cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25386/genetics.10673792
title: Supplemental Material for Heft et al., 2020

description: Sequences encoding Olduvai protein
domains (formerly DUF1220) show the greatest human lineage-specific increase in
copy number of any coding region in the genome and have been associated, in a
dosage-dependent manner, with brain size, cognitive aptitude, autism, and
schizophrenia. Tandem intragenic duplications of a three-domain block, termed
the Olduvai triplet, in four <i>NBPF</i> genes
in the chromosomal 1q21.1-.2 region are primarily responsible for the striking
human-specific copy number increase. Interestingly, most of the Olduvai
triplets are adjacent to, and transcriptionally co-regulated with, three
human-specific <i>NOTCH2NL</i> genes that have been shown to promote cortical
neurogenesis. Until now, the underlying genomic events that drove the Olduvai
hyper-amplification in humans have remained unexplained. Here, we show that the
presence or absence of an alternative first exon of the Olduvai triplet
perfectly discriminates between amplified (58/58) and unamplified (0/12)
triplets. We provide sequence and breakpoint analyses that suggest the
alternative exon was produced by an NAHR-based mechanism involving the
duplicative transposition of an existing Olduvai exon found in the CON3 domain
that typically occurs at the carboxy end of <i>NBPF</i>
genes. We also provide suggestive <i>in
vitro</i> evidence that the alternative exon may promote instability through a putative
G-quadraplex-based (pG4) mechanism. Lastly, we use single-molecule optical
mapping to characterize the intragenic structural variation observed in <i>NBPF</i> genes in 154 unrelated individuals
and 52 related individuals from 16 families and show that the presence of pG4-containing
Olduvai triplets is strongly correlated with high levels of Olduvai copy number
variation. These results suggest that the same driver of genomic instability
that allowed the evolutionarily recent, rapid, and extreme human-specific Olduvai
expansion remains highly active in the human genome.
DOI: 10.25386/genetics.10673792.v1
title: Supplemental Material for Heft et al., 2020

description: Sequences encoding Olduvai protein
domains (formerly DUF1220) show the greatest human lineage-specific increase in
copy number of any coding region in the genome and have been associated, in a
dosage-dependent manner, with brain size, cognitive aptitude, autism, and
schizophrenia. Tandem intragenic duplications of a three-domain block, termed
the Olduvai triplet, in four <i>NBPF</i> genes
in the chromosomal 1q21.1-.2 region are primarily responsible for the striking
human-specific copy number increase. Interestingly, most of the Olduvai
triplets are adjacent to, and transcriptionally co-regulated with, three
human-specific <i>NOTCH2NL</i> genes that have been shown to promote cortical
neurogenesis. Until now, the underlying genomic events that drove the Olduvai
hyper-amplification in humans have remained unexplained. Here, we show that the
presence or absence of an alternative first exon of the Olduvai triplet
perfectly discriminates between amplified (58/58) and unamplified (0/12)
triplets. We provide sequence and breakpoint analyses that suggest the
alternative exon was produced by an NAHR-based mechanism involving the
duplicative transposition of an existing Olduvai exon found in the CON3 domain
that typically occurs at the carboxy end of <i>NBPF</i>
genes. We also provide suggestive <i>in
vitro</i> evidence that the alternative exon may promote instability through a putative
G-quadraplex-based (pG4) mechanism. Lastly, we use single-molecule optical
mapping to characterize the intragenic structural variation observed in <i>NBPF</i> genes in 154 unrelated individuals
and 52 related individuals from 16 families and show that the presence of pG4-containing
Olduvai triplets is strongly correlated with high levels of Olduvai copy number
variation. These results suggest that the same driver of genomic instability
that allowed the evolutionarily recent, rapid, and extreme human-specific Olduvai
expansion remains highly active in the human genome.
DOI: 10.6084/m9.figshare.14337454.v1
title: Additional file 2 of The effects on pain, physical function, and quality of life of quadriceps strengthening exercises combined with Baduanjin qigong in older adults with knee osteoarthritis: a quasi-experimental study

description: Additional file 2. The dataset supporting the conclusions of this article.
DOI: 10.48457/iopan-7bdc0d42-b80a-48f7-b89b-b5d7954c14d5
title: GELATINOUS ZOOPLANKTON OFF THE NORTHEAST GREENLAND COAST

