cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6109508
title: Additional file 6: of Expression levels of long non-coding RNAs are prognostic for AML outcome

description: LncRNA expression data. Description of data: LncRNA expression data and corresponding AML subtypes. (CSV 8427 kb)
DOI: 10.6084/m9.figshare.6109508.v1
title: Additional file 6: of Expression levels of long non-coding RNAs are prognostic for AML outcome

description: LncRNA expression data. Description of data: LncRNA expression data and corresponding AML subtypes. (CSV 8427 kb)
DOI: 10.6084/m9.figshare.6109532
title: Additional file 8: of Expression levels of long non-coding RNAs are prognostic for AML outcome

description: lncRNA in de novo vs. non-de novo AML. Description of data: Differentially expressed lncRNA in de novo vs. non-de novo AML patients. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.6111464
title: Raw cell viability data for culturing time and IRE treatments.xlsx

description: Raw cell viability data for culturing time and IRE treatments for a statistical model of IRE.
DOI: 10.6084/m9.figshare.6118949
title: pathogens_rep_set.fasta

description: This is a dataset about the root-associated pathogen community in a 50ha subtropical forest plot in Southern China
DOI: 10.6084/m9.figshare.6118949.v1
title: pathogens_rep_set.fasta

description: This is a dataset about the root-associated pathogen community in a 50ha subtropical forest plot in Southern China
DOI: 10.6084/m9.figshare.6118961
title: Rare species advantage or disadvantage? Insights from root-associated pathogens

description: This dataset is about the root-associated pathogens in a 50ha subtropical forest plot in Southern China
DOI: 10.6084/m9.figshare.6118961.v1
title: Rare species advantage or disadvantage? Insights from root-associated pathogens

description: This dataset is about the root-associated pathogens in a 50ha subtropical forest plot in Southern China
DOI: 10.6084/m9.figshare.6119276
title: Additional file 6: of Postoperative infection caused by Acinetobacter baumannii misdiagnosed as a free-living amoeba species in a humeral head hemiarthroplasty patient: a case report

description: Table 1. Comparison of the obtained sequence using prokaryotic universal primers pair 16Â s-27F /16Â s-1390R with the top ten Species from the Blast. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.6119276.v1
title: Additional file 6: of Postoperative infection caused by Acinetobacter baumannii misdiagnosed as a free-living amoeba species in a humeral head hemiarthroplasty patient: a case report

description: Table 1. Comparison of the obtained sequence using prokaryotic universal primers pair 16Â s-27F /16Â s-1390R with the top ten Species from the Blast. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.6119300
title: Additional file 7: of Postoperative infection caused by Acinetobacter baumannii misdiagnosed as a free-living amoeba species in a humeral head hemiarthroplasty patient: a case report

description: Table 2. Comparison of obtained sequence (using prokaryotic universal primers pair 16 s-27F /16 s-1390R) with Acinetobacter baumannii strain KAB05, complete genome. Query = obtained sequence; Sbjct = Acinetobacter baumannii strain KAB05, complete genome. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.6119300.v1
title: Additional file 7: of Postoperative infection caused by Acinetobacter baumannii misdiagnosed as a free-living amoeba species in a humeral head hemiarthroplasty patient: a case report

description: Table 2. Comparison of obtained sequence (using prokaryotic universal primers pair 16 s-27F /16 s-1390R) with Acinetobacter baumannii strain KAB05, complete genome. Query = obtained sequence; Sbjct = Acinetobacter baumannii strain KAB05, complete genome. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.6121343
title: Identification of G2/M phase transition by sequential nuclear and cytoplasmic changes and molecular markers in mice intestinal epithelial cells

description: Although the regulatory network of G2/M phase transition has been intensively studied in mammalian cell lines, the identification of morphological and molecular markers to identify G2/M phase transition <i>in vivo</i> remains elusive. In this study, we found no obvious morphological changes between the S phase and G2 phase in mice intestinal epithelial cells. The G2 phase could be identified by Brdu incorporation resistance, marginal and scattered foci of histone H3 phosphorylated at Ser10 (pHH3), and relatively intact Golgi ribbon. Prophase starts with nuclear transformation <i>in situ</i>, which was identified by a series of prophase markers including nuclear translocation of cyclinB1, fragmentation of the Golgi complex, and a significant increase in pHH3. The nucleus started to move upwards in the late prophase and finally rounded up at the apical surface. Then, metaphase was initiated as the level of pHH3 peaked. During anaphase and telophase, pHH3 sharply decreased, while Ki67 was obviously bound to chromosomes, and PCNA was distributed throughout the whole cell. Based on the aforementioned markers and Brdu pulse labeling, it was estimated to take about one hour for most crypt cells to go through the G2 phase and about two hours to go through the G2-M phase. It took much longer for crypt base columnar (CBC) stem cells to undergo G2-prophase than rapid transit amplifying cells. In summary, a series of sequentially presenting markers could be used to indicate the progress of G2/M events in intestinal epithelial cells and other epithelial systems <i>in vivo</i>.
DOI: 10.6084/m9.figshare.6121343.v1
title: Identification of G2/M phase transition by sequential nuclear and cytoplasmic changes and molecular markers in mice intestinal epithelial cells

