Quantifying DNA damage following light sheet and confocal imaging of the mammalian embryo.

Embryo quality assessment by optical imaging is increasing in popularity. Among available optical techniques, light sheet microscopy has emerged as a superior alternative to confocal microscopy due to its geometry, enabling faster image acquisition with reduced photodamage to the sample. However, previous assessments of photodamage induced by imaging may have failed to measure more subtle impacts.

Learning algorithms for identification of whisky using portable Raman spectroscopy.

Reliable identification of high-value products such as whisky is vital due to rising issues of brand substitution and quality control in the industry. We have developed a novel framework that can perform whisky analysis directly from raw spectral data with no human intervention by integrating machine learning models with a portable Raman device. We demonstrate that machine learning models can achieve over 99% accuracy in brand or product identification across twenty-eight commercial samples.

UVA Hyperspectral Light-Sheet Microscopy for Volumetric Metabolic Imaging: Application to Preimplantation Embryo Development.

Cellular metabolism is a key regulator of energetics, cell growth, regeneration, and homeostasis. Spatially mapping the heterogeneity of cellular metabolic activity is of great importance for unraveling the overall cell and tissue health. In this regard, imaging the endogenous metabolic cofactors, nicotinamide adenine dinucleotide (phosphate) (NAD(P)H) and flavin adenine dinucleotide (FAD), with subcellular resolution and in a noninvasive manner would be useful to determine tissue and cell viability in a clinical environment, but practical use is limited by current imaging techniques.

Multimodal Raman spectroscopy and optical coherence tomography for biomedical analysis.

Optical techniques hold great potential to detect and monitor disease states as they are a fast, non-invasive toolkit. Raman spectroscopy (RS) in particular is a powerful label-free method capable of quantifying the biomolecular content of tissues. Still, spontaneous Raman scattering lacks information about tissue morphology due to its inability to rapidly assess a large field of view.

The effect of discrete wavelengths of visible light on the developing murine embryo.

Purpose: A current focus of the IVF field is non-invasive imaging of the embryo to quantify developmental potential. Such approaches use varying wavelengths to gain maximum biological information. The impact of irradiating the developing embryo with discrete wavelengths of light is not fully understood.

Protein detection enabled using functionalised silk-binding peptides on a silk-coated optical fibre.

We present a new coating procedure to prepare optical fibre sensors suitable for use with protein analytes. We demonstrate this through the detection of AlexaFluor-532 tagged streptavidin by its binding to D-biotin that is functionalised onto an optical fibre, incorporation in a silk fibroin fibre coating. The D-biotin was covalently attached to a silk-binding peptide to provide SBP-biotin, which adheres the D-biotin to the silk-coated fibre tip.

Tailored Multi-Color Dispersive Wave Formation in Quasi-Phase-Matched Exposed Core Fibers.

Widely wavelength-tunable femtosecond light sources in a compact, robust footprint play a central role in many prolific research fields and technologies, including medical diagnostics, biophotonics, and metrology. Fiber lasers are on the verge in the development of such sources, yet widespan spectral tunability of femtosecond pulses remains a pivotal challenge. Dispersive wave generation, also known as Cherenkov radiation, offers untapped potentials to serve these demands.

Scalable Functionalization of Optical Fibers Using Atomically Thin Semiconductors.

Atomically thin transition metal dichalcogenides are highly promising for integrated optoelectronic and photonic systems due to their exciton-driven linear and nonlinear interactions with light. Integrating them into optical fibers yields novel opportunities in optical communication, remote sensing, and all-fiber optoelectronics. However, the scalable and reproducible deposition of high-quality monolayers on optical fibers is a challenge.

All-fiber all-optical quantitative polymerase chain reaction (qPCR).

Quantitative polymerase chain reaction (qPCR), the real-time amplification and measurement of a targeted DNA molecule, has revolutionized the biological sciences and is routinely applied in areas such as medical diagnostics, forensics, and agriculture. Despite widescale use of qPCR technology in the lab, the availability of low-cost and high-speed portable systems remains one of the barriers to routine in-field implementation. Here we propose and demonstrate a potential solution using a photonics-based qPCR system.

A biophotonic approach to measure pH in small volumes in vitro: Quantifiable differences in metabolic flux around the cumulus-oocyte-complex (COC).

Unfertilised eggs (oocytes) release chemical biomarkers into the medium surrounding them. This provides an opportunity to monitor cell health and development during assisted reproductive processes if detected in a non-invasive manner. Here we report the measurement of pH using an optical fibre probe, OFP1, in 5 μL drops of culture medium containing single mouse cumulus oocyte complexes (COCs).

Quantum noise limited nanoparticle detection with exposed-core fiber.

Label-free biosensors are important tools for clinical diagnostics and for studying biology at the single molecule level. The development of optical label-free sensors has allowed extreme sensitivity but can expose the biological sample to photodamage. Moreover, the fragility and complexity of these sensors can be prohibitive to applications.

Minocycline attenuates 3,4-methylenedioxymethamphetamine-induced hyperthermia in the rat brain.

