cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14300067.v1
title: Additional file 5 of m7GDisAI: N7-methylguanosine (m7G) sites and diseases associations inference based on heterogeneous network

description: Additional file 5. Table S5: m7G chemical similarity matrix ACSN.
DOI: 10.6084/m9.figshare.14300073.v1
title: Additional file 7 of m7GDisAI: N7-methylguanosine (m7G) sites and diseases associations inference based on heterogeneous network

description: Additional file 7. Table S7: Disease semantic similarity network ADD.
DOI: 10.6084/m9.figshare.14300070.v1
title: Additional file 6 of m7GDisAI: N7-methylguanosine (m7G) sites and diseases associations inference based on heterogeneous network

description: Additional file 6. Table S6: m7G CNF similarity matrix ACNFSN.
DOI: 10.6084/m9.figshare.14300073
title: Additional file 7 of m7GDisAI: N7-methylguanosine (m7G) sites and diseases associations inference based on heterogeneous network

description: Additional file 7. Table S7: Disease semantic similarity network ADD.
DOI: 10.6084/m9.figshare.14300076
title: Additional file 8 of m7GDisAI: N7-methylguanosine (m7G) sites and diseases associations inference based on heterogeneous network

description: Additional file 8. Table S8: Predicted ovarian cancer related m7G sites and their host genes.
DOI: 10.6084/m9.figshare.22688685.v1
title: Additional file 13 of Positive mood-related gut microbiota in a long-term closed environment: a multiomics study based on the “Lunar Palace 365” experiment

description: Additional file 13: Table S1. The key species with VIP score ≥ 1 in more than 50% of the psychological factors.
DOI: 10.6084/m9.figshare.12202985.v1
title: A new choristodere (Reptilia: Choristodera) from an Aptian–Albian coal deposit in China

description: Choristoderes are a small clade of freshwater aquatic reptiles known from deposits of Jurassic–Miocene age. They show their greatest diversity in the Early Cretaceous of Asia, with seven recorded genera including longirostrine and brevirostine taxa, long- and short-necked taxa, and representatives of both neochoristoderes and non-neochoristoderes. The latter, informal grouping, comprising <i>Monjurosuchus</i>, <i>Philydrosaurus</i>, <i>Hyphalosaurus</i>, <i>Khurendukhosaurus</i> and, probably, <i>Shokawa</i>, is distinguished by the closure of the lower temporal fenestra. This differentiates them from typically diapsid stem choristoderes like the Jurassic Euramerican <i>Cteniogenys</i> and from all neochoristoderes like <i>Champsosaurus</i> and <i>Simoeodosaurus</i>. The recent description of <i>Coeruleodraco jurassicus</i> from the Callovian/Oxfordian of China provided the first example of an Asian non-neochoristodere with an open lower temporal fenestra. Here, we describe a second, geologically younger, genus and species from the Shahai Formation of Badaohao locality in western Liaoning, considered to be Aptian–Albian in age. This adds an eighth choristodere genus to the Early Cretaceous Asian record. The new species shares the diapsid skull morphology of <i>C. jurassicus</i>, demonstrating that a lineage of small, brevirostrine choristoderes with fully diapsid skulls persisted in Asia until the latter part of the Early Cretaceous. https://zoobank.org:pub:2D0B390A-6291-4C29-A72A-4F6A507C608B
DOI: 10.6084/m9.figshare.22688697
title: Additional file 17 of Positive mood-related gut microbiota in a long-term closed environment: a multiomics study based on the “Lunar Palace 365” experiment

description: Additional file 17: Table S5.The key metabolites with VIP score ≥ 1 in all the potential psychobiotics.
DOI: 10.6084/m9.figshare.23208037
title: Additional file 1 of Identification of Vitis vinifera MYB transcription factors and their response against grapevine berry inner necrosis virus

description: Additional file 1: Table S1. Summary information of physiological and biochemical properties of the VvMYB proteins.
DOI: 10.6084/m9.figshare.12202985
title: A new choristodere (Reptilia: Choristodera) from an Aptian–Albian coal deposit in China

