1/f Noise Mitigation in an Opto-Mechanical Sensor with a Fabry-Pérot Interferometer.

Low-frequency and 1/f noise are common measurement limitations that arise in a variety of physical processes. Mitigation methods for these noises are dependent on their source. Here, we present a method for removing 1/f noise of optical origin using a micro-cavity Fabry-Pérot (FP) interferometer. A mechanical modulation of the FP cavity length was applied to a previously studied opto-mechanical sensor. It effectively mimics an up-conversion of the laser frequency, shifting signals to a region where lower white-noise sources dominate and 1/f noise is not present. Demodulation of this signal shifts the results back to the desired frequency range of observation with the reduced noise floor of the higher frequencies. This method was found to improve sensitivities by nearly two orders of magnitude at 1 Hz and eliminated 1/f noise in the range from 1 Hz to 4 kHz. A mathematical model for low-finesse FP cavities is presented to support these results. This study suggests a relatively simple and efficient method for 1/f noise suppression and improving the device sensitivity of systems with an FP interferometer readout.

The language of blame: Exploring the effects of non-native accents on post-accident blame attributions.

This peer commentary investigates how individuals assign blame to non-native supervisors after an accident where an employee suffers a workplace accident in a multilingual organization. Extending research presented in the focal article by Obenauer and Kalsher's (2023), the authors propose that supervisors with non-native accents are likely to be blamed after an accident they tried to prevent due to stereotypes and increased cognitive effort in processing accented speech. The authors discuss scenarios where, even when supervisors effectively conduct a verbal safety briefing warning employees about possible dangers, they are not excepted from blame. Additionally, the authors suggest that biases against non-native supervisors may extend to native speakers with strong regional or foreign sounding accents. Moving forward, this commentary encourages more nuanced theorizing around non-native accents and more research differentiating between various Latin/Hispanic accents.

Domestication signatures in the non-conventional yeast Lachancea cidri.

Evaluating domestication signatures beyond model organisms is essential for a thorough understanding of the genotype-phenotype relationship in wild and human-related environments. Structural variations (SVs) can significantly impact phenotypes playing an important role in the physiological adaptation of species to different niches, including during domestication. A detailed characterization of the fitness consequences of these genomic rearrangements, however, is still limited in non-model systems, largely due to the paucity of direct comparisons between domesticated and wild isolates. Here, we used a combination of sequencing strategies to explore major genomic rearrangements in a Lachancea cidri yeast strain isolated from cider (CBS2950) and compared them to those in eight wild isolates from primary forests. Genomic analysis revealed dozens of SVs, including a large reciprocal translocation (~16 kb and 500 kb) present in the cider strain, but absent from all wild strains. Interestingly, the number of SVs was higher relative to single-nucleotide polymorphisms in the cider strain, suggesting a significant role in the strain's phenotypic variation. The set of SVs identified directly impacts dozens of genes and likely underpins the greater fermentation performance in the L. cidri CBS2950. In addition, the large reciprocal translocation affects a proline permease (PUT4) regulatory region, resulting in higher PUT4 transcript levels, which agrees with higher ethanol tolerance, improved cell growth when using proline, and higher amino acid consumption during fermentation. These results suggest that SVs are responsible for the rapid physiological adaptation of yeast to a human-related environment and demonstrate the key contribution of SVs in adaptive fermentative traits in non-model species.IMPORTANCEThe exploration of domestication signatures associated with human-related environments has predominantly focused on studies conducted on model organisms, such as Saccharomyces cerevisiae, overlooking the potential for comparisons across other non-Saccharomyces species. In our research, employing a combination of long- and short-read data, we found domestication signatures in Lachancea cidri, a non-model species recently isolated from fermentative environments in cider in France. The significance of our study lies in the identification of large array of major genomic rearrangements in a cider strain compared to wild isolates, which underly several fermentative traits. These domestication signatures result from structural variants, which are likely responsible for the phenotypic differences between strains, providing a rapid path of adaptation to human-related environments.

Compressive video via IR-pulsed illumination.

We propose and demonstrate a compressive temporal imaging system based on pulsed illumination to encode temporal dynamics into the signal received by the imaging sensor during exposure time. Our approach enables >10x increase in effective frame rate without increasing camera complexity. To mitigate the complexity of the inverse problem during reconstruction, we introduce two keyframes: one before and one after the coded frame. We also craft what we believe to be a novel deep learning architecture for improved reconstruction of the high-speed scenes, combining specialized convolutional and transformer architectures. Simulation and experimental results clearly demonstrate the reconstruction of high-quality, high-speed videos from the compressed data.

