A Comparative Study of Desktop, Fishtank, and Cave Systems for the Exploration of Volume Rendered Confocal Data Sets

We present a participant study that compares biological data exploration tasks using volume renderings of laser confocal microscopy data across three environments that vary in level of immersion: a desktop, fishtank, and cave system. For the tasks, data, and visualization approach used in our study, we found that subjects qualitatively preferred and quantitatively performed better in the cave compared with the fishtank and desktop. Subjects performed real-world biological data analysis tasks that emphasized understanding spatial relationships including characterizing the general features in a volume, identifying colocated features, and reporting geometric relationships such as whether clusters of cells were coplanar. After analyzing data in each environment, subjects were asked to choose which environment they wanted to analyze additional data sets in - subjects uniformly selected the cave environment.

Element speciation and behaviour in metal-rich Boreal river and estuarine systems using ultrafiltration and chemical modelling

The bioavailability of metals and their potential for environmental pollution depends not simply on total concentrations, but is to a great extent determined by their chemical form. Consequently, knowledge of aqueous metal species is essential in investigating potential metal toxicity and mobility. The overall aim of this thesis is, thus, to determine the species of major and trace elements and the size distribution among the different forms (e.g. ions, molecules and mineral particles) in selected metal-enriched Boreal river and estuarine systems by utilising filtration techniques and geochemical modelling. On the basis of the spatial physicochemical patterns found, the fractionation and complexation processes of elements (mainly related to input of humic matter and pH-change) were examined. Dissolved (<1 kDa), colloidal (1 kDa-0.45 μm) and particulate (>0.45 μm) size fractions of sulfate, organic carbon (OC) and 44 metals/metalloids were investigated in the extremely acidic Vörå River system and its estuary in W Finland, and in four river systems in SW Finland (Sirppujoki, Laajoki, Mynäjoki and Paimionjoki), largely affected by soil erosion and acid sulfate (AS) soils. In addition, geochemical modelling was used to predict the formation of free ions and complexes in these investigated waters. One of the most important findings of this study is that the very large amounts of metals known to be released from AS soils (including Al, Ca, Cd, Co, Cu, Mg, Mn, Na, Ni, Si, U and the lanthanoids) occur and can prevail mainly in toxic forms throughout acidic river systems; as free ions and/or sulfate-complexes. This has serious effects on the biota and especially dissolved Al is expected to have acute effects on fish and other organisms, but also other potentially toxic dissolved elements (e.g. Cd, Cu, Mn and Ni) can have fatal effects on the biota in these environments. In upstream areas that are generally relatively forested (higher pH and contents of OC) fewer bioavailable elements (including Al, Cu, Ni and U) may be found due to complexation with the more abundantly occurring colloidal OC. In the rivers in SW Finland total metal concentrations were relatively high, but most of the elements occurred largely in a colloidal or particulate form and even elements expected to be very soluble (Ca, K, Mg, Na and Sr) occurred to a large extent in colloidal form. According to geochemical modelling, these patterns may only to a limited extent be explained by in-stream metal complexation/adsorption. Instead there were strong indications that the high metal concentrations and dominant solid fractions were largely caused by erosion of metal bearing phyllosilicates. A strong influence of AS soils, known to exist in the catchment, could be clearly distinguished in the Sirppujoki River as it had very high concentrations of a metal sequence typical of AS soils in a dissolved form (Ba, Br, Ca, Cd, Co, K, Mg, Mn, Na, Ni, Rb and Sr). In the Paimionjoki River, metal concentrations (including Ba, Cs, Fe, Hf, Pb, Rb, Si, Th, Ti, Tl and V; not typical of AS soils in the area) were high, but it was found that the main cause of this was erosion of metal bearing phyllosilicates and thus these metals occurred dominantly in less toxic colloidal and particulate fractions. In the two nearby rivers (Laajoki and Mynäjoki) there was influence of AS soils, but it was largely masked by eroded phyllosilicates. Consequently, rivers draining clay plains sensitive to erosion, like those in SW Finland, have generally high background metal concentrations due to erosion. Thus, relying on only semi-dissolved (<0.45 μm) concentrations obtained in routine monitoring, or geochemical modelling based on such data, can lead to a great overestimation of the water toxicity in this environment. The potentially toxic elements that are of concern in AS soil areas will ultimately be precipitated in the recipient estuary or sea, where the acidic metalrich river water will gradually be diluted/neutralised with brackish seawater. Along such a rising pH gradient Al, Cu and U will precipitate first together with organic matter closest to the river mouth. Manganese is relatively persistent in solution and, thus, precipitates further down the estuary as Mn oxides together with elements such as Ba, Cd, Co, Cu and Ni. Iron oxides, on the contrary, are not important scavengers of metals in the estuary, they are predicted to be associated only with As and PO4.

