Application of molecular biological methods for studying probiotics and the gut flora

Increasingly, the microbiological scientific community is relying on molecular biology to define the complexity of the gut flora and to distinguish one organism from the next. This is particularly pertinent in the field of probiotics, and probiotic therapy, where identifying probiotics from the commensal flora is often warranted. Current techniques, including genetic fingerprinting, gene sequencing, oligonucleotide probes and specific primer selection, discriminate closely related bacteria with varying degrees of success. Additional molecular methods being employed to determine the constituents of complex microbiota in this area of research are community analysis, denaturing gradient gel electrophoresis (DGGE)/temperature gradient gel electrophoresis (TGGE), fluorescent in situ hybridisation (FISH) and probe grids. Certain approaches enable specific aetiological agents to be monitored, whereas others allow the effects of dietary intervention on bacterial populations to be studied. Other approaches demonstrate diversity, but may not always enable quantification of the population. At the heart of current molecular methods is sequence information gathered from culturable organisms. However, the diversity and novelty identified when applying these methods to the gut microflora demonstrates how little is known about this ecosystem. Of greater concern is the inherent bias associated with some molecular methods. As we understand more of the complexity and dynamics of this diverse microbiota we will be in a position to develop more robust molecular-based technologies to examine it. In addition to identification of the microbiota and discrimination of probiotic strains from commensal organisms, the future of molecular biology in the field of probiotics and the gut flora will, no doubt, stretch to investigations of functionality and activity of the microflora, and/or specific fractions. The quest will be to demonstrate the roles of probiotic strains in vivo and not simply their presence or absence.

Effective elements of cognitive behaviour therapy for psychosis: results of a novel type of subgroup analysis based on principal stratification

Background. Meta-analyses show that cognitive behaviour therapy for psychosis (CBT-P) improves distressing positive symptoms. However, it is a complex intervention involving a range of techniques. No previous study has assessed the delivery of the different elements of treatment and their effect on outcome. Our aim was to assess the differential effect of type of treatment delivered on the effectiveness of CBT-P, using novel statistical methodology. Method. The Psychological Prevention of Relapse in Psychosis (PRP) trial was a multi-centre randomized controlled trial (RCT) that compared CBT-P with treatment as usual (TAU). Therapy was manualized, and detailed evaluations of therapy delivery and client engagement were made. Follow-up assessments were made at 12 and 24 months. In a planned analysis, we applied principal stratification (involving structural equation modelling with finite mixtures) to estimate intention-to-treat (ITT) effects for subgroups of participants, defined by qualitative and quantitative differences in receipt of therapy, while maintaining the constraints of randomization. Results. Consistent delivery of full therapy, including specific cognitive and behavioural techniques, was associated with clinically and statistically significant increases in months in remission, and decreases in psychotic and affective symptoms. Delivery of partial therapy involving engagement and assessment was not effective. Conclusions. Our analyses suggest that CBT-P is of significant benefit on multiple outcomes to patients able to engage in the full range of therapy procedures. The novel statistical methods illustrated in this report have general application to the evaluation of heterogeneity in the effects of treatment.

Gut microbial activity, implications for health and disease: the potential role of metabolite analysis

Microbial metabolism of proteins and amino acids by human gut bacteria generates a variety of compounds including phenol, indole, and sulfur compounds and branched chain fatty acids, many of which have been shown to elicit a toxic effect on the lumen. Bacterial fermentation of amino acids and proteins occurs mainly in the distal colon, a site that is often fraught with symptoms from disorders including ulcerative colitis (UC) and colorectal cancer (CRC). In contrast to carbohydrate metabolism by the gut microbiota, proteolysis is less extensively researched. Many metabolites are low molecular weight, volatile compounds. This review will summarize the use of analytical methods to detect and identify compounds in order to elucidate the relationship between specific dietary proteinaceous substrates, their corresponding metabolites, and implications for gastrointestinal health.

A comparative review of dimension reduction methods in approximate Bayesian computation

Approximate Bayesian computation (ABC) methods make use of comparisons between simulated and observed summary statistics to overcome the problem of computationally intractable likelihood functions. As the practical implementation of ABC requires computations based on vectors of summary statistics, rather than full data sets, a central question is how to derive low-dimensional summary statistics from the observed data with minimal loss of information. In this article we provide a comprehensive review and comparison of the performance of the principal methods of dimension reduction proposed in the ABC literature. The methods are split into three nonmutually exclusive classes consisting of best subset selection methods, projection techniques and regularization. In addition, we introduce two new methods of dimension reduction. The first is a best subset selection method based on Akaike and Bayesian information criteria, and the second uses ridge regression as a regularization procedure. We illustrate the performance of these dimension reduction techniques through the analysis of three challenging models and data sets.

