Model for Interpreting Discordant SARS-CoV-2 Diagnostic Test Results.

We devised a model to interpret discordant SARS-CoV-2 test results. We estimate that, during March 2020-May 2022, a patient in the United States who received a positive rapid antigen test result followed by a negative nucleic acid test result had only a 15.4% (95% CI 0.6%-56.7%) chance of being infected.

Disproportionate impacts of COVID-19 in a large US city.

COVID-19 has disproportionately impacted individuals depending on where they live and work, and based on their race, ethnicity, and socioeconomic status. Studies have documented catastrophic disparities at critical points throughout the pandemic, but have not yet systematically tracked their severity through time. Using anonymized hospitalization data from March 11, 2020 to June 1, 2021 and fine-grain infection hospitalization rates, we estimate the time-varying burden of COVID-19 by age group and ZIP code in Austin, Texas. During this 15-month period, we estimate an overall 23.7% (95% CrI: 22.5-24.8%) infection rate and 29.4% (95% CrI: 28.0-31.0%) case reporting rate. Individuals over 65 were less likely to be infected than younger age groups (11.2% [95% CrI: 10.3-12.0%] vs 25.1% [95% CrI: 23.7-26.4%]), but more likely to be hospitalized (1,965 per 100,000 vs 376 per 100,000) and have their infections reported (53% [95% CrI: 49-57%] vs 28% [95% CrI: 27-30%]). We used a mixed effect poisson regression model to estimate disparities in infection and reporting rates as a function of social vulnerability. We compared ZIP codes ranking in the 75th percentile of vulnerability to those in the 25th percentile, and found that the more vulnerable communities had 2.5 (95% CrI: 2.0-3.0) times the infection rate and only 70% (95% CrI: 60%-82%) the reporting rate compared to the less vulnerable communities. Inequality persisted but declined significantly over the 15-month study period. Our results suggest that further public health efforts are needed to mitigate local COVID-19 disparities and that the CDC's social vulnerability index may serve as a reliable predictor of risk on a local scale when surveillance data are limited.

Improving probabilistic infectious disease forecasting through coherence.

With an estimated $10.4 billion in medical costs and 31.4 million outpatient visits each year, influenza poses a serious burden of disease in the United States. To provide insights and advance warning into the spread of influenza, the U.S. Centers for Disease Control and Prevention (CDC) runs a challenge for forecasting weighted influenza-like illness (wILI) at the national and regional level. Many models produce independent forecasts for each geographical unit, ignoring the constraint that the national wILI is a weighted sum of regional wILI, where the weights correspond to the population size of the region. We propose a novel algorithm that transforms a set of independent forecast distributions to obey this constraint, which we refer to as probabilistically coherent. Enforcing probabilistic coherence led to an increase in forecast skill for 79% of the models we tested over multiple flu seasons, highlighting the importance of respecting the forecasting system's geographical hierarchy.

Approach to classify, separate, and enrich objects in groups using ensemble sorting.

The sorting of objects into groups is a fundamental operation, critical in the preparation and purification of populations of cells, crystals, beads, or droplets, necessary for research and applications in biology, chemistry, and materials science. Most of the efforts exploring such purification have focused on two areas: the degree of separation and the measurement precision required for effective separation. Conventionally, achieving good separation ultimately requires that the objects are considered one by one (which can be both slow and expensive), and the ability to measure the sorted objects by increasing sensitivity as well as reducing sorting errors. Here we present an approach to sorting that addresses both critical limitations with a scheme that allows us to approach the theoretical limit for the accuracy of sorting decisions. Rather than sorting individual objects, we sort the objects in ensembles, via a set of registers which are then in turn sorted themselves into a second symmetric set of registers in a lossless manner. By repeating this process, we can arrive at high sorting purity with a low set of constraints. We demonstrate both the theory behind this idea and identify the critical parameters (ensemble population and sorting time), and show the utility and robustness of our method with simulations and experimental systems spanning several orders of scale, sorting populations of macroscopic beads and microfluidic droplets. Our method is general in nature and simplifies the sorting process, and thus stands to enhance many different areas of science, such as purification, enrichment of rare objects, and separation of dynamic populations.

Reversal of orbital angular momentum arising from an extreme Doppler shift.

