cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6297371
title: SILVA ver. 132 database

description: SILVA ver 132 16S rRNA database formatted for the mg_pipeline; it has been dereplicated and now has 649,326 sequences.<br>It is compressed with MFCompress from the original 983 Mb file. To uncompress it, get the software (http://sweet.ua.pt/ap/software/mfcompress/MFCompress-src-1.01.tgz) and run:MFCompressD SILVA_132_derep.fasta.mfc
DOI: 10.6084/m9.figshare.6297371.v1
title: SILVA ver. 132 database

description: SILVA ver 132 16S rRNA database formatted for the mg_pipeline; it has been dereplicated and now has 649,326 sequences.<br>It is compressed with MFCompress from the original 983 Mb file. To uncompress it, get the software (http://sweet.ua.pt/ap/software/mfcompress/MFCompress-src-1.01.tgz) and run:MFCompressD SILVA_132_derep.fasta.mfc
DOI: 10.6084/m9.figshare.6297209
title: Complete data set for Nadtochiy et al. 2018 J. Mol. Cell Cardiol. paper on NMN cardioprotection

description: Complete data set in Excel format for all the Figures in the JMCC paper<br>
DOI: 10.6084/m9.figshare.6297209.v1
title: Complete data set for Nadtochiy et al. 2018 J. Mol. Cell Cardiol. paper on NMN cardioprotection

description: Complete data set in Excel format for all the Figures in the JMCC paper<br>
DOI: 10.6084/m9.figshare.6297182
title: experiment.json

description: IORE experiment description file for a Cartesian dataset-based workload.
DOI: 10.6084/m9.figshare.6297182.v1
title: experiment.json

description: IORE experiment description file for a Cartesian dataset-based workload.
DOI: 10.6084/m9.figshare.6297041
title: HiC.100kb.chr1.btr

description: HiC.100kb.chr1.btr
DOI: 10.6084/m9.figshare.6297041.v1
title: HiC.100kb.chr1.btr

description: HiC.100kb.chr1.btr
DOI: 10.6084/m9.figshare.6296987
title: The distinction of CPR bacteria from other bacteria based on protein family content

description: this fileset contains the data generated in the paper "The distinction of CPR bacteria from other bacteria based on protein family content". The zip file contains 22,977 fasta files, one file per family. the binary matrix used to create the figures 2, 3 and 4 are also provided.
DOI: 10.6084/m9.figshare.6296987.v1
title: Biological capacities clearly define a major subdivision in Domain Bacteria

description: this fileset contains the data generated in the paper "Biological capacities clearly define a major subdivision in Domain Bacteria". The zip file contains 786 fasta files, one file per family. the binary matrix used to create the figures 2, 3 and 4 are also provided.
DOI: 10.6084/m9.figshare.6296987.v3
title: The distinction of CPR bacteria from other bacteria based on protein family content

description: this fileset contains the data generated in the paper "The distinction of CPR bacteria from other bacteria based on protein family content". The zip file contains 22,977 fasta files, one file per family. the binary matrix used to create the figures 2, 3 and 4 are also provided.
DOI: 10.6084/m9.figshare.6296987.v2
title: Biological capacities clearly define a major subdivision in Domain Bacteria

description: this fileset contains the data generated in the paper "The distinction of CPR bacteria from other bacteria based on protein family content". The zip file contains 22,977 fasta files, one file per family. the binary matrix used to create the figures 2, 3 and 4 are also provided.
DOI: 10.6084/m9.figshare.6296291
title: Data

description: The data has been obtained from numerous and extensive set of experiments conducted in Fluid Mechanics Laboratory of Mechanical Engineering, Indian Institute of Science, Bangalore - 560012, INDIA.<br>
DOI: 10.6084/m9.figshare.6296291.v1
title: Data

description: The data has been obtained from numerous and extensive set of experiments conducted in Fluid Mechanics Laboratory of Mechanical Engineering, Indian Institute of Science, Bangalore - 560012, INDIA.<br>
DOI: 10.6084/m9.figshare.6295211
title: Data for Experiments 1 & 2 from The high-level basis of body adaptation

description: Data for Experiment 1 (first worksheet) and Experiment 2 (second worksheet) for all conditions, in Microsoft Excel format
DOI: 10.6084/m9.figshare.6295076
title: All data_Spinal Deformities.xlsx from Evolution in caves: selection from darkness causes spinal deformities in teleost fishes

