Find research datasets worth reusing

Figure 1 from: Smirnova L, Mergen P, Groom Q, De Wever A, Penev L, Stoev P, Pe'er I, Runnel V, Camacho A, Vincent T, Agosti D, Arvanitidis C, Bonet F, Saarenmaa H (2016) Data sharing tools adopted by the European Biodiversity Observation Network Project. Research Ideas and Outcomes 2: e9390. https://doi.org/10.3897/rio.2.e9390

Figure 1 - ARPHA consists of two integrated workflows: in ARPHA-XML, the manuscript is written and processed via the ARPHA Writing Tool, and in ARPHA-DOC, the manuscript is submitted and processed as document file(s).

Figure 3 from: Molino J, Lubiana Alves T, Ferreira-Camargo L, Croce M, Tanaka A, Buson F, Ribeiro P, Campos-Salazar A, Antonio E, Maizel A, Siratuti V, Costa C, Wlodarczyk S, de Souza Lima R, Mello F, Mayfield S, Carvalho J (2016) Chimeric spider silk production in microalgae: a modular bionanomaterial. Research Ideas and Outcomes 2: e9342. https://doi.org/10.3897/rio.2.e9342

Figure 3 - Cassette construction to be inserted in C. renhardtii nuclear genome for the expression of desired proteins. Promoter hsp70A/rbcs2: fusion of the promoters hsp70A and rbcs2 (Eichler-Stahlberg et al. 2009, Schroda et al. 2000). Sh-Ble: gene that gives resistance to Zeomycin. 2A: self-cleavage peptide obtained from Foot and Mouth Disease Virus (FMDV) (Rasala et al. 2012). PS: Secretion signal peptide of the gene Ars1. GOI: gene of interest coding the proteins to be used in the project. His: coding sequence of six histidines (histidine tag). RbcS2 3'UTR: terminal sequence (untranslated region) of the gene RbcS2 (Fuhrmann et al. 1999)

Figure 1 from: Molino J, Lubiana Alves T, Ferreira-Camargo L, Croce M, Tanaka A, Buson F, Ribeiro P, Campos-Salazar A, Antonio E, Maizel A, Siratuti V, Costa C, Wlodarczyk S, de Souza Lima R, Mello F, Mayfield S, Carvalho J (2016) Chimeric spider silk production in microalgae: a modular bionanomaterial. Research Ideas and Outcomes 2: e9342. https://doi.org/10.3897/rio.2.e9342

Figure 1 - Project overview. Schematic representation of spider web structure from macro to nano scale. A representation of: enzybiotic protein from a bacteriophage; a spider silk protein with repetitive domains and N and C terminals; host expression system Chlamydomonas reinhardtii and a chimeric protein envisioned in this project; and the final product, a biopatch produced from recombinant silk proteins and chimeric proteins.

Figure 2 from: Molino J, Lubiana Alves T, Ferreira-Camargo L, Croce M, Tanaka A, Buson F, Ribeiro P, Campos-Salazar A, Antonio E, Maizel A, Siratuti V, Costa C, Wlodarczyk S, de Souza Lima R, Mello F, Mayfield S, Carvalho J (2016) Chimeric spider silk production in microalgae: a modular bionanomaterial. Research Ideas and Outcomes 2: e9342. https://doi.org/10.3897/rio.2.e9342

Figure 2 - Schematic representation of spider silk proteins and chimeric protein. A: MaSp1 - Major ampullate spidroin 1, MaSp2 - Major ampullate spidroin 2 B: Chimeric protein of a enzybiotic with N and C terminals domains of spider silk proteins.

Figure 8b from: Kramer B, Bosman J, Ignac M, Kral C, Kalleinen T, Koskinen P, Bruno I, Buckland A, Callaghan S, Champieux R, Chapman C, Hagstrom S, Martone M, Murphy F, O'Donnell D (2016) Defining the Scholarly Commons - Reimagining Research Communication. Report of Force11 SCWG Workshop, Madrid, Spain, February 25-27, 2016. Research Ideas and Outcomes 2: e9340. https://doi.org/10.3897/rio.2.e9340

Figure 8b - Visualizaton showing all groups' visions as interconnected elements (triples), with common elements overlapping.

Figure 8a from: Kramer B, Bosman J, Ignac M, Kral C, Kalleinen T, Koskinen P, Bruno I, Buckland A, Callaghan S, Champieux R, Chapman C, Hagstrom S, Martone M, Murphy F, O'Donnell D (2016) Defining the Scholarly Commons - Reimagining Research Communication. Report of Force11 SCWG Workshop, Madrid, Spain, February 25-27, 2016. Research Ideas and Outcomes 2: e9340. https://doi.org/10.3897/rio.2.e9340

Figure 8a - Visualization showing all ideas generated collectively in the first round (session 3, dark grey) or second round (session 4, light grey), and those generated by the respective groups (solid colors) as part of their vision of scholarly communication.

