Continuous GRASP with a local active-set method for bound-constrained global optimization

Global optimization seeks a minimum or maximum of a multimodal function over a discrete or continuous domain. In this paper, we propose a hybrid heuristic-based on the CGRASP and GENCAN methods-for finding approximate solutions for continuous global optimization problems subject to box constraints. Experimental results illustrate the relative effectiveness of CGRASP-GENCAN on a set of benchmark multimodal test functions.

A simplified minimal residual disease polymerase chain reaction method at early treatment points can stratify children with acute lymphoblastic leukemia into good and poor outcome groups

Background Minimal residual disease is an important independent prognostic factor in childhood acute lymphoblastic leukemia. The classical detection methods such as multiparameter flow cytometry and real-time quantitative polymerase chain reaction analysis are expensive, time-consuming and complex, and require considerable technical expertise. Design and Methods We analyzed 229 consecutive children with acute lymphoblastic leukemia treated according to the GBTLI-99 protocol at three different Brazilian centers. Minimal residual disease was analyzed in bone marrow samples at diagnosis and on days 14 and 28 by conventional homo/heteroduplex polymerase chain reaction using a simplified approach with consensus primers for IG and TCR gene rearrangements. Results At least one marker was detected by polymerase chain reaction in 96.4%, of the patients. By combining the minimal residual disease results obtained on days 14 and 28, three different prognostic groups were identified: minimal residual disease negative on days 14 and 28, positive on day 14/negative on day 28, and positive on both. Five-year event-free survival rates were 85%, 75.6%,, and 27.8%, respectively (p<0.0001). The same pattern of stratification held true for the group of intensively treated children. When analyzed in other subgroups of patients such as those at standard and high risk at diagnosis, those with positive B-derived CD10, patients positive for the TEL/AML1 transcript, and patients in morphological remission on a day 28 marrow, the event-free survival rate was found to be significantly lower in patients with positive minimal residual disease on day 28. Multivariate analysis demonstrated that the detection of minimal residual disease on day 28 is the most significant prognostic factor. Conclusions This simplified strategy for detection of minimal residual disease was feasible, reproducible, cheaper and simpler when compared with other methods, and allowed powerful discrimination between children with acute lymphoblastic leukemia with a good and poor outcome.

Continuum-continuum coupling and polarization potentials for weakly bound systems

We investigate the influence of couplings among continuum states in collisions of weakly bound nuclei. For this purpose, we compare cross sections for complete fusion, breakup, and elastic scattering evaluated by continuum discretized coupled channel (CDCC) calculations, including and not including these couplings. In our study, we discuss this influence in terms of the polarization potentials that reproduces the elastic wave function of the coupled channel method in single channel calculations. We find that the inclusion of couplings among continuum states renders the real part of the polarization potential more repulsive, whereas it leads to weaker absorption to the breakup channel. We show that the noninclusion of continuum-continuum couplings in CDCC calculations may lead to qualitative and quantitative wrong conclusions.

Crystallization and preliminary X-ray diffraction analysis of human IL-22 bound to its soluble decoy receptor IL-22BP

Interleukin-22 (IL-22) is a pleiotropic cytokine that is involved in inflammatory responses. Human IL-22 was incubated with its soluble decoy receptor IL-22BP (IL-22 binding protein) and the IL-22 -IL-22BP complex was crystallized in hanging drops using the vapour-diffusion method. Suitable crystals were obtained from polyethylene glycol solutions and diffraction data were collected to 2.75 angstrom resolution. The crystal belonged to the tetragonal space group P41, with unit-cell parameters a = b = 67.9, c = 172.5 angstrom, and contained two IL-22-IL- 22BP complexes per asymmetric unit.

Exploring the emission intensities of ICP OES aided by chemometrics in the geographical discrimination of mineral waters

A rapid method for classification of mineral waters is proposed. The discrimination power was evaluated by a novel combination of chemometric data analysis and qualitative multi-elemental fingerprints of mineral water samples acquired from different regions of the Brazilian territory. The classification of mineral waters was assessed using only the wavelength emission intensities obtained by inductively coupled plasma optical emission spectrometry (ICP OES), monitoring different lines of Al, B, Ba, Ca, Cl, Cu, Co, Cr, Fe, K, Mg, Mn, Na, Ni, P, Pb, S, Sb, Si, Sr, Ti, V, and Zn, and Be, Dy, Gd, In, La, Sc and Y as internal standards. Data acquisition was done under robust (RC) and non-robust (NRC) conditions. Also, the combination of signal intensities of two or more emission lines for each element were evaluated instead of the individual lines. The performance of two classification-k-nearest neighbor (kNN) and soft independent modeling of class analogy (SIMCA)-and preprocessing algorithms, autoscaling and Pareto scaling, were evaluated for the ability to differentiate between the various samples in each approach tested (combination of robust or non-robust conditions with use of individual lines or sum of the intensities of emission lines). It was shown that qualitative ICP OES fingerprinting in combination with multivariate analysis is a promising analytical tool that has potential to become a recognized procedure for rapid authenticity and adulteration testing of mineral water samples or other material whose physicochemical properties (or origin) are directly related to mineral content.

