Avoimet julkaisuarkistot ja niiden tekniikka

Open Access -liike pyrkii vapauttamaan tieteellisen tiedon kaupallisuuden rajoitteista edesauttamalla artikkeleiden rinnakkaisversioiden avointa ja esteetöntä verkkotallennusta. Sen mahdollistamiseksi verkkoon perustetaan julkaisuarkistoja, joiden toiminta-ajatuksena on säilöä taustayhteisönsä tieteellinen tuotanto avoimesti ja keskitetysti yhteen paikkaan. Avoimen lähdekoodin arkistosovellukset jakavat sisältönsä OAI-protokollan avulla ja muodostavat näin globaalin virtuaalisen tietoverkon. Suurten tietomäärien käsittelyssä on huomioitava erityisesti kuvailutiedon rooli tehokkaiden hakujen toteuttamisessa sekä tiedon yksilöiminen verkossa erilaisten pysyvien tunnisteiden, kuten Handle:n tai URN:n avulla. Tieteellisen tiedon avoimella saatavuudella on merkittävä vaikutus myös oppimisen näkökulmasta. Julkaisuarkistot tarjoavat oppimateriaalin lisäksi uusia mahdollisuuksia julkaisukanavan ja oppimisymp äristön integroimiseen. Työssä esitellään avoimen saatavuuden keskeisiä teemoja sekä sen käytännön toteutusta varten kehitettyjä teknisiä ratkaisuja. Näiden pohjalta toteutetaan Meilahden kampuksen avoin julkaisuarkisto. Työssä pohditaan myös julkaisuarkistojen soveltuvuutta oppimisprosessin tukemiseen tutkivan- ja sulautuvan oppimisen viitekehyksessä. ACM Computing Classification System (CCS): H.3 [INFORMATION STORAGE AND RETRIEVAL], H.3.7 [Digital Libraries], H.3.3 [Information Search and Retrieval], H.3.5 [Online Information Services], K.3 [COMPUTERS AND EDUCATION], K.3.1 [Computer Uses in Education]

Remote sensing of leaf area index: enhanced retrieval from close-range and remotely sensed optical observations

A wide range of models used in agriculture, ecology, carbon cycling, climate and other related studies require information on the amount of leaf material present in a given environment to correctly represent radiation, heat, momentum, water, and various gas exchanges with the overlying atmosphere or the underlying soil. Leaf area index (LAI) thus often features as a critical land surface variable in parameterisations of global and regional climate models, e.g., radiation uptake, precipitation interception, energy conversion, gas exchange and momentum, as all areas are substantially determined by the vegetation surface. Optical wavelengths of remote sensing are the common electromagnetic regions used for LAI estimations and generally for vegetation studies. The main purpose of this dissertation was to enhance the determination of LAI using close-range remote sensing (hemispherical photography), airborne remote sensing (high resolution colour and colour infrared imagery), and satellite remote sensing (high resolution SPOT 5 HRG imagery) optical observations. The commonly used light extinction models are applied at all levels of optical observations. For the sake of comparative analysis, LAI was further determined using statistical relationships between spectral vegetation index (SVI) and ground based LAI. The study areas of this dissertation focus on two regions, one located in Taita Hills, South-East Kenya characterised by tropical cloud forest and exotic plantations, and the other in Gatineau Park, Southern Quebec, Canada dominated by temperate hardwood forest. The sampling procedure of sky map of gap fraction and size from hemispherical photographs was proven to be one of the most crucial steps in the accurate determination of LAI. LAI and clumping index estimates were significantly affected by the variation of the size of sky segments for given zenith angle ranges. On sloping ground, gap fraction and size distributions present strong upslope/downslope asymmetry of foliage elements, and thus the correction and the sensitivity analysis for both LAI and clumping index computations were demonstrated. Several SVIs can be used for LAI mapping using empirical regression analysis provided that the sensitivities of SVIs at varying ranges of LAI are large enough. Large scale LAI inversion algorithms were demonstrated and were proven to be a considerably efficient alternative approach for LAI mapping. LAI can be estimated nonparametrically from the information contained solely in the remotely sensed dataset given that the upper-end (saturated SVI) value is accurately determined. However, further study is still required to devise a methodology as well as instrumentation to retrieve on-ground green leaf area index . Subsequently, the large scale LAI inversion algorithms presented in this work can be precisely validated. Finally, based on literature review and this dissertation, potential future research prospects and directions were recommended.

