cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh3416343.08fu
title: SH3416343.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh3416344.08fu
title: SH3416344.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh3416345.08fu
title: SH3416345.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh3416346.08fu
title: SH3416346.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh3416347.08fu
title: SH3416347.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh3416348.08fu
title: SH3416348.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh3416349.08fu
title: SH3416349.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh3416350.08fu
title: SH3416350.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh3416351.08fu
title: SH3416351.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.6084/m9.figshare.19619120
title: Additional file 17 of Systematic trait dissection in oilseed rape provides a comprehensive view, further insight, and exact roadmap for yield determination

description: Additional file 17: Table S10. The DEGs identified by RNA-seq of SAM in the initial stage of floral bud differentiation between Zhongshuang11 and No.73290.
DOI: 10.6084/m9.figshare.19619123
title: Additional file 18 of Systematic trait dissection in oilseed rape provides a comprehensive view, further insight, and exact roadmap for yield determination

description: Additional file 18: Table S11. List of primers used in this study, including fine-mapping, gene cloning, and qRT-PCR.
DOI: 10.6084/m9.figshare.13332813
title: Synthesis and crystal structure of two new Zn(II) and Ni(II) coordination polymers with anti-ovarian cancer activity

description: By using a mixed-ligand approach, two new coordination polymers with the chemical formula of {[Zn(L)(ip)·H<sub>2</sub>O]<sub>8</sub>}<sub>n</sub> (<b>1</b>, H<sub>2</sub>ip = isophthalic acid and L = 1,1’-(2-methylpropane-1,3-diyl)bis(1H-benzo[d]imidazole)) and {[Ni(L)(tdc)·2H<sub>2</sub>O]<sub>2</sub>}<sub>n</sub> (<b>2</b>, H<sub>2</sub>tdc = 2,5-thiophenedicarboxylic acid) have been hydrothermally synthesized and structurally characterized by single-crystal X-ray diffraction analyses, powder X-ray diffraction, thermogravimetric analysis and elemental analysis. In addition, <i>in vitro</i> anticancer activity of compounds <b>1</b> and <b>2</b> on four human ovarian cancer cells (CoC1, A2780, 3AO and OVCAR) was further determined. The results showed that compared with their organic ligands, the two compounds displayed efficient antitumor activity.
DOI: 10.6084/m9.figshare.14381185.v1
title: Diagnostic and prognostic value of ABC transporter family member ABCG1 gene in clear cell renal cell carcinoma

description: As the most common histologic subtype of renal cancer, clear cell renal cell carcinoma (ccRCC) poses a serious threat to public health. However, there are no specific molecular-targeted drugs for ccRCC at present. Human ATP-binding cassette (ABC) transporter family plays an important role in homeostasis maintenance. This study aimed to evaluate the potential diagnostic value of <i>ABC</i> genes in ccRCC. A total of 952 samples of ccRCC patients (707) and controls (245) from three different datasets were included for analysis. Receiver operating characteristic analysis and t-test were used to analyze the differential expression of <i>ABC</i> genes in ccRCC patients and control samples at mRNA level during screening and validations. The Cancer Genome Atlas (TCGA-ccRCC) dataset was utilized to investigate the correlation between ABC genes expression and prognostic value in ccRCC. We then investigated the interactions between <i>ABCG1</i> and proteins in the Comparative Toxicogenomics Database (CTD). Finally, we found that ATP-binding cassette transporter G member 1 (<i>ABCG1</i>) was over-expressed in ccRCC patients compared with healthy samples at mRNA level. Cox regression analysis and Kaplan–Meier analysis showed that ccRCC patients with high <i>ABCG1</i> expression had better overall survival (OS) than those patients with low expression (hazard ratio (HR) = 0.662, <i>p</i> = 0.007). This study demonstrated that <i>ABCG1</i> is a potential diagnostic and prognostic biomarker in ccRCC and discussed the molecular mechanisms underlying the relationship between ccRCC and <i>ABCG1</i>, which might provide guidance for better management and treatment of ccRCC in the future.
DOI: 10.6084/m9.figshare.7041194
title: Additional file 2: of Three new Diplozoidae mitogenomes expose unusual compositional biases within the Monogenea class: implications for phylogenetic studies

description: Nucleotide composition and skewness comparison of different elements of the mitochondrial genomes of Paradiplozoon opsariichthydis, Sindiplozoon sp. and Eudiplozoon sp.. NCR: non-coding region; PCG: protein-coding gene. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.19619117.v1
title: Additional file 16 of Systematic trait dissection in oilseed rape provides a comprehensive view, further insight, and exact roadmap for yield determination

description: Additional file 16: Table S9. The annotated genes in the fine-mapped genomic regions of four representative hub-QTL clusters.
DOI: 10.6084/m9.figshare.13332813.v1
title: Synthesis and crystal structure of two new Zn(II) and Ni(II) coordination polymers with anti-ovarian cancer activity

