Relation between sequence and structure of HIV-1 protease inhibitor complexes: a model system for the analysis of protein flexibility.

The flexibility of different regions of HIV-1 protease was examined by using a database consisting of 73 X-ray structures that differ in terms of sequence, ligands or both. The root-mean-square differences of the backbone for the set of structures were shown to have the same variation with residue number as those obtained from molecular dynamics simulations, normal mode analyses and X-ray B-factors. This supports the idea that observed structural changes provide a measure of the inherent flexibility of the protein, although specific interactions between the protease and the ligand play a secondary role. The results suggest that the potential energy surface of the HIV-1 protease is characterized by many local minima with small energetic differences, some of which are sampled by the different X-ray structures of the HIV-1 protease complexes. Interdomain correlated motions were calculated from the structural fluctuations and the results were also in agreement with molecular dynamics simulations and normal mode analyses. Implications of the results for the drug-resistance engendered by mutations are discussed briefly.

On Modelling, System Identification and Control of Servo-Systems with a Flexible Load

The present study was done with two different servo-systems. In the first system, a servo-hydraulic system was identified and then controlled by a fuzzy gainscheduling controller. The second servo-system, an electro-magnetic linear motor in suppressing the mechanical vibration and position tracking of a reference model are studied by using a neural network and an adaptive backstepping controller respectively. Followings are some descriptions of research methods. Electro Hydraulic Servo Systems (EHSS) are commonly used in industry. These kinds of systems are nonlinearin nature and their dynamic equations have several unknown parameters.System identification is a prerequisite to analysis of a dynamic system. One of the most promising novel evolutionary algorithms is the Differential Evolution (DE) for solving global optimization problems. In the study, the DE algorithm is proposed for handling nonlinear constraint functionswith boundary limits of variables to find the best parameters of a servo-hydraulic system with flexible load. The DE guarantees fast speed convergence and accurate solutions regardless the initial conditions of parameters. The control of hydraulic servo-systems has been the focus ofintense research over the past decades. These kinds of systems are nonlinear in nature and generally difficult to control. Since changing system parameters using the same gains will cause overshoot or even loss of system stability. The highly non-linear behaviour of these devices makes them ideal subjects for applying different types of sophisticated controllers. The study is concerned with a second order model reference to positioning control of a flexible load servo-hydraulic system using fuzzy gainscheduling. In the present research, to compensate the lack of dampingin a hydraulic system, an acceleration feedback was used. To compare the results, a pcontroller with feed-forward acceleration and different gains in extension and retraction is used. The design procedure for the controller and experimental results are discussed. The results suggest that using the fuzzy gain-scheduling controller decrease the error of position reference tracking. The second part of research was done on a PermanentMagnet Linear Synchronous Motor (PMLSM). In this study, a recurrent neural network compensator for suppressing mechanical vibration in PMLSM with a flexible load is studied. The linear motor is controlled by a conventional PI velocity controller, and the vibration of the flexible mechanism is suppressed by using a hybrid recurrent neural network. The differential evolution strategy and Kalman filter method are used to avoid the local minimum problem, and estimate the states of system respectively. The proposed control method is firstly designed by using non-linear simulation model built in Matlab Simulink and then implemented in practical test rig. The proposed method works satisfactorily and suppresses the vibration successfully. In the last part of research, a nonlinear load control method is developed and implemented for a PMLSM with a flexible load. The purpose of the controller is to track a flexible load to the desired position reference as fast as possible and without awkward oscillation. The control method is based on an adaptive backstepping algorithm whose stability is ensured by the Lyapunov stability theorem. The states of the system needed in the controller are estimated by using the Kalman filter. The proposed controller is implemented and tested in a linear motor test drive and responses are presented.

The role of community and population ecology in applying mycorrhizal fungi for improved food security.