Comparison between dSPACE and NI systems based on real-time intelligent control of a teleoperated hydraulic servo system

The Laboratory of Intelligent Machine researches and develops energy-efficient power transmissions and automation for mobile construction machines and industrial processes. The laboratory's particular areas of expertise include mechatronic machine design using virtual technologies and simulators and demanding industrial robotics. The laboratory has collaborated extensively with industrial actors and it has participated in significant international research projects, particularly in the field of robotics. For years, dSPACE tools were the lonely hardware which was used in the lab to develop different control algorithms in real-time. dSPACE's hardware systems are in widespread use in the automotive industry and are also employed in drives, aerospace, and industrial automation. But new competitors are developing new sophisticated systems and their features convinced the laboratory to test new products. One of these competitors is National Instrument (NI). In order to get to know the specifications and capabilities of NI tools, an agreement was made to test a NI evolutionary system. This system is used to control a 1-D hydraulic slider. The objective of this research project is to develop a control scheme for the teleoperation of a hydraulically driven manipulator, and to implement a control algorithm between human and machine interaction, and machine and task environment interaction both on NI and dSPACE systems simultaneously and to compare the results.

ORCIDs in the Wild: Implementing ORCIDs into Research Support and Repository Systems

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

Combined effects of diethylpropion and alcohol on locomotor activity of mice: participation of the dopaminergic and opioid systems

The widespread consumption of anorectics and combined anorectic + alcohol misuse are problems in Brazil. In order to better understand the interactive effects of ethanol (EtOH) and diethylpropion (DEP) we examined the locomotion-activating effects of these drugs given alone or in combination in mice. We also determined whether this response was affected by dopamine (DA) or opioid receptor antagonists. A total of 160 male Swiss mice weighing approximately 30 g were divided into groups of 8 animals per group. The animals were treated daily for 7 consecutive days with combined EtOH + DEP (1.2 g/kg and 5.0 mg/kg, ip), EtOH (1.2 g/kg, ip), DEP (5.0 mg/kg, ip) or the control solution coadministered with the DA antagonist haloperidol (HAL, 0.075 mg/kg, ip), the opioid antagonist naloxone (NAL, 1.0 mg/kg, ip), or vehicle. On days 1, 7 and 10 after the injections, mice were assessed in activity cages at different times (15, 30, 45 and 60 min) for 5 min. The acute combination of EtOH plus DEP induced a significantly higher increase in locomotor activity (day 1: 369.5 ± 34.41) when compared to either drug alone (day 1: EtOH = 232.5 ± 23.79 and DEP = 276.0 ± 12.85) and to control solution (day 1: 153.12 ± 7.64). However, the repeated administration of EtOH (day 7: 314.63 ± 26.79 and day 10: 257.62 ± 29.91) or DEP (day 7: 309.5 ± 31.65 and day 10: 321.12 ± 39.24) alone or in combination (day 7: 459.75 ± 41.28 and day 10: 427.87 ± 33.0) failed to induce a progressive increase in the locomotor response. These data demonstrate greater locomotion-activating effects of the EtOH + DEP combination, probably involving DA and/or opioid receptor stimulation, since the daily pretreatment with HAL (day 1: EtOH + DEP = 395.62 ± 11.92 and EtOH + DEP + HAL = 371.5 ± 6.76; day 7: EtOH + DEP = 502.5 ± 42.27 and EtOH + DEP + HAL = 281.12 ± 16.08; day 10: EtOH + DEP = 445.75 ± 16.64 and EtOH + DEP + HAL = 376.75 ± 16.4) and NAL (day 1: EtOH + DEP = 553.62 ± 38.15 and EtOH + DEP + NAL = 445.12 ± 55.67; day 7: EtOH + DEP = 617.5 ± 38.89 and EtOH + DEP + NAL = 418.25 ± 61.18; day 10: EtOH + DEP = 541.37 ± 32.86 and EtOH + DEP + NAL = 427.12 ± 51.6) reduced the locomotor response induced by combined administration of EtOH + DEP. These findings also suggest that a major determinant of combined anorectic-alcohol misuse may be the increased stimulating effects produced by the combination.

