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1,453 results for “Outcome research”
Figure 5 from: Dupont S, Humphries J, Butcher AJ, Baker E, Balcells L, Price BW (2020) Ahead of the curve: three approaches to mass digitisation of vials with a focus on label data capture. Research Ideas and Outcomes 6: e53606. https://doi.org/10.3897/rio.6.e53606
Figure 5 MALICE: Image output of MALICE including original output image (a) and the final processed image (b).
Figure 7 from: Dupont S, Humphries J, Butcher AJ, Baker E, Balcells L, Price BW (2020) Ahead of the curve: three approaches to mass digitisation of vials with a focus on label data capture. Research Ideas and Outcomes 6: e53606. https://doi.org/10.3897/rio.6.e53606
Figure 7 ReVILE: Two Rollout photography outputs of ReVILE. Left to right: a frame from the video (rotated 90° clockwise) showing the vial itself; the uncropped rollout image, covering more than one full rotation; the cropped rollout image, showing only one 360° rotation; the cropped rollout image, "shifted" across (by transferring a manually-defined block of pixel columns from the left side of the image to the right) to show the complete label
Figure 4 from: Prieß-Buchheit J, Aro AR, Demirova I, Lanzerath D, Stoev P, Wilder N (2020) Rotatory role-playing and role-models to enhance the research integrity culture. Research Ideas and Outcomes 6: e53921. https://doi.org/10.3897/rio.6.e53921
Figure 4 Quotes from Pierre Curie (2012) Marie Curie: With Autobiographical Notes by Marie Curie, Dover Publication: Mineola New York, p.70 and Russell, Bertrand (2004) History of Western Philosophy, London, p.864. Figures designed by Freepik from www.flaticon.com.
Figure 1 from: Stefanoudis PV, Talma S, Samimi-Namin K, Woodall LC (2020) Deep reef ecosystems of the Western Indian Ocean: addressing the great unknown. Research Ideas and Outcomes 6: e53913. https://doi.org/10.3897/rio.6.e53913
Figure 1 Top left to centre right: Photographs representing the different training activities that took place during the workshop. Bottom: Group photo of participants.
Figure 1 from: Samuel S, Shadaydeh M, Böcker S, Brügmann B, Bucher SF, Deckert V, Denzler J, Dittrich P, von Eggeling F, Güllmar D, Guntinas-Lichius O, König-Ries B, Löffler F, Maicher L, Marz M, Migliavacca M, R. Reichenbach J, Reichstein M, Römermann C, Wittig A (2020) A virtual "Werkstatt" for digitization in the sciences. Research Ideas and Outcomes 6: e54106. https://doi.org/10.3897/rio.6.e54106
Figure 1 Integration of the "Werkstatt" in the Friedrich Schiller University and the research center of Jena.
Supplementary material 1 from: Cunha MR, Génio L, Pradillon F, Clavel Henry M, Beaulieu S, Birch J, Campuzano FJ, Carretón M, De Leo F, Gula J, Laming S, Lindsay D, Matos FL, Metaxas A, Meyer-Kaiser K, Mills S, Queiroga H, Rodrigues CF, Sarrazin J, Watanabe H, Young R, Young CM (2020) Foresight Workshop on Advances in Ocean Biological Observations: a sustained system for deep-ocean meroplankton. Research Ideas and Outcomes 6: e54284. https://doi.org/10.3897/rio.6.e54284
Abstracts of keynote talks
Figure 2 from: Cunha MR, Génio L, Pradillon F, Clavel Henry M, Beaulieu S, Birch J, Campuzano FJ, Carretón M, De Leo F, Gula J, Laming S, Lindsay D, Matos FL, Metaxas A, Meyer-Kaiser K, Mills S, Queiroga H, Rodrigues CF, Sarrazin J, Watanabe H, Young R, Young CM (2020) Foresight Workshop on Advances in Ocean Biological Observations: a sustained system for deep-ocean meroplankton. Research Ideas and Outcomes 6: e54284. https://doi.org/10.3897/rio.6.e54284
Figure 2 Sustained meroplankton observations - a basin-scale approach. Low-cost samplers for deep-ocean observations (colonization modules coupled with larval traps) deployed at moorings or mounted on landers of the EMSO-ERIC distributed observatories and covering different water masses (Project LO3CATED; Génio, Cunha and Young). NACW: North Atlantic Central Water; AIW: Antarctic Intermediate Water; MOW: Mediterranean Outflow Water; NADW: North Atlantic Deep Water; MABW: Modified Antarctic Bottom Water.
