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FIGURE 2 in Bathyraja (Arctoraja) sexoculata sp. nov., a new softnose skate (Rajiformes Arhynchobatidae) from Simushir Island, Kuril Islands (western North Pacific) with special reference to geographic variations in Bathyraja (Arctoraja) smirnovi
FIGURE 2. Bathyraja sexoculata sp. nov., ZMMU-P 24098, holotype, 346 mm TL, immature male, preserved. (A) dorsal view, (B) ventral view
FIGURE 11 in Bathyraja (Arctoraja) sexoculata sp. nov., a new softnose skate (Rajiformes Arhynchobatidae) from Simushir Island, Kuril Islands (western North Pacific) with special reference to geographic variations in Bathyraja (Arctoraja) smirnovi
FIGURE 11. Frequency distribution of selected meristic counts in Bathyraja sexoculata sp. nov. and B. smirnovi. (A) total tail thorns (predorsal + interdorsal), (B) nuchal thorns, (C) predorsal caudal vertebrae. Red, B. sexoculata; black, B. smirnovi from southern Sea of Japan; gray, B. smirnovi from northern Sea of Japan; white, B. smirnovi from Sea of Okhotsk
Data from: Estimating the molecular evolutionary rates of mitochondrial genes referring to Quaternary Ice Age events with inferred population expansions and dispersals in Japanese Apodemus
Background: Determining reliable evolutionary rates of molecular markers is essential in illustrating historical episodes with phylogenetic inferences. Although emerging evidence has suggested a high evolutionary rate for intraspecific genetic variation, it is unclear how long such high evolutionary rates persist because a recent calibration point is rarely available. Other than using fossil evidence, it is possible to estimate evolutionary rates by relying on the well-established temporal framework of the Quaternary glacial cycles that would likely have promoted both rapid expansion events and interisland dispersal events. Results: We examined mitochondrial cytochrome b (Cytb) and control region (CR) gene sequences in two Japanese wood mouse species, Apodemus argenteus and A. speciosus, of temperate origin and found signs of rapid expansion in the population from Hokkaido, the northern island of Japan. Assuming that global warming after the last glacial period 7–10 thousand years before present (kyr BP) was associated with the expansion, the evolutionary rates (sites per million years, myr) of Cytb and CR were estimated as 11–16% and 22–32%, respectively, for A. argenteus, and 12–17% and 17–24%, respectively, for A. speciosus. Additionally, the significant signature of rapid expansion detected in the mtDNA sequences of A. speciosus from the remaining southern main islands, Honshu, Shikoku, and Kyushu, provided an estimated Cytb evolutionary rate of 3.1%/site/myr under the assumption of a postglacial population expansion event long ago, most probably at 130 kyr BP. Bayesian analyses using the higher evolutionary rate of 11–17%/site/myr for Cytb supported the recent demographic or divergence events associated with the Last Glacial Maximum. However, the slower evolutionary rate of 3.1%/site/myr would be reasonable for several divergence events that were associated with glacial periods older than 130 kyr BP. Conclusions: The faster and slower evolutionary rates of Cytb can account for divergences associated with the last and earlier glacial maxima, respectively, in the phylogenetic inference of murine rodents. The elevated evolutionary rate seemed to decline within 100,000 years.
Data from: Avoidable errors in the modeling of outbreaks of emerging pathogens, with special reference to Ebola
As an emergent infectious disease outbreak unfolds, public health response is reliant on information on key epidemiological quantities, such as transmission potential and serial interval. Increasingly, transmission models fit to incidence data are used to estimate these parameters and guide policy. Some widely used modelling practices lead to potentially large errors in parameter estimates and, consequently, errors in model-based forecasts. Even more worryingly, in such situations, confidence in parameter estimates and forecasts can itself be far overestimated, leading to the potential for large errors that mask their own presence. Fortunately, straightforward and computationally inexpensive alternatives exist that avoid these problems. Here, we first use a simulation study to demonstrate potential pitfalls of the standard practice of fitting deterministic models to cumulative incidence data. Next, we demonstrate an alternative based on stochastic models fit to raw data from an early phase of 2014 West Africa Ebola virus disease outbreak. We show not only that bias is thereby reduced, but that uncertainty in estimates and forecasts is better quantified and that, critically, lack of model fit is more readily diagnosed. We conclude with a short list of principles to guide the modelling response to future infectious disease outbreaks.
