cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8107610
title: Multi-level control architecture for Bionic Handling Assistant robot augmented by learning from demonstration for apple-picking

description: The control of soft continuum robots is challenging owing to their mechanical elasticity and complex dynamics. An additional challenge emerges when we want to apply Learning from Demonstration (LfD) and need to collect necessary demonstrations due to the inherent control difficulty. In this paper, we provide a multi-level architecture from low-level control to high-level motion planning for the Bionic Handling Assistant (BHA) robot. We deploy learning across all levels to enable the application of LfD for a real-world manipulation task. To record the demonstrations, an actively compliant controller is used. A variant of dynamical systems' application that are able to encode both position and orientation then maps the recorded 6D end-effector pose data into a virtual attractor space. A recent LfD method encodes the pose attractors within the same model for point-to-point motion planning. In the proposed architecture, hybrid models that combine an analytical approach and machine learning techniques are used to overcome the inherent slow dynamics and model imprecision of the BHA. The performance and generalization capability of the proposed multi-level approach are evaluated in simulation and with the real BHA robot in an apple-picking scenario which requires high accuracy to control the pose of the robot's end-effector.
DOI: 10.6084/m9.figshare.8107646.v2
title: Data used to apply the three-step strategy for predicting algae growth inhibition toxicity [1].

description: Table I lists the names of the 309 chemicals selected from the data set of 425 chemicals in Kusk et al. [2], along with the SMILES strings used to calculate their physicochemical properties (log <i>P</i>, log <i>D</i> at pH10, log <i>S</i><sub>0</sub>, and log <i>S</i><sub>w</sub>) by means of ACD/Labs [3]. Tables II, III, and IV list log (1/48h-algal EC<sub>50</sub> [mM]) values, physicochemical properties, and values used for Steps 1–3 of the three-step strategy [1]; values are from the algal toxicity data set of Kusk et al. [2].<br>Log <i>P</i>: log of octanol–water partition coefficient, calculated with ACD/Labs using Consensus LogP values. <br>Log <i>D</i> at pH 10: log of octanol–water distribution coefficient at pH 10 (log <i>D</i><sub>pH10</sub> in Tables II, III, and IV), calculated with ACD/Labs using the Consensus LogP and GALAS pKa modules.<br>Log <i>S</i><sub>0</sub>: log of intrinsic solubility (i.e., solubility of the neutral form [mol L<sup>−1</sup>]) in water at 25 °C, calculated with the GALAS algorithm in ACD/Labs.<br>Log <i>S</i><sub>w</sub>: log of solubility in pure water along with pH of the resulting solution (mol L<sup>−1</sup> with a defined pH), calculated with the GALAS algorithm in ACD/Labs.<br>Values of log (1/48h-algal EC<sub>50</sub> [mM]) were calculated by converting EC<sub>50</sub> values in milligrams per liter to the corresponding millimolar values by using the molecular weights listed in the supplemental data of ref. [2]. <br><br>[1] Furuhama A, Hasunuma K, Hayashi TI, Tatarazako N (2016) Predicting algal growth inhibition toxicity: three-step strategy using structural and physicochem-ical properties. SAR QSAR Environ Res 27:343–362.<br>[2] Kusk KO, Christensen AM, Nyholm N (2018) Algal growth inhibition test re-sults of 425 organic chemical substances. Chemosphere 204:405–412.<br>[3] ACD/Labs, version 2018 (2018). Advanced Chemistry Development, Inc., To-ronto, ON, Canada.<br><br>
DOI: 10.6084/m9.figshare.8107646.v1
title: Data used to apply the three-step strategy for predicting algae growth inhibition toxicity [1].

