cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.714098.v1
title: Brain networks in bipolar disorder II: a resting-state fMRI study

description: Bipolar disorder II (BD-II) is characterized by hypomanic and depressive episodes, accompanied by mild cognitive deficits, which can be postulated to be due to emotional and cognitive dyscontrol, with attention as the binding factor. Structural and functional magnetic resonance imaging (fMRI) have implicated several brain regions across the BD spectrum, including the prefrontal cortex (PFC), cingulate cortex and amygdala. Newer studies also look at whole brain networks using resting-state fMRI (RS-fMRI). A notable RS network is the default-mode network (DMN), typically activated at rest and associated with mind wandering. The aim of the current study was to characterize functional brain networks specifically in BD-II patients (n = 32) by assessing of within and between network connectivity against healthy controls (n = 35) through RS-fMRI (age 18-50). We also assessed the subjects on working memory measures using the RAVLT and BVMT-R. Independent component analysis and dual regression was used for within-network analysis, and FSLNets was used for between-network connectivity and network modeling. Based on earlier findings, we predicted aberrant connectivity within the DMN, increased connectivity within the anterior cingulate cortex, decreased connectivity between the ventrolateral PFC and amygdala, and decreased connectivity between the posterior cingulate cortex and DMN. We also expected visual networks to display increased connectivity to the amygdala. Decreased test performance was observed on the BVMT-R, and decreased delayed recall on the RAVLT. We found no statistically significant changes in connectivity within or between networks, indicating that brain networks in BD-II are not significantly different from healthy individuals.
DOI: 10.6084/m9.figshare.713940.v1
title: 1654 targets ranked by compounds

description: This is the supplimentary data from the paper below. It can be used to intersect with other target protein lists you care to compare with via standard identifiers (we would be grateful if you cite the results) J Cheminform. 2011 May 13;3(1):14. doi: 10.1186/1758-2946-3-14.<br>Analysis of in vitro bioactivity data extracted from drug discovery literature and patents: Ranking 1654 human protein targets by assayed compounds and molecular scaffolds. Southan C, Boppana K, Jagarlapudi SA, Muresan S. BACKGROUND: Since the classic Hopkins and Groom druggable genome review in 2002, there have been a number of publications updating both the hypothetical and successful human drug target statistics. However, listings of research targets that define the area between these two extremes are sparse because of the challenges of collating published information at the necessary scale. We have addressed this by interrogating databases, populated by expert curation, of bioactivity data extracted from patents and journal papers over the last 30 years. RESULTS: From a subset of just over 27,000 documents we have extracted a set of compound-to-target relationships for biochemical in vitro binding-type assay data for 1,736 human proteins and 1,654 gene identifiers. These are linked to 1,671,951 compound records derived from 823,179 unique chemical structures. The distribution showed a compounds-per-target average of 964 with a maximum of 42,869 (Factor Xa). The list includes non-targets, failed targets and cross-screening targets. The top-278 most actively pursued targets cover 90% of the compounds. We further investigated target ranking by determining the number of molecular frameworks and scaffolds. These were compared to the compound counts as alternative measures of chemical diversity on a per-target basis. CONCLUSIONS: The compounds-per-protein listing generated in this work (provided as a supplementary file) represents the major proportion of the human drug target landscape defined by published data. We supplemented the simple ranking by the number of compounds assayed with additional rankings by molecular topology. These showed significant differences and provide complementary assessments of chemical tractability.
DOI: 10.6084/m9.figshare.713233
title: Bennett et al. 2012

description: Data, Tables and Figures for Bennett, GM, Pantoja, NA, and O’Grady, PM 2012. Diversity and phylogenetic relationships of Wolbachia in Drosophila and other native Hawaiian insects. Fly 6(4): 273-283.
DOI: 10.6084/m9.figshare.712620
title: OGrady et al. 2002b

description: Figures for O’Grady, PM, Vela, D, and Rafael, V. 2002. Zygothrica desallei: A new species of Drosophilidae (Diptera) from Ecuador. Annals of the Entomological Society of America 31(3): 314-315.
DOI: 10.6084/m9.figshare.713289
title: posters

description: This fileset is intended to be a collection of my posters so it is easier for me to find them.
DOI: 10.6084/m9.figshare.713289.v1
title: posters