description: Gelatinous zooplankton are useful indicators of climate-driven shifts in the ocean; hence our study goal was to determine their diversity and distribution in the poorly investigated area of the Northeast Greenland shelf and adjacent waters. Zooplankton samples were collected vertically using a MultiNet in August and September 2017, at 9 stations along two transects: northern and southern. Eleven taxa were identified, of which Plotocnide borealis had the largest share within the assemblage in both transects. Gelatinous zooplankton biodiversity was the highest in the north. The local bathymetry and hydrology both shaped the distribution of the gelatinous zooplankton, leading to the emergence of three ecological groups: 1) taxa typically associated with, or found exclusively, in the intermediate, colder shelf waters (e.g. Plotocnide borealis); 2) organisms associated with higher temperatures and greater depths, mainly of the off-shelf waters (e.g. Aglantha digitale); 3) organisms whose distribution depended mainly on salinity and oxygen saturation (e.g. Aeginopsis laurentii). Additionally, A. digitale was associated with the presence of the warmer waters of Atlantic origin, the presence of which on both sides of the Fram Strait allowed to compare our findings with better studied gelatinous zooplankton from the West Spitsbergen Current, leading to the conclusion that the existent evidence of progressing Atlantification suggests that such impacts might also be expected off the Northeast Greenland coast.
DOI: 10.6084/m9.figshare.14337454
title: Additional file 2 of The effects on pain, physical function, and quality of life of quadriceps strengthening exercises combined with Baduanjin qigong in older adults with knee osteoarthritis: a quasi-experimental study

description: Additional file 2. The dataset supporting the conclusions of this article.
DOI: 10.6084/m9.figshare.24305365
title: <b>Estimating building height in China from ALOS AW3D30</b>

description: This study developed a method to estimate building height for all of China based on the Advanced Land Observing Satellite (ALOS) World 3D-30 m (AW3D30) DSM and other ancillary data including the Global Artificial Impervious Area (GAIA) dataset, the NASADEM dataset and the Global Roads Inventory Project (GRIP) dataset. The proposed method enabled us to accurately estimate building height with a special slope correction algorithm, improving the accuracy of building height estimation. The outcome of our procedure is a map of building height for China at a spatial resolution of 30 m. Compared to field-measured building height data and reference building height data from Baidu map, results indicate that the proposed method performed well (root mean square error (RMSE) of 4.26 m and 4.98 m, respectively). The new building height map of China contributes to the improved management of urban areas and further studies of urban environments.Reference: https://doi.org/10.1016/j.isprsjprs.2022.01.022.
DOI: 10.6084/m9.figshare.24305428
title: <b>Leveraging Chinese GaoFen-7 imagery for high-resolution building height estimation in multiple cities</b>

description: This is a building height dataset estimated from Chinese Gaofen-7 imagery. The estimated building heights in the different cities (Tianjin, Lanzhou, Chongqing, Ningbo, Guangzhou, and Shenzhen) are highly consistent with the reference building height data obtained from field-measured building height data, building floor data, and airborne light detection and ranging (LiDAR) data. The R<sup>2</sup> varies from 0.75 to 0.90, while the root mean square error (RMSE) ranges from 4.06 m to 8.06 m. The validation of the estimated building heights over 106,366 buildings using airborne LiDAR height data yielded R<sup>2</sup> and RMSE of 0.90 and 6.72 m for Shenzhen and 0.89 and 4.06 m for Hong Kong, respectively. Note that the Viewing angles for the GF-7Backward image are -5°, so there is a small offset between the building roof derived from GF-7 image and the building roof derived from other images. Reference: https://doi.org/10.1016/j.rse.2023.113802.
DOI: 10.6084/m9.figshare.16965487
title: Dataset S2 Co-adaption between of tRNA gene frequency and codon usage at the synonymous codon level and the amino acid level of individual genes of A. japonicus. from tRNA copy number and codon usage in the sea cucumber genome provide insights to adaptive translation for saponin biosynthesis