description: Choristoderes are a small clade of freshwater aquatic reptiles known from deposits of Jurassic–Miocene age. They show their greatest diversity in the Early Cretaceous of Asia, with seven recorded genera including longirostrine and brevirostine taxa, long- and short-necked taxa, and representatives of both neochoristoderes and non-neochoristoderes. The latter, informal grouping, comprising <i>Monjurosuchus</i>, <i>Philydrosaurus</i>, <i>Hyphalosaurus</i>, <i>Khurendukhosaurus</i> and, probably, <i>Shokawa</i>, is distinguished by the closure of the lower temporal fenestra. This differentiates them from typically diapsid stem choristoderes like the Jurassic Euramerican <i>Cteniogenys</i> and from all neochoristoderes like <i>Champsosaurus</i> and <i>Simoeodosaurus</i>. The recent description of <i>Coeruleodraco jurassicus</i> from the Callovian/Oxfordian of China provided the first example of an Asian non-neochoristodere with an open lower temporal fenestra. Here, we describe a second, geologically younger, genus and species from the Shahai Formation of Badaohao locality in western Liaoning, considered to be Aptian–Albian in age. This adds an eighth choristodere genus to the Early Cretaceous Asian record. The new species shares the diapsid skull morphology of <i>C. jurassicus</i>, demonstrating that a lineage of small, brevirostrine choristoderes with fully diapsid skulls persisted in Asia until the latter part of the Early Cretaceous. https://zoobank.org:pub:2D0B390A-6291-4C29-A72A-4F6A507C608B
DOI: 10.6084/m9.figshare.22688694.v1
title: Additional file 16 of Positive mood-related gut microbiota in a long-term closed environment: a multiomics study based on the “Lunar Palace 365” experiment

description: Additional file 16: Table S4. Prediction of potential psychobiotics with PLS regression models based on metabolites. (xlsx 12 kb).
DOI: 10.6084/m9.figshare.22688706
title: Additional file 20 of Positive mood-related gut microbiota in a long-term closed environment: a multiomics study based on the “Lunar Palace 365” experiment

description: Additional file 20: Table S8. Major nutrients intake during the “Lunar Palace 365” experiment.
DOI: 10.6084/m9.figshare.16921517
title: Additional file 4 of SVDNVLDA: predicting lncRNA-disease associations by Singular Value Decomposition and node2vec

description: Additional file 4. The precision results of different features in classifiers.
DOI: 10.6084/m9.figshare.16921529.v1
title: Additional file 6 of SVDNVLDA: predicting lncRNA-disease associations by Singular Value Decomposition and node2vec

description: Additional file 6. The complete case study results of lung cancer.
DOI: 10.6084/m9.figshare.16921517.v1
title: Additional file 4 of SVDNVLDA: predicting lncRNA-disease associations by Singular Value Decomposition and node2vec

description: Additional file 4. The precision results of different features in classifiers.
DOI: 10.6084/m9.figshare.16921523.v1
title: Additional file 5 of SVDNVLDA: predicting lncRNA-disease associations by Singular Value Decomposition and node2vec

description: Additional file 5. The complete case study results of breast cancer.
DOI: 10.6084/m9.figshare.16921535
title: Additional file 7 of SVDNVLDA: predicting lncRNA-disease associations by Singular Value Decomposition and node2vec

description: Additional file 7. The complete case study results of pancreatic cancer.
DOI: 10.6084/m9.figshare.16921505
title: Additional file 1 of SVDNVLDA: predicting lncRNA-disease associations by Singular Value Decomposition and node2vec

description: Additional file 1. The numerical values of diagonal elements in the importance matrix Σ.
DOI: 10.6084/m9.figshare.16921505.v1
title: Additional file 1 of SVDNVLDA: predicting lncRNA-disease associations by Singular Value Decomposition and node2vec

