Simultaneous Localization and Mapping in Repeating Environments

Master's thesis Mechatronics MAS500 - University of Agder 2018Konfidensiell til / confidential until 01.07.202

Correlation analysis of two-dimensional gel electrophoretic protein patterns and biological variables

BACKGROUND: Two-dimensional gel electrophoresis (2DE) is a powerful technique to examine post-translational modifications of complexly modulated proteins. Currently, spot detection is a necessary step to assess relations between spots and biological variables. This often proves time consuming and difficult when working with non-perfect gels. We developed an analysis technique to measure correlation between 2DE images and biological variables on a pixel by pixel basis. After image alignment and normalization, the biological parameters and pixel values are replaced by their specific rank. These rank adjusted images and parameters are then put into a standard linear Pearson correlation and further tested for significance and variance. RESULTS: We validated this technique on a set of simulated 2DE images, which revealed also correct working under the presence of normalization factors. This was followed by an analysis of p53 2DE immunoblots from cancer cells, known to have unique signaling networks. Since p53 is altered through these signaling networks, we expected to find correlations between the cancer type (acute lymphoblastic leukemia and acute myeloid leukemia) and the p53 profiles. A second correlation analysis revealed a more complex relation between the differentiation stage in acute myeloid leukemia and p53 protein isoforms. CONCLUSION: The presented analysis method measures relations between 2DE images and external variables without requiring spot detection, thereby enabling the exploration of biosignatures of complex signaling networks in biological systems

Genes of cell-cell interactions, chemotherapy detoxification and apoptosis are induced during chemotherapy of acute myeloid leukemia

<p>Abstract</p> <p>Background</p> <p>The molecular changes <it>in vivo </it>in acute myeloid leukemia cells early after start of conventional genotoxic chemotherapy are incompletely understood, and it is not known if early molecular modulations reflect clinical response.</p> <p>Methods</p> <p>The gene expression was examined by whole genome 44 k oligo microarrays and 12 k cDNA microarrays in peripheral blood leukocytes collected from seven leukemia patients before treatment, 2–4 h and 18–24 h after start of chemotherapy and validated by real-time quantitative PCR. Statistically significantly upregulated genes were classified using gene ontology (GO) terms. Parallel samples were examined by flow cytometry for apoptosis by annexin V-binding and the expression of selected proteins were confirmed by immunoblotting.</p> <p>Results</p> <p>Significant differential modulation of 151 genes were found at 4 h after start of induction therapy with cytarabine and anthracycline, including significant overexpression of 31 genes associated with p53 regulation. Within 4 h of chemotherapy the BCL2/BAX and BCL2/PUMA ratio were attenuated in proapoptotic direction. FLT3 mutations indicated that non-responders (5/7 patients, 8 versus 49 months survival) are characterized by a unique gene response profile before and at 4 h. At 18–24 h after chemotherapy, the gene expression of p53 target genes was attenuated, while genes involved in chemoresistance, cytarabine detoxification, chemokine networks and T cell receptor were prominent. No signs of apoptosis were observed in the collected cells, suggesting the treated patients as a physiological source of pre-apoptotic cells.</p> <p>Conclusion</p> <p>Pre-apoptotic gene expression can be monitored within hours after start of chemotherapy in patients with acute myeloid leukemia, and may be useful in future determination of therapy responders. The low number of patients and the heterogeneity of acute myeloid leukemia limited the identification of gene expression predictive of therapy response. Therapy-induced gene expression reflects the complex biological processes involved in clinical cancer cell eradication and should be explored for future enhancement of therapy.</p

Barns rett til vitnefritak overfor nærstående: Harmonerer straffeprosessloven §122 om at «Fritak for vitneplikt gjelder ikke for fornærmede eller vitner under 12 år», med Den Europeiske Menneskerettighetskonvensjon og FNs barnekonvensjon?

Master i rettsvitenskapJUS399MAJU

Rapport fra prosjektet "Spesialpedagogisk kompetanseutvikling Norge-Nordvest-Russland 2002-2005"

Denne rapporten oppsummerer prosjektet ”Spesialpedagogisk kompetanseutvikling Norge–-Nordvest-Russland 2002–2005”. Det er den avsluttende delen av et norsk-russisk samarbeid som har strukket seg over perioden 1998–2005. Prosjektet er grundig beskrevet i prosjektplanen som ble utarbeidet i sin endelige form i mars 2003 (vedlagt). Første del av samarbeidet, perioden 1998–2001, var organisert i prosjektet ”Spesialpedagogikk Ark-hangelsk”. Det er først beskrevet i prosjektplanen fra juli 1998 og oppsummert i prosjektrapporten som ble utarbeidet høsten 2001 (begge er vedlagt)