description: This fileset is intended to be a collection of my posters so it is easier for me to find them.
DOI: 10.6084/m9.figshare.712601
title: OGrady 2002a

description: Figures for O'Grady, PM. 2002. Notes on the nomenclature of the endemic Hawaiian Drosophilidae. Bishop Museum Occasional Papers 65: 36-40.
DOI: 10.6084/m9.figshare.712612
title: OGrady and Kidwell 2002

description: Data, Tables and Figures for O’Grady, PM, and Kidwell, MG. 2002. Phylogeny of the subgenus <em>Sophophora (Diptera: Drosophilidae) inferred using the 28S, alcohol dehydrogenase, and cytochrome oxidase II genes. Molecular Phylogenetics and Evolution: 22(3): 442-453.</em>
DOI: 10.6084/m9.figshare.712618
title: OGrady et al. 2002a

description: Data, Tables and Figures for O'Grady, PM, Durando, CM, Heed, WB, Wasserman, M, Etges, W, and DeSalle, R. 2002. Genetic divergence within the <em>Drosophila mayaguanasubcluster, a closely related triad of Caribbean species in the repleta species group. Hereditas: 136(3): 240-226.</em>
DOI: 10.6084/m9.figshare.712620.v1
title: OGrady et al. 2002b

description: Figures for O’Grady, PM, Vela, D, and Rafael, V. 2002. Zygothrica desallei: A new species of Drosophilidae (Diptera) from Ecuador. Annals of the Entomological Society of America 31(3): 314-315.
DOI: 10.6084/m9.figshare.712601.v1
title: OGrady 2002a

description: Figures for O'Grady, PM. 2002. Notes on the nomenclature of the endemic Hawaiian Drosophilidae. Bishop Museum Occasional Papers 65: 36-40.
DOI: 10.6084/m9.figshare.712618.v1
title: OGrady et al. 2002

description: Data, Tables and Figures for O'Grady, PM, Durando, CM, Heed, WB, Wasserman, M, Etges, W, and DeSalle, R. 2002. Genetic divergence within the <em>Drosophila mayaguanasubcluster, a closely related triad of Caribbean species in the repleta species group. Hereditas: 136(3): 240-226.</em>
DOI: 10.6084/m9.figshare.712618.v2
title: OGrady et al. 2002a

description: Data, Tables and Figures for O'Grady, PM, Durando, CM, Heed, WB, Wasserman, M, Etges, W, and DeSalle, R. 2002. Genetic divergence within the <em>Drosophila mayaguanasubcluster, a closely related triad of Caribbean species in the repleta species group. Hereditas: 136(3): 240-226.</em>
DOI: 10.6084/m9.figshare.712592
title: OGrady and Markow 2012

description: O’Grady, PM and Markow, TA 2012. Rapid morphological, behavioral, and ecological evolution in Drosophila: Comparisons between the endemic Hawaiian Drosophila and the cactophilic repleta species group. In Rapidly Evolving Genes and Genetic Systems (RS Singh, J Xu and RJ Kulanthial, eds). Oxford University Press.
DOI: 10.6084/m9.figshare.712612.v2
title: OGrady and Kidwell 2002

description: Data, Tables and Figures for O’Grady, PM, and Kidwell, MG. 2002. Phylogeny of the subgenus <em>Sophophora (Diptera: Drosophilidae) inferred using the 28S, alcohol dehydrogenase, and cytochrome oxidase II genes. Molecular Phylogenetics and Evolution: 22(3): 442-453.</em>
DOI: 10.6084/m9.figshare.712592.v1
title: OGrady and Markow 2012

description: O’Grady, PM and Markow, TA 2012. Rapid morphological, behavioral, and ecological evolution in Drosophila: Comparisons between the endemic Hawaiian Drosophila and the cactophilic repleta species group. In Rapidly Evolving Genes and Genetic Systems (RS Singh, J Xu and RJ Kulanthial, eds). Oxford University Press.
DOI: 10.6084/m9.figshare.712612.v1
title: OGrady and Kidwell

