Compared to the field of X-ray crystallography, the field of single particle three-dimensional electron microscopy has few reliable metrics for assessing the quality of 3D reconstructions. New ...metrics are needed that can determine whether a given 3D reconstruction accurately reflects the structure of the particles from which it was derived or instead depicts a plausible though incorrect structure due to coarse misalignment of particles. Here an empirical procedure is presented for differentiating between a reconstruction with well-aligned particles and a reconstruction with grossly misclassified particles. For a given dataset, 3D reconstructions are computed from subsets of particles with decreasing numbers of particles contributing to the reconstruction. A plot of inverse resolution vs. the logarithm of the number of particles (a “ResLog” plot) provides metrics for the reliability of the reconstruction and the overall quality of the dataset and processing. Specifically, the y-intercept of a regression line provides a measure of the relative accuracy of the particle alignment and classification, and the slope is an indicator of the overall data quality including the imaging conditions and processing steps. ResLog plots can also be used to optimize conditions for data collection and reconstruction parameters. Although resolution estimates can vary by method of calculation, ResLog-derived parameters are consistent whether calculated by Fourier shell correlation or Fourier neighbor correlation, or a new coordinate-based metric that serves as a yardstick for structures where atomic coordinates are available. ResLog plots could become part of a standard set of parameters to be included in 3D reconstruction reports.
Human gene therapy has advanced from twentieth-century conception to twenty-first-century reality. The recombinant Adeno-Associated Virus (rAAV) is a major gene therapy vector. Research continues to ...improve rAAV safety and efficacy using a variety of AAV capsid modification strategies. Significant factors influencing rAAV transduction efficiency include neutralizing antibodies, attachment factor interactions and receptor binding. Advances in understanding the molecular interactions during rAAV cell entry combined with improved capsid modulation strategies will help guide the design and engineering of safer and more efficient rAAV gene therapy vectors.
Trauma-induced coagulopathy (TIC) is associated with a fourfold increased risk of mortality. Hyperfibrinolysis is a component of TIC, but its mechanism is poorly understood. Plasminogen activation ...inhibitor (PAI-1) degradation by activated protein C has been proposed as a mechanism for deregulation of the plasmin system in hemorrhagic shock, but in other settings of ischemia, tissue plasminogen activator (tPA) has been shown to be elevated. We hypothesized that the hyperfibrinolysis in TIC is not the result of PAI-1 degradation but is driven by an increase in tPA, with resultant loss of PAI-1 activity through complexation with tPA.
Eighty-six consecutive trauma activation patients had blood collected at the earliest time after injury and were screened for hyperfibrinolysis using thrombelastography (TEG). Twenty-five hyperfibrinolytic patients were compared with 14 healthy controls using enzyme-linked immunosorbent assays for active tPA, active PAI-1, and PAI-1/tPA complex. Blood was also subjected to TEG with exogenous tPA challenge as a functional assay for PAI-1 reserve.
Total levels of PAI-1 (the sum of the active PAI-1 species and its covalent complex with tPA) are not significantly different between hyperfibrinolytic trauma patients and healthy controls: median, 104 pM (interquartile range IQR, 48-201 pM) versus 115 pM (IQR, 54-202 pM). The ratio of active to complexed PAI-1, however, was two orders of magnitude lower in hyperfibrinolytic patients than in controls. Conversely, total tPA levels (active + complex) were significantly higher in hyperfibrinolytic patients than in controls: 139 pM (IQR, 68-237 pM) versus 32 pM (IQR, 16-37 pM). Hyperfibrinolytic trauma patients displayed increased sensitivity to exogenous challenge with tPA (median LY30 of 66.8% compared with 9.6% for controls).
Depletion of PAI-1 in TIC is driven by an increase in tPA, not PAI-1 degradation. The tPA-challenged TEG, based on this principle, is a functional test for PAI-1 reserves. Exploration of the mechanism of up-regulation of tPA is critical to an understanding of hyperfibrinolysis in trauma.
Prognostic and epidemiologic study, level II.
