Stratification of responders towards eculizumab using a structural epitope mapping strategy

The complement component 5 (C5)-binding antibody eculizumab is used to treat patients with paroxysmal nocturnal hemoglobinuria (PNH) and atypical haemolytic uremic syndrome (aHUS). As recently reported there is a need for a precise classification of eculizumab responsive patients to allow for a safe and cost-effective treatment. To allow for such stratification, knowledge of the precise binding site of the drug on its target is crucial. Using a structural epitope mapping strategy based on bacterial surface display, flow cytometric sorting and validation via haemolytic activity testing, we identified six residues essential for binding of eculizumab to C5. This epitope co-localizes with the contact area recently identified by crystallography and includes positions in C5 mutated in non-responders. The identified epitope also includes residue W917, which is unique for human C5 and explains the observed lack of cross-reactivity for eculizumab with other primates. We could demonstrate that Ornithodorus moubata complement inhibitor (OmCI), in contrast to eculizumab, maintained anti-haemolytic function for mutations in any of the six epitope residues, thus representing a possible alternative treatment for patients non-responsive to eculizumab. The method for stratification of patients described here allows for precision medicine and should be applicable to several other diseases and therapeutics

Movement Patterns for a Critically Endangered Species, the Leatherback Turtle (Dermochelys coriacea), Linked to Foraging Success and Population Status

Foraging success for pelagic vertebrates may be revealed by horizontal and vertical movement patterns. We show markedly different patterns for leatherback turtles in the North Atlantic versus Eastern Pacific, which feed on gelatinous zooplankton that are only occasionally found in high densities. In the Atlantic, travel speed was characterized by two modes, indicative of high foraging success at low speeds (<15 km d−1) and transit at high speeds (20–45 km d−1). Only a single mode was evident in the Pacific, which occurred at speeds of 21 km d−1 indicative of transit. The mean dive depth was more variable in relation to latitude but closer to the mean annual depth of the thermocline and nutricline for North Atlantic than Eastern Pacific turtles. The most parsimonious explanation for these findings is that Eastern Pacific turtles rarely achieve high foraging success. This is the first support for foraging behaviour differences between populations of this critically endangered species and suggests that longer periods searching for prey may be hindering population recovery in the Pacific while aiding population maintenance in the Atlantic

Rampfeber hos lärar- och civilingenjörsstudenter

Stage fright is a large problem even for college students, who have chosen an occupation direction where standing on a scene is a common occurrence. Stage fright can imply that individuals abandon occupation directions they are interested in and can impair performances and health. The purpose with this thesis is to examine whether there is any differences between teacher- and engineering students at the LTU, when it comes to stage fright. A first hypothesis is that stage fright is lower in the college program, where public performances happen regularly and in this case the teacher programs. A second hypothesis is that the teacher students apply coping strategies to a smaller degree and a third hypothesis is that stage fright is lower for men. A questionnaire was administered to four college classes. The results show that the engineering students experienced public speaking occasions as more stressful than the teacher students, which confirms the hypothesis. Moreover, it turned out that the teacher students applied more coping strategies than the engineering students, but the difference was not statistically significant and the hypothesis was rejected. Finally, the results show that women experience public performance occasions as more stressful than men, especially during the presentation act when they were exposed to more symptoms, which is in accordance to the hypothesis.Validerat; 20150626 (global_studentproject_submitter

