Effects of fumonisin B1 on selected biological responses and performance of broiler chickens

The objective of this study was to determine the effects of three doses of fumonisin B1 (0, 100, and 200mg/kg of feed) on biological variables (relative weight of liver [RWL], total plasma protein [TPP], albumin [Alb], calcium [Ca], phosphorus [P], uric acid [UA], alanine aminotransferase [ALT], aspartate aminotransferase [AST], gamma glutamyltransferase [GGT], alkaline phosphatase [AP], total cholesterol [Chol], triglycerides [Tri], sphinganine-to-sphingosine ratio [SA:SO], and C-reactive protein [CRP]), morphological evaluation of the small intestine (villus height [VH], crypt depth [CD], and villus-to-crypt ratio [V:C]), histological evaluation, and on performance (body weight [BW], feed intake [FI], and feed conversion rate [FCR]) of broiler chickens. Significant effects of FB were observed on BW and FI (reduced), on RWL, TPP, Ca, ALT, AST, GGT, Chol, and Tri (increased) at both 14 and 28 days evaluations. In addition, significant increase was observed on FCR, Alb, P, SA:SO, and CRP and significant reduction in UA, VH, and V:C only at the 28 days evaluation. Significant histological lesions were observed on liver and kidney of FB inoculated broilers at 14 and 28 days. Those results show that FB has a significant effect on biological and histological variables and on performance of broiler chickens.

Concomitant infection of Neospora caninum and Bovine Herpesvirus type 5 in spontaneous bovine abortions

Bovine Herpesvirus type 5 (BoHV-5) has not been conclusively demonstrated to cause bovine abortion. Brain lesions produced by Neospora caninum and Bovine Herpesvirus type 1 (BoHV-1) exhibit common features. Therefore, careful microscopic evaluation and additional diagnostic procedures are required to achieve an accurate final etiological diagnosis. The aim of the present work was to investigate the occurrence of infections due to BoHV-1, BoHV-5 and N. caninum in 68 cases of spontaneous bovine abortions which showed microscopic lesions in the fetal central nervous system. This study allowed the identification of 4 (5.9%) fetuses with dual infection by BoHV-5 and N. caninum and 33 (48.5%) cases in which N. caninum was the sole pathogen identified. All cases were negative to BoHV-1. The results of this study provide evidence that dual infection by BoHV-5 and N. caninum occur during pregnancy in cattle; however, the role of BoHV-5 as a primary cause of bovine abortion needs further research. Molecular diagnosis of BoHV-5 and N. caninum confirmed the importance of applying complementary assays to improve the sensitivity of diagnosing bovine abortion.

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.

Methods of genetic diversity creation and functional display for directed evolution experiments

Protein engineering aims to improve the properties of enzymes and affinity reagents by genetic changes. Typical engineered properties are affinity, specificity, stability, expression, and solubility. Because proteins are complex biomolecules, the effects of specific genetic changes are seldom predictable. Consequently, a popular strategy in protein engineering is to create a library of genetic variants of the target molecule, and render the population in a selection process to sort the variants by the desired property. This technique, called directed evolution, is a central tool for trimming protein-based products used in a wide range of applications from laundry detergents to anti-cancer drugs. New methods are continuously needed to generate larger gene repertoires and compatible selection platforms to shorten the development timeline for new biochemicals. In the first study of this thesis, primer extension mutagenesis was revisited to establish higher quality gene variant libraries in Escherichia coli cells. In the second study, recombination was explored as a method to expand the number of screenable enzyme variants. A selection platform was developed to improve antigen binding fragment (Fab) display on filamentous phages in the third article and, in the fourth study, novel design concepts were tested by two differentially randomized recombinant antibody libraries. Finally, in the last study, the performance of the same antibody repertoire was compared in phage display selections as a genetic fusion to different phage capsid proteins and in different antibody formats, Fab vs. single chain variable fragment (ScFv), in order to find out the most suitable display platform for the library at hand. As a result of the studies, a novel gene library construction method, termed selective rolling circle amplification (sRCA), was developed. The method increases mutagenesis frequency close to 100% in the final library and the number of transformants over 100-fold compared to traditional primer extension mutagenesis. In the second study, Cre/loxP recombination was found to be an appropriate tool to resolve the DNA concatemer resulting from error-prone RCA (epRCA) mutagenesis into monomeric circular DNA units for higher efficiency transformation into E. coli. Library selections against antigens of various size in the fourth study demonstrated that diversity placed closer to the antigen binding site of antibodies supports generation of antibodies against haptens and peptides, whereas diversity at more peripheral locations is better suited for targeting proteins. The conclusion from a comparison of the display formats was that truncated capsid protein three (p3Δ) of filamentous phage was superior to the full-length p3 and protein nine (p9) in obtaining a high number of uniquely specific clones. Especially for digoxigenin, a difficult hapten target, the antibody repertoire as ScFv-p3Δ provided the clones with the highest affinity for binding. This thesis on the construction, design, and selection of gene variant libraries contributes to the practical know-how in directed evolution and contains useful information for scientists in the field to support their undertakings.

