Identification of spermatogenesis in individual seminiferous tubules and testicular tissue of adult normal and busulfan-treated mice employing Raman spectroscopy and principal component analysis.

The present study aims to identify spermatogenesis in testicular seminiferous tubules (ST) and testicular tissue of adult normal and busulfan-treated mice utilizing PCA and Raman spectroscopy. Raman measurements were conducted on single tubules and testes samples from adult and immature mice, comparing them with those from busulfan-treated adult mice, with validation through histological examination. The analysis revealed a higher signal variability (30 %-40 % at the peaks), prompting scrutiny of individual Raman spectra as a means of spermatogenesis measurement. However, principal component analysis (PCA) demonstrated significant cluster separation between the ST of mature and immature mice. Similar investigations were performed to compare ST from normal mature mice and those from busulfan-treated (BS-treated) mature mice, revealing substantial separation along PC1 and PC2 for all comparison sets. Additionally, comparing testicular samples from mature and immature mice revealed distinct separation in PCA. The study concludes that the combined approach of PCA and Raman spectroscopy proves to be a noninvasive and potentially valuable method for identifying spermatogenesis in seminiferous tubules and testicular samples.

Compressive hyperspectral microscopy for cancer detection.

Significance: Hyperspectral microscopy grants the ability to characterize unique properties of tissues based on their spectral fingerprint. The ability to label and measure multiple molecular probes simultaneously provides pathologists and oncologists with a powerful tool to enhance accurate diagnostic and prognostic decisions. As the pathological workload grows, having an objective tool that provides companion diagnostics is of immense importance. Therefore, fast whole-slide spectral imaging systems are of immense importance for automated cancer prognostics that meet current and future needs. Aim: We aim to develop a fast and accurate hyperspectral microscopy system that can be easily integrated with existing microscopes and provide flexibility for optimizing measurement time versus spectral resolution. Approach: The method employs compressive sensing (CS) and a spectrally encoded illumination device integrated into the illumination path of a standard microscope. The spectral encoding is obtained using a compact liquid crystal cell that is operated in a fast mode. It provides time-efficient measurements of the spectral information, is modular and versatile, and can also be used for other applications that require rapid acquisition of hyperspectral images. Results: We demonstrated the acquisition of breast cancer biopsies hyperspectral data of the whole camera area within ∼1 s. This means that a typical 1×1 cm2 biopsy can be measured in ∼10 min. The hyperspectral images with 250 spectral bands are reconstructed from 47 spectrally encoded images in the spectral range of 450 to 700 nm. Conclusions: CS hyperspectral microscopy was successfully demonstrated on a common lab microscope for measuring biopsies stained with the most common stains, such as hematoxylin and eosin. The high spectral resolution demonstrated here in a rather short time indicates the ability to use it further for coping with the highly demanding needs of pathological diagnostics, both for cancer diagnostics and prognostics.

Label-Free Direct Detection of Cylindrospermopsin via Graphene-Enhanced Surface Plasmon Resonance Aptasensor.

In this work, we report a novel method for the label-free detection of cyanotoxin molecules based on a direct assay utilizing a graphene-modified surface plasmon resonance (SPR) aptasensor. Molecular dynamic simulation of the aptamer's interaction with cylindrospermopsin (CYN) reveals the strongest binding sites between C18-C26 pairs. To modify the SPR sensor, the wet transfer method of CVD monolayer graphene was used. For the first time, we report the use of graphene functionalized by an aptamer as a bioreceptor in conjunction with SPR for the detection of CYN. In a direct assay with an anti-CYN aptamer, we demonstrated a noticeable change in the optical signal in response to the concentrations far below the maximum tolerable level of 1 µg/L and high specificity.

Biofilm growth monitoring using guided wave ultralong-range Surface Plasmon Resonance: A proof of concept.