Optical truss interferometer for the LISA telescope.

The Laser Interferometer Space Antenna telescopes must exhibit an optical path length stability of p m/H z in the mHz observation band to meet mission requirements. The optical truss interferometer is a proposed method to aid in the ground testing of the telescopes, as well as a risk-mitigation plan for flight units. This consists of three Fabry-Perot cavities mounted to the telescope, which are used to monitor structural displacements. We have designed and developed a fiber-based cavity injection system that integrates fiber components, mode matching optics, and a cavity input mirror into a compact input stage. The input stages, paired with return mirror stages, can be mounted to the telescope to form optical truss cavities. We performed a thorough sensitivity analysis using various simulation methods to support the fabrication and assembly of three first-generation prototype cavities, each of which exhibited satisfactory performance based on our models.

Multispectral Filter Array Design by Optimal Sphere Packing.

Multispectral imaging (MSI) collects a datacube of spatio-spectral information of a scene. Many acquisition methods for spectral imaging use scanning, preventing its widespread usage for dynamic scenes. On the other hand, the conventional color filter array (CFA) method often used to sample color images has also been extended to snapshot MSI using a Multispectral Filter Array (MSFA), which is a mosaic of selective spectral filters placed over the Focal Plane Array (FPA). However, even state-ofthe- art MSFAs coding patterns produce artifacts and distortions in the reconstructed spectral images, which might be due to the nonoptimal distribution of the spectral filters. To reduce the appearance of artifacts and provide tools for the optimal design of MSFAs, this paper proposes a novel mathematical framework to design MSFAs using a Sphere Packing (SP) approach. By assuming that each sampled filter can be represented by a sphere within the discrete datacube, SP organizes the position of the equal-size and disjoint spheres's centers in a cubic container. Our method is denoted Multispectral Filter Array by Optimal Sphere Packing (MSFA-OSP), which seeks filter positions that maximize the minimum distance between the spheres's centers. Simulation results show an image quality improvement of up to 2 dB and a remarkable boost in spectral similarity when using our proposed MSFA design approach for a variety of reconstruction algorithms. Moreover, MSFA-OSP notably reduces the appearance of false colors and zipper effect artifacts, often seen when using state-of-the-art demosaicking algorithms. Experiments using synthetic and real data prove that the proposed MSFA-OSP outperforms state-of-the-art MSFAs in terms of spatial and spectral fidelity. The code that reproduces the figures of this article is available at https://github.com/nelson10/DemosaickingMultispectral3DSpherePacking.git.

Gyro-Free Inertial Navigation Systems Based on Linear Opto-Mechanical Accelerometers.

High-sensitivity uniaxial opto-mechanical accelerometers provide very accurate linear acceleration measurements. In addition, an array of at least six accelerometers allows the estimation of linear and angular accelerations and becomes a gyro-free inertial navigation system. In this paper, we analyze the performance of such systems considering opto-mechanical accelerometers with different sensitivities and bandwidths. In the six-accelerometer configuration adopted here, the angular acceleration is estimated using a linear combination of accelerometers' read-outs. The linear acceleration is estimated similarly but requires a correcting term that includes angular velocities. Accelerometers' colored noise from experimental data is used to derive, analytically and through simulations, the performance of the inertial sensor. Results for six accelerometers, separated by 0.5 m in a cube configuration show noise levels of 10-7 m s-2 and 10-5 m s-2 (in Allan deviation) for time scales of one second for the low-frequency (Hz) and high-frequency (kHz) opto-mechanical accelerometers, respectively. The Allan deviation for the angular velocity at one second is 10-5 rad s-1 and 5×10-4 rad s-1. Compared to other technologies such as MEMS-based inertial sensors and optical gyroscopes, the high-frequency opto-mechanical accelerometer exhibits better performance than tactical-grade MEMS for time scales shorter than 10 s. For angular velocity, it is only superior for time scales less than a few seconds. The linear acceleration of the low-frequency accelerometer outperforms the MEMS for time scales up to 300 s and for angular velocity only for a few seconds. Fiber optical gyroscopes are orders of magnitude better than the high- and low-frequency accelerometers in gyro-free configurations. However, when considering the theoretical thermal noise limit of the low-frequency opto-mechanical accelerometer, 5×10-11 m s-2, linear acceleration noise is orders of magnitude lower than MEMS navigation systems. Angular velocity precision is around 10-10 rad s-1 at one second and 5×10-7 rad s-1 at one hour, which is comparable to fiber optical gyroscopes. While experimental validation is yet not available, the results shown here indicate the potential of opto-mechanical accelerometers as gyro-free inertial navigation sensors, provided the fundamental noise limit of the accelerometer is reached, and technical limitations such as misalignments and initial conditions errors are well controlled.

