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Supplementary material 3 from: Egloff W, Agosti D, Patterson D, Hoffmann A, Mietchen D, Kishor P, Penev L (2016) Data Policy Recommendations for Biodiversity Data. EU BON Project Report. Research Ideas and Outcomes 2: e8458. https://doi.org/10.3897/rio.2.e8458
MS241: Specification for registry and metadata catalogue
Supplementary material 2 from: Egloff W, Agosti D, Patterson D, Hoffmann A, Mietchen D, Kishor P, Penev L (2016) Data Policy Recommendations for Biodiversity Data. EU BON Project Report. Research Ideas and Outcomes 2: e8458. https://doi.org/10.3897/rio.2.e8458
MS971: Data sharing agreement
Supplementary material 1 from: Wojnarski M, Hanken Kurtz D (2016) Paperity Central: An Open Catalog of All Scholarly Literature. Research Ideas and Outcomes 2: e8462. https://doi.org/10.3897/rio.2.e8462
An introductory video presenting our Open Science Prize project.
Supplementary material 1 from: Martone M, Murray-Rust P, Molloy J, Arrow T, MacGillivray M, Kittel C, Kasberger S, Steel G, Oppenheim C, Ranganathan A, Tennant J, Udell J (2016) ContentMine/Hypothes.is Proposal. Research Ideas and Outcomes 2: e8424. https://doi.org/10.3897/rio.2.e8424
Video showing ContentMine software applied to EPMC papers mentioning Zika virus.
Figure 2 from: von Rintelen K, Arida E, Häuser C (2017) A review of biodiversity-related issues and challenges in megadiverse Indonesia and other Southeast Asian countries. Research Ideas and Outcomes 3: e20860. https://doi.org/10.3897/rio.3.e20860
Figure 2 - The changing pathways of biodiversity in Indonesian society (without any claim of completeness and time scale). The oldest forms of biodiversity-related knowledge changed over time and (local) space, also from rather bottom-up (local knowledge) to more top-down pathways (e.g., governmental programmes) (continuous line). However, modern pathways also rely on older pathways and the whole process is not only unidirectional (dashed line) as older pathway (traditional knowledge and medicine) are often making a comeback.
Figure 1 from: von Rintelen K, Arida E, Häuser C (2017) A review of biodiversity-related issues and challenges in megadiverse Indonesia and other Southeast Asian countries. Research Ideas and Outcomes 3: e20860. https://doi.org/10.3897/rio.3.e20860
Figure 1 - Map of Southeast Asia. The ten member states of the Association of Southeast Asian Nations (ASEAN) in Southeast Asia. The map shows the isolated islands of Indonesia and the Philippines. Their complex biogeographical and geological history led to the evolution of an extraordinary biodiversity and endemism. Map modified from d-maps.com (the original map was downloaded from http://www.d-maps.com/carte.php?num_car=28675&lang=en).
Figure 5 from: Vyshedskiy A, Mahapatra S, Dunn R (2017) Linguistically deprived children: meta-analysis of published research underlines the importance of early syntactic language use for normal brain development. Research Ideas and Outcomes 3: e20696. https://doi.org/10.3897/rio.3.e20696
Figure 5 - Flexible syntax, prepositions, adjectives, verb tenses, and other common elements of grammar, all facilitate the human ability to communicate an infinite number of novel images with the use of a finite number of words. The graph shows the number of distinct images that can be transmitted with high fidelity in a communication system with 1,000 nouns as a function of the number of spatial prepositions. In a communication system with no spatial prepositions and other recursive elements, 1000 nouns can communicate 1000 images to a listener. Adding just one spatial preposition allows for the formation of three-word phrases (such as: 'a bowl behind a cup' or 'a cup behind a bowl') and increases the number of distinct images that can be communicated to a listener from 1000 to one million (1000x1x1000). Adding a second spatial preposition and allowing for five-word sentences of the form object-preposition-object-preposition-object (such as: a bowl on a cup behind a plate) increases the number of distinct images that can be communicated to four billion (1000x2x1000x2x1000). The addition of a third spatial preposition increases the number of distinct images to 27 trillion (1000x3x1000x3x1000x3x1000), and so on. In general, the number of distinct images communicated by three-word sentences of the structure object-preposition-object equals the number of object-words times the number of prepositions times the number of object-words. A typical language with 1000 nouns and 100 spatial prepositions can theoretically communicate 1000101 x 100100 distinct images. This number is significantly greater than the total number of atoms in the universe. For all practical purposes, an infinite number of distinct images can be communicated by a syntactic communication system with just 1000 words and a few prepositions. Prepositions, adjectives, and verb tenses dramatically facilitate the capacity of a syntactic communication system with a finite number of words to communicate an infinite number of distinct images. Linguists refer to this property of human languages as recursion. The "infiniteness" of human language has been explicitly recognized by "Galileo, Descartes, and the 17th-century 'philosophical grammarians' and their successors, notably von Humboldt" (Hauser et al. 2002). The infiniteness of all human languages stand in stark contrast to finite homesign communication systems that are lacking spatial prepositions, syntax, and other recursive elements of a formal sign language.
