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Fig. 18 in Phylogenetic Studies On Didelphid Marsupials Ii. Nonmolecular Data And New Irbp Sequences: Separate And Combined Analyses Of Didelphine Relationships With Denser Taxon Sampling
Fig. 18. Strict consensus of 252 equally mostparsimonious trees obtained by a heuristic analysis of IRBP sequences described in this report (see table 4 for summary dataset characteristics and tree statistics). Bremer support and bootstrap values are provided above and below each branch, repectively. For simplicity, conspecific sequences (analyzed separately in PAUP*) have been condensed to single terminals in this diagram. Outgroup taxa are indicated with asterisks. All parsimonyequivalent resolutions of the basal ingroup polytomy are shown in figure 19A–E.
Fig. 5 in Tridacna noae (Röding, 1798) - a valid giant clam species separated from T. maxima (Röding, 1798) by morphological and genetic data
Fig. 5. Neighbour joining tree of Tridacninae using Kimura 2-parameter model based on 28S rRNA gene sequence. Bootstrap values: 1,000; outgroup: Corculum cardissa.
Fig. 19 in Phylogenetic Studies On Didelphid Marsupials Ii. Nonmolecular Data And New Irbp Sequences: Separate And Combined Analyses Of Didelphine Relationships With Denser Taxon Sampling
Fig. 19. All equally mostparsimonious resolutions of the basal didelphine polytomy in figures 18 and 21. A, Resolution supported by 72 mostparsimonious trees (MPTs) from the IRBP1 analysis and 6 MPTs from the IRBP2 analysis; B, resolution supported by 72 MPTs from the IRBP1 analysis and 6 MPTs from the IRBP2 analysis; C, resolution supported by 36 MPTs from the IRBP1 analysis and 3 MPTs from the IRBP2 analysis; D, resolution supported by 36 MPTs from the IRBP1 analysis, 6 MPTs from the IRBP2 analysis, and 8 MPTs from the combined analysis; E, resolution supported by 36 MPTs from the IRBP1 analysis, 6 MPTs from the IRBP2 analysis, and 8 MPTs from the combined analysis; F, resolution supported by 18 MPTs from the combined analysis only.
Fig. 7 in Tridacna noae (Röding, 1798) - a valid giant clam species separated from T. maxima (Röding, 1798) by morphological and genetic data
Fig. 7. Mantle colour pattern and hyaline organs of Tridacna maxima (A, B) and Tridacna noae (C, D). E, Enlarged hyaline organs of T. maxima; F, Enlarged hyaline organs of T. noae. →: Hyaline organs.
Fig. 13 in Phylogenetic Studies On Didelphid Marsupials Ii. Nonmolecular Data And New Irbp Sequences: Separate And Combined Analyses Of Didelphine Relationships With Denser Taxon Sampling
Fig. 13. Anterolingual views of left M3 illustrating taxonomic differences in cingular morphology. Left, Marmosa murina (AMNH 272870) with preprotocrista and anterolabial cingulum joined to form a continuous shelf along the anterior margin of the tooth crown. Right, Monodelphis adusta (AMNH 272781) with separate crista and cingulum (no continuous shelf).
Text-fig. 4. Neogene generic diversity in rodents for the three study areas separately and combined. in Generically Speaking, A Survey On Neogene Rodent Diversity At The Genus Level In The Now Database
Text-fig. 4. Neogene generic diversity in rodents for the three study areas separately and combined.
Text-fig. 7. PGLS regressions for Mylodontidae, "Orophodontidae", and the rest of the sloths considered separately, Mylodontidae: dash double-dot line (-..-), "Orophodontidae": dash-dot line (-.-), rest of sloths: dash line (--). in Unexpected Inhibitory Cascade In The Molariforms Of Sloths (Folivora, Xenarthra): A Case Study In Xenarthrans Honouring Gerhard Storch'S Open-Mindedness
Text-fig. 7. PGLS regressions for Mylodontidae, "Orophodontidae", and the rest of the sloths considered separately, Mylodontidae: dash double-dot line (-..-), "Orophodontidae": dash-dot line (-.-), rest of sloths: dash line (--).
