NaOCl effect on biofilm produced by Staphylococcus aureus isolated from the milking environment and mastitis infected cows

Biofilms constitute a physical barrier, protecting the encased bacteria from detergents and sanitizers. The objective of this work was to analyze the effectiveness of sodium hypochlorite (NaOCl) against strains of Staphylococcus aureus isolated from raw milk of cows with subclinical mastitis and Staphylococcus aureus isolated from the milking environment (blowers and milk conducting tubes). The results revealed that, in the presence of NaOCl (150ppm), the number of adhered cells of the twelve S. aureus strains was significantly reduced. When the same strains were evaluated in biofilm condition, different results were obtained. It was found that, after a contact period of five minutes with NaOCl (150ppm), four strains (two strains from milk , one from the blowers and one from a conductive rubber) were still able to grow. Although with the increasing contact time between the bacteria and the NaOCl (150ppm), no growth was detected for any of the strains. Concerning the efficiency of NaOCl on total biofilm biomass formation by each S. aureus strain, a decrease was observed when these strains were in contact with 150 ppm NaOCl for a total period of 10 minutes. This study highlights the importance of a correct sanitation protocol of all the milk processing units which can indeed significantly reduce the presence of microorganisms, leading to a decrease of cow´s mastitis and milk contamination.

Real-time Image-based RGB-D Camera Motion Tracking and Environment Mapping

In this work, image based estimation methods, also known as direct methods, are studied which avoid feature extraction and matching completely. Cost functions use raw pixels as measurements and the goal is to produce precise 3D pose and structure estimates. The cost functions presented minimize the sensor error, because measurements are not transformed or modified. In photometric camera pose estimation, 3D rotation and translation parameters are estimated by minimizing a sequence of image based cost functions, which are non-linear due to perspective projection and lens distortion. In image based structure refinement, on the other hand, 3D structure is refined using a number of additional views and an image based cost metric. Image based estimation methods are particularly useful in conditions where the Lambertian assumption holds, and the 3D points have constant color despite viewing angle. The goal is to improve image based estimation methods, and to produce computationally efficient methods which can be accomodated into real-time applications. The developed image-based 3D pose and structure estimation methods are finally demonstrated in practise in indoor 3D reconstruction use, and in a live augmented reality application.

Video transcoding in a distributed cloud computing environment

Video transcoding refers to the process of converting a digital video from one format into another format. It is a compute-intensive operation. Therefore, transcoding of a large number of simultaneous video streams requires a large amount of computing resources. Moreover, to handle di erent load conditions in a cost-e cient manner, the video transcoding service should be dynamically scalable. Infrastructure as a Service Clouds currently offer computing resources, such as virtual machines, under the pay-per-use business model. Thus the IaaS Clouds can be leveraged to provide a coste cient, dynamically scalable video transcoding service. To use computing resources e ciently in a cloud computing environment, cost-e cient virtual machine provisioning is required to avoid overutilization and under-utilization of virtual machines. This thesis presents proactive virtual machine resource allocation and de-allocation algorithms for video transcoding in cloud computing. Since users' requests for videos may change at di erent times, a check is required to see if the current computing resources are adequate for the video requests. Therefore, the work on admission control is also provided. In addition to admission control, temporal resolution reduction is used to avoid jitters in a video. Furthermore, in a cloud computing environment such as Amazon EC2, the computing resources are more expensive as compared with the storage resources. Therefore, to avoid repetition of transcoding operations, a transcoded video needs to be stored for a certain time. To store all videos for the same amount of time is also not cost-e cient because popular transcoded videos have high access rate while unpopular transcoded videos are rarely accessed. This thesis provides a cost-e cient computation and storage trade-o strategy, which stores videos in the video repository as long as it is cost-e cient to store them. This thesis also proposes video segmentation strategies for bit rate reduction and spatial resolution reduction video transcoding. The evaluation of proposed strategies is performed using a message passing interface based video transcoder, which uses a coarse-grain parallel processing approach where video is segmented at group of pictures level.

