cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4991087.v1
title: Is rheumatoid arthritis associated with a declined immunogenicity of influenza vaccination? A systematic review and meta-analysis

description: <b>Objective:</b> To determine whether immunogenicity and safety of influenza vaccination in rheumatoid arthritis (RA) patients are significantly different from those in healthy population. <b>Methods:</b> PubMed, MEDLINE, Embase, Cochrane Library and Web of Science were searched on 31 August 2016. Studies were included when they met the inclusion criteria. Two reviewers independently extracted data on study characteristics, methodological quality and outcomes. The primary outcome was seroprotection (SP) rate after immunization. <b>Results:</b> 13 studies were included. The SP rates did not significantly differ between the RA patients and healthy controls for the H3N2 (RR = 0.96, 95% CI, 0.82 to 1.13, p = 0.64) and B strain (RR = 0.95, 95% CI 0.84 to 1. 08, p = 0.44). Nevertheless, RA was associated with a significant decrease of SP rate for the H1N1 strain (RR = 0.72, 95% CI 0.60 to 0.86, p <b>Conclusions:</b> The immunogenicity was significantly different between RA patients and the healthy controls for H1N1 strain, but not for H3N2 or B strains. Adverse event rates were higher in RA patients. Adjuvant and special kinds of immunosuppressive biologics may play an important role in immunogenicity of inactivated influenza vaccines for RA patients.
DOI: 10.6084/m9.figshare.4990982
title: Distribution and Drivers of Global Mangrove Forest Change 1996-2010

description: This study undertook an analysis of 1168 1<sup>o</sup>x1<sup>o</sup> radar mosaic composite images, combining 1996 JERS-1 and 2007 and 2010 ALOS PALSAR mosaic imagery across the geographical range of mangrove forests. The composite imagery was visually interrogated to determine the location and distribution of changes in extent over the period 1996-2010. In addition, these composites were used to establish the perceived drivers of the change in Land Cover and Land Use Change (LCLUC). Validation of the observed changes and their drivers was undertaken through reference to the dense time-series of Landsat optical imagery and high-resolution imagery via Google Earth.The data for this work was made available for use to the Global Mangrove Watch (GMW), an international coalition conceived through JAXA’s Kyoto & Carbon (K&C) Initiative to demonstrate the potential of time-series Japanese L-band Synthetic Aperture Radar (SAR) for characterising, mapping and monitoring mangroves at regional to global scales.Time-series of JERS-1 imagery from 1996 and ALOS PALSAR imagery data from 2007 and 2010 were compiled, in KML format for Google Earth, to generate temporal colour composite (1996, 2007 and 2010 in Red, Green and Blue bands) tiles measuring 1<sup>o</sup>x1<sup>o</sup> in extent at 25 m pixel resolution. Only the HH polarisation channel was used. The total geographical extent of the colour composite dataset was defined using the mangrove map of Giri et al 2011. The tiles were imported into Google Earth for the visual analysis of change visible as colours in the RGB composite images. Each region was manually interpreted to identify evidence of changes in mangrove extent to a predefined set of categories. These categories were selected using reference to the literature on the causes of mangrove forest loss and expert knowledge. The categories of change identified were: 1) Intact, 2) Prior Disturbance, 3) Erosion, 4) Deposition/Regrowth, 5) Aquaculture/Agriculture, 6) Dieback 7) Logging.AcknowledgmentsThe authors are thankful to the Japanese Aerospace Exploration Agency (JAXA) for providing JERS-1/ALOS color composite imagery for this work. The authors are particularly grateful to Mr Takuya Itoh for compiling the dataset and making it available to the project. The Global Mangrove WatchThe Global Mangrove Watch (GMW) is an international science collaboration initiated in 2011 by the Japanese Space Agency. The GMW is part of the Wetlands Theme of the ALOS Kyoto & Carbon Initiative. The GMW homepage is: http://www.eorc.jaxa.jp/ALOS/en/kyoto/mangrovewatch.htm and is on Twitter as @GlobalMangroves.
DOI: 10.6084/m9.figshare.4990976
title: Appendix_Data

description: Supplement of Master's Thesis: "Modeling and analysis of colon-microbiota interactions in inflammatory bowel disease" by Georgios Marinos, CAU zu Kiel, Germany<br>Part: Appendix_Data
DOI: 10.6084/m9.figshare.4990976.v1
title: Appendix_Data

