Discovery and validation of serologic biomarkers for the diagnosis and prognosis of invasive candidiasis by computational immunomics

Invasive candidiasis (IC) is an opportunistic systemic mycosis caused by Candida species (commonly Candida albicans) that continues to pose a significant public health problem worldwide. Despite great advances in antifungal therapy and changes in clinical practices, IC remains a major infectious cause of morbidity and mortality in severely immunocompromised or critically ill patients, and further accounts for substantial healthcare costs. Its impact on patient clinical outcome and economic burden could be ameliorated by timely initiation of appropriate antifungal therapy. However, early detection of IC is extremely difficult because of its unspecific clinical signs and symptoms, and the inadequate accuracy and time delay of the currently available diagnostic or risk stratification methods. In consequence, the diagnosis of IC is often attained in advanced stages of infection (leading to delayed therapeutic interventions and ensuing poor clinical outcomes) or, unfortunately, at autopsy. In addition to the difficulties encountered in diagnosing IC at an early stage, the initial therapeutic decision-making process is also hindered by the insufficient accuracy of the currently available tools for predicting clinical outcomes in individual IC patients at presentation. Therefore, it is not surprising that clinicians are generally unable to early detect IC, and identify those IC patients who are most likely to suffer fatal clinical outcomes and may benefit from more personalized therapeutic strategies at presentation. Better diagnostic and prognostic biomarkers for IC are thus needed to improve the clinical management of this life-threatening and costly opportunistic fungal infection...

Design and Applications of a Decade-Spanning Terahertz Frequency Comb Spectrometer: Doppler-limited Rotational Spectroscopy of Methanol and Methanol-OD

This thesis details the design and applications of a terahertz (THz) frequency comb spectrometer. The spectrometer employs two offset locked Ti:Sapphire femtosecond oscillators with repetition rates of approximately 80 MHz, offset locked at 100 Hz to continuously sample a time delay of 12.5 ns at a maximum time delay resolution of 15.6 fs. These oscillators emit continuous pulse trains, allowing the generation of a THz pulse train by the master, or pump, oscillator and the sampling of this THz pulse train by the slave, or probe, oscillator via the electro-optic effect. Collecting a train of 16 consecutive THz pulses and taking the Fourier transform of this pulse train produces a decade-spanning frequency comb, from 0.25 to 2.5 THz, with a comb tooth width of 5 MHz and a comb tooth spacing of ~80 MHz. This frequency comb is suitable for Doppler-limited rotational spectroscopy of small molecules. Here, the data from 68 individual scans at slightly different pump oscillator repetition rates were combined, producing an interleaved THz frequency comb spectrum, with a maximum interval between comb teeth of 1.4 MHz, enabling THz frequency comb spectroscopy.

The accuracy of the THz frequency comb spectrometer was tested, achieving a root mean square error of 92 kHz measuring selected absorption center frequencies of water vapor at 10 mTorr, and a root mean square error of 150 kHz in measurements of a K-stack of acetonitrile. This accuracy is sufficient for fitting of measured transitions to a model Hamiltonian to generate a predicted spectrum for molecules of interest in the fields of astronomy and physical chemistry. As such, the rotational spectra of methanol and methanol-OD were acquired by the spectrometer. Absorptions from 1.3 THz to 2.0 THz were compared to JPL catalog data for methanol and the spectrometer achieved an RMS error of 402 kHz, improving to 303 kHz when excluding low signal-to-noise absorptions. This level of accuracy compares favorably with the ~100 kHz accuracy achieved by JPL frequency multiplier submillimeter spectrometers. Additionally, the relative intensity performance of the THz frequency comb spectrometer is linear across the entire decade-spanning bandwidth, making it the preferred instrument for recovering lineshapes and taking absolute intensity measurements in the THz region. The data acquired by the Terahertz Frequency Comb Spectrometer for methanol-OD is of comparable accuracy to the methanol data and may be used to refine the fit parameters for the predicted spectrum of methanol-OD.

Design of an Experimental Rig to Characterize the Gust Response of Small Wind Turbines and Autorotating Seeds

This thesis investigates the rotational behavior of abstracted small-wind-turbine rotors exposed to a sudden increase in oncoming flow velocity, i.e. a gust. These rotors consisted of blades with aspect ratios characteristic of samara seeds, which are known for their ability to maintain autorotation in unsteady wind. The models were tested in a towing tank using a custom-built experimental rig. The setup was designed and constructed to allow for the measurement of instantaneous angular velocity of a rotor model towed at a prescribed kinematic profile along the tank. The conclusions presented in this thesis are based on the observed trends in effective angle-of-attack distribution, tip speed ratio, angular velocity, and time delay in the rotational response for each of rotors over prescribed gust cases. It was found that the blades with the higher aspect ratio had higher tip speed ratios and responded faster than the blades with a lower aspect ratio. The decrease in instantaneous tip speed ratio during the onset of a prescribed gust correlated with the time delay in each rotor model's rotational response. The time delays were found to increase nonlinearly with decreasing durations over which the simulated gusts occurred.

