cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh3296730.08fu
title: SH3296730.08FU

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/sh3296731.08fu
title: SH3296731.08FU

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/sh3296732.08fu
title: SH3296732.08FU

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/sh3296733.08fu
title: SH3296733.08FU

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/sh3296734.08fu
title: SH3296734.08FU

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/sh3296735.08fu
title: SH3296735.08FU

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/sh3296736.08fu
title: SH3296736.08FU

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.12601255
title: Propensity Score Matched Analysis Comparing Robotic-Assisted with Laparoscopic Posterior Retroperitoneal Adrenalectomy

description: To compare the perioperative outcomes between robotic posterior retroperitoneal adrenalectomy (RPRA) with laparoscopic posterior retroperitoneal adrenalectomy (LPRA) for adrenal tumors and to identify which group of patients may benefit from RPRA. A total of 401 patients who fulfilled the inclusion criteria were collected and analyzed; among them, 86 and 315 patients underwent RPRA and LPRA, respectively. To adjust for potential baseline confounders, propensity score matching (PSM) was conducted at a 1:1 ratio. Patient demographics and perioperative outcomes were compared between the two groups. After matching, no differences were found between the two groups in patient demographics or tumor characteristics. The median length of postoperative stay (3 vs. 4 days, <i>p</i> = 0.001) was significantly shorter in the RPRA group, but this group also showed a higher median total hospitalization cost (8121.89 vs. 4107.92 $, <i>p</i> &lt; 0.001). There was no difference in the median operative duration (100 vs. 110 min, <i>p</i> = 0.554), median estimated blood loss (50 vs. 50 ml, <i>p</i> = 0.730), transfusion rate (<i>p</i> = 0.497) or incidence of postoperative complications (<i>p</i> = 0.428). According to our research, RPRA leads to a shorter postoperative hospitalization stay but a higher total hospitalization cost than LPRA after propensity score matching.
DOI: 10.6084/m9.figshare.24500197
title: GI_urchin BRUV_051123.csv

description: dataset showing Gonad Index (GI, %) for the urchins <i>Centrostephanus rodgersii </i>(long-spined urchin) and <i>Heliocidaris erythrogramma </i>(short-spined urchin) "before", "during" and "after" a Baited Remote Underwater Video (BRUV) experiment using tethered urchins in Wollongong, NSW, Australia.
DOI: 10.6084/m9.figshare.24500197.v1
title: GI_urchin BRUV_051123.csv

description: dataset showing Gonad Index (GI, %) for the urchins <i>Centrostephanus rodgersii </i>(long-spined urchin) and <i>Heliocidaris erythrogramma </i>(short-spined urchin) "before", "during" and "after" a Baited Remote Underwater Video (BRUV) experiment using tethered urchins in Wollongong, NSW, Australia.
DOI: 10.6084/m9.figshare.13123333.v1
title: The epidemic of erythromycin-resistant <i>Bordetella pertussis</i> with limited genome variation associated with pertussis resurgence in China

description: The resurgence of <i>Bordetella pertussis</i> infections leading to whooping cough is a concern in many parts of the world. The number of pertussis cases in China has increased significantly since 2013. In this study, whole-genome sequencing analysis was performed for 388 <i>B. pertussis</i> strains isolated in China from the 1970s to 2018, combining 594 published strains from around the world. This study revealed that lineage V diverged about 50 years ago in China, while lineage IV is dominant in the other countries. It also revealed that the erythromycin-resistant sub-lineages Va, Vb, and Vc with limited genomic variation emerged 11 ~ 12 years ago. These three sub-lineages were identified after the co-purified acellular vaccines (cp-ACVs) completely replaced the previous whole cell vaccines (WCVs) after the national immunization program of 2012. It suggests that the cp-ACVs cannot induce immunity that is potent enough to restrict the spread of the lineage V, antibiotic abuse further favors the spread of this lineage in China. These findings demand a reassessment of the immunization strategy and development of new vaccines in China to stop the resurgence and drug resistance of <i>B. pertussis</i>.
DOI: 10.6084/m9.figshare.13123377.v2
title: Rapid humoral immune responses are required for recovery from haemorrhagic fever with renal syndrome patients

description: Haemorrhagic fever with renal syndrome (HFRS) following Hantaan virus (HTNV) infection displays variable clinical signs. Humoral responses elicited during HTNV infections are considered important, however, this process remains poorly understood. Herein, we have investigated the phenotype, temporal dynamics, and characteristics of B-cell receptor (BCR) repertoire in an HFRS cohort. The serological proﬁles were characterized by a lowered expression level of nucleoprotein (NP)-speciﬁc antibody in severe cases. Importantly, B-cell subsets were activated and proliferated within the first two weeks of symptom onset and moderate cases reacted more rapidly. BCR analysis in the recovery phase revealed a dramatic increase in the immunoglobulin gene diversity which was more significantly progressed in moderate infections. In severe cases, B-cell-related transcription was lower with inflammatory sets overactivated. Taken together, these data suggest the clinical signs and disease recovery in HFRS patients were positively impacted by rapid and efficacious humoral responses.
DOI: 10.6084/m9.figshare.12599391
title: Additional file 1 of LcMYB4, an unknown function transcription factor gene from sheepgrass, as a positive regulator of chilling and freezing tolerance in transgenic Arabidopsis

