An intercomparison of bio-optical techniques for detecting dominant phytoplankton size class from satellite remote sensing

Satellite remote sensing of ocean colour is the only method currently available for synoptically measuring wide-area properties of ocean ecosystems, such as phytoplankton chlorophyll biomass. Recently, a variety of bio-optical and ecological methods have been established that use satellite data to identify and differentiate between either phytoplankton functional types (PFTs) or phytoplankton size classes (PSCs). In this study, several of these techniques were evaluated against in situ observations to determine their ability to detect dominant phytoplankton size classes (micro-, nano- and picoplankton). The techniques are applied to a 10-year ocean-colour data series from the SeaWiFS satellite sensor and compared with in situ data (6504 samples) from a variety of locations in the global ocean. Results show that spectral-response, ecological and abundance-based approaches can all perform with similar accuracy. Detection of microplankton and picoplankton were generally better than detection of nanoplankton. Abundance-based approaches were shown to provide better spatial retrieval of PSCs. Individual model performance varied according to PSC, input satellite data sources and in situ validation data types. Uncertainty in the comparison procedure and data sources was considered. Improved availability of in situ observations would aid ongoing research in this field.     

Parameterization of computational domain in isogeometric analysis: Methods and comparison

Parameterization of computational domain plays an important role in isogeometric analysis as mesh generation in finite element analysis. In this paper, we investigate this problem in the 2D case, i.e., how to parametrize the computational domains by planar B-spline surface from the given CAD objects (four boundary planar B-spline curves). Firstly, two kinds of sufficient conditions for injective B-spline parameterization are derived with respect to the control points. Then we show how to find good parameterization of computational domain by solving a constraint optimization problem, in which the constraint condition is the injectivity sufficient conditions of planar B-spline parameterization, and the optimization term is the minimization of quadratic energy functions related to the first and second derivatives of planar B-spline parameterization. By using this method, the resulted parameterization has no self-intersections, and the isoparametric net has good uniformity and orthogonality. After introducing a posteriori error estimation for isogeometric analysis, we propose r-refinement method to optimize the parameterization by repositioning the inner control points such that the estimated error is minimized. Several examples are tested on isogeometric heat conduction problem to show the effectiveness of the proposed methods and the impact of the parameterization on the quality of the approximation solution. Comparison examples with known exact solutions are also presented.     

Binding of the tautomeric forms of isoniazid-NAD adducts to the active site of the Mycobacterium tuberculosis enoyl-ACP reductase (InhA): a theoretical approach

The front-line antituberculosis drug isoniazid (INH) inhibits InhA, the NADH-dependent fatty acid biosynthesis enoyl ACP-reductase from Mycobacterium tuberculosis, via formation of covalent adducts with NAD (INH-NAD adducts). While ring tautomers were found the main species formed in solution, only the 4S chain INH-NAD tautomer was evidenced in the crystallized InhA:INH-NAD complex. In this study we attempted to explore the modes of interaction and energy binding of the different isomers placed in the active site of InhA with the help of various molecular modelling techniques. Ligand and enzyme models were generated with the help of the Vega ZZ program package. Resulting ligands were then docked into the InhA active site individually using computational automated docking package AUTODOCK 3.0.5. The more relevant docked conformations were then used to compute the interaction energy between the ligands and the InhA cavity. The AM1 Hamiltonian and the QM/MM ONIOM methodologies were used and the results compared. The various tautomers were found docked in almost the same place where INH-NAD was present as predicted by earlier X-ray crystallographic studies. However, some changes of ligand conformation and of the interactions ligand-protein were evidenced. The lower binding energy was observed for the 4S chain adduct that probably represents the effective active form of the INH-NAD adducts, as compared to the 4R epimer. The two 4S,7R and 4R,7S ring tautomers show intermediate and similar binding energies contrasting with their different experimental inhibitory potency on InhA. As a possible explanation based on calculated conformations, we formulated the hypothesis of an initial binding of the two ring tautomers to InhA followed by opening of only the ring hemiamidal 4S,7R tautomer (possibly catalyzed by Tyr158 phenolate basic group) to give the 4S chain INH-NAD tight-binding inhibitor. The predictions of ligand-protein interactions at the molecular level can be of primary importance in elucidating the mechanisms of action of isoniazid and InhA-related resistances, in identifying the effective mycobactericidal entities and, in further step, in the design of a new generation of antitubercular drugs.     

MetaMol: high-quality visualization of molecular skin surface

Modeling and visualizing molecular surfaces is an important and challenging task in bioinformatics. Such surfaces play an essential role in better understanding the chemical and physical properties of molecules. However, constructing and displaying molecular surfaces requires complex algorithms. In this article we introduce MetaMol, a new program that generates high-quality images in interactive time. In contrast with existing software that discretizes the surface with triangles or grids, our program is based on a GPU accelerated ray-casting algorithm that directly uses the piecewise-defined algebraic equation of the molecular skin surface. As a result, both better performances and higher quality are obtained.     

Top-down proteomic analysis by MALDI-TOF profiling: Concentration-independent biomarkers

Although numerous protein biomarkers have been correlated with advanced disease states, no new clinical assays have been developed. Goals often anticipate disease-specific protein changes that exceed values among healthy individuals, a property common to acute phase reactants. This review considers somewhat different approaches. It focuses on intact protein isoform ratios that present a biomarker without change in the total concentration of the protein. These will seldom be detected by peptide level analysis or by most antibody-based assays. For example, application of an inexpensive method to large sample groups resulted in observation of several polymorphisms, including the first structural polymorphism of apolipoprotein C1. Isoform distribution of this protein was altered and was eventually linked to increased obesity. Numerous other protein isoforms included C- and N-terminal proteolysis, changes of glycoisoform ratios and certain types of sulfhydryl oxidation. While many of these gave excellent statistical correlation with advanced disease, clinical utility was not apparent. More important may be that protein isoform ratios were very stable in each individual. Diagnosis by longitudinal analysis of the same individual might increase sensitivity of protein biomarkers by 20-fold or more. Protein changes that exceed the range of values found among healthy individuals may be uncommon.     

