Urban energy fluxes in Helsinki and their high frequency spectral corrections

Inadvertent climate modification has led to an increase in urban temperatures compared to the surrounding rural area. The main reason for the temperature rise is the altered energy portioning of input net radiation to heat storage and sensible and latent heat fluxes in addition to the anthropogenic heat flux. The heat storage flux and anthropogenic heat flux have not yet been determined for Helsinki and they are not directly measurable. To the contrary, turbulent fluxes of sensible and latent heat in addition to net radiation can be measured, and the anthropogenic heat flux together with the heat storage flux can be solved as a residual. As a result, all inaccuracies in the determination of the energy balance components propagate to the residual term and special attention must be paid to the accurate determination of the components. One cause of error in the turbulent fluxes is the fluctuation attenuation at high frequencies which can be accounted for by high frequency spectral corrections. The aim of this study is twofold: to assess the relevance of high frequency corrections to water vapor fluxes and to assess the temporal variation of the energy fluxes. Turbulent fluxes of sensible and latent heat have been measured at SMEAR III station, Helsinki, since December 2005 using the eddy covariance technique. In addition, net radiation measurements have been ongoing since July 2007. The used calculation methods in this study consist of widely accepted eddy covariance data post processing methods in addition to Fourier and wavelet analysis. The high frequency spectral correction using the traditional transfer function method is highly dependent on relative humidity and has an 11% effect on the latent heat flux. This method is based on an assumption of spectral similarity which is shown not to be valid. A new correction method using wavelet analysis is thus initialized and it seems to account for the high frequency variation deficit. Anyhow, the resulting wavelet correction remains minimal in contrast to the traditional transfer function correction. The energy fluxes exhibit a behavior characteristic for urban environments: the energy input is channeled to sensible heat as latent heat flux is restricted by water availability. The monthly mean residual of the energy balance ranges from 30 Wm-2 in summer to -35 Wm-2 in winter meaning a heat storage to the ground during summer. Furthermore, the anthropogenic heat flux is approximated to be 50 Wm-2 during winter when residential heating is important.

Role of heat treatment in the processing and quality of oat flakes

This thesis reports on investigations into the influence of heat treatment on the manufacturing of oat flakes. Sources of variation in the oat flake quality are reviewed, including the whole chain from the farm to the consumer. The most important quality parameters of oat flakes are the absence of lipid hydrolysing enzymes, specific weight, thickness, breakage (fines), water absorption. Flavour, colour and pasting properties are also important, but were not included in the experimental part of this study. Of particular interest was the role of heat processing. The first possible heat treatment may occur already during grain drying, which in Finland generally happens at the farm. At the mill, oats are often kilned to stabilise the product by inactivating lipid hydrolysing enzymes. Almost invariably steaming is used during flaking, to soften the groats and reduce flake breakage. This thesis presents the use of a material science approach to investigating a complex system, typical of food processes. A combination of fundamental and empirical rheological measurements was used together with a laboratory scale process to simulate industrial processing. The results were verified by means of industrial trials. Industrially produced flakes at three thickness levels (nominally 0.75, 0.85 and 0.90 mm) were produced from kilned and unkilned oat groats, and the flake strength was measured at different moisture contents. Kilning was not found to significantly affect the force required to puncture a flake with a 2mm cylindrical probe, which was taken as a measure of flake strength. To further investigate how heat processing contributes to flake quality, dynamic mechanical analysis was used to characterise the effect of heat on the mechanical properties of oats. A marked stiffening of the groat, of up to about 50% increase in storage modulus, was observed during first heating at around 36 to 57°C. This was also observed in tablets prepared from ground groats and extracted oat starch. This stiffening was thus attributed to increased adhesion between starch granules. Groats were steamed in a laboratory steamer and were tempered in an oven at 80 110°C for 30 90 min. The maximum force required to compress the steamed groats to 50% strain increased from 50.7 N to 57.5 N as the tempering temperature was increased from 80 to 110°C. Tempering conditions also affected water absorption. A significantly higher moisture content was observed for kilned (18.9%) compared to unkilned (17.1%) groats, but otherwise had no effect on groat height, maximum force or final force after a 5 s relaxation time. Flakes were produced from the tempered groats using a laboratory flaking machine, using a roll gap of 0.4 mm. Apart from specific weight, flake properties were not influenced by kilning. Tempering conditions however had significant effects on the specific weight, thickness and water absorption of the flakes, as well as on the amount of fine material (<2 mm) produced during flaking. Flake strength correlated significantly with groat strength and flake thickness. Trial flaking at a commercial mill confirmed that groat temperature after tempering influenced water absorption. Variation in flake strength was observed , but at the groat temperatures required to inactivate lipase, it was rather small. Cold flaking of groats resulted in soft, floury flakes. The results presented in this thesis suggest that heating increased the adhesion between starch granules. This resulted in an increase in the stiffness and brittleness of the groat. Brittle fracture, rather than plastic flow, during flaking could result in flaws and cracks in the flake. These would be expected to increase water absorption. This was indeed observed as tempering temperature increased. Industrial trials, conducted with different groat temperatures, confirmed the main findings of the laboratory experiments. The approach used in the present study allowed the systematic study of the effect of interacting process parameters on product quality. There have been few scientific studies of oat processing, and these results can be used to understand the complex effects of process variables on flake quality. They also offer an insight into what happens as the oat groat is deformed into a flake.

