cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4832344.v2
title: Nasal Colonization and Bacterial Contamination of Mobile Phones Carried by Medical Staff in the Operating Room

description: <b>The characteristics of including medical staff; proportion and distribution of isolated bacteria; and genotyping of isolated staphylococcus aureus.</b>
DOI: 10.25430/researchdata.cab.unipd.it.00000376
title: Taking the pulse of river networks: climate-driven dynamics of the active channel length in temporary streams - DATASET

description: Dataset containing the geometry and status (over time) of the stream networks analyzed in the "Taking the pulse of river networks: climate-driven dynamics of the active channel length in temporary streams" research paper.
DOI: 10.6084/m9.figshare.4831855
title: Aish Slope Table

description: <b>Aish Slope Table: Periodic Table Recreation Incorporating Electron Filling Pattern In An Orbital</b><br> Advanced version of periodic table covering all the demerits of periodic table. This includes periodic table, electronic configuration information, orbitals information, electron filling pattern information and more of the characteristics including Aufbau principle in a single table. <br><b>This is the natural solution for the term The Periodic Table.</b> Any objections are welcome to be negotiated.
DOI: 10.6084/m9.figshare.4831855.v2
title: Aish Slope Table

description: <b>Aish Slope Table: Periodic Table Recreation Incorporating Electron Filling Pattern In An Orbital</b><br> Advanced version of periodic table covering all the demerits of periodic table. This includes periodic table, electronic configuration information, orbitals information, electron filling pattern information and more of the characteristics including Aufbau principle in a single table. <br><b>This is the natural solution for the term The Periodic Table.</b> Any objections are welcome to be negotiated.
DOI: 10.6084/m9.figshare.4830016
title: survey_data_messy_quality_control

description: Spreadsheet for Sorting Exersize in Data Carpentry Ecology Lesson
DOI: 10.6084/m9.figshare.4831780
title: GBStags_StripeRustResistanceInPI480035.fasta

description: FASTA formatted file for GBS (genotyping-by-sequencing) tags used for linkage mapping and quantitative trait loci mapping for AvS x PI 480035 population.
DOI: 10.6084/m9.figshare.4831780.v1
title: GBStags_StripeRustResistanceInPI480035.fasta

description: FASTA formatted file for GBS (genotyping-by-sequencing) tags used for linkage mapping and quantitative trait loci mapping for AvS x PI 480035 population.
DOI: 10.6084/m9.figshare.4829599
title: PLOSONE_Uncertainty_Dataset.zip

description: fMRI raw (de-identified) dataset
DOI: 10.6084/m9.figshare.4829602
title: Role of a geodatabase to assess the distribution of plants of conservation interest in a large protected area: A case study for a major national park in Italy

description: We use a geodatabase to investigate the distribution patterns of an important subset of floristic reports recorded for the <i>Parco Nazionale delle Foreste Casentinesi, Monte Falterona, Campigna</i> in the northern Apennines, Italy. This database was analysed using spatial statistical techniques and a digital elevation model. Significant relationships between species presence, sampling effort and species richness were then analysed in relation to topographical variables and to an existing vegetation map. Report-based rarefaction techniques were used to compare areas having different numbers of species recorded. Overall, the analysis shows that some areas of the park are richer in species of conservation interest than others, and that these have been more intensely investigated. Meanwhile, for other areas, botanical knowledge is scarce or even absent. This has led to clustering and redundancy of floristic data in some areas. The study confirms that the existence of a complete and up-to-date geodatabase creates a valuable resource which enables information gaps to be bridged. Such gaps often exist in biological databases for rare and narrowly distributed species. The wider application of these analyses should also give useful indications of how the incidences of these species of conservation interest are associated with particular environmental variables.
DOI: 10.6084/m9.figshare.4829602.v1
title: Role of a geodatabase to assess the distribution of plants of conservation interest in a large protected area: A case study for a major national park in Italy

