Mass Spectrometry Informatics in Systems Biology

Mass spectrometry (MS) became a standard tool for identifying metabolites in biological tissues, and metabolomics is slowly acknowledged as a legitimate research discipline for characterizing biological conditions. The computational analyses of metabolomics, however, lag behind compared with the rapid advances in analytical aspects for two reasons. First is the lack of standardized data repository for mass spectra: each research institution is flooded with gigabytes of mass-spectral data from its own analytical groups and cannot host a world-class repository for mass spectra. The second reason is the lack of informatics experts that are fully experienced with spectral analyses. The two barriers must be overcome to establish a publicly free data server for MS analysis in metabolomics as does GenBank in genomics and UniProt in proteomics. The workshop brought together bioinformaticians working on mass spectral analyses in Finland and Japan with the goal to establish a consortium to freely exchange and publicize mass spectra of metabolites measured on various platforms computational tools to analyze spectra spectral knowledge that are computationally predicted from standardized data. This book contains the abstracts of the presentations given in the workshop. The programme of the workshop consisted of oral presentations from Japan and Finland, invited lectures from Steffen Neumann (Leibniz Institute of Plant Biochemistry), Matej Oresic (VTT), Merja Penttila (VTT) and Nicola Zamboni (ETH Zurich) as well as free form discussion among the participants. The event was funded by Academy of Finland (grants 139203 and 118653), Japan Society for the Promotion of Science (JSPS Japan-Finland Bilateral Semi- nar Program 2010) and Department of Computer Science University of Helsinki. We would like to thank all the people contributing to the technical pro- gramme and the sponsors for making the workshop possible. Helsinki, October 2010 Masanori Arita, Markus Heinonen and Juho Rousu

Isomerisations of substituted β-keto-esters - Part II. Isomerisation of ethyl 1-ethoxycarbonyl 2oxocyclopentyl acetate into 2, 3-diethoxycarbonylcyclohexanone

A mechanism for the isomerisation of ethyl 1-ethoxycarbonyl-2-oxocyclopentylacetate (I) into a cyclohexane β-keto-ester as proceeding through an intermediate bicyclic /gb-diketone (VII) has been considered as an alternative mechanism to one earlier suggested.1 The determination of the structure of the isomerised β-keto-ester as 2, 3-diethoxycarbonylcyclohexanone (V) has provided support for the earlier mechanism.

The Philosophical Age. Almanac. Issue 36. The Northern Lights

keywords: Enlightenment, Northern countries, Finland, Russia, Scotland In the 36 th edition of the almanac "Philosophical Age" published materials of international symposium «The Northern Lights - Facets of Enlightenment Culture», (held September 25-26, 2009) in The Aleksanteri Institute the University of Helsinki. Contents: Vesa Oittinen Between Radicalism and Utilitarianism — On the Profile of the Finnish Enlightenment Tatiana Artemyeva The Status of Intellectual Values in the Russian Enlightenment Oili Pulkkinen The Cosmopolitan Experience, Theoretical Histories and the Universal Science of the Scottish Enlightenment Аlla Zlatopolskaya L’autocritique des Lumières chez Rousseau et le rousseauisme russe Johannes Remy Alexander Radishchev, Ethical Consuming, and North American Quakers Kimmo Sarje Anders Chydenius and Radical Swedish Enlightenment Johan Sten Anders Johan Lexell: A Finnish Astronomer at St. Petersburg Academy of Sciences and His European Contacts Mikhail Mikeshin A Russian Adam Smith in French Style: An Example of the Transfer of Ideas Larisa Agamalian The Library of an Enlightened Russian Landowner

Novel Approaches to the Sampling of Atmospheric Aerosols and Determination of Chemical Composition