description: By using a mixed-ligand approach, two new coordination polymers with the chemical formula of {[Zn(L)(ip)·H<sub>2</sub>O]<sub>8</sub>}<sub>n</sub> (<b>1</b>, H<sub>2</sub>ip = isophthalic acid and L = 1,1’-(2-methylpropane-1,3-diyl)bis(1H-benzo[d]imidazole)) and {[Ni(L)(tdc)·2H<sub>2</sub>O]<sub>2</sub>}<sub>n</sub> (<b>2</b>, H<sub>2</sub>tdc = 2,5-thiophenedicarboxylic acid) have been hydrothermally synthesized and structurally characterized by single-crystal X-ray diffraction analyses, powder X-ray diffraction, thermogravimetric analysis and elemental analysis. In addition, <i>in vitro</i> anticancer activity of compounds <b>1</b> and <b>2</b> on four human ovarian cancer cells (CoC1, A2780, 3AO and OVCAR) was further determined. The results showed that compared with their organic ligands, the two compounds displayed efficient antitumor activity.
DOI: 10.6084/m9.figshare.13332601
title: Transcriptome analysis of azacitidine (5-AzaC)-treatment affecting the development of early somatic embryogenesis in longan

description: DNA methylation plays key roles in regulating genes which control somatic embryogenesis (SE) in plant. 5-Azacytidine (5-AzaC) was considered as a common inhibitor of DNA methylation. Longan (<i>Dimocarpus longan</i> Lour.) SE has been established and used as model system for studying mechanism of SE in woody plants. However, effects of 5-AzaC on longan EC and the underlying mechanism at molecular level are rarely understood. In this study, RNA-seq was performed for transcriptome analysis of longan EC treated with or without 5-AzaC were analysed. A total of 29,232 expressed genes were obtained by aligned to longan reference genome and 1,617 differentially expressed genes (DEGs) were got in the pairwise comparisons of CK_<i>vs</i>_T. Integrating the KEGG enrichment pathway analysis showed that ‘butanoate metabolism’, ‘C5-branched dibasic acid metabolism’, ‘sulphur metabolism’, ‘selenocompound metabolism’, ‘pantothenate and CoA biosynthesis’, ‘phagosome’, and ‘plant hormone signal transduction’ were significantly enriched pathways, while the analysis of DEGs revealed that 5-AzaC-treatment could alter genes expression which related to the SE to adjust the complicated metabolic pathways. Therefore, these results indicated that 5-AzaC-treatment positively impact the development of early SE from longan and a decrease in the global DNA methylation level during early SE in longan.
DOI: 10.6084/m9.figshare.13332601.v1
title: Transcriptome analysis of azacitidine (5-AzaC)-treatment affecting the development of early somatic embryogenesis in longan

description: DNA methylation plays key roles in regulating genes which control somatic embryogenesis (SE) in plant. 5-Azacytidine (5-AzaC) was considered as a common inhibitor of DNA methylation. Longan (<i>Dimocarpus longan</i> Lour.) SE has been established and used as model system for studying mechanism of SE in woody plants. However, effects of 5-AzaC on longan EC and the underlying mechanism at molecular level are rarely understood. In this study, RNA-seq was performed for transcriptome analysis of longan EC treated with or without 5-AzaC were analysed. A total of 29,232 expressed genes were obtained by aligned to longan reference genome and 1,617 differentially expressed genes (DEGs) were got in the pairwise comparisons of CK_<i>vs</i>_T. Integrating the KEGG enrichment pathway analysis showed that ‘butanoate metabolism’, ‘C5-branched dibasic acid metabolism’, ‘sulphur metabolism’, ‘selenocompound metabolism’, ‘pantothenate and CoA biosynthesis’, ‘phagosome’, and ‘plant hormone signal transduction’ were significantly enriched pathways, while the analysis of DEGs revealed that 5-AzaC-treatment could alter genes expression which related to the SE to adjust the complicated metabolic pathways. Therefore, these results indicated that 5-AzaC-treatment positively impact the development of early SE from longan and a decrease in the global DNA methylation level during early SE in longan.
DOI: 10.6084/m9.figshare.19619108.v1
title: Additional file 13 of Systematic trait dissection in oilseed rape provides a comprehensive view, further insight, and exact roadmap for yield determination

description: Additional file 13: Table S6. Polymorphism of SNPs within the pericentromere region of the 19 chromosomes.
DOI: 10.6084/m9.figshare.19619120.v1
title: Additional file 17 of Systematic trait dissection in oilseed rape provides a comprehensive view, further insight, and exact roadmap for yield determination

description: Additional file 17: Table S10. The DEGs identified by RNA-seq of SAM in the initial stage of floral bud differentiation between Zhongshuang11 and No.73290.
DOI: 10.6084/m9.figshare.11760030
title: Additional file 6 of Whole-transcriptome sequencing uncovers core regulatory modules and gene signatures of human fetal growth restriction

