cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4892063
title: Fig_3_Data_for_naive

description: Data for Fig. 3. Contains the desired result, measured result, and masked and full residuals for scan patterns of three different lengths.
DOI: 10.6084/m9.figshare.4892066.v1
title: Fig_4_Data_for_L_iteration

description: Data for Fig. 4. Contains impulse response, time-inverse impulse response, voltage mask, cropped and padded residual, cropped and full expected result, cropped desired result, initial input voltage, and correction voltages. Contains data for each panel in flow chart.
DOI: 10.6084/m9.figshare.4892072
title: Fig_5_Data_for_linear_decon

description: Data for Fig. 5. Contains the optimization results, including the desired result, achieved result, and masked and unmasked residual for 1 iterations. Also includes data from Fig. 3 for comparison.
DOI: 10.6084/m9.figshare.4892078.v1
title: Fig_7_Data_for_full_method

description: Data for Fig. 7. Contains a series of optimization results, including the desired result, achieved result, masked and unmasked residual, and voltage mask for 5 iterations.
DOI: 10.6084/m9.figshare.4892063.v1
title: Fig_3_Data_for_naive

description: Data for Fig. 3. Contains the desired result, measured result, and masked and full residuals for scan patterns of three different lengths.
DOI: 10.6084/m9.figshare.4892000
title: Novel Aggregate Deletion/Substitution/Addition Learning Algorithms for Recursive Partitioning

description: Many complex diseases are caused by a variety of both genetic and environmental factors acting in conjunction. To help understand these relationships, nonparametric methods that use aggregate learning have been developed such as <i>random forests</i> and <i>conditional forests</i>. Molinaro et al. (2010) described a powerful, single model approach called <i>partDSA</i> that has the advantage of producing interpretable models. We propose two extensions to the <i>partDSA</i> algorithm called <i>bagged partDSA</i> and <i>boosted partDSA</i>. These algorithms achieve higher prediction accuracies than individual <i>partDSA</i> objects through aggregating over a set of <i>partDSA</i> objects. Further, by using <i>partDSA</i> objects in the ensemble, each base learner creates decision rules using both “and” and “or” statements, which allows for natural logical constructs. We also provide four variable ranking techniques that aid in identifying the most important individual factors in the models. In the regression context, we compared bagged partDSA and boosted partDSA to random forests and conditional forests. Using simulated and real data, we found that bagged partDSA had lower prediction error than the other methods if the data were generated by a simple logic model, and that it performed similarly for other generating mechanisms. We also found that <i>boosted partDSA</i> was effective for a particularly complex case. Taken together these results suggest that the new methods are useful additions to the ensemble learning toolbox. We implement these algorithms as part of the partDSA R package. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.4892072.v1
title: Fig_5_Data_for_linear_decon

description: Data for Fig. 5. Contains the optimization results, including the desired result, achieved result, and masked and unmasked residual for 1 iterations. Also includes data from Fig. 3 for comparison.
DOI: 10.6084/m9.figshare.4891712
title: Breeding Propensity Data

description: 1. Capture histories of individual piping plovers. File contains individual id, capture history, individual count (always 1 in this dataset) as well as covariates for: sex (standardized such that 0 = unknown, 1.05 = female, and -0.946 = male), and time specific covariates (50 columns each) for minimum known age (1 = first year known breeding, 0 = all else) and minimum known linear age (from 1 to 10 years since first known breeding). 2. Data for condition analysis. Includes id, mass, year, reproductive output, and sex (standardized such that 0 = unknown, 1.05 = female, and -0.946 = male)3.arrival departure data. Includes id, year, standard arrival date, standard departure date minimum age, reproductive output, and sex (standardized such that 0 = unknown, 1.05 = female, and -0.946 = male)
DOI: 10.6084/m9.figshare.4891904
title: How plant neighborhood composition influences herbivory: Testing four mechanisms of associational resistance and susceptibility

description: These are the data used in Kim (2017). How plant neighborhood composition influences herbivory: Testing four mechanisms of associational resistance and susceptibility. PLoS ONE 12(5): e0176499. https://doi.org/10.1371/journal.pone.0176499<br>
DOI: 10.6084/m9.figshare.4891904.v1
title: How plant neighborhood composition influences herbivory: Testing four mechanisms of associational resistance and susceptibility

