Coffee water use in agroforestry system with rubber trees

Water uptake and use by plants are essentially energy processes that can be largely modified by percentage of soil cover, plant type; foliage area and its distribution; phenological stage and several environmental factors. Coffee trees (Coffea arabica - cv. Obatã IAC 1669-20) in Agrforestry System (AFS) spaced 3.4x0.9m apart, were planted inside and along rows of 12- year-old rubber trees (Hevea spp.) in Piracicaba-SP, Brazil (22 42'30" S, 47 38'00" W - altitude: 546m). Sap flow of one-year-old coffee plants exposed to 35; 45; 80; 95 and 100% of total solar radiation was estimated by the heat balance technique (Dynamax Inc.). Coffee plants under shade showed greater water loss per unit of incident irradiance. On the other hand, plants in monocrop (full sun) had the least water loss per unit of incident irradiance. For the evaluated positions average water use was (gH2O.m-2Leaf area.MJ-1): 64.71; 67.75; 25.89; 33.54; 27.11 in Dec./2002 and 97.14; 72.50; 40.70; 32.78; 26.13 in Feb./2003. This fact may be attributed to the higher stomata sensitivity of the coffee plants under more illuminated conditions, thus plants under full sun presented the highest water use efficiency. Express transpiration by leaf mass can be a means to access plant adaptation to the various environments, which is inaccessible when the approach is made by leaf area.

Automated Software Testing in Machine Automation

The problem of software (SW) defaults is becoming more and more topical because of increasing amount of the SW and its complication. The majority of these defaults are founded during the test part that consumes about 40-50% of the development efforts. Test automation allows reducing the cost of this process and increasing testing effectiveness. In the middle of 1980 the first tools for automated testing appeared and the automated process was implemented in different kinds of SW testing. In short time, it became obviously, automated testing can cause many problems such as increasing product cost, decreasing reliability and even project fail. This thesis describes automated testing process, its concept, lists main problems, and gives an algorithm for automated test tools selection. Also this work presents an overview of the main automated test tools for embedded systems.

REPRODUCTIVE SYSTEM AND POLLEN FLOW IN PROGENIES OF Qualea grandiflora Mart., A TYPICAL SPECIES OF THE BRAZILIAN CERRADO

This study analyzed the reproductive system and the pollen dispersion pattern of Qualea grandiflora progenies. This is a typical species from the Brazilian Cerrado about which there are not too many studies from the genetics point of view. The study was conducted in an area of 2.2 hectares located in the Conservation Unit managed by the Forest Institute of the state of São Paulo, Brazil (Assis State Forest). Total genomic DNA of 300 seeds from 25 plants (12 seeds from each plant) was extracted and amplified using specific primers to obtain microsatellite markers. Results showed that selfing is frequent among adults and progenies, and the species reproduces by outcrossing between related and unrelated individuals (0.913). The single-locus outcrossing rate was 0.632, which indicates that mating between unrelated individuals is more frequent than between related plants. The selfing rate was low (0.087), that is, the species is allogamous and self-fertilization is reduced. About 35% of the plants in the progenies were full-sibs, and about 57%, half-sibs. Besides, about 8% of the progenies were selfing siblings. The genetic differentiation coefficient within progenies was 0.139, whereas the fixation rate was about 27%. The estimate of the effective size revealed that the genetic representativeness of descent was lower than expected in random mating progenies: The analyzed samples corresponded to only 13.2 individuals of an ideal panmictic population. In environmental recovery programs, seeds, preferably from different fruits, should be collected from 95 trees to preserve the genetic diversity of the species.

