cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21602967.v1
title: Targeted Next-Generation Sequencing Reveals a Large Novel β-Thalassemia Deletion that Removes the Entire <i>HBB</i> Gene

description: β-Thalassemia (β-thal) is one of the most common monogenic recessive inherited diseases worldwide. The mutation spectrum of β-thal has been increasingly broadened by various genetic testing methods. The discovery and identification of novel and rare pathogenic thalassemia variants enable better disease prevention, especially in high prevalence regions. In this study, a Chinese thalassemia family with an unclear etiology was recruited to the Thalassemia Screening Program. Blood samples collected from them were primarily screened by hematology analysis and clinical routine genetic screening. Subsequently, targeted next-generation sequencing (NGS) and Sanger sequencing were performed to find and identify a novel deletion variant. The deletion, discovered by targeted NGS, was validated through real-time quantitative polymerase chain reaction (qPCR). First, a large novel β-thal deletion (3488 bp) related to a high Hb F level, NC_000011.9: g.5245533_5249020del (Chongqing deletion) (GRCh37/hg19), was found and identified in the proband and her mother. The deletion removed the entire β-globin gene and led to absent β-globin (β<sup>0</sup>). We then validated this large novel deletion in the proband and her mother by qPCR. We first discovered and identified a large novel β-thal deletion related to elevated Hb F level, it helps broaden the spectrum of pathogenic mutants that may cause β-thal intermedia (β-TI) or β-thal major (β-TM), paving the way for effective thalassemia screening. Next-generation sequencing has the potential of finding rare and novel thalassemia mutants.
DOI: 10.6084/m9.figshare.21603037.v1
title: Long non-coding RNA NCK1-AS1 functions as a ceRNA to regulate cell viability and invasion in esophageal squamous cell carcinoma via microRNA-133b/ENPEP axis

description: This study is designed to explore the role of long non-coding RNAs (lncRNAs) NCK1-AS1 in proliferative and invasive activities of esophageal squamous cell carcinoma (ESCC) cells by binding to microRNA-133b (miR-133b) to regulate ENPEP. Differentially expressed lncRNAs, miRs, genes and their targeting relationships were screened on ESCC-related gene expression datasets GSE17351 and GSE6188. The targeting relationships among NCK1-AS1, miR-133b, and ENPEP were verified using functional assays. Loss- and gain- of function assays were carried out to examine the roles of NCK1-AS1, miR-133b, and ENPEP in ESCC cell proliferative, invasive, migrative and apoptotic abilities as well as tumorigenesis <i>in vivo</i>. Elevated NCK1-AS1 and ENPEP but reduced miR-133b expression were found in ESCC. NCK1-AS1 knockdown or miR-133b overexpression inhibited the malignant properties of ESCC cells as well as tumorigenesis <i>in vivo</i>. NCK1-AS1 regulated the ENPEP expression by competitively binding to miR-133b. ENPEP overexpression reversed inhibition of NCK1-AS1 knockdown on the function of ESCC cells. This study provides evidence that silencing NCK1-AS1 inhibits expression of ENPEP by sponging miR-133b, thereby suppressing ESCC.
DOI: 10.6084/m9.figshare.7971320
title: p-value from ks-test comparing different osmotic stress condition

description: p-value from ks-test comparing different osmotic stress condition
DOI: 10.6084/m9.figshare.13214445.v1
title: Composition and consistence of the bacterial microbiome in upper, middle and lower esophagus before and after Lugol’s iodine staining in the esophagus cancer screening

