cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.17148965.v1
title: 16S rRNA gene sequencing of colon content samples from mouse treated with or without κ-carrageenan

description: The fecal samples collected from the colon lumen of mice at necropsy were used to extract microbial genomic DNA using CTAB method. Gel electrophoresis was used to monitor the concentration and evaluate the purity of DNA. The hypervariable V3-V4 regions of the 16S rRNA gene were sequenced with specific primers (forward primer, 341F: CCTAYGGGRBGCASCAG; reverse primer, 806R: GGACTACNNGGGTATCTAAT) tagged with barcodes. The PCR reactions were carried out with Phusion® High-Fidelity PCR Master Mix (New England Biolabs). The sequencing library was generated using TruSeq® DNA PCR-Free Sample Preparation Kit (Illumina, USA) and was sequenced on an Illumina NovaSeq platform.
DOI: 10.6084/m9.figshare.17148965
title: 16S rRNA gene sequencing of colon content samples from mouse treated with or without κ-carrageenan

description: The fecal samples collected from the colon lumen of mice at necropsy were used to extract microbial genomic DNA using CTAB method. Gel electrophoresis was used to monitor the concentration and evaluate the purity of DNA. The hypervariable V3-V4 regions of the 16S rRNA gene were sequenced with specific primers (forward primer, 341F: CCTAYGGGRBGCASCAG; reverse primer, 806R: GGACTACNNGGGTATCTAAT) tagged with barcodes. The PCR reactions were carried out with Phusion® High-Fidelity PCR Master Mix (New England Biolabs). The sequencing library was generated using TruSeq® DNA PCR-Free Sample Preparation Kit (Illumina, USA) and was sequenced on an Illumina NovaSeq platform.
DOI: 10.5281/zenodo.5771203
title: SIS2 restart files part.2

description: SIS2 restart files part2
DOI: 10.5281/zenodo.5771202
title: SIS2 restart files part.2

description: SIS2 restart files part2
DOI: 10.6084/m9.figshare.17155787.v2
title: Supplementary materials- (Chapter 3).xlsx

description: Supplementary materials -(Chapter 3)<br>
DOI: 10.3886/e156861
title: Teacher Day Reconstruction Method Analysis Files, 2020-2021

description: The attached syntax file provides the R script for the analyses included in the following publication:<br><br>Jones, N. D., Camburn, E., Kelcery, B., & Quintero, E. (In Press). Teachers' time use and affect before and after COVID-19 school closures, AERA Open.<br><br>Full data for this paper are available upon request. You can email the first author (ndjones@bu.edu) with inquiries about the project data. Full data will be released through OpenICPSR at the conclusion of the grant period.<br>
DOI: 10.3886/e156861v1
title: Teacher Day Reconstruction Method Analysis Files, 2020-2021

description: The attached syntax file provides the R script for the analyses included in the following publication:<br><br>Jones, N. D., Camburn, E., Kelcery, B., & Quintero, E. (In Press). Teachers' time use and affect before and after COVID-19 school closures, AERA Open.<br><br>Full data for this paper are available upon request. You can email the first author (ndjones@bu.edu) with inquiries about the project data. Full data will be released through OpenICPSR at the conclusion of the grant period.<br>
DOI: 10.6084/m9.figshare.17151980
title: Metabolites characterisation of colon content samples from mouse treated with or without κ-carrageenan using LC–MS-based method

description: Untargeted metabolomics analysis was conducted using colon contents from mice. Briefly, individual samples were accurately weighed. After the precipitation of proteins with methanol, the extracted metabolites from the samples were characterized by an Ultra-performance liquid chromatography (UPLC) tandem mass spectrometer (UPLC-MS/MS), consisting of a Vanquish UHPLC system (ThermoFisher, Germany) coupled with an Orbitrap Q Exactive<sup>TM</sup>HF-X mass spectrometer (Thermo Fisher，Germany). The raw data were processed using the Compound Discoverer 3.1 (CD3.1, ThermoFisher) to perform peak alignment, peak picking, and quantitation for each metabolite. And then peaks were matched with the mzCloud (https://www.mzcloud.org/), mzVault and MassList database to obtain the accurate qualitative and relative quantitative results.
DOI: 10.6084/m9.figshare.17151980.v1
title: Metabolites characterisation of colon content samples from mouse treated with or without κ-carrageenan using LC–MS-based method