description: Data, Tables and Figures for O’Grady, PM, and Kidwell, MG. 2002. Phylogeny of the subgenus <em>Sophophora (Diptera: Drosophilidae) inferred using the 28S, alcohol dehydrogenase, and cytochrome oxidase II genes. Molecular Phylogenetics and Evolution: 22(3): 442-453.</em>
DOI: 10.6084/m9.figshare.712582
title: OGrady et al. 2001

description: Figure for O’Grady, PM,Val, FC, Hardy, DE, and Kaneshiro, KY. 2001. The rustica species group of Hawaiian Drosophila (Diptera: Drosophilidae). Pan-Pacific Entomologist 77(4): 254-260.
DOI: 10.6084/m9.figshare.712586
title: CAP Cardiac MICCAI 2013 - Individual Images

description: This is the 3D version of the 4D CAP input data. Each individual has an average template and a corresponding segmentation.
DOI: 10.6084/m9.figshare.712587
title: Plasmodium 3D7 Genome Assembly With PacBio Data and CLEAR

description: This fileset contains data, code and IPython Notebooks demostrating<br>how to assemble the hard to assemble 80% AT-rich Plasmodium 3D7 genome. The first thing you might want to do is probably to read through<br>''P3D7_CLEAR_NOTE.pdf'' to know what this dataset is about. You will have to "gunzip" the two main data file ''preads.fa.gz'' and<br>''pr_pr_strigent.m4.gz'' to use them. The IPython Notebook ''P3D7_CLEAR_NOTE.ipynb'' and ''P3D7_CLEAR_NOTE_P2.ipynb''<br>can be run to generate the assembly if you have proper computation environment. There are also the PDF verison of the notebooks, ''P3D7_CLEAR_NOTE.pdf''<br>and ''P3D7_CLEAR_NOTE_P2.pdf''. Some requirement on how to reproduce the<br>computational experiment can be found in ''P3D7_CLEAR_NOTE.pdf''. Thanks Carsten Russ (Broad Institute) and Sarah Volkmann (Harvard School of Public Health) for providing the DNA sample.
DOI: 10.6084/m9.figshare.712571
title: Etges et al. 2001

description: Figures for Etges, WJ, Armella, MA, O'Grady, PM, and Heed, WB. 2001. Two new species of Drosophila (Diptera; Drosophilidae) in the repleta group from Mexico. Annals of the Entomological Society of America94(1): 16-20.
DOI: 10.6084/m9.figshare.712582.v1
title: OGrady et al. 2001

description: Figure for O’Grady, PM,Val, FC, Hardy, DE, and Kaneshiro, KY. 2001. The rustica species group of Hawaiian Drosophila (Diptera: Drosophilidae). Pan-Pacific Entomologist 77(4): 254-260.
DOI: 10.6084/m9.figshare.712571.v1
title: Etges et al. 2001

description: Figures for Etges, WJ, Armella, MA, O'Grady, PM, and Heed, WB. 2001. Two new species of Drosophila (Diptera; Drosophilidae) in the repleta group from Mexico. Annals of the Entomological Society of America94(1): 16-20.
DOI: 10.6084/m9.figshare.712586.v1
title: CAP Cardiac MICCAI 2013 - Individual Images

description: This is the 3D version of the 4D CAP input data. Each individual has an average template and a corresponding segmentation.
DOI: 10.6084/m9.figshare.712588.v1
title: Spectroscopic measurements of EUV ejecta emission in a CME: a high-blueshift trailing thread

description: The mass of erupting prominence material can be inferred from the obscuration of emission behind this mass of cool plasma thanks to the rapid cadence of SDO/AIA images in the short EUV wavelength range (Poster #9, by Carlyle et al.). In comparing this approach with spectral observations from Hinode/EIS, to monitor contributions from emission seen around the erupting prominence material, we have found an intriguing component of blue-shifted emission, trailing the erupting prominence, with Doppler shifts of order ~350 km s-1 in both He II and Fe XII bright lines. This emission indicates (1) that plasma heating is taking place in the wake of the prominence, and (2) that this plasma is moving at supersonic velocities. This poster was presented at IAU Symposium 300 in Paris in June 2013.
DOI: 10.6084/m9.figshare.712587.v1
title: Plasmodium 3D7 Genome Assembly With PacBio Data and CLEAR

