Development of a cross-European virtual sample repository and HIV resistance database

BACKGROUND: Several European HIV observational data bases have, over the last decade, accumulated a substantial number of resistance test results and developed large sample repositories, There is a need to link these efforts together, We here describe the development of such a novel tool that allows to bind these data bases together in a distributed fashion for which the control and data remains with the cohorts rather than classic data mergers.METHODS: As proof-of-concept we entered two basic queries into the tool: available resistance tests and available samples. We asked for patients still alive after 1998-01-01, and between 180 and 195 cm of height, and how many samples or resistance tests there would be available for these patients, The queries were uploaded with the tool to a central web server from which each participating cohort downloaded the queries with the tool and ran them against their database, The numbers gathered were then submitted back to the server and we could accumulate the number of available samples and resistance tests.RESULTS: We obtained the following results from the cohorts on available samples/resistance test: EuResist: not availableI11,194; EuroSIDA: 20,71611,992; ICONA: 3,751/500; Rega: 302/302; SHCS: 53,78311,485, In total, 78,552 samples and 15,473 resistance tests were available amongst these five cohorts. Once these data items have been identified, it is trivial to generate lists of relevant samples that would be usefuI for ultra deep sequencing in addition to the already available resistance tests, Saon the tool will include small analysis packages that allow each cohort to pull a report on their cohort profile and also survey emerging resistance trends in their own cohort,CONCLUSIONS: We plan on providing this tool to all cohorts within the Collaborative HIV and Anti-HIV Drug Resistance Network (CHAIN) and will provide the tool free of charge to others for any non-commercial use, The potential of this tool is to ease collaborations, that is, in projects requiring data to speed up identification of novel resistance mutations by increasing the number of observations across multiple cohorts instead of awaiting single cohorts or studies to reach the critical number needed to address such issues.

Blind channel estimation and data detection using hidden Markov models theory

In this correspondence, we propose applying the hiddenMarkov models (HMM) theory to the problem of blind channel estimationand data detection. The Baum–Welch (BW) algorithm, which is able toestimate all the parameters of the model, is enriched by introducingsome linear constraints emerging from a linear FIR hypothesis on thechannel. Additionally, a version of the algorithm that is suitable for timevaryingchannels is also presented. Performance is analyzed in a GSMenvironment using standard test channels and is found to be close to thatobtained with a nonblind receiver.

Control and Simulation of Batch Crystallization

Concerning process control of batch cooling crystallization the present work focused on the cooling profile and seeding technique. Secondly, the influence of additives on batch-wise precipitation process was investigated. Moreover, a Computational Fluid Dynamics (CFD) model for simulation of controlled batch cooling crystallization was developed. A novel cooling model to control supersaturation level during batch-wise cooling crystallization was introduced. The crystallization kinetics together with operating conditions, i.e. seed loading, cooling rate and batch time, were taken into account in the model. Especially, the supersaturation- and suspension density- dependent secondary nucleation was included in the model. The interaction between the operating conditions and their influence on the control target, i.e. the constant level of supersaturation, were studied with the aid of a numerical solution for the cooling model. Further, the batch cooling crystallization was simulated with the ideal mixing model and CFD model. The moment transformation of the population balance, together with the mass and heat balances, were solved numerically in the simulation. In order to clarify a relationship betweenthe operating conditions and product sizes, a system chart was developed for anideal mixing condition. The utilization of the system chart to determine the appropriate operating condition to meet a required product size was introduced. With CFD simulation, batch crystallization, operated following a specified coolingmode, was studied in the crystallizers having different geometries and scales. The introduced cooling model and simulation results were verified experimentallyfor potassium dihydrogen phosphate (KDP) and the novelties of the proposed control policies were demonstrated using potassium sulfate by comparing with the published results in the literature. The study on the batch-wise precipitation showed that immiscible additives could promote the agglomeration of a derivative of benzoic acid, which facilitated the filterability of the crystal product.

Warlike outlines of the securitarian state. Life control and the exclusion of people

Present book collects some of the thoughts developed during the 5 years (2004-2009) of work in the frame of the CHALLENGE project, "The Changing Landscape of European Liberty and Security". The project has related academic knowledge and research with the analysis of the policies and practices of the member States of the European Union [EU] around the couple liberty and security

Mittausjärjestelmä IGBT:n lämpötilan määrittämiseen

Tässä diplomityössä tutustutaan IGBT:n ja tehodiodin rakenteisiin, lämmön muodostumiseen kyseisissä komponenteissa sekä menetelmiin, joilla komponenttien lämpötilat voidaan määrittää. Työssä suunnitellaan ja rakennetaan mittausjärjestelmä, jolla IGBT:n ja tehodiodin lämpötilat voidaan määrittää suoraan mittaamalla sekä matemaattisten mallien avulla. Mittausjärjestelmä koostuu DC-chopper -kytkennästä, kuormavirran, välipiirin jännitteen sekä lämpötilan mittauksista. Lämpötilan mittauksissa käytettiin komponenttien pintoihin liitettyjä termopareja. Matemaattisia malleja varten mittausjärjestelmään lisättiin välipiirin jännitteen sekä kuormavirran mittaus. Laitteiston ohjaus sekä mittaustulosten tallentaminen toteutettiin dSPACE -laitteistolla. Mittausjärjestelmän toimivuus testattiin Lappeenrannan teknillisen yliopiston Säätötekniikan laboratoriossa tehdyillä mittauksilla.

