cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.2009025.v1
title: Edwards Aquifer data/regression analysis

description: The tables data were used to comparatively plot regressions between two factors affecting the Edwards Aquifer. Through these plots it can be observed which factors like well discharge and J-17 well levels can correlate with one another. The higher the R^2 value, the better and closer the fit is for the correlation between corresponding factors.
DOI: 10.6084/m9.figshare.2008977
title: Kinect controlled dinosaur simulations for education and public outreach

description: Dinosaurs are a source of enormous public interest and as such are useful for fostering greater interest in basic science and technology. With the increasing popularity of dinosaur films that claim to portray realistic dinosaur behaviour, one question that is regularly posed for palaeontologists to answer is how we know that our reconstructions are accurate. Dinosaur locomotion is no exception to this line of questioning and one technique for estimating how dinosaurs may have moved is multibody dynamic simulation (MBDA) of high biofidelity musculoskeletal computer models. Such simulations uses Newton's Law's of Motion to calculate how the different parts of the animals body would have moved depending on the internal forces generated by the muscles and the external forces due to gravity and physical contact with the ground. In this project we designed a system that allowed the user to directly control the muscles forces generated using a Kinect for Xbox One sensor attached to a PC using the Kinect Adaptor for Windows. The Kinect output is used to drive the muscles using customised software and models (<i>Tyrannosaurus</i>, <i>Triceratops</i>, <i>Brachiosaurus</i>, <i>Edmontonia</i>, <i>Edmontosaurus</i>, <i>Gorgosaurus</i>) based on our standard GaitSym MBDA system. The initial system was trialled over 7 days at the 2015 Cheltenham Science Festival which showed that the bipedal models were relatively easy to control using human body movements and provided a good vehicle to explain how the physics and physiology behind dinsoaur locomotor reconstruction. The quadrupedal models in their current form are much more difficult to control and further work is needed in this area. The 3D models and software for this project are freely available to download (http://www.animalsimulation.org) and it is hoped that they will find further uses in areas such as 3D printing for anatomical education and virtual world simulations.
DOI: 10.6084/m9.figshare.2008995
title: PowerPoint Presentation and Excel Graphs Used in Twinery

description: Final PowerPoint presentation and excel graphs used in Twinery model
DOI: 10.6084/m9.figshare.2008944
title: Edwards Aquifer data/regression analysis

description: The tables data were used to comparatively plot regressions between two factors affecting the Edwards Aquifer. Through these plots it can be observed which factors like well discharge and J-17 well levels can correlate with one another. The higher the R^2 value, the better and closer the fit is for the correlation between corresponding factors.
DOI: 10.6084/m9.figshare.2008938
title: Edward's Aquifer Case Study

description: PowerPoint presentation on the Edward's Aquifer case study and models.
DOI: 10.6084/m9.figshare.2008944.v1
title: Edwards Aquifer data/regression analysis

description: The tables data were used to comparatively plot regressions between two factors affecting the Edwards Aquifer. Through these plots it can be observed which factors like well discharge and J-17 well levels can correlate with one another. The higher the R^2 value, the better and closer the fit is for the correlation between corresponding factors.
DOI: 10.6084/m9.figshare.2008926
title: AZ1.0

description: Background The <em>Azadirachta indica</em> (neem) tree is a source of a wide number of natural products, including the potent biopesticide azadirachtin. In spite of its widespread applications in agriculture and medicine, the molecular aspects of the biosynthesis of neem terpenoids remain largely unexplored. The current report describes the draft genome and four transcriptomes of <em>A. indica</em> and attempts to contextualise the sequence information in terms of its molecular phylogeny, transcript expression and terpenoid biosynthesis pathways. <em>A. indica</em> is the first member of the family <em>Meliaceae</em> to be sequenced using next generation sequencing approach. Results The genome and transcriptomes of <em>A. indica</em> were sequenced using multiple sequencing platforms and libraries. The <em>A. indica</em> genome is AT-rich, bears few repetitive DNA elements and comprises about 20,000 genes. The molecular phylogenetic analyses grouped <em>A. indica</em> together with <em>Citrus sinensis</em> from the <em>Rutaceae</em> family validating its conventional taxonomic classification. Comparative transcript expression analysis showed either exclusive or enhanced expression of known genes involved in neem terpenoid biosynthesis pathways compared to other sequenced angiosperms. Genome and transcriptome analyses in <em>A. indica</em> led to the identification of repeat elements, nucleotide composition and expression profiles of genes in various organs. Conclusions This study on <em>A. indica</em> genome and transcriptomes will provide a model for characterization of metabolic pathways involved in synthesis of bioactive compounds, comparative evolutionary studies among various <em>Meliaceae</em> family members and help annotate their genomes. A better understanding of molecular pathways involved in the azadirachtin synthesis in <em>A. indica</em> will pave ways for bulk production of environment friendly biopesticides.
DOI: 10.6084/m9.figshare.2008938.v1
title: Edward's Aquifer Case Study

