Fakultet for naturvitenskap og teknologi

Synthesis of Potential Metallo-beta-Lactamase Inhibitors

Paulsen, Britt — Mon, 14 Nov 2011 23:00:00 GMT

Paulsen, Britt

Protein-protein binding affinities calculated using the LIE method

Andberg, Tor Arne Heim — Mon, 14 Nov 2011 23:00:00 GMT

Andberg, Tor Arne Heim
Absolute binding free energies for the third domain of the turkey ovomucoid inhibitor in complex with Streptomyces griseus proteinase B and porcine pancreatic elastase has been calculated using the linear interaction energy method.

Design and Evaluation of a Medical Microwave Radiometer for Observing Temperature Gradients Subcutaneously in the Human Body

Klemetsen, Øystein — Tue, 31 Jan 2012 23:00:00 GMT

Klemetsen, Øystein
The topic covered in this thesis is medical temperature measurement of subcutaneous parts of human tissue with use of microwave radiometry. Radiometry is a completely non-invasive, non-toxic and relatively inexpensive sensing modality. The radiometric technique is based on the measurement of electromagnetic noise power emitted by lossy materials. The method has explicit low investment costs and low technological complexity, but relatively low spatial resolution. Still the method can be useful for some dedicated medical applications. Fundamental radiometric theory and dielectrical properties of biological tissues are derived. The process to realize a miniaturized radiometer is going from active antenna configuration to a complete miniaturized radiometer and finally to a modular radiometer, that is used \textsl{in-vivo} on humans. Different radiometers were designed, simulated, built and tested on realistic human phantoms. \textit{In vivo} experiments were also conducted to verify the prototype radiometer and to test the ability to be used in tailored medical diagnostics. The primary application covered is temperature gradient measurement during microwave hyperthermia and in pediatric vesicouretaral reflux (VUR) detection. Hyperthermia is a therapeutic technique in which cancerous tissue is heated to 40-45$^\circ$C, inducing vascular and cellular changes that improve the therapeutic effectiveness when used in conjunction with chemotherapy or radiation therapy. VUR is abnormal flow of urine from the bladder back to the upper urinary tract. Another application where this radiometer can be of great interest is in breast cancer diagnostic. Breast cancer is a type of cancer that forms in tissues of the breast; usually in the ducts and lobules and can occur in both men and woman. We present results from radiometric measurement on human phantoms during a hyperthermia heating sequence. Experimental evidence shows that radiometry can be used for temperature quality assurance of the heated volume in depth. In VUR detection, the first step is to heat the bladder prior to detection of the reflux. We present results from measurements \textsl{in-vivo} with a water filled balloon in the human mouth, that mimics pediatric bladder heating. Results show that the radiometer can be used as the first step in the novel VUR detection. Radiometry antennas are one of the most critical components in a radiometer system. An elliptical printed circuit board antenna is designed and matched to the human body. Further, an antenna with suction, with use of negative pressure to mount the antenna onto the human body for improved radiometric performance, was also proposed