Qualidade da operação na cultura da cana-de-açúcar utilizando cartas de controle

Pós-graduação em Agronomia (Ciência do Solo) - FCAV

Low-Cost Ultra-Wide Genotyping Using Roche/454 Pyrosequencing for Surveillance of HIV Drug Resistance

Background: Great efforts have been made to increase accessibility of HIV antiretroviral therapy (ART) in low and middle-income countries. The threat of wide-scale emergence of drug resistance could severely hamper ART scale-up efforts. Population-based surveillance of transmitted HIV drug resistance ensures the use of appropriate first-line regimens to maximize efficacy of ART programs where drug options are limited. However, traditional HIV genotyping is extremely expensive, providing a cost barrier to wide-scale and frequent HIV drug resistance surveillance. Methods/Results: We have developed a low-cost laboratory-scale next-generation sequencing-based genotyping method to monitor drug resistance. We designed primers specifically to amplify protease and reverse transcriptase from Brazilian HIV subtypes and developed a multiplexing scheme using multiplex identifier tags to minimize cost while providing more robust data than traditional genotyping techniques. Using this approach, we characterized drug resistance from plasma in 81 HIV infected individuals collected in Sao Paulo, Brazil. We describe the complexities of analyzing next-generation sequencing data and present a simplified open-source workflow to analyze drug resistance data. From this data, we identified drug resistance mutations in 20% of treatment naive individuals in our cohort, which is similar to frequencies identified using traditional genotyping in Brazilian patient samples. Conclusion: The developed ultra-wide sequencing approach described here allows multiplexing of at least 48 patient samples per sequencing run, 4 times more than the current genotyping method. This method is also 4-fold more sensitive (5% minimal detection frequency vs. 20%) at a cost 3-5 x less than the traditional Sanger-based genotyping method. Lastly, by using a benchtop next-generation sequencer (Roche/454 GS Junior), this approach can be more easily implemented in low-resource settings. This data provides proof-of-concept that next-generation HIV drug resistance genotyping is a feasible and low-cost alternative to current genotyping methods and may be particularly beneficial for in-country surveillance of transmitted drug resistance.

Multi-criteria analysis in the strategic environmental assessment of the sugar and alcohol sector

The Strategic Environmental Assessment (SEA) of the sugar and alcohol sector guides a territorial and sectoral planning that benefits most of the local society and supports this economic activity in all its stages. In this way, the present work aims to determine an index of aggregation of the indicators generated in the baseline of the SEA process, called Index of Sustainability of Expansion of the Sugar and Alcohol Sector (IScana). For this, it was used the normalization of the indicators of each city by the fuzzy logic and attribution of weights by the Analytic Hierarchy Process (AHP). Then, the IScana values had been spatialized in the region of 'Grande Dourados'-Mato Grosso do Sul State. The northern portion concentrated the highest values of IScana, 0.48 and 0.55, referring to the cities of Nova Alvorada do Sul and Rio Brilhante, while, in the central portion, the city of Dourados presented the lowest value, 0.10. The selection of the set of indicators forming the IScana, and their relative importance, was satisfactory for the application of fuzzy logic and AHP techniques. The IScana index supplies objective information regarding the diagnosis of the region for the application of SEA.

Competition on counter measures to 2-D facial spoofing attacks

[EN]Spoofing identities using photographs is one of the most common techniques to attack 2-D face recognition systems. There seems to exist no comparative stud- ies of di erent techniques using the same protocols and data. The motivation behind this competition is to com- pare the performance of di erent state-of-the-art algo- rithms on the same database using a unique evaluation method. Six di erent teams from universities around the world have participated in the contest.

TCAD approaches to multidimensional simulation of advanced semiconductor devices

Technology scaling increasingly emphasizes complexity and non-ideality of the electrical behavior of semiconductor devices and boosts interest on alternatives to the conventional planar MOSFET architecture. TCAD simulation tools are fundamental to the analysis and development of new technology generations. However, the increasing device complexity is reflected in an augmented dimensionality of the problems to be solved. The trade-off between accuracy and computational cost of the simulation is especially influenced by domain discretization: mesh generation is therefore one of the most critical steps and automatic approaches are sought. Moreover, the problem size is further increased by process variations, calling for a statistical representation of the single device through an ensemble of microscopically different instances. The aim of this thesis is to present multi-disciplinary approaches to handle this increasing problem dimensionality in a numerical simulation perspective. The topic of mesh generation is tackled by presenting a new Wavelet-based Adaptive Method (WAM) for the automatic refinement of 2D and 3D domain discretizations. Multiresolution techniques and efficient signal processing algorithms are exploited to increase grid resolution in the domain regions where relevant physical phenomena take place. Moreover, the grid is dynamically adapted to follow solution changes produced by bias variations and quality criteria are imposed on the produced meshes. The further dimensionality increase due to variability in extremely scaled devices is considered with reference to two increasingly critical phenomena, namely line-edge roughness (LER) and random dopant fluctuations (RD). The impact of such phenomena on FinFET devices, which represent a promising alternative to planar CMOS technology, is estimated through 2D and 3D TCAD simulations and statistical tools, taking into account matching performance of single devices as well as basic circuit blocks such as SRAMs. Several process options are compared, including resist- and spacer-defined fin patterning as well as different doping profile definitions. Combining statistical simulations with experimental data, potentialities and shortcomings of the FinFET architecture are analyzed and useful design guidelines are provided, which boost feasibility of this technology for mainstream applications in sub-45 nm generation integrated circuits.