description: Although the regulatory network of G2/M phase transition has been intensively studied in mammalian cell lines, the identification of morphological and molecular markers to identify G2/M phase transition <i>in vivo</i> remains elusive. In this study, we found no obvious morphological changes between the S phase and G2 phase in mice intestinal epithelial cells. The G2 phase could be identified by Brdu incorporation resistance, marginal and scattered foci of histone H3 phosphorylated at Ser10 (pHH3), and relatively intact Golgi ribbon. Prophase starts with nuclear transformation <i>in situ</i>, which was identified by a series of prophase markers including nuclear translocation of cyclinB1, fragmentation of the Golgi complex, and a significant increase in pHH3. The nucleus started to move upwards in the late prophase and finally rounded up at the apical surface. Then, metaphase was initiated as the level of pHH3 peaked. During anaphase and telophase, pHH3 sharply decreased, while Ki67 was obviously bound to chromosomes, and PCNA was distributed throughout the whole cell. Based on the aforementioned markers and Brdu pulse labeling, it was estimated to take about one hour for most crypt cells to go through the G2 phase and about two hours to go through the G2-M phase. It took much longer for crypt base columnar (CBC) stem cells to undergo G2-prophase than rapid transit amplifying cells. In summary, a series of sequentially presenting markers could be used to indicate the progress of G2/M events in intestinal epithelial cells and other epithelial systems <i>in vivo</i>.
DOI: 10.6084/m9.figshare.6124046
title: Using a new framework of two-phase generalized additive models to incorporate prey abundance in spatial distribution models of juvenile slender lizardfish in Haizhou Bay, China

description: The predictive skill of species distribution models depends on the quality and quantity of input information. In addition to the physical environmental variables, prey availability is also one of the main drivers regulating spatial distribution of marine species. However, prey distribution data have rarely been considered in habitat models due to the lack of information on non-commercial prey species. This may lead to an incomplete view of species distributions and biased model predictions. In this study, we developed a new framework of two-phase generalized additive models (GAMs) based on the Tweedie distribution to incorporate the predicted prey abundance as covariates in habitat models, and applied this framework to juvenile slender lizardfish <i>Saurida elongata</i> in Haizhou Bay, China. This study demonstrated that the predictive skill of habitat models could be greatly improved through incorporating prey abundance as explanatory variables. The importance of prey distribution data in the habitat model confirms the essentiality of including prey data while modelling species distribution. Spatial overlap and GAM analysis demonstrated that not all dominant prey can be selected as potential explanatory variables and only those prey species showing high spatiotemporal occurrences with predators should be incorporated. The framework derived in this study could be extended to other marine organisms to improve the predictive skill of habitat models and enhance our understanding of the ecological mechanisms underlying the distribution of marine species.
DOI: 10.6084/m9.figshare.6124046.v1
title: Using a new framework of two-phase generalized additive models to incorporate prey abundance in spatial distribution models of juvenile slender lizardfish in Haizhou Bay, China

description: The predictive skill of species distribution models depends on the quality and quantity of input information. In addition to the physical environmental variables, prey availability is also one of the main drivers regulating spatial distribution of marine species. However, prey distribution data have rarely been considered in habitat models due to the lack of information on non-commercial prey species. This may lead to an incomplete view of species distributions and biased model predictions. In this study, we developed a new framework of two-phase generalized additive models (GAMs) based on the Tweedie distribution to incorporate the predicted prey abundance as covariates in habitat models, and applied this framework to juvenile slender lizardfish <i>Saurida elongata</i> in Haizhou Bay, China. This study demonstrated that the predictive skill of habitat models could be greatly improved through incorporating prey abundance as explanatory variables. The importance of prey distribution data in the habitat model confirms the essentiality of including prey data while modelling species distribution. Spatial overlap and GAM analysis demonstrated that not all dominant prey can be selected as potential explanatory variables and only those prey species showing high spatiotemporal occurrences with predators should be incorporated. The framework derived in this study could be extended to other marine organisms to improve the predictive skill of habitat models and enhance our understanding of the ecological mechanisms underlying the distribution of marine species.
DOI: 10.6084/m9.figshare.6125237
title: Investigation on Friction and Wear Properties of High-Temperature Bearing Steel 9Cr18Mo