description: Esophageal bacteria, as the integral composition of human ecosystem, have been reported to be associated with esophageal lesions. However, few studies focus on microbial compositions in different esophageal segments, especially after Lugol’s iodine staining (LIS) in the endoscopic examination for the screening of esophageal cancer. We aim to investigate the composition of the bacterial microbiome in upper, middle and lower esophagus and if LIS would affect the detection of bacteria. A total of 141 fasting samples including the upper, middle and lower esophagus from 27 participants were collected by brushing the mucosal surface of the esophagus before (Eso) and after (Lug) LIS. Bacterial V3–V4 region of 16S rRNA gene was amplified and sequenced by Illumina’s sequencing platform. The top six abundant bacterial phyla taxa among three locations from both Eso and Lug groups were Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Fusobacteria and TM7. In terms of genera, the bacterium in three locations from two groups was all characterized by a highest relative abundance of <i>Streptococcus</i>. Bacteria diversity and the relative abundance between Eso and Lug were comparable (<i>p</i> &gt; .05). Bacteria diversity was consistent in different esophageal locations within the individual. The bacterial microbiome in healthy esophagus are highly diverse and consistent even among three physiological sites at all clades. Lugol’s iodine staining would not change local microenvironment in term of microbial composition. These findings provide an essential baseline for future studies investigating local and systemic bacterial microbiome and esophageal diseases.
DOI: 10.6084/m9.figshare.13214445
title: Composition and consistence of the bacterial microbiome in upper, middle and lower esophagus before and after Lugol’s iodine staining in the esophagus cancer screening

description: Esophageal bacteria, as the integral composition of human ecosystem, have been reported to be associated with esophageal lesions. However, few studies focus on microbial compositions in different esophageal segments, especially after Lugol’s iodine staining (LIS) in the endoscopic examination for the screening of esophageal cancer. We aim to investigate the composition of the bacterial microbiome in upper, middle and lower esophagus and if LIS would affect the detection of bacteria. A total of 141 fasting samples including the upper, middle and lower esophagus from 27 participants were collected by brushing the mucosal surface of the esophagus before (Eso) and after (Lug) LIS. Bacterial V3–V4 region of 16S rRNA gene was amplified and sequenced by Illumina’s sequencing platform. The top six abundant bacterial phyla taxa among three locations from both Eso and Lug groups were Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Fusobacteria and TM7. In terms of genera, the bacterium in three locations from two groups was all characterized by a highest relative abundance of <i>Streptococcus</i>. Bacteria diversity and the relative abundance between Eso and Lug were comparable (<i>p</i> &gt; .05). Bacteria diversity was consistent in different esophageal locations within the individual. The bacterial microbiome in healthy esophagus are highly diverse and consistent even among three physiological sites at all clades. Lugol’s iodine staining would not change local microenvironment in term of microbial composition. These findings provide an essential baseline for future studies investigating local and systemic bacterial microbiome and esophageal diseases.
DOI: 10.6084/m9.figshare.17006972
title: Additional file 7 of Whole-transcriptome sequencing reveals a vernalization-related ceRNA regulatory network in chinese cabbage (Brassica campestris L. ssp. pekinensis)

description: Table S7. Summary of ceRNA relationships.
DOI: 10.6084/m9.figshare.13212380.v1
title: Additional file 12 of Gene expression kinetics of Exaiptasia pallida innate immune response to Vibrio parahaemolyticus infection

description: Additional file 12 : Supplementary Table 8.
DOI: 10.6084/m9.figshare.17006972.v1
title: Additional file 7 of Whole-transcriptome sequencing reveals a vernalization-related ceRNA regulatory network in chinese cabbage (Brassica campestris L. ssp. pekinensis)

description: Table S7. Summary of ceRNA relationships.
DOI: 10.6084/m9.figshare.13212395
title: Additional file 4 of Gene expression kinetics of Exaiptasia pallida innate immune response to Vibrio parahaemolyticus infection

description: Additional file 4 : Supplementary Figure 3.
DOI: 10.6084/m9.figshare.5350429
title: Origin of the Cretaceous ore-bearing granitoids in the Beihuaiyang Zone, northern margin of the Dabie Orogen, Eastern China