description: Additional file 1. The numerical values of diagonal elements in the importance matrix Σ.
DOI: 10.6084/m9.figshare.16921541.v1
title: Additional file 8 of SVDNVLDA: predicting lncRNA-disease associations by Singular Value Decomposition and node2vec

description: Additional file 8. The statistical overview of experimental data.
DOI: 10.6084/m9.figshare.16921523
title: Additional file 5 of SVDNVLDA: predicting lncRNA-disease associations by Singular Value Decomposition and node2vec

description: Additional file 5. The complete case study results of breast cancer.
DOI: 10.6084/m9.figshare.16921529
title: Additional file 6 of SVDNVLDA: predicting lncRNA-disease associations by Singular Value Decomposition and node2vec

description: Additional file 6. The complete case study results of lung cancer.
DOI: 10.6084/m9.figshare.16921541
title: Additional file 8 of SVDNVLDA: predicting lncRNA-disease associations by Singular Value Decomposition and node2vec

description: Additional file 8. The statistical overview of experimental data.
DOI: 10.6084/m9.figshare.16921508
title: Additional file 2 of SVDNVLDA: predicting lncRNA-disease associations by Singular Value Decomposition and node2vec

description: Additional file 2. The sensitivity results of different features in classifiers.
DOI: 10.6084/m9.figshare.16921535.v1
title: Additional file 7 of SVDNVLDA: predicting lncRNA-disease associations by Singular Value Decomposition and node2vec

description: Additional file 7. The complete case study results of pancreatic cancer.
DOI: 10.6084/m9.figshare.16921508.v1
title: Additional file 2 of SVDNVLDA: predicting lncRNA-disease associations by Singular Value Decomposition and node2vec

description: Additional file 2. The sensitivity results of different features in classifiers.
DOI: 10.6084/m9.figshare.16921511.v1
title: Additional file 3 of SVDNVLDA: predicting lncRNA-disease associations by Singular Value Decomposition and node2vec

description: Additional file 3. The specificity results of different features in classifiers.
DOI: 10.6084/m9.figshare.22688706.v1
title: Additional file 20 of Positive mood-related gut microbiota in a long-term closed environment: a multiomics study based on the “Lunar Palace 365” experiment

description: Additional file 20: Table S8. Major nutrients intake during the “Lunar Palace 365” experiment.
DOI: 10.6084/m9.figshare.23208040
title: Additional file 2 of Identification of Vitis vinifera MYB transcription factors and their response against grapevine berry inner necrosis virus

description: Additional file 2: Table S2. The VvMYB transcription factors distributed on different subgroups.
DOI: 10.6084/m9.figshare.23208049
title: Additional file 4 of Identification of Vitis vinifera MYB transcription factors and their response against grapevine berry inner necrosis virus

description: Additional file 4: Table S4. Summary information of VvMYBs and AtMYBs amino acid sequence FASTA file.
DOI: 10.6084/m9.figshare.23208049.v1
title: Additional file 4 of Identification of Vitis vinifera MYB transcription factors and their response against grapevine berry inner necrosis virus

description: Additional file 4: Table S4. Summary information of VvMYBs and AtMYBs amino acid sequence FASTA file.
DOI: 10.6084/m9.figshare.7484513
title: Time-course analysis of nuclear events during conjugation in the marine ciliate <i>Euplotes vannus</i> and comparison with other ciliates (Protozoa, Ciliophora)

