DSpace REST API: an Interface for Reusing DSpace Content, and Practical Applications

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

Fedora 4 as a Shared Linked Data repository for the Art Institute of Chicago Collections

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

Lipase and omega-transaminase catalysis in preparation of alcohol and amine enantiomers

Enantiopure intermediates are of high value in drug synthesis. Biocatalysis alone or combined with chemical synthesis provides powerful tools to access enantiopure compounds. In biocatalysis, chemo-, regio- and enantioselectivity of enzymes are combined with their inherent environmentally benign nature. Enzymes can be applied in versatile chemical reactions with non-natural substrates under synthesis conditions. Immobilization of an enzyme is a crucial part of an efficient biocatalytic synthesis method. Successful immobilization enhances the catalytic performance of an enzyme and enables its reuse in successive reactions. This thesis demonstrates the feasibility of biocatalysis in the preparation of enantiopure secondary alcohols and primary amines. Viability and synthetic usability of the studied biocatalytic methods have been addressed throughout this thesis. Candida antarctica lipase B (CAL-B) catalyzed enantioselective O-acylation of racemic secondary alcohols was successfully incorporated with in situ racemization in the dynamic kinetic resolution, affording the (R)-esters in high yields and enantiopurities. Side reactions causing decrease in yield and enantiopurity were suppressed. CAL-B was also utilized in the solvent-free kinetic resolution of racemic primary amines. This method produced the enantiomers as (R)-amides and (S)-amines under ambient conditions. An in-house sol-gel entrapment increased the reusability of CAL-B. Arthrobacter sp. omega-transaminase was entrapped in sol-gel matrices to obtain a reusable catalyst for the preparation enantiopure primary amines in an aqueous medium. The obtained heterogeneous omega-transaminase catalyst enabled the enantiomeric enrichment of the racemic amines to their (S)-enantiomers. The synthetic usability of the sol-gel catalyst was demonstrated in five successive preparative kinetic resolutions.

Horizontal projections of area 17 in Cebus monkeys: metric features, and modular and laminar distribution

Metric features and modular and laminar distributions of intrinsic projections of area 17 were studied in Cebus apella. Anterogradely and retrogradely labeled cell appendages were obtained using both saturated pellets and iontophoretic injections of biocytin into the operculum. Laminar and modular distributions of the labeled processes were analyzed using Nissl counterstaining, and/or cytochrome oxidase and/or NADPH-diaphorase histochemistry. We distinguished three labeled cell types: pyramidal, star pyramidal and stellate cells located in supragranular cortical layers (principally in layers IIIa, IIIb a, IIIb ß and IIIc). Three distinct axon terminal morphologies were found, i.e., Ia, Ib and II located in granular and supragranular layers. Both complete and partial segregation of group I axon terminals relative to the limits of the blobs of V1 were found. The results are compatible with recent evidence of incomplete segregation of visual information flow in V1 of Old and New World primates

