How inquilinism shaped breeding systems in a termite host-inquiline relationship.

Social insects have developed a broad diversity of nesting and foraging strategies. One of these, inquilinism, occurs when one species (the inquiline) inhabits the nest built and occupied by another species (the host). Obligatory inquilines must overcome strong constraints upon colony foundation and development, due to limited availability of host colonies. To reveal how inquilinism shapes reproductive strategies in a termite host-inquiline dyad, we carried out a microsatellite marker study on Inquilinitermes inquilinus and its host Constrictotermes cavifrons. The proportion of simple, extended and mixed families was recorded in both species, as well as the presence of neotenics, parthenogenesis and multiple foundations. Most host colonies (95%) were simple families and all were monodomous. By contrast, the inquiline showed a higher proportion of extended (30%) and mixed (5%) families, and frequent neotenics (in 25% of the nests). This results from the simultaneous foundation in host nests of numerous incipient colonies, which, as they grow, may compete, fight, or merge. We also documented the use of parthenogenesis by female-female pairs. In conclusion, the classical monogamous colony pattern of the host species suggests uneventful development of simple foundations dispersed in the environment, in accordance with the wide distribution of their resources. By contrast, the multiple reproductive patterns displayed by the inquiline species reveal strong constraints on foundation sites: founders first concentrate into host nests, then must attempt to outcompete or absorb the neighbouring foundations to gain full control of the resources provided by the host nest.

Redox Reporter - Ligand Competition to Support Signaling in the Cocaine-Binding Electrochemical Aptamer-Based Biosensor.

Electrochemical aptamer-based (E-AB) biosensors have demonstrated capabilities in monitoring molecules directly in undiluted complex matrices and in the body with the hopes of addressing personalized medicine challenges. This sensing platform relies on an electrode-bound, redox-reporter-modified aptamer. The electrochemical signal is thought to originate from the aptamer undergoing a binding-induced conformational change capable of moving the redox reporter closer to the electrode surface. While this is the generally accepted mechanism, it is notable that there is limited evidence demonstrating conformational change or distance-dependent change in electron transfer rates in E-AB sensors. In response, we investigate here the signal transduction of the well-studied cocaine-binding aptamer with different analytical methods and found that this sensor relies on a redox-reporter - ligand competition mechanism rather than a ligand-induced structure formation mechanism. Our results show that the covalently bound redox reporter, methylene blue, binds at or near the ligand binding site on the aptamer resulting in a folded conformation of the cocaine-binding aptamer. Addition of ligand then competes with the redox reporter for binding, altering its electron transfer rate. While we show this for the cocaine-binding aptamer, given the prevalence of methylene blue in E-AB sensors, a similar competition-based may occur in other systems.

Ordering Eyeglasses Using 3D Head Scan Technology versus Established Online and Storefront Clinic Methods.

SIGNIFICANCE: This study investigates how a new smartphone scanning technology compares with established online and storefront vendors in providing remote measurement and adjustment of prescription eyeglasses. PURPOSE: This study aimed to evaluate a new technology for ordering prescription eyeglasses online. METHODS: Thirty participants with 2.00 to 2.75 D of presbyopia (aged 49 to 74 years) were asked to order eyeglasses with progressive addition lenses from four vendors: one online vendor using a new head scan technology (Topology, San Francisco, CA), two established Web site-based vendors (vendors A and B), and one storefront vendor: Université de Montréal's Vision Clinic (UMVC). The resulting measurements were compared with those of opticians. Participant-reported preferences on visual and physical comfort of eyeglasses were collected after 15-minute trials of eyeglasses from each vendor. RESULTS: Pupillary half-distance measured with Topology matched optician measurements, but online vendors A and B diverged (mean difference, - 0.80 mm [ Z = -2.79; P = .005]). Topology and vendor B segment addition heights were similar to optician measurements, but vendor A diverged (mean, -1.40 mm [ Z = -2.58; P = .01]). The personalization parameter values obtained with Topology were different from optician measurements for pantoscopic angle (-5.30° [ Z = -4.12; P < .001]) and face wrap angle (+1.25° [ Z = -2.94; P = .003]). The UMVC eyeglasses scored best for adjustment (8.71/10 [ Z = -5.53; P < .001]), with Topology coming second (7.23/10). Topology scores were equivalent to UMVC scores for all eight items of patient-reported preferences (nonparametric Friedman analysis of variance, P < .05). CONCLUSIONS: Basic lens centration measurements obtained with Topology compare well with those of opticians, but some aspects of the methodology for measuring personalization parameters could be improved. In comparison with two established online vendors, resulting measurements with Topology are more consistent. Initial wearer satisfaction with Topology eyeglasses was also better.