Figure 7 from: Underwood E, Grace M (2017) The use of biodiversity data in rural development programming. Research Ideas and Outcomes 3: e20369. https://doi.org/10.3897/rio.3.e20369
Figure 7 - Records added to the National Biodiversity Network Gateway, 2004 to 2015. From UK Biodiversity Indicators 2015, http://jncc.defra.gov.uk/page-4229 Source: NBN Gateway and NBN Atlas.
Figure 4 from: Vyshedskiy A, Mahapatra S, Dunn R (2017) Linguistically deprived children: meta-analysis of published research underlines the importance of early syntactic language use for normal brain development. Research Ideas and Outcomes 3: e20696. https://doi.org/10.3897/rio.3.e20696
Figure 4 - Synchronicity has to be understood in terms of synchronicity of the arrival of action potentials to a target neuron rather than absolute equality of action potential conduction times over different paths. Consider the following example: suppose neuron A is receiving excitatory input from neurons B and C via two different pathways (neuron A is the target neuron for both neurons B and C). Suppose that the action potential conduction time is 2ms from neuron B to neuron A and 22ms from neuron C to neuron A (i.e., the axonal pathway B-A has a significantly shorter conduction time than the axonal pathway C-A). Does it mean that the connections B-A and C-A are always asynchronous? No. The answer depends on the predominant neural activity rhythm in this network. At the firing rate of 50Hz (inter-spike interval of 20ms that correspond to Gamma rhythm), neurons B and C can actually be considered synchronous in relationship to neuron A: consider a train of action potentials synchronously fired by neurons B and C. The first action potential from neuron B will reach neuron A in 2ms and the first action potential from neuron C will reach neuron A in 22ms. Obviously, there would be no coincidence in the arrival times of the 1st action potentials from neurons B and C. However the second action potential from neuron B will arrive to neuron A in 22ms, concurrently with the 1st action potential from neuron C. Thus, starting with the second action potential, neuron A will receive synchronous activation from neurons B and C. The synchronous activation has a significantly greater probability of enhancing synaptic connections between neurons A and B, and A and C (Hebbian learning: 'neurons that fire together, wire together' (Hebb 1949). Thus, synchronicity does not need to imply absolute equality in the conduction time over different pathways. Rather synchronicity implies near-zero phase-shift between the two firing trains of action potentials at the postsynaptic cells. This phase-shift depends on conduction times over each pathway and also on the dominant firing frequency in the neural network.
Figure 1 from: Underwood E, Grace M (2017) The use of biodiversity data in rural development programming. Research Ideas and Outcomes 3: e20369. https://doi.org/10.3897/rio.3.e20369
Figure 1 - Use of CMEF indicators in CAP monitoring and evaluation (reproduced from European Commission 2015)
Figure 2 from: Vyshedskiy A, Mahapatra S, Dunn R (2017) Linguistically deprived children: meta-analysis of published research underlines the importance of early syntactic language use for normal brain development. Research Ideas and Outcomes 3: e20696. https://doi.org/10.3897/rio.3.e20696
Figure 2 - A typical question testing subject's ability to mentally rotate an object is shown here as a 2x2 matrix with six answer choices displayed below the problem. The top row of the matrix indicates the rule: "the object in the right column is the result of 45° clockwise rotation." Applying this rule to the bottom row, we arrive at the correct answer depicted on the right.
Figure 6 from: Underwood E, Grace M (2017) The use of biodiversity data in rural development programming. Research Ideas and Outcomes 3: e20369. https://doi.org/10.3897/rio.3.e20369
Figure 6 - The German HNV monitoring methodology and results - HNV value decline In Germany, the HNV monitoring methodology has enabled an initial assessment of the trend in HNV value of farmland. Between 2009 and 2013, there was a significant decline of HNV value, in particular in the HNV class III, which represents the lowest value (in terms of species richness and structure). Graph reproduced from (Benzler et al. 2015).
