Entorn de gestió de dades d'ornitologia

Des de fa uns anys, des de l’EPS de la UVic, s’està duent a terme el desenvolupament d’un dispositiu electrònic que proporciona la capacitat de capturar dades sobre un niu d’ocells. El projecte e-niu, que es pot seguir a www.tutara.info/e-niu, està actualment en una fase de test., i s’ha desenvolupat sobretot la part hardware. Aquest projecte té com a objectiu principal crear un entorn web per poder gestionar les dades que s’obtenen del niu d’ocells informatitzat (e-niu). Les dades que ens arriben dels e-nius estan en un arxiu de text, i el que es pretén és que l’usuari que controla el niu, pugui fer diversos anàlisis de les dades d’aquest. A més de poder veure els resultats en diversos tipus de gràfics, també se li vol donar la opció de treure els resultats en format taula o en format Excel, un format aquest últim, molt interessant, ja que donaria a les dades una gran possibilitat de ser tractades posteriorment, com fer seleccions del tipus de dades, treure percentatges, crear altres tipus de gràfics, etc. L’altre gran objectiu és el fet de poder treballar en la creació d’un entorn web complert a nivell gairebé professional amb l’aprenentatge que això comporta, ja que s’ha aplicat la tecnologia client-servidor, és a dir, que el llenguatge de programació està dins el servidor, i quan algun usuari l’executa, el sistema només li envia la presentació en HTML. El sistema de programació que es fa servir és el de les tres capes. La capa de dades, que està formada per una base de dades relacional del tipus MySQL i és on emmagatzemarem tota la informació. La capa de programació de la que s’encarrega el llenguatge PHP, és on s’efectua tot el tractament de les dades i finalment, la capa de presentació, que és la que s’encarrega de mostrar les dades al client en el navegador mitjançant els templates de HTML.

Tropical biodiversity: has it been a potential source of secondary metabolites useful for medicinal chemistry?

The use of natural products has definitely been the most successful strategy in the discovery of novel medicines. Secondary metabolites from terrestrial and marine organisms have found considerable use in the treatment of numerous diseases and have been considered lead molecules both in their natural form and as templates for medicinal chemistry. This paper seeks to show the great value of secondary metabolites and emphasize the rich chemical diversity of Brazilian biodiversity. This natural chemical library remains understudied, but can be a useful source of new secondary metabolites with potential application as templates for drug discovery.

SÍNTESE E CARACTERIZAÇÃO DE COMPÓSITOS ORGÂNICO-INORGÂNICOS MACROPOROSOS PARA O SENSORIAMENTO DE H2O2

Electrodes modified with poly(5-amino-1-naphthol)/Prussian blue (poly(5-NH2-1-NAP)/PB) hybrid films are able to electrochemically reduce H2O2 in medium containing an excess of Na+ cations. This is an important advantage for biosensing applications over electrodes in which only conventionally (electro) deposited Prussian blue is present. Consequently, the aim of this work was to examine the application of templates of ordered arrays of colloidal poly(styrene) spheres (800, 450 and 100 nm in diameter) to produce inverse opal structures of poly(5-NH2-1-NAP)/PB hybrid platforms, in an effort to study the influence of the increase in surface area/volume ratio and higher exposition of the mediator active sites on material performance during H2O2 determination employing the different sized porous structures. Moreover, since the accentuated hydrophilic character of poly(5-NH2-1-NAP)/PB also allows H2O2 electrochemical reduction in inner active sites, issues concerning the amount of mediator electrodeposited on the electrode were also reflected in the observed results.

Chiral separations of mandelic acid by HPLC using molecularly imprinted polymers

Styrene is used in a variety of chemical industries. Environmental and occupational exposures to styrene occur predominantly through inhalation. The major metabolite of styrene is present in two enantiomeric forms, chiral R- and S- hydroxy-1-phenyl-acetic acid (R-and S-mandelic acid, MA). Thus, the concentration of MA, particularly of its enantiomers, has been used in urine tests to determine whether workers have been exposed to styrene. This study describes a method of analyzing mandelic acid using molecular imprinting techniques and HPLC detection to perform the separation of diastereoisomers of mandelic acid. The molecularly imprinted polymer (MIP) was prepared by non-covalent molecular imprinting using (+) MA, (-) MA or (+) phenylalanine, (-) phenylalanine as templates. Methacrylic acid (MAA) and ethylene glycol dimethacrylate (EGDMA) were copolymerized in the presence of the template molecules. The bulk polymerization was carried out at 4ºC under UV radiation. The resulting MIP was grounded into 25~44¼m particles, which were slurry packed into analytical columns. After the template molecules were removed, the MIP-packed columns were found to be effective for the chromatographic resolution of (±)-mandelic acid. This method is simpler and more convenient than other chromatographic methods.

