cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccdc.csd.cc2f2lty
title: CCDC 2236830: Experimental Crystal Structure Determination

description: Related Article: Yingying Qin, Yongmei Kang, Lei Zhang, Jianping Sun, Zhijing Zhang, Jialei Xu, Fanlong Zeng, Anyang Li, Wenyuan Wang, Weiqun Shi|2024|Chin.Chem.Lett.|35|108691|doi:10.1016/j.cclet.2023.108691
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.cc2fyqz3
title: CCDC 2262906: Experimental Crystal Structure Determination

description: Related Article: Pingping Wang, Huixian Miao, Kechuan Sheng, Bin Wang, Fan Feng, Xuankun Cai, Wei Huang, Dayu Wu|2024|Chin.Chem.Lett.|35|108600|doi:10.1016/j.cclet.2023.108600
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.cc2fyr05
title: CCDC 2262907: Experimental Crystal Structure Determination

description: Related Article: Pingping Wang, Huixian Miao, Kechuan Sheng, Bin Wang, Fan Feng, Xuankun Cai, Wei Huang, Dayu Wu|2024|Chin.Chem.Lett.|35|108600|doi:10.1016/j.cclet.2023.108600
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.cc2gqjd4
title: CCDC 2285766: Experimental Crystal Structure Determination

description: Related Article: Zhiguo Zhang, Bingbing Shi, Xiyang Cao, Nana Ma, Hao Wu, Xingjie Zhang, Guisheng Zhang|2024|Chin.Chem.Lett.|35|109184|doi:10.1016/j.cclet.2023.109184
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.7802195
title: Additional file 2: of MetaCHIP: community-level horizontal gene transfer identification through the combination of best-match and phylogenetic approaches

description: Metadata of downloaded 2094 genomes. (TXT 157 kb)
DOI: 10.6084/m9.figshare.7802195.v1
title: Additional file 2: of MetaCHIP: community-level horizontal gene transfer identification through the combination of best-match and phylogenetic approaches

description: Metadata of downloaded 2094 genomes. (TXT 157 kb)
DOI: 10.6084/m9.figshare.7802201
title: Additional file 3: of MetaCHIP: community-level horizontal gene transfer identification through the combination of best-match and phylogenetic approaches

description: MetaCHIP identified 10,255 HGTs from the 2094 genomes. (TXT 805 kb)
DOI: 10.26188/25222604
title: Indexed RefSeq database

description: Indexed NCBI RefSeq database, containing both bacterial and fungal genomes.<br>to download form the command line, use:curl "https://mediaflux.researchsoftware.unimelb.edu.au:443/mflux/share.mfjp?_token=Lqaic1pBmpDdqX8ofv1C1128247855&browser=true&filename=RefSeq_bf.zip" -d browser=false -o RefSeq_bf.zip<br><br>
DOI: 10.26188/25222604.v1
title: Indexed RefSeq database

description: Indexed NCBI RefSeq database, containing both bacterial and fungal genomes.<br>to download form the command line, use:curl "https://mediaflux.researchsoftware.unimelb.edu.au:443/mflux/share.mfjp?_token=Lqaic1pBmpDdqX8ofv1C1128247855&browser=true&filename=RefSeq_bf.zip" -d browser=false -o RefSeq_bf.zip<br><br>
DOI: 10.6084/m9.figshare.7802201.v1
title: Additional file 3: of MetaCHIP: community-level horizontal gene transfer identification through the combination of best-match and phylogenetic approaches

description: MetaCHIP identified 10,255 HGTs from the 2094 genomes. (TXT 805 kb)
DOI: 10.6084/m9.figshare.7802204
title: Additional file 4: of MetaCHIP: community-level horizontal gene transfer identification through the combination of best-match and phylogenetic approaches

description: Nucleic acid sequences MetaCHIP identified 10,255 HGTs. (FASTA 16796 kb)
DOI: 10.6084/m9.figshare.7802204.v1
title: Additional file 4: of MetaCHIP: community-level horizontal gene transfer identification through the combination of best-match and phylogenetic approaches

description: Nucleic acid sequences MetaCHIP identified 10,255 HGTs. (FASTA 16796 kb)
DOI: 10.6084/m9.figshare.7802216
title: Additional file 5: of MetaCHIP: community-level horizontal gene transfer identification through the combination of best-match and phylogenetic approaches