description: This fileset contains data, code and IPython Notebooks demostrating<br>how to assemble the hard to assemble 80% AT-rich Plasmodium 3D7 genome. The first thing you might want to do is probably to read through<br>''P3D7_CLEAR_NOTE.pdf'' to know what this dataset is about. You will have to "gunzip" the two main data file ''preads.fa.gz'' and<br>''pr_pr_strigent.m4.gz'' to use them. The IPython Notebook ''P3D7_CLEAR_NOTE.ipynb'' and ''P3D7_CLEAR_NOTE_P2.ipynb''<br>can be run to generate the assembly if you have proper computation environment. There are also the PDF verison of the notebooks, ''P3D7_CLEAR_NOTE.pdf''<br>and ''P3D7_CLEAR_NOTE_P2.pdf''. Some requirement on how to reproduce the<br>computational experiment can be found in ''P3D7_CLEAR_NOTE.pdf''.
DOI: 10.6084/m9.figshare.712512
title: 1936-1940 OK Counties General Highway Maps GEOREF

description: This zip file includes a georeferenced (Projected &gt; UTM &gt; NAD 1927 &gt; Zone 14 North) set of Oklahoma Counties General Highway and Transportation Maps. The maps range in date from 1936 to 1940. 76 of the 77 Oklahoma counties are represented; this set is missing a LeFlore County map.
DOI: 10.6084/m9.figshare.712487
title: Raw data of ETHZ Provenance Challenge 2012

description: Raw data in ALPS HDF5 format needed to reproduce the figures in the ETHZ Provenance Challenge 2012 paper. Data for different temperatures around the critical point.
DOI: 10.6084/m9.figshare.712587.v2
title: Plasmodium 3D7 Genome Assembly With PacBio Data and CLEAR

description: This fileset contains data, code and IPython Notebooks demostrating<br>how to assemble the hard to assemble 80% AT-rich Plasmodium 3D7 genome. The first thing you might want to do is probably to read through<br>''P3D7_CLEAR_NOTE.pdf'' to know what this dataset is about. You will have to "gunzip" the two main data file ''preads.fa.gz'' and<br>''pr_pr_strigent.m4.gz'' to use them. The IPython Notebook ''P3D7_CLEAR_NOTE.ipynb'' and ''P3D7_CLEAR_NOTE_P2.ipynb''<br>can be run to generate the assembly if you have proper computation environment. There are also the PDF verison of the notebooks, ''P3D7_CLEAR_NOTE.pdf''<br>and ''P3D7_CLEAR_NOTE_P2.pdf''. Some requirement on how to reproduce the<br>computational experiment can be found in ''P3D7_CLEAR_NOTE.pdf''.
DOI: 10.6084/m9.figshare.712588.v2
title: Poster: Spectroscopic measurements of EUV ejecta emission in a CME: a high-blueshift trailing thread

description: The mass of erupting prominence material can be inferred from the obscuration of emission behind this mass of cool plasma thanks to the rapid cadence of SDO/AIA images in the short EUV wavelength range (Poster #9, by Carlyle et al.). In comparing this approach with spectral observations from Hinode/EIS, to monitor contributions from emission seen around the erupting prominence material, we have found an intriguing component of blue-shifted emission, trailing the erupting prominence, with Doppler shifts of order ~350 km s-1 in both He II and Fe XII bright lines. This emission indicates (1) that plasma heating is taking place in the wake of the prominence, and (2) that this plasma is moving at supersonic velocities. This poster was presented at IAU Symposium 300 in Paris in June 2013.
DOI: 10.6084/m9.figshare.712487.v1
title: Raw data of ETHZ Provenance Challenge 2012

description: Raw data in ALPS HDF5 format needed to reproduce the figures in the ETHZ Provenance Challenge 2012 paper. Data for different temperatures around the critical point.
DOI: 10.6084/m9.figshare.712275
title: Heed and OGrady 2000

description: Figures associated with Heed and O'Grady 2000.
DOI: 10.6084/m9.figshare.712277
title: OGrady and DeSalle 2000

description: Figure 1. Showing variation in wing maculations on the phylogeny of the Hawaiian Drosophilidae.
DOI: 10.6084/m9.figshare.712277.v1
title: OGrady and DeSalle 2000