description: Data underlying our analyses
DOI: 10.6084/m9.figshare.6295001.v1
title: Conditional Extremes in Asymmetric Financial Markets

description: The global financial crisis of 2007–2009 revealed the great extent to which systemic risk can jeopardize the stability of the entire financial system. An effective methodology to quantify systemic risk is at the heart of the process of identifying the so-called systemically important financial institutions for regulatory purposes as well as to investigate key drivers of systemic contagion. The paper proposes a method for dynamic forecasting of CoVaR, a popular measure of systemic risk. As a first step, we develop a semi-parametric framework using asymptotic results in the spirit of extreme value theory (EVT) to model the conditional probability distribution of a bivariate random vector given that one of the components takes on a large value, taking into account important features of financial data such as asymmetry and heavy tails. In the second step, we embed the proposed EVT method into a dynamic framework via a bivariate GARCH process. An empirical analysis is conducted to demonstrate and compare the performance of the proposed methodology relative to a very flexible fully parametric alternative.
DOI: 10.6084/m9.figshare.6294998.v1
title: Optimal designs for multi-response nonlinear regression models with several factors via semi-definite programming

description: We use semi-definite programming (SDP) to find a variety of optimal designs for multi-response linear models with multiple factors, and for the first time, extend the methodology to find optimal designs for multi-response nonlinear models and generalized linear models with multiple factors. We construct transformations that (i) facilitate improved formulation of the optimal design problems into SDP problems, (ii) enable us to extend SDP methodology to find optimal designs from linear models to nonlinear multi-response models with multiple factors and (iii) correct erroneously reported optimal designs in the literature caused by formulation issues. We also derive invariance properties of optimal designs and their dependence on the covariance matrix of the correlated errors, which are helpful for reducing the computation time for finding optimal designs. Our applications include finding A-, A<sub><i>s</i></sub>-, c- and D-optimal designs for multi-response multi-factor polynomial models, locally c- and D-optimal designs for a bivariate <i>E</i><sub><i>max</i></sub> response model and for a bivariate Probit model useful in the biosciences.
DOI: 10.6084/m9.figshare.6294998.v3
title: Optimal Designs for Multi-Response Nonlinear Regression Models With Several Factors via Semidefinite Programming

description: We use semidefinite programming (SDP) to find a variety of optimal designs for multi-response linear models with multiple factors, and for the first time, extend the methodology to find optimal designs for multi-response nonlinear models and generalized linear models with multiple factors. We construct transformations that (i) facilitate improved formulation of the optimal design problems into SDP problems, (ii) enable us to extend SDP methodology to find optimal designs from linear models to nonlinear multi-response models with multiple factors and (iii) correct erroneously reported optimal designs in the literature caused by formulation issues. We also derive invariance properties of optimal designs and their dependence on the covariance matrix of the correlated errors, which are helpful for reducing the computation time for finding optimal designs. Our applications include finding A-, A<sub><i>s</i></sub>-, c-, and D-optimal designs for multi-response multi-factor polynomial models, locally c- and D-optimal designs for a bivariate Emax response model and for a bivariate Probit model useful in the biosciences.
DOI: 10.6084/m9.figshare.6294998.v2
title: Optimal Designs for Multi-Response Nonlinear Regression Models With Several Factors via Semidefinite Programming

description: We use semidefinite programming (SDP) to find a variety of optimal designs for multi-response linear models with multiple factors, and for the first time, extend the methodology to find optimal designs for multi-response nonlinear models and generalized linear models with multiple factors. We construct transformations that (i) facilitate improved formulation of the optimal design problems into SDP problems, (ii) enable us to extend SDP methodology to find optimal designs from linear models to nonlinear multi-response models with multiple factors and (iii) correct erroneously reported optimal designs in the literature caused by formulation issues. We also derive invariance properties of optimal designs and their dependence on the covariance matrix of the correlated errors, which are helpful for reducing the computation time for finding optimal designs. Our applications include finding A-, A<sub><i>s</i></sub>-, c-, and D-optimal designs for multi-response multi-factor polynomial models, locally c- and D-optimal designs for a bivariate Emax response model and for a bivariate Probit model useful in the biosciences.
DOI: 10.6084/m9.figshare.6294995
title: A Penalized Likelihood Method for Classification With Matrix-Valued Predictors

