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Figure 10 from: Mingorance Gámez C (2018) Epigenetic function of Granulocytic nuclei? Designing a new line of research. Research Ideas and Outcomes 4: e29438. https://doi.org/10.3897/rio.4.e29438
Figure 10 Regulatory RNA would function in the same lobe as it was transcribed, affecting only genes distributed along with its own locus.
Figure 1 from: Mingorance Gámez C (2018) Epigenetic function of Granulocytic nuclei? Designing a new line of research. Research Ideas and Outcomes 4: e29438. https://doi.org/10.3897/rio.4.e29438
Figure 1 Possible distributions of both copies of a gene in a basophil or eosinophil (left) and how we would perceive them through the microscope (right).
Figure 8 from: Mingorance Gámez C (2018) Epigenetic function of Granulocytic nuclei? Designing a new line of research. Research Ideas and Outcomes 4: e29438. https://doi.org/10.3897/rio.4.e29438
Figure 8 When hybridising with intronic hnRNA, we would need an additional probe in order to discard false positives because of a copy of the gene not being transcribed and it would only work in heterozygotes. In this case, using red and green probes for different alleles would show as yellow if both copies are transcribing in the same lobe or as red or green if only one of them is being transcribed.
Figure 9 from: Mingorance Gámez C (2018) Epigenetic function of Granulocytic nuclei? Designing a new line of research. Research Ideas and Outcomes 4: e29438. https://doi.org/10.3897/rio.4.e29438
Figure 9 Distribution between lobes can help both copies of the unused sequence to be modified to become NETs (A), but it can also help to modify only one copy of a used gene (B) by containing the modifying enzymes in one lobe and keeping a functional copy of the gene for normal transcription.
Figure 3 from: Mingorance Gámez C (2018) Epigenetic function of Granulocytic nuclei? Designing a new line of research. Research Ideas and Outcomes 4: e29438. https://doi.org/10.3897/rio.4.e29438
Figure 3 Possible distributions of both copies of a gene in a neutrophil with four lobes (left) and how we would perceive them through the microscope (right).
Figure 7 from: Mingorance Gámez C (2018) Epigenetic function of Granulocytic nuclei? Designing a new line of research. Research Ideas and Outcomes 4: e29438. https://doi.org/10.3897/rio.4.e29438
Figure 7 Frequencies of joint random pattern studying a single target (A) or two (B) in a neutrophil with three lobes. Even if we find 2 populations of neutrophils with a pattern of joint distribution in a fixed lobe and showing the same frequencies and distributions shown in A, these two populations would show only two of the distributions shown in B with the same frequencies found before if the pattern is not actually independent of the lobe.
Figure 4 from: Mingorance Gámez C (2018) Epigenetic function of Granulocytic nuclei? Designing a new line of research. Research Ideas and Outcomes 4: e29438. https://doi.org/10.3897/rio.4.e29438
Figure 4 Probability of finding each distribution of the alleles in a basophil or eosinophil through the microscope, assuming an independent pattern (A, assuming an equal chance for both lobes), pattern of interdependent location independent of lobe (B) or pattern of interdependent location in a fixed lobe (C). In cases B and C, since these cells only have two lobes, we would find only cells with one of the distributions, so we would be unable to tell one of the patterns apart from the other.
Figure 2 from: Mingorance Gámez C (2018) Epigenetic function of Granulocytic nuclei? Designing a new line of research. Research Ideas and Outcomes 4: e29438. https://doi.org/10.3897/rio.4.e29438
Figure 2 Possible distributions of both copies of a gene in a neutrophil with three lobes (left) and how we would perceive them through the microscope (right).