The global human population is expected to reach ∼9 billion by 2050. Feeding this many people represents a major challenge requiring global crop yield increases of up to 100%. Microbial symbionts of plants such as arbuscular mycorrhizal fungi (AMF) represent a huge, but unrealized resource for improving yields of globally important crops, especially in the tropics. We argue that the application of AMF in agriculture is too simplistic and ignores basic ecological principals. To achieve this challenge, a community and population ecology approach can contribute greatly. First, ecologists could significantly improve our understanding of the determinants of the survival of introduced AMF, the role of adaptability and intraspecific diversity of AMF and whether inoculation has a direct or indirect effect on plant production. Second, we call for extensive metagenomics as well as population genomics studies that are crucial to assess the environmental impact that introduction of non-local AMF may have on native AMF communities and populations. Finally, we plead for an ecologically sound use of AMF in efforts to increase food security at a global scale in a sustainable manner.

Evolution of the mating system in colonizing plants.

Colonization is likely to be more successful for species with an ability to self-fertilize and thus to establish new populations as single individuals. As a result, self-compatibility should be common among colonizing species. This idea, labelled 'Baker's law', has been influential in discussions of sexual-system and mating-system evolution. However, its generality has been questioned, because models of the evolution of dispersal and the mating system predict an association between high dispersal rates and outcrossing rather than selfing, and because of many apparent counter examples to the law. The contrasting predictions made by models invoking Baker's law versus those for the evolution of the mating system and dispersal urges a reassessment of how we should view both these traits. Here, I review the literature on the evolution of mating and dispersal in colonizing species, with a focus on conceptual issues. I argue for the importance of distinguishing between the selfing or outcrossing rate and a simple ability to self-fertilize, as well as for the need for a more nuanced consideration of dispersal. Colonizing species will be characterized by different phases in their life pattern: dispersal to new habitat, implying an ecological sieve on dispersal traits; establishment and a phase of growth following colonization, implying a sieve on reproductive traits; and a phase of demographic stasis at high density, during which new trait associations can evolve through local adaptation. This dynamic means that the sorting of mating-system and dispersal traits should change over time, making simple predictions difficult.

Micronization of Pharmaceuticals and Food Ingredients using Supercritical Fluid Techniques

Micronization techniques based on supercritical fluids (SCFs) are promising for the production of particles with controlled size and distribution. The interest of the pharmaceutical field in the development of SCF techniques is increasing due to the need for clean processes, reduced consumption of energy, and to their several possible applications. The food field is still far from the application of SCF micronization techniques, but there is increasing interest mainly for the processing of products with high added value. The aim of this study is to use SCF micronization techniques for the production of particles of pharmaceuticals and food ingredients with controlled particle size and morphology, and to look at their production on semi-industrial scale. The results obtained are also used to understand the processes from the perspective of broader application within the pharmaceutical and food industries. Certain pharmaceuticals, a biopolymer and a food ingredient have been tested using supercritical antisolvent micronization (SAS) or supercritical assisted atomization (SAA) techniques. The reproducibility of the SAS technique has been studied using physically different apparatuses and on both laboratory and semi-industrial scale. Moreover, a comparison between semi-continuous and batch mode has been performed. The behaviour of the system during the SAS process has been observed using a windowed precipitation vessel. The micronized powders have been characterized by particle size and distribution, morphology and crystallinity. Several analyses have been performed to verify if the SCF process modified the structure of the compound or caused degradation or contamination of the product. The different powder morphologies obtained have been linked to the position of the process operating point with respect to the vapour-liquid equilibrium (VLE) of the systems studied, that is, mainly to the position of the mixture critical point (MCP) of the mixture. Spherical micro, submicro- and nanoparticles, expanded microparticles (balloons) and crystals were obtained by SAS. The obtained particles were amorphous or with different degrees of crystallinity and, in some cases, had different pseudo-polymorphic or polymorphic forms. A compound that could not be processed using SAS was micronized by SAA, and amorphous particles were obtained, stable in vials at room temperature. The SCF micronization techniques studied proved to be effective and versatile for the production of particles for several uses. Furthermore, the findings of this study and the acquired knowledge of the proposed processes can allow a more conscious application of SCF techniques to obtain products with the desired characteristics and enable the use of their principles for broader applications.

