Approaching the ground states of the random maximum two-satisfiability problem by a greedy single-spin flipping process

In this brief report we explore the energy landscapes of two spin glass models using a greedy single-spin flipping process, {\tt Gmax}. The ground-state energy density of the random maximum two-satisfiability problem is efficiently approached by {\tt Gmax}. The achieved energy density $e(t)$ decreases with the evolution time $t$ as $e(t)-e(\infty)=h (\log_{10} t)^{-z}$ with a small prefactor $h$ and a scaling coefficient $z > 1$, indicating an energy landscape with deep and rugged funnel-shape regions. For the $\pm J$ Viana-Bray spin glass model, however, the greedy single-spin dynamics quickly gets trapped to a local minimal region of the energy landscape.Comment: 5 pages with 4 figures included. Accepted for publication in Physical Review E as a brief repor

An Efficient Local Search for Partial Latin Square Extension Problem

A partial Latin square (PLS) is a partial assignment of n symbols to an nxn grid such that, in each row and in each column, each symbol appears at most once. The partial Latin square extension problem is an NP-hard problem that asks for a largest extension of a given PLS. In this paper we propose an efficient local search for this problem. We focus on the local search such that the neighborhood is defined by (p,q)-swap, i.e., removing exactly p symbols and then assigning symbols to at most q empty cells. For p in {1,2,3}, our neighborhood search algorithm finds an improved solution or concludes that no such solution exists in O(n^{p+1}) time. We also propose a novel swap operation, Trellis-swap, which is a generalization of (1,q)-swap and (2,q)-swap. Our Trellis-neighborhood search algorithm takes O(n^{3.5}) time to do the same thing. Using these neighborhood search algorithms, we design a prototype iterated local search algorithm and show its effectiveness in comparison with state-of-the-art optimization solvers such as IBM ILOG CPLEX and LocalSolver.Comment: 17 pages, 2 figure

Effect of farnesol on structure and composition of staphylococcus epidermidis biofilm matrix

Staphylococcus epidermidis is the most frequent cause of nosocomial sepsis and catheter-related infections in which biofilm formation is considered to be one of the main virulence mechanisms. Moreover, their increased resistance to conventional antibiotic therapy enhances the need to develop new therapeutical agents. Farnesol, a natural sesquiterpenoid present in many essential oils, has been described as impairing bacterial growth. The aim of this study was to evaluate the effect of farnesol on the structure and composition of biofilm matrix of S. epidermidis. Biofilms formed in the presence of farnesol (300 μM) contained less biomass, and displayed notable changes in the composition of the biofilm matrix. Changes in the spacial structure were also verified by confocal scanning laser microscopy (CSLM). The results obtained by the quantification of extracellular polymers and by wheat germ agglutinin (WGA) fluorescent detection of glycoproteins containing β(1→4)-N-acetyl-d-glucosamine support the hypothesis that farnesol causes disruption of the cytoplasmic membrane and consequently release of cellular content.Fernanda Gomes and Pilar Teixeira fully acknowledge the financial support of Fundacao para a Ciencia e Tecnologia (FCT) through the grants SFRH/BD/32126/2006 and SFRH/BPD/26803/2006, respectively

“A Good Death” - Palliative Surgery in Trisomy 18

A trissomia 18 caracteriza-se por múltiplas anomalias, incluindo doença cardíaca em 60 a 90% dos casos e elevada mortalidade. O mau prognóstico global, conduz habitualmente a uma politica de “cuidados mínimos” mas, paliar, é também nestas situações, um imperativo ético. Descreve-se o caso de uma recém-nascida sem diagnóstico pré natal, mas com confirmação por cariotipo, com cardiopatia, que condicionou insuficiência cardíaca congestiva e angústia respiratória crescente, inviabilizando alta hospitalar, como era desejo da família. Após consenso entre os pais e o corpo clínico responsável, foi decidida intervenção cirúrgica cardíaca paliativa, que possibilitou melhoria clínica e alta para o domicílio. Os autores defendem que a cirurgia cardíaca pode ser uma atitude a considerar em casos de trissomia 18, pois pode aliviar o sofrimento

Heparan sulphate mediates swine vesicular disease virus attachment to the host cell

Heparan sulphate (HS) has been found to serve as receptor for initial cell binding of numerous viruses. Different glycosaminoglycans (GAGs), including heparin and HS, were analysed for their ability to bind swine vesicular disease virus (SVDV), a picornavirus with close homology to human coxsackie B5 virus. Binding of SVDV was established by heparin-affinity chromatography. In addition, infection of IB-RS-2 epithelial porcine cells was inhibited by treating the virus with soluble HS, heparin, and chondroitin sulphate B (CS-B), as well as by enzymic digestion of cell surface GAGs. Analysis of the infection course showed that SVDV uses cellular HS for its binding to the cell surface and that this interaction occurs during attachment of the virus, prior to its internalization into the cell. Sequence analysis of SVDV variants selected for their lack of sensitivity to heparin inhibition in vitro led to the identification of two residues (A2135V and 11 266K) potentially involved in heparin/HS interaction. The location of these residues in a three-dimensional model shows that they are clustered in a well-exposed region of the capsid, providing a physical mechanism that could account for the heparin-binding phenotype