and built. The simple and elegant solution for the coupling of the antenna with use of negative pressure, documents improved performance in estimating the true temperature as well as exhibiting smaller fluctuation in the radiometric signal.; Bakgrunnen for avhandlingen er at nåværende metoder som brukes til screening av brystkreft hos kvinner er røntgenbaserte gjennomlysningsmetoder med assosierte utfordringer som tilgjengelighet og stor grad av feildiagnostisering. Videre er vesicouretral refluks en tilstand med tilbakestrøm av urin fra blære, opp via urinleder til nyre, og som i visse tilfeller kan forårsake nyreskade. Denne diagnosen blir ofte stilt i barneår, hvor barnet da må i gjennom diagnostiske prosedyrer som kan oppleves smertefulle. Vi ønsker å finne ut om det er mulig å lage et lite og fungerende mikrobølgeinstrument som er fullstendig ufarlig for pasienten og som kan brukes til medisinsk diagnostikk av disse sykdommene. Vi har designet, simulert og bygget et mikrobølgeinstrument som på fagspråk betegnes et radiometer. Radiometeret er bygget av kommersielt masseproduserte og lett tilgjengelige komponenter. Ved å velge en slik konstruksjonsmetode, kan kostnadene holdes nede og størrelsen på selve instrumentet blir minimalisert. Deteksjonsprinsippet som ligger til grunn for instrumenteringen er å måle naturlig varmestråling fra kroppen for å kunne avdekke temperaturdifferanser inne i selve vevet. Det er kjent fra studier at kreftsvulster har høyere temperatur (opptil 5C) enn normalt friskt vev. Denne temperaturkontrasten kan man avlese med dette instrumentet om temperaturdifferansen er tilstrekkelig høy. Videre kan instrumentet potensielt brukes i en helt ny metode for detektering av refluks av urin fra blære til nyrer. Instrumenteringen har vært testet på mennesker, hvor man har klart å lage et måleoppsett som simulerer oppvarming av en pediatrisk blære. Denne oppvarmingen av blæren er en forutsetning for videre deteksjon av refluks av urin fra blære til en eller begge nyrene.
The papers of this thesis are not available in Munin:
1. Ø. Klemetsen, Y. Birkelund, and S. K. Jacobsen: 'Design of medical radiometer front-end for improved performance', Progress In Electromagnetics Research B (2011) Vol. 27, 289–306. Available at http://www.jpier.org/PIERB/pier.php?paper=10101204
2. Øystein Klemetsen, Svein Jacobsen and Yngve Birkelund: 'Radiometric temperature reading of a hot ellipsoidal object inside the oral cavity by a shielded microwave antenna put flush to the cheek' (paper in review)
3. Øystein Klemetsen and Svein Jacobsen: 'Improved Radiometric Performance Attained by an Elliptical Microwave Antenna With Suction', IEEE transactions on biomedical engineering (2012)59(1):263-271. Available at http://dx.doi.org/10.1109/TBME.2011.2172441
4. Yngve Birkelund, Øystein Klemetsen, Svein K. Jacobsen, Kavitha Arunachalam, Paolo Maccarini, and Paul R. Stauffer: 'Vesicoureteral Reflux in children : a phantom study of microwave heating and radiometric thermometry of pediatric bladder', IEEE transactions on biomedical engineering (2011)58(11):3269-3278. Available at http://dx.doi.org/10.1109/TBME.2011.2167148
5. Svein Jacobsen and Øystein Klemetsen: 'Improved detectability in medical microwave radio-thermometers as obtained by active antennas', IEEE transactions on biomedical engineering (2008)55(12):2778-2785. Available at http://dx.doi.org/10.1109/TBME.2008.2002156

