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Figure 3. Haplotype networks for Rattus exulans, R in Expanding Population Edge Craniometrics and Genetics Provide Insights into Dispersal of Commensal Rats through Nusa Tenggara, Indonesia
Figure 3. Haplotype networks for Rattus exulans, R. argentiventer, and Rattus rattus Complex LIV. Sunda refers to the islands of Borneo, Java, and Sumatra; the Indonesian sample (brown) lacks further collection information.
Data from: Rtapas: An R package to assess cophylogenetic signal between two evolutionary histories
<p class="MsoNormal"><span>Cophylogeny represents a framework to understand how ecological and evolutionary process influence lineage diversification. The recently developed algorithm Random Tanglegram Partitions provides a directly interpretable statistic to quantify the strength of cophylogenetic signal and incorporates phylogenetic uncertainty into its estimation, and maps onto a tanglegram the contribution to cophylogenetic signal of individual host-symbiont associations. We introduce </span><span>Rtapas</span><span>, an R package to perform Random Tanglegram Partitions. </span><span>Rtapas</span><span> </span><span>applies a given global-fit method to random partial tanglegrams of a fixed size to identify the associations, terminals, and internal nodes that maximize phylogenetic congruence. This new package extends the original implementation with a new algorithm that examines the contribution to phylogenetic incongruence of each host-symbiont association and adds ParaFit, a method designed to test for topological congruence between two phylogenies, to the list of global-fit methods than can be applied. </span><span>Rtapas</span><span> </span><span>facilitates and speeds up cophylogenetic analysis, as it can handle large phylogenies (100+ terminals) in affordable computational time as illustrated with two real-world examples. </span><span>Rtapas</span><span> </span><span>can particularly cater for the need for causal inference in cophylogeny in two domains: (i) Analysis of complex and intricate host-symbiont evolutionary histories and (ii) assessment of topological (in)congruence between phylogenies produced with different DNA markers and specifically identify subsets of loci for phylogenetic analysis that are most likely to reflect gene-tree evolutionary histories.</span></p>
Input data for the case study reported in "DREAM: an R package for druggability evaluation of human complex diseases".
<p>The data included in this record constituted the input for the case study reported in the manuscript "DREAM: an R package for druggability evaluation of human complex diseases", by Antonio Federico, Michele Fratello, Alisa Pavel, Lena Möbus, Giusy del Giudice, Angela Serra, Dario Greco. The data derive from transcriptomics experiments executed on lesional skin from atopic dermatitis patients and unaffected skin counterparts. The data consists of two files in ".txt" format reporting gene expression data in tabular format, where on the rows are reported genes and on the columns are reported samples. The data is an aggregated and batch-corrected collection of datasets originally downloaded by Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/). The file "GE_Mic_AD_Pamr_MAARS.txt" reports gene expression estimates of lesional skin of atopic dermatitis patients, while the file "GE_Mic_AD_Pamr_nl_MAARS.txt" reports gene expression estimates of non-lesional skin of atopic dermatitis patients.</p>
Figure 3 in A NEW SPECIES IN THE RHEOCRICOTOPUS (R.) EFFUSUS GROUP FROM CANADA WITH A REVIEW OF THE NEARCTIC SPECIES OF RHEOCRICOTOPUS AND PARAMETRIOCNEMUS (CHIRONOMIDAE: ORTHOCLADIINAE) Abstract
Figure 3. Rheocricotopus (R.) reduncusoides sp. n. male. a) wing, b) hypopygium, arrow indicates the sternapodeme, c) superior volsella caudomedian projection.
Figure 2 in A NEW SPECIES IN THE RHEOCRICOTOPUS (R.) EFFUSUS GROUP FROM CANADA WITH A REVIEW OF THE NEARCTIC SPECIES OF RHEOCRICOTOPUS AND PARAMETRIOCNEMUS (CHIRONOMIDAE: ORTHOCLADIINAE) Abstract
Figure 2. Rheocricotopus (R.) reduncusoides sp. n. male. a) head, b) antenna, c) thorax lateral view.
Figure 1 in A NEW SPECIES IN THE RHEOCRICOTOPUS (R.) EFFUSUS GROUP FROM CANADA WITH A REVIEW OF THE NEARCTIC SPECIES OF RHEOCRICOTOPUS AND PARAMETRIOCNEMUS (CHIRONOMIDAE: ORTHOCLADIINAE) Abstract
Figure 1. Parametriocnemus hamatus (Johannsen) male. a) antenna, b) head, c) thorax lateral view, d) wing, e) hypopygium.