Flexible constrained sampling with guarantees for pattern mining

Pattern sampling has been proposed as a potential solution to the infamous pattern explosion. Instead of enumerating all patterns that satisfy the constraints, individual patterns are sampled proportional to a given quality measure. Several sampling algorithms have been proposed, but each of them has its limitations when it comes to 1) flexibility in terms of quality measures and constraints that can be used, and/or 2) guarantees with respect to sampling accuracy. We therefore present Flexics, the first flexible pattern sampler that supports a broad class of quality measures and constraints, while providing strong guarantees regarding sampling accuracy. To achieve this, we leverage the perspective on pattern mining as a constraint satisfaction problem and build upon the latest advances in sampling solutions in SAT as well as existing pattern mining algorithms. Furthermore, the proposed algorithm is applicable to a variety of pattern languages, which allows us to introduce and tackle the novel task of sampling sets of patterns. We introduce and empirically evaluate two variants of Flexics: 1) a generic variant that addresses the well-known itemset sampling task and the novel pattern set sampling task as well as a wide range of expressive constraints within these tasks, and 2) a specialized variant that exploits existing frequent itemset techniques to achieve substantial speed-ups. Experiments show that Flexics is both accurate and efficient, making it a useful tool for pattern-based data exploration.Comment: Accepted for publication in Data Mining & Knowledge Discovery journal (ECML/PKDD 2017 journal track

Decadal changes of the Western Arabian sea ecosystem

Historical data from oceanographic expeditions and remotely sensed data on outgoing longwave radiation, temperature, wind speed and ocean color in the western Arabian Sea (1950–2010) were used to investigate decadal trends in the physical and biochemical properties of the upper 300 m. 72 % of the 29,043 vertical profiles retrieved originated from USA and UK expeditions. Increasing outgoing longwave radiation, surface air temperatures and sea surface temperature were identified on decadal timescales. These were well correlated with decreasing wind speeds associated with a reduced Siberian High atmospheric anomaly. Shoaling of the oxycline and nitracline was observed as well as acidification of the upper 300 m. These physical and chemical changes were accompanied by declining chlorophyll-a concentrations, vertical macrofaunal habitat compression, declining sardine landings and an increase of fish kill incidents along the Omani coast

Chiral Polymerization in Open Systems From Chiral-Selective Reaction Rates

We investigate the possibility that prebiotic homochirality can be achieved exclusively through chiral-selective reaction rate parameters without any other explicit mechanism for chiral bias. Specifically, we examine an open network of polymerization reactions, where the reaction rates can have chiral-selective values. The reactions are neither autocatalytic nor do they contain explicit enantiomeric cross-inhibition terms. We are thus investigating how rare a set of chiral-selective reaction rates needs to be in order to generate a reasonable amount of chiral bias. We quantify our results adopting a statistical approach: varying both the mean value and the rms dispersion of the relevant reaction rates, we show that moderate to high levels of chiral excess can be achieved with fairly small chiral bias, below 10%. Considering the various unknowns related to prebiotic chemical networks in early Earth and the dependence of reaction rates to environmental properties such as temperature and pressure variations, we argue that homochirality could have been achieved from moderate amounts of chiral selectivity in the reaction rates.Comment: 15 pages, 6 figures, accepted for publication in Origins of Life and Evolution of Biosphere

Wind-pv-thermal power aggregator in electricity market

This paper addresses the aggregation of wind, photovoltaic and thermal units with the aim to improve bidding in an electricity market. Market prices, wind and photovoltaic powers are assumed as data given by a set of scenarios. Thermal unit modeling includes start-up costs, variables costs and bounds due to constraints of technical operation, such as: ramp up/down limits and minimum up/down time limits. The modeling is carried out in order to develop a mathematical programming problem based in a stochastic programming approach formulated as a mixed integer linear programming problem. A case study comparison between disaggregated and aggregated bids for the electricity market of the Iberian Peninsula is presented to reveal the advantage of the aggregation

Enzymatic degradation of starch thermoplastic blends using samples of different thickness

The material studied was a thermoplastic blend of corn starch with a poly(ethylene-vinyl alcohol) copolymer, SEVA-C. The influence of both the material’s exposed surface and enzyme concentration on degradation kinetics was studied. As α-amylase is present in the blood plasma, experiments were performed, varying the material thickness and the α-amylase between 50 and 100 units/l, at 37°C, lasting up to 90 days. Four different batches using SEVA-C and starch samples of different thickness were performed. The positive correlation between degradation rate and the exposed material surface was confirmed, since thin films with larger exposed surfaces were degraded faster than thick square plates having the same total mass. The degradation extent depends on the total amount of amorphous starch present in the formulation rather than on the amount of enzyme used and the minimum thickness to ensure maximum degradation was estimated to be close to 0.25 mm