description: This paper presented a study of friction and wear on 9Cr18Mo when rubbed against other materials (steel-304, steel-440C, steel-GCr15 or silicon nitride ceramic ball) at high temperature conditions. Friction and wear tests were carried out with universal a friction and wear testing machine. The wear morphology was analyzed by a Nanovea three-dimensional profilometer and trinocular positive Gang metallurgical microscope. The Vickers hardness of 9Cr18Mo at different temperatures was tested by means of a high temperature vacuum hardometer. Results showed that the friction and wear on the contact surface of the 9Cr18Mo sample are higher when the hardness of counter materials is higher than or similar to that of the sample. Under dry sliding conditions, the 9Cr18Mo sample surface presented various degrees of adhesion, plowing and pit, particularly if tested in the presence of a high temperature environment. During the worn stages, the counter materials on the worn surface successively produced cracks, crack growth, and wear debris under the action of load. Moreover, the frictional pair 9Cr18Mo-ceramic showed good anti-wear behavior at 400 °C that proved the anti high temperature performance of 9Cr18Mo.
DOI: 10.6084/m9.figshare.6125237.v1
title: Investigation on Friction and Wear Properties of High-Temperature Bearing Steel 9Cr18Mo

description: This paper presented a study of friction and wear on 9Cr18Mo when rubbed against other materials (steel-304, steel-440C, steel-GCr15 or silicon nitride ceramic ball) at high temperature conditions. Friction and wear tests were carried out with universal a friction and wear testing machine. The wear morphology was analyzed by a Nanovea three-dimensional profilometer and trinocular positive Gang metallurgical microscope. The Vickers hardness of 9Cr18Mo at different temperatures was tested by means of a high temperature vacuum hardometer. Results showed that the friction and wear on the contact surface of the 9Cr18Mo sample are higher when the hardness of counter materials is higher than or similar to that of the sample. Under dry sliding conditions, the 9Cr18Mo sample surface presented various degrees of adhesion, plowing and pit, particularly if tested in the presence of a high temperature environment. During the worn stages, the counter materials on the worn surface successively produced cracks, crack growth, and wear debris under the action of load. Moreover, the frictional pair 9Cr18Mo-ceramic showed good anti-wear behavior at 400 °C that proved the anti high temperature performance of 9Cr18Mo.
DOI: 10.6084/m9.figshare.6125360
title: Short-term insulin intensive therapy decreases MCP-1 and NF-κB expression of peripheral blood monocyte and the serum MCP-1 concentration in newlydiagnosed type 2 diabetics

description: ABSTRACT Objective To observe the effect of short-term insulin intensive treatment on the monocyte chemoattractant protein-1 (MCP-1) as well as on the nuclear factor-kappa B (NF-κB) expression of peripheral blood monocyte. This is also in addition to observing the serum MCP-1 level in newlydiagnosed type 2 diabetic patients and probing its anti-inflammation effects. Subjects and methods Twenty newly-diagnosed type 2 diabetic patients were treated with an insulin intensive treatment for 2 weeks. MCP-1 and NF-κB expression on the monocyte surface were measured with flow cytometry, the serum MCP-1 level was measured by enzyme linked immunosorbent assay (ELISA) during pretreatment and post-treatment. Results After 2 weeks of the treatment, MCP-1 and NF-κB protein expression of peripheral blood monocyte and serum MCP-1 levels decreased significantly compared with those of pre-treatment, which were (0.50 ± 0.18)% vs (0.89 ± 0.26)% (12.22 ± 2.80)% vs (15.53 ± 2.49)% and (44.53 ± 3.97) pg/mL vs (49.53 ± 3.47) pg/mL, respectively (P &lt; 0.01). The MCP-1 expression on monocyte surface had a significant positive relationship with serum MCP-1 levels (r = 0.47, P &lt; 0.01). Conclusions Short-term insulin intensive therapy plays a role in alleviating the increased inflammation reaction in type 2 diabetics.
DOI: 10.6084/m9.figshare.6125360.v1
title: Short-term insulin intensive therapy decreases MCP-1 and NF-κB expression of peripheral blood monocyte and the serum MCP-1 concentration in newlydiagnosed type 2 diabetics