Machine Learning Enables Selection of Epistatic Enzyme Mutants for Stability Against Unfolding and Detrimental Aggregation.

Machine learning (ML) has pervaded most areas of protein engineering, including stability and stereoselectivity. Using limonene epoxide hydrolase as the model enzyme and innov'SAR as the ML platform, comprising a digital signal process, we achieved high protein robustness that can resist unfolding with concomitant detrimental aggregation. Fourier transform (FT) allows us to take into account the order of the protein sequence and the nonlinear interactions between positions, and thus to grasp epistatic phenomena. The innov'SAR approach is interpolative, extrapolative and makes outside-the-box, predictions not found in other state-of-the-art ML or deep learning approaches. Equally significant is the finding that our approach to ML in the present context, flanked by advanced molecular dynamics simulations, uncovers the connection between epistatic mutational interactions and protein robustness.

Demonstration of terabit coherent on-chip optical interconnects employing mode-division multiplexing.

We experimentally demonstrate a net capacity per wavelength of 1.23 Tb/s with 30 GBaud 16-ary quadrature amplitude modulation (16-QAM) mode-division multiplexing (MDM) signals over a single silicon-on-insulator (SOI) multimode waveguide for optical interconnects employing $11 \times 11$ multiple-in-multiple-out (MIMO) digital signal processing. In order to simplify the receiver architecture for coherent optical interconnects, we further propose and evaluate an on-chip self-homodyne coherent detection (SHCD) scheme. In the experiment, 30 Gbaud quadrature phase shift keying (QPSK) signals carried by 10 waveguide modes are successfully recovered with bit error rates (BERs) below 7% forward error correction (FEC) threshold using the pilot tone delivered by ${{\rm TE}_0}$ mode as a local oscillator. Around 10% penalty on error vector magnitude (EVM) is observed due to modal cross talk compared to homodyne detection.

Experimental characterization of group and phase delays induced by bending and twisting in multi-core fibers.

The local variations of group and phase propagation delays induced by bending and twisting a coupled core three-core fiber are experimentally characterized, for the first time, to the best of our knowledge, along the fiber length, with millimeter-scale spatial resolution. The measurements are performed by means of spectral correlation analysis on the fiber's Rayleigh backscattered signal, enabling for a distributed measurement of the perturbation effects along the fiber length. A mathematical model validating the experimental results is also reported.

Photonic lantern tip/tilt detector for adaptive optics systems.

In this work, we demonstrate a four-core multicore fiber photonic lantern tip/tilt wavefront sensor. To diagnose the low-order Zernike aberrations, we exploit the ability of the photonic lantern to encode the characteristics of a complex incoming beam at the multimode facet of the sensor to intensity distributions at the multicore fiber output. Here, we provide a comprehensive numerical analysis capable of predicting the performance of fabricated devices and experimentally demonstrate the concept. Two receiver architectures are implemented to discern tip/tilt information by (i) imaging the four-core fiber facet on a 2D detector and (ii) direct power measurement of the single mode outputs using a multicore fiber multiplexer and photodetectors. For both receiver schemes, an angular detection window of ∼0.4∘ at 1064 nm can be achieved. Our results are expected to further facilitate the development of intensity-based fiber wavefront sensors for adaptive optics systems.

Phase retrieval with fast convergence employing parallel alternative projections and phase reset for coherent communications.

