Técnicas de análise do perfil de execução e otimização de programas em química computacional

In this paper we review the basic techniques of performance analysis within the UNIX environment that are relevant in computational chemistry, with particular emphasis on the execution profile using the gprof tool. Two case studies (in ab initio and molecular dynamics calculations) are presented in order to illustrate how execution profiling can be used to effectively identify bottlenecks and to guide source code optimization. Using these profiling and optimization techniques it was possible to obtain significant speedups (of up to 30%) in both cases.

Uso de redes neurais recorrentes na determinação das constantes de acidez para a 7-epiclusianona em misturas etanol-água

This work propose a recursive neural network to solve inverse equilibrium problem. The acidity constants of 7-epiclusianone in ethanol-water binary mixtures were determined from multiwavelength spectrophotmetric data. A linear relationship between acidity constants and the %w/v of ethanol in the solvent mixture was observed. The proposed method efficiency is compared with the Simplex method, commonly used in nonlinear optimization techniques. The neural network method is simple, numerically stable and has a broad range of applicability.

Valuation models and Simon's bounded rationality

This paper aims at reconciling the evidence that sophisticated valuation models are increasingly used by companies in their investment appraisal with the literature of bounded rationality, according to which objective optimization is impracticable in the real world because it would demand an immense level of sophistication of the analytical and computational processes of human beings. We show how normative valuation models should rather be viewed as forms of reality representation, frameworks according to which the real world is perceived, fragmented for a better understanding, and recomposed, providing an orderly method for undertaking a task as complex as the investment decision.

Optimization of random amplified polymorphic DNA techniques for use in genetic studies of Cuban triatominae

Random amplified polymorphic DNA (RAPD) technique is a simple and reliable method to detect DNA polymorphism. Several factors can affect the amplification profiles, thereby causing false bands and non-reproducibility of assay. In this study, we analyzed the effect of changing the concentration of primer, magnesium chloride, template DNA and Taq DNA polymerase with the objective of determining their optimum concentration for the standardization of RAPD technique for genetic studies of Cuban Triatominae. Reproducible amplification patterns were obtained using 5 pmoL of primer, 2.5 mM of MgCl2, 25 ng of template DNA and 2 U of Taq DNA polymerase in 25 µL of the reaction. A panel of five random primers was used to evaluate the genetic variability of T. flavida. Three of these (OPA-1, OPA-2 and OPA-4) generated reproducible and distinguishable fingerprinting patterns of Triatominae. Numerical analysis of 52 RAPD amplified bands generated for all five primers was carried out with unweighted pair group method analysis (UPGMA). Jaccard's Similarity Coefficient data were used to construct a dendrogram. Two groups could be distinguished by RAPD data and these groups coincided with geographic origin, i.e. the populations captured in areas from east and west of Guanahacabibes, Pinar del Río. T. flavida present low interpopulation variability that could result in greater susceptibility to pesticides in control programs. The RAPD protocol and the selected primers are useful for molecular characterization of Cuban Triatominae.

Land cover classification of Lago Grande de Curuai floodplain (Amazon, Brazil) using multi-sensor and image fusion techniques

Given the limitations of different types of remote sensing images, automated land-cover classifications of the Amazon várzea may yield poor accuracy indexes. One way to improve accuracy is through the combination of images from different sensors, by either image fusion or multi-sensor classifications. Therefore, the objective of this study was to determine which classification method is more efficient in improving land cover classification accuracies for the Amazon várzea and similar wetland environments - (a) synthetically fused optical and SAR images or (b) multi-sensor classification of paired SAR and optical images. Land cover classifications based on images from a single sensor (Landsat TM or Radarsat-2) are compared with multi-sensor and image fusion classifications. Object-based image analyses (OBIA) and the J.48 data-mining algorithm were used for automated classification, and classification accuracies were assessed using the kappa index of agreement and the recently proposed allocation and quantity disagreement measures. Overall, optical-based classifications had better accuracy than SAR-based classifications. Once both datasets were combined using the multi-sensor approach, there was a 2% decrease in allocation disagreement, as the method was able to overcome part of the limitations present in both images. Accuracy decreased when image fusion methods were used, however. We therefore concluded that the multi-sensor classification method is more appropriate for classifying land cover in the Amazon várzea.

