cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8240636.v1
title: Additional file 1: of Genetic and morphological divergence among three closely related Phrynocephalus species (Agamidae)

description: Table S1. Mensural and meristic data, expressed as mean ± SE and range, collected from adults of three viviparous Phrynocephalus species. (XLS 60 kb)
DOI: 10.6084/m9.figshare.8240651
title: Additional file 3: of Genetic and morphological divergence among three closely related Phrynocephalus species (Agamidae)

description: Table S3. Loading of the first two axes of a principal components (PC) analysis on 22 morphological variables for both sexes. Size effects are removed in all cases by using residuals from the regressions on SVL. Variables with the main contribution to each factor are in bold. Species with different superscripts differ significantly (Tukey’s test, α = 0.05; a &gt; b &gt; c). (XLSX 14 kb)
DOI: 10.6084/m9.figshare.8240498.v1
title: Additional file 1: of A survey of transcriptome complexity using PacBio single-molecule real-time analysis combined with Illumina RNA sequencing for a better understanding of ricinoleic acid biosynthesis in Ricinus communis

description: Table S1. Statistics of sequencing data for three SMRT cells (1–2 k, 2-3 k and 3-6 k) by PacBio SMRT sequencing. Table S2. Statistics of reads of insert (ROI) for three SMRT cells (1–2 k, 2-3 k and 3-6 k) by PacBio SMRT sequencing. Table S3. Statistics of full-length reads for three SMRT cells (1–2 k, 2-3 k and 3-6 k) by PacBio SMRT sequencing. Table S4. Statistics of iterative clustering for error correction (ICE) for all isoforms by PacBio SMRT analysis. Table S5. The gene structure optimization information by PacBio SMRT sequencing. Table S6. The annotated information of 21,122 novel genes. Table S7. Detailed information on 250 fusion genes. Table S8. The list of 1356 TF genes. Table S9. Statistics of sequencing data for strains 349 and 1115 at three time points (7 DAF, 14 DAF and 21 DAF) by Illumina RNA sequencing. Table S10. Comparison of transcriptome sequencing reads with genome references by Illumina RNA sequencing. Table S11. The primers for quantitative real-time PCR in this study. (ZIP 1535 kb)
DOI: 10.5517/ccdc.csd.cc2g0jbc
title: CCDC 2264622: Experimental Crystal Structure Determination

description: Related Article: Hiroaki Imoto, Kensuke Naka, Ryoto Inaba, Takashi Kikuchi|2024|Synlett|35|437|doi:10.1055/a-2112-9605
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2g0jcd
title: CCDC 2264623: Experimental Crystal Structure Determination

description: Related Article: Hiroaki Imoto, Kensuke Naka, Ryoto Inaba, Takashi Kikuchi|2024|Synlett|35|437|doi:10.1055/a-2112-9605
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2g0jdf
title: CCDC 2264624: Experimental Crystal Structure Determination

description: Related Article: Hiroaki Imoto, Kensuke Naka, Ryoto Inaba, Takashi Kikuchi|2024|Synlett|35|437|doi:10.1055/a-2112-9605
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.14532170
title: Additional file 5 of Multi-omics reveals age-related differences in the diaphragm response to mechanical ventilation: a pilot study

description: Additional file 5. Supplemental Table 4: Enriched KEGG pathways in the diaphragm.
DOI: 10.6084/m9.figshare.8240504
title: Additional file 2: of A survey of transcriptome complexity using PacBio single-molecule real-time analysis combined with Illumina RNA sequencing for a better understanding of ricinoleic acid biosynthesis in Ricinus communis

description: Figure S1. Correlation thermograms between 18 samples from Illumina RNA sequencing. Figure S2. ROI read length distribution of each size (1–2 k, 2-3 k and 3-6 k) of bins in the cDNA database. Figure S3. GO classification according to cellular component, molecular function and biological process of differentially expressed genes. Strain 349 vs. strain 1115 at 7 DAF (A), 14 DAF (B), and 21 DAF (C). Figure S4. KEGG classification and Pathway enrichment statistics of differentially expressed genes. (A) KEGG classification between strains 349 and 1115 at 7 DAF. (B) KEGG classification between 349 and 1115 at 14 DAF. (C) KEGG classification between 349 and 1115 at 21 DAF. (D) Pathway enrichment statistics between 349 and 1115 at 7 DAF. (E) Pathway enrichment statistics between 349 and 1115 at 14 DAF. (F) Pathway enrichment statistics between 349 and 1115 at 14 DAF. Figure S5. COG function classification of differentially expressed genes. (A) 349 vs. 1115 at 7 DAF. (B) 349 vs. 1115 at 14 DAF. (C) 349 vs. 1115 at 21 DAF. (ZIP 29130 kb)
DOI: 10.6084/m9.figshare.14532167.v1
title: Additional file 4 of Multi-omics reveals age-related differences in the diaphragm response to mechanical ventilation: a pilot study

