Investigation and data adaptive analysis of CARS spectra

In this diploma work advantages of coherent anti-Stokes Raman scattering spectrometry (CARS) and various methods of the quantitative analysis of substance structure with its help are considered. The basic methods and concepts of the adaptive analysis are adduced. On the basis of these methods the algorithm of automatic measurement of a scattering strip size of a target component in CARS spectrum is developed. The algorithm uses known full spectrum of target substance and compares it with a CARS spectrum. The form of a differential spectrum is used as a feedback to control the accuracy of matching. To exclude the influence of a background in CARS spectra the differential spectrum is analysed by means of its second derivative. The algorithm is checked up on the simulated simple spectra and on the spectra of organic compounds received experimentally.

Breast Imaging Reporting and Data System - BI-RADS®: valor preditivo positivo das categorias 3, 4 e 5. revisão sistemática da literatura

OBJETIVO: Avaliar artigos, na literatura, que verificam o valor preditivo positivo das categorias 3, 4 e 5 do Breast Imaging Reporting and Data System (BI-RADS®). MATERIAIS E MÉTODOS: Foi realizada pesquisa na base de dados Medline utilizando os termos "predictive value" e "BI-RADS". Foram incluídos 11 artigos nesta revisão. RESULTADOS: O valor preditivo positivo das categorias 3, 4 e 5 variou entre 0% e 8%, 4% e 62%, 54% e 100%, respectivamente. Três artigos avaliaram, concomitantemente, os critérios morfológicos das lesões que apresentaram maior valor preditivo positivo na mamografia, sendo nódulo espiculado o critério com maior valor preditivo positivo. CONCLUSÃO: Houve grande variabilidade do valor preditivo positivo das categorias 3, 4 e 5 do BI-RADS® em todos os estudos, porém foram identificadas diferenças metodológicas que limitaram a comparação desses estudos.

Valor preditivo positivo das categorias 3, 4 e 5 do Breast Imaging Reporting and Data System (BI-RADS®)

OBJETIVO: O objetivo deste trabalho foi avaliar o BI-RADS® como fator preditivo de suspeição de malignidade em lesões mamárias não palpáveis nas categorias 3, 4 e 5, correlacionando as mamografias com os resultados histopatológicos através do cálculo do valor preditivo positivo do exame mamográfico. MATERIAIS E MÉTODOS: Trezentas e setenta e uma pacientes encaminhadas a um serviço de referência em tratamento de câncer em Teresina, PI, para realização de exames histopatológicos em mama no período de julho de 2005 a março de 2008, por terem mamografia de categorias 3, 4 ou 5, tiveram seus exames revisados. Das 371 pacientes, 265 foram submetidas a biópsia por agulha grossa e 106, a marcação pré-cirúrgica. RESULTADOS: Em relação às mamografias, 11,32% foram classificadas como categoria 3, 76,28% como categoria 4 e 12,4% como categoria 5. Os resultados histológicos demonstraram 24% de exames positivos para malignidade. Os valores preditivos positivos das categorias 3, 4 e 5 foram, respectivamente, de 7,14%, 16,96% e 82,61%. Foram calculados os valores preditivos positivos, separadamente, para as biópsias percutâneas (7,14%, 15,76%, 76,47%) e para as marcações pré-cirúrgicas (7,14%, 20%, 100%). CONCLUSÃO: Achados malignos foram subestimados pelo laudo radiológico e houve superestimação de achados benignos, o que resultou na realização desnecessária de alguns procedimentos invasivos.

Positive predictive values of Breast Imaging Reporting and Data System (BI-RADS®) categories 3, 4 and 5 in breast lesions submitted to percutaneous biopsy

Objective To evaluate the BI-RADS as a predictive factor of suspicion for malignancy in breast lesions by correlating radiological with histological results and calculating the positive predictive value for categories 3, 4 and 5 in a breast cancer reference center in the city of São Paulo. Materials and Methods Retrospective, analytical and cross-sectional study including 725 patients with mammographic and/or sonographic findings classified as BI-RADS categories 3, 4 and 5 who were referred to the authors' institution to undergo percutaneous biopsy. The tests results were reviewed and the positive predictive value was calculated by means of a specific mathematical equation. Results Positive predictive values found for categories 3, 4 and 5 were respectively the following: 0.74%, 33.08% and 92.95%, for cases submitted to ultrasound-guided biopsy, and 0.00%, 14.90% and 100% for cases submitted to stereotactic biopsy. Conclusion The present study demonstrated high suspicion for malignancy in lesions classified as category 5 and low risk for category 3. As regards category 4, the need for systematic biopsies was observed.

