cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22922080.v1
title: Complete mitochondrial genome of the little-known regional endemic <i>Aporia hastata</i> (Oberthür, 1892) (Lepidoptera: Pieridae)

description: The present study reports the mitochondrial genome of <i>A. hastata</i> (Oberthür, 1892), a little-known <i>Aporia</i> species endemic to the southern margin of the Hengduan Mountains in Yunnan Province. This genome is circular, 15,148 bp in length, and consists of 13 PCGs, 22 tRNAs, and two rRNAs. The Bayesian phylogenetic tree clusters <i>A. hastata</i> with other <i>Aporia</i> taxa inside tribe Pierini Duponchel, [1835]. The findings of this study add valuable new information to the genus <i>Aporia</i> and are beneficial to a better understanding of phylogeography of these butterflies.
DOI: 10.6084/m9.figshare.20300788.v1
title: Antimicrobial resistance in <i>Vibrio cholerae</i> O1/O139 clinical isolates: a systematic review and meta-analysis

description: <i>Vibrio cholerae</i> O1/O139 is responsible for cholera epidemics that remains a huge public health menace across the globe. Furthermore, an increasing resistance rate among <i>V. cholerae</i> strains has been reported around the world. Therefore, the objective of this meta-analysis was to evaluate the weighted pooled resistance (WPR) rates in clinical <i>V. cholerae</i> O1/O139 isolates based on different years, areas, antimicrobial susceptibility testing, and resistance rates. We searched the studies in PubMed, Scopus, Embase, and Web of Science (until January 2020). Statistical analyses were conducted using STATA software (ver. 14.0). A total of 139 studies investigating 24,062 <i>V. cholerae</i> O1/O139 isolates were analyzed. The majority of the studies originated in Asia (<i>n</i> = 102). The WPR rates were as follows: azithromycin 1%, erythromycin 36%, ciprofloxacin 3%, cotrimoxazole 79%, doxycycline 7%, and tetracycline 20%. There was increased resistance to cotrimoxazole, ciprofloxacin, and tetracycline during the 1980–2020 years. Temporal changes in antibiotic resistance rate found in this study demonstrated the critical continuous surveillance of antibiotic resistance. Also, ciprofloxacin, azithromycin, gentamicin, cephalexin, imipenem, ofloxacin, and norfloxacin were found to be the best antibiotics against <i>V. cholera</i>, with the highest and the lowest effectiveness resistance rate.
DOI: 10.6084/m9.figshare.7717820
title: Time resolved gene expression analysis during tamoxifen adaption of MCF-7 cells identifies long non-coding RNAs with prognostic impact

description: Acquired tamoxifen resistance is a persistent problem for the treatment of estrogen receptor positive, premenopausal breast cancer patients and predictive biomarkers are still elusive. We here analyzed gene expression changes in a cellular model to identify early and late changes upon tamoxifen exposure and thereby novel prognostic biomarkers. Estrogen receptor positive MCF-7 cells were incubated with 4OH-tamoxifen (10 nM) and gene expression analyzed by array hybridization during 12 weeks. Array results were confirmed by nCounter- and qRT-PCR technique. Pathway enrichment analysis revealed that early responses concerned mainly amine synthesis and NRF2-related signaling and evolved into a stable gene expression pattern within 4 weeks characterized by changes in glucuronidation-, estrogen metabolism-, nuclear receptor- and interferon signaling pathways. As a large number of long non coding RNAs was subject to regulation, we investigated 5 of these (linc01213, linc00632 linc0992, LOC101929547 and XR_133213) in more detail. From these, only linc01213 was upregulated but all were less abundant in estrogen-receptor negative cell lines (MDA-MB 231, SKBR-3 and UACC3199). In a web-based survival analysis linc01213 and linc00632 turned out to have prognostic impact. Linc01213 was investigated further by plasmid-mediated over-expression as well as siRNA down-regulation in MCF-7 cells. Nevertheless, this had no effect on proliferation or expression of tamoxifen regulated genes, but migration was increased. In conclusion, the cellular model identified a set of lincRNAs with prognostic relevance for breast cancer. One of these, linc01213 although regulated by 4OH-tamoxifen, is not a central regulator of tamoxifen adaption, but interferes with the regulation of migration.
DOI: 10.6084/m9.figshare.7193516
title: Additional file 1: of Non-target site-based resistance to tribenuron-methyl and essential involved genes in Myosoton aquaticum (L.)