description: Untargeted metabolomics analysis was conducted using colon contents from mice. Briefly, individual samples were accurately weighed. After the precipitation of proteins with methanol, the extracted metabolites from the samples were characterized by an Ultra-performance liquid chromatography (UPLC) tandem mass spectrometer (UPLC-MS/MS), consisting of a Vanquish UHPLC system (ThermoFisher, Germany) coupled with an Orbitrap Q Exactive<sup>TM</sup>HF-X mass spectrometer (Thermo Fisher，Germany). The raw data were processed using the Compound Discoverer 3.1 (CD3.1, ThermoFisher) to perform peak alignment, peak picking, and quantitation for each metabolite. And then peaks were matched with the mzCloud (https://www.mzcloud.org/), mzVault and MassList database to obtain the accurate qualitative and relative quantitative results.
DOI: 10.6084/m9.figshare.14749512
title: Supplementary Data for Beaulieu et al. "Diversification of ergot alkaloids and heritable fungal symbionts in morning glories"

description: <b>Supplementary Data 1. Sampling information and results.</b> Naming authority and geographic information were collected from the World Checklist of Selected Families at https://wcsp.science.kew.org. <br> <b>Supplementary Data 2.</b> Accession information of all sequences included in the ITS phylogeny. <br> <b>Supplementary Data 3.</b> ITS phylogeny of morning glories with EAs. ITS phylogeny adapted from Muñoz-Rodríguez et al. (2019) colorized with our EA data. Orange species are EA- and blue species are EA+. <br> <b>Supplementary Data 4.</b> All herbarium specimens used in the study. <br><b>Supplementary Data 5</b>. <i>Ipomoea, Argyrei, Stictocardia, </i>and <i>Turbina</i> occurence data from GBIF. Source data for Figure 1. <b>Supplementary Data 6.</b> RaxML phylogeny. Source data for Figure 2, 3, and 4. <b>Supplementary Data 7.</b> Metadata for species in the phylogeny. Source data for Figure 2. <b>Supplementary Data 8.</b> Ergot alkaloid data for species in the phylogeny. Source data for Figure 4.<br> <b>Supplementary Data 9.</b> Source data for Figure 5.<br><br>
DOI: 10.6084/m9.figshare.17031240
title: An archetype-based energy modelling approach for a remote, subarctic community

description: For many remote communities, fossil fuels are used for both heating and electricity generation; however, while electricity use is measured by the distributor, the proportion of thermal energy end-use is rarely known because of the individual nature of heating and hot water systems. Consequently, most renewable energy studies target only the production of electricity, overlooking the significant fossil fuel use for space and hot water heating in cold climates. To address the existing bias, this study implements a bottom-up approach for simulating thermal energy demand in a remote, subarctic community. The proposed method relies on six novel residential archetypes appropriate to the region, which are shown to deliver better accuracy than the existing United States Department of Energy Climate Zone 8 archetypes. Simulation results indicate that thermal energy demands account for half of fossil fuel consumption in the community and are therefore an important consideration in energy system decarbonization strategies.
DOI: 10.6084/m9.figshare.17031240.v1
title: An archetype-based energy modelling approach for a remote, subarctic community

description: For many remote communities, fossil fuels are used for both heating and electricity generation; however, while electricity use is measured by the distributor, the proportion of thermal energy end-use is rarely known because of the individual nature of heating and hot water systems. Consequently, most renewable energy studies target only the production of electricity, overlooking the significant fossil fuel use for space and hot water heating in cold climates. To address the existing bias, this study implements a bottom-up approach for simulating thermal energy demand in a remote, subarctic community. The proposed method relies on six novel residential archetypes appropriate to the region, which are shown to deliver better accuracy than the existing United States Department of Energy Climate Zone 8 archetypes. Simulation results indicate that thermal energy demands account for half of fossil fuel consumption in the community and are therefore an important consideration in energy system decarbonization strategies.
DOI: 10.6084/m9.figshare.16903288
title: VIB5 database

