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167 results for “Twist”
Chromophore carbonyl twisting in fluorescent biosensors encodes direct readout of protein conformations with multicolor switching
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Data from: Anomalous thermal transport in Eshelby twisted van der Waals nanowires
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Strain fields in twisted bilayer graphene: Dataset 18 of 19
<p>See supplemental materials of Kazmierczak & Van Winkle et al for more information.</p> <p>02262020_3.h5 : dataset s1-3 corresponding to a mean angle of 0.9999</p>
Strain fields in twisted bilayer graphene: Dataset 19 of 19
<p>See supplemental materials of Kazmierczak & Van Winkle et al for more information.</p> <p>02262020_6.h5 : dataset s1-6 corresponding to a mean angle of 1.2592</p>
Data from: Polyphyly of Arundinoideae (Poaceae) and evolution of the twisted geniculate lemma awn
Background and Aims: Subfamily Arundinoideae represents one of the last unsolved taxonomic mysteries in the grass family (Poaceae) due to the narrow and remote distributions of many of its 19 morphologically and ecologically heterogeneous genera. Resolving the phylogenetic relationships of these genera could have substantial implications for understanding character evolution in the grasses, for example the twisted geniculate awn – a hygroscopic awn that has been shown to be important in seed germination for some grass species. In this study, the phylogenetic positions of most arundinoid genera were determined using DNA from herbarium specimens, and their placement affects interpretation of this ecologically important trait. Methods: A phylogenetic analysis was conducted on a matrix of full-plastome sequences from 123 species in 107 genera representing all grass subfamilies, with 15 of the 19 genera in subfamily Arundinoideae. Parsimony and maximum likelihood mapping approaches were used to estimate ancestral states for presence of a geniculate lemma awn with a twisted column across Poaceae. Lastly, anatomical characters were examined for former arundinoid taxa using light microscopy and scanning electron microscopy. Key Results: Four genera traditionally included in Arundinoideae fell outside the subfamily in the plastome phylogeny, with the remaining 11 genera forming Arundinoideae sensu stricto. The twisted geniculate awn has originated independently at least five times in the PACMAD grasses, in the subfamilies Panicoideae, Danthonioideae/Chloridoideae and Arundinoideae. Morphological and anatomical characters support the new positions of the misplaced arundinoid genera in the phylogeny, but also highlight convergent and parallel evolution in the grasses. Conclusions: In placing the majority of arundinoid genera in a phylogenetic framework, our study answers one of the last remaining big questions in grass taxonomy while highlighting examples of convergent evolution in an ecologically important trait, the hygroscopic, twisted geniculate awn.
Twisted Cordate Hand Axe
Source: Objaverse 1.0 / Sketchfab
Flux Emergence Photospheric Data from Simulation with Twist 0
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Flux Emergence Photospheric Data from Simulation with Twist 0.5
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Flux Emergence Photospheric Data from Simulation with Twist 1
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Twisted Cordate Handaxe
University of Manchester Archaeology Teaching Collection Source: Objaverse 1.0 / Sketchfab
Twist - torsion coupling in beating axonemes
<p>The dataset published here was used to measure a<strong> high resolution 3D wavefom </strong>of isolated and <strong>reactivated axonemes from <em>Chlamydomonas reinhardtii</em></strong>.</p> <p><a href="https://doi.org/10.1101/2024.03.18.585533"><span><span>doi:</span> https://doi.org/10.1101/2024.03.18.585533 </span></a></p> <p>It was further used to show <strong>twist-torsion coupling </strong>in these axonemes.</p> <p>The data is organized in six folders:</p> <p><strong>1) high resoluton 3D averaged waveform of isolated and reactivated axonemes from <em>Chlamydomonas Reinhardtii</em>.</strong><br>Data files (MATLAB and txt format) contain the 3D coordinates (along the 3D arc-length) of 32 axonemal shapes that comprise one beat cycle. <br>A corresponding txt file describes the details of the dataset. </p> <p><strong>2) 3D waveforms of single isolated and reactivated axonemes from <em>Chlamydomonas Reinhardtii</em>.