Susteinable steelmaking by process integration

Environmental issues, including global warming, have been serious challenges realized worldwide, and they have become particularly important for the iron and steel manufacturers during the last decades. Many sites has been shut down in developed countries due to environmental regulation and pollution prevention while a large number of production plants have been established in developing countries which has changed the economy of this business. Sustainable development is a concept, which today affects economic growth, environmental protection, and social progress in setting up the basis for future ecosystem. A sustainable headway may attempt to preserve natural resources, recycle and reuse materials, prevent pollution, enhance yield and increase profitability. To achieve these objectives numerous alternatives should be examined in the sustainable process design. Conventional engineering work cannot address all of these substitutes effectively and efficiently to find an optimal route of processing. A systematic framework is needed as a tool to guide designers to make decisions based on overall concepts of the system, identifying the key bottlenecks and opportunities, which lead to an optimal design and operation of the systems. Since the 1980s, researchers have made big efforts to develop tools for what today is referred to as Process Integration. Advanced mathematics has been used in simulation models to evaluate various available alternatives considering physical, economic and environmental constraints. Improvements on feed material and operation, competitive energy market, environmental restrictions and the role of Nordic steelworks as energy supplier (electricity and district heat) make a great motivation behind integration among industries toward more sustainable operation, which could increase the overall energy efficiency and decrease environmental impacts. In this study, through different steps a model is developed for primary steelmaking, with the Finnish steel sector as a reference, to evaluate future operation concepts of a steelmaking site regarding sustainability. The research started by potential study on increasing energy efficiency and carbon dioxide reduction due to integration of steelworks with chemical plants for possible utilization of available off-gases in the system as chemical products. These off-gases from blast furnace, basic oxygen furnace and coke oven furnace are mainly contained of carbon monoxide, carbon dioxide, hydrogen, nitrogen and partially methane (in coke oven gas) and have proportionally low heating value but are currently used as fuel within these industries. Nonlinear optimization technique is used to assess integration with methanol plant under novel blast furnace technologies and (partially) substitution of coal with other reducing agents and fuels such as heavy oil, natural gas and biomass in the system. Technical aspect of integration and its effect on blast furnace operation regardless of capital expenditure of new operational units are studied to evaluate feasibility of the idea behind the research. Later on the concept of polygeneration system added and a superstructure generated with alternative routes for off-gases pretreatment and further utilization on a polygeneration system producing electricity, district heat and methanol. (Vacuum) pressure swing adsorption, membrane technology and chemical absorption for gas separation; partial oxidation, carbon dioxide and steam methane reforming for methane gasification; gas and liquid phase methanol synthesis are the main alternative process units considered in the superstructure. Due to high degree of integration in process synthesis, and optimization techniques, equation oriented modeling is chosen as an alternative and effective strategy to previous sequential modelling for process analysis to investigate suggested superstructure. A mixed integer nonlinear programming is developed to study behavior of the integrated system under different economic and environmental scenarios. Net present value and specific carbon dioxide emission is taken to compare economic and environmental aspects of integrated system respectively for different fuel systems, alternative blast furnace reductants, implementation of new blast furnace technologies, and carbon dioxide emission penalties. Sensitivity analysis, carbon distribution and the effect of external seasonal energy demand is investigated with different optimization techniques. This tool can provide useful information concerning techno-environmental and economic aspects for decision-making and estimate optimal operational condition of current and future primary steelmaking under alternative scenarios. The results of the work have demonstrated that it is possible in the future to develop steelmaking towards more sustainable operation.

Potential and Challenges of Analog Reconfigurable Computation in Modern and Future CMOS

In this work, the feasibility of the floating-gate technology in analog computing platforms in a scaled down general-purpose CMOS technology is considered. When the technology is scaled down the performance of analog circuits tends to get worse because the process parameters are optimized for digital transistors and the scaling involves the reduction of supply voltages. Generally, the challenge in analog circuit design is that all salient design metrics such as power, area, bandwidth and accuracy are interrelated. Furthermore, poor flexibility, i.e. lack of reconfigurability, the reuse of IP etc., can be considered the most severe weakness of analog hardware. On this account, digital calibration schemes are often required for improved performance or yield enhancement, whereas high flexibility/reconfigurability can not be easily achieved. Here, it is discussed whether it is possible to work around these obstacles by using floating-gate transistors (FGTs), and analyze problems associated with the practical implementation. FGT technology is attractive because it is electrically programmable and also features a charge-based built-in non-volatile memory. Apart from being ideal for canceling the circuit non-idealities due to process variations, the FGTs can also be used as computational or adaptive elements in analog circuits. The nominal gate oxide thickness in the deep sub-micron (DSM) processes is too thin to support robust charge retention and consequently the FGT becomes leaky. In principle, non-leaky FGTs can be implemented in a scaled down process without any special masks by using “double”-oxide transistors intended for providing devices that operate with higher supply voltages than general purpose devices. However, in practice the technology scaling poses several challenges which are addressed in this thesis. To provide a sufficiently wide-ranging survey, six prototype chips with varying complexity were implemented in four different DSM process nodes and investigated from this perspective. The focus is on non-leaky FGTs, but the presented autozeroing floating-gate amplifier (AFGA) demonstrates that leaky FGTs may also find a use. The simplest test structures contain only a few transistors, whereas the most complex experimental chip is an implementation of a spiking neural network (SNN) which comprises thousands of active and passive devices. More precisely, it is a fully connected (256 FGT synapses) two-layer spiking neural network (SNN), where the adaptive properties of FGT are taken advantage of. A compact realization of Spike Timing Dependent Plasticity (STDP) within the SNN is one of the key contributions of this thesis. Finally, the considerations in this thesis extend beyond CMOS to emerging nanodevices. To this end, one promising emerging nanoscale circuit element - memristor - is reviewed and its applicability for analog processing is considered. Furthermore, it is discussed how the FGT technology can be used to prototype computation paradigms compatible with these emerging two-terminal nanoscale devices in a mature and widely available CMOS technology.

