cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6344888.v1
title: Fecal source identification using random forest

description: Script_RF_V6.R: Code to perform the source identification using random forest classification (creation/training of the classifiers + prediction of new samples).<br>RF_SourceIdentification_v6.RData: R-objects that contains the training/testing V6-databases used in the publication. <br>ClostridialesBacteroiales_v6.fa: File containing the sequences of the V6- Clostridiales/Bacteroidales amplicon sequence variants.<br><br>RF_training_outputs.zip: Folder containing the outputs of the random forest classifications performed to train the V6-classifiers.<br>Confusion_Matrix_V6.xlsx: Excel spreadsheet containing the confusion matrix for each V6-classifiers.<br>
DOI: 10.6084/m9.figshare.6344876
title: Data and code from the paper "Modeling the impact of changes in day-care contact patterns on the dynamics of varicella transmission in France between 1991 and 2015 "

description: Data and code from the paper "Modeling the impact of changes in day-care contact patterns on the dynamics of varicella transmission in France between 1991 and 2015 " submitted to PLOS Computational Biology
DOI: 10.6084/m9.figshare.6344876.v1
title: Data and code from the paper "Modeling the impact of changes in day-care contact patterns on the dynamics of varicella transmission in France between 1991 and 2015 "

description: Data and code from the paper "Modeling the impact of changes in day-care contact patterns on the dynamics of varicella transmission in France between 1991 and 2015 " submitted to PLOS Computational Biology
DOI: 10.6084/m9.figshare.6344870
title: Age-dependent changes in biometrics indicate senescence in the European Blackbird <i>Turdus merula</i>

description: <b>Capsule:</b> A 19-year study of European Blackbirds <i>Turdus merula</i> confirms that senescence is associated with a decrease in condition measured by wing length but bills become progressively longer with age. <b>Aims:</b> To explore the correlations between biometrics of Blackbirds and age, to identify possible links with senescence. <b>Methods:</b> During the 19 years of the study, 801 birds of known age were measured: 431 males and 370 females, aged from 2 to 10 years. Among these 91 males and 50 females were retrapped at least one moult later. For each bird, there were at least one set of measurements when fully grown. <b>Results:</b> Wing length increased until the sixth year of life after which it started to decrease. An increase in bill length throughout the lifetime was found in both sexes. <b>Conclusion:</b> Changes in wing length correspond with an earlier study of this population suggesting the onset of senescence after the fifth to sixth calendar year of life.
DOI: 10.6084/m9.figshare.6344870.v1
title: Age-dependent changes in biometrics indicate senescence in the European Blackbird <i>Turdus merula</i>

description: <b>Capsule:</b> A 19-year study of European Blackbirds <i>Turdus merula</i> confirms that senescence is associated with a decrease in condition measured by wing length but bills become progressively longer with age. <b>Aims:</b> To explore the correlations between biometrics of Blackbirds and age, to identify possible links with senescence. <b>Methods:</b> During the 19 years of the study, 801 birds of known age were measured: 431 males and 370 females, aged from 2 to 10 years. Among these 91 males and 50 females were retrapped at least one moult later. For each bird, there were at least one set of measurements when fully grown. <b>Results:</b> Wing length increased until the sixth year of life after which it started to decrease. An increase in bill length throughout the lifetime was found in both sexes. <b>Conclusion:</b> Changes in wing length correspond with an earlier study of this population suggesting the onset of senescence after the fifth to sixth calendar year of life.
DOI: 10.6084/m9.figshare.6344843
title: Construction and Visualization of Confidence Sets for Frequentist Distributional Forecasts

description: The focus of this article is on the quantification of sampling variation in frequentist probabilistic forecasts. We propose a method of constructing confidence sets that respects the functional nature of the forecast distribution, and use animated graphics to visualize the impact of parameter uncertainty on the location, dispersion, and shape of the distribution. The confidence sets are derived via the inversion of a Wald test, and the ellipsoid that defines the boundary of the set computed numerically. A wide range of linear and nonlinear time series models—encompassing long memory, state space, and mixture specifications—is used to demonstrate the procedure, based on artificially generated data. An empirical example in which distributional forecasts of both financial returns and its stochastic volatility are produced is then used to illustrate the practical importance of accommodating sampling variation in the manner proposed.
DOI: 10.6084/m9.figshare.6344843.v1
title: Construction and Visualization of Confidence Sets for Frequentist Distributional Forecasts