description: Table I lists the names of the 309 chemicals selected from the data set of 425 chemicals in Kusk et al. [2], along with the SMILES strings used to calculate their physicochemical properties (log <i>P</i>, log <i>D</i> at pH10, log <i>S</i><sub>0</sub>, and log <i>S</i><sub>w</sub>) by means of ACD/Labs [3]. Tables II, III, and IV list log (1/48h-algal EC<sub>50</sub> [mM]) values, physicochemical properties, and values used for Steps 1–3 of the three-step strategy [1]; values are from the algal toxicity data set of Kusk et al. [2].<br>Log <i>P</i>: log of octanol–water partition coefficient, calculated with ACD/Labs using Consensus LogP values. <br>Log <i>D</i> at pH 10: log of octanol–water distribution coefficient at pH 10 (log <i>D</i><sub>pH10</sub> in Tables II, III, and IV), calculated with ACD/Labs using the Consensus LogP and GALAS pKa modules.<br>Log <i>S</i><sub>0</sub>: log of intrinsic solubility (i.e., solubility of the neutral form [mol L<sup>−1</sup>]) in water at 25 °C, calculated with the GALAS algorithm in ACD/Labs.<br>Log <i>S</i><sub>w</sub>: log of solubility in pure water along with pH of the resulting solution (mol L<sup>−1</sup> with a defined pH), calculated with the GALAS algorithm in ACD/Labs.<br>Values of log (1/48h-algal EC<sub>50</sub> [mM]) were calculated by converting EC<sub>50</sub> values in milligrams per liter to the corresponding millimolar values by using the molecular weights listed in the supplemental data of ref. [2]. <br><br>[1] Furuhama A, Hasunuma K, Hayashi TI, Tatarazako N (2016) Predicting algal growth inhibition toxicity: three-step strategy using structural and physicochem-ical properties. SAR QSAR Environ Res 27:343–362.<br>[2] Kusk KO, Christensen AM, Nyholm N (2018) Algal growth inhibition test re-sults of 425 organic chemical substances. Chemosphere 204:405–412.<br>[3] ACD/Labs, version 2018 (2018). Advanced Chemistry Development, Inc., To-ronto, ON, Canada.<br><br>
DOI: 10.6084/m9.figshare.8107610.v1
title: Multi-level control architecture for Bionic Handling Assistant robot augmented by learning from demonstration for apple-picking

description: The control of soft continuum robots is challenging owing to their mechanical elasticity and complex dynamics. An additional challenge emerges when we want to apply Learning from Demonstration (LfD) and need to collect necessary demonstrations due to the inherent control difficulty. In this paper, we provide a multi-level architecture from low-level control to high-level motion planning for the Bionic Handling Assistant (BHA) robot. We deploy learning across all levels to enable the application of LfD for a real-world manipulation task. To record the demonstrations, an actively compliant controller is used. A variant of dynamical systems' application that are able to encode both position and orientation then maps the recorded 6D end-effector pose data into a virtual attractor space. A recent LfD method encodes the pose attractors within the same model for point-to-point motion planning. In the proposed architecture, hybrid models that combine an analytical approach and machine learning techniques are used to overcome the inherent slow dynamics and model imprecision of the BHA. The performance and generalization capability of the proposed multi-level approach are evaluated in simulation and with the real BHA robot in an apple-picking scenario which requires high accuracy to control the pose of the robot's end-effector.
DOI: 10.6084/m9.figshare.8105939
title: Additional file 3: of Staphylococci phages display vast genomic diversity and evolutionary relationships

description: Average nucleotide sequence identity values. Average nucleotide sequence identities (ANIs) of 205 staphylococcal phage genomes were made using Kalign algorithm. Heat map was created in excel. (XLSX 41 kb)
DOI: 10.6084/m9.figshare.8105942
title: Additional file 4: of Staphylococci phages display vast genomic diversity and evolutionary relationships

description: Shared gene content. Biopython functions were used to assignment gene content similarity using the Phamerator output (2139 phams, of which 745 are orphams). Heat map was created in excel. (XLSX 223 kb)
DOI: 10.6084/m9.figshare.8105933
title: Additional file 34: of Staphylococci phages display vast genomic diversity and evolutionary relationships

description: Integrases, attB sites and virulence genes. The dataset includes all cluster B staphylococcal siphoviruses (n = 132), for which five integrases types, five attB sites and 13 virulence factors were identified. The integrases were identified through Phamerator and BLASTP. The attB site was found through BLASTP using best host species hit similar to the one originally used to isolate the phage. The virulence genes were retrieved from Additional file 2 and re-organized. (XLSX 72 kb)
DOI: 10.6084/m9.figshare.8105936
title: Additional file 35: of Staphylococci phages display vast genomic diversity and evolutionary relationships

description: Endolysin genes. The dataset includes 205 staphylococcal phages, for which four distinct organization strategies were found (single gene, two genes spliced, two genes adjacent and single gene with inter-lytic-domain secondary translational start site). The corresponding nucleotide and amino acid sequences and functional encoding domains (catalytic and binding) detected through the structural database HHpred are given. All genes spliced with group I introns were manually curated. (XLSX 99 kb)
DOI: 10.6084/m9.figshare.8105939.v1
title: Additional file 3: of Staphylococci phages display vast genomic diversity and evolutionary relationships