Unwelcomed biofilms are problematic in food industries, surgical devices, marine applications, and wastewater treatment plants, essentially everywhere where there is moisture. Very recently, label-free advanced sensors such as localized and extended surface plasmon resonance (SPR) have been explored as tools for monitoring biofilm formation. However, conventional noble metal SPR substrates suffer from low penetration depth (100-300 nm) into the dielectric medium above the surface, preventing the reliable detection of large entities of single or multi-layered cell assemblies like biofilms which can grow up to a few micrometers or more. In this study, we propose using a plasmonic insulator-metal-insulator (IMI) structure (SiO2-Ag-SiO2) with a higher penetration depth based on a diverging beam single wavelength format of Kretschmann configuration in a portable SPR device. An SPR line detection algorithm for locating the reflectance minimum of the device helps to view changes in refractive index and accumulation of the biofilm in real-time down to 10-7 RIU precision. The optimized IMI structure exhibits strong penetration dependence on wavelength and incidence angle. Within the plasmonic resonance, different angles penetrate different depths, showing a maximum near the critical angle. At the wavelength of 635 nm, a high penetration depth of more than 4 µm was obtained. Compared to a thin gold film substrate, for which the penetration depth is only ∼200 nm, the IMI substrate provides more reliable results. The average thickness of the biofilm after 24 h of growth was found to be between 6 and 7 µm with ∼63% live cell volume, as estimated from confocal microscopic images using an image processing tool. To explain this saturation thickness, a graded index biofilm structure is proposed in which the refractive index decreases with the distance from the interface. Furthermore, when plasma-assisted degeneration of biofilms was studied in a semi-real-time format, there was almost no effect on the IMI substrate compared to the gold substrate. The growth rate over the SiO2 surface was higher than on gold, possibly due to differences between surface charge effects. On the gold, the excited plasmon generates an oscillating cloud of electrons, while for the SiO2 case, this does not happen. This methodology can be utilized to detect and characterize biofilms with better signal reliability with respect to concentration and size dependence.

Real-Time Ellipsometric Surface Plasmon Resonance Sensor Using Polarization Camera May Provide the Ultimate Detection Limit.

Ellipsometric Surface Plasmon Resonance (SPR) sensors are known for their relatively simple optical configuration compared to interferometric and optical heterodyne phase interrogation techniques. However, most of the previously explored ellipsometric SPR sensors based on intensity measurements are limited by their real-time applications because phase or polarization shifts are conducted serially. Here we present an ellipsometric SPR sensor based on a Kretschmann-Raether (KR) diverging beam configuration and a pixelated microgrid polarization camera. The proposed methodology has the advantage of real-time and higher precision sensing applications. The short-term stability of the measurement using the ellipsometric parameters tanψ and cos(Δ) is found to be superior over direct SPR or intensity measurements, particularly with fluctuating sources such as laser diodes. Refractive index and dynamic change measurements in real-time are presented together with Bovine Serum Albumin (BSA)-anti-BSA antibody binding to demonstrate the potential of the developed sensor for biological sensing applications with a resolution of sub-nM and down to pM with additional optimization. The analysis shows that this approach may provide the ultimate detection limit for SPR sensors.

Preparation of Nickel Oxide Nanoflakes for Carrier Extraction and Transport in Perovskite Solar Cells.

Hole transport layers (HTLs) with high conductivity, charge extraction ability, and carrier transport capability are highly important for fabricating perovskite solar cells (PSCs) with high power conversion efficiency and device stability. Low interfacial recombination between the HTL and perovskite absorber is also crucial to the device performance of PSCs. In this work, we developed a three-stage method to prepare NiOx nanoflakes as the HTL in the inverted PSCs. Due to the addition of the nanoflake layer, the deposited perovskite films with larger grain sizes and fewer boundaries were obtained, implying higher photogenerated current and fill factors in our PSCs. Meanwhile, the downshifted valence band of the NiOx HTL improved hole extraction from the perovskite absorber and open-circuit voltages of PSCs. The optimized device based on the NiOx nanoflakes showed the highest efficiency of 14.21% and a small hysteresis, which outperformed the NiOx thin film as the HTL. Furthermore, the device maintained 83% of its initial efficiency after 60 days of storage. Our results suggest that NiOx nanoflakes provide great potential for constructing PSCs with high efficiency and long-term stability.

Bacterial DNA Recognition by SERS Active Plasma-Coupled Nanogold.

It is shown that surface-enhanced Raman spectroscopy (SERS) can identify bacteria based on their genomic DNA composition, acting as a "sample-distinguishing marker". Successful spectral differentiation of bacterial species was accomplished with nanogold aggregates synthesized through single-step plasma reduction of the ionic gold-containing vapored precursor. A high enhancement factor (EF = 107) in truncated coupled plasmonic particulates allowed SERS-probing at nanogram sample quantities. Simulations confirmed the occurrence of the strongest electric field confinement within nanometric gaps between gold dimers/chains from where the molecular fingerprints of bacterial DNA fragments gained photon scattering enhancement. The most prominent Raman modes linked to fundamental base-pair molecular vibrations were deconvoluted and used to proceed with nitrogenous base content estimation. The genomic composition (percentage of guanine-cytosine and adenine-thymine) was successfully validated by third-generation sequencing using nanopore technology, further proving that the SERS technique can be employed to swiftly specify bioentities by the discriminative principal-component statistical approach.

Phase unwrapping using the extracted degree of coherence and phase from phase shifting interferometry systems.