Biohiilen teknillistaloudelliset käyttömahdollisuudet meesauuneissa

Diplomityön tavoitteena oli tutkia biohiilen teknillisiä ja taloudellisia käyttömahdollisuuksia meesauunien polttoaineena. Suomessa meesauunit käyttävät polttoaineinaan yleensä maakaasua ja polttoöljyä. Näiden polttoaineiden käytön korvaamisessa ja vähentämisessä halvemmilla biopolttoaineilla on saatavilla suuret säästöt ja päästöjen vähennykset. Työssä keskityttiin erityisesti tutkimaan biohiilen mahdollisia polttotapoja, biohiilen polton tuottamien vierasaineiden määrää ja biohiilen käytön taloudellista kannattavuutta meesauunien polttoaineena. Työn pohjalta voidaan sanoa, että biohiilen käyttö meesauunien polttoaineena on mahdollista ja kannattavaa. Biohiiltä voidaan käyttää polttoaineena meesauuneissa samoilla polttotavoilla, mitä on käytetty sellu- ja sementtiteollisuudessa polttamaan biohiilen kaltaisia polttoaineita. Biohiilen polton tuottamien vierasaineiden määrä on samaa suuruusluokkaa kuin puun pölypolton tuottamien vierasaineiden määrä. Vierasaineiden pitoisuuksia voidaan hallita avaamalla kemikaalikiertoa. Biohiilen kanssa kilpaileviin puun pölypolttoon ja kaasutukseen nähden biohiilelle löydettiin etuja.

α-Pinene oxide and verbenol oxide isomerizations over heterogeneous catalysts

Terpenes are a valuable natural resource for the production of fine chemicals. Turpentine, obtained from biomass and also as a side product of softwood industry, is rich in monoterpenes such as α-pinene and β-pinene, which are widely used as raw materials in the synthesis of flavors, fragrances and pharmaceutical compounds. The rearrangement of their epoxides has been thoroughly studied in recent years, as a method to obtain compounds which are further used in the fine chemical industry. The industrially most desired products of α-pinene oxide isomerization are campholenic aldehyde and trans-carveol. Campholenic aldehyde is an intermediate for the manufacture of sandalwood-like fragrances such as santalol. Trans-carveol is an expensive constituent of the Valencia orange essence oil used in perfume bases and food flavor composition. Furthermore it has been found to exhibit chemoprevention of mammary carcinogenesis. A wide range of iron and ceria supported catalysts were prepared, characterized and tested for α-pinene oxide isomerization in order to selective synthesis of above mentioned products. The highest catalytic activity in the preparation of campholenic aldehyde over iron modified catalysts using toluene as a solvent at 70 °C (total conversion of α-pinene oxide with a selectivity of 66 % to the desired aldehyde) was achieved in the presence of Fe-MCM-41. Furthermore, Fe-MCM-41 catalyst was successfully regenerated without deterioration of catalytic activity and selectivity. The most active catalysts in the synthesis of trans-carveol from α-pinene oxide over iron and ceria modified catalysts in N,N-dimethylacetamide as a solvent at 140 °C (total conversion of α-pinene oxide with selectivity 43 % to trans-carveol) were Fe-Beta-300 and Ce-Si-MCM-41. These catalysts were further tested for an analogous reaction, namely verbenol oxide isomerization. Verbenone is another natural organic compound which can be found in a variety of plants or synthesized by allylic oxidation of α-pinene. An interesting product which is synthesized from verbenone is (1R,2R,6S)-3-methyl-6-(prop-1-en-2-yl)cyclohex-3-ene-1,2-diol. It has been discovered that this diol possesses potent anti-Parkinson activity. The most effective way leading to desired diol starts from verbenone and includes three stages: epoxidation of verbenone to verbenone oxide, reduction of verbenone oxide and subsequent isomerization of obtained verbenol oxide, which is analogous to isomerization of α-pinene oxide. In the research focused on the last step of these synthesis, high selectivity (82 %) to desired diol was achieved in the isomerization of verbenol oxide at a conversion level of 96 % in N,N-dimethylacetamide at 140 °C using iron modified zeolite, Fe-Beta-300. This reaction displayed surprisingly high selectivity, which has not been achieved yet. The possibility of the reuse of heterogeneous catalysts without activity loss was demonstrated.