Network Device Driver Design and Implementation for Symbian Operating System

Tämä diplomityö esittää Symbianin käyttöjärjestelmän verkkoarkkitehtuuriin perustuvan paikallisverkkokortin (LAN) käyttöönottoa. Pääajatus oli keskitetty langattoman LAN— kortin (WLAN) ajureiden käyttöönottoon. Jokainen Symbianin käyttöjärjestelmän verkkoarkkitehtuurin komponentti oli huolellisesti tutkittu, painottaen mahdollista langattoman yhteyden uudelleenkäyttöä. Myös olemassaolevan Ethernetkortin ajureiden uudelleenkäyttö oli huolellisesti otettu huomioon. Diplomityöprojektin aikana esimerkki WLAN-kortin ajurin lähdekoodista oli esitetty. Tämä ajuri on kirjoitettu NOKIA DTN-20 WLAN-korttia varten. Havaittiin myös, että suurin osa Symbianin käyttöjärjestelmän verkkoarkkitehtuurista voidaan käyttää myös WLAN-pohjaisessa yhteydessä ilman muutoksia.. Esitetty ajuri käyttää myös tiettyjä olemassaolevan Ethernetkortin ajureita, esim. Logical Device Driver (LDD):tä.

The Value System of Consumer Board Packaging

Olemassa olevien teollisuuden rakenteiden ja arvoketjujen muutos on usein onnistuneiden liiketoimintainnovaatioiden takana. Yritysten tulisikin olla tietoisia rakenteista, jotka määrittelevät arvon jakaantumista niiden arvoketjuissa. Tämän työn tavoitteena oli tutkia ja arvioida kartongin pakkausketjujen rakenteita kartongintuottajalta aina kauppiaalle asti. Työn kuluessa yritysketjujen arviointia varten oli kehitettävä uudenlainen analysointityökalu. Työssä käsitellyt kartonkipakkausketjut olivat nestekartonkipakkaaminen, elintarvikepakkaaminen, lääkepakkaaminen sekä graafisten kartonkien ketju. Jokaista edellä mainituista ketjuista arvioitiin käyttämällä kehitettyä analysointityökalua. Työn merkittävin tulos on kehitetty työkalu, jolla pakkausketjuja sekä myös muita yritysketjuja on mahdollista analysoida. Kehitettyä työkalua käyttämällä oli mahdollista tehdä johtopäätöksiä vertikaalin integraation mahdollisuudesta sekä pakkausketjujen suotuisuudesta uusille bisnesmalleille. Sekä analysointityökalua että saatuja johtopäätöksiä voidaan käyttää hyväksi, kun kartongintuottaja suunnittelee tulevaisuuden toimenpiteitä.

Business potential evaluation of wireless local area networks: Teleoperator’s view

The objective of the thesis was to evaluate business potential of wireless local area networks (WLAN, Wireless LAN). At first, the scope of business potential evaluation of technology was introduced. Next, a general framework of business potential evaluation of technology based on literature was presented. In addition, convergence of cellular networks and data networks was studied in order to get an insight of current situation of mobile telecommunications industry. Finally, wireless local area networks business potential was evaluated. A wireless local area network is a data communication system, which combines data connectivity with mobility and is implemented in unlicensed frequency bands, allowing new business opportunities to emerge. The main markets of WLAN are corporate networks, public area networks and access networks. At the moment the penetration of WLAN terminals is low which derives to low demand of wireless LAN services. In addition, unlicensed spectrum forces the teleoperators to set the service price relatively low. The business potential is in integrating wireless LANs to cellular networks and in offering value added services to end users. The future of wireless LAN is to be complementary network to cellular networks. In this vision cellular networks provide voice and low data services and broadband wireless networks enable multimedia services.