description: Taxonomic classification of the human gut and North Sea genome bins. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.7802216.v1
title: Additional file 5: of MetaCHIP: community-level horizontal gene transfer identification through the combination of best-match and phylogenetic approaches

description: Taxonomic classification of the human gut and North Sea genome bins. (XLSX 17 kb)
DOI: 10.26188/25222610
title: Indexed NCBI nt database - original

description: Indexed NCBI nucleotide database, used to benchmark CCMetagen in its original publication.<br>To download from the command line, use:curl "https://mediaflux.researchsoftware.unimelb.edu.au:443/mflux/share.mfjp?_token=i8yedNiYfdjrBfGJ8Y5z1128247857&browser=true&filename=ncbi_nt_kma.zip" -d browser=false -o ncbi_nt_kma.zip<br>
DOI: 10.26188/25222610.v1
title: Indexed NCBI nt database - original

description: Indexed NCBI nucleotide database, used to benchmark CCMetagen in its original publication.<br>To download from the command line, use:curl "https://mediaflux.researchsoftware.unimelb.edu.au:443/mflux/share.mfjp?_token=i8yedNiYfdjrBfGJ8Y5z1128247857&browser=true&filename=ncbi_nt_kma.zip" -d browser=false -o ncbi_nt_kma.zip<br>
DOI: 10.6084/m9.figshare.6753656
title: Additional file 10: of LTR-retrotransposon transcriptome modulation in response to endotoxin-induced stress in PBMCs

description: Table S3. HERVs or MaLRs with the same expression profiles as genes within pathways. (XLS 53 kb)
DOI: 10.6084/m9.figshare.6753656.v1
title: Additional file 10: of LTR-retrotransposon transcriptome modulation in response to endotoxin-induced stress in PBMCs

description: Table S3. HERVs or MaLRs with the same expression profiles as genes within pathways. (XLS 53 kb)
DOI: 10.6084/m9.figshare.24849654.v6
title: Marketing Mix Modelling (MMM) data for a large panel of eCommerce brands provided by Conjura (https://www.conjura.com)

description: This data was made publicly available by <b>Conjura (https://www.conjura.com)</b> under Creative Commons license to support the advancement of <b>Marketing Mix Modelling (MMM)</b> for eCommerce brands. The data provides a daily-level of marketing spend and web purchases for a large cross-section of eCommerce brands and is suitable for modelling the cost of acquiring customers (CAC) and return on advertising spend (ROAS). If using the data please refer to the data dictionary provided for important details.
DOI: 10.6084/m9.figshare.24849654.v5
title: Marketing Mix Modelling (MMM) data for a large panel of eCommerce brands (https://www.conjura.com)

description: This data was made public by Conjura (https://www.conjura.com) to support the advancement of Marketing Mix Modelling (MMM) for eCommerce brands. The data can be used to the model the cost of acquiring customers (CAC) and return on advertising spend (ROAS) from a large cross-section of eCommerce brands in order to find robust MMM models.
DOI: 10.15468/429a9w
title: Red list of flora and fauna of Donetsk region of Ukraine

description: The checklist consists of species of animals and plants that are rare or endangered in the territory of the Donetsk region of Ukraine. The checklist was implemented by the decision of the Donetsk Regional Council dated February 29, 2000 #23/11-255 and order of the Ministry of Ecology and Natural Resources of Ukraine dated September 11, 2017 #333 "On Approval of the List of Animal Species Subject to Special Protection in the Territory of Donetsk Oblast".
DOI: 10.6084/m9.figshare.6753665
title: MOESM2 of DDIT4 promotes gastric cancer proliferation and tumorigenesis through the p53 and MAPK pathways

description: Additional file 2: Table S1. The effect of DDIT4-knockdown on phosphorylation of signal protein.
DOI: 10.6084/m9.figshare.6753665.v1
title: MOESM2 of DDIT4 promotes gastric cancer proliferation and tumorigenesis through the p53 and MAPK pathways

description: Additional file 2: Table S1. The effect of DDIT4-knockdown on phosphorylation of signal protein.
DOI: 10.5281/zenodo.10724779
title: Tracking Brand-Associated Polarity-Bearing Topics in User Reviews
DOI: 10.5281/zenodo.10724780
title: Tracking Brand-Associated Polarity-Bearing Topics in User Reviews
DOI: 10.6084/m9.figshare.8850857
title: SelS promote cell survive