Figure 1 from: Cunha MR, Génio L, Pradillon F, Clavel Henry M, Beaulieu S, Birch J, Campuzano FJ, Carretón M, De Leo F, Gula J, Laming S, Lindsay D, Matos FL, Metaxas A, Meyer-Kaiser K, Mills S, Queiroga H, Rodrigues CF, Sarrazin J, Watanabe H, Young R, Young CM (2020) Foresight Workshop on Advances in Ocean Biological Observations: a sustained system for deep-ocean meroplankton. Research Ideas and Outcomes 6: e54284. https://doi.org/10.3897/rio.6.e54284
Figure 1 Workshop participants "under the microscope" at the campus of Universidade de Aveiro: Back row, left to right: Fábio Matos, Jonathan Gula, Henrique Queiroga, Rob Young, Sven Laming, Kirstin Meyer-Kaiser, Jozée Sarrazin, Craig M. Young, Fabio De Leo. Front row, left to right: Jim Birch, Morane Clavel Henry, Marina R. Cunha, Clara Rodrigues, Florence Pradillon, Anna Metaxas.
Figure 1 from: Senapati S, Dash J, Sethi M, Chakraborty S (2020) Bioengineered probiotics to control SARS-CoV-2 infection. Research Ideas and Outcomes 6: e54802. https://doi.org/10.3897/rio.6.e54802
<p>Figure 1 Bioengineered probiotics to control SARS-CoV-2 infection. (a) Pathogenesis of SARS-CoV-2 depends on interaction between S protein of virus and angiotensin-converting enzyme 2 (ACE2) expressed on the surface of host cells. (b (1)) Engineered probiotics with expression of cell bound ACE2, sequesters the virus by making it bind to the ACE2 receptor on its surface thus inhibiting the viral entry into gut epithelial cells. (b (2)) The secreted form of ACE2 (sACE2) produced by probiotics confiscates the virus by binding to S proteins and masking their binding sites for gut epithelial ACE2. (c) The sACE2 could also have systemic effects due to its absorption into circulation and inhibiting the virus binding at distant organs like lungs.</p>
Figure 1 from: Petersen M, Pramann B, Toepfer R, Neumann J, Enke H, Hoffmann J, Mauer R (2020) Research Data Management - Current status and future challenges for German non-university research institutions. Research Ideas and Outcomes 6: e55141. https://doi.org/10.3897/rio.6.e55141
Figure 1 Main results of the World Café on experts' opinion to different aspects and challenges in research data management. Shown are the five stations ('Community Perspective', 'Reflection', 'Technology', 'Society & Values', and 'Personal Objectives') and the main points raised and discussed by the participants during the sessions.
Supplementary material 1 from: Petersen M, Pramann B, Toepfer R, Neumann J, Enke H, Hoffmann J, Mauer R (2020) Research Data Management - Current status and future challenges for German non-university research institutions. Research Ideas and Outcomes 6: e55141. https://doi.org/10.3897/rio.6.e55141
Programm FDM-Expert*innentreffen 18.06.2019 (german)
Supplementary material 2 from: Petersen M, Pramann B, Toepfer R, Neumann J, Enke H, Hoffmann J, Mauer R (2020) Research Data Management - Current status and future challenges for German non-university research institutions. Research Ideas and Outcomes 6: e55141. https://doi.org/10.3897/rio.6.e55141
Forschungsdatenmanagement mit NFDI: Wie sind wir vorbereitet? Wie partizipieren wir?
Supplementary material 4 from: Petersen M, Pramann B, Toepfer R, Neumann J, Enke H, Hoffmann J, Mauer R (2020) Research Data Management - Current status and future challenges for German non-university research institutions. Research Ideas and Outcomes 6: e55141. https://doi.org/10.3897/rio.6.e55141
Photographs of notes from the discussions in the Leibniz Sessions
Figure 4 from: Padilla-Sanchez V (2020) In silico analysis of SARS-CoV-2 spike glycoprotein and insights into antibody binding. Research Ideas and Outcomes 6: e55281. https://doi.org/10.3897/rio.6.e55281
Figure 4 Docking energies and interface score charts. A shows the Rosetta Dock results, binding energies from PDBEPISA server in B shows good results for ΔG. Developability of this antibody shows all green flags in C.
