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- Andersson, Anna, et al.
(author)
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Gene expression profiling of leukemic cell lines reveals conserved molecular signatures among subtypes with specific genetic aberrations
- 2005
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In: Leukemia. - : Springer Science and Business Media LLC. - 1476-5551 .- 0887-6924. ; 19:6, s. 1042-1050
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Journal article (peer-reviewed)abstract
- Hematologic malignancies are characterized by fusion genes of biological/clinical importance. Immortalized cell lines with such aberrations are today widely used to model different aspects of leukemogenesis. Using cDNA microarrays, we determined the gene expression profiles of 40 cell lines as well as of primary leukemias harboring 11q23/MLL rearrangements, t(1;19)[TCF3/PBX1], t(12;21)[ETV6/RUNX1], t(8;21)[RUNX1/CBFA2T1], t(8;14) [IGH@/MYC], t(8;14)[TRA@/MYC], t(9;22)[BCR/ABL1], t(10;11) [PICALM/MLLT10], t(15;17)[PML/RARA], or inv(16)[CBFB/MYH11]. Unsupervised classification revealed that hematopoietic cell lines of diverse origin, but with the same primary genetic changes, segregated together, suggesting that pathogenetically important regulatory networks remain conserved despite numerous passages. Moreover, primary leukemias cosegregated with cell lines carrying identical genetic rearrangements, further supporting that critical regulatory pathways remain intact in hematopoietic cell lines. Transcriptional signatures correlating with clinical subtypes/primary genetic changes were identified and annotated based on their biological/molecular properties and chromosomal localization. Furthermore, the expression profile of tyrosine kinase-encoding genes was investigated, identifying several differentially expressed members, segregating with primary genetic changes, which may be targeted with tyrosine kinase inhibitors. The identified conserved signatures are likely to reflect regulatory networks of importance for the transforming abilities of the primary genetic changes and offer important pathogenetic insights as well as a number of targets for future rational drug design.
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| 3. |
- Andersson, Anna, et al.
(author)
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Microarray-based classification of a consecutive series of 121 childhood acute leukemias: prediction of leukemic and genetic subtype as well as of minimal residual disease status.
- 2007
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In: Leukemia. - : Springer Science and Business Media LLC. - 1476-5551 .- 0887-6924. ; 21:6, s. 1198-1203
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Journal article (peer-reviewed)abstract
- Gene expression analyses were performed on 121 consecutive childhood leukemias (87 B-lineage acute lymphoblastic leukemias (ALLs), 11 T-cell ALLs and 23 acute myeloid leukemias (AMLs)), investigated during an 8-year period at a single center. The supervised learning algorithm k-nearest neighbor was utilized to build gene expression predictors that could classify the ALLs/AMLs according to clinically important subtypes with high accuracy. Validation experiments in an independent data set verified the high prediction accuracies of our classifiers. B-lineage ALLs with uncharacteristic cytogenetic aberrations or with a normal karyotype displayed heterogeneous gene expression profiles, resulting in low prediction accuracies. Minimal residual disease status (MRD) in T-cell ALLs with a high (40.1%) MRD at day 29 could be classified with 100% accuracy already at the time of diagnosis. In pediatric leukemias with uncharacteristic cytogenetic aberrations or with a normal karyotype, unsupervised analysis identified two novel subgroups: one consisting mainly of cases remaining in complete remission (CR) and one containing a few patients in CR and all but one of the patients who relapsed. This study of a consecutive series of childhood leukemias confirms and extends further previous reports demonstrating that global gene expression profiling provides a valuable tool for genetic and clinical classification of childhood leukemias.
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- Andersson, Patrik, 1974, et al.
(author)
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Framtidsbilder för samhällsbyggnad
- 2006
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Reports (other academic/artistic)abstract
- Framtidsbilder för samhällsbyggnad 2020De kommande 15 åren står institutionen för Bygg- och miljöteknik inför stora förändringar. Därför har institutionen initierat projektet Framtidsbilder 2020 där man engagerat en framtidspanel bestående av elva yngre disputerade forskare. Arbetet inleddes med ett breddgruppsmöte där 110 personer representerande institutionens personal och studenter deltog. Vid mötet identifierades ett antal trender och osäkra utvecklingar som påverkar framtiden inom samhällsbyggnadsområdet. Deltagarna bidrog också med idéer till en önskvärd utveckling, vilket har sammanställts och utgör grunden till en gemensam önskvärd framtid/vision för institutionen. Materialet från breddgruppsmötet har bearbetats av Framtidspanelen och resulterat i fyra scenarier som beskriver hur samhällsbyggnadsområdet kan se ut år 2020. Syftet med framtidsbilderna är att de ska vara vägledande för institutionens beslut och förhållningssätt under de kommande åren.Fyra scenarierTurning TorsoSamhället präglas av en ekonomi som är på uppgång, och av ett nytänkande och öppet samhälle. Materiell status och individualism är viktigt. Detta leder till en hög arbetsbelastning samt krav på exklusiva varor av hög kvali-tet. Det finns en stor medvetenhet om miljöpåverkan och klimatförändringar och lösningarna för att klara energiförsörjningen är innovativa.Eco-metropolenDet sveper en grön våg genom dagens samhälle. Under de senaste 15 åren har vi insett att jorden skall vara en bebolig plats även åt dem som kommer efter oss. Vi söker ständigt efter nya, mer förfinade metoder att tillvarata de resurser vi har. Samhället och individen är i balans. Ekonomin är god och vi är miljömedvetna, trygga och integrerade. Nytänkande premieras och icke- materialistiska värderingar står högt i kurs. Vi tänker individuellt, men agerar mer än gärna för kollektivets bästa. Utbildning är gratis TrädgårdsstadenEtt samhälle där vi lärt oss hantera stress, men känner oss otrygga och helst umgås i slutna sociala sammanhang. Vi bor enkelt inne i stan, eller gärna på landsbygden nära storstäderna. Minskade behov av högutbildade i samhället gör att vi har svårt att rekrytera studenter till teknikutbildningar. Det traditionella tankesättet leder till kulturkrockar med företag och personer från andra länder.Gated communitiesFörsämrad ekonomi och ökad egoism har lett fram till ett stressat, otryggt och segregerat samhälle. Accelererande klimatförändringar och ökad miljö-påverkan skrämmer oss, men trots det åtgärdar vi inte problemen, utan koncentrerar oss på konsekvenserna. Arbetslöshet i samhällsbyggnadssek-torn leder till sänkt status för samhällsbyggaren. Vi har därför svårt att rekrytera studenter, och även forskningen har låg status.
