Tapping the wealth of microbial data in high-throughput metabolic model reconstruction

Genome-scale metabolic models are valuable tools in the metabolic engineering process, based on the ability of these models to integrate diverse sources of data to produce global predictions of organism behavior. At the most basic level, these models require only a genome sequence to construct, and once built, they may be used to predict essential genes, culture conditions, pathway utilization, and the modifications required to enhance a desired organism behavior. In this chapter, we address two key challenges associated with the reconstruction of metabolic models: (a) leveraging existing knowledge of microbiology, biochemistry, and available omics data to produce the best possible model; and (b) applying available tools and data to automate the reconstruction process. We consider these challenges as we progress through the model reconstruction process, beginning with genome assembly, and culminating in the integration of constraints to capture the impact of transcriptional regulation. We divide the reconstruction process into ten distinct steps: (1) genome assembly from sequenced reads; (2) automated structural and functional annotation; (3) phylogenetic tree-based curation of genome annotations; (4) assembly and standardization of biochemistry database; (5) genome-scale metabolic reconstruction; (6) generation of core metabolic model; (7) generation of biomass composition reaction; (8) completion of draft metabolic model; (9) curation of metabolic model; and (10) integration of regulatory constraints. Each of these ten steps is documented in detail.

Use of automated external defibrillators in a Brazilian airline. A 1-year experience

After the incorporation of automated external defibrilators by other airlines and the support of the Brazilian Society of cardiology, Varig Airlines Began the onboard defibrilation program with the initial purpose of equiping wide-body aircrafts frequently used in international flights and that airplanes use in the Rio - São Paulo route. With all fight attendants trained, the automated. External defibrilation devides were incorporated to 34 airplanes of a total pleet of 80 aircrats. The devices were intalled in the bagage compartments secured with velero straps and 2 pairs of electrods, one or which pre-conected to the device to minimize application time. Later, a portable monitor was addres to the ressocitation kit in the long flights. The expansion of the knowledge of the basic life support fundamentors and the correted implantation of the survival chain and of the automated external defibrilators will increase the extense of recovery of cardiorespiratory arrest victins in aircrafts.

BIOMedical search engine framework: lightweight and customized implementation of domain-specific biomedical search engines

The Smart Drug Search is publicly accessible at http://sing.ei.uvigo.es/sds/. The BIOMedical Search Engine Framework is freely available for non-commercial use at https://github.com/agjacome/biomsef

Validation study of an automated wrist monitor, omron model HEM-608, compared with the standard methods for blood pressure measurement

OBJECTIVE - The aim of our study was to assess the profile of a wrist monitor, the Omron Model HEM-608, compared with the indirect method for blood pressure measurement. METHODS - Our study population consisted of 100 subjects, 29 being normotensive and 71 being hypertensive. Participants had their blood pressure checked 8 times with alternate techniques, 4 by the indirect method and 4 with the Omron wrist monitor. The validation criteria used to test this device were based on the internationally recognized protocols. RESULTS - Our data showed that the Omron HEM-608 reached a classification B for systolic and A for diastolic blood pressure, according to the one protocol. The mean differences between blood pressure values obtained with each of the methods were -2.3 +7.9mmHg for systolic and 0.97+5.5mmHg for diastolic blood pressure. Therefore, we considered this type of device approved according to the criteria selected. CONCLUSION - Our study leads us to conclude that this wrist monitor is not only easy to use, but also produces results very similar to those obtained by the standard indirect method.

Assessment of the DIXTAL DX-2710 Automated Oscillometric Device for Blood Pressure Measurement with the Validation Protocols of the British Hypertension Society (BHS) and the Association for the Advancement of Medical Instrumentation (AAMI)

OBJECTIVE: To assess the Dixtal DX2710 automated oscillometric device used for blood pressure measurement according to the protocols of the BHS and the AAMI. METHODS: Three blood pressure measurements were taken in 94 patients (53 females 15 to 80 years). The measurements were taken randomly by 2 observers trained to measure blood pressure with a mercury column device connected with an automated device. The device was classified according to the protocols of the BHS and AAMI. RESULT: The mean of blood pressure levels obtained by the observers was 148±38/93±25 mmHg and that obtained with the device was 148±37/89±26 mmHg. Considering the differences between the measurements obtained by the observer and those obtained with the automated device according to the criteria of the BHS, the following classification was adopted: "A" for systolic pressure (69% of the differences < 5; 90% < 10; and 97% < 15 mmHg); and "B" for diastolic pressure (63% of the differences < 5; 83% < 10; and 93% < 15 mmHg). The mean and standard deviation of the differences were 0±6.27 mmHg for systolic pressure and 3.82±6.21 mmHg for diastolic pressure. CONCLUSION: The Dixtal DX2710 device was approved according to the international recommendations.

Verificación Formal de Sistemas basada Formal Software Verification based on Automated Analysisen Análisis Automático.

