Investigation of a new GRASP-based clustering algorithm applied to biological data

A large amount of biological data has been produced in the last years. Important knowledge can be extracted from these data by the use of data analysis techniques. Clustering plays an important role in data analysis, by organizing similar objects from a dataset into meaningful groups. Several clustering algorithms have been proposed in the literature. However, each algorithm has its bias, being more adequate for particular datasets. This paper presents a mathematical formulation to support the creation of consistent clusters for biological data. Moreover. it shows a clustering algorithm to solve this formulation that uses GRASP (Greedy Randomized Adaptive Search Procedure). We compared the proposed algorithm with three known other algorithms. The proposed algorithm presented the best clustering results confirmed statistically. (C) 2009 Elsevier Ltd. All rights reserved.

Infeasibility handling in genetic algorithm using nested domains for production planning

In this paper we present a genetic algorithm with new components to tackle capacitated lot sizing and scheduling problems with sequence dependent setups that appear in a wide range of industries, from soft drink bottling to food manufacturing. Finding a feasible solution to highly constrained problems is often a very difficult task. Various strategies have been applied to deal with infeasible solutions throughout the search. We propose a new scheme of classifying individuals based on nested domains to determine the solutions according to the level of infeasibility, which in our case represents bands of additional production hours (overtime). Within each band, individuals are just differentiated by their fitness function. As iterations are conducted, the widths of the bands are dynamically adjusted to improve the convergence of the individuals into the feasible domain. The numerical experiments on highly capacitated instances show the effectiveness of this computational tractable approach to guide the search toward the feasible domain. Our approach outperforms other state-of-the-art approaches and commercial solvers. (C) 2009 Elsevier Ltd. All rights reserved.

Heuristics for the one-dimensional cutting stock problem with limited multiple stock lengths

This paper deals with the classical one-dimensional integer cutting stock problem, which consists of cutting a set of available stock lengths in order to produce smaller ordered items. This process is carried out in order to optimize a given objective function (e.g., minimizing waste). Our study deals with a case in which there are several stock lengths available in limited quantities. Moreover, we have focused on problems of low demand. Some heuristic methods are proposed in order to obtain an integer solution and compared with others. The heuristic methods are empirically analyzed by solving a set of randomly generated instances and a set of instances from the literature. Concerning the latter. most of the optimal solutions of these instances are known, therefore it was possible to compare the solutions. The proposed methods presented very small objective function value gaps. (C) 2008 Elsevier Ltd. All rights reserved.

Lot sizing and furnace scheduling in small foundries

A lot sizing and scheduling problem prevalent in small market-driven foundries is studied. There are two related decision levels: (I the furnace scheduling of metal alloy production, and (2) moulding machine planning which specifies the type and size of production lots. A mixed integer programming (MIP) formulation of the problem is proposed, but is impractical to solve in reasonable computing time for non-small instances. As a result, a faster relax-and-fix (RF) approach is developed that can also be used on a rolling horizon basis where only immediate-term schedules are implemented. As well as a MIP method to solve the basic RF approach, three variants of a local search method are also developed and tested using instances based on the literature. Finally, foundry-based tests with a real-order book resulted in a very substantial reduction of delivery delays and finished inventory, better use of capacity, and much faster schedule definition compared to the foundry`s own practice. (c) 2006 Elsevier Ltd. All rights reserved.

Magnetism of Co overlayers and nanostructures on W(001): A first-principles study

The magnetic properties of Co nanostructures and a Co monolayer on W(001) have been studied in the framework of density functional theory. Different geometries such as planar and three-dimensional clusters have been considered, with cluster sizes varying between 2 and 13 atoms. The calculations were performed using the real-space linear muffin-tin orbital method (RS-LMTO-ASA). With respect to the stability of the magnetic state, we predict an antiferromagnetic (AFM) structure for the ground state of the planar Co clusters and a ferromagnetic (FM) state for the three-dimensional clusters. For the three-dimensional clusters, one of the AFM arrangements leads to frustration due to the competing FM and AFM exchange interactions between different atoms in the cluster, and gives rise to a non-collinear state with energy close to that of the FM ground state. The relative role of the Co-Co and Co-W exchange interactions is also investigated. (C) 2007 Elsevier B.V. All rights reserved.