Figure 1d from: Liversage K, Byrne M (2018) A note on life-history traits and conservation concerns for viviparous Australian seastars (Parvulastra parvivipara and P. vivipara). Research Ideas and Outcomes 4: e29766. https://doi.org/10.3897/rio.4.e29766
Figure 1d Photographs from P. parvivipara and P. vivipara habitat, and graph of P. vivipara population trends. - Trends from the largest P. vivipara population at Pitt Water. Each point is the mean of adult densities from numerous sampling events over each 2 year period. During 1976-83 a fixed 1 m2 quadrat was sampled (Prestedge 1998) while a different method was used from 2001-04 involving 25 m transects being sampled across the site (Ecomarine 2014). Other survey types (timed-search) have also found large population declines (see section 2.).
Figure 1b from: Liversage K, Byrne M (2018) A note on life-history traits and conservation concerns for viviparous Australian seastars (Parvulastra parvivipara and P. vivipara). Research Ideas and Outcomes 4: e29766. https://doi.org/10.3897/rio.4.e29766
Figure 1b Photographs from P. parvivipara and P. vivipara habitat, and graph of P. vivipara population trends. - Photograph of a boulder underside in P. parvivipara habitat with extensive encrustation of oyster shells that includes invasive Pacific oysters (bar = 5 cm).
Figure 1a from: Liversage K, Byrne M (2018) A note on life-history traits and conservation concerns for viviparous Australian seastars (Parvulastra parvivipara and P. vivipara). Research Ideas and Outcomes 4: e29766. https://doi.org/10.3897/rio.4.e29766
Figure 1a Photographs from P. parvivipara and P. vivipara habitat, and graph of P. vivipara population trends. - Photograph taken during surveys of Liversage (2015) showing P. parvivipara giving birth, with the bright orange juvenile emerging from parent's dorsal side (bar = 1 cm).
Figure 1c from: Liversage K, Byrne M (2018) A note on life-history traits and conservation concerns for viviparous Australian seastars (Parvulastra parvivipara and P. vivipara). Research Ideas and Outcomes 4: e29766. https://doi.org/10.3897/rio.4.e29766
Figure 1c Photographs from P. parvivipara and P. vivipara habitat, and graph of P. vivipara population trends. - Photograph of P. vivipara during 1992 at Pit Water. Populations have become reduced in subsequent years which may be associated with increased siltation and overgrowth from encrusting species (bar = 5 cm).
Figure 4 from: Seltmann K, Lafia S, Paul D, James S, Bloom D, Rios N, Ellis S, Farrell U, Utrup J, Yost M, Davis E, Emery R, Motz G, Kimmig J, Shirey V, Sandall E, Park D, Tyrrell C, Thackurdeen R, Collins M, O'Leary V, Prestridge H, Evelyn C, Nyberg B (2018) Georeferencing for Research Use (GRU): An integrated geospatial training paradigm for biocollections researchers and data providers. Research Ideas and Outcomes 4: e32449. https://doi.org/10.3897/rio.4.e32449
Figure 4 Initial expertise (color of the bar) vs final confidence (y-axis) after the GRU workshop for participants responding to final survey. Example for how to interpret this graphic: the blue color bar at the top indicates that before the workshop roughly 50% of respondents said their knowledge of GEOLocate was "neither high nor low" but after the workshop these same respondents selected "much higher" for their knowledge of GEOLocate.
Figure 3 from: Seltmann K, Lafia S, Paul D, James S, Bloom D, Rios N, Ellis S, Farrell U, Utrup J, Yost M, Davis E, Emery R, Motz G, Kimmig J, Shirey V, Sandall E, Park D, Tyrrell C, Thackurdeen R, Collins M, O'Leary V, Prestridge H, Evelyn C, Nyberg B (2018) Georeferencing for Research Use (GRU): An integrated geospatial training paradigm for biocollections researchers and data providers. Research Ideas and Outcomes 4: e32449. https://doi.org/10.3897/rio.4.e32449
Figure 3 An illustrative example of the two methods of uncertainty capture when georeferencing specimens. Method A, or polygon, creates a shape around the river (in blue). Method B, or point-radius, creates a circle of uncertainty around the origin. The illustration is based on output from GeoLocate software (Rios 2018) for both polygon and point-radius.