AMB system for high-speed motors using automatic commissioning

The general trend towards increasing e ciency and energy density drives the industry to high-speed technologies. Active Magnetic Bearings (AMBs) are one of the technologies that allow contactless support of a rotating body. Theoretically, there are no limitations on the rotational speed. The absence of friction, low maintenance cost, micrometer precision, and programmable sti ness have made AMBs a viable choice for highdemanding applications. Along with the advances in power electronics, such as signi cantly improved reliability and cost, AMB systems have gained a wide adoption in the industry. The AMB system is a complex, open-loop unstable system with multiple inputs and outputs. For normal operation, such a system requires a feedback control. To meet the high demands for performance and robustness, model-based control techniques should be applied. These techniques require an accurate plant model description and uncertainty estimations. The advanced control methods require more e ort at the commissioning stage. In this work, a methodology is developed for an automatic commissioning of a subcritical, rigid gas blower machine. The commissioning process includes open-loop tuning of separate parts such as sensors and actuators. The next step is to apply a system identi cation procedure to obtain a model for the controller synthesis. Finally, a robust model-based controller is synthesized and experimentally evaluated in the full operating range of the system. The commissioning procedure is developed by applying only the system components available and a priori knowledge without any additional hardware. Thus, the work provides an intelligent system with a self-diagnostics feature and an automatic commissioning.

One chip solution for low-cost active magnetic bearing system

In this work the implementation of the active magnetic bearing control system in a single FPGA is studied. Requirements for the full magnetic bearing control system are reviewed. Different control methods for active magnetic bearings are described shortly. Flux and the current base controllers are implemented in a FPGA. Suitability of the con-trollers for a low-cost magnetic bearing application is studied. Floating-point arithmetic’s are used in the controllers to ease designing burden and improve calculation precision. Per-formance of the flux controller is verified with simulations.

Automated Purchase to Pay Process Value Modeling and Comparative Process Speeds

The importance of efficient supply chain management has increased due to globalization and the blurring of organizational boundaries. Various supply chain management technologies have been identified to drive organizational profitability and financial performance. Organizations have historically been concentrating heavily on the flow of goods and services, while less attention has been dedicated to the flow of money. While supply chains are becoming more transparent and automated, new opportunities for financial supply chain management have emerged through information technology solutions and comprehensive financial supply chain management strategies. This research concentrates on the end part of the purchasing process which is the handling of invoices. Efficient invoice processing can have an impact on organizations working capital management and thus provide companies with better readiness to face the challenges related to cash management. Leveraging a process mining solution the aim of this research was to examine the automated invoice handling process of four different organizations. The invoice data was collected from each organizations invoice processing system. The sample included all the invoices organizations had processed during the year 2012. The main objective was to find out whether e-invoices are faster to process in an automated invoice processing solution than scanned invoices (post entry into invoice processing solution). Other objectives included looking into the longest lead times between process steps and the impact of manual process steps on cycle time. Processing of invoices from maverick purchases was also examined. Based on the results of the research and previous literature on the subject, suggestions for improving the process were proposed. The results of the research indicate that scanned invoices were processed faster than e-invoices. This is mostly due to the more complex processing of e-invoices. It should be noted however that the manual tasks related to turning a paper invoice into electronic format through scanning are ignored in this research. The transitions with the longest lead times in the invoice handling process included both pre-automated steps as well as manual steps performed by humans. When the most common manual steps were examined in more detail, it was clear that these steps had a prolonging impact on the process. Regarding invoices from maverick purchases the evidence shows that these invoices were slower to process than invoices from purchases conducted through e-procurement systems and from preferred suppliers. Suggestions on how to improve the process included: increasing invoice matching, reducing of manual steps and leveraging of different value added services such as invoice validation service, mobile solutions and supply chain financing services. For companies that have already reaped all the process efficiencies the next step is to engage in collaborative financial supply chain management strategies that can benefit the whole supply chain.