description: Average nucleotide sequence identity values. Average nucleotide sequence identities (ANIs) of 205 staphylococcal phage genomes were made using Kalign algorithm. Heat map was created in excel. (XLSX 41 kb)
DOI: 10.6084/m9.figshare.8105942.v1
title: Additional file 4: of Staphylococci phages display vast genomic diversity and evolutionary relationships

description: Shared gene content. Biopython functions were used to assignment gene content similarity using the Phamerator output (2139 phams, of which 745 are orphams). Heat map was created in excel. (XLSX 223 kb)
DOI: 10.6084/m9.figshare.8105933.v1
title: Additional file 34: of Staphylococci phages display vast genomic diversity and evolutionary relationships

description: Integrases, attB sites and virulence genes. The dataset includes all cluster B staphylococcal siphoviruses (n = 132), for which five integrases types, five attB sites and 13 virulence factors were identified. The integrases were identified through Phamerator and BLASTP. The attB site was found through BLASTP using best host species hit similar to the one originally used to isolate the phage. The virulence genes were retrieved from Additional file 2 and re-organized. (XLSX 72 kb)
DOI: 10.6084/m9.figshare.8105936.v1
title: Additional file 35: of Staphylococci phages display vast genomic diversity and evolutionary relationships

description: Endolysin genes. The dataset includes 205 staphylococcal phages, for which four distinct organization strategies were found (single gene, two genes spliced, two genes adjacent and single gene with inter-lytic-domain secondary translational start site). The corresponding nucleotide and amino acid sequences and functional encoding domains (catalytic and binding) detected through the structural database HHpred are given. All genes spliced with group I introns were manually curated. (XLSX 99 kb)
DOI: 10.6084/m9.figshare.8105918
title: Additional file 2: of Staphylococci phages display vast genomic diversity and evolutionary relationships

description: Phams. The dataset includes 205 staphylococcal phages, encoding 20,579 predicted ORFs, a total of 2139 phams (gene with related sequences) of which 745 orphams (genes without related sequences) were identified generated based on kclust alignments performed in Phamerator. Phams are ordered by highest conservation among phage members. The phage-ORF column reflects the positioning of genes locus of the genome map generated by Phamerator. Biopython functions were used to retrieved and list in a table with several features associated to the phages. * An alternative nomenclature system for Cluster B phage integrases is provided as in Goerke et al. 2009 (29). (XLSX 216 kb)
DOI: 10.6084/m9.figshare.8105918.v1
title: Additional file 2: of Staphylococci phages display vast genomic diversity and evolutionary relationships

description: Phams. The dataset includes 205 staphylococcal phages, encoding 20,579 predicted ORFs, a total of 2139 phams (gene with related sequences) of which 745 orphams (genes without related sequences) were identified generated based on kclust alignments performed in Phamerator. Phams are ordered by highest conservation among phage members. The phage-ORF column reflects the positioning of genes locus of the genome map generated by Phamerator. Biopython functions were used to retrieved and list in a table with several features associated to the phages. * An alternative nomenclature system for Cluster B phage integrases is provided as in Goerke et al. 2009 (29). (XLSX 216 kb)
DOI: 10.6084/m9.figshare.8105894
title: Additional file 2: of Prognostic impact of tumor location in colon cancer: the Monitoring of Cancer Incidence in Japan (MCIJ) project

description: Figure S2. A. 5-year net survivals for patients with right- and left-sided colon cancer in stage localized. B 5-year net survivals for patients with right- and left-sided colon cancer in stage regional. C 5-year net survival for patients with right- and left-sided colon cancer in stage distant. (ZIP 139 kb)
DOI: 10.6084/m9.figshare.8105888
title: Additional file 1: of Prognostic impact of tumor location in colon cancer: the Monitoring of Cancer Incidence in Japan (MCIJ) project

description: Figure S1. A. 5-year net survivals for patients with right- and left-sided colon cancer in those aged less than 40 years old. B 5-year net survivals for patients with right- and left-sided colon cancer in those aged 40–54 years old. C 5-year net survivals for patients with right- and left-sided colon cancer in those aged 55–70 years old. D 5-year net survivals for patients with right- and left-sided colon cancer in those aged &gt; 70 years old. (ZIP 186 kb)
DOI: 10.6084/m9.figshare.8105894.v1
title: Additional file 2: of Prognostic impact of tumor location in colon cancer: the Monitoring of Cancer Incidence in Japan (MCIJ) project

