Phase-variable bacteria simultaneously express multiple capsules

Capsular polysaccharides (CPSs) protect bacteria from host and environmental factors. Many bacteria can express different CPSs and these CPSs are phase variable. For example, Bacteroides thetaiotaomicron (B. theta) is a prominent member of the human gut microbiome and expresses eight different capsular polysaccharides. Bacteria, including B. theta, have been shown to change their CPSs to adapt to various niches such as immune, bacteriophage, and antibiotic perturbations. However, there are limited tools to study CPSs and fundamental questions regarding phase variance, including if gut bacteria can express more than one capsule at the same time, remain unanswered. To better understand the roles of different CPSs, we generated a B. theta CPS1-specific antibody and a flow cytometry assay to detect CPS expression in individual bacteria in the gut microbiota. Using these novel tools, we report for the first time that bacteria can simultaneously express multiple CPSs. We also observed that nutrients such as glucose and salts had no effect on CPS expression. The ability to express multiple CPSs at the same time may provide bacteria with an adaptive advantage to thrive amid changing host and environmental conditions, especially in the intestine.

Comparative study of optical coherence tomography angiography algorithms for rodent retinal imaging

Optical coherence tomography angiography (OCTA) is a functional extension of optical coherence tomography for non-invasive in vivo three-dimensional imaging of the microvasculature of biological tissues. Several algorithms have been developed to construct OCTA images from the measured optical coherence tomography signals. In this study, we compared the performance of three OCTA algorithms that are based on the variance of phase, amplitude, and the complex representations of the optical coherence tomography signals for rodent retinal imaging, namely the phase variance, improved speckle contrast, and optical microangiography. The performance of the different algorithms was evaluated by comparing the quality of the OCTA images regarding how well the vasculature network can be resolved. Quantities that are widely used in ophthalmic studies including blood vessel density, vessel diameter index, vessel perimeter index, vessel complexity index were also compared. Results showed that both the improved speckle contrast and optical microangiography algorithms are more robust than phase variance, and they can reveal similar vasculature features while there are statistical differences in the calculated quantities.

GECORIS: An Open-Source Toolbox for Analyzing Time Series of Corner Reflectors in InSAR Geodesy

Artificial radar reflectors, such as corner reflectors or transponders, are commonly used for radiometric and geometric Synthetic Aperture Radar (SAR) sensor calibration, SAR interferometry (InSAR) applications over areas with few natural coherent scatterers, and InSAR datum connection and geodetic integration. Despite the current abundance of regular SAR time series, no free and open-source software (FOSS) dedicated to analyzing SAR time series of artificial radar reflectors exists. In this paper, we present a FOSS Python toolbox for efficient and automatic estimation of: (i) the clutter level of a particular site before a corner reflector installation, (ii) the Radar Cross Section (RCS) to track a corner reflector’s performance and detect outliers, for example, due to damage or debris accumulation, (iii) the Signal-to-Clutter Ratio (SCR) to predict the positioning precision and the InSAR phase variance, (iv) the InSAR displacement time series of a corner reflector network. We use the toolbox to analyze Sentinel-1 SAR time series of the network of 23 corner reflectors for InSAR monitoring of landslides in Slovakia.

Reliability analysis of seismic attribute in the detection of fault-karst

In the Tarim Basin, various irregular fractured-vuggy reservoirs have developed along with the main faults. These reservoirs are geologically defined as carbonate fault karst. In the past few years, seismic attributes have been widely used for the identification and evaluation of fault karst. However, there has been less reliability analysis regarding their usage. Imaging using the theoretical fault-karst velocity model can reflect the shapes and distributions of fractures and vugs, whereas imaging using the background velocity can simulate seismic data in real cases. We have adopted an approach based on typical fault-karst theoretical forward modeling to evaluate the reliability of seismic attributes in practical applications. First, we extract various attributes from the images using the theoretical velocity and the background velocity using similarity estimation between them to optimize the sensitive attributes. The analysis result indicates that the instantaneous phase, variance, amplitude gradient, coherence, and texture entropy are more suitable to characterize the anomalies of fractures and vugs with prediction accuracy of 71.7%. Because fracture orientation and density are the key parameters for quantifying the differences between the two images, taking coherence as an example, we extract the fracture traces through circular scanlines and circular windows based on the optimized attributes. The coincidence rate between the predicted fracture density and the known model reaches 83%, and that between the predicted fracture orientation and the known model is greater than 95%. With this remarkable coincidence, we can conclude that optimized seismic attributes are reliable for characterizing fractured-vuggy reservoirs.