</strong><br>Data files (MATLAB and txt format) contain the 3D shapes of 17 individual axonemes obtained from defocused darkfield-microsopy images. <br>A corresponding txt file describes the details of the dataset.</p> <p><strong>3) Image Raw Data of single isolated and reactivated axonemes used to reconstruct the 3D waveform<br></strong>Movie files (multi-layer tif) of reactivated axonemes imaged with defocused-darkfield-microscopy. <br>A corresponding txt file describes the details of the dataset.<strong><br></strong></p> <p><strong>4) Calibration of defocused darkfield-microscopy. <br></strong>Data file (MATLAB) contains the relationship between the z-position relative to the focal plane and the full-width-at-half-maximum (FWHM) of the axoneme signal, measured normal to the centerline as well as the z-stack of imges (multi-layer tif) used to extract this relation. <br>A corresponding txt file describes the details of the dataset.</p> <p><strong>5)</strong> <strong>Distance between gold nano paricle (GNP) and the axonemal centerline as a function of the beat cycle</strong><br>Data file (MATLAB) contains 20 measurements of d_C (where d_C is the normal distance between the center position of the GNP and the axoneme centerline in 2D images) as a function of time. A corresponding txt file describes the details of the dataset.</p> <p><strong>6) Image Raw Data of single isolated and reactivated axonemes with attached GNPs used to measure d_C. <br></strong>Movie files (multi-layer tif) of reactivated axonemes with attached gold nano particles (GNPs) imaged with darkfield-microscopy. <br>A corresponding txt file describes the details of the dataset.</p>
Dataset for 'Mapping twist-tuned multi-band topology in bilayer WSe$_2$'
<p>Datasets and code for the manuscript 'Mapping twist-tuned multi-band topology in bilayer WSe2.' See 'README.txt' for further details. </p>
Fig. 1 in Phytochemical genomics of the Madagascar periwinkle: Unravelling the last twists of the alkaloid engine
Fig. 1. Overview of the MIA biosynthetic pathway highlighting the preferential distribution of MIAs within Catharanthus roseus.
Fig. 2 in Phytochemical genomics of the Madagascar periwinkle: Unravelling the last twists of the alkaloid engine
Fig. 2. Model for the alkaloid plant cell factories in Catharanthus roseus leaves. The biosynthesis of MIAs sequentially involves internal phloem associated parenchyma (IPAP) cells, pavimentous epidermal cells (upper and lower) and specialized cells (laticifers and idioblasts). The biosynthetic pathway leading to vindoline is shown in the margins of the leaf diagram. Known single enzymatic steps in each cell type are indicated by grey arrows and abbreviation of enzyme names. Broken grey arrows indicate unknown enzymatic steps. No specific cellular localization for NMT has been determined. A DNA helix is shown besides proteins encoded by genes characterized by exploiting C. roseus transcriptomic resources. In the leaf diagram, dashed arrows indicate conversion of pyruvate (A) and GAP (B) to loganic acid (C) in IPAP cells; conversion of loganic acid (C) to 16-methoxy-tabersonine (D) in epidermis (for simplification, only the conversion in the upper epidermis is shown) and conversion of desacetoxyvindoline (E) to vindoline (F) in laticifers and idioblasts. The blue arrows indicate intercellular metabolite translocation for loganic acid (C) and secretion to the leaf surface for catharantine. Broken blue arrows indicate that the translocated metabolite is uncharacterized/unknown. DXS, 1-deoxy-D-xylulose-5-phosphate (DXP) synthase; DXR, DXP reductoisomerase; CMS, 4- (cytidine 50-diphospho)-2C-methyl-D-erythritol (CM) synthase; CMK, CM kinase; MECS, 2C-methyl-D-erythritol-2,4-cyclodiphosphate (MEC) synthase; HDS, hydroxymethylbutenyl 4-diphosphate (HD) synthase; HDR, HD reductase; IDI, isopentenyl diphosphate isomerase; GPPS, geranyl diphosphate synthase; GES, geraniol synthase; G10H (CYP76B6), geraniol 10-hydroxylase; CPR, cytochrome P450-reductase; 10HGO, 10-hydroxygeraniol oxidoreductase; IS, iridoid synthase; 7DLGT, 7-deoxyloganetic acid glucosyltransferase; 7DLH, 7-deoxyloganic acid hydroxylase; LAMT, loganic acid O-methyltransferase; SLS (CYP72A1), secologanin synthase; TDC, tryptophan decarboxylase; STR, strictosidine synthase; SGD, strictosidine b-glucosidase; T16H2 (CYP71D351), tabersonine 16-hydroxylase 2; 16OMT, 16-hydroxytabersonine O-methyltransferase; TPT2, catharanthine transporter from pleiotropic drug resistance (PDR) family of ABC transporters; D4H, desacetoxyvindoline 4-hydroxylase; DAT, deacetylvindoline 4-Oacetyltransferase. DMAPP, dimethylallyl diphosphate; GAP, glyceraldehyde 3-phosphate; IPP, isopentenyl diphosphate. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