Identificación y caracterización del problema. Uno de los problemas más importantes asociados con la construcción de software es la corrección del mismo. En busca de proveer garantías del correcto funcionamiento del software, han surgido una variedad de técnicas de desarrollo con sólidas bases matemáticas y lógicas conocidas como métodos formales. Debido a su naturaleza, la aplicación de métodos formales requiere gran experiencia y conocimientos, sobre todo en lo concerniente a matemáticas y lógica, por lo cual su aplicación resulta costosa en la práctica. Esto ha provocado que su principal aplicación se limite a sistemas críticos, es decir, sistemas cuyo mal funcionamiento puede causar daños de magnitud, aunque los beneficios que sus técnicas proveen son relevantes a todo tipo de software. Poder trasladar los beneficios de los métodos formales a contextos de desarrollo de software más amplios que los sistemas críticos tendría un alto impacto en la productividad en tales contextos. Hipótesis. Contar con herramientas de análisis automático es un elemento de gran importancia. Ejemplos de esto son varias herramientas potentes de análisis basadas en métodos formales, cuya aplicación apunta directamente a código fuente. En la amplia mayoría de estas herramientas, la brecha entre las nociones a las cuales están acostumbrados los desarrolladores y aquellas necesarias para la aplicación de estas herramientas de análisis formal sigue siendo demasiado amplia. Muchas herramientas utilizan lenguajes de aserciones que escapan a los conocimientos y las costumbres usuales de los desarrolladores. Además, en muchos casos la salida brindada por la herramienta de análisis requiere cierto manejo del método formal subyacente. Este problema puede aliviarse mediante la producción de herramientas adecuadas. Otro problema intrínseco a las técnicas automáticas de análisis es cómo se comportan las mismas a medida que el tamaño y complejidad de los elementos a analizar crece (escalabilidad). Esta limitación es ampliamente conocida y es considerada crítica en la aplicabilidad de métodos formales de análisis en la práctica. Una forma de atacar este problema es el aprovechamiento de información y características de dominios específicos de aplicación. Planteo de objetivos. Este proyecto apunta a la construcción de herramientas de análisis formal para contribuir a la calidad, en cuanto a su corrección funcional, de especificaciones, modelos o código, en el contexto del desarrollo de software. Más precisamente, se busca, por un lado, identificar ambientes específicos en los cuales ciertas técnicas de análisis automático, como el análisis basado en SMT o SAT solving, o el model checking, puedan llevarse a niveles de escalabilidad superiores a los conocidos para estas técnicas en ámbitos generales. Se intentará implementar las adaptaciones a las técnicas elegidas en herramientas que permitan su uso a desarrolladores familiarizados con el contexto de aplicación, pero no necesariamente conocedores de los métodos o técnicas subyacentes. Materiales y métodos a utilizar. Los materiales a emplear serán bibliografía relevante al área y equipamiento informático. Métodos. Se emplearán los métodos propios de la matemática discreta, la lógica y la ingeniería de software. Resultados esperados. Uno de los resultados esperados del proyecto es la individualización de ámbitos específicos de aplicación de métodos formales de análisis. Se espera que como resultado del desarrollo del proyecto surjan herramientas de análisis cuyo nivel de usabilidad sea adecuado para su aplicación por parte de desarrolladores sin formación específica en los métodos formales utilizados. Importancia del proyecto. El principal impacto de este proyecto será la contribución a la aplicación práctica de técnicas formales de análisis en diferentes etapas del desarrollo de software, con la finalidad de incrementar su calidad y confiabilidad. A crucial factor for software quality is correcteness. Traditionally, formal approaches to software development concentrate on functional correctness, and tackle this problem basically by being based on well defined notations founded on solid mathematical grounds. This makes formal methods better suited for analysis, due to their precise semantics, but they are usually more complex, and require familiarity and experience with the manipulation of mathematical definitions. So, their acceptance by software engineers is rather restricted, and formal methods applications have been confined to critical systems. Nevertheless, it is obvious that the advantages that formal methods provide apply to any kind of software system. It is accepted that appropriate software tool support for formal analysis is essential, if one seeks providing support for software development based on formal methods. Indeed, some of the relatively recent sucesses of formal methods are accompanied by good quality tools that automate powerful analysis mechanisms, and are even integrated in widely used development environments. Still, most of these tools either concentrate on code analysis, and in many cases are still far from being simple enough to be employed by software engineers without experience in formal methods. Another important problem for the adoption of tool support for formal methods is scalability. Automated software analysis is intrinsically complex, and thus techniques do not scale well in the general case. In this project, we will attempt to identify particular modelling, design, specification or coding activities in software development processes where to apply automated formal analysis techniques. By focusing in very specific application domains, we expect to find characteristics that might be exploited to increase the scalability of the corresponding analyses, compared to the general case.

Efficient similarity-based operations for data integration

Similarity-based operations, similarity join, similarity grouping, data integration

Walking Tree - Organisation neuer Forschung in der Wissenschaft : Zusammenarbeit zwischen Integration und Differenzierung

Magdeburg, Univ., Fak. für Geistes-, Sozial- und Erziehungswiss., Diss., 2011

Stimulus-, aufgaben- und aufmerksamkeitsrelatierte Determinanten audiovisueller Integration

Magdeburg, Univ., Fak. für Naturwiss., Diss., 2011

Aufnahme von Flüchtlingen und Vertriebenen sowie Aspekte und Bestrebungen ihrer Eingliederung/Integration im Kreis Salzwedel 1945 bis 1948/49

Flight and displacement, Research about displaced people, Displaced people in Saxony- Anhalt and in the district of Salzwedel, Arrival and reception, Integration into social life, Administrative activities, Housing, Integration into the labour market, Social welfare activities

stochastic method for automated matching of horizons across a fault in 3D seismic data

Seismic analysis, horizon matching, fault tracking, marked point process,stochastic annealing

Robust acoustic and semantic modeling in a telephone-based spoken dialog system

Magdeburg, Univ., Fak. für Elektrotechnik und Informationstechnik, Diss., 2009

Integration of appetitive and aversive reinforcers and the neuromodulation of reward seeking and pain avoidance

Magdeburg, Univ., Fak. für Naturwiss., Diss., 2010

Zwischen Isolation, Anpassung und räumlicher Mobilität : eine Untersuchung zur Integration von Binnenwanderern in Deutschland

Magdeburg, Univ., Fak. für Geistes-, Sozial- und Erziehungswiss., Diss., 2011

Minimal-invasive provenance integration into data-intensive systems

Magdeburg, Univ., Fak. für Informatik, Diss., 2014