Text-fig. 2. Phylogeography based on mitochondrial phylogeny showing several evolutionary lineages of Arvicola and the separation of the Italian lineage of Arvicola, currently A. italicus (lineage A1), from European and Euro-Asiatic groups. From Wust-Saucy (1998: fig. 27), modified. in Independent Water Vole (Mimomys Savini, Arvicola: Rodentia, Mammalia) Lineages In Italy And Central Europe
Text-fig. 2. Phylogeography based on mitochondrial phylogeny showing several evolutionary lineages of Arvicola and the separation of the Italian lineage of Arvicola, currently A. italicus (lineage A1), from European and Euro-Asiatic groups. From Wust-Saucy (1998: fig. 27), modified.
Text-fig. 12. Scanning electron microscope (SEM) images of pollen of Sergipea sp. from a group of probable fragmentary pollen sacs; Torres Vedras locality, Portugal. a) Cluster of probable fragmentary pollen sacs that yielded the pollen in this Text-figure; b, c) Pollen grains showing the robust longitudinal ribs separated by prominent areas of granular exine; note the groove along the margins of the longitudinal ribs (arrowheads); d) Pollen grain showing the granular exine flanked by two robust ribs; note the groove along the margins of the longitudinal ribs (arrowheads). Specimen, TV44-S148012 (a–d). Scale bars 150 Μm (a), 12 Μm (c), 6 Μm (b, d). in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community
Text-fig. 12. Scanning electron microscope (SEM) images of pollen of Sergipea sp. from a group of probable fragmentary pollen sacs; Torres Vedras locality, Portugal. a) Cluster of probable fragmentary pollen sacs that yielded the pollen in this Text-figure; b, c) Pollen grains showing the robust longitudinal ribs separated by prominent areas of granular exine; note the groove along the margins of the longitudinal ribs (arrowheads); d) Pollen grain showing the granular exine flanked by two robust ribs; note the groove along the margins of the longitudinal ribs (arrowheads). Specimen, TV44-S148012 (a–d). Scale bars 150 Μm (a), 12 Μm (c), 6 Μm (b, d).
Text-fig. 13. Scanning electron microscope (SEM) images of pollen or spore clump with pollen grains or spores of unknown affinity that occur separately or adhering together in dyads, triads and tetrads; Torres Vedras locality, Portugal. a) Clump of pollen or spores that yielded the pollen or spores in this Text-figure; b–f) Grains adhering together in twos, threes or fours (b–e) or occurring singly and apparently with a proximal trilete mark (f); note that the adhering grains are connected by a smooth bandlike covering, perhaps remains of the microspore mother cell; note also abundant orbicules of various sizes among and over the grains. Specimen, TV44-S148149. Scale bars 300 Μm (a), 30 Μm (b–f). in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community
Text-fig. 13. Scanning electron microscope (SEM) images of pollen or spore clump with pollen grains or spores of unknown affinity that occur separately or adhering together in dyads, triads and tetrads; Torres Vedras locality, Portugal. a) Clump of pollen or spores that yielded the pollen or spores in this Text-figure; b–f) Grains adhering together in twos, threes or fours (b–e) or occurring singly and apparently with a proximal trilete mark (f); note that the adhering grains are connected by a smooth bandlike covering, perhaps remains of the microspore mother cell; note also abundant orbicules of various sizes among and over the grains. Specimen, TV44-S148149. Scale bars 300 Μm (a), 30 Μm (b–f).
Fig. 16. A. Vertebral line normally separated from the parietal region. B in Phylogenetic relationships based on morphological data and taxonomy of the genus Salvadora Baird & Girard, 1853 (Reptilia, Colubridae)
Fig. 16. A. Vertebral line normally separated from the parietal region. B. Vertebral line reaching the parietal region.