Current phase unwrapping methods for non-scanning interferometry systems with one wavelength are not robust in the presence of high steps while still having a limited step height and range using two wavelengths configurations. Here, a new phase unwrapping method is proposed, allowing imaging steps with a height up to 15 times the wavelength using one wavelength or up to 1500 times using two wavelengths. It is based on a one-time computational model fitting of calibration measurements that allows to extract the degree of coherence and phase from two phase-shifted images per wavelength, perform phase unwrapping and accurately reconstruct the 3D structure of the sample. The proposed method has a nanometric axial accuracy and can operate in real-time. The algorithms and methodology for one and two wavelengths are presented and confirmed experimentally.

Label-Free Mycotoxin Raman Identification by High-Performing Plasmonic Vertical Carbon Nanostructures.

Mycotoxins are widespread chemical entities in the agriculture and food industries that can induce cancer growth and immune deficiency, posing a serious health threat for humankind. These hazardous compounds are produced naturally by various molds (fungi) that contaminate different food products and can be detected in cereals, nuts, spices, and other food products. However, their detection, especially at minimally harmful concentrations, remains a serious analytical challenge. This research shows that high-performing plasmonic substrates (analytical enhancement factor = 5 × 107 ) based on plasma-grown vertical hollow carbon nanotubes can be applied for immediate detection of the most toxic mycotoxins. Due to excellent sensitivity allowing operation at ppb concentrations, it is possible to collect vibrational fingerprints of aflatoxin B1 , zearalenone, alternariol, and fumonisin B1 , highlighting the key spectral differences between them using principal component analysis. Regarding time-consuming conventional methods, including thin-layer chromatography, gas chromatography, high-performance liquid chromatography, and enzyme-linked immunosorbent assay, the designed surface-enhanced Raman spectroscopy substrates provide a clear roadmap to reducing the detection time-scale of mycotoxins down to seconds.

Helical Nanostructures of Ferroelectric Liquid Crystals as Fast Phase Retarders for Spectral Information Extraction Devices: A Comparison with the Nematic Liquid Crystal Phase Retarders.

Extraction of spectral information using liquid crystal (LC) retarders has recently become a topic of great interest because of its importance for creating hyper- and multispectral images in a compact and inexpensive way. However, this method of hyperspectral imaging requires thick LC-layer retarders (50 µm-100 µm and above) to obtain spectral modulation signals for reliable signal reconstruction. This makes the device extremely slow in the case of nematic LCs (NLCs), since the response time of NLCs increases proportionally to the square of the LC-layer thickness, which excludes fast dynamic processes monitoring. In this paper, we explore two approaches for solving the speed problem: the first is based on the use of faster nanospiral ferroelectric liquid crystals as an alternative to NLCs, and the second is based on using a passive multiband filter and focuses on multispectral extraction rather than hyperspectral. A detailed comparative study of nematic and ferroelectric devices is presented. The study is carried out using a 9-spectral bands passive spectral filter, covering the visible and near-infrared ranges. We propose the concept of multispectral rather than hyperspectral extraction, where a small number of wavelengths are sufficient for specific applications.

Detection of necrotrophic DNA marker of anthracnose causing Colletotrichum gloeosporioides fungi in harvested produce using surface plasmon resonance.

Agriculture and food crops monitoring is extremely important for securing the food supply chain to human society. Here, we developed a highly specific detection method for monitoring pathogenic fungus Colletotrichum gloeosporioides using necrotrophic DNA biomarker as the recognition element and surface plasmon resonance (SPR) as transducing mechanism in the prism coupling configuration. The sensor shows its response for a wide range of concentrations from pM to µM of target DNA sequence using a complementary DNA probe immobilized on the sensor surface, which could detect concentrations as low as 7 pM. The detection limit is found to be comparable with conventional molecular-based detection platforms, achieved due to optimized spectral SPR bimetallic substrate with subpixel resolution obtained by post processing. The response time of the sensor for detection is less than 30 min at room temperature. The quick detection scheme of the sensor may facilitate the screening of a large number of samples acquired for the sorting of harvested produce. This sensor is fast, reliable, cost-effective, and can be miniaturized for portability for the screening of real samples (mRNA) in the field and packaging house.

Resonant Subwavelength and Nano-Scale Grating Structures for Biosensing Application: A Comparative Study.