Tools and data services registry: a community effort to document bioinformatics resources.

Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand.Here we present a community-driven curation effort, supported by ELIXIR-the European infrastructure for biological information-that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners.As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools.

Trigger and data link system for CMS Resistive Plate Chambers at the LHC accelerator

The purpose of the work was to realize a high-speed digital data transfer system for RPC muon chambers in the CMS experiment on CERN’s new LHC accelerator. This large scale system took many years and many stages of prototyping to develop, and required the participation of tens of people. The system interfaces to Frontend Boards (FEB) at the 200,000-channel detector and to the trigger and readout electronics in the control room of the experiment. The distance between these two is about 80 metres and the speed required for the optic links was pushing the limits of available technology when the project was started. Here, as in many other aspects of the design, it was assumed that the features of readily available commercial components would develop in the course of the design work, just as they did. By choosing a high speed it was possible to multiplex the data from some the chambers into the same fibres to reduce the number of links needed. Further reduction was achieved by employing zero suppression and data compression, and a total of only 660 optical links were needed. Another requirement, which conflicted somewhat with choosing the components a late as possible was that the design needed to be radiation tolerant to an ionizing dose of 100 Gy and to a have a moderate tolerance to Single Event Effects (SEEs). This required some radiation test campaigns, and eventually led to ASICs being chosen for some of the critical parts. The system was made to be as reconfigurable as possible. The reconfiguration needs to be done from a distance as the electronics is not accessible except for some short and rare service breaks once the accelerator starts running. Therefore reconfigurable logic is extensively used, and the firmware development for the FPGAs constituted a sizable part of the work. Some special techniques needed to be used there too, to achieve the required radiation tolerance. The system has been demonstrated to work in several laboratory and beam tests, and now we are waiting to see it in action when the LHC will start running in the autumn 2008.

Automatic evaluation and data generation for analytical chemistry instrumental analysis exercises

In general, laboratory activities are costly in terms of time, space, and money. As such, the ability to provide realistically simulated laboratory data that enables students to practice data analysis techniques as a complementary activity would be expected to reduce these costs while opening up very interesting possibilities. In the present work, a novel methodology is presented for design of analytical chemistry instrumental analysis exercises that can be automatically personalized for each student and the results evaluated immediately. The proposed system provides each student with a different set of experimental data generated randomly while satisfying a set of constraints, rather than using data obtained from actual laboratory work. This allows the instructor to provide students with a set of practical problems to complement their regular laboratory work along with the corresponding feedback provided by the system's automatic evaluation process. To this end, the Goodle Grading Management System (GMS), an innovative web-based educational tool for automating the collection and assessment of practical exercises for engineering and scientific courses, was developed. The proposed methodology takes full advantage of the Goodle GMS fusion code architecture. The design of a particular exercise is provided ad hoc by the instructor and requires basic Matlab knowledge. The system has been employed with satisfactory results in several university courses. To demonstrate the automatic evaluation process, three exercises are presented in detail. The first exercise involves a linear regression analysis of data and the calculation of the quality parameters of an instrumental analysis method. The second and third exercises address two different comparison tests, a comparison test of the mean and a t-paired test.

Spectrophotometric study of iron oxidation in the iron(II)/thiocyanate/acetone system and some analytical applications

The possibility of using thiocyanate to determine iron(II) and/or iron(III) in water-acetone mixture has been re-examined as part of a systematic and comparative study involving metallic complexes of pseudohalide ligands. Some parameters that affect the complete oxidation of the ferrous cations, their subsequent complexation and the system stability have been studied to optimize the experimental conditions. Our results show the viability and potentiality of this simply methodology as an alternative analytical procedure to determine iron cations with high sensitivity, precision and accuracy. Studies on the calibration, stability, precision, and effect of various different ions have been carried out by using absorbance values measured at 480 nm. The analytical curve for the total iron determination obeys Beer's law (r = 0.9993), showing a higher sensitivity (molar absorptivity of 2.10x10(4) L cm-1 mol-1) when compared with other traditional systems (ligands) or even with the "similar" azide ion [1.53x10(4) L cm-1 mol-1, for iron-III/azide complexes, in 70% (v/v) tetrahydrofuran/water, at 396 nm]. Under such optimized experimental conditions, it is possible to determine iron in the concentration range from 0.5 to 2 ppm (15-65% T for older equipments, quartz cells of 1.00 cm). Analytical applications have been tested for some different materials (iron ores), also including pharmaceutical products for anemia, and results were compared with atomic absorption determinations. Very good agreement was obtained with these two different techniques, showing the potential of the present experimental conditions for the total iron spectrophotometric determinations (errors < 5%). The possibility of iron speciation was made evident by using another specific and auxiliary method for iron(II) or (III).