Modelling and PI Control of an Irrigation Canal

The main goal of this paper is to expose and validate a methodology to design efficient automatic controllers for irrigation canals, based on the Saint-Venant model. This model-based methodology enables to design controllers at the design stage (when the canal is not already built). The methodology is applied on an experimental canal located in Portugal. First the full nonlinear PDE model is calibrated, using a single steady-state experiment. The model is then linearized around a functioning point, in order to design linear PI controllers. Two classical control strategies are tested (local upstream control and distant downstream control) and compared on the canal. The experimental results show the effectiveness of the model.

Effect of pulsed electromagnetic fields (pemfs) on muscle activity, tissue oxygenation and vo2 during exercise.

PEMF are a medical and non-invasive therapy successfully used for clinical treatments of bone disease, due to the piezoelectric effect that improve bone mass and density, by the stimulation of osteoblastogenesis, with modulation of calcium storages and mineral metabolism. PEMF enhance tissue oxygenation, microcirculation and angiogenesis, in rats and cells erythrocytes, in cells-free assay. Such responses could be caused by a modulation of nitric oxide signal and interaction between PEMF and Ca2+/NO/cGMP/PKG signal. PEMF improve blood flow velocity of smallest vein without changing their diameter. PEMF therapy helpful in patients with diabetes, due to increased microcirculation trough enhance capillary blood velocity and diameter. We investigated the influence of stimulation on muscular activity, tissue oxygenation and pulmonary VO2, during exercise, on different intensity, as heavy or moderate, different subjects, as a athlete or sedentary, and different sport activity, as a cycling or weightlifting. In athletes, we observed a tendency for a greater change and a faster kinetic of HHb concentration. PEMF increased the velocity and the quantity of muscle O2 available, leading to accelerate the HHb kinetics. Stimulation induced a bulk muscle O2 availability and a greater muscle O2 extraction, leading to a reduced time delay of the HHb slow component. Stimulation increased the amplitude of muscle activity under different conditions, likely caused by the effect of PEMF on contraction mechanism of muscular fibers, by the change of membrane permeability and Ca2+ channel conduction. In athletes, we observed an increase of overall activity during warm-up. In sedentary people, stimulation increased the magnitude of muscle activity during moderate constant-load exercise and warm-up. In athletes and weightlifters, stimulation caused an increase of blood lactate concentration during exercise, confirming a possible influence of stimulation on muscle activity and on glycolytic metabolism of type-II muscular fibers.

Discrete-time mean variance optimal control of linear systems with Markovian jumps and multiplicative noise

In this article, we consider the stochastic optimal control problem of discrete-time linear systems subject to Markov jumps and multiplicative noise under three kinds of performance criterions related to the final value of the expectation and variance of the output. In the first problem it is desired to minimise the final variance of the output subject to a restriction on its final expectation, in the second one it is desired to maximise the final expectation of the output subject to a restriction on its final variance, and in the third one it is considered a performance criterion composed by a linear combination of the final variance and expectation of the output of the system. We present explicit sufficient conditions for the existence of an optimal control strategy for these problems, generalising previous results in the literature. We conclude this article presenting a numerical example of an asset liabilities management model for pension funds with regime switching.

Demand response in electrical energy supply: an optimal real time pricing approach

In competitive electricity markets with deep concerns for the efficiency level, demand response programs gain considerable significance. As demand response levels have decreased after the introduction of competition in the power industry, new approaches are required to take full advantage of demand response opportunities. This paper presents DemSi, a demand response simulator that allows studying demand response actions and schemes in distribution networks. It undertakes the technical validation of the solution using realistic network simulation based on PSCAD. The use of DemSi by a retailer in a situation of energy shortage, is presented. Load reduction is obtained using a consumer based price elasticity approach supported by real time pricing. Non-linear programming is used to maximize the retailer’s profit, determining the optimal solution for each envisaged load reduction. The solution determines the price variations considering two different approaches, price variations determined for each individual consumer or for each consumer type, allowing to prove that the approach used does not significantly influence the retailer’s profit. The paper presents a case study in a 33 bus distribution network with 5 distinct consumer types. The obtained results and conclusions show the adequacy of the used methodology and its importance for supporting retailers’ decision making.

