A simple model for the estimation of congenital malformation frequency in racially mixed populations

A simple model is proposed, using the method of maximum likelihood to estimate malformation frequencies in racial groups based on data obtained from hospital services. This model uses the proportions of racial admixture, and the observed malformation frequency. It was applied to two defects: postaxial polydactyly and cleft lip, the frequencies of which are recognizedly heterogeneous among racial groups. The frequencies estimated in each racial group were those expected for these malformations, which proves the applicability of the method.

Differences between remaining ability and loss of capacity in maximum aerobic impairment

In the evaluation of exercise intolerance of patients with respiratory diseases the American Medical Association (AMA) and the American Thoracic Society (ATS) have proposed similar classifications for rating aerobic impairment using maximum oxygen uptake (VO2max) normalized for total body weight (ml min-1 kg-1). However, subjects with the same VO2max weight-corrected values may have considerably different losses of aerobic performance (VO2max expressed as % predicted). We have proposed a new, specific method for rating loss of aerobic capacity (VO2max, % predicted) and we have compared the two classifications in a prospective study involving 75 silicotic claimants. Logistic regression analysis showed that the disagreement between rating systems (higher dysfunction by the AMA/ATS classification) was associated with age >50 years (P<0.005) and overweight (P = 0.04). Interestingly, clinical (dyspnea score) and spirometric (FEV1) normality were only associated with the VO2max, % predicted, normal values (P<0.01); therefore, in older and obese subjects the AMA/ATS classification tended to overestimate the aerobic dysfunction. We conclude that in the evaluation of aerobic impairment in patients with respiratory diseases, the loss of aerobic capacity (VO2max, % predicted) should be used instead of the traditional method (remaining aerobic ability, VO2max, in ml min-1 kg-1).

pp-Blast: a "pseudo-parallel" Blast

We have developed a software called pp-Blast that uses the publicly available Blast package and PVM (parallel virtual machine) to partition a multi-sequence query across a set of nodes with replicated or shared databases. Benchmark tests show that pp-Blast running in a cluster of 14 PCs outperformed conventional Blast running in large servers. In addition, using pp-Blast and the cluster we were able to map all human cDNAs onto the draft of the human genome in less than 6 days. We propose here that the cost/benefit ratio of pp-Blast makes it appropriate for large-scale sequence analysis. The source code and configuration files for pp-Blast are available at http://www.ludwig.org.br/biocomp/tools/pp-blast.

Simulating the dynamics of silver market using computational market dynamics

Traditional econometric approaches in modeling the dynamics of equity and commodity markets, have, made great progress in the past decades. However, they assume rationality among the economic agents and and do not capture the dynamics that produce extreme events (black swans), due to deviation from the rationality assumption. The purpose of this study is to simulate the dynamics of silver markets by using the novel computational market dynamics approach. To this end, the daily data from the period of 1st March 2000 to 1st March 2013 of closing prices of spot silver prices has been simulated with the Jabłonska-Capasso-Morale(JCM) model. The Maximum Likelihood approach has been employed to calibrate the acquired data with JCM. Statistical analysis of the simulated series with respect to the actual one has been conducted to evaluate model performance. The model captures the animal spirits dynamics present in the data under evaluation well.

An EDTA-β-cyclodextrin adsorbent for the adsorption of rare earth elements and its application in preconcentration of ultratrace rare earth elements from seawater

The objectives of this work were synthesizing an EDTA-β-CD adsorbent and investigating its adsorption potential and applications in preconcentration of REEs from aqueous phase. The adsorption capacity of EDTA-β-CD was investigated. The adsorption studies were performed by batch techniques both in one- and multi-component systems. The effects of pH, contact time and initial concentration were evaluated. The analytical detection methods and characterization methods were presented. EDTA-β-CD adsorbent was synthesized successfully with high EDTA coverage. The maximum REEs uptake was 0.310 mmol g-1 for La(III), 0.337 mmol g-1 for Ce(III) and 0.353 mmol g-1 for Eu(III), respectively. The kinetics of REEs onto EDTA-β-CD fitted well to pseudo-second-order model and the adsorption rate was affected by intra-particle diffusion. The experimental data of one component studies fitted to Langmuir isotherm model indicating the homogeneous surface of the adsorbent. The extended Sips model was applicable for the isotherm studies in three-component system. The electrostatic interaction, chelation and complexation were all involved in the adsorption mechanism. The preconcentration of RE ions and regeneration of EDTA-β-CD were successful. Overall, EDTA-β-CD is an effective adsorbent in adsorption and preconcentration of REEs.