Structural and operational optimisation : applications in energy systems

In this work mathematical programming models for structural and operational optimisation of energy systems are developed and applied to a selection of energy technology problems. The studied cases are taken from industrial processes and from large regional energy distribution systems. The models are based on Mixed Integer Linear Programming (MILP), Mixed Integer Non-Linear Programming (MINLP) and on a hybrid approach of a combination of Non-Linear Programming (NLP) and Genetic Algorithms (GA). The optimisation of the structure and operation of energy systems in urban regions is treated in the work. Firstly, distributed energy systems (DES) with different energy conversion units and annual variations of consumer heating and electricity demands are considered. Secondly, district cooling systems (DCS) with cooling demands for a large number of consumers are studied, with respect to a long term planning perspective regarding to given predictions of the consumer cooling demand development in a region. The work comprises also the development of applications for heat recovery systems (HRS), where paper machine dryer section HRS is taken as an illustrative example. The heat sources in these systems are moist air streams. Models are developed for different types of equipment price functions. The approach is based on partitioning of the overall temperature range of the system into a number of temperature intervals in order to take into account the strong nonlinearities due to condensation in the heat recovery exchangers. The influence of parameter variations on the solutions of heat recovery systems is analysed firstly by varying cost factors and secondly by varying process parameters. Point-optimal solutions by a fixed parameter approach are compared to robust solutions with given parameter variation ranges. In the work enhanced utilisation of excess heat in heat recovery systems with impingement drying, electricity generation with low grade excess heat and the use of absorption heat transformers to elevate a stream temperature above the excess heat temperature are also studied.

Avaliação de microcalcificações mamárias de acordo com as classificações do Breast Imaging Reporting and Data System (BI-RADS TM) e de Le Gal

OBJETIVO: avaliar a acurácia da mamografia para o diagnóstico de microcalcificações mamárias suspeitas, com as classificações do Breast Imaging Reporting and Data System (BI-RADS TM) e Le Gal em comparação com o resultado histopatológico utilizado como padrão-ouro. MÉTODOS: foram selecionados dos arquivos dos blocos cirúrgicos, 130 casos operados com mamografias contendo somente microcalcificações mamárias, inicialmente classificadas como suspeitas sem lesões detectáveis ao exame clínico. Estas foram reclassificadas por dois examinadores, utilizando as classificações de Le Gal e BI-RADS TM, obtendo-se diagnóstico de consenso. As biópsias foram revistas por dois patologistas e foi obtido diagnóstico de consenso. A leitura das mamografias e a revisão das lâminas foram feitas em duplo-cego. As análises estatísticas utilizadas neste estudo foram o teste do chi2, o modelo Fleiss quadrático para VPP e o programa Epi-Info 6.0. RESULTADOS: a correlação entre a análise histopatológica e mamográfica, usando BI-RADS TM e Le Gal, mostrou a mesma sensibilidade de 96,4%, especificidade de 55,9 e 30,3%, valor preditivo positivo (VPP) de 37,5% e 27,5% e acurácia de 64,6 e 44,6%, respectivamente. Quando discriminamos por categorias de BI-RADS TM, obtivemos VPPs: categoria 2, 0%; categoria 3, 1,8%; categoria 4, 31,6% e categoria 5, 60%. Os VPPs pela classificação de Le Gal foram: categoria 2, 3,1%; categoria 3, 18,1 %; categoria 4, 26,4%; categoria 5, 66,7% e não classificável, 5,2%. CONCLUSÕES: observou-se uma maior precisão com a classificação de BI-RADS TM, porém não se conseguiu reduzir a ambigüidade na avaliação das microcalcificações mamárias.

E-thesis repository – processes and data

Poster at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Targeted Annotation of Scientific Literature and Data Resources in Invenio Digital Libraries

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Building Dynamic Data Centers for Fast Delivery of New Data and Data Updates

Poster at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014