cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh1181479.09fu
title: SH1181479.09FU

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/sh1181480.09fu
title: SH1181480.09FU

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.21151342
title: Additional file 5 of Key factors for differential drought tolerance in two contrasting wild materials of Artemisia wellbyi identified using comparative transcriptomics

description: Additional file 5: Table S5. Drought-induced DETs in the drought-tolerant A.wellbyi under drought stress.
DOI: 10.6084/m9.figshare.21151300
title: Additional file 11 of Key factors for differential drought tolerance in two contrasting wild materials of Artemisia wellbyi identified using comparative transcriptomics

description: Additional file 11: Table S11. Photosynthesis-related genes in the drought-sensitive A.wellbyi under drought stress.
DOI: 10.6084/m9.figshare.5427271
title: Hierarchical Low Rank Approximation of Likelihoods for Large Spatial Datasets

description: Datasets in the fields of climate and environment are often very large and irregularly spaced. To model such datasets, the widely used Gaussian process models in spatial statistics face tremendous challenges due to the prohibitive computational burden. Various approximation methods have been introduced to reduce the computational cost. However, most of them rely on unrealistic assumptions for the underlying process and retaining statistical efficiency remains an issue. We develop a new approximation scheme for maximum likelihood estimation. We show how the composite likelihood method can be adapted to provide different types of hierarchical low rank approximations that are both computationally and statistically efficient. The improvement of the proposed method is explored theoretically; the performance is investigated by numerical and simulation studies; and the practicality is illustrated through applying our methods to two million measurements of soil moisture in the area of the Mississippi River basin, which facilitates a better understanding of the climate variability. Supplementary material for this article is available online.
DOI: 10.6084/m9.figshare.7524497
title: Additional file 7: of Comparative analysis of the mitochondrial genomes of oriental spittlebug trible Cosmoscartini: insights into the relationships among closely related taxa

description: Table S5. Primer used in this study. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.19583431.v1
title: Melatonin promotes apoptosis of thyroid cancer cells via regulating the signaling of microRNA-21 (miR-21) and microRNA-30e (miR-30e)

description: Melatonin (MEL) is an effective therapeutic choice for thyroid cancer treatment. In this study, we aimed to explored the potential effect of MEL upon the drug sensitivity of cancer cells and the according underlying mechanisms. Thyroid cancer mice were established as a control group and a MEL group to observe the in vivo effect of MEL. Tumor size and weight in nude mice were detected to evaluate the effect of MEL on tumor growth. Immunohistochemistry assay (IHC) and Western blot were performed to analyze the expression of PTEN protein in tumor cells or tumor cells. After 32 days of cancer cell implantation, MEL was found to significantly repress tumor growth in nude mice approximately by half. Moreover, MEL also suppressed tumor cell proliferation, while apparently activating the apoptosis of tumor cells. In addition, hydrogen sulfide (H<sub>2</sub>S) production was obviously elevated by MEL treatment. Mechanistically, the expression of phosphatase and tensin homolog (PTEN) was remarkably activated by MEL treatment in tumor tissues of implanted TPC-1 and BCPaP cells in nude mice. Meanwhile, MEL inhibited the expression of miR-21 and miR-30e and promoted the expression of lncRNA-cancer susceptibility candidate 7 (CASC7). Both miR-21 and miR-30e could suppress PTEN expression, while miR-21 could also inhibit the expression of lncRNA-CASC7. In conclusion, the results demonstrated that the MEL administration could downregulate the expression of miR-21 and miR-30e, which resulted in increased expression of PTEN, a pro-apoptotic tumor suppressor, to promote the apoptosis of thyroid cancer cells.
DOI: 10.6084/m9.figshare.7524554
title: Additional file 1: of Analysis of repeated leukocyte DNA methylation assessments reveals persistent epigenetic alterations after an incident myocardial infarction