Figure 7b from: Kramer B, Bosman J, Ignac M, Kral C, Kalleinen T, Koskinen P, Bruno I, Buckland A, Callaghan S, Champieux R, Chapman C, Hagstrom S, Martone M, Murphy F, O'Donnell D (2016) Defining the Scholarly Commons - Reimagining Research Communication. Report of Force11 SCWG Workshop, Madrid, Spain, February 25-27, 2016. Research Ideas and Outcomes 2: e9340. https://doi.org/10.3897/rio.2.e9340

Figure 7b - Example of Trello card comment with link to another idea. #dep_on - idea depends on another idea; "https://trello.com/c/RaNcbKSe" - is the short link to the Trello card with the connected idea. In the visualization it would be represented as a line connecting two ideas.

Figure 7a from: Kramer B, Bosman J, Ignac M, Kral C, Kalleinen T, Koskinen P, Bruno I, Buckland A, Callaghan S, Champieux R, Chapman C, Hagstrom S, Martone M, Murphy F, O'Donnell D (2016) Defining the Scholarly Commons - Reimagining Research Communication. Report of Force11 SCWG Workshop, Madrid, Spain, February 25-27, 2016. Research Ideas and Outcomes 2: e9340. https://doi.org/10.3897/rio.2.e9340

Figure 7a - Example of Trello card with tags. "using the public domain" - the idea name; #G2 - the idea came from the Group 2; #viz - the idea is ready to be included in the visualization; #triple - the idea has a link to another idea in the group's vision.

Figure 4 from: Molino J, Lubiana Alves T, Ferreira-Camargo L, Croce M, Tanaka A, Buson F, Ribeiro P, Campos-Salazar A, Antonio E, Maizel A, Siratuti V, Costa C, Wlodarczyk S, de Souza Lima R, Mello F, Mayfield S, Carvalho J (2016) Chimeric spider silk production in microalgae: a modular bionanomaterial. Research Ideas and Outcomes 2: e9342. https://doi.org/10.3897/rio.2.e9342

Figure 4 - Experimental Flowchart. (A) Wild Cells incubated with built vectors. (B) Wild-cell transformation by electroporation. (C) Selection of mutants resistant to Zeocin. (D) Screening of antibiotic resistant cells by PCR. (E) Cultivation of PCR positive cells. (F) Fractions to be tested for the presence of recombinant proteins. (G) Detection of recombinant proteins present in the fractions by Western Blot. (H) Protein Purification. (I) Quantification via ELISA. (J) Spider silk polymerization reaction.

Figure 1 from: Hartgerink C, Wicherts J, van Assen M (2016) The value of statistical tools to detect data fabrication. Research Ideas and Outcomes 2: e8860. https://doi.org/10.3897/rio.2.e8860

Figure 1 - The applied statistical methods to test for data fabrication in Project 1, depicting those that are combined into an overall test for data fabrication with the Fisher method. Benford's law is excluded from the overall tests because of an expected lack of utility.

Figure 2 from: Hartgerink C, Wicherts J, van Assen M (2016) The value of statistical tools to detect data fabrication. Research Ideas and Outcomes 2: e8860. https://doi.org/10.3897/rio.2.e8860

Figure 2 - Scatterplot reporting the accompanying correlation value. The raw data for variables X and Y is available in the individual points and can be extracted. Statistical methods such as terminal digit analysis can be applied to these raw data to detect data anomalies.

Figure 9 from: Klein A (2016) Crowdsourcing voice editing and quality assessment of data collected from the largest mobile phone-based research study of Parkinson disease. Research Ideas and Outcomes 2: e8848. https://doi.org/10.3897/rio.2.e8848

Figure 9 - Timeline. We will prepare and update the Web app (Aim 2) as we develop it for use in annotating gold standard audio data (Aim 1) and as we get feedback on its use in connection with Amazon's Mechanical Turk (Aim 2). Year 2 will consist primarily of testing the aggregation of annotated audio data for further analysis (Aim 2), to train an automated approach (Exploratory Aim), and to publish and present our findings.