Hyperthermia is most dangerous clinical symptom of acute MDMA administration, and a key factor related to potentially life-threatening MDMA-induced complications. MDMA induces a consistently faster onset of brain hyperthermia when compared to a delayed and moderate hyperthermia in the body, and the most harmful effects of MDMA are related to its modulation of neural functions. The primary focus of this study was to investigate the effects of minocycline, a centrally acting tetracycline derivative on MDMA-induced brain hyperthermia at high ambient temperature.

Tunable multi-wavelength third-harmonic generation using exposed-core microstructured optical fiber.

We demonstrate that exposed-core microstructured optical fibers offer multiple degrees of freedom for tailoring third-harmonic generation through the core diameter, input polarization, and nanofilm deposition. Varying these parameters allows control of the phase-matching position between an infrared pump wavelength and the generated visible wavelengths. In this Letter, we show how increasing the core diameter over previous experiments (2.

Improved method for optical fiber temperature probe implantation in brains of free-moving rats.

Background: The localized monitoring of brain temperature is crucial to the understanding of the mechanisms underlying brain hyperthermia, such as that caused by stimulant drugs. Many animal studies investigating brain hyperthermia have utilized thermocouple electrodes for temperature measurement, however optical fiber sensors have proven to be an attractive alternative to conventional measurement techniques. Despite their advantages, optical fiber sensors in their current form have struggled to find effective use in studies involving free-moving animals.

Miniaturized single-fiber-based needle probe for combined imaging and sensing in deep tissue.

The ability to visualize structure while simultaneously measuring chemical or physical properties of a biological tissue has the potential to improve our understanding of complex biological processes. We report the first miniaturized single-fiber-based imaging+sensing probe capable of simultaneous optical coherence tomography (OCT) imaging and temperature sensing. An OCT lens is fabricated at the distal end of a double-clad fiber, including a thin layer of rare-earth-doped tellurite glass to enable temperature measurements.

Cancer Detection in Human Tissue Samples Using a Fiber-Tip pH Probe.

Intraoperative detection of tumorous tissue is an important unresolved issue for cancer surgery. Difficulty in differentiating between tissue types commonly results in the requirement for additional surgeries to excise unremoved cancer tissue or alternatively in the removal of excess amounts of healthy tissue. Although pathologic methods exist to determine tissue type during surgery, these methods can compromise postoperative pathology, have a lag of minutes to hours before the surgeon receives the results of the tissue analysis, and are restricted to excised tissue.

Portable optical fiber probe for in vivo brain temperature measurements.

This work reports on the development of an optical fiber based probe for in vivo measurements of brain temperature. By utilizing a thin layer of rare-earth doped tellurite glass on the tip of a conventional silica optical fiber a robust probe, suitable for long-term in vivo measurements of temperature can be fabricated. This probe can be interrogated using a portable optical measurement setup, allowing for measurements to be performed outside of standard optical laboratories.

Quantification of the fluorescence sensing performance of microstructured optical fibers compared to multi-mode fiber tips.

Microstructured optical fibers, particularly those with a suspended-core geometry, have frequently been argued as efficient evanescent-field fluorescence-based sensors. However, to date there has not been a systematic comparison between such fibers and the more common geometry of a multi-mode fiber tip sensor. In this paper we make a direct comparison between these two fiber sensor geometries both theoretically and experimentally.

A Dual Sensor for pH and Hydrogen Peroxide Using Polymer-Coated Optical Fibre Tips.

This paper demonstrates the first single optical fibre tip probe for concurrent detection of both hydrogen peroxide (H₂O₂) concentration and pH of a solution. The sensor is constructed by embedding two fluorophores: carboxyperoxyfluor-1 (CPF1) and seminaphtharhodafluor-2 (SNARF2) within a polymer matrix located on the tip of the optical fibre. The functionalised fibre probe reproducibly measures pH, and is able to accurately detect H₂O₂ over a biologically relevant concentration range.

Boronate probes for the detection of hydrogen peroxide release from human spermatozoa.

Human spermatozoa are compromised by production of reactive oxygen species (ROS), and detection of ROS in spermatozoa is important for the diagnosis of male infertility. The probes 2',7'-dichlorohydrofluorescein diacetate (DCFH), dihydroethidium (DHE), and MitoSOX red (MSR) are commonly used for detecting ROS by flow cytometry; however, these probes lack sensitivity to hydrogen peroxide (H2O2), which is particularly damaging to mammalian sperm cells. This study reports the synthesis and use of three aryl boronate probes, peroxyfluor-1 (PF1), carboxyperoxyfluor-1, and a novel probe, 2-(2-ethoxyethoxy)ethoxyperoxyfluor-1 (EEPF1), in human spermatozoa.

Generating and measuring photochemical changes inside the brain using optical fibers: exploring stroke.

We report here on the development of a method for inducing a stroke in a specific location within a mouse brain through the use of an optical fiber. By capturing the emitted fluorescence signal generated using the same fiber it is possible to monitor photochemical changes within the brain in real-time, and directly measure the concentration of the stroke-inducing dye, Rose Bengal, at the infarct site. This technique reduces the requirement for post-operative histology to determine if a stroke has successfully been induced within the animal, and therefore opens up the opportunity to explore the recovery of the brain after the stroke event.