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Supplementary material 2 from: Barroso CX, Pereira de Freitas JE, Matthews-Cascon H, Arruda Bezerra LE, da Cruz Lotufo TM (2020) Molecular evidences confirm the taxonomic separation of two sympatric congeneric species (Mollusca, Gastropoda, Neritidae, Neritina). ZooKeys 904: 117-130. https://doi.org/10.3897/zookeys.904.46790
Radulae of the Neritina meleagris (A) and Neritina virginea (B) analysed
Supplementary material 1 from: Barroso CX, Pereira de Freitas JE, Matthews-Cascon H, Arruda Bezerra LE, da Cruz Lotufo TM (2020) Molecular evidences confirm the taxonomic separation of two sympatric congeneric species (Mollusca, Gastropoda, Neritidae, Neritina). ZooKeys 904: 117-130. https://doi.org/10.3897/zookeys.904.46790
Alignments used to construct the phylogenetic trees and statistical parsimony network analysis
Ultramicroporous iron-isonicotinate MOFs combining size-exclusion kinetics and thermodynamics for efficient CO2/N2 gas separation
<p>Relevant Data for the publication with DOI: <a title="Link to landing page via DOI" href="https://doi.org/10.1039/D2TA08934C">10.1039/D2TA08934C</a></p>
STUDY OF FACTORS AFFECTING THE PRINCIPLE OF OPERATION OF THE COTTON SEPARATOR DEVICE
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Crataegus bretschneideri (Rosaceae), a separate species endemic to Northeast of China
<p><span><i>Crataegus b</i></span><span><i>retschneideri</i> is considered a variety of <i>Crataegus pinnatifida</i>, but it has also been proposed as a separate species. We used ITS and three cpDNA sequence fragments (<i>psbA-trnH, trnG-trnS, trnH-trnK</i>) to perform maximum parsimony, maximum likelihood, Bayesian interence and neighbor-joining molecular phylogenetic tree analysis with 108 individuals of 19 hawthorn (<i>Crataegus</i>) species and 4 outgroups (<i>Malus</i>). ITS, cpDNA and cpDNA-ITS molecular phylogenetic trees constructed using 4 methods have similar consistency respectively.</span></p> <p><span>In the cpDNA-ITS molecular phylogenetic tree, <i>C. bretschneideri</i> is an independent clade separated from <i>Crataegus maximowiczii </i>and <i>C. pinnatifida</i>, which provides a separate species condition. In the ITS (nuclear inheritance) molecular phylogenetic tree, <i>C. bretschneideri</i> and <i>C. pinnatifida</i> are closely related and are distantly related to <i>C. maximowiczii</i>. The cpDNA (maternal inheritance) molecular phylogenetic tree indicated that <i>C. bretschneideri</i> is closely related to <i>C. maximowiczii</i> but distantly related to <i>C. pinnatifida</i>. Furthermore, the 108 <i>Crataegus</i> individuals belonged to 15 chloroplast haplotypes, as determined using the DNASP analysis; <i>C. bretschneideri</i> and <i>C. maximowiczii</i> have the same chloroplast haplotype, H1; <i>C. pinnatifida </i>contains three haplotypes, H13-H15. Taken together with previous results of our laboratory, we confirm that <i>C. bretschneideri</i> is not a variety of <i>C. pinnatifida,</i> but a separate species that gradually developed from natural hybrid offspring in mixed forest areas with <i>C. maximowiczii</i> as the female parent and <i>C. pinnatifida</i> as the male parent. </span></p>
Genomic and acoustic differences separate Lilian's Meadowlark (Sturnella magna lilianae) from Eastern (S. magna) and Western (S. neglecta) Meadowlarks
<p>Examining differences among recently diverged populations can provide insight into the traits and evolutionary mechanisms that drive or maintain divergence. The genus <i>Sturnella</i> includes two recently diverged species, <i>Sturnella magna </i>(Eastern Meadowlark) and <i>S. neglecta </i>(Western Meadowlark), the former of which has a complex of subspecies distributed across the Americas. Of the <i>S. magna</i> subspecies that occur in the United States, <i>S. m. lilianae </i>is the only one with a disjunct range, occurring in the southwestern U.S. and central Mexico. It also has markedly different song patterns than all other <i>S. magna</i> subspecies. In order to assess population differentiation, we performed whole-genome sequencing of 35 birds, and analyzed song characteristics from 85 birds. Songs from each species and <i>S. m. lilianae</i> were diagnosable using linear discriminant function analysis and support divergence in song between all taxa. Phylogenetic analysis and admixture proportions support three distinct clades within North American meadowlarks, and tests of introgression failed to detect a significant signal. Overall, our results indicate that <i>S. m</i>. <i>lilianae</i> exhibits high levels of genetic and vocal differentiation from both<i> S. magna</i> and <i>S. neglecta</i>, with no evidence of introgression between any group, and forms a distinct evolutionary lineage. We thus recommend the elevation of <i>S. m. lilianae </i>to species status.</p>