Gap junctions in the cardiovascular and immune systems

Gap junctions are clusters of intercellular channels directly connecting the cytoplasm of adjacent cells. These channels are formed by proteins named connexins and are present in all metazoan organisms where they serve diverse functions ranging from control of cell growth and differentiation to electric conduction in excitable tissues. In this overview we describe the presence of connexins in the cardiovascular and lympho-hematopoietic systems giving the reader a summary of the topics to be covered throughout this edition and a historical perspective of the discovery of gap junctions in the immune system.

Novel genes and regulatory systems in epididymal differentiation and sperm maturation of the mouse.

Mammalian spermatozoa gain their fertilizing ability during maturation in the epididymis. Proteins and lipids secreted into the epididymal lumen remodel the sperm membrane, thereby providing the structure necessary for progressive motility and oocyte interaction. In the current study, genetically modified mouse models were utilized to determine the role of novel genes and regulatory systems in the postnatal development and function of the epididymis. Ablation of the mouse β-defensin, Defb41, altered the flagellar movements of sperm and reduced the ability of sperm to bind to the oocyte in vitro. The Defb41-deficient iCre knock-in mouse model was furthermore utilized to generate Dicer1 conditional knock-out (cKO) mice. DICER1 is required for production of mature microRNAs in the regulation of gene expression by RNA interference. Dicer1 cKO gave rise to dedifferentiation of the epididymal epithelium and an altered expression of genes involved in lipid synthesis. As a consequence, the cholesterol:polyunsaturated fatty acid ratio of the Dicer1 cKO sperm membrane was increased, which resulted in membrane instability and infertility. In conclusion, the results of the Defb41 study further support the important role of β-defensin family members in sperm maturation. The regulatory role of Dicer1 was also shown to be required for epididymal development. In addition, the study is the first to show a clear connection between lipid homeostasis in the epididymis and sperm membrane integrity. Taken together, the results give important new evidence on the regulatory system guiding epididymal development and function

Evaluation of the PetrifilmTM and TEMPO® systems and the conventional method for counting microorganisms in pasteurized milk

New microbiological methods have been developed and commercialized, but their performance must be guaranteed. The aim of the present study was to evaluate the PetrifilmTM and TEMPO® systems compared to the conventional method for counting microorganisms in pasteurized milk. A total of 141 samples of pasteurized milk were analyzed by counting mesophilic aerobic, Coliforms at 35 ºC, Coliforms at 45 ºC, and Escherichia coli microorganisms. High correlation was found between the methods for counting Coliforms at 35 ºC, but low correlation was found for counting mesophilic aerobic, Coliforms at 45 ºC, and Escherichia coli. No significant statistical difference was found among the three methods for counting Coliforms at 35 ºC; however, the mean counts of mesophilic aerobic, Coliforms at 45 ºC, and Escherichia coli showed significant statistical difference. PetrifilmTM and TEMPO® systems had satisfactory results for Coliforms at 35 ºC in pasteurized milk but low performance for mesophilic aerobic, Coliforms at 45 ºC and Escherichia coli.