Identification and characterization of novel mammalian alcohol dehydrogenases

The vertebrate medium chain alcohol dehydrogenases are dimeric zinc metalloenzymes that catalyze the reversible oxidation/reduction of alcohols/aldehydes using NAD+/NADH as coenzyme. In mammals, six classes of ADH have been defined (ADH1-ADH6) whereof five have been identified in humans. These enzymes are further divided into isozymes, and the presence of allelozymes, which have been detected for a number of gene loci, adds additional multiplicity to this enzyme system. Only a few ADHs have been assigned specific metabolic functions, e.g. glutathione dependent formaldehyde oxidation by ADH3, whereas other ADHs seem to contribute in the general defense against xenobiotics and endogenously formed alcohols and aldehydes. This thesis aims to provide insights into ADH structure and function, with emphasis on the identification and characterization of novel ADH forms, A cDNA coding for a mouse ADH2 was cloned, which showed high structural similarity with the rat ortholog but lower identity with other species variants. Interestingly, the mouse and rat ADH2 forms share the same residue replacements, as compared to other ADHs, at positions important for catalysis and substrate specificity. Kinetic measurements displayed that rodent ADH2s are low activity enzymes, but the activity could be restored by substituting a unique Pro47 for Ms. Large substrate isotope effects for octanol oxidation showed that hydride transfer is rate- limiting for turnover. Altogether, these results indicate that the rodent enzymes form an ADH2 subgroup within the ADH family. The mechanisms of mammalian ADH2 enzymes were studied further and an ordered mechanism with coenzyme binding as the first reactant was suggested for both human and mouse ADH2. The enzymes display strong pH dependence with pK values for kcat and kcat/Km several pH units higher than fot the ADH1 enzymes. Additional replacements at position 47 in the mouse enzyme (Pro47Ala and Pro47Gln) also increased oxidative activity and we propose that the rigid ring structure of Pro47 causes coenzyme binding that is unfavorable for efficient catalysis. This also shows that a His at position 47 does not act as a catalytic base in the deprotonation of the alcohol substrate. Experiments with deuterated substrates and transient kinetic measurements indicate that dissociation of coenzyme is rate-limiting for human ADH2 whereas hydride transfer is rate-limiting for all mouse ADH2 forms. Polymorphisms in both the ADH2 and the ADH3 genes were found by single strand conformational polymorphism (SSCP) analysis. The ADH2 polymorphism affects the coding region and results in an lle308Val substitution. Homology modeling located position 308 in the subunit interface of the molecule and in the vicinity of the active site pocket entrance. Characterization of the two allelozymes showed that the 308Val substitution decreases protein stability as compared to the 308Ile variant and that Km-values, for a number of model substrates, were higher for the 308Val enzyme. The ADH3 polymorphisms were detected within the 5'-flanking region. A reporter gene assay showed a significant reduction in promoter activity for a rare C+9 g T+9 transition, which could arise from decreased binding of nuclear proteins, as indicated by electrophoretic mobility shift assays. ADH5 and ADH6 have been identified only at the nucleic acid level in human and deermouse, respectively. These enzymes share 67% structural identity and could possibly belong to the same diverged class. Previous reports indicated that human ADH5 differs from other ADHs in exon/intron organization, lacking the last exon and thus should be expressed in a truncated form. However, we were able to identify full-length ADH5 transcripts and the presence of a ninth exon was also confirmed by sequencing of genomic DNA. Northern blot analyses established the full-length variant as the major transcript with the strongest signal from adult liver. We conclude that the ADH5 gene contains a composite internal/terminal exon, which can be differentially processed as a result of competition between polyadenylation and splicing. In addition, a new ADH was identified in rat which showed 78% identity with the deermouse ADH6 variant. No soluble ADH5 or ADH6 protein could be recombinantly expressed in E. coli, but using a protocol of refolding insoluble proteins from inclusion bodies, milligram amounts of ADH-GST fusion proteins of both human ADH5 and rat ADH6 could be isolated. The purified proteins were not stable without the GST tag and no activity was observed with a number substrates, which could be a result of an incorrect fold of the ADH part of the fusion protein. In vitro translation experiments and expression of ADH-GFP fusion protein in COS cells indicate that soluble ADH5 and ADH6 protein could be produced in mammalian cells

Applying Goal Modeling to API Ecosystems: A Cross-Company Case Study

APIs play a major role in software ecosystems and must continuously evolve to meet the demands of these ecosystems. In this paper we identify a new ecosystem around each API within software ecosystems and apply goal modeling to map such ecosystem. The authors collaborated with two software intense companies in a cross-case study. The outcome of this research was that by visualizing the relations between the actors within the API ecosystem, companies can better understand the ecosystem. An API ecosystem can be challenging to model and it is recommended that the mapping is done by an individual with experience in goal modeling. However, both, the modeling process and the mapped API ecosystem provide analytical benefits for an organization

CURTAIN WALLS : A comparison between site-builtand prefabricated construction methods

