First dice your dill – new methods and techniques in sample handling

This book is dedicated to celebrate the 60th birthday of Professor Rainer Huopalahti. Professor Rainer “Repe” Huopalahti has had, and in fact is still enjoying a distinguished career in the analysis of food and food related flavor compounds. One will find it hard to make any progress in this particular field without a valid and innovative sample handling technique and this is a field in which Professor Huopalahti has made great contributions. The title and the front cover of this book honors Professor Huopahti’s early steps in science. His PhD thesis which was published on 1985 is entitled “Composition and content of aroma compounds in the dill herb, Anethum graveolens L., affected by different factors”. At that time, the thesis introduced new technology being applied to sample handling and analysis of flavoring compounds of dill. Sample handling is an essential task that in just about every analysis. If one is working with minor compounds in a sample or trying to detect trace levels of the analytes, one of the aims of sample handling may be to increase the sensitivity of the analytical method. On the other hand, if one is working with a challenging matrix such as the kind found in biological samples, one of the aims is to increase the selectivity. However, quite often the aim is to increase both the selectivity and the sensitivity. This book provides good and representative examples about the necessity of valid sample handling and the role of the sample handling in the analytical method. The contributors of the book are leading Finnish scientists on the field of organic instrumental analytical chemistry. Some of them are also Repe’ s personal friends and former students from the University of Turku, Department of Biochemistry and Food Chemistry. Importantly, the authors all know Repe in one way or another and are well aware of his achievements on the field of analytical chemistry. The editorial team had a great time during the planning phase and during the “hard work editorial phase” of the book. For example, we came up with many ideas on how to publish the book. After many long discussions, we decided to have a limited edition as an “old school hard cover book” – and to acknowledge more modern ways of disseminating knowledge by publishing an internet version of the book on the webpages of the University of Turku. Downloading the book from the webpage for personal use is free of charge. We believe and hope that the book will be read with great interest by scientists working in the fascinating field of organic instrumental analytical chemistry. We decided to publish our book in English for two main reasons. First, we believe that in the near future, more and more teaching in Finnish Universities will be delivered in English. To facilitate this process and encourage students to develop good language skills, it was decided to be published the book in English. Secondly, we believe that the book will also interest scientists outside Finland – particularly in the other member states of the European Union. The editorial team thanks all the authors for their willingness to contribute to this book – and to adhere to the very strict schedule. We also want to thank the various individuals and enterprises who financially supported the book project. Without that support, it would not have been possible to publish the hardcover book.

Data mining techniques for identification of spectrally homogeneous areas using NDVI temporal profiles of soybean crop

The aim of this study was to group temporal profiles of 10-day composites NDVI product by similarity, which was obtained by the SPOT Vegetation sensor, for municipalities with high soybean production in the state of Paraná, Brazil, in the 2005/2006 cropping season. Data mining is a valuable tool that allows extracting knowledge from a database, identifying valid, new, potentially useful and understandable patterns. Therefore, it was used the methods for clusters generation by means of the algorithms K-Means, MAXVER and DBSCAN, implemented in the WEKA software package. Clusters were created based on the average temporal profiles of NDVI of the 277 municipalities with high soybean production in the state and the best results were found with the K-Means algorithm, grouping the municipalities into six clusters, considering the period from the beginning of October until the end of March, which is equivalent to the crop vegetative cycle. Half of the generated clusters presented spectro-temporal pattern, a characteristic of soybeans and were mostly under the soybean belt in the state of Paraná, which shows good results that were obtained with the proposed methodology as for identification of homogeneous areas. These results will be useful for the creation of regional soybean "masks" to estimate the planted area for this crop.

The Possibilities and Dosimetric Limitations of MLC-Based Intensity-Modulated Radiotherapy Delivery and Optimization Techniques

