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Fig. 3 in A report of 38 unrecorded bacterial species in Korea within the classes Bacilli and Deinococci isolated from various sources
Fig. 3. Neighbor-joining phylogenetic tree based on 16S rRNA sequences, showing the relationship between the isolates and their relatives of the order Lactobacillales. Bootstrap values (>70%) are shown. Escherichia coli DSM 30083T (X801725) was used as an outgroup. Bar, 0.05 substitutions per nucleotide position.
The CNN classifier at the class level for fungal identification
<p>The CNN classifier was trained based on the CNN model using the WI-CBS ITS barcode dataset.</p>
Figure 3. Coral morphology class score for 13 in Current status of coral reefs in Tioman Island, Peninsular Malaysia
Figure 3. Coral morphology class score for 13 reef sites in Tioman Island. Most of the reef sites were plotted under mixed coral morphologies and received class 4 (C 4). Three reef sites (Tomok Island, Gado Bay, and Tulai Bay) dominated by stress-tolerator corals and received class 1 (C 1). One reef site (Bayan Bay) dominated by competitor corals and received class 2 (C 2).
CREATIVE ACTIVITY IN PREPARING PRIMARY CLASS TEACHERS TO DIRECT NATIONAL PROFESSIONS
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EduLifeDesks Archive: 2010 Field Museum Class in Phylogenetics
eNemo
IMPORTANCE OF RASING STUDENTS' AWARENESS ABOUT CLIMATE JUSTICE IN LANGUAGE CLASSES
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STUDENTS' NEED TO DEVELOP PERSONAL VALUES IN EDUCATIONAL CLASSES
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Figure 8 in Comparative genomics reveals the evolutionary history of the unicellular eukaryote class Litostomatea and its adaptive evolution based on biochemical metabolic capacity
Figure 8. RSCU of 14 newly sequenced litostomatean genomes/transcriptomes. Each codon is ploưed.
Morphometrics of taxa in the genus Sphenopsis, recorded from adult male (n = 21) and female (n = 15) study skins in the Academy of Natural Sciences of Drexel University, Philadelphia (ANSP) and Delaware Museum of Nature & Science, Greenville (DMNH) collections. Sample sizes and means (± SD) are given for each taxon, within each sex class (female, male), for the following variables: (WG) wing length, (TR) tarsometatarsus length, (TL) tail length, (BL) bill length, and (BW) bill width. All measurements in mm. in Taxonomic status of the Western Hemispingus Sphenopsis ochracea (Thraupidae) and a review of species limits in the genus Sphenopsis P. L. Sclater, 1861
Morphometrics of taxa in the genus Sphenopsis, recorded from adult male (n = 21) and female (n = 15) study skins in the Academy of Natural Sciences of Drexel University, Philadelphia (ANSP) and Delaware Museum of Nature & Science, Greenville (DMNH) collections. Sample sizes and means (± SD) are given for each taxon, within each sex class (female, male), for the following variables: (WG) wing length, (TR) tarsometatarsus length, (TL) tail length, (BL) bill length, and (BW) bill width. All measurements in mm.
Table ¹: Comparison of analysis of variance results for skull (occlusal view) and mandible (side view) shape in Rhipidomys mastacalis from three vegetation classes in Brazil. Object asymmetry and correspondence methods were employed to assess asymmetry for skulls and mandibles, respectively. in Morphological symmetry of Rhipidomys mastacalis (Mammalia, Rodentia, Cricetidae) in fragmented habitats of the Atlantic Forest in Northeastern Brazil: a study on the influence of the environment on an endemic species
