cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7819598
title: Supplementary Material for: Long-Term Efficacy and Safety of Molidustat for Anemia in Chronic Kidney Disease: DIALOGUE Extension Studies

description: <b><i>Background:</i></b> Molidustat, a novel hypoxia-inducible factor-prolyl hydroxylase inhibitor, is being investigated for the treatment of anemia associated with chronic kidney disease (CKD). The efficacy and safety of molidustat were recently evaluated in three 16-week phase 2b studies. Here, we report the results of two long-term extension studies of molidustat. <b><i>Methods:</i></b> Both studies were parallel-group, open-label, multicenter studies of ≤36 months’ duration, in patients with anemia due to CKD, and included an erythropoiesis-stimulating agent as active control. One study enrolled patients not receiving dialysis (<i>n</i> = 164), and the other enrolled patients receiving hemodialysis (<i>n</i> = 88). The primary efficacy variable for both studies was change in blood hemoglobin (Hb) level from baseline to each post-baseline visit, and safety outcomes included adverse events (AEs). <b><i>Results:</i></b> In patients not on dialysis, the mean ± SD Hb concentrations at baseline were 11.28 ± 0.55 g/dL for molidustat and 11.08 ± 0.51 g/dL for darbepoetin. The mean ± SD blood Hb concentrations throughout the study (defined as mean of each patient’s overall study Hb levels) were 11.10 ± 0.508 and 10.98 ± 0.571 g/dL in patients treated with molidustat and darbepoetin, respectively. Similar proportions of patients reported at least one AE in the molidustat (85.6%) and darbepoetin (85.7%) groups. In patients on dialysis, mean ± SD Hb levels at baseline were 10.40 ± 0.70 and 10.52 ± 0.53 g/dL in the molidustat and epoetin groups, respectively. The mean ± SD blood Hb concentrations during the study were 10.37 ± 0.56 g/dL in the molidustat group and 10.52 ± 0.47 g/dL in the epoetin group. Proportions of patients who reported at least one AE were 91.2% in the molidustat group and 93.3% in the epoetin group. <b><i>Conclusions:</i></b> Molidustat was well tolerated for up to 36 months and appears to be an effective alternative to darbepoetin and epoetin in the long-term management of anemia associated with CKD.
DOI: 10.6084/m9.figshare.7819595
title: GoL glider

description: Frames showing a Game of Life glider.
DOI: 10.6084/m9.figshare.7819598.v1
title: Supplementary Material for: Long-Term Efficacy and Safety of Molidustat for Anemia in Chronic Kidney Disease: DIALOGUE Extension Studies

description: <b><i>Background:</i></b> Molidustat, a novel hypoxia-inducible factor-prolyl hydroxylase inhibitor, is being investigated for the treatment of anemia associated with chronic kidney disease (CKD). The efficacy and safety of molidustat were recently evaluated in three 16-week phase 2b studies. Here, we report the results of two long-term extension studies of molidustat. <b><i>Methods:</i></b> Both studies were parallel-group, open-label, multicenter studies of ≤36 months’ duration, in patients with anemia due to CKD, and included an erythropoiesis-stimulating agent as active control. One study enrolled patients not receiving dialysis (<i>n</i> = 164), and the other enrolled patients receiving hemodialysis (<i>n</i> = 88). The primary efficacy variable for both studies was change in blood hemoglobin (Hb) level from baseline to each post-baseline visit, and safety outcomes included adverse events (AEs). <b><i>Results:</i></b> In patients not on dialysis, the mean ± SD Hb concentrations at baseline were 11.28 ± 0.55 g/dL for molidustat and 11.08 ± 0.51 g/dL for darbepoetin. The mean ± SD blood Hb concentrations throughout the study (defined as mean of each patient’s overall study Hb levels) were 11.10 ± 0.508 and 10.98 ± 0.571 g/dL in patients treated with molidustat and darbepoetin, respectively. Similar proportions of patients reported at least one AE in the molidustat (85.6%) and darbepoetin (85.7%) groups. In patients on dialysis, mean ± SD Hb levels at baseline were 10.40 ± 0.70 and 10.52 ± 0.53 g/dL in the molidustat and epoetin groups, respectively. The mean ± SD blood Hb concentrations during the study were 10.37 ± 0.56 g/dL in the molidustat group and 10.52 ± 0.47 g/dL in the epoetin group. Proportions of patients who reported at least one AE were 91.2% in the molidustat group and 93.3% in the epoetin group. <b><i>Conclusions:</i></b> Molidustat was well tolerated for up to 36 months and appears to be an effective alternative to darbepoetin and epoetin in the long-term management of anemia associated with CKD.
DOI: 10.6084/m9.figshare.7819583
title: Random GoL Patterns

