74 resultados para NEST REUSE


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

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Biomedical natural language processing (BioNLP) is a subfield of natural language processing, an area of computational linguistics concerned with developing programs that work with natural language: written texts and speech. Biomedical relation extraction concerns the detection of semantic relations such as protein-protein interactions (PPI) from scientific texts. The aim is to enhance information retrieval by detecting relations between concepts, not just individual concepts as with a keyword search. In recent years, events have been proposed as a more detailed alternative for simple pairwise PPI relations. Events provide a systematic, structural representation for annotating the content of natural language texts. Events are characterized by annotated trigger words, directed and typed arguments and the ability to nest other events. For example, the sentence “Protein A causes protein B to bind protein C” can be annotated with the nested event structure CAUSE(A, BIND(B, C)). Converted to such formal representations, the information of natural language texts can be used by computational applications. Biomedical event annotations were introduced by the BioInfer and GENIA corpora, and event extraction was popularized by the BioNLP'09 Shared Task on Event Extraction. In this thesis we present a method for automated event extraction, implemented as the Turku Event Extraction System (TEES). A unified graph format is defined for representing event annotations and the problem of extracting complex event structures is decomposed into a number of independent classification tasks. These classification tasks are solved using SVM and RLS classifiers, utilizing rich feature representations built from full dependency parsing. Building on earlier work on pairwise relation extraction and using a generalized graph representation, the resulting TEES system is capable of detecting binary relations as well as complex event structures. We show that this event extraction system has good performance, reaching the first place in the BioNLP'09 Shared Task on Event Extraction. Subsequently, TEES has achieved several first ranks in the BioNLP'11 and BioNLP'13 Shared Tasks, as well as shown competitive performance in the binary relation Drug-Drug Interaction Extraction 2011 and 2013 shared tasks. The Turku Event Extraction System is published as a freely available open-source project, documenting the research in detail as well as making the method available for practical applications. In particular, in this thesis we describe the application of the event extraction method to PubMed-scale text mining, showing how the developed approach not only shows good performance, but is generalizable and applicable to large-scale real-world text mining projects. Finally, we discuss related literature, summarize the contributions of the work and present some thoughts on future directions for biomedical event extraction. This thesis includes and builds on six original research publications. The first of these introduces the analysis of dependency parses that leads to development of TEES. The entries in the three BioNLP Shared Tasks, as well as in the DDIExtraction 2011 task are covered in four publications, and the sixth one demonstrates the application of the system to PubMed-scale text mining.

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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.

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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.

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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.

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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.

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Tämän sivuainetutkielman aiheena on pienviljelijäliike. Kysymykseni on, miten pienviljelijäliikettä tuotiin esille Pienviljelijä-lehdessä? Aihetta lähestytään osuustoiminnan ja poliittisuuden kautta. Osuustoiminnan ja poliittisuuden tutkiminen keskittyy tutkimuksessani lehden kyseisistä aiheista käsittelemiin artikkeleihin. Osuustoiminta nähdään tässä tutkimuksessa taloudellisena yhteistoimintana, jossa päämääränä on parantaa siihen osallistuvien taloudellista asemaa. Poliittisuus puolestaan nähdään työväenaatteena, vasemmistolaisuutena. Pienviljelijä on tutkimuksessani itsenäinen maataviljelevä henkilö, joka on torpparivapautuksessa lunastanut muutaman hehtaarin suuruisen maatilan itsensä ja perheensä elatukseen. Olen käyttänyt metodina historiallis-kvalitatiivista eli laadullista tutkimusta pyrkien pelkistämään havaintoja ja sitä kautta ratkaisemaan arvoituksen eli vastaamaan niihin kysymyksiin, joita olen tutkielmalleni asettanut. Tutkimukseni pääasiallinen lähdeaineisto on vuosina 1920—1929 ilmestyneet Pienviljelijä-lehden numerot. Alkuperäisaineiston lisäksi käytän tutkimuskirjallisuutta, josta tärkeimmäksi nousee Arvo Santosen väitöskirja Järjestäytymiskysymys ja pienviljelijäjärjestöjen vakiintuminen Suomessa. Tutkimus maatalouden pienviljelyspoliittisesta murrosvaiheesta 1930-luvun alkuun mennessä. Muuta tutkimuskirjallisuutta olen käyttänyt soveltuvin osin Poliittisuus liittyy tutkimuksessani lehden artikkeleihin, jotka käsittelivät sekä osuus-toimintaa että kunnallis- ja eduskuntavaaleja. Yhteistä molemmissa oli poliittisuuden muuttuminen vuosikymmenen aikana. Vuosikymmenen alussa lehden kannat poliittisuuteen olivat selkeitä, mutta tultaessa vuosikymmenen lopulle niitä pyrittiin häivyttämään ja tilalle tulivat kannanotot, joissa korostettiin pienviljelijäin ammatillisen ja taloudellisen aseman parantamisen merkitystä. Osuustoiminnassa poliittisuus näkyi vaihtoehtona kapitalistiselle talousjärjestelmälle. Osuustoiminnan avulla oli mahdollista saavuttaa sosialistinen järjestelmä. Vaalien alla kirjoittajat olivat huolissaan äänestämisestä ja siitä, että lehden lukijat osasivat valita oikeat ehdokkaat. Alku vuosikymmenellä vaihtoehto ilmaistiin selkeästi, työväen ehdokkaat. Loppuvuosikymmenellä lehdessä ei haluttu selkeästi määrittää ketä tuli äänestää. Lehti ilmoittikin olevansa puolueeton vaalitaisteluiden melskeessä.

