Second shot at cyno genome assembly
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PROVIDER: PRJEB51627 | ENA |
REPOSITORIES: ENA
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Project description:Real-time imaging of countless femtosecond dynamics requires extreme speeds orders of magnitude beyond the limits of electronic sensors. Existing femtosecond imaging modalities either require event repetition or provide single-shot acquisition with no more than 1013 frames per second (fps) and 3 × 102 frames. Here, we report compressed ultrafast spectral photography (CUSP), which attains several new records in single-shot multi-dimensional imaging speeds. In active mode, CUSP achieves both 7 × 1013 fps and 103 frames simultaneously by synergizing spectral encoding, pulse splitting, temporal shearing, and compressed sensing-enabling unprecedented quantitative imaging of rapid nonlinear light-matter interaction. In passive mode, CUSP provides four-dimensional (4D) spectral imaging at 0.5 × 1012 fps, allowing the first single-shot spectrally resolved fluorescence lifetime imaging microscopy (SR-FLIM). As a real-time multi-dimensional imaging technology with the highest speeds and most frames, CUSP is envisioned to play instrumental roles in numerous pivotal scientific studies without the need for event repetition.
| S-EPMC7190645 | biostudies-literature
Project description:The capture of transient scenes at high imaging speed has been long sought by photographers, with early examples being the well known recording in 1878 of a horse in motion and the 1887 photograph of a supersonic bullet. However, not until the late twentieth century were breakthroughs achieved in demonstrating ultrahigh-speed imaging (more than 10(5) frames per second). In particular, the introduction of electronic imaging sensors based on the charge-coupled device (CCD) or complementary metal-oxide-semiconductor (CMOS) technology revolutionized high-speed photography, enabling acquisition rates of up to 10(7) frames per second. Despite these sensors' widespread impact, further increasing frame rates using CCD or CMOS technology is fundamentally limited by their on-chip storage and electronic readout speed. Here we demonstrate a two-dimensional dynamic imaging technique, compressed ultrafast photography (CUP), which can capture non-repetitive time-evolving events at up to 10(11) frames per second. Compared with existing ultrafast imaging techniques, CUP has the prominent advantage of measuring an x-y-t (x, y, spatial coordinates; t, time) scene with a single camera snapshot, thereby allowing observation of transient events with temporal resolution as tens of picoseconds. Furthermore, akin to traditional photography, CUP is receive-only, and so does not need the specialized active illumination required by other single-shot ultrafast imagers. As a result, CUP can image a variety of luminescent--such as fluorescent or bioluminescent--objects. Using CUP, we visualize four fundamental physical phenomena with single laser shots only: laser pulse reflection and refraction, photon racing in two media, and faster-than-light propagation of non-information (that is, motion that appears faster than the speed of light but cannot convey information). Given CUP's capability, we expect it to find widespread applications in both fundamental and applied sciences, including biomedical research.
| S-EPMC4270006 | biostudies-literature
Project description:BackgroundSeveral approaches can be used to determine the order of loci on chromosomes and hence develop maps of the genome. However, all mapping approaches are prone to errors either arising from technical deficiencies or lack of statistical support to distinguish between alternative orders of loci. The accuracy of the genome maps could be improved, in principle, if information from different sources was combined to produce integrated maps. The publicly available bovine genomic sequence assembly with 6x coverage (Btau_2.0) is based on whole genome shotgun sequence data and limited mapping data however, it is recognised that this assembly is a draft that contains errors. Correcting the sequence assembly requires extensive additional mapping information to improve the reliability of the ordering of sequence scaffolds on chromosomes. The radiation hybrid (RH) map described here has been contributed to the international sequencing project to aid this process.ResultsAn RH map for the 30 bovine chromosomes is presented. The map was built using the Roslin 3000-rad RH panel (BovGen RH map) and contains 3966 markers including 2473 new loci in addition to 262 amplified fragment-length polymorphisms (AFLP) and 1231 markers previously published with the first generation RH map. Sequences of the mapped loci were aligned with published bovine genome maps to identify inconsistencies. In addition to differences in the order of loci, several cases were observed where the chromosomal assignment of loci differed between maps. All the chromosome maps were aligned with the current 6x bovine assembly (Btau_2.0) and 2898 loci were unambiguously located in the bovine sequence. The order of loci on the RH map for BTA 5, 7, 16, 22, 25 and 29 differed substantially from the assembled bovine sequence. From the 2898 loci unambiguously identified in the bovine sequence assembly, 131 mapped to different chromosomes in the BovGen RH map.ConclusionAlignment of the BovGen RH map with other published RH and genetic maps showed higher consistency in marker order and chromosome assignment than with the current 6x sequence assembly. This suggests that the bovine sequence assembly could be significantly improved by incorporating additional independent mapping information.
| S-EPMC1636650 | biostudies-literature
Project description:An outstanding hurdle for defect spin qubits in silicon carbide (SiC) is single-shot readout, a deterministic measurement of the quantum state. Here, we demonstrate single-shot readout of single defects in SiC via spin-to-charge conversion, whereby the defect's spin state is mapped onto a long-lived charge state. With this technique, we achieve over 80% readout fidelity without pre- or postselection, resulting in a high signal-to-noise ratio that enables us to measure long spin coherence times. Combined with pulsed dynamical decoupling sequences in an isotopically purified host material, we report single-spin T2 > 5 seconds, over two orders of magnitude greater than previously reported in this system. The mapping of these coherent spin states onto single charges unlocks both single-shot readout for scalable quantum nodes and opportunities for electrical readout via integration with semiconductor devices.
