Systematic structural studies of iron superoxide dismutases from human parasites and a statistical coupling analysis of metal binding specificity

Superoxide dismutases (SODs) are a crucial class of enzymes in the combat against intracellular free radical damage. They eliminate superoxide radicals by converting them into hydrogen peroxide and oxygen. In spite of their very different life cycles and infection strategies, the human parasites Plasmodium falciparum, Trypanosoma cruzi and Trypanosoma brucei are known to be sensitive to oxidative stress. Thus the parasite Fe-SODs have become attractive targets for novel drug development. Here we report the crystal structures of FeSODs from the trypanosomes T. brucei at 2.0 angstrom and T. cruzi at 1.9 angstrom resolution, and that from P. falciparum at a higher resolution (2.0 angstrom) to that previously reported. The homodimeric enzymes are compared to the related human MnSOD with particular attention to structural aspects which are relevant for drug design. Although the structures possess a very similar overall fold, differences between the enzymes at the entrance to the channel which leads to the active site could be identified. These lead to a slightly broader and more positively charged cavity in the parasite enzymes. Furthermore, a statistical coupling analysis (SCA) for the whole Fe/MnSOD family reveals different patterns of residue coupling for Mn and Fe SODs, as well as for the dimeric and tetrameric states. In both cases, the statistically coupled residues lie adjacent to the conserved core surrounding the metal center and may be expected to be responsible for its fine tuning, leading to metal ion specificity.

Crystal structure and statistical coupling analysis of highly glycosylated peroxidase from royal palm tree (Roystonea regia)

Royal palm tree peroxidase (RPTP) is a very stable enzyme in regards to acidity, temperature, H(2)O(2), and organic solvents. Thus, RPTP is a promising candidate for developing H(2)O(2)-sensitive biosensors for diverse applications in industry and analytical chemistry. RPTP belongs to the family of class III secretory plant peroxidases, which include horseradish peroxidase isozyme C, soybean and peanut peroxidases. Here we report the X-ray structure of native RPTP isolated from royal palm tree (Roystonea regia) refined to a resolution of 1.85 angstrom. RPTP has the same overall folding pattern of the plant peroxidase superfamily, and it contains one heme group and two calcium-binding sites in similar locations. The three-dimensional structure of RPTP was solved for a hydroperoxide complex state, and it revealed a bound 2-(N-morpholino) ethanesulfonic acid molecule (MES) positioned at a putative substrate-binding secondary site. Nine N-glycosylation sites are clearly defined in the RPTP electron-density maps, revealing for the first time conformations of the glycan chains of this highly glycosylated enzyme. Furthermore, statistical coupling analysis (SCA) of the plant peroxidase superfamily was performed. This sequence-based method identified a set of evolutionarily conserved sites that mapped to regions surrounding the heme prosthetic group. The SCA matrix also predicted a set of energetically coupled residues that are involved in the maintenance of the structural folding of plant peroxidases. The combination of crystallographic data and SCA analysis provides information about the key structural elements that could contribute to explaining the unique stability of RPTP. (C) 2009 Elsevier Inc. All rights reserved.

Statistical coupling analysis of aspartic proteinases based on crystal structures of the Trichoderma reesei enzyme and its complex with pepstatin A

The crystal structures of an aspartic proteinase from Trichoderma reesei (TrAsP) and of its complex with a competitive inhibitor, pepstatin A, were solved and refined to crystallographic R-factors of 17.9% (R(free)=21.2%) at 1.70 angstrom resolution and 15.81% (R(free) = 19.2%) at 1.85 angstrom resolution, respectively. The three-dimensional structure of TrAsP is similar to structures of other members of the pepsin-like family of aspartic proteinases. Each molecule is folded in a predominantly beta-sheet bilobal structure with the N-terminal and C-terminal domains of about the same size. Structural comparison of the native structure and the TrAsP-pepstatin complex reveals that the enzyme undergoes an induced-fit, rigid-body movement upon inhibitor binding, with the N-terminal and C-terminal lobes tightly enclosing the inhibitor. Upon recognition and binding of pepstatin A, amino acid residues of the enzyme active site form a number of short hydrogen bonds to the inhibitor that may play an important role in the mechanism of catalysis and inhibition. The structures of TrAsP were used as a template for performing statistical coupling analysis of the aspartic protease family. This approach permitted, for the first time, the identification of a network of structurally linked residues putatively mediating conformational changes relevant to the function of this family of enzymes. Statistical coupling analysis reveals coevolved continuous clusters of amino acid residues that extend from the active site into the hydrophobic cores of each of the two domains and include amino acid residues from the flap regions, highlighting the importance of these parts of the protein for its enzymatic activity. (C) 2008 Elsevier Ltd. All rights reserved.