description: Quality assessment of the reads generated from RNA-Seq for the resistant (MR) and susceptible (S) Mysoton aquaticum populations. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.11912052.v1
title: Predicting (in)correctly: listeners rapidly use unexpected information to revise their predictions

description: Comprehenders can incorporate rich contextual information to predict upcoming input on the fly, and cues that conflict with their predictions are quickly detected. The present study examined whether and how comprehenders may revise their existing predictions upon encountering a prediction-inconsistent cue. We took advantage of the rich classifier system in Mandarin Chinese and tracked participants’ eye-movements as they listened to sentences in which the final noun is preceded by a classifier which was either compatible with the most expected noun, incompatible with the most expected noun but indicative of another contextually suitable noun, or uninformative. We found that, upon hearing a prediction-inconsistent classifier, listeners quickly directed their eye gaze away from the originally expected object and immediately onto the (initially) unexpected but contextually suitable object. This provides initial evidence that listeners can quickly use prediction-mismatching cues to revise their existing predictions on the fly.
DOI: 10.6084/m9.figshare.7193504.v1
title: Additional file 7: of Transcriptome analysis reveals the molecular mechanisms of the defense response to gray leaf spot disease in maize

description: Up-regulated and down-regulated wall-associated kinases in ‘Yayu889’ and ‘Zhenghong532’ at 89, 91, and 93 days post planting, respectively. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.7717820.v1
title: Time resolved Gene Expression Analysis during Tamoxifen adaption of MCF-7 cells identifies long non-coding RNAs with prognostic Impact

description: Acquired tamoxifen resistance is a persistent problem for the treatment of estrogen receptor positive, premenopausal breast cancer patients and predictive biomarkers are still elusive. We here analyzed gene expression changes in a cellular model to identify early and late changes upon tamoxifen exposure and thereby novel prognostic biomarkers. Estrogen receptor positive MCF-7 cells were incubated with 4OH-tamoxifen (10 nM) and gene expression analyzed by array hybridization during 12 weeks. Array results were confirmed by nCounter- and qRT-PCR technique. Pathway enrichment analysis revealed that early responses concerned mainly amine synthesis and NRF2-related signaling and evolved into a stable gene expression pattern within 4 weeks characterized by changes in glucuronidation-, estrogen metabolism-, nuclear receptor- and interferon signaling pathways. As a large number of long non coding RNAs was subject to regulation, we investigated 5 of these (linc01213, linc00632 linc0992, LOC101929547 and XR_133213) in more detail. From these, only linc01213 was upregulated but all were less abundant in estrogen-receptor negative cell lines (MDA-MB 231, SKBR-3 and UACC3199). In a web-based survival analysis linc01213 and linc00632 turned out to have prognostic impact. Linc01213 was investigated further by plasmid-mediated over-expression as well as siRNA down-regulation in MCF-7 cells. Nevertheless, this had no effect on proliferation or expression of tamoxifen regulated genes, but migration was increased. In conclusion, the cellular model identified a set of lincRNAs with prognostic relevance for breast cancer. One of these, linc01213 although regulated by 4OH-tamoxifen, is not a central regulator of tamoxifen adaption, but interferes with the regulation of migration.
DOI: 10.6084/m9.figshare.14526212.v1
title: Additional file 12 of Basic leucine zipper (bZIP) transcription factor genes and their responses to drought stress in ginseng, Panax ginseng C.A. Meyer

description: Table S8. Primers used for qRT-PCR analysis.
DOI: 10.6084/m9.figshare.7193495.v1
title: Additional file 6: of Transcriptome analysis reveals the molecular mechanisms of the defense response to gray leaf spot disease in maize

description: Up-regulated and down-regulated PR genes in ‘Yayu889’ and ‘Zhenghong532’ at 89, 91, and 93 days post planting, respectively. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.14526218.v1
title: Additional file 2 of Basic leucine zipper (bZIP) transcription factor genes and their responses to drought stress in ginseng, Panax ginseng C.A. Meyer