The Phase Shift Correlation function uncovers periodic Ulcerative Colitis microbiome relationships without temporal sampling

Correlation analysis is a fundamental technique to determine potential relationships within biological processes. However, many biological processes have been shown to function in a periodic manner. When modeling correlations, the fluctuations that are associated with periodicity cause significant issues. We have implemented a Phase Shift Correlation (PSC) algorithm, with a corresponding value PSCrho, to address the periodicity and phase variance associated with features that vary with the same frequency -- but are phase shifted. The phase shift could well indicate causality with one feature’s quantitative change leading to the change in the other feature.We applied the PSC algorithm to Ulcerative Colitis (UC) microbiome data and compared the resulting feature relationships with the equivalent Spearman correlation function results. PSC located many instances of higher phase shifted correlations, where the corresponding Pearson correlation was low.

Robustness of prediction for extreme adaptive optics systems under various observing conditions

Context. For high-contrast imaging systems, such as VLT/SPHERE, the performance of the system at small angular separations is contaminated by the wind-driven halo in the science image. This halo is a result of the servo-lag error in the adaptive optics (AO) system due to the finite time between measuring the wavefront phase and applying the phase correction. One approach to mitigating the servo-lag error is predictive control. Aims. We aim to estimate and understand the potential on-sky performance that linear data-driven prediction would provide for VLT/SPHERE under various turbulence conditions. Methods. We used a linear minimum mean square error predictor and applied it to 27 different AO telemetry data sets from VLT/SPHERE taken over many nights under various turbulence conditions. We evaluated the performance of the predictor using residual wavefront phase variance as a performance metric. Results. We show that prediction always results in a reduction in the temporal wavefront phase variance compared to the current VLT/SPHERE AO performance. We find an average improvement factor of 5.1 in phase variance for prediction compared to the VLT/SPHERE residuals. When comparing to an idealised VLT/SPHERE, we find an improvement factor of 2.0. Under our 27 different cases, we find the predictor results in a smaller spread of the residual temporal phase variance. Finally, we show there is no benefit to including spatial information in the predictor in contrast to what might have been expected from the frozen flow hypothesis. A purely temporal predictor is best suited for AO on VLT/SPHERE. Conclusions. Linear prediction leads to a significant reduction in phase variance for VLT/SPHERE under a variety of observing conditions and reduces the servo-lag error. Furthermore, prediction improves the reliability of the AO system performance, making it less sensitive to different conditions.

The minimum of the time-delay wavefront error in Adaptive Optics

An analytical expression is given for the minimum of the time-delay induced wavefront error (also known as the servo-lag error) in Adaptive Optics systems under temporal prediction filtering. The analysis is based on the von Kármán model for the spectral density of refractive index fluctuations and the hypothesis of frozen flow. An optimal, temporal predictor can achieve up to a factor 1.77 more reduction of the wavefront phase variance compared to the zero-order prediction strategy, which is commonly used in Adaptive Optics systems. Alternatively, an optimal predictor can allow for a 1.41 times longer time-delay to arrive at the same residual phase variance. Generally, the performance of the optimal, temporal predictor depends on the very product of time-delay, wind speed and the reciprocal of turbulence outer scale.

Probing gravity by holding atoms for 20 seconds

Atom interferometers are powerful tools for both measurements in fundamental physics and inertial sensing applications. Their performance, however, has been limited by the available interrogation time of freely falling atoms in a gravitational field. By suspending the spatially separated atomic wave packets in a lattice formed by the mode of an optical cavity, we realize an interrogation time of 20 seconds. Our approach allows gravitational potentials to be measured by holding, rather than dropping, atoms. After seconds of hold time, gravitational potential energy differences from as little as micrometers of vertical separation generate megaradians of interferometer phase. This trapped geometry suppresses the phase variance due to vibrations by three to four orders of magnitude, overcoming the dominant noise source in atom-interferometric gravimeters.