| 1. |
- Nord, Helena, 1980-
(författare)
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Application of Genomic and Expression Arrays for Identification of new Cancer Genes
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Copy number variation (CNV) comprises a recently discovered kind of variation involving deletion and duplication of DNA segments of variable size, ranging from a few hundred basepairs to several million. By altering gene dosage levels or disrupting proximal or distant regulatory elements CNVs create human diversity. They represent also an important factor in human evolution and play a role in many disorders including cancer. Array-based comparative genomic hybridization as well as expression arrays are powerful and suitable methods for determination of copy number variations or gene expression changes in the human genome. In paper I we established a 32K clone-based genomic array, covering 99% of the current assembly of the human genome with high resolution and applied it in the profiling of 71 healthy individuals from three ethnic groups. Novel and previously reported CNVs, involving ~3.5% of the genome, were identified. Interestingly, 87% of the detected CNV regions overlapped with known genes indicating that they probably have phenotypic consequences. In papers II through IV we applied this platform to different tumor types, namely two collections of brain tumors, glioblastoma (paper II) and medulloblastoma (paper III), and a set of bladder carcinoma (paper IV) to identify chromosomal alterations at the level of DNA copy number that could be related to tumor initiation/progression. Tumors of the central nervous system represent a heterogeneous group of both benign and malignant neoplasms that affect both children and adults. Glioblastoma and medulloblastoma are two malignant forms. Glioblastoma often affects adults while the embryonal tumor medulloblastoma is the most common malignant brain tumor among children. The detailed profiling of 78 glioblastomas, allowed us to identify a complex pattern of aberrations including frequent and high copy number amplicons (detected in 79% of samples) as well as a number of homozygously deleted loci. These regions encompassed not only previously reported oncogenes and tumor suppressor genes but also numerous novel genes. In paper III, a subset of 26 medulloblastomas was analyzed using the same genomic array. We observed that alterations involving chromosome 17, especially isochromosome 17q, were the most common genomic aberrations in this tumor type, but copy number alterations involving other chromosomes: 1, 7 and 8 were also frequent. Focal amplifications, on chromosome 1 and 3, not previously described, were also detected. These loci may encompass novel genes involved in medulloblastoma development. In paper IV we examined for the presence of DNA copy number alterations and their effect on gene expression in a subset of 21 well-characterized Ta bladder carcinomas, selected for the presence or absence of recurrences. We identified a number of novel genes as well as a significant association between amplifications and high-grade and recurrent tumors which might be clinically useful. The results derived from these studies increase our understanding of the genetic alterations leading to the development of these tumor forms and point out candidate genes that may be used in future as targets for new diagnostic and therapeutic strategies.
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| 2. |
- Abazajian, Kevork, et al.
(författare)
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CMB-S4 : Forecasting Constraints on Primordial Gravitational Waves
- 2022
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Ingår i: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 926:1
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Tidskriftsartikel (refereegranskat)abstract
- CMB-S4—the next-generation ground-based cosmic microwave background (CMB) experiment—is set to significantly advance the sensitivity of CMB measurements and enhance our understanding of the origin and evolution of the universe. Among the science cases pursued with CMB-S4, the quest for detecting primordial gravitational waves is a central driver of the experimental design. This work details the development of a forecasting framework that includes a power-spectrum-based semianalytic projection tool, targeted explicitly toward optimizing constraints on the tensor-to-scalar ratio, r, in the presence of Galactic foregrounds and gravitational lensing of the CMB. This framework is unique in its direct use of information from the achieved performance of current Stage 2–3 CMB experiments to robustly forecast the science reach of upcoming CMB-polarization endeavors. The methodology allows for rapid iteration over experimental configurations and offers a flexible way to optimize the design of future experiments, given a desired scientific goal. To form a closed-loop process, we couple this semianalytic tool with map-based validation studies, which allow for the injection of additional complexity and verification of our forecasts with several independent analysis methods. We document multiple rounds of forecasts for CMB-S4 using this process and the resulting establishment of the current reference design of the primordial gravitational-wave component of the Stage-4 experiment, optimized to achieve our science goals of detecting primordial gravitational waves for r > 0.003 at greater than 5σ, or in the absence of a detection, of reaching an upper limit of r < 0.001 at 95% CL.
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| 3. |
- Adamsson, Inger, et al.