<p><b>Table ¹:</b> Comparison of analysis of variance results for skull (occlusal view) and mandible (side view) shape in <i>Rhipidomys mastacalis</i> from three vegetation classes in Brazil.Object asymmetry and correspondence methods were employed to assess asymmetry for skulls and mandibles,respectively.</p><table><tbody><tr><th><b>Shape procrustes ANOVA</b></th></tr></tbody><tbody><tr><th><b>Effect Sum of squares</b></th><td><b>Mean squares</b></td><td><b>Degrees of freedom</b></td><td><i>F statistic</i></td><td><i>p -Value</i></td><td><b>Pillai tr.</b></td><td><i>p -Value</i></td></tr><tr><th><b>Skulls</b></th></tr><tr><th><b>Forested vegetation</b></th></tr><tr><th>Individual</th><td>0.19908517</td><td>0.0004253957</td><td>468</td><td>22.36</td><td><0.0001</td><td>–</td><td>–</td></tr><tr><th>Side</th><td>0.00366522</td><td>0.0002036232</td><td>18</td><td>10.70</td><td><0.0001</td><td>–</td><td>–</td></tr><tr><th>Individual × side</th><td>0.00890443</td><td>0.0000190266</td><td>468</td><td>2.24</td><td><0.0001</td><td>–</td><td>–</td></tr><tr><th>Error 1</th><td>0.00825565</td><td>0.0000084935</td><td>972</td><td>–</td><td>–</td><td>–</td><td>–</td></tr><tr><th><b>Occupancy mosaics in forested areas</b></th></tr><tr><th>Individual</th><td>0.37829478</td><td>0.0003965354</td><td>954</td><td>18.57</td><td><0.0001</td><td>–</td><td>–</td></tr><tr><th>Side</th><td>0.00547536</td><td>0.0003041869</td><td>18</td><td>14.25</td><td><0.0001</td><td>–</td><td>–</td></tr><tr><th>Individual × side</th><td>0.02037065</td><td>0.0000213529</td><td>954</td><td>1.89</td><td><0.0001</td><td>–</td><td>–</td></tr><tr><th>Error 1</th><td>0.02201359</td><td>0.0000113239</td><td>1944</td><td>–</td><td>–</td><td>–</td><td>–</td></tr><tr><th><b>Cocoa plantations</b></th></tr><tr><th>Individual</th><td>0.0645902300</td><td>0.0001302222</td><td>496</td><td>5.18</td><td><0.0001</td><td>–</td><td>–</td></tr><tr><th>Side</th><td>0.0113531900</td><td>0.0007095741</td><td>16</td><td>28.23</td><td><0.0001</td><td>–</td><td>–</td></tr><tr><th>Individual × side</th><td>0.0124666800</td><td>0.0000251344</td><td>496</td><td>1.88</td><td><0.0001</td><td>–</td><td>–</td></tr><tr><th>Error 1</th><td>0.0136608800</td><td>0.0000133407</td><td>1024</td><td>–</td><td>–</td><td>–</td><td>–</td></tr><tr><th><b>Mandibles</b></th></tr><tr><th><b>Forested vegetation</b></th></tr><tr><th>Individual</th><td>0.70443879</td><td>0.0012579264</td><td>560</td><td>8.10</td><td><0.0001</td><td>14.16</td><td><0.0001</td></tr><tr><th>Side</th><td>0.00549957</td><td>0.0002749783</td><td>20</td><td>1.77</td><td>0.0207</td><td>0.0207</td><td>0.0069</td></tr><tr><th>Individual × side</th><td>0.08696012</td><td>0.0001552859</td><td>560</td><td>2.46</td><td><0.0001</td><td>10.75</td><td><0.0001</td></tr><tr><th>Error 1</th><td>0.07312665</td><td>0.0000387718</td><td>1160</td><td>–</td><td>–</td><td>–</td><td>–</td></tr><tr><th><b>Occupancy mosaics in forested areas</b></th></tr><tr><th>Individual</th><td>1.19843989</td><td>0.0011984399</td><td>1000</td><td>8.16</td><td><0.0001</td><td>14.70</td><td><0.0001</td></tr><tr><th>Side</th><td>0.01169771</td><td>0.0005848855</td><td>20</td><td>3.98</td><td><0.0001</td><td>0.74</td><td>0.0001</td></tr><tr><th>Individual × side</th><td>0.14685738</td><td>0.0001468574</td><td>1000</td><td>3.03</td><td><0.0001</td><td>11.21</td><td><0.0001</td></tr><tr><th>Error 1</th><td>0.09880745</td><td>0.0000484350</td><td>2040</td><td>–</td><td>–</td><td>–</td><td>–</td></tr><tr><th><b>Cocoa plantations</b></th></tr><tr><th>Individual</th><td>0.3269927600</td><td>0.0004808717</td><td>680</td><td>4.52</td><td><0.0001</td><td>14.14</td><td><0.0001</td></tr><tr><th>Side</th><td>0.0143644400</td><td>0.0007182221</td><td>20</td><td>6.75</td><td><0.0001</td><td>0.86</td><td>0.0017</td></tr><tr><th>Individual × side</th><td>0.0723474900</td><td>0.0001063934</td><td>680</td><td>2.39</td><td><0.0001</td><td>10.41</td><td>0.0017</td></tr><tr><th>Error 1</th><td>0.0622041800</td><td>0.0000444316</td><td>1400</td><td>–</td><td>–</td><td>–</td><td>–</td></tr></tbody></table>