description: These are the data used in Kim (2017). How plant neighborhood composition influences herbivory: Testing four mechanisms of associational resistance and susceptibility. PLoS ONE 12(5): e0176499. https://doi.org/10.1371/journal.pone.0176499<br>
DOI: 10.6084/m9.figshare.4892000.v2
title: Novel Aggregate Deletion/Substitution/Addition Learning Algorithms for Recursive Partitioning

description: Many complex diseases are caused by a variety of both genetic and environmental factors acting in conjunction. To help understand these relationships, nonparametric methods that use aggregate learning have been developed such as <i>random forests</i> and <i>conditional forests</i>. Molinaro et al. (2010) described a powerful, single model approach called <i>partDSA</i> that has the advantage of producing interpretable models. We propose two extensions to the <i>partDSA</i> algorithm called <i>bagged partDSA</i> and <i>boosted partDSA</i>. These algorithms achieve higher prediction accuracies than individual <i>partDSA</i> objects through aggregating over a set of <i>partDSA</i> objects. Further, by using <i>partDSA</i> objects in the ensemble, each base learner creates decision rules using both “and” and “or” statements, which allows for natural logical constructs. We also provide four variable ranking techniques that aid in identifying the most important individual factors in the models. In the regression context, we compared bagged partDSA and boosted partDSA to random forests and conditional forests. Using simulated and real data, we found that bagged partDSA had lower prediction error than the other methods if the data were generated by a simple logic model, and that it performed similarly for other generating mechanisms. We also found that <i>boosted partDSA</i> was effective for a particularly complex case. Taken together these results suggest that the new methods are useful additions to the ensemble learning toolbox. We implement these algorithms as part of the partDSA R package. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.4891712.v1
title: Breeding Propensity Data

description: 1. Capture histories of individual piping plovers. File contains individual id, capture history, individual count (always 1 in this dataset) as well as covariates for: sex (standardized such that 0 = unknown, 1.05 = female, and -0.946 = male), and time specific covariates (50 columns each) for minimum known age (1 = first year known breeding, 0 = all else) and minimum known linear age (from 1 to 10 years since first known breeding). 2. Data for condition analysis. Includes id, mass, year, reproductive output, and sex (standardized such that 0 = unknown, 1.05 = female, and -0.946 = male)3.arrival departure data. Includes id, year, standard arrival date, standard departure date minimum age, reproductive output, and sex (standardized such that 0 = unknown, 1.05 = female, and -0.946 = male)
DOI: 10.6084/m9.figshare.4892000.v1
title: Novel aggregate deletion/substitution/addition learning algorithms for recursive partitioning

description: <b>Motivation</b>: Many complex diseases are caused by a variety of both genetic and environmental factors acting in conjunction. To help understand these relationships, non-parametric methods that utilize aggregate learning have been developed such as <i>Random Forests</i> and <i>Conditional Forests</i>. Molinaro et al. (2010) described a powerful, single model approach called <i>partDSA</i> that has the advantage of producing interpretable models. <b>Methods</b>: We propose two extensions to the <i>partDSA</i> algorithm called <i>Bagged partDSA</i> and <i>Boosted partDSA</i>. These algorithms achieve higher prediction accuracies than individual <i>partDSA</i> objects through aggregating over a set of independent <i>partDSA</i> objects. Further, by utilizing <i>partDSA</i> objects in the ensemble, each base learner creates decision rules using both ‘and’ and ‘or’ statements, which allows for natural logical constructs. We also provide four variable ranking techniques that aid in identifying the most important individual factors in the models. <b>Results</b>: In the regression context, we compared <i>Bagged partDSA</i> and <i>Boosted partDSA</i> to <i>Random Forests</i> and <i>Conditional Forests</i>. Using simulated and real data, we found that <i>Bagged partDSA</i> had lower prediction error than the other methods if the data were generated by a simple logic model, and that it performed similarly for other generating mechanisms. We also found that <i>Boosted partDSA</i> was effective for a particularly complex case. Taken together these results suggest that the new methods are useful additions to the ensemble learning toolbox. We implement these algorithms as part of the partDSA R package.
DOI: 10.6084/m9.figshare.4888772
title: Metz_2017_Thesis_Data.zip

description: This data set contains data sets analyzed in the 2017 Alfred University PhD thesis by Peter C. Metz. These data include:i. Synthetic PDF data produced using DIFFaXii. Experimental X-ray and Neutron PDF data collected using APS 11-ID-B (APS, ANL) and NOMAD (SNS, ORNL)ii. Experimental X-ray PDF data collected using APS 11-ID-B (APS, ANL).
DOI: 10.6084/m9.figshare.4888568
title: Daily oscillation of odorant detection in the rat olfactory epithelium