Developing a Temperature-Inducible Transcriptional Rheostat in Neurospora crassa.

Heat shock protein (HSP)-encoding genes (hsp), part of the highly conserved heat shock response (HSR), are known to be induced by thermal stress in several organisms. In Neurospora crassa, three hsp genes, hsp30, hsp70, and hsp80, have been characterized; however, the role of defined cis elements in their responses to discrete changes in temperature remains largely unexplored. To fill this gap, while also aiming to obtain a reliable fungal heat shock-inducible system, we analyzed different sections of each hsp promoter by assessing the expression of real-time transcriptional reporters. Whereas all three promoters and their resected versions were acutely induced by high temperatures, only hsp30 displayed a broad range of expression and high tunability, amply exceeding other inducible promoter systems existing in Neurospora, such as quinic acid- or light-inducible ones. As proof of concept, we employed one of these promoters to control the expression of clr-2, which encodes the master regulator of Neurospora cellulolytic capabilities. The resulting strain fails to grow on cellulose at 25°C, whereas it grows robustly if heat shock pulses are delivered daily. Additionally, we designed two hsp30 synthetic promoters and characterized them, as well as the native promoters, using a gradient of high temperatures, yielding a wide range of responses to thermal stimuli. Thus, Neurospora hsp30-based promoters represent a new set of modular elements that can be used as transcriptional rheostats to adjust the expression of a gene of interest or for the implementation of regulated circuitries for synthetic biology and biotechnological strategies. IMPORTANCE A timely and dynamic response to strong temperature fluctuations is paramount for organismal biology. At the same time, inducible promoters are a powerful tool for fungal biotechnological and synthetic biology endeavors. In this work, we analyzed the activity of several N. crassa heat shock protein (hsp) promoters at a wide range of temperatures, observing that hsp30 exhibits remarkable sensitivity and a dynamic range of expression as we charted the response of this promoter to subtle increases in temperature, and also as we built and analyzed synthetic promoters based on hsp30 cis elements. As proof of concept, we tested the ability of hsp30 to provide tight control of a central process, cellulose degradation. While this study provides an unprecedented description of the regulation of the N. crassa hsp genes, it also contributes a noteworthy addition to the molecular toolset of transcriptional controllers in filamentous fungi.

Fiber-based two-wavelength heterodyne laser interferometer.

Displacement measuring interferometry is a crucial component in metrology applications. In this paper, we propose a fiber-based two-wavelength heterodyne interferometer as a compact and highly sensitive displacement sensor that can be used in inertial sensing applications. In the proposed design, two individual heterodyne interferometers are constructed using two different wavelengths, 1064 nm and 1055 nm; one of which measures the target displacement and the other monitors the common-mode noise in the fiber system. A narrow-bandwidth spectral filter separates the beam paths of the two interferometers, which are highly common and provide a high rejection ratio to the environmental noise. The preliminary test shows a sensitivity floor of 7.5pm/Hz at 1 Hz when tested in an enclosed chamber. We also investigated the effects of periodic errors due to imperfect spectral separation on the displacement measurement and propose algorithms to mitigate these effects.

Quasi-monolithic heterodyne laser interferometer for inertial sensing.

We present a compact heterodyne laser interferometer developed for high-sensitivity displacement sensing applications. This interferometer consists of customized prisms and wave plates assembled as a quasi-monolithic unit to realize a miniaturized system. The interferometer design adopts a common-mode rejection scheme to provide a high rejection ratio to common environmental noise. Experimental tests in vacuum show a displacement sensitivity level of 11p m/H z at 100m H z and as low as 0.6p m/H z above 1p m. The prototype unit is 20m m×20m m×10m m in size and weighs 4.5g, allowing subsequent integration in compact systems.