Figure 3 from: Underwood E, Grace M (2017) The use of biodiversity data in rural development programming. Research Ideas and Outcomes 3: e20369. https://doi.org/10.3897/rio.3.e20369
Figure 3 - Extract of the Danish HNV map. Available at http://arealinformation.miljoeportal.dk/distribution/
Figure 1 from: Vyshedskiy A, Mahapatra S, Dunn R (2017) Linguistically deprived children: meta-analysis of published research underlines the importance of early syntactic language use for normal brain development. Research Ideas and Outcomes 3: e20696. https://doi.org/10.3897/rio.3.e20696
Figure 1 - Visual information processing in the cortex. From the primary visual cortex (V1, shown in yellow), the visual information is passed in two streams. The neurons along the ventral stream also known as the ventral visual cortex (shown in purple) are primarily concerned with what the object is. The ventral visual stream runs into the inferior temporal lobe. The neurons along the dorsal stream also known the dorsal visual cortex (shown in green) are primarily concerned with where the object is. The dorsal visual stream runs into the parietal lobe.
Figure 3 from: Vyshedskiy A, Mahapatra S, Dunn R (2017) Linguistically deprived children: meta-analysis of published research underlines the importance of early syntactic language use for normal brain development. Research Ideas and Outcomes 3: e20696. https://doi.org/10.3897/rio.3.e20696
Figure 3 - Linguistic isolates performance in verbal and nonverbal tests. This Figure is also available as a Power Point slide in Suppl. material 1.
Figure 5 from: Underwood E, Grace M (2017) The use of biodiversity data in rural development programming. Research Ideas and Outcomes 3: e20369. https://doi.org/10.3897/rio.3.e20369
Figure 5 - Opinions of RDP policy evaluators on data availability and bottlenecks. Results reproduced from ENRD 2012. A group of 58 RDP policy evaluators were asked about data availability and bottlenecks to data use for agricultural policy impact evaluation in 2007-2013. In response to the question: "To what extent are sound data available to carry out RDP impact evaluations?" 2% (1) replied 'fully available', 24% (14) replied 'largely available', 72% (42) replied 'partly available', 2% (1) replied 'not available'. The answers to the question "What are the major bottlenecks in providing sound data for the assessment of RDP impact in 2007-2013?" are shown in the graph.
Figure 2 from: Underwood E, Grace M (2017) The use of biodiversity data in rural development programming. Research Ideas and Outcomes 3: e20369. https://doi.org/10.3897/rio.3.e20369
Figure 2 - Workflow of the production of the EU Farmland Bird Index. Adapted from source: http://www.ebcc.info/wpimages/schema2016_big.jpg
Figure 1 from: Kissling WD (2017) Has frugivory influenced the macroecology and diversification of a tropical keystone plant family? Research Ideas and Outcomes 3: e14944. https://doi.org/10.3897/rio.3.e14944
Figure 1 - Global functional trait distributions of palms (n = 2469) and frugivorous consumers (n = 3835, incl. birds and mammals), showing large-scale co-variation between (a) palm fruit size (length in cm) and (b) consumer body size (mass in kg). Symbols are plotted for the mass centroids of geographic units ('botanical countries', TDWG level 3 units) and represent mean values across all species in a given unit. Values are calculated across a total of 29,032 species-level occurrences (5,218 for palms, 23,814 for consumers).
Figure 2 from: Kissling WD (2017) Has frugivory influenced the macroecology and diversification of a tropical keystone plant family? Research Ideas and Outcomes 3: e14944. https://doi.org/10.3897/rio.3.e14944
Figure 2 - Global diversification of palms. Branches are coloured by mean diversification rates across the time-calibrated generic-level phylogeny of palms estimated using Bayesian Analysis of Macroevolutionary Mixtures (BAMM).
Figure 4 from: Kissling WD, Seijmonsbergen AC, Foppen RPB, Bouten W (2017) eEcoLiDAR, eScience infrastructure for ecological applications of LiDAR point clouds: reconstructing the 3D ecosystem structure for animals at regional to continental scales. Research Ideas and Outcomes 3: e14939. https://doi.org/10.3897/rio.3.e14939
Figure 4 - Time table for the eEcoLiDAR project (assuming a start in March 2017). The work plan covers tasks for the NLeSC engineers, the proposed PhD student, and two associated Postdoc projects.
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.