description: Random patterns of the Game of Life, by episodes of 10 time steps.
DOI: 10.6084/m9.figshare.7819583.v2
title: Random GoL Patterns

description: Random patterns of the Game of Life, by episodes of 10 time steps.
DOI: 10.6084/m9.figshare.7819571
title: Supplementary material of López-Escardo et al. 2019 submitted to Philosophical transactions of the Royal Society B

description: Supplementary material of the work: Reconstruction of protein domain evolution using single-cell amplified genomes of uncultured choanoflagellates sheds light on the origin of animals by López-Escardo et al. 2019 submitted to Philosophical transactions of the Royal Society B
DOI: 10.6084/m9.figshare.7819541
title: BUSCO Result

description: This fileset contains following contents;<br>Visualization of BUSCO result of Liparis tanakae draft genome by using actinopterygii_odb9 database.<br>Full table of BUSCO result of Liparis tanakae draft genome<br>Short summarized table of BUSCO result of Liparis tanakae draft genome
DOI: 10.6084/m9.figshare.7819595.v2
title: GoL glider

description: Frames showing a Game of Life glider.
DOI: 10.6084/m9.figshare.7819535
title: Dataset for: Molecular evolution of proteins mediating mitochondrial fission-fusion dynamics

description: Eukaryotes employ a subset of dynamins to mediate mitochondrial fusion and fission dynamics. Here we report the molecular evolution and diversification of the dynamin-related mitochondrial proteins that drive the fission (Drp1) and the fusion processes (mitofusin and Opa1). We demonstrate that the three paralogs emerged concurrently in an early mitochondriate eukaryotic ancestor. Furthermore, multiple independent duplication events from an ancestral bifunctional fission protein gave rise to specialized fission proteins. The evolutionary history of these proteins is marked by transformations that include independent gain and loss events occurring at the levels of entire genes, specific functional domains, and intronic regions. The domain level variations primarily comprise loss-gain of lineage specific domains that are present in the terminal regions of the sequences.
DOI: 10.6084/m9.figshare.7819541.v1
title: BUSCO Result

description: This fileset contains following contents;<br>Visualization of BUSCO result of Liparis tanakae draft genome by using actinopterygii_odb9 database.<br>Full table of BUSCO result of Liparis tanakae draft genome<br>Short summarized table of BUSCO result of Liparis tanakae draft genome
DOI: 10.6084/m9.figshare.7819535.v1
title: Dataset for: Molecular evolution of proteins mediating mitochondrial fission-fusion dynamics

description: Eukaryotes employ a subset of dynamins to mediate mitochondrial fusion and fission dynamics. Here we report the molecular evolution and diversification of the dynamin-related mitochondrial proteins that drive the fission (Drp1) and the fusion processes (mitofusin and Opa1). We demonstrate that the three paralogs emerged concurrently in an early mitochondriate eukaryotic ancestor. Furthermore, multiple independent duplication events from an ancestral bifunctional fission protein gave rise to specialized fission proteins. The evolutionary history of these proteins is marked by transformations that include independent gain and loss events occurring at the levels of entire genes, specific functional domains, and intronic regions. The domain level variations primarily comprise loss-gain of lineage specific domains that are present in the terminal regions of the sequences.
DOI: 10.6084/m9.figshare.7819505
title: TD_Shapefile_Data.rar

description: Habitat features pertinent to the success of European Turtle Dove were mapped using ArcGIS polygons. Polygons were classified based on a predefined suitability factor. Rasters were created to visualise the interactions of suitable habitat features using the site selection and suitability analysis. Data contained here include ArcGIS vector shapefiles and raster files.
DOI: 10.6084/m9.figshare.7819526
title: GO Result

description: This fileset contains following contents;<br>GO_chart.svg: Visualized result of GO functional annotation of L. tanakae draft genome<br>Liparis_tanakai_GO_blast.xlsx: Table of GO functional annotation result of L. tanakae draft genome<br>GO_information.xlsx: Brief summary of GO functional annotation result of L. tanakae draft genome<br><br><br>
DOI: 10.6084/m9.figshare.7819505.v2
title: TD_Shapefile_Data.rar

