CASANDRA: a prototype implementation of a system of network progressive transmission of medical digital images

In this paper, a prototype for progressive transmission of medical digital 2D images through the network, called CASANDRA, is presented. The prototype consists of the server part and the client part. In the server part, the images are acquired, stored, computed their wavelet transform and the wavelet coefficients stored, then transmitted progressively, when required, via TCP to the client. In the client part, with the inverse wavelet transform, the received wavelet coefficients are used to build successive improved reconstructions of the image.This prototype has been implemented and is being tested in the Radiotherapy Service of the Valencia University Hospital (Valencia, Spain).     

Simple multichannel system for the measurement of the net water flux across biological tissues

This paper describes the development of a simple system for measurement of net water movement through biological membrane barriers. The system is based on the detection of a water meniscus inside a polyethylene tube, which reflects the water movement inside one hemichamber of a modified Ussing chamber containing a membrane barrier. The detection device consists of a commercial computer-controlled flat bed scanner and specifically developed software. This system allows one to perform a relatively high number of individual experiments per physical unit. It is a flexible and affordable device, which allows comparatively more information per unit to be obtained than previously described methods.     

Arity and alternation: a proper hierarchy in higher order logics

We study the effect of simultaneously bounding the maximal-arity of the higher-order variables and the alternation of quantifiers in higher-order logics, as to their expressive power on finite structures (or relational databases). Let $\mathit{AA}^i(r,m)$ be the class of (i?+?1)-th order logic formulae where all quantifiers are grouped together at the beginning of the formulae, forming m alternating blocks of consecutive existential and universal quantifiers, and such that the maximal-arity (a generalization of the concept of arity, not just the maximal of the arities of the quantified variables) of the higher-order variables is bounded by r. Note that, the order of the quantifiers in the prefix may be mixed. We show that, for every i?≥?1, the resulting $\mathit{AA}^i(r,m)$ hierarchy of formulae of (i?+?1)-th order logic is proper. This extends a result by Makowsky and Pnueli who proved that the same hierarchy in second-order logic is proper. In both cases the strategy used to prove the results consists in considering formulae which, represented as finite structures, satisfy themselves. As the well known diagonalization argument applies here, this gives rise, for each order i and each level of the $\mathit{AA}^i(r,m)$ hierarchy of arity and alternation, to a class of formulae which is not definable in that level, but which is definable in a higher level of the same hierarchy. We then use a similar argument to prove that the classes of $\Sigma^i_m \cup \Pi^i_m$ formulae in which the higher-order variables of all orders up to i?+?1 have maximal-arity at most r, also induce a proper hierarchy in each higher-order logic of order i?≥?3. It is not known whether the correspondent hierarchy in second-order logic is proper. Using the concept of finite model truth definitions introduced by M. Mostowski, we give a sufficient condition for that to be the case.     

Protein radial distribution function (P-RDF) and Bayesian-Regularized Genetic Neural Networks for modeling protein conformational stability: chymotrypsin inhibitor 2 mutants

Development of novel computational approaches for modeling protein properties is a main goal in applied Proteomics. In this work, we reported the extension of the radial distribution function (RDF) scores formalism to proteins for encoding 3D structural information with modeling purposes. Protein-RDF (P-RDF) scores measure spherical distributions on protein 3D structure of 48 amino acids/residues properties selected from the AAindex data base. P-RDF scores were tested for building predictive models of the change of thermal unfolding Gibbs free energy change (DeltaDeltaG) of chymotrypsin inhibitor 2 upon mutations. In this sense, an ensemble of Bayesian-Regularized Genetic Neural Networks (BRGNNs) yielded an optimum nonlinear model for the conformational stability. The ensemble predictor described about 84% and 70% variance of the data in training and test sets, respectively.     

Privacy-preserving boosting

We describe two algorithms, BiBoost (Bipartite Boosting) and MultBoost (Multiparty Boosting), that allow two or more participants to construct a boosting classifier without explicitly sharing their data sets. We analyze both the computational and the security aspects of the algorithms. The algorithms inherit the excellent generalization performance of AdaBoost. Experiments indicate that the algorithms are better than AdaBoost executed separately by the participants, and that, independently of the number of participants, they perform close to AdaBoost executed using the entire data set. Responsible Editor: Charu Aggarwal.     

Logical Representation of a Conceptual Model for Spatial Data Warehouses

The MultiDimER model is a conceptual model used for representing a multidimensional view of data for Data Warehouse (DW) and On-Line Analytical Processing (OLAP) applications. This model includes a spatial extension allowing spatiality in levels, hierarchies, fact relationships, and measures. In this way decision-making users can represent in an abstract manner their analysis needs without considering complex implementation issues and spatial OLAP tools developers can have a common vision for representing spatial data in a multidimensional model. In this paper we propose the transformation of a conceptual schema based on the MultiDimER constructs to an object-relational schema. We based our mapping on the SQL:2003 and SQL/MM standards giving examples of commercial implementation using Oracle 10g with its spatial extension. Further we use spatial integrity constraints to ensure the semantic equivalence of the conceptual and logical schemas. We also show some examples of Oracle spatial functions, including aggregation functions required for the manipulation of spatial data. The described mappings to the object-relational model along with the examples using a commercial system show the feasibility of implementing spatial DWs in current commercial DBMSs. Further, using integrated architectures, where spatial and thematic data is defined within the same DBMS, facilitates the system management simplifying data definition and manipulation.

