Predicting class I major histocompatibility complex (MHC) binders using multivariate statistics:comparison of discriminant analysis and multiple linear regression

The accurate in silico identification of T-cell epitopes is a critical step in the development of peptide-based vaccines, reagents, and diagnostics. It has a direct impact on the success of subsequent experimental work. Epitopes arise as a consequence of complex proteolytic processing within the cell. Prior to being recognized by T cells, an epitope is presented on the cell surface as a complex with a major histocompatibility complex (MHC) protein. A prerequisite therefore for T-cell recognition is that an epitope is also a good MHC binder. Thus, T-cell epitope prediction overlaps strongly with the prediction of MHC binding. In the present study, we compare discriminant analysis and multiple linear regression as algorithmic engines for the definition of quantitative matrices for binding affinity prediction. We apply these methods to peptides which bind the well-studied human MHC allele HLA-A*0201. A matrix which results from combining results of the two methods proved powerfully predictive under cross-validation. The new matrix was also tested on an external set of 160 binders to HLA-A*0201; it was able to recognize 135 (84%) of them.

Transfer characteristics and propagation effects of a multi-resonance ring resonator-based optical device

We describe the linear and nonlinear optical transfer characteristics of a multi-resonance device consisting of two optical ring resonators coupled one to the other and to an optical waveguide. The propagation effects displayed by the device are compared with those of a sequence of fundamental ring resonators coupled to a waveguide.

Fiber Bragg grating Sensor interrogation using chirped fiber grating-based sagnac loop

We have investigated numerically and experimentally a fiber Bragg grating (FBG) sensor interrogation scheme utilizing a linear chirped grating-based Sagnac loop as a wavelength-dependent receiver. The scheme is suitable for both static and dynamic sensor interrogation with advantages of stable and linear readout response and easily-adjustable sensing resolution and dynamic range. Static and dynamic strain resolutions as high as ± 4.2 με and 0.406 με/√ Hz have been demonstrated using this scheme.

NLSE-based model of a random distributed feedback fiber laser

In this work we propose a NLSE-based model of power and spectral properties of the random distributed feedback (DFB) fiber laser. The model is based on coupled set of non-linear Schrödinger equations for pump and Stokes waves with the distributed feedback due to Rayleigh scattering. The model considers random backscattering via its average strength, i.e. we assume that the feedback is incoherent. In addition, this allows us to speed up simulations sufficiently (up to several orders of magnitude). We found that the model of the incoherent feedback predicts the smooth and narrow (comparing with the gain spectral profile) generation spectrum in the random DFB fiber laser. The model allows one to optimize the random laser generation spectrum width varying the dispersion and nonlinearity values: we found, that the high dispersion and low nonlinearity results in narrower spectrum that could be interpreted as four-wave mixing between different spectral components in the quasi-mode-less spectrum of the random laser under study could play an important role in the spectrum formation. Note that the physical mechanism of the random DFB fiber laser formation and broadening is not identified yet. We investigate temporal and statistical properties of the random DFB fiber laser dynamics. Interestingly, we found that the intensity statistics is not Gaussian. The intensity auto-correlation function also reveals that correlations do exist. The possibility to optimize the system parameters to enhance the observed intrinsic spectral correlations to further potentially achieved pulsed (mode-locked) operation of the mode-less random distributed feedback fiber laser is discussed.

Broadband tunable all-fiber polarization interference filter based on 45° tilted fiber gratings

We have theoretically and experimentally designed and demonstrated an all-fiber polarization interference filter (AFPIF), which is formed by a polarization-maintaining (PM) fiber cavity structure utilizing two 45° tilted fiber gratings (45°-TFGs) inscribed by UV laser on the PM fiber. Such a filter could generate modulated transmission of linear polarization status. It has been revealed that the modulation depth of the transmission depends on the coupling angle between the 45°-TFGs and the PM fiber cavity. When the two 45°-TFGs in PM fiber are oriented at 45° to the principal axis of the PM fiber cavity, the maximum modulation depth is achievable. Due to the thermal effect on birefringence of the PM fiber, the AFPIF can be tuned over a broad wavelength range just by simple thermal tuning of the cavity. The experiment results show that the temperature tuning sensitivity is proportional to the length ratio of the PM fiber cavity under heating. For 18 and 40 cm long cavities with 6 cm part under heating, the thermal tuning sensitivities are 0.616 and 0.31 nm/° C, respectively, which are almost two orders of magnitude higher than normal fiber Bragg gratings. © 1983-2012 IEEE.

Probabilistic multiple model neural network based leak detection system:experimental study

This paper presents an effective decision making system for leak detection based on multiple generalized linear models and clustering techniques. The training data for the proposed decision system is obtained by setting up an experimental pipeline fully operational distribution system. The system is also equipped with data logging for three variables; namely, inlet pressure, outlet pressure, and outlet flow. The experimental setup is designed such that multi-operational conditions of the distribution system, including multi pressure and multi flow can be obtained. We then statistically tested and showed that pressure and flow variables can be used as signature of leak under the designed multi-operational conditions. It is then shown that the detection of leakages based on the training and testing of the proposed multi model decision system with pre data clustering, under multi operational conditions produces better recognition rates in comparison to the training based on the single model approach. This decision system is then equipped with the estimation of confidence limits and a method is proposed for using these confidence limits for obtaining more robust leakage recognition results.