Elektrokinetik konzentrierter kolloidaler Suspensionen

In dieser Arbeit wurden wässrige Suspensionen ladungsstabilisierter kolloidaler Partikel bezüglich ihres Verhaltens unter dem Einfluss elektrischer Felder untersucht. Insbesondere wurde die elektrophoretische Mobilität µ über einen weiten Partikelkonzentrationsbereich studiert, um das individuelle Verhalten einzelner Partikel mit dem bisher nur wenig untersuchten kollektiven Verhalten von Partikelensembles (speziell von fluid oder kristallin geordneten Ensembles) zu vergleichen. Dazu wurde ein superheterodynes Dopplervelocimetrisches Lichtstreuexperiment mit integraler und lokaler Datenerfassung konzipiert, das es erlaubt, die Geschwindigkeit der Partikel in elektrischen Feldern zu studieren. Das Experiment wurde zunächst erfolgreich im Bereich nicht-ordnender und fluid geordneter Suspensionen getestet. Danach konnte mit diesem Gerät erstmals das elektrophoretische Verhalten von kristallin geordneten Suspensionen untersucht werden. Es wurde ein komplexes Fließverhalten beobachtet und ausführlich dokumentiert. Dabei wurden bisher in diesem Zusammenhang noch nicht beobachtete Effekte wie Blockfluss, Scherbandbildung, Scherschmelzen oder elastische Resonanzen gefunden. Andererseits machte dieses Verhalten die Entwicklung einer neuen Auswertungsroutine für µ im kristallinen Zustand notwendig, wozu die heterodyne Lichtstreutheorie auf den superheterodynen Fall mit Verscherung erweitert werden musste. Dies wurde zunächst für nicht geordnete Systeme durchgeführt. Diese genäherte Beschreibung genügte, um unter den gegebenen Versuchbedingungen auch das Lichtstreuverhalten gescherter kristalliner Systeme zu interpretieren. Damit konnte als weiteres wichtiges Resultat eine generelle Mobilitäts-Konzentrations-Kurve erhalten werden. Diese zeigt bei geringen Partikelkonzentrationen den bereits bekannten Anstieg und bei mittleren Konzentrationen ein Plateau. Bei hohen Konzentrationen sinkt die Mobilität wieder ab. Zur Interpretation dieses Verhaltens bzgl. Partikelladung stehen derzeit nur Theorien für nicht wechselwirkende Partikel zur Verfügung. Wendet man diese an, so findet man eine überraschend gute Übereinstimmung der elektrophoretisch bestimmten Partikelladung Z*µ mit numerisch bestimmten effektiven Partikelladungen Z*PBC.

Marine biodiversity survey in the Northern Red Sea: a large-scale monitoring carried out in collaboration with volunteer divers

Concerns over global change and its effect on coral reef survivorship have highlighted the need for long-term datasets and proxy records, to interpret environmental trends and inform policymakers. Citizen science programs have showed to be a valid method for collecting data, reducing financial and time costs for institutions. This study is based on the elaboration of data collected by recreational divers and its main purpose is to evaluate changes in the state of coral reef biodiversity in the Red Sea over a long term period and validate the volunteer-based monitoring method. Volunteers recreational divers completed a questionnaire after each dive, recording the presence of 72 animal taxa and negative reef conditions. Comparisons were made between records from volunteers and independent records from a marine biologist who performed the same dive at the same time. A total of 500 volunteers were tested in 78 validation trials. Relative values of accuracy, reliability and similarity seem to be comparable to those performed by volunteer divers on precise transects in other projects, or in community-based terrestrial monitoring. 9301 recreational divers participated in the monitoring program, completing 23,059 survey questionnaires in a 5-year period. The volunteer-sightings-based index showed significant differences between the geographical areas. The area of Hurghada is distinguished by a medium-low biodiversity index, heavily damaged by a not controlled anthropic exploitation. Coral reefs along the Ras Mohammed National Park at Sharm el Sheikh, conversely showed high biodiversity index. The detected pattern seems to be correlated with the conservation measures adopted. In our experience and that of other research institutes, citizen science can integrate conventional methods and significantly reduce costs and time. Involving recreational divers we were able to build a large data set, covering a wide geographic area. The main limitation remains the difficulty of obtaining an homogeneous spatial sampling distribution.