description: PowerPoint presentation on the Edward's Aquifer case study and models.
DOI: 10.6084/m9.figshare.2008926.v1
title: AZ1.0

description: Background The <em>Azadirachta indica</em> (neem) tree is a source of a wide number of natural products, including the potent biopesticide azadirachtin. In spite of its widespread applications in agriculture and medicine, the molecular aspects of the biosynthesis of neem terpenoids remain largely unexplored. The current report describes the draft genome and four transcriptomes of <em>A. indica</em> and attempts to contextualise the sequence information in terms of its molecular phylogeny, transcript expression and terpenoid biosynthesis pathways. <em>A. indica</em> is the first member of the family <em>Meliaceae</em> to be sequenced using next generation sequencing approach. Results The genome and transcriptomes of <em>A. indica</em> were sequenced using multiple sequencing platforms and libraries. The <em>A. indica</em> genome is AT-rich, bears few repetitive DNA elements and comprises about 20,000 genes. The molecular phylogenetic analyses grouped <em>A. indica</em> together with <em>Citrus sinensis</em> from the <em>Rutaceae</em> family validating its conventional taxonomic classification. Comparative transcript expression analysis showed either exclusive or enhanced expression of known genes involved in neem terpenoid biosynthesis pathways compared to other sequenced angiosperms. Genome and transcriptome analyses in <em>A. indica</em> led to the identification of repeat elements, nucleotide composition and expression profiles of genes in various organs. Conclusions This study on <em>A. indica</em> genome and transcriptomes will provide a model for characterization of metabolic pathways involved in synthesis of bioactive compounds, comparative evolutionary studies among various <em>Meliaceae</em> family members and help annotate their genomes. A better understanding of molecular pathways involved in the azadirachtin synthesis in <em>A. indica</em> will pave ways for bulk production of environment friendly biopesticides.
DOI: 10.6084/m9.figshare.2008923
title: COPS

description: Copy Number Alterations (CNAs) such as deletions and duplications; compose a larger percentage of genetic variations than single nucleotide polymorphisms or other structural variations in cancer genomes that undergo major chromosomal re-arrangements. It is, therefore, imperative to identify cancer-specific somatic copy number alterations (SCNAs), with respect to matched normal tissue, in order to understand their association with the disease. We have devised an accurate, sensitive, and easy-to-use tool, COPS, COpy number using Paired Samples, for detecting SCNAs. We rigorously tested the performance of COPS using short sequence simulated reads at various sizes and coverage of SCNAs, read depths, read lengths and also with real tumor:normal paired samples. We found COPS to perform better in comparison to other known SCNA detection tools for all evaluated parameters, namely, sensitivity (detection of true positives), specificity (detection of false positives) and size accuracy. COPS performed well for sequencing reads of all lengths when used with most upstream read alignment tools. Additionally, by incorporating a downstream boundary segmentation detection tool, the accuracy of SCNA boundaries was further improved. Here, we report an accurate, sensitive and easy to use tool in detecting cancer-specific SCNAs using short-read sequence data. In addition to cancer, COPS can be used for any disease as long as sequence reads from both disease and normal samples from the same individual are available. An added boundary segmentation detection module makes COPS detected SCNA boundaries more specific for the samples studied. COPS is available at ftp://115.119.160.213 with username “cops” and password “cops”.
DOI: 10.6084/m9.figshare.2008908
title: AugmentingAssembly