description: Supplement of Master's Thesis: "Modeling and analysis of colon-microbiota interactions in inflammatory bowel disease" by Georgios Marinos, CAU zu Kiel, Germany<br>Part: Appendix_Data
DOI: 10.6084/m9.figshare.4990919
title: Fluctuations in coral reef fish densities after environmental disturbances on the northern Great Barrier Reef

description: The Great Barrier Reef around Lizard Island has suffered from severe tropical cyclones Ita (2014) and Nathan (2015) and a massive coral bleaching due to El Niño (2016). We compared fish density from before the disturbances to data collected after the disturbances. Overall, we recorded up to 68% declines in fish density after the environmental perturbations. Thus, environmental perturbations due to extreme climate events appear to have strong detrimental consequences for reef fish densities.
DOI: 10.6084/m9.figshare.4990913
title: VASA-data-4282017-NG.zip

description: 2014 Verbal/Social Autopsy Study in Nigeria
DOI: 10.6084/m9.figshare.4990694
title: Data in R

description: These files include the scripts used for test phylogenetic signal for ventral and dorsal anchors in Ligophorus spp., Also, the data set in format CSV for ventral and dorsal anchors.
DOI: 10.6084/m9.figshare.4990685
title: Ligophorus_Alignment.nex

description: This file contain the alignment of the species of Ligophorus.
DOI: 10.6084/m9.figshare.4990682
title: Ligosmedi_ML.nex

description: This file contain the tree in nexus format.
DOI: 10.6084/m9.figshare.4990694.v1
title: Data in R

description: These files include the scripts used for test phylogenetic signal for ventral and dorsal anchors in Ligophorus spp., Also, the data set in format CSV for ventral and dorsal anchors.
DOI: 10.6084/m9.figshare.4990670
title: Robot-assisted excision gastro intestinal stromal tumors of stomach with the da Vinci Si and Xi regardless location site

description: In this retrospective study we report on a single centre series of 12 robotically-assisted resections performed chronologically using the da Vinci Si and compare these with the more recent and Xi platform.Data of patients undergoing robot-assisted treatment of gastric GIST were retrieved from the prospectively-collected Institutional database for the retrospective analysis of the patients stratified according to tumor location of the tumor.
DOI: 10.6084/m9.figshare.4990682.v1
title: Ligosmedi_ML.nex

description: This file contain the tree in nexus format.
DOI: 10.6084/m9.figshare.4990685.v1
title: Ligophorus_Alignment.nex

description: This file contain the alignment of the species of Ligophorus.
DOI: 10.6084/m9.figshare.4990670.v1
title: Robot-assisted excision gastro intestinal stromal tumors of stomach with the da Vinci Si and Xi regardless location site

description: In this retrospective study we report on a single centre series of 12 robotically-assisted resections performed chronologically using the da Vinci Si and compare these with the more recent and Xi platform.Data of patients undergoing robot-assisted treatment of gastric GIST were retrieved from the prospectively-collected Institutional database for the retrospective analysis of the patients stratified according to tumor location of the tumor.
DOI: 10.6084/m9.figshare.4990598
title: Mumps raw data based on 20 randomly selected sequences

description: Raw data for the graphs linking conservation, entropy and DynaMine results for the mumps virus proteins, based on 20 randomly selected sequences.
DOI: 10.6084/m9.figshare.4990586
title: Graphs for the mumps proteins based on 20 randomly selected sequences

description: Graphs linking conservation, entropy and DynaMine results for the mumps proteins based on 20 randomly selected sequences
DOI: 10.6084/m9.figshare.4990598.v1
title: Mumps raw data based on 20 randomly selected sequences

description: Raw data for the graphs linking conservation, entropy and DynaMine results for the mumps virus proteins, based on 20 randomly selected sequences.
DOI: 10.6084/m9.figshare.4990562
title: Parida-etal-Table S2.pdf