Data from: The plover neurotranscriptome assembly: transcriptomic analysis in an ecological model species without a reference genome
We assembled a de novo transcriptome of short-read Illumina RNA-Seq data generated from telencephalon and diencephalon tissue samples from the Kentish plover, Charadrius alexandrinus. This is a species of considerable interest in behavioural ecology for its highly variable mating system and parental behaviour, but it lacks genomic resources and is evolutionarily distant from the few available avian draft genome sequences. We assembled and identified over 21 000 transcript contigs with significant expression in our samples, showing high homology to exonic sequences in avian draft genomes. From these, we identified >31 000 high-quality SNPs and > 2500 simple sequence repeats (SSRs). We also analysed expression patterns in our data to identify potential candidate genes related to differences in male and female behaviour, identifying over 200 nonoverlapping putative autosomal transcripts that show significant expression differences between males and females. Gene ontology analysis revealed that female-biased transcripts were significantly enriched for cerebral functions related to learning, cognition and memory, and male-biased transcripts were mostly enriched for terms related to neural function such as neuron projection and synapses. This data set provides one of the first de novo transcriptome assemblies from non-normalized short-read next-generation data and outlines an effective strategy for measuring sequence and expression variability simultaneously without the aid of a reference genome.
3D Deconvolution reference dataset
<p>Paired airy-light-sheet data with fluorescent bead and sample data acquired at NPL.</p>
FIGURES 410–413 in The Italian species of the Chthonius ischnocheles group (Arachnida, Pseudoscorpiones, Chthoniidae), with reference to neighbouring countries
FIGURES 410–413. Distribution maps for the Italian species of the Chthonius ischnocheles group. 410, Chthonius caoduroi Callaini, 1987, Chthonius gallettii n. sp., Chthonius inguscioi n. sp., Chthonius marciai n. sp. and Chthonius multidentatus Beier, 1963; 411, Chthonius caprai Gardini, 1977, Chthonius jonicus Beier, 1931 and Chthonius leoi (Callaini, 1988); 412, Chthonius halberti Kew, 1916, Chthonius nicolosii n. sp., Chthonius ressli Beier, 1956 and Chthonius stammeri Beier, 1942; 413, Chthonius horridus Beier, 1934, Chthonius italicus Beier, 1930 and Chthonius lanai n. sp.
FIGURES 406–409 in The Italian species of the Chthonius ischnocheles group (Arachnida, Pseudoscorpiones, Chthoniidae), with reference to neighbouring countries
FIGURES 406–409. Distribution maps for the Italian species of the Chthonius ischnocheles group. 406, Chthonius densedentatus Beier, 1938; 407, Chthonius ischnocheles (Hermann, 1804); 408, Chthonius pygmaeus Beier, 1934; 409, Chthonius euganeus Gardini, 1991, Chthonius gentianae n. sp., Chthonius herminii n. sp. and Chthonius paolettii Beier, 1973.
FIGURES 387–393. Chthonius stammeri Beier, 1942 in The Italian species of the Chthonius ischnocheles group (Arachnida, Pseudoscorpiones, Chthoniidae), with reference to neighbouring countries
FIGURES 387–393. Chthonius stammeri Beier, 1942, Grava dell'Occhio, 3.II.1999 (Laurino, Salerno). 387, male, anterior margin of carapace; 388, female, id.; 389, male, carapace; 390, male, right chelicera; 391, female, movable finger of right chelicera; 392, male, right chelal hand, dorsal view; 393, female, id.