description: VIB5 database:<br>Lina Zhang, Shuang Zhang, Alec Owens, Sergei N. Yurchenko, Pavlo O. Dral, "Accurate ab initio quantum chemical molecular potential energy surfaces", Sci. Data, 2021, submitted.<br>VIB5.zip contains the database in json format.<br>extraction_data.py is a script for extracting data from the VIB5 database in a convenient format. Run command to get help of how to use the script:python3 extraction_data.py -h<br>
DOI: 10.5281/zenodo.5771253
title: Lateral hypothalamic neuronal ensembles regulate pre-sleep nest-building behavior

description: Data and codes for the paper "Lateral hypothalamic neuronal ensembles regulate pre-sleep nest-building behavior".
DOI: 10.6084/m9.figshare.17140172.v2
title: Data from "Many-Body Effects in the X-ray Absorption Spectra of Liquid Water"

description: This dataset contains all data related to the publication "Many-Body Effects in the X-ray Absorption Spectra of Liquid Water", by F. Tang et al., 2021. In this work, we used deepmd to generate snapshots of H<sub>2</sub>O, D<sub>2</sub>O at different temperatures. Then we used these snapshots to compute the GW-BSE XAS spectra and the related analysis reported in the paper. This dataset contains links to all software used, all data generated as part of this work, as well as scripts to generate and analyze all data and generate the plots reported in the publication.
DOI: 10.15468/7usrnx
title: Rediscovery of the endemic Afrotropical genus Spathioplites (Hymenoptera, Braconidae, Doryctinae) with major range extension records for Spathioplites phreneticus

description: This dataset contains the digitized treatments in Plazi based on the original journal article Noort 1,2, Simon van, Belokobylskij 3,4, Sergey A., Touret-Alby 5, Agniele (2021): Rediscovery of the endemic Afrotropical genus Spathioplites (Hymenoptera, Braconidae, Doryctinae) with major range extension records for Spathioplites phreneticus. African Invertebrates 62 (2): 497-520, DOI: http://dx.doi.org/10.3897/afrinvertebr.62.74103, URL: http://dx.doi.org/10.3897/afrinvertebr.62.74103
DOI: 10.15468/hxs474
title: Phelypaea boissieri f. lutea (Orobanchaceae), a peculiar new form from Turkey and typification of the name of this species

description: This dataset contains the digitized treatments in Plazi based on the original journal article Subasi, Uemit, Pedraja, Oscar Sanchez, Piwowarczyk, Renata (2021): Phelypaea boissieri f. lutea (Orobanchaceae), a peculiar new form from Turkey and typification of the name of this species. PhytoKeys 186: 159-167, DOI: http://dx.doi.org/10.3897/phytokeys.186.77575, URL: http://dx.doi.org/10.3897/phytokeys.186.77575
DOI: 10.15468/my65ev
title: On the identity of Thymus humifusus var. aureopunctatus (Lamiaceae) and taxonomic notes on the Th. richardii complex

description: This dataset contains the digitized treatments in Plazi based on the original journal article Saez, Llorenc, Bogunic, Faruk, Cambria, Salvatore, Riera, Jesus, Bogdanovic, Sandro (2021): On the identity of Thymus humifusus var. aureopunctatus (Lamiaceae) and taxonomic notes on the Th. richardii complex. PhytoKeys 186: 139-158, DOI: http://dx.doi.org/10.3897/phytokeys.186.75412, URL: http://dx.doi.org/10.3897/phytokeys.186.75412
DOI: 10.15468/aqy2vr
title: Dipteris shenzhenensis, a new endangered species of Dipteridaceae from Shenzhen, southern China