Phase-retrieval (PR) receivers can reconstruct complex-valued signals using only direct detection without the use of any optical carriers. We propose and demonstrate two PR receiver solutions with faster and better convergence. First, we demonstrate a PR receiver based on parallel alternative projections that are produced by propagating the signal through an array of dispersive elements of increasing length followed by direct detection. Fast convergence and high retrieved phase accuracy are achieved using a modified Gerchberg-Saxton (GS) algorithm that uses each projection as an intensity constraint. Second, we achieve similar performances employing an enhanced single projection GS algorithm with selective phase reset using symbol-wise GS errors. We experimentally reconstruct a 30 Gbaud QPSK signal after 55 km single-mode fiber transmission using the proposed solutions with a reduced number of iterations.

Temporal and spectral coding over amplified spontaneous emission for secure optical coherent communications.

We demonstrate secure optical coherent communications employing low-coherence matched detection based on the randomness of amplified spontaneous emission (ASE) noise. Two-level physical-layer optical encryption is achieved through temporal and spectral coding over a broadband ASE source. An ASE-carried signal and unmodulated carrier are polarization multiplexed, transmitted over a same single-mode fiber (SMF), and separated with the aid of polarization tracking before having matched detection at the receiving side. The impact of chromatic dispersion on the low-coherence matched detection system is analyzed and experimentally investigated. We experimentally realize optically coded 20 Gbaud QPSK and 8-PSK signals transmission over a 43 km SMF span with a maximum line rate of 60 Gbits/s.

Carrier-less phase retrieval receiver leveraging digital upsampling.

Phase retrieval (PR) receivers can reconstruct the full electrical field of the signal using only intensity measurements without any optical carrier. In this Letter, we investigate the requirement of digital upsampling and receiver bandwidth of the PR receiver based on alternative projection employing a dispersive element. An iteration scheme averaging the interleaved upsampled symbols to maintain two samples per symbol for the estimated complex-valued signal is proposed and experimentally demonstrated with fast algorithm convergence. The PR uses a modified Gerchberg-Saxton algorithm. Experimentally, we measure Nyquist-shaped 30-GBaud quadrature phase shift keying signals after 55-km single-mode fiber transmission using only 110 and 250 iterations to reach, respectively, the 20% and 7% forward-error correction threshold levels.

Multiport swept-wavelength interferometer with laser phase noise mitigation employing a broadband ultra-weak FBG array.

Optical vector network analyzers (OVNAs) based on swept-wavelength interferometry are applied widely in optical metrology and sensing to measure the complex transfer functions of optical components, devices, and fibers. Phase noise from laser sweep nonlinearities degrades the measurement quality as the distance increases and limits the usage of the OVNA in characterizing systems with long impulse responses as required in space-division multiplexing links with a high mode count or in the presence of large modal differential group delay (DGD). In this Letter, we use a densely distributed broadband ultra-weak fiber Bragg grating array to directly measure the distortion due to phase noise at a 5-m increment up to 400 m and use this measured data to directly eliminate the distortion. We experimentally extend the measurement range of the swept-wavelength OVNA over 400 m and successfully characterize a 2-km six-mode multimode fiber link with an accumulated impulse response as wide as 20 ns.

One-shot optimization of multiple enzyme parameters: Tailoring glucose oxidase for pH and electron mediators.

Enzymes are biological catalysts with many industrial applications, but natural enzymes are usually unsuitable for industrial processes because they are not optimized for the process conditions. The properties of enzymes can be improved by directed evolution, which involves multiple rounds of mutagenesis and screening. By using mathematical models to predict the structure-activity relationship of an enzyme, and by defining the optimal combination of mutations in silico, we can significantly reduce the number of bench experiments needed, and hence the time and investment required to develop an optimized product. Here, we applied our innovative sequence-activity relationship methodology (innov'SAR) to improve glucose oxidase activity in the presence of different mediators across a range of pH values. Using this machine learning approach, a predictive model was developed and the optimal combination of mutations was determined, leading to a glucose oxidase mutant (P1) with greater specificity for the mediators ferrocene-methanol (12-fold) and nitrosoaniline (8-fold), compared to the wild-type enzyme, and better performance in three pH-adjusted buffers. The kcat /KM ratio of P1 increased by up to 121 folds compared to the wild type enzyme at pH 5.5 in the presence of ferrocene methanol.