Assessment and control of Bacillus cereus emetic toxin in food

Despite of improving levels of hygiene, the incidence of registered food borne disease has been at the same level for many years: there were 40 to 90 epidemics in which 1000-9000 persons contracted food poisoning through food or drinking water in Finland. Until the year 2004 salmonella and campylobacter were the most common bacterial causes of food borne diseases, but in years 2005-2006 Bacillus cereus was the most common. Similar developement has been published i.e. in Germany already in the 1990´s. One reason for this can be Bacillus cereus and its emetic toxin, cereulide. Bacillus cereus is a common environmental bacterium that contaminates raw materials of food. Otherwise than salmonella and campylobacter, Bacillus cereus is a heat resistant bacterium, capable of surviving most cooking procedures due to the production of highly thermo resistant spores. The food involved has usually been heat treated and surviving spores are the source of the food poisoning. The heat treatment induces germination of the spore and the vegetative cells then produce toxins. This doctoral thesis research focuses on developing methods for assessing and eliminating risks to food safety by cereulide producing Bacillus cereus. The biochemistry and physiology of cereulide production was investigated and the results were targeted to offer tools for minimizing toxin risk in food during the production. I developed methods for the extraction and quantitative analysis of cereulide directly from food. A prerequisite for that is knowledge of the chemical and physical properties of the toxin. Because cereulide is practically insoluble in water, I used organic solvents; methanol, ethanol and pentane for the extraction. For extraction of bakery products I used high temperature (100C) and pressure (103.4 bars). Alternaties for effective extraction is to flood the plain food with ethanol, followed by stationary equilibration at room temperature. I used this protocol for extracting cereulide from potato puree and penne. Using this extraction method it is also possible also extract cereulide from liquid food, like milk. These extraction methods are important improvement steps for studying of Bacillus cereus emetic food poisonings. Prior my work, cereulide extraction was done using water. As the result, the yield was poor and variable. To investigate suspected food poisonings, it is important to show actual toxicity of the incriminated food. Many toxins, but not cereulide, inactivate during food processing like heating. The next step is to identify toxin by chemical methods. I developed with my colleague Maria Andesson a rapid assay for the detection of cereulide toxicity, within 5 to 15 minutes. By applying this test it is possible to rapidly detect which food was causing the food poisoning. The chemical identification of cereulide was achieved using mass spectrometry. I used cereulide specific molecular ions, m/z (+/-0.3) 1153.8 (M+H+), 1171.0 (M+NH4+), 1176.0 (M+Na+) and 1191.7 (M+K+) for reliable identification. I investigated foods to find out their amenability to accumulate cereulide. Cereulide was formed high amounts (0.3 to 5.5 microg/g wet wt) when of cereulide producing B. cereus strains were present in beans, rice, rice-pastry and meat-pastry, if stored at non refrigerated temperatures (21-23C). Rice and meat pastries are frequently consumed under conditions where no cooled storage is available e.g. picnics and outdoor events. Bacillus cereus is a ubiquitous spore former and is therefore difficult to eliminate from foods. It is therefore important to know which conditions will affect the formation of cereulide in foods. My research showed that the cereulide content was strongly (10 to 1000 fold differences in toxin content) affected by the growth environment of the bacterium. Storage of foods under nitrogen atmosphere (> 99.5 %) prevented the production of cereulide. But when also carbon dioxide was present, minimizing the oxygen contant (< 1%) did not protect the food from formation of cereulide in preliminary experiments. Also food supplements affected cereulide production at least in the laboratory. Adding free amino acids, leucine and valine, stimulated cereulide production 10 to 20 fold. In peptide bonded form these amino acids are natural constituents in all proteins. Interestingly, adding peptide bonded leucine and valine had no significant effect on cereulide production. Free amino acids leucine and valine are approved food supplements and widely used as flawour modifiers in food technology. My research showed that these food supplements may increase food poisoning risk even though they are not toxic themselves.