Binary Classification as a Phase Separation Process (data repository)
<p><strong>For version 0.0.2 (from 2021) see below:</strong></p> <p>This is a data repository for the paper "Binary classification as a phase separation process", by Rafael Monteiro.</p> <ul> <li>Website with description of this project: <a href="https://rafael-a-monteiro-math.github.io/Binary_classification_phase_separation/index.html">https://rafael-a-monteiro-math.github.io/Binary_classification_phase_separation/index.html</a></li> <li>Github: <a href="https://github.com/rafael-a-monteiro-math/Binary_classification_phase_separation">https://github.com/rafael-a-monteiro-math/Binary_classification_phase_separation</a></li> </ul> <p>This is a second version, which I wrote using tensorflow. It is much smaller (5 Gb when decompressed), a remarkable improvement when compared to the more than 100 Gb of the previous version).</p> <p>The new files are </p> <ul> <li>PSBC_BCs.tar.gz</li> <li>PSBC_classifier_PCA.tar.gz</li> <li>PSBC_dataset.tar.gz</li> <li>PSBC_libs_grids_statistics.tar.gz</li> <li> PSBC_notebooks.tar.gz</li> </ul> <p>Their content is explained in the file README_v2.pdf</p> <p><strong>UPDATE: <a href="https://drive.google.com/drive/folders/18l_92HuHDWJDkZnvXRuyGedcyC_3YZ2M?usp=sharing">a Google Colab folder is also available</a>. You can also find all the data and libraries there, unpacked.</strong></p> <p>For usage, see the Git-hub. </p> <blockquote> <p><strong>NOTE)</strong> I will keep the content for the previous version available in my Github as well. It is still a "nice exercise" to do all that is done in this new version in numpy, as done there. <strong><em>(Or, I should say, they should be studied as a cautionary tale of what to avoid.)</em></strong></p> </blockquote> <p> </p> <p><strong>For version 0.0.1 (from 2020) see below:</strong></p> <p>This is a data repository for the paper "Binary classification as a phase separation process", by Rafael Monteiro.</p> <ul> <li>Website with description of this project: <a href="https://rafael-a-monteiro-math.github.io/Binary_classification_phase_separation/index.html">https://rafael-a-monteiro-math.github.io/Binary_classification_phase_separation/index.html</a></li> <li>Github: <a href="https://github.com/rafael-a-monteiro-math/Binary_classification_phase_separation">https://github.com/rafael-a-monteiro-math/Binary_classification_phase_separation</a></li> </ul> <p>Therein you will find</p> <ul> <li>Examples</li> <li>1D toy model examples</li> <li>Computational statistics</li> <li>Several trained PSBC on MNIST dataset, with different parameter configurations</li> <li>Extra simulations, investigating normalization properties, low dimensional models that fail due to "too much" model compression, and comparison among ANNs, KNNs, and the PSBC in 1D</li> </ul> <p>If you want to know</p> <ol> <li>how to read the data</li> <li>how to access computational statistics, raw data, and examples</li> <li>how to use the data stored in this data repository</li> </ol> <p>see the guide README.pdf on GitHub page at <a href="https://github.com/rafael-a-monteiro-math/Binary_Classification_Phase_Separation">Binary_Classification_Phase_Separation</a>, where a script that downloads (and organizes) all this data is also available ("download_PSBC.sh).</p> <p>I did not include a copy of the train-test set (0-1dubset of the MNIST database) in every folder with simulations. But you can find a copy of the normalized dataset in the tar ball "PSBC_Examples.tar.gz" as</p> <p>data_test_normalized_MNIST.csv and data_train_normalized_MNIST.csv.</p> <p> </p>
Open Dataset for publication: Resonant laser ionization and mass separation of Ac-225
<p>The dataset for publication in preparation:</p> <p>Resonant laser ionization and mass separation of Ac-225.</p> <p> </p> <p>Includes all data analysed for results given in the publication.</p>
Cooperative action of separate interaction domains promotes high-affinity DNA binding of Arabidopsis thaliana ARF transcription factors
<p>The repository contains the smFRET and SAXS data presented in the preprint https://doi.org/10.1101/2022.11.16.516730 (BioRxiv)</p>