In conjunction with today’s increasing competition within the construction sector, more pressure is being placed on building contractors. Efficiency and improvements are necessary but without impairment to an ergonomic and safe construction site. This in is in order to reduce the construction costs and time but to retain the ability to deliver a high-quality contract. Various methods and prefabrication degrees are used, depending on the project's requirements and conditions. This analysis sets out to investigate and exhibit what qualifications are important when choosing a construction method for curtain walls. Advantages and disadvantages with each method have been analyzed and recommendations have been given to show when different methods are best suited. This diploma work is limited to the study of site-built, semi-prefabricated and fully-prefabricated curtain walls. The study was conducted in collaboration with Peab Bostad AB Uppsala, Sweden, who utilizes the studied methods within their company. Relevant information was obtained throughout a comprehensive study of literature, on-site examinations and interviews with people working with the different methods of constructing curtain walls. The study shows that half-prefabricated curtain walls are the best method in today´s current circumstances. This method makes the building phase shorter, reduces stress- and strain-related injuries compared to on-site built methods and allows estimators to make a more accurate project budget. On-site built curtain walls are to be used in renovation and restoration projects or if special conditions occur, for example to keep company labors busy during a low conjunction. The method is slower and makes staffing charts irregular. The use of fully prefabricated curtain wall is fast, but it is also the method containing the greatest risks, mainly problems with moisture. The method will become more common in the future as safer designs and more precise handling will be possible.I samband med dagens ökade konkurrens i byggbranschen sätts det press på byggentreprenörer. Effektiviseringar, material- och metodval blir allt mer viktiga för att kunna minska byggtid, reducera kostnader men även leverera en entreprenad med hög kvalitet samt med ergonomiska- och säkra utföranden. Idag används olika metoder och prefabriceringsgrader beroende på projekts olika förutsättningar. Detta examensarbete syftar till att redovisa vilka förutsättningar som är av vikt vid val av utfackningsmetod. Studien behandlar även för- och nackdelar med olika metodval samt när dessa bör användas eller undvikas. Rapporten är avgränsad till studier av platsbyggda, halvprefabricerade och helprefabricerade utfackningsväggar. Studien har gjorts i sammarbete med PEAB Bostad AB Uppsala, som tillämpar de här studerade metoderna inom företaget. Metoder för att få fram relevant och intressant information har främst gjorts i form av litteraturstudier, arbetsplatsbesök och intervjuer med nyckelpersoner i produktionen. Studien redovisar att halvprefabricerade utfackningsväggar är det bästa alternativet i dagsläget, för att kunna uppnå god kvalitet, minska kostnader och reducera byggtider. Metoden är snabb och minskar belastnings- och förslitningsskador jämfört med platsbyggnation samt att de ekonomiska riskerna är små vilket gör att en pricksäker budget kan göras före byggstart. Vid renoverings- och tilläggsarbeten samt vid mindre projekt kan platsbyggnation vara lönsamt men bör undvikas i allmänhet då arbetsmiljön och ergonomin försämras. Metoden tar även längre tid och bemanningskurvan blir ojämnare. Helprefabricerade utfackningsväggar är den snabbaste metoden men innefattar även de största riskerna. Metoden kommer att bli vanligare i framtiden i takt med säkrare utföranden och noggrannare hantering. I dagsläget är denna metod problematisk då eventuella problem kan vara omfattande

A utility-eye view of the CO2 compliance-decision process in the European power-sector

The purpose of this paper is to provide a utility eye-view of the European power-sector's CO2-compliance decision process under a tradable emissions scheme. The cost analysis indicates that, in the medium term, many utilities are likely to consider options based on traditional power technologies such as converting existing coal-fired capacity to burn gas, extending the lives of nuclear capacity, and replacing old coal-fired plants with more efficient gas- or even coal-fired units. The long-term economic potential of future options is highly uncertain, and utilities are likely to respond to this by maintaining flexibility in fuel choices and avoid large investments that lock them into a specific compliance method before more efficient and cleaner technologies have crystallized. Given the multitude of possible CO2-mitigation options, there is a strong case for emissions trading and for refraining from policies that build on mandatory fuel-requirements, higher rates of capital stock turnover and technology standards.Climate policy Power generation Compliance methods Europe