Oxidative stability of phytosterols in food models and foods

An important safety aspect to be considered when foods are enriched with phytosterols and phytostanols is the oxidative stability of these lipid compounds, i.e. their resistance to oxidation and thus to the formation of oxidation products. This study concentrated on producing scientific data to support this safety evaluation process. In the absence of an official method for analyzing of phytosterol/stanol oxidation products, we first developed a new gas chromatographic - mass spectrometric (GC-MS) method. We then investigated factors affecting these compounds' oxidative stability in lipid-based food models in order to identify critical conditions under which significant oxidation reactions may occur. Finally, the oxidative stability of phytosterols and stanols in enriched foods during processing and storage was evaluated. Enriched foods covered a range of commercially available phytosterol/stanol ingredients, different heat treatments during food processing, and different multiphase food structures. The GC-MS method was a powerful tool for measuring the oxidative stability. Data obtained in food model studies revealed that the critical factors for the formation and distribution of the main secondary oxidation products were sterol structure, reaction temperature, reaction time, and lipid matrix composition. Under all conditions studied, phytostanols as saturated compounds were more stable than unsaturated phytosterols. In addition, esterification made phytosterols more reactive than free sterols at low temperatures, while at high temperatures the situation was the reverse. Generally, oxidation reactions were more significant at temperatures above 100°C. At lower temperatures, the significance of these reactions increased with increasing reaction time. The effect of lipid matrix composition was dependent on temperature; at temperatures above 140°C, phytosterols were more stable in an unsaturated lipid matrix, whereas below 140°C they were more stable in a saturated lipid matrix. At 140°C, phytosterols oxidized at the same rate in both matrices. Regardless of temperature, phytostanols oxidized more in an unsaturated lipid matrix. Generally, the distribution of oxidation products seemed to be associated with the phase of overall oxidation. 7-ketophytosterols accumulated when oxidation had not yet reached the dynamic state. Once this state was attained, the major products were 5,6-epoxyphytosterols and 7-hydroxyphytosterols. The changes observed in phytostanol oxidation products were not as informative since all stanol oxides quantified represented hydroxyl compounds. The formation of these secondary oxidation products did not account for all of the phytosterol/stanol losses observed during the heating experiments, indicating the presence of dimeric, oligomeric or other oxidation products, especially when free phytosterols and stanols were heated at high temperatures. Commercially available phytosterol/stanol ingredients were stable during such food processes as spray-drying and ultra high temperature (UHT)-type heating and subsequent long-term storage. Pan-frying, however, induced phytosterol oxidation and was classified as a rather deteriorative process. Overall, the findings indicated that although phytosterols and stanols are stable in normal food processing conditions, attention should be paid to their use in frying. Complex interactions between other food constituents also suggested that when new phytosterol-enriched foods are developed their oxidative stability must first be established. The results presented here will assist in choosing safe conditions for phytosterol/stanol enrichment.