Hoitotyön koulutuksen opiskelijavalinnat. Seurantatutkimus kahden valintakoemenetelmän yhteydestä opiskelijoiden osaamiseen ja opiskelumotivaatioon

Hoitotyön koulutukseen pyritään valitsemaan alalle soveltuvia, motivoituneita sekä teoreettisissa ja kliinisissä opinnoissa menestyviä opiskelijoita. Tämän seurantatutkimuksen tarkoituksena oli vertailla soveltuvuuskokeella ja kirjallisella kokeella valittujen hoitotyön opiskelijoiden osaamista ja opiskelumotivaatiota. Tutkimuksen tavoitteena oli tehdä tutkimustulosten perusteella hoitotyön koulutuksen opiskelijavalintoihin liittyviä kehittämisehdotuksia. Tutkimuksen kohderyhmänä olivat yhteen ammattikorkeakouluun syksyn 2002 ja syksyn 2004 välisenä aikana hoitotyön koulutukseen kahdella eri valintakoemenetelmällä valitut hoitotyön opiskelijat (N=626) (sairaanhoitotyö, terveydenhoitotyö, kätilötyö). Opiskelijaryhmistä muodostettiin kaksi kohorttia valintakoemenetelmän perusteella: soveltuvuuskoe (VAL1, N=368) ja kirjallinen koe (VAL2, N=258). Seurantatutkimuksen aineisto kerättiin opiskelijoiden opintorekisteristä sekä kahdella strukturoidulla mittarilla, joilla kartoitettiin hoitotyön opiskelijoiden itsearvioitua hoitotyön osaamista (OSAA-mittari) ja opiskelumotivaatiota (MOTI-mittari). Seurantatutkimuksen aineistonkeruu ajoittui opiskelijoiden kolmannelle lukukaudella (1. mittaus, 2004‒2006, VAL1 n=234, VAL2 n=126) ja valmistumisvaiheeseen (2. mittaus, 2006‒2009, VAL1 n=149, VAL2 n=108). Ensimmäisen mittauksen vastausprosentti oli 75,0 % ja toisen mittauksen 92,4 %. Aineistojen analysoinnissa käytettiin pitkittäistutkimukseen soveltuvia monimuuttujamenetelmiä. Kahdella valintakoemenetelmällä valikoitui pienistä eroista huolimatta osaamiseltaan ja opiskelumotivaatioltaan hyvin samanlaisia opiskelijoita. Soveltuvuuskokeella valitut opiskelijat kokivat ryhmän kannustavuuden vahvemmaksi valmistumisvaiheessa kuin kirjallisella kokeella valitut. Kirjallisella kokeella valittujen opiskelijoiden kolmannen lukukauden arvosanoihin perustuva osaaminen oli parempaa kuin soveltuvuuskokeella valittujen opiskelijoiden. Suuntautumisvaihtoehto, hoitoalan työkokemus, peruskoulutus ja hakusija olivat merkittävimmin yhteydessä opiskelijoiden osaamiseen ja opiskelumotivaatioon. Valintakoemenetelmä selitti eniten opiskelijoiden osaamisessa ja opiskelumotivaatiossa ilmenneitä eroja, joskin selitysosuudet jäivät alhaisiksi. Kehittämisehdotukset kohdistuvat valintakoemenetelmien kehittämiseen ja säännölliseen arviointiin sekä alalle motivoituneisuuden määrittelyyn ja mittaamisen kehittämiseen. Jatkotutkimusaiheina ehdotetaan eri valintakoemenetelmien testaamista ja tutkimuksessa käytettyjen mittareiden edelleen kehittämistä.

