Quantitative morphology of femtosecond laser-written point-by-point optical fiber Bragg gratings.

We investigate the morphology of femtosecond laser, single pulse-inscribed, point-by-point (PbP) fiber Bragg gratings. Direct measurement of a PbP grating's refractive index profile was carried out with micro-reflectivity analysis. PbP gratings were imaged at sub-micrometer scale with scanning electron microscopy, Raman and photoluminescence studies were performed to probe the structural and electronic changes. Comparison of results from different characterisation techniques suggests that the creation of an increased refractive index region around the micro-void is due to contributions from both densification and the formation of highly polarizable non-bridging oxygen bonds.

Noise in Brillouin based information storage.

We theoretically and numerically study the efficiency of Brillouin-based opto-acoustic data storage in a photonic waveguide in the presence of thermal noise and laser phase noise. We compare the physics of the noise processes and how they affect different storage techniques, examining both amplitude and phase storage schemes. We investigate the effects of storage time and pulse properties on the quality of the retrieved signal and find that phase storage is less sensitive to thermal noise than amplitude storage.

Picosecond acoustic dynamics in stimulated Brillouin scattering.

Recent experiments demonstrating storage of optical pulses in acoustic phonons via stimulated Brillouin scattering raise questions about the spectral and temporal capacities of such protocols and the limitations of the theoretical frameworks routinely used to describe them. We consider the dynamics of photon-phonon scattering induced by optical pulses with temporal widths comparable to the period of acoustic oscillations. We revisit the widely adopted classical formalism of coupled modes and demonstrate its breakdown. We use a simple extension to the formulation and find potentially measurable consequences in the dynamics of Brillouin experiments involving ultrashort pulses.

Colorectal adenocarcinomas diagnosed following a negative faecal immunochemical test show high-risk pathological features in a colon screening programme.

AIMS: The faecal immunochemical test (FIT) is used every 2 years to screen average-risk British Columbians aged 50-74 years, with follow-up colonoscopy for positive results. Non-screen-detected colorectal adenocarcinomas are defined as those detected within 25 months following a negative FIT. We aimed to more clearly characterise these malignancies. METHODS AND RESULTS: A medical chart and focused pathology review of colorectal malignancies from 926 individuals who completed FIT in the British Columbia Colon Screening Program in 2014, and whose pathology reports were available for review, was conducted. This cohort was divided into two groups: individuals with colorectal adenocarcinomas diagnosed following a positive FIT (screen-detected) and individuals with colorectal adenocarcinoma diagnosed within 25 months of a negative FIT (FIT-interval cancers). Rates of clinically relevant pathological parameters, as outlined in the American Joint Committee on Cancer (AJCC), 8th edition, were compared between the screen-detected and FIT-interval cancer groups. A total of 876 screen-detected and 50 FIT-interval cancers were identified. FIT-interval cancers exhibited higher rates of high-grade differentiation (including poorly differentiated and undifferentiated cases; P < 0.01) and aggressive histotype (signet ring cell and mucinous carcinomas; P < 0.01) than did screen-detected cancers after Bonferroni correction. Colorectal adenocarcinoma diagnosed after a negative FIT may therefore be associated with worse prognostic determinants than screen-detected cancers. CONCLUSION: FIT-interval cancers are associated with high-risk pathological features; the possibility that more aggressive, fast-growing lesions which arise in the interval after truly negative FITs cannot be ruled out. Further study of a larger cohort of FIT-interval cancers controlling for interaction among the different pathologic parameters will be undertaken.

Transformation of aqueous protein attenuated total reflectance infra-red absorbance spectroscopy to transmission.

Infrared (IR) spectroscopy is increasingly being used to probe the secondary structure of proteins, especially for high-concentration samples and biopharmaceuticals in complex formulation vehicles. However, the small path lengths required for aqueous protein transmission experiments, due to high water absorbance in the amide I region of the spectrum, means that the path length is not accurately known, so only the shape of the band is ever considered. This throws away a dimension of information. Attenuated total reflectance (ATR) IR spectroscopy is much easier to implement than transmission IR spectroscopy and, for a given instrument and sample, gives reproducible spectra. However, the ATR-absorbance spectrum varies with sample concentration and instrument configuration, and its wavenumber dependence differs significantly from that observed in transmission spectroscopy. In this paper, we determine, for the first time, how to transform water and aqueous protein ATR spectra into the corresponding transmission spectra with appropriate spectral shapes and intensities. The approach is illustrated by application to water, concanavalin A, haemoglobin and lysozyme. The transformation is only as good as the available water refractive index data. A hybrid of literature data provides the best results. The transformation also allows the angle of incidence of an ATR crystal to be determined. This opens the way to using both spectral shape and spectra intensity for protein structure fitting.