Landscape unit discrimination for pedological surveys by orbital spectral response

Landscape unit discrimination for pedological surveys by orbital spectral response. The objective of tins study was compare two soil survey methods. The first was performed by methods traditionally used to distinguish landscape units and soil class discrimination. The second was based on soil class distinction through orbital spectral response. In order to establish soil characteristics and their classification, soil samples were collected at two depths in a grid system, with a distance of 500 meters between points. With these samples, physical and chemical analyses were carried out. In the sampling points, the apparent reflectance of the soil, front the orbital image, was determined and, through cluster analysis landscape units were established. In order to evaluate the resemblance reliability between the landscape units established in each method, the Kappa index was used, the value set for the confusion matrix was 0.43, indicating high quality in the comparison, showing that the non-conventional method was as close as the one carried out by photointerpretation.

Hyperplane navigation: A method to set individual scores in fMRI group datasets

Recent studies have demonstrated that spatial patterns of fMRI BOLD activity distribution over the brain may be used to classify different groups or mental states. These studies are based on the application of advanced pattern recognition approaches and multivariate statistical classifiers. Most published articles in this field are focused on improving the accuracy rates and many approaches have been proposed to accomplish this task. Nevertheless, a point inherent to most machine learning methods (and still relatively unexplored in neuroimaging) is how the discriminative information can be used to characterize groups and their differences. In this work, we introduce the Maximum Uncertainty Linear Discrimination Analysis (MLDA) and show how it can be applied to infer groups` patterns by discriminant hyperplane navigation. In addition, we show that it naturally defines a behavioral score, i.e., an index quantifying the distance between the states of a subject from predefined groups. We validate and illustrate this approach using a motor block design fMRI experiment data with 35 subjects. (C) 2008 Elsevier Inc. All rights reserved.

Patient based method of assessing adverse events in clinical trials in rheumatology: the revised Stanford Toxicity Index

We describe the progress towards developing a patient rated toxicity index that meets all of the patient-important attributes defined by the OMERACT Drug Safety Working Party, These attributes are frequency, severity. importance to patient, importance to the clinician, impact on economics, impact on activities, and integration of adverse effects with benefits. The Stanford Toxicity Index (STI) has been revised to collect all attributes with the exception of impact on activities. However, since the STI is a part of the Health Assessment Questionnaire (HAQ). impact on activities is collected by the HAQ. In particular, a new question asks patients to rate overall satisfaction, taking into consideration both benefits and adverse effects. The nest step in the development of this tool is to ensure that the STI meets the OMERACT filter of truth, discrimination, and feasibility. Although truth and feasibility have been confirmed by comparisons within the ARAMIS database, discrimination needs to be assessed in clinical trials.

Lanczos subspace filter diagonalization: Homogeneous recursive filtering and a low-storage method for the calculation of matrix elements

We develop a new iterative filter diagonalization (FD) scheme based on Lanczos subspaces and demonstrate its application to the calculation of bound-state and resonance eigenvalues. The new scheme combines the Lanczos three-term vector recursion for the generation of a tridiagonal representation of the Hamiltonian with a three-term scalar recursion to generate filtered states within the Lanczos representation. Eigenstates in the energy windows of interest can then be obtained by solving a small generalized eigenvalue problem in the subspace spanned by the filtered states. The scalar filtering recursion is based on the homogeneous eigenvalue equation of the tridiagonal representation of the Hamiltonian, and is simpler and more efficient than our previous quasi-minimum-residual filter diagonalization (QMRFD) scheme (H. G. Yu and S. C. Smith, Chem. Phys. Lett., 1998, 283, 69), which was based on solving for the action of the Green operator via an inhomogeneous equation. A low-storage method for the construction of Hamiltonian and overlap matrix elements in the filtered-basis representation is devised, in which contributions to the matrix elements are computed simultaneously as the recursion proceeds, allowing coefficients of the filtered states to be discarded once their contribution has been evaluated. Application to the HO2 system shows that the new scheme is highly efficient and can generate eigenvalues with the same numerical accuracy as the basic Lanczos algorithm.

Application of the maximum entropy method to the (2 + 1)D four-fermion model

We investigate spectral functions extracted using the maximum entropy method from correlators measured in lattice simulations of the (2+1)-dimensional four-fermion model. This model is particularly interesting because it has both a chirally broken phase with a rich spectrum of mesonic bound states and a symmetric phase where there are only resonances. In the broken phase we study the elementary fermion, pion, sigma, and massive pseudoscalar meson; our results confirm the Goldstone nature of the π and permit an estimate of the meson binding energy. We have, however, seen no signal of σ→ππ decay as the chiral limit is approached. In the symmetric phase we observe a resonance of nonzero width in qualitative agreement with analytic expectations; in addition the ultraviolet behavior of the spectral functions is consistent with the large nonperturbative anomalous dimension for fermion composite operators expected in this model.