Hybrid tilted fiber grating based refractive index and liquid level sensing system

We report a refractive index (RI) and liquid level sensing system based on a hybrid grating structure comprising of a 45° and an 81° tilted fiber gratings (TFGs) that have been inscribed into a single mode fiber in series. In this structure, the 45°-TFG is used as a polarizer to filter out the transverse electric (TE) component and enable the 81°-TFG operating at single polarization for RI and level sensing. The experiment results show a lower temperature cross-sensitivity, only about 7.33 pm/°C, and a higher RI sensitivity, being around 180 nm/RIU at RI=1.345 and 926 nm/RIU at RI=1.412 region, which are significantly improved in comparison with long period fiber gratings. The hybrid grating structure has also been applied as a liquid level sensor, showing 3.06 dB/mm linear peak ratio sensitivity.

Fibre laser using a microchannel based loss tuning element for refractive index sensing

We have proposed and demonstrated a fibre laser system using a microchannel as a cavity loss tuning element for surrounding medium refractive index (SRI) sensing. A ~6µm width microchannel was created by femtosecond (fs) laser inscription assisted chemical etching in the cavity fibre, which offers a direct access to the external liquids. When the SRI changes, the microchannel behaves as a loss tuning element, hence modulating the laser cavity loss and output power. The results indicate that the presented laser sensing system has a linear response to the SRI with a sensitivity in the order of 10-5. Using higher pump power and more sensitive photodetector, the SRI sensitivity could be further enhanced.

High performance liquid level monitoring system based on polymer fiber Bragg gratings embedded in silicone rubber diaphragm

Liquid-level sensing technologies have attracted great prominence, because such measurements are essential to industrial applications, such as fuel storage, flood warning and in the biochemical industry. Traditional liquid level sensors are based on electromechanical techniques; however they suffer from intrinsic safety concerns in explosive environments. In recent years, given that optical fiber sensors have lots of well-established advantages such as high accuracy, costeffectiveness, compact size, and ease of multiplexing, several optical fiber liquid level sensors have been investigated which are based on different operating principles such as side-polishing the cladding and a portion of core, using a spiral side-emitting optical fiber or using silica fiber gratings. The present work proposes a novel and highly sensitive liquid level sensor making use of polymer optical fiber Bragg gratings (POFBGs). The key elements of the system are a set of POFBGs embedded in silicone rubber diaphragms. This is a new development building on the idea of determining liquid level by measuring the pressure at the bottom of a liquid container, however it has a number of critical advantages. The system features several FBG-based pressure sensors as described above placed at different depths. Any sensor above the surface of the liquid will read the same ambient pressure. Sensors below the surface of the liquid will read pressures that increase linearly with depth. The position of the liquid surface can therefore be approximately identified as lying between the first sensor to read an above-ambient pressure and the next higher sensor. This level of precision would not in general be sufficient for most liquid level monitoring applications; however a much more precise determination of liquid level can be made by linear regression to the pressure readings from the sub-surface sensors. There are numerous advantages to this multi-sensor approach. First, the use of linear regression using multiple sensors is inherently more accurate than using a single pressure reading to estimate depth. Second, common mode temperature induced wavelength shifts in the individual sensors are automatically compensated. Thirdly, temperature induced changes in the sensor pressure sensitivity are also compensated. Fourthly, the approach provides the possibility to detect and compensate for malfunctioning sensors. Finally, the system is immune to changes in the density of the monitored fluid and even to changes in the effective force of gravity, as might be obtained in an aerospace application. The performance of an individual sensor was characterized and displays a sensitivity (54 pm/cm), enhanced by more than a factor of 2 when compared to a sensor head configuration based on a silica FBG published in the literature, resulting from the much lower elastic modulus of POF. Furthermore, the temperature/humidity behavior and measurement resolution were also studied in detail. The proposed configuration also displays a highly linear response, high resolution and good repeatability. The results suggest the new configuration can be a useful tool in many different applications, such as aircraft fuel monitoring, and biochemical and environmental sensing, where accuracy and stability are fundamental. © (2015) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.

Energy-based damage and fracture framework for viscoelastic asphalt concrete

A framework based on the continuum damage mechanics and thermodynamics of irreversible processes using internal state variables is used to characterize the distributed damage in viscoelastic asphalt materials in the form of micro-crack initiation and accumulation. At low temperatures and high deformation rates, micro-cracking is considered as the source of nonlinearity and thus the cause of deviation from linear viscoelastic response. Using a non-associated damage evolution law, the proposed model shows the ability to describe the temperature-dependent processes of micro-crack initiation, evolution and macro-crack formation with good comparison to the material response in the Superpave indirect tensile (IDT) strength test.

Practical photovoltaic simulator with a cross tackling control strategy based on the first-hand duty cycle processing

This paper proposes a methodological scheme for the photovoltaic (PV) simulator design. With the advantages of a digital controller system, linear interpolation is proposed for precise fitting with higher computational efficiency. A novel control strategy that directly tackles two different duty cycles is proposed and implemented to achieve a full-range operation including short circuit (SC) and open circuit (OC) conditions. Systematic design procedures for both hardware and algorithm are explained, and a prototype is built. Experimental results confirm an accurate steady state performance under different load conditions, including SC and OC. This low power apparatus can be adopted for PV education and research with a limited budget.