Support vector classification of proteomic profile spectra based on feature extraction with the bi-orthogonal discrete wavelet transform

Automatic classification of high-resolution mass spectrometry data has increasing potential to support physicians in diagnosis of diseases like cancer. The proteomic data exhibit variations among different disease states. A precise and reliable classification of mass spectra is essential for a successful diagnosis and treatment. The underlying process to obtain such reliable classification results is a crucial point. In this paper such a method is explained and a corresponding semi automatic parameterization procedure is derived. Thereby a simple straightforward classification procedure to assign mass spectra to a particular disease state is derived. The method is based on an initial preprocessing stage of the whole set of spectra followed by the bi-orthogonal discrete wavelet transform (DWT) for feature extraction. The approximation coefficients calculated from the scaling function exhibit a high peak pattern matching property and feature a denoising of the spectrum. The discriminating coefficients, selected by the Kolmogorov–Smirnov test are finally used as features for training and testing a support vector machine with both a linear and a radial basis kernel. For comparison the peak areas obtained with the it ClinProt-System ¹ [33] were analyzed using the same support vector machines. The introduced approach was evaluated on clinical MALDI-MS data sets with two classes each originating from cancer studies. The cross validated error rates using the wavelet coefficients where better than those obtained from the peak areas².     

Bringing law and order to IEEE 802.11 networks—A case for DiscoSec

To improve the tarnished reputation of WLAN security, the new IEEE 802.11i standard provides means for mutual user authentication and assures confidentiality of user data. However, the IEEE 802.11 link-layer is still highly vulnerable to a plethora of simple, yet effective attacks which further jeopardize the already fragile security of wireless communications.Some of these vulnerabilities are related to limited hardware capabilities of access points and their abuse may result in serious degradation of control over the wireless connection, which, especially in the case of broadcast communication, allows for client hijacking attacks. Although these issues are known and their impact is expected to be less prevalent on modern equipment, this work demonstrates the opposite. In our experimental analysis, we tested frequently used access points, and by forcing them to operate on their performance limits, we identified significant operational anomalies and demonstrated their impact on security by implementing a novel version of the Man-In-The-Middle attack, to which we refer as the Muzzle attack.Secondly, this work describes DiscoSec, a solution for “patching” WLANs against a variety of such link-layer attacks. DiscoSec provides DoS-resilient key exchange, an efficient frame authentication, and a performance-oriented implementation. By means of extensive real-world measurements DiscoSec is evaluated, showing that even on very resource-limited devices the network throughput is decreased by only 22% compared to the throughput without any authentication, and by 6% on more performance-capable hardware. To demonstrate its effectiveness, DiscoSec is available as an open-source IEEE 802.11 device driver utilizing well-established cryptographic primitives provided by the Linux Crypto API and OpenSSL library.     

A combinatorial intra-enterprise exchange for logistics services

The exchange of cargo capacities is a well established approach in logistics. However, only few logistics marketplaces are able to take into consideration synergies that can be generated by combining different transportation routes of different logistics carrierps. In order to exploit these synergies, we designed and implemented the combinatorial exchange mechanism ComEx for the intra-enterprise exchange of delivery orders in a logistics company organized in a profit center structure. Each profit center is able to release delivery orders to an adjacent profit center if the geographic locations of the customers allow for a reduced-cost delivery by the adjacent profit center. We demonstrate that by using the ComEx mechanism, the total cost of transportation of our logistics company can be reduced by up to 14%. Since our iterative auction mechanism is very complex and therefore resource-intensive, we reduce the complexity by applying a convex hull approach combined with a distance-based cost estimator.

Nonlinear vehicle side-slip estimation with friction adaptation

A nonlinear observer for estimation of the longitudinal velocity, lateral velocity, and yaw rate of a vehicle, designed for the purpose of vehicle side-slip estimation, is modified and extended in order to work for different road surface conditions. The observer relies on a road-tire friction model and is therefore sensitive to changes in the adhesion characteristics of the road surface. The friction model is parametrized with a single friction parameter, and an update law is designed. The adaptive observer is proven to be uniformly globally asymptotically stable and uniformly locally exponentially stable under a persistency-of-excitation condition and a set of technical assumptions, using results related to Matrosov's theorem. The observer is tested on recorded data from two test vehicles and shows good results on a range of road surfaces.     

A graph-based framework for model-driven optimization facilitating impact analysis of mutation operator properties

Optimization problems in software engineering typically deal with structures as they occur in the design and maintenance of software systems. In model-driven optimization (MDO), domain-specific models are used to represent these structures while evolutionary algorithms are often used to solve optimization problems. However, designing appropriate models and evolutionary algorithms to represent and evolve structures is not always straightforward. Domain experts often need deep knowledge of how to configure an evolutionary algorithm. This makes the use of model-driven meta-heuristic search difficult and expensive. We present a graph-based framework for MDO that identifies and clarifies core concepts and relies on mutation operators to specify evolutionary change. This framework is intended to help domain experts develop and study evolutionary algorithms based on domain-specific models and operators. In addition, it can help in clarifying the critical factors for conducting reproducible experiments in MDO. Based on the framework, we are able to take a first step toward identifying and studying important properties of evolutionary operators in the context of MDO. As a showcase, we investigate the impact of soundness and completeness at the level of mutation operator sets on the effectiveness and efficiency of evolutionary algorithms.