Avalon Media System project update: a Hydra solution for digital audio and video access

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

Biomedical Event Extraction with Machine Learning

Biomedical natural language processing (BioNLP) is a subfield of natural language processing, an area of computational linguistics concerned with developing programs that work with natural language: written texts and speech. Biomedical relation extraction concerns the detection of semantic relations such as protein-protein interactions (PPI) from scientific texts. The aim is to enhance information retrieval by detecting relations between concepts, not just individual concepts as with a keyword search. In recent years, events have been proposed as a more detailed alternative for simple pairwise PPI relations. Events provide a systematic, structural representation for annotating the content of natural language texts. Events are characterized by annotated trigger words, directed and typed arguments and the ability to nest other events. For example, the sentence “Protein A causes protein B to bind protein C” can be annotated with the nested event structure CAUSE(A, BIND(B, C)). Converted to such formal representations, the information of natural language texts can be used by computational applications. Biomedical event annotations were introduced by the BioInfer and GENIA corpora, and event extraction was popularized by the BioNLP'09 Shared Task on Event Extraction. In this thesis we present a method for automated event extraction, implemented as the Turku Event Extraction System (TEES). A unified graph format is defined for representing event annotations and the problem of extracting complex event structures is decomposed into a number of independent classification tasks. These classification tasks are solved using SVM and RLS classifiers, utilizing rich feature representations built from full dependency parsing. Building on earlier work on pairwise relation extraction and using a generalized graph representation, the resulting TEES system is capable of detecting binary relations as well as complex event structures. We show that this event extraction system has good performance, reaching the first place in the BioNLP'09 Shared Task on Event Extraction. Subsequently, TEES has achieved several first ranks in the BioNLP'11 and BioNLP'13 Shared Tasks, as well as shown competitive performance in the binary relation Drug-Drug Interaction Extraction 2011 and 2013 shared tasks. The Turku Event Extraction System is published as a freely available open-source project, documenting the research in detail as well as making the method available for practical applications. In particular, in this thesis we describe the application of the event extraction method to PubMed-scale text mining, showing how the developed approach not only shows good performance, but is generalizable and applicable to large-scale real-world text mining projects. Finally, we discuss related literature, summarize the contributions of the work and present some thoughts on future directions for biomedical event extraction. This thesis includes and builds on six original research publications. The first of these introduces the analysis of dependency parses that leads to development of TEES. The entries in the three BioNLP Shared Tasks, as well as in the DDIExtraction 2011 task are covered in four publications, and the sixth one demonstrates the application of the system to PubMed-scale text mining.

Mating system in Myracrodruon urundeuva (Anarcadiaceae): implications for conservation genetics

The aims of this study were to investigate the mating system of a fragmented population of the dioecious tropical tree Myracrodruon urundeuva Allemão, using five microsatellite loci and the mixed mating and correlated mating models. The study was conducted in the Estação Ecológica de Paulo de Farias (436 ha), where the population occupies about 142 ha. The mating system was estimated using 514 open-pollinated offspring, collected from 30 seed-trees. Estimates of the multilocus outcrossing rate confirm that the species is dioecious (t m = 1.0). Low levels of mating among relatives were detected in the population (1 - t s = 0.020). The estimate of paternity correlation (r p(m)) indicated that offsprings were composed of mixtures of half-sibs and full-sibs, with the latter occurring at a low frequency (average of 0.148). The estimated coancestry coefficient within families (Θ = 0.147) was larger and the effective population size (Ne(v)) was lower (Ne(v) = 2.98) than expected in progenies from panmictic populations (Θ = 0.125, Ne(v) = 4, respectively). In terms of conservation, the results indicate that to retain an effective population size of 150, is necessary to collect seeds from at least 50 seed-trees.

