Quantification of uncertainty in aerosol optical thickness retrieval arising from aerosol microphysical model and other sources, applied to Ozone Monitoring Instrument (OMI) measurements

Satellite instruments are nowadays successfully utilised for measuring atmospheric aerosol in many applications as well as in research. Therefore, there is a growing need for rigorous error characterisation of the measurements. Here, we introduce a methodology for quantifying the uncertainty in the retrieval of aerosol optical thickness (AOT). In particular, we concentrate on two aspects: uncertainty due to aerosol microphysical model selection and uncertainty due to imperfect forward modelling. We apply the introduced methodology for aerosol optical thickness retrieval of the Ozone Monitoring Instrument (OMI) on board NASA's Earth Observing System (EOS) Aura satellite, launched in 2004. We apply statistical methodologies that improve the uncertainty estimates of the aerosol optical thickness retrieval by propagating aerosol microphysical model selection and forward model error more realistically. For the microphysical model selection problem, we utilise Bayesian model selection and model averaging methods. Gaussian processes are utilised to characterise the smooth systematic discrepancies between the measured and modelled reflectances (i.e. residuals). The spectral correlation is composed empirically by exploring a set of residuals. The operational OMI multi-wavelength aerosol retrieval algorithm OMAERO is used for cloud-free, over-land pixels of the OMI instrument with the additional Bayesian model selection and model discrepancy techniques introduced here. The method and improved uncertainty characterisation is demonstrated by several examples with different aerosol properties: weakly absorbing aerosols, forest fires over Greece and Russia, and Sahara desert dust. The statistical methodology presented is general; it is not restricted to this particular satellite retrieval application

