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.     

Models wagging the dog: are circuits constructed with disparate parameters?

In a recent article, Prinz, Bucher, and Marder (2004) addressed the fundamental question of whether neural systems are built with a fixed blueprint of tightly controlled parameters or in a way in which properties can vary largely from one individual to another, using a database modeling approach. Here, we examine the main conclusion that neural circuits indeed are built with largely varying parameters in the light of our own experimental and modeling observations. We critically discuss the experimental and theoretical evidence, including the general adequacy of database approaches for questions of this kind, and come to the conclusion that the last word for this fundamental question has not yet been spoken.     

Local Stability of an Endoreversible Heat Engine Working in an Ecological Regime

We present a local stability analysis of an endoreversible engine working in an ecological regime, for three common heat transfer laws. From our local stability analysis we conclude that the system is stable for every value of the heat conductivity g, the heat capacity C and the ratio of temperatures with T ₁ > T ₂. After a small perturbation the system decays exponentially to the steady state determined by two different relaxation times. We observe that the stability of the system improves as increases whereas the steady-state energetic properties of the engine decline. Moreover, we compare the stability properties of the engine working in the ecological regime and under maximum power output. Finally, qualitative phase-space portraits for the evolution of the system are presented for representative cases.     

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.     

Efficient computation of Morse-Smale complexes for three-dimensional scalar functions

The Morse-Smale complex is an efficient representation of the gradient behavior of a scalar function, and critical points paired by the complex identify topological features and their importance. We present an algorithm that constructs the Morse-Smale complex in a series of sweeps through the data, identifying various components of the complex in a consistent manner. All components of the complex, both geometric and topological, are computed, providing a complete decomposition of the domain. Efficiency is maintained by representing the geometry of the complex in terms of point sets.     

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 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.