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Bumblebees are a very essential group of pollinating insects, but their populations have declined drastically during the past decades. We need to understand why their numbers are decreasing and what can be done to reverse this trend. Climate change-related phenomena, such as changes in the overwintering temperatures and spring conditions, are among the most prominent threats to bumblebees. Queens have a special role in the lifecycle of bumblebees because they overwinter and start new colonies the next year. Their successful performance: survival, overwintering ability, longevity, immune competence, and nest establishing capability in spring, is highly important for bumblebee populations. However, the effects of climate change on bumblebee queen performance remain unknown. The main objective of this thesis was to assess how temperature affects the performance of bumblebee queens during and after overwintering. The effects of warm temperature predicted by climate change scenarios on queen survival and stress-tolerance were studied by a four-month artificial diapause of bumblebee queens at two temperatures (9°C and 1.8°C). Bumblebee colonies were also reared in a laboratory and factors affecting colony characteristics were examined. In addition, queen performance during spring was studied in a starvation experiment using two temperatures (15°C as normal; 24°C as warmer than average) and queens collected from nature right after their emergence. My research revealed how temperature affects queen performance, and queen size was found to be an important factor determining the direction of some of these effects. We found a 0.4g weight threshold for bumblebee queens to be able to survive overwintering. In addition, during mild winters, larger queens have a higher chance than smaller ones to survive through winter and also to cope with immunological stresses after overwintering. During cold conditions, which are normal in the current climatic situation, this advantage disappears. In the spring starvation experiment, the starved queens survived approximately eight days longer in 15°C than in 24°C, which means that starvation risk rises significantly with increasing spring temperature, in a situation where food is scarce due to for example frost damage or asynchrony between bumblebees and their important food plants. These results could mean that in the future climate, larger queens are better able to survive the winter, initiate their nests and start rearing their offspring. This may be problematic, because I also detected two alternative strategies of colony development that differ between large and small queens; larger queens start to lay eggs earlier at nest initiation, their colonies mature later, they produce more workers, and they have a more strongly male biased sex allocation compared with smaller queens. If larger queens have a greater change of producing offspring after a mild winter, this could lead to a significant decline in the total production of new queens at a population level. Thus, it seems that queen size could act as one mechanism regulating the population level outcomes in different temperatures. The new information presented in my thesis reinforces that basic research, monitoring, and local species conservation of bumblebees both in Finland and globally must be increased to ensure that this highly important pollinator group survives in the face of climate change.

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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.

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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.

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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.

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Tässä kandidaatintyössä tutkittiin sähkö- ja hybridiajoneuvojen akkujen uusiokäyttöä. Tutkimus toteutettiin kirjallisuustyönä. Tavoitteena oli selvittää voidaanko sähkö- ja hybridiajoneuvojen akkuja uusiokäyttää, mitä ongelmia mahdollisesti uusiokäyttöön liittyy, minkälaisissa sovelluksissa käytettyjä akkuja voisi käyttää ja uusiokäytetäänkö kyseisenlaisia akkuja jo nykyään. Työssä esiteltiin myös yleisimpiä akkutekniikoita sekä niiden kierrätystä. Tutkimuksessa havaittiin, että akuissa on runsaasti kapasiteettia jäljellä ajoneuvokäytön jälkeen. Uusiokäytössä akku voi kestää jopa yhtä paljon käyttöä kuin ajoneuvokäytössä. Ongelmat uusiokäytössä liittyvät akkujen vaihtelevaan kuntoon ja kapasiteettiin. Ennen uusiokäyttöä akut tulisi tarkastaa ja jos mahdollista, poistaa huonokuntoiset ja vialliset kennot. Käytettyjen akkujen uusiokäyttöön soveltuvista laitteistoista on tehty muutamia prototyyppejä, jotka ovat teholtaan ja kapasiteetiltaan hyvin vaihtelevia. Sopivalla valvontajärjestelmällä varustettuna käytettyjä akkuja voitaneen käyttää myös olemassa olevissa, akkuja sisältävissä järjestelmissä. Käytettyjä akkuja voitaneen käyttää muun muassa uusiutuvan energian varastointiin, sähköverkon kulutushuippujen kompensointiin ja sähköajoneuvojen pikalatauksen puskurina. Etenkin litiumioniakkujen uusiokäyttö on järkevää, koska kierrätys ei ole kovin tehokasta ainakaan vielä.

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Kirjallisuusarvostelu

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Kirjallisuusarvostelu