description: Figure S2. A. 5-year net survivals for patients with right- and left-sided colon cancer in stage localized. B 5-year net survivals for patients with right- and left-sided colon cancer in stage regional. C 5-year net survival for patients with right- and left-sided colon cancer in stage distant. (ZIP 139 kb)
DOI: 10.6084/m9.figshare.8105888.v1
title: Additional file 1: of Prognostic impact of tumor location in colon cancer: the Monitoring of Cancer Incidence in Japan (MCIJ) project

description: Figure S1. A. 5-year net survivals for patients with right- and left-sided colon cancer in those aged less than 40 years old. B 5-year net survivals for patients with right- and left-sided colon cancer in those aged 40–54 years old. C 5-year net survivals for patients with right- and left-sided colon cancer in those aged 55–70 years old. D 5-year net survivals for patients with right- and left-sided colon cancer in those aged &gt; 70 years old. (ZIP 186 kb)
DOI: 10.6084/m9.figshare.8105867
title: Additional file 1: of Staphylococci phages display vast genomic diversity and evolutionary relationships

description: Staphylococcal phage genome characteristics. Biopython package was used to retrieve complete genome sequences at June of 2018 from NCBI and list in a table with several features associated to the phage. *Numbers in parentheses indicate the size of DNA regions (in bp) homologous to regions of known terminal repeats. DTR, direct terminal repeat; COS, cohesive end site. CoPS, coagulase-positive species, CoVS, coagulase-variable species, CoNS, coagulase-negative species. (XLSX 29 kb)
DOI: 10.6084/m9.figshare.8105867.v1
title: Additional file 1: of Staphylococci phages display vast genomic diversity and evolutionary relationships

description: Staphylococcal phage genome characteristics. Biopython package was used to retrieve complete genome sequences at June of 2018 from NCBI and list in a table with several features associated to the phage. *Numbers in parentheses indicate the size of DNA regions (in bp) homologous to regions of known terminal repeats. DTR, direct terminal repeat; COS, cohesive end site. CoPS, coagulase-positive species, CoVS, coagulase-variable species, CoNS, coagulase-negative species. (XLSX 29 kb)
DOI: 10.6084/m9.figshare.8105849
title: Additional file 2: of Scientific and technological contributions of Latin America and Caribbean countries to the Zika virus outbreak

description: ZIKAV-related patents with earliest priority date up to 12/31/2017 (XLSX 1728 kb)
DOI: 10.6084/m9.figshare.8105849.v1
title: Additional file 2: of Scientific and technological contributions of Latin America and Caribbean countries to the Zika virus outbreak

description: ZIKAV-related patents with earliest priority date up to 12/31/2017 (XLSX 1728 kb)
DOI: 10.6084/m9.figshare.8105843
title: Additional file 1: of Scientific and technological contributions of Latin America and Caribbean countries to the Zika virus outbreak

description: ZIKAV-related publications up to December 2017, retrieved from WoS, PubMed, and Scopus. (CSV 1513 kb)
DOI: 10.25934/00003506.0
title: Available IPD datapackage for study 'A Randomised, Double-blind, Placebo-controlled Parallel Group Efficacy and Safety Study of BI 1356 (One Dose, e.g. 5 mg), Administered Orally Once Daily Over 24 Weeks, With an Open Label Extension to 80 Weeks (Placebo Patients Switched to BI 1356), in Type 2 Diabetic Patients With Insufficient Glycaemic Control Despite Metformin Therapy'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.6084/m9.figshare.8105843.v1
title: Additional file 1: of Scientific and technological contributions of Latin America and Caribbean countries to the Zika virus outbreak

description: ZIKAV-related publications up to December 2017, retrieved from WoS, PubMed, and Scopus. (CSV 1513 kb)
DOI: 10.25934/00003506.1
title: IPD datapackage for study 'A Randomised, Double-blind, Placebo-controlled Parallel Group Efficacy and Safety Study of BI 1356 (One Dose, e.g. 5 mg), Administered Orally Once Daily Over 24 Weeks, With an Open Label Extension to 80 Weeks (Placebo Patients Switched to BI 1356), in Type 2 Diabetic Patients With Insufficient Glycaemic Control Despite Metformin Therapy' and research request: 'Stratification of SGLT2 inhibitor glucose lowering therapy in Type 2 diabetes'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.6084/m9.figshare.8105816
title: MOESM3 of Development of microsatellite loci for two New World vultures (Cathartidae)