description: The Beihuaiyang Zone (BHY) is one of the most important Mo–Pb–Zn polymetallic metallogenic belts in China, and the BHY deposits are genetically and geographically associated with Cretaceous magmatic rocks. In this article, we present new zircon U–Pb ages and Hf isotope data, whole-rock major and trace-element analytical results, and Sr–Nd–Pb isotope data for the granite porphyry of the Shapinggou (SPG) Mo deposit and the quartz monzonite porphyry of the Gongdongchong (GDC) Pb–Zn deposit. The high contents of SiO<sub>2</sub>, crust-like rare-earth-element and trace element patterns, and the enriched Sr–Nd–Pb–Hf isotopic compositions indicate that both porphyries originated from crustal melting. Inherited Neoproterozoic zircons are common in both porphyries, which implies that their crustal sources were the South China Block rather than the North China Block. Whole-rock <i>ε</i><sub>Nd</sub>(<i>t</i>) values (−10.8 to −9.8 for the GDC deposit, −12.9 to −12.4 for the SPG deposit) and zircon <i>ε</i><sub>Hf</sub>(<i>t</i>) values (−14.3 to −11.1 for the GDC deposit, −18.4 to −13.3 for the SPG deposit) for the ore-bearing rocks are significantly higher than the values found in the widespread and older ore-barren rocks, indicating that the magma sources of the ore-bearing rocks were younger than those of the ore-barren rocks. An integrated study of the Sr–Nd–Pb–Hf isotope contents shows that these younger source rocks are similar to the gneisses found in the South and Central Dabie units, which represent the upper crust of the subducted South China Block. Given the geochemical behaviour of molybdenum, a surface enrichment process would have been an essential prerequisite for the formation of the large Mo deposit. The early Paleozoic Mo–Pb–Zn-enriched black shales, which are widespread in the upper layers of the South China Block, might have been scraped off during Triassic subduction and then transported to deep-crustal levels below the BHY, thus forming an ideal source for the ore-bearing porphyries. An upper-crustal origin for the ore-bearing magmatic rocks is also consistent with the data for most other deposits distributed in the BHY of the Dabie Orogen.
DOI: 10.6084/m9.figshare.7447592
title: Overexpression of Fbxo6 inactivates spindle checkpoint by interacting with Mad2 and BubR1

description: The spindle assembly checkpoint prevents chromosome mis-segregation during mitosis by delaying sister chromatid separation. Several F-box protein members play critical roles in maintaining genome stability and regulating cell cycle progress via ubiquitin-mediated protein degradation. Here, we showed that Fbxo6 critically regulated spindle checkpoint and chromosome segregation. Fbxo6 was phosphorylated during mitosis. Overexpression of Fbxo6 lead to faster exit from nocodazole-induced mitosis arrest through premature sister chromatid separation. Moreover, we found substantially more binuclear and multilobed nuclei cells accompanied with impaired cell viability in Fbxo6-overexpressed HeLa cells. Mechanistically, Fbxo6 interacted with spindle checkpoint proteins including Mad2 and BubR1 leading to the premature exit from mitosis. Overall, we revealed a novel role of Fbxo6 in regulating spindle checkpoint, which may shed light on the regulation of genome instability of cancer cells.
DOI: 10.6084/m9.figshare.7447592.v1
title: Overexpression of Fbxo6 inactivates spindle checkpoint by interacting with Mad2 and BubR1

description: The spindle assembly checkpoint prevents chromosome mis-segregation during mitosis by delaying sister chromatid separation. Several F-box protein members play critical roles in maintaining genome stability and regulating cell cycle progress via ubiquitin-mediated protein degradation. Here, we showed that Fbxo6 critically regulated spindle checkpoint and chromosome segregation. Fbxo6 was phosphorylated during mitosis. Overexpression of Fbxo6 lead to faster exit from nocodazole-induced mitosis arrest through premature sister chromatid separation. Moreover, we found substantially more binuclear and multilobed nuclei cells accompanied with impaired cell viability in Fbxo6-overexpressed HeLa cells. Mechanistically, Fbxo6 interacted with spindle checkpoint proteins including Mad2 and BubR1 leading to the premature exit from mitosis. Overall, we revealed a novel role of Fbxo6 in regulating spindle checkpoint, which may shed light on the regulation of genome instability of cancer cells.
DOI: 10.6084/m9.figshare.25195535
title: Work related MD in OT