description: cell death was quantified by TUNEL and PI staining <br>
DOI: 10.6084/m9.figshare.8850860
title: Acute Deletion of METTL14 in β-cells of adult mice results in glucose intolerance

description: <b>Introduction</b>: To understand the molecular mechanism of glucose intolerance, we performed RNA sequencing to detect the gene expression in beta-cell <i>Mettl14</i> special knockout mice and wild type mice.<b> Material and Methods</b>: Polyadenylated RNA was further enriched from total RNA by using Dyabeads mRNA Purification Kit. All samples were sequenced using Illumina Hiseq 4000 at the University of Chicago Genomic Facility. Sequence reads were aligned to mouse transcriptome (GRCm38.vM17 downloaded from genecode) and quantified using Kallisto at pair-end mode with 30 tomes bootstrap. Transcript level differential expression analysis was performed using sleuth. Inference of differential expression between WT and beta KO mice was made by likelihood ratio and log fold change was obtained using the Wald test. The inference leveraged bootstrap to take uncertainty of quantification into account and leveraged biological replicates to take account the biological variability.<b> Result: </b>The expression levels of 106 transcripts were significantly altered in beta KO islets compared to WT islets. Among those altered genes, 104 genes were upregulated and 2 genes were downregulated.<b>Conclusion:</b><i> Mettl14</i> special knockout in beta-cell induces glucose intolerance by changing genes trascription.<br>
DOI: 10.6084/m9.figshare.11996595
title: Scalable Hyperparameter Selection for Latent Dirichlet Allocation

description: Latent Dirichlet allocation (LDA) is a heavily used Bayesian hierarchical model used in machine learning for modeling high-dimensional sparse count data, for example, text documents. As a Bayesian model, it incorporates a prior on a set of latent variables. The prior is indexed by some hyperparameters, which have a big impact on inference regarding the model. The ideal estimate of the hyperparameters is the empirical Bayes estimate which is, by definition, the maximizer of the marginal likelihood of the data with all the latent variables integrated out. This estimate cannot be obtained analytically. In practice, the hyperparameters are chosen either in an ad-hoc manner, or through some variants of the EM algorithm for which the theoretical basis is weak. We propose an MCMC-based fully Bayesian method for obtaining the empirical Bayes estimate of the hyperparameter. We compare our method with other existing approaches both on synthetic and real data. The comparative experiments demonstrate that the LDA model with hyperparameters specified by our method outperforms models with the hyperparameters estimated by other methods. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.11996595.v2
title: Scalable Hyperparameter Selection for Latent Dirichlet Allocation

description: Latent Dirichlet allocation (LDA) is a heavily used Bayesian hierarchical model used in machine learning for modeling high-dimensional sparse count data, for example, text documents. As a Bayesian model, it incorporates a prior on a set of latent variables. The prior is indexed by some hyperparameters, which have a big impact on inference regarding the model. The ideal estimate of the hyperparameters is the empirical Bayes estimate which is, by definition, the maximizer of the marginal likelihood of the data with all the latent variables integrated out. This estimate cannot be obtained analytically. In practice, the hyperparameters are chosen either in an ad-hoc manner, or through some variants of the EM algorithm for which the theoretical basis is weak. We propose an MCMC-based fully Bayesian method for obtaining the empirical Bayes estimate of the hyperparameter. We compare our method with other existing approaches both on synthetic and real data. The comparative experiments demonstrate that the LDA model with hyperparameters specified by our method outperforms models with the hyperparameters estimated by other methods. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.11996595.v1
title: Scalable Hyperparameter Selection for Latent Dirichlet Allocation

description: Latent Dirichlet Allocation (LDA) is a heavily-used Bayesian hierarchical model used in machine learning for modelling high-dimensional sparse count data, for example, text documents. As a Bayesian model, it incorporates a prior on a set of latent variables. The prior is indexed by some hyperparameters, which have a big impact on inference regarding the model. The ideal estimate of the hyperparameters is the empirical Bayes estimate which is, by definition, the maximizer of the marginal likelihood of the data with all the latent variables integrated out. This estimate cannot be obtained analytically. In practice, the hyperparameters are chosen either in an ad-hoc manner, or through some variants of the EM algorithm for which the theoretical basis is weak. We propose an MCMC-based fully-Bayesian method for obtaining the empirical Bayes estimate of the hyperparameter. We compare our method with other existing approaches both on synthetic and real data. The comparative experiments demonstrate that the LDA model with hyperparameters specified by our method outperforms models with the hyperparameters estimated by other methods. Supplemental materials for the paper are available online.
DOI: 10.6084/m9.figshare.6753716
title: Additional file 2: of LTR-retrotransposon transcriptome modulation in response to endotoxin-induced stress in PBMCs