Trap parameters for the fast OSL signal component obtained through analytical separation for various quartz samples
<p>Dataset for article</p> <p>Trap parameters for the fast OSL signal component obtained through analytical separation for various quartz samples</p>
Data from: Membrane phase separation drives responsive assembly of receptor signaling domains
<p>Plasma membrane heterogeneity has been tied to a litany of cellular functions and is often explained by analogy to membrane phase separation, yet models based on phase separation alone fall short of describing the rich organization available within cell membranes. We present comprehensive experimental evidence motivating an updated model of plasma membrane heterogeneity in which membrane domains assemble in response to protein scaffolds. Quantitative super-resolution nanoscopy measurements in live B lymphocytes detect membrane domains that emerge upon clustering B cell receptors (BCR). These domains enrich and retain membrane proteins based on their preference for the liquid-ordered phase. Unlike phase separated membranes that consist of binary phases with defined compositions, membrane composition at BCR clusters is modulated through the protein constituents in clusters or the composition of the membrane overall. This tunable domain structure is detected through the variable sorting of membrane probes and impacts the magnitude of BCR activation.</p>
Text-fig. 42. Scanning electron microscope (SEM, a, b, e) and synchrotron radiation X-ray tomographic microscopy (SRXTM, c, d, f–g) images of "Tricarpellate flower sp. 1"; Catefica locality, Portugal. a, b) Flower bud in two different lateral views showing semiinferior ovary and perianth; c) Longitudinal section (orthoslice yz0340) through flower bud in (a and b) showing the semi-inferior gynoecium and perigynous insertion of other floral parts; d) Volume rendering of flower bud with pedicel preserved; note the depression/split in one of the corner apparently separating two perianth lobes of the outer perianth whorl (t-o) and exposing one tepal of the inner whorl (t-i); e) Flower bud with pedicel preserved; note broad tepals of the outer whorl (t-o) and tepal of the inner whorl abraded exposing a broad stamen (st); f, g) Transverse sections through flower bud in (a and b) at two different levels above the insertion of the perianth (f, rec-file 1310; g, xy0280) showing the trimerous organization of the flower and the free, laterally flattened carpels; yellow indicates the two whorls of the androecium, each with three stamens. Specimens, Catefica 50-S171520 (a–c, f), Catefica 50-S174902 (d), Catefica MM154-P0271 (e), Catefica 49-S175354 (g). Scale bars = 300 Μm (a–e). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 42. Scanning electron microscope (SEM, a, b, e) and synchrotron radiation X-ray tomographic microscopy (SRXTM, c, d, f–g) images of "Tricarpellate flower sp. 1"; Catefica locality, Portugal. a, b) Flower bud in two different lateral views showing semiinferior ovary and perianth; c) Longitudinal section (orthoslice yz0340) through flower bud in (a and b) showing the semi-inferior gynoecium and perigynous insertion of other floral parts; d) Volume rendering of flower bud with pedicel preserved; note the depression/split in one of the corner apparently separating two perianth lobes of the outer perianth whorl (t-o) and exposing one tepal of the inner whorl (t-i); e) Flower bud with pedicel preserved; note broad tepals of the outer whorl (t-o) and tepal of the inner whorl abraded exposing a broad stamen (st); f, g) Transverse sections through flower bud in (a and b) at two different levels above the insertion of the perianth (f, rec-file 1310; g, xy0280) showing the trimerous organization of the flower and the free, laterally flattened carpels; yellow indicates the two whorls of the androecium, each with three stamens. Specimens, Catefica 50-S171520 (a–c, f), Catefica 50-S174902 (d), Catefica MM154-P0271 (e), Catefica 49-S175354 (g). Scale bars = 300 Μm (a–e).