Variability and Trends of Phytoplankton in the Baltic Sea and Kattegat-Skagerrak

The aim of the report is to describe results from analyses of time series of phytoplankton data from the Swedish marine monitoring programs. One issue is if it is possible to describe environmental change with the current sampling frequency. The three main aims are: (I) to investigate the statistical strength of time series of phytoplankton biomass, (II) to investigate the variability of species composition between stations and (III) to investigate the temporal variability regarding species composition. Results indicate how long time series are needed to detect change at a certain level. Also the variability in biodiversity is shown with some examples.   To quantify the biomass of phytoplankton different parameters may be investigated, e.g. chlorophyll content and the biovolume of phytoplankton. Chlorophyll a is designated in directives for describing the environmental status of the seas as an indicator for eutrophication. Sampling for chlorophyll is usually made using two different methods in the seas surrounding Sweden. Samples are collected using a hose, normally from 0-10 m depth, or by sampling at discrete depths, e.g. 1, 5 and 10 m. No difference was observed when comparing data from the hose sampling with depth-averaged data from the discrete depths. Thus the data from hose-sampling can be used together with the data based on sampling at discrete depths. To investigate if chlorophyll a works as a proxy for phytoplankton biomass data on total biovolume of phytoplankton, based on cell counts and cell volume estimates, was compared to chlorophyll a data. The data set include data from 1983 to 2014. A large part of the data emanates from 2010 and later. In the investigated data set there is a significant, but weak, correlation between chlorophyll a and total biovolume (n= 3119, p &lt;0.01, R2 = 0.439).   Results about the statistical strength (power) of the time series of total biovolume of phytoplankton indicate that it on average takes 23 years to detect a change of 1% (p&lt;0.01, power = 80%). A change of 10% is detected after 7 years and a change of 40% is detected in 5 years. Results regarding the statistical strength of time series of chlorophyll a show that it on average takes 33 years to detect a change of 1%. A change of 10% is detected after 14 years and a change of 40% in 7 years. Please note that these figures are based on data from monitoring programs that include the variability observed. When the data set was divided into geographical areas called the type areas it was evident that the amount of available data in the different type areas varies a lot. In some areas there is not enough data to carry out an analysis of the statistical strength. Another conclusion is that there is substantially less data on phytoplankton biodiversity and biomass based on cell counts and cell volume estimates compared to the amount of data on chlorophyll a.   Data was also split according to sea basins to show the statistical strength in the data if sampling frequency continues as up to now. To detect a change of Swedish Agency for Marine and Water Management report 2015:33  8 5% of chlorophyll a with the power of 80% the number of years needed if the present sampling frequency continues is on average: - The Kattegat-Skagerrak: 16 years - The Sound and the Southern Baltic Proper: 11 years - The Baltic Proper: 7-&gt;50 years - The Bothnian Sea: 19-41 years - The Bothnian Bay: 13-35 years   To investigate differences in biodiversity, data from intense sampling campaigns made in the period 2010-2012 was used. The sampling was made at a much larger number of locations compared to the normal monitoring program. Results of cluster analysis (Euclidian distance) on the species composition show that weekly sampling describes the natural variability in phytoplankton biodiversity well while sampling once a month does not resolve the natural variability in biodiversity. When investigating the spatial variability, i.e. the differences in species composition between stations, results indicate that samples from the same water mass, e.g. the southern Kattegat, are similar. The differences in closely located bays and fjords are large in regard to plankton biodiversity.Rapporten syftar till att beskriva resultat från analys av tidsserier från marina miljöövervakningsprogram i Sverige med avseende på växtplankton. En övergripande fråga är om den svenska miljöövervakningen kan fånga upp förändringar med nuvarande provtagningsfrekvens. De tre huvudsyftena är att: (I) analysera statistisk styrka för tidsserier av växtplanktonbiomassa, (II) analysera hur statistiskt lika stationer är med avseende på artsammansättning och (III) analysera tidsmässig variabilitet vad gäller artsammansättning. Resultaten kan ge en fingervisning om hur långa mätserier som krävs beroende på vilken fråga som skall besvaras, d.v.s. vilken storlek på förändring över tid som behöver detekteras. Resultaten ger även inblick i hur stor variabiliteten i växtplanktons biodiversitet är mellan stationerna, eller enklare utryckt hur lika stationer är.  För att kvantifiera hur mycket växtplankton som finns kan olika parametrar undersökas, exempelvis klorofyll och biovolym. Klorofyll är specificerat i direktiv för att beskriva miljöstatus i havet som en indikator för eutrofiering. Klorofyllprovtagning sker med huvudsakligen två olika metoder i haven runt Sverige. Prover tas dels med slang, normalt 0-10 m, och dels med vattenhämtare från fasta djup. När medelvärden från provtagning vid fasta djup jämfördes med data från slangprovtagning kunde ingen skillnad påvisas. En slutsats är att klorofylldata baserad på slangprovtagning kan användas tillsammans med medelvärdesbildade data från fasta djup. För att undersöka om klorofyll a fungerar som en så kallad proxy (~ersättare) för växtplanktonbiomassa jämfördes data på total biovolym av växtplankton med mängden klorofyll a i ett datamaterial från 1983 till 2014. En stor del av data kommer från 2010 och senare. I det undersökta datamaterialet finns en signifikant, men svag, korrelation mellan växtplanktonbiomassa, mätt som biovolym, och klorofyll a. (n= 3119, p &lt;0.01, R2 = 0.439).  Resultat gällande statistisk styrka på tidsserier av total biovolym av växtplankton visar att det i medeltal tar 23 år att upptäcka en förändring på 1% (p&lt;0.05, power = 80%). En förändring på 10% upptäcks på 7 år och en förändring på 40% på 5 år. Resultat gällande statistisk styrka på tidsserier av klorofyll a visar att det i medeltal tar 33 år att upptäcka en förändring på 1%. En förändring på 10% upptäcks på 14 år och en förändring på 40% på 7 år. Det är värt att notera att dessa siffror är baserade på verkliga data från miljöövervakningen och den variabilitet som finns i datamaterialet. När data delades upp i olika geografiska områden enligt den så kallade typindelningen av kustvatten visade det sig att datamängden i de olika typerna varierar stort. Det innebär att det i vissa områden i stort sett saknas dataunderlag för att göra en analys av statistisk styrka. En annan slutsats är att det finns en betydligt mindre mängd data gällande växtplanktons biodiverstitet och biomassa baserat på cellräkning och cellvolymsbestämningar jämfört med mängden data på klorofyll a.  Data delades även in havsområdesvis för att visa vilken statistisk säkerhet datamaterialet ger om provtagningar fortsätter med samma frekvens som hittills. För att upptäcka en förändring på 5% i klorofyll med en statistisk säkerhet på 80% krävs det i medeltal:   Kattegatt-Skagerrak: 16 års data  Öresund och södra Egentliga Östersjön: 11 års data  Egentliga Östersjön: 7-&gt; 50 års data  Bottenhavet: 19-41 års data  Bottenviken: 13-35 års data  För att undersöka skillnader i biodiversitet användas data från de så kallade kampanjårs-studierna som genomfördes under perioden 2010 - 2012. Då genomfördes provtagning av växtplankton på betydligt fler stationer än i de normala övervakningsprogrammen. Resultat av klusteranalys (Euclidian distance) på artsammansättning visar att en provtagningsfrekvens på en gång i veckan fångar den naturliga variationen i biodiversitet. Provtagning en gång i månaden fångar inte den naturliga variabiliteten i biodiversitet. När det gäller rumslig upplösning så har stationer inom samma vattenmassa, t.ex. södra Kattegatt, ungefär samma artsammansättning. När det gäller stationer nära kusten, finns betydande skillnader i biodiversitet mellan prover insamlade i närliggande vikar och fjärdar/fjordar.

