Clustering high dimensional data: A graph-based relaxed optimization approach

There is no doubt that clustering is one of the most studied data mining tasks. Nevertheless, it remains a challenging problem to solve despite the many proposed clustering approaches. Graph-based approaches solve the clustering task as a global optimization problem, while many other works are based on local methods. In this paper, we propose a novel graph-based algorithm “GBR” that relaxes some well-defined method even as improving the accuracy whilst keeping it simple. The primary motivation of our relaxation of the objective is to allow the reformulated objective to find well distributed cluster indicators for complicated data instances. This relaxation results in an analytical solution that avoids the approximated iterative methods that have been adopted in many other graph-based approaches. The experiments on synthetic and real data sets show that our relaxation accomplishes excellent clustering results. Our key contributions are: (1) we provide an analytical solution to solve the global clustering task as opposed to approximated iterative approaches; (2) a very simple implementation using existing optimization packages; (3) an algorithm with relatively less computation time over the number of data instances to cluster than other well defined methods in the literature.     

Modeling the leadership – project performance relation: radial basis function,Gaussian and Kriging methods as alternatives to linear regression

The purpose of this paper is to analyze alternative forecasting methods that produce results at least similar to or better than linear regression (MLR) that can be used in the modeling of social systems. While organizations may be considered as typically non-linear systems, the common feature of most models found in literature continues to be the use of linear regression techniques. From a case study, advanced statistical methods of Gaussian and Kriging are evaluated, as well as an artificial intelligence (AI) tool, the radial basis function (RBF). The results show the best performance of the suggested methods compared to MLR, especially RBF, because of its uniform prediction behavior throughout all ranges of evaluation. These techniques, although somewhat unconventional in social systems modeling, present a potential contribution in increasing the accuracy and precision of the predictions allowing a more accurate assessment of the impact of certain strategies on the project performance to be made before the allocation of material, human and financial resources.     

MOSFET threshold voltage: Definition,extraction, and some applications

This paper exploits a universal current-based definition of the threshold voltage (V_T) and discusses some direct methods to measure it. The consistency, accuracy, and sensitivity of the extraction procedures to second-order effects are examined through numerical simulations and experimental measurements. In addition to three procedures based on dc current measurements we propose an automatic V_T-extractor circuit which allows the direct determination of the threshold voltage with minimum influence of second-order effects.     

The Expression of Active CD11b Monocytes in Blood and Disease Progression in Amyotrophic Lateral Sclerosis

Monocytes expressing the inflammation suppressing active CD11b, a beta2 integrin, may regulate neuroinflammation and modify clinical outcomes in amyotrophic lateral sclerosis (ALS). In this single site, retrospective study, peripheral blood mononuclear cells from 38 individuals living with ALS and 20 non-neurological controls (NNC) were investigated using flow cytometry to study active CD11b integrin classical (CM), intermediate (IM) and non-classical (NCM) monocytes during ALS progression. Seventeen ALS participants were sampled at the baseline (V1) and at two additional time points (V2 and V3) for longitudinal analysis. Active CD11b+ CM frequencies increased steeply between the baseline and V3 (ANOVA repeated measurement, p < 0.001), and the V2/V1 ratio negatively correlated with the disease progression rate, similar to higher frequencies of active CD11b+ NCM at the baseline (R = −0.6567; p = 0.0031 and R = 0.3862; p = 0.0168, respectively). CD11b NCM, clinical covariates and neurofilament light-chain plasma concentration at the baseline predicted shorter survival in a multivariable and univariate analysis (CD11b NCM—HR: 1.05, CI: 1.01–1.11, p = 0.013. Log rank: above median: 43 months and below median: 21.22 months; p = 0.0022). Blood samples with the highest frequencies of active CD11b+ IM and NCM contained the lowest concentrations of soluble CD11b. Our preliminary data suggest that the levels of active CD11b+ monocytes and NCM in the blood predict different clinical outcomes in ALS.     