description: Table S1. Detection of the HERV transcriptome in PBMCs. (XLSX 145 kb)
DOI: 10.6084/m9.figshare.6753716.v1
title: Additional file 2: of LTR-retrotransposon transcriptome modulation in response to endotoxin-induced stress in PBMCs

description: Table S1. Detection of the HERV transcriptome in PBMCs. (XLSX 145 kb)
DOI: 10.18434/mds2-3184
title: Hurricane Maria Wind-Field Model for Puerto Rico
DOI: 10.6084/m9.figshare.25308679
title: 2023 Approved small-molecule drugs

description: From blogpost https://cdsouthan.blogspot.com/2024/01/patent-mapping-2023-drug-approvals.html
DOI: 10.6084/m9.figshare.6753782
title: Additional file 6: of LTR-retrotransposon transcriptome modulation in response to endotoxin-induced stress in PBMCs

description: Table S2. Differential expression of HERV-V3 chip repertoires induced by stimulation state changes in endotoxin tolerance model. (XLSX 41775 kb)
DOI: 10.6084/m9.figshare.6753782.v1
title: Additional file 6: of LTR-retrotransposon transcriptome modulation in response to endotoxin-induced stress in PBMCs

description: Table S2. Differential expression of HERV-V3 chip repertoires induced by stimulation state changes in endotoxin tolerance model. (XLSX 41775 kb)
DOI: 10.6084/m9.figshare.5705278
title: Phylogenetic and expression analysis of the magnesium transporter family in pear, and functional verification of <i>PbrMGT7</i> in pear pollen

description: The magnesium ion (Mg<sup>2+</sup>) is the most abundant divalent cation in living cells, and it plays essential roles in various cellular functions. Mg<sup>2+</sup> homeostasis in plant cells is crucial for plant growth. The <i>MRS2</i>/<i>MGT</i> family of proteins localise to various membranes, and they function during Mg<sup>2+</sup> transport in plants, but their functions are largely unknown in fruit trees. In this study, we performed a genome-wide analysis to identify the <i>MGT</i> gene family members in the pear <i>Pyrus bretschneideri</i>. Sixteen <i>MGT</i> genes were identified. Analysis of the activity of pear pollen showed that a low-concentration magnesium ion treatment was beneficial for pollen germination and pollen tube growth. None of the 16 <i>MGT</i> genes were expressed in any unique tissue, including pollen, and their expression in magnesium-treated pollen varied greatly, where <i>PbrMGT7</i> was the most sensitive and it was tested as a representative. <i>PbrMGT7</i> could functionally complement a bacterial strain deficient in Mg<sup>2+</sup>, thereby indicating a role in magnesium transport. A co-localisation experiment confirmed that <i>PbrMGT7</i> was localised in the mitochondria, which suggests that <i>PbrMGT7</i> could mediate Mg-trafficking between the mitochondria and cytosol. Overall, these results suggest that <i>PbrMGT7</i> is related to Mg<sup>2+</sup> homeostasis during pear pollen tube growth.​​
DOI: 10.6084/m9.figshare.5705278.v1
title: Phylogenetic and expression analysis of the magnesium transporter family in pear, and functional verification of <i>PbrMGT7</i> in pear pollen

description: The magnesium ion (Mg<sup>2+</sup>) is the most abundant divalent cation in living cells, and it plays essential roles in various cellular functions. Mg<sup>2+</sup> homeostasis in plant cells is crucial for plant growth. The <i>MRS2</i>/<i>MGT</i> family of proteins localise to various membranes, and they function during Mg<sup>2+</sup> transport in plants, but their functions are largely unknown in fruit trees. In this study, we performed a genome-wide analysis to identify the <i>MGT</i> gene family members in the pear <i>Pyrus bretschneideri</i>. Sixteen <i>MGT</i> genes were identified. Analysis of the activity of pear pollen showed that a low-concentration magnesium ion treatment was beneficial for pollen germination and pollen tube growth. None of the 16 <i>MGT</i> genes were expressed in any unique tissue, including pollen, and their expression in magnesium-treated pollen varied greatly, where <i>PbrMGT7</i> was the most sensitive and it was tested as a representative. <i>PbrMGT7</i> could functionally complement a bacterial strain deficient in Mg<sup>2+</sup>, thereby indicating a role in magnesium transport. A co-localisation experiment confirmed that <i>PbrMGT7</i> was localised in the mitochondria, which suggests that <i>PbrMGT7</i> could mediate Mg-trafficking between the mitochondria and cytosol. Overall, these results suggest that <i>PbrMGT7</i> is related to Mg<sup>2+</sup> homeostasis during pear pollen tube growth.​​
DOI: 10.6084/m9.figshare.8326727
title: Additional file 2: of Mining traits for the enrichment and isolation of not-yet-cultured populations