Leikki ja lasten muu toiminta päiväkotiympäristöjen suunnittelussa

Tiivistelmä. Diplomityöni on tutkielma, jossa perehdyn lasten leikkiin ja muuhun toimintaan päiväkotiympäristöissä. Pyrin löytämään keinoja, kuinka päiväkotiympäristöjen suunnittelussa voitaisiin ottaa huomioon leikki ja lasten muu toiminta. Viitekehyksenä työssäni on erityisesti varhaiskasvatusta käsittelevä kasvatustieteen alan kirjallisuus, sekä Rakennustietosäätiön ohjekortiston ohjekortti. Paneudun myös lasten toiminnallisuutta käsittelevään arkkitehtuurin kirjallisuuteen. Käsittelen kasvatustieteen kirjallisuudesta esille nousevia teemoja kolmen esimerkkikohteen kautta, sekä esitän konseptiluonnoksissani lasten omaehtoista toimintaa tukevia ratkaisuja. Kirjallisuudessa painottuu ympäristön toiminnallisuus ja lasten toiminta. Lasten maailmankuva perustuu paljolti toiminnan kautta ympäristöön tutustumiseen. Voidaankin todeta, että ympäristön luominen on enemmän kuin pelkän fyysisen ympäristön luomista. Se on kulttuurin luomista. Koska toiminnallisuus on lasten kokemusmaailmassa ensisijainen vaikuttamisen väylä, olen jättänyt materiaalit ja tilojen visuaalisuuden työssäni vähemmälle huomiolle, jotta katse kiinnittyisi vahvemmin toiminnallisuuteen ja kokemuksellisuuteen. Suurin yksittäinen esiin nouseva teema on leikki ja leikin alalajina erityisesti pitkäkestoinen leikki. Etsin leikkiä edesauttavia ilmiöitä ja pyrin niiden pohjalta löytämään luonnosmaisissa konseptiesityksissäni ratkaisuja laadukkaan leikkiympäristön syntymiseksi. Työssäni esitän ratkaisuja myös pitkäkestoisen leikin turvaamiseksi ja leikkimaailman säilyttämiseksi katkojen ajaksi. Terminä paljon esillä on ’tarjouma’, joka tarkoittaa ympäristön tarjoamia virikkeitä lasten leikille ja muulle toiminnalle. Teemana esille nousee myös minuutta tukeva ympäristö, joka edellyttää usein ympäristöltä persoonallisuutta. Kuten nuoren omassa huoneessa tila tehdään oman näköiseksi julisteiden avulla, tulisi vastaavan tapainen toiminta mahdollistaa myös pienille lapsille heidän päivähoitoympäristöissään. Perinteisesti tämä on mahdollistettu esimerkiksi valokuvilla lasten omien paikkojen, kuten päiväunivuoteiden yhteydessä. Havaintojeni mukaan personoinnin voisi mahdollistaa jo rakennuksen suunnitteluvaiheessa ja kytkeä sen näin aidosti osaksi ympäristöä. Lasten oma toiminta voidaan näin nähdä ympäristölle mahdollisuutena, ei uhkana. Muita tärkeitä esille nousseita teemoja ovat ympäristön moniaistillisuus, tilojen jäsentelyn vaikutus lasten toimintaan, ympäristön vaikutus päiväkodin hierarkiaan, sekä lasten näkökulma. Teemojen pohjalta olen suunnitellut konseptitasoisia luonnoksia, joissa esittelen ideoita leikkiä ja lasten muuta toimintaa tukevan päiväkotiympäristön aikaansaamiseksi. Konsepteissa painottuvat lasten toiminta ja päiväkodin tapahtumat. Esitän mahdollisuuksia liikkuvien leikkien lisäksi myös rauhoittumista ja lepoa tukevien ratkaisujen löytämiseksi.Play and other activities of children in the design of daycare environments. Abstract. In my Master’s Thesis my focus is on children’s play and other activities in daycare centre environments. My aim is to find out means of design how to better take into account children’s activities at daycare centre environments. The literary framework for my Thesis lies on studies concerning theory about early childhood education. Also, The Rules and Information File concerning Daycare environments of Finnish Building Information Group’s (RT) targeted for designers is one of my main sources. In addition, I will focus on architectural literature about children’s activity in environments. The themes pointed out in educational literature I will discuss through three architectural case studies. Further, I will present my design concepts demonstrating solutions supporting children’s spontaneous activities. In the literature, environments’ functionality and childrens activities are widely emphasized. Child’s worldview is mainly based on exploring the environment through actions. Therefore, creating the environment is more than just creating the physical environment, but it is about creating culture. Since, the emphasis in my Thesis is on actions and activities in children’s environments, I have left material studies and the overall spatial visuality to a smaller role. Hence, my aim is to focus on functionality and experiential aspects. The biggest single theme in my Thesis is childrens play, especially long lasting play. My aim is to find phenomena to foster play and further, to find design solutions for high quality children’s play environments through conceptual design proposals. Affordance is often referred concept, meaning cues inspiring the play and other children’s action offered by the environment. As a theme there also child’s selfdom supporting environment is emphasized, meaning that environment has to be personal or be personalized in some way. Similarly, youngsters have posters in their room, should also the little children be able to personalize their environments. Usually in Finland personalization has been made possible by placing pictures of children or their family nearby their own places like beds. According to my findings, personalization could be taken into consideration already in the architectural design phase and thereby, it could be genuine feature of the whole environment. Hence, children’s action would be seen as an opportunity, not a threat. Other important themes in my Diploma Thesis are ’using all the senses’, ’the impact of space orientation on childrens activity’, ’the impacts of the environment on the daycare centre’s hierarchy’ and ’children’s view’. Based on the aforementioned themes I have designed conceptual sketches to support play and other children’s activities in daycare centre environments. The focus is on design concepts for children’s actions and other activities in the daycare centre environments. In addition to design solutions for children’s independent moving plays, I will also offer proposals for design concepts concerning rest and relax

Quantitative proteomic analysis of bronchoalveolar lavage fluid in West Highland white terriers with canine idiopathic pulmonary fibrosis

Background Canine idiopathic pulmonary fibrosis (CIPF) is a chronic, progressive, interstitial fibrosing lung disease, manifesting as cough, exercise intolerance and ultimately, dyspnea and respiratory failure. It mainly affects West Highland white terriers (WHWTs), lacks curable treatment and has a poor prognosis. Aspiration of gastroesophageal refluxate may play a role in the development of CIPF. In the first part of this study, we completed label-free quantitative proteomic analysis of bronchoalveolar lavage fluid (BALF) from CIPF and healthy WHWTs. In the second part, we evaluated potential protein markers of reflux aspiration from canine gastric juice and vomitus and whether these were present in BALF from the two groups. Results Across all BALF samples, 417 proteins were identified, and of these, 265 proteins were identified by two or more unique tryptic peptides. Using the 265 high confidence assignments, the quantitative proteome profiles were very similar in the two cohorts, but they could be readily resolved by principal component analysis on the basis of differential protein expression. Of the proteins that were differentially abundant in the two groups, several (including inflammatory and fibrotic markers) were elevated in CIPF, and a smaller, more diverse group of proteins were diminished in CIPF. No protein markers indicative of reflux aspiration were identified. Conclusions Label-free proteomics allowed discrimination between CIPF and healthy WHWTs, consistent with fibrotic process but did not provide clear evidence for gastrointestinal aspiration. The measurement of proteins may provide a proteomics signature of CIPF that could be used to evaluate treatment options.Peer reviewe