Optical Studies of the Antarctic Glacio-Oceanic System

The Antarctic system comprises of the continent itself, Antarctica, and the ocean surrounding it, the Southern Ocean. The system has an important part in the global climate due to its size, its high latitude location and the negative radiation balance of its large ice sheets. Antarctica has also been in focus for several decades due to increased ultraviolet (UV) levels caused by stratospheric ozone depletion, and the disintegration of its ice shelves. In this study, measurements were made during three Austral summers to study the optical properties of the Antarctic system and to produce radiation information for additional modeling studies. These are related to specific phenomena found in the system. During the summer of 1997-1998, measurements of beam absorption and beam attenuation coefficients, and downwelling and upwelling irradiance were made in the Southern Ocean along a S-N transect at 6°E. The attenuation of photosynthetically active radiation (PAR) was calculated and used together with hydrographic measurements to judge whether the phytoplankton in the investigated areas of the Southern Ocean are light limited. By using the Kirk formula the diffuse attenuation coefficient was linked to the absorption and scattering coefficients. The diffuse attenuation coefficients (Kpar) for PAR were found to vary between 0.03 and 0.09 1/m. Using the values for KPAR and the definition of the Sverdrup critical depth, the studied Southern Ocean plankton systems were found not to be light limited. Variabilities in the spectral and total albedo of snow were studied in the Queen Maud Land region of Antarctica during the summers of 1999-2000 and 2000-2001. The measurement areas were the vicinity of the South African Antarctic research station SANAE 4, and a traverse near the Finnish Antarctic research station Aboa. The midday mean total albedos for snow were between 0.83, for clear skies, and 0.86, for overcast skies, at Aboa and between 0.81 and 0.83 for SANAE 4. The mean spectral albedo levels at Aboa and SANAE 4 were very close to each other. The variations in the spectral albedos were due more to differences in ambient conditions than variations in snow properties. A Monte-Carlo model was developed to study the spectral albedo and to develop a novel nondestructive method to measure the diffuse attenuation coefficient of snow. The method was based on the decay of upwelling radiation moving horizontally away from a source of downwelling light. This was assumed to have a relation to the diffuse attenuation coefficient. In the model, the attenuation coefficient obtained from the upwelling irradiance was higher than that obtained using vertical profiles of downwelling irradiance. The model results were compared to field measurements made on dry snow in Finnish Lapland and they correlated reasonably well. Low-elevation (below 1000 m) blue-ice areas may experience substantial melt-freeze cycles due to absorbed solar radiation and the small heat conductivity in the ice. A two-dimensional (x-z) model has been developed to simulate the formation and water circulation in the subsurface ponds. The model results show that for a physically reasonable parameter set the formation of liquid water within the ice can be reproduced. The results however are sensitive to the chosen parameter values, and their exact values are not well known. Vertical convection and a weak overturning circulation is generated stratifying the fluid and transporting warmer water downward, thereby causing additional melting at the base of the pond. In a 50-year integration, a global warming scenario mimicked by a decadal scale increase of 3 degrees per 100 years in air temperature, leads to a general increase in subsurface water volume. The ice did not disintegrate due to the air temperature increase after the 50 year integration.

Storage and retrieval of individual genomes

A repetitive sequence collection is one where portions of a base sequence of length n are repeated many times with small variations, forming a collection of total length N. Examples of such collections are version control data and genome sequences of individuals, where the differences can be expressed by lists of basic edit operations. Flexible and efficient data analysis on a such typically huge collection is plausible using suffix trees. However, suffix tree occupies O(N log N) bits, which very soon inhibits in-memory analyses. Recent advances in full-text self-indexing reduce the space of suffix tree to O(N log σ) bits, where σ is the alphabet size. In practice, the space reduction is more than 10-fold, for example on suffix tree of Human Genome. However, this reduction factor remains constant when more sequences are added to the collection. We develop a new family of self-indexes suited for the repetitive sequence collection setting. Their expected space requirement depends only on the length n of the base sequence and the number s of variations in its repeated copies. That is, the space reduction factor is no longer constant, but depends on N / n. We believe the structures developed in this work will provide a fundamental basis for storage and retrieval of individual genomes as they become available due to rapid progress in the sequencing technologies.

Information Technology in Construction – Domain Definition and Research Issues

This article discusses the scope of research on the application of information technology in construction (ITC). A model of the information and material activities which together constitute the construction process is presented, using the IDEF0 activity modelling methodology. Information technology is defined to include all kinds of technology used for the storage, transfer and manipulation of information, thus also including devices such as copying machines, faxes and mobile phones. Using the model the domain of ITC research is defined as the use of information technology to facilitate and re-engineer the information process component of construction. Developments during the last decades in IT use in construction is discussed against a background of a simplified model of generic information processing tasks. The scope of ITC is compared with the scopes of research in related areas such as design methodology, construction management and facilities management. Health care is proposed as an interesting alternative (to the often used car manufacturing industry), as an IT application domain to compare with. Some of the key areas of ITC research in recent years; expert systems, company IT strategies, and product modelling are shortly discussed. The article finishes with a short discussion of the problems of applying standard scientific methodology in ITC research, in particular in product model research.