(författare)
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Comparative effects of omeprazole, amoxycillin plus metronidazole versus omeprazole, clarithromycin plus metronidazole on the oral, gastric and intestinal microflora in Helicobacter pylori-infected patients
- 1999
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Ingår i: Journal of Antimicrobial Chemotherapy. - : Nature Publishing Group. - 0305-7453 .- 1460-2091. ; 45, s. A8-A8
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Tidskriftsartikel (refereegranskat)abstract
- Fourteen patients with Helicobacter pylori infection were treated with 20 mg omeprazole, 1 g amoxycillin and 400 mg metronidazole bd for 7 days (OAM), and 16 patients were treated with 20 mg omeprazole, 250 mg clarithromycin and 400 mg metronidazole bd for 7 days (OCM). Saliva, gastric biopsies and faecal samples were collected before, during (day 7) and 4 weeks after treatment in order to analyse alterations of the normal microflora and to determine antimicrobial susceptibility. Both treatment regimens resulted in marked quantitative and qualitative alterations. A selection of resistant streptococcal strains were noticed in both treatment groups, most apparent in the OCM group where a shift from susceptible to resistant strains was recorded. In the OAM group, six patients had overgrowth of resistant Enterobacteriaceae during treatment compared with none in the OCM group, in the gastric microflora. The MICs for Enterococcus spp. and Enterobacteriaceae in faeces increased significantly during treatment in both groups. Nine patients in the OAM group became intestinally colonized by yeasts during treatment. The total anaerobic microflora was strongly suppressed in both treatment groups, although most pronounced in the OCM group, where the frequency of clarithromycin-resistant bacteroides strains increased from 2 to 76% during treatment, and remained at 59% 4 weeks post-treatment. Even if the treatment outcome was better in the OCM group (100%) than in the OAM group (71%), the amoxycillin-based treatment might be preferable from an ecological point of view, since the qualitative alterations in terms of emergence and persistence of resistant strains seemed to be most pronounced in the clarithromycin-treated group.
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| 4. |
- Adlerberth, Ingegerd, 1959, et al.
(författare)
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Toxin-producing Clostridium difficile strains as long-term gut colonizers of healthy infants.
- 2014
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Ingår i: Journal of clinical microbiology. - 1098-660X. ; 52:1, s. 173-179
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Tidskriftsartikel (refereegranskat)abstract
- Clostridium difficile is a colonizer of the human gut, and toxin-producing strains may cause diarrhea if infectious burden is heavy. Infants are more frequently colonized than adults, but rarely develop C. difficile disease. It is not known whether strains of C. difficile differ in capacity to colonize and persist in the human gut microbiota. Here, we strain-typed isolates of C. difficile colonizing 42 healthy infants followed from birth to ≥12 months of age, using PCR ribotyping of the 16S-23S rRNA intergenic spacer region. The isolates were also characterized regarding carriage of the toxin genes tcdA, tcdB and cdtA/B, and capacity to produce toxin B in vitro. Most strains (71%) were toxin-producers, and 51% belonged to the 001 or 014 ribotypes, that often cause disease in adults. These ribotypes were significantly more likely than other ones to persist for ≥6 months in the infant micobiota, and were isolated from 13/15 children carrying such long-term colonizing strains. Ribotype 001 strains were often acquired in the first week of life and attained higher population counts than other C. difficile ribotypes in newborn infants' faeces. Several toxin-negative ribotypes were identified, two of which (GI and GIII) were long-term colonizers, each in one infant. Our results suggest that the toxin-producing C. difficile ribotypes 001 and 014 have special fitness in the infantile gut microbiota. Toxin-producing strains colonizing young children for long time periods may represent a reservoir for strains causing disease in adults.
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| 5. |
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| 6. |
- Behrendt, Lars, et al.
(författare)
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Life in the dark : far-red absorbing cyanobacteria extend photic zones deep into terrestrial caves
- 2020
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Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 22:3, s. 952-963
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Tidskriftsartikel (refereegranskat)abstract
- Chlorophyll (Chl) f and d are the most recently discovered chlorophylls, enabling cyanobacteria to harvest near-infrared radiation (NIR) at 700-780 nm for oxygenic photosynthesis. Little is known about the occurrence of these pigments in terrestrial habitats. Here, we provide first details on spectral photon irradiance within the photic zones of four terrestrial cave systems in concert with a detailed investigation of photopigmentation, light reflectance and microbial community composition. We frequently found Chl f and d along the photic zones of caves characterized by low light enriched in NIR and inhabited by cyanobacteria producing NIR-absorbing pigments. Surprisingly, deeper parts of caves still contained NIR, an effect likely attributable to the reflectance of specific wavelengths by the surface materials of cave walls. We argue that the stratification of microbial communities across the photic zones of cave entrances resembles the light-driven species distributions in forests and aquatic environments.
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| 7. |
- Bjurstrom, Johan, et al.
(författare)
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Energy harvesting feasibility for safety belt buckle
- 2024
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Ingår i: 2024 IEEE Wireless Power Technology Conference and Expo (WPTCE). - : Institute of Electrical and Electronics Engineers (IEEE). - 9798350349139 ; , s. 409-413
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Konferensbidrag (refereegranskat)abstract
- Technology is to an increasing degree becoming spatially distributed, as Internet of Things or sensors in vehicles. With this comes challenges in power supply, with either cumbersome amounts of batteries or power cables. In this paper we examine the potential of energy harvesting for powering a safety sensor on a belt buckle. Concluding that that the vibrations on this site are impractically small, we propose an energy harvester for transducing human induced mechanical energy. The electromagnetic energy harvester converts vertical buckle-in/-out events into rotations of a circular array of magnets, varying the flux through a coil. Both measurements and simulations are performed, the later showing a potential energy of 4mJ for a single buckle-in event. © 2024 IEEE.