Computational models for and from biology : simple gene assembly and reaction systems

The advancement of science and technology makes it clear that no single perspective is any longer sufficient to describe the true nature of any phenomenon. That is why the interdisciplinary research is gaining more attention overtime. An excellent example of this type of research is natural computing which stands on the borderline between biology and computer science. The contribution of research done in natural computing is twofold: on one hand, it sheds light into how nature works and how it processes information and, on the other hand, it provides some guidelines on how to design bio-inspired technologies. The first direction in this thesis focuses on a nature-inspired process called gene assembly in ciliates. The second one studies reaction systems, as a modeling framework with its rationale built upon the biochemical interactions happening within a cell. The process of gene assembly in ciliates has attracted a lot of attention as a research topic in the past 15 years. Two main modelling frameworks have been initially proposed in the end of 1990s to capture ciliates’ gene assembly process, namely the intermolecular model and the intramolecular model. They were followed by other model proposals such as templatebased assembly and DNA rearrangement pathways recombination models. In this thesis we are interested in a variation of the intramolecular model called simple gene assembly model, which focuses on the simplest possible folds in the assembly process. We propose a new framework called directed overlap-inclusion (DOI) graphs to overcome the limitations that previously introduced models faced in capturing all the combinatorial details of the simple gene assembly process. We investigate a number of combinatorial properties of these graphs, including a necessary property in terms of forbidden induced subgraphs. We also introduce DOI graph-based rewriting rules that capture all the operations of the simple gene assembly model and prove that they are equivalent to the string-based formalization of the model. Reaction systems (RS) is another nature-inspired modeling framework that is studied in this thesis. Reaction systems’ rationale is based upon two main regulation mechanisms, facilitation and inhibition, which control the interactions between biochemical reactions. Reaction systems is a complementary modeling framework to traditional quantitative frameworks, focusing on explicit cause-effect relationships between reactions. The explicit formulation of facilitation and inhibition mechanisms behind reactions, as well as the focus on interactions between reactions (rather than dynamics of concentrations) makes their applicability potentially wide and useful beyond biological case studies. In this thesis, we construct a reaction system model corresponding to the heat shock response mechanism based on a novel concept of dominance graph that captures the competition on resources in the ODE model. We also introduce for RS various concepts inspired by biology, e.g., mass conservation, steady state, periodicity, etc., to do model checking of the reaction systems based models. We prove that the complexity of the decision problems related to these properties varies from P to NP- and coNP-complete to PSPACE-complete. We further focus on the mass conservation relation in an RS and introduce the conservation dependency graph to capture the relation between the species and also propose an algorithm to list the conserved sets of a given reaction system.

Design of traction transmission and suspension systems for an omni-directional mobile robot

This project aims to design and manufacture a mobile robot with two Universal Robot UR10 mainly used indoors. In order to obtain omni-directional maneuverability, the mobile robot is constructed with Mecanum wheels. The Mecanum wheel can move in any direction with a series of rollers attached to itself. These rollers are angled at 45º about the hub’s circumference. This type of wheels can be used in both driving and steering with their any-direction property. This paper is focused on the design of traction system and suspension system, and the velocity control of Mecanum wheels in the close-loop control system. The mechanical design includes selection of bearing housing, couplers which are act as connection between shafts, motor parts, and other needed components. The 3D design software SolidWorks is utilized to assemble all the components in order to get correct tolerance. The driving shaft is designed based on assembled structure via the software as well. The design of suspension system is to compensate the assembly error of Mecanum wheels to guarantee the stability of the robot. The control system of motor drivers is realized through the Robot Operating System (ROS) on Ubuntu Linux. The purpose of inverse kinematics is to obtain the relationship among the movements of all Mecanum wheels. Via programming and interacting with the computer, the robot could move with required speed and direction.