description: Genomic tRNA copy numbers determine cytoplasmic tRNA abundances, which in turn influence translation efficiency, but the underlying mechanism is not well understood. Here, using the sea cucumber <i>Apostichopus japonicus</i> as a model, we combined genomic sequence, transcriptome expression and ecological food resource data to study its codon usage adaptation. The results showed that, unlike intragenic ncRNAs, tRNAs tended to be transcribed independently. This may be attributed to their specific Pol III promoters that lack transcriptional regulation, which may underlie the correlation between genomic copy number and cytoplasmic abundance of tRNAs. Moreover, codon usage optimization was mostly restrained by a gene's amino acid sequence that might be a compromise between functionality and translation efficiency. Genes for stress responses were highly optimized for most echinoderms, while enzymes for saponin biosynthesis (LAS, CYPs and UGTs) were especially optimized in sea cucumbers, which might promote saponin synthesis as a defence strategy. The genomic tRNA content of <i>A. japonicas</i> was positively correlated to amino acid content in its natural food particles, which should promote its efficiency in protein synthesis. We propose that coevolution between genomic tRNA content and codon usage of sea cucumbers facilitate their saponin synthesis and survival on food resource with low nutrient content.
DOI: 10.6084/m9.figshare.16965490
title: Table S2 Translation efficiency and protein stability from tRNA copy number and codon usage in the sea cucumber genome provide insights to adaptive translation for saponin biosynthesis

description: Genomic tRNA copy numbers determine cytoplasmic tRNA abundances, which in turn influence translation efficiency, but the underlying mechanism is not well understood. Here, using the sea cucumber <i>Apostichopus japonicus</i> as a model, we combined genomic sequence, transcriptome expression and ecological food resource data to study its codon usage adaptation. The results showed that, unlike intragenic ncRNAs, tRNAs tended to be transcribed independently. This may be attributed to their specific Pol III promoters that lack transcriptional regulation, which may underlie the correlation between genomic copy number and cytoplasmic abundance of tRNAs. Moreover, codon usage optimization was mostly restrained by a gene's amino acid sequence that might be a compromise between functionality and translation efficiency. Genes for stress responses were highly optimized for most echinoderms, while enzymes for saponin biosynthesis (LAS, CYPs and UGTs) were especially optimized in sea cucumbers, which might promote saponin synthesis as a defence strategy. The genomic tRNA content of <i>A. japonicas</i> was positively correlated to amino acid content in its natural food particles, which should promote its efficiency in protein synthesis. We propose that coevolution between genomic tRNA content and codon usage of sea cucumbers facilitate their saponin synthesis and survival on food resource with low nutrient content.
DOI: 10.6084/m9.figshare.16965493
title: Data set S3. Correlation between TAAI, stAI and gene length in different deuterostomes.; Data set S4. Protein sequences of sea cucumber-specific CYPs and UGTs and their closest homologs. from tRNA copy number and codon usage in the sea cucumber genome provide insights to adaptive translation for saponin biosynthesis

description: Genomic tRNA copy numbers determine cytoplasmic tRNA abundances, which in turn influence translation efficiency, but the underlying mechanism is not well understood. Here, using the sea cucumber <i>Apostichopus japonicus</i> as a model, we combined genomic sequence, transcriptome expression and ecological food resource data to study its codon usage adaptation. The results showed that, unlike intragenic ncRNAs, tRNAs tended to be transcribed independently. This may be attributed to their specific Pol III promoters that lack transcriptional regulation, which may underlie the correlation between genomic copy number and cytoplasmic abundance of tRNAs. Moreover, codon usage optimization was mostly restrained by a gene's amino acid sequence that might be a compromise between functionality and translation efficiency. Genes for stress responses were highly optimized for most echinoderms, while enzymes for saponin biosynthesis (LAS, CYPs and UGTs) were especially optimized in sea cucumbers, which might promote saponin synthesis as a defence strategy. The genomic tRNA content of <i>A. japonicas</i> was positively correlated to amino acid content in its natural food particles, which should promote its efficiency in protein synthesis. We propose that coevolution between genomic tRNA content and codon usage of sea cucumbers facilitate their saponin synthesis and survival on food resource with low nutrient content.
DOI: 10.6084/m9.figshare.16965496
title: Table S1 Correlation between isoaccepting tRNA gene frequencies and synonymous codon usage in the transcriptome of A. japonicus. from tRNA copy number and codon usage in the sea cucumber genome provide insights to adaptive translation for saponin biosynthesis