description: We use a geodatabase to investigate the distribution patterns of an important subset of floristic reports recorded for the <i>Parco Nazionale delle Foreste Casentinesi, Monte Falterona, Campigna</i> in the northern Apennines, Italy. This database was analysed using spatial statistical techniques and a digital elevation model. Significant relationships between species presence, sampling effort and species richness were then analysed in relation to topographical variables and to an existing vegetation map. Report-based rarefaction techniques were used to compare areas having different numbers of species recorded. Overall, the analysis shows that some areas of the park are richer in species of conservation interest than others, and that these have been more intensely investigated. Meanwhile, for other areas, botanical knowledge is scarce or even absent. This has led to clustering and redundancy of floristic data in some areas. The study confirms that the existence of a complete and up-to-date geodatabase creates a valuable resource which enables information gaps to be bridged. Such gaps often exist in biological databases for rare and narrowly distributed species. The wider application of these analyses should also give useful indications of how the incidences of these species of conservation interest are associated with particular environmental variables.
DOI: 10.6084/m9.figshare.4829599.v1
title: PLOSONE_Uncertainty_Dataset.zip

description: fMRI raw (de-identified) dataset
DOI: 10.6084/m9.figshare.4829584
title: Inter-individual variability in discourse informativeness in elderly populations

description: An increasing number of studies focus on discourse production in patients with neurodegenerative diseases and underline its clinical usefulness. However, if this is to be used as a clinical tool, one needs to consider how normal discourse varies within cognitively unimpaired elderly populations. In the current study, the aim has been to investigate discourse macrolinguistic variability. For this, 123 participants aged between 55 and 84 were recruited. A cluster analysis of their discourse macrolinguistic features was conducted. Then, cluster characterisation based on socio-demographic and linguistic performance was tested (fluency, naming, syntax and spelling). This method aims to identify various profiles of speaker and informativeness and then see if inter-individual variability may be related to socio-demographic and/or linguistic aspects. Four clusters of informativeness were found but no socio-demographic features appeared significant. The fourth cluster, defined as ‘off topic’, had lower performance during linguistic tasks than others and thus the boundary between normality and pathology should be questioned.
DOI: 10.6084/m9.figshare.4829527
title: Dataset for: Structural study of 1-(2´, 3´-<i>O</i>-isopropylidene-(α-D-allo and –β-L-talofuranosyluron)-5´-cyanohydrin)uracil stereoisomers by NMR spectroscopy and theoretical methods.

description: The stereochemistry of nucleoside derivatives determines their pharmacological activity such as anticancer, antiviral, against human immunodeficiency virus (HIV) and antimycotic. Therefore, it is necessary to elucidate the structure of each stereoisomer. The isolation and spectroscopic characterization of the 1-(2´, 3´-<i>O</i>-isopropylidene-(α-D-allo and -β-L-talofuranosyluron)-5´-cyanohydrin)uracil stereoisomer is of great importance because these compounds are intermediaries in the development of novel nucleoside derivatives. In this study, we elucidated the structure of 5´(<i>R</i>) and (<i>S</i>)-cyanohydrin stereoisomers by NMR spectroscopy and tridimensional analysis. The structure was modeled based on the conformer with the local minimized energy. 1D-NOESY gave a detailed information about the tridimensional structure of each diastereoisomer. The ratio of the diastereoisomers determined by NMR, using DMSO-d<sub>6</sub> as solvent, was 65% of 5´(<i>R</i>)-cyanohydrin (<b>A</b>) and 35% of 5´(<i>S</i>)-cyanohydrin (<b>B</b>).
DOI: 10.6084/m9.figshare.4829533
title: Morphological and nutritional characteristics of fruits dispersed by birds.

description: Description of some fruit characteristics including fruit size, seed size, fruit energetic content and proportion of lipids, proteins and carbohydrates in the pulpDatabase used in the article:Sebastián-González, E. Drivers of species role in avian seed-dispersal mutualistic networks. Journal of Animal Ecology (Accepted for publication).
DOI: 10.6084/m9.figshare.4829524
title: Frugivorous birds morphological and ecological characteristics

description: Description of some frugivorous bird characteristics including bird size, bill length and width, degree of frugivory (from 1, consumes fruits sporadically to 5, consumes only fruits), threatening degree by the IUCN.Database used in the article:Sebastián-González, E. Drivers of species role in avian seed-dispersal mutualistic networks. Journal of Animal Ecology (Accepted for publication).<br><br>
DOI: 10.6084/m9.figshare.4829527.v1
title: Dataset for: Structural study of 1-(2´, 3´-<i>O</i>-isopropylidene-(α-D-allo and –β-L-talofuranosyluron)-5´-cyanohydrin)uracil stereoisomers by NMR spectroscopy and theoretical methods.