p53 protein biosignatures in acute myeloid leukemia

p53 is a tumor suppressor protein often regarded as the guardian of the genome. It is a highly connected protein involved in many signaling processes in the cell. The inactivation of p53 through genetic mutations in TP53 is common in human cancers and can be detected in more than 50% of malignant tumors. In acute leukemia however, p53 inactivation is not normally a part of leukemogenesis and TP53 is found to be wild-type in >90% of the cases. This thesis has sought to elucidate the nature of the p53 protein regulation in acute myeloid leukemia to increase our understanding of disease development. The experiments have proposed that p53 is wild type, expressed and capable of transactivation of target genes. However, p53 phosphorylation could be correlated to expression of the anti-apoptotic protein Bcl-2 suggesting that Bcl-2 can function as a downstream block to p53-mediated apoptosis. Furthermore, Bcl-2 levels could be associated to a specific mutation in the receptor tyrosine kinase Flt3. Flt3 mutation has been found to be a strong predictor of disease relapse in AML, and driving Bcl-2 expression, thereby inhibiting the p53 pathway, may propose a new important event in leukemogenesis. This thesis has further shown that p53 exists as two main isoforms in patient material from acute myeloid leukemia. The expression of these was influenced by chemotherapy in vivo and induction of one specific form correlated to induction of known p53 target genes. The p53 protein has many known sites for post-translational modifications and serves as a substrate for many enzymes. The p53 protein may thus be a central node in a large network of proteins whose activities are critical for cell life and death. This may suggest that specific p53 signatures could serve as a ‘read-out’ for the p53 network. The expression of the described p53 isoforms were, using a novel correlation algorithm, found to be correlated to several clinical parameters including survival, remission and Flt3 mutation. This could imply that p53 may be used as a possible biomarker for clinical stratification of leukemia patients

Biochar - A market analysis and predictions for the future

In the light of the increasing focus on climate changes biochar is now considered one of the Negative Emission Technologies (NET) in the toolbox. Biochar is the product of pyrolyzed biomass and has a variety of applications besides capturing and storing carbon (PyCCS). This includes the established soil improvement application and newer, less explored applications as an additive in concrete or solar dye cells. Research for new applications is ongoing. Pyrolyzed wood feedstock, called biocarbon, is already being used in the metallurgical industry to replace fossil coal. The biochar market is still immature; the production is very low and so is the demand. This thesis analyzes the market state of affairs with the objective of predicting the future of biochar as an economically viable product. Some key points for new entrants are established through Porter’s five forces model and Value Chain Analysis. Some points on optimal production plant are presented. The analysis demonstrates that biochar plant size should not exceed a yearly production of 50 000 tons biochar because the costs of logistics become too large. This is due to biological constraint that limits the quantity of biomass that can be collected per area. The area required for producing the millions of tons biocarbon needed for the metallurgical industry is too large so biocarbon will not be able to replace fossil coal completely. The potential demand in the agricultural industry for biochar is even larger, several hundreds of thousands of tons, will neither be possible to produce. The potential supply will never reach the potential demand. This thesis demonstrates why the best chance of success is within the biochar for the agriculture market

Mat, klær og møbler: En studie av ulike avhendingsprosesser

Denne studien ser nærmere på mekanismene rundt hvorfor, hvordan og når man velger å kvitte seg med ting fra husholdningen. Forbruksforskning har lenge vært en veletablert nisje innen økonomi, antropologi, kultur-studier og sosiologi, men her er det den første delen av forbruket, det å tilegne seg ting, som tradisjonelt har stått i fokus. Avfall og handlinger som gjør noe til avfall er noe som ofte tas for gitt og som oversees, men å studere dette kan gi stor innsikt i våre sosiale handlingsmønstre og samfunnsstrukturer. Hvordan og hvorfor mennesker kvitter seg med ting er en viktig del av forbruket og har, som forbruket, implikasjoner for sosial status, identitet, tilhørighet og estetiske idealer. Fordi det finnes lite forskning på området, og spesielt lite norsk forskning, har jeg valgt å gjøre en eksplorerende empirisk studie hvor jeg bruker sensitiverende begreper i analysen av datamaterialet. Problemstillingen for studien kan deles inn i to hovedspørsmål: 1) Hvorfor velger man å kvitte seg med noe fra husholdningen? 2) Hva påvirker når og hvordan man velger å kvitte seg med noe fra husholdningen? I et forsøk på å få et helhetlig bilde av hvilke vurderinger som gjøres når man skal kvitte seg med eiendeler og hvordan disse vurderingene eventuelt varierer mellom forskjellige kategorier av ting har jeg valgt å gå bredt ut og ser på tre typer eiendeler: det en konsumerer (mat og dens tilhørende emballasje), det en kler seg med (klær og sko) og det en omgir seg med i hjemmet (bruksting og møbler). For å belyse problemstillingen har jeg gjort dybdeintervjuer med ni personer, fem menn og fire kvinner jevnt fordelt på aldersgruppene 20-30 år og 50-60 år. Ved å se på et så bredt utvalg av eiendeler får jeg ikke bare et innblikk i hvorfor og hvordan man kvitter seg med dem, men også hva som er forholdet mellom dem. Gjennom en «grounded» analyse viste blant annet tid seg som et sensitiverende konsept som både separerer de tre typene eiendeler og binder dem sammen. For å illustrere dette har jeg laget to forløpsmodeller som viser avhendingsprosessen i et tidsperspektiv. Den underliggende tidslinjen skiller de tre kategoriene av eiendeler da de har forskjellige livsløpslengder i husholdningen. Mat og emballasje har det korteste livsløpet på grunn av matens materialitet og emballasjens tap av primærfunksjon så snart maten er pakket ut. Disse utgjør også mesteparten av hverdagsavfallet som krever tid i hverdagen for å håndteres. Klær, sko, bruksting og møbler er underlagt samme forløpsmodell, men klær og sko har generelt et kortere livsløp i husholdningen og er nærmere knyttet til kroppen enn bruksting og møbler som også i større grad utgjør en del av «hjemmet». Ved hjelp av forløpsmodellene har jeg forsøkt å illustrere at hvorfor og hvordan vi kvitter oss med ting er en kompleks prosess. Det er lite i studien som tyder på at det å kvitte seg med ting er en tankeløs handling som drives av et umettelig behov for det nye. Tvert imot krever det mye energi og nøye vurderinger, ikke bare i forhold til hvorvidt man ønsker å bli kvitt eller beholde, men også hvordan man eventuelt skal kvitte seg med det. Forhandlinger rundt hva man vil kvitte seg med skjer heller ikke i et vakuum, men i en hverdagssetting under konstant påvirkning fra sosiale og strukturelle forhold. Her har det også vært særlig fruktbart å trekke frem informantenes egne livsløpsfaser for å belyse at hvordan hverdagslivet er..