The use of intensity-modulated radiotherapy (IMRT) has increased extensively in the modern radiotherapy (RT) treatments over the past two decades. Radiation dose distributions can be delivered with higher conformality with IMRT when compared to the conventional 3D-conformal radiotherapy (3D-CRT). Higher conformality and target coverage increases the probability of tumour control and decreases the normal tissue complications. The primary goal of this work is to improve and evaluate the accuracy, efficiency and delivery techniques of RT treatments by using IMRT. This study evaluated the dosimetric limitations and possibilities of IMRT in small (treatments of head-and-neck, prostate and lung cancer) and large volumes (primitive neuroectodermal tumours). The dose coverage of target volumes and the sparing of critical organs were increased with IMRT when compared to 3D-CRT. The developed split field IMRT technique was found to be safe and accurate method in craniospinal irradiations. By using IMRT in simultaneous integrated boosting of biologically defined target volumes of localized prostate cancer high doses were achievable with only small increase in the treatment complexity. Biological plan optimization increased the probability of uncomplicated control on average by 28% when compared to standard IMRT delivery. Unfortunately IMRT carries also some drawbacks. In IMRT the beam modulation is realized by splitting a large radiation field to small apertures. The smaller the beam apertures are the larger the rebuild-up and rebuild-down effects are at the tissue interfaces. The limitations to use IMRT with small apertures in the treatments of small lung tumours were investigated with dosimetric film measurements. The results confirmed that the peripheral doses of the small lung tumours were decreased as the effective field size was decreased. The studied calculation algorithms were not able to model the dose deficiency of the tumours accurately. The use of small sliding window apertures of 2 mm and 4 mm decreased the tumour peripheral dose by 6% when compared to 3D-CRT treatment plan. A direct aperture based optimization (DABO) technique was examined as a solution to decrease the treatment complexity. The DABO IMRT technique was able to achieve treatment plans equivalent with the conventional IMRT fluence based optimization techniques in the concave head-and-neck target volumes. With DABO the effective field sizes were increased and the number of MUs was reduced with a factor of two. The optimality of a treatment plan and the therapeutic ratio can be further enhanced by using dose painting based on regional radiosensitivities imaged with functional imaging methods.

Software Development Process Modeling. Developers Perspective to Contemporary Modeling Techniques

Formal software development processes and well-defined development methodologies are nowadays seen as the definite way to produce high-quality software within time-limits and budgets. The variety of such high-level methodologies is huge ranging from rigorous process frameworks like CMMI and RUP to more lightweight agile methodologies. The need for managing this variety and the fact that practically every software development organization has its own unique set of development processes and methods have created a profession of software process engineers. Different kinds of informal and formal software process modeling languages are essential tools for process engineers. These are used to define processes in a way which allows easy management of processes, for example process dissemination, process tailoring and process enactment. The process modeling languages are usually used as a tool for process engineering where the main focus is on the processes themselves. This dissertation has a different emphasis. The dissertation analyses modern software development process modeling from the software developers’ point of view. The goal of the dissertation is to investigate whether the software process modeling and the software process models aid software developers in their day-to-day work and what are the main mechanisms for this. The focus of the work is on the Software Process Engineering Metamodel (SPEM) framework which is currently one of the most influential process modeling notations in software engineering. The research theme is elaborated through six scientific articles which represent the dissertation research done with process modeling during an approximately five year period. The research follows the classical engineering research discipline where the current situation is analyzed, a potentially better solution is developed and finally its implications are analyzed. The research applies a variety of different research techniques ranging from literature surveys to qualitative studies done amongst software practitioners. The key finding of the dissertation is that software process modeling notations and techniques are usually developed in process engineering terms. As a consequence the connection between the process models and actual development work is loose. In addition, the modeling standards like SPEM are partially incomplete when it comes to pragmatic process modeling needs, like light-weight modeling and combining pre-defined process components. This leads to a situation, where the full potential of process modeling techniques for aiding the daily development activities can not be achieved. Despite these difficulties the dissertation shows that it is possible to use modeling standards like SPEM to aid software developers in their work. The dissertation presents a light-weight modeling technique, which software development teams can use to quickly analyze their work practices in a more objective manner. The dissertation also shows how process modeling can be used to more easily compare different software development situations and to analyze their differences in a systematic way. Models also help to share this knowledge with others. A qualitative study done amongst Finnish software practitioners verifies the conclusions of other studies in the dissertation. Although processes and development methodologies are seen as an essential part of software development, the process modeling techniques are rarely used during the daily development work. However, the potential of these techniques intrigues the practitioners. As a conclusion the dissertation shows that process modeling techniques, most commonly used as tools for process engineers, can also be used as tools for organizing the daily software development work. This work presents theoretical solutions for bringing the process modeling closer to the ground-level software development activities. These theories are proven feasible by presenting several case studies where the modeling techniques are used e.g. to find differences in the work methods of the members of a software team and to share the process knowledge to a wider audience.