Lyophilized disaccharides – the effect of water during storage

Nearly one fourth of new medicinal molecules are biopharmaceutical (protein, antibody or nucleic acid derivative) based. However, the administration of these compounds is not always that straightforward due to the fragile nature of aforementioned domains in GI-tract. In addition, these molecules often exhibit poor bioavailability when administered orally. As a result, parenteral administration is commonly preferred. In addition, shelf-life of these molecules in aqueous environments is poor, unless stored in low temperatures. Another approach is to bring these molecules to anhydrous form via lyophilization resulting in enhanced stability during storage. Proteins cannot most commonly be freeze dried by themselves so some kind of excipients are nearly always necessary. Disaccharides are commonly utilized excipients in freeze-dried formulations since they provide a rigid glassy matrix to maintain the native conformation of the protein domain. They also act as "sink"-agents, which basically mean that they can absorb some moisture from the environment and still help to protect the API itself to retain its activity and therefore offer a way to robust formulation. The aim of the present study was to investigate how four amorphous disaccharides (cellobiose, melibiose, sucrose and trehalose) behave when they are brought to different relative humidity levels. At first, solutions of each disaccharide were prepared, filled into scintillation vials and freeze dried. Initial information on how the moisture induced transformations take place, the lyophilized amorphous disaccharide cakes were placed in vacuum desiccators containing different relative humidity levels for defined period, after which selected analyzing methods were utilized to further examine the occurred transformations. Affinity to crystallization, water sorption of the disaccharides, the effect of moisture on glass transition and crystallization temperature were studied. In addition FT-IR microscopy was utilized to map the moisture distribution on a piece of lyophilized cake. Observations made during the experiments backed up the data mentioned in a previous study: melibiose and trehalose were shown to be superior over sucrose and cellobiose what comes to the ability to withstand elevated humidity and temperature, and to avoid crystallization with pharmaceutically relevant moisture contents. The difference was made evident with every utilized analyzing method. In addition, melibiose showed interesting anomalies during DVS runs, which were absent with other amorphous disaccharides. Particularly fascinating was the observation made with polarized light microscope, which revealed a possible small-scale crystallization that cannot be observed with XRPD. As a result, a suggestion can safely be made that a robust formulation is most likely obtained by utilizing either melibiose or trehalose as a stabilizing agent for biopharmaceutical freeze-dried formulations. On the other hand, more experiments should be conducted to obtain more accurate information on why these disaccharides have better tolerance for elevating humidities than others.

Water quality estimation by optical remote sensing in boreal lakes

In lake-rich regions, the gathering of information about water quality is challenging because only a small proportion of the lakes can be assessed each year by conventional methods. One of the techniques for improving the spatial and temporal representativeness of lake monitoring is remote sensing from satellites and aircrafts. The experimental material included detailed optical measurements in 11 lakes, air- and spaceborne remote sensing measurements with concurrent field sampling, automatic raft measurements and a national dataset of routine water quality measurements from over 1100 lakes. The analyses of the spatially high-resolution airborne remote sensing data from eutrophic and mesotrophic lakes showed that one or a few discrete water quality observations using conventional monitoring can yield a clear over- or underestimation of the overall water quality in a lake. The use of TM-type satellite instruments in addition to routine monitoring results substantially increases the number of lakes for which water quality information can be obtained. The preliminary results indicated that coloured dissolved organic matter (CDOM) can be estimated with TM-type satellite instruments, which could possibly be utilised as an aid in estimating the role of lakes in global carbon budgets. Based on the results of reflectance modelling and experimental data, MERIS satellite instrument has optimal or near-optimal channels for the estimation of turbidity, chlorophyll a and CDOM in Finnish lakes. MERIS images with a 300 m spatial resolution can provide water quality information in different parts of large and medium-sized lakes, and in filling in the gaps resulting from conventional monitoring. Algorithms that would not require simultaneous field data for algorithm training would increase the amount of remote sensing-based information available for lake monitoring. The MERIS Boreal Lakes processor, trained with the optical data and concentration ranges provided by this study, enabled turbidity estimations with good accuracy without the need for algorithm correction with field measurements, while chlorophyll a and CDOM estimations require further development of the processor. The accuracy of interpreting chlorophyll a via semi empirical algorithms can be improved by classifying lakes prior to interpretation according to their CDOM level and trophic status. Optical modelling indicated that the spectral diffuse attenuation coefficient can be estimated with reasonable accuracy from the measured water quality concentrations. This provides more detailed information on light attenuation from routine monitoring measurements than is available through the Secchi disk transparency. The results of this study improve the interpretation of lake water quality by remote sensing and encourage the use of remote sensing in lake monitoring.