Column and batch reactive transport experiment parameter estimation using a genetic algorithm

This paper focuses on the application of a genetic algorithm (GA) in estimating the fate and transport parameters of a reacting solute from the column and batch experiments involving a saturated porous medium. A program is developed using C++ to model the column and batch data using kinetically controlled one- or two-site sorption models including linear and/or nonlinear forms. The objective of the algorithm is to minimize the sum of squared differences between the measured and modeled solute concentration data associated with column effluent (i.e., “breakthrough curves”). The GA is capable of estimating transport and reactions parameters such as forward and reverse reaction rates and parameters of the nonlinear reaction models, from a given set of measured data. Further simulations have been performed to estimate the appropriate configurations of the GA, which assist the method in estimating the fate and transport parameters more efficiently. It is shown that a wide range of the GA parameters can lead to convergence to appropriate estimations. The results obtained from this study show that the capability of GAs to fit the column and batch experiment data is promising.     

Aberrant protein expression in plasma and kidney tissue during experimental obstructive nephropathy

Kidney failure is a major health problem worldwide. Patients with end-stage renal disease require intensive medical support by dialysis or kidney transplantation. Current methods for diagnosis of kidney disease are either invasive or insensitive, and renal function may decline by as much as 50% before it can be detected using current techniques. The goal of this study was, therefore, to identify biomarkers of kidney disease (associated with renal fibrosis) that can be used for the development of a non-invasive clinical test for early disease detection. We utilized two protein-profiling technologies (SELDI-TOF MS and 2-D) to screen the plasma and kidney proteome for aberrantly expressed proteins in an experimental mouse model of unilateral uretric obstruction, which mimics the pathology of human renal disease. Several differentially regulated proteins were detected at the plasma level of day-3-obstructed animals, which included serum amyloid A1, fibrinogen α, haptoglobin precursor protein, haptoglobin and major urinary proteins 11 and 8. Differentially expressed proteins detected at the tissue level included ras-like activator protein 2, haptoglobin precursor protein, malate dehydrogenase, α enolase and murine urinary protein (all p<0.05 versus controls). Immunohistochemistry was used to confirm the up-regulation of fibrinogen. Interestingly, these proteins are largely separated into four major classes: (i) acute-phase reactants (ii) cell-signaling molecules (iii) molecules involved in cell growth and metabolism and (iv) urinary proteins. These results provide new insights into the pathology of obstructive nephropathy and may facilitate the development of specific assay(s) to detect and monitor renal fibrosis.     

Mammogram Learning System for Breast Cancer Diagnosis Using Deep Learning SVM

The most common form of cancer for women is breast cancer. Recent advances in medical imaging technologies increase the use of digital mammograms to diagnose breast cancer. Thus, an automated computerized system with high accuracy is needed. In this study, an efficient Deep Learning Architecture (DLA) with a Support Vector Machine (SVM) is designed for breast cancer diagnosis. It combines the ideas from DLA with SVM. The state-of-the-art Visual Geometric Group (VGG) architecture with 16 layers is employed in this study as it uses the small size of 3 × 3 convolution filters that reduces system complexity. The softmax layer in VGG assumes that the training samples belong to exactly only one class, which is not valid in a real situation, such as in medical image diagnosis. To overcome this situation, SVM is employed instead of the softmax layer in VGG. Data augmentation is also employed as DLA usually requires a large number of samples. VGG model with different SVM kernels is built to classify the mammograms. Results show that the VGG-SVM model has good potential for the classification of Mammographic Image Analysis Society (MIAS) database images with an accuracy of 98.67%, sensitivity of 99.32%, and specificity of 98.34%.     

Adapting application execution in CMPs using helper threads

In parallel to the changes in both the architecture domain–the move toward chip multiprocessors (CMPs)–and the application domain–the move toward increasingly data-intensive workloads–issues such as performance, energy efficiency and CPU availability are becoming increasingly critical. The CPU availability can change dynamically due to several reasons such as thermal overload, increase in transient errors, or operating system scheduling. An important question in this context is how to adapt, in a CMP, the execution of a given application to CPU availability change at runtime. Our paper studies this problem, targeting the energy-delay product (EDP) as the main metric to optimize. We first discuss that, in adapting the application execution to the varying CPU availability, one needs to consider the number of CPUs to use, the number of application threads to accommodate and the voltage/frequency levels to employ (if the CMP has this capability). We then propose to use helper threads to adapt the application execution to CPU availability change in general with the goal of minimizing the EDP. The helper thread runs parallel to the application execution threads and tries to determine the ideal number of CPUs, threads and voltage/frequency levels to employ at any given point in execution. We illustrate this idea using four applications (Fast Fourier Transform, MultiGrid, LU decomposition and Conjugate Gradient) under different execution scenarios. The results collected through our experiments are very promising and indicate that significant EDP reductions are possible using helper threads. For example, we achieved up to 66.3%, 83.3%, 91.2%, and 94.2% savings in EDP when adjusting all the parameters properly in applications FFT, MG, LU, and CG, respectively. We also discuss how our approach can be extended to address multi-programmed workloads.     