Automatisering av nationellt dataflöde till ICES genom skördning - en förstudie

SMHI är, på uppdrag av Havs- och vattenmyndigheten (HaV), datavärd för svenska marina miljöövervakningsdata. En central del i uppdraget är att årligen rapportera nationellt insamlad data till nternationella Havsforskningsrådet, ICES. För biologiska data sker en årlig rapportering av data levererade från föregående års övervakning. Leveranserna sker på ett format definierat av ICES. Leveransernas innehåll valideras av SMHI mot ICES valideringstjänst DATSU via uppladdning till en webbsida. När samtliga fel är rättade skickas leveranserna till ICES via e-post. SMHI har fått ett uppdrag från HaV att utreda om det finns en möjlighet att låta ICES skörda data som ersättning för den nuvarande hanteringen med manuella leveranser. ICES har också ett intresse av att utreda om skördning av data är en lämplig metod för framtida inhämtande av data. ICES vill även testa möjligheterna att byta leveransformat till ett nytt XML-baserat format. SMHI föreslår en lösning där SMHI:s tjänst för maskin-maskin-kommunikation, SHARKdata, används. SHARKdata kommer att utökas för att kunna generera exportpaket i enlighet med ICES nya XML-baserade format. ICES har även kompletterat sin valideringstjänst DATSU med ett gränssnitt för maskin-maskinkommunikation så att man med automatik kan anropa DATSU och validera exportpaket. En prototyp har utvecklats för att visa hur SHARKdata kan användas för denna typ av hantering med skördning. I prototypen ingår även konvertering till en inledande testversion av XML-formatet för datatypen Zoobenthos. Det fortsatta projektet efter denna förstudie planeras som ett samarbete mellan SMHI och ICES. SMHI utvecklar fortlöpande SHARKdata i takt med att ICES släpper specifikationer på format för nya datatyper, parallellt med att data rapporteras på nuvarande sätt. Detta arbete beräknas pågå under 2016 och 2017, med varierande intensitet. Efter denna test- och utvecklingsperiod antas ICES släppa en ny version av sitt rapporteringformat och då kan SMHI gå över till det nya rapporteringssättet