Table ²: Comparison of the results of analysis of variance on the shape of scapulae (occlusal view) and pelvis (side view) in Rhipidomys mastacalis from three vegetation classes in Brazil. Correspondence asymmetry was the only method used for asymmetry analysis. in Morphological symmetry of Rhipidomys mastacalis (Mammalia, Rodentia, Cricetidae) in fragmented habitats of the Atlantic Forest in Northeastern Brazil: a study on the influence of the environment on an endemic species
<p><b>Table ²:</b> Comparison of the results of analysis of variance on the shape of scapulae (occlusal view) and pelvis (side view) in <i>Rhipidomys mastacalis</i> from three vegetation classes in Brazil. Correspondence asymmetry was the only method used for asymmetry analysis.</p><table><tbody><tr><th><b>Shape procrustes ANOVA</b></th></tr></tbody><tbody><tr><th><b>Effect Sum of squares</b></th><td><b>Mean squares</b></td><td><b>Degrees of freedom</b></td><td><i>F statistic</i></td><td><i>p -Value</i></td><td><b>Pillai tr.</b></td><td><i>p -Value</i></td></tr><tr><th><b>Scapulae</b></th></tr><tr><th><b>Forested vegetation</b></th></tr><tr><th>Individual</th><td>0.0941373400</td><td>0.0010459705</td><td>90</td><td>3</td><td><0.0001</td><td>–</td><td>–</td></tr><tr><th>Side</th><td>0.0100439600</td><td>0.0010043960</td><td>2.88</td><td>0.0037</td><td>0.0003</td><td>–</td><td>–</td></tr><tr><th>Individual × side</th><td>0.0314069500</td><td>0.0003489662</td><td>90</td><td>5.89</td><td><0.0001</td><td>4.91</td><td><0.0001</td></tr><tr><th>Error 1</th><td>0.0118544100</td><td>0.0000592721</td><td>200</td><td>–</td><td>–</td><td>–</td><td>–</td></tr><tr><th><b>Occupancy mosaics in forested areas</b></th></tr><tr><th>Individual</th><td>0.2064168200</td><td>0.0010320841</td><td>200</td><td>4.82</td><td><0.0001</td><td>7.15</td><td><0.0001</td></tr><tr><th>Side</th><td>0.0262808000</td><td>0.0026280796</td><td>10</td><td>12.28</td><td><0.0001</td><td>0.86</td><td>0.0022</td></tr><tr><th>Individual × side</th><td>0.0428160400</td><td>0.0002140802</td><td>200</td><td>2.68</td><td><0.0001</td><td>4.98</td><td><0.0001</td></tr><tr><th>Error 1</th><td>0.0335675700</td><td>0.0000799228</td><td>420</td><td>–</td><td>–</td><td>–</td><td>–</td></tr><tr><th><b>Cocoa plantations</b></th></tr><tr><th>Individual</th><td>0.2508635400</td><td>0.0009291242</td><td>270</td><td>4.07</td><td><0.0001</td><td>7.11</td><td><0.0001</td></tr><tr><th>Side</th><td>0.0256608100</td><td>0.0025660812</td><td>10</td><td>11.24</td><td><0.0001</td><td>0.87</td><td><0.0001</td></tr><tr><th>Individual × side</th><td>0.0616394000</td><td>0.0002282941</td><td>270</td><td>3.10</td><td><0.0001</td><td>5.72</td><td><0.0001</td></tr><tr><th>Error 1</th><td>0.0412323300</td><td>0.0000736292</td><td>560</td><td>–</td><td>–</td><td>–</td><td>–</td></tr><tr><th><b>Pelvis</b></th></tr><tr><th><b>Forested vegetation</b></th></tr><tr><th>Individual</th><td>0.0543411200</td><td>0.0004312787</td><td>126</td><td>4.63</td><td><0.0001</td><td></td><td></td></tr><tr><th>Side</th><td>0.0043155600</td><td>0.0003082544</td><td>14</td><td>3.31</td><td>0.0002</td><td></td><td></td></tr><tr><th>Individual × side</th><td>0.0117297800</td><td>0.0000930935</td><td>126</td><td>2.31</td><td><0.0001</td><td>6.07</td><td><0.0001</td></tr><tr><th>Error 1</th><td>0.0112943700</td><td>0.000040337</td><td>280</td><td>–</td><td>–</td><td>–</td><td>–</td></tr><tr><th><b>Occupancy mosaics in forested