description: The focus of this paper is on the quantification of sampling variation in frequentist probabilistic forecasts. We propose a method of constructing confidence sets that respects the functional nature of the forecast distribution, and use animated graphics to visualize the impact of parameter uncertainty on the location, dispersion and shape of the distribution. The confidence sets are derived via the inversion of a Wald test, and the ellipsoid that defines the boundary of the set computed numerically. A wide range of linear and non-linear time series models - encompassing long memory, state space and mixture specifications - is used to demonstrate the procedure, based on artificially generated data. An empirical example in which distributional forecasts of both financial returns and its stochastic volatility are produced is then used to illustrate the practical importance of accommodating sampling variation in the manner proposed.
DOI: 10.6084/m9.figshare.6344843.v3
title: Construction and Visualization of Confidence Sets for Frequentist Distributional Forecasts

description: The focus of this article is on the quantification of sampling variation in frequentist probabilistic forecasts. We propose a method of constructing confidence sets that respects the functional nature of the forecast distribution, and use animated graphics to visualize the impact of parameter uncertainty on the location, dispersion, and shape of the distribution. The confidence sets are derived via the inversion of a Wald test, and the ellipsoid that defines the boundary of the set computed numerically. A wide range of linear and nonlinear time series models—encompassing long memory, state space, and mixture specifications—is used to demonstrate the procedure, based on artificially generated data. An empirical example in which distributional forecasts of both financial returns and its stochastic volatility are produced is then used to illustrate the practical importance of accommodating sampling variation in the manner proposed.
DOI: 10.6084/m9.figshare.6344843.v2
title: Construction and Visualization of Confidence Sets for Frequentist Distributional Forecasts

description: The focus of this article is on the quantification of sampling variation in frequentist probabilistic forecasts. We propose a method of constructing confidence sets that respects the functional nature of the forecast distribution, and use animated graphics to visualize the impact of parameter uncertainty on the location, dispersion, and shape of the distribution. The confidence sets are derived via the inversion of a Wald test, and the ellipsoid that defines the boundary of the set computed numerically. A wide range of linear and nonlinear time series models—encompassing long memory, state space, and mixture specifications—is used to demonstrate the procedure, based on artificially generated data. An empirical example in which distributional forecasts of both financial returns and its stochastic volatility are produced is then used to illustrate the practical importance of accommodating sampling variation in the manner proposed.
DOI: 10.6084/m9.figshare.6344825
title: Summary of counts of different categories of skeletal taxa and of footprints. The Carnian Pluvial Episode and the origin of dinosaurs

description: Summary of counts of different categories of skeletal taxa, by tetrapod fauna and summary of counts of different categories of footprints, by ichnofauna
DOI: 10.6084/m9.figshare.6344825.v1
title: Summary of counts of different categories of skeletal taxa and of footprints. The Carnian Pluvial Episode and the origin of dinosaurs

description: Summary of counts of different categories of skeletal taxa, by tetrapod fauna and summary of counts of different categories of footprints, by ichnofauna
DOI: 10.6084/m9.figshare.6344666
title: npj biofilms and microbiomes manuscript datasets

description: FTIR- Figure 1TGA- Figure 2OCT- Figure 3AFM- Figure 4OCE- Figure 5
DOI: 10.6084/m9.figshare.6344348
title: Monolithic rod columns for HPLC based on divinylbenzene-styrene copolymer with 1-vinylimidazole and 4-vinylpyridine

description: Monolithic chromatographic columns for HPLC based on divinylbenzene-styrene both with 1-vinylimidazole and with 4-vinylpyridine are prepared. The monoliths were synthesized in glass tubes with the inner diameter of 2 mm. Texture, hydrodynamic and chromatographic properties of the prepared columns were studied. Linear solvation energy relationships model was applied for the characterization of columns selectivity It is shown that changing the on 1-vinylimidazole or 4-vinylpyridine content in the initial solution allows to change the selectivity of the columns. An examples of small molecules and some proteins separations are presented.
DOI: 10.6084/m9.figshare.6344348.v1
title: Monolithic rod columns for HPLC based on divinylbenzene-styrene copolymer with 1-vinylimidazole and 4-vinylpyridine