Low-cost automatic activity data recording system

We describe a low-cost, high quality device capable of monitoring indirect activity by detecting touch-release events on a conducting surface, i.e., the animal's cage cover. In addition to the detecting sensor itself, the system includes an IBM PC interface for prompt data storage. The hardware/software design, while serving for other purposes, is used to record the circadian activity rhythm pattern of rats with time in an automated computerized fashion using minimal cost computer equipment (IBM PC XT). Once the sensor detects a touch-release action of the rat in the upper portion of the cage, the interface sends a command to the PC which records the time (hours-minutes-seconds) when the activity occurred. As a result, the computer builds up several files (one per detector/sensor) containing a time list of all recorded events. Data can be visualized in terms of actograms, indicating the number of detections per hour, and analyzed by mathematical tools such as Fast Fourier Transform (FFT) or cosinor. In order to demonstrate method validation, an experiment was conducted on 8 Wistar rats under 12/12-h light/dark cycle conditions (lights on at 7:00 a.m.). Results show a biological validation of the method since it detected the presence of circadian activity rhythm patterns in the behavior of the rats

Rapid detection of multidrug-resistant Mycobacterium tuberculosis using the mycobacteria growth indicator tube (MGIT) system

The emergence of multidrug-resistant strains of Mycobacterium tuberculosis has increased the need for rapid drug susceptibility tests, which are needed for adequate patient treatment. The objective of the present study was to evaluate the mycobacteria growth indicator tube (MGIT) system to detect multidrug-resistant M. tuberculosis strains. The MGIT system was compared with two standard methods (proportion and resistance ratio methods). One hundred clinical M. tuberculosis isolates [25 susceptible to isoniazid (INH) and rifampicin (RIF), 20 resistant to INH, 30 resistant to INH-RIF, and 25 resistant to INH-RIF and other drugs] obtained in the State of São Paulo were tested for INH and RIF susceptibility. Full agreement among the tests was found for all sensitive and all INH-resistant strains. For RIF-resistant strains results among the tests agreed for 53 (96.4%) of 55 isolates. Results were obtained within 6 days (range, 5 to 8 days), 28 days and 12 days when using MGIT, the proportion method and the resistance ratio methods, respectively. The MGIT system presented an overall agreement of 96% when compared with two standard methods. These data show that the MGIT system is rapid, sensitive and efficient for the early detection of multidrug-resistant M. tuberculosis.

A clinical gamma camera-based pinhole collimated system for high resolution small animal SPECT imaging

The main objective of the present study was to upgrade a clinical gamma camera to obtain high resolution tomographic images of small animal organs. The system is based on a clinical gamma camera to which we have adapted a special-purpose pinhole collimator and a device for positioning and rotating the target based on a computer-controlled step motor. We developed a software tool to reconstruct the target’s three-dimensional distribution of emission from a set of planar projections, based on the maximum likelihood algorithm. We present details on the hardware and software implementation. We imaged phantoms and heart and kidneys of rats. When using pinhole collimators, the spatial resolution and sensitivity of the imaging system depend on parameters such as the detector-to-collimator and detector-to-target distances and pinhole diameter. In this study, we reached an object voxel size of 0.6 mm and spatial resolution better than 2.4 and 1.7 mm full width at half maximum when 1.5- and 1.0-mm diameter pinholes were used, respectively. Appropriate sensitivity to study the target of interest was attained in both cases. Additionally, we show that as few as 12 projections are sufficient to attain good quality reconstructions, a result that implies a significant reduction of acquisition time and opens the possibility for radiotracer dynamic studies. In conclusion, a high resolution single photon emission computed tomography (SPECT) system was developed using a commercial clinical gamma camera, allowing the acquisition of detailed volumetric images of small animal organs. This type of system has important implications for research areas such as Cardiology, Neurology or Oncology.