description: Figure 1. Showing variation in wing maculations on the phylogeny of the Hawaiian Drosophilidae.
DOI: 10.6084/m9.figshare.712588.v3
title: Poster: Spectroscopic measurements of EUV ejecta emission in a CME: a high-blueshift trailing thread

description: Pending publication.
DOI: 10.6084/m9.figshare.712272
title: PSU First Thursday Talk June 2013 - CT Modelling

description: Various forms of slides for a talk at Portland State University, June 6, 2013
DOI: 10.6084/m9.figshare.712512.v1
title: 1936-1940 OK Counties General Highway Maps

description: This zip file includes a georeferenced (Projected &gt; UTM &gt; NAD 1927 &gt; Zone 14 North) set of Oklahoma Counties General Highway and Transportation Maps. The maps range in date from 1890 to 1916. 76 of the 77 Oklahoma counties are represented; this set is missing a LeFlore County map.
DOI: 10.6084/m9.figshare.712587.v3
title: Plasmodium 3D7 Genome Assembly With PacBio Data and CLEAR

description: This fileset contains data, code and IPython Notebooks demostrating<br>how to assemble the hard to assemble 80% AT-rich Plasmodium 3D7 genome. The first thing you might want to do is probably to read through<br>''P3D7_CLEAR_NOTE.pdf'' to know what this dataset is about. You will have to "gunzip" the two main data file ''preads.fa.gz'' and<br>''pr_pr_strigent.m4.gz'' to use them. The IPython Notebook ''P3D7_CLEAR_NOTE.ipynb'' and ''P3D7_CLEAR_NOTE_P2.ipynb''<br>can be run to generate the assembly if you have proper computation environment. There are also the PDF verison of the notebooks, ''P3D7_CLEAR_NOTE.pdf''<br>and ''P3D7_CLEAR_NOTE_P2.pdf''. Some requirement on how to reproduce the<br>computational experiment can be found in ''P3D7_CLEAR_NOTE.pdf''.
DOI: 10.6084/m9.figshare.711835
title: OGrady et al. 1998

description: This set contains all data, tables and figures in: Phylogeny of the Drosophila saltans species group based on combined analysis of nuclear and mitochondrial DNA sequences. Nexus files of all novel sequences generated in this study are included. Individual sequence files were downloaded from NCBI and aligned in Geneious.
DOI: 10.6084/m9.figshare.712264
title: OGrady 1999

description: Data, Tables and Figures from Reevaluation of Phylogeny in the Drosophila obscura Species Group Based on Combined Analysis of Nucleotide Sequences
DOI: 10.6084/m9.figshare.712272.v1
title: PSU First Thursday Talk June 2013 - CT Modelling

description: Various forms of slides for a talk at Portland State University, June 6, 2013
DOI: 10.6084/m9.figshare.712275.v2
title: Heed and OGrady 2000

description: Figures associated with Heed and O'Grady 2000.
DOI: 10.6084/m9.figshare.711798
title: Hospital Air 16S Sequences

description: Bacterial 16S sequence data collected from air in a hospital in Oregon Data collection procedures are described in the paper "Architectural design influences the diversity and structure of the built environment microbiome" by Kembel et al. (2012, ISME Journal). http://www.nature.com/ismej/journal/v6/n8/abs/ismej2011211a.html <strong>File list</strong> run1.sff.zip and run2.sff.zip - raw 454 sequencing data from two runs in SFF format air454.fastq.zip - sequences from both runs in FASTQ format air454_barcodes.txt - barcode sequences identifying samples
DOI: 10.6084/m9.figshare.711798.v1
title: Hospital Air 16S Sequences

description: Bacterial 16S sequence data collected from air in a hospital in Oregon Data collection procedures are described in the paper "Architectural design influences the diversity and structure of the built environment microbiome" by Kembel et al. (2012, ISME Journal). http://www.nature.com/ismej/journal/v6/n8/abs/ismej2011211a.html <strong>File list</strong> run1.sff.zip and run2.sff.zip - raw 454 sequencing data from two runs in SFF format air454.fastq.zip - sequences from both runs in FASTQ format air454_barcodes.txt - barcode sequences identifying samples
DOI: 10.6084/m9.figshare.712275.v1
title: Heed and OGrady 2000 Journal of the New York Entomological Society 108(1-2): 97-104