Web-käyttöliittymän ajonaikainen parametripohjainen luominen

Työssä tutkitaan eri tekniikoita, joilla web-käyttöliittymä voidaan toteuttaa. Tutkituista tekniikoista valitaan työn tavoitteisiin ja rajoitteisiin parhaiten soveltuvat tekniikat, joita käytetään hyväksi luotaessa varsinainen käyttöliittymäkerros olemassa olevalle web-sovellukselle. Varsinaiset käyttöliittymät luodaan automaattisesti työn aikana toteutettavalla käyttöliittymägeneraattorilla, joka käyttää hyväkseen käyttöliittymiä kuvaavia XML-kuvaustiedostoja. Tekniikoista parhaiten tarpeisiimme soveltui AJAX-lähestymistapa, joka mahdollistaa sivun osittaisen päivittämisen ja täten työpöytäsovellusmaisemman käytettävyyden nopeamman sivun päivityksen vuoksi. Käyttöliittymägeneraattorin käyttämät kuvaustiedostot puolestaan mahdollistavat käyttöliittymäkontrollien valmiin mallintamisen yleisessä kontrollikuvaustiedostossa sekä niiden helpon muokkaamisen ja sijoittelun sivu-kohtaisesti. Lisäksi käyttöliittymäkerros sisältää monipuoliset käyttöliittymäkontrollit.

Esisuunnitteluohjelmiston kehitys BFB-höyrykattiloille

Tämä diplomityö käsittelee Andritz Oy:n BFB-voimalaitosten tarjoustoimintaan kehitettävää esisuunnitteluohjelmistoa. Tässä työssä on esitelty kattiloiden tarjoustoimintaan liittyviä seikkoja etenkin laskennan ja tekniikan näkökulmasta. Työssä on myös koottu tietoa polttoaineista ja BFB-kattiloiden suunnittelusta ja mitoituksesta. Työn aikana kehitettiin ohjelmisto, jolla on mahdollista luoda eri BFB-kattila tarjousprojekteja. Projekteille on mahdollista luoda useita eri taselaskelmia eri lähtöarvoilla ja useilla eri polttoaineilla, sekä niiden seoksilla. Ohjelmakehityksessä painotettiin suunnittelun joustavuutta eri konfiguraatioille, mahdollisimman tarkkaa laskentaa ja ylläpidon merkitystä. Ohjelmistokehityksessä päätettiin käyttää Microsoft Excel ohjelmistoa laskentaympäristönä. Tällöin pystyttiin luomaan käyttäjille tuttu käyttöympäristö ja mahdollistaa vanhojen hyväksi todettujen laskentapohjien käyttö apuna kehityksessä. Tämä mahdollistaa myös ylläpidon toimialueen ammattilaisten toimesta jatkossa.

Tiedonhallinnan kehittäminen prosessikuvausten ja sähköisen dokumentoinnin avulla

Tämän diplomityön tavoitteena on selkeyttää apteekin ydinprosesseja mallintamalla prosessit ja tehostaa apteekin tiedonhallintaa sähköisen toimintajärjestelmän avulla. Ydinprosessien mallintaminen lisää apteekin työntekijöiden tietoisuutta prosessien oikeasta suoritustavasta. Dokumenttien sijoittaminen yhteen paikkaan helpottaa niiden löytymistä ja käytettävyyttä. Tässä työssä tutkittiin yhtä yritystä, joten tutkimusmenetelmänä käytettiin tapaustutkimusta. Työn keskeinen sisältö rakentuu tiedonhallinnan, prosessijohtamisen sekä sähköisen toimintajärjestelmän teorioiden pohjalta. Teoriaa hyödynnetään käytännön tutkimuksessa, jossa kartoitetaan apteekin dokumentit ja kehitetään niiden organisointia. Työssä tunnistetaan ja mallinnetaan apteekin ydinprosessit sekä kerätään tietoa niiden ongelmakohdista. Apteekin ydinprosesseiksi tunnistettiin reseptiasiakkaan palvelu ja neuvonta, itsehoitoasiakkaan palvelu ja neuvonta, kotisairaanhoidon ja hoivakotien palvelu sekä tavaranhallinta. Apteekissa luodut dokumentit luokiteltiin toimintaohjeiksi, työohjeiksi, lomakkeiksi ja rekisteriselosteiksi. Työn tuloksena apteekin tiedonhallinta tehostui dokumenttien sähköistämisellä ja organisoinnilla toimintajärjestelmään. Ydinprosessien mallintaminen selkeytti apteekin ydinprosesseja sekä lisäsi työntekijöiden tietoisuutta prosessien oikeasta toimintatavasta.