Cogset : A High-Performance MapReduce Engine

Viken Valvåg, Steffen — Sun, 29 Jan 2012 23:00:00 GMT

Viken Valvåg, Steffen
MapReduce has become a widely employed programming model for large-scale data-intensive computations. Traditional MapReduce engines employ dynamic routing of data as a core mechanism for fault tolerance and load balancing. An alternative mechanism is static routing, which reduces the need to store temporary copies of intermediate data, but requires a tighter coupling between the components for storage and processing. The initial intuition motivating our work is that reading and writing less temporary data could improve performance, while the tight coupling of storage and processing could be leveraged to improve data locality. We therefore conjecture that a high-performance MapReduce engine can be based on static routing, while preserving the non-functional properties associated with traditional engines. To investigate this thesis, we design, implement, and experiment with Cogset, a distributed MapReduce engine that deviates considerably from the traditional design. We evaluate the performance of Cogset by comparing it to a widely used traditional MapReduce engine using a previously established benchmark. The results confirm our thesis that a high-performance MapReduce engine can be based on static routing, although analysis indicates that the reasons for Cogset's performance improvements are more subtle than expected. Through our work we develop a better understanding of static routing, its benefits and limitations, and its ramifications for a MapReduce engine. A secondary goal of our work is to explore how higher-level abstractions that are commonly built on top of MapReduce will interact with an execution engine based on static routing. Cogset is therefore designed with a generic, low-level core interface, upon which MapReduce is implemented as a relatively thin layer, as one of several supported programming interfaces. At its core, Cogset provides a few fundamental mechanisms for reliable and distributed storage of data, and parallel processing of statically partitioned data. While this dissertation mainly focuses on how these capabilities are leveraged to implement a distributed MapReduce engine, we also demonstrate how two other higher-level abstractions were built on top of Cogset. These may serve as alternative access points for data-intensive applications, and illustrate how some of the lessons learned from Cogset can be applicable in a broader context.
The papers of this thesis are not available in Munin:
1. Steffen Viken Valvåg and Dag Johansen: 'Oivos : simple and efficient distributed data processing' (2008). In Proceedings of the 2008 Tenth IEEE International Conference on High Performance Computing and Communications (HPCC 2008), pages 113– 122. IEEE Computer Society. Available at http://dx.doi.org/10.1109/HPCC.2008.105
2. Steffen Viken Valvåg and Dag Johansen: 'Update Maps : a new abstraction for High-Throughput Batch processing' (2009). In Proceedings of the 2009 IEEE International Conference on Networking, Architecture, and Storage (NAS 2009), pages 431–438. IEEE Computer Society. Available at http://dx.doi.org/10.1109/NAS.2009.73
3. Steffen Viken Valvåg and Dag Johansen: 'Cogset : a unified engine for reliable storage and parallel processing' (2009). In Proceedings of the 2009 Sixth IFIP International Conference on Network and Parallel Computing (NPC 2009), pages 174– 181. IEEE Computer Society. Available at http://dx.doi.org/10.1109/NPC.2009.23
4. Steffen Viken Valvåg, Dag Johansen, and Åge Kvalnes: 'Cogset vs. Hadoop : measurements and analysis', (2010). In Proceedings of the 2010 Second IEEE International Conference on Cloud Computing Technology and Science (CloudCom 2010), pages 768–775. IEEE Computer Society. Available at http://dx.doi.org/10.1109/CloudCom.2010.103

Estimating production loss due to icing on wind turbines

Haaland, Silje Sanderud — Tue, 31 May 2011 22:00:00 GMT

Haaland, Silje Sanderud
Icing on wind turbines are known to lower their performance, but the exact relationship between wind, ice and power production is not known. In this thesis power loss due to icing on turbine blades at Aapua wind park is investigated for the winter season 2009-2010. The total loss is found to be 30%, whereof 25% is concluded being due to icing. Three different methods are presented to estimate a power output model P(V,I), based on empirical data of wind speed, ice load and power production from a wind turbine. The models estimate power output from wind speed and ice load observations. Their performance are compared using correlation and root mean square error (RMSE), and the kriging method, using a weighted mean to calculate power output, is found best. A comparison of the proposed kriging model to an existing model show a 10% increase in performance for the kriging method. Testing shows that kriging works well for low wind speeds and low ice loads, but tends to overestimate production during high ice loads. For the season as a whole, the modelled power output underestimates the power production with 1%. Time series of modelled, measured and expected power output, together with ice load and temperature measurements, are investigated. Results show that sublimation, shedding, melting and accretion processes on the turbine wings, are not fully captured by the model. Mismatch between ice loads on measuring equipment compared to turbine blades, together with insufficient number of observation data, are found to be the main reasons for inaccuracy in the model.

The Dayside Open/Closed Field line Boundary -Ground-based optical determination and examination