description: Figures associated with Heed and O'Grady 2000.
DOI: 10.6084/m9.figshare.712587.v4
title: Plasmodium 3D7 Genome Assembly With PacBio Data and CLEAR

description: This fileset contains data, code and IPython Notebooks demostrating<br>how to assemble the hard to assemble 80% AT-rich Plasmodium 3D7 genome. The first thing you might want to do is probably to read through<br>''P3D7_CLEAR_NOTE.pdf'' to know what this dataset is about. You will have to "gunzip" the two main data file ''preads.fa.gz'' and<br>''pr_pr_strigent.m4.gz'' to use them. The IPython Notebook ''P3D7_CLEAR_NOTE.ipynb'' and ''P3D7_CLEAR_NOTE_P2.ipynb''<br>can be run to generate the assembly if you have proper computation environment. There are also the PDF verison of the notebooks, ''P3D7_CLEAR_NOTE.pdf''<br>and ''P3D7_CLEAR_NOTE_P2.pdf''. Some requirement on how to reproduce the<br>computational experiment can be found in ''P3D7_CLEAR_NOTE.pdf''.
DOI: 10.6084/m9.figshare.711785
title: Design-oriented research methods

description: This diagram shows the connections between design-oriented research methods. Read more on my blog about how to publish design-based research (see link below). <strong>References</strong> Anderson, T., & Shattuck, J. (2012). Design-based research: A decade of progress in education research? Educational Researcher, 41(1), 16–25. doi:10.3102/0013189X11428813 Brown, A. L. (1992). Design experiments: Theoretical and methodological challenges in creating complex interventions. Journal of the Learning Sciences, 2(2), 141–178. doi:10.1207/s15327809jls0202_2 Cole, R., Purao, S., Rossi, M., & Sein, M. (2005). Being proactive: Where action research meets design research. Proceedings of the 26th International Conference on Information Systems (ICIS 2005). Collins, A. (1992). Toward a design science of education. In E. Scanlon & T. O’Shea (Eds.), New directions in educational technology. Berlin: Springer-Verlag. Collins, A., Joseph, D., & Bielaczyc, K. (2004). Design research: Theoretical and methodological Iissues. Journal of the Learning Sciences, 13(1), 15–42. doi:10.1207/s15327809jls1301 The Design-Based Research Collective. (2003). Design-based research: An emerging paradigm for educational inquiry. Educational Researcher, 32(1), 5–8. doi:10.3102/0013189X032001005 Hevner, A. R., March, S. T., Park, J., & Ram, S. (2004). Design science in information systems research. MIS Quarterly, 28(1), 75–105. Iivari, J., & Venable, J. (2009). Action research and design science research: Seemingly similar but decisively dissimilar. 17th European Conference on Information Systems (ECIS 2009). March, S. T., & Smith, G. (1995). Design and natural science research on information technology. Decision Support Systems, 15(4), 251-266. doi:10.1016/0167-9236(94)00041-2 Peffers, K., Tuunanen, T., Rothenberger, M., & Chatterjee, S. (2007). A design science research methodology for information systems research. Journal of Management Information Systems, 24(3), 45-77. doi:10.2753/MIS0742-1222240302 Schön, D. A. (1983). The reflective practitioner: How professionals think in action. Basic Books. Sein, M. K., Henfridsson, O., Purao, S., Rossi, M., & Lindgren, R. (2011). Action design research. MIS Quarterly, 35(1), 37–56. Simon, H. A. (1969). The Sciences of the Artificial. Cambridge, MA: MIT Press.
DOI: 10.6084/m9.figshare.711112
title: Crowd4Discovery striatal primary neuronal culture experiment 2

description: Primary striatal neuronal culture troubleshooting experiment. As described in the C4D Spring update (link below), these cells were stained with a variety of markers to assess autophagy induction as a positive control in response to rapamycin treatment, a known inducer of autophagy. These cells were treated with rapamycin.
DOI: 10.6084/m9.figshare.712264.v2
title: OGrady 1999

description: Data, Tables and Figures from Reevaluation of Phylogeny in the Drosophila obscura Species Group Based on Combined Analysis of Nucleotide Sequences