description: Genomic tRNA copy numbers determine cytoplasmic tRNA abundances, which in turn influence translation efficiency, but the underlying mechanism is not well understood. Here, using the sea cucumber <i>Apostichopus japonicus</i> as a model, we combined genomic sequence, transcriptome expression and ecological food resource data to study its codon usage adaptation. The results showed that, unlike intragenic ncRNAs, tRNAs tended to be transcribed independently. This may be attributed to their specific Pol III promoters that lack transcriptional regulation, which may underlie the correlation between genomic copy number and cytoplasmic abundance of tRNAs. Moreover, codon usage optimization was mostly restrained by a gene's amino acid sequence that might be a compromise between functionality and translation efficiency. Genes for stress responses were highly optimized for most echinoderms, while enzymes for saponin biosynthesis (LAS, CYPs and UGTs) were especially optimized in sea cucumbers, which might promote saponin synthesis as a defence strategy. The genomic tRNA content of <i>A. japonicas</i> was positively correlated to amino acid content in its natural food particles, which should promote its efficiency in protein synthesis. We propose that coevolution between genomic tRNA content and codon usage of sea cucumbers facilitate their saponin synthesis and survival on food resource with low nutrient content.
DOI: 10.6084/m9.figshare.16965499
title: Dataset S1. tRNA gene structures of A. japonicus. from tRNA copy number and codon usage in the sea cucumber genome provide insights to adaptive translation for saponin biosynthesis

description: Genomic tRNA copy numbers determine cytoplasmic tRNA abundances, which in turn influence translation efficiency, but the underlying mechanism is not well understood. Here, using the sea cucumber <i>Apostichopus japonicus</i> as a model, we combined genomic sequence, transcriptome expression and ecological food resource data to study its codon usage adaptation. The results showed that, unlike intragenic ncRNAs, tRNAs tended to be transcribed independently. This may be attributed to their specific Pol III promoters that lack transcriptional regulation, which may underlie the correlation between genomic copy number and cytoplasmic abundance of tRNAs. Moreover, codon usage optimization was mostly restrained by a gene's amino acid sequence that might be a compromise between functionality and translation efficiency. Genes for stress responses were highly optimized for most echinoderms, while enzymes for saponin biosynthesis (LAS, CYPs and UGTs) were especially optimized in sea cucumbers, which might promote saponin synthesis as a defence strategy. The genomic tRNA content of <i>A. japonicas</i> was positively correlated to amino acid content in its natural food particles, which should promote its efficiency in protein synthesis. We propose that coevolution between genomic tRNA content and codon usage of sea cucumbers facilitate their saponin synthesis and survival on food resource with low nutrient content.
DOI: 10.6084/m9.figshare.23257013
title: Supplementary raw sequence data

description: The effects of  warming, precipitation reduction and their combination on soil bacterial and fungal communities in a semi-arid grassland on the Loess Plateau.
DOI: 10.6084/m9.figshare.24305653
title: Exploration of the potential mechanism of Duhuo Jisheng Decoction in osteoarthritis treatment by using network pharmacology and molecular dynamics simulation

description: In this study, the active ingredients of 15 Chinese herbal medicines of Duhuo Jisheng Decoction and their corresponding targets were obtained from the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database. The microarray data of Osteoarthritis (OA) were obtained through the GEO database for differential analysis and then a drug target-OA-related gene protein-protein interaction (PPI) network was established. The potential targets of Duhuo Jisheng Decoction in the treatment of OA were acquired by intersecting the OA-associated genes with the target genes of active ingredients. Random walk with restart (RWR) analysis of PPI networks was performed using potential targets as seed, and the top 50 genes of affinity coefficients were used as key action genes of Duhuo Jisheng Decoction in the treatment of OA. A drug-active ingredient-gene interaction network was established. AKT1, a key target of Duhuo Jisheng Decoction in the treatment of OA, was obtained by topological analysis of the gene interaction network. Molecular docking and molecular dynamics verified the binding of AKT1 to its corresponding drug active ingredients. CETSA assay demonstrated that the combination of luteolin and AKT1 increased the stability of AKT1, and the combination efficiency was high. In conclusion, the molecular mechanism of Duhuo Jisheng Decoction in treating OA featured by multiple components, targets, and pathways had been further investigated in this study, which is of significance for discovering as well as developing new drugs for this disease. The findings can also offer personalized diagnosis and treatment strategies for patients with OA in clinical practice.
DOI: 10.6084/m9.figshare.24305653.v1
title: Exploration of the potential mechanism of Duhuo Jisheng Decoction in osteoarthritis treatment by using network pharmacology and molecular dynamics simulation