The Purdue University Research Repository (PURR): An institutional data management service with a virtual research environment, data publication, and archiving

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

Novel virtual environment and real-time simulation based methods for improving life-cycle efficiency of non-road mobile machinery

Virtual environments and real-time simulators (VERS) are becoming more and more important tools in research and development (R&D) process of non-road mobile machinery (NRMM). The virtual prototyping techniques enable faster and more cost-efficient development of machines compared to use of real life prototypes. High energy efficiency has become an important topic in the world of NRMM because of environmental and economic demands. The objective of this thesis is to develop VERS based methods for research and development of NRMM. A process using VERS for assessing effects of human operators on the life-cycle efficiency of NRMM was developed. Human in the loop simulations are ran using an underground mining loader to study the developed process. The simulations were ran in the virtual environment of the Laboratory of Intelligent Machines of Lappeenranta University of Technology. A physically adequate real-time simulation model of NRMM was shown to be reliable and cost effective in testing of hardware components by the means of hardware-in-the-loop (HIL) simulations. A control interface connecting integrated electro-hydraulic energy converter (IEHEC) with virtual simulation model of log crane was developed. IEHEC consists of a hydraulic pump-motor and an integrated electrical permanent magnet synchronous motorgenerator. The results show that state of the art real-time NRMM simulators are capable to solve factors related to energy consumption and productivity of the NRMM. A significant variation between the test drivers is found. The results show that VERS can be used for assessing human effects on the life-cycle efficiency of NRMM. HIL simulation responses compared to that achieved with conventional simulation method demonstrate the advances and drawbacks of various possible interfaces between the simulator and hardware part of the system under study. Novel ideas for arranging the interface are successfully tested and compared with the more traditional one. The proposed process for assessing the effects of operators on the life-cycle efficiency will be applied for wider group of operators in the future. Driving styles of the operators can be analysed statistically from sufficient large result data. The statistical analysis can find the most life-cycle efficient driving style for the specific environment and machinery. The proposed control interface for HIL simulation need to be further studied. The robustness and the adaptation of the interface in different situations must be verified. The future work will also include studying the suitability of the IEHEC for different working machines using the proposed HIL simulation method.

Quantification of Toxin Biosynthesis Genes In Cyanobacteria and Dinoflagellates - Genetic Factors as Predictors of Toxin Production in the Environment

Harmful algal blooms (HABs) are events caused by the massive proliferation of microscopic, often photosynthetic organisms that inhabit both fresh and marine waters. Although HABs are essentially a natural phenomenon, they now cause worldwide concern. Recent anthropogenic effects, such as climate change and eutrophication via nutrient runoff, can be seen in their increased prevalence and severity. Cyanobacteria and dinoflagellates are often the causative organisms of HABs. In addition to adverse effects caused by the sheer biomass, certain species produce highly potent toxic compounds: hepatotoxic microcystins are produced exclusively by cyanobacteria and neurotoxic saxitoxins, also known as paralytic shellfish toxins (PSTs), by both cyanobacteria and dinoflagellates. Specific biosynthetic genes in the cyanobacterial genomes direct the production of microcystin and paralytic shellfish toxins. Recently also the first paralytic shellfish toxin gene sequences from dinoflagellate genomes have been elucidated. The public health risks presented by HABs are evident, but the monitoring and prediction of toxic events is challenging. Characterization of the genetic background of toxin biosynthesis, including that of microcystins and paralytic shellfish toxins, has made it possible to develop highly sensitive molecular tools which have shown promise in the monitoring and study of potentially toxic microalgae. In this doctoral work, toxin-specific genes were targeted in the developed PCR and qPCR assays for the detection and quantification of potentially toxic cyanobacteria and dinoflagellates in the environment. The correlation between the copy numbers of the toxin biosynthesis genes and toxin production were investigated to assess whether the developed methods could be used to predict toxin concentrations. The nature of the correlation between gene copy numbers and amount of toxin produced varied depending on the targeted gene and the producing organism. The combined mcyB copy numbers of three potentially microcystin-producing cyanobacterial genera showed significant positive correlation to the observed total toxin production. However, the presence of PST-specific sxtA, sxtG, and sxtB genes of cyanobacterial origin was found to be a poor predictor of toxin production in the studied area. Conversely, the dinoflagellate sxtA4 was a good qualitative indicator of a neurotoxic bloom both in the laboratory and in the field, and population densities reflected well the observed toxin concentrations. In conclusion, although the specificity of each potential targeted toxin biosynthesis gene must be assessed individually during method development, the results obtained in this doctoral study support the use of quantitative PCR -based approaches in the monitoring of toxic cyanobacteria and dinoflagellates.

Automated UI testing. WBCT, a computer-automated user test environment tool.

Today, the user experience and usability in software application are becoming a major design issue due to the adaptation of many processes using new technologies. Therefore, the study of the user experience and usability might be included in every software development project and, thus, they should be tested to get traceable results. As a result of different testing methods to evaluate the concepts, a non-expert on the topic might have doubts on which option he/she should opt for and how to interpret the outcomes of the process. This work aims to create a process to ease the whole testing methodology based on the process created by Seffah et al. and a supporting software tool to follow the procedure of these testing methods for the user experience and usability.