Social tagging within task management

Social tagging evolved in response to a need to tag heterogeneous objects, the automated tagging of which is usually not feasible by current technological means. Social tagging can be used for more flexible competence management within organizations. The profiles of employees can be built in the form of groups of tags, as employees tag each other, based on their familiarity of each other’s expertise. This can serve as a replacement for the more traditional competence management approaches, which usually become outdated due to social and organizational hurdles, and obsolete data. These limitations can be overcome by people tagging, as the information revealed by such tags is usually based on most recent employee interaction and knowledge. Task management as part of personal information management aims at the support of users’ individual task handling. This can include collaborating with other individuals, sharing one’s knowledge, both functional and process-related, and distributing documents and web resources. In this context, Task patterns can be used as templates that collect information and experience around tasks associated to it during run time, facilitating agility. The effective collaboration among contributors necessitates the means to find the appropriate individuals to work with on the task, and this can be made possible by using social tagging to describe individual competencies. The goal of this study is to support finding and tagging people within task management, through the effective exploitation of the work/task context. This involves the utilization of knowledge of the workers’ expertise, nature of the task/task pattern and information available from the documents and web resources attached to the task. Vice versa, task management provides an excellent environment for social tagging due to the task context that already provides suitable tags. The study also aims at assisting users of the task management solution with the collaborative construction of light-weight ontology by inferring semantic relations between tags. The thesis project aims at an implementation of people finding & tagging within the java application for task management that consumes web services, which provide the required ontology for the organization.

Regioselective modification of galactose-containing polysaccharides in aqueous media

Biorefining is defined as sustainable conversion of biomass into marketable products and energy. Forests cover almost one third of earth’s land area, and account for approximately 40% of the total annual biomass production. In forest biorefining, the wood components are, in addition to the traditional paper and board products, converted into chemicals and biofuels. The major components in wood are cellulose, hemicelluloses, and lignin. The main hemicellulose in softwoods, which are of interest especially for the Nordic forest industry, is O-acetyl galactoglucomannan (GGM). GGM can be isolated in industrial scale from the waste waters of the mechanical pulping process, but is not yet today industrially utilized. In order to attain desired properties of GGM for specific end-uses, chemical and enzymatic modifications can be performed. Regioselective modifications of GGM, and other galactose-containing polysaccharides were done by oxidations, and by combining oxidations with subsequent derivatizations of the formed carbonyl or carboxyl groups. Two different pathways were investigated: activation of the C-6 positions in different sugar units by TEMPO-mediated oxidation, and activation of C-6 position in only galactose-units by oxidation catalyzed by the enzyme galactose oxidase. The activated sites were further selectively derivatized; TEMPO-oxidized GGM by a carbodiimide-mediated reaction forming amides, and GO-oxidized GGM by indium-mediated allylation introducing double or triple bonds to the molecule. In order to better understand the reaction, and to develop a MALDI-TOF-MS method for characterization of regioselectively allylated GGM, α-D-galactopyranoside and raffinose were used as model compounds. All reactions were done in aqueous media. To investigate the applicability of the modified polysaccharides for, e.g., cellulose surface functionalization, their sorption onto pulp fibres was studied. Carboxylation affects the sorption tendency significantly; a higher degree of oxidation leads to lower sorption. By controlling the degree of oxidation of the polysaccharides and the ionic strength of the sorption media, high degrees of sorption of carboxylated polysaccharides onto cellulose could, however, be obtained. Anionic polysaccharides were used as templates during laccase-catalyzed polymerization of aniline, offering a green, chemo-enzymatic route for synthesis of conducting polyaniline (PANI) composite materials. Different polysaccharide templates, such as, native GGM, TEMPO-oxidized GGM, naturally anionic κ-carrageenan, and nanofibrillated cellulose produced by TEMPO-oxidation, were assessed. The conductivity of the synthesized polysaccharide/PANI biocomposites varies depending on the polysaccharide template; κ-CGN, the anionic polysaccharide with the lowest pKa value, produces the polysaccharide/PANI biocomposites with the highest conductivity. The presented derivatization, sorption, and polymerization procedures open new application windows for polysaccharides, such as spruce GGM. The modified polysaccharides and the conducting biocomposites produced provide potential applications in biosensors, electronic devices, and tissue engineering.