description: <b>Work-Related Musculoskeletal Disorders Among Occupational Therapists in Turkey: A Cross-Sectional Study</b>
DOI: 10.6084/m9.figshare.16884700.v1
title: Characterization of the first complete chloroplast genome of <i>Amaranthus hybridus</i> (Caryophyllales: Amaranthaceae) with phylogenetic implications

description: In the present study, the complete chloroplast genome of <i>Amaranthus hybridus</i> was sequenced and assembled. The complete chloroplast genome of <i>Amaranthus hybridus</i> is 150,709 in size, with the GC content of 36.56%. The chloroplast genome of <i>Amaranthus hybridus</i> contained 86 protein-coding genes (PCGs), eight ribosomal RNA (rRNA) genes, and 37 transfer RNA (tRNA) genes. Phylogenetic analysis based on combined chloroplast gene dataset indicated that the <i>Amaranthus hybridus</i> exhibited a close relationship with <i>A. hypochondriacus</i> and <i>A. caudatus</i>.
DOI: 10.6084/m9.figshare.5350393
title: Generation of AMBER force field parameters for zinc centres of M1 and M17 family aminopeptidases

description: The M1 and M17 aminopeptidases are metallo-exopeptidases that rely on the presence of divalent cations, usually zinc, in their active site for proteolytic activity. They are from separate protease superfamilies, however, members often have overlapping substrate specificity. Inhibitors of one or both enzymes can be used to modulate hypertension, reduce proliferation of certain types of cancers and control malaria parasites. Current inhibitors act to chelate the zinc ions in the active site, locking the enzymes in an inactive transition state. We were interested in using a computational approach to understand the structure and dynamics of the M1 and M17 aminopeptidases, however, the presence of the essential metal ions in the proteases presents a challenge to classical molecular dynamics (MD) simulation. The zinc amber force field does not contain applicable descriptions of the zinc coordination environment present in either of these two protease families. To provide tools for the study of these two enzymes, we have used the metal centre parameter builder to generate new hybrid bonded/nonbonded force field (FF) parameters to correctly describe the active site architecture for each enzyme. The new parameters were evaluated by fitting the normal mode frequencies of molecular mechanics to the quantum mechanics frequencies and validated by performing short MD simulations. The new FF parameters now enable more accurate and reliable MD simulations for any member of the M1 or M17 aminopeptidase superfamilies.
DOI: 10.48544/132ef38b-c373-4df5-a42e-7360f5ac8097
title: Interventies voor het stimuleren van gezond en duurzaam voedingsgedrag
DOI: 10.6084/m9.figshare.14787568.v1
title: Flash cold sintering of Nb<sub>2</sub>O<sub>5</sub>: polarity and electrolyte effects

description: We report on a novel consolidation technique based on the combination of a liquid (cold sintering) and electricity (flash sintering). The evolution of hydrogen from electrolysis of the solvent triggered the Flash Cold Sintering (FCS) event without need for external heating. Electrochemical effects became pronounced in the presence of acetic acid solution as the electrolyte had an increased conductivity compared to pure water. By adjusting the acetic acid molar concentration to 0.5 M and by inverting the polarity during FCS a 5 mm diameter 0.8 mm thick Nb<sub>2</sub>O<sub>5</sub> sample was evenly sintered up to 99% in 100 s at a temperature as low as 350°C. Conventional sintered counterparts achieved a 95% relative density when dwelled for 240 min at 1400°C. The inherent complexity of the proposed FCS approach resulted in enhanced densification and weakly translucent samples.
DOI: 10.6084/m9.figshare.5350429.v1
title: Origin of the Cretaceous ore-bearing granitoids in the Beihuaiyang Zone, northern margin of the Dabie Orogen, Eastern China