Surgical techniques for maxillary bone grafting - literature review

For oral rehabilitation with implant-supported prostheses, there are required procedures to create the bone volume needed for installation of the implants. Thus, bone grafts from intraoral or extraoral donor sites represent a very favorable opportunity. This study aimed to review the literature on the subject, seeking to discuss parameters for the indications, advantages and complications of techniques for autogenous bone grafts.

Comparison of three diagnostic techniques for the detection of leptospires in the kidneys of wild house mice (Mus musculus)

Forty-one wild house mice (Mus musculus) were trapped in an urban area, near railways, in Santa Fe city, Argentina. Both kidneys from each mouse were removed for bacteriological and histological examination. One kidney was inoculated into Fletcher semi-solid medium and isolates were serologically typed. The other kidney was microscopically examined after hematoxylin-eosin, silver impregnation and immunohistochemical stains. Leptospires, all of them belonging to the Ballum serogroup, were isolated from 16 (39%) out of 41 samples. The presence of the agent was recorded in 18 (44%) and in 19 (46%) out of 41 silver impregnated and immunohistochemically stained samples respectively. Additionally, leptospires were detected in high number on the apical surface of epithelial cells and in the lumen of medullary tubules and they were less frequently seen on the apical surface of epithelial cells or in the lumen of the cortical tubules, which represents an unusual finding in carrier animals. Microscopic lesions consisting of focal mononuclear interstitial nephritis, glomerular shrinkage and desquamation of tubular epithelial cells were observed in 13 of 19 infected and in 10 of 22 non-infected mice; differences in presence of lesions between infected and non-infected animals were not statistically significant (P=0,14). The three techniques, culture, silver impregnation and immunohistochemistry, had a high agreement (k³0.85) and no significant differences between them were detected (P>0.05). In addition, an unusual location of leptospires in kidneys of carrier animals was reported, but a relationship between lesions and presence of leptospires could not be established.

Using passive techniques for vibration damping in mechanical systems

This paper examines two passive techniques for vibration reduction in mechanical systems: the first one is based on dynamic vibration absorbers (DVAs) and the second uses resonant circuit shunted (RCS) piezoceramics. Genetic algorithms are used to determine the optimal design parameters with respect to performance indexes, which are associated with the dynamical behavior of the system over selected frequency bands. The calculation of the frequency response functions (FRFs) of the composite structure (primary system + DVAs) is performed through a substructure coupling technique. A modal technique is used to determine the frequency response function of the structure containing shunted piezoceramics which are bonded to the primary structure. The use of both techniques simultaneously on the same structure is investigated. The methodology developed is illustrated by numerical applications in which the primary structure is represented by simple Euler-Bernoulli beams. However, the design aspects of vibration control devices presented in this paper can be extended to more complex structures.

Performance evaluation of 3D computer vision techniques

This work presents the implementation and comparison of three different techniques of three-dimensional computer vision as follows: • Stereo vision - correlation between two 2D images • Sensorial fusion - use of different sensors: camera 2D + ultrasound sensor (1D); • Structured light The computer vision techniques herein presented took into consideration the following characteristics: • Computational effort ( elapsed time for obtain the 3D information); • Influence of environmental conditions (noise due to a non uniform lighting, overlighting and shades); • The cost of the infrastructure for each technique; • Analysis of uncertainties, precision and accuracy. The option of using the Matlab software, version 5.1, for algorithm implementation of the three techniques was due to the simplicity of their commands, programming and debugging. Besides, this software is well known and used by the academic community, allowing the results of this work to be obtained and verified. Examples of three-dimensional vision applied to robotic assembling tasks ("pick-and-place") are presented.

Optimal design of 3R manipulators by using classical techniques and simulated annealin

In this paper, the optimum design of 3R manipulators is formulated and solved by using an algebraic formulation of workspace boundary. A manipulator design can be approached as a problem of optimization, in which the objective functions are the size of the manipulator and workspace volume; and the constrains can be given as a prescribed workspace volume. The numerical solution of the optimization problem is investigated by using two different numerical techniques, namely, sequential quadratic programming and simulated annealing. Numerical examples illustrate a design procedure and show the efficiency of the proposed algorithms.