description: Supplemental methods, Table S1. CpGs from KORA EWAS. Those CpGs with a false discovery rate P &lt; 0.15 in an epigenome-wide association study in KORA using the difference in methylation between the baseline and follow-up exams as the outcome (after adjustment for technical factors) and the occurrence of an MI as the predictor while adjusting for clinical covariates (at both baseline and follow-up) in a generalized estimating equations model. Table S2. The 174 CpGs which were retained from the initial elastic net model performed in KORA. Table S3. Epigenetic loci with non-zero coefficients from the NAS elastic net model. Table S4. AUC for the model fit with the loci with non-zero betas from the NAS elastic net in KORA, NAS, and InCHIANTI. Table S5. Medication usage in KORA at baseline and follow-up. We divide out the medication usage in KORA at (a) baseline and (b) follow-up for those individuals who did not develop and incident MI during the observation time (MI free) vs those that did (MI cases). Table S6. Association between 11 epigenetic fingerprint loci and medications. Associations were performed relative to both starting and stopping six classes of medications: diuretic, beta-blockers, anti-platelet, calcium channel blocker, statins, ACE-inhibitor, and angiotensin inhibitor. Table S7. Count of the genes within 1 Mb of each epigenetic fingerprint loci. Table S8. Integration of methylation, gene expression, and metabolomics for the suggestive (P &lt; 0.001) gene expression-metabolite associations. Figure S1. Post hoc power estimations for the observed effects at our FDR cutoff of 0.15 for the initial screening EWAS. (ZIP 196 kb)
DOI: 10.6084/m9.figshare.7524599
title: Additional file 7: of DNA methylation age is not affected in psoriatic skin tissue

description: Table S6. Three hundred and one candidates Ps-dependent age-associated CpGs contrasted by PN and PP using a loose cut-off (Pâ &lt;â 0.01). (XLSX 79Â kb)
DOI: 10.6084/m9.figshare.21680513.v1
title: Dataset1.zip

description: Additional projected images from simulations and experiments
DOI: 10.6084/m9.figshare.21151956.v1
title: Additional file 1 of The clinical characteristics and treatment of ovarian malignant mesoderm mixed tumor: a systematic review

description: Additional file 1.
DOI: 10.6084/m9.figshare.21152066.v1
title: Additional file 5 of A circular RNA derived from GLIS3 accelerates the proliferation of glioblastoma cells through competitively binding with miR-449c-5p to upregulate CAPG and GLIS3

description: Additional file 5: Table S3. Sequences for FISH probes targeting circGLIS3, CAPG and GLIS3.
DOI: 10.6084/m9.figshare.21151300.v1
title: Additional file 11 of Key factors for differential drought tolerance in two contrasting wild materials of Artemisia wellbyi identified using comparative transcriptomics

description: Additional file 11: Table S11. Photosynthesis-related genes in the drought-sensitive A.wellbyi under drought stress.
DOI: 10.6084/m9.figshare.8280746
title: <i>De novo</i> lipogenesis at the mitotic exit is used for nuclear envelope reassembly/expansion. Implications for combined chemotherapy

description: Mitosis has been traditionally considered a metabolically inactive phase. We have previously shown, however, that extensive alterations in lipids occur as the cells traverse mitosis, including increased <i>de novo</i> fatty acid (FA) and phosphatidylcholine (PtdCho) synthesis and decreased lysophospholipid content. Given the diverse structural and functional properties of these lipids, we sought to study their metabolic fate and their importance for cell cycle completion. Here we show that FA and PtdCho synthesized at the mitotic exit are destined to the nuclear envelope. Importantly, FA and PtdCho synthesis, but not the decrease in lysophospholipid content, are necessary for cell cycle completion beyond G<sub>2</sub>/M. Moreover, the presence of alternative pathways for PtdCho synthesis renders the cells less sensitive to its inhibition than to the impairment of FA synthesis. FA synthesis, thus, represents a cell cycle-related metabolic vulnerability that could be exploited for combined chemotherapy. We explored the combination of fatty acid synthase (FASN) inhibition with agents that act at different phases of the cell cycle. Our results show that the effect of FASN inhibition may be enhanced under some drug combinations.
DOI: 10.6084/m9.figshare.8301089
title: Identification of proteins associated with splicing factors Ntr1, Ntr2, Brr2 and Gpl1 in the fission yeast <i>Schizosaccharomyces pombe</i>