Text-fig. 26. Scanning electron microscope (SEM) images of stamens and pollen grains of Elasmostemon paisii gen. et sp. nov. (a–c) and laminar stamens with monocolpate reticulate pollen sp. (d–g); Catefica locality, Portugal. a) Stamen fragment with basal portion missing showing two pairs of pollen sacs on one surface of the stamen close to the margin and separated by a broad connective, except near the apex where the thecae meet; note that the thecae are dehisced with the walls of the pollen sacs curled back; b) Pollen grains inside a dehisced pollen sac; note variation in size and development of the reticulum; c) Detail of (b) showing monocolpate, reticulate pollen with lumen of reticulum varying markedly in size but partly obscured by residual organic material; d) Stamen with apical and basal part of anther preserved showing two pairs of pollen sacs (asterisks) on the curved, perhaps ventral, surface close to the stamen margin; e) Detail of crack in the anther showing the inner anther wall with densely spaced spherical orbicules that vary greatly in size; f) Pollen exposed in the crack in the anther; note coarsely foveolate to coarsely reticulate pollen wall and densely spaced orbicules; g) Folded pollen grains with reticulate pollen wall and also showing the inner anther wall with densely spaced spherical orbicules that vary greatly in size. Specimens, Catefica 49-S172560 (a–c), Catefica 50- S170384 (d–g). Scale bars = 600 Μm (a, d), 20 Μm (b, e), 6 Μm (c, f, g). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 26. Scanning electron microscope (SEM) images of stamens and pollen grains of Elasmostemon paisii gen. et sp. nov. (a–c) and laminar stamens with monocolpate reticulate pollen sp. (d–g); Catefica locality, Portugal. a) Stamen fragment with basal portion missing showing two pairs of pollen sacs on one surface of the stamen close to the margin and separated by a broad connective, except near the apex where the thecae meet; note that the thecae are dehisced with the walls of the pollen sacs curled back; b) Pollen grains inside a dehisced pollen sac; note variation in size and development of the reticulum; c) Detail of (b) showing monocolpate, reticulate pollen with lumen of reticulum varying markedly in size but partly obscured by residual organic material; d) Stamen with apical and basal part of anther preserved showing two pairs of pollen sacs (asterisks) on the curved, perhaps ventral, surface close to the stamen margin; e) Detail of crack in the anther showing the inner anther wall with densely spaced spherical orbicules that vary greatly in size; f) Pollen exposed in the crack in the anther; note coarsely foveolate to coarsely reticulate pollen wall and densely spaced orbicules; g) Folded pollen grains with reticulate pollen wall and also showing the inner anther wall with densely spaced spherical orbicules that vary greatly in size. Specimens, Catefica 49-S172560 (a–c), Catefica 50- S170384 (d–g). Scale bars = 600 Μm (a, d), 20 Μm (b, e), 6 Μm (c, f, g).