description: This dataset contains the digitized treatments in Plazi based on the original journal article Wei, Zuo-Ying, Gu, Yu-Feng, Xia, Zeng-Qiang, Chen, Li-Jun, Wang, Ting, Zhang, Shou-Zhou, Zhao, Guo-Hua, Chen, Jian-Bing, Cao, Jian-Guo, Yan, Yue-Hong (2021): Dipteris shenzhenensis, a new endangered species of Dipteridaceae from Shenzhen, southern China. PhytoKeys 186: 111-120, DOI: http://dx.doi.org/10.3897/phytokeys.186.73739, URL: http://dx.doi.org/10.3897/phytokeys.186.73739
DOI: 10.15468/7jqbyx
title: The re-description of Synoecnema hirsutum Timm, 1959 (Synoecneminae, Ungellidae, Drilonematoidea) from a pheretimoid earthworm in Vietnam with the analysis of its phylogenetic relationships

description: This dataset contains the digitized treatments in Plazi based on the original journal article Ivanova, Elena S., Efeykin, Boris D., Spiridonov, Sergei E. (2021): The re-description of Synoecnema hirsutum Timm, 1959 (Synoecneminae, Ungellidae, Drilonematoidea) from a pheretimoid earthworm in Vietnam with the analysis of its phylogenetic relationships. ZooKeys 1076: 135-150, DOI: http://dx.doi.org/10.3897/zookeys.1076.75932, URL: http://dx.doi.org/10.3897/zookeys.1076.75932
DOI: 10.15468/b3jvtp
title: Discovery of the genus Platycotylus Olliff, 1883 (Coleoptera, Tenebrionidae) in Japan: Description of a new and remarkable species

description: This dataset contains the digitized treatments in Plazi based on the original journal article Yoshida 1, Takahiro, Ando 2, Kiyoshi (2021): Discovery of the genus Platycotylus Olliff, 1883 (Coleoptera, Tenebrionidae) in Japan: Description of a new and remarkable species. ZooKeys 1076: 125-133, DOI: http://dx.doi.org/10.3897/zookeys.1076.75846, URL: http://dx.doi.org/10.3897/zookeys.1076.75846
DOI: 10.15468/uxkgmj
title: New relictual genera in Cyrtoquediini and Indoquediini (Coleoptera: Staphylinidae: Staphylininae)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Brunke, Adam J. (2021): New relictual genera in Cyrtoquediini and Indoquediini (Coleoptera: Staphylinidae: Staphylininae). ZooKeys 1076: 109-124, DOI: http://dx.doi.org/10.3897/zookeys.1076.73103, URL: http://dx.doi.org/10.3897/zookeys.1076.73103
DOI: 10.6084/m9.figshare.15085892
title: Additional file 2 of Molecular features and vulnerabilities of recurrent chordomas

description: Additional file 2: Table 3. Filtered exonic variants in the primary tumor tissue (11PT) and the cell lines U-CH11 and U-CH11R.
DOI: 10.6084/m9.figshare.15085892.v1
title: Additional file 2 of Molecular features and vulnerabilities of recurrent chordomas

description: Additional file 2: Table 3. Filtered exonic variants in the primary tumor tissue (11PT) and the cell lines U-CH11 and U-CH11R.
DOI: 10.6084/m9.figshare.15085898
title: Additional file 3 of Molecular features and vulnerabilities of recurrent chordomas

description: Additional file 3: Table 4. List of up- and downregulated genes in U-CH11R versus U-CH11 based on the microarray gene expression analysis.
DOI: 10.6084/m9.figshare.15085898.v1
title: Additional file 3 of Molecular features and vulnerabilities of recurrent chordomas

description: Additional file 3: Table 4. List of up- and downregulated genes in U-CH11R versus U-CH11 based on the microarray gene expression analysis.
DOI: 10.6084/m9.figshare.15085901
title: Additional file 4 of Molecular features and vulnerabilities of recurrent chordomas

description: Additional file 4: Table 5. GSEA of differentially expressed genes in U-CH11R and U-CH11
DOI: 10.6084/m9.figshare.15085904
title: Additional file 5 of Molecular features and vulnerabilities of recurrent chordomas