description: The spliceosome is a complex molecular machine assembled from many components, which catalyzes the removal of introns from mRNA precursors. Our previous study revealed that the Nrl1 (NRDE-2 like 1) protein associates with spliceosome proteins and regulates pre-mRNA splicing and homologous recombination-dependent R-loop formation in the fission yeast <i>Schizosaccharomyces pombe</i>. Here, we identify proteins associated with splicing factors Ntr1, Ntr2, Brr2 and Gpl1, a poorly characterized G-patch domain-containing protein required for efficient splicing. This work provides new evidence that Nrl1 and splicing factors physically interact and reveals additional insights into the protein interaction network of the spliceosome. We discuss implications of these findings in the light of recent progress in our understanding of how Nrl1 and splicing factors ensure genome stability.
DOI: 10.6084/m9.figshare.13292518.v1
title: Episodic Neoproterozoic extension-related magmatism in the Altyn Tagh, NW China: implications for extension and breakup processes of Rodinia supercontinent

description: Episodic Neoproterozoic magmatic suites in the Altyn Tagh, NW China, are thought to be related break-up of the Rodinia supercontinent. These suites resulted from long-term extension of the lithosphere during orogenic collapse and subsequent rifting. New geochemical and U-Pb-Hf zircon data indicate that the 825 Ma Hongliugou granite displays the characteristics of A-type granites derived from a juvenile source. Gneissic granites (780–760 Ma) are characterized by high Rb (&gt;200 × 10<sup>−6</sup>), low Zr/Hf (23.28–29.28) and low Nb/Ta (4.20–12.99) typical of highly fractionated granites. A diabase exhibits trace element patterns between OIB and E-MORB which we infer as derivation from an enriched asthenosphere mantle. Combined with previous reported ca. 850 Ma and 620 Ma extension-related magmatism in this region, we interpreted the Altyn Tagh sequences as part of a lengthy supercontinental break-up process. Neoproterozoic magmatism in the Altyn Tagh is broadly correlative with magmatism in East Kunlun and North Qaidam orogenic belts around the Qaidam basin. Collectively, the Qaidam block, exposed mainly in the Altyn Tagh, East Kunlun and North Qaidam, represents a succession of accretionary orogenic, postorogenic, and within plate magmatism between 1200 and 620 Ma. The similarity in age of magmatism and metamorphism in the Altyn Tagh-North Qaidam-East Kunlun regions indicate that these Precambrian sequences collectively represent the basement of Qaidam block.
DOI: 10.6084/m9.figshare.8050154
title: Additional file 4: of Translation of the circular RNA circÎ˛-catenin promotes liver cancer cell growth through activation of the Wnt pathway

description: Table S3. The mass spectrometry analysis data (XLSX 78 kb)
DOI: 10.6084/m9.figshare.8050154.v1
title: Additional file 4: of Translation of the circular RNA circÎ˛-catenin promotes liver cancer cell growth through activation of the Wnt pathway

description: Table S3. The mass spectrometry analysis data (XLSX 78 kb)
DOI: 10.5281/zenodo.10575682
title: Memory access traces and results for ABACuS
DOI: 10.5281/zenodo.10575683
title: Memory access traces and results for ABACuS
DOI: 10.6084/m9.figshare.8050139.v1
title: Additional file 3: of Identification of the defense-related gene VdWRKY53 from the wild grapevine Vitis davidii using RNA sequencing and ectopic expression analysis in Arabidopsis

description: Details of the KEGG pathways investigated in this study. (XLSX 122 kb)
DOI: 10.6084/m9.figshare.21680617
title: Additional file 9 of LncRNA CEBPA-DT promotes liver cancer metastasis through DDR2/β-catenin activation via interacting with hnRNPC

description: Additional file 9. Supplementary RNA sequencing results.
DOI: 10.6084/m9.figshare.8050151
title: Additional file 4: of Identification of the defense-related gene VdWRKY53 from the wild grapevine Vitis davidii using RNA sequencing and ectopic expression analysis in Arabidopsis