description: Table S3. The raw reads and normalized metatranscriptomic data as RPKM, MRPKM, CRPKM, and LCRPKM for clades IB and IIA. (XLSX 2562 kb)
DOI: 10.6084/m9.figshare.8326727.v1
title: Additional file 2: of Mining traits for the enrichment and isolation of not-yet-cultured populations

description: Table S3. The raw reads and normalized metatranscriptomic data as RPKM, MRPKM, CRPKM, and LCRPKM for clades IB and IIA. (XLSX 2562 kb)
DOI: 10.6084/m9.figshare.23531107
title: Electron transfer processes associated with structural Fe in clay minerals

description: Fe-bearing clay minerals are widely distributed in soils, sediments, and rocks, representing a significant Fe pool in the Earth’s crust. The electron transfer (ET) from/to structural Fe in clay minerals is a crucial electron and energy flux in the natural environment, which drives numerous biogeochemical processes and contaminant transformation. Depending on the types and properties of both clay minerals and exogenous reactants as well as aqueous chemistry, the ET processes could involve interfacial ET through edge/basal planes and interior ET inside clay minerals. This paper reviews the important ET reactions between Fe-bearing clay minerals and various reactants, including Fe-cycling microbes, redox-active organic compounds, and heavy metals. Moreover, we discuss the physical-chemical mechanisms of interfacial and interior ET processes and develop models to illustrate the thermodynamic and kinetic constraints on the ET rate and extent. On this basis, we emphasize the environmental implications of ET associated with clay minerals, such as their roles in serving as biogeobatteries for biogeochemical processes and contaminant transformation, coevolution with microbes, and regulation of greenhouse gas formation. Finally, research needs are proposed to advance our molecular-scale understanding of ET processes and utilize them for environmental mitigation and human health.
DOI: 10.6084/m9.figshare.6753893
title: Additional file 10: of CDC42 controls the activation of primordial follicles by regulating PI3K signaling in mouse oocytes

description: Individual data values. (XLSX 30 kb)
DOI: 10.6084/m9.figshare.6753893.v1
title: Additional file 10: of CDC42 controls the activation of primordial follicles by regulating PI3K signaling in mouse oocytes

description: Individual data values. (XLSX 30 kb)
DOI: 10.25592/uhhfdm.9611
title: An ALNS algorithm for the static dial-a-ride problem with ride and waiting time minimization - instance data

description: This data set includes the instances used in the paper "An ALNS algorithm for the static dial-a-ride problem with ride and waiting time minimization" <em>OR Spectrum</em> <strong>44, </strong>87–119 (2022). Both the instances used for the final calculations as well as the ones used for the preliminary studies and parameter tuning in the appendix are present.
DOI: 10.25592/uhhfdm.9610
title: An ALNS algorithm for the static dial-a-ride problem with ride and waiting time minimization - instance data

description: This data set includes the instances used in the paper "An ALNS algorithm for the static dial-a-ride problem with ride and waiting time minimization" <em>OR Spectrum</em> <strong>44, </strong>87–119 (2022). Both the instances used for the final calculations as well as the ones used for the preliminary studies and parameter tuning in the appendix are present.
DOI: 10.6084/m9.figshare.19336816
title: Table S2. Genetic maps constructed in the study from Evolution of the sex-determining region in <i>Ginkgo biloba</i>

description: The file lists location of SNP markers for 12 chromosomes in the male and female genetic maps
DOI: 10.6084/m9.figshare.19336816.v1
title: Table S2. Genetic maps constructed in the study from Evolution of the sex-determining region in <i>Ginkgo biloba</i>

description: The file lists location of SNP markers for 12 chromosomes in the male and female genetic maps