The functional fit between collaborative software and work systems:Qualification of work system needs to software functionality

The study develops an approach that tries to validate software functionality to work systems needs in SMEs. The formulated approach is constructed by using a SAAS based software i.e., work collaboration service (WCS), and SMEs as the elements of study. Where the WCS’s functionality is qualified to the collaboration needs that exist in operational and project work within SMEs. For this research constructivist approach and case study method is selected because the nature of the current study requires an in depth study of the work collaboration service as well as a detailed study of the work systems within different enterprises. Four different companies are selected in which fourteen interviews are conducted to gather data pertaining. The work systems method and framework are used as a central part of the approach to collect, analyze and interpret the enterprises work systems model and the underlying collaboration needs on operational and project work. On the other hand, the functional model of the WCS and its functionality is determined from functional model analysis, software testing, documentation and meetings with the service vendor. The enterprise work system model and the WCS model are compared to reveal how work progression differs between the two and make visible unaddressed stages of work progression. The WCS functionality is compared to work systems collaboration needs to ascertain if the service will suffice the needs of the project and operational work under study. The unaddressed needs provide opportunities to improve the functionality of the service for better conformity to the needs of enterprise and work. The results revealed that the functional models actually differed in how operational and project work progressed within the stages. WCS shared similar stages of work progression apart from the stages of identification and acceptance, and progress and completion stages were only partially addressed. Conclusion is that the identified unaddressed needs such as, single point of reference, SLA and OLA inclusion etc., should be implemented or improved within the WCS at appropriate stages of work to gain better compliance of the service to the needs of the enterprise an work itself. The developed approach can hence be used to carry out similar analysis for the conformance of pre-built software functionality to work system needs with SMEs.

Biotransformations of water insoluble substrates in aqueous, two-phase and encapsulated systems /

The biotransformation of water insoluble substrates by mammalian and bacterial cells has been problematic, since these whole cell reactions are primarily performed in an aqueous environment The implementation of a twophase or encapsulated system has the advantages of providing a low water system along with the physiological environment the cells require to sustain themselves. Encapsulation of mammalian cells by formation of polyamide capsules via interfacial polymerization illustrated that the cells could not survive this type of encapsulation process. Biotransformation of the steroid spironolactone [3] by human kidney carcinoma cells was performed in a substrate-encapsulated system, yielding canrenone [4] in 70% yield. Encapsulation of nitrile-metabolizing Rhodococcus rhodochrous cells using a polyamide membrane yielded leaky capsules, but biotransformation of 2-(4- chlorophenyl)-3-methylbutyronitrile (CPIN) [6] in a free cell system yielded CPIN amide [7] in 40% yield and 94% ee. A two-phase biotransformation of CPIN consisting of a 5:1 ratio of tris buffer, pH 7.2 to octane respectively, gave CPIN acid [8] in 30% yield and 97% ee. It was concluded that Rhodococcus rhodochrous ATCC 17895 contained a nonselective nitrile hydratase and a highly selective amidase enzyme.

Bis-and tris (amidine) fluoroboron cations and related systems studies by Multinuclear NMR and fast atom bombardment mass spectometry