Verifying Object-based Graph Grammars

The development of concurrent and reactive systems is gaining importance since they are well-suited to modern computing platforms, such as the Internet. However, the development of correct concurrent and reactive systems is a non-trivial task. Object-based graph grammar (OBGG) is a visual formal language suitable for the specification of this class of systems. In previous work, a translation from OBGG to PROMELA (the input language of the SPIN model checker) was defined, enabling the verification of OBGG models using SPIN. In this paper we extend this approach in two different ways: (1) the approach for property specification is improved, enabling to prove properties not only about possible OBGG derivations, but also about the internal state of involved objects; (2) an approach is defined to interpret PROMELA races as OBGG derivations, generating graphical counter-examples for properties that are not true for a given OBGG model. Another contribution of this paper is (3) the definition of a method for model checking partial systems (isolated objects or a set of objects) using an assume-guarantee approach. A gas station system modeled with OBGGs is used to illustrate the contributions.This work is partially sponsored by projects IQ-MObile (CNPq-Brazil/CNR-Italy) and PLATUS (CNPq).Osmar Marchi dos Santos is partially sponsored by CAPES-Brazil.     

An expert protein loop refinement protocol by molecular dynamics simulations with restraints

Protein structure prediction (PSP) is a long standing problem in structural biology and bioinformatics. Within the PSP problem loop refinement is a major bottleneck. In this article we report the latest version of the CReF expert predictor system for the PSP problem with emphasis on loop refinement of the approximate 3-D structure 1ZDD_P of the Z34C mini protein predicted by CReF. We designed a loop refinement protocol based on seven molecular dynamics (MD) simulations runs at different temperatures. We found that, by letting the loop residues move freely during dynamics at 325 K and restraining the internal coordinates of the correctly predicted helical structures, while allowing them to move relative to each other, the refinement protocol was very effective in predicting an accurate loop conformation in the first 100 ps of a 1000 ps MD simulation. The quality of the predictions was confirmed by the RMSD between refined and experimental structures which varied from 0.6 to 1.3 Å. In addition, stereochemical analyses showed that 100% of all residues of the refined 1ZDD_P, including those in the loop, populates the most favorable core regions of the Ramachandran plot. Our study suggests that the proposed protocol may be suitable to refine more complex mini proteins with different classes and architectures.     

Complete and non-overlapping marching along a closed regular intersection curve

In this paper we present an algorithm for estimating the rotation index of a closed regular intersection curve from its singular points. On the basis of this index we have also devised a procedure that guarantees that a closed intersection curve will be traced completely, without overlapping. Combining this procedure with marching steps derived from differential geometric properties has resulted in a robust intersection technique.     

Influence of the insecticide pyriproxyfen on the flight muscle differentiation of Apis mellifera (Hymenoptera, Apidae)

The Brazilian africanized Apis mellifera is currently considered as one of the most important pollinators threatened by the use of insecticides due to its frequent exposition to their toxic action while foraging in the crops it pollinated. Among the insecticides, the most used in the control of insect pragues has as active agent the pyriproxyfen, analogous to the juvenile hormone (JH). Unfortunately the insecticides used in agriculture affect not only the target insects but also beneficial nontarget ones as bees compromising therefore, the growth rate of their colonies at the boundaries of crop fields. Workers that forage for provisions in contaminated areas can introduce contaminated pollen or/and nectar inside the beehives. As analogous to JH the insecticide pyriproxyfen acts in the bee's larval growth and differentiation during pupation or metamorphosis timing. The flighty muscle is not present in the larvae wingless organisms, but differentiates during pupation/metamorphosis. This work aimed to investigate the effect of pyriproxyfen insecticide on differentiation of such musculature in workers of Brazilian africanized honey bees fed with artificial diet containing the pesticide. The results show that the bees fed with contaminated diet, independent of the insecticide concentration used, show a delay in flight muscle differentiation when compared to the control.     

Effects of hydroxyl group distribution on the reactivity, stability and optical properties of fullerenols

We investigate the impact of hydroxyl groups on the properties of C(60)(OH)(n) systems, with n = 1, 2, 3, 4, 8, 10, 16, 18, 24, 32 and 36 by means of first-principles density functional theory calculations. A detailed analysis from the local density of states has shown that adsorbed OH groups can induce dangling bonds in specific carbon atoms around the adsorption site. This increases the tendency to form polyhydroxylated fullerenes (fullerenols). The structural stability is analyzed in terms of the calculated formation enthalpy of each species. Also, a careful examination of the electron density of states for different fullerenols shows the possibility of synthesizing single molecules with tunable optical properties.