Kalman filter for computational market dynamics

Kalman filter is a recursive mathematical power tool that plays an increasingly vital role in innumerable fields of study. The filter has been put to service in a multitude of studies involving both time series modelling and financial time series modelling. Modelling time series data in Computational Market Dynamics (CMD) can be accomplished using the Jablonska-Capasso-Morale (JCM) model. Maximum likelihood approach has always been utilised to estimate the parameters of the JCM model. The purpose of this study is to discover if the Kalman filter can be effectively utilized in CMD. Ensemble Kalman filter (EnKF), with 50 ensemble members, applied to US sugar prices spanning the period of January, 1960 to February, 2012 was employed for this work. The real data and Kalman filter trajectories showed no significant discrepancies, hence indicating satisfactory performance of the technique. Since only US sugar prices were utilized, it would be interesting to discover the nature of results if other data sets are employed.

Use of magnitude-squared coherence to identify the maximum driving response band of the somatosensory evoked potential

The present study proposes to apply magnitude-squared coherence (MSC) to the somatosensory evoked potential for identifying the maximum driving response band. EEG signals, leads [Fpz'-Cz'] and [C3'-C4'], were collected from two groups of normal volunteers, stimulated at the rate of 4.91 (G1: 26 volunteers) and 5.13 Hz (G2: 18 volunteers). About 1400 stimuli were applied to the right tibial nerve at the motor threshold level. After applying the anti-aliasing filter, the signals were digitized and then further low-pass filtered (200 Hz, 6th order Butterworth and zero-phase). Based on the rejection of the null hypothesis of response absence (MSC(f) > 0.0060 with 500 epochs and the level of significance set at a = 0.05), the beta and gamma bands, 15-66 Hz, were identified as the maximum driving response band. Taking both leads together ("logical-OR detector", with a false-alarm rate of a = 0.05, and hence a = 0.0253 for each derivation), the detection exceeded 70% for all multiples of the stimulation frequency within this range. Similar performance was achieved for MSC of both leads but at 15, 25, 35, and 40 Hz. Moreover, the response was detected in [C3'-C4'] at 35.9 Hz and in [Fpz'-Cz'] at 46.2 Hz for all members of G2. Using the "logical-OR detector" procedure, the response was detected at the 7th multiple of the stimulation frequency for the series as a whole (considering both groups). Based on these findings, the MSC technique may be used for monitoring purposes.

A clinical gamma camera-based pinhole collimated system for high resolution small animal SPECT imaging

The main objective of the present study was to upgrade a clinical gamma camera to obtain high resolution tomographic images of small animal organs. The system is based on a clinical gamma camera to which we have adapted a special-purpose pinhole collimator and a device for positioning and rotating the target based on a computer-controlled step motor. We developed a software tool to reconstruct the target’s three-dimensional distribution of emission from a set of planar projections, based on the maximum likelihood algorithm. We present details on the hardware and software implementation. We imaged phantoms and heart and kidneys of rats. When using pinhole collimators, the spatial resolution and sensitivity of the imaging system depend on parameters such as the detector-to-collimator and detector-to-target distances and pinhole diameter. In this study, we reached an object voxel size of 0.6 mm and spatial resolution better than 2.4 and 1.7 mm full width at half maximum when 1.5- and 1.0-mm diameter pinholes were used, respectively. Appropriate sensitivity to study the target of interest was attained in both cases. Additionally, we show that as few as 12 projections are sufficient to attain good quality reconstructions, a result that implies a significant reduction of acquisition time and opens the possibility for radiotracer dynamic studies. In conclusion, a high resolution single photon emission computed tomography (SPECT) system was developed using a commercial clinical gamma camera, allowing the acquisition of detailed volumetric images of small animal organs. This type of system has important implications for research areas such as Cardiology, Neurology or Oncology.