Damage tolerance analysis for Blackshape BS 115 programme, EASA CS VLA & CS-23

The thesis project has been developed in partnership with the Design Department of Blackshape Spa, a carbon – fiber ultra – light airplane company in Monopoli (Bari, Italy). The main goal is the assessment of a starting point for a damage tolerant concept during the design and certification phases of the Blackshape BS 115 airplane, with respect to EASA CS VLA & CS 23 Regulations. This approach has been carried out starting from an initial literary review as far as the way of modeling composites fractures is concerned. Further on, three finite element models have been generated and implemented in order to simulate defects occurring during manufacturing and service phases. At last, the procedures of non - destructive inspections have been taken into account, in order to establish how to investigate primary structures defects and delaminations during maintenance.

Does published orthodontic research account for clustering effects during statistical data analysis?

In orthodontics, multiple site observations within patients or multiple observations collected at consecutive time points are often encountered. Clustered designs require larger sample sizes compared to individual randomized trials and special statistical analyses that account for the fact that observations within clusters are correlated. It is the purpose of this study to assess to what degree clustering effects are considered during design and data analysis in the three major orthodontic journals. The contents of the most recent 24 issues of the American Journal of Orthodontics and Dentofacial Orthopedics (AJODO), Angle Orthodontist (AO), and European Journal of Orthodontics (EJO) from December 2010 backwards were hand searched. Articles with clustering effects and whether the authors accounted for clustering effects were identified. Additionally, information was collected on: involvement of a statistician, single or multicenter study, number of authors in the publication, geographical area, and statistical significance. From the 1584 articles, after exclusions, 1062 were assessed for clustering effects from which 250 (23.5 per cent) were considered to have clustering effects in the design (kappa = 0.92, 95 per cent CI: 0.67-0.99 for inter rater agreement). From the studies with clustering effects only, 63 (25.20 per cent) had indicated accounting for clustering effects. There was evidence that the studies published in the AO have higher odds of accounting for clustering effects [AO versus AJODO: odds ratio (OR) = 2.17, 95 per cent confidence interval (CI): 1.06-4.43, P = 0.03; EJO versus AJODO: OR = 1.90, 95 per cent CI: 0.84-4.24, non-significant; and EJO versus AO: OR = 1.15, 95 per cent CI: 0.57-2.33, non-significant). The results of this study indicate that only about a quarter of the studies with clustering effects account for this in statistical data analysis.

Statistical shape analysis via principal factor analysis

Statistical shape analysis techniques commonly employed in the medical imaging community, such as active shape models or active appearance models, rely on principal component analysis (PCA) to decompose shape variability into a reduced set of interpretable components. In this paper we propose principal factor analysis (PFA) as an alternative and complementary tool to PCA providing a decomposition into modes of variation that can be more easily interpretable, while still being a linear efficient technique that performs dimensionality reduction (as opposed to independent component analysis, ICA). The key difference between PFA and PCA is that PFA models covariance between variables, rather than the total variance in the data. The added value of PFA is illustrated on 2D landmark data of corpora callosa outlines. Then, a study of the 3D shape variability of the human left femur is performed. Finally, we report results on vector-valued 3D deformation fields resulting from non-rigid registration of ventricles in MRI of the brain.

Optical Tolerance Analysis of the Multi-Beam Limb Viewing Instrument STEAMR

In this paper, we report on an optical tolerance analysis of the submillimeter atmospheric multi-beam limb sounder, STEAMR. Physical optics and ray-tracing methods were used to quantify and separate errors in beam pointing and distortion due to reflector misalignment and primary reflector surface deformations. Simulations were performed concurrently with the manufacturing of a multi-beam demonstrator of the relay optical system which shapes and images the beams to their corresponding receiver feed horns. Results from Monte Carlo simulations show that the inserts used for reflector mounting should be positioned with an overall accuracy better than 100 μm (~ 1/10 wavelength). Analyses of primary reflector surface deformations show that a deviation of magnitude 100 μm can be tolerable before deployment, whereas the corresponding variations should be less than 30 μm during operation. The most sensitive optical elements in terms of misalignments are found near the focal plane. This localized sensitivity is attributed to the off-axis nature of the beams at this location. Post-assembly mechanical measurements of the reflectors in the demonstrator show that alignment better than 50 μm could be obtained.