Analysis of the HLA class I associated peptide repertoire in a hepatocellular carcinoma cell line reveals tumor-specific peptides as putative targets for immunotherapy

HLA class I molecules present peptides on the cell surface to CD8(+) T cells. The repertoire of peptides that associate to class I molecules represents the cellular proteome. Therefore, cells expressing different proteomes could generate different class I-associated peptide repertoires. A large number of peptides have been sequenced from HLA class I alleles, mostly from lymphoid cells. On the other hand, T cell immunotherapy is a goal in the fight against cancer, but the identification of T cell epitopes is a laborious task. Proteomic techniques allow the definition of putative T cell epitopes by the identification of HLA natural ligands in tumor cells. In this study, we have compared the HLA class I-associated peptide repertoire from the hepatocellular carcinoma (HCC) cell line SK-Hep-1 with that previously described from lymphoid cells. The analysis of the peptide pool confirmed that, as expected, the peptides from SK-Hep-1 derive from proteins localized in the same compartments as in lymphoid cells. Within this pool, we have identified 12 HLA class I peptides derived from HCC-related proteins. This confirms that tumor cell lines could be a good source of tumor associated antigens to be used, together with MS, to define putative epitopes for cytotoxic T cells from cancer patients.     

The tauola-photos-F environment for the TAUOLA and PHOTOS packages, release II

We present the system for maintaining the versions of two packages: the TAUOLA of τ-lepton decay and PHOTOS for radiative corrections in decays. The following features can be chosen in an automatic or semi-automatic way: (1) format of the common block HEPEVT; (2) version of the physics input (for TAUOLA): as published, as initialized by the CLEO collaboration, as initialized by the ALEPH collaboration (it is suggested to use this version only with the help of the collaboration advice), new optional parametrization of matrix elements in 4π decay channels; (3) type of application: stand-alone, universal interface based on the information stored in the HEPEVT common block including longitudinal spin effects in the elementary Z/γ^∗→τ⁺τ⁻ process, extended version of the standard universal interface including full spin effects in the H/A→τ⁺τ⁻ decay, interface for KKMC Monte Carlo, (4) random number generators; (5) compiler options. The last section of the paper contains documentation of the programs updates introduced over the last two years.

Program summary

Title of program:tauola-photos-F, release IICatalogue identifier:ADXO_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXO_v1_0Programs obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandComputer: PC running GNU/Linux operating systemProgramming languages and tools used:CPP: standard C-language preprocessor, GNU Make builder tool, also FORTRAN compilerNo. of lines in distributed program, including test data, etc.: 194 118No. of bytes in distributed program, including test data, etc.:2 481 234Distribution format: tar.gzCatalogue identifier:ADXO_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXO_v2_0No. of lines in distributed program, including test data, etc.:308 235No. of bytes in distributed program, including test data, etc.:2 988 363Distribution format:tar.gzDoes the new version supersede the previous version:YesNature of the physical problem: The code of Monte Carlo generators often has to be tuned to the needs of large HEP Collaborations and experiments. Usually, these modifications do not introduce important changes in the algorithm, but rather modify the initialization and form of the hadronic current in τ decays. The format of the event record (HEPEVT common block) used to exchange information between building blocks of Monte Carlo systems often needs modification. Thus, there is a need to maintain various, slightly modified versions of the same code. The package presented here allows the production of ready-to-compile versions of TAUOLA [S. Jadach, Z. Wa?s, R. Decker, J.H. Kühn, Comput. Phys. Comm. 76 (1993) 361; A.E. Bondar, et al., Comput. Phys. Comm. 146 (2002) 139] and PHOTOS [E. Barberio, Z. Wa?s, Comput. Phys. Comm. 79 (1994) 291] Monte Carlo generators with appropriate demonstration programs. The new algorithm, universal interface of TAUOLA to work with the HEPEVT common block, is also documented here. Finally, minor technical improvements of TAUOLA and PHOTOS are also listed.Method of solution: The standard UNIX tool: the C-language preprocessor is used to produce a ready-to-distribute version of TAUOLA and PHOTOS code. The final FORTRAN code is produced from the library of ‘pre-code’ that is included in the package.Reasons for new version: The functionality of the version of TAUOLA and PHOTOS changed over the last two years. The changes, and their reasons, are documented in Section 9, and our new papers cited in this section.Additional comments: The updated version includes new features described in Section 9 of the paper. PHOTOS and TAUOLA were first submitted to the library as separate programs. Summary details of these previous programs are obtainable from the CPC Program Library.Typical running time: Depends on the speed of the computer used and the demonstration program chosen. Typically a few seconds.     

The introduction of sit-stand worktables; aspects of attitudes, compliance and satisfaction

The introduction of sit-stand worktables was examined in this study. Purchasers at four companies were interviewed regarding preparations prior to purchase, follow-up after installation, and if expectations had been fulfilled. Personnel at the four companies answered a questionnaire examining use of the worktables' sit-stand function, and the influence of some variables on this. Utilisation of the sit-stand function was less than what could be expected to relieve static musculoskeletal loading during VDU work. Pain experienced during the past year, and education on the use of the worktable gave rise to modest increases in utilisation. Investment in sit-stand worktables was satisfactory to purchasers, in terms of providing flexible furniture to suit modern organisational dynamics. Users were, in general, positive to the worktables, but showed poor compliance in using them. User and purchaser satisfaction with regard to improving individual health ergonomics was questionable in respect of the low level of usage.