description: Additional file 4. Supplemental Table 3: Enriched GO terms in the diaphragm.
DOI: 10.6084/m9.figshare.14532164.v1
title: Additional file 3 of Multi-omics reveals age-related differences in the diaphragm response to mechanical ventilation: a pilot study

description: Additional file 3. Supplemental Table 2: CMV-induced DEPs in the plasma.
DOI: 10.6084/m9.figshare.14532164
title: Additional file 3 of Multi-omics reveals age-related differences in the diaphragm response to mechanical ventilation: a pilot study

description: Additional file 3. Supplemental Table 2: CMV-induced DEPs in the plasma.
DOI: 10.6084/m9.figshare.14532161.v1
title: Additional file 2 of Multi-omics reveals age-related differences in the diaphragm response to mechanical ventilation: a pilot study

description: Additional file 2. Supplemental Table 1: CMV-induced DEGs and DEPs in the diaphragm.
DOI: 10.6084/m9.figshare.14532170.v1
title: Additional file 5 of Multi-omics reveals age-related differences in the diaphragm response to mechanical ventilation: a pilot study

description: Additional file 5. Supplemental Table 4: Enriched KEGG pathways in the diaphragm.
DOI: 10.6084/m9.figshare.14532173
title: Additional file 6 of Multi-omics reveals age-related differences in the diaphragm response to mechanical ventilation: a pilot study

description: Additional file 6. Supplemental Table 5: Enriched KEGG pathways in the plasma.
DOI: 10.5281/zenodo.10684095
title: PRIORITY DIRECTIONS OF OUTSAFFING AND OUTSOURCING IN UZBEKISTAN.
DOI: 10.5281/zenodo.10684096
title: PRIORITY DIRECTIONS OF OUTSAFFING AND OUTSOURCING IN UZBEKISTAN.
DOI: 10.6084/m9.figshare.14532188.v1
title: Additional file 12 of Maternal karyogene and cytoplasmic genotype affect the induction efficiency of doubled haploid inducer in Brassica napus

description: Additional file 12. Statistics of the number of SNPs of heterozygous loci in the hybrid F1 generation.
DOI: 10.6084/m9.figshare.14532191.v1
title: Additional file 13 of Maternal karyogene and cytoplasmic genotype affect the induction efficiency of doubled haploid inducer in Brassica napus

description: Additional file 13. F1 generation paternal parent infiltrated SNP site.
DOI: 10.6084/m9.figshare.14532218
title: Additional file 7 of Maternal karyogene and cytoplasmic genotype affect the induction efficiency of doubled haploid inducer in Brassica napus

description: Additional file 7. SNP homozygosity rate and inheritance rate.
DOI: 10.6084/m9.figshare.6143600
title: Genetic diversity and population genetic structure of the only population of Aoluguya Reindeer (<i>Rangifer tarandus</i>) in China

description: Aoluguya Reindeer is the only reindeer species in China and currently approximately 1000 Aoluguya Reindeer remain semi-domesticated. A relative low diversity estimate was found by investigating genetic variability and demographic history of its population. Mismatch distribution curve of its nucleotide sequences and neutral test indicate its population has not experienced expansion. Genetic diversity and population structure were also analysed by using its mtDNA and microsatellites technology. Statistical results of these analyses showed there were varying degrees of population inbreeding and suggested that gene flow existed among its populations at one time. Three mutation models were also used to detect the bottleneck effect of reindeer population. The genetic variation of eight populations is relatively small. In addition, the clustering program STRUCTURE was used to analyse Aoluguya Reindeer population structure, to determine its optimal <i>K</i> and first time to analyse the phylogenetic status of Aoluguya Reindeer among other reindeer subspecies. It is recommended that the government establish a natural conservation area in Aoluguya Reindeer growing geography, forbade the trade and hunting of Aoluguya Reindeer, and strengthen the protection of this endangered species.
DOI: 10.6084/m9.figshare.14532218.v1
title: Additional file 7 of Maternal karyogene and cytoplasmic genotype affect the induction efficiency of doubled haploid inducer in Brassica napus