Text-fig. 25. Scanning electron microscope (SEM) images of stamens and pollen grains of Elasmostemon paisii gen. et sp. nov.; Catefica locality, Portugal. a) Stamen fragment showing two pairs of pollen sacs along the margins of the stamen with a broad connective that separates the thecae, except near the apex where the thecae meet; b) Detail of surface of pollen sacs showing larger cells (arrows), interpreted as ethereal oil cells; c) Pollen in situ from specimen in (a); d) Stamen fragment with apical and basal portion missing and surface slightly abraded and compressed obscuring cellular details; note remains of another stamen attached to the underside of the stamen; e–h) Pollen in situ from specimen in (d) showing long aperture (e) and pollen wall with heterobrochate reticulum (e–h); note narrow muri with flatten and smooth surface and short columellae (h). Specimens, Catefica 49-S115859 (a–c), Catefica 151-S105281 (holotype, d–h). Scale bars = 600 Μm (a, d), 50 Μm (b), 6 Μm (c, e–g), 1.5 Μm (h). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 25. Scanning electron microscope (SEM) images of stamens and pollen grains of Elasmostemon paisii gen. et sp. nov.; Catefica locality, Portugal. a) Stamen fragment showing two pairs of pollen sacs along the margins of the stamen with a broad connective that separates the thecae, except near the apex where the thecae meet; b) Detail of surface of pollen sacs showing larger cells (arrows), interpreted as ethereal oil cells; c) Pollen in situ from specimen in (a); d) Stamen fragment with apical and basal portion missing and surface slightly abraded and compressed obscuring cellular details; note remains of another stamen attached to the underside of the stamen; e–h) Pollen in situ from specimen in (d) showing long aperture (e) and pollen wall with heterobrochate reticulum (e–h); note narrow muri with flatten and smooth surface and short columellae (h). Specimens, Catefica 49-S115859 (a–c), Catefica 151-S105281 (holotype, d–h). Scale bars = 600 Μm (a, d), 50 Μm (b), 6 Μm (c, e–g), 1.5 Μm (h).
Text-fig. 28. Scanning electron microscope (SEM) images of stamens and pollen of Endressistemon cateficensis gen. et sp. nov.; Catefica locality, Portugal. a, b) Staminal structure with two lateral stamens and one median structure seen in ventral and dorsal view (orientation unknown) showing that each stamen has a prominent apical extension and two pairs of pollen sacs separated by a narrow connective; both stamens are borne on a common base together with the median structure and their anthers are sessile on the common stalk; note the apical projection of the median structure (asterisk) between the two stamens and the ribs over probable vascular bundles that extend from the common base into the apical projections of both stamens and the median structure (arrows); c) Staminal structure showing two stamens with prominent apical projections and median axis-like structure between the two stamens (arrow); d) Staminal structure showing two stamens with prominent apical projections borne on a common base; e) Staminal structure in (a) and (b), from the same orientation as (b), showing the ribs over probable vascular bundles (yellow) that extend into the apical projections; f) Detail of staminal structure in (a) and (b) showing the fused or strongly adhering apical projections of the two lateral stamens and the median structure (asterisk); g) Monocolpate, reticulate pollen grains from the pollen sacs of stamen in (d). Specimens, Catefica 49-S107778 (holotype, a, b, e, f), Catefica 49-S107769 (c), Catefica 49-S107751 (d, g). Scale bars = 600 Μm (a–d), 300 Μm (e), 100 Μm (f), 6 Μm (g). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 28. Scanning electron microscope (SEM) images of stamens and pollen of Endressistemon cateficensis gen. et sp. nov.; Catefica locality, Portugal. a, b) Staminal structure with two lateral stamens and one median structure seen in ventral and dorsal view (orientation unknown) showing that each stamen has a prominent apical extension and two pairs of pollen sacs separated by a narrow connective; both stamens are borne on a common base together with the median structure and their anthers are sessile on the common stalk; note the apical projection of the median structure (asterisk) between the two stamens and the ribs over probable vascular bundles that extend from the common base into the apical projections of both stamens and the median structure (arrows); c) Staminal structure showing two stamens with prominent apical projections and median axis-like structure between the two stamens (arrow); d) Staminal structure showing two stamens with prominent apical projections borne on a common base; e) Staminal structure in (a) and (b), from the same orientation as (b), showing the ribs over probable vascular bundles (yellow) that extend into the apical projections; f) Detail of staminal structure in (a) and (b) showing the fused or strongly adhering apical projections of the two lateral stamens and the median structure (asterisk); g) Monocolpate, reticulate pollen grains from the pollen sacs of stamen in (d). Specimens, Catefica 49-S107778 (holotype, a, b, e, f), Catefica 49-S107769 (c), Catefica 49-S107751 (d, g). Scale bars = 600 Μm (a–d), 300 Μm (e), 100 Μm (f), 6 Μm (g).
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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.