description: The stereochemistry of nucleoside derivatives determines their pharmacological activity such as anticancer, antiviral, against human immunodeficiency virus (HIV) and antimycotic. Therefore, it is necessary to elucidate the structure of each stereoisomer. The isolation and spectroscopic characterization of the 1-(2´, 3´-<i>O</i>-isopropylidene-(α-D-allo and -β-L-talofuranosyluron)-5´-cyanohydrin)uracil stereoisomer is of great importance because these compounds are intermediaries in the development of novel nucleoside derivatives. In this study, we elucidated the structure of 5´(<i>R</i>) and (<i>S</i>)-cyanohydrin stereoisomers by NMR spectroscopy and tridimensional analysis. The structure was modeled based on the conformer with the local minimized energy. 1D-NOESY gave a detailed information about the tridimensional structure of each diastereoisomer. The ratio of the diastereoisomers determined by NMR, using DMSO-d<sub>6</sub> as solvent, was 65% of 5´(<i>R</i>)-cyanohydrin (<b>A</b>) and 35% of 5´(<i>S</i>)-cyanohydrin (<b>B</b>).
DOI: 10.6084/m9.figshare.4829500
title: cacamobilegeneNetwork_20.txt.tagged.subnets

description: Sequence similarity network<br>
DOI: 10.6084/m9.figshare.4829500.v1
title: cacamobilegeneNetwork_20.txt.tagged.subnets

description: Sequence similarity network<br>
DOI: 10.6084/m9.figshare.4829497
title: Long-term safety and effectiveness of adalimumab for the treatment of Japanese patients with rheumatoid arthritis: 3-year results from a postmarketing surveillance of 552 patients

description: <b>Objectives:</b> To determine the safety and effectiveness of and identify associated factors in long-term adalimumab (ADA) treatment of Japanese patients with rheumatoid arthritis (RA). <b>Methods:</b> Of 7740 patients participating in the all-case postmarketing surveillance study, 552 were enrolled in the present study and observed for 3 years. The safety and effectiveness of ADA were analyzed in 509 and 430 patients, respectively. <b>Results:</b> Adverse drug reactions (ADRs) were reported in 34.2% of patients (23.3/100 person-years [PYs]); serious ADRs (SADRs) were reported in 10.6% (5.9/100 PYs). The most common ADRs and SADRs were infection (16.5%) and serious infection (6.1%), respectively. Seven patients (1.4%) developed malignancies. Multivariate analysis revealed that the risk factors for SADRs were age ≥65 years and respiratory disorder at baseline. The proportion of patients who achieved remission (28-joint count Disease Activity Score based on four erythrocyte sedimentation rates &lt;2.6) increased from 3.3% at baseline to 49.2% at 36 months. Significant predictors of failure to achieve remission were female sex, age ≥65 years, blood disorders and advanced structural change at baseline. <b>Conclusions:</b> Overall, no unknown safety issues were noted during the 3-year treatment with ADA in Japanese patients with RA.
DOI: 10.6084/m9.figshare.4829533.v1
title: Fruit characteristics including fruit and seed size, pulp energetic content and some nutritional contents of the pulp. Fruits dispersed by birds.

description: Description of some fruit characteristics including fruit size, seed size, fruit energetic content and proportion of lipids, proteins and carbohydrates in the pulpDatabase used in the article:Sebastián-González, E. Drivers of species role in avian seed-dispersal mutualistic networks. Journal of Animal Ecology (Accepted for publication).
DOI: 10.6084/m9.figshare.4829491
title: Bayesian Nonparametric Modeling for Multivariate Ordinal Regression