The formation and the isolation of fluoroboron salts, (D2BF2+)(PF6-), (DD'BF2+)(PF6-) and (D3BF2+)(PF6-)2, have been carried out. 1,8-Diazabicyclo [5,4.0]undec-7-ene (DBU) and 1,5-diazabicyclo[4,3,O]non-5-ene (DBN), extremely strong organic bases, were introduced into the fluoroboron cation systems and induced a complicated redistribution reaction in the D/BF3/BC13 systems. The result was the formation of all BFnCI4-n-, D.BFnCI3-n and fluoroboron cation species which were detected by 19p and 11B NMR spectrometry. The displacement reaction of CI- from these D.BFnCI3-n (n = 1 and 2) species by the second entering ligand is much faster than in other nitrogen donor containing systems which have been previously studied. Tetramethylguanidine, oxazolines and thiazolines can also produce similar reactions in D/BF3/BCI3 systems, but no significant BFnC4-n- species were observed. As well as influences of their basicity and their steric hindrance, N=C-R(X) (X = N, 0 or S) and N=C( X)2 (X = N or S) structures of ligands have significant effects on the fonnationof fluoroboron cations and the related NMR parameters. D3BF2+ and some D2BF2+ show the expected inertness, but (DBU)2BF2+ shows an interestingly high reactivity. (D2BF2+)(X-) formed from weak organic bases such as pyridine can react with stronger organic bases and form DD'BF2+ and D'2BF2+ in acetone or nitromethane. Fast atom bombardment mass spectrometry is doubly meaningful to this work. Firstly, FABMS can be directly applied to the complicated fluoroboron cation containing solution systems as an excellent complementary technique to multinuclear NMR. Secondly, the gas-phase ion substitution reaction of (D2BF2+)(PF6-) with the strong organic bases is successfully observed in a FABMS ion source when the B-N bond is not too strong in these cations.

Interactions between the cholinergic and dopaminergic systems during the production of ultrasonic vocalizations in rats

Rats produce ultrasonic vocalizations that can be categorized into two types of ultrasonic calls based on their sonographic structure. One group contains 22-kHz ultrasonic vocalization (USVs), characterized by relatively constant (flat) frequency with peak frequency ranging from 19 to 28-kHz, and a call duration ranging between 100 – 3000 ms. These vocalization can be induced by cholinomimetic agents injected into the ascending mesolimbic cholinergic system that terminates in the anterior hypothalamic-preoptic area (AH-MPO) and lateral septum (LS). The other group of USVs contains 50-kHz USVs, characterized by high peak frequency, ranging from 39 to 90-kHz, short duration ranging from 10-90 ms, and varying frequency and complex sonographic morphology. These vocalizations can be induced by dopaminergic agents injected into the nucleus accumbens, the target area for the mesolimbic dopaminergic system. 22-kHz USVs are emitted in situations that are highly aversive, such as proximity of a predator or anticipation of a foot shock, while 50 kHz USVs are emitted in rewarding and appetitive situations, such as juvenile play behaviour or anticipation of rewarding electrical brain stimulation. The activities of these two mesolimbic systems were postulated to be antagonistic to each other. The current thesis is focused on the interaction of these systems indexed by emission of relevant USVs. It was hypothesized that emission of 22 kHz USVs will be antagonized by prior activation of the dopaminergic system while emission of 50 kHz will be antagonized by prior activation of the cholinergic system. It was found that injection of apomorphine into the shell of the nucleus accumbens significantly decreased the number of carbachol-induced 22 kHz USVs from both AH-MPO and LS. Injection of carbachol into the LS significantly decreased the number of apomorphine-induced 50 kHz USVs from the shell of the nucleus accumbens. The results of the study supported the main hypotheses that the mesolimbic dopaminergic and cholinergic systems function in antagonism to each other.

Educational Leadership: Exploring the Influence of Managed and Living Systems in Educational Leadership Discourse

A conceptual analysis of educational leadership explored the influence of managed and living systems on 21st century leadership discourse. Drawing on a detailed understanding of managed and living systems theory compiled from the work of Capra (2002), Morgan (1997), Mitchell and Sackney (2009), and Wheatley (2007), this study draws attention to the managed systems systemic concepts of efficiency, control, and standardization, and the living systems concepts of collaboration, shared meaning, change, and interconnection as markers of systems theory that find resonance within leadership literature. Using these systemic concepts as a framework, this study provides important insights into the espousal of managed and living systems concepts within the leadership discourse.