•Ongoing severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection may occur in immunocompromised hosts.•Sequencing of repeat samples demonstrated an increasing repertoire of ...mutations.•Viral culture can be used to confirm the presence of infectious SARS-CoV-2.
This article reports a case of a 21-year-old woman with refractory B-cell acute lymphocytic leukaemia who presented with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). She remained positive for SARS-CoV-2 by viral culture for 78 days and by polymerase chain reaction (PCR) for 97 days. Sequencing of repeat samples over time demonstrated an increasing and dynamic repertoire of mutations.
The spin vector of a spin-1 system, unlike that of a spin−1/2 system, can lie anywhere on or inside the Bloch sphere representing the phase space. As a consequence, the geometrical and topological ...properties of the spin-1 phase space of quantum states are richer and require a generalization of Berry's phase. For special trajectories passing through the center of the Bloch sphere (singular loops), the geometric phase has a non-Abelian nature. Here, we experimentally explore this geometric phase for singular loops in a spin-1 quantum system using ultracold Rb87 atoms confined in an optical trap using microwave and rf control fields.
Robust road boundary extraction and completion play an important role in providing guidance to all road users and supporting high-definition (HD) maps. The significant challenges remain in remarkable ...and accurate road boundary recovery from poor road boundary conditions. This paper presents a novel deep learning framework, named BoundaryNet, to extract and complete road boundaries by using both mobile laser scanning (MLS) point clouds and high-resolution satellite imagery. First, road boundaries are extracted by conducting a curb-based extraction method. Such extracted 3D road boundary lines are used as inputs to feed into a U-shaped network for erroneous boundary denoising. Then, a convolutional neural network (CNN) model is proposed to complete the road boundaries. Next, to achieve more complete and accurate road boundaries, a conditional deep convolutional generative adversarial network (c-DCGAN) with the assistance of road centerlines extracted from satellite images is developed. Finally, according to the completed road boundaries, the inherent road geometries are calculated. The proposed methods were evaluated using satellite imagery and four MLS point cloud datasets with varying densities and road conditions in urban environments. The quality evaluation metrics of 82.88%, 82.43%, 88.86%, and 84.89% were achieved for four data sets. The experimental results indicate that the BoundaryNet model can provide a promising solution for road boundary completion and road geometry estimation.
Both tissue plasminogen activator (tPA) in the circulation and urokinase (uPA) in tissues cleave plasminogen (PLG) to plasmin to promote clot lysis. Tranexamic acid (TXA) blocks both the ...tPA-dependent generation of plasmin on blood clots as well as active plasmin binding to polymerized fibrin, and is commonly administered for bleeding in trauma to limit fibrinolysis. In addition to lysing clots, however, active plasmin also cleaves complement proteins, potentially enhancing inflammation. Because TXA does not block uPA-dependent plasmin generation from PLG and instead augments it, we hypothesized that administration of TXA could enhance or inhibit proinflammatory C5a formation in a PLG activator-dependent manner.
Citrate platelet-poor plasma (PPP) and PPP depleted of complement protein C3 or PLG were obtained from healthy donors and commercial sources. Platelet-poor plasma was treated ex vivo with or without TXA and either with or without tPA or with or without uPA. Clotting was then induced by calcium and thrombin in clotted PPP experiments, while unclotted PPP experiments were treated with vehicle controls. C5a levels were measured via enzyme-linked immunosorbent assay. Data were expressed as mean ± SEM.
Plasmin-mediated fibrinolysis by tPA in clotted PPP led to an approximately threefold increase in C5a production (p < 0.0001), which was significantly inhibited by TXA (p < 0.001). Paradoxically, when fibrinolysis was induced by uPA, TXA treatment led to further increases in C5a production beyond uPA alone (p < 0.0001). Furthermore, clotting was not required for C5a generation from uPA + TXA. C3 depletion had no effect on C5a production, while depletion of PLG eliminated it.