description: Ciliates represent a morphologically and genetically distinct group of single-celled eukaryotes that segregate germline and somatic functions into two types of nuclei and exhibit complex cytogenetic events during the sexual process of conjugation, which is under the control of the so-called “mating type systems”. Studying conjugation in ciliates may provide insight into our understanding of the origins and evolution of sex and fertilization. In the present work, we studied in detail the sexual process of conjugation using the model species <i>Euplotes vannus</i>, and compared these nuclear events with those occurring in other ciliates. Our results indicate that in <i>E. vannus</i>: 1) conjugation requires about 75 hours to complete: the longest step is the development of the new macronucleus (ca. 64h), followed by the nuclear division of meiosis I (5h); the mitotic divisions usually take only 2h; 2) there are three prezygotic divisions (mitosis and meiosis I and II), and two of the eight resulting nuclei become pronuclei; 3) after the exchange and fusion of the pronuclei, two postzygotic divisions occur; two of the four products differentiate into the new micronucleus and macronucleus, respectively, and the parental macronucleus degenerates completely; 4) comparison of the nuclear events during conjugation in different ciliates reveals that there are generally three prezygotic divisions while the number of postzygotic divisions is highly variable. These results can serve as reference to investigate the mating type system operating in this species and to analyze genes involved in the different steps of the sexual process.
DOI: 10.6084/m9.figshare.23208055
title: Additional file 6 of Identification of Vitis vinifera MYB transcription factors and their response against grapevine berry inner necrosis virus

description: Additional file 6: Table S6. Expression patterns of 41 VvMYB genes during the process of GINV infection by qRT-PCR.
DOI: 10.6084/m9.figshare.7484516
title: LncRNA MIAT overexpression reduced neuron apoptosis in a neonatal rat model of hypoxic-ischemic injury through miR-211/GDNF

description: <b>Objective</b>: To investigate the underlying mechanism of lncRNA myocardial infarction-associated transcript (MIAT) in hypoxic-ischemic (HI)-induced neonatal cerebral palsy. <b>Materials and methods</b>: Neonatal rat model of HI injury was established to detect the motor function. LncRNA MIAT, miR-211, glial cell line-derived neurotrophic factor (GDNF) and caspase-3 expressions were measured by qRT-PCR or western blot. The apoptosis of Neuro2A cells was detected by flow cytometry. RNA immunoprecipitation (RIP) and RNA pull-down assays were performed to confirm the interaction between MIAT and miR-211. <b>Results</b>: Compared with control group, lncRNA MIAT and GDNF were downregulated in striatal tissues of neonatal rats in HI group and oxygen glucose deprivation (OGD)-induced ischemic injury of Neuro2A cells, whereas miR-211 was up-regulated in striatal tissues of HI group and OGD-induced ischemic injury of Neuro2A cells. LncRNA MIAT interacted with miR-211, and lncRNA MIAT overexpression reduced neuron apoptosis through miR-211. Besides, GDNF expression was positively regulated by lncRNA MIAT and negatively regulated by miR-211 in Neuro2A cells. <i>In vivo</i> experiment proved MIAT promoted motor function and relieved HI injury. <b>Conclusion</b>: MIAT overexpression reduced apoptosis of Neuro2A cells through miR-211/GDNF, which relieved HI injury of neonatal rats.
DOI: 10.6084/m9.figshare.23213185
title: Effect of chlorpyrifos on the expression and regulation of salivary gland protein of <i>Haemaphysalis longicornis</i>

description: The aim of this study is to explore the detoxification and homoeostasis functions of salivary glands, and to look for possible target proteins of new drugs for tick prevention and treatment. Different concentrations of chlorpyrifos to deal with the semi-engorged female <i>Haemaphysalis longicornis</i>, through the DIA quantitative proteomics method to quantitatively determine of all the proteins in the salivary glands, and through a variety of the depth of the bioinformatics methods for protein analysis and function mining, explain the molecular mechanism of detoxification function of salivary glands. Quantitative information from 5 normal groups and 8 different treatment groups showed that a total of 3152 proteins were identified. The expression levels of these proteins changed with the chlorpyrifos different concentration and treatment times. However, after the overall analysis, it was found that after the action of chlorpyrifos, the proteins involved in detoxification, such as glutathione S-transferase and glutamine synthetase, the heat shock proteins involved in stress, and the acid sphingomyelinase involved in maintaining the body’s homoeostasis had corresponding changes. We found and explained the functions of detoxification, stress, and homoeostasis of salivary glands. The regulatory strategies of proteins that played a key role in these functions were explored.
DOI: 10.6084/m9.figshare.23213185.v1
title: Effect of chlorpyrifos on the expression and regulation of salivary gland protein of <i>Haemaphysalis longicornis</i>