description: Table S2. The 62 PgbZIP genes that were spliced into transacripts having full-length ORFs and their putative protein sequences.
DOI: 10.6084/m9.figshare.14526236
title: Additional file 8 of Basic leucine zipper (bZIP) transcription factor genes and their responses to drought stress in ginseng, Panax ginseng C.A. Meyer

description: Table S6. Expressions of the 273 PgbZIP transcripts in the four-year-old roots of 42 genotypes, 14 tissues of a four-year-old plant and 4 different year-old roots.
DOI: 10.6084/m9.figshare.14526212
title: Additional file 12 of Basic leucine zipper (bZIP) transcription factor genes and their responses to drought stress in ginseng, Panax ginseng C.A. Meyer

description: Table S8. Primers used for qRT-PCR analysis.
DOI: 10.6084/m9.figshare.12436517
title: COVID-19 severity correlates with airway epithelium-immune cell interactions identified by single-cell analysis

description: <b>Single-cell RNA-Seq of airway samples of COVID-19 patients and healthy controls</b><br>This dataset comprises single-cell RNA-Seq data of nasopharyngeal, protected specimen brush, and bronchial lavage samples of 19 COVID-19 patients (eight moderate and eleven critical according to the WHO classification) and five healthy controls, for a total of 36 samples. <br>An in-depth description is presented in the manuscript "Cross-talk between the airway epithelium and activated immune cells defines severity in COVID-19" (https://www.medrxiv.org/content/10.1101/2020.04.29.20084327v1). <br>The data is uploaded as two .rds files of Seurat objects that can be imported into R. The _main file contains all samples from the nasopharynx, while the _loc file contains data from nasopharyngeal, protected specimen brush, and bronchial lavage samples of two patients. <br>A quantification of viral RNA reads (as CPM, in total over cells and background) is provided as .xlsx file. Please note that these values may differ from viral load estimates obtained from diagnostic procedures and may be less accurate.Raw count values (cellranger output) are provided in the file count_matrices_NBT.tar.<br>
DOI: 10.6084/m9.figshare.14526233
title: Additional file 7 of Basic leucine zipper (bZIP) transcription factor genes and their responses to drought stress in ginseng, Panax ginseng C.A. Meyer

description: Table S5. Annotation and GO categorization of the 273 PgbZIP transcripts.
DOI: 10.20393/c4b5ae62-4c8d-11ee-be56-0242ac120002
title: Herring Spawning Areas

description: Herring eggs are deposited on the seabed in discrete gravel beds or flat stone and the herring are completely reliant on these spawning beds for reproduction. Spawning beds refers to known discrete gravel beds used by herring. Nearby spawning beds are grouped into spawning grounds, which may contain one or more spawning beds. Spawning grounds are further grouped into spawning areas.
DOI: 10.6084/m9.figshare.7193516.v1
title: Additional file 1: of Non-target site-based resistance to tribenuron-methyl and essential involved genes in Myosoton aquaticum (L.)

description: Quality assessment of the reads generated from RNA-Seq for the resistant (MR) and susceptible (S) Mysoton aquaticum populations. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7717820.v2
title: Time resolved gene expression analysis during tamoxifen adaption of MCF-7 cells identifies long non-coding RNAs with prognostic impact