Figure 4 in A NEW SPECIES IN THE RHEOCRICOTOPUS (R.) EFFUSUS GROUP FROM CANADA WITH A REVIEW OF THE NEARCTIC SPECIES OF RHEOCRICOTOPUS AND PARAMETRIOCNEMUS (CHIRONOMIDAE: ORTHOCLADIINAE) Abstract
Figure 4. Rheocricotopus (R.) reduncus Saether and Schnell, male paratypes from Norway. a) caudomedian projection and inferior volsella, b) variation of the caudomedian projection and inferior volsella, c) sternapodeme (black arrow) and phallapodeme (white arrows).
Mitglieder des EVB geniessen im Hotel in Grandvillard Freiburger Spezialitäten: René Renz, Bene Jost, Jürgen Hensle, Ursula Beutler Aarun und Christoph Germann (v. l. n. r.). (Foto Elisabeth Friedli) in Vereinsausflug des EVB 2017 in die Region des Moléson: Die Sonne macht sich rar
Mitglieder des EVB geniessen im Hotel in Grandvillard Freiburger Spezialitäten: René Renz, Bene Jost, Jürgen Hensle, Ursula Beutler Aarun und Christoph Germann (v. l. n. r.). (Foto Elisabeth Friedli)
Data and R scripts for KCC plots in Douville (2023)
<p>Data and R scripts for plotting Fig. 3 and Fig.4 in Douville (2023)</p> <p>Douville H. (2023) Robust and perfectible constraints on human-induced Arctic climate change. Communications Earth & Environment (revised)</p>
Fig. 2. Sardinian Rhithrodytes species. A – R in A new, putatively semisubterranean, Rhithrodytes diving beetle from southwestern Sardinia (Coleoptera: Dytiscidae)
Fig. 2. Sardinian Rhithrodytes species. A – R. pantaleonii sp. nov., paratype, dorsal habitus; B – R. sexguttatus (Aubé, 1838), dorsal habitus; C – R. pantaleonii sp. nov., holotype, male genitalia; D – R. sexguttatus (Aubé, 1838), male genitalia. In C & D, images represent, from left to right: median lobe, lateral view; median lobe, ventral view; median lobe apex; paramere. Scale bars A & B = 1 mm; C & D = 100 μm.
Figure 2 in Rhyacophila siparantum sp. nov. (Trichoptera: Rhyacophilidae), a new species of the R. philopotamoides species group from the Republic of Kosovo with molecular and ecological notes
Figure 2. Picture of the type locality of Rhyacophila siparantum sp. nov.: Bogë Stream, Rugovë Mountain, Kosovo.
Figure 4 in Rhyacophila siparantum sp. nov. (Trichoptera: Rhyacophilidae), a new species of the R. philopotamoides species group from the Republic of Kosovo with molecular and ecological notes
Figure 4. Lateral profile of segment X: A. Rhyacophila siparantum sp. nov. (Kosovo); B. Rhyacophila schmidinarica (Croatia); C. Rhyacophila hirticornis (Croatia).
Figure 3 in Rhyacophila siparantum sp. nov. (Trichoptera: Rhyacophilidae), a new species of the R. philopotamoides species group from the Republic of Kosovo with molecular and ecological notes
Figure 3. Lateral profile of: A. Rhyacophila schmidinarica (Croatia); B. Rhyacophila siparantum sp. nov. (Kosovo); C. Rhyacophila hirticornis (Croatia).
Figure 9 in Rhyacophila siparantum sp. nov. (Trichoptera: Rhyacophilidae), a new species of the R. philopotamoides species group from the Republic of Kosovo with molecular and ecological notes
Figure 9. Maximum likelihood phylogenetic tree based on the analysis of the COI sequences of Rhyacophila species. Numbers near nodes indicate maximum likelihood (ML) ultrafast bootstrap support values (BS), and Bayesian posterior probabilities (BPP). The result of morphological examination is shown by the first row of vertical bars where each color indicates a different species. The results of species delimitations are represented with the following vertical bars, from left to right, indicate the OTUs inferred by ABGD and mPTP. Terminal codes present BOLD ID, as in Table 1.
Figure 8. Segment X in Rhyacophila siparantum sp. nov. (Trichoptera: Rhyacophilidae), a new species of the R. philopotamoides species group from the Republic of Kosovo with molecular and ecological notes
Figure 8. Segment X and anal sclerites with apical band in ventrocaudal position (A); anal sclerites with apical band in dorsocaudal position (B).