Optimal design of 3R manipulators by using classical techniques and simulated annealin

In this paper, the optimum design of 3R manipulators is formulated and solved by using an algebraic formulation of workspace boundary. A manipulator design can be approached as a problem of optimization, in which the objective functions are the size of the manipulator and workspace volume; and the constrains can be given as a prescribed workspace volume. The numerical solution of the optimization problem is investigated by using two different numerical techniques, namely, sequential quadratic programming and simulated annealing. Numerical examples illustrate a design procedure and show the efficiency of the proposed algorithms.

Optimization of image analysis techniques for quality assessment of whole-wheat breads made with fat replacer

The cellular structure of healthy food products, with added dietary fiber and low in calories, is an important factor that contributes to the assessment of quality, which can be quantified by image analysis of visual texture. This study seeks to compare image analysis techniques (binarization using Otsu’s method and the default ImageJ algorithm, a variation of the iterative intermeans method) for quantification of differences in the crumb structure of breads made with different percentages of whole-wheat flour and fat replacer, and discuss the behavior of the parameters number of cells, mean cell area, cell density, and circularity using response surface methodology. Comparative analysis of the results achieved with the Otsu and default ImageJ algorithms showed a significant difference between the studied parameters. The Otsu method demonstrated the crumb structure of the analyzed breads more reliably than the default ImageJ algorithm, and is thus the most suitable in terms of structural representation of the crumb texture.

O planejamento econômico no Brasil: considerações críticas

In the past thirty years, a series of plans have been developed by successive Brazilian governments in a continuing effort to maximize the nation's resources for economic and social growth. This planning history has been quantitatively rich but qualitatively poor. The disjunction has stimulated Professor Mello e Souza to address himself to the problem of national planning and to offer some criticisms of Brazilian planning experience. Though political instability has obviously been a factor promoting discontinuity, his criticisms are aimed at the attitudes and strategic concepts which have sought to link planning to national goals and administration. He criticizes the fascination with techniques and plans to the exclusion of proper diagnosis of the socio-political reality, developing instruments to coordinate and carry out objectives, and creating an administrative structure centralized enough to make national decisions and decentralized enough to perform on the basis of those decisions. Thus, fixed, quantified objectives abound while the problem of functioning mechanisms for the coordinated, rational use of resources has been left unattended. Although his interest and criticism are focused on the process and experience of national planning, he recognized variation in the level and results of Brazilian planning. National plans have failed due to faulty conception of the function of planning. Sectorial plans, save in the sector of the petroleum industry under government responsibility, ha e not succeeded in overcoming the problems of formulation and execution thereby repeating old technical errors. Planning for the private sector has a somewhat brighter history due to the use of Grupos Executivos which has enabled the planning process to transcend the formalism and tradition-bound attitudes of the regular bureaucracy. Regional planning offers two relatively successful experiences, Sudene and the strategy of the regionally oriented autarchy. Thus, planning history in Brazil is not entirely black but a certain shade of grey. The major part of the article, however, is devoted to a descriptive analysis of the national planning experience. The plans included in this analysis are: The Works and Equipment Plan (POE); The Health, Food, Transportation and Energy Plan (Salte); The Program of Goals; The Trienal Plan of Economic and Social Development; and the Plan of Governmental Economic Action (Paeg). Using these five plans for his historical experience the author sets out a series of errors of formulation and execution by which he analyzes that experience. With respect to formulation, he speaks of a lack of elaboration of programs and projects, of coordination among diverse goals, and of provision of qualified staff and techniques. He mentions the absence of the definition of resources necessary to the financing of the plan and the inadequate quantification of sectorial and national goals due to the lack of reliable statistical information. Finally, he notes the failure to coordinate the annual budget with the multi-year plans. He sees the problems of execution as beginning in the absence of coordination between the various sectors of the public administration, the failure to develop an operative system of decentralization, the absence of any system of financial and fiscal control over execution, the difficulties imposed by the system of public accounting, and the absence of an adequate program of allocation for the liberation of resources. He ends by pointing to the failure to develop and use an integrated system of political economic tools in a mode compatible with the objective of the plans. The body of the article analyzes national planning experience in Brazil using these lists of errors as rough model of criticism. Several conclusions emerge from this analysis with regard to planning in Brazil and in developing countries, in general. Plans have generally been of little avail in Brazil because of the lack of a continuous, bureaucratized (in the Weberian sense) planning organization set in an instrumentally suitable administrative structure and based on thorough diagnoses of socio-economic conditions and problems. Plans have become the justification for planning. Planning has come to be conceived as a rational method of orienting the process of decisions through the establishment of a precise and quantified relation between means and ends. But this conception has led to a planning history rimmed with frustration, and failure, because of its rigidity in the face of flexible and changing reality. Rather, he suggests a conception of planning which understands it "as a rational process of formulating decisions about the policy, economy, and society whose only demand is that of managing the instrumentarium in a harmonious and integrated form in order to reach explicit, but not quantified ends". He calls this "planning without plans": the establishment of broad-scale tendencies through diagnosis whose implementation is carried out through an adjustable, coherent instrumentarium of political-economic tools. Administration according to a plan of multiple, integrated goals is a sound procedure if the nation's administrative machinery contains the technical development needed to control the multiple variables linked to any situation of socio-economic change. Brazil does not possess this level of refinement and any strategy of planning relevant to its problems must recognize this. The reforms which have been attempted fail to make this recognition as is true of the conception of planning informing the Brazilian experience. Therefore, unworkable plans, ill-diagnosed with little or no supportive instrumentarium or flexibility have been Brazil's legacy. This legacy seems likely to continue until the conception of planning comes to live in the reality of Brazil.