description: Univariate or multivariate ordinal responses are often assumed to arise from a latent continuous parametric distribution, with covariate effects that enter linearly. We introduce a Bayesian nonparametric modeling approach for univariate and multivariate ordinal regression, which is based on mixture modeling for the joint distribution of latent responses and covariates. The modeling framework enables highly flexible inference for ordinal regression relationships, avoiding assumptions of linearity or additivity in the covariate effects. In standard parametric ordinal regression models, computational challenges arise from identifiability constraints and estimation of parameters requiring nonstandard inferential techniques. A key feature of the nonparametric model is that it achieves inferential flexibility, while avoiding these difficulties. In particular, we establish full support of the nonparametric mixture model under fixed cut-off points that relate through discretization the latent continuous responses with the ordinal responses. The practical utility of the modeling approach is illustrated through application to two datasets from econometrics, an example involving regression relationships for ozone concentration, and a multirater agreement problem. Supplementary materials with technical details on theoretical results and on computation are available online.
DOI: 10.6084/m9.figshare.4829494
title: Split-Plot and Multi-Stratum Designs for Statistical Inference

description: It is increasingly recognized that many industrial and engineering experiments use split-plot or other multi-stratum structures. Much recent work has concentrated on finding optimum, or near-optimum, designs for estimating the fixed effects parameters in multi-stratum designs. However, often inference, such as hypothesis testing or interval estimation, will also be required and for inference to be unbiased in the presence of model uncertainty requires pure error estimates of the variance components. Most optimal designs provide few, if any, pure error degrees of freedom. Gilmour and Trinca (2012) introduced design optimality criteria for inference in the context of completely randomized and block designs. Here these criteria are used stratum-by-stratum to obtain multi-stratum designs. It is shown that these designs have better properties for performing inference than standard optimum designs. Compound criteria, which combine the inference criteria with traditional point estimation criteria, are also used and the designs obtained are shown to compromise between point estimation and inference. Designs are obtained for two real split-plot experiments and an illustrative split–split-plot structure. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.4829497.v1
title: Long-term safety and effectiveness of adalimumab for the treatment of Japanese patients with rheumatoid arthritis: 3-year results from a postmarketing surveillance of 552 patients

description: <b>Objectives:</b> To determine the safety and effectiveness of and identify associated factors in long-term adalimumab (ADA) treatment of Japanese patients with rheumatoid arthritis (RA). <b>Methods:</b> Of 7740 patients participating in the all-case postmarketing surveillance study, 552 were enrolled in the present study and observed for 3 years. The safety and effectiveness of ADA were analyzed in 509 and 430 patients, respectively. <b>Results:</b> Adverse drug reactions (ADRs) were reported in 34.2% of patients (23.3/100 person-years [PYs]); serious ADRs (SADRs) were reported in 10.6% (5.9/100 PYs). The most common ADRs and SADRs were infection (16.5%) and serious infection (6.1%), respectively. Seven patients (1.4%) developed malignancies. Multivariate analysis revealed that the risk factors for SADRs were age ≥65 years and respiratory disorder at baseline. The proportion of patients who achieved remission (28-joint count Disease Activity Score based on four erythrocyte sedimentation rates &lt;2.6) increased from 3.3% at baseline to 49.2% at 36 months. Significant predictors of failure to achieve remission were female sex, age ≥65 years, blood disorders and advanced structural change at baseline. <b>Conclusions:</b> Overall, no unknown safety issues were noted during the 3-year treatment with ADA in Japanese patients with RA.
DOI: 10.6084/m9.figshare.4829491.v1
title: Bayesian Nonparametric Modeling for Multivariate Ordinal Regression

description: Univariate or multivariate ordinal responses are often assumed to arise from a latent continuous parametric distribution, with covariate effects that enter linearly. We introduce a Bayesian nonparametric modeling approach for univariate and multivariate ordinal regression, which is based on mixture modeling for the joint distribution of latent responses and covariates. The modeling framework enables highly flexible inference for ordinal regression relationships, avoiding assumptions of linearity or additivity in the covariate effects. In standard parametric ordinal regression models, computational challenges arise from identifiability constraints and estimation of parameters requiring nonstandard inferential techniques. A key feature of the nonparametric model is that it achieves inferential flexibility, while avoiding these difficulties. In particular, we establish full support of the nonparametric mixture model under fixed cut-off points that relate through discretization the latent continuous responses with the ordinal responses. The practical utility of the modeling approach is illustrated through application to two datasets from econometrics, an example involving regression relationships for ozone concentration, and a multirater agreement problem. Supplementary materials with technical details on theoretical results and on computation are available online.
DOI: 10.6084/m9.figshare.4829494.v1
title: Split-Plot and Multi-Stratum Designs for Statistical Inference