description: Researchers interested in studying and constructing transcriptomes, especially for non-model species, face the conundrum of choosing from a number of available <i>de novo</i> and genome-guided assemblers. None of the popular assembly tools in use today achieve requisite sensitivity, specificity or recovery of full-length transcripts on their own. Here, we present a comprehensive comparative study of the performance of various assemblers. Additionally, we present an approach to combinatorially augment transciptome assembly by using both <i>de novo</i> and genome-guided tools. In our study, we obtained the best recovery and most full-length transcripts with Trinity and TopHat1-Cufflinks, respectively. The sensitivity of the assembly and isoform recovery was superior, without compromising much on the specificity, when transcripts from Trinity were augmented with those from TopHat1-Cufflinks.
DOI: 10.6084/m9.figshare.2008923.v1
title: COPS

description: Copy Number Alterations (CNAs) such as deletions and duplications; compose a larger percentage of genetic variations than single nucleotide polymorphisms or other structural variations in cancer genomes that undergo major chromosomal re-arrangements. It is, therefore, imperative to identify cancer-specific somatic copy number alterations (SCNAs), with respect to matched normal tissue, in order to understand their association with the disease. We have devised an accurate, sensitive, and easy-to-use tool, COPS, COpy number using Paired Samples, for detecting SCNAs. We rigorously tested the performance of COPS using short sequence simulated reads at various sizes and coverage of SCNAs, read depths, read lengths and also with real tumor:normal paired samples. We found COPS to perform better in comparison to other known SCNA detection tools for all evaluated parameters, namely, sensitivity (detection of true positives), specificity (detection of false positives) and size accuracy. COPS performed well for sequencing reads of all lengths when used with most upstream read alignment tools. Additionally, by incorporating a downstream boundary segmentation detection tool, the accuracy of SCNA boundaries was further improved. Here, we report an accurate, sensitive and easy to use tool in detecting cancer-specific SCNAs using short-read sequence data. In addition to cancer, COPS can be used for any disease as long as sequence reads from both disease and normal samples from the same individual are available. An added boundary segmentation detection module makes COPS detected SCNA boundaries more specific for the samples studied. COPS is available at ftp://115.119.160.213 with username “cops” and password “cops”.
DOI: 10.6084/m9.figshare.2008908.v1
title: AugmentingAssembly

description: Researchers interested in studying and constructing transcriptomes, especially for non-model species, face the conundrum of choosing from a number of available <i>de novo</i> and genome-guided assemblers. None of the popular assembly tools in use today achieve requisite sensitivity, specificity or recovery of full-length transcripts on their own. Here, we present a comprehensive comparative study of the performance of various assemblers. Additionally, we present an approach to combinatorially augment transciptome assembly by using both <i>de novo</i> and genome-guided tools. In our study, we obtained the best recovery and most full-length transcripts with Trinity and TopHat1-Cufflinks, respectively. The sensitivity of the assembly and isoform recovery was superior, without compromising much on the specificity, when transcripts from Trinity were augmented with those from TopHat1-Cufflinks.
DOI: 10.6084/m9.figshare.2008857
title: Mental Modeler files

description: These iterations of a concept map surrounding the idea of being sustainable with the Edwards Aquifer. The less specific mental modeler concept map is the final product showing how the most positive and negative factors can relate to one another in affecting the aquifer itself. This allowed the understanding of how to interrelate these factors on the respective programs of Insight Maker, Matlab, and Twine in creating our models.
DOI: 10.6084/m9.figshare.2008902
title: AZ2.0

description: Neem (Azadirachta indica A. Juss.), an evergreen tree of the Meliaceae family, is known for its<br>medicinal, cosmetic, pesticidal and insecticidal properties. We had previously sequenced and <br>published the draft genome of the plant, using mainly short read sequencing data. In this report, we <br>present an improved genome assembly generated using additional short reads from Illumina and <br>long reads from Pacific Biosciences SMRT sequencer. We assembled short reads and error-<br>corrected long reads using Platanus, an assembler designed to perform well for heterozygous <br>genomes. The updated genome assembly (v2.0) yielded 3- and 3.5-fold increase in N50 and N75, <br>respectively; 2.6-fold decrease in the total number of scaffolds; 1.25-fold increase in the number of <br>valid transcriptome alignments; 13.4-fold less mis-assembly and 1.85-fold increase in the <br>percentage repeat, resulted due to removal of mis-assembly and closure of gaps fromover the earlier <br>assembly (v1.0). The current assembly also maps better to the genes known to be involved in the <br>terpenoid biosynthesis pathway. Together, the data represents an improved assembly of the A. <br>indica genome.<br><br>The raw data described in this manuscript are submitted to the NCBI Short Read Archive under <br>the accession numbers SRX1074131, SRX1074132, SRX1074133, and SRX1074134 , under <br>(SRP013453).
DOI: 10.6084/m9.figshare.2008839
title: Twine Pictures

