| 1. |
- Lindblad-Toh, Kerstin, et al.
(författare)
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Genome sequence, comparative analysis and haplotype structure of the domestic dog.
- 2005
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 438:7069, s. 803-19
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Tidskriftsartikel (refereegranskat)abstract
- Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.
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| 2. |
- Iacobaeus, E, et al.
(författare)
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Analysis of cerebrospinal fluid and cerebrospinal fluid cells from patients with multiple sclerosis for detection of JC virus DNA
- 2009
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Ingår i: Multiple sclerosis (Houndmills, Basingstoke, England). - : SAGE Publications. - 1352-4585 .- 1477-0970. ; 15:1, s. 28-35
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Tidskriftsartikel (refereegranskat)abstract
- Objective1) To determine whether JC virus (JCV) DNA was present in the cerebrospinal fluid (CSF) and blood from patients with multiple sclerosis (MS) in comparison with controls and 2) to find out if our clinical material, based on presence of JCV DNA, included any patient at risk for progressive multifocal leukoencephalopathy (PML).MethodsThe prevalence of JCV DNA was analyzed in CSF and plasma from 217 patients with MS, 86 patients with clinically isolated syndrome (CIS), and 212 patients with other neurological diseases (OND). In addition, we analyzed CSF cells, the first report of JCV DNA in CSF cells in a single sample, and peripheral blood cells in a subgroup of MS ( n = 49), CIS ( n = 14) and OND ( n = 53).ResultsA low copy number of JCV DNA was detected in one MS cell free CSF sample and in one MS CSF cell samples. None of these had any signs of PML or developed this disease during follow-up. In addition, two OND plasma samples were JCV DNA positive, whereas all the other samples had no detectable virus.ConclusionA low copy number of JCV DNA may occasionally be observed both in MS and other diseases and may occur as part of the normal biology of JC virus in humans. This study does not support the hypothesis that patients with MS would be at increased risk to develop PML, and consequently screening of CSF as a measurable risk for PML is not useful.
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| 3. |
- Bhadauria, Major, et al.
(författare)
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Accomodating diversity in CMPs with heterogeneous frequencies
- 2009
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Ingår i: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). - Berlin, Heidelberg : Springer Berlin Heidelberg. - 1611-3349 .- 0302-9743. - 9783540929895 ; 5409 LNCS, s. 248-262
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Konferensbidrag (refereegranskat)abstract
- Shrinking process technologies and growing chip sizes have profound effects on process variation. This leads to Chip Multiprocessors (CMPs) where not all cores operate at maximum frequency. Instead of simply disabling the slower cores or using guard banding (running all at the frequency of the slowest logic block), we investigate keeping them active, and examine performance and power efficiency of using frequency-heterogeneous CMPs on multithreaded workloads. With uniform workload partitioning, one might intuitively expect slower cores to degrade performance. However, with non-uniform workload partitioning, we find that using both low and high frequency cores improves performance and reduces energy consumption over just running faster cores. Thread scheduling and workload partitioning naturally play significant roles in these improvements. We find that using under-performing cores improves performance by 16% on average and saves CPU energy by up to 16% across the NAS and SPEC-OMP benchmarks on a quad-core AMD platform. Workload balancing via dynamic partitioning yields results within 5% of the overall ideal value. Finally, we show feasible methods to determine at run time whether using a heterogeneous configuration is beneficial. We validate our work through evaluation on a real CMP.
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| 4. |
- Bhadauria, Major, et al.
(författare)
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Understanding parsec performance on contemporary CMPS
- 2009
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Ingår i: Proceedings of the 2009 IEEE International Symposium on Workload Characterization, IISWC 2009. - 9781424451562 ; , s. 98-107
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Konferensbidrag (refereegranskat)abstract
- PARSEC is a reference application suite used in industry and academia to assess new Chip Multiprocessor (CMP) designs. No investigation to date has profiled PARSEC on real hardware to better understand scaling properties and bottlenecks. This understanding is crucial in guiding future CMP designs for these kinds of emerging workloads. We use hardware performance counters, taking a systems-level approach and varying common architectural parameters: number of out-of-order cores, memory hierarchy configu- rations, number of multiple simultaneous threads, number of memory channels, and processor frequencies. We find these programs to be largely compute-bound, and thus lim- ited by number of cores, micro-architectural resources, and cache-to-cache transfers, rather than by off-chip memory or system bus bandwidth. Half the suite fails to scale lin- early with increasing number of threads, and some applica- tions saturate performance at few threads on all platforms tested. Exploiting thread level parallelism delivers greater payoffs than exploiting instruction level parallelism. To re- duce power and improve performance, we recommend in- creasing the number of arithmetic units per core, increasing support for TLP, and reducing support for ILP.
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