Local Features in Image and Video Processing - Object Class Matching and Video Shot Detection

The usage of digital content, such as video clips and images, has increased dramatically during the last decade. Local image features have been applied increasingly in various image and video retrieval applications. This thesis evaluates local features and applies them to image and video processing tasks. The results of the study show that 1) the performance of different local feature detector and descriptor methods vary significantly in object class matching, 2) local features can be applied in image alignment with superior results against the state-of-the-art, 3) the local feature based shot boundary detection method produces promising results, and 4) the local feature based hierarchical video summarization method shows promising new new research direction. In conclusion, this thesis presents the local features as a powerful tool in many applications and the imminent future work should concentrate on improving the quality of the local features.

In search of information systems value : a case study of the EHR benefits realisation efforts of three Swedish hospitals.

The Swedish public health care organisation could very well be undergoing its most significant change since its specialisation during the late 19th and early 20th century. At the heart of this change is a move from using manual patient journals to electronic health records (EHR). EHR are complex integrated organisational wide information systems (IS) that promise great benefits and value as well as presenting great challenges to the organisation. The Swedish public health care is not the first organisation to implement integrated IS, and by no means alone in their quest for realising the potential benefits and value that it has to offer. As organisations invest in IS they embark on a journey of value-creation and capture. A journey where a costbased approach towards their IS-investments is replaced with a value-centric focus, and where the main challenges lie in the practical day-to-day task of finding ways to intertwine technology, people and business processes. This has however proven to be a problematic task. The problematic situation arises from a shift of perspective regarding how to manage IS in order to gain value. This is a shift from technology delivery to benefits delivery; from an ISimplementation plan to a change management plan. The shift gives rise to challenges related to the inability of IS and the elusiveness of value. As a response to these challenges the field of IS-benefits management has emerged offering a framework and a process in order to better understand and formalise benefits realisation activities. In this thesis the benefits realisation efforts of three Swedish hospitals within the same county council are studied. The thesis focuses on the participants of benefits analysis projects; their perceptions, judgments, negotiations and descriptions of potential benefits. The purpose is to address the process where organisations seek to identify which potential IS-benefits to pursue and realise, this in order to better understand what affects the process, so that realisation actions of potential IS-benefits could be supported. A qualitative case study research design is adopted and provides a framework for sample selection, data collection, and data analysis. It also provides a framework for discussions of validity, reliability and generalizability. Findings displayed a benefits fluctuation, which showed that participants’ perception of what constituted potential benefits and value changed throughout the formal benefits management process. Issues like structure, knowledge, expectation and experience affected perception differently, and this in the end changed the amount and composition of potential benefits and value. Five dimensions of benefits judgment were identified and used by participants when finding accommodations of potential benefits and value to pursue. Identified dimensions affected participants’ perceptions, which in turn affected the amount and composition of potential benefits. During the formal benefits management process participants shifted between judgment dimensions. These movements emerged through debates and interactions between participants. Judgments based on what was perceived as expected due to one’s role and perceived best for the organisation as a whole were the two dominant benefits judgment dimensions. A benefits negotiation was identified. Negotiations were divided into two main categories, rational and irrational, depending on participants’ drive when initiating and participating in negotiations. In each category three different types of negotiations were identified having different characteristics and generating different outcomes. There was also a benefits negotiation process identified that displayed management challenges corresponding to its five phases. A discrepancy was also found between how IS-benefits are spoken of and how actions of IS benefits realisation are understood. This was a discrepancy between an evaluation and a realisation focus towards IS value creation. An evaluation focus described IS-benefits as well-defined and measurable effects and a realisation focus spoke of establishing and managing an on-going place of value creation. The notion of valuescape was introduced in order to describe and support the understanding of IS value creation. Valuescape corresponded to a realisation focus and outlined a value configuration consisting of activities, logic, structure, drivers and role of IS.

It’s a workflow engine. It’s working with linked data. It’s repository! – Supporting electronic thesis related processes in University of Helsinki library

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

E-thesis repository – processes and data

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

Integrating CRIS and repository – an overview of the situation in Finland and in three other Nordic countries

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

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

Ovule ontogeny of Tabebuia pulcherrima Sandwith (Bignoniaceae): megasporogenesis and integument development

The ovule of Tabebuia pulcherrima is anatropous, unitegmic and tenuinucellate. The nucellus shows a trizonate structural organization. The integument is initiated by periclinal divisions in the dermal layer (zone I), around the base of the archesporium. Subsequently, cells derived from the subdermal layer (zone II) start to push the dermal cells, so that they shift toward the micropylar region. The archesporial cell differentiates directly into the megaspore mother cell, undergoes meiosis, and originates a linear tetrad of megaspores. The mature embryo sac mother cell is elongated, possess a conspicuous central nucleus, and a characteristic bipolar vacuome with fibrous-granulated content. The inner cell layers of the integument differentiate into an amyloplast-rich endothelium. Patterns of callose deposition in the tetrad and selection of the functional megaspore, as well as the taxonomic value of some characters are discussed.

