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Mach-Zehnder interferometers are integrated photonic sensors that have yielded excellent detection limits down to 10-7 RIU. They are of particular interest due to their large design freedom, allowing for example application in promising point-of-care compatible read-out schemes. The attainable detection limit of such sensors can interact with the sensor design in different ways, depending on the dominant origin of noise which can either be influencing a single sensor arm, both sensor arms or can be unrelated to the sensor itself. In this work, the interaction of these three noise regimes with the sensor design is examined. The regimes are combined into a framework that predicts the limit of detection as a function of sensor design. A set of experimental results confirms the validity of this obtained theoretical framework. This analysis provides a blueprint for optimization of MZI photonic sensors under any combination of read-out method and measurement circumstances.

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We report on the label-free real-time optical monitoring of DNA hybridization upon exposure to a flow of complementary DNA at different concentrations. The biosensor is composed of a silicon nitride integrated unbalanced Mach-Zehnder interferometer (MZI), with an integrated arrayed waveguide grating as a spectral filter. This MZI has been shown to have both sufficient multiplexing capability and limit of detection on the order of 10 - 6 RIU. Probe DNA, consisting of a 36-mer fragment is covalently immobilized on the silicon nitride integrated biosensor. The wavelength shift is monitored upon complementary DNA targets being flown over the sensor. Concentrations of 1 pM can be easily detected. Also, an alternative route to modify the sensor surface with carboxylic groups using the photochemical reaction of fatty acids is proposed and preliminary XPS results are presented. Moreover, preliminary results for DNA obtained from a rolling circle amplification (RCA-DNA) process and spiked in a realistic amplification buffer are presented.

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Tuberculosis (TB) is the leading global cause of death from a single infectious agent. Registered incidence rates are low, especially in low-resource countries with weak health systems, due to the disadvantages of current diagnostic techniques. A major effort is directed to develop a point-of-care (POC) platform to reduce TB deaths with a prompt and reliable low-cost technique. In the frame of the European POCKET Project, a novel POC platform for the direct and noninvasive detection of TB in human urine was developed. The photonic sensor chip is integrated in a disposable cartridge and is based on a highly sensitive Mach-Zehnder Interferometer (MZI) transducer combined with an on-chip spectral filter. The required elements for the readout are integrated in an instrument prototype, which allows real-time monitoring and data processing. In this work, the novel POC platform has been employed for the direct detection of lipoarabinomannan (LAM), a lipopolysaccharide found in the mycobacterium cell wall. After the optimization of several parameters, a limit of detection of 475 pg/mL (27.14 pM) was achieved using a direct immunoassay in undiluted human urine in less than 15 min. A final validation of the technique was performed using 20 clinical samples from TB patients and healthy donors, allowing the detection of TB in people regardless of HIV coinfection. The results show excellent correlation to those obtained with standard techniques. These promising results demonstrate the high sensitivity, specificity and applicability of our novel POC platform, which could be used during routine check-ups in developing countries.

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Cone-beam CTs (CBCTs) installed on a linear accelerator can be used to provide fast and accurate automatic six degrees of freedom (6DoF) vector displacement information of the patient position just prior to radiotherapy. These displacement corrections can be made with 6DoF couches, which are primarily used for patient setup correction during stereotactic treatments. When position corrections are performed daily prior to treatment, the correction is deemed "online". However, the interface between the first generation 6DoF couches and the imaging software is suboptimal. The system requires the user to select manually the patient and type the match result by hand. The introduction of 6DoF setup correction for treatments, other than stereotactic radiotherapy, is hindered by both the high workload associated with the online protocol and the interface issues. For these reasons, we developed software that fully integrates the 6DoF couch with the linear accelerator. To further reduce both the workload and imaging dose, three off-line 6DoF correction protocols were analyzed. While the protocols require significantly less imaging, the analysis assessed their ability to reduce the systematic rotation setup correction. CBCT scans were acquired for 19 patients with intracranial meningioma. The total number of CBCT scans was 856, acquired before and after radiotherapy treatment fractions. The patient positions were corrected online using a 6DoF robotic couch. The effects on the residual rotational setup error for three off-line protocols were simulated. The three protocols used were two known off-line protocols, the no action level (NAL) and the extended no action level (eNAL), and one new off-line protocol (eNAL++). The residual setup errors were compared using the systematic and random components of the total setup error. The reduction of the rotational setup error of these protocols was optimized with respect to the required workload (i.e., number of CBCTs required). Rotational errors up to 3.2° were found after initial patient setup. The eNAL++ protocol achieved a reduction of the systematic rotational setup error similar to that of the online protocol (pitch from 0.8° to 0.3°), while requiring 70% fewer CBCTs. With a 6DoF robotic couch, translation, and rotation patient position corrections can be performed off-line to reduce the systematic setup error, workload, and patient scan dose.

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A microcavity-based deoxyribonucleic acid (DNA) optical biosensor is demonstrated for the first time using synthetic sapphire for the optical cavity. Transmitted and elastic scattering intensity at 1510 nm are analyzed from a sapphire microsphere (radius 500 µm, refractive index 1.77) on an optical fiber half coupler. The 0.43 nm angular mode spacing of the resonances correlates well with the optical size of the sapphire sphere. Probe DNA consisting of a 36-mer fragment was covalently immobilized on a sapphire microsphere and hybridized with a 29-mer target DNA. Whispering gallery modes (WGMs) were monitored before the sapphire was functionalized with DNA and after it was functionalized with single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA). The shift in WGMs from the surface modification with DNA was measured and correlated well with the estimated thickness of the add-on DNA layer. It is shown that ssDNA is more uniformly oriented on the sapphire surface than dsDNA. In addition, it is shown that functionalization of the sapphire spherical surface with DNA does not affect the quality factor (Q . ≈ 04) of the sapphire microspheres. The use of sapphire is especially interesting because this material is chemically resilient, biocompatible, and widely used for medical implants.

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