description: Habitat features pertinent to the success of European Turtle Dove were mapped using ArcGIS polygons. Polygons were classified based on a predefined suitability factor. Rasters were created to visualise the interactions of suitable habitat features using the site selection and suitability analysis. Data contained here include ArcGIS vector shapefiles and raster files.
DOI: 10.6084/m9.figshare.7819487
title: Artifact and instructions to generate experimental results for TACAS 2019 paper: StocHy: automated verification and synthesis of stochastic processes

description: We provide an artifact of the tool called StocHy. This serves as an accompaniment to the tool paper titled StocHy: automated verification and synthesis of stochastic processes. The artifact consists of a compiled version of StocHy which allows you to generate all the results within the experimental evaluation section (i.e. Sec. 4). Within the tool paper, we present four different case studies highlighting the novelty, strengths and use of StocHy. The first case study deals with the application of formal verification via two abstraction techniques: FAUST 2 or IMDP based and their comparison in terms of computational times and abstraction error for varying grid sizes. Using the artifact, this analysis can be performed for all the different grids or a subset of the grids used (as desired). In the second case study, we perform strategy synthesis over an unbounded time horizon. Consequently, running the artifact results in generating the policy itself, the probability of satisfying the property of interest when using this policy and the maximum abstraction error. The third case study, shows how we can scale in the number of continuous variables (up to 12 dimensions) when performing formal verification.<br>The artifacts gives the option to run the verification procedure for all (or<br>a subset of) the dimensions considered. Lastly, it performs the simulation for the stochastic hybrid system considered in the fourth case study. We intend to employ the artifact as a demo of StocHy with the aim of highlighting its ease of use and scalability.
DOI: 10.6084/m9.figshare.7819505.v1
title: TD_Shapefile_Data.rar

description: Habitat features pertinent to the success of European Turtle Dove were mapped using ArcGIS polygons. Polygons were classified based on a predefined suitability factor. Rasters were created to visualise the interactions of suitable habitat features using the site selection and suitability analysis. Data contained here include ArcGIS vector shapefiles and raster files.
DOI: 10.6084/m9.figshare.7819526.v1
title: GO Result

description: This fileset contains following contents;<br>GO_chart.svg: Visualized result of GO functional annotation of L. tanakae draft genome<br>Liparis_tanakai_GO_blast.xlsx: Table of GO functional annotation result of L. tanakae draft genome<br>GO_information.xlsx: Brief summary of GO functional annotation result of L. tanakae draft genome<br><br><br>
DOI: 10.6084/m9.figshare.7819469
title: Ortholog Result

description: This fileset contains ortholgous gene analysis results as csv format files and a txt file for summarizing their stats. OrthoMCL analysis was conducted by comparing L. tanakae genome with H. sapiens, M. musculus, D. rerio, and L. crocea reference genomes accessed from NCBI.
DOI: 10.6084/m9.figshare.7819487.v1
title: Artifact and instructions to generate experimental results for TACAS 2019 paper: StocHy: automated verification and synthesis of stochastic processes

description: We provide an artifact of the tool called StocHy. This serves as an accompaniment to the tool paper titled StocHy: automated verification and synthesis of stochastic processes. The artifact consists of a compiled version of StocHy which allows you to generate all the results within the experimental evaluation section (i.e. Sec. 4). Within the tool paper, we present four different case studies highlighting the novelty, strengths and use of StocHy. The first case study deals with the application of formal verification via two abstraction techniques: FAUST 2 or IMDP based and their comparison in terms of computational times and abstraction error for varying grid sizes. Using the artifact, this analysis can be performed for all the different grids or a subset of the grids used (as desired). In the second case study, we perform strategy synthesis over an unbounded time horizon. Consequently, running the artifact results in generating the policy itself, the probability of satisfying the property of interest when using this policy and the maximum abstraction error. The third case study, shows how we can scale in the number of continuous variables (up to 12 dimensions) when performing formal verification.<br>The artifacts gives the option to run the verification procedure for all (or<br>a subset of) the dimensions considered. Lastly, it performs the simulation for the stochastic hybrid system considered in the fourth case study. We intend to employ the artifact as a demo of StocHy with the aim of highlighting its ease of use and scalability.
DOI: 10.6084/m9.figshare.7819469.v1
title: Ortholog Result