Introducing the new and improved DMPTool

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

Yrityksen tuoterakenteen määrittäminen olioparadigmalla

Tässä työssä tutkitaan yrityksen tuoterakenteen toteuttamista olioparadigmalla osana vanhenevan tuotannonohjausjärjestelmän uudistamista. Työssä on tunnistettu olioparadigman keskeiset rakenteet sekä tarkasteltu suunnittelumalleja, joita hyödyntämällä voidaan määrittää ja toteuttaa monimutkaisia sekä laajennettavia tuoterakenteita. Työn tavoitteena oli muodostaa tuoterakenteen runko, jota muokkaamalla on mahdollista toteuttaa erityyppisiä tuoterakenteita. Työ on rajattu siten, että todellista tuoterakennetta ei toteuteta. Tutkimuksen tuloksena havaittiin, että oliokeskeisyydellä voidaan toteuttaa tuoterakenteita, joita on mahdollista tulevaisuudessa muokata yrityksen tarpeisiin mukauttaen siten, että tuoterakenteen runkoon ei tarvitse tehdä suuria muutoksia. Olioperusteisella lähestymisellä voidaan mallintaa hyvin erityyppisiä ja ymmärrettäviä käsitteitä. Oliokeskeisellä lähestymistavalla voidaan toteuttaa myös muut vanhenevan tuotannonohjausjärjestelmän osa-alueet.

From protein structure to function with bioinformatics

It has long been known that amino acids are the building blocks for proteins and govern their folding into specific three-dimensional structures. However, the details of this process are still unknown and represent one of the main problems in structural bioinformatics, which is a highly active research area with the focus on the prediction of three-dimensional structure and its relationship to protein function. The protein structure prediction procedure encompasses several different steps from searches and analyses of sequences and structures, through sequence alignment to the creation of the structural model. Careful evaluation and analysis ultimately results in a hypothetical structure, which can be used to study biological phenomena in, for example, research at the molecular level, biotechnology and especially in drug discovery and development. In this thesis, the structures of five proteins were modeled with templatebased methods, which use proteins with known structures (templates) to model related or structurally similar proteins. The resulting models were an important asset for the interpretation and explanation of biological phenomena, such as amino acids and interaction networks that are essential for the function and/or ligand specificity of the studied proteins. The five proteins represent different case studies with their own challenges like varying template availability, which resulted in a different structure prediction process. This thesis presents the techniques and considerations, which should be taken into account in the modeling procedure to overcome limitations and produce a hypothetical and reliable three-dimensional structure. As each project shows, the reliability is highly dependent on the extensive incorporation of experimental data or known literature and, although experimental verification of in silico results is always desirable to increase the reliability, the presented projects show that also the experimental studies can greatly benefit from structural models. With the help of in silico studies, the experiments can be targeted and precisely designed, thereby saving both money and time. As the programs used in structural bioinformatics are constantly improved and the range of templates increases through structural genomics efforts, the mutual benefits between in silico and experimental studies become even more prominent. Hence, reliable models for protein three-dimensional structures achieved through careful planning and thoughtful executions are, and will continue to be, valuable and indispensable sources for structural information to be combined with functional data.