Shuffled rolling shutter for snapshot temporal imaging.

We propose a modification to the rolling shutter mechanism found in CMOS detectors by shuffling the pixels in every scanline. This potential hardware modification improves the sampling of the space-time datacube, allowing the recovery of high-speed videos from a single image using either tensor completion methods or reconstruction algorithms often used for compressive temporal video. We also present a design methodology for optimal sampling schemes and compare them to random shuffling. Simulations, and experimental results obtained by optically emulating the hardware, demonstrate the ability of the shuffled rolling shutter to capture images that allow reconstructing videos, which would otherwise be impossible when using the traditional rolling shutter mechanism.

Estimation and Error Analysis for Optomechanical Inertial Sensors.

A sensor model and methodology to estimate the forcing accelerations measured using a novel optomechanical inertial sensor with the inclusion of stochastic bias and measurement noise processes is presented. A Kalman filter for the estimation of instantaneous sensor bias is developed; the outputs from this calibration step are then employed in two different approaches for the estimation of external accelerations applied to the sensor. The performance of the system is demonstrated using simulated measurements and representative values corresponding to a bench-tested 3.76 Hz oscillator. It is shown that the developed methods produce accurate estimates of the bias over a short calibration step. This information enables precise estimates of acceleration over an extended operation period. These results establish the feasibility of reliably precise acceleration estimates using the presented methods in conjunction with state of the art optomechanical sensing technology.

Investigation and Mitigation of Noise Contributions in a Compact Heterodyne Interferometer.

We present a noise estimation and subtraction algorithm capable of increasing the sensitivity of heterodyne laser interferometers by one order of magnitude. The heterodyne interferometer is specially designed for dynamic measurements of a test mass in the application of sub-Hz inertial sensing. A noise floor of 3.31×10-11m/Hz at 100 mHz is achieved after applying our noise subtraction algorithm to a benchtop prototype interferometer that showed a noise level of 2.76×10-10m/Hz at 100 mHz when tested in vacuum at levels of 3×10-5 Torr. Based on the previous results, we investigated noise estimation and subtraction techniques of non-linear optical pathlength noise, laser frequency noise, and temperature fluctuations in heterodyne laser interferometers. For each noise source, we identified its contribution and removed it from the measurement by linear fitting or a spectral analysis algorithm. The noise correction algorithm we present in this article can be generally applied to heterodyne laser interferometers.

Compressive temporal imaging using a rolling shutter camera array.

In this work, we present a novel camera array that exploits the electronic rolling shutter to achieve high speed compressive temporal imaging. Traditional compressive temporal imaging makes use of mechanical coded apertures, despite implementation and calibration challenges. Instead, we propose to model the inherent spatial and temporal coding provided by the distinctive rolling shutter sampling from each camera of the array as a compressive temporal imaging system matrix. Thus, we can recover a high speed video from a set of snapshots from the camera array by using compressive sensing reconstruction algorithms. We present both simulation and experimental results for a 4-camera array system with different orientation angles, reconstructing up to 56 high-speed sub-frames from a set of simultaneously triggered snapshots from the array, achieving a compression rate of up to 14X.

Boosting the deep learning wavefront sensor for real-time applications [Invited].

The deep learning wavefront sensor (DLWFS) allows the direct estimate of Zernike coefficients of aberrated wavefronts from intensity images. The main drawback of this approach is related to the use of massive convolutional neural networks (CNNs) that are lengthy to train or estimate. In this paper, we explore several options to reduce both the training and estimation time. First, we develop a CNN that can be rapidly trained without compromising accuracy. Second, we explore the effects given smaller input image sizes and different amounts of Zernike modes to be estimated. Our simulation results demonstrate that the proposed network using images of either 8×8, 16×16, or 32×32 will dramatically reduce training time and even boost the estimation accuracy of Zernike coefficients. From our experimental results, we can confirm that a 16×16 DLWFS can be quickly trained and is able to estimate the first 12 Zernike coefficients-skipping piston, tip, and tilt-without sacrificing accuracy and significantly speeding up the prediction time to facilitate low-cost, real-time adaptive optics systems.

A global search for novel transcription factors impacting the Neurospora crassa circadian clock.