Interaction between repeated restraint stress and concomitant midazolam administration on sweet food ingestion in rats

Emotional changes can influence feeding behavior. Previous studies have shown that chronically stressed animals present increased ingestion of sweet food, an effect reversed by a single dose of diazepam administered before testing the animals. The aim of the present study was to evaluate the response of animals chronically treated with midazolam and/or submitted to repeated restraint stress upon the ingestion of sweet food. Male adult Wistar rats were divided into two groups: controls and exposed to restraint 1 h/day, 5 days/week for 40 days. Both groups were subdivided into two other groups treated or not with midazolam (0.06 mg/ml in their drinking water during the 40-day treatment). The animals were placed in a lighted area in the presence of 10 pellets of sweet food (Froot loops®). The number of ingested pellets was measured during a period of 3 min, in the presence or absence of fasting. The group chronically treated with midazolam alone presented increased ingestion when compared to control animals (control group: 2.0 ± 0.44 pellets and midazolam group: 3.60 ± 0.57 pellets). The group submitted to restraint stress presented an increased ingestion compared to controls (control group: 2.0 ± 0.44 pellets and stressed group: 4.18 ± 0.58 pellets). Chronically administered midazolam reduced the ingestion in stressed animals (stressed/water group: 4.18 ± 0.58 pellets; stressed/midazolam group: 3.2 ± 0.49 pellets). Thus, repeated stress increases appetite for sweet food independently of hunger and chronic administration of midazolam can decrease this behavioral effect.

Attraction to amino acids by Lymnaea acuminata, the snail host of Fasciola species

Adult Lymnaea acuminata (average length 20-22 mm) were collected locally from lakes and low-lying submerged fields from Gorakhpur. The chemoattraction studies were made in round glass aquaria measuring 30 cm in diameter and filled to a depth of 10 mm with 500 ml dechlorinated tap water. Each aquarium was divided into four concentric zones. At the starting time of the assay 10 snails were placed on the circumference of outermost zone 0. Snail attractant pellets (SAP) were added simultaneously in the center of central zone 3. SAP of different amino acids were prepared at concentrations of 10, 20, 50, 80 and 100 mM/2% agar solution and, subsequently, spread to a uniform thickness of 5 mm. After cooling, SAP were cut in small pieces of 5 mm in diameter. Lymnaea acuminata's attraction to amino acids was studied using different amino acid concentrations in SAP. Pellets containing amino acids with non-polar R groups (proline and tryptophan), a charged polar group (arginine) and uncharged polar R groups (serine, citrulline and asparagine) were tested. The snails were more attracted to the uncharged polar R group amino acid serine than to other groups of amino acids. The preferred amino acid concentration was 80 mM. The attraction of snails to different amino acids was concentration dependent. Snails could discriminate amongst the different amino acids at > or = 50 mM.

