions are crucial for accurately approximating lattice energies within 1 kJ/mol and might also be needed for further improvement of lattice constants and hence cell volumes. Finally, vibrational properties are already very well captured at the monomer and dimer level, making it possible to approximate vibrational free energies at room temperature within 1 kJ/mol. This supporting dataset includes results of PBE0+MBD, PBE+MBD, and multimer embedding calculations for the X23 set of molecular crystals. See the included README.md file for more details. The related preprint can be found at https://doi.org/10.48550/arXiv.2209.02687.
DOI: 10.5281/zenodo.10022727
title: MatKG 1.3

description: MatKG is a comprehensive Knowledge Graph of Materials Science that captures a diverse rangeof entities and relationships from scientific literature. MatKG includes materials, properties, applications, characterization methods,synthesis methods, symmetry phase labels, and descriptors, among other entities, which are extracted automatically usingadvanced natural language processing methods from over 5 million papers in the domain. Relationships between these entities are established using statistical means, resulting in a knowledge graph with over 150,000 entities and 3.5 million unique triples. MatKG is the largest knowledge graph in the field of materials science at the time of writing, and its development represents a significant advance in the organization and accessibility of materials science data
DOI: 10.34740/kaggle/dsv/6984024
title: Melody Metrics:Popularity
DOI: 10.6084/m9.figshare.24578689
title: <b>STEM Clubs and their role in the future of education</b>

description: <b>Background and Context:</b> STEM Clubs in higher education represent authentic real-life approaches to assess computational thinking (CT) skills
DOI: 10.5281/zenodo.10138317
title: GitHub Public Pull Request Comments

description: Over 13 MILLION pull request comments
Dataset used for the master's thesis "LLMs for Code Comment Consistency." Covers the languages Go, Java, JavaScript, TypeScripp, and Python. All data is mined from permissively-licensed GitHub public projects with at least 25 stars and 25 pull requests submitted at the time of access.
 
This dataset pertains specifically to **pull request comments that are made on files.** In other words, every comment in this dataset is linked to a specific file in a pull request.
 
### What can I do with this data?
Anything you want, of course, but here are some starter ideas:
- Sentiment analysis of comments, is there a correlation between number of contributions and positivity of reviews?
- Pull request comment generation: can we automatically make code review comments?
- PR text mining: can we mine out examples of a specific type of comment? (in my project, this was comments about function documentation)
 
The mining code is publicly accessible.
 
Each file is a JSON object where each key is a Github repository, and each value is a pull request comment in that repository.
DOI: 10.5281/zenodo.10138316
title: GitHub Public Pull Request Comments

description: Over 13 MILLION pull request comments
Dataset used for the master's thesis "LLMs for Code Comment Consistency." Covers the languages Go, Java, JavaScript, TypeScripp, and Python. All data is mined from permissively-licensed GitHub public projects with at least 25 stars and 25 pull requests submitted at the time of access.
 
This dataset pertains specifically to **pull request comments that are made on files.** In other words, every comment in this dataset is linked to a specific file in a pull request.
 
### What can I do with this data?
Anything you want, of course, but here are some starter ideas:
- Sentiment analysis of comments, is there a correlation between number of contributions and positivity of reviews?
- Pull request comment generation: can we automatically make code review comments?
- PR text mining: can we mine out examples of a specific type of comment? (in my project, this was comments about function documentation)
 
The mining code is publicly accessible.
 
Each file is a JSON object where each key is a Github repository, and each value is a pull request comment in that repository.
DOI: 10.5281/zenodo.10138302
title: Multilingual paired code and comment changes

description: Dataset used for the master's thesis "LLMs for Code Comment Consistency." Covers the languages Go, Java, JavaScript, TypeScript, and Python. All data is mined from permissively-licensed GitHub public projects.
This dataset consists of pairs of function/method code blocks and their documentation comments, before and after commits.Examples are labeled 0 if the comment was not changed before and after, and 1 if the comment was changed. For the purpose of comment consistency, that means a 1-labeled example has an old comment that is inconsistent with the new code.If you're training a code summarization or comment generation task, then of course ignore the classification label.

All-22k contains the training, validation, and test set used in the models trained in the paper. The examples are balanced by language and between the positive and negative classes. Any code repository is only present in one of these sets.