description: Results and statistical analysis using Prism software. See reference for detailled M&M.<br><br>EJN Minor Revision<br>
DOI: 10.6084/m9.figshare.4888568.v1
title: Daily oscillation of odorant detection in the rat olfactory epithelium

description: Results and statistical analysis using Prism software. See reference for detailled M&M.<br><br>EJN Minor Revision<br>
DOI: 10.6084/m9.figshare.4888391
title: A critical reexamination of doing arithmetic nonconsciously: Supplementary Materials

description: These html and R Markdown files contain the code used and supplementary analyses reported in: <br>Moors, P., Hesselmann, G. (2017). A critical reexamination of doing arithmetic nonconsciously. Psychonomic Bulletin & Review.
DOI: 10.6084/m9.figshare.4888358
title: Dataset_SAI_RMT.xlsx

description: <b>This is the data repository for our manuscript in European Journal of Neuroscience. If you have any questions please do not hesitate to contact me (s.bonni@hsantalucia.it)</b>
DOI: 10.6084/m9.figshare.4888358.v1
title: Dataset_SAI_RMT.xlsx

description: <b>This is the data repository for our manuscript in European Journal of Neuroscience. If you have any questions please do not hesitate to contact me (s.bonni@hsantalucia.it)</b>
DOI: 10.6084/m9.figshare.4888391.v2
title: A critical reexamination of doing arithmetic nonconsciously: Supplementary Materials

description: These html and R Markdown files contain the code used and supplementary analyses reported in: <br>Moors, P., Hesselmann, G. (2017). A critical reexamination of doing arithmetic nonconsciously. Psychonomic Bulletin & Review.
DOI: 10.6084/m9.figshare.4888316
title: Helianthus annuus

description: CRootbox parameter file for Helianthus annuus.<br><br>from:<br><br>Potential and actual root growth variations in root systems: modeling them with a two-step stochastic approach Pages L, Xie J, Serra V Plant and Soil, 373, 723-735, 2013
DOI: 10.6084/m9.figshare.4888283
title: Database for the ampC alleles in Acinetobacter baumannii

description: ampC - DNA sequences AmpC - Amino acid sequences
DOI: 10.6084/m9.figshare.4888283.v1
title: Database for the ampC alleles in Acinetobacter baumannii

description: ampC - DNA sequences AmpC - Amino acid sequences
DOI: 10.6084/m9.figshare.4888280
title: <i>Superstesaster promissor</i> gen. et sp. nov., a new starfish (Echinodermata, Asteroidea) from the Early Triassic of Utah, USA, filling a major gap in the phylogeny of asteroids

description: We describe <i>Superstesaster promissor</i> gen. et sp. nov., a starfish from the Smithian (Early Triassic) of Utah (USA) that fills a major gap in the fossil record of the Asteroidea. The post-Palaeozoic crown group Asteroidea are distinct from any of the diverse Palaeozoic forms. However, current understanding of the Palaeozoic–Mesozoic transition is blurred by a large gap in the fossil record between the Early Permian and the Middle Triassic. Building on the newly described taxon, a phylogenetic analysis investigates the relationships between Palaeozoic and Mesozoic Asteroidea. Including 30 species and 70 morphological characters, it is the most comprehensive phylogeny produced for fossil starfishes so far. Relationships among Palaeozoic forms remain poorly resolved, but their position in the tree is grossly consistent with stratigraphy. The tree topology implies the appearance of a wide range of morphologies during the Ordovician, a bottleneck during the end-Devonian events, and a second diversification during the Carboniferous, before a diversity decline at the end of the Permian. <i>Superstesaster promissor</i> nests above Palaeozoic taxa and appears as the sister group to the post-Palaeozoic Asteroidea. It represents the first record of a member of the stem group in the Mesozoic, and it likely reflects the ancestral morphology of the crown group. <i>S. promissor</i> shares with the crown group typical ambulacral and adambulacral plate shape and articulation. Phylogenetic relationships within the crown group remain poorly resolved, although three clades are consistent with molecular and morphological phylogenies available for extant forms: Valvatacea (<i>Comptoniaster</i>, <i>Pentasteria</i>, <i>Advenaster</i>, <i>Noviaster</i>), Forcipulatacea (<i>Germanasterias</i>, <i>Argoviaster</i>) and Velatida (<i>Tropidaster</i>, <i>Protremaster</i>). A Triassic and Jurassic radiation of the crown group is confirmed. Most Triassic and Jurassic forms do not share all synapomorphies with extant clades and usually represent separate clades or stem members of modern clades rather than true members of modern families. http://zoobank.org/urn:lsid:zoobank.org:pub:8CAC421A-DC0C-4EEB-B872-C7505FA8C2EA
DOI: 10.6084/m9.figshare.4888280.v1
title: <i>Superstesaster promissor</i> gen. et sp. nov., a new starfish (Echinodermata, Asteroidea) from the Early Triassic of Utah, USA, filling a major gap in the phylogeny of asteroids