Figure 3 from: Padilla-Sanchez V (2020) In silico analysis of SARS-CoV-2 spike glycoprotein and insights into antibody binding. Research Ideas and Outcomes 6: e55281. https://doi.org/10.3897/rio.6.e55281
Figure 3 Docking interface between the modified 80R antibody and the RBD of the SARS-CoV-2 spike protein. The model shows the structural interface with the 80R antibody above and the RBD below. The seven substitutions in 80R are shown in magenta and RBD residues are shown in cyan. Notice how the substitutions in 80R allow new aromatic-aromatic interactions that improve binding to the RBD and are not present in wild type 80R. E484 is shown pointing towards the beta strand of 80R and a glycine substitution was therefore introduced to avoid clashes.
Figure 6 from: Padilla-Sanchez V (2020) In silico analysis of SARS-CoV-2 spike glycoprotein and insights into antibody binding. Research Ideas and Outcomes 6: e55281. https://doi.org/10.3897/rio.6.e55281
Figure 6 m396 mutations docking results. A shows Rosetta Dock funnels for the original partners SARS-CoV and m396, SARS-CoV-2 and m396 and the SARS-CoV-2 and mutated m396. Notice how the binding is improved to the level of the original partners. B shows the ΔG energies again notice the improvement of binding when the mutations are introduced. Finally, C shows the developability flags with only one warning that is not that far from green flag.
Figure 5 from: Padilla-Sanchez V (2020) In silico analysis of SARS-CoV-2 spike glycoprotein and insights into antibody binding. Research Ideas and Outcomes 6: e55281. https://doi.org/10.3897/rio.6.e55281
Figure 5 Docking interface between the modified m396 antibody and SARS-CoV-2 spike protein RBD. In magenta is m396 mutant and in cyan SARS-CoV-2 RBD. These five mutations introduce many electrostatic interactions between the partners therefore stabilizing very much the binding.
Figure 2 from: Padilla-Sanchez V (2020) In silico analysis of SARS-CoV-2 spike glycoprotein and insights into antibody binding. Research Ideas and Outcomes 6: e55281. https://doi.org/10.3897/rio.6.e55281
Figure 2 Structural analysis of SARS-CoV spike glycoprotein. In A the SARS-CoV spike protein (PDB ID: 6ACG) is shown bound to ACE2 (brown) and 80R antibody (cyan), superimposed on the same binding site. In B the spike protein is shown bound only to the 80R antibody (PDB ID: 2GHW), with the structural model of the RBD of the SARS-CoV-2 spike protein (magenta) containing the missing loops. This homology model served as the basis for the docking experiments. In C it is shown a spike colored by subunit and showing the glycans. There are only two possible glycans in RBD region at 331 and 343 and neither of these sites affect the 80R binding.
Figure 1 from: Padilla-Sanchez V (2020) In silico analysis of SARS-CoV-2 spike glycoprotein and insights into antibody binding. Research Ideas and Outcomes 6: e55281. https://doi.org/10.3897/rio.6.e55281
Figure 1 Structural model of SARS-CoV-2 infection. This structural model was built with UCSF Chimera using high-performance computers (Bridges Large and Frontera). The model shows 16 viruses, with the spike proteins shown in green (PDB ID: 6VSB) and an actual lipid bilayer membrane, with ACE2 dimers shown in magenta. All these structures are at atomic resolution. The length of the membrane is approximately 1 micrometer.
Figure 8 from: Steinbeck C, Koepler O, Bach F, Herres-Pawlis S, Jung N, Liermann JC, Neumann S, Razum M, Baldauf C, Biedermann F, Bocklitz TW, Boehm F, Broda F, Czodrowski P, Engel T, Hicks MG, Kast SM, Kettner C, Koch W, Lanza G, Link A, Mata RA, Nagel WE, Porzel A, Schlörer N, Schulze T, Weinig H-G, Wenzel W, Wessjohann LA, Wulle S (2020) NFDI4Chem - Towards a National Research Data Infrastructure for Chemistry in Germany. Research Ideas and Outcomes 6: e55852. https://doi.org/10.3897/rio.6.e55852
Figure 8 Components of TA2, Smart Lab, and connection to TA3: Seamless data transfer from devices via the ELN to repositories. Grey panels: modular software plugins, orange panels: modular software plugins for ELN and repositories, blue panels: software developed for the ELN. OC, IC, PC, PolyCC and AC represent the modules of the subdisciplines to be developed (see list of abbreviations in the last section of the Grant Proposal and the table to it).
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.