description: Additional file 7. SNP homozygosity rate and inheritance rate.
DOI: 10.6084/m9.figshare.14532161
title: Additional file 2 of Multi-omics reveals age-related differences in the diaphragm response to mechanical ventilation: a pilot study

description: Additional file 2. Supplemental Table 1: CMV-induced DEGs and DEPs in the diaphragm.
DOI: 10.6084/m9.figshare.14532167
title: Additional file 4 of Multi-omics reveals age-related differences in the diaphragm response to mechanical ventilation: a pilot study

description: Additional file 4. Supplemental Table 3: Enriched GO terms in the diaphragm.
DOI: 10.6084/m9.figshare.14532191
title: Additional file 13 of Maternal karyogene and cytoplasmic genotype affect the induction efficiency of doubled haploid inducer in Brassica napus

description: Additional file 13. F1 generation paternal parent infiltrated SNP site.
DOI: 10.6084/m9.figshare.14532203.v1
title: Additional file 2 of Maternal karyogene and cytoplasmic genotype affect the induction efficiency of doubled haploid inducer in Brassica napus

description: Additional file 2. Flow cytometry results statistics. The ploidy of rape was calculated by fluorescence intensity, and the peak value range represents the fluorescence signal value of mitotic G1 phase of flow cytometry. There are some differences in the fluorescence signal value of each material under the same ploidy, and there significant differences in the fluorescence signal value between ploidy.
DOI: 10.6084/m9.figshare.14532188
title: Additional file 12 of Maternal karyogene and cytoplasmic genotype affect the induction efficiency of doubled haploid inducer in Brassica napus

description: Additional file 12. Statistics of the number of SNPs of heterozygous loci in the hybrid F1 generation.
DOI: 10.6084/m9.figshare.14532221
title: Additional file 8 of Maternal karyogene and cytoplasmic genotype affect the induction efficiency of doubled haploid inducer in Brassica napus

description: Additional file 8. Test material information. The same number of materials used represents the same karyogene, “A” represents sterile line, “B” represents maintainer line, pol CMS was bred by backcross with 15 generations of maintainer line, and ogu CMS was bred by backcross with 12 generations of the same maintainer line, only cytoplasmic genotype differences, but 0068 and 0933 have similar sources. The collection and breeding of the Brassica napus materials we use has obtained local permits in China, which is in line with national policies. The Brassica napus used in this study is commonly grown oil crop used species native to China and does not fall under the Nagoya protocol.
DOI: 10.6084/m9.figshare.14532173.v1
title: Additional file 6 of Multi-omics reveals age-related differences in the diaphragm response to mechanical ventilation: a pilot study

description: Additional file 6. Supplemental Table 5: Enriched KEGG pathways in the plasma.
DOI: 10.6084/m9.figshare.14532185.v1
title: Additional file 11 of Maternal karyogene and cytoplasmic genotype affect the induction efficiency of doubled haploid inducer in Brassica napus

description: Additional file 11. Genotyping raw data.
DOI: 10.6084/m9.figshare.14532194
title: Additional file 14 of Maternal karyogene and cytoplasmic genotype affect the induction efficiency of doubled haploid inducer in Brassica napus

description: Additional file 14. Statistics of identification results of different identification methods.
DOI: 10.6084/m9.figshare.14532203
title: Additional file 2 of Maternal karyogene and cytoplasmic genotype affect the induction efficiency of doubled haploid inducer in Brassica napus

description: Additional file 2. Flow cytometry results statistics. The ploidy of rape was calculated by fluorescence intensity, and the peak value range represents the fluorescence signal value of mitotic G1 phase of flow cytometry. There are some differences in the fluorescence signal value of each material under the same ploidy, and there significant differences in the fluorescence signal value between ploidy.
DOI: 10.6084/m9.figshare.14532206
title: Additional file 3 of Maternal karyogene and cytoplasmic genotype affect the induction efficiency of doubled haploid inducer in Brassica napus