Molecular determinants of phase separation for Drosophila DNA replication licensing factors
<p>Liquid-liquid phase separation (LLPS) of intrinsically disordered regions (IDRs) in proteins can drive the formation of membraneless compartments in cells. Phase-separated structures enrich for specific partner proteins and exclude others. Previously, we showed that the IDRs of metazoan DNA replication initiators drive DNA-dependent phase separation <i>in vitro</i> and chromosome binding <i>in vivo</i>, and that initiator condensates selectively recruit partner proteins (Parker et al., 2019). How initiator IDRs facilitate LLPS and maintain compositional specificity is unknown. Here, using <i>D. melanogaster (Dm)</i> Cdt1 as a model initiation factor, we show that phase separation results from a synergy between electrostatic DNA-bridging interactions and hydrophobic inter-IDR contacts. Both sets of interactions depend on sequence composition (but not sequence order), are resistant to 1,6-hexanediol, and do not depend on aromaticity. These findings demonstrate that distinct sets of interactions drive condensate formation and specificity across different phase-separating systems and advance efforts to predict IDR LLPS propensity and partner selection <i>a priori</i>.</p>
Synergistic phase separation of two pathways promotes integrin clustering and nascent adhesion formation
<p><span><span><span><span><span><span><span><span><span><span><span>Integrin adhesion complexes (IACs) are integrin-based plasma membrane-associated compartments where cells sense environmental cues. The physical mechanisms and molecular interactions that mediate initial IAC formation are unclear. We found that both p130Cas ("Cas") and Focal adhesion kinase ("FAK") undergo liquid-liquid phase separation <i>in vitro</i>under physiologic conditions. Cas- and FAK- driven phase separation is sufficient to reconstitute kindlin-dependent integrin clustering <i>in vitro </i>with recombinant mammalian proteins. <i>In vitro</i> condensates and IACs in mouse embryonic fibroblasts (MEFs) exhibit similar sensitivities to environmental perturbations including changes in temperature and pH. Furthermore, mutations that inhibit or enhance phase separation <i>in vitro</i> reduce or increase the number of IACs in MEFs, respectively. Finally, we find that the Cas and FAK pathways act synergistically to promote phase separation, integrin clustering, IAC formation and partitioning of key components <i>in vitro</i> and in cells. We propose that Cas- and FAK- driven phase separation provides an intracellular trigger for integrin clustering and nascent IAC formation.</span></span></span></span></span></span></span></span></span></span></span></p>
Distribution. Known only from two localities separated by a few kilometers in W Sudan. in Muridae
Distribution. Known only from two localities separated by a few kilometers in W Sudan.
Supplementary material 3 from: Ren J, Bai M, Yang X-K, Zhang R-Z, Ge S-Q (2017) Geometric morphometrics analysis of the hind wing of leaf beetles: proximal and distal parts are separate modules. ZooKeys 685: 131-149. https://doi.org/10.3897/zookeys.685.13084
Coordinates data of landmarks. :
Figure 4 from: Ren J, Bai M, Yang X-K, Zhang R-Z, Ge S-Q (2017) Geometric morphometrics analysis of the hind wing of leaf beetles: proximal and distal parts are separate modules. ZooKeys 685: 131-149. https://doi.org/10.3897/zookeys.685.13084
Figure 4 - Modularity test results. A The hypothesized partition: proximal part landmarks 1-6, 23, 24, and 26–36 and distal part landmarks 7–22, 25; different colour presents different modules B The partition with minimal covariance in all evaluated 104 partitions by RV coefficient C The partition with minimal covariance in all evaluated 106 partitions by RV coefficient.