description: Details of genes classified in subcluster K03. (XLSX 69 kb)
DOI: 10.6084/m9.figshare.14865087.v2
title: Structure and dynamics of major histocompatibility class Ib molecule H2-M3 complexed with mitochondrial-derived peptides

description: Presentation of antigenic peptides to T-cell receptors is an essential step in the adaptive immune response. In the mouse the class Ib major histocompatibility complex molecule, H2-M3, presents bacterial- and mitochondrial-derived peptides to T-cell receptors on cytotoxic T cells. Four mitochondrial heptapeptides, differing only at residue 6, form complexes with H2-M3 which can be distinguished by T cells. No structures of relevant receptors are available. To investigate the structural basis for this distinction, crystal structures were determined and molecular dynamics simulations over one microsecond were done for each complex. In the crystal structures of the heptapeptide complexes with H2-M3, presented here, the side chains of the peptide residues at position 6 all point into the H2-M3 binding groove, and are thus inaccessible, so that the very similar structures do not suggest how recognition and initiation of responses by the T cells may occur. However, conformational differences, which could be crucial to T-cell discrimination, appear within one microsecond during molecular dynamics simulations of the four complexes. Specifically, the three C-terminal residues of peptide ligands with alanine or threonine at position 6 partially exit the binding groove; this does not occur in peptide ligands with isoleucine or valine at position 6. Structural changes associated with partial peptide exit from the binding groove, along with relevant peptide binding energetics and immunological results are discussed. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13292463
title: Long non-coding RNA HOTAIR regulates myeloid differentiation through the upregulation of p21 via miR-17-5p in acute myeloid leukaemia

description: Long non-coding RNA HOTAIR has been reported to play a key role in regulating various biological processes in various cancers. However, the roles and mechanisms of HOTAIR in acute myeloid leukaemia (AML) are still unclear and need to be investigated. In this study, we induced differentiation of four AML cell lines by all-trans retinoic acid (ATRA) and found HOTAIR was significantly upregulated in the process. Chromatin immunoprecipitation (ChIP) assays indicated that C/EBPβ upregulated HOTAIR during ATRA induced differentiation in HL-60 cells. By gain- and loss-of-function analysis, we then observed that HOTAIR expression was positively correlated with ATRA-induced differentiation and negatively regulated G1 phase arrest in HL-60 cells. In addition, we found that HOTAIR promoted ATRA-induced differentiation via the regulation of the cell cycle regulator p21 via miR-17-5p. Moreover, we detected the expression of HOTAIR in 84 de novo AML patients, HOTAIR was found significantly downregulated in the AML patients compared to the iron deficiency anaemia (IDA) control group, negatively correlated with the platelet level in M2 patients. In all, our data suggest that HOTAIR may be subtype-specific in AML-M2 patients, also HOTAIR regulates AML differentiation by C/EBPBβ/HOTAIR/miR-17-5p/p21 pathway. The findings of the present study provide a novel insight into the mechanism of lncRNA-mediated differentiation and indicate that HOTAIR may be a promising therapeutic target for leukaemia, especially for AML with M2 type. <b>Abbreviation:</b> AML: acute myeloid leukaemia; APL: acute promyelocytic leukaemia; ATRA: all-trans retinoic acid; CCK8: cell Counting Kit-8; CDKs: cyclin-dependent kinases ; CeRNA: competing endogenous RNAs; ChIP: chromatin immunoprecipitation; CHX: cycloheximide; FAB: French–American–British; FCM: flow cytometry; HOTAIR: HOX transcript antisense RNA; IDA: iron-deficiency anemia; lncRNA: long non-coding RNA; 3′UTR: 3′untranslated region; MT: Mutation type; WT: Wild type; qRT-PCR: Quantitative real-time PCR
DOI: 10.6084/m9.figshare.19584094
title: MicroRNA-642b-3p functions as an oncomiR in gastric cancer by down-regulating the CUB and sushi multiple domains protein 1/smad axis