description: ABSTRACT Objective To observe the effect of short-term insulin intensive treatment on the monocyte chemoattractant protein-1 (MCP-1) as well as on the nuclear factor-kappa B (NF-κB) expression of peripheral blood monocyte. This is also in addition to observing the serum MCP-1 level in newlydiagnosed type 2 diabetic patients and probing its anti-inflammation effects. Subjects and methods Twenty newly-diagnosed type 2 diabetic patients were treated with an insulin intensive treatment for 2 weeks. MCP-1 and NF-κB expression on the monocyte surface were measured with flow cytometry, the serum MCP-1 level was measured by enzyme linked immunosorbent assay (ELISA) during pretreatment and post-treatment. Results After 2 weeks of the treatment, MCP-1 and NF-κB protein expression of peripheral blood monocyte and serum MCP-1 levels decreased significantly compared with those of pre-treatment, which were (0.50 ± 0.18)% vs (0.89 ± 0.26)% (12.22 ± 2.80)% vs (15.53 ± 2.49)% and (44.53 ± 3.97) pg/mL vs (49.53 ± 3.47) pg/mL, respectively (P &lt; 0.01). The MCP-1 expression on monocyte surface had a significant positive relationship with serum MCP-1 levels (r = 0.47, P &lt; 0.01). Conclusions Short-term insulin intensive therapy plays a role in alleviating the increased inflammation reaction in type 2 diabetics.
DOI: 10.6084/m9.figshare.6125813
title: MOESM1 of Liraglutide suppresses non-esterified free fatty acids and soluble vascular cell adhesion molecule-1 compared with metformin in patients with recent-onset type 2 diabetes

description: Additional file 1: Table S1. Changes of plasma lipids and lipoprotein metabolism parameters before and after 8-week treatment with liraglutide and metfotmin. Table S2. Comparisons of body weight, plasma glucose and insulin secretion capacity before and after 8-week treatment between two groups. Table S3. Comparisons of sVCAM-1,sICAM-1,PAI-1 levels before and after 8-week treatment between two groups. Table S4. Spearman rank correlations in ΔNEFA with ΔsVCAM-1, ΔAUCins and ΔI30/ΔG30 after 8-week treatment.
DOI: 10.6084/m9.figshare.6125813.v1
title: MOESM1 of Liraglutide suppresses non-esterified free fatty acids and soluble vascular cell adhesion molecule-1 compared with metformin in patients with recent-onset type 2 diabetes

description: Additional file 1: Table S1. Changes of plasma lipids and lipoprotein metabolism parameters before and after 8-week treatment with liraglutide and metfotmin. Table S2. Comparisons of body weight, plasma glucose and insulin secretion capacity before and after 8-week treatment between two groups. Table S3. Comparisons of sVCAM-1,sICAM-1,PAI-1 levels before and after 8-week treatment between two groups. Table S4. Spearman rank correlations in ΔNEFA with ΔsVCAM-1, ΔAUCins and ΔI30/ΔG30 after 8-week treatment.
DOI: 10.6084/m9.figshare.6125912
title: Additional file 1: of Correction to: Dual RNA-seq reveals viral infections in asthmatic children without respiratory illness which are associated with changes in the airway transcriptome

description: Table S2. Gene count table for 48 RNA-seq nasal brushing subjects from GALA cohort. (XLSX 5732 kb)
DOI: 10.6084/m9.figshare.6125912.v1
title: Additional file 1: of Correction to: Dual RNA-seq reveals viral infections in asthmatic children without respiratory illness which are associated with changes in the airway transcriptome

description: Table S2. Gene count table for 48 RNA-seq nasal brushing subjects from GALA cohort. (XLSX 5732 kb)
DOI: 10.6084/m9.figshare.6126005
title: Additional file 1: of DNA methylation profiles correlated to striped bass sperm fertility

description: Table S1. Primers used for pyrosequencing validation of differentially methylated regions (DMRs) identified by MBD-Seq(XLS). (XLS 29Â kb)
DOI: 10.6084/m9.figshare.6126005.v1
title: Additional file 1: of DNA methylation profiles correlated to striped bass sperm fertility

description: Table S1. Primers used for pyrosequencing validation of differentially methylated regions (DMRs) identified by MBD-Seq(XLS). (XLS 29Â kb)
DOI: 10.6084/m9.figshare.6126020
title: MOESM2 of New World feline APOBEC3 potently controls inter-genus lentiviral transmission