The Earth s climate is a highly dynamic and complex system in which atmospheric aerosols have been increasingly recognized to play a key role. Aerosol particles affect the climate through a multitude of processes, directly by absorbing and reflecting radiation and indirectly by changing the properties of clouds. Because of the complexity, quantification of the effects of aerosols continues to be a highly uncertain science. Better understanding of the effects of aerosols requires more information on aerosol chemistry. Before the determination of aerosol chemical composition by the various available analytical techniques, aerosol particles must be reliably sampled and prepared. Indeed, sampling is one of the most challenging steps in aerosol studies, since all available sampling techniques harbor drawbacks. In this study, novel methodologies were developed for sampling and determination of the chemical composition of atmospheric aerosols. In the particle-into-liquid sampler (PILS), aerosol particles grow in saturated water vapor with further impaction and dissolution in liquid water. Once in water, the aerosol sample can then be transported and analyzed by various off-line or on-line techniques. In this study, PILS was modified and the sampling procedure was optimized to obtain less altered aerosol samples with good time resolution. A combination of denuders with different coatings was tested to adsorb gas phase compounds before PILS. Mixtures of water with alcohols were introduced to increase the solubility of aerosols. Minimum sampling time required was determined by collecting samples off-line every hour and proceeding with liquid-liquid extraction (LLE) and analysis by gas chromatography-mass spectrometry (GC-MS). The laboriousness of LLE followed by GC-MS analysis next prompted an evaluation of solid-phase extraction (SPE) for the extraction of aldehydes and acids in aerosol samples. These two compound groups are thought to be key for aerosol growth. Octadecylsilica, hydrophilic-lipophilic balance (HLB), and mixed phase anion exchange (MAX) were tested as extraction materials. MAX proved to be efficient for acids, but no tested material offered sufficient adsorption for aldehydes. Thus, PILS samples were extracted only with MAX to guarantee good results for organic acids determined by liquid chromatography-mass spectrometry (HPLC-MS). On-line coupling of SPE with HPLC-MS is relatively easy, and here on-line coupling of PILS with HPLC-MS through the SPE trap produced some interesting data on relevant acids in atmospheric aerosol samples. A completely different approach to aerosol sampling, namely, differential mobility analyzer (DMA)-assisted filter sampling, was employed in this study to provide information about the size dependent chemical composition of aerosols and understanding of the processes driving aerosol growth from nano-size clusters to climatically relevant particles (>40 nm). The DMA was set to sample particles with diameters of 50, 40, and 30 nm and aerosols were collected on teflon or quartz fiber filters. To clarify the gas-phase contribution, zero gas-phase samples were collected by switching off the DMA every other 15 minutes. Gas-phase compounds were adsorbed equally well on both types of filter, and were found to contribute significantly to the total compound mass. Gas-phase adsorption is especially significant during the collection of nanometer-size aerosols and needs always to be taken into account. Other aims of this study were to determine the oxidation products of β-caryophyllene (the major sesquiterpene in boreal forest) in aerosol particles. Since reference compounds are needed for verification of the accuracy of analytical measurements, three oxidation products of β-caryophyllene were synthesized: β-caryophyllene aldehyde, β-nocaryophyllene aldehyde, and β-caryophyllinic acid. All three were identified for the first time in ambient aerosol samples, at relatively high concentrations, and their contribution to the aerosol mass (and probably growth) was concluded to be significant. Methodological and instrumental developments presented in this work enable fuller understanding of the processes behind biogenic aerosol formation and provide new tools for more precise determination of biosphere-atmosphere interactions.

Medium access control schemes for local area networks with multiple priority function

This paper deals with the development and performance evaluation of three modified versions of a scheme proposed for medium access control in local area networks. The original scheme implements a collision-free and fair medium arbitration by using a control wire in conjunction with a data bus. The modifications suggested in this paper are intended to realize the multiple priority function in local area networks.