Tranexamic acid administration can have proinflammatory or anti-inflammatory effects through regulating C5a generation by plasmin, depending on the predominating PLG activator. Tranexamic acid may cause significant inflammatory C5a elevations in injured tissues by augmenting uPA-mediated plasmin generation in a fibrin-independent manner. In contrast, TXA reduces C5a generation during tPA-mediated fibrinolysis that may reduce inflammatory responses. In vivo validation of these novel ex vivo findings is warranted and may have important clinical consequences.
We have observed sub-Poissonian spin correlations generated by collisionally induced spin mixing in a spin-1 Bose-Einstein condensate. We measure a quantum noise reduction of -7 dB (-10 dB corrected ...for detection noise) below the standard quantum limit for the corresponding coherent spin states. The spin fluctuations are detected as atom number differences in the spin states using fluorescent imaging that achieves a detection noise floor of 8 atoms per spin component for a probe time of 100 μs.
ABSTRACT
We present the Emission Line Galaxy (ELG) sample of the extended Baryon Oscillation Spectroscopic Survey from the Sloan Digital Sky Survey IV Data Release 16. We describe the observations ...and redshift measurement for the 269 243 observed ELG spectra, and then present the large-scale structure catalogues, used for the cosmological analysis, and made of 173 736 reliable spectroscopic redshifts between 0.6 and 1.1. We perform a spherically averaged baryon acoustic oscillations (BAO) measurement in configuration space, with density field reconstruction: the data two-point correlation function shows a feature consistent with that of the BAO, the BAO model being only weakly preferred over a model without BAO (Δχ2 < 1). Fitting a model constrained to have a BAO feature provides a 3.2 per cent measurement of the spherically averaged BAO distance DV(zeff)/rdrag = 18.23 ± 0.58 at the effective redshift zeff = 0.845.
Adeno-associated virus (AAV) vectors have made great progress in their use for gene therapy; however, fundamental aspects of AAV's capsid assembly remain poorly characterized. In this regard, the ...discovery of assembly-activating protein (AAP) sheds new light on this crucial part of AAV biology and vector production. Previous studies have shown that AAP is essential for assembly; however, how its mechanistic roles in assembly might differ among AAV serotypes remains uncharacterized. Here, we show that biological properties of AAPs and capsid assembly processes are surprisingly distinct among AAV serotypes 1 to 12. In the study, we investigated subcellular localizations and assembly-promoting functions of AAP1 to -12 (i.e., AAPs derived from AAV1 to -12, respectively) and examined the AAP dependence of capsid assembly processes of these 12 serotypes using combinatorial approaches that involved immunofluorescence and transmission electron microscopy, barcode-Seq (i. e., a high-throughput quantitative method using DNA barcodes and a next-generation sequencing technology), and quantitative dot blot assays. This study revealed that AAP1 to -12 are all localized in the nucleus with serotype-specific differential patterns of nucleolar association; AAPs and assembled capsids do not necessarily colocalize; AAPs are promiscuous in promoting capsid assembly of other serotypes, with the exception of AAP4, -5, -11, and -12; assembled AAV5, -8, and -9 capsids are excluded from the nucleolus, in contrast to the nucleolar enrichment of assembled AAV2 capsids; and, surprisingly, AAV4, -5, and -11 capsids are not dependent on AAP for assembly. These observations highlight the serotype-dependent heterogeneity of the capsid assembly process and challenge current notions about the role of AAP and the nucleolus in capsid assembly.
Assembly-activating protein (AAP) is a recently discovered adeno-associated virus (AAV) protein that promotes capsid assembly and provides new opportunities for research in assembly. Previous studies on AAV serotype 2 (AAV2) showed that assembly takes place in the nucleolus and is dependent on AAP and that capsids colocalize with AAP in the nucleolus during the assembly process. However, through the investigation of 12 different AAV serotypes (AAV1 to -12), we find that AAP is not an essential requirement for capsid assembly of AAV4, -5, and -11, and AAP, assembled capsids, and the nucleolus do not colocalize for all the serotypes. In addition, we find that there are both serotype-restricted and serotype-promiscuous AAPs in their assembly roles. These findings challenge widely held beliefs about the importance of the nucleolus and AAP in AAV assembly and show the heterogeneous nature of the assembly process within the AAV family.
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