Tidal volume single breath washout of two tracer gases--a practical and promising lung function test

Background Small airway disease frequently occurs in chronic lung diseases and may cause ventilation inhomogeneity (VI), which can be assessed by washout tests of inert tracer gas. Using two tracer gases with unequal molar mass (MM) and diffusivity increases specificity for VI in different lung zones. Currently washout tests are underutilised due to the time and effort required for measurements. The aim of this study was to develop and validate a simple technique for a new tidal single breath washout test (SBW) of sulfur hexafluoride (SF6) and helium (He) using an ultrasonic flowmeter (USFM). Methods The tracer gas mixture contained 5% SF6 and 26.3% He, had similar total MM as air, and was applied for a single tidal breath in 13 healthy adults. The USFM measured MM, which was then plotted against expired volume. USFM and mass spectrometer signals were compared in six subjects performing three SBW. Repeatability and reproducibility of SBW, i.e., area under the MM curve (AUC), were determined in seven subjects performing three SBW 24 hours apart. Results USFM reliably measured MM during all SBW tests (n = 60). MM from USFM reflected SF6 and He washout patterns measured by mass spectrometer. USFM signals were highly associated with mass spectrometer signals, e.g., for MM, linear regression r-squared was 0.98. Intra-subject coefficient of variation of AUC was 6.8%, and coefficient of repeatability was 11.8%. Conclusion The USFM accurately measured relative changes in SF6 and He washout. SBW tests were repeatable and reproducible in healthy adults. We have developed a fast, reliable, and straightforward USFM based SBW method, which provides valid information on SF6 and He washout patterns during tidal breathing.

Capturing How Objects Flow At Runtime

Most of today's dynamic analysis approaches are based on method traces. However, in the case of object-orientation understanding program execution by analyzing method traces is complicated because the behavior of a program depends on the sharing and the transfer of object references (aliasing). We argue that trace-based dynamic analysis is at a too low level of abstraction for object-oriented systems. We propose a new approach that captures the life cycle of objects by explicitly taking into account object aliasing and how aliases propagate during the execution of the program. In this paper, we present in detail our new meta-model and discuss future tracks opened by it.

Effectively Selecting a Target Population for a Future Comparative Study

When comparing a new treatment with a control in a randomized clinical study, the treatment effect is generally assessed by evaluating a summary measure over a specific study population. The success of the trial heavily depends on the choice of such a population. In this paper, we show a systematic, effective way to identify a promising population, for which the new treatment is expected to have a desired benefit, using the data from a current study involving similar comparator treatments. Specifically, with the existing data we first create a parametric scoring system using multiple covariates to estimate subject-specific treatment differences. Using this system, we specify a desired level of treatment difference and create a subgroup of patients, defined as those whose estimated scores exceed this threshold. An empirically calibrated group-specific treatment difference curve across a range of threshold values is constructed. The population of patients with any desired level of treatment benefit can then be identified accordingly. To avoid any ``self-serving'' bias, we utilize a cross-training-evaluation method for implementing the above two-step procedure. Lastly, we show how to select the best scoring system among all competing models. The proposals are illustrated with the data from two clinical trials in treating AIDS and cardiovascular diseases. Note that if we are not interested in designing a new study for comparing similar treatments, the new procedure can also be quite useful for the management of future patients who would receive nontrivial benefits to compensate for the risk or cost of the new treatment.

On the Accelerated Failure Time Model for Current Status and Interval Censored Data

This paper introduces a novel approach to making inference about the regression parameters in the accelerated failure time (AFT) model for current status and interval censored data. The estimator is constructed by inverting a Wald type test for testing a null proportional hazards model. A numerically efficient Markov chain Monte Carlo (MCMC) based resampling method is proposed to simultaneously obtain the point estimator and a consistent estimator of its variance-covariance matrix. We illustrate our approach with interval censored data sets from two clinical studies. Extensive numerical studies are conducted to evaluate the finite sample performance of the new estimators.