Structural and functional characteristics of xenavidin, the first frog avidin from Xenopus tropicalis

<p>Abstract</p> <p>Background</p> <p>Avidins are proteins with extraordinarily high ligand-binding affinity, a property which is used in a wide array of life science applications. Even though useful for biotechnology and nanotechnology, the biological function of avidins is not fully understood. Here we structurally and functionally characterise a novel avidin named xenavidin, which is to our knowledge the first reported avidin from a frog.</p> <p>Results</p> <p>Xenavidin was identified from an EST sequence database for <it>Xenopus tropicalis </it>and produced in insect cells using a baculovirus expression system. The recombinant xenavidin was found to be homotetrameric based on gel filtration analysis. Biacore sensor analysis, fluorescently labelled biotin and radioactive biotin were used to evaluate the biotin-binding properties of xenavidin - it binds biotin with high affinity though less tightly than do chicken avidin and bacterial streptavidin. X-ray crystallography revealed structural conservation around the ligand-binding site, while some of the loop regions have a unique design. The location of structural water molecules at the entrance and/or within the ligand-binding site may have a role in determining the characteristic biotin-binding properties of xenavidin.</p> <p>Conclusion</p> <p>The novel data reported here provide information about the biochemically and structurally important determinants of biotin binding. This information may facilitate the discovery of novel tools for biotechnology.</p

Modification of the loops in the ligand-binding site turns avidin into a steroid-binding protein

<p>Abstract</p> <p>Background</p> <p>Engineered proteins, with non-immunoglobulin scaffolds, have become an important alternative to antibodies in many biotechnical and therapeutic applications. When compared to antibodies, tailored proteins may provide advantageous properties such as a smaller size or a more stable structure.</p> <p>Results</p> <p>Avidin is a widely used protein in biomedicine and biotechnology. To tailor the binding properties of avidin, we have designed a sequence-randomized avidin library with mutagenesis focused at the loop area of the binding site. Selection from the generated library led to the isolation of a steroid-binding avidin mutant (sbAvd-1) showing micromolar affinity towards testosterone (K_d~ 9 μM). Furthermore, a gene library based on the sbAvd-1 gene was created by randomizing the loop area between <it>β</it>-strands 3 and 4. Phage display selection from this library led to the isolation of a steroid-binding protein with significantly decreased biotin binding affinity compared to sbAvd-1. Importantly, differential scanning calorimetry and analytical gel-filtration revealed that the high stability and the tetrameric structure were preserved in these engineered avidins.</p> <p>Conclusions</p> <p>The high stability and structural properties of avidin make it an attractive molecule for the engineering of novel receptors. This methodology may allow the use of avidin as a universal scaffold in the development of novel receptors for small molecules.</p

A 96-well format for a high-throughput baculovirus generation, fast titering and recombinant protein production in insect and mammalian cells

<p>Abstract</p> <p>Background</p> <p>Baculovirus expression vector system (BEVS) has become a standard in recombinant protein production and virus-like particle preparation for numerous applications.</p> <p>Findings</p> <p>We describe here protocols which adapt baculovirus generation into 96-well format.</p> <p>Conclusion</p> <p>The established methodology allows simple baculovirus generation, fast virus titering within 18 h and efficient recombinant protein production in a high-throughput format. Furthermore, the produced baculovirus vectors are compatible with gene expression in vertebrate cells <it>in vitro </it>and <it>in vivo</it>.</p

Avidin related protein 2 shows unique structural and functional features among the avidin protein family