| S-EPMC8809532 | biostudies-literature
Project description:PurposeTo evaluate the feasibility of an abbreviated gadoxetic acid-enhanced MRI protocol including second-shot arterial phase (SSAP) imaging for liver metastasis evaluation.Materials and methodsFor this retrospective study, a total of 197 patients with cancer (117 men and 80 women; mean age, 62.9 years) were included who underwent gadoxetic acid-enhanced MRI performed by using a modified injection protocol for liver metastasis evaluation from July to August 2017. The modified injection protocol included routine dynamic imaging after a first injection of 6 mL and SSAP imaging after a second injection of 4 mL. Image set 1 was obtained with the full original protocol. Image set 2 consisted of T2-weighted, diffusion-weighted, hepatobiliary phase, and SSAP images (the simulated abbreviated protocol). Acquisition time was measured in each image set. The diagnostic performance of each image set was compared by using a jackknife alternative free-response receiver operating characteristic analysis. Image quality evaluation and visual assessment of vascularity were performed on the original arterial phase images, the SSAP images, and their subtraction images.ResultsThe acquisition time was significantly shorter in image set 2 than in image set 1 (18.6 vs 6.2 minutes, P <.0001). The reader-averaged figure-of-merit was not significantly different between image sets 1 and 2 (P = .197). The mean motion artifact score was significantly lower for the SSAP images than for the original arterial phase images (P <.001). All hypervascular metastases (n = 72) showed hyperintensity on the SSAP and/or the second subtraction images.ConclusionAn abbreviated MRI protocol including SSAP is feasible for liver metastasis evaluation, providing faster image acquisition while preserving diagnostic performance, image quality, and visual vascularity.Keywords: Abdomen/GI, Comparative Studies, Liver, MR-Imaging, Metastases© RSNA, 2019Supplemental material is available for this article.
| S-EPMC7983790 | biostudies-literature
Project description: Not available
| S-EPMC9630605 | biostudies-literature
Project description:The Pacific oyster Crassostrea gigas, a widely cultivated marine bivalve mollusc, is becoming a genetically and genomically enabled model for highly fecund marine metazoans with complex life-histories. A genome sequence is available for the Pacific oyster, as are first-generation, low-density, linkage and gene-centromere maps mostly constructed from microsatellite DNA makers. Here, higher density, second-generation, linkage maps are constructed from more than 1100 coding (exonic) single-nucleotide polymorphisms (SNPs), as well as 66 previously mapped microsatellite DNA markers, all typed in five families of Pacific oysters (nearly 172,000 genotypes). The map comprises 10 linkage groups, as expected, has an average total length of 588 cM, an average marker-spacing of 1.0 cM, and covers 86% of a genome estimated to be 616 cM. All but seven of the mapped SNPs map to 618 genome scaffolds; 260 scaffolds contain two or more mapped SNPs, but for 100 of these scaffolds (38.5%), the contained SNPs map to different linkage groups, suggesting widespread errors in scaffold assemblies. The 100 misassembled scaffolds are significantly longer than those that map to a single linkage group. On the genetic maps, marker orders and intermarker distances vary across families and mapping methods, owing to an abundance of markers segregating from only one parent, to widespread distortions of segregation ratios caused by early mortality, as previously observed for oysters, and to genotyping errors. Maps made from framework markers provide stronger support for marker orders and reasonable map lengths and are used to produce a consensus high-density linkage map containing 656 markers.
| S-EPMC4592983 | biostudies-literature
Project description:We create a new assembly of the Drosophila simulans genome using 142 million paired short-read sequences and previously published data for strain w(501). Our assembly represents a higher-quality genomic sequence with greater coverage, fewer misassemblies, and, by several indexes, fewer sequence errors. Evolutionary analysis of this genome reference sequence reveals interesting patterns of lineage-specific divergence that are different from those previously reported. Specifically, we find that Drosophila melanogaster evolves faster than D. simulans at all annotated classes of sites, including putatively neutrally evolving sites found in minimal introns. While this may be partly explained by a higher mutation rate in D. melanogaster, we also find significant heterogeneity in rates of evolution across classes of sites, consistent with historical differences in the effective population size for the two species. Also contrary to previous findings, we find that the X chromosome is evolving significantly faster than autosomes for nonsynonymous and most noncoding DNA sites and significantly slower for synonymous sites. The absence of a X/A difference for putatively neutral sites and the robustness of the pattern to Gene Ontology and sex-biased expression suggest that partly recessive beneficial mutations may comprise a substantial fraction of noncoding DNA divergence observed between species. Our results have more general implications for the interpretation of evolutionary analyses of genomes of different quality.
| S-EPMC3530686 | biostudies-literature
Project description:We demonstrate single-shot multi-frame imaging of quasi-2D cylindrically converging shock waves as they propagate through a multi-layer target sample assembly. We visualize the shock with sequences of up to 16 images, using a Fabry-Perot cavity to generate a pulse train that can be used in various imaging configurations. We employ multi-frame shadowgraph and dark-field imaging to measure the amplitude and phase of the light transmitted through the shocked target. Single-shot multi-frame imaging tracks geometric distortion and additional features in our images that were not previously resolvable in this experimental geometry. Analysis of our images, in combination with simulations, shows that the additional image features are formed by a coupled wave structure resulting from interface effects in our targets. This technique presents a new capability for tabletop imaging of shock waves that can be extended to experiments at large-scale facilities.
| S-EPMC6403302 | biostudies-literature