Ligation dependent allele specific quantification (LASQ) of CFTR cDNA on the LightCycler using MLPA hybridization probes

BACKGROUND: As for Cystic Fibrosis (CF) and many other hereditary diseases there is still a lack in understanding the relationship between genetic (e.g. allelic) and phenotypic diversity. Therefore methods which allow fine quantification of allelic proportions of mRNA transcripts are of high importance. METHODS: We used either genomic DNA (gDNA) or total RNA extracted from nasal cells as starting nucleic acid template for our assay. The subjects included in this study were 9 CF patients compound heterozygous for the F508del mutation and each one F508del homozygous and one wild type homozygous respectively. We established a novel ligation based quantification method which allows fine quantification of the allelic proportions of ss and ds CFTR cDNA. To verify reliability and accuracy of this novel assay we compared it with semiquantitative fluorescent PCR (SQF-PCR). RESULTS: We established a novel assay for allele specific quantification of gene expression which combines the benefits of the specificity of the ligation reaction and the accuracy of quantitative real-time PCR. The comparison with SQF-PCR clearly demonstrates that LASQ allows fine quantification of allelic proportions. CONCLUSION: This assay represents an alternative to other fine quantitative methods such as ARMS PCR and Pyrosequencing.

Transactional Memory in a Dynamic Language

Concurrency control is mostly based on locks and is therefore notoriously difficult to use. Even though some programming languages provide high-level constructs, these add complexity and potentially hard-to-detect bugs to the application. Transactional memory is an attractive mechanism that does not have the drawbacks of locks, however the underlying implementation is often difficult to integrate into an existing language. In this paper we show how we have introduced transactional semantics into Smalltalk by using the reflective facilities of the language. Our approach is based on method annotations, incremental parse tree transformations and an optimistic commit protocol. The implementation does not depend on modifications to the virtual machine and therefore can be changed at the language level. We report on a practical case study, benchmarks and further and on-going work.

Aus der Krise lernen – Wirtschaftlichkeit durch Flexibilität und Wandlungsfähigkeit sichern

Flexible und wandelbare Fabrikstrukturen sind von hoher Bedeutung, wenn Produktionsstätten in einem turbulenten Umfeld langfristig wettbewerbsfähig bleiben sollen; darin sind sich Forschung und Praxis einig. Während der jüngsten weltweiten Wirtschaftskrise wurden Experten aus dem Airline-Catering-Umfeld befragt, wie Betriebe dieser Branche auf starke Veränderungen vorbereitet sind. Vorgespräche und Analysen des Autors legten die Vermutung nahe, dass diese Dienstleistungsbranche besonderen Flexibilitätsanforderungen unterliegt. Im Rahmen einer detaillierten Studie, deren Erkenntnisse in einer Dissertation zusammengefasst werden, sind Interviews mit Experten geführt worden. Aus den Ergebnissen der Interviews wurden Schlussfolgerungen auf erforderliche, flexible Materialflusstechniklösungen, im Speziellen Elektrohängebahnen (EHB), und bauliche Anpassungen nach dem „Konzept Internet der Dinge“ gezogen. Szenarioanalysen zu Wirtschaftlichkeits- und Risikoaspekten durchleuchteten die generierten Ansätze. Anschließend an die quantitative Analyse wurden die Ansätze ebenfalls durch eine qualitative Bewertung herkömmlichen Lösungen gegenübergestellt. Die aufgebaute Bewertungsmethode ist sowohl geeignet, um in zukünftigen Projekten die Entscheidung für oder gegen eine wandelbare Ausführung zu treffen, als auch andere Branchen auf die grundsätzliche Sinnhaftigkeit des Einsatzes wandelbarer Materialflusstechnik zu überprüfen.

Das prognosebasierte Reservierungsverfahren - ein Ansatz zur Reduzierung der mittleren Fahrzeit in einer Regalfläche

Die neu entwickelte Belegungsstrategie basiert auf prognostizierten Verweildauern (VWD) und Zwischenankunftszeiten der Ladeeinheiten (LE) des Sortiments. Für jede Ladeeinheit, die im Lager ankommt wird berechnet, wie viele Ladeeinheiten während der Verweildauer dieser aktuellen Ladeeinheit voraussichtlich ankommen und das Lager auch in diesem VWD-Zeitraum wieder verlassen. In Abhängigkeit der aktuellen Lagerbelegung werden für die in dem Zeitraum ankommenden Ladeeinheiten Lagerfächer reserviert und erst anschließend die eingehende Ladeeinheit in das fahrzeitgünstigste, freie und nicht reservierte Lagerfach eingelagert. Eine zusätzliche Berücksichtigung des Energiebedarfes für die Ein- und Auslagerung ist möglich. Das prognosebasierte Reservierungsverfahren wurde neben den gängigen Belegungsstrategien in einem parametrisierbaren Simulationsmodell umgesetzt. Die Belegungsstrategien wurden anhand verschiedener Szenarien getestet und verglichen. Ein zusätzlich entwickelter Benchmark gibt Auskunft über die Qualität der Simulationsergebnisse.