Process of burnout: structure, antecedents, and consequences

The major changes that have been witnessed in today's workplaces are challenging the mental well-being of employed people. Stress and burnout are considered to be modern epidemics, and their importance to physical health and work ability has been acknowledged world-wide. The aim of the thesis was to study the concept of burnout as a process proceeding from its antecedents, through the development of the syndrome, and to its outcomes. Several work-related factors considered antecedents of burnout were studied in different occupational groups. The syndrome of burnout is seen as consisting of three dimensions - exhaustion, cynicism and lack of professional efficacy - and different alternatives for the sequential development of these dimensions were tested. Furthermore, several indicators of the severely detrimental health and work ability outcomes of burnout were investigated in a longitudinal study design. The research questions were as follows. 1) Is burnout, as measured with the Maslach Burnout Inventory - General Survey (MBI-GS), a three-dimensional construct and how invariant is the factorial structure across occupations (Finnish) and national samples (Finnish, Swedish and Dutch)? How persistent is exhaustion over time? 2) What is the sequential process of burnout? Is it similar across occupations? How do work stressors relate to the process? 3) How does burnout relate to severe health consequences as well as temporary and chronic work disability according to hospitalization periods, sick-leave episodes and receiving disability pensions? The data were collected between 1986 and 2005. The population of the study consisted of respondents to a company-wide questionnaire survey carried out in 1996-1997 (N=9705, response rate 63%). The participants comprised 6025 blue-collar workers and 3680 white-collar workers. The majority were men (N=7494) and the average age was 43.7 years. In addition, a sample from the population had responded to a questionnaire survey in 1988, which was combined with the 1996 data to form panel data on 713 respondents. The register-based data were collected between 1986 and 2005 from 1) the company's occupational health services' records for a sample of respondents from the 1996 questionnaire survey (sick-leave data), 2) hospitalization records from the Hospital discharge register, and 3) disability pension records from the Finnish Centre for Pensions. These data were combined person by person with the 1996 questionnaire survey data with the help of personal identification numbers which were saved with the study numbers by the researchers. The results showed that burnout consists of three separate but correlating symptoms: exhaustion, cynicism and lack of professional efficacy. As a syndrome, burnout was strongly related to job stressors at work, and seemed to develop from exhaustion through cynicism to lack of professional efficacy in a similar manner among white-collar and blue-collar employees. The results also showed that exhaustion persisted even after eight years of follow-up but did not predict cynicism or lack of professional efficacy after that amount of time. Nor were job stressors longitudinally related to burnout. Longitudinal results were obtained for the severe health-related consequences of burnout. The investigated outcomes represented different phases of health deterioration ranging from sick-leaves and hospitalization periods to receiving work disability pensions. The results showed that burnout syndrome, and its elements of exhaustion and cynicism, were related to future mental and cardiovascular disorders as indicated by hospitalization periods. Burnout was also related to future sick-leave periods due to mental, cardiovascular and musculoskeletal disorders. Of the separate elements, exhaustion was related to the same three categories of disorder, cynicism to mental, musculoskeletal and digestive disorders, and lack of professional efficacy to mental and musculoskeletal disorders. Burnout also predicted receiving disability pensions due to mental and musculoskeletal disorders among initially healthy subjects. Exhaustion was related to receiving disability pensions even when self-reported chronic illness was taken into account. The results suggest that burnout is a multidimensional, chronic, work-related syndrome, which may have serious consequences for health and work ability.

Fuzzy Coherence: Making Sense of Continuity in Hypertext Narratives

Hypertexts are digital texts characterized by interactive hyperlinking and a fragmented textual organization. Increasingly prominent since the early 1990s, hypertexts have become a common text type both on the Internet and in a variety of other digital contexts. Although studied widely in disciplines like hypertext theory and media studies, formal linguistic approaches to hypertext continue to be relatively rare. This study examines coherence negotiation in hypertext with particularly reference to hypertext fiction. Coherence, or the quality of making sense, is a fundamental property of textness. Proceeding from the premise that coherence is a subjectively evaluated property rather than an objective quality arising directly from textual cues, the study focuses on the processes through which readers interact with hyperlinks and negotiate continuity between hypertextual fragments. The study begins with a typological discussion of textuality and an overview of the historical and technological precedents of modern hypertexts. Then, making use of text linguistic, discourse analytical, pragmatic, and narratological approaches to textual coherence, the study takes established models developed for analyzing and describing conventional texts, and examines their applicability to hypertext. Primary data derived from a collection of hyperfictions is used throughout to illustrate the mechanisms in practice. Hypertextual coherence negotiation is shown to require the ability to cognitively operate between local and global coherence by means of processing lexical cohesion, discourse topical continuities, inferences and implications, and shifting cognitive frames. The main conclusion of the study is that the style of reading required by hypertextuality fosters a new paradigm of coherence. Defined as fuzzy coherence, this new approach to textual sensemaking is predicated on an acceptance of the coherence challenges readers experience when the act of reading comes to involve repeated encounters with referentially imprecise hyperlinks and discourse topical shifts. A practical application of fuzzy coherence is shown to be in effect in the way coherence is actively manipulated in hypertext narratives.