Use of Information Visualization Methods Eliminating Cross Talk in Multiple Sensing Units Investigated for a Light-Addressable Potentiometric Sensor

The integration of nanostructured films containing biomolecules and silicon-based technologies is a promising direction for reaching miniaturized biosensors that exhibit high sensitivity and selectivity. A challenge, however, is to avoid cross talk among sensing units in an array with multiple sensors located on a small area. In this letter, we describe an array of 16 sensing units, of a light-addressable potentiometric sensor (LAPS), which was made with layer-by-Layer (LbL) films of a poly(amidomine) dendrimer (PAMAM) and single-walled carbon nanotubes (SWNTs), coated with a layer of the enzyme penicillinase. A visual inspection of the data from constant-current measurements with liquid samples containing distinct concentrations of penicillin, glucose, or a buffer indicated a possible cross talk between units that contained penicillinase and those that did not. With the use of multidimensional data projection techniques, normally employed in information Visualization methods, we managed to distinguish the results from the modified LAPS, even in cases where the units were adjacent to each other. Furthermore, the plots generated with the interactive document map (IDMAP) projection technique enabled the distinction of the different concentrations of penicillin, from 5 mmol L(-1) down to 0.5 mmol L(-1). Data visualization also confirmed the enhanced performance of the sensing units containing carbon nanotubes, consistent with the analysis of results for LAPS sensors. The use of visual analytics, as with projection methods, may be essential to handle a large amount of data generated in multiple sensor arrays to achieve high performance in miniaturized systems.

Boundary and internal conditions for adjoint fluid-flow problems

The ever-increasing robustness and reliability of flow-simulation methods have consolidated CFD as a major tool in virtually all branches of fluid mechanics. Traditionally, those methods have played a crucial role in the analysis of flow physics. In more recent years, though, the subject has broadened considerably, with the development of optimization and inverse design applications. Since then, the search for efficient ways to evaluate flow-sensitivity gradients has received the attention of numerous researchers. In this scenario, the adjoint method has emerged as, quite possibly, the most powerful tool for the job, which heightens the need for a clear understanding of its conceptual basis. Yet, some of its underlying aspects are still subject to debate in the literature, despite all the research that has been carried out on the method. Such is the case with the adjoint boundary and internal conditions, in particular. The present work aims to shed more light on that topic, with emphasis on the need for an internal shock condition. By following the path of previous authors, the quasi-1D Euler problem is used as a vehicle to explore those concepts. The results clearly indicate that the behavior of the adjoint solution through a shock wave ultimately depends upon the nature of the objective functional.

What determines the use of capital budgeting methods? : Evidence from Swedish listed companies

Purpose: This paper aims to extend and contribute to prior research on the association between company characteristics and choice of capital budgeting methods (CBMs). Design/methodology/approach: A multivariate regression analysis on questionnaire data from 2005 and 2008 is used to study which factors determine the choice of CBMs in Swedish listed companies. Findings: Our results supported hypotheses that Swedish listed companies have become more sophisticated over the years (or at least less unsophisticated) which indicates a closing of the theory-practice gap; that companies with greater leverage used payback more often; and that companies with stricter debt targets and less management ownership employed accounting rate of return more frequent. Moreover, larger companies used CBMs more often. Originality/value: The paper contributes to prior research within this field by being the first Swedish study to examine the association between use of CBMs and as many as twelve independent variables, including changes over time, by using multivariate regression analysis. The results are compared to a US and a continental European study.

Comparison of different analysis techniques for the determination of muscle onset in individuals with patellofemoral pain syndrome

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Comparison of space analysis performed on plaster vs. digital dental casts applying Tanaka and Johnston's equation

OBJETIVO: comparar medidas de tamanhos dentários, suas reprodutibilidades e a aplicação da equação de regressão de Tanaka e Johnston na predição do tamanho dos caninos e pré-molares em modelos de gesso e digital. MÉTODOS: trinta modelos de gesso foram escaneados para obtenção dos modelos digitais. As medidas do comprimento mesiodistal dos dentes foram obtidas com paquímetro digital nos modelos de gesso e nos modelos digitais utilizando o software O3d (Widialabs). A somatória do tamanho dos incisivos inferiores foi utilizada para obter os valores de predição do tamanho dos pré-molares e caninos utilizando equação de regressão, e esses valores foram comparados ao tamanho real dos dentes. Os dados foram analisados estatisticamente, aplicando-se aos resultados o teste de correlação de Pearson, a fórmula de Dahlberg, o teste t pareado e a análise de variância (p < 0,05). RESULTADOS: excelente concordância intraexaminador foi observada nas medidas realizadas em ambos os modelos. O erro aleatório não esteve presente nas medidas obtidas com paquímetro, e o erro sistemático foi mais frequente no modelo digital. A previsão de espaço obtida pela aplicação da equação de regressão foi maior que a somatória dos pré-molares e caninos presentes nos modelos de gesso e nos modelos digitais. CONCLUSÃO: apesar da boa reprodutibilidade das medidas realizadas em ambos os modelos, a maioria das medidas dos modelos digitais foram superiores às do modelos de gesso. O espaço previsto foi superestimado em ambos os modelos e significativamente maior nos modelos digitais.