description: Additional file 1: Table S1. All primers used in this study.
DOI: 10.6084/m9.figshare.13123377.v1
title: Rapid humoral immune responses are required for recovery from haemorrhagic fever with renal syndrome patients

description: Haemorrhagic fever with renal syndrome (HFRS) following Hantaan virus (HTNV) infection displays variable clinical signs. Humoral responses elicited during HTNV infections are considered important, however, this process remains poorly understood. Herein, we have investigated the phenotype, temporal dynamics, and characteristics of B-cell receptor (BCR) repertoire in an HFRS cohort. The serological proﬁles were characterized by a lowered expression level of nucleoprotein (NP)-speciﬁc antibody in severe cases. Importantly, B-cell subsets were activated and proliferated within the first two weeks of symptom onset and moderate cases reacted more rapidly. BCR analysis in the recovery phase revealed a dramatic increase in the immunoglobulin gene diversity which was more significantly progressed in moderate infections. In severe cases, B-cell-related transcription was lower with inflammatory sets overactivated. Taken together, these data suggest the clinical signs and disease recovery in HFRS patients were positively impacted by rapid and efficacious humoral responses.
DOI: 10.6084/m9.figshare.13123377.v3
title: Rapid humoral immune responses are required for recovery from haemorrhagic fever with renal syndrome patients

description: Haemorrhagic fever with renal syndrome (HFRS) following Hantaan virus (HTNV) infection displays variable clinical signs. Humoral responses elicited during HTNV infections are considered important, however, this process remains poorly understood. Herein, we have investigated the phenotype, temporal dynamics, and characteristics of B-cell receptor (BCR) repertoire in an HFRS cohort. The serological proﬁles were characterized by a lowered expression level of nucleoprotein (NP)-speciﬁc antibody in severe cases. Importantly, B-cell subsets were activated and proliferated within the first two weeks of symptom onset and moderate cases reacted more rapidly. BCR analysis in the recovery phase revealed a dramatic increase in the immunoglobulin gene diversity which was more significantly progressed in moderate infections. In severe cases, B-cell-related transcription was lower with inflammatory sets overactivated. Taken together, these data suggest the clinical signs and disease recovery in HFRS patients were positively impacted by rapid and efficacious humoral responses.
DOI: 10.6084/m9.figshare.13647263
title: Additional file 2 of CRISPRi enables isoform-specific loss-of-function screens and identification of gastric cancer-specific isoform dependencies

description: Additional file 2: Table S1. Transcript specific RNA-Seq (using the Salomon algorithm) in 4 gastric cancer cell lines. Table S2. Spacer sequences of sgRNAs used in pooled library. Table S3. Gastric cancer specific altered and un-altered transcripts. Table S4. Results from CRISPRi screen. Data was generated using the MAGeCK algorithm. Table S5. Phospho-proteomic mass spectrometry in YCC3 cells following CRISPRi mediated suppression of CIT expression. Table S6. RNA-Seq in YCC3 cells following CRISPRi mediated suppression of CIT expression. Table S7. Primers used in this study for qPCR and generation of sgRNAs.
DOI: 10.6084/m9.figshare.12599220
title: Additional file 1 of Fasciclin-like arabinogalactan gene family in Nicotiana benthamiana: genome-wide identification, classification and expression in response to pathogens

description: Additional file 1: Table S1. List of NbFLA CDS and protein sequences.
DOI: 10.6084/m9.figshare.12599241.v1
title: Additional file 8 of Fasciclin-like arabinogalactan gene family in Nicotiana benthamiana: genome-wide identification, classification and expression in response to pathogens

description: Additional file 8: Table S5. Primers used in this study.
DOI: 10.6084/m9.figshare.12599229
title: Additional file 4 of Fasciclin-like arabinogalactan gene family in Nicotiana benthamiana: genome-wide identification, classification and expression in response to pathogens

description: Additional file 4: Table S3. Cis-acting elements in NbFLAs.
DOI: 10.6084/m9.figshare.12599389.v1
title: Additional file 1 of Desiccation does not drastically increase the accessibility of exogenous DNA to nuclear genomes: evidence from the frequency of endosymbiotic DNA transfer

description: Additional file 1: Table S1. The NUMT/NUPT contents (contributed by organellar transcribed sequences) of desiccation-tolerant species and their controls. Table S2. The information used in assembling mitochondrial genomes. Table S3. The information used in assigning desiccation-tolerant species and their controls. Table S4. Genome information of the eukaryotes used in this study. Table S5. The NUMT/NUPT contents (contributed by organellar genomes) of desiccation-tolerant species and their controls.
DOI: 10.6084/m9.figshare.13646899.v1
title: Additional file 3 of Putative ligand binding sites of two functionally characterized bark beetle odorant receptors