description: This fileset contains ortholgous gene analysis results as csv format files and a txt file for summarizing their stats. OrthoMCL analysis was conducted by comparing L. tanakae genome with H. sapiens, M. musculus, D. rerio, and L. crocea reference genomes accessed from NCBI.
DOI: 10.6084/m9.figshare.7819475
title: KEGG Result

description: This fileset contains KEGG based functional annotation using blastp function (DB : 20170102 fish DB, option : -comp_based_stats 0, -evalue 1e-5).
DOI: 10.6084/m9.figshare.7819484
title: Phylogeny Result

description: This fileset contains following contents;<br>BUSCO_single_copy_gene_tree.zip: a supermatrix aln.faa file containing BUSCO based single copy homologous genes between L. tanakae and H. sapiens, M. musculus, D. rerio, L. crocea, a nwk (newick) format file converted from the aln.faa file, and resulted phylogenetic tree as a pdf file.<br>OrthoMCL_single_copy_gene_tree.zip: a supermatrix aln.faa file containing OrthoMCL based single copy homologous genes between L. tanakae and H. sapiens, M. musculus, D. rerio, L. crocea, a nwk (newick) format file converted from the aln.faa file, and resulted phylogenetic tree as a pdf file.<br>BUSCO analysis was conducted by using default option and vertebrata_odb9 as a reference database. OrthoMCL analysis was conducted by using following options; (config option : percentMatchCutoff=50, evalueExponentCutoff=-5) and orthomclFilterFasta step (10 20), blastp step (option -evalue 1e-5), mcl step (-I 1.5). Options and steps not described in here were tested as their default values.
DOI: 10.6084/m9.figshare.7819466
title: Supplementary Material for: Inappropriate Use of the “Rosowski Criteria” and “Modified Rosowski Criteria” for Assessing the Normal Function of Human Temporal Bones

description: Important research by Rosowski et al. [Twenty-Seventh Meeting of the Association for Research in Otolaryngology, 2004, p. 275] has led to a standard practice by the American Society for Testing Materials [West Conshohocken: ASTM International; 2014] to assess normal function of temporal bones used in the development of novel middle ear actuators and sensors. Rosowki et al. [Audiol Neurotol. 2007; 12(4): 265–76] have since suggested that the original criteria are too restrictive and have proposed modified criteria. We show that both the original and modified criteria are inappropriate for assessing individual temporal bones. Moreover, we suggest that both the original and modified Rosowski criteria should be applied with caution when assessing whether mean data from a study are within physiological norms because the multiple comparisons resulting from verification at each frequency will lead to very liberal rejection. The standard practice, however, has led to the collection of more extensive and consistent data. We suggest that it is now opportune to use these data to further modify the Rosowski criteria.
DOI: 10.6084/m9.figshare.7819484.v1
title: Phylogeny Result

description: This fileset contains following contents;<br>BUSCO_single_copy_gene_tree.zip: a supermatrix aln.faa file containing BUSCO based single copy homologous genes between L. tanakae and H. sapiens, M. musculus, D. rerio, L. crocea, a nwk (newick) format file converted from the aln.faa file, and resulted phylogenetic tree as a pdf file.<br>OrthoMCL_single_copy_gene_tree.zip: a supermatrix aln.faa file containing OrthoMCL based single copy homologous genes between L. tanakae and H. sapiens, M. musculus, D. rerio, L. crocea, a nwk (newick) format file converted from the aln.faa file, and resulted phylogenetic tree as a pdf file.<br>BUSCO analysis was conducted by using default option and vertebrata_odb9 as a reference database. OrthoMCL analysis was conducted by using following options; (config option : percentMatchCutoff=50, evalueExponentCutoff=-5) and orthomclFilterFasta step (10 20), blastp step (option -evalue 1e-5), mcl step (-I 1.5). Options and steps not described in here were tested as their default values.
DOI: 10.6084/m9.figshare.7819457
title: Functional Annotation

description: This fileset contains a result of functional annotation. Genbank NR database, UniProt, GO, InterPro, Pfam, CD, TIGRFAM, and EggNOG were used to annotate predicted genes of L. tanake draft genome. These functional annotation datasets were merged.
DOI: 10.6084/m9.figshare.7819436
title: Annotation Result

description: This fileset contains following contents about basic annotation of L. tanakae draft genome;<br>Liparis_tanaka.faa: FastA format file of annotated L. tanakae draft genome containing predicted amino-acid sequences.<br>Liparis_tanakai.gff: gff format (Genera Feature Format) file of annotated L. tanakae draft genome containing general information sets of annotated sequences in genome assembly.<br>The basic annotation was conducted by using Seqping pipeline with default options.<br>
DOI: 10.6084/m9.figshare.7819457.v1
title: Functional Annotation