description: Additional file 5: Table 6. GSEA of RRHO Plot Quadrant A.
DOI: 10.6084/m9.figshare.15085907
title: Additional file 6 of Molecular features and vulnerabilities of recurrent chordomas

description: Additional file 6: Table 7. List of potential miR-196a-5p target genes in recurrent chordoma cell lines.
DOI: 10.6084/m9.figshare.15085907.v1
title: Additional file 6 of Molecular features and vulnerabilities of recurrent chordomas

description: Additional file 6: Table 7. List of potential miR-196a-5p target genes in recurrent chordoma cell lines.
DOI: 10.6084/m9.figshare.15085901.v1
title: Additional file 4 of Molecular features and vulnerabilities of recurrent chordomas

description: Additional file 4: Table 5. GSEA of differentially expressed genes in U-CH11R and U-CH11
DOI: 10.6084/m9.figshare.15085904.v1
title: Additional file 5 of Molecular features and vulnerabilities of recurrent chordomas

description: Additional file 5: Table 6. GSEA of RRHO Plot Quadrant A.
DOI: 10.15468/preagk
title: Two new Cypridopsinae Kaufmann, 1900 (Crustacea, Ostracoda) from southern Africa

description: This dataset contains the digitized treatments in Plazi based on the original journal article Szwarc, Agata, Martens, Koen, Namiotko, Tadeusz (2021): Two new Cypridopsinae Kaufmann, 1900 (Crustacea, Ostracoda) from southern Africa. ZooKeys 1076: 83-107, DOI: http://dx.doi.org/10.3897/zookeys.1076.76123, URL: http://dx.doi.org/10.3897/zookeys.1076.76123
DOI: 10.6084/m9.figshare.17156921
title: Additional file 2 of An interferon-related signature characterizes the whole blood transcriptome profile of insulin-resistant individuals—the CODAM study

description: Additional file 2: Table S1.
DOI: 10.6084/m9.figshare.17156921.v1
title: Additional file 2 of An interferon-related signature characterizes the whole blood transcriptome profile of insulin-resistant individuals—the CODAM study

description: Additional file 2: Table S1.
DOI: 10.6084/m9.figshare.17156927
title: Additional file 3 of An interferon-related signature characterizes the whole blood transcriptome profile of insulin-resistant individuals—the CODAM study

description: Additional file 3: Table S2.
DOI: 10.6084/m9.figshare.17156930
title: Additional file 4 of An interferon-related signature characterizes the whole blood transcriptome profile of insulin-resistant individuals—the CODAM study

description: Additional file 4: Table S3.
DOI: 10.6084/m9.figshare.17156927.v1
title: Additional file 3 of An interferon-related signature characterizes the whole blood transcriptome profile of insulin-resistant individuals—the CODAM study

description: Additional file 3: Table S2.
DOI: 10.6084/m9.figshare.17156930.v1
title: Additional file 4 of An interferon-related signature characterizes the whole blood transcriptome profile of insulin-resistant individuals—the CODAM study

description: Additional file 4: Table S3.
DOI: 10.6084/m9.figshare.17156933
title: Additional file 5 of An interferon-related signature characterizes the whole blood transcriptome profile of insulin-resistant individuals—the CODAM study

description: Additional file 5: Table S4.
DOI: 10.6084/m9.figshare.17156933.v1
title: Additional file 5 of An interferon-related signature characterizes the whole blood transcriptome profile of insulin-resistant individuals—the CODAM study

description: Additional file 5: Table S4.
DOI: 10.6084/m9.figshare.17156936.v1
title: Additional file 6 of An interferon-related signature characterizes the whole blood transcriptome profile of insulin-resistant individuals—the CODAM study

description: Additional file 6: Table S5.
DOI: 10.6084/m9.figshare.17156936
title: Additional file 6 of An interferon-related signature characterizes the whole blood transcriptome profile of insulin-resistant individuals—the CODAM study

description: Additional file 6: Table S5.
DOI: 10.6084/m9.figshare.17156939
title: Additional file 7 of An interferon-related signature characterizes the whole blood transcriptome profile of insulin-resistant individuals—the CODAM study