description: Additional file 3. PAL_FINDER results for turkey vulture (Cathartes aura) next-generation sequencing run on Illumina MiSeq. MiSeq run files were submitted to the National Center for Biotechnology Information Sequence Read Archive (accession number PRJNA498072).
DOI: 10.6084/m9.figshare.8105816.v1
title: MOESM3 of Development of microsatellite loci for two New World vultures (Cathartidae)

description: Additional file 3. PAL_FINDER results for turkey vulture (Cathartes aura) next-generation sequencing run on Illumina MiSeq. MiSeq run files were submitted to the National Center for Biotechnology Information Sequence Read Archive (accession number PRJNA498072).
DOI: 10.6084/m9.figshare.8105810
title: MOESM2 of Development of microsatellite loci for two New World vultures (Cathartidae)

description: Additional file 2. PAL_FINDER results for black vulture (Coragyps atratus) next-generation sequencing run on Illumina MiSeq. MiSeq run files were submitted to the National Center for Biotechnology Information Sequence Read Archive (accession number PRJNA498072).
DOI: 10.6084/m9.figshare.8105810.v1
title: MOESM2 of Development of microsatellite loci for two New World vultures (Cathartidae)

description: Additional file 2. PAL_FINDER results for black vulture (Coragyps atratus) next-generation sequencing run on Illumina MiSeq. MiSeq run files were submitted to the National Center for Biotechnology Information Sequence Read Archive (accession number PRJNA498072).
DOI: 10.6084/m9.figshare.8105726
title: Additional file 2: of GScluster: network-weighted gene-set clustering analysis

description: Table S1, Table S2, and Table S3. Supplementary tables. Gene-set clustering results of the colon cancer, type II diabetes, and AMLÂ examples using three different distance measures.Â (XLSX 139â kb)
DOI: 10.6084/m9.figshare.8105693
title: Additional file 3: of System-level analysis of metabolic trade-offs during anaerobic photoheterotrophic growth in Rhodopseudomonas palustris

description: SBML format of the RP model. (XML 1614 kb)
DOI: 10.6084/m9.figshare.8105693.v1
title: Additional file 3: of System-level analysis of metabolic trade-offs during anaerobic photoheterotrophic growth in Rhodopseudomonas palustris

description: SBML format of the RP model. (XML 1614 kb)
DOI: 10.6084/m9.figshare.8105684
title: Additional file 2: of System-level analysis of metabolic trade-offs during anaerobic photoheterotrophic growth in Rhodopseudomonas palustris

description: RP model and gene knockout results. (XLSX 133 kb)
DOI: 10.6084/m9.figshare.8105684.v1
title: Additional file 2: of System-level analysis of metabolic trade-offs during anaerobic photoheterotrophic growth in Rhodopseudomonas palustris

description: RP model and gene knockout results. (XLSX 133 kb)
DOI: 10.6084/m9.figshare.8105519
title: Additional file 5: of Prognostic relevance of topoisomerase II Îą and minichromosome maintenance protein 6 expression in colorectal cancer

description: Table S2. Coherence of minichromosome maintenance protein 6 IHC expression to clinical and histological criteria. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.8105513
title: Additional file 4: of Prognostic relevance of topoisomerase II Îą and minichromosome maintenance protein 6 expression in colorectal cancer

description: Table S1. Coherence of topoisomerase II alpha IHC expression to clinical and histological criteria. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.8105519.v1
title: Additional file 5: of Prognostic relevance of topoisomerase II Îą and minichromosome maintenance protein 6 expression in colorectal cancer

description: Table S2. Coherence of minichromosome maintenance protein 6 IHC expression to clinical and histological criteria. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.8105513.v1
title: Additional file 4: of Prognostic relevance of topoisomerase II Îą and minichromosome maintenance protein 6 expression in colorectal cancer

description: Table S1. Coherence of topoisomerase II alpha IHC expression to clinical and histological criteria. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.8105441
title: Additional file 5: of Integrated omics-based pathway analyses uncover CYP epoxygenase-associated networks as theranostic targets for metastatic triple negative breast cancer

description: Quantitative proteomic data of eight paired TNBC tumors and adjacent normal tissues using iTRAQ. (XLS 3510 kb)
DOI: 10.6084/m9.figshare.8105435
title: Additional file 1: of Within-sample co-methylation patterns in normal tissues

description: All R scripts for the analysis of this paper. (ZIP 20 kb)