Promoting Growth in the Use of Bioenergy in Europe by Converting Existing Coal-Fired Power Plants to Biomass

Repowering existing power plants by replacing coal with biomass might offer an interesting option to ease the transition from fossil fuels to renewable energy sources and promote a fur-ther expansion of bioenergy in Europe, on account of the potential to decrease greenhouse gas emissions, as well as other pollutants (SOx, NOx, etcetera). In addition, a great part of the appeal of repowering projects comes from the opportunity to reuse the vast existing invest-ment and infrastructure associated with coal-based power generation. Even so, only a limited number of experiences with repowering are found. Therefore, efforts are required to produce technical and scientific evidence to determine whether said technology might be considered feasible for its adoption within European conditions. A detailed evaluation of the technical and economic aspects of this technology constitutes a powerful tool for decision makers to define the energy future for Europe. To better illustrate this concept, a case study is analyzed. A Slovakian pulverized coal plant was used as the basis for determining the effects on perfor-mance, operation, maintenance and cost when fuel is shifted to biomass. It was found that biomass fuel properties play a crucial role in plant repowering. Furthermore, results demon-strate that this technology offers renewable energy with low pollutant emissions at the cost of reduced capacity, relatively high levelized cost of electricity and sometimes, a maintenance-intensive operation. Lastly, regardless of the fact that existing equipment can be reutilized for the most part, extensive additions/modifications may be required to ensure a safe operation and an acceptable performance.

Espoon puhdistamolietteen käsittelymenetelmien selvitys Ämmässuon käsittelykeskukselle

Ravinteiden kierrätys yhä enemmän luonnonvaroja kuluttavassa yhteiskunnassa on noussut tärkeäksi. Hyötykäyttämällä luonnollisesti syntyvät orgaaniset virrat yhteiskunnasta voidaan kierrättää pellolta nostetut ravinteet takaisin. Tässä diplomityössä on tarkasteltu Helsingin seudun ympäristöpalveluiden toteuttamaa mädätetyn puhdistamolietteen käsittelyä ja pohdittu sen käsittelymahdollisuuksia erityisesti Ämmässuon käsittelykeskuksessa. Tarkastelussa on keskitytty kahteen yleisimpään kompostointimenetelmään, eli auma- ja tunnelikompostointiin. Kompostointimenetelmien tarkastelussa on pyritty löytämään optimaalinen tukiaine sekä prosessiaika käsiteltävälle lietteelle Ämmässuolla olemassa olleilla resursseilla. Tutkimuksessa toteutettiin käytännön pilot -kokeita sekä toteutettiin teoreettista prosessin parametrien laskentaa mukaan lukien kustannukset ja resurssit. Tutkimuksen perusteella voidaan todeta, että kyseisen tyyppisellä käsittelyalueella tunneli-kompostointi on näillä parametreilla testattuna paras vaihtoehto. Menetelmällä voidaan saavuttaa nopeampi käsittelyaika sekä vähentää kompostoinnista aiheutuvia hajuhaittoja ympäristöön. Tukiaineseoksessa voidaan korvata yleisestikin käytetty turve vastaanotettavalla lehti-puru viherjäteseoksella sekä risuhakkeella ja prosessiaika on noin 12 -16 viikkoa. Käsittelyn kustannukset verrattuna tämän hetkiseen käsittelyyn Metsäpirtissä eivät olleet merkittävästi suuremmat ja ympäristövaikutusarvioinnin perusteella syntypaikkaa lähellä oleva käsittelyalue sekä prosessin pienemmät vaikutukset tuovat ympäristöedun käsittelylle Ämmässuolla.