Proteomic examination of Leishmania chagasi plasma membrane proteins: Contrast between avirulent and virulent (metacyclic) parasite forms

Purpose: About two million new cases of leishmaniasis with 50 000 associated deaths occur worldwide each year. Promastigotes of the causative Leishmania spp. develop from the procyclic stage to the highly virulent metacyclic stage within the sand fly vector. We hypothesized that proteins important for promastigote virulence might be uniquely represented in the plasma membrane of metacyclic, but not procyclic, promastigotes. Experimental design: Procyclic (logarithmic) promastigotes and purified metacyclic promastigotes from stationary phase cultures of Leishmania chagasi were used to prepare membrane preparations either by surface biotinylation‐streptavidin affinity separation or by octyl glucoside detergent extraction. Results: These membrane fractions were enriched over 130‐ and 250‐fold, respectively, as estimated by Western blotting for the plasma membrane's major surface protease. Hundreds or dozens of proteins were identified by LC‐MS/MS in the surface biotinylation or detergent extraction, respectively. Confocal microscopy suggested the difference between the lists was due to the fact that proteins localized both on the surface membrane and within the flagellar pocket were accessible to surface biotinylation, whereas only proteins on the membrane were obtained by detergent extraction. Using detergent extraction, we found different proteins were present in membranes of the procyclic stage compared to metacyclic stage promastigotes. Several dozen were stage specific. Conclusions and clinical relevance: These data provide a foundation for identifying virulence factors in the plasma membranes of Leishmania spp. promastigotes during metacyclogenesis.     

Automatic detection of breast cancers in mammograms using structured support vector machines

Breast cancer is one of the most common cancers diagnosed in women. Large margin classifiers like the support vector machine (SVM) have been reported effective in computer-assisted diagnosis systems for breast cancers. However, since the separating hyperplane determination exclusively relies on support vectors, the SVM is essentially a local classifier and its performance can be further improved. In this work, we introduce a structured SVM model to determine if each mammographic region is normal or cancerous by considering the cluster structures in the training set. The optimization problem in this new model can be solved efficiently by being formulated as one second order cone programming problem. Experimental evaluation is performed on the Digital Database for Screening Mammography (DDSM) dataset. Various types of features, including curvilinear features, texture features, Gabor features, and multi-resolution features, are extracted from the sample images. We then select the salient features using the recursive feature elimination algorithm. The structured SVM achieves better detection performance compared with a well-tested SVM classifier in terms of the area under the ROC curve.     

Leader’s dilemma game: An experimental design for cyber insider threat research

One of the problems with insider threat research is the lack of a complete 360° view of an insider threat dataset due to inadequate experimental design. This has prevented us from modeling a computational system to protect against insider threat situations. This paper provides a contemporary methodological approach for using online games to simulate insider betrayal for predictive behavioral research. The Leader’s Dilemma Game simulates an insider betrayal scenario for analyzing organizational trust relationships, providing an opportunity to examine the trustworthiness of focal individuals, as measured by humans as sensors engaging in computer-mediated communication. This experimental design provides a window into trustworthiness attribution that can generate a rigorous and relevant behavioral dataset, and contributes to building a cyber laboratory that advances future insider threat study.     

Optimization of Geoscience Laser Altimeter System waveform metrics to support vegetation measurements

The Geoscience Laser Altimeter System (GLAS) has collected over 250 million measurements of vegetation height over forests globally. Accurate vegetation heights can be determined using waveform metrics that include vertical extent and extent of the waveform's trailing and leading edges. All three indices are highly dependent upon the signal strength, background noise and signal-to-noise ratio of the waveform, as the background noise contribution to the waveforms has to be removed before their calculation. Over the last six years, GLAS has collected data during thirteen observation periods using illumination from three different lasers. The power levels of these lasers have changed over time, resulting in variable signal power and noise characteristics. Atmospheric conditions vary continuously, also influencing signal power and noise.To minimize these effects, we optimized a noise coefficient which could be constant or vary according to observation period or noise metric. This parameter is used with the mean and standard deviation of the background noise to determine a noise level threshold that is removed from each waveform. An optimization analysis was used with a global dataset of waveforms that are near-coincident with waveforms from other observation periods; the goal of the optimization was to minimize the difference in vertical extent between spatially overlapping GLAS observations. Optimizations based on absolute difference in height led to situations in which the total extent was minimized as well; further optimizations reduced a normalized difference in height extent. The simplest optimizations were based on a constant value to be applied to all observations; noise coefficients of 2.7, 3.2, 3.4 and 4.0 were determined for datasets consisting of global forests, global vegetation, forest in the legal Amazon basin and boreal forests respectively. Optimizations based on the power level or the signal-to-noise ratio of waveforms best minimized differences in waveform extent, decreasing the percent root mean squared height difference by 25-54% over the constant value approach. Further development of methods to ensure temporal consistency of waveform indices will be necessary to support long-term satellite lidar missions and will result in more accurate and precise estimates of canopy height.     

Fuzzy clustering of time series in the frequency domain

Traditional and fuzzy cluster analyses are applicable to variables whose values are uncorrelated. Hence, in order to cluster time series data which are usually serially correlated, one needs to extract features from the time series, the values of which are uncorrelated. The periodogram which is an estimator of the spectral density function of a time series is a feature that can be used in the cluster analysis of time series because its ordinates are uncorrelated. Additionally, the normalized periodogram and the logarithm of the normalized periodogram are also features that can be used. In this paper, we consider a fuzzy clustering approach for time series based on the estimated cepstrum. The cepstrum is the spectrum of the logarithm of the spectral density function. We show in our simulation studies for the typical generating processes that have been considered, fuzzy clustering based on the cepstral coefficients performs very well compared to when it is based on other features.