Hyperfine and magnetic properties of Fe-Cu clusters and Fe precipitates embedded in a Cu matrix

Using the first-principles real-space linear muffin-tin orbital method within the atomic sphere approximation (RS-LMTO-ASA) we study hyperfine and local magnetic properties of substituted pure Fe and Fe-Cu clusters in an fcc Cu matrix. Spin and orbital contributions to magnetic moments, hyperfine fields and the Mossbauer isomer shifts at the Fe sites in Fe precipitates and Fe-Cu alloy clusters of sizes up to 60 Fe atoms embedded in the Cu matrix are calculated and the influence of the local environment on these properties is discussed.

New and improved results for packing identical unitary radius circles within triangles, rectangles and strips

The focus of study in this paper is the class of packing problems. More specifically, it deals with the placement of a set of N circular items of unitary radius inside an object with the aim of minimizing its dimensions. Differently shaped containers are considered, namely circles, squares, rectangles, strips and triangles. By means of the resolution of non-linear equations systems through the Newton-Raphson method, the herein presented algorithm succeeds in improving the accuracy of previous results attained by continuous optimization approaches up to numerical machine precision. The computer implementation and the data sets are available at http://www.ime.usp.br/similar to egbirgin/packing/. (C) 2009 Elsevier Ltd, All rights reserved.

Three-dimensional packings with rotations

We present approximation algorithms for the three-dimensional strip packing problem, and the three-dimensional bin packing problem. We consider orthogonal packings where 90 degrees rotations are allowed. The algorithms we show for these problems have asymptotic performance bounds 2.64, and 4.89, respectively. These algorithms are for the more general case in which the bounded dimensions of the bin given in the input are not necessarily equal (that is, we consider bins for which the length. the width and the height are not necessarily equal). Moreover, we show that these problems-in the general version-are as hard to approximate as the corresponding oriented version. (C) 2009 Elsevier Ltd. All rights reserved.

Minimizing the object dimensions in circle and sphere packing problems

Given a fixed set of identical or different-sized circular items, the problem we deal with consists on finding the smallest object within which the items can be packed. Circular, triangular, squared, rectangular and also strip objects are considered. Moreover, 2D and 3D problems are treated. Twice-differentiable models for all these problems are presented. A strategy to reduce the complexity of evaluating the models is employed and, as a consequence, instances with a large number of items can be considered. Numerical experiments show the flexibility and reliability of the new unified approach. (C) 2007 Elsevier Ltd. All rights reserved.

Hur retusch påverkar skönhetsannonsers attraktion : En studie om målgruppens åsikter och köplust

Tidigare studier som gjorts inom området visade att kvinnor anser att kvinnors skönhet inte är värderad enligt rimliga normer i vårt samhälle. Hård retuschering motarbetas på många håll, bland annat genom att organisationer som ASA (Advertising Standards Authority) och politiska partier som Liberaldemokraterna i Storbritannien arbetar för att missledande retuschering ska försvinna. En studie har visat att det, för att öka annonsers attraktionskraft, är viktigt att den ökade skönheten hos en modell är relevant för produktens användningsområde, då betraktaren anstränger sig intellektuellt vid betraktandet av bilden. Det finns dock inga tidigare studier som bevisar om en retuscherad modell faktiskt ökar målgruppens köplust av skönhetsprodukter vid rådande samhällsattityder och skönhetsideal. Två enkätundersökningar gjordes därför med sammanlagt 1480 deltagare. Produkten i studien var en fiktiv hudkräm. Genom att i den ena undersökningen låta betraktaren möta modellbilden i en situation som efterliknade verkligheten, på så sätt att de inte fick veta om den var retuscherad, kunde studien svara på om retuschering ökade köplusten. Bilder med bortretuscherade skönhetsfläckar och utväxt prefererades. Att retuschera bort flyghår ökade inte köplusten. I den andra jämförande undersökningen kunde betraktaren jämföra den retuscherade med den oretuscherade modellbilden. Resultaten visade att skönhetsfläckar och flyghår tillåts och prefereras borttagna, men inte utväxt. I intervjuer med fem kvinnor hördes målgruppens attityder om vad som ansågs var tillåtet att retuschera. Svaren tydde på att en relevant och försiktig retuschering prefererades. Att lämna några födelsemärken ökade trovärdigheten.