Weed mapping using techniques of precision agriculture

The aim of this study was to identify and map the weed population in a no-tillage area. Geostatistical techniques were used in the mapping in order to assess this information as a tool for the localized application of herbicides. The area of study is 58.08 hectares wide and was sampled in a fixed square grid (which point spaced 50 m, 232 points) using a GPS receiver. In each point the weeds species and population were analyzed in a square with a 0.25 m2 fixed area. The species Ipomoea grandifolia, Gnaphalium spicatum, Richardia spp. and Emilia sonchifolia have presented no spatial dependence. However, the species Conyza spp., C. echinatus and E. indica have shown a spatial correlation. Among the models tested, the spherical model has shown had a better fit for Conyza spp. and Eleusine indica and the Gaussian model for Cenchrus echinatus. The three species have a clumped spatial distribution. The mapping of weeds can be a tool for localized control, making herbicide use more rational, effective and economical.

Phytotoxic Activity of Parthenium Against Wheat and Canola Differ With Plant Parts and Bioassays Techniques

Phytotoxic effects of invasive weed Parthenium hysterophorus were studied by using whole plant, leaf and root aqueous extracts at 0, 2.5, 5.0, 7.5 and 10% (w/v) concentrations against germination and early seedling growth of wheat and canola. Studies were carried out both in Petri plates with filter paper as substratum placed in controlled conditions and soil-filled plastic pots placed in open environments. Pronounced variation was noted for phytotoxic activity of different plant parts of parthenium, aqueous extract concentrations, test species, and bioassay techniques. Aqueous parthenium extracts either inhibited or delayed the germination and suppressed seedling growth of test species over control. For both test species, all the germination attributes were suppressed to a greater extent in Petri plates than in plastic pots. Leaf extracts were more suppressive to germination of test species than whole plant and root extracts. Increasing extract concentration beyond 2.5% caused significant reduction in seedling dry biomass of both test species. Aqueous parthenium extract diminished chlorophyll contents of wheat and canola by 32-63% and 29 69%, respectively. Nevertheless, an increase of 9-172% and 22-60% in phenolic contents of wheat and canola was recorded. Canola appeared to be more susceptible than wheat at all extract concentrations. Present study concluded that bioassays conducted under controlled condition using filter paper as substratum may be misleading due to over estimation of allelopathic response and variation in potential of receiver and donor species. Furthermore, it implies that threshold concentrations of allelochemicals for test species in Petri plates are rarely reached under field conditions.

Geo-enabling repositories - techniques, tools, and challenges

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

Chromosome damage in underground coal miners: detection by conventional cytogenetic techniques and by submitting lymphocytes of unexposed individuals to plasma from at-risk groups

Chromosome abnormalities and the mitotic index in lymphocyte cultures and micronuclei in buccal mucosa cells were investigated in a sample of underground mineral coal miners from Southern Brazil. A decreased mitotic index, an excess of micronuclei and a higher frequency of chromosome abnormalities (fragments, polyploidy and overall chromosome alterations) were observed in the miners when compared to age-paired normal controls from the same area. An alternative assay for clastogenesis in occupational exposition was tested by submitting lymphocytes from non-exposed individuals to a pool of plasmas from the exposed population. This assay proved to be very convenient, as the lymphocytes obtained from the same individuals can be used as target as well as control cells. Also, it yielded a larger number of metaphases and of successful cultures than with common lymphocyte cultures from miners. A significantly higher frequency of chromatid gaps, fragments and overall alterations were observed when lymphocytes from control subjects were exposed to miner plasma pools. Control plasma pools did not significantly induce any type of chromosome alterations in the cultures of normal subjects, thus indicating that the results are not due to the effect of the addition of plasma pools per se.

Evaluation of techniques for C and ASG banding of the mitotic chromosomes of Anastrepha species (Diptera, Tephritidae)

Methods previously described by Canovai et al. (Caryologia 47: 241-247, 1994) which produced C and ASG bands in mitotic chromosomes of Ceratitis capitata were applied to the chromosomes of several Anastrepha species. Metaphase plate yield was substantially increased by use of imaginal disks together with cerebral ganglia. The C-bands were quite prominent allowing the resolution of tiny blocks of heterochromatin. The ASG method produced G-like banded chromosomes, which permitted recognition of each individual chromosome. These simple techniques do not require special equipment and may be valuable for karyotype variability studies in fruit flies and other Diptera