Thinking outside the shell: novel sensors designed from plasmon-enhanced fluorescent concentric nanoparticles.

The alteration of photophysical properties of fluorophores in the vicinity of a metallic nanostructure, a phenomenon termed plasmon- or metal-enhanced fluorescence (MEF), has been investigated extensively and used in a variety of proof-of-concept demonstrations over the years. A particularly active area of development in this regard has been the design of nanostructures where fluorophore and metallic core are held in a stable geometry that imparts improved luminosity and photostability to a plethora of organic fluorophores. This minireview presents an overview of MEF-based concentric core-shell sensors developed in the past few years. These architectures expand the range of applications of nanoparticles (NPs) beyond the uses possible with fluorescent molecules. Design aspects that are being described include the influence of the nanocomposite structure on MEF, notably the dependence of fluorescence intensity and lifetime on the distance to the plasmonic core. The chemical composition of nanocomposites as a design feature is also discussed, taking as an example the use of non-noble plasmonic metals such as indium as core materials to enhance multiple fluorophores throughout the UV-Vis range and tune the sensitivity of halide-sensing fluorophores operating on the principle of collisional quenching. Finally, the paper describes how various solid substrates can be functionalized with MEF-based nanosensors to bestow them with intense and photostable pH-sensitive properties for use in fields such as medical therapy and diagnostics, dentistry, biochemistry and microfluidics.

Beyond the display: phase-only liquid crystal on Silicon devices and their applications in photonics [Invited].

Existing for almost four decades, liquid crystal on Silicon (LCOS) technology is rapidly growing into photonic applications. We review the basics of the technology, from the wafer to the driving solutions, the progress over the last decade and the future outlook. Furthermore we review the most exciting industrial and scientific applications of the LCOS technology.

Novel Descriptors and Digital Signal Processing- Based Method for Protein Sequence Activity Relationship Study.

The work aiming to unravel the correlation between protein sequence and function in the absence of structural information can be highly rewarding. We present a new way of considering descriptors from the amino acids index database for modeling and predicting the fitness value of a polypeptide chain. This approach includes the following steps: (i) Calculating Q elementary numerical sequences (Ele_SEQ) depending on the encoding of the amino acid residues, (ii) determining an extended numerical sequence (Ext_SEQ) by concatenating the Q elementary numerical sequences, wherein at least one elementary numerical sequence is a protein spectrum obtained by applying fast Fourier transformation (FFT), and (iii) predicting a value of fitness for polypeptide variants (train and/or validation set). These new descriptors were tested on four sets of proteins of different lengths (GLP-2, TNF alpha, cytochrome P450, and epoxide hydrolase) and activities (cAMP activation, binding affinity, thermostability and enantioselectivity). We show that the use of multiple physicochemical descriptors coupled with the implementation of the FFT, taking into account the interactions between residues of amino amides within the protein sequence, could lead to very significant improvement in the quality of models and predictions. The choice of the descriptor or of the combination of descriptors and/or FFT is dependent on the couple protein/fitness. This approach can provide potential users with value added to existing mutant libraries where screening efforts have so far been unsuccessful in finding improved polypeptide mutants for useful applications.

Application of fourier transform and proteochemometrics principles to protein engineering.