The linear Doppler shift is familiar as the rise and fall in pitch of a siren as it passes by. Less well known is the rotational Doppler shift, proportional to the rotation rate between source and receiver, multiplied by the angular momentum carried by the beam. In extreme cases the Doppler shift can be larger than the rest-frame frequency and for a red shift, the observed frequency then becomes "negative." In the linear case, this effect is associated with the time reversal of the received signal, but it can be observed only with supersonic relative motion between the source and receiver. However, the rotational case is different; if the radius of rotation is smaller than the wavelength, then the velocities required to observe negative frequencies are subsonic. Using an acoustic source at [Formula: see text]100 Hz we create a rotational Doppler shift larger than the laboratory-frame frequency. We observe that once the red-shifted wave passes into the "negative frequency" regime, the angular momentum associated with the sound is reversed in sign compared with that of the laboratory frame. These low-velocity laboratory realizations of extreme Doppler shifts have relevance to superoscillatory fields and offer unique opportunities to probe interactions with rotating bodies and aspects of pseudorelativistic frame translation.

Single-pixel imaging 12 years on: a review.

Modern cameras typically use an array of millions of detector pixels to capture images. By contrast, single-pixel cameras use a sequence of mask patterns to filter the scene along with the corresponding measurements of the transmitted intensity which is recorded using a single-pixel detector. This review considers the development of single-pixel cameras from the seminal work of Duarte et al. up to the present state of the art. We cover the variety of hardware configurations, design of mask patterns and the associated reconstruction algorithms, many of which relate to the field of compressed sensing and, more recently, machine learning. Overall, single-pixel cameras lend themselves to imaging at non-visible wavelengths and with precise timing or depth resolution. We discuss the suitability of single-pixel cameras for different application areas, including infrared imaging and 3D situation awareness for autonomous vehicles.

Dual-band single-pixel telescope.

Single-pixel imaging systems can obtain images from a wide range of wavelengths at low-cost compared to those using conventional multi-pixel, focal-plane array sensors, especially at wavelengths outside the visible spectrum. The ability to sense short-wave infrared radiation with single-pixel techniques extends imaging capability to adverse weather conditions and environments, such as fog, haze, or night time. In this work, we demonstrate a dual-band single-pixel telescope for imaging at both visible (VIS) and short-wave infrared (SWIR) spectral regions simultaneously under some of these outdoor weather conditions. At 64 × 64 pixel-resolution, our system has achieved continuous VIS and SWIR imaging of various objects at a frame rate up to 2.4 Hz. Visual and contrast comparison between the reconstructed VIS and SWIR images emphasizes the significant contribution of infrared observation using the single-pixel technique. The single-pixel telescope provides an alternative cost-effective imaging solution for synchronized dual-waveband optical applications.

Developing a portable gas imaging camera using highly tunable active-illumination and computer vision.

We have developed a portable gas imaging camera for identifying methane leaks in real-time. The camera uses active illumination from distributed feedback InGaAs laser diodes tuned to the 1653 nm methane absorption band. An InGaAs focal plane sensor array images the active illumination. The lasers are driven off resonance every alternate frame so that computer vision can extract the gas data. A colour image is captured simultaneously and the data is superimposed to guide the operator. Image stabilisation has been employed to allow detection with a moving camera, successfully imaging leaks from mains pressure gas supplies at a range of up to 3 m and flow rates as low as 0.05 L min-1.

Accuracy of real-time multi-model ensemble forecasts for seasonal influenza in the U.S.

Seasonal influenza results in substantial annual morbidity and mortality in the United States and worldwide. Accurate forecasts of key features of influenza epidemics, such as the timing and severity of the peak incidence in a given season, can inform public health response to outbreaks. As part of ongoing efforts to incorporate data and advanced analytical methods into public health decision-making, the United States Centers for Disease Control and Prevention (CDC) has organized seasonal influenza forecasting challenges since the 2013/2014 season. In the 2017/2018 season, 22 teams participated. A subset of four teams created a research consortium called the FluSight Network in early 2017. During the 2017/2018 season they worked together to produce a collaborative multi-model ensemble that combined 21 separate component models into a single model using a machine learning technique called stacking. This approach creates a weighted average of predictive densities where the weight for each component is determined by maximizing overall ensemble accuracy over past seasons. In the 2017/2018 influenza season, one of the largest seasonal outbreaks in the last 15 years, this multi-model ensemble performed better on average than all individual component models and placed second overall in the CDC challenge. It also outperformed the baseline multi-model ensemble created by the CDC that took a simple average of all models submitted to the forecasting challenge. This project shows that collaborative efforts between research teams to develop ensemble forecasting approaches can bring measurable improvements in forecast accuracy and important reductions in the variability of performance from year to year. Efforts such as this, that emphasize real-time testing and evaluation of forecasting models and facilitate the close collaboration between public health officials and modeling researchers, are essential to improving our understanding of how best to use forecasts to improve public health response to seasonal and emerging epidemic threats.

Photon Bunching in a Rotating Reference Frame.