Wireless Authentication and Authorization, case Wireless Access Control System

Lyhyen kantaman radiotekniikoiden hyödyntäminen mahdollistaa uudenlaisten paikallisten palveluiden käytön ja vanhojen palveluiden kehittämisen. Kulunvalvonta on päivittäisenä palveluna valittu työn esimerkkisovellukseksi. Useita tunnistus- ja valtuutustapoja tutkitaan, ja julkisen avaimen infrastruktuuri on esitellään tarkemmin. Langattomat tekniikat Bluetooth, Zigbee, RFID ja IrDA esitellän yleisellä tasolla langattomat tekniikat –luvussa. Bluetooth-tekniikan rakennetta, mukaan lukien sen tietoturva-arkkitehtuuria, tutkitaan tarkemmin. Bluetooth-tekniikkaa käytetään työssä suunnitellun langattoman kulunvalvontajärjestelmän tietojen siirtoon. Kannettava päätelaite toimii käyttäjän henkilökohtaisena luotettuna laitteena, jota voi käyttää avaimena. Käyttäjän tunnistaminen ja valtuuttaminen perustuu julkisen avaimen infrastruktuuriin. Ylläpidon allekirjoittamat varmenteet sisältävät käyttäjän julkisen avaimen lisäksi tietoa hänestä ja hänen oikeuksistaan. Käyttäjän tunnistaminen kulunvalvontapisteissä tehdään julkisen ja salaisen avaimen käyttöön perustuvalla haaste-vastaus-menetelmällä. Lyhyesti, järjestelmässä käytetään Bluetooth-päätelaitteita langattomina avaimina.

Local thermodynamics and the generalized Gibbs-Duhem equation in systems with long-range interactions

The local thermodynamics of a system with long-range interactions in d dimensions is studied using the mean-field approximation. Long-range interactions are introduced through pair interaction potentials that decay as a power law in the interparticle distance. We compute the local entropy, Helmholtz free energy, and grand potential per particle in the microcanonical, canonical, and grand canonical ensembles, respectively. From the local entropy per particle we obtain the local equation of state of the system by using the condition of local thermodynamic equilibrium. This local equation of state has the form of the ideal gas equation of state, but with the density depending on the potential characterizing long-range interactions. By volume integration of the relation between the different thermodynamic potentials at the local level, we find the corresponding equation satisfied by the potentials at the global level. It is shown that the potential energy enters as a thermodynamic variable that modifies the global thermodynamic potentials. As a result, we find a generalized Gibbs-Duhem equation that relates the potential energy to the temperature, pressure, and chemical potential. For the marginal case where the power of the decaying interaction potential is equal to the dimension of the space, the usual Gibbs-Duhem equation is recovered. As examples of the application of this equation, we consider spatially uniform interaction potentials and the self-gravitating gas. We also point out a close relationship with the thermodynamics of small systems.

The effects of cocoa on the immune system

Cocoa is a food relatively rich in polyphenols, which makes it a potent antioxidant. Due to its activity as an antioxidant, as well as through other mechanisms, cocoa consumption has been reported to be beneficial for cardiovascular health, brain functions, and cancer prevention. Furthermore, cocoa influences the immune system, in particular the inflammatory innate response and the systemic and intestinal adaptive immune response. Preclinical studies have demonstrated that a cocoa-enriched diet modifies T-cell functions that conduce to a modulation of the synthesis of systemic and gut antibodies. In this regard, it seems that a cocoa diet in rats produces changes in the lymphocyte composition of secondary lymphoid tissues and the cytokines secreted by T cells. These results suggest that it is possible that cocoa could inhibit the function of Th2 cells, and in line with this, the preventive effect of cocoa on IgE synthesis in a rat allergy model has been reported, which opens up new perspectives when considering the beneficial effects of cocoa compounds. On the other hand, cocoa intake modifies the functionality of gut-associated lymphoid tissue by means of modulating IgA secretion and intestinal microbiota. The mechanisms involved in these influences are discussed here. Further research may elucidate the cocoa compounds involved in such an effect and also the possible medical approaches to these repercussions