description: We propose a penalized likelihood method to fit the linear discriminant analysis model when the predictor is matrix valued. We simultaneously estimate the means and the precision matrix, which we assume has a Kronecker product decomposition. Our penalties encourage pairs of response category mean matrix estimators to have equal entries and also encourage zeros in the precision matrix estimator. To compute our estimators, we use a blockwise coordinate descent algorithm. To update the optimization variables corresponding to response category mean matrices, we use an alternating minimization algorithm that takes advantage of the Kronecker structure of the precision matrix. We show that our method can outperform relevant competitors in classification, even when our modeling assumptions are violated. We analyze three real datasets to demonstrate our method’s applicability. Supplementary materials, including an R package implementing our method, are available online.
DOI: 10.6084/m9.figshare.6294995.v2
title: A Penalized Likelihood Method for Classification With Matrix-Valued Predictors

description: We propose a penalized likelihood method to fit the linear discriminant analysis model when the predictor is matrix valued. We simultaneously estimate the means and the precision matrix, which we assume has a Kronecker product decomposition. Our penalties encourage pairs of response category mean matrix estimators to have equal entries and also encourage zeros in the precision matrix estimator. To compute our estimators, we use a blockwise coordinate descent algorithm. To update the optimization variables corresponding to response category mean matrices, we use an alternating minimization algorithm that takes advantage of the Kronecker structure of the precision matrix. We show that our method can outperform relevant competitors in classification, even when our modeling assumptions are violated. We analyze three real datasets to demonstrate our method’s applicability. Supplementary materials, including an R package implementing our method, are available online.
DOI: 10.6084/m9.figshare.6294995.v1
title: A penalized likelihood method for classification with matrix-valued predictors

description: We propose a penalized likelihood method to fit the linear discriminant analysis model when the predictor is matrix valued. We simultaneously estimate the means and the precision matrix, which we assume has a Kronecker product decomposition. Our penalties encourage pairs of response category mean matrix estimators to have equal entries and also encourage zeros in the precision matrix estimator. To compute our estimators, we use a blockwise coordinate descent algorithm. To update the optimization variables corresponding to response category mean matrices, we use an alternating minimization algorithm that takes advantage of the Kronecker structure of the precision matrix. We show that our method can outperform relevant competitors in classification, even when our modeling assumptions are violated. We analyze three real datasets to demonstrate our method's applicability. Supplementary materials, including an R package implementing our method, are available online.
DOI: 10.6084/m9.figshare.6294791
title: Albacore + Porechop nanopore reads

description: These files contain the nanopore long reads produced by R9.4 MinION, basecalled and demultiplexed by Albacore v2.1.3, followed by a further demultiplexing step by Porechop v0.2.3.<br>Half of each strain's sample underwent FFPE repair, and half did not - these were sequenced under different barcodes. The samples here are tagged "ER" (FFPE repair), "noER" (no FFPE repair) and "all" (FFPE repaired and non-FFPE repaired reads pooled together)<br><br>The "all" sets of reads will also be available from SRA (accessions SAMN09500966 to SAMN09500970).
DOI: 10.6084/m9.figshare.6294791.v2
title: Albacore + Porechop nanopore reads

description: These files contain the nanopore long reads produced by R9.4 MinION, basecalled and demultiplexed by Albacore v2.1.3, followed by a further demultiplexing step by Porechop v0.2.3.<br>Half of each strain's sample underwent FFPE repair, and half did not - these were sequenced under different barcodes. The samples here are tagged "ER" (FFPE repair), "noER" (no FFPE repair) and "all" (FFPE repaired and non-FFPE repaired reads pooled together)<br><br>The "all" sets of reads will also be available from SRA (accessions SAMN09500966 to SAMN09500970).
DOI: 10.6084/m9.figshare.6294791.v1
title: Albacore basecalled nanopore reads

description: These files contain the nanopore long reads produced by R9.4 MinION, basecalled and demultiplexed by Albacore v2.1.3.<br>Half of each strain's sample underwent end repair, and half did not - these were sequenced under different barcodes. The samples here are tagged "ER" (end repair), "noER" (no end repair) and "all" (end repaired and non-end repaired reads pooled together)<br><br>The "all" sets of reads (after additional demultiplexing by Porechop v0.2.3) will be available from SRA ASAP.
DOI: 10.6084/m9.figshare.6293960
title: Pollen morphology of selected species from the family Solanaceae