description: We describe <i>Superstesaster promissor</i> gen. et sp. nov., a starfish from the Smithian (Early Triassic) of Utah (USA) that fills a major gap in the fossil record of the Asteroidea. The post-Palaeozoic crown group Asteroidea are distinct from any of the diverse Palaeozoic forms. However, current understanding of the Palaeozoic–Mesozoic transition is blurred by a large gap in the fossil record between the Early Permian and the Middle Triassic. Building on the newly described taxon, a phylogenetic analysis investigates the relationships between Palaeozoic and Mesozoic Asteroidea. Including 30 species and 70 morphological characters, it is the most comprehensive phylogeny produced for fossil starfishes so far. Relationships among Palaeozoic forms remain poorly resolved, but their position in the tree is grossly consistent with stratigraphy. The tree topology implies the appearance of a wide range of morphologies during the Ordovician, a bottleneck during the end-Devonian events, and a second diversification during the Carboniferous, before a diversity decline at the end of the Permian. <i>Superstesaster promissor</i> nests above Palaeozoic taxa and appears as the sister group to the post-Palaeozoic Asteroidea. It represents the first record of a member of the stem group in the Mesozoic, and it likely reflects the ancestral morphology of the crown group. <i>S. promissor</i> shares with the crown group typical ambulacral and adambulacral plate shape and articulation. Phylogenetic relationships within the crown group remain poorly resolved, although three clades are consistent with molecular and morphological phylogenies available for extant forms: Valvatacea (<i>Comptoniaster</i>, <i>Pentasteria</i>, <i>Advenaster</i>, <i>Noviaster</i>), Forcipulatacea (<i>Germanasterias</i>, <i>Argoviaster</i>) and Velatida (<i>Tropidaster</i>, <i>Protremaster</i>). A Triassic and Jurassic radiation of the crown group is confirmed. Most Triassic and Jurassic forms do not share all synapomorphies with extant clades and usually represent separate clades or stem members of modern clades rather than true members of modern families. http://zoobank.org/urn:lsid:zoobank.org:pub:8CAC421A-DC0C-4EEB-B872-C7505FA8C2EA
DOI: 10.6084/m9.figshare.4888250
title: Refining palaeoenvironmental analysis using integrated quantitative granulometry and palynology

description: Dataset: Grain size results
DOI: 10.6084/m9.figshare.4888244
title: Supplementary Material for: Patterns of Disease in Patients with Middle-Lobe Predominant Bronchiectasis

description: <b><i>Background:</i></b> Middle-lobe predominant bronchiectasis affecting the right middle-lobe and/or lingula (RMLP) is classically described in asthenic, elderly females with skeletal abnormalities or associated nontuberculous mycobacterial (NTM) infection. <b><i>Objectives:</i></b> We aimed to evaluate the frequency and clinical characteristics of patients with an RMLP phenotype in a cohort of newly diagnosed bronchiectasis patients and determine associations with disease severity. <b><i>Methods:</i></b> A retrospective observational cross-sectional cohort study of consecutive bronchiectasis patients in our institution was performed. Data were collected on baseline variables, microbiology status, lung function, and radiology according to the modified Bhalla score. Disease severity was assessed using bronchiectasis severity index (BSI) and FACED severity scores. <b><i>Results:</i></b> Of 81 patients (mean age [SD] 62.6 [12.4], females 55 [67.9%], BMI 26.9 [5.7%]), 20 (24.7%) had RMLP disease. These patients were significantly younger, female, and with lower BMIs than patients with the classical bronchiectasis phenotype (<i>p</i> = 0.03, 0.01, and <i>p</i> &lt;0.01, respectively). Fewer symptoms of cough and daily sputum (<i>p</i> = 0.01 and &lt;0.01), prior exacerbation frequency (<i>p</i> = 0.03), and higher baseline forced expiratory volume (<i>p</i> = 0.04) were noted. A higher incidence of NTM at diagnosis was demonstrated (<i>p</i> = 0.01). BSI and FACED severity scores in RMLP patients were significantly lower than their counterparts (both <i>p</i> &lt; 0.001). <b><i>Conclusions:</i></b> The RMLP phenotype is associated with younger patients than classically described in the literature. An increased rate of NTM infection in this phenotype was noted, particularly in females, but much lower than previously described. Lung function and disease severity scores in this patient group are relatively normal, suggesting a milder phenotype in patients with this form of the disease.
DOI: 10.6084/m9.figshare.4888250.v1
title: Refining palaeoenvironmental analysis using integrated quantitative granulometry and palynology