Detection of mycoplasmas in urethral swabs from HIV-1 infected patients and control individuals using culture techniques and polymerase chain reaction

The objective of the present study was to determine the prevalence of certain mycoplasma species, i.e., Mycoplasma hominis, Ureaplasma urealyticum and Mycoplasma penetrans, in urethral swabs from HIV-1 infected patients compared to swabs from a control group. Mycoplasmas were detected by routine culture techniques and by the Polymerase Chain Reaction (PCR) technique, using 16SrRNA generic primers of conserved region and Mycoplasma penetrans specific primers. The positivity rates obtained with the two methods were comparable. Nevertheless, PCR was more sensitive, while the culture techniques allowed the quantification of the isolates. The results showed no significant difference (p < 0.05) in positivity rates between the methods used for mycoplasma detection.

Analysis of molecular biology techniques for the diagnosis of human papillomavirus infection and cervical cancer prevention

The objective of the present study was to evaluate the usefulness of molecular methodologies to access human papillomavirus genome in the genital tract. Samples from 136 women aged 17 to 52 years old obtained from the Dr. Sérgio Franco Laboratories between 2000 and 2001, were analyzed by the hybrid capture assay and amplified by PCR with generic primers MY09/MY11 and specific primers for types 16, 18, 31, 33, 35, 58. Viral genome was detected in 71.3% of the samples by hybrid capture and 75% by amplification. When cytopathology was used as a reference method for screening lesions, hybrid capture (p=0) and amplification (p=0.002) presented positive association. The 3 methods showed absolute agreement when cytopathology confirmed papillomavirus infection and high grade intraepithelial lesion. Disagreements occurred for 10 cases: seven inflammatory cases positive by PCR and negative for hybrid capture and 3 low squamous intraepithelial lesions positive for hybrid capture but negative for amplification. In conclusion, hybrid capture was shown to be sensitive and specific enough for use in clinical routines. Moreover, the evaluation of viral load values obtained by this method were shown to be related to the severity of the lesion and merit further studies to analyze the possible association with risk of progression to malignancy.

Implications of the Hemodynamic Optimization Approach Guided by Right Heart Catheterization in Patients with Severe Heart Failure

OBJECTIVE: To report the hemodynamic and functional responses obtained with clinical optimization guided by hemodynamic parameters in patients with severe and refractory heart failure. METHODS: Invasive hemodynamic monitoring using right heart catheterization aimed to reach low filling pressures and peripheral resistance. Frequent adjustments of intravenous diuretics and vasodilators were performed according to the hemodynamic measurements. RESULTS: We assessed 19 patients (age = 48±12 years and ejection fraction = 21±5%) with severe heart failure. The intravenous use of diuretics and vasodilators reduced by 12 mm Hg (relative reduction of 43%) pulmonary artery occlusion pressure (P<0.001), with a concomitant increment of 6 mL per beat in stroke volume (relative increment of 24%, P<0.001). We observed significant associations between pulmonary artery occlusion pressure and mean pulmonary artery pressure (r=0.76; P<0.001) and central venous pressure (r=0.63; P<0.001). After clinical optimization, improvement in functional class occurred (P< 0.001), with a tendency towards improvement in ejection fraction and no impairment to renal function. CONCLUSION: Optimization guided by hemodynamic parameters in patients with refractory heart failure provides a significant improvement in the hemodynamic profile with concomitant improvement in functional class. This study emphasizes that adjustments in blood volume result in imme-diate benefits for patients with severe heart failure.