description: Identification of functionally relevant potential genomic loci using an economical, simpler and user-friendly genomics-assisted breeding strategy is vital for rapid genetic dissection of complex flowering time quantitative trait in chickpea. A high-throughput multiple QTL-seq strategy was employed in two inter (<i>C. arietinum</i> <i>desi</i> accession ICC 4958 × <i>C. reticulatum</i> wild accession ICC 17160)- and intra (ICC 4958 × <i>C. arietinum</i> <i>kabuli</i> accession ICC 8261)-specific RIL mapping population to identify the major QTL genomic regions governing flowering time in chickpea. The whole genome resequencing discovered 446475 and 150434 SNPs exhibiting differentiation between early- and late-flowering mapping parents and bulks, constituted by pooling the homozygous individuals of extreme flowering time phenotypic trait from each of two aforesaid RIL populations. The multiple QTL-seq analysis using these mined SNPs in two RIL mapping populations narrowed-down two longer (907.1 kb and 1.99 Mb) major flowering time QTL genomic regions into the high-resolution shorter (757.7 kb and 1.39 Mb) QTL intervals on chickpea chromosome 4. This essentially identified regulatory as well as coding (non-synonymous/synonymous) novel SNP allelic variants from two <i>efl1</i> (early flowering 1) and <i>GI</i> (<i>GIGANTEA</i>) genes regulating flowering time in chickpea. Interestingly, strong natural allelic diversity reduction (88-91%) of two known flowering genes especially mapped at major QTL intervals as compared to that of background genomic regions (where no flowering time QTLs were mapped) (61.8%) in cultivated vis-à-vis wild <i>Cicer</i> gene pools was evident inferring the significant impact of evolutionary bottlenecks on these loci during chickpea domestication. Higher association potential of coding non-synonymous and regulatory SNP alleles mined from <i>efl1</i> (36-49%) and <i>GI</i> (33-42%) known flowering genes for early and late flowering time differentiation among chickpea accessions was evident. The robustness and validity of two functional allelic variants-containing genes localized at major flowering time QTLs was apparent by their identification from multiple intra-/inter-specific mapping populations of chickpea. The functionally relevant molecular tags delineated can be of immense use for deciphering the natural allelic diversity-based domestication pattern of flowering time and expediting genomics-aided crop improvement to develop early flowering cultivars of chickpea.
DOI: 10.6084/m9.figshare.4990586.v1
title: Graphs for the mumps proteins based on 20 randomly selected sequences

description: Graphs linking conservation, entropy and DynaMine results for the mumps proteins based on 20 randomly selected sequences
DOI: 10.6084/m9.figshare.4990562.v1
title: Parida-etal-Table S2.pdf

description: Identification of functionally relevant potential genomic loci using an economical, simpler and user-friendly genomics-assisted breeding strategy is vital for rapid genetic dissection of complex flowering time quantitative trait in chickpea. A high-throughput multiple QTL-seq strategy was employed in two inter (<i>C. arietinum</i> <i>desi</i> accession ICC 4958 × <i>C. reticulatum</i> wild accession ICC 17160)- and intra (ICC 4958 × <i>C. arietinum</i> <i>kabuli</i> accession ICC 8261)-specific RIL mapping population to identify the major QTL genomic regions governing flowering time in chickpea. The whole genome resequencing discovered 446475 and 150434 SNPs exhibiting differentiation between early- and late-flowering mapping parents and bulks, constituted by pooling the homozygous individuals of extreme flowering time phenotypic trait from each of two aforesaid RIL populations. The multiple QTL-seq analysis using these mined SNPs in two RIL mapping populations narrowed-down two longer (907.1 kb and 1.99 Mb) major flowering time QTL genomic regions into the high-resolution shorter (757.7 kb and 1.39 Mb) QTL intervals on chickpea chromosome 4. This essentially identified regulatory as well as coding (non-synonymous/synonymous) novel SNP allelic variants from two <i>efl1</i> (early flowering 1) and <i>GI</i> (<i>GIGANTEA</i>) genes regulating flowering time in chickpea. Interestingly, strong natural allelic diversity reduction (88-91%) of two known flowering genes especially mapped at major QTL intervals as compared to that of background genomic regions (where no flowering time QTLs were mapped) (61.8%) in cultivated vis-à-vis wild <i>Cicer</i> gene pools was evident inferring the significant impact of evolutionary bottlenecks on these loci during chickpea domestication. Higher association potential of coding non-synonymous and regulatory SNP alleles mined from <i>efl1</i> (36-49%) and <i>GI</i> (33-42%) known flowering genes for early and late flowering time differentiation among chickpea accessions was evident. The robustness and validity of two functional allelic variants-containing genes localized at major flowering time QTLs was apparent by their identification from multiple intra-/inter-specific mapping populations of chickpea. The functionally relevant molecular tags delineated can be of immense use for deciphering the natural allelic diversity-based domestication pattern of flowering time and expediting genomics-aided crop improvement to develop early flowering cultivars of chickpea.
DOI: 10.6084/m9.figshare.4990445
title: Supplementary Material for: A Novel Approach of Synthesizing and Evaluating the Anticancer Potential of Silver Oxide Nanoparticles in vitro