Energy efficient scheduling for cluster-tree wireless sensor networks with time-bounded data flows: application to IEEE 802.15.4/ZigBee

Cluster scheduling and collision avoidance are crucial issues in large-scale cluster-tree Wireless Sensor Networks (WSNs). The paper presents a methodology that provides a Time Division Cluster Scheduling (TDCS) mechanism based on the cyclic extension of RCPS/TC (Resource Constrained Project Scheduling with Temporal Constraints) problem for a cluster-tree WSN, assuming bounded communication errors. The objective is to meet all end-to-end deadlines of a predefined set of time-bounded data flows while minimizing the energy consumption of the nodes by setting the TDCS period as long as possible. Sinceeach cluster is active only once during the period, the end-to-end delay of a given flow may span over several periods when there are the flows with opposite direction. The scheduling tool enables system designers to efficiently configure all required parameters of the IEEE 802.15.4/ZigBee beaconenabled cluster-tree WSNs in the network design time. The performance evaluation of thescheduling tool shows that the problems with dozens of nodes can be solved while using optimal solvers.

Optimal approximation of fractional derivatives through discrete-time fractions using genetic algorithms

This study addresses the optimization of rational fraction approximations for the discrete-time calculation of fractional derivatives. The article starts by analyzing the standard techniques based on Taylor series and Padé expansions. In a second phase the paper re-evaluates the problem in an optimization perspective by tacking advantage of the flexibility of the genetic algorithms.

Measuring end-to-end delay in real-time auralisation systems

One of the major challenges in the development of an immersive system is handling the delay between the tracking of the user’s head position and the updated projection of a 3D image or auralised sound, also called end-to-end delay. Excessive end-to-end delay can result in the general decrement of the “feeling of presence”, the occurrence of motion sickness and poor performance in perception-action tasks. These latencies must be known in order to provide insights on the technological (hardware/software optimization) or psychophysical (recalibration sessions) strategies to deal with them. Our goal was to develop a new measurement method of end-to-end delay that is both precise and easily replicated. We used a Head and Torso simulator (HATS) as an auditory signal sensor, a fast response photo-sensor to detect a visual stimulus response from a Motion Capture System, and a voltage input trigger as real-time event. The HATS was mounted in a turntable which allowed us to precisely change the 3D sound relative to the head position. When the virtual sound source was at 90º azimuth, the correspondent HRTF would set all the intensity values to zero, at the same time a trigger would register the real-time event of turning the HATS 90º azimuth. Furthermore, with the HATS turned 90º to the left, the motion capture marker visualization would fell exactly in the photo-sensor receptor. This method allowed us to precisely measure the delay from tracking to displaying. Moreover, our results show that the method of tracking, its tracking frequency, and the rendering of the sound reflections are the main predictors of end-to-end delay.

Time is Running Out: The 2°C Target and Optimal Climate Policies

The quintessence of recent natural science studies is that the 2 degrees C target can only be achieved with massive emission reductions in the next few years. The central twist of this paper is the addition of this limited time to act into a non-perpetual real options framework analysing optimal climate policy under uncertainty. The window-of-opportunity modelling setup shows that the limited time to act may spark a trend reversal in the direction of low-carbon alternatives. However, the implementation of a climate policy is evaded by high uncertainty about possible climate pathways.

New delay-dependent stability criteria for uncertain neutral systems with mixed time-varying delays and nonlinear perturbations

The problem of stability analysis for a class of neutral systems with mixed time-varying neutral, discrete and distributed delays and nonlinear parameter perturbations is addressed. By introducing a novel Lyapunov-Krasovskii functional and combining the descriptor model transformation, the Leibniz-Newton formula, some free-weighting matrices, and a suitable change of variables, new sufficient conditions are established for the stability of the considered system, which are neutral-delay-dependent, discrete-delay-range dependent, and distributeddelay-dependent. The conditions are presented in terms of linear matrix inequalities (LMIs) and can be efficiently solved using convex programming techniques. Two numerical examples are given to illustrate the efficiency of the proposed method

Efficient T cell activation requires an optimal dwell-time of interaction between the TCR and the pMHC complex.

Cytotoxic T cell (CTL) activation by antigen requires the specific detection of peptide-major histocompatibility class I (pMHC) molecules on the target-cell surface by the T cell receptor (TCR). We examined the effect of mutations in the antigen-binding site of a Kb-restricted TCR on T cell activation, antigen binding and dissociation from antigen.These parameters were also examined for variants derived from a Kd-restricted peptide that was recognized by a CTL clone. Using these two independent systems, we show that T cell activation can be impaired by mutations that either decrease or increase the binding half-life of the TCR-pMHC interaction. Our data indicate that efficient T cell activation occurs within an optimal dwell-time range of TCR-pMHC interaction. This restricted dwell-time range is consistent with the exclusion of either extremely low or high affinity T cells from the expanded population during immune responses.