Analysis of Nonlinear Optical Properties of Photonic Crystal Beam-splitters

The paper analyses electromagnetic wave propagation through nonlinear photonic crystal beam-splitters. Different lattice configurations of Y-junction beam-splitters are simulated and propagation properties are investigated with introducing nonlinearity with varying the rod size in crystal lattice. It is seen that nonlinear photonic crystal shows a considerable band-gap even at low refractive contrast. The division of power in both arms of beam-splitters can be controlled by varying the nonlinearity.

Näkemyksiä käsityöopetuksen kehitystarpeista yhtenäisessä perusopetuksessa

The objective of this study was to find out what development targets craft teachers could identify in the comprehensive school classes 1 through 9 after the curriculum of the year 2004 had declared craft education uniform in textile and technical craft. Earlier research had shown that after this curricular reform craft education had been carried out in dissimilar ways in different municipalities and schools. This causes differences in the contents of teaching and thus in learning outcomes on national level. The most problematic situations occur on the 7th grade when the classes contain pupils with very heterogeneous skill levels. My intention is to find general themes in craft education that are significant when considering developmental objectives. The problem was explored by four research questions as follows: What kind of problems have craft teachers confronted during the application of the curriculum 2004, what are the most important objectives and contents in craft for the comprehensive school, how craft education should be arranged in the future and what prerequisites should be considered to generate high quality craft education? The study was carried out by a qualitative research approach. The informants consisted of 21 persons, out of which 15 were textile or technical teachers and six were textile or technical teacher students. The research data was collected in the form of short open narratives, based on a partially structured inquiry. Respectively content analysis was applied for analysis of the narratives. Research results revealed that craft teachers were mainly satisfied in uniform craft and hoped that both textile and technical craft could be compulsory school subjects for both genders. Textile and technical craft should be defined as separate independent school subjects, both of which should be developed with broader and high quality contents. Craft subjects should be allocated more teaching time. Teachers asked for a more logically proceeding curriculum, initiating from the beginning to the end of the compulsory school. It was suggested that this could be done by a qualified subject teacher. A uniform curriculum solution must be found for the whole country.

Helsingin kävelykeskustan suunnittelu ydinkeskustan kadunvarsiliikeyrittäjien näkökulmasta

Aiempien tutkimusten mukaan keskustayrittäjien kielteinen asenne on olennaisesti vaikeuttanut kävelykatujen toteuttamista kaupunkikeskustoissa. Yrittäjät pelkäävät ostokykyisten asiakkaiden kaikkoavan ja liikevaihtonsa pienenevän kävelykeskustauudistusten myötä. Yrittäjien kielteiset asenteet ovat usein myös painottuneet suuriin kaupunkeihin. Etenkin ydinkeskustassa sijaitsevat kadunvarsiliikeyrittäjät ovat kokeneet kävelykadut ongelmiksi. Tämän tutkimuksen tavoitteena on selvittää, mikä on ydinkeskustan kadunvarsiliikeyrittäjien näkemys Helsingin kävelykeskustan suunnittelusta, millaisena ydinkeskustan kadunvarsiliikeyrittäjät näkevät sijaintikatunsa kävelykeskustan suunnittelupäämäärien kautta tarkasteltuna, ja onko kävelykatuyrittäjien ja kävelykatujen ulkopuolella sijaitsevien yrittäjien näkemysten välillä eroja. Taustana tälle tarkastellaan Helsingin kävelykeskustaa pohjoismaisessa kontekstissa, ja käydään läpi Helsingin kävelykeskustan suunnittelun ja rakentumisen historiaa ja päämääriä. Tutkimuksen aineisto koostuu Helsingin ydinkeskustan kadunvarsiliikeyrittäjille tehdystä kyselystä, kävelykeskustoihin liittyvistä tutkimuksista ja selvityksistä, kaupunkisuunnitteluun ja -tutkimukseen liittyvästä tutkimuskirjallisuudesta, sanomalehtiartikkeleista, ydinkeskustassa tehdystä empiirisestä havainnoinnista ja kahdesta asiantuntijahaastattelusta. Kyselyaineistoa analysoidaan tutkimuksessa tilastollisten menetelmien avulla. Helsingin kävelykeskustan suunnittelu ja rakentuminen on ollut pitkällinen prosessi. Vuoden 1 989 kävelykeskustan periaatesuunnitelmasta on konkretisoitunut Kluuvikatu ja Mikonkatu. Keskustatunnelihanke on vaakalaudalla, minkä vuoksi kävelykeskustan uuden periaatesuunnitelman toteutuminen on epävarmaa. Kävelykeskustan rakentuminen kuitenkin etenee. Keskuskatu ja Kalevankadun itäpää muutetaan kävelykaduiksi ja ydinkeskustan jalankulkuympäristöä parannetaan ja kehitetään jatkuvasti. Tällä hetkellä kävelykeskustan suunnittelun painopiste on Aleksanterinkadun kortteleiden ympäristössä, ja suunnittelun tärkeimpiä päämääriä ovat viihtyisyyden, turvallisuuden, kaupallisen vetovoimaisuuden ja saavutettavuuden parantaminen. Kyselyyn vastanneiden yrittäjien mielestä kävelykeskustaa tulisi laajentaa, sillä laajemman kävelykeskustan nähdään kasvattavan liikevaihtoa ja lisäävän yleisesti ydinkeskustan vetovoimaa. Kävelykatuyrittäjien näkemykset kävelykeskustan suunnittelusta ja kehittämisestä olivat kävelykatujen ulkopuolisia yrittäjiä kielteisempiä. Em. yrittäjien asenteisiin vaikuttavat oletettavasti tutkituilla kävelykaduilla ilmenneet ongelmat. Kyse voi myös olla siitä, että uusien kävelykatujen rakentaminen haittaa kävelykatujen saavutettavuutta. Kadunvarsiliikeyrittäjien yleinen suhtautuminen kävelykeskustan kehittämiseen ja suunnittelupäämääriin on kuitenkin pääosin positiivista. Jatkotutkimuksen kannalta olisi kiinnostavaa selvittää, onko muiden ydinkeskustassa toimivien yritysten, kuten esimerkiksi tavaratalojen ja kauppakeskusten johdon ja kiinteistösijoittajien ja -omistajien suhtautuminen kävelykeskustan kehittämiseen myös positiivista. Tämän lisäksi olisi mielenkiintoista selvittää keskustan käyttäjien ja keskustassa asuvien asenteita kävelykeskustan suunnitteluun, ja verrata tuloksia tässä tutkimuksessa selvitettyihin kadunvarsiliikeyrittäjien näkemyksiin.