description: Additional file 2: Table S1. Primers used in this study. A full list of the primers used in this study.
DOI: 10.6084/m9.figshare.6126020.v1
title: MOESM2 of New World feline APOBEC3 potently controls inter-genus lentiviral transmission

description: Additional file 2: Table S1. Primers used in this study. A full list of the primers used in this study.
DOI: 10.6084/m9.figshare.6126050
title: Additional file 3: of DNA methylation profiles correlated to striped bass sperm fertility

description: Table S2. Differentially methylated regions (DMRs) between high- and sub-fertility striped bass sperm at a strict false discovery rate (FDR) &lt;â 0.1 (XLS). (XLS 53Â kb)
DOI: 10.6084/m9.figshare.6126050.v1
title: Additional file 3: of DNA methylation profiles correlated to striped bass sperm fertility

description: Table S2. Differentially methylated regions (DMRs) between high- and sub-fertility striped bass sperm at a strict false discovery rate (FDR) &lt;â 0.1 (XLS). (XLS 53Â kb)
DOI: 10.6084/m9.figshare.6126065
title: Additional file 4: of DNA methylation profiles correlated to striped bass sperm fertility

description: Table S3. Annotation of the identified differentially methylated regions (DMRs) in striped bass sperm from high- and sub-fertility groups. Genes present on contigs with DMRs are indicated in the column to the left (DMRs) and are numbered according to the striped bass genome assembly files provided at http://appliedecology.cals.ncsu.edu/striped-bass-genome-project/data-downloads/ . Additional information including start and end of the gene transcripts on each of the contigs, length of the DMR site (Width), methylation levels in fish from the sub-fertile (Conc_Low) and high-fertile (Conc_High) groups, methylation fold-difference between fertility groups (negative value indicates greater in the high fertility group in reference to the low fertility group), p-value, false discovery rate (FDR), gene name (Name), approved gene symbol (Gene), gene position on each of the contigs (Gene Position), and method of annotation (ID) either from the striped bass genome or BLAST of the National Center for Biotechnology Information (XLS). (XLS 91Â kb)
DOI: 10.6084/m9.figshare.6126065.v1
title: Additional file 4: of DNA methylation profiles correlated to striped bass sperm fertility

description: Table S3. Annotation of the identified differentially methylated regions (DMRs) in striped bass sperm from high- and sub-fertility groups. Genes present on contigs with DMRs are indicated in the column to the left (DMRs) and are numbered according to the striped bass genome assembly files provided at http://appliedecology.cals.ncsu.edu/striped-bass-genome-project/data-downloads/ . Additional information including start and end of the gene transcripts on each of the contigs, length of the DMR site (Width), methylation levels in fish from the sub-fertile (Conc_Low) and high-fertile (Conc_High) groups, methylation fold-difference between fertility groups (negative value indicates greater in the high fertility group in reference to the low fertility group), p-value, false discovery rate (FDR), gene name (Name), approved gene symbol (Gene), gene position on each of the contigs (Gene Position), and method of annotation (ID) either from the striped bass genome or BLAST of the National Center for Biotechnology Information (XLS). (XLS 91Â kb)
DOI: 10.6084/m9.figshare.6127760
title: Sequences of spike-ins used to evaluate TAPS

description: Sequences of spike-ins used for testing TAPS.
DOI: 10.6084/m9.figshare.6127760.v1
title: Sequences of spike-ins used to evaluate TAPS

description: Sequences of spike-ins used for testing TAPS.
DOI: 10.6084/m9.figshare.6131024
title: Unweighted UniFrac distances

description: The unweighted UniFrac distance (Lozupone and Knight AEM 2005) matrix of the 9511 fecal samples used in the American Gut paper. UniFrac was computed using Striped UniFrac (https://github.com/biocore/unifrac). Prior to execution of UniFrac, Deblur (Amir et al mSystems 2017) was run on the samples, all bloom sOTUs were removed (Amir et al mSystems 2017), and samples were rarefied to a depth of 1250 reads (Weiss et al Microbiome 2017). For the phylogeny, fragments were inserted using SEPP (Mirarab et al Pac Symp Biocomput 2012) into the Greengenes 13_5 99% OTU tree (McDonald et al ISME 2012).
DOI: 10.6084/m9.figshare.6131672
title: Additional file 1: of iSeg: an efficient algorithm for segmentation of genomic and epigenomic data

description: The zipped supplementary file submitted with this manuscript contains Coriell (Snijders et al.) profiles, BACarray profiles, and simulated data files. (ZIP 1970kb)