Food and Indoor Air Isolated Bacillus Non-Protein Toxins: : Structures, Physico-Chemical Properties and Mechanisms of Effects on Eukaryotic Cells

We report here the structures and properties of heat-stable, non-protein, and mammalian cell-toxic compounds produced by spore-forming bacilli isolated from indoor air of buildings and from food. Little information is available on the effects and occurrence of heat-stable non-protein toxins produced by bacilli in moisture-damaged buildings. Bacilli emit spores that move in the air and can serve as the carriers of toxins, in a manner similar to that of the spores of toxic fungi found in contaminated indoor air. Bacillus spores in food cause problems because they tolerate the temperatures applied in food manufacture and the spores later initiate growth when food storage conditions are more favorable. Detection of the toxic compounds in Bacillus is based on using the change in mobility of boar spermatozoa as an indicator of toxic exposure. GC, LC, MS, and nuclear magnetic resonance NMR spectroscopy were used for purification, detection, quantitation, and analysis of the properties and structures of the compounds. Toxicity and the mechanisms of toxicity of the compounds were studied using boar spermatozoa, feline lung cells, human neural cells, and mitochondria isolated from rat liver. The ionophoric properties were studied using the BLM (black-lipid membrane) method. One novel toxin, forming ion channels permeant to K+ > Na+ > Ca2+, was found and named amylosin. It is produced by B. amyloliquefaciens isolated from indoor air of moisture-damaged buildings. Amylosin was purified with an RP-HPLC and a monoisotopic mass of 1197 Da was determined with ESI-IT-MS. Furthermore, acid hydrolysis of amylosin followed by analysis of the amino acids with the GS-MS showed that it was a peptide. The presence of a chromophoric polyene group was found using a NMR spectroscopy. The quantification method developed for amylosin based on RP-HPLC-UV, using the macrolactone polyene, amphotericin B (MW 924), as a reference compound. The B. licheniformis strains isolated from a food poisoning case produced a lipopeptide, lichenysin A, that ruptured mammalian cell membranes and was purified with a LC. Lichenysin A was identified by its protonated molecules and sodium- and potassium- cationized molecules with MALDI-TOF-MS. Its protonated forms were observed at m/z 1007, 1021 and 1035. The amino acids of lichenysin A were analyzed with ESI-TQ-MS/MS and, after acid hydrolysis, the stereoisomeric forms of the amino acids with RP-HPLC. The indoor air isolates of the strain of B. amyloliquefaciens produced not only amylosin but also lipopeptides: the cell membrane-damaging surfactin and the fungicidal fengycin. They were identified with ESI-IT-MS observing their protonated molecules, the sodium- and potassium-cationized molecules and analysing the MS/MS spectra. The protonated molecules of surfactin and fengycin showed m/z values of 1009, 1023, and 1037 and 1450, 1463, 1493, and 1506, respectively. Cereulide (MW 1152) was purified with RP-HPLC from a food poisoning strain of B. cereus. Cereulide was identified with ESI-TQ-MS according to the protonated molecule observed at m/z 1154 and the ammonium-, sodium- and potassium-cationized molecules observed at m/z 1171, 1176, and 1192, respectively. The fragment ions of the MS/MS spectrum obtained from the protonated molecule of cereulide at m/z 1154 were also interpreted. We developed a quantification method for cereulide, using RP-HPLC-UV and valinomycin (MW 1110, which structurally resembles cereulide) as the reference compound. Furthermore, we showed empirically, using the BLM method, that the emetic toxin cereulide is a specific and effective potassium ionophore of whose toxicity target is especially the mitochondria.

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.

Rigorous scaling law for the heat current in disordered harmonic chain

We study the energy current in a model of heat conduction, first considered in detail by Casher and Lebowitz. The model consists of a one-dimensional disordered harmonic chain of n i.i.d. random masses, connected to their nearest neighbors via identical springs, and coupled at the boundaries to Langevin heat baths, with respective temperatures T_1 and T_n. Let EJ_n be the steady-state energy current across the chain, averaged over the masses. We prove that EJ_n \sim (T_1 - T_n)n^{-3/2} in the limit n \to \infty, as has been conjectured by various authors over the time. The proof relies on a new explicit representation for the elements of the product of associated transfer matrices.