The core characteristics and nursing care activities in psychiatric intensive care units in Sweden

Internationally, research on psychiatric intensive care units (PICUs) commonly reportsresults from demographic studies such as criteria for admission, need for involuntary treatment, andthe occurrence of violent behaviour. A few international studies describe the caring aspect of thePICUs based specifically on caregivers’ experiences. The concept of PICU in Sweden is not clearlydefined. The aim of this study is to describe the core characteristics of a PICU in Sweden and todescribe the care activities provided for patients admitted to the PICUs. Critical incident techniquewas used as the research method. Eighteen caregivers at a PICU participated in the study bycompleting a semistructured questionnaire. In-depth interviews with three nurses and two assistantnurses also constitute the data. An analysis of the content identified four categories that characterizethe core of PICU: the dramatic admission, protests and refusal of treatment, escalating behaviours, andtemporarily coercive measure. Care activities for PICUs were also analysed and identified as controlling– establishing boundaries, protecting – warding off, supporting – giving intensive assistance, andstructuring the environment. Finally, the discussion put focus on determining the intensive aspect ofpsychiatric care which has not been done in a Swedish perspective before. PICUs were interpreted asa level of care as it is composed by limited structures and closeness in care.

Självet, rollerna och pågående koordinationer av mänskliga handlingar : Om att försöka se ’samhället’ som något annat än fängelse eller marionetteater

The self, roles and the ongoing coordination of human action. Trying to see ‘society’ as neither prison nor puppet theatre In the article it is argued that structural North-American role-sociology may be integrated with theories emphasizing ‘society’ as ongoing processes (f. ex. Giddens’ theory of structuration). This is possible if the concept of role is defined as a recurrence oriented to the action of others standing out as a regularity in a societal process. But this definition makes it necessary to in a fundamental way understand what kind of social being the role-actor is. This is done with the help of Hans Joas’ theory of creativity and Merleau-Pontys concept of ‘flesh’ arguing that Meads concept of the ‘I’ maybe understood as an embodied self-asserting I, which at least in reflexive modernity has the creative power to split Meads ‘me’ into a self-voiced subject-me and an other voiced object-me. The embodied I communicating with the subject-me may be viewed as that role-actor which is something else than the role played. But this kind of role-actor is making for new troubles because it is hard to understand how this kind of self is creating self-coherence by using Meads concept of ‘the generalized other’. This trouble is handled by using Alain Touraines concept of the ‘subject’ and arguing that the generalized other is dissolving in de-modernized modernity. In split modernity self-coherence may instead be created by what in the article is called the generalized subject. This concept means a kind of communicative future based evaluation, which has its base in the ‘subject’ opposing the split powers of both the instrumentality of markets and of life-worlds trying to create ‘fundamentalistic’ self-identities. This kind of self is communicative because it also must respect the other as ‘subject’. It exists only in the battle against the forces of the market or a community. It never constructs an ideal city or a higher type of individual. It creates and protects a clearing that is constantly being invaded, to use the words of the old Frenchman himself. Asa kind of test-case it is by the way in the article shown how Becks concept of individualization may be understood in a deeply social and role-sociological way.

Large-scale metabolomic profiling identifies novel biomarkers for incident coronary heart disease

Analyses of circulating metabolites in large prospective epidemiological studies could lead to improved prediction and better biological understanding of coronary heart disease (CHD). We performed a mass spectrometry-based non-targeted metabolomics study for association with incident CHD events in 1,028 individuals (131 events; 10 y. median follow-up) with validation in 1,670 individuals (282 events; 3.9 y. median follow-up). Four metabolites were replicated and independent of main cardiovascular risk factors [lysophosphatidylcholine 18∶1 (hazard ratio [HR] per standard deviation [SD] increment = 0.77, P-value<0.001), lysophosphatidylcholine 18∶2 (HR = 0.81, P-value<0.001), monoglyceride 18∶2 (MG 18∶2; HR = 1.18, P-value = 0.011) and sphingomyelin 28∶1 (HR = 0.85, P-value = 0.015)]. Together they contributed to moderate improvements in discrimination and re-classification in addition to traditional risk factors (C-statistic: 0.76 vs. 0.75; NRI: 9.2%). MG 18∶2 was associated with CHD independently of triglycerides. Lysophosphatidylcholines were negatively associated with body mass index, C-reactive protein and with less evidence of subclinical cardiovascular disease in additional 970 participants; a reverse pattern was observed for MG 18∶2. MG 18∶2 showed an enrichment (P-value = 0.002) of significant associations with CHD-associated SNPs (P-value = 1.2×10-7 for association with rs964184 in the ZNF259/APOA5 region) and a weak, but positive causal effect (odds ratio = 1.05 per SD increment in MG 18∶2, P-value = 0.05) on CHD, as suggested by Mendelian randomization analysis. In conclusion, we identified four lipid-related metabolites with evidence for clinical utility, as well as a causal role in CHD development.