description: Additional file 3. Fertility identification results.
DOI: 10.6084/m9.figshare.14532206.v1
title: Additional file 3 of Maternal karyogene and cytoplasmic genotype affect the induction efficiency of doubled haploid inducer in Brassica napus

description: Additional file 3. Fertility identification results.
DOI: 10.6084/m9.figshare.15056821.v1
title: Identification of microRNA transcriptome throughout the lifespan of yak (<i>Bos grunniens</i>) corpus luteum

description: The corpus luteum (CL) is a temporary organ that plays a critical role for female fertility by maintaining the estrous cycle. MicroRNA (miRNA) is a class of non-coding RNAs involved in various biological processes. However, there exists limited knowledge of the role of miRNA in yak CL. In this study, we used high-throughput sequencing to study the transcriptome dynamics of miRNA in yak early (eCL), middle (mCL) and late-stage CL (lCL). A total of 6,730 miRNAs were identified, including 5,766 known and 964 novels miRNAs. Three miRNAs, including bta-miR-126-3p, bta-miR-143 and bta-miR-148a, exhibited the highest expressions in yak CLs of all the three stages. Most of the miRNAs were 20–24 nt in length and the peak was at 22 nt. Besides, most miRNAs with different lengths displayed significant uracil preference at the 5'-end. Furthermore, 1,067, 280 and 112 differentially expressed (DE) miRNAs were found in eCL vs. mCL, mCL vs. lCL, and eCL vs. lCL, respectively. Most of the DE miRNAs were down-regulated in the eCL vs. mCL and eCL vs. lCL groups, and up-regulated in the mCL vs. lCL group. A total of 18,904 target genes were identified, with 18,843 annotated. Pathway enrichment analysis of the DE miRNAs target genes illustrated that the most enriched cellular process in each group included pathways in cancer, PI3K-Akt pathway, endocytosis, and focal adhesion. A total of 20 putative target genes in 47 DE miRNAs were identified to be closely associated with the formation, function or regression of CL. Three DE miRNAs, including bta-miR-11972, novel-miR-619 and novel-miR-153, were proved to directly bind to the 3'-UTR of their predicated target mRNAs, including <i>CDK4</i>, <i>HSD17B1</i> and <i>MAP1LC3C</i>, respectively. Both of these DE miRNAs and their target mRNAs exhibited dynamic expression profiles across the lifespan of yak CL. This study presents a general basis for understanding of the regulation of miRNA on yak CL and also provides a novel genetic resource for future analysis of the gene network during the estrous cycle in the yak.
DOI: 10.6084/m9.figshare.14532215
title: Additional file 6 of Maternal karyogene and cytoplasmic genotype affect the induction efficiency of doubled haploid inducer in Brassica napus

description: Additional file 6. 6 K SNP chip raw data.
DOI: 10.6084/m9.figshare.14532221.v1
title: Additional file 8 of Maternal karyogene and cytoplasmic genotype affect the induction efficiency of doubled haploid inducer in Brassica napus

description: Additional file 8. Test material information. The same number of materials used represents the same karyogene, “A” represents sterile line, “B” represents maintainer line, pol CMS was bred by backcross with 15 generations of maintainer line, and ogu CMS was bred by backcross with 12 generations of the same maintainer line, only cytoplasmic genotype differences, but 0068 and 0933 have similar sources. The collection and breeding of the Brassica napus materials we use has obtained local permits in China, which is in line with national policies. The Brassica napus used in this study is commonly grown oil crop used species native to China and does not fall under the Nagoya protocol.
DOI: 10.6084/m9.figshare.6143861
title: Spontaneous single nucleotide polymorphism in porcine microRNA-378 seed region leads to functional alteration