description: aaaa
DOI: 10.6084/m9.figshare.2008857.v1
title: Mental Modeler files

description: These iterations of a concept map surrounding the idea of being sustainable with the Edwards Aquifer. The less specific mental modeler concept map is the final product showing how the most positive and negative factors can relate to one another in affecting the aquifer itself. This allowed the understanding of how to interrelate these factors on the respective programs of Insight Maker, Matlab, and Twine in creating our models.
DOI: 10.6084/m9.figshare.2008788
title: Code File 1.pdf

description: The electrical permittivity and magnetic permeability coefficients of 109 compounds used in the present investigation as different layers.
DOI: 10.6084/m9.figshare.2008902.v2
title: AZ2.0

description: Neem (Azadirachta indica A. Juss.), an evergreen tree of the Meliaceae family, is known for its<br>medicinal, cosmetic, pesticidal and insecticidal properties. We had previously sequenced and <br>published the draft genome of the plant, using mainly short read sequencing data. In this report, we <br>present an improved genome assembly generated using additional short reads from Illumina and <br>long reads from Pacific Biosciences SMRT sequencer. We assembled short reads and error-<br>corrected long reads using Platanus, an assembler designed to perform well for heterozygous <br>genomes. The updated genome assembly (v2.0) yielded 3- and 3.5-fold increase in N50 and N75, <br>respectively; 2.6-fold decrease in the total number of scaffolds; 1.25-fold increase in the number of <br>valid transcriptome alignments; 13.4-fold less mis-assembly and 1.85-fold increase in the <br>percentage repeat, resulted due to removal of mis-assembly and closure of gaps fromover the earlier <br>assembly (v1.0). The current assembly also maps better to the genes known to be involved in the <br>terpenoid biosynthesis pathway. Together, the data represents an improved assembly of the A. <br>indica genome.<br><br>The raw data described in this manuscript are submitted to the NCBI Short Read Archive under <br>the accession numbers SRX1074131, SRX1074132, SRX1074133, and SRX1074134 , under <br>(SRP013453).
DOI: 10.6084/m9.figshare.2008767
title: Dataset 'Fixed muscle synergies and their potential to improve the intuitive control of myoelectric assistive technology for upper extremities.'

description: Data set on which conclusions of Valk et al. (2019): 'Fixed muscle synergies and their potential to improve the intuitive control of myoelectric assistive technology for upper extremities.' are based.
DOI: 10.6084/m9.figshare.2008788.v1
title: Code File 1.pdf

description: The electrical permittivity and magnetic permeability coefficients of 109 compounds used in the present investigation as different layers.
DOI: 10.6084/m9.figshare.2008839.v3
title: Twine Pictures

description: aaaa
DOI: 10.6084/m9.figshare.2008902.v1
title: AZ2.0

description: Neem (Azadirachta indica A. Juss.), an evergreen tree of the Meliaceae family, is known for its<br>medicinal, cosmetic, pesticidal and insecticidal properties. We had previously sequenced and <br>published the draft genome of the plant, using mainly short read sequencing data. In this report, we <br>present an improved genome assembly generated using additional short reads from Illumina and <br>long reads from Pacific Biosciences SMRT sequencer. We assembled short reads and error-<br>corrected long reads using Platanus, an assembler designed to perform well for heterozygous <br>genomes. The updated genome assembly (v2.0) yielded 3- and 3.5-fold increase in N50 and N75, <br>respectively; 2.6-fold decrease in the total number of scaffolds; 1.25-fold increase in the number of <br>valid transcriptome alignments; 13.4-fold less mis-assembly and 1.85-fold increase in the <br>percentage repeat, resulted due to removal of mis-assembly and closure of gaps fromover the earlier <br>assembly (v1.0). The current assembly also maps better to the genes known to be involved in the <br>terpenoid biosynthesis pathway. Together, the data represents an improved assembly of the A. <br>indica genome.<br><br>The raw data described in this manuscript are submitted to the NCBI Short Read Archive under <br>the accession numbers SRX1074131, SRX1074132, SRX1074133, and SRX1074134 , under <br>(SRP013453).
DOI: 10.6084/m9.figshare.2008734
title: Data from - Contrasting Role of Temperature in Structuring Regional Patterns of Invasive and Native Pestilential Stink Bugs - PLoS ONE 11(2): e0150649. doi:10.1371/journal.pone.0150649