Design of User Authentication System for Multi-operator wireless LANs

Langattomat lähiverkot ovat viime vuosikymmeninä saavuttaneet suuren suosion. Tässä työssä käsitellään käyttäjien todentamisjärjestelmän suunnittelua ja kehitystä langattomaan monioperaattoriverkkoon. Langattomassa monioperaattoriverkossa käyttäjillä on mahdollisuus käyttää eri operaattoreiden palveluita. Aluksi käsitellään olemassa olevia todentamismenetelmiä ja -järjestelmiä. minkä jälkeen kuvaillaan todentamisjärjestelmä langattomille monioperaattoriverkoille. Todentamisjärjestelmän ratkaisuvaihtoehtoja esitellään kaksi, niin sanotut moni- istunto - ja yksittäisistuntomalli. Moni-istuntomalli on normaali lähestymistapa käyttäjien todentamiseen tietokonejärjestelmissä. Siinä käyttäjän pitää tunnistautua ja todentaa itsensä jokaiselle verkon palvelulle erikseen. Yksittäisistuntomallissa pyritään parempaan luotettavuuteen ja käytettävyyteen. Siinä käyttäjä todentaa itsensä vain kerran ja voi sen jälkeen päästä useisiin palveluihin. Työn loppuosassa kuvaillaan suunnitellun järjestelmän toteutusta. Lisäksi ehdotetaan vaihtoehtoisia toteutustapoja, analysoidaan järjestelmän heikkouksia ja kerrotaan jatkokehitysmahdoillisuuksista.

Software methods for HTML files protection in local / corporate networks: review and implementation

Tässä luomistyössä on esitetty tutkimus informaation suojaamisen menetelmien osalta paikallisissa ja ryhmäkuntaisissa verkoissa. Tutkimukseen kuuluu nykyaikaisten kryptagraafisten järjestelmien, Internetin/Intranetin ohjelmointikeinojen ja pääsyoikeuksien jakelumenetelmien analyysi. Tutkimusten perusteella on laadittu ohjelmiston prototyyppi HTML-tiedostojen suojaamista varten. Ohjelmiston laatimisprosessi on sisältänyt vaatimusten, järjestelmän ja suojelukomponenttien suunnittelun ja protytyypin testauksen. Ohjelmiston realisoinnin jälkeen kirjoitettiin käyttöohjeet. Ohjelmiston prototyyppi suojaa informaatiota HTML-tiedoston koko käytön aikana ja eri yrityksissä voidaan käyttää sitä pienien laajennuksien jälkeen.

Potential of local bio-geoengineering to mitigate dangerous temperature increases in a global warming scenario

Crops and forests are already responding to rising atmospheric carbon dioxide and air temperatures. Increasing atmospheric CO2 concentrations are expected to enhance plant photosynthesis. Nevertheless, after long-term exposure, plants acclimate and show a reduction in photosynthetic activity (i.e. down-regulation). If in the future the Earth"s temperature is allowed to rise further, plant ecosystems and food security will both face significant threats. The scientific community has recognized that an increase in global temperatures should remain below 2°C in order to combat climate change. All this evidence suggests that, in parallel with reductions in CO2 emissions, a more direct approach to mitigate global warming should be considered. We propose here that global warming could be partially mitigated directly through local bio-geoengineering approaches. For example, this could be done through the management of solar radiation at surface level, i.e. by increasing global albedo. Such an effect has been documented in the south-eastern part of Spain, where a significant surface air temperature trend of -0.3°C per decade has been observed due to a dramatic expansion of greenhouse horticulture.

The genetic basis of color-related local adaptation in a ring-like colonization around the Mediterranean.

Uncovering the genetic basis of phenotypic variation and the population history under which it established is key to understand the trajectories along which local adaptation evolves. Here, we investigated the genetic basis and evolutionary history of a clinal plumage color polymorphism in European barn owls (Tyto alba). Our results suggest that barn owls colonized the Western Palearctic in a ring-like manner around the Mediterranean and meet in secondary contact in Greece. Rufous coloration appears to be linked to a recently evolved nonsynonymous-derived variant of the melanocortin 1 receptor (MC1R) gene, which according to quantitative genetic analyses evolved under local adaptation during or following the colonization of Central Europe. Admixture patterns and linkage disequilibrium between the neutral genetic background and color found exclusively within the secondary contact zone suggest limited introgression at secondary contact. These results from a system reminiscent of ring species provide a striking example of how local adaptation can evolve from derived genetic variation.