Roll manufacturing of flexible microfluidic devices in thin PMMA and COC foils by embossing and lamination

Microfluidics on foil is gaining momentum due to a number of advantages of employing thin films combined with the capability of cost-effective high-volume manufacturing of devices. In this work, ultra-thin, flexible Y-microreactors with microchannels of 100 μm width and 30 μm depth were fabricated in thermoplastic polymer foils. The fluidic pattern was hot roll embossed in 125 μm thick poly-methyl-methacrylate (PMMA) and 130 μm thick cyclic-olefin-copolymer (COC) films using a dry-etched microstructured silicon wafer as a flat embossing tool in a laminator. The sealing of the channels was performed with two different techniques, one based on lamination of SU8 dry film resist (DFR) and the other one based on spin-coated poly-dimethylsiloxane (PDMS). Testing of the interconnected microreactor was carried out using two dye colorant solutions to demonstrate mixing.     

Somatosensory Processing and Schizophrenia Liability: Proprioception, Exteroceptive Sensitivity, and Graphesthesia Performance in the Biological Relatives of Schizophrenia Patients.

In the present study, the authors examined somatosensory processing in 30 biological relatives of persons with schizophrenia (hereafter called "schizophrenia relatives"), 30 biological relatives of persons with bipolar affective disorder (psychiatric family control subjects), and 30 healthy control subjects with no family history of psychopathology. All 3 groups completed a weight discrimination task, a 2-point discrimination task, and a complex cognitive somatosensory task (i.e., graphesthesia). The schizophrenia relatives performed significantly worse on all 3 somatosensory tasks compared with both the healthy control subjects and the bipolar relatives. The healthy control subjects and psychiatric family control subjects showed no significant differences on any of the somatosensory tasks. Within the weight discrimination and 2-point discrimination tasks, schizophrenia relatives showed group differences on the d' index, the measure of sensitivity, whereas all 3 groups did not differ on lnβ, the measure of response bias, suggesting a genuine difference in weight and touch sensitivity. The d' value of the weight discrimination task was significantly associated with both the cognitive-perceptual factor and negative symptom factor of the clinical questionnaire (e.g., Schizotypal Personality Questionnaire; SPQ), whereas the 2-point discrimination d' value and graphesthesia scores were significantly associated only with the cognitive-perceptual factor of the SPQ. Implications for the possible relation between somatosensory task performance and schizophrenia liability are discussed. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Comparing the effects of text size and format on the readibility of computer-displayed Times New Roman and Arial text

Times New Roman and Arial typefaces in 10- and 12-point, dot-matrix and anti-aliased format conditions were compared for readability (accuracy, reading speed, and accuracy/reading speed), as well as perceptions of typeface legibility, sharpness, ease of reading, and general preference. In assessing readability, the 10-point anti-aliased Arial typeface was read slower than the other type conditions. Examining perceptions of typeface legibility, sharpness, and ease of reading detected significant effects for typeface, size, and format. Overall, the 12-point dot-matrix Arial typeface was preferred to the other typefaces. Recommendations for appropriate typeface combinations for computer-displayed text are discussed.     

An Autonomous Spacecraft Agent Prototype

This paper describes the New Millennium Remote Agent (NMRA) architecture for autonomous spacecraft control systems. The architecture supports challenging requirements of the autonomous spacecraft domain not usually addressed in mobile robot architectures, including highly reliable autonomous operations over extended time periods in the presence of tight resource constraints, hard deadlines, limited observability, and concurrent activity. A hybrid architecture, NMRA integrates traditional real-time monitoring and control with heterogeneous components for constraint-based planning and scheduling, robust multi-threaded execution, and model-based diagnosis and reconfiguration. Novel features of this integrated architecture include support for robust closed-loop generation and execution of concurrent temporal plans and a hybrid procedural/deductive executive.We implemented a prototype autonomous spacecraft agent within the architecture and successfully demonstrated the prototype in the context of a challenging autonomous mission scenario on a simulated spacecraft. As a result of this success, the integrated architecture has been selected to fly as an autonomy experiment on Deep Space One (DS-1), the first flight of NASA';s New Millennium Program (NMP), which will launch in 1998. It will be the first AI system to autonomously control an actual spacecraft.     

Management of imprecision and uncertainty for production activity control

The operational levels of production management, often called production activity control (PAC) or manufacturing process control, require increasing reaction capabilities in order to adapt the workshop management to the changes of its environment. It often implies giving more responsibilities to the low decision levels. However, the management of the corresponding degrees of freedom is generally unusual. In such a situation, decision support systems (DSSs) provide a way to reconcile the satisfaction of mid-level objectives and the reaction requirements. A conceptual model is described that provides a design framework for a PAC DSS. Since the available knowledge lies mainly in expertise, a DSS has been implemented using a knowledge-based system. The uncertainty and imprecision of the managed information led to the use of fuzzy logic as a modeling tool. Moreover, various inference semantics have been implemented in the expert rules because different kinds of reasoning have been identified. Two versions of the DSS are described and several examples of implemented reasoning processes are developed.