description: The aim of this study is to explore the detoxification and homoeostasis functions of salivary glands, and to look for possible target proteins of new drugs for tick prevention and treatment. Different concentrations of chlorpyrifos to deal with the semi-engorged female <i>Haemaphysalis longicornis</i>, through the DIA quantitative proteomics method to quantitatively determine of all the proteins in the salivary glands, and through a variety of the depth of the bioinformatics methods for protein analysis and function mining, explain the molecular mechanism of detoxification function of salivary glands. Quantitative information from 5 normal groups and 8 different treatment groups showed that a total of 3152 proteins were identified. The expression levels of these proteins changed with the chlorpyrifos different concentration and treatment times. However, after the overall analysis, it was found that after the action of chlorpyrifos, the proteins involved in detoxification, such as glutathione S-transferase and glutamine synthetase, the heat shock proteins involved in stress, and the acid sphingomyelinase involved in maintaining the body’s homoeostasis had corresponding changes. We found and explained the functions of detoxification, stress, and homoeostasis of salivary glands. The regulatory strategies of proteins that played a key role in these functions were explored.
DOI: 10.6084/m9.figshare.7484678.v1
title: Supplemental tables from Social affiliation predicts mitochondrial DNA copy number in female rhesus macaques

description: Study subject information, summary statistics, and model results.
DOI: 10.6084/m9.figshare.23208037.v1
title: Additional file 1 of Identification of Vitis vinifera MYB transcription factors and their response against grapevine berry inner necrosis virus

description: Additional file 1: Table S1. Summary information of physiological and biochemical properties of the VvMYB proteins.
DOI: 10.6084/m9.figshare.23208043.v1
title: Additional file 3 of Identification of Vitis vinifera MYB transcription factors and their response against grapevine berry inner necrosis virus

description: Additional file 3: Table S3. Distribution of VvMYB genes on grapevine chromosomes.
DOI: 10.6084/m9.figshare.22688787.v1
title: Additional file 2 of A graph neural network-based interpretable framework reveals a novel DNA fragility–associated chromatin structural unit

description: Additional file 2: Table S1. Robustness evaluation for DSB-GNN against different Hi-C processing parameters. Table S2. Results of ablation experiments. Table S3. Performance comparison between DSB-GNN, LightGBM and Random Forest with different subsets of features. Table S4. The distribution of 1D genomic distance from prediction site to 1-hop and 2-hop neighbours. Table S5. 1242 loops with at least one anchor developing DSBs. Table S6. Comparison of different thresholds for contact counts. Table S7. Comparison of different numbers of GAT or GCN layers.
DOI: 10.6084/m9.figshare.7484678
title: Supplemental tables from Social affiliation predicts mitochondrial DNA copy number in female rhesus macaques

description: Study subject information, summary statistics, and model results.
DOI: 10.6084/m9.figshare.22688787
title: Additional file 2 of A graph neural network-based interpretable framework reveals a novel DNA fragility–associated chromatin structural unit

description: Additional file 2: Table S1. Robustness evaluation for DSB-GNN against different Hi-C processing parameters. Table S2. Results of ablation experiments. Table S3. Performance comparison between DSB-GNN, LightGBM and Random Forest with different subsets of features. Table S4. The distribution of 1D genomic distance from prediction site to 1-hop and 2-hop neighbours. Table S5. 1242 loops with at least one anchor developing DSBs. Table S6. Comparison of different thresholds for contact counts. Table S7. Comparison of different numbers of GAT or GCN layers.
DOI: 10.6084/m9.figshare.22688745
title: Additional file 2 of Genome-wide identification and expression analysis of BZR gene family and associated responses to abiotic stresses in cucumber (Cucumis sativus L.)

description: Supplementary Material 2
DOI: 10.15156/bio/sh319493.07fu
title: SH319493.07FU

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/sh1683106.08fu
title: SH1683106.08FU

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/sh1683107.08fu
title: SH1683107.08FU

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.