description: It is increasingly recognized that many industrial and engineering experiments use split-plot or other multi-stratum structures. Much recent work has concentrated on finding optimum, or near-optimum, designs for estimating the fixed effects parameters in multi-stratum designs. However, often inference, such as hypothesis testing or interval estimation, will also be required and for inference to be unbiased in the presence of model uncertainty requires pure error estimates of the variance components. Most optimal designs provide few, if any, pure error degrees of freedom. Gilmour and Trinca (2012) introduced design optimality criteria for inference in the context of completely randomized and block designs. Here these criteria are used stratum-by-stratum to obtain multi-stratum designs. It is shown that these designs have better properties for performing inference than standard optimum designs. Compound criteria, which combine the inference criteria with traditional point estimation criteria, are also used and the designs obtained are shown to compromise between point estimation and inference. Designs are obtained for two real split-plot experiments and an illustrative split–split-plot structure. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.4829533.v4
title: Morphological and nutritional characteristics of fruits dispersed by birds.

description: Description of some fruit characteristics including fruit size, seed size, fruit energetic content and proportion of lipids, proteins and carbohydrates in the pulpDatabase used in the article:Sebastián-González, E. Drivers of species role in avian seed-dispersal mutualistic networks. Journal of Animal Ecology (Accepted for publication).
DOI: 10.6084/m9.figshare.4829401
title: Dataset for: Modulation of host cell SUMOylation facilitates efficient development of Plasmodium berghei and Toxoplasma gondii

description: SUMOylation is a reversible post translational modification of proteins that regulates protein stabilization, nucleocytoplasmic transport and protein-protein interactions. Several viruses and bacteria modulate host SUMOylation machinery for efficient infection. Plasmodium sporozoites are infective forms of malaria parasite that infect hepatocytes and transforms into exoerythrocytic forms (EEFs). Here we show that, during EEF development, the distribution of SUMOylated proteins in host cell nuclei was significantly reduced and expression of the SUMOylation enzymes was downregulated. Plasmodium EEFs destabilized the host cytoplasmic protein SMAD4 by inhibiting its SUMOylation. SUMO1 overexpression was detrimental to EEF growth and insufficiency of the only conjugating enzyme Ubc9/E2 promoted EEF growth. The expression of genes involved in suppression of host cell defense pathways during infection was reversed during SUMO1 overexpression, as revealed by transcriptomic analysis. The inhibition of host cell SUMOylation was also observed in Toxoplasma. We provide a hitherto unknown mechanism of regulating host gene expression through altering host SUMOylation by Apicomplexan parasites.
DOI: 10.6084/m9.figshare.4829401.v1
title: Dataset for: Modulation of host cell SUMOylation facilitates efficient development of Plasmodium berghei and Toxoplasma gondii

description: SUMOylation is a reversible post translational modification of proteins that regulates protein stabilization, nucleocytoplasmic transport and protein-protein interactions. Several viruses and bacteria modulate host SUMOylation machinery for efficient infection. Plasmodium sporozoites are infective forms of malaria parasite that infect hepatocytes and transforms into exoerythrocytic forms (EEFs). Here we show that, during EEF development, the distribution of SUMOylated proteins in host cell nuclei was significantly reduced and expression of the SUMOylation enzymes was downregulated. Plasmodium EEFs destabilized the host cytoplasmic protein SMAD4 by inhibiting its SUMOylation. SUMO1 overexpression was detrimental to EEF growth and insufficiency of the only conjugating enzyme Ubc9/E2 promoted EEF growth. The expression of genes involved in suppression of host cell defense pathways during infection was reversed during SUMO1 overexpression, as revealed by transcriptomic analysis. The inhibition of host cell SUMOylation was also observed in Toxoplasma. We provide a hitherto unknown mechanism of regulating host gene expression through altering host SUMOylation by Apicomplexan parasites.
DOI: 10.6084/m9.figshare.4829533.v3
title: Morphological and nutritional characteristics of fruits dispersed by birds.

description: Description of some fruit characteristics including fruit size, seed size, fruit energetic content and proportion of lipids, proteins and carbohydrates in the pulpDatabase used in the article:Sebastián-González, E. Drivers of species role in avian seed-dispersal mutualistic networks. Journal of Animal Ecology (Accepted for publication).