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- Aulchenko, Yurii S, et al.
(author)
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Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts
- 2009
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In: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 41:1, s. 47-55
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Journal article (peer-reviewed)abstract
- Recent genome-wide association (GWA) studies of lipids have been conducted in samples ascertained for other phenotypes, particularly diabetes. Here we report the first GWA analysis of loci affecting total cholesterol (TC), low-density lipoprotein (LDL) cholesterol, high-density lipoprotein (HDL) cholesterol and triglycerides sampled randomly from 16 population-based cohorts and genotyped using mainly the Illumina HumanHap300-Duo platform. Our study included a total of 17,797-22,562 persons, aged 18-104 years and from geographic regions spanning from the Nordic countries to Southern Europe. We established 22 loci associated with serum lipid levels at a genome-wide significance level (P < 5 x 10(-8)), including 16 loci that were identified by previous GWA studies. The six newly identified loci in our cohort samples are ABCG5 (TC, P = 1.5 x 10(-11); LDL, P = 2.6 x 10(-10)), TMEM57 (TC, P = 5.4 x 10(-10)), CTCF-PRMT8 region (HDL, P = 8.3 x 10(-16)), DNAH11 (LDL, P = 6.1 x 10(-9)), FADS3-FADS2 (TC, P = 1.5 x 10(-10); LDL, P = 4.4 x 10(-13)) and MADD-FOLH1 region (HDL, P = 6 x 10(-11)). For three loci, effect sizes differed significantly by sex. Genetic risk scores based on lipid loci explain up to 4.8% of variation in lipids and were also associated with increased intima media thickness (P = 0.001) and coronary heart disease incidence (P = 0.04). The genetic risk score improves the screening of high-risk groups of dyslipidemia over classical risk factors.
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- Axelsson, Jesper, et al.
(author)
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Bus fire safety
- 2008
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Reports (peer-reviewed)
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| 8. |
- Björklund, Patrik, 1970-
(author)
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Applications of Resource Optimization in Wireless Networks
- 2006
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Doctoral thesis (other academic/artistic)abstract
- The demand for wireless communications is increasing every year, but the available resources are not increasing at the same rate. It is very important that the radio resources are used in an efficient way allowing the networks to support as many users as possible. The three types of networks studied in this thesis are frequency hopping GSM networks, ad hoc multi-hop networks and WCDMA networks.One type of network with a promising future is ad hoc multi-hop networks. The users in this kind of networks communicate with each other without base stations. Instead the signal can be sent directly between two users, or relayed over one or several other users before the final destination is reached. Resources are shared by letting the users transmit in time slots. The problem studied is to minimize the number of time slots used, when the users broadcast. Two different optimization models are developed for assigning time slots to the users. A reduction of the number of time slots means a shorter delay for a user to transmit next time.The rapid growth of the number of subscribers in cellular networks requires efficient cell planning methods. The trend of smaller cell sizes in urban areas for higher capacity raise the need for more efficient spectrum usage. Since the infrastructure of a second generation cellular system, such as GSM, already exists, and the available bandwidth of an operator is limited, frequency planning methods are of utmost importance. Because of the limited bandwidth in a GSM network, the frequencies must be reused. When planning a GSM network the frequencies can not be reused too tightly due to interference. The frequency planning problem in a GSM network is a very complex task. In this thesis an optimization model for frequency assignment in a frequency hopping GSM network is developed. The problem is to assign frequencies to the cells in the network, while keeping the interference to a minimum. Different meta heuristic methods such as tabu search and simulated annealing are used to solve the problem. The results show that the interference levels can be reduced to allow a capacity increase.The demand for sending more information over the wireless communication systems requires more bandwidth. Voice communication was handled well by the second generation cellular systems. The third generation of mobile telecommunication systems will handle data transmissions in a greater extent. The last type of network considered in the thesis is a WCDMA cellular network. The aim is to schedule the transmission of packet data from the base station to the users. Scheduling models that maximize the utility are developed for both the downlink shared channel and the high speed downlink shared channel.
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