A flexible architecture for privacy-aware trust management

In service-oriented systems a constellation of services cooperate, sharing potentially sensitive information and responsibilities. Cooperation is only possible if the different participants trust each other. As trust may depend on many different factors, in a flexible framework for Trust Management (TM) trust must be computed by combining different types of information. In this paper we describe the TAS3 TM framework which integrates independent TM systems into a single trust decision point. The TM framework supports intricate combinations whilst still remaining easily extensible. It also provides a unified trust evaluation interface to the (authorization framework of the) services. We demonstrate the flexibility of the approach by integrating three distinct TM paradigms: reputation-based TM, credential-based TM, and Key Performance Indicator TM. Finally, we discuss privacy concerns in TM systems and the directions to be taken for the definition of a privacy-friendly TM architecture.\u

Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score

©2008 Pandit and Skolnick; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. This article is available from: http://www.biomedcentral.com/1471-2105/9/531doi:10.1186/1471-2105-9-531Background: Protein tertiary structure comparisons are employed in various fields of contemporary structural biology. Most structure comparison methods involve generation of an initial seed alignment, which is extended and/or refined to provide the best structural superposition between a pair of protein structures as assessed by a structure comparison metric. One such metric, the TM-score, was recently introduced to provide a combined structure quality measure of the coordinate root mean square deviation between a pair of structures and coverage. Using the TM-score, the TM-align structure alignment algorithm was developed that was often found to have better accuracy and coverage than the most commonly used structural alignment programs; however, there were a number of situations when this was not true. Results: To further improve structure alignment quality, the Fr-TM-align algorithm has been developed where aligned fragment pairs are used to generate the initial seed alignments that are then refined using dynamic programming to maximize the TM-score. For the assessment of the structural alignment quality from Fr-TM-align in comparison to other programs such as CE and TMalign, we examined various alignment quality assessment scores such as PSI and TM-score. The assessment showed that the structural alignment quality from Fr-TM-align is better in comparison to both CE and TM-align. On average, the structural alignments generated using Fr-TM-align have a higher TM-score (~9%) and coverage (~7%) in comparison to those generated by TM-align. Fr- TM-align uses an exhaustive procedure to generate initial seed alignments. Hence, the algorithm is computationally more expensive than TM-align. Conclusion: Fr-TM-align, a new algorithm that employs fragment alignment and assembly provides better structural alignments in comparison to TM-align. The source code and executables of Fr- TM-align are freely downloadable at: http://cssb.biology.gatech.edu/skolnick/files/FrTMalign/

Trajectory mapping: A tool for validation of trace gas observations

We investigate the effectiveness of trajectory mapping(TM) as a data validation tool. TM combines a dynamical model of the atmosphere with trace gas observations to provide more statistically robust estimates of instrument performance over much broader geographic areas than traditional techniques are able to provide. We present four detailed case studies selected so that the traditional techniques are expected to work well. In each case the TM results are equivalent to or improve upon the measurement comparisons performed with traditional approaches. The TM results are statistically more robust than those achieved using traditional approaches since the TM comparisons occur over a much larger range of geophysical variability. In the first case study we compare ozone data from the Halogen Occultation Experiment (HALOE) with Microwave Limb Sounder(MLS). TM comparisons appear to introduce little to no error as compared to the traditional approach. In the second case study we compare ozone data from HALOE with that from the Stratospheric Aerosol and Gas Experiment TT(SAGE TT). TM results in differences of less than 5% as compared to the traditional approach at altitudes between 18 and 25 km and less than 10% at altitudes between 25 and 40 km.In the third case study we show that ozone profiles generated from HALOE data using TM compare well with profiles from five European ozonesondes. In the fourth case study we evaluate the precision of MLS H20 using TM and find typical precision uncertainties of 3-7% at most latitudes and altitudes. The TM results agree well with previous estimates but are the result of a global analysis of the data rather than an analysis in the limited latitude bands in which traditional approaches work. Finally, sensitivity studies using the MLS H20 data show the following: (1) a combination of forward and backward trajectory calculations minimize uncertainties in isentropic TM; (2) although the uncertainty of the technique increases with trajectory duration,TM calculations of up to 14 days can provide reliable information for use in data validation studies; (3) a correlation coincidence criterion of 400 km produces the best TM results under most circumstances; (4) TM performs well compared to (and sometimes better than) traditional approaches at all latitudes and in most seasons and; (5) TM introduces no statistically significant biases at altitudes between 22 and 40 km

Modified protein expression in the tectorial membrane of the cochlea reveals roles for the striated sheet matrix

The tectorial membrane (TM) of the mammalian cochlea is a complex extracellular matrix which, in response to acoustic stimulation, displaces the hair bundles of outer hair cells (OHCs), thereby initiating sensory transduction and amplification. Here, using TM segments from the basal, high-frequency region of the cochleae of genetically modified mice (including models of human hereditary deafness) with missing or modified TM proteins, we demonstrate that frequency-dependent stiffening is associated with the striated sheet matrix (SSM). Frequency-dependent stiffening largely disappeared in all three TM mutations studied where the SSM was absent either entirely or at least from the stiffest part of the TM overlying the OHCs. In all three TM mutations, dissipation of energy is decreased at low (<8 kHz) and increased at high (>8 kHz) stimulus frequencies. The SSM is composed of polypeptides carrying fixed charges, and electrostatic interaction between them may account for frequency-dependent stiffness changes in the material properties of the TM. Through comparison with previous in vivo measurements, it is proposed that implementation of frequency-dependent stiffening of the TM in the OHC attachment region facilitates interaction among tones, backward transmission of energy, and amplification in the cochlea

Metastases risk in thin cutaneous melanoma: Prognostic value of clinical-pathologic characteristics and mutation profile

Background: A high percentage of patients with thin melanoma (TM), defined as lesions with Breslow thickness ≤1 mm, presents excellent long-term survival, however, some patients develop metastases. Existing prognostic factors cannot reliably differentiate TM patients at risk for metastases. Objective: We aimed at characterizing the clinical-pathologic and mutation profile of metastatic and not-metastatic TM in order to distinguish lesions at risk of metastases. Methods: Clinical-pathologic characteristics were recorded for the TM cases analyzed. We used a Next Generation Sequencing (NGS) multi-gene panel to characterize TM for multiple somatic mutations. Results: A statistically significant association emerged between the presence of metastases and Breslow thickness ≥0.6 mm (p=0.003). None of TM with lymph-node involvement had Breslow thickness < 0.6 mm. Somatic mutations were identified in 19 of 21 TM analyzed (90.5%). No mutations were observed in two not-metastatic cases with the lowest Breslow thickness (≤0.4 mm), whereas mutations in more than one gene were detected in one metastatic case with the highest Breslow thickness (1.00 mm). Conclusion: Our study indicates Breslow thickness ≥0.6 mm as a valid prognostic factor to distinguish TM at risk for metastases