areas</b></th></tr><tr><th>Individual</th><td>0.1059661700</td><td>0.0003440460</td><td>308</td><td>4.42</td><td><0.0001</td><td>9.69</td><td><0.0001</td></tr><tr><th>Side</th><td>0.0049395300</td><td>0.0003528236</td><td>14</td><td>4.53</td><td><0.0001</td><td>0.85</td><td>0.0311</td></tr><tr><th>Individual × side</th><td>0.0239852500</td><td>0.0000778742</td><td>308</td><td>2.00</td><td><0.0001</td><td>6.64</td><td><0.0001</td></tr><tr><th>Error 1</th><td>0.0251368400</td><td>0.0000390324</td><td>644</td><td>–</td><td>–</td><td>–</td><td>–</td></tr><tr><th><b>Cocoa plantations</b></th></tr><tr><th>Individual</th><td>0.1292837500</td><td>0.0003420205</td><td>378</td><td>5.68</td><td><0.0001</td><td>10.51</td><td><0.0001</td></tr><tr><th>Side</th><td>0.0043550500</td><td>0.0003110747</td><td>14</td><td>5.17</td><td><0.0001</td><td>0.84</td><td>0.0016</td></tr><tr><th>Individual × side</th><td>0.0227608400</td><td>0.0000602139</td><td>378</td><td>2.24</td><td><0.0001</td><td>6.17</td><td><0.0001</td></tr><tr><th>Error 1</th><td>0.0210413800</td><td>0.0000268385</td><td>714</td><td>–</td><td>–</td><td>–</td><td>–</td></tr></tbody></table>
Linked collectors and determiners for: Illustrated and online catalog of the type specimens of birds (Class: Aves) in the Ornithological Collection at the Instituto de Investigación de Recursos Biológicos Alexander von Humboldt (IAvH-A), Colombia.
Natural history specimen data linked to collectors and determiners held within, "Illustrated and online catalog of the type specimens of birds (Class: Aves) in the Ornithological Collection at the Instituto de Investigación de Recursos Biológicos Alexander von Humboldt (IAvH-A), Colombia". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/e679a1e4-43cc-4ab1-bb7d-e788fc23dc7a">https://bionomia.net/dataset/e679a1e4-43cc-4ab1-bb7d-e788fc23dc7a</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/e679a1e4-43cc-4ab1-bb7d-e788fc23dc7a">https://gbif.org/dataset/e679a1e4-43cc-4ab1-bb7d-e788fc23dc7a</a>. Formatted as a Frictionless Data package.
DIFFERENTIATION STRATEGIES FOR ENHANCING STUDENTS' PROFESSIONAL COMMUNICATIVE COMPETENCE IN CLIL CLASSES
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TEACHING STUDENTS TO SOLVE LOGICAL PROBLEMS IN PRIMARY CLASS MATHEMATICS LESSONS
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ON THE VALUABILITY OF STUDENTS' LOGICAL THINKING IN PRIMARY CLASS MATHEMATICS LESSONS
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Data from: PCR-based isolation of multigene families: lessons from the avian MHC class IIB
The amount of sequence data available today highly facilitates the access to genes from many gene families. Primers amplifying the desired genes over a range of species are readily obtained by aligning conserved gene regions, and laborious gene isolation procedures can often be replaced by quicker PCR-based approaches. However, in the case of multigene families, PCR-based approaches bear the often ignored risk of incomplete isolation of family members. This problem is most prominent in gene families with highly variable and thus unpredictable number of gene copies among species, such as in the major histocompatibility complex (MHC). In the present study we (i) report new primers for the isolation of the MHC class IIB (MHCIIB) gene family in birds, and (ii) share our experience with isolating MHCIIB genes from an unprecedented number of avian species from all over the avian phylogeny. We report important and usually underappreciated problems encountered during PCR-based multigene family isolation, and provide a collection of measures to help significantly improving the chance of successfully isolating complete multigene families using PCR-based approaches.