description: Sequence variation in a microRNA (miRNA) seed region can influence its biogenesis and effects on target mRNAs; however, in mammals, few seed region mutations leading to functional alterations have been reported to date. Here, we report the identification of a single nucleotide polymorphism (SNP) with functional consequence located in the seed region of porcine miR-378. <i>In vitro</i> analysis of this rs331295049 A17G SNP showed significantly up-regulated expression of the mature miR-378 (miR-378/G). <i>In silico</i> target prediction indicated that the SNP would modulate secondary structure and result in functional loss affecting &gt;85% of the known target genes of the wild-type miR-378 (miR-378/A), and functional gain affecting &gt;700 new target genes, and dual-luciferase reporter assay verified this result. This report of a SNP in the seed region of miR-378 leads to functional alteration and indicates the potential for substantive functional consequences to the molecular physiology of a mammalian organism. The SNP changed the secondary structure of pre-miR-378 and increased the production of mutant miR-378. Functionally, the SNP lead to loss and gain of miR-378 targets.
DOI: 10.6084/m9.figshare.6143861.v1
title: Spontaneous single nucleotide polymorphism in porcine microRNA-378 seed region leads to functional alteration

description: Sequence variation in a microRNA (miRNA) seed region can influence its biogenesis and effects on target mRNAs; however, in mammals, few seed region mutations leading to functional alterations have been reported to date. Here, we report the identification of a single nucleotide polymorphism (SNP) with functional consequence located in the seed region of porcine miR-378. <i>In vitro</i> analysis of this rs331295049 A17G SNP showed significantly up-regulated expression of the mature miR-378 (miR-378/G). <i>In silico</i> target prediction indicated that the SNP would modulate secondary structure and result in functional loss affecting &gt;85% of the known target genes of the wild-type miR-378 (miR-378/A), and functional gain affecting &gt;700 new target genes, and dual-luciferase reporter assay verified this result. This report of a SNP in the seed region of miR-378 leads to functional alteration and indicates the potential for substantive functional consequences to the molecular physiology of a mammalian organism. The SNP changed the secondary structure of pre-miR-378 and increased the production of mutant miR-378. Functionally, the SNP lead to loss and gain of miR-378 targets.
DOI: 10.6084/m9.figshare.14532615
title: Additional file 3 of Artificial intelligence-based computational framework for drug-target prioritization and inference of novel repositionable drugs for Alzheimer’s disease

description: Additional file 3 A list of all candidate repositionable compounds for Alzheimer’s disease.
DOI: 10.6084/m9.figshare.14532612.v1
title: Additional file 2 of Artificial intelligence-based computational framework for drug-target prioritization and inference of novel repositionable drugs for Alzheimer’s disease

description: Additional file 2 A list of potential therapeutic targets for Alzheimer’s disease.
DOI: 10.6084/m9.figshare.14532615.v1
title: Additional file 3 of Artificial intelligence-based computational framework for drug-target prioritization and inference of novel repositionable drugs for Alzheimer’s disease

description: Additional file 3 A list of all candidate repositionable compounds for Alzheimer’s disease.
DOI: 10.6084/m9.figshare.20299722
title: Late Carboniferous extension-related magmatism in the southwestern Alxa block of NW China: geochronology, geochemistry, and tectonic implications

description: Whether the northern margin of the North China Craton (NCC) was a continental arc or in a lithospheric extensional setting during the Carboniferous is the primary divergence among different tectonic models about the terminal evolutionary history of the southeastern Central Asian Orogenic Belt (CAOB). The Alxa block is the western segment of the northern NCC and contiguous to the southeastern CAOB, and therefore the tectonic setting of the Carboniferous magmatic intrusions in this block can shed light on this controversy. In this contribution, new zircon U–Pb ages, elemental geochemistry, and Sr-Nd isotopes are presented for thirteen Late Carboniferous (~318–300 Ma) magmatic intrusions in the southwestern Alxa block. Among them, seven calc-alkaline I-type granites and one aluminous A2-type granite were probably generated by the partial melting and crystallization differentiation of various crustal sources (perhaps including earlier orogenic materials) under different temperature conditions. Four quartz diorites and one hornblende gabbro may be the partial melts of subduction-modified basaltic lower crust sources and sub-continental lithospheric mantle sources, respectively. According to the integration of the new results and regional geological correlations, the Alxa block and the southeastern CAOB were most likely in a uniform tectonic regime during the Carboniferous. At that time, this region was characterized by the lithospheric extension-related magmatic rock associations, the increasing mantle inputs over time, the clockwise P–T paths of high temperature-low pressure metamorphic rocks, and the transgression sedimentary sequences. All these lines of evidence suggest an intra-continental lithospheric extensional setting rather than a continental arc setting for the southeastern CAOB during the Carboniferous.