POLITICAL ENVIRONMENT AND BUSINESS DEVELOPMENT IN THE ARCTIC Strategic opportunities and threats for Finnish companies

The Arctic environment is changing constantly. There are several factors that constitute to the rate and immensity of the development. The region differs from the surrounding markets that most of the countries in the region have been used to. Therefore the purpose of the study was to understand how the political environment affects Finnish companies’ strategies and business operations. The issues analyzed were the political environment in the region, the business environment and economic development, and the opportunities and threats that the Finnish companies have in Arctic. The main theories were found from strategic management and market analysis tools. The different theories and definitions were gone through in order to understand the context of the study. This is a qualitative study that uses content analysis as its main method of analyzing the data. Therefore the data analyzed was gathered from already existing material and it was analyzed until the saturation point was found. This was done in order to minimize the risks related to using secondary data. The data collected was then categorized into themes accordingly. First the general political environment in the Arctic was studied, especially the Arctic Council and its work as the main political entity. From there the focus shifted to the business environment and the general opportunities and threats that are found from Arctic economic development. China offered another point of view to this as it represented a non-Arctic state with a keen interest on the region. Lastly the two previous objectives were combined and looked through from a Finnish perspective. Finnish companies have a great starting point to Arctic business and the operational business environment gives them the framework with which they have to operate in. As a conclusion it can be said that there are three main factors leading the Arctic economic development; the climate change, the development of technology, and the political environment. These set the framework with which the companies operating in the region must comply with. The industry that is likely to lead the development is the marine industry. Furthermore it became evident that the Finnish companies operating in the Arctic face many opportunities as well as threats which can be utilized, taken advantage of or controlled through effective strategic management. The key characteristics needed in the region are openness and understanding of the challenging environment and the ability to face and manage the arising challenges.

Childlessness in a child-centered environment : the experiences of voluntarily childless female teachers /

In the literature on voluntary childlessness there is a lack of research on the types of occupations held by women who choose not to mother and how their fertility choice influences their occupational experiences. At the same time, the experience ofwomen with regard to the childfree choice has not been adequately addressed in contemporary feminist literature. In the field of education, much has been written about the association between mothering and teaching. Thus, childfree teachers become particularly interesting since they made seemingly paradoxical choices in that they chose not to bear and rear children yet they chose an occupation in which they are surrounded by and responsible for the daily care of many children. To gain an understanding of the work-related experiences of childfree women, in-depth interviews were conducted with 7 voluntarily childless female elementary school teachers from Southern Ontario. In addition, a focus group interview in which 3 of the 7 childfree teachers participated was conducted. Findings revealed that these women's "choice" to be childless was the result of complex circumstances and multiple motivations. Also, despite their decision to forgo the traditional female role of mother, these women held surprisingly conventional beliefs with regard to family and gender roles. In addition, these childfree women at times identified themselves as mother-like when teaching, yet at other times distanced themselves as teachers from mothers. Finally, results showed that these women experienced both direct and indirect pronatalist pressures outside as well as inside the workplace as a result of their childfree status.

The Social Enterprise as an Alternative Work Option for Persons with Developmental Disabilities: A Case Study of Staff Perspectives at Common Ground Co-operative

Traditional employment options for persons with developmental disabilities are lacking. Employment options available for persons with developmental disabilities are reflective of the medical and social model perspectives of disability; with segregated and supported employment reinforcing the idea that persons with developmental disabilities are incapable and competitive employment missing the necessary accommodations for persons to be successful. This study examined social enterprises as an alternative employment option that can balance both medical and social model perspectives by accommodating for weaknesses or limitations and recognizing the strengths and capabilities of persons with developmental disabilities in the workplace. Moreover, this study is part of a broader case study which is examining the nature and impacts of a social enterprise, known as Common Ground Co-operative (CGC), which supports five social purpose businesses that are owned and operated by persons with developmental disabilities. This study is part of the Social Business and Marginalized Social Groups Community-University Research Alliance. To date, a case study has been written describing the nature and impacts of CGC and its related businesses from the perspectives of the Partners, board members, funders and staff (Owen, Readhead, Bishop, Hope & Campbell, in press & Readhead, 2012). The current study used a descriptive case study approach to provide a detailed account of the perceptions and opinions of CGC staff members who support each of the Partners in the five related businesses. Staff members were chosen for the focus of this study because of the integral role that they play in the successful outcomes of the persons they support. This study was conducted in two phases. In the first phase five staff members were interviewed. During this stage of interviews, several themes were presented which needed to be examined in further detail, specifically staff stress and burnout and duty of care for business Partners versus the promotion of their autonomy. A second phase of interviews was then conducted with one individual participant and a focus group of seven. During both interview phases, Staff participants described an employment model that creates a non-judgemental environment for the business Partners that promotes their strengths, accommodates for their limitations, provides educational opportunities and places the responsibility for the businesses on the persons with developmental disabilities cultivating equality and promoting independence. Staff described the nature of their role including risk factors for stress, the protective factors that buffer stress, and the challenges associated with balancing many role demands. Issues related to the replication of this social enterprise model are described.