Data from: Chloroplast phylogenomic analysis resolves deep-level relationships within the green algal class Trebouxiophyceae
Background: The green algae represent one of the most successful groups of photosynthetic eukaryotes, but compared to their land plant relatives, surprisingly little is known about their evolutionary history. This is in great part due to the difficulty of recognizing species diversity behind morphologically similar organisms. The Trebouxiophyceae is a species-rich class of the Chlorophyta that includes symbionts (e.g. lichenized algae) as well as free-living green algae. Members of this group display remarkable ecological variation, occurring in aquatic, terrestrial and aeroterrestrial environments. Because a reliable backbone phylogeny is essential to understand the evolutionary history of the Trebouxiophyceae, we sought to identify the relationships among the major trebouxiophycean lineages that have been previously recognized in nuclear-encoded 18S rRNA phylogenies. To this end, we used a chloroplast phylogenomic approach. Results: We determined the sequences of 29 chlorophyte chloroplast genomes and assembled amino acid and nucleotide data sets derived from 79 chloroplast genes of 61 chlorophytes, including 35 trebouxiophyceans. The amino acid- and nucleotide-based phylogenies inferred using maximum likelihood and Bayesian methods and various models of sequence evolution revealed essentially the same relationships for the trebouxiophyceans. Two major groups were identified: a strongly supported clade of 29 taxa (core trebouxiophyceans) that is sister to the Chlorophyceae + Ulvophyceae and a clade comprising the Chlorellales and Pedinophyceae that represents a basal divergence relative to the former group. The core trebouxiophyceans form a grade of strongly supported clades that include a novel lineage represented by the desert crust alga Pleurastrosarcina brevispinosa. The assemblage composed of the Oocystis and Geminella clades is the deepest divergence of the core trebouxiophyceans. Like most of the chlorellaleans, early-diverging core trebouxiophyceans are predominantly planktonic species, whereas core trebouxiophyceans occupying more derived lineages are mostly terrestrial or aeroterrestrial algae. Conclusions: Our phylogenomic study provides a solid foundation for addressing fundamental questions related to the biology and ecology of the Trebouxiophyceae. The inferred trees reveal that this class is not monophyletic; they offer new insights not only into the internal structure of the class but also into the lifestyle of its founding members and subsequent adaptations to changing environments.
Data from: Becoming pure: identifying generational classes of admixed individuals within lesser and greater scaup populations
Estimating the frequency of hybridization is important to understand its evolutionary consequences and its effects on conservation efforts. In this study, we examined the extent of hybridization in two sister species of ducks that hybridize. We used mitochondrial control region sequences and 3,589 double-digest restriction-associated DNA sequences (ddRADseq) to identify admixture between wild lesser scaup (Aythya affinis) and greater scaup (A. marila). Among 111 individuals, we found one introgressed mitochondrial DNA haplotype in lesser scaup and four in greater scaup. Likewise, based on the site-frequency spectrum from autosomal DNA, gene flow was asymmetrical, with higher rates from lesser into greater scaup. However, using ddRADseq nuclear DNA all individuals were assigned to their respective species with > 0.95 posterior assignment probability. To examine the power for detecting admixture, we simulated a breeding experiment in which empirical data were used to create F1 hybrids and nine generations (F2-F10) of backcrossing. F1 hybrids and F2, F3, and most F4 backcrosses were clearly distinguishable from pure individuals, but evidence of admixed histories was effectively lost after the fourth generation. Thus, we conclude that low interspecific assignment probabilities (0.011 – 0.043) for two lesser and nineteen greater scaup were consistent with admixed histories beyond the F3 generation. These results indicate that the propensity of these species to hybridize in the wild is low and largely asymmetric. When applied to species-specific cases, our approach offers powerful utility for examining concerns of hybridization in conservation efforts, especially for determining the generational time until admixed histories are effectively lost through backcrossing.
TNT file for phylogenetic analysis of the moss class Polytrichopsida composed of morphological and sequence level characters
<p>PREMISE OF THE STUDY: When fossils are sparse in morphologically divergent lineages, phylogenetic analyses based on morphology may support hypotheses of relationships incongruent with those supported by gene sequence data. Integration of morphological and sequence data from conservative gene regions may reconcile such situations by circumscribing the search space of combined analyses.</p> <p>METHODS: We revisited the phylogeny of Polytrichopsida, a highly divergent group of mosses, in parsimony analyses. We supplemented the existing morphological matrix with sequence data of four genes (nt 18S, cp rbcL & rps4, mt nad5) commonly used in mosses; we included both fossils and extant terminals that lack sequence data.</p> <p>KEY RESULTS: We recovered patterns of relationships largely congruent with those supported by analyses of sequence data from a higher number of terminals. Analyses including all terminals recovered one optimal tree with Alophosia and the fossil Meantoinea forming a clade sister to the rest of the ingroup. Outgroup sampling experiments produced congruent topologies for most ingroup relationships.</p> <p>CONCLUSIONS: The potential of total-evidence analyses sampling conservative genes to alleviate conflict with morphology-based hypotheses should be tested in groups with denser fossil record. Although bryophyte fossils have been deemed fragmentary, it was recently shown that integrating fossils in total-evidence analyses may not reduce phylogenetic resolution. Therefore, total-evidence analyses incorporating fossils bear promise for clarifying bryophyte phylogenetic relationships. In Polytrichopsida, a group with a long evolutionary history, we cannot assume, a priori, that currently known fossils, which date back to only c. 140 Ma ago, represent the oldest lineages.</p>
Exploring the impact of a mindfulness meditation class on college student stress levels and quality of life.
<p>Data set from study exploring a mindfulness meditation class vs control group.</p>
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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.