Resonant-based sensors are attractive optical structures due to the easy detection of shifts in the resonance location in response to variations in the analyte refractive index (RI) in comparison to non-resonant-based sensors. In particular, due to the rapid progress of nanostructures fabrication methods, the manufacturing of subwavelength and nano-scale gratings in a large area and at a low cost has become possible. A comparative study is presented involving analysis and experimental work on several subwavelength and nanograting structures, highlighting their nano-scale features' high potential in biosensing applications, namely: (i) Thin dielectric grating on top of thin metal film (TDGTMF), which can support the excitation of extended surface plasmons (ESPs), guided mode resonance, or leaky mode; (ii) reflecting grating for conventional ESP resonance (ESPR) and cavity modes (CMs) excitation; (iii) thick dielectric resonant subwavelength grating exhibiting guided mode resonance (GMR) without a waveguide layer. Among the unique features, we highlight the following: (a) Self-referenced operation obtained using the TDGTMF geometry; (b) multimodal operation, including ESPR, CMs, and surface-enhanced spectroscopy using reflecting nanograting; (c) phase detection as a more sensitive approach in all cases, except the case of reflecting grating where phase detection is less sensitive than intensity or wavelength detection. Additionally, intensity and phase detection modes were experimentally demonstrated using off-the-shelf grating-based optical compact discs as a low-cost sensors available for use in a large area. Several flexible designs are proposed for sensing in the visible and infrared spectral ranges based on the mentioned geometries. In addition, enhanced penetration depth is also proposed for sensing large entities such as cells and bacteria using the TDGTMF geometry.

A comprehensive review on plasmonic-based biosensors used in viral diagnostics.

The proliferation and transmission of viruses has become a threat to worldwide biosecurity, as exemplified by the current COVID-19 pandemic. Early diagnosis of viral infection and disease control have always been critical. Virus detection can be achieved based on various plasmonic phenomena, including propagating surface plasmon resonance (SPR), localized SPR, surface-enhanced Raman scattering, surface-enhanced fluorescence and surface-enhanced infrared absorption spectroscopy. The present review covers all available information on plasmonic-based virus detection, and collected data on these sensors based on several parameters. These data will assist the audience in advancing research and development of a new generation of versatile virus biosensors.

Two-color optically addressed spatial light modulator as a generic spatiotemporal system.

Nonlinear spatiotemporal systems are the basis for countless physical phenomena in such diverse fields as ecology, optics, electronics, and neuroscience. The canonical approach to unify models originating from different fields is the normal form description, which determines the generic dynamical aspects and different bifurcation scenarios. Realizing different types of dynamical systems via one experimental platform that enables continuous transition between normal forms through tuning accessible system parameters is, therefore, highly relevant. Here, we show that a transmissive, optically addressed spatial light modulator under coherent optical illumination and optical feedback coupling allows tuning between pitchfork, transcritical, and saddle-node bifurcations of steady states. We demonstrate this by analytically deriving the system's dynamical equations in correspondence to the normal forms of the associated bifurcations and confirm these results via extensive numerical simulations. Our model describes a nematic liquid crystal device using nano-dimensional dichalcogenide (a-As 2S 3) glassy thin films as photo sensors and alignment layers, and we use device parameters obtained from experimental characterization. Optical coupling, for example, using diffraction, holography, or integrated unitary maps allows implementing a variety of system topologies of technological relevance for neural networks and potentially Ising or XY-Hamiltonian models with ultralow energy consumption.

Femtosecond Laser-Induced Vanadium Oxide Metamaterial Nanostructures and the Study of Optical Response by Experiments and Numerical Simulations.

Surface patterning is a popular approach to produce photonic metasurfaces that are tunable when electro-optic, thermo-optic, or magneto-optic materials are used. Vanadium oxides (VyOx) are well-known phase change materials with many applications, especially when used as tunable metamaterial photonic structures. Particularly, VO2 is a well-known thermochromic material for its near-room-temperature phase transition from the insulating to the metallic state. One-dimensional (1D) VO2 nanograting structures are studied by numerical simulation, and the simulation results reveal that the VO2 nanograting structures could enhance the luminous transmittance (Tlum) compared with a pristine flat VO2 surface. It is worth mentioning that Tlum is also polarization-dependent, and both larger grating height and smaller grating periodicity give enhanced Tlum, particularly at TE polarization in both insulating (20 °C) and metallic (90 °C) states of VO2. Femtosecond laser-patterned VO2 films exhibiting nanograting structures with an average periodicity of ≈500-700 nm have been fabricated for the first time to enhance thermochromic properties. Using X-ray photoelectron spectroscopy, it is shown that at the optimum laser processing conditions, VO2 dominates the film composition, while under extra processing, the existence of other vanadium oxide phases such as V2O3 and V2O5 increases. Such structures show enhanced transmittance in the near-infrared (NIR) region, with an improvement in NIR and solar modulation abilities (ΔTNIR = 10.8%, ΔTsol = 10.9%) compared with a flat VO2 thin film (ΔTNIR = 8%, ΔTsol = 10.2%). The slight reduction in transmittance in the visible region is potentially due to the scattering caused by the imperfect nanograting structures. This new patterning approach helps understand the polarization-dependent optical response of VO2 thin films and opens a new gateway for smart devices.