description: Additional file 3: Supplementary Data 1. Multiple sequence alignment used to generate the ItypOR models.
DOI: 10.6084/m9.figshare.12599392
title: Additional file 2 of Desiccation does not drastically increase the accessibility of exogenous DNA to nuclear genomes: evidence from the frequency of endosymbiotic DNA transfer

description: Additional file 2: Data S1. The mitochondrial genome sequences assembled in this study.
DOI: 10.6084/m9.figshare.23084013.v1
title: Additional file 1 of Whole genome sequencing and analysis of Armillaria gallica Jzi34 symbiotic with Gastrodia elata

description: Additional file 1: TableS1. Ka/Ks value for the collinear P450 gene pairs between A. gallica Jzi34 and other Armillaria.
DOI: 10.6084/m9.figshare.12599241
title: Additional file 8 of Fasciclin-like arabinogalactan gene family in Nicotiana benthamiana: genome-wide identification, classification and expression in response to pathogens

description: Additional file 8: Table S5. Primers used in this study.
DOI: 10.6084/m9.figshare.12599229.v1
title: Additional file 4 of Fasciclin-like arabinogalactan gene family in Nicotiana benthamiana: genome-wide identification, classification and expression in response to pathogens

description: Additional file 4: Table S3. Cis-acting elements in NbFLAs.
DOI: 10.6084/m9.figshare.12599232
title: Additional file 5 of Fasciclin-like arabinogalactan gene family in Nicotiana benthamiana: genome-wide identification, classification and expression in response to pathogens

description: Additional file 5: Table S4. Potential transcription factors of NbFLAs.
DOI: 10.6084/m9.figshare.12599410
title: Additional file 4 of Cow manure application effectively regulates the soil bacterial community in tea plantation

description: Additional file 4: Table S1. The relative abundance of the dominant phyla and P/A ratio in soil bacterial communities.
DOI: 10.6084/m9.figshare.12599146.v1
title: Additional file 3 of Experimental immunization of mice with a recombinant bovine enterovirus vaccine expressing BVDV E0 protein elicits a long-lasting serologic response

description: Additional file 3: Table S1. The raw data of the anti-BEV VP1 antibodies detection in experimental mice Table S2. The raw data of the anti-BVDV E0 antibodies detection in experimental mice
DOI: 10.6084/m9.figshare.12599146
title: Additional file 3 of Experimental immunization of mice with a recombinant bovine enterovirus vaccine expressing BVDV E0 protein elicits a long-lasting serologic response

description: Additional file 3: Table S1. The raw data of the anti-BEV VP1 antibodies detection in experimental mice Table S2. The raw data of the anti-BVDV E0 antibodies detection in experimental mice
DOI: 10.6084/m9.figshare.23609519
title: m<sup>6</sup>A mRNA Methylation Analysis Provides Novel Insights into Pigmentation in Sheep Skin

description: N6-methyladenosine (m<sup>6</sup>A) is the most universal post-transcriptional modification of mRNA which may play important roles in verious species. However, the potential roles of m<sup>6</sup>A in the pigmentation of skin are not completely understood. To explore the role of m6A modification in pigmentation of sheep skin, we used MeRIP-seq and RNA-seq to profile the skin transcriptome in black and white coat color (<i>n=</i>3). Our results showed that an average of 7701 m<sup>6</sup>A peaks were obtained for all samples and the average length was 305.89 bp. The GGACUU sequence was the most enrichment motif and shared in black skin and white skin. The m<sup>6</sup>A peaks were mainly enriched in the CDS, 3'UTR and 5'UTR, especially in CDS region near the stop codon of the transcript. 235 signiﬁcantly differential peaks were found in black skin vs. white skin. The KEGG signaling pathways of downregulated and upregulated m<sup>6</sup>A peaks were mainly enriched in AGE-RAGE signaling pathway in diabetic complications, Viral carcinogenesis, Transcriptional misregulation in cancer, ABC transporters, Basal transcription factors and Thyroid hormone synthesis (<i>P</i> value &lt;0.05). For RNA-seq, 71 differently expressed genes (DEGs) were scanned in black skin vs. white skin. DEGs were significantly enriched in tyrosine metabolism, melanogenesis, neuroactive ligand-receptor interaction pathway (<i>P</i> value &lt;0.05). Combined m<sup>6</sup>A-seq and RNA-seq analysis showed that the hyper-up genes and hypo-up genes were both enriched in ErbB signaling pathway (<i>P</i> value &lt;0.05). In conclusion, it provide a basis for further research into the functions of m<sup>6</sup>A methylation modiﬁcations in pigmentation.
DOI: 10.6084/m9.figshare.12599437.v1
title: Additional file 4 of Time-resolved multi-omics analysis reveals the role of nutrient stress-induced resource reallocation for TAG accumulation in oleaginous fungus Mortierella alpina

description: Additional file 4. Unsupervised time-resolved trend clustering analyses.