A new approach to the design of electronic exchanges

Electronic Exchanges are double-sided marketplaces that allows multiple buyers to trade with multiple sellers, with aggregation of demand and supply across the bids to maximize the revenue in the market. In this paper, we propose a new design approach for an one-shot exchange that collects bids from buyers and sellers and clears the market at the end of the bidding period. The main principle of the approach is to decouple the allocation from pricing. It is well known that it is impossible for an exchange with voluntary participation to be efficient and budget-balanced. Budget-balance is a mandatory requirement for an exchange to operate in profit. Our approach is to allocate the trade to maximize the reported values of the agents. The pricing is posed as payoff determination problem that distributes the total payoff fairly to all agents with budget-balance imposed as a constraint. We devise an arbitration scheme by axiomatic approach to solve the payoff determination problem using the added-value concept of game theory.

A Multi-layer Perceptron based Non-linear Mixture Model to estimate class abundance from mixed pixels

Sub-pixel classification is essential for the successful description of many land cover (LC) features with spatial resolution less than the size of the image pixels. A commonly used approach for sub-pixel classification is linear mixture models (LMM). Even though, LMM have shown acceptable results, pragmatically, linear mixtures do not exist. A non-linear mixture model, therefore, may better describe the resultant mixture spectra for endmember (pure pixel) distribution. In this paper, we propose a new methodology for inferring LC fractions by a process called automatic linear-nonlinear mixture model (AL-NLMM). AL-NLMM is a three step process where the endmembers are first derived from an automated algorithm. These endmembers are used by the LMM in the second step that provides abundance estimation in a linear fashion. Finally, the abundance values along with the training samples representing the actual proportions are fed to multi-layer perceptron (MLP) architecture as input to train the neurons which further refines the abundance estimates to account for the non-linear nature of the mixing classes of interest. AL-NLMM is validated on computer simulated hyperspectral data of 200 bands. Validation of the output showed overall RMSE of 0.0089±0.0022 with LMM and 0.0030±0.0001 with the MLP based AL-NLMM, when compared to actual class proportions indicating that individual class abundances obtained from AL-NLMM are very close to the real observations.