Figure 2 from: Seltmann K, Lafia S, Paul D, James S, Bloom D, Rios N, Ellis S, Farrell U, Utrup J, Yost M, Davis E, Emery R, Motz G, Kimmig J, Shirey V, Sandall E, Park D, Tyrrell C, Thackurdeen R, Collins M, O'Leary V, Prestridge H, Evelyn C, Nyberg B (2018) Georeferencing for Research Use (GRU): An integrated geospatial training paradigm for biocollections researchers and data providers. Research Ideas and Outcomes 4: e32449. https://doi.org/10.3897/rio.4.e32449
Figure 2 This specimen record is an example from the University of California Collection Network Symbiota Portal. The large image is an edit of the record to include a medium size version of the image for easier viewing in this article. The portal software is open source and it is freely available for reuse through the Symbiota GitHub repository. The image is an example of a specimen record that includes an image of the specimen with label data. The image is contributed by the UCSB Invertebrate Zoology Collection at the Cheadle Center for Biodiversity and Ecological Restoration. The usage rights for the image is Creative Commons 0 (public domain).
Figure 1 from: Seltmann K, Lafia S, Paul D, James S, Bloom D, Rios N, Ellis S, Farrell U, Utrup J, Yost M, Davis E, Emery R, Motz G, Kimmig J, Shirey V, Sandall E, Park D, Tyrrell C, Thackurdeen R, Collins M, O'Leary V, Prestridge H, Evelyn C, Nyberg B (2018) Georeferencing for Research Use (GRU): An integrated geospatial training paradigm for biocollections researchers and data providers. Research Ideas and Outcomes 4: e32449. https://doi.org/10.3897/rio.4.e32449
Figure 1 Map created using SimpleMappr (Shorthouse 2010) that illustrates geolocated specimens for Genus=Cicindela in California as found on iDigBio.
Figure 1 from: Petersen M, Hoffmann J, Glöckler F (2019) Access to Geosciences – Ways and Means to share and publish collection data. Research Ideas and Outcomes 5: e32987. https://doi.org/10.3897/rio.5.e32987
Figure 1 Types of collection objects. Given are the frequencies of particular objects the survey participants' institution or department holds. Other objects include soil, crystal models, historical instruments, boreholes, etc.
Figure 5 from: Petersen M, Hoffmann J, Glöckler F (2019) Access to Geosciences – Ways and Means to share and publish collection data. Research Ideas and Outcomes 5: e32987. https://doi.org/10.3897/rio.5.e32987
Figure 5 Elements identified by workshop and survey participants as being important for the publication of geoscientific collection objects. The four different object classes (fossils, rocks, meteorites, and minerals) are highlighted in different shades of green, terms important for the respective class are assigned around the object name and likewise colored, terms in the center (grey) are relevant for all four object classes. Note: The figure only summarizes the mentioned terms, there might be more properties that are important for the publication of collection object associated data for the different object classes and / or more terms mentioned for one class only but important for several.
Figure 4 from: Petersen M, Hoffmann J, Glöckler F (2019) Access to Geosciences – Ways and Means to share and publish collection data. Research Ideas and Outcomes 5: e32987. https://doi.org/10.3897/rio.5.e32987
Figure 4 Awareness and usage of Geoscientific Collection Access Service (GeoCASe). Shown is the frequency of answers regarding the awareness of GeoCASe (a), the data provision through the GeoCASe portal (b), the readiness to support the progress of improvements (c), and the interest of being part of the GeoCASe community (d).
Supplementary material 1 from: Petersen M, Hoffmann J, Glöckler F (2019) Access to Geosciences – Ways and Means to share and publish collection data. Research Ideas and Outcomes 5: e32987. https://doi.org/10.3897/rio.5.e32987
Sheet on the survey on geoscientific collection data
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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)
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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.