Optimizing Computational Frameworks to Study the Influence of the Protein Environment on the Individual Site Energies of Chromophores in Photosystem II of Photosynthesis

Photosynthesis is a process in which electromagnetic radiation is converted into chemical energy. Photosystems capture photons with chromophores and transfer their energy to reaction centers using chromophores as a medium. In the reaction center, the excitation energy is used to perform chemical reactions. Knowledge of chromophore site energies is crucial to the understanding of excitation energy transfer pathways in photosystems and the ability to compute the site energies in a fast and accurate manner is mandatory for investigating how protein dynamics ef-fect the site energies and ultimately energy pathways with time. In this work we developed two software frameworks designed to optimize the calculations of chro-mophore site energies within a protein environment. The first is for performing quantum mechanical energy optimizations on molecules and the second is for com-puting site energies of chromophores in a fast and accurate manner using the polar-izability embedding method. The two frameworks allow for the fast and accurate calculation of chromophore site energies within proteins, ultimately allowing for the effect of protein dynamics on energy pathways to be studied. We use these frame-works to compute the site energies of the eight chromophores in the reaction center of photosystem II (PSII) using a 1.9 Å resolution x-ray structure of photosystem II. We compare our results to conflicting experimental data obtained from both isolat-ed intact PSII core preparations and the minimal reaction center preparation of PSII, and find our work more supportive of the former.

Pollution Routing in a Tropical Estuarine Environment

This thesis attempts to gain insight on the mathematical approach to estuarine oceanographic systems; also to closely understand the governing processes in the estuarine environment as well as in the adjoining river reaches. The main aim was to conduct pollution routing for tropical estuarine environment namely, for the Cochin estuary. In this context, attempts have been made to apply, verify and validate the application of models, pre- prepared with necessary modifications to suit the area of interest by use of RIVMIX and WASP tools. Finally the thesis concludes by highlighting the advantages and limitations in modelling water bodies and concurrentlysimulates most of the possible scenarios within the purview of this work.

Synergic Reactions in the Estuarine Environment leading to Modulation of Aluminium metal during Transport Processes (in Cochin Estuary)

The research work which was carried out to Synergic Reactions in the Estuarine Environment leading to Modulation of Aluminium metal during Transport Processes (in Cochin Estuary)Estuaries are considered as sink or source for terrestrial and various anthropogenically generated materials. These include naturally occurring elements Al, Si, Fe or trace inorganics or industrial pollutants of different types. There have been reports on both positive and negative impacts by the introduction of above materials into the ecosystem.This thesis deals with the trace metal Aluminium (Al) whose average concentration (about 8%) in the earths crust is surpassed only by that of Oxygen and Silicon. There can be no doubt that most of the land derived materials reaches the ocean through rivers via estuaries. An important aspect noticed here is that the concentration of dissolved Al is much lower in sea water than in river water.On critically analysing Cochin estuary, for the entire cycles, covering monsoon, postmonsoon and premonsoon, the following salient features are documented as hereunder. Dissolved Al exhibits high and variable trends in Cochin estuary, the influencing parameters being salinity, SPM, pH and dissolved Si. A general profile showed removal in upper/mid estuary followed by regeneration in the mid/lower estuary and further decrease seawards in the southern/northem arms.Distribution appears to be a function of freshwater input, the monsoon season exhibiting very high concentrations throughout the estuary. As the river discharge decreased with the progress of seasons, dissolved Al concentration also decreased, the metal limiting itself to the upper and mid estuary.

Influence of the buffer environment on the Relative Biological Effectiveness of carbon ion radiation, investigated by Scanning Force Microscopy and gel electrophoresis