Voimalaitoksen energiaraportoinnin kehittäminen

Diplomityössä tarkasteltiin Metsä Board Simpeleen voimalaitoksen energiaraportointi kokonaisuutta. Tarkastelun kohteena olivat lämpö-, sähkö- ja polttoaine-energiat. Tarkastelun pääpaino oli energian määritykseen tarvittavissa mittapisteissä sekä niistä muodostuvissa raporteissa. Työn tavoitteena oli saada luotettavat energiaraportit, jotka ovat jaoteltu selkeästi ja johdonmukaisesti. Tavoitteena oli myös vähentää kuukausiraportoinnin muodostamiseen tarvittavaa henkilötyöaikaa. Teoriaosuudessa käsitellään yleisesti voimalaitosprosessin toimintaa sekä siinä käytettäviä polttoaineita. Energiataseen muodostamisen perusteita tarkasteltiin voimalaitosprosessin kannalta. Energian määrityksiin käytettävät prosessimittaukset käytiin läpi. Raportointivelvollisuudet selvitettiin, niin tilastokeskuksien, kuin viranomaistenkin suuntaan. Työosuudessa perehdyttiin käytössä oleviin raportointikäytäntöihin sekä raporttipohjiin. Energialaskentayhtälöt ja parametrit tarkastettiin tarvittavilta osin. Työnaikana havaittiin nopeasti, että raportointi muodostetaan pitkälti Microsoft Excel-taulukkolaskentaohjelmiston avulla. Olemassa olevia automatisoituja raportteja ei hyödynnetty ollenkaan, koska niitä pidettiin epäluotettavina. Työn tuloksena automatisoidut kuukausiraportit tarkastettiin, virheet korjattiin ja ne otettiin käyttöön. Automaattisiin raportteihin tehtiin päivitysehdotukset uusista raporttipohjista. Viralliseen kuukausiraportointiin rakennettiin myös kokonaan uudet raportointipohjat, jotka hyödyntävät automaattisesti muodostuvia raportteja. Uudet raporttipohjat nopeuttivat raportointityötä merkittävästi. Polttoaine-energian hallintajärjestelmä todettiin vanhanaikaiseksi ja sen uusimista suositellaan. Uusinnalla raportointityö helpottuisi ja sen avulla siitä saataisiin kattavampi.

Metal oxides prepared through the nanocasting approach-mechanistic study, surface interactions and applications in separation

Mesoporous metal oxides are nowadays widely used in various technological applications, for instance in catalysis, biomolecular separations and drug delivery. A popular technique used to synthesize mesoporous metal oxides is the nanocasting process. Mesoporous metal oxide replicas are obtained from the impregnation of a porous template with a metal oxide precursor followed by thermal treatment and removal of the template by etching in NaOH or HF solutions. In a similar manner to the traditional casting wherein the product inherits the features of the mold, the metal oxide replicas are supposed to have an inverse structure of the starting porous template. This is however not the case, as broken or deformed particles and other structural defects have all been experienced during nanocasting experiments. Although the nanocasting technique is widely used, not all the processing steps are well understood. Questions over the fidelity of replication and morphology control are yet to be adequately answered. This work therefore attempts to answer some of these questions by elucidating the nanocasting process, pin pointing the crucial steps involved and how to harness this knowledge in making wholesome replicas which are a true replication of the starting templates. The rich surface chemistry of mesoporous metal oxides is an important reason why they are widely used in applications such as catalysis, biomolecular separation, etc. At times the surface is modified or functionalized with organic species for stability or for a particular application. In this work, nanocast metal oxides (TiO2, ZrO2 and SnO2) and SiO2 were modified with amino-containing molecules using four different approaches, namely (a) covalent bonding of 3-aminopropyltriethoxysilane (APTES), (b) adsorption of 2-aminoethyl dihydrogen phosphate (AEDP), (c) surface polymerization of aziridine and (d) adsorption of poly(ethylenimine) (PEI) through electrostatic interactions. Afterwards, the hydrolytic stability of each functionalization was investigated at pH 2 and 10 by zeta potential measurements. The modifications were successful except for the AEDP approach which was unable to produce efficient amino-modification on any of the metal oxides used. The APTES, aziridine and PEI amino-modifications were fairly stable at pH 10 for all the metal oxides tested while only AZ and PEI modified-SnO2 were stable at pH 2 after 40 h. Furthermore, the functionalized metal oxides (SiO2, Mn2O3, ZrO2 and SnO2) were packed into columns for capillary liquid chromatography (CLC) and capillary electrochromatography (CEC). Among the functionalized metal oxides, aziridinefunctionalized SiO2, (SiO2-AZ) showed good chemical stability, and was the most useful packing material in both CLC and CEC. Lastly, nanocast metal oxides were synthesized for phosphopeptide enrichment which is a technique used to enrich phosphorylated proteins in biological samples prior to mass spectrometry analysis. By using the nanocasting technique to prepare the metal oxides, the surface area was controlled within a range of 42-75 m2/g thereby enabling an objective comparison of the metal oxides. The binding characteristics of these metal oxides were compared by using samples with different levels of complexity such as synthetic peptides and cell lysates. The results show that nanocast TiO2, ZrO2, Fe2O3 and In2O3 have comparable binding characteristics. Furthermore, In2O3 which is a novel material in phosphopeptide enrichment applications performed comparably with standard TiO2 which is the benchmark for such phosphopeptide enrichment procedures. The performance of the metal oxides was explained by ranking the metal oxides according to their isoelectric points and acidity. Overall, the clarification of the nanocasting process provided in this work will aid the synthesis of metal oxides with true fidelity of replication. Also, the different applications of the metal oxides based on their surface interactions and binding characteristics show the versatility of metal oxide materials. Some of these results can form the basis from which further applications and protocols can be developed.