description: The pollen grains of 38 species and one variety of 17 genera in the family Solanaceae were studied using light microscopy (LM) and scanning electron microscopy (SEM). Among them, the pollen morphology of 13 species was described for the first time. Our results suggested that the exine ornamentation of pollen grains could be divided into 11 types, made up of three types (cerebroid, granulate-perforate-punctate and rugulate-perforate) which were observed for the first time in Solanaceae, and other normal types (granulate, granulate-perforate, punctate, reticulate, rugulate, rugulate-striate, spinulose-perforate, striate). In addition, the studied species have pollen grains that differ in size, shape, equatorial view, polar view, aperture features and exine ornamentation, confirming that Solanaceae is a eurypalynous family. Furthermore, the intergeneric and intrageneric relationships of Solanaceae were explored. These results could provide a palynological basis for classification and systematic study of Solanaceae.
DOI: 10.6084/m9.figshare.6293960.v1
title: Pollen morphology of selected species from the family Solanaceae

description: The pollen grains of 38 species and one variety of 17 genera in the family Solanaceae were studied using light microscopy (LM) and scanning electron microscopy (SEM). Among them, the pollen morphology of 13 species was described for the first time. Our results suggested that the exine ornamentation of pollen grains could be divided into 11 types, made up of three types (cerebroid, granulate-perforate-punctate and rugulate-perforate) which were observed for the first time in Solanaceae, and other normal types (granulate, granulate-perforate, punctate, reticulate, rugulate, rugulate-striate, spinulose-perforate, striate). In addition, the studied species have pollen grains that differ in size, shape, equatorial view, polar view, aperture features and exine ornamentation, confirming that Solanaceae is a eurypalynous family. Furthermore, the intergeneric and intrageneric relationships of Solanaceae were explored. These results could provide a palynological basis for classification and systematic study of Solanaceae.
DOI: 10.6084/m9.figshare.6293918
title: The Strandja Massif and the İstanbul Zone were once parts of the same palaeotectonic unit: new data from Triassic detrital zircons

description: Spatially continuous rock assemblages that share similar environmental evolution or structural features can be classified as a single tectonic unit. This approach enables to link dispersed units or massifs with each other and sometimes can be subjective, depending on the classification criteria. The relationship and the nature of the contact between the Strandja Massif and the İstanbul Zone have been controversial due to the Cainozoic cover. Amalgamation of these units was claimed as early as the Aptian-Albian. Lower Triassic sedimentary rocks, which are overlain by the Carboniferous flysch with a N-verging thrust fault are exposed NW of the İstanbul Zone. This study reveals the spatial relationship between the Strandja Massif and the İstanbul Zone deduced from the U-Pb dating and Lu-Hf isotopes of the detrital zircons from these Lower Triassic clastics. Our results show that the early Triassic basin was fed from a provenance that included arc-related Upper Carboniferous-Lower Permian magmatic rocks which is much more likely to be the Strandja Massif than the İstanbul Zone. The second outcome of this study is that a unit that previously assigned to Palaeozoic turned out to be Triassic, which brings the Strandja Massif farther to the east, into the northern İstanbul Zone.
DOI: 10.6084/m9.figshare.6293918.v1
title: The Strandja Massif and the İstanbul Zone were once parts of the same palaeotectonic unit: new data from Triassic detrital zircons