description: This file contains the data used for multi-scale spatial analysis for patterns of stink bug distribution and abundance in the mid-Atlantic United states. Stink bug data were collected from field surveys, and environmental variables were derived from freely available data on topography, climate, and land use factors. Please see the methods section and the supplementary data in the manuscript for the descriptions of the environmental variables. <br>
DOI: 10.6084/m9.figshare.2008758
title: Survival

description: p { margin-bottom: 0.25cm; direction: ltr; line-height: 120%; text-align: left; }a:link { } Oral tongue squamous cell carcinomas (OTSCC) are a homogenous group of head and neck tumors characterized with aggressive behavior among younger age group of patients. In this report, we have analysed genetic, transcriptomic, and epigenetic variants across genomes of 50 oral tongue primary tumors along with the human papilloma virus infection to find significant association with disease free survival. Our data identified somatic mutations in the genes <i>NOTCH2</i>, <i>TP53</i> and LOH in <i>11p</i>, and DNA methylation in <i>SLC38A8</i> to be significantly associated with better disease free survival in HPV positive patients (<i>P</i> = 0.000175), but not in HPV negative patients (<i>P</i> = 0.974). We validated the latter using patients without HPV infection from TCGA (<i>P</i> = 0.679, N = 15 for TCGA_OralTongue; <i>P</i> = 0.262, N = 43 for all TCGA_HNSCC patients).
DOI: 10.6084/m9.figshare.2008839.v2
title: Twine Pictures

description: These are the figures used in the interface. Two show the 3rd and 5th critical stages of the Edwards Aquifer J17 index well, while another is a map of the Edwards Aquifer. These figures are from the Aquiferium Project headed by Encompass Labs, the Edwards Aquifer Authority, and the University of Texas at Austin. One shows a representative picture of the user as a tomato farmer, while another shows the user as a corn farmer. The former is from NaturalAwakeningsMag.com and the latter is from RestoringMinistry.org.The final picture is of the San Marcos Salamander, created by Seth Patterson at flickR.
DOI: 10.6084/m9.figshare.2008758.v1
title: Survival

description: p { margin-bottom: 0.25cm; direction: ltr; line-height: 120%; text-align: left; }a:link { } Oral tongue squamous cell carcinomas (OTSCC) are a homogenous group of head and neck tumors characterized with aggressive behavior among younger age group of patients. In this report, we have analysed genetic, transcriptomic, and epigenetic variants across genomes of 50 oral tongue primary tumors along with the human papilloma virus infection to find significant association with disease free survival. Our data identified somatic mutations in the genes <i>NOTCH2</i>, <i>TP53</i> and LOH in <i>11p</i>, and DNA methylation in <i>SLC38A8</i> to be significantly associated with better disease free survival in HPV positive patients (<i>P</i> = 0.000175), but not in HPV negative patients (<i>P</i> = 0.974). We validated the latter using patients without HPV infection from TCGA (<i>P</i> = 0.679, N = 15 for TCGA_OralTongue; <i>P</i> = 0.262, N = 43 for all TCGA_HNSCC patients).
DOI: 10.6084/m9.figshare.2008767.v2
title: Dataset 'Fixed muscle synergies and their potential to improve the intuitive control of myoelectric assistive technology for upper extremities.'

description: Data set on which conclusions of Valk et al. (2019): 'Fixed muscle synergies and their potential to improve the intuitive control of myoelectric assistive technology for upper extremities.' are based.
DOI: 10.6084/m9.figshare.2008767.v1
title: Dataset 'Fixed muscle synergies and their potential to improve the intuitive control of myoelectric assistive technology for upper extremities.'

description: Data set on which conclusions of Valk et al., (2018): 'Fixed muscle synergies and their potential to improve the intuitive control of myoelectric assistive technology for upper extremities.' are based.
DOI: 10.6084/m9.figshare.2008722
title: Supporting information MS Gersemiols 2015

description: outputs from Gaussian NMR calculations<br>
DOI: 10.6084/m9.figshare.2008764.v1
title: Data Rod Reaching

description: Joint Angle trajectories, end-effector kinematics and UCM-varaibles