Figure 2 from: Klein A (2016) Crowdsourcing voice editing and quality assessment of data collected from the largest mobile phone-based research study of Parkinson disease. Research Ideas and Outcomes 2: e8848. https://doi.org/10.3897/rio.2.e8848

Figure 2 - Mockup of audio recording annotation tool – Step 1: Selection. This figure shows a mockup of what an audio annotation Web application tool could look like. In this first step, (A) the Worker presses the Play icon to listen to the voice recording, (B) selects a problematic segment by clicking and dragging the mouse over the waveform, and (C) replays the recording if necessary and selects other problematic segments.

Figure 2 from: Klein A, Ghosh S (2016) Graph-based clinical diagnosis and prediction using multi-modal neuroimaging data. Research Ideas and Outcomes 2: e8835. https://doi.org/10.3897/rio.2.e8835

Figure 2 - Examples of automatically extracted features (MRI) (a) Example structural features (left lateral views of volumes, surfaces, curves, and points) (b) Schematic feature hierarchy: 3-D gyrii surround a 2-D sulcal ribbon with 1-D fundus containing 0-D pits

Figure 3 from: Klein A (2016) Visual Parkinson's Disease Rating Scale: A Universal Iconic Questionnaire for Epidemiological Studies in India. Research Ideas and Outcomes 2: e8834. https://doi.org/10.3897/rio.2.e8834

Figure 3 - Timeline This Gantt chart provides an estimate of the relative timing and duration for achieving each of the Aims.

Figure 1 from: Klein A (2016) Visual Parkinson's Disease Rating Scale: A Universal Iconic Questionnaire for Epidemiological Studies in India. Research Ideas and Outcomes 2: e8834. https://doi.org/10.3897/rio.2.e8834

Figure 1 - First pass at a VPDRS static graphic Figure 1 corresponds to the first self-administered MDS-UPDRS question: 1.7 SLEEP PROBLEMS. Over the past week, have you had trouble going to sleep at night or staying asleep through the night? Consider how rested you felt after waking up in the morning. 0: Normal: No problems. 1: Slight: Sleep problems are present but usually do not cause trouble getting a full night of sleep. 2: Mild: Sleep problems usually cause some difficulties getting a full night of sleep. 3: Moderate: Sleep problems cause a lot of difficulties getting a full night of sleep, but I still usually sleep for more than half the night. 4: Severe: I usually do not sleep for most of the night."

Figure 5 from: Klein A (2016) Crowdsourcing voice editing and quality assessment of data collected from the largest mobile phone-based research study of Parkinson disease. Research Ideas and Outcomes 2: e8848. https://doi.org/10.3897/rio.2.e8848

Figure 5 - DARPA-funded seedling project. This schematic represents our DARPA-funded seedling project to assess the feasibility of collecting phone voice recordings from PD patients for use in a competition.

Figure 1 from: Klein A, Ghosh S (2016) Graph-based clinical diagnosis and prediction using multi-modal neuroimaging data. Research Ideas and Outcomes 2: e8835. https://doi.org/10.3897/rio.2.e8835

Figure 1 - Examples of graph-based representations of scientific data among hundreds on the www.visualcomplexity.com website (categories on the site include biology, food webs and semantic, social, and knowledge networks). Lower left images of DTI, connectome, and network hubs are from Olaf Sporns (2010, Scholarpedia, 5(2):5584).

Figure 4 from: Klein A (2016) Crowdsourcing voice editing and quality assessment of data collected from the largest mobile phone-based research study of Parkinson disease. Research Ideas and Outcomes 2: e8848. https://doi.org/10.3897/rio.2.e8848

Figure 4 - Audio recording annotation tool – Step 3: Rating. Following Figures 2 and 3, here the Worker rates how serious the problem is that is affecting the highlighted segment of the recording. In this example, the Worker indicates that the background noise (wind) is not good, but that it doesn't interfere with his/her ability to hear the voice in the recording.

Figure 7 from: Klein A (2016) Crowdsourcing voice editing and quality assessment of data collected from the largest mobile phone-based research study of Parkinson disease. Research Ideas and Outcomes 2: e8848. https://doi.org/10.3897/rio.2.e8848

Figure 7 - Example mPower patient voice data. In the mPower app, PD patients are prompted to perform the voice activity three times per day: once before taking their medication, a second time when they feel they are at their best after taking their medication, and a third "random" time. This figure shows example voice data for a single patient on medication (top) and at a "random" time, very likely off medication (bottom). On the left are waveforms, showing the acoustic voice signal over time (0-10 seconds), from which one can clearly see that the patient's voice trailed off to a minimum (bottom left) compared to after medication (top left). On the right are spectrograms, representing signal amplitude at different frequencies (0-5 kHz) over time (0-10 seconds). The spectrogram after medication (top right) has more uniform frequency bands across the recording compared to the rather "muddled" spectrogram recorded at the random time (bottom right).