description: Aberrant expression of microRNAs (miRNAs or miRs) has been involved in the progression of gastric cancer (GC). Our analysis of GC-related gene expression profiles identified the significantly up-regulated miR-642b-3p expression, which has been reported as a mediator in various cancers but rarely mentioned in researches on GC. Herein, this study intends to investigate the role of miR-642b-3p in GC development. Bioinformatics analysis was conducted to predict the downstream target gene of miR-642b-3p. Expression patterns of miR-642b-3p and CUB and sushi multiple domains protein 1 (CSMD1) in GC tissues and cell lines was then determined. Immunofluorescence, wound healing and Transwell invasion assays were performed to observe the malignant behaviors of GC cells with altered expression of miR-642b-3p and CSMD1. Nude mice with xenograft tumors were developed for <i>in vivo</i> validation. miR-642b-3p expression was increased in GC tissues and cell lines. miR-642b-3p targeted CSMD1 and reduced the expression of CSMD1, thereby inhibiting the activation of Smad signaling pathway. By this mechanism, the epithelial–mesenchymal transition (EMT), invasive and migratory potentials of GC cells were repressed. Meanwhile, <i>in vivo</i> data verified that miR-642b-3p enhanced the tumor growth of GC cells, which was associated with blockade of CSMD1-dependent activation of the Smad signaling pathway. Overall, miR-642b-3p acts as an oncomiR promoting tumor development in GC through suppressing CSMD1 expression and inactivating the Smad signaling pathway, which may enable the development of new therapeutic strategies for treatment of GC.
DOI: 10.25387/g3.11719890.v1
title: Supplemental Material for Lu et al., 2020

description: Figure
S1. Estimates of divergence time. File S1.
Codon sequences with evidences of positive selection in FASTA format. File S2.
Protein sequences containing convergent/parallel substitutions in FASTA format. File S3.
Protein sequences containing multiple amino acid substitutions specific to
Shedao pit-viper in FASTA format. File S4.
Codon sequence alignments of all single-copy genes used in this study in FASTA
format. Table S1. Genomic data, assembly version, and data sources used in this study. Table S2. Calibration points used in divergence date estimation. Table S3. List of genes that bear signals of positive selection in the Shedao pit-viper.Table S4. List of genes that possess sites of convergent substitutions. Table S5. List of genes that possess sites of parallel substitutions.
DOI: 10.6084/m9.figshare.13292518
title: Episodic Neoproterozoic extension-related magmatism in the Altyn Tagh, NW China: implications for extension and breakup processes of Rodinia supercontinent

description: Episodic Neoproterozoic magmatic suites in the Altyn Tagh, NW China, are thought to be related break-up of the Rodinia supercontinent. These suites resulted from long-term extension of the lithosphere during orogenic collapse and subsequent rifting. New geochemical and U-Pb-Hf zircon data indicate that the 825 Ma Hongliugou granite displays the characteristics of A-type granites derived from a juvenile source. Gneissic granites (780–760 Ma) are characterized by high Rb (&gt;200 × 10<sup>−6</sup>), low Zr/Hf (23.28–29.28) and low Nb/Ta (4.20–12.99) typical of highly fractionated granites. A diabase exhibits trace element patterns between OIB and E-MORB which we infer as derivation from an enriched asthenosphere mantle. Combined with previous reported ca. 850 Ma and 620 Ma extension-related magmatism in this region, we interpreted the Altyn Tagh sequences as part of a lengthy supercontinental break-up process. Neoproterozoic magmatism in the Altyn Tagh is broadly correlative with magmatism in East Kunlun and North Qaidam orogenic belts around the Qaidam basin. Collectively, the Qaidam block, exposed mainly in the Altyn Tagh, East Kunlun and North Qaidam, represents a succession of accretionary orogenic, postorogenic, and within plate magmatism between 1200 and 620 Ma. The similarity in age of magmatism and metamorphism in the Altyn Tagh-North Qaidam-East Kunlun regions indicate that these Precambrian sequences collectively represent the basement of Qaidam block.