description: Monolithic chromatographic columns for HPLC based on divinylbenzene-styrene both with 1-vinylimidazole and with 4-vinylpyridine are prepared. The monoliths were synthesized in glass tubes with the inner diameter of 2 mm. Texture, hydrodynamic and chromatographic properties of the prepared columns were studied. Linear solvation energy relationships model was applied for the characterization of columns selectivity It is shown that changing the on 1-vinylimidazole or 4-vinylpyridine content in the initial solution allows to change the selectivity of the columns. An examples of small molecules and some proteins separations are presented.
DOI: 10.6084/m9.figshare.6343280
title: data

description: This file contains a folder with the data gathered from a set of projects when experimenting with Descartes, Gregor and PITest.The <b>project.json</b> file contains a record for each project with the name, identifier, repository origin and the commit identifier of the state in which the project was inspected.For each project there is a folder that contains the following <b>JSON</b> files: <b>lines.json</b>: The number of lines as counter by <b>cloc</b> (https://github.com/AlDanial/cloc).<b>descartes.json</b>: The mutation result obtained with Descartes.<b>gregor.json</b>: The mutation result obtained with Gregor.<b>methods.json</b>: A classification of each method in the project according to its metadata.<b>worthiness.json</b>: A classification of the potential issues found in the project as worthy or not of additional testing actions. This file does not appear for all projects.
DOI: 10.6084/m9.figshare.6343280.v2
title: data

description: This file contains a folder with the data gathered from a set of projects when experimenting with Descartes, Gregor and PITest.The <b>project.json</b> file contains a record for each project with the name, identifier, repository origin and the commit identifier of the state in which the project was inspected.For each project there is a folder that contains the following <b>JSON</b> files: <b>lines.json</b>: The number of lines as counter by <b>cloc</b> (https://github.com/AlDanial/cloc).<b>descartes.json</b>: The mutation result obtained with Descartes.<b>gregor.json</b>: The mutation result obtained with Gregor.<b>methods.json</b>: A classification of each method in the project according to its metadata.<b>worthiness.json</b>: A classification of the potential issues found in the project as worthy or not of additional testing actions. This file does not appear for all projects.
DOI: 10.6084/m9.figshare.6343280.v1
title: data

description: This file contains a folder with the data gathered from a set of projects when experimenting with Descartes, Gregor and PITest.The <b>project.json</b> file contains a record for each project with the name, identifier, repository origin and the commit identifier of the state in which the project was inspected.For each project there is a folder that contains the following <b>JSON</b> files: <b>lines.json</b>: The number of lines as counter by <b>cloc</b> (https://github.com/AlDanial/cloc).<b>descartes.json</b>: The mutation result obtained with Descartes.<b>gregor.json</b>: The mutation result obtained with Gregor.<b>methods.json</b>: A classification of each method in the project according to its metadata.<b>worthiness.json</b>: A classification of the potential issues found in the project as worthy or not of additional testing actions. This file does not appear for all projects.
DOI: 10.6084/m9.figshare.6341435
title: Karyotype of the Neotropical mangrove species <i>Pelliciera Rhizophorae</i> Triana and Planchon (Tetrameristaceae)

description: <i>Pelliciera rhizophorae</i> is the sole survivor of the Eocene mangroves inhabiting the Isthmus of Panama. Two populations of <i>Pelliciera rhizophorae</i>, a small morphotype at the Pacific coast and a tall morphotype at the Caribbean coast, display significant morphological and molecular differences. The patterns of differentiation between these two morphotypes were not determined by the isthmus itself, but are probably due to a process of adaptation in response to the climate that resulted in specific traits for the two populations. Aiming to verify if the ecological isolation also caused changes in the karyotype of the two morphotypes, we investigated the number of chromosomes, size, morphology, distribution of CMA, DAPI bands and nuclear DNA content of the Atlantic and Pacific populations of <i>P. rhizophorae.</i> A diploid chromosome number of 2<i>n</i> = 34 was found in both morphotypes, exhibiting small metacentric, submetacentric and acrocentric chromosomes. The acrocentric chromosomes presented the largest CMA+bands which are often associated with the nucleolus. Nuclear DNA content was similar in both variants (2.52 pg and 2. 56 pg for the small and tall morphotypes respectively), evidencing a small genome. Although the two morphotypes were karyotypically very similar, we observed a consistent difference in digestibility of their root tips in cellulase–pectinase solution and in the stainability of their cytoplasm. The cytotaxonomical relationship between <i>Pelliciera</i> and the related taxa is also discussed.
DOI: 10.6084/m9.figshare.6341435.v1
title: Karyotype of the Neotropical mangrove species <i>Pelliciera Rhizophorae</i> Triana and Planchon (Tetrameristaceae)