Odor emission control and reduce in betaine manufacture

This thesis was made in Naantali plant of Finnfeeds Finland Oy. In this thesis the main study was in reducing, controlling, measuring and processing odour effluents in various methods. Also are considered legislation, marketing issues and environmental requirements of reducing of odour effluents. The literature review introduces odours complications, legislations and various methods of odour removal. There is also a review of volatile organic compounds detection and measuring methods. The experimental section consists TD-GC-MS-measurements and expansive measurements with electronic nose. Electronic nose is a new solution for recognition and measuring industrial odours. In this thesis the electronic nose was adapted into reliable recognition and measuring method. Measurements with electronic nose was made in betaine factory and main targets were odour removal process and other odours from factory. As a result of experimental work with TD-GC-MS-measurements becomes odour compound of 2-and 3- methylbutanal and dimethyldisulfide, which odour is sweet and fug. Extensive study with electronic nose found many developmental subjects. Odour balance measurements of factory and after calculation made adjustment of odour removal process, over all odour effluent to environment will reduce 25 %.

Breast imaging reporting and data system (BI-RADS™): como tem sido utilizado?

O Breast Imaging Reporting and Data System (BI-RADS™), do American College of hRadiology, foi concebido para padronizar o laudo mamográfico e reduzir os fatores de confusão na descrição e interpretação das imagens, além de facilitar o monitoramento do resultado final. OBJETIVO: Identificar a maneira como vem sendo utilizado o BI-RADS™, gerando informações que possam auxiliar o Colégio Brasileiro de Radiologia a desenvolver estratégias para aperfeiçoar o seu uso. MATERIAIS E MÉTODOS: Os dados foram coletados na cidade de Goiânia, GO. Foram solicitados os exames de mamografia anteriores a todas as mulheres que se dirigiram ao serviço para realização de mamografia entre janeiro/2003 e junho/2003. Foram incluídos na análise exames anteriores, realizados entre 1/7/2001 e 30/6/2003. RESULTADOS: Foram coletados 104 laudos anteriores, emitidos por 40 radiologistas de 33 diferentes serviços. Dos 104 laudos, 77% (n = 80) utilizavam o BI-RADS™. Destes, apenas 15% (n = 12) eram concisos, nenhum utilizava a estrutura e organização recomendadas pelo sistema, 98,75% (n = 79) não respeitavam o léxico e 65% (n = 51) não faziam recomendação de conduta. CONCLUSÃO: O BI-RADS™, apesar de bastante utilizado, não foi reconhecido como sistema para padronização dos laudos. Foi usado quase exclusivamente como forma de classificação final dos exames.

New kernel functions and learning methods for text and data mining

Recent advances in machine learning methods enable increasingly the automatic construction of various types of computer assisted methods that have been difficult or laborious to program by human experts. The tasks for which this kind of tools are needed arise in many areas, here especially in the fields of bioinformatics and natural language processing. The machine learning methods may not work satisfactorily if they are not appropriately tailored to the task in question. However, their learning performance can often be improved by taking advantage of deeper insight of the application domain or the learning problem at hand. This thesis considers developing kernel-based learning algorithms incorporating this kind of prior knowledge of the task in question in an advantageous way. Moreover, computationally efficient algorithms for training the learning machines for specific tasks are presented. In the context of kernel-based learning methods, the incorporation of prior knowledge is often done by designing appropriate kernel functions. Another well-known way is to develop cost functions that fit to the task under consideration. For disambiguation tasks in natural language, we develop kernel functions that take account of the positional information and the mutual similarities of words. It is shown that the use of this information significantly improves the disambiguation performance of the learning machine. Further, we design a new cost function that is better suitable for the task of information retrieval and for more general ranking problems than the cost functions designed for regression and classification. We also consider other applications of the kernel-based learning algorithms such as text categorization, and pattern recognition in differential display. We develop computationally efficient algorithms for training the considered learning machines with the proposed kernel functions. We also design a fast cross-validation algorithm for regularized least-squares type of learning algorithm. Further, an efficient version of the regularized least-squares algorithm that can be used together with the new cost function for preference learning and ranking tasks is proposed. In summary, we demonstrate that the incorporation of prior knowledge is possible and beneficial, and novel advanced kernels and cost functions can be used in algorithms efficiently.

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.