     

Long‐term effects of angiotensin II blockade with irbesartan on inflammatory markers in hemodialysis patients: A randomized double blind placebo controlled trial (SAFIR study)

Introduction: Low‐grade chronic inflammation is common in hemodialysis (HD) patients. Previous studies suggest an anti‐inflammatory effect of angiotensin II receptor blocker (ARB) treatment. The aim of this study was to compare the effect of ARB vs. placebo on plasma concentrations of inflammatory markers in HD patients. Methods: Adult HD patients were randomized for double‐blind treatment with the ARB irbesartan 150–300 mg/day or placebo. At baseline, 1 week, 3, 6, 9, and 12 months plasma high sensitivity C‐reactive protein (hsCRP), interleukin (IL)?1β, IL‐6, IL‐8, IL‐18, and transforming growth factor‐β (TGF‐β) were measured using Luminex and enzyme‐linked immunosorbent assay (ELISA) technology. Findings: Eighty‐two patients were randomized (placebo/ARB: 41/41). The groups did not differ in initial levels of any of the inflammatory markers (placebo/ARB median(range)): hsCRP 3.3(0.2–23.4)/2.7(0.2–29.6) μg/mL; IL‐1β 1.1(0.0–45.9)/1.1(0.0‐7.2) pg/mL; IL‐6 10(1–90)/12(1–84) pg/mL; IL‐8 31(9–134)/34(5–192) pg/mL; IL‐18 364(188–1343)/377(213–832) pg/mL; TGF‐β 3.2(0.8–13.9)/3.6(1.3–3.8) ng/mL. Overall, there was no significant difference in hsCRP, IL‐6, IL‐8, and TGF‐β between placebo and ARB‐treated patients during the study period, and hsCRP, IL‐6, IL‐8, and TGF‐β were relatively stable during the study period (P ≥ 0.18 in all tests for parallel curves, equal levels, and constant levels). The IL‐1β level was slightly different in the two groups over time, but not significantly (P = 0.09 in test for parallel curves) and it was also relatively stable during the study period (P ≥ 0.49 in tests for equal levels and constant level). IL‐18 was the only inflammatory marker which was not constant during the study period (P = 0.001 in test for constant level), but there was no significant difference between placebo and ARB‐treated (P ≥ 0.51 in tests for parallel curves and equal levels). Discussion: Inflammatory biomarkers were neither acutely, nor in the long‐term significantly affected by the ARB irbesartan. Our findings suggest that ARB treatment in HD patients does not offer protective anti‐inflammatory effects.     

Quality of life development during initial hemodialysis therapy and association with loss of residual renal function

Introduction: Health related quality of life (HRQOL) is markedly reduced in hemodialysis patients compared to the general population. We investigated the course of self‐reported HRQOL over time and the association with selected factors, focusing on changes in glomerular filtration rate (GFR). Methods: Eighty‐two newly started hemodialysis patients from the SAFIR cohort filled out the Kidney Disease Quality of Life Short Form Version 1.3 (KDQOL‐SF^TM) questionnaire at baseline, 6 and 12 months. The SAFIR study was a randomized, placebo‐controlled, double‐blind intervention study, examining the effects of the angiotensin II receptor blocker irbesartan. HRQOL was a secondary outcome measure. Main inclusion criteria: Dialysis vintage <1 year, left ventricular ejection fraction >30% and urinary output >300 mL/day. GFR was measured with mean creatinine and urea clearance from 24‐hour urine collections at baseline, 6 and 12 months. Findings: Irbesartan treatment did not affect HRQOL. Patients were pooled into one group for further analyses. Decline in GFR correlated significantly with decreasing HRQOL over time. HRQOL was stable over time, with a slight nonsignificant tendency toward improved HRQOL. The largest HRQOL‐differences (positive values equal improved HRQOL) observed during the 12 month study period were (mean[95% confidence interval]): Burden of kidney disease:6.4[?2.2;15.0], Role limitations‐physical:12.7[?2.1;27.5], and Role limitations‐emotional:9.7[?5.2;24.6]. Comorbidity, especially diabetes, hospital admissions, female gender, and age were strongly associated with lower HRQOL in cross sectional analysis. Discussion: Preservation of residual renal function seems to be important for HRQOL. In newly started HD patients, HRQOL showed little change after 12 months. HRQOL was negatively affected by comorbidity, especially diabetes, hospital admissions, female gender, and age.     

Cytosolic Calcium Concentration Changes in Neuronal Cells Under Clinorotation and in Parabolic Flight Missions

All life on earth has been established under conditions of stable gravity of 1g. Nevertheless, in numerous experiments the direct gravity dependence of biological processes has been shown on all levels of organization, from single molecules to humans. To study the effects especially of microgravity on biological systems, a variety of platforms are available, from drop towers to the ISS. Due to the costs of these platforms and their limited availability, as an alternative, numerous simulators have been developed for so called “simulated” microgravity. A classical systems is a clinostat, basically rotating a sample around one axis, and by integration of the gravity vector for 360° arguing that thus the effects of gravity are depleted. Indeed, a variety of studies has shown that taking out the direction of gravity from a biological system often results in consequences similar to the exposure of the system to real microgravity. Nevertheless, the opposite has been shown, too, and as a consequence the relevance of clinostats in microgravity research is still under discussion. To get some more insight into this problem we have constructed a small fluorescence clinostat and have studied the effects of clinorotation on the cytosolic calcium concentration of neuroglioma cells. The results have been compared to experiments with identical cells in real microgravity, utilizing parabolic flight missions. Our results show that in case of a cell suspension used in a small florescence clinostat within a tube diameter of 2mm, the effects of clinorotation are comparable to those under real microgravity, both showing a significant increase in intracellular calcium concentration.