BACKGROUND: The chicken avidin gene family consists of avidin and several avidin related genes (AVRs). Of these gene products, avidin is the best characterized and is known for its extremely high affinity for D-biotin, a property that is utilized in numerous modern life science applications. Recently, the AVR genes have been expressed as recombinant proteins, which have shown different biotin-binding properties as compared to avidin. RESULTS: In the present study, we have employed multiple biochemical methods to better understand the structure-function relationship of AVR proteins focusing on AVR2. Firstly, we have solved the high-resolution crystal structure of AVR2 in complex with a bound ligand, D-biotin. The AVR2 structure reveals an overall fold similar to the previously determined structures of avidin and AVR4. Major differences are seen, especially at the 1–3 subunit interface, which is stabilized mainly by polar interactions in the case of AVR2 but by hydrophobic interactions in the case of AVR4 and avidin, and in the vicinity of the biotin binding pocket. Secondly, mutagenesis, competitive dissociation analysis and differential scanning calorimetry were used to compare and study the biotin-binding properties as well as the thermal stability of AVRs and avidin. These analyses pinpointed the importance of residue 109 for biotin binding and stability of AVRs. The I109K mutation increased the biotin-binding affinity of AVR2, whereas the K109I mutation decreased the biotin-binding affinity of AVR4. Furthermore, the thermal stability of AVR2(I109K) increased in comparison to the wild-type protein and the K109I mutation led to a decrease in the thermal stability of AVR4. CONCLUSION: Altogether, this study broadens our understanding of the structural features determining the ligand-binding affinities and stability as well as the molecular evolution within the protein family. This novel information can be applied to further develop and improve the tools already widely used in avidin-biotin technology

Removal of cell surface heparan sulfate increases TACE activity and cleavage of ErbB4 receptor

<p>Abstract</p> <p>Background</p> <p>Nuclear localization of proteolytically formed intracellular fragment of ErbB4 receptor tyrosine kinase has been shown to promote cell survival, and nuclear localization of ErbB4 receptor has been described in human breast cancer. Tumor necrosis factor alpha converting enzyme (TACE) initiates the proteolytic cascade leading to ErbB4 intracellular domain formation. Interactions between matrix metalloproteases and heparan sulfate have been described, but the effect of cell surface heparan sulfate on TACE activity has not been previously described.</p> <p>Results</p> <p>As indicated by immunodetection of increased ErbB4 intracellular domain formation and direct enzyme activity analysis, TACE activity was substantially amplified by enzymatic removal of cell surface heparan sulfate but not chondroitin sulfate.</p> <p>Conclusion</p> <p>In this communication, we suggest a novel role for cell surface heparan sulfate. Removal of cell surface heparan sulfate led to increased formation of ErbB4 intracellular domain. As ErbB4 intracellular domain has previously been shown to promote cell survival this finding may indicate a novel mechanism how HS degradation active in tumor tissue may favor cell survival.</p

Structure and characterization of a novel chicken biotin-binding protein A (BBP-A)

BACKGROUND: The chicken genome contains a BBP-A gene showing similar characteristics to avidin family genes. In a previous study we reported that the BBP-A gene may encode a biotin-binding protein due to the high sequence similarity with chicken avidin, especially at regions encoding residues known to be located at the ligand-binding site of avidin. RESULTS: Here, we expand the repertoire of known macromolecular biotin binders by reporting a novel biotin-binding protein A (BBP-A) from chicken. The BBP-A recombinant protein was expressed using two different expression systems and purified with affinity chromatography, biochemically characterized and two X-ray structures were solved – in complex with D-biotin (BTN) and in complex with D-biotin D-sulfoxide (BSO). The BBP-A protein binds free biotin with high, "streptavidin-like" affinity (K(d )~ 10(-13 )M), which is about 50 times lower than that of chicken avidin. Surprisingly, the affinity of BBP-A for BSO is even higher than the affinity for BTN. Furthermore, the solved structures of the BBP-A – BTN and BBP-A – BSO complexes, which share the fold with the members of the avidin and lipocalin protein families, are extremely similar to each other. CONCLUSION: BBP-A is an avidin-like protein having a β-barrel fold and high affinity towards BTN. However, BBP-A differs from the other known members of the avidin protein family in thermal stability and immunological properties. BBP-A also has a unique ligand-binding property, the ability to bind BTN and BSO at comparable affinities. BBP-A may have use as a novel material in, e.g. modern bio(nano)technological applications