BACKGROUND: Connecting the dots between the protein sequence and its function is of fundamental interest for protein engineers. In-silico methods are useful in this quest especially when structural information is not available. In this study we propose a mutant library screening tool called iSAR (innovative Sequence Activity Relationship) that relies on the physicochemical properties of the amino acids, digital signal processing and partial least squares regression to uncover these sequence-function correlations. RESULTS: We show that the digitalized representation of the protein sequence in the form of a Fourier spectrum can be used as an efficient descriptor to model the sequence-activity relationship of proteins. The iSAR methodology that we have developed identifies high fitness mutants from mutant libraries relying on physicochemical properties of the amino acids, digital signal processing and regression techniques. iSAR correlates variations caused by mutations in spectra with biological activity/fitness. It takes into account the impact of mutations on the whole spectrum and does not focus on local fitness alone. The utility of the method is illustrated on 4 datasets: cytochrome P450 for thermostability, TNF-alpha for binding affinity, GLP-2 for potency and enterotoxins for thermostability. The choice of the datasets has been made such as to illustrate the ability of the method to perform when limited training data is available and also when novel mutations appear in the test set, that have not been featured in the training set. CONCLUSION: The combination of Fast Fourier Transform and Partial Least Squares regression is efficient in capturing the effects of mutations on the function of the protein. iSAR is a fast algorithm which can be implemented with limited computational resources and can make effective predictions even if the training set is limited in size.

Inter-polarization mixers for coherent detection of optical signals.

Electro-magnetic (EM) mixers are fundamental building blocks in communication systems. They are used in frequency/wavelength filters, interferometric modulators, amplitude-phase receivers, to name a few. Traditional EM mixers have two or more input ports and work only for co-polarized signal and local-oscillator (LO) incident on its inputs. Here we report on novel designs, in silicon, of inter-polarization EM mixers operating at 1550 nm wavelength. The 180-degree optical mixer comprising a single input port is demonstrated to coherently mix orthogonally polarized signal and LO. Using the proposed 180-degree mixer, we report on a novel design for a 90-degree optical mixer on silicon with small footprint, broadband response, low loss and good fabrication tolerance. It exploits birefringence of a waveguide to achieve broadband and fabrication-tolerant 90° phase difference between the signal/LO relative phase in the in-phase and quadrature components. A monolithic silicon photonics coherent receiver is demonstrated using the reported 90-degree mixer, and its operation at 22 Gbaud and 44 Gbaud is shown. These mixers pave the way for novel coherent receiver architectures in long-haul, metro, passive optical networks and data-center interconnect applications.

Triple-clad photonic lanterns for mode scaling.

We propose a novel triple-clad photonic lanterns for mode scaling. This novel structure alleviates the adiabatic tapering requirement for the fabrication of large photonic lanterns. A 10-mode photonic lantern with insertion losses ranging from 0.6 to 2.0 dB across all the modes and a record-low pairwise 4-dB mode-dependent loss at C-band was demonstrated.

Photonic lantern broadband orbital angular momentum mode multiplexer.

Optical vortex beams that carry orbital angular momentum (OAM), also known as OAM modes, have attracted considerable interest in recent years as they can comprise an additional degree of freedom for a variety of advanced classical and quantum optical applications. While canonical methods of OAM mode generation are effective, a method that can simultaneously generate and multiplex OAM modes with low loss and over broad spectral range is still in great demand. Here, via novel design of an optical fiber device referred to as a photonic lantern, where the radial mode index ("m") is neglected, for the first time we demonstrate the simultaneous generation and multiplexing of OAM modes with low loss and over the broadest spectral range to date (550 nm). We further confirm the potential of this approach to preserve the quality of studied OAM modes by fusion splicing the end-facet of the fabricated device to a delivery ring-core fiber (RCF).

Broadband and low-loss mode scramblers using CO2-laser inscribed long-period gratings.

We demonstrate broadband and low-loss three-mode and six-mode scramblers employing CO2-laser inscribed long-period gratings (LPGs) for space-division multiplexing. Step-index (SI) few-mode fibers are used to avoid mode coupling to the cladding modes. We characterize the mode scramblers using a swept-wavelength interferometer. Mode-dependent loss (MDL) and modal transfer matrices over the C+L band are presented. Demonstrated LPGs with negligible MDL and low insertion loss contributed to high-performance CO2-laser inscription. The total MDLs induced by the SI fiber with LPGs in three-mode and six-mode scramblers are measured to be 2 and 4 dB, respectively.