description: In this study, the active ingredients of 15 Chinese herbal medicines of Duhuo Jisheng Decoction and their corresponding targets were obtained from the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database. The microarray data of Osteoarthritis (OA) were obtained through the GEO database for differential analysis and then a drug target-OA-related gene protein-protein interaction (PPI) network was established. The potential targets of Duhuo Jisheng Decoction in the treatment of OA were acquired by intersecting the OA-associated genes with the target genes of active ingredients. Random walk with restart (RWR) analysis of PPI networks was performed using potential targets as seed, and the top 50 genes of affinity coefficients were used as key action genes of Duhuo Jisheng Decoction in the treatment of OA. A drug-active ingredient-gene interaction network was established. AKT1, a key target of Duhuo Jisheng Decoction in the treatment of OA, was obtained by topological analysis of the gene interaction network. Molecular docking and molecular dynamics verified the binding of AKT1 to its corresponding drug active ingredients. CETSA assay demonstrated that the combination of luteolin and AKT1 increased the stability of AKT1, and the combination efficiency was high. In conclusion, the molecular mechanism of Duhuo Jisheng Decoction in treating OA featured by multiple components, targets, and pathways had been further investigated in this study, which is of significance for discovering as well as developing new drugs for this disease. The findings can also offer personalized diagnosis and treatment strategies for patients with OA in clinical practice.
DOI: 10.6084/m9.figshare.8052767
title: Amifostine showed an inhibition effect on the differentiation of Raw264.7 cells to osteoclasts under 2Gy radiation by reducing ROS

description: the raw data of the article "Amifostine showed an inhibition effect on the differentiation of Raw264.7 cells to osteoclasts under 2Gy radiation by reducing ROS"
DOI: 10.6084/m9.figshare.8046212.v1
title: A novel function of anaphase promoting complex subunit 10 in tumor progression in non-small cell lung cancer

description: The anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated E3 ubiquitin ligase, is responsible for the transition from metaphase to anaphase and the exit from mitosis. The anaphase promoting complex subunit 10 (APC10), a subunit of the APC/C, executes a vital function in substrate recognition. However, no research has reported the connection between APC10 and cancer until now. In this study, we uncovered a novel, unprecedented role of APC10 in tumor progression, which is independent of APC/C. First, aberrant increase of APC10 expression was validated in non-small cell lung cancer (NSCLC) cells and tissues, and the absence of APC10 repressed cell proliferation and migration. Of great interest, we found that APC10 inhibition induced cell cycle arrest at the G0/G1 phase and reduced the expression of the APC/C substrate, Cyclin B1; this finding is different from the conventional concept of the accumulation of Cyclin B1 and cell cycle arrest in metaphase. Further, APC10 was found to interact with glutaminase C (GAC), and the inhibition of APC10 weakened glutamine metabolism and induced excessive autophagy. Taken together, these findings identify a novel function of APC10 in the regulation of NSCLC tumorigenesis and point to the possibility of APC10 as a new target for cancer therapy.
DOI: 10.6084/m9.figshare.17125979
title: Additional file 3 of Cardiovascular and connective tissue disorder features in FLNA-related PVNH patients: progress towards a refined delineation of this syndrome

description: Additional file 3: Data S3. Cohort 2.
DOI: 10.6084/m9.figshare.17125982.v1
title: Additional file 4 of Cardiovascular and connective tissue disorder features in FLNA-related PVNH patients: progress towards a refined delineation of this syndrome

description: Additional file 4: Data S4. Literature patients.
DOI: 10.6084/m9.figshare.17125976
title: Additional file 2 of Cardiovascular and connective tissue disorder features in FLNA-related PVNH patients: progress towards a refined delineation of this syndrome

description: Additional file 2: Data S2. Data for Venn Diagram.
DOI: 10.6084/m9.figshare.17125976.v1
title: Additional file 2 of Cardiovascular and connective tissue disorder features in FLNA-related PVNH patients: progress towards a refined delineation of this syndrome

description: Additional file 2: Data S2. Data for Venn Diagram.