This work focuses on the analysis of the influence of environment on the relative biological effectiveness (RBE) of carbon ions on molecular level. Due to the high relevance of RBE for medical applications, such as tumor therapy, and radiation protection in space, DNA damages have been investigated in order to understand the biological efficiency of heavy ion radiation. The contribution of this study to the radiobiology research consists in the analysis of plasmid DNA damages induced by carbon ion radiation in biochemical buffer environments, as well as in the calculation of the RBE of carbon ions on DNA level by mean of scanning force microscopy (SFM). In order to study the DNA damages, besides the common electrophoresis method, a new approach has been developed by using SFM. The latter method allows direct visualisation and measurement of individual DNA fragments with an accuracy of several nanometres. In addition, comparison of the results obtained by SFM and agarose gel electrophoresis methods has been performed in the present study. Sparsely ionising radiation, such as X-rays, and densely ionising radiation, such as carbon ions, have been used to irradiate plasmid DNA in trishydroxymethylaminomethane (Tris buffer) and 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES buffer) environments. These buffer environments exhibit different scavenging capacities for hydroxyl radical (HO0), which is produced by ionisation of water and plays the major role in the indirect DNA damage processes. Fragment distributions have been measured by SFM over a large length range, and as expected, a significantly higher degree of DNA damages was observed for increasing dose. Also a higher amount of double-strand breaks (DSBs) was observed after irradiation with carbon ions compared to X-ray irradiation. The results obtained from SFM measurements show that both types of radiation induce multiple fragmentation of the plasmid DNA in the dose range from D = 250 Gy to D = 1500 Gy. Using Tris environments at two different concentrations, a decrease of the relative biological effectiveness with the rise of Tris concentration was observed. This demonstrates the radioprotective behavior of the Tris buffer solution. In contrast, a lower scavenging capacity for all other free radicals and ions, produced by the ionisation of water, was registered in the case of HEPES buffer compared to Tris solution. This is reflected in the higher RBE values deduced from SFM and gel electrophoresis measurements after irradiation of the plasmid DNA in 20 mM HEPES environment compared to 92 mM Tris solution. These results show that HEPES and Tris environments play a major role on preventing the indirect DNA damages induced by ionising radiation and on the relative biological effectiveness of heavy ion radiation. In general, the RBE calculated from the SFM measurements presents higher values compared to gel electrophoresis data, for plasmids irradiated in all environments. Using a large set of data, obtained from the SFM measurements, it was possible to calculate the survive rate over a larger range, from 88% to 98%, while for gel electrophoresis measurements the survive rates have been calculated only for values between 96% and 99%. While the gel electrophoresis measurements provide information only about the percentage of plasmids DNA that suffered a single DSB, SFM can count the small plasmid fragments produced by multiple DSBs induced in a single plasmid. Consequently, SFM generates more detailed information regarding the amount of the induced DSBs compared to gel electrophoresis, and therefore, RBE can be calculated with more accuracy. Thus, SFM has been proven to be a more precise method to characterize on molecular level the DNA damage induced by ionizing radiations.

Decent work?

Pastoralism and ranching are two different rangeland-based livestock systems in dryland areas of East Africa. Both usually operate under low and irregular rainfall and consequently low overall primary biomass production of high spatial and temporal heterogeneity. Both are usually located far from town centres, market outlets and communication, medical, educational, banking, insurance and other infrastructure. Whereas pastoralists can be regarded as self-employed, gaining their livelihood from managing their individually owned livestock on communal land, ranches mostly employ herders as wage labourers to manage the livestock owned by the ranch on the ranches’ own land property. Both production systems can be similarly labour intensive and – with regard to the livestock management – require the same type of work, whether carried out as self-employed pastoralist or as employed herder on a work contract. Given this similarity, the aim of this study was to comparatively assess how pastoralists and employed herders in northern Kenya view their working conditions, and which criteria they use to assess hardship and rewards in their daily work and their working life. Their own perception is compared with the concept of Decent Work developed by the International Labour Organisation (ILO). Samburu pastoralists in Marsabit and Samburu Districts as well as herders on ranches in Laikipia District were interviewed. A qualitative analysis of 47 semi-structured interviews yielded information about daily activities, income, free time, education and social security. Five out of 22 open interviews with pastoralists and seven out of 13 open interviews with employed herders fully transcribed and subjected to qualitative content analysis to yield life stories of 12 informants. Pastoralists consider it important to have healthy and satisfied animals. The ability to provide food for their family especially for the children has a high priority. Hardships for the pastoralists are, if activities are exhausting, and challenging, and dangerous. For employed herders, decent conditions are if their wages are high enough to be able to provide food for their family and formal education for their children. It is further most important for them to do work they are experienced and skilled in. Most employed herders were former pastoralists, who had lost their animals due to drought or raids. There are parallels between the ILO ‘Decent Work’ concept and the perception of working conditions of pastoralists and employed herders. These are, for example, that remuneration is of importance and the appreciation by either the employer or the community is desired. Some aspects that are seen as important by the ILO such as safety at work and healthy working conditions only play a secondary role to the pastoralists, who see risky and dangerous tasks as inherent characteristics of their efforts to gain a livelihood in their living environment.