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| 8. |
- Brånhult, Anna, et al.
(författare)
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Kartanalys för Sydsveriges agrara landskap : metodstudie om den genetiska mångfalden och det genetiska kulturarvet i dagens landskap / rapport från projektet Genetisk variation som kulturarv i Sydsveriges agrara landskap (GRAAL)
- 2013
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- ”Genetisk variation som kulturarv i Sydsveriges agrara landskap” (GRAAL) är ett projekt som nyligen initierats och bedrivs i samarbete mellan Sveriges Lantbruksuniversitet (SLU), Centrum för Biologisk Mångfald (CBM) och Nordiskt Genresurscenter (NordGen). Projektets syfte är att studera den genetiska mångfalden och föreslå bevarandeåtgärder kring det genetiska kulturarvet i träd och buskar i dagens landskap. Projektet avser således att identifiera och åldersbestämma samt att bedöma den genetiska variationen hos stubbskottsträd i det skånska kulturlandskapet. Projektet avser också att som ett led i detta arbete ta fram ett tvärvetenskapligt och tvärsektoriellt arbetssätt där moderna genetiska analyser samspelar med nya arkeologiska och historiska metoder och landskapsanalys. Denna rapport presenterar en historisk kartstudie som går ut på att identifiera områden där gamla flerstammiga träd med sockel kan påträffas.
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| 9. |
- Csenki, Leonard, et al.
(författare)
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Proof of principle of a generalized fuzzy Hough transform approach to peak alignment of one-dimensional 1H NMR data
- 2007
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Ingår i: Analytical and Bioanalytical Chemistry. - : Springer Science and Business Media LLC. - 1618-2642 .- 1618-2650. ; 389:3, s. 875-885
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Tidskriftsartikel (refereegranskat)abstract
- In metabolic profiling, multivariate data analysis techniques are used to interpret one-dimensional (1D) 1H NMR data. Multivariate data analysis techniques require that peaks are characterised by the same variables in every spectrum. This location constraint is essential for correct comparison of the intensities of several NMR spectra. However, variations in physicochemical factors can cause the locations of the peaks to shift. The location prerequisite may thus not be met, and so, to solve this problem, alignment methods have been developed. However, current state-of-the-art algorithms for data alignment cannot resolve the inherent problems encountered when analysing NMR data of biological origin, because they are unable to align peaks when the spatial order of the peaks changes—a commonly occurring phenomenon. In this paper a new algorithm is proposed, based on the Hough transform operating on an image representation of the NMR dataset that is capable of correctly aligning peaks when existing methods fail. The proposed algorithm was compared with current state-of-the-art algorithms operating on a selected plasma dataset to demonstrate its potential. A urine dataset was also processed using the algorithm as a further demonstration. The method is capable of successfully aligning the plasma data but further development is needed to address more challenging applications, for example urine data.
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| 10. |
- Daraei, Mahsa, 1991-
(författare)
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Production planning of CHP plants integrated with bioethanol production and local renewables
- 2019
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Production planning of an energy system is dependent on parameters such as energy demand and energy conversion technologies, which are influential in making decisions on operation strategy and optimal performance of the system. In accordance with the European Union energy policy, the share of renewable resources in the energy supply is growing. Improvement in energy technology is considered to be a pathway to achieve the target of 100% renewable power supply in Sweden by 2040. Increased utilization of renewable resources in energy systems and transportation sectors as well as improved energy conversion technologies would add complexity to the systems. Development of such complex systems depends on several key parameters, including availability of local resources, changes in daily energy use behavior, market price and weather conditions. Therefore, optimization and long-term production planning of such systems will be crucial considering the alternating nature of renewable resources. The aim of this thesis is to develop an optimization model for a regional energy system to provide advanced knowledge for production planning for combined heat and power (CHP) plants. The energy system in the county of Västmanland in central Sweden is used as the case for study. The regional system consists of CHP plants, heat only boilers and renewable resources. Two different optimization cases are developed for the analysis, one with increased energy supply from local renewables, and the other with integrated transport fuels production in a polygeneration system. The model includes the whole chain from availability of resources to the final energy use. The effect of different parameters relating to trends in energy demand and supply on operational strategy of the studied system is investigated by developing different scenarios. The potential solar power production from grid-connected solar cells installed on the rooftops of buildings in the region is added to the system in the base scenario. Then, the first scenario analyzes the increased application of heat pumps to replace the district heating in some of the buildings in the region. The influence of electrification of the transportation system as a result of increased penetration of electric vehicles is investigated in the second scenario. Two further scenarios evaluate the effects of integration of bioethanol production with existing CHP plants and increased application of bioethanol cars and hybrid vehicles in the regional transportation system. The study demonstrates the importance of production planning of the energy system at the regional scale in relation to resource availability and energy imports. The main conclusion of this thesis is that the polygeneration and increased use of heat pumps could influence the production planning of the system in terms of fuel use, plants operation, fossil-based emissions, and energy demand and import. However, increased use of hybrid vehicles represents the optimal case for the mentioned parameters.
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