Plasma cytokine response, lipid peroxidation and NF-κB activation in skeletal muscle following maximum progressive swimming

Our objective was to determine lipid peroxidation and nuclear factor-κB (NF-κB) activation in skeletal muscle and the plasma cytokine profile following maximum progressive swimming. Adult male Swiss mice (N = 15) adapted to the aquatic environment were randomly divided into three groups: immediately after exercise (EX1), 3 h after exercise (EX2) and control. Animals from the exercising groups swam until exhaustion, with an initial workload of 2% of body mass attached to the tail. Control mice did not perform any exercise but were kept immersed in water for 20 min. Maximum swimming led to reactive oxygen species (ROS) generation in skeletal muscle, as indicated by increased thiobarbituric acid reactive species (TBARS) levels (4062.67 ±1487.10 vs 19,072.48 ± 8738.16 nmol malondialdehyde (MDA)/mg protein, control vs EX1). Exercise also promoted NF-κB activation in soleus muscle. Cytokine secretion following exercise was marked by increased plasma interleukin-6 (IL-6) levels 3 h post-exercise (P < 0.05). Interleukin-10 (IL-10) levels were reduced following exercise and remained reduced 3 h post-exercise (P < 0.05). Plasma levels of other cytokines investigated, monocyte chemotactic protein-1 (MCP-1), tumor necrosis factor-alpha (TNF-α), interferon-gamma (IFN-γ) and interleukin-12 (IL-12), were not altered by exercise. The present findings showed that maximum swimming, as well as other exercise models, led to lipid peroxidation and NF-κB activation in skeletal muscle and increased plasma IL-6 levels. The plasma cytokine response was also marked by reduced IL-10 levels. These results were attributed to exercise type and intensity.

Performance assessment of the single photon emission microscope: high spatial resolution SPECT imaging of small animal organs

The single photon emission microscope (SPEM) is an instrument developed to obtain high spatial resolution single photon emission computed tomography (SPECT) images of small structures inside the mouse brain. SPEM consists of two independent imaging devices, which combine a multipinhole collimator, a high-resolution, thallium-doped cesium iodide [CsI(Tl)] columnar scintillator, a demagnifying/intensifier tube, and an electron-multiplying charge-coupling device (CCD). Collimators have 300- and 450-µm diameter pinholes on tungsten slabs, in hexagonal arrays of 19 and 7 holes. Projection data are acquired in a photon-counting strategy, where CCD frames are stored at 50 frames per second, with a radius of rotation of 35 mm and magnification factor of one. The image reconstruction software tool is based on the maximum likelihood algorithm. Our aim was to evaluate the spatial resolution and sensitivity attainable with the seven-pinhole imaging device, together with the linearity for quantification on the tomographic images, and to test the instrument in obtaining tomographic images of different mouse organs. A spatial resolution better than 500 µm and a sensitivity of 21.6 counts·s-1·MBq-1 were reached, as well as a correlation coefficient between activity and intensity better than 0.99, when imaging 99mTc sources. Images of the thyroid, heart, lungs, and bones of mice were registered using 99mTc-labeled radiopharmaceuticals in times appropriate for routine preclinical experimentation of <1 h per projection data set. Detailed experimental protocols and images of the aforementioned organs are shown. We plan to extend the instrument's field of view to fix larger animals and to combine data from both detectors to reduce the acquisition time or applied activity.

Bayesian analysis of SEIR epidemic models

This thesis concerns the analysis of epidemic models. We adopt the Bayesian paradigm and develop suitable Markov Chain Monte Carlo (MCMC) algorithms. This is done by considering an Ebola outbreak in the Democratic Republic of Congo, former Zaïre, 1995 as a case of SEIR epidemic models. We model the Ebola epidemic deterministically using ODEs and stochastically through SDEs to take into account a possible bias in each compartment. Since the model has unknown parameters, we use different methods to estimate them such as least squares, maximum likelihood and MCMC. The motivation behind choosing MCMC over other existing methods in this thesis is that it has the ability to tackle complicated nonlinear problems with large number of parameters. First, in a deterministic Ebola model, we compute the likelihood function by sum of square of residuals method and estimate parameters using the LSQ and MCMC methods. We sample parameters and then use them to calculate the basic reproduction number and to study the disease-free equilibrium. From the sampled chain from the posterior, we test the convergence diagnostic and confirm the viability of the model. The results show that the Ebola model fits the observed onset data with high precision, and all the unknown model parameters are well identified. Second, we convert the ODE model into a SDE Ebola model. We compute the likelihood function using extended Kalman filter (EKF) and estimate parameters again. The motivation of using the SDE formulation here is to consider the impact of modelling errors. Moreover, the EKF approach allows us to formulate a filtered likelihood for the parameters of such a stochastic model. We use the MCMC procedure to attain the posterior distributions of the parameters of the SDE Ebola model drift and diffusion parts. In this thesis, we analyse two cases: (1) the model error covariance matrix of the dynamic noise is close to zero , i.e. only small stochasticity added into the model. The results are then similar to the ones got from deterministic Ebola model, even if methods of computing the likelihood function are different (2) the model error covariance matrix is different from zero, i.e. a considerable stochasticity is introduced into the Ebola model. This accounts for the situation where we would know that the model is not exact. As a results, we obtain parameter posteriors with larger variances. Consequently, the model predictions then show larger uncertainties, in accordance with the assumption of an incomplete model.