Johnsen, Magnar Gullikstad — Mon, 19 Dec 2011 23:00:00 GMT

Johnsen, Magnar Gullikstad
The Open/Closed eld line Boundary (OCB) is the most important boundary in the magnetospheric system. On the dayside, the equatorward edge of the 6300 Å[OI] cusp aurora can be used as a proxy for the OCB. This work, which is a dissertation for the degree of philosophiæ Doctor consists of three scienti c papers focusing on the latitude of the optical cusp OCB and one paper focusing on polar cap patch generation mechanisms in the vicinity of the OCB. In Paper I we use modeling to demonstrate the variability of the cusp aurora with respect to vertical volume emission rate pro les and horizontal modulation owing to neutral wind. A meridian scanning photometer (MSP) simulator has been developed in order to study the manifestation of the cusp aurora in the MSP data from Svalbard. A method for obtaining the OCB location and nding the correct mapping altitude in order to transform the OCB location from MSP scan angle to magnetic latitude is found by simulating the horizontal movement of a reference cusp aurora. The reference cusp aurora, which is based on expected ionospheric and atmospheric conditions and electron precipitation characteristics, is de ned from the modeling results. Uncertainties in the scan angle to magnetic latitude transformation are found by simulating a wide range of realistic cusp auroras deviating from the reference cusp aurora. In Paper II the method of Paper I for finding the OCB is tested on real MSP data and compared with the OCB as obtained by satellite energetic particle measurements with very successful results. In Paper III the method of Paper I is used on 15 years of MSP data from Svalbard in order to study the statistical behavior of the cusp OCB. A possible relationship between the OCB latitude in the cusp and the solar cycle is revealed, and a possible expansion is brie y discussed. By comparing the OCB latitude with solar wind parameters, solar wind-magnetosphere coupling functions and geomagnetic indices, good correlations are found, which are in concurrence with previous satellite based, statistical studies. We nd a relationship between the OCB latitude and the ring current density (SYM/H), demonstrating great complexity in the physics behind the OCB location. We argue that the balance between reconnection dynamics on the dayside and nightside as well as the history or integral of previous events in the magnetospheric system are important factors for governing the cusp OCB latitude. Paper IV gives an overview of the solar wind and ionospheric conditions as measured during the Investigation of Cusp Irregularities 2 sounding rocket campaign. The rocket was launched through a newly produced polar cap patch. Based on the measurements performed in-situ by the rocket instrumentation and with groundbased optics and radars, a new creation mechanism, which partly involves ionization by both particle precipitation and solar irradiation and upwelling from sub F-layer altitudes, is suggested.
The papers of this thesis are not available in Munin:
1. M. G. Johnsen, D. A. Lorentzen, J, M. Holmes and U. P. Løvhaug: 'A model based method for obtaining the open/closed field line boundary from the cusp auroral 6300 Å[OI] red line' Journal of Geophysical research (forthcomming paper).
2. M. G. Johnsen and D. A. Lorentzen: 'The dayside open/closed eld line boundary as seen from space- and ground-based instrumentation' Journal of Geophysical research (forthcomming paper).
3. M. G. Johnsen and D. A. Lorentzen: 'A statistical analysis of the optical dayside open/closed field line boundary' Journal of Geophysical research (in press). Availavle at http://dx.doi.org/10.1029/2011JA016984
4. D. A. Lorentzen, J. Moen, K. Oksavik, F. Sigernes, Y. Saito and M. G. Johnsen: 'In situ measurement of a newly created polar cap patch', Journal of Geophysical research (2010), vol. 115, A12323. Available at http://dx.doi.org/10.1029/2010JA015710

Demetalation of metallocorroles

Capar, Can — Tue, 30 Sep 2008 22:00:00 GMT

Capar, Can
Although the chemistry of corroles has grown spectacularly in recent years, the field has been marred by the lack of convenient protocols for demetalation of metallocorroles. In this thesis, I have developed a superior procedure for demetalating copper corroles with concentrated H2SO4 and 5-200 equiv FeCl2 or SnCl2. The yields obtained with this reductive procedure are generally substantially better than with HCl3/H2SO4, CH2Cl2/H2SO4, or H2SO4 alone. With an oxidation-prone metallocorrole such as Cu[T(p-OMeP)C], the reductive protocol was essential for obtaining any measurable yield of the free base at all. Free-base β-octabromo-mesotriarylcorroles were also obtained in pure form, in good yields, and with relative ease via this procedure.