Roles of calcium and IP3 in impaired colon contractility of rats following multiple organ dysfunction syndrome

The purpose of the present study was to explore changes in rat colon motility, and determine the roles of calcium and inositol (1,4,5)-triphosphate (IP3) in colon dysmotility induced by multiple organ dysfunction syndrome (MODS) caused by bacteria peritonitis. The number of stools, the contractility of the muscle strips and the length of smooth muscle cells (SMC) in the colon, the concentration of calcium and IP3 in SMC, and serum nitric oxide were measured. Number of stools, fecal weight, IP3 concentration in SMC and serum nitric oxide concentration were 0.77 ± 0.52 pellets, 2.51 ± 0.39 g, 4.14 ± 2.07 pmol/tube, and 113.95 ± 37.89 µmol/L, respectively, for the MODS group (N = 11) vs 1.54 ± 0.64 pellets, 4.32 ± 0.57 g, 8.19 ± 3.11 pmol/tube, and 37.42 ± 19.56 µmol/L for the control group (N = 20; P < 0.05). After treatment with 0.1 mM acetylcholine and 0.1 M potassium chloride, the maximum contraction stress of smooth muscle strips, the length of SMC and the changes of calcium concentration were 593 ± 81 and 458 ± 69 g/cm³, 48.1 ± 11.8 and 69.2 ± 15.7 µM, 250 ± 70 and 167 ± 48%, respectively, for the control group vs 321 ± 53 and 284 ± 56 g/cm³, 65.1 ± 18.5 and 87.2 ± 23.7 µM, 127 ± 35 and 112 ± 35% for the MODS group (P < 0.05). Thus, colon contractility was decreased in MODS, a result possibly related to reduced calcium concentration and IP3 in SMC.

Effect of skilled and unskilled training on nerve regeneration and functional recovery

The most disabling aspect of human peripheral nerve injuries, the majority of which affect the upper limbs, is the loss of skilled hand movements. Activity-induced morphological and electrophysiological remodeling of the neuromuscular junction has been shown to influence nerve repair and functional recovery. In the current study, we determined the effects of two different treatments on the functional and morphological recovery after median and ulnar nerve injury. Adult Wistar male rats weighing 280 to 330 g at the time of surgery (N = 8-10 animals/group) were submitted to nerve crush and 1 week later began a 3-week course of motor rehabilitation involving either "skilled" (reaching for small food pellets) or "unskilled" (walking on a motorized treadmill) training. During this period, functional recovery was monitored weekly using staircase and cylinder tests. Histological and morphometric nerve analyses were used to assess nerve regeneration at the end of treatment. The functional evaluation demonstrated benefits of both tasks, but found no difference between them (P > 0.05). The unskilled training, however, induced a greater degree of nerve regeneration as evidenced by histological measurement (P < 0.05). These data provide evidence that both of the forelimb training tasks used in this study can accelerate functional recovery following brachial plexus injury.

Kartonkikoneen tuoreveden käytön vähentäminen kemiallisesti puhdistettua jätevesikirkastetta hyödyntäen

Tämän diplomityön tarkoituksena oli tutkia mahdollisuutta hyödyntää kemiallisesti puh-distettua jätevettä prosessivetenä. Vedensäästöpotentiaalin perusteella tutkimuskohteeksi valittiin kartonkikone 4. Tutkimuksen tavoite oli tuoreveden käytön ja jätevesipäästöjen vähentäminen Stora Enso Imatran tehtailla. Työn kirjallisuusosa keskittyy kemialliseen jätevedenkäsittelyyn, kartonkikoneen veden käyttöön ja prosessiveden laatuun vaikuttaviin tekijöihin. Työn kokeellisessa osassa laa-dittiin vesitase tuoreveden käyttökohteiden ja veden tarpeen määrittämiseksi. Kemialli-sesti puhdistetun jäteveden ja prosessiveden ominaisuudet määritettiin, jotta saatiin sel-ville ne ominaisuudet, jotka voisivat estää jätevesikirkasteen hyötykäytön. Laboratoriomääritykset osoittivat, että hyötykäytön esteenä ovat jätevesikirkasteen kiin-toaine-, sulfaatti- ja karbonaattipitoisuus sekä mikrobitaso ja väri. Metallien ja suolaionien haittavaikutusten selvittäminen vaatii lisätutkimusta. Lisäpuhdistusmenetelmien avulla, kuten käänteisosmoosi, jätevesikirkasteen laatu saataisiin vastaamaan prosessiveden tasoa ja hyötykäyttö olisi mahdollista myös kartonkikone 4:n ulkopuolella.