Optimization of NMR Data Utilization on Valhall - a Brown Chalk Oilfield

The Valhall field started production in 1982 and has been producing since. A vast amount of data has been gathered and interpreted since then. Because of its complexity, there are still many questions left unanswered. Some are questions related to the water flooding system; in-fill wells are drilled, and logging data detects unexpected water. Where does the water come from and why? Others are related to the confidence in estimated target parameters such as water saturation, porosity and permeability. Can this data contribute to increase the confidence in them? Valhall is a brown chalk field. It is a complex, mature field and consists of tight, fractured chalk. Successful reservoir management requires good understanding of the reservoir and the data. The Nuclear Magnetic Resonance is a fairly old technology and is well understood. It has a great potential of providing useful information along the wellbore. Data have been acquired from the reservoir but the applications in the Valhall reservoir management has not been exploited to its full potential. It has been used as a secondary source of porosity and saturation and used if no other source of such information has been available. The objective of the present study is to optimize the utilization of NMR data on Valhall through investigation of the current applications and possible additional applications. Investigations are done on the data quality, porosity, fluid saturations, permeability and the possibility of improving the understanding of water flooding. Moreover parameters are optimized to better fit conventional logs. Its applicability for well placement and Geosteering are discussed. The results lead to the conclusion that data is useful, trustworthy, and recommended for use in future operations. The extra information NMR provides regarding bound and movable water is added value and very useful in waterflood surveillance. NMR data provides important information about key reservoir properties

Impact of hull cleaning and crew performance on bunker consumption: Classification and optimization of underwater hull cleaning intervals under data uncertainty

This thesis investigates the impact of underwater hull cleaning and crew performance on bunker consumption using noon reports. Biofouling imposes increased resistance on oceangoing vessels over time, and hull cleanings are subsequently performed to remove marine growth and reduce resistance. With uncertain data, a classification model is proposed to identify hull cleaning dates. The hull cleaning dates classified by the proposed model outperform the company-reported dates in terms of fitting expectations. A model to economically optimize hull cleaning intervals is further defined, achieving savings of 0.3 – 1.4 % over a three-year period, by applying optimal intervals to vessels with two hull cleanings. Adding an additional hull cleaning resulted in fuel savings of 2.1 – 3.2 %. Although results are found under strict assumptions, they are similar to savings made by advanced continuous monitoring systems. Individual crew members are analyzed to find whether certain crew over- or underperforms in terms of fuel expenditure. Findings suggest that several masters and chief engineers have significant deviations in mean consumption even after controlling for all known covariates, although the causality of deviations remains unexplained. Using fixed effects regression models, the impact of hull cleaning on fuel consumption is estimated to be approximately 1 % for Panamax and Medium Range vessels, and 9 % for Suezmax vessels. Crew members are estimated to explain between 3 – 4 % of variation in fuel consumption. Several machine learning models were tested to measure effects on prediction accuracy. Linear models achieved prediction accuracies of 63.5 – 67.5 %, increasing by 3 – 8 %, while advanced non-linear models achieved prediction accuracies of 77.1 – 78.2 %, increasing by 2.5 – 3 %. The thesis’ findings contributes to existing literature by quantifying the impact of underwater hull cleaning and crew performance on bunker consumption under data uncertainty, by providing a model to identify hull cleanings and to observe potential savings of optimizing intervals