description: Dataset: Grain size results
DOI: 10.6084/m9.figshare.4888205
title: Phylogeny taxon sampling from How do seemingly non-vagile clades accomplish trans-marine dispersal? Trait and dispersal evolution in the landfowl (Aves: Galliformes)

description: Table of species, institution, sample ID, tissue type, and NCBI Bioproject accession for each sample used in phylogenetic analysis
DOI: 10.6084/m9.figshare.4888202
title: Table S1 from Genetic diversity is largely unpredictable but scales with museum occurrences in a species-rich clade of Australian lizards

description: Data on individuals included in this study
DOI: 10.6084/m9.figshare.4888205.v1
title: Phylogeny taxon sampling from How do seemingly non-vagile clades accomplish trans-marine dispersal? Trait and dispersal evolution in the landfowl (Aves: Galliformes)

description: Table of species, institution, sample ID, tissue type, and NCBI Bioproject accession for each sample used in phylogenetic analysis
DOI: 10.6084/m9.figshare.4888187
title: Fossils used to time-calibrate ultrametric tree from How do seemingly non-vagile clades accomplish trans-marine dispersal? Trait and dispersal evolution in the landfowl (Aves: Galliformes)

description: Taxa, localiy, stratigraphy, node calibrated, hard minmum age of fossils used to time-calibrate the ultrametric tree
DOI: 10.6084/m9.figshare.4888202.v1
title: Table S1 from Genetic diversity is largely unpredictable but scales with museum occurrences in a species-rich clade of Australian lizards

description: Data on individuals included in this study
DOI: 10.6084/m9.figshare.4888187.v1
title: Fossils used to time-calibrate ultrametric tree from How do seemingly non-vagile clades accomplish trans-marine dispersal? Trait and dispersal evolution in the landfowl (Aves: Galliformes)

description: Taxa, localiy, stratigraphy, node calibrated, hard minmum age of fossils used to time-calibrate the ultrametric tree
DOI: 10.6084/m9.figshare.4888175
title: Evolutionary model testing from How do seemingly non-vagile clades accomplish trans-marine dispersal? Trait and dispersal evolution in the landfowl (Aves: Galliformes)

description: Model testing results to identify appropriate comparative evolutionary models for character state reconstructions
DOI: 10.6084/m9.figshare.4888175.v1
title: Evolutionary model testing from How do seemingly non-vagile clades accomplish trans-marine dispersal? Trait and dispersal evolution in the landfowl (Aves: Galliformes)

description: Model testing results to identify appropriate comparative evolutionary models for character state reconstructions
DOI: 10.6084/m9.figshare.4888169
title: Table S5 from Genetic diversity is largely unpredictable but scales with museum occurrences in a species-rich clade of Australian lizards

description: Data on studies included in our literature survey on the drivers of genetic diversity
DOI: 10.6084/m9.figshare.4888169.v1
title: Table S5 from Genetic diversity is largely unpredictable but scales with museum occurrences in a species-rich clade of Australian lizards

description: Data on studies included in our literature survey on the drivers of genetic diversity
DOI: 10.6084/m9.figshare.4888154
title: DATABASE_Prevalence of anemia and associated factors in children living in urban and rural settings from Bata District, Equatorial Guinea, 2013.xlsx

description: Anemia in children under 5 years of age is a global public health problem. According to the World Health Organization the current rate of anemia among preschool aged children in Equatorial Guinea is 66%. No information is available above this age. The cross-sectional Prevamal Survey was conducted in 2013 aimed at providing baseline data on malaria prevalence in children aged 2 months-15 years old. Sampling was carried out with the use of a multistage, stratified cluster strategy in the district of Bata, Equatorial Guinea. The excel database provide the individual data and an extra sheet with variables' information.