On the efficacy of texture analysis for crowd monitoring

The goal of this work is to assess the efficacy of texture measures for estimating levels of crowd densities ill images. This estimation is crucial for the problem of crowd monitoring. and control. The assessment is carried out oil a set of nearly 300 real images captured from Liverpool Street Train Station. London, UK using texture measures extracted from the images through the following four different methods: gray level dependence matrices, straight lille segments. Fourier analysis. and fractal dimensions. The estimations of dowel densities are given in terms of the classification of the input images ill five classes of densities (very low, low. moderate. high and very high). Three types of classifiers are used: neural (implemented according to the Kohonen model). Bayesian. and an approach based on fitting functions. The results obtained by these three classifiers. using the four texture measures. allowed the conclusion that, for the problem of crowd density estimation. texture analysis is very effective.

The STATFLUX code: a statistical method for calculation of flow and set of parameters, based on the Multiple-Compartment Biokinetical Model

The code STATFLUX, implementing a new and simple statistical procedure for the calculation of transfer coefficients in radionuclide transport to animals and plants, is proposed. The method is based on the general multiple-compartment model, which uses a system of linear equations involving geometrical volume considerations. Flow parameters were estimated by employing two different least-squares procedures: Derivative and Gauss-Marquardt methods, with the available experimental data of radionuclide concentrations as the input functions of time. The solution of the inverse problem, which relates a given set of flow parameter with the time evolution of concentration functions, is achieved via a Monte Carlo Simulation procedure.Program summaryTitle of program: STATFLUXCatalogue identifier: ADYS_v1_0Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADYS_v1_0Program obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandLicensing provisions: noneComputer for which the program is designed and others on which it has been tested: Micro-computer with Intel Pentium III, 3.0 GHzInstallation: Laboratory of Linear Accelerator, Department of Experimental Physics, University of São Paulo, BrazilOperating system: Windows 2000 and Windows XPProgramming language used: Fortran-77 as implemented in Microsoft Fortran 4.0. NOTE: Microsoft Fortran includes non-standard features which are used in this program. Standard Fortran compilers such as, g77, f77, ifort and NAG95, are not able to compile the code and therefore it has not been possible for the CPC Program Library to test the program.Memory, required to execute with typical data: 8 Mbytes of RAM memory and 100 MB of Hard disk memoryNo. of bits in a word: 16No. of lines in distributed program, including test data, etc.: 6912No. of bytes in distributed Program, including test data, etc.: 229 541Distribution format: tar.gzNature of the physical problem: the investigation of transport mechanisms for radioactive substances, through environmental pathways, is very important for radiological protection of populations. One such pathway, associated with the food chain, is the grass-animal-man sequence. The distribution of trace elements in humans and laboratory animals has been intensively studied over the past 60 years [R.C. Pendlenton, C.W. Mays, R.D. Lloyd, A.L. Brooks, Differential accumulation of iodine-131 from local fallout in people and milk, Health Phys. 9 (1963) 1253-1262]. In addition, investigations on the incidence of cancer in humans, and a possible causal relationship to radioactive fallout, have been undertaken [E.S. Weiss, M.L. Rallison, W.T. London, W.T. Carlyle Thompson, Thyroid nodularity in southwestern Utah school children exposed to fallout radiation, Amer. J. Public Health 61 (1971) 241-249; M.L. Rallison, B.M. Dobyns, F.R. Keating, J.E. Rall, F.H. Tyler, Thyroid diseases in children, Amer. J. Med. 56 (1974) 457-463; J.L. Lyon, M.R. Klauber, J.W. Gardner, K.S. Udall, Childhood leukemia associated with fallout from nuclear testing, N. Engl. J. Med. 300 (1979) 397-402]. From the pathways of entry of radionuclides in the human (or animal) body, ingestion is the most important because it is closely related to life-long alimentary (or dietary) habits. Those radionuclides which are able to enter the living cells by either metabolic or other processes give rise to localized doses which can be very high. The evaluation of these internally localized doses is of paramount importance for the assessment of radiobiological risks and radiological protection. The time behavior of trace concentration in organs is the principal input for prediction of internal doses after acute or chronic exposure. The General Multiple-Compartment Model (GMCM) is the powerful and more accepted method for biokinetical studies, which allows the calculation of concentration of trace elements in organs as a function of time, when the flow parameters of the model are known. However, few biokinetics data exist in the literature, and the determination of flow and transfer parameters by statistical fitting for each system is an open problem.Restriction on the complexity of the problem: This version of the code works with the constant volume approximation, which is valid for many situations where the biological half-live of a trace is lower than the volume rise time. Another restriction is related to the central flux model. The model considered in the code assumes that exist one central compartment (e.g., blood), that connect the flow with all compartments, and the flow between other compartments is not included.Typical running time: Depends on the choice for calculations. Using the Derivative Method the time is very short (a few minutes) for any number of compartments considered. When the Gauss-Marquardt iterative method is used the calculation time can be approximately 5-6 hours when similar to 15 compartments are considered. (C) 2006 Elsevier B.V. All rights reserved.