Parallel spectroscopic ellipsometry for ultra-fast thin film characterization.

Spectroscopic ellipsometer (SE) is an essential optical metrology tool commonly used to characterize thin films and monitor fabrication processes. However, it relies on mechanical rotation of a polarizer or a photo-elastic phase modulator which are limited in speed and prone to errors when handling dynamic processes. The constant trend of micro-electronics dimensions shrinkage and increase of the wafer area necessitates faster and more accurate tools. A fast SE design based on parallel snapshot detection of three signals at different polarizations is proposed and demonstrated. Not relying on mechanical rotation nor serial phase modulation, it is more accurate and can reach acquisition rates of hundreds of measurements per second.

Functionalized silicon dioxide self-referenced plasmonic chip as point-of-care biosensor for stroke biomarkers NT-proBNP and S100ß.

Surface plasmon resonance (SPR) biosensors are often used in the detection of solid, liquid or gaseous samples in diagnostics, pharmaceutics and military defense. Plasmon waveguide resonance (PWR) mode is obtained when a dielectric waveguide layer is added to the metal film. In this study, a self-referenced PWR (SRPWR) silicon dioxide (SiO2) chip was examined. The self-referenced measurement is important to compensate for temperature fluctuations, other instabilities and allows RI signal measurement without an additional reference sample, thus minimising the sample volume needed. The chip was fabricated with a multi-layer of metals and dielectrics, consisting of a 420 nm SiO2 layer, a 40 nm Ag layer and another 480 nm SiO2 layer. This chip was shown to give one internal plasmon excited on the bottom interface SiO2/Ag, which is used as self-reference in the detection. The top layer acts as a waveguide layer and can be designed to give modes with ultrahigh penetration depth. A direct assay was developed, where the recognition molecule (specific antibody) was immobilized onto the SiO2 plasmonic chip surface, via a covalent coupling protocol based on 3-aminopropyltriethoxysilane (APTES) and glutaraldehyde. The SRPWR biosensor was developed for the sensing of two chosen stroke biomarkers: NT-proBNP and S100ß, which are sensitive and specific for stroke diagnostics. For both biomarkers, a linear decreasing pattern in the RI signal was recognized with the increasing biomarkers concentrations. Biomarkers detection was conducted in deionized water and validation was done in spiked porcine plasma. The SiO2 based plasmonic chip demonstrates a limit-of-detection of less than 1 ng/mL that is clinically relevant for both stroke biomarkers.

Dual-camera design for hyperspectral and panchromatic imaging, using a wedge shaped liquid crystal as a spectral multiplexer.

In this paper, we present a new hyperspectral compact camera which is designed to have high spatial and spectral resolutions, to be vibrations tolerant, and to achieve state-of-the-art high optical throughput values compared to existing nanosatellite hyperspectral imaging payloads with space heritage. These properties make it perfect for airborne and spaceborne remote sensing tasks. The camera has both hyperspectral and panchromatic imaging capabilities, achieved by employing a wedge-shaped liquid crystal cell together with computational image processing. The hyperspectral images are acquired through passive along-track spatial scanning when no voltage is applied to the cell, and the panchromatic images are quickly acquired in a single snapshot at a high signal-to-noise ratio when the cell is voltage driven.

Plasmonic nanoparticle-film-assisted photoelectrochemical catalysis across the entire visible-NIR region.

Low solar light absorption and high electron-hole pair recombination are still the main challenges for solar energy conversion. Here, we design a plasmonic nanoparticle (NP)-film with a unique structure combining the advantages of a Au NP and film, which exhibits strong broadband absorption from the visible to near-infrared (NIR) wavelength range. In addition, the high density of sub-1 nm inter-particle gaps in the Au NP-film supports electromagnetic field enhancement of several orders of magnitude that greatly promotes the generation and separation of electron-hole pairs. Accordingly, the plasmonic NP-film-assisted photocatalyst (TiO2/90Au/TiO2) leads to an 88-fold increase in the photocurrent density at 0.75 V vs. RHE in 25% methanol solution under visible-NIR light irradiation (λ > 420 nm) compared to a TiO2 film, which is higher than those of the ever reported Au/TiO2 photocatalysts in the entire visible-NIR range. Our finding indicates a promising way to explore full solar spectrum photocatalysts, which can be easily extended to other energy conversion applications.