Should you repeat mismatch repair testing in cases of tumour recurrence? An evaluation of repeat mismatch repair testing by the use of immunohistochemistry in recurrent tumours of the gastrointestinal and gynaecological tracts.

AIMS: The role of mismatch repair (MMR) testing has evolved from identifying Lynch syndrome patients to predicting response to immune checkpoint inhibitors. This has led to requests from clinicians to retest recurrences of MMR-proficient primary tumours in the hope that the recurrence may show a different MMR status and qualify the patient for treatment. We aimed to determine whether repeat testing is warranted. METHODS AND RESULTS: We evaluated recurrent tumours (local recurrences or metastases) from 137 patients with MMR-proficient primary tumours of the gastrointestinal and gynaecological tracts. The local recurrences and metastases all occurred at least 30 days after resection of the primary tumour. We used a combination of a tissue microarray and whole slide staining to perform immunohistochemistry (IHC) for PMS2, MLH1, MSH2, and MSH6, and compared the results with the MMR status of the primary tumour. Three of 137 (2%) initially showed a discordant staining pattern. However, further investigation showed that these discordances were attributable to some of the known pitfalls associated with MMR IHC interpretation - post-radiotherapy loss of MSH6 expression and subclonal loss of MLH1 staining. We did not identify any cases with a genuine discordance in MMR status. CONCLUSION: We conclude that repeat MMR IHC testing of recurrences is not warranted, as MMR status does not change relative to that of the primary tumour.

Emission and nonradiative decay of nanodiamond NV centers in a low refractive index environment.

The nitrogen vacancy (NV) center is the most widely studied single optical defect in diamond with great potential for applications in quantum technologies. Development of practical single-photon devices requires an understanding of the emission under a range of conditions and environments. In this work, we study the properties of a single NV center in nanodiamonds embedded in an air-like silica aerogel environment which provides a new domain for probing the emission behavior of NV centers in nanoscale environments. In this arrangement, the emission rate is governed primarily by the diamond crystal lattice with negligible contribution from the surrounding environment. This is in contrast to the conventional approach of studying nanodiamonds on a glass coverslip. We observe an increase in the mean lifetime due to the absence of a dielectric interface near the emitting dipoles and a distribution arising from the irregularities in the nanodiamond geometry. Our approach results in the estimation of the mean quantum efficiency (~0.7) of the nanodiamond NV emitters.

Cladding mode coupling in highly localized fiber Bragg gratings II: complete vectorial analysis.

Highly localized fiber Bragg gratings can be inscribed point-by-point with focused ultrashort pulses. The transverse localization of the resonant grating causes strong coupling to cladding modes of high azimuthal and radial order. In this paper, we show how the reflected cladding modes can be fully analyzed, taking their vectorial nature, orientation and degeneracies into account. The observed modes' polarization and intensity distributions are directly tied to the dispersive properties and show abrupt transitions in nature, strongly correlated with changes in the coupling strengths.

Characterization and modeling of Fano resonances in chalcogenide photonic crystal membranes.

We demonstrate resonant guiding in a chalcogenide glass photonic crystal membrane. We observe strong resonances in the optical transmission spectra at normal incidence, associated with Fano coupling between free space and guided modes. We obtain good agreement with modeling results based on three-dimensional finite-difference time-domain simulations, and identify the guided modes near the centre of the first Brillouin zone responsible for the main spectral features.

Transverse characterization of high air-fill fraction tapered photonic crystal fiber.

We demonstrate tapering of a high air-fill fraction photonic crystal fiber by using the flame-brushing technique. Transverse probing along the taper allows us to ascertain how the microstructure is preserved during tapering. Experimental results are compared with numerical simulations performed with the finite-difference time-domain and plane-wave expansion methods. Through this investigation we find that the fiber geometry is well preserved throughout the tapering process and we resolve the apparent discrepancies between simulation and experiment that arise through the finite extent of the fiber microstructure.

Leakage of the fundamental mode in photonic crystal fiber tapers.

We report detailed measurements of the optical properties of tapered photonic crystal fibers (PCFs). We observe a striking long-wavelength loss as the fiber diameter is reduced, despite the minimal airhole collapse along the taper. We associate this loss with a transition of the fundamental core mode as the fiber dimensions contract: At wavelengths shorter than this transition wavelength, the core mode is strongly confined in the fiber microstructure, whereas at longer wavelengths the mode expands beyond the microstructure and couples out to higher-order modes. These experimental results are discussed in the context of the so-called fundamental mode cutoff described by Kuhlmey et al. [Opt. Express 10, 1285 (2002)], which apply to PCFs with a finite microstructure.