Although quantum physics is well understood in inertial reference frames (flat spacetime), a current challenge is the search for experimental evidence of nontrivial or unexpected behavior of quantum systems in noninertial frames. Here, we present a novel test of quantum mechanics in a noninertial reference frame: we consider Hong-Ou-Mandel (HOM) interference on a rotating platform and study the effect of uniform rotation on the distinguishability of the photons. Both theory and experiments show that the rotational motion induces a relative delay in the photon arrival times at the exit beam splitter and that this delay is observed as a shift in the position of the HOM dip. This experiment can be extended to a full general relativistic test of quantum physics using satellites in Earth's orbit and indicates a new route toward the use of photonic technologies for investigating quantum mechanics at the interface with relativity.

Holographic optical trapping Raman micro-spectroscopy for non-invasive measurement and manipulation of live cells.

We present a new approach for combining holographic optical tweezers with confocal Raman spectroscopy. Multiple laser foci, generated using a liquid-crystal spatial light modulator, are individually used for both optical trapping and excitation of spontaneous Raman spectroscopy from trapped objects. Raman scattering from each laser focus is spatially filtered using reflective apertures on a digital micro-mirror device, which can be reconfigured with flexible patterns at video rate. We discuss operation of the instrument, and performance and viability considerations for biological measurements. We then demonstrate the capability of the instrument for fast, flexible, and interactive manipulation with molecular measurement of interacting live cell systems.

Experimental demonstration of ray-rotation sheets.

We have built microstructured sheets that rotate, on transmission, the direction of light rays by an arbitrary, but fixed, angle around the sheet normal. These ray-rotation sheets comprise two pairs of confocal lenticular arrays. In addition to rotating the direction of transmitted light rays, our sheets also offset ray position sideways on the scale of the diameter of the lenticules. If this ray offset is sufficiently small so that it cannot be resolved, our ray-rotation sheets appear to perform generalized refraction.

Sub-shot-noise shadow sensing with quantum correlations.

The quantised nature of the electromagnetic field sets the classical limit to the sensitivity of position measurements. However, techniques based on the properties of quantum states can be exploited to accurately measure the relative displacement of a physical object beyond this classical limit. In this work, we use a simple scheme based on the split-detection of quantum correlations to measure the position of a shadow at the single-photon light level, with a precision that exceeds the shot-noise limit. This result is obtained by analysing the correlated signals of bi-photon pairs, created in parametric downconversion and detected by an electron multiplying CCD (EMCCD) camera employed as a split-detector. By comparing the measured statistics of spatially anticorrelated and uncorrelated photons we were able to observe a significant noise reduction corresponding to an improvement in position sensitivity of up to 17% (0.8dB). Our straightforward approach to sub-shot-noise position measurement is compatible with conventional shadow-sensing techniques based on the split-detection of light-fields, and yields an improvement that scales favourably with the detector's quantum efficiency.

Real-time imaging of methane gas leaks using a single-pixel camera.

We demonstrate a camera which can image methane gas at video rates, using only a single-pixel detector and structured illumination. The light source is an infrared laser diode operating at 1.651µm tuned to an absorption line of methane gas. The light is structured using an addressable micromirror array to pattern the laser output with a sequence of Hadamard masks. The resulting backscattered light is recorded using a single-pixel InGaAs detector which provides a measure of the correlation between the projected patterns and the gas distribution in the scene. Knowledge of this correlation and the patterns allows an image to be reconstructed of the gas in the scene. For the application of locating gas leaks the frame rate of the camera is of primary importance, which in this case is inversely proportional to the square of the linear resolution. Here we demonstrate gas imaging at ~25 fps while using 256 mask patterns (corresponding to an image resolution of 16×16). To aid the task of locating the source of the gas emission, we overlay an upsampled and smoothed image of the low-resolution gas image onto a high-resolution color image of the scene, recorded using a standard CMOS camera. We demonstrate for an illumination of only 5mW across the field-of-view imaging of a methane gas leak of ~0.2 litres/minute from a distance of ~1 metre.

DMD-based software-configurable spatially-offset Raman spectroscopy for spectral depth-profiling of optically turbid samples.

Spectral depth-profiling of optically turbid samples is of high interest to a broad range of applications. We present a method for measuring spatially-offset Raman spectroscopy (SORS) over a range of length scales by incorporating a digital micro-mirror device (DMD) into a sample-conjugate plane in the detection optical path. The DMD can be arbitrarily programmed to collect/reject light at spatial positions in the 2D sample-conjugate plane, allowing spatially offset Raman measurements. We demonstrate several detection geometries, including annular and simultaneous multi-offset modalities, for both macro- and micro-SORS measurements, all on the same instrument. Compared to other SORS modalities, DMD-based SORS provides more flexibility with only minimal additional experimental complexity for subsurface Raman collection.

Comparing the information capacity of Laguerre-Gaussian and Hermite-Gaussian modal sets in a finite-aperture system.