Perunan Y-viruksen testaaminen korkeassa happi-hiilidioksidipitoisuudessa idätetyistä perunoista

Perunalla (Solanum tuberosum L.) tällä hetkellä maailmanlaajuisesti eniten sato- ja laatutappioita aiheuttaa perunan Y-virus (PVY). Vaikka pelkän Y-viruksen aiheuttamaa satotappiota on vaikea mitata, on sen arvioitu olevan 20-80 %. Viruksen tärkein leviämistapa on viroottinen siemenperuna. Korkealaatuinen siemenperuna on edellytys ruoka-, ruokateollisuus- ja tärkkelysperunan tuotannolle. Kasvuston silmämääräinen tarkastelu aliarvioi yleensä Y-viruksen esiintyvyyttä. Laboratoriotestauksen avulla saadaan tarkempi tieto pellolta korjatun sadon saastunta-asteesta. Ongelmana Y-viruksen testaamisessa on, että sitä ei havaita dormanssissa olevista perunoista otetuista näytteistä yhtä luotettavasti kuin jo dormanssin ohittaneista perunoista testattaessa. Erilaisia menetelmiä kemikaaleista (Rindite, bromietaani) kasvihormoneihin (mm. gibberelliinihappo) ja varastointiolosuhteiden muutoksiin (kylmä- ja lämpökäsittely) on kokeiltu perunan dormanssin purkamiseen, mutta tulokset ovat olleet vaihtelevia. Tässä tutkielmassa perunan dormanssin purkamiseen käytettiin happi-hiilidioksidikäsittelyä (O2 40 % ja CO2 20 %) eripituisina käsittelyaikoina. Tarkoituksena oli selvittää, vaikuttaako käsittely perunan itämiseen ja dormanssin luontaista aikaisempaan purkautumiseen tai Y-viruksen havaitsemiseen. Lisäksi haluttiin selvittää, voiko Y-viruksen määrittämisen ELISA-testillä (Enzyme Linked Immunosorbent Assay) tehdä yhtä luotettavasti myös muista kasvinosista (mukula, itu), kuin tällä hetkellä yleisesti käytetystä perunan lehdestä. Idätyskäsittelyn vaikutuksista dormanssin purkautumiseen saatiin vaihtelevia, eikä kovinkaan yleistettäviä tuloksia. Käsittelyn ei myöskään havaittu vaikuttavan PYY-viroottisuuden havaitsemiseen eri näytemateriaaleilla testattaessa. Kun eri kasvinosien toimivuutta testissä vertailtiin, mukulamateriaalin todettiin aliarvioivan PVY-viroottisuutta kaikissa kokeissa. Myös itumateriaali aliarvioi pääsääntöisesti PVY-viroottisuutta ELISA:lla tehdyissä määrityksissä. Luotettavin testimateriaali oli perunan lehti.

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.

Reynolds stress and heat flux in spherical shell convection

Context. Turbulent fluxes of angular momentum and heat due to rotationally affected convection play a key role in determining differential rotation of stars. Aims. We compute turbulent angular momentum and heat transport as functions of the rotation rate from stratified convection. We compare results from spherical and Cartesian models in the same parameter regime in order to study whether restricted geometry introduces artefacts into the results. Methods. We employ direct numerical simulations of turbulent convection in spherical and Cartesian geometries. In order to alleviate the computational cost in the spherical runs and to reach as high spatial resolution as possible, we model only parts of the latitude and longitude. The rotational influence, measured by the Coriolis number or inverse Rossby number, is varied from zero to roughly seven, which is the regime that is likely to be realised in the solar convection zone. Cartesian simulations are performed in overlapping parameter regimes. Results. For slow rotation we find that the radial and latitudinal turbulent angular momentum fluxes are directed inward and equatorward, respectively. In the rapid rotation regime the radial flux changes sign in accordance with earlier numerical results, but in contradiction with theory. The latitudinal flux remains mostly equatorward and develops a maximum close to the equator. In Cartesian simulations this peak can be explained by the strong 'banana cells'. Their effect in the spherical case does not appear to be as large. The latitudinal heat flux is mostly equatorward for slow rotation but changes sign for rapid rotation. Longitudinal heat flux is always in the retrograde direction. The rotation profiles vary from anti-solar (slow equator) for slow and intermediate rotation to solar-like (fast equator) for rapid rotation. The solar-like profiles are dominated by the Taylor-Proudman balance.