FIGURES 373–379. Chthonius ressli Beier, 1956, Gaibola near Bologna. 373 in The Italian species of the Chthonius ischnocheles group (Arachnida, Pseudoscorpiones, Chthoniidae), with reference to neighbouring countries
FIGURES 373–379. Chthonius ressli Beier, 1956, Gaibola near Bologna. 373, male, anterior margin of carapace; 374, female, id.; 375, male, carapace; 376, male, right chelicera; 377, female, movable finger of right chelicera; 378, male, right chelal hand, dorsal view; 379, female, id.
FIGURES 365–372. Chthonius pygmaeus Beier, 1934 in The Italian species of the Chthonius ischnocheles group (Arachnida, Pseudoscorpiones, Chthoniidae), with reference to neighbouring countries
FIGURES 365–372. Chthonius pygmaeus Beier, 1934, near Passo di Tanamea, 6.X.1997 (Lusevera, Udine). 365, male, right chela, antiaxial view; 366, male, detail of fingers at the chelal tip, antiaxial view; 367, male, detail of fingers at level of trichobothria est-it and st-t, antiaxial view; 368, male, detail of fingers at level of trichobothrium sb, antiaxial view; 369, female, right chela, antiaxial view; 370, female, detail of fingers at the chelal tip, antiaxial view; 371, female, detail of fingers at level of trichobothria est-it and st-t, antiaxial view; 372, female, detail of fingers at level of trichobothrium sb, antiaxial view.
FIGURES 380–386. Chthonius ressli Beier, 1956, Gaibola near Bologna. 380 in The Italian species of the Chthonius ischnocheles group (Arachnida, Pseudoscorpiones, Chthoniidae), with reference to neighbouring countries
FIGURES 380–386. Chthonius ressli Beier, 1956, Gaibola near Bologna. 380, male, right chela, antiaxial view; 381, male, detail of fingers at the distal half of chela, antiaxial view; 382, male, detail of fingers at level of trichobothrium sb, antiaxial view; 383, female, right chela, antiaxial view; 384, female, detail of fingers at the chelal tip, antiaxial view; 385, female, detail of fingers at level of trichobothria est-it and st-t, antiaxial view; 386, female, detail of fingers at level of trichobothrium sb, antiaxial view.
FIGURES 402–405 in The Italian species of the Chthonius ischnocheles group (Arachnida, Pseudoscorpiones, Chthoniidae), with reference to neighbouring countries
FIGURES 402–405. Distribution maps for the Italian species of the Chthonius ischnocheles group. 402, Chthonius agazzii Beier, 1966 and Chthonius comottii Inzaghi, 1987; 403, Chthonius alpicola Beier, 1951; 404, Chthonius carinthiacus Beier, 1951; 405, Chthonius guglielmii Callaini, 1986 and Chthonius ilvensis Beier, 1963.
FIGURES 354–357. Chthonius paolettii Beier, 1973 in The Italian species of the Chthonius ischnocheles group (Arachnida, Pseudoscorpiones, Chthoniidae), with reference to neighbouring countries
FIGURES 354–357. Chthonius paolettii Beier, 1973, female, Covol dei Siori (Valstagna, Vicenza). 354, left chela, antiaxial view; 355, id., detail of fingers at the chelal tip, antiaxial view; 356, id., detail of fingers at level of trichobothria est-it and st-t, antiaxial view; 357, id., detail of fingers at level of trichobothrium sb, antiaxial view.
FIGURES 327–334. Chthonius multidentatus Beier, 1963 in The Italian species of the Chthonius ischnocheles group (Arachnida, Pseudoscorpiones, Chthoniidae), with reference to neighbouring countries
FIGURES 327–334. Chthonius multidentatus Beier, 1963, Grotta del Conzo, 26.VI.2019 (Syracuse). 327, male, right chela, antiaxial view; 328, male, detail of fingers at the chelal tip, antiaxial view; 329, male, detail of fingers at level of trichobothria est-it and st-t, antiaxial view; 330, male, detail of fingers at level of trichobothrium sb, antiaxial view; 331, female, right chela, antiaxial view; 332, female, detail of fingers at the chelal tip, antiaxial view; 333, female, detail of fingers at level of trichobothria est-it and st-t, antiaxial view; 334, female, detail of fingers at level of trichobothrium sb, antiaxial view.