description: <b><i>Background:</i></b> Development of novel strategies to kill cancer by sparing normal cells is of utmost importance. Apart from their known antimicrobial activity, only limited information has been recorded regarding the antitumor potential of biocompatible silver oxide nanoparticles (AgONPs). There is a need to evaluate the anticancer potential of biocompatible AgONPs in vitro. <b><i>Methods:</i></b> A new approach of utilizing the leaf extract of <i>Excoecaria agallocha</i> was used to synthesize AgONPs. This was then characterized by ultraviolet-visible spectrophotometry, nanoparticle-tracking analysis, and ζ-potential analysis. Cytotoxicity and apoptotic potential were evaluated with an MTT assay and an annexin V-binding assay against the murine melanoma (B16F10), murine colon cancer (CT26), murine lung adenocarcinoma (3LL), and murine Ehrlich ascites carcinoma (EAC) cell lines. Cellular localization of AgONPs was evaluated on fluorescence microscopy. <b><i>Results:</i></b> UV peaks at 270 and 330 nm indicated the formation of nanoparticles (NPs) and the NP-tracking analyzer revealed them to have a size of 228 nm. AgONPs exerted initial cytotoxicity, specifically against all the experimental malignant cells by sparing the normal cell lines. Moreover, AgONPs exert apoptosis equally on all the malignant cells in vitro and ex vivo. This cytotoxicity possibly occurs via the nuclear translocation of AgONPs as analyzed in B16F10 cells. <b><i>Conclusions:</i></b> AgONPs utilizing natural sources would be a new medicinal approach against a broad spectrum of malignancy.
DOI: 10.6084/m9.figshare.4990448
title: Supplementary Material for: A Novel Ataxic Mutant Mouse Line Having Sensory Neuropathy Shows Heavy Iron Deposition in Kidney

description: <b><i>Background/Aims:</i></b> A novel ataxic mouse line was established from the offspring of a male mouse administered cyclophosphamide in a juvenile period. <b><i>Methods:</i></b> We have attempted to examine the phenotype and histopathological changes of affected mice. Furthermore, linkage analysis and sequencing of the mutant was performed to reveal the causative gene locus. <b><i>Results and Conclusion:</i></b> The affected mouse was characterized by heavy hind limb ataxia with gait disorder, which was first recognized at about 4 weeks of age and slowly progressed with advancing age. The phenotype was inherited in an autosomal recessive pattern. The genetic locus associated with the phenotype was named <i>hak</i> and mapped to 107,305,356-108,637,615 on chromosome 2qE3, non-coding sequences in the vicinity of <i>Bdnf</i> gene. Many spheroids were noticed in the cerebellar medulla and the brain stem. In the peripheral nerves, some sensory ganglionic cells showed deposition of NF-200 in the perikaryon and NF-200-positive spheroids in nerve fibers. No inflammatory cell infiltration was observed. In addition, the adult affected mouse had distinct iron deposition in the kidney and the liver, but not in the heart, the skeletal muscle and the central nervous system. These results suggest that the <i>hak</i> mouse has a tissue-specific impairment in the expression of a type of <i>Bdnf</i> transcripts.
DOI: 10.6084/m9.figshare.4990442
title: Supplementary Material for: Sulfatase 2 Modulates Fate Change from Motor Neurons to Oligodendrocyte Precursor Cells through Coordinated Regulation of Shh Signaling with Sulfatase 1

description: Sulfatases (Sulfs) are a group of endosulfatases consisting of Sulf1 and Sulf2, which specifically remove sulfate from heparan sulfate proteoglycans. Although several studies have shown that Sulf1 acts as a regulator of sonic hedgehog (Shh) signaling during embryonic ventral spinal cord development, the detailed expression pattern and function of Sulf2 in the spinal cord remains to be determined. In this study, we found that Sulf2 also modulates the cell fate change from motor neurons (MNs) to oligodendrocyte precursor cells (OPCs) by regulating Shh signaling in the mouse ventral spinal cord in coordination with Sulf1. In the mouse, Sulf mRNAs colocalize with Shh mRNA and gradually expand dorsally from embryonic day (E) 10.5 to E12.5, following strong Patched1 signals (a target gene of Shh signaling). This coordinated expression pattern led us to hypothesize that in the mouse, strong Shh signaling is induced when Shh is released by Sulf1/2, and this strong Shh signaling subsequently induces the dorsal expansion of Shh and Sulf1/2 expression. Consistent with this hypothesis, in the ventral spinal cord of Sulf1 knockout (KO) or Sulf2 KO mice, the expression patterns of Shh and Patched1 differed from that in wild-type mice. Moreover, the position of the pMN and p3 domains were shifted ventrally, MN generation was prolonged, and OPC generation was delayed at E12.5 in both Sulf1 KO and Sulf2 KO mice. These results demonstrated that in addition to Sulf1, Sulf2 also plays an important and overlapping role in the MN-to-OPC fate change by regulating Shh signaling in the ventral spinal cord. However, neither Sulf1 nor Sulf2 could compensate for the loss of the other in the developing mouse spinal cord. In vitro studies showed no evidence of an interaction between Sulf1 and Sulf2 that could increase sulfatase activity. Furthermore, Sulf1/2 double heterozygote and Sulf1/2 double KO mice exhibited phenotypes similar to the Sulf1 KO and Sulf2 KO mice. These results indicate that there is a threshold for sulfatase activity (which is likely reflected in the dose of Shh) required to induce the MN-to-OPC fate change, and Shh signaling requires the coordinated activity of Sulf1 and Sulf2 in order to reach that threshold in the mouse ventral spinal cord.
DOI: 10.6084/m9.figshare.4990442.v1
title: Supplementary Material for: Sulfatase 2 Modulates Fate Change from Motor Neurons to Oligodendrocyte Precursor Cells through Coordinated Regulation of Shh Signaling with Sulfatase 1