description: Additional file 6: Table S6. GSEA of key signaling pathway enrichment.
DOI: 10.6084/m9.figshare.19619099
title: Additional file 10 of Systematic trait dissection in oilseed rape provides a comprehensive view, further insight, and exact roadmap for yield determination

description: Additional file 10: Table S3. Summary statistics of the correlation among 21 traits investigated in six environments.
DOI: 10.4121/ca5b3196-ac7c-4753-93cd-099d82277a99
title: Code underlying the MSc thesis: Observing human gait and detecting falls: A model-based approach based on wearable sensors

description: Code complementing the thesis by Sachin Umans for the degree of MSc Systems & Control from the TU Delft. Contains a model-based, pre-impact fall detector algorithm based on a single wearable IMU sensor. MSc thesis: <strong>Observing human gait and detecting falls</strong>
DOI: 10.6084/m9.figshare.25218434
title: Automated model building and protein identification in cryo-EM maps

description: Atomic models described in the main text of the ModelAngelo paper by Jamali et al. in Nature (2024) and built by ModelAngelo.
DOI: 10.6084/m9.figshare.11760012
title: Additional file 4 of Whole-transcriptome sequencing uncovers core regulatory modules and gene signatures of human fetal growth restriction

description: Additional file 4: Table S4. Differentially expressed protein-coding genes, lncRNAs, and miRNAs.
DOI: 10.6084/m9.figshare.11760030.v1
title: Additional file 6 of Whole-transcriptome sequencing uncovers core regulatory modules and gene signatures of human fetal growth restriction

description: Additional file 6: Table S6. GSEA of key signaling pathway enrichment.
DOI: 10.6084/m9.figshare.7565726
title: Supporting information from Photodegradation of naphthalene over Fe<sub>3</sub>O<sub>4</sub> under visible light irradiation

description: Using FeCl<sub>3</sub> and FeSO<sub>4</sub> as precursors, Fe<sub>3</sub>O<sub>4</sub> were prepared by co-precipitation method via FeCl<sub>3</sub> and FeSO<sub>4</sub> aqueous solutions successively added in NaOH solution. The sample was proved by X-ray powder diffraction, transmission electron microscope, ultraviolet–visible spectrophotometry and magnetic measurement. The results showed that the prepared Fe<sub>3</sub>O<sub>4</sub> material was composed of an average diameter of about 15 nm particles and nano rods with well-crystallized magnetite and stronger superparamagnetic, getting a saturation magnetization of 49.5 emu g<sup>−1</sup>. This Fe<sub>3</sub>O<sub>4</sub> material was found to be an effective catalyst for photodegradation of naphthalene with or without H<sub>2</sub>O<sub>2</sub> under visible light irradiation, getting 81.1% and 74.3% degradation rate in these two cases, respectively. The degradation pathway in the absence and presence of H<sub>2</sub>O<sub>2</sub> was analysed via measurement of the distribution of degradation products by GC-MS and adsorption of reactants on the surface of the catalyst by <i>in situ</i> DRIFTS spectra.
DOI: 10.6084/m9.figshare.7565726.v1
title: Supporting information from Photodegradation of naphthalene over Fe<sub>3</sub>O<sub>4</sub> under visible light irradiation

description: Using FeCl<sub>3</sub> and FeSO<sub>4</sub> as precursors, Fe<sub>3</sub>O<sub>4</sub> were prepared by co-precipitation method via FeCl<sub>3</sub> and FeSO<sub>4</sub> aqueous solutions successively added in NaOH solution. The sample was proved by X-ray powder diffraction, transmission electron microscope, ultraviolet–visible spectrophotometry and magnetic measurement. The results showed that the prepared Fe<sub>3</sub>O<sub>4</sub> material was composed of an average diameter of about 15 nm particles and nano rods with well-crystallized magnetite and stronger superparamagnetic, getting a saturation magnetization of 49.5 emu g<sup>−1</sup>. This Fe<sub>3</sub>O<sub>4</sub> material was found to be an effective catalyst for photodegradation of naphthalene with or without H<sub>2</sub>O<sub>2</sub> under visible light irradiation, getting 81.1% and 74.3% degradation rate in these two cases, respectively. The degradation pathway in the absence and presence of H<sub>2</sub>O<sub>2</sub> was analysed via measurement of the distribution of degradation products by GC-MS and adsorption of reactants on the surface of the catalyst by <i>in situ</i> DRIFTS spectra.
DOI: 10.6084/m9.figshare.11760042
title: Additional file 7 of Whole-transcriptome sequencing uncovers core regulatory modules and gene signatures of human fetal growth restriction

description: Additional file 7: Table S7. GSEA of key hallmark enrichment.