description: <i>Pelliciera rhizophorae</i> is the sole survivor of the Eocene mangroves inhabiting the Isthmus of Panama. Two populations of <i>Pelliciera rhizophorae</i>, a small morphotype at the Pacific coast and a tall morphotype at the Caribbean coast, display significant morphological and molecular differences. The patterns of differentiation between these two morphotypes were not determined by the isthmus itself, but are probably due to a process of adaptation in response to the climate that resulted in specific traits for the two populations. Aiming to verify if the ecological isolation also caused changes in the karyotype of the two morphotypes, we investigated the number of chromosomes, size, morphology, distribution of CMA, DAPI bands and nuclear DNA content of the Atlantic and Pacific populations of <i>P. rhizophorae.</i> A diploid chromosome number of 2<i>n</i> = 34 was found in both morphotypes, exhibiting small metacentric, submetacentric and acrocentric chromosomes. The acrocentric chromosomes presented the largest CMA+bands which are often associated with the nucleolus. Nuclear DNA content was similar in both variants (2.52 pg and 2. 56 pg for the small and tall morphotypes respectively), evidencing a small genome. Although the two morphotypes were karyotypically very similar, we observed a consistent difference in digestibility of their root tips in cellulase–pectinase solution and in the stainability of their cytoplasm. The cytotaxonomical relationship between <i>Pelliciera</i> and the related taxa is also discussed.
DOI: 10.6084/m9.figshare.6340862
title: Peach 480 SVs

description: To detect the breeding footprints, we sequenced 480 peach accessions, including 52 wild relative accessions, 213 landrace accessions, and 215 improved cultivars. Using this resequencing date, we detected the genomic changes during domestication and improvement.
DOI: 10.6084/m9.figshare.6340862.v1
title: Peach.480.SVs

description: To detect the breeding footprints, we sequenced 480 peach accessions, including 52 wild relative accessions, 213 landrace accessions, and 215 improved cultivars. Using this resequencing date, we detected the genomic change during domestication and improvement.
DOI: 10.6084/m9.figshare.6340661
title: DLBCL case summary.xls

description: Currently risk factors associated with chemotherapy-induced thrombocytopenia(CIT) in patients with Diffuse Large B Cell Lymphoma (DLBCL) is still undefined. Our research aims to analyse the effects of risk factors on thrombocytopenia. Moreover, it also aims to analyse the optimal threshold for infusion platelets of CIT patients who have received platelet transfusions.We conducted a retrospective analysis of 523 patients with DLBCL from 2011 to 2013 . Clinical and demographic parameters were extracted and analyse the risk factors associated with CIT. The threshold for platelet transfusions in DLBCL patients with central venous catheter (CVC) was evaluated.227 (43.4%) DLBCL patients had thrombocytopenia and 63 (12%) had thrombocytopenia without concomitant cytopenias. We identified that the choice of chemotherapy regimen was positively correlated with thrombocytopenia (p &lt;0.001). The chemotherapy regimens that are most likely to result in thrombocytopenia were DHAP (92.3%), ICE (89.7%), GDP (89.7%) and Gemox (69%) respectively. Aside from this, high LDH (P = 0.006) and Ann Arbor Stage III / IV (P = 0.025) were determined to be risk factors leading to thrombocytopenia. 40 patients (17.6%) had transfused platelets, and all of them were placed in the central venous. The high-threshold group (Platelet count PC≤20×10<sup>9</sup>/L) has a significant lower amount of platelet transfusions than the low-threshold group (PC≤10×10<sup>9</sup>/L). The platelet transfusion amount was1.44 ± 0.77 vs 2.05 ± 1.13(p = 0.047).In conclusion,The chemotherapy regimens that were DHAP, ICE, GDP and Gemox can easily lead to thrombocytopenia. A high level of LDH in peripheral blood and Ann Arbor Stage III / IV are also risk factors accountable for thrombocytopenia. A 20×10<sup>9</sup>/L prophylactic platelet transfusion threshold value is safe and effective and a better choice for the DLBCL patients with CVC.
DOI: 10.6084/m9.figshare.6340661.v1
title: DLBCL case summary.xls