description: Spatially continuous rock assemblages that share similar environmental evolution or structural features can be classified as a single tectonic unit. This approach enables to link dispersed units or massifs with each other and sometimes can be subjective, depending on the classification criteria. The relationship and the nature of the contact between the Strandja Massif and the İstanbul Zone have been controversial due to the Cainozoic cover. Amalgamation of these units was claimed as early as the Aptian-Albian. Lower Triassic sedimentary rocks, which are overlain by the Carboniferous flysch with a N-verging thrust fault are exposed NW of the İstanbul Zone. This study reveals the spatial relationship between the Strandja Massif and the İstanbul Zone deduced from the U-Pb dating and Lu-Hf isotopes of the detrital zircons from these Lower Triassic clastics. Our results show that the early Triassic basin was fed from a provenance that included arc-related Upper Carboniferous-Lower Permian magmatic rocks which is much more likely to be the Strandja Massif than the İstanbul Zone. The second outcome of this study is that a unit that previously assigned to Palaeozoic turned out to be Triassic, which brings the Strandja Massif farther to the east, into the northern İstanbul Zone.
DOI: 10.6084/m9.figshare.6293915
title: Mitochondrial genomes of the South American electric knifefishes <i>Eigenmannia humboldtii</i> (Steindachner 1878), <i>Eigenmannia limbata</i> (Schreiner and Miranda Ribeiro 1903), <i>Sternopygus aequilabiatus</i> (Humboldt 1805) and <i>Sternopygus macrurus</i> (Bloch and Schneider 1801), (Gymnotiformes, Sternopygidae)

description: We report four mitochondrial genomes of South American electric knifefishes, derived from target capture and Illumina sequencing (HiSeq 2500 PE100). Two trans-Andean species <i>Eigenmannia humboldtii</i> (mitochondrial consensus genome of 25 individuals) and <i>Sternopygus aequilabiatus</i> (mitochondrial consensus genome of 30 individuals) from Colombia and two cis-Andean species <i>Eigenmannia limbata</i> from Suriname and <i>Sternopygus macrurus</i> from Argentina. Regarding <i>Eigenmannia humboldtii</i>, <i>Eigenmannia limbata,</i> and <i>Sternopygus macrurus</i> mitochondrial genomes have 13 protein-coding genes, 1 D-loop, 2 ribosomal RNAs, 22 transfer RNAs, and are 13,394 bp, 10,921 bp, and 13,013 bp in length respectively, for <i>Sternopygus aequilabiatus</i> mitochondrial genomes have 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and is 14,270 bp in length.
DOI: 10.6084/m9.figshare.6293915.v1
title: Mitochondrial genomes of the South American electric knifefishes <i>Eigenmannia humboldtii</i> (Steindachner 1878), <i>Eigenmannia limbata</i> (Schreiner and Miranda Ribeiro 1903), <i>Sternopygus aequilabiatus</i> (Humboldt 1805) and <i>Sternopygus macrurus</i> (Bloch and Schneider 1801), (Gymnotiformes, Sternopygidae)

description: We report four mitochondrial genomes of South American electric knifefishes, derived from target capture and Illumina sequencing (HiSeq 2500 PE100). Two trans-Andean species <i>Eigenmannia humboldtii</i> (mitochondrial consensus genome of 25 individuals) and <i>Sternopygus aequilabiatus</i> (mitochondrial consensus genome of 30 individuals) from Colombia and two cis-Andean species <i>Eigenmannia limbata</i> from Suriname and <i>Sternopygus macrurus</i> from Argentina. Regarding <i>Eigenmannia humboldtii</i>, <i>Eigenmannia limbata,</i> and <i>Sternopygus macrurus</i> mitochondrial genomes have 13 protein-coding genes, 1 D-loop, 2 ribosomal RNAs, 22 transfer RNAs, and are 13,394 bp, 10,921 bp, and 13,013 bp in length respectively, for <i>Sternopygus aequilabiatus</i> mitochondrial genomes have 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and is 14,270 bp in length.
DOI: 10.6084/m9.figshare.6293834
title: 3D seismic reflection data - the geological Hubble

description: Presentation give to Leon H. Charney School of Marine Sciences, Haifa, Israel (Monday 21st May 2018)<br>
DOI: 10.17028/rd.lboro.6293513
title: Data for paper "Aerodrome Situational Awareness of Unmanned Aircraft: An Integrated Self-Learning Approach with Bayesian Network Semantic Segmentation"

description: The .rar file contains:1. GPS location data CSV2. Processed input videos to algorithm3. Output videos to algorithm4. Code to run algorithm<br>
DOI: 10.17028/rd.lboro.6293513.v1
title: Data for paper "Aerodrome Situational Awareness of Unmanned Aircraft: An Integrated Self-Learning Approach with Bayesian Network Semantic Segmentation"

description: The .rar file contains:1. GPS location data CSV2. Processed input videos to algorithm3. Output videos to algorithm4. Code to run algorithm<br>