description: The Beihuaiyang Zone (BHY) is one of the most important Mo–Pb–Zn polymetallic metallogenic belts in China, and the BHY deposits are genetically and geographically associated with Cretaceous magmatic rocks. In this article, we present new zircon U–Pb ages and Hf isotope data, whole-rock major and trace-element analytical results, and Sr–Nd–Pb isotope data for the granite porphyry of the Shapinggou (SPG) Mo deposit and the quartz monzonite porphyry of the Gongdongchong (GDC) Pb–Zn deposit. The high contents of SiO<sub>2</sub>, crust-like rare-earth-element and trace element patterns, and the enriched Sr–Nd–Pb–Hf isotopic compositions indicate that both porphyries originated from crustal melting. Inherited Neoproterozoic zircons are common in both porphyries, which implies that their crustal sources were the South China Block rather than the North China Block. Whole-rock <i>ε</i><sub>Nd</sub>(<i>t</i>) values (−10.8 to −9.8 for the GDC deposit, −12.9 to −12.4 for the SPG deposit) and zircon <i>ε</i><sub>Hf</sub>(<i>t</i>) values (−14.3 to −11.1 for the GDC deposit, −18.4 to −13.3 for the SPG deposit) for the ore-bearing rocks are significantly higher than the values found in the widespread and older ore-barren rocks, indicating that the magma sources of the ore-bearing rocks were younger than those of the ore-barren rocks. An integrated study of the Sr–Nd–Pb–Hf isotope contents shows that these younger source rocks are similar to the gneisses found in the South and Central Dabie units, which represent the upper crust of the subducted South China Block. Given the geochemical behaviour of molybdenum, a surface enrichment process would have been an essential prerequisite for the formation of the large Mo deposit. The early Paleozoic Mo–Pb–Zn-enriched black shales, which are widespread in the upper layers of the South China Block, might have been scraped off during Triassic subduction and then transported to deep-crustal levels below the BHY, thus forming an ideal source for the ore-bearing porphyries. An upper-crustal origin for the ore-bearing magmatic rocks is also consistent with the data for most other deposits distributed in the BHY of the Dabie Orogen.
DOI: 10.6084/m9.figshare.13212391.v1
title: Additional file 2 of Uterine transcriptome analysis reveals mRNA expression changes associated with the ultrastructure differences of eggshell in young and aged laying hens

description: Additional file 2. The information of differentially expressed genes (DEGs) in uterus between young (42 wk. of age) and aged hen groups (72 wk. of age).
DOI: 10.25549/usctheses-c89-355626
title: etd-DankwaLind-8852-b
DOI: 10.6084/m9.figshare.13212452.v1
title: Additional file 3 of Comprehensive analysis of single-cell RNA sequencing data from healthy human marrow hematopoietic cells

description: Additional file 3: Table S1. GO terms of genes dynamically changed along hematopoietic lineage differentiation.
DOI: 10.6084/m9.figshare.10071542
title: MOESM2 of Genomic characteristics and comparative genomics analysis of the endophytic fungus Sarocladium brachiariae

description: Additional file 2: Table S1.1. BUSCO analysis of S. brachiariae scaffolds assembly; Table S1.2. Statistics of RNAseq data; Table S1.3. Mapping rate of NGS data; Table 2. RNA statistics of S. brachiariae; Table S3. Repeative sequence statistic of S. brachiariae; Table S4. Gene annotation statistic of S. brachiariae; Table S5.1. KOG distribution of predicted proteins from S. brachiariae; Table S5.2. KOG distribution of predicted proteins from S. oryzae; Table S6.1. Secreated proteins of S. brachiariae and S. oryzae; Table S6.2. CAZymes distribution of predicted proteins from S. brachiariae; Table S6.3. CAZymes distribution of predicted proteins from S. oryzae; Table S7.1. SM Clusters coordinates of S. brachiariae scaffolds assembly; Table S7.2. SM Clusters coordinates of S. oryzae scaffolds assembly; Table S8. Cytochrome P450 distribution of predicted proteins from S. brachiariae; Table S9. Genes chosen for PCR validation of in silico gene prediction result of S. brachiariae and primers design.
DOI: 10.6084/m9.figshare.10071542.v1
title: MOESM2 of Genomic characteristics and comparative genomics analysis of the endophytic fungus Sarocladium brachiariae