FIGURES 266–273. Chthonius italicus Beier, 1930 in The Italian species of the Chthonius ischnocheles group (Arachnida, Pseudoscorpiones, Chthoniidae), with reference to neighbouring countries
FIGURES 266–273. Chthonius italicus Beier, 1930, Grotta dei Surgentin, 29.III.2015 (Pigna, Imperia) (unless otherwise stated). 266, male, anterior margin of carapace; 267, female, id.; 268, male, carapace; 269, male, right chelicera; 270, female, movable finger of right chelicera; 271, male (Buco del Dré, Roaschia), id.; 272, male, right chelal hand, dorsal view; 273, female, id.
FIGURES 289–296. Chthonius jonicus Beier, 1931 in The Italian species of the Chthonius ischnocheles group (Arachnida, Pseudoscorpiones, Chthoniidae), with reference to neighbouring countries
FIGURES 289–296. Chthonius jonicus Beier, 1931, Riserva Naturale dello Zingaro, 31.XII.1994 (Scopello, Trapani). 289, male, right chela, antiaxial view; 290, male, detail of fingers at the chelal tip, antiaxial view; 291, male, detail of fingers at level of trichobothria est-it and st-t, antiaxial view; 292, male, detail of fingers at level of trichobothrium sb, antiaxial view; 293, female, right chela, antiaxial view; 294, female, detail of fingers at the chelal tip, antiaxial view; 295, female, detail of fingers at level of trichobothria est-it and st-t, antiaxial view; 296, female, detail of fingers at level of trichobothrium sb, antiaxial view.
FIGURES 394–401. Chthonius stammeri Beier, 1942 in The Italian species of the Chthonius ischnocheles group (Arachnida, Pseudoscorpiones, Chthoniidae), with reference to neighbouring countries
FIGURES 394–401. Chthonius stammeri Beier, 1942, Grava dell'Occhio, 3.II.1999 (Laurino, Salerno). 394, male, right chela, antiaxial view; 395, male, detail of fingers at the chelal tip, antiaxial view; 396, male, detail of fingers at level of trichobothria est-it and st-t, antiaxial view; 397, male, detail of fingers at level of trichobothrium sb, antiaxial view; 398, female, right chela, antiaxial view; 399, female, detail of fingers at the chelal tip, antiaxial view; 400, female, detail of fingers at level of trichobothria est-it and st-t, antiaxial view; 401, female, detail of fingers at level of trichobothrium sb, antiaxial view.
FIGURES 245–252 in The Italian species of the Chthonius ischnocheles group (Arachnida, Pseudoscorpiones, Chthoniidae), with reference to neighbouring countries
FIGURES 245–252. Chthonius ischnocheles (Hermann, 1804), Castiglione delle Stiviere (Mantova). 245, male, right chela, antiaxial view (hand granulation omitted); 246, male, detail of fingers at the chelal tip, antiaxial view; 247, male, detail of fingers at level of trichobothria est-it and st-t, antiaxial view; 248, male, detail of fingers at level of trichobothrium sb, antiaxial view; 249, female, right chela, antiaxial view (hand granulation omitted); 250, female, detail of fingers at the chelal tip, antiaxial view; 251, female, detail of fingers at level of trichobothria est-it and st-t, antiaxial view; 252, female, detail of fingers at level of trichobothrium sb, antiaxial view.
FIGURES 237–244 in The Italian species of the Chthonius ischnocheles group (Arachnida, Pseudoscorpiones, Chthoniidae), with reference to neighbouring countries
FIGURES 237–244. Chthonius ischnocheles (Hermann, 1804), Castiglione delle Stiviere (Mantova). 237, male, anterior margin of carapace; 238, female, id.; 239, male, carapace; 240, male, right ocular area; 241, male, right chelicera (dorsal granulation omitted); 242, female, movable finger of right chelicera; 243, male, right chelal hand, dorsal view (granulation omitted); 244, female, id. (granulation omitted).
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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.