Efficient analysis of protein expression by using two-dimensional electrophoresis (2-DE) data relies on the use of automated image processing techniques. The overall success of this research depends critically on the accuracy and the reliability of the analysis software. In addition, the software has a profound effect on the interpretation of the results obtained, and the amount of user intervention demanded during the analysis. The choice of analysis software that best meets specific needs is therefore of interest to the research laboratory. In this paper we compare two advanced analysis software packages, PDQuest and Progenesis. Their evaluation is based on quantitative tests at three different levels of standard 2-DE analysis: spot detection, gel matching and spot quantitation. As test materials we use three gel sets previously used in a similar comparison of Z3 and Melanie, and three sets of gels from our own research. It was observed that the quality of the test gels critically influences the spot detection and gel matching results. Both packages were sensitive to the parameter or filter settings with respect to the tendency of finding true positive and false positive spots. Quantitation results were very accurate for both analysis software packages.

We discuss quantum annealing of the two-dimensional transverse-field Ising model on a D-Wave device, encoded on L × L lattices with L ≤ 32. Analyzing the residual energy and deviation from maximal magnetization in the final classical state, we find an optimal L dependent annealing rate v for which the two quantities are minimized. The results are well described by a phenomenological model with two powers of v and L-dependent prefactors to describe the competing effects of reduced quantum fluctuations (for which we see evidence of the Kibble-Zurek mechanism) and increasing noise impact when v is lowered. The same scaling form also describes results of numerical solutions of a transverse-field Ising model with the spins coupled to noise sources. We explain why the optimal annealing time is much longer than the coherence time of the individual qubits.The prospect of simulating theoretical quantum manybody Hamiltonians with controllable engineered systems is now an important motivation for atomic and quantum device physics [1-3]. Systems explored for creating such "synthetic quantum matter" include ultracold gases [4][5][6][7][8][9], photonic devices [10][11][12][13][14], polaritons [15], and trapped ions [16][17][18][19][20][21][22]. Another emerging simulation platform is large arrays of superconducting qubits [23][24][25][26][27][28][29], which were originally envisioned in the context of quantum annealing (QA) as efficient solvers of classical optimization problems mapped to Ising like Hamiltonians [30][31][32][33][34][35][36][37][38][39][40][41][42][43]. To reach the classical ground state (the problem solution) in a QA process, strong quantum fluctuations are initially induced by applying a transverse field, which is quasi-adiabatically reduced to zero. QA devices operating according to this principle have entered industrial production and applications beyond the academic setting [23], motivated by the hope of more efficient solutions of NP-hard problems [33,44] and, more recently, quantum enhanced machine learning [45,46]. It is still unclear what systems (classes of optimization problems) are amenable to significant speedup, and to what extent QA can be realized in actual devices [41,[47][48][49][50][51][52][53][54][55].While the question of quantum speedups is essential, the potential of using QA devices as generic quantum many-body emulators motivates a broader range of investigations into the devices and how they can be exploited for probing various quantum phenomena. As an example, recently a QA device produced by D-Wave Systems was used in an impressive study of a quantum phase transition of a quantum spin glass [29]. An important question in applications of QA devices, for optimization or quantum simulation, is whether the desired adiabatic evolution is sufficiently realized in the presence of noise (the environment) and finite annealing time. This question motivates studies of the dependence of measured properties on the annealing time [27,[57][58][59], which also impacts the effects of noise. For this...

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Separable binary-phase array illuminators for fan-out up to 1024 x 1024 and ~65% two-dimensional efficiency are designed by simulated annealing with constraints for maximizing the minimum feature size. A new nonseparable trapezoidal coding technique is introduced and applied to design high-efficiency (~75%-80%) array generators for fan-out up to 16 x 16. A rigorous electromagnetic diffraction theory is used to evaluate the range of validity of the scalar designs (both grating period and input angle are considered), to analyze fabrication errors (slanted groove walls and undercutting), and to design binary resonance-domain one-dimensional array generators with 90%-100% efficiency. Trapezoidal gratings for low fan-out (8 x 8), separable gratings for high fan-out (up to 128 x 128), and a 1 x 5 resonance domain (100% efficient) reflection grating are demonstrated experimentally.

Two-dimensional electrophoresis is a widely used method for separating a large number of proteins from complex protein mixtures and for revealing differential patterns of protein expressions. In the computer-assisted proteome research, the comparison of protein separation profiles involves several heuristic steps, ranging from protein spot detection to matching of unknown spots. An important prerequisite for efficient protein spot matching is the image warping step, where the geometric relationship between the gel profiles is modeled on the basis of a given set of known corresponding spots, so-called landmarks, and the locations of unknown spots are predicted using the optimized model. Traditionally, polynomial functions together with least squares optimization has been used, even though this approach is known to be incapable of modeling all the complex distortions inherent in electrophoretic data. To satisfy the need of more flexible gel distortion correction, a hierarchical grid transformation method with stochastic optimization is presented. The method provides an adaptive multiresolution model between the gels, and good correction performance in the practical cross-validation tests suggests that automatic warping of gel images could be based on this approach. We believe that the proposed model also has significance in the ultimate comparison of corresponding protein spots since the matching process should benefit from the closeness of the true spot pairs.

Utilization of movement data from mobile sports tracking applications is affected by its inherent biases and sensitivity, which need to be understood when developing value-added services for, e.g., application users and city planners. We have developed a method for generating a privacy-preserving heat map with user diversity (ppDIV), in which the density of trajectories, as well as the diversity of users, is taken into account, thus preventing the bias effects caused by participation inequality. The method is applied to public cycling workouts and compared with privacy-preserving kernel density estimation (ppKDE) focusing only on the density of the recorded trajectories and privacy-preserving user count calculation (ppUCC), which is similar to the quadrat-count of individual application users. An awareness of privacy was introduced to all methods as a data pre-processing step following the principle of k-Anonymity. Calibration results for our heat maps using bicycle counting data gathered by the city of Helsinki are good (R 2 N 0.7) and raise high expectations for utilizing heat maps in a city planning context. This is further supported by the diurnal distribution of the workouts indicating that, in addition to sports-oriented cyclists, many utilitarian cyclists are tracking their commutes. However, sports tracking data can only enrich official in-situ counts with its high spatio-temporal resolution and coverage, not replace them.

A computer-generated binary amplitude hologram is used to transform an initial Gaussian electromagnetic field with spherical phase front at 310 GHz into a non-diffracting Bessel beam. The beam profile is measured with the help of a near field scanner. In contrast to the situation in the optical region, both amplitude and phase information is readily obtainable from the generated field.

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