Assessment of physiological potential of cucumber seeds using the software Seedling Vigor Imaging System® (SVIS®)

The software Seed Vigor Imaging System (SVIS®), has been successfully used to evaluate seed physiological potential by automated analyses of scanned seedlings. In this research, the efficiency of this system was compared to other tests accepted for assessing cucumber (Cucumis sativus L.) seed vigor of distinct seed lots of Supremo and Safira cultivars. Seeds were subjected to germination, traditional and saturated salt accelerated aging, seedling emergence, seedling length and SVIS analyses (determination of vigor indices and seedling growth uniformity, lengths of primary root, hypocotyl and whole seedlings). It was also determined whether the definition of seedling growth/uniformity ratios affects the sensitivity of the SVIS®. Results showed that analyses SVIS have provided consistent identification of seed lots performance, and have produced information comparable to those from recommended seed vigor tests, thus demonstrating a suitable sensitivity for a rapid and objective evaluation of physiological potential of cucumber seeds. Analyses of four-days-old cucumber seedlings using the SVIS® are more accurate and growth/uniformity does not affect the precision of results.

Controlling full penetration in MAG welding by the application of infrared thermography and neural network

In this study, an infrared thermography based sensor was studied with regard to usability and the accuracy of sensor data as a weld penetration signal in gas metal arc welding. The object of the study was to evaluate a specific sensor type which measures thermography from solidified weld surface. The purpose of the study was to provide expert data for developing a sensor system in adaptive metal active gas (MAG) welding. Welding experiments with considered process variables and recorded thermal profiles were saved to a database for further analysis. To perform the analysis within a reasonable amount of experiments, the process parameter variables were gradually altered by at least 10 %. Later, the effects of process variables on weld penetration and thermography itself were considered. SFS-EN ISO 5817 standard (2014) was applied for classifying the quality of the experiments. As a final step, a neural network was taught based on the experiments. The experiments show that the studied thermography sensor and the neural network can be used for controlling full penetration though they have minor limitations, which are presented in results and discussion. The results are consistent with previous studies and experiments found in the literature.

The development of automated methods for the determination of trace concentrations of carbomate pesticides in water using solid sorbent pre-concentration methods and high performance liquid chromatography /

Several automated reversed-phase HPLC methods have been developed to determine trace concentrations of carbamate pesticides (which are of concern in Ontario environmental samples) in water by utilizing two solid sorbent extraction techniques. One of the methods is known as on-line pre-concentration'. This technique involves passing 100 milliliters of sample water through a 3 cm pre-column, packed with 5 micron ODS sorbent, at flow rates varying from 5-10 mUmin. By the use of a valve apparatus, the HPLC system is then switched to a gradient mobile phase program consisting of acetonitrile and water. The analytes, Propoxur, Carbofuran, Carbaryl, Propham, Captan, Chloropropham, Barban, and Butylate, which are pre-concentrated on the pre-column, are eluted and separated on a 25 cm C-8 analytical column and determined by UV absorption at 220 nm. The total analytical time is 60 minutes, and the pre-column can be used repeatedly for the analysis of as many as thirty samples. The method is highly sensitive as 100 percent of the analytes present in the sample can be injected into the HPLC. No breakthrough of any of the analytes was observed and the minimum detectable concentrations range from 10 to 480 ng/L. The developed method is totally automated for the analysis of one sample. When the above mobile phase is modified with a buffer solution, Aminocarb, Benomyl, and its degradation product, MBC, can also be detected along with the above pesticides with baseline resolution for all of the analytes. The method can also be easily modified to determine Benomyl and MBC both as solute and as particulate matter. By using a commercially available solid phase extraction cartridge, in lieu of a pre-column, for the extraction and concentration of analytes, a completely automated method has been developed with the aid of the Waters Millilab Workstation. Sample water is loaded at 10 mL/min through a cartridge and the concentrated analytes are eluted from the sorbent with acetonitrile. The resulting eluate is blown-down under nitrogen, made up to volume with water, and injected into the HPLC. The total analytical time is 90 minutes. Fifty percent of the analytes present in the sample can be injected into the HPLC, and recoveries for the above eight pesticides ranged from 84 to 93 percent. The minimum detectable concentrations range from 20 to 960 ng/L. The developed method is totally automated for the analysis of up to thirty consecutive samples. The method has proven to be applicable to both purer water samples as well as untreated lake water samples.