description: Sulfatases (Sulfs) are a group of endosulfatases consisting of Sulf1 and Sulf2, which specifically remove sulfate from heparan sulfate proteoglycans. Although several studies have shown that Sulf1 acts as a regulator of sonic hedgehog (Shh) signaling during embryonic ventral spinal cord development, the detailed expression pattern and function of Sulf2 in the spinal cord remains to be determined. In this study, we found that Sulf2 also modulates the cell fate change from motor neurons (MNs) to oligodendrocyte precursor cells (OPCs) by regulating Shh signaling in the mouse ventral spinal cord in coordination with Sulf1. In the mouse, Sulf mRNAs colocalize with Shh mRNA and gradually expand dorsally from embryonic day (E) 10.5 to E12.5, following strong Patched1 signals (a target gene of Shh signaling). This coordinated expression pattern led us to hypothesize that in the mouse, strong Shh signaling is induced when Shh is released by Sulf1/2, and this strong Shh signaling subsequently induces the dorsal expansion of Shh and Sulf1/2 expression. Consistent with this hypothesis, in the ventral spinal cord of Sulf1 knockout (KO) or Sulf2 KO mice, the expression patterns of Shh and Patched1 differed from that in wild-type mice. Moreover, the position of the pMN and p3 domains were shifted ventrally, MN generation was prolonged, and OPC generation was delayed at E12.5 in both Sulf1 KO and Sulf2 KO mice. These results demonstrated that in addition to Sulf1, Sulf2 also plays an important and overlapping role in the MN-to-OPC fate change by regulating Shh signaling in the ventral spinal cord. However, neither Sulf1 nor Sulf2 could compensate for the loss of the other in the developing mouse spinal cord. In vitro studies showed no evidence of an interaction between Sulf1 and Sulf2 that could increase sulfatase activity. Furthermore, Sulf1/2 double heterozygote and Sulf1/2 double KO mice exhibited phenotypes similar to the Sulf1 KO and Sulf2 KO mice. These results indicate that there is a threshold for sulfatase activity (which is likely reflected in the dose of Shh) required to induce the MN-to-OPC fate change, and Shh signaling requires the coordinated activity of Sulf1 and Sulf2 in order to reach that threshold in the mouse ventral spinal cord.
DOI: 10.6084/m9.figshare.4990394
title: Yarrowia lipolytica DGA1 RNAseq, metabolomics, proteomics and genome-scale models

description: Additional information to the mBio paper "Leucine biosynthesis is involved in regulating high lipid accumulation in <i>Yarrowia lipolytica" </i>(https://doi.org/10.1128/mBio.00857-17)<i>.</i><i><br></i>* models.zip contains condition-specific genome-scale models of <i>Yarrowia lipolytica </i>metabolism* proteomics_log2_counts.xlsx contains the log2 transformed proteomics counts* proteomics_crossCompare.xlsx contains results from cross-comparison differential expression analysis of proteomics data<br>* proteomics_lineaModel.xlsx contains results from general linear model differential expression analysis of proteomics data<br>* RNAseq_log2_counts.xlsx contains the log2 transformed RNAseq counts* RNAseq_crossCompare.xlsx contains results from cross-comparison differential expression analysis of RNAseq data<br>* RNAseq_crossCompare.xlsx contains results from general linear model differential expression analysis of RNAseq data<br><br>For more details regarding the experimental setup and data-generation, please see the paper.