Using a spontaneous parametric down-conversion process to create entangled spatial states, we compare the information capacity associated with measurements in the Hermite-Gaussian and Laguerre-Gaussian modal basis in an optical system of finite aperture. We show that the cross-talk imposed by the aperture restriction degrades the information capacity. However, the Laguerre-Gaussian mode measurements show greater resilience to cross talk than the Hermite-Gaussian, suggesting that the Laguerre-Gaussian modal set may still offer real-world advantages over other modal sets.

Improving the signal-to-noise ratio of single-pixel imaging using digital microscanning.

Single-pixel cameras provide a means to perform imaging at wavelengths where pixelated detector arrays are expensive or limited. The image is reconstructed from measurements of the correlation between the scene and a series of masks. Although there has been much research in the field in recent years, the fact that the signal-to-noise ratio (SNR) scales poorly with increasing resolution has been one of the main limitations prohibiting the uptake of such systems. Microscanning is a technique that provides a final higher resolution image by combining multiple images of a lower resolution. Each of these low resolution images is subject to a sub-pixel sized lateral displacement. In this work we apply a digital microscanning approach to an infrared single-pixel camera. Our approach requires no additional hardware, but is achieved simply by using a modified set of masks. Compared to the conventional Hadamard based single-pixel imaging scheme, our proposed framework improves the SNR of reconstructed images by ∼ 50 % for the same acquisition time. In addition, this strategy also provides access to a stream of low-resolution 'preview' images throughout each high-resolution acquisition.

Polymer micronozzle array for multiple electrosprays produced by templated synthesis and etching of microstructured fibers.

Microstructured fibers (MSFs) having raised polymer nozzles in each channel are custom designed, fabricated, and tested for use as multiple electrospray (MES) emitters for mass spectrometry (MS). There is strong motivation to develop electrospray emitters that operate at practical flow rates but give the much greater ionization efficiency associated with lower (nano) flow rates. This can be accomplished by splitting the flow into many lower-volume electrosprays, an approach known as MES. To couple with most modern mass spectrometers, the MES emitter must have a small diameter to allow efficient ion collection into the MS. In this work, a MSF, defined as a fiber having many empty channels running along its length, was designed to have 9 channels, 9 µm each, >100 µm apart arranged in a radial pattern, all in a fiber having a compatible diameter with both front-end LC equipment and typical MS inlets. This design seeks to promote independent electrospray from each channel while maintaining electric field homogeneity. While the MSFs themselves do not support MES, the formation of polymer nozzles protruding from each channel at the tip face enables independent electrospray from each nozzle. Microscope imaging, electrospray current measurement, and ESI-MS detection of a model analyte all confirm the MES behavior of the 9-nozzle emitter, showing significant signal enhancement relative to a single-nozzle emitter at the same total flow rate. LC/MS data from a protein digest obtained at an independent laboratory demonstrates the applicability and robustness of the emitter for real scientific challenges using modern LC/MS equipment.

Mechanical Faraday effect for orbital angular momentum-carrying beams.

When linearly polarised light is transmitted through a spinning window, the plane of polarisation is rotated. This rotation arises through a phase change that is applied to the circularly polarised states corresponding to the spin angular momentum (SAM). Here we show an analogous effect for the orbital angular momentum (OAM), where a differential phase between the positive and negative modes (±â„“) is observed as a rotation of the transmitted image. For normal materials, this rotation is on the order of a micro radian, but by using a slow-light medium, we show a rotation of a few degrees. We also note that, within the bounds of our experimental parameters, this rotation angle does not exceed the scale of the spatial features in the beam profile.

Optically trapped bacteria pairs reveal discrete motile response to control aggregation upon cell-cell approach.

Aggregation of bacteria plays a key role in the formation of many biofilms. The critical first step is cell-cell approach, and yet the ability of bacteria to control the likelihood of aggregation during this primary phase is unknown. Here, we use optical tweezers to measure the force between isolated Bacillus subtilis cells during approach. As we move the bacteria towards each other, cell motility (bacterial swimming) initiates the generation of repulsive forces at bacterial separations of ~3 µm. Moreover, the motile response displays spatial sensitivity with greater cell-cell repulsion evident as inter-bacterial distances decrease. To examine the environmental influence on the inter-bacterial forces, we perform the experiment with bacteria suspended in Tryptic Soy Broth, NaCl solution and deionised water. Our experiments demonstrate that repulsive forces are strongest in systems that inhibit biofilm formation (Tryptic Soy Broth), while attractive forces are weak and rare, even in systems where biofilms develop (NaCl solution). These results reveal that bacteria are able to control the likelihood of aggregation during the approach phase through a discretely modulated motile response. Clearly, the force-generating motility we observe during approach promotes biofilm prevention, rather than biofilm formation.