Fig. 4 in Phytochemical genomics of the Madagascar periwinkle: Unravelling the last twists of the alkaloid engine
Fig. 4. Virus-induced gene silencing monitored in C. roseus by targeting phytoene desaturase (PDS). (A) Control plant. (B) Photobleaching phenoptype of upper leaves as a marker of PDS silenced tissues in plant co-infiltrated with Agrobacterium tumefaciens strain GV3101 containing pTRV1 and pTRV2-PDS (T-DNA vectors carrying, respectively RNA1 and RNA2 TRV genome) (S. Besseau and V. Courdavault, personal data). Seedlings were grown at 28 °C and transferred at 21 °C after transformation to improve VIGS efficiency as suggested by Sung et al. (2014).
Fig. 3 in Phytochemical genomics of the Madagascar periwinkle: Unravelling the last twists of the alkaloid engine
Fig. 3. The use of high-throughput transcriptomic data for discovery of MIA biosynthetic genes. Two non-exclusive strategies may be used: orthology comparison with other species (left panel) and clustering of gene expression (right panel). The former approach requires transcriptomic data from candidate species with specific alkaloid metabolisms (e.g. secologanin (11)-producing (purple inset) and non secologanin (11)-producing (blue inset) species). Such data are available from the MPGR and PhytoMetaSyn projects. A first orthology comparison using the OrthoMCL algorithm (Li et al., 2003) could help identify conserved genes encoding enzymes involved in the biosynthesis of common precursors in MIA-producing species (Camptotheca acuminata, Rauwolfia serpentina, C. roseus) but also specific enzymatic activities dedicated to the synthesis of particular alkaloids, such as the C. roseus specific genes. A second orthology analysis can be further performed on the set of conserved genes found in the MIAproducing species to isolate candidates from the secoiridoid pathway by comparing with transcriptomic data from non secologanin (11)-producing enzymes. The second strategy relies on transcriptome analyses from diverse experimental conditions to construct a reference transcriptome which will be used to estimate the abundance of each transcript in each condition in order to cluster genes according to their expression levels. The more experimental conditions are available, the more the clustering analysis will be efficient to group co-regulated genes. Note that this reference transcriptome could also serve to the orthology analysis depicted in the left panel, and also to verify expression levels of candidate genes resulting from this kind of approach. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
Dataset: Polarization-driven band topology evolution in twisted MoTe2 and WSe2
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Band gap formation in commensurate twisted bilayer graphene/hBN moiré lattices
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Data set for "The effect of pulling and twisting forces on chameleon sequence peptides"
<p>Data set for the publication "The effect of pulling and twisting forces on chameleon sequence peptides"<br> <br> The data contains all energy landscapes explored, structures extracted and analysed, and the necessary utility scripts, written by James Meadows. The README details which data is in each directory. The image directory contains the disconnectivity graphs associated with this data.</p>
Data for "Hofstadter spectrum of Chern bands in twisted transition metal dichalcogenides"
<p>Data used to generate each Figure is in files denoted fig....hdf5. <br>These files contain results for multiple parameter values. The group "data" can be read into a pandas dataframe, providing an index and scalar data.<br>Vector valued data is stored in individual datasets, indexed by the index in "data" along 0-th axis.<br>For an example readout, see "example.py".</p> <p>See README.txt for notes on individual files.</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.