Devices and Techniques for Blood Pressure Measurement and Criteria for Hypertension Adopted by Brazilian Physicians: Exploratory Study

OBJECTIVE: To determine technical procedures and criteria used by Brazilian physicians for measuring blood pressure and diagnosing hypertension. METHODS: A questionnaire with 5 questions about practices and behaviors regarding blood pressure measurement and the diagnosis of hypertension was sent to 25,606 physicians in all Brazilian regions through a mailing list. The responses were compared with the recommendations of a specific consensus and descriptive analysis. RESULTS: Of the 3,621 (14.1%) responses obtained, 57% were from the southeastern region of Brazil. The following items were reported: use of an aneroid device by 67.8%; use of a mercury column device by 14.6%; 11.9% of the participants never calibrated the devices; 35.7% calibrated the devices at intervals < 1 year; 85.8% measured blood pressure in 100% of the medical visits; 86.9% measured blood pressure more than once and on more than one occasion. For hypertension diagnosis, 55.7% considered the patient's age, and only 1/3 relied on consensus statements. CONCLUSION: Despite the adequate frequency of both practices, it was far from that expected, and some contradictions between the diagnostic criterion for hypertension and the number of blood pressure measurements were found. The results suggest that, to include the great majority of the medical professionals, disclosure of consensus statements and techniques for blood pressure measurement should go beyond the boundaries of medical events and specialized journals.

Assessment of the techniques of blood pressure measurement by health professionals

OBJECTIVE: To assess blood pressure measurement by health professionals of a public hospital in São Paulo State. METHODS: Semi-structured interviews and direct observation were performed with a verification list according to the criteria reported by Perloff et al. One hundred and five health professionals took part in the study. After measuring blood pressure, the level of concordance between the way the procedure was performed and the recommended one was assessed. RESULTS: Nurses and nurse's aides abided by 40% of the recommended procedures for adequate blood pressure measurement. The other categories of health professionals (nursing and medicine teachers, physicians, residents, and nursing students) abided by approximately 70%. CONCLUSION: Permanent educational activities aiming at standardizing blood pressure measurement should be implemented among the different categories of health professionals.

Protein recovery, separation and purification: selection of optimal techniques using an expert system

The paper discusses the utilization of new techniques ot select processes for protein recovery, separation and purification. It describesa rational approach that uses fundamental databases of proteins molecules to simplify the complex problem of choosing high resolution separation methods for multi component mixtures. It examines the role of modern computer techniques to help solving these questions.

Molecular Genetic Analysis of Multi-drug Resistance in Indian Isolates of Mycobacterium tuberculosis

A total of 116 isolates from patients attending the out-patient department at the All India Institute of Medical Sciences, New Delhi and the New Delhi Tuberculosis Centre, New Delhi, India were collected. They were analyzed for resistance to drugs prescribed in the treatment for tuberculosis. The drug resistance was initially determined by microbiological techniques. The Bactec 460TB system was employed to determine the type and level of resistance in each isolate. The isolates were further characterized at molecular level. The multi-drug loci corresponding to rpo b, gyr A, kat G were studied for mutation(s) by the polymerase chain reaction-single strand conformational polymorphism (PCR-SSCP) technique. The SSCP positive samples were sequenced to characterize the mutations in rpo b, and gyr A loci. While previously reported mutations in the gyr A and rpo b loci were found to be present, several novel mutations were also scored in the rpo b locus. Interestingly, analysis of the gyr A locus showed the presence of point mutation(s) that could not be detected by PCR-SSCP. Furthermore, rifampicin resistance was found to be an important marker for checking multi-drug resistance (MDR) in clinical isolates of Mycobacterium tuberculosis. This is the first report on molecular genetic analysis of MDR tuberculosis one from India, highlights the increasing incidence of MDR in the Indian isolates of M. tuberculosis.