Green supplier selection via Multiple Criteria Data Envelopment Analysis

An appropriate supplier selection and its profound effects on increasing the competitive advantage of companies has been widely discussed in supply chain management (SCM) literature. By raising environmental awareness among companies and industries they attach more importance to sustainable and green activities in selection procedures of raw material providers. The current thesis benefits from data envelopment analysis (DEA) technique to evaluate the relative efficiency of suppliers in the presence of carbon dioxide (CO2) emission for green supplier selection. We incorporate the pollution of suppliers as an undesirable output into DEA. However, to do so, two conventional DEA model problems arise: the lack of the discrimination power among decision making units (DMUs) and flexibility of the inputs and outputs weights. To overcome these limitations, we use multiple criteria DEA (MCDEA) as one alternative. By applying MCDEA the number of suppliers which are identified as efficient will be decreased and will lead to a better ranking and selection of the suppliers. Besides, in order to compare the performance of the suppliers with an ideal supplier, a “virtual” best practice supplier is introduced. The presence of the ideal virtual supplier will also increase the discrimination power of the model for a better ranking of the suppliers. Therefore, a new MCDEA model is proposed to simultaneously handle undesirable outputs and virtual DMU. The developed model is applied for green supplier selection problem. A numerical example illustrates the applicability of the proposed model.

Dietary fiber intake, stool frequency and colonic transit time in chronic functional constipation in children

The objective of the present study was to evaluate associations between fiber intake, colonic transit time and stool frequency. Thirty-eight patients aged 4 to 14 years were submitted to alimentary evaluation and to measurement of colonic transit time. The median fiber intake of the total sample was age + 10.3 g/day. Only 18.4% of the subjects presented a daily dietary fiber intake below the levels recommended by the American Health Foundation. In this group, the median left colonic transit time was shorter than in the group with higher dietary fiber intake (11 vs 17 h, P = 0.067). The correlation between stool frequency and colonic transit time was negative and weak for left colon (r = -0.3, P = 0.04), and negative and moderate for rectosigmoid and total colon (r = -0.5, P<0.001 and r = -0.5, P<0.001, respectively). The stool frequency was lower in the group with slow transit time (0.8 vs 2.3 per week, P = 0.014). In conclusion, most patients with chronic functional constipation had adequate dietary fiber intake. The negative correlation between stool frequency and colonic transit time increased progressively from proximal segments to distal segments of the colon. Patients with normal and prolonged colonic transit time differ in terms of stool frequency.

Optimization and Measuring Techniques for Collect-and-Place Machines in Printed Circuit Board Industry

This thesis considers optimization problems arising in printed circuit board assembly. Especially, the case in which the electronic components of a single circuit board are placed using a single placement machine is studied. Although there is a large number of different placement machines, the use of collect-and-place -type gantry machines is discussed because of their flexibility and increasing popularity in the industry. Instead of solving the entire control optimization problem of a collect-andplace machine with a single application, the problem is divided into multiple subproblems because of its hard combinatorial nature. This dividing technique is called hierarchical decomposition. All the subproblems of the one PCB - one machine -context are described, classified and reviewed. The derived subproblems are then either solved with exact methods or new heuristic algorithms are developed and applied. The exact methods include, for example, a greedy algorithm and a solution based on dynamic programming. Some of the proposed heuristics contain constructive parts while others utilize local search or are based on frequency calculations. For the heuristics, it is made sure with comprehensive experimental tests that they are applicable and feasible. A number of quality functions will be proposed for evaluation and applied to the subproblems. In the experimental tests, artificially generated data from Markov-models and data from real-world PCB production are used. The thesis consists of an introduction and of five publications where the developed and used solution methods are described in their full detail. For all the problems stated in this thesis, the methods proposed are efficient enough to be used in the PCB assembly production in practice and are readily applicable in the PCB manufacturing industry.