description: Additional file 7: Table S6.
DOI: 10.6084/m9.figshare.17156939.v1
title: Additional file 7 of An interferon-related signature characterizes the whole blood transcriptome profile of insulin-resistant individuals—the CODAM study

description: Additional file 7: Table S6.
DOI: 10.6084/m9.figshare.17156942
title: Additional file 8 of An interferon-related signature characterizes the whole blood transcriptome profile of insulin-resistant individuals—the CODAM study

description: Additional file 8: Table S7.
DOI: 10.6084/m9.figshare.17156942.v1
title: Additional file 8 of An interferon-related signature characterizes the whole blood transcriptome profile of insulin-resistant individuals—the CODAM study

description: Additional file 8: Table S7.
DOI: 10.6084/m9.figshare.17156945
title: Additional file 9 of An interferon-related signature characterizes the whole blood transcriptome profile of insulin-resistant individuals—the CODAM study

description: Additional file 9: Table S8.
DOI: 10.6084/m9.figshare.17156945.v1
title: Additional file 9 of An interferon-related signature characterizes the whole blood transcriptome profile of insulin-resistant individuals—the CODAM study

description: Additional file 9: Table S8.
DOI: 10.6084/m9.figshare.17156955
title: Additional file 4 of Functional screening of a human saliva metagenomic DNA reveal novel resistance genes against sodium hypochlorite and chlorhexidine

description: Additional file 4. BlastN results of the metagenomic sequencing data of each saliva oral metagenomic DNA against the resistance genes detected in this study.
DOI: 10.6084/m9.figshare.17156955.v1
title: Additional file 4 of Functional screening of a human saliva metagenomic DNA reveal novel resistance genes against sodium hypochlorite and chlorhexidine

description: Additional file 4. BlastN results of the metagenomic sequencing data of each saliva oral metagenomic DNA against the resistance genes detected in this study.
DOI: 10.6084/m9.figshare.17156976
title: Additional file 4 of Risk factors of asthma in the Asian population: a systematic review and meta-analysis

description: Additional file 4: Table S3. Study characteristics and reported asthma-associated risk factors of 289 studies included in the systematic review process.
DOI: 10.6084/m9.figshare.17156976.v1
title: Additional file 4 of Risk factors of asthma in the Asian population: a systematic review and meta-analysis

description: Additional file 4: Table S3. Study characteristics and reported asthma-associated risk factors of 289 studies included in the systematic review process.
DOI: 10.6084/m9.figshare.17156702
title: Columbine Lake lead models from serac package

description: Lead model (CFCS, CRS, and CIC) outputs from the package serac v0.1.0.
DOI: 10.15468/88qpgx
title: Gems of the southern Japanese seas - four new species of Edwardsianthus (Anthozoa, Actiniaria, Edwardsiidae) with redescriptions of two species

description: This dataset contains the digitized treatments in Plazi based on the original journal article Izumi, Takato, Fujii, Takuma (2021): Gems of the southern Japanese seas - four new species of Edwardsianthus (Anthozoa, Actiniaria, Edwardsiidae) with redescriptions of two species. ZooKeys 1076: 151-182, DOI: http://dx.doi.org/10.3897/zookeys.1076.69025, URL: http://dx.doi.org/10.3897/zookeys.1076.69025
DOI: 10.15468/wzzhng
title: First record of the genus Discorhabdella (Porifera, Demospongiae, Poecilosclerida, Crambeidae) from Sagami Bay, Japan with description of two new species

description: This dataset contains the digitized treatments in Plazi based on the original journal article Ise, Yuji, Vacelet, Jean, Izumi, Takato, Woo, Sau Pinn, Tan, Shau Hwai (2021): First record of the genus Discorhabdella (Porifera, Demospongiae, Poecilosclerida, Crambeidae) from Sagami Bay, Japan with description of two new species. ZooKeys 1076: 67-81, DOI: http://dx.doi.org/10.3897/zookeys.1076.37278, URL: http://dx.doi.org/10.3897/zookeys.1076.37278