Inflammation, oxidative stress, glomerular filtration rate, and albuminuria in elderly men : a cross-sectional study

BACKGROUND: The role of inflammation and oxidative stress in mild renal impairment in the elderly is not well studied. Accordingly, we aimed at investigating the associations between estimated glomerular filtration rate (eGFR), albumin/creatinine ratio (ACR), and markers of different inflammatory pathways and oxidative stress in a community based cohort of elderly men. FINDINGS: Cystatin C-based GFR, ACR, and biomarkers of cytokine-mediated inflammation (interleukin-6, high-sensitivity C-reactive protein[CRP], serum amyloid A[SAA]), cyclooxygenase-mediated inflammation (urinary prostaglandin F2alpha [PGF2alpha]), and oxidative stress (urinary F2 isoprostanes) were assessed in the Uppsala Longitudinal Study of Adult Men(n = 647, mean age 77 years). RESULTS: In linear regression models adjusting for age, BMI, smoking, blood pressure, LDL-cholesterol, HDL-cholesterol, triglycerides, and treatment with statins, ACE-inhibitors, ASA, and anti-inflammatory agents, eGFR was inversely associated with CRP, interleukin-6, and SAA (beta-coefficient -0.13 to -0.19, p < 0.001 for all), and positively associated with urinary F2-isoprostanes (beta-coefficient 0.09, p = 0.02). In line with this, ACR was positively associated with CRP, interleukin-6, and SAA (beta- coefficient 0.09-0.12, p < 0.02 for all), and negatively associated with urinary F2-isoprostanes (beta-coefficient -0.12, p = 0.002). The associations were similar but with lower regression coefficients in a sub-sample with normal eGFR (>60 ml/min/1.73 m2, n = 514), with the exception that F2-isoprostane and SAA were no longer associated with eGFR. CONCLUSION: Our data indicate that cytokine-mediated inflammation is involved in the early stages of impaired kidney function in the elderly, but that cyclooxygenase-mediated inflammation does not play a role at this stage. The unexpected association between higher eGFR/lower albuminuria and increased F2-isoprostanes in urine merits further studies.

Comparação dos principais constituintes químicos de duas espécies de arnica: Cravorana (Porophyllum Ruderale [Jacq.] Cass) e Varão-de-Ouro (Solidago SP.)

Diferentes espécies vegetais são denominadas popularmente como arnica, devido ao uso em ferimentos, traumatismos e contusões, semelhantes ao da espécie oficial Arnica montana L. Dentre elas, destacam-se as seguintes: Porophyllum ruderale (Jacq.) Cass., nativa do Brasil, com maior frequência na região Sudeste, constituída por óleo essencial, flavonoides, taninos, alcaloides e saponinas; Solidago sp., planta originária da América do Sul e encontrada em vários terrenos brasileiros, constituída por flavonoides, óleo essencial e saponinas. Este trabalho teve por objetivo realizar a avaliação farmacognóstica das espécies Porophyllum ruderale e Solidago sp. A parte aérea seca das espécies foi pulverizada e tamisada, e analisaram-se as características organolépticas dos pós: aspecto, cor, odor e sabor; a triagem fitoquímica foi realizada a partir de métodos tradicionais. Verificou-se a presença de taninos condensados e flavonoides em ambas as espécies, e não foi confirmada a presença de saponinas e alcaloides em nenhuma das amostras.