Sen kenozoisk sedimentasjonsmiljø på kontinentalmarginen utenfor Troms

Rydningen, Tom Arne — Sun, 18 Apr 2010 22:00:00 GMT

Rydningen, Tom Arne
Batymetriske og seismiske data er analysert for å utrede den senkenozoiske utviklingen av kontinentalmarginen utenfor Troms. Prograderende kiler av glasigene avsetninger er identifisert nær munningen av de glasiale trauene Andfjorden og Malangsdjupet. En seismisk stratigrafi med to hovedenheter, S1 og S2, er definert. Enhet S2 viser hovedsakelig et prograderende mønster mot nordvest, mens S2 er aggraderende på kontinentalhylla og prograderende på skråninga. En utviklingsmodell for studieområdet er utledet, der en tidlig (glasi-)fluvial fase er etterfulgt av en fase karakterisert av større isdekker som nådde ut til eggakanten gjentatte ganger. Landformer på havbunnen er beskrevet og genesen til disse er tolket. Tre grupper av landformer er identifisert: subglasiale formelementer, formelementer dannet ved breranden, og post-glasiale formelementer. Under siste glasiale maksimum beveget isstrømmer seg i trauene, mens bankene var okkupert av en mer passiv is. Deglasiasjonen av studieområdet var trolig hurtig i trauene, da megaskala glasiale lineasjoner er godt bevart på havbunnen. Lineasjonene er overlagret av avsetninger som viser noen stopp eller mindre fremrykk under tilbaketrekningen. Forekomsten av en serie frontavsetninger på banken tyder på at tilbaketrekningen var langsommere her. Etter at området var deglasiert har havstrømmer og vertikal migrasjon av fluider modifisert havbunnen.

Air temperature at 90 km altitude in the Artic obtained using meteor radar : validation, characterization and climate change.

Kluken, Lars Grytbakk — Thu, 29 Sep 2011 22:00:00 GMT

Kluken, Lars Grytbakk
Temperatures at 90 km altitude above Ramfjordmoen (69°N, 19°E) have been obtained with the Nippon/Norwegian Tromsø Meteor Radar. The temperatures have been derived from meteor radar decay rates using two techniques: the pressure based and the temperature gradient based methods. The results have been compared to the Microwave Limb Sounder (MLS) instrument on board the Aura spacecraft. It was found that the pressure method was simpler to implement than the temperature gradient method and gave better results in relation to the MLS temperatures. With the use of a technique for statistical comparison of geophysical data, the intrinsic uncertainty of the radar temperatures was estimated to be less than 4 K. Two attempts to combine the two techniques in order to measure both temperatures and pressure with the meteor radar have been carried out. One of the approaches proved to be feasible and gave promising results. This indicates that the meteor radar may have the potential of producing continuous temperature and pressure measurements virtually independent of external data. A new collocated sodium lidar is introduced and some initial comparisons are carried out between the two instruments. At times there were large discrepancies, but more data is necessary in order to obtain reliable results. Finally, some possible uses of the radar temperatures are proposed. A method for investigating long term trends is discussed in detail. The data available resulted in a trend of - 2.2 K per decade, but more data is required to establish a trend with higher confidence. It was estimated that approximately 13 years of data are needed to determine the trend with a probability of 90 %.

Purification and characterization of a salt tolerant metallo-beta-lactamase from Aliivibrio salmonicida

Kristiansen, Anders — Thu, 30 Jun 2011 22:00:00 GMT

Kristiansen, Anders
Beta-lactamases are enzymes that inactivate beta-lactam antibiotics by hydrolyzing the amide bond that exists in the beta-lactam ring, disrupting the ring structure and make the antibiotics nonfunctional against bacteria. Metallo-beta-lactamases (MBLs) are a group of beta-lactamases which needs metal ions bound to its active site in order to function and are an important factor in many bacteria in order to be resistant to antibiotics. Resistance to antibiotics is a serious health problem which increases with excessive use of antibiotics. This study is based on the purification and characterization of MBL from the psychrophilic organism Aliivibrio salmonicida which is the causative agent for the Hitra disease, or cold-water vibrosis, in seawater-farmed Atlantic salmon (Salmo salar). Characterization of asMBL has revealed interesting properties in regards of temperature-, salt-, pH optimum and enzyme kinetics. asMBL properties have been compared to VIM-7, a MBL isolated from hospital which thrives in mesophilic conditions. Compared to VIM-7, asMBL proves to be adapted to the colder and saltier environment of the seawater. asMBL enzyme kinetics have also been compared to MBLs from human pathogenic bacteria and asMBL showed a general lower enzymatic efficiency in terms of lower kcat and higher Km at the same experimental conditions as the other MBLs. Nitrocefin, the substrate used for the characterization of asMBL, had its stability in temperature, pH and Tris investigated. From these investigations it seems plausible that nitrocefin is auto-hydrolyzed in a synergetic matter when present at high pH and in Tris buffer. An attempt to crystallize the protein and retrieve a structure was unsuccessful as it turns out that the protein seems to be aggregating at high concentrations.