Densitometry, radiography, and histological assessment of collagen as methods to evaluate femoral bones in an experimental model of osteoporosis

All methods to detect experimental loss of bone present technique limitations. The sensitivities of image and histological analyses to detect the effects of teriparatide in rats with bone loss after ovariectomy were evaluated. All methods were qualitatively valid.The standardization of methods to assess bone loss after ovariectomy is crucial to establish the degree of experimental osteoporosis. In general, methods per image or histological techniques are used. To validate these two ways to determine the degree of bone loss in ovariectomized rats, we evaluated the sensitivities of bone densitometry, conventional radiography, and histological analysis of the area occupied by collagen, detecting the effects of teriparatide treatment in the femur of ovariectomized rats with bone loss.Wistar rats were divided into three groups: a control group, in which the animals were only subjected to laparotomy; an ovariectomized group, in which bilateral removal of the ovaries was performed; and an ovariectomized + teriparatide group, in which bilateral removal of the ovaries was performed, and the animals were treated with 3 mu g/100 g/day of teriparatide. Three months following the ovariectomy, bone densitometry, radiographic densitometry, and histological analysis of the area occupied by collagen fibers were carried out in the femur diaphysis.The bone densitometry revealed 11.2% reduction in femur density; in the conventional radiography, the loss of bone mass was 14.5%, and with the histological analysis, a 40.9% reduction in the area occupied by collagen was detected in the femur diaphysis.In conclusion, histological analysis could not be quantitatively compared with the methods of bone densitometry and conventional radiography; however, all of these methods were qualitatively valid for assessing the loss of bone stemming from ovariectomy and the therapeutic effect of teriparatide in the prevention of osteoporosis.

Precision of yule-walker methods for the arma spectral model

In this work a new method is proposed of separated estimation for the ARMA spectral model based on the modified Yule-Walker equations and on the least squares method. The proposal of the new method consists of performing an AR filtering in the random process generated obtaining a new random estimate, which will reestimate the ARMA model parameters, given a better spectrum estimate. Some numerical examples will be presented in order to ilustrate the performance of the method proposed, which is evaluated by the relative error and the average variation coefficient.

Evaluation of the effects of different extraction methods for main volatile compounds from Bambusa textilis leaves

Bambusa textilis is widely used in popular medicine to treat all kinds of wound inflammation, chronic fever, pulmonary and infectious diseases. The aim of this study was to compare the chemical composition of the extracts of B. textilis leaves obtained by three different extraction methods: solid/liquid extraction, Soxhlet and Clevenger system using gas chromatography with flame ionization detector (GC-FID) and gas chromatography with mass spectrometry (GC-MS) analyses. The analytical characteristics of the extracts showed some differences and the GC-MS analysis indicated the presence of higher concentrations of nitro compounds and alkalis. © VSP 2005.

Fusion of fingerprint recognition methods for robust human identification

Biometrics is one of the biggest tendencies in human identification. The fingerprint is the most widely used biometric. However considering the automatic fingerprint recognition a completely solved problem is a common mistake. The most popular and extensively used methods, the minutiae-based, do not perform well on poor-quality images and when just a small area of overlap between the template and the query images exists. The use of multibiometrics is considered one of the keys to overcome the weakness and improve the accuracy of biometrics systems. This paper presents the fusion of a minutiae-based and a ridge-based fingerprint recognition method at rank, decision and score level. The fusion techniques implemented leaded to a reduction of the Equal Error Rate by 31.78% (from 4.09% to 2.79%) and a decreasing of 6 positions in the rank to reach a Correct Retrieval (from rank 8 to 2) when assessed in the FVC2002-DB1A database. © 2008 IEEE.