description: Acquired tamoxifen resistance is a persistent problem for the treatment of estrogen receptor positive, premenopausal breast cancer patients and predictive biomarkers are still elusive. We here analyzed gene expression changes in a cellular model to identify early and late changes upon tamoxifen exposure and thereby novel prognostic biomarkers. Estrogen receptor positive MCF-7 cells were incubated with 4OH-tamoxifen (10 nM) and gene expression analyzed by array hybridization during 12 weeks. Array results were confirmed by nCounter- and qRT-PCR technique. Pathway enrichment analysis revealed that early responses concerned mainly amine synthesis and NRF2-related signaling and evolved into a stable gene expression pattern within 4 weeks characterized by changes in glucuronidation-, estrogen metabolism-, nuclear receptor- and interferon signaling pathways. As a large number of long non coding RNAs was subject to regulation, we investigated 5 of these (linc01213, linc00632 linc0992, LOC101929547 and XR_133213) in more detail. From these, only linc01213 was upregulated but all were less abundant in estrogen-receptor negative cell lines (MDA-MB 231, SKBR-3 and UACC3199). In a web-based survival analysis linc01213 and linc00632 turned out to have prognostic impact. Linc01213 was investigated further by plasmid-mediated over-expression as well as siRNA down-regulation in MCF-7 cells. Nevertheless, this had no effect on proliferation or expression of tamoxifen regulated genes, but migration was increased. In conclusion, the cellular model identified a set of lincRNAs with prognostic relevance for breast cancer. One of these, linc01213 although regulated by 4OH-tamoxifen, is not a central regulator of tamoxifen adaption, but interferes with the regulation of migration.
DOI: 10.6084/m9.figshare.7193561
title: Additional file 5: of Non-target site-based resistance to tribenuron-methyl and essential involved genes in Myosoton aquaticum (L.)

description: The respective numbers of overlapping up-regulated genes in comparative treatment groups. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7193552.v1
title: Additional file 4: of Non-target site-based resistance to tribenuron-methyl and essential involved genes in Myosoton aquaticum (L.)

description: The annotation for unigenes of Myosoton aquaticum. (XLSX 14194 kb)
DOI: 10.6084/m9.figshare.15058005.v1
title: Anti-neoplastic characteristics and potential targets of calycosin against bisphenol A-related osteosarcoma: bioinformatics analysis

description: Environmentally, bisphenol A (BPA) is a well-known pollutant caused human health risk, including osteosarcoma (OS). OS, a deadly bone neoplasia, may occur in children and adults. However, the anti-OS pharmacotherapy prescribes limitedly in clinical practice. Interestingly, previous experimental evidences indicate calycosin-exerting potential anti-OS actions. Thus, in this report, we aimed to further characterize and detail the therapeutic targets and molecular mechanisms of calycosin-anti-BPA-related OS by using network pharmacology and molecular docking analyses. In results, the bioinformatics data disclosed all mapped, core targets, biological functions, molecular pathways of calycosin to treat BPA-related OS. The computational analysis using molecular docking indicated that potential binding ability of core targets in calycosin to treat BPA-related OS was identified. Moreover, detailed biological functions and optimal pathways of calycosin-anti-BPA-related OS were revealed, as shown in integrated network maps. Taken together, these network pharmacology and structural biology findings illustrate the core biotargets, pharmacological functions and pathways of calycosin-anti-BPA-related OS. Potentially, these core targets identified by molecular docking may attribute to the potential clinical application of calycosin against BPA-related OS.
DOI: 10.6084/m9.figshare.14526236.v1
title: Additional file 8 of Basic leucine zipper (bZIP) transcription factor genes and their responses to drought stress in ginseng, Panax ginseng C.A. Meyer

description: Table S6. Expressions of the 273 PgbZIP transcripts in the four-year-old roots of 42 genotypes, 14 tissues of a four-year-old plant and 4 different year-old roots.
DOI: 10.6084/m9.figshare.7193552
title: Additional file 4: of Non-target site-based resistance to tribenuron-methyl and essential involved genes in Myosoton aquaticum (L.)

description: The annotation for unigenes of Myosoton aquaticum. (XLSX 14194 kb)
DOI: 10.6084/m9.figshare.14526215.v1
title: Additional file 1 of Basic leucine zipper (bZIP) transcription factor genes and their responses to drought stress in ginseng, Panax ginseng C.A. Meyer

description: Table S1. The PgbZIP genes identified in this study and their transcript sequences.
DOI: 10.6084/m9.figshare.14526209
title: Additional file 11 of Basic leucine zipper (bZIP) transcription factor genes and their responses to drought stress in ginseng, Panax ginseng C.A. Meyer

description: Table S7. Plant materials used for this study.
DOI: 10.15156/bio/sh507610.07fu
title: SH507610.07FU

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/sh507611.07fu
title: SH507611.07FU

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/sh2775046.08fu
title: SH2775046.08FU

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/sh2775047.08fu
title: SH2775047.08FU

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/sh2775048.08fu
title: SH2775048.08FU

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/sh507612.07fu
title: SH507612.07FU

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.