Identification and minisequencing-based discrimination of SHV beta-lactamases in nosocomial infection-associated Klebsiella pneumoniae in Brisbane, Australia

Extended-spectrum beta-lactamases (ESBLs) are active against oxyimino cephalosporins and monobactams. Twenty-one Klebsiella pneumoniae isolates obtained between 1991 and 1995 at the Princess Alexandra Hospital in Brisbane, Australia, were subject to amplification and sequencing of the SHV beta-lactamase-encoding genes. Thirteen strains were phenotypically ESBL positive. Of these, six strains carried the bla(SHV-2a) gene and seven strains carried the bla(SHV-12) gene. Eight strains were phenotypically ESBL negative. Of these, seven strains carried the non-ESBL bla(SHV-11) gene and one strain carried the non-ESBL bla(SHV-1) gene. There was complete correspondence between the ESBL phenotype and the presence or absence of an ESBL-encoding gene(s). In addition, it was determined that of the 13 ESBL-positive strains, at least 4 carried copies of a non-ESBL-encoding gene in addition to the bla(SHV-2a) or bla(SHV12) gene. A minisequencing-based assay was developed to discriminate the different SHV classes. This technique, termed first-nucleotide change, involves the identification of the base added to a primer in a single-nucleotide extension reaction. The assay targeted polymorphisms at the first bases of codons 238 and 240 and reliably discriminated ESBL-positive strains from ESBL-negative strains and also distinguished strains carrying bla(SHV-2a) from strains carrying bla(SHV-12). In addition, this method was used to demonstrated an association between the relative copy numbers of bla(SHV) genes in individual strains and the levels of antibiotic resistance.

Calculation of bound and resonance states of HO2 for nonzero total angular momentum

Bound and resonance states of HO2 have been calculated quantum mechanically by the Lanczos homogeneous filter diagonalization method [Zhang and Smith, Phys. Chem. Chem. Phys. 3, 2282 (2001); J. Chem. Phys. 115, 5751 (2001)] for nonzero total angular momentum J = 1,2,3. For lower bound states, agreement between the results in this paper and previous work is quite satisfactory; while for high lying bound states and resonances these are the first reported results. A helicity quantum number V assignment (within the helicity conserving approximation) is performed and the results indicate that for lower bound states it is possible to assign the V quantum numbers unambiguously, but for resonances it is impossible to assign the V helicity quantum numbers due to strong mixing. In fact, for the high-lying bound states, the mixing has already appeared. These results indicate that the helicity conserving approximation is not good for the resonance state calculations and exact quantum calculations are needed to accurately describe the reaction dynamics for HO2 system. Analysis of the resonance widths shows that most of the resonances are overlapping and the interferences between them lead to large fluctuations from one resonance to another. In accord with the conclusions from earlier J = 0 calculations, this indicates that the dissociation of HO2 is essentially irregular. (C) 2003 American Institute of Physics.

An improved preemption delay upper bound for floating non-preemptive region

In embedded systems, the timing behaviour of the control mechanisms are sometimes of critical importance for the operational safety. These high criticality systems require strict compliance with the offline predicted task execution time. The execution of a task when subject to preemption may vary significantly in comparison to its non-preemptive execution. Hence, when preemptive scheduling is required to operate the workload, preemption delay estimation is of paramount importance. In this paper a preemption delay estimation method for floating non-preemptive scheduling policies is presented. This work builds on [1], extending the model and optimising it considerably. The preemption delay function is subject to a major tightness improvement, considering the WCET analysis context. Moreover more information is provided as well in the form of an extrinsic cache misses function, which enables the method to provide a solution in situations where the non-preemptive regions sizes are small. Finally experimental results from the implementation of the proposed solutions in Heptane are provided for real benchmarks which validate the significance of this work.

Finding an upper bound on the increase in execution time due to contention on the memory bus in COTS-based multicore systems

Contention on the memory bus in COTS based multicore systems is becoming a major determining factor of the execution time of a task. Analyzing this extra execution time is non-trivial because (i) bus arbitration protocols in such systems are often undocumented and (ii) the times when the memory bus is requested to be used are not explicitly controlled by the operating system scheduler; they are instead a result of cache misses. We present a method for finding an upper bound on the extra execution time of a task due to contention on the memory bus in COTS based multicore systems. This method makes no assumptions on the bus arbitration protocol (other than assuming that it is work-conserving).

Calculating an upper bound on the finishing time of a group of threads executing on a GPU: a preliminary case study

Graphics processor units (GPUs) today can be used for computations that go beyond graphics and such use can attain a performance that is orders of magnitude greater than a normal processor. The software executing on a graphics processor is composed of a set of (often thousands of) threads which operate on different parts of the data and thereby jointly compute a result which is delivered to another thread executing on the main processor. Hence the response time of a thread executing on the main processor is dependent on the finishing time of the execution of threads executing on the GPU. Therefore, we present a simple method for calculating an upper bound on the finishing time of threads executing on a GPU, in particular NVIDIA Fermi. Developing such a method is nontrivial because threads executing on a GPU share hardware resources at very fine granularity.