description: This fileset contains a result of functional annotation. Genbank NR database, UniProt, GO, InterPro, Pfam, CD, TIGRFAM, and EggNOG were used to annotate predicted genes of L. tanake draft genome. These functional annotation datasets were merged.
DOI: 10.6084/m9.figshare.7819427
title: Supplementary Material for: Body Mass Index at Diagnosis as a Prognostic Factor for Early-Stage Invasive Breast Cancer after Surgical Resection

description: <b><i>Background:</i></b> The aim of this study was to investigate the association between body mass index (BMI) and prognosis of Chinese women with breast cancer. <b><i>Patients and</i></b> <b><i>Methods:</i></b> 3,380 primary breast cancer patients who underwent surgery from 2010 to 2012 were selected and classified as low BMI group (BMI <i>Results:</i> The high BMI group showed more aggressive pathological features. BMI was negatively associated with OS (hazard ratio (HR) 1.33, 95% confidence interval (CI) 1.06–1.66; p = 0.012) but not DFS (HR 1.15, 95% CI 0.94–1.40; p = 0.17). Furthermore, when stratified by age, BMI was significantly and negatively associated with OS (HR 1.43, 95% CI 1.05–1.95; p = 0.025) in patients above 50 years of age, but this effect was not detected in younger patients. <b><i>Conclusion:</i></b> BMI was an independent prognostic factor of OS in Chinese women with breast cancer, and age might be a mitigating factor. Among patients above 50 years of age, those with a high BMI were at greater risk of poor prognosis compared to individuals with a low BMI.
DOI: 10.6084/m9.figshare.7819436.v1
title: Annotation Result

description: This fileset contains following contents about basic annotation of L. tanakae draft genome;<br>Liparis_tanaka.faa: FastA format file of annotated L. tanakae draft genome containing predicted amino-acid sequences.<br>Liparis_tanakai.gff: gff format (Genera Feature Format) file of annotated L. tanakae draft genome containing general information sets of annotated sequences in genome assembly.<br>The basic annotation was conducted by using Seqping pipeline with default options.<br>
DOI: 10.6084/m9.figshare.7819418
title: Assembly Result

description: This file contains fasta-formatted scaffold sequences of L. tanakae draft genome.<br>Platanus was used to assemble contigs into scaffolds and gaps between them with all options and steps were conducted as their default values.
DOI: 10.6084/m9.figshare.7819418.v1
title: Assembly Result

description: This file contains fasta-formatted scaffold sequences of L. tanakae draft genome.<br>Platanus was used to assemble contigs into scaffolds and gaps between them with all options and steps were conducted as their default values.
DOI: 10.6084/m9.figshare.7819361
title: Age-related Changes of Macular Ganglion Cell-Inner Plexiform Layer Thickness in Korean elderly subjects

description: Age-related Changes of Macular Ganglion Cell-Inner Plexiform Layer Thickness in Korean elderly subjects
DOI: 10.6084/m9.figshare.7819346
title: Spraying 6-BA could alleviate the harmful impacts of waterlogging on dry matter accumulation and grain yield of wheat

description: <b>Fig. 1. </b>Daily sunshine duration, daily average temperature and daily rainfall during the wheat growth seasons at experimental station from 2011 to 2013. <b>Fig. 2. </b>Rainfall in ten days of each month during the whole wheat season from Jingzhou Weather Station from 1983 to 2012. <b>Fig. 3.</b> The effect of different treatments on the dry matter accumulation at maturity<b></b> <b>Fig. 4. </b>The effect of different treatments on photosynthetic rate from flag leaf after booting stage <b>Fig. 5.</b> The effect of different treatments on MDA content in flag leaf (a, c) and the third leaf from top (b,d) at 25 DAA (2011-2012 and 2012-2013).<b>Table 1.</b> The nutrient statuses of soil in the top 20 cm layer.<b>Table 2.</b> Effect of different treatments on grain yield, kernel number per spike and 1000 kernel weight.
DOI: 10.6084/m9.figshare.7819343
title: Influence of groundwater table fluctuation on the transport of volatile organic contaminants in the vadose zone.xlsx

description: These data contain information about the influence of groundwater table fluctuation on the transport of VOCs from groundwater to the atmosphere.