description: Currently risk factors associated with chemotherapy-induced thrombocytopenia(CIT) in patients with Diffuse Large B Cell Lymphoma (DLBCL) is still undefined. Our research aims to analyse the effects of risk factors on thrombocytopenia. Moreover, it also aims to analyse the optimal threshold for infusion platelets of CIT patients who have received platelet transfusions.We conducted a retrospective analysis of 523 patients with DLBCL from 2011 to 2013 . Clinical and demographic parameters were extracted and analyse the risk factors associated with CIT. The threshold for platelet transfusions in DLBCL patients with central venous catheter (CVC) was evaluated.227 (43.4%) DLBCL patients had thrombocytopenia and 63 (12%) had thrombocytopenia without concomitant cytopenias. We identified that the choice of chemotherapy regimen was positively correlated with thrombocytopenia (p &lt;0.001). The chemotherapy regimens that are most likely to result in thrombocytopenia were DHAP (92.3%), ICE (89.7%), GDP (89.7%) and Gemox (69%) respectively. Aside from this, high LDH (P = 0.006) and Ann Arbor Stage III / IV (P = 0.025) were determined to be risk factors leading to thrombocytopenia. 40 patients (17.6%) had transfused platelets, and all of them were placed in the central venous. The high-threshold group (Platelet count PC≤20×10<sup>9</sup>/L) has a significant lower amount of platelet transfusions than the low-threshold group (PC≤10×10<sup>9</sup>/L). The platelet transfusion amount was1.44 ± 0.77 vs 2.05 ± 1.13(p = 0.047).In conclusion,The chemotherapy regimens that were DHAP, ICE, GDP and Gemox can easily lead to thrombocytopenia. A high level of LDH in peripheral blood and Ann Arbor Stage III / IV are also risk factors accountable for thrombocytopenia. A 20×10<sup>9</sup>/L prophylactic platelet transfusion threshold value is safe and effective and a better choice for the DLBCL patients with CVC.
DOI: 10.6084/m9.figshare.6340658
title: The engagement of cortical areas preceding exogenous vergence eye movements

description: Data underlying the findings reported in a submitted manuscript entitled <b>The engagement of cortical areas preceding exogenous vergence eye movements</b><br>
DOI: 10.6084/m9.figshare.6340547
title: Raw Data for 'Microscopic structure of the polymer-induced liquid precursor for calcium carbonate'

description: The data in the archive file are labelled in the following levels: <br>1st: polymer systems (ds-DNA, pAsp, pAH, pAA or no polymer) <br>2nd: characterization methods<br>3rd: detailed experimental conditions<br><br>The Matlab script used for morphological analysis of the Tomo results could be found in the "code folder", together with the scripts for reading and writting the Tomo stacks.<br>Please feel free to contact us if you need any further information about the data.
DOI: 10.6084/m9.figshare.6340331
title: MAPLE 2.3.0: an improved system for evaluating the functionomes of genomes and metagenomes

description: MAPLE is an automated system for inferring the potential comprehensive functions harbored by genomes and metagenomes. To reduce runtime in MAPLE analyzing the massive amino acid datasets of over 1 million sequences, we improved it by adapting the KEGG automatic annotation server to use GHOSTX and verified no substantial difference in the MAPLE results between the original and new implementations.
DOI: 10.6084/m9.figshare.6340331.v1
title: MAPLE 2.3.0: an improved system for evaluating the functionomes of genomes and metagenomes

description: MAPLE is an automated system for inferring the potential comprehensive functions harbored by genomes and metagenomes. To reduce runtime in MAPLE analyzing the massive amino acid datasets of over 1 million sequences, we improved it by adapting the KEGG automatic annotation server to use GHOSTX and verified no substantial difference in the MAPLE results between the original and new implementations.