Sulphuric acid scarification effects on Brachiaria brizantha, B. humidicola and Panicum maximum seed dormancy release

Most tropical forage grass species have dormant seeds, which reduce percentages in germination tests. The objective of this study was to evaluate H2SO4 scarification effects on seed dormancy releasing, through germination time (T50) and variability among germination test replicates, in 630, 94 and 82 seed samples of B. brizantha, B. humidicola and P. maximum, respectively, tested at the Central Seed Testing Laboratory, Campinas, Brazil, from 1991 to 1999. Germination tests used two 4 x 100 replicates of intact and scarified seeds (15-, 10-, 5-minute treatments, respectively). Mean germination time (T50) and variability among germination replicates were also analysed. Statistical analysis was performed by t-test paired samples for means. Scarification promoted general decreases in T50, while variability among germination test replicates was reduced in B. brizantha. Scarification increase germination in B. brizantha and P. maximum, but is deleterious in B. humidicola.

Avaliação da viabilidade de sementes de Panicum maximum Jacq pelo teste de tetrazólio

O Brasil tem muitas áreas com Panicum maximum Jacq, sendo produtor, consumidor e exportador de suas sementes. Contudo, a qualidade das sementes produzidas é duvidosa. O teste de germinação não é eficiente para estimar a viabilidade de sementes desta espécie, principalmente logo após a colheita, quando se tem alto percentual de sementes dormentes, sendo necessária a realização do teste de tetrazólio. Com o objetivo de avaliar as metodologias mais utilizadas na condução do teste de tetrazólio determinou-se a viabilidade de quatro lotes da cultivar Tanzânia, com diferentes qualidades fisiológicas e intensidades de dormência, através das seguintes metodologias e concentrações da solução de 2,3,5 trifenil cloreto tetrazólio: 1,0% (conforme metodologia prescrita pela International Seed Testing Association - ISTA); 0,2% com descarte de metade da sementes e 0,1% sem descarte de uma metade da semente. Como referencial, o teste de germinação foi realizado com e sem tratamento para superação da dormência, sendo as avaliações realizadas em quatro épocas trimestrais. Como tratamento para superação da dormência utilizou-se a temperatura de 42° C durante 72 horas. Não houve diferenças significativas entre as diferentes metodologias utilizadas para o teste de tetrazólio. A visualização da estrutura embrionária foi facilitada quando foram avaliadas as duas metades das sementes. Não houve diferença siginifcativa entre a viabilidade, pelo teste de tetrazólio, e a germinação de lotes sem sementes dormentes. O tratamento para superação da dormência não foi eficiente para todas as sementes e prejudicou a germinação, quando não havia mais dormência. Os lotes que não possuíam sementes dormentes não apresentaram diferenças significativas entre os resultados dos testes de germinação e tetrazólio.

A beleza no ritmo pseudo-dionisiano da processão/conversão

No contexto da Metafísica Medieval, a «beleza» foi pensada como um conceito ambíguo: ora atribuído a Deus, ora atribuído ao Mundo. O propósito deste artigo é clarificar o sentido desta ambiguidade no âmbito da filosofia do Pseudo-Dionísio Areopagita. Se, portanto, o conceito de «beleza» é, em primeiro lugar, despojado do seu carácter sensível e mundano, para ser apropriado à natureza divina, ele é, num segundo momento, aposto à própria criação, de forma a designar a manifestação visível da beleza transcendente e o chamamento vital para a perscrutação teológica.