Figure 2 from: Ren J, Bai M, Yang X-K, Zhang R-Z, Ge S-Q (2017) Geometric morphometrics analysis of the hind wing of leaf beetles: proximal and distal parts are separate modules. ZooKeys 685: 131-149. https://doi.org/10.3897/zookeys.685.13084
Figure 2 - PCA and CVA results. A Centroid size graph of hind wing landmarks (Procrustes fit) B PCA results, the shape changes associated with the first three PCs: the relative size of the apical area which could be considered the main feature (variance contribution ratio was 45.01%) to influence of the overall variance of the hind wing, the changes of cross vein cv in the middle area (variance contribution ratio was 12.39%), and relative size of the anal area size (variance contribution ratio was 10.56%) C CVA results, the axis of CV1 and CV2 presented the first two large shape variance of all variance; points with different colours indicated different subtribes' specimens; the ellipse is presented as an equal-frequency ellipse with a given probability level of 90%, which contains approximately 90% of the data points.
Figure 1 from: Ren J, Bai M, Yang X-K, Zhang R-Z, Ge S-Q (2017) Geometric morphometrics analysis of the hind wing of leaf beetles: proximal and distal parts are separate modules. ZooKeys 685: 131-149. https://doi.org/10.3897/zookeys.685.13084
Figure 1 - Leaf beetle hind wing (Chrysomela populi Linnaeus), with landmark locations (the dot with number), vein nomenclature and regional division. The nomenclature of the wing venation follows that of Kukalová-Peck & Lawrence (1993, 2004). Radial area: green, central area: blue, medial area: purple, anal area: yellow, apical (folding) area: red. Proximal part landmarks 1–6, 23, 24, and 26–36 mainly include radial, medial, and anal areas; distal part landmarks 7–22 and 25 include the central area, radial cell, and apical area. Abbreviations: Costa (C), Subcosta (Sc), Subcosta Anterior (ScA), Subcosta Posterior (ScP), Radius Anterior (RA), Radius Posterior (RP), Radial cross veins (r3, r4), Media Posterior (MP), Radio-medial cross veins (rp-mp1, rp-mp2), medial cross vein (cv), Cubitus Anterior (CuA), Medio-cubital Cross-vein or Arculus (mp-cua), Anal Anterior (AA), Anal posterior (AP). "+" indicates fused veins. The sub-number of veins reflects vein branches.
Figure 3 from: Ren J, Bai M, Yang X-K, Zhang R-Z, Ge S-Q (2017) Geometric morphometrics analysis of the hind wing of leaf beetles: proximal and distal parts are separate modules. ZooKeys 685: 131-149. https://doi.org/10.3897/zookeys.685.13084
Figure 3 - PLS analysis results. A Scatter plot of the PLS1 of two blocks B Shape changes associated with the first PLS axes of two blocks: each diagram shows the block change along the PLS1 in the positive or negative direction, corresponding to Figure 3A.
Online repository for: "Compensation of capacitive currents in high-throughput dielectrophoretic separators"
<p>Please check the readme.odt file for details.</p>
Uncovering intermolecular interactions driving liquid-liquid phase separation of TDP-43 low complexity domain
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Demonstration of the tunnel transfer method for non-aversive handling used to perform daily dam-pup separation sessions as part of the MSEW protocol on PDs 2-13
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Longitudinal chiral forces in photonic integrated waveguides to separate particles with realistically small chirality
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Online repository for: "Using Rectangular Waveforms in Dielectrophoresis Application to Increase Separation and Sorting Efficiency"
<p>Please consult the README file for information on the content of this online repository.</p>
Source Separation Dataset for Knowledge Boosting (Part 2)
<p><strong>Part 2 of the Source Separation Dataset</strong> as described in <em>Knowledge boosting during low-latency inference</em> (Interspeech 2024)</p> <p><strong>Abstract:</strong> Models for low-latency, streaming applications could benefit from the knowledge capacity of larger models, but edge devices cannot run these models due to resource constraints. A possible solution is to transfer hints during inference from a large model running remotely to a small model running on-device. However, this incurs a communication delay that breaks real-time requirements and does not guarantee that both models will operate on the same data at the same time. We propose knowledge boosting, a novel technique that allows a large model to operate on time-delayed input during inference, while still boosting small model performance. Using a streaming neural network that processes 8 ms chunks, we evaluate different speech separation and enhancement tasks with communication delays of up to six chunks or 48 ms. Our results show larger gains where the performance gap between the small and large models is wide, demonstrating a promising method for large-small model collaboration for low-latency applications. </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.