Data and R scrips for "Exposure to closed-loop scrubber washwater alters biodiversity, reproduction, and grazing of marine zooplankton"
<p>Research data and scripts associated with the article "Exposure to closed-loop scrubber washwater alters biodiversity, reproduction, and grazing of marine zooplankton" by Jönander et al.</p>
R SCRIPT: INFLUENCE OF ENVIRONMENTAL FACTORS ON THE POWER PRODUCED BY PHOTOVOLTAIC PANELS ARTIFICIALLY WEATHERED
<p>The files describe the r-script code and data base used in the article titled: "INFLUENCE OF ENVIRONMENTAL FACTORS ON THE POWER PRODUCED BY PHOTOVOLTAIC PANELS ARTIFICIALLY WEATHERED"</p>
Final abundances used in "Impact of level densities and gamma-strength functions on r-process simulations"
<p>Dataset of final abundances used in the article "Impact of level densities and gamma-strength functions on r-process simulations", found on ArXiv at https://arxiv.org/abs/2305.03664.</p> <p>The five files named "final_y_x_ext_REACLIB" contain the abundances calculated using the REACLIB rates and the x trajectory.</p> <p>The five folders represent the five different trajectories used, and they each contain 48 final abundance files. These were calculated using the 48 different neutron-capture rate combinations from the 6 nuclear level density and the 8 gamma-strength function models available in TALYS 1.95. The names indicate the trajectory, the mass model, the nuclear level density, the gamma-strength function and the optical model potential used. For example, the file named "b_output_m2n1s7o2_noDZ" contains the final abundances obtained using trajectory "b", mass model 2, nuclear level density 1, strength 7 and optical model potential 2 (in this case meaning keyword "localomp n" in TALYS 1.95). For details and references, see the article.</p> <p>The first column in all files indicates the mass number A, the second column the final abundance Y.</p>
Рис. 26. Сравнение среΑних значений частоты изменчивости эΛементов рисунка и инΑекса пигментации Mesobuthus eupeus в посеΛениях из разнотипных (А) и оΑнотипных (В) биотопов в кажΑой из выборок: I – Северо-ЗапаΑный Гобустан; II – Северо-Восточный Гобустан; III – ЦентраΛьный Гобустан; IV – Юго-Восточный Гобустан; V – Юго-Восточный Ширван. ИнΑекс корреΛяции r в преΑеΛах 0.744–0.989; p <0.05. Fig. 26. Comparison of the average values of the frequency of variability of pattern elements and the pigmentation index of Mesobuthus eupeus in conglomerations from habitats of different types (A) and of the same type (B) in each sample: I – northwestern Gobustan; II – northeastern Gobustan; III – central Gobustan; IV – southeastern Gobustan; V – southeastern Shirvan. Correlation index r = 0.744–0.989; p <0.05. in Materials on the colour pattern variability of Mesobuthus eupeus (C.L. Koch, 1839) (Arachnida: Scorpiones) in southeastern Shirvan and Gobustan (Eastern Azerbaijan)
Рис. 26. Сравнение среΑних значений частоты изменчивости эΛементов рисунка и инΑекса пигментации Mesobuthus eupeus в посеΛениях из разнотипных (А) и оΑнотипных (В) биотопов в кажΑой из выборок: I – Северо-ЗапаΑный Гобустан; II – Северо-Восточный Гобустан; III – ЦентраΛьный Гобустан; IV – Юго-Восточный Гобустан; V – Юго-Восточный Ширван. ИнΑекс корреΛяции r в преΑеΛах 0.744–0.989; p <0.05. Fig. 26. Comparison of the average values of the frequency of variability of pattern elements and the pigmentation index of Mesobuthus eupeus in conglomerations from habitats of different types (A) and of the same type (B) in each sample: I – northwestern Gobustan; II – northeastern Gobustan; III – central Gobustan; IV – southeastern Gobustan; V – southeastern Shirvan. Correlation index r = 0.744–0.989; p <0.05.
Fig. 2 in A new R package and web application for detecting bilateral asymmetry in parasitic infections
Fig. 2. Histogram showing distribution of fold differences in abundance of Diplostomum spp. metacercariae between left and right eyes (excluding lenses). For each host the number of parasites in the right eye was divided by the number of parasites in the left eye, and the result was binary log transformed. The log 2 ratio will be negative if there are more parasites in the left than right eye, and positive if there are more parasites in the right than left eye. A log 2 ratio of one corresponds to a one-fold difference, i.e. double the number of parasites. Perfect symmetry is a log 2 ratio of zero.
ScienceDex guides
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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)
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.