description: Additional file 2: Table S1.1. BUSCO analysis of S. brachiariae scaffolds assembly; Table S1.2. Statistics of RNAseq data; Table S1.3. Mapping rate of NGS data; Table 2. RNA statistics of S. brachiariae; Table S3. Repeative sequence statistic of S. brachiariae; Table S4. Gene annotation statistic of S. brachiariae; Table S5.1. KOG distribution of predicted proteins from S. brachiariae; Table S5.2. KOG distribution of predicted proteins from S. oryzae; Table S6.1. Secreated proteins of S. brachiariae and S. oryzae; Table S6.2. CAZymes distribution of predicted proteins from S. brachiariae; Table S6.3. CAZymes distribution of predicted proteins from S. oryzae; Table S7.1. SM Clusters coordinates of S. brachiariae scaffolds assembly; Table S7.2. SM Clusters coordinates of S. oryzae scaffolds assembly; Table S8. Cytochrome P450 distribution of predicted proteins from S. brachiariae; Table S9. Genes chosen for PCR validation of in silico gene prediction result of S. brachiariae and primers design.
DOI: 10.6084/m9.figshare.10071551
title: MOESM3 of Genomic characteristics and comparative genomics analysis of the endophytic fungus Sarocladium brachiariae

description: Additional file 3: Table S1. Helvolic acid biosynthetic gene cluster found in S. oryzae; Table S2. Possible proteins involved in helvolic acid biosynthesis found in S. brachiariae.
DOI: 10.6084/m9.figshare.13212458
title: Additional file 4 of Comprehensive analysis of single-cell RNA sequencing data from healthy human marrow hematopoietic cells

description: Additional file 4: Table S2. Top 50 genes dynamically expressed along pseudotime ordering.
DOI: 10.6084/m9.figshare.10071551.v1
title: MOESM3 of Genomic characteristics and comparative genomics analysis of the endophytic fungus Sarocladium brachiariae

description: Additional file 3: Table S1. Helvolic acid biosynthetic gene cluster found in S. oryzae; Table S2. Possible proteins involved in helvolic acid biosynthesis found in S. brachiariae.
DOI: 10.6084/m9.figshare.10071557
title: MOESM4 of Genomic characteristics and comparative genomics analysis of the endophytic fungus Sarocladium brachiariae

description: Additional file 4. Annotation (BLASTp) of genes in PKS, NRPS and PKS/NRPS gene clusters of S. brachiariae.
DOI: 10.6084/m9.figshare.10071557.v1
title: MOESM4 of Genomic characteristics and comparative genomics analysis of the endophytic fungus Sarocladium brachiariae

description: Additional file 4. Annotation (BLASTp) of genes in PKS, NRPS and PKS/NRPS gene clusters of S. brachiariae.
DOI: 10.6084/m9.figshare.10071566
title: MOESM5 of Genomic characteristics and comparative genomics analysis of the endophytic fungus Sarocladium brachiariae

description: Additional file 5. Annotation (BLASTp) of genes in PKS, NRPS and PKS/NRPS gene clusters of S. oryzae.
DOI: 10.6084/m9.figshare.10071566.v1
title: MOESM5 of Genomic characteristics and comparative genomics analysis of the endophytic fungus Sarocladium brachiariae

description: Additional file 5. Annotation (BLASTp) of genes in PKS, NRPS and PKS/NRPS gene clusters of S. oryzae.