Fault Tolerance Analysis and Self-Healing Strategy of Autonomous, Evolvable Hardware Systems

This paper presents an analysis of the fault tolerance achieved by an autonomous, fully embedded evolvable hardware system, which uses a combination of partial dynamic reconfiguration and an evolutionary algorithm (EA). It demonstrates that the system may self-recover from both transient and cumulative permanent faults. This self-adaptive system, based on a 2D array of 16 (4×4) Processing Elements (PEs), is tested with an image filtering application. Results show that it may properly recover from faults in up to 3 PEs, that is, more than 18% cumulative permanent faults. Two fault models are used for testing purposes, at PE and CLB levels. Two self-healing strategies are also introduced, depending on whether fault diagnosis is available or not. They are based on scrubbing, fitness evaluation, dynamic partial reconfiguration and in-system evolutionary adaptation. Since most of these adaptability features are already available on the system for its normal operation, resource cost for self-healing is very low (only some code additions in the internal microprocessor core)

Role of the Department of Commerce in federal statistical gathering, analysis, and dissemination, and opportunities for reform and consolidation : hearing before the Subcommittee on Oversight of Government Management, Restructuring, and the District of Columbia of the Committee on Governmental Affairs, United States Senate, One Hundred Fifth Congress, first session, April 9, 1997.

Shipping list no.: 98-0027-P.

Genetic algorithms in statistical tolerancing

An important aspect in manufacturing design is the distribution of geometrical tolerances so that an assembly functions with given probability, while minimising the manufacturing cost. This requires a complex search over a multidimensional domain, much of which leads to infeasible solutions and which can have many local minima. As well, Monte-Carlo methods are often required to determine the probability that the assembly functions as designed. This paper describes a genetic algorithm for carrying out this search and successfully applies it to two specific mechanical designs, enabling comparisons of a new statistical tolerancing design method with existing methods. (C) 2003 Elsevier Ltd. All rights reserved.

A statistical-mechanical analysis of coded CDMA with regular LDPC codes

We analyze, using the replica method of statistical mechanics, the theoretical performance of coded code-division multiple-access (CDMA) systems in which regular low-density parity-check (LDPC) codes are used for channel coding.

Statistical mechanics analysis of LDPC coding in MIMO Gaussian channels

Using analytical methods of statistical mechanics, we analyse the typical behaviour of a multiple-input multiple-output (MIMO) Gaussian channel with binary inputs under low-density parity-check (LDPC) network coding and joint decoding. The saddle point equations for the replica symmetric solution are found in particular realizations of this channel, including a small and large number of transmitters and receivers. In particular, we examine the cases of a single transmitter, a single receiver and symmetric and asymmetric interference. Both dynamical and thermodynamical transitions from the ferromagnetic solution of perfect decoding to a non-ferromagnetic solution are identified for the cases considered, marking the practical and theoretical limits of the system under the current coding scheme. Numerical results are provided, showing the typical level of improvement/deterioration achieved with respect to the single transmitter/receiver result, for the various cases. © 2007 IOP Publishing Ltd.

Composite CDMA—a statistical mechanics analysis

Code division multiple access (CDMA) in which the spreading code assignment to users contains a random element has recently become a cornerstone of CDMA research. The random element in the construction is particularly attractive as it provides robustness and flexibility in utilizing multiaccess channels, whilst not making significant sacrifices in terms of transmission power. Random codes are generated from some ensemble; here we consider the possibility of combining two standard paradigms, sparsely and densely spread codes, in a single composite code ensemble. The composite code analysis includes a replica symmetric calculation of performance in the large system limit, and investigation of finite systems through a composite belief propagation algorithm. A variety of codes are examined with a focus on the high multi-access interference regime. We demonstrate scenarios both in the large size limit and for finite systems in which the composite code has typical performance exceeding those of sparse and dense codes at equivalent signal to noise ratio.