Sedimentology and micromorphology of drumlin sediments at Chimney Bluffs State Park, New York, United States of America

The drumlin sediments at Chimney Bluffs, New York appear to represent a block-inmatrix style glacial melange. This melange comprises sand stringers, lenses and intraclasts juxtaposed in an apparently massive diamicton. Thin section examination of these glacigenic deposits has revealed microstructures indicative of autokinetic subglacial defonnation which are consistent with a deformable bed origin for the diamicton. These features include banding and. necking of matrix grains, oriented plasma fabrics and the formation of pressure shadows at the long axis ends of elongate clasts. Preservation of primary stratification within the sand intraclasts appears to suggest that these features were pre-existing up-ice deposits that were frozen, entrained, then deposited as part of a defonning till layer beneath an advancing ice sheet. Multi-directional micro-shearing within the sand blocks is thought to reflect the frozen nature of the sand units in such a high strain environment. It is also contended that dewatering of the sediment pile leading to the eventual immobilisation of the defonning till layer was responsible for opening sub-horizontal fissures within the diamicton. These features were subsequently infilled with mass flow poorly sorted sands and silts which were subjected to ductile defonnation during the waning stages of an actively deforming till layer. Microstructures indicative of the dewatering processes in the sand units include patches of fine-grained particles within a coarser-grained matrix and the presence of concentrated zones of translocated clays. However, these units were probably confined within an impermeable diamicton casing that prevented massive pore water influxes from the deforming till layer~ Hence, these microstructures probably reflect localised dewatering of the sand intraclasts. A layered subglacial shear zone model is proposed for the various features exhibited by the drumlin sediments. The complexity of these structures is explained in terms of ii superposing deformation styles in response to changing pore water pressures. Constructional glaciotectonics, as implied by the occurrence of sub-horizontal fissuring, is suggested as the mechanism for the stacking of the sand intraclast units within the diamicton. The usefulness of micromorphology in complimenting the traditional sedimentology of glacigenic deposits is emphasised by the current study. An otherwise massive diamicton was shown to contain microstructures indicative of the very high strain rates expected in a complexly deforming till layer. . It is quite obvious from this investigation that the classification of diamictons needs to be re-examined for evidence of microstructures that could lead to the re-interpretation of diamicton forming processes. RESUME Le pacquet de sediments drumlinaire de Chimney Bluffs, New York, represent un "bloc-en-matrice" genre de melange glaciale. Des structures microscopique comprennent l'evidence pour la defonnation intrinseque attribuee a l'origine lit non resistant du drumlin. PreselVation des structures primaires au coeur des blocs arenaces suggere que ceux sont des depots preexistant qui furent geles, entraines et par la suite sedimentes au milieu d'une couche de debris sous-glaciaires en voie de deformation. Des failles microscopiques a l'interieur des blocs arenaces appuient aussi l'idee d'un bloc cohesif (c'est-a-dire gele) au centre d'un till non resistant. Des implications significatives s'emergent de cette etude pour les conditions sous-glaciaire et les processus de la formation des drumlin.