Eukaryotic circadian oscillators share a common circuit architecture, a negative feedback loop in which a positive element activates the transcription of a negative one that then represses the action of the former, inhibiting its own expression. While studies in mammals and insects have revealed additional transcriptional inputs modulating the expression of core clock components, this has been less characterized in the model Neurospora crassa, where the participation of other transcriptional components impacting circadian clock dynamics remains rather unexplored. Thus, we sought to identify additional transcriptional regulators modulating the N. crassa clock, following a reverse genetic screen based on luminescent circadian reporters and a collection of transcription factors (TFs) knockouts, successfully covering close to 60% of them. Besides the canonical core clock components WC-1 and -2, none of the tested transcriptional regulators proved to be essential for rhythmicity. Nevertheless, we identified a set of 23 TFs that when absent lead to discrete, but significant, changes in circadian period. While the current level of analysis does not provide mechanistic information about how these new players modulate circadian parameters, the results of this screen reveal that an important number of light and clock-regulated TFs, involved in a plethora of processes, are capable of modulating the clockworks. This partial reverse genetic clock screen also exemplifies how the N. crassa knockout collection continues to serve as an expedite platform to address broad biological questions.

Novel CRISPR-based sequence specific enrichment methods for target loci and single base mutations.

The programmable sequence specificity of CRISPR has found uses in gene editing and diagnostics. This manuscript describes an additional application of CRISPR through a family of novel DNA enrichment technologies. CAMP (CRISPR Associated Multiplexed PCR) and cCAMP (chimeric CRISPR Associated Multiplexed PCR) utilize the sequence specificity of the Cas9/sgRNA complex to target loci for the ligation of a universal adapter that is used for subsequent amplification. cTRACE (chimeric Targeting Rare Alleles with CRISPR-based Enrichment) also applies this method to use Cas9/sgRNA to target loci for the addition of universal adapters, however it has an additional selection for specific mutations through the use of an allele-specific primer. These three methods can produce multiplex PCR that significantly reduces the optimization required for every target. The methods are also not specific to any downstream analytical platform. We additionally will present a mutation specific enrichment technology that is non-amplification based and leaves the DNA in its native state: TRACE (Targeting Rare Alleles with CRISPR-based Enrichment). TRACE utilizes the Cas9/sgRNA complex to sterically protect the ends of targeted sequences from exonuclease activity which digests both the normal variant as well as any off-target sequences.

A compact high-precision periodic-error-free heterodyne interferometer.

We present the design, bench-top setup, and experimental results of a compact heterodyne interferometer that achieves picometer-level displacement sensitivities in air over frequencies above 100 MHz. The optical configuration with spatially separated beams prevents frequency and polarization mixing, and therefore eliminates periodic errors. The interferometer is designed to maximize common-mode optical laser beam paths to obtain high rejection of environmental disturbances, such as temperature fluctuations and acoustics. The results of our experiments demonstrate the short- and long-term stabilities of the system during stationary and dynamic measurements. In addition, we provide measurements that compare our interferometer prototype with a commercial system, verifying our higher sensitivity of 3 pm, higher thermal stability by a factor of two, and periodic-error-free performance.

Optomechanical lasers for inertial sensing.

We have developed an inertially sensitive optomechanical laser by combining a vertical-external-cavity surface-emitting laser (VECSEL) with a monolithic fused silica resonator. By placing the external cavity mirror of the VECSEL onto the optomechanical resonator test mass, we create a sensor where external accelerations are directly transcribed onto the lasing frequency. We developed a proof-of-principle laboratory prototype and observe test mass oscillations at the resonance frequency of the sensor through the VECSEL lasing frequency, 4.18±0.03Hz. In addition, we set up an ancillary heterodyne interferometer to track the motion of the mechanical oscillator's test mass, observing a resonance of 4.194±0.004Hz. The interferometer measurements validate the VECSEL results, confirming the feasibility of using optomechanical lasers for inertial sensing.

Quantum hybrid optomechanical inertial sensing.

We discuss the design of quantum hybrid inertial sensor that combines an optomechanical inertial sensor with the retroreflector of a cold atom interferometer. This sensor fusion approach provides absolute and high-accuracy measurements with cold atom interferometers, while utilizing the optomechanical inertial sensor at frequencies above the repetition rate of the atom interferometer. This improves the overall measurement bandwidth as well as the robustness and field deployment capabilities of these systems. We evaluate which parameters yield an optimal acceleration sensitivity, from which we anticipate a noise floor at nano-g levels from DC to 1 kHz.