| 1. |
|
|
| 2. |
- Munkberg, Jacob, et al.
(author)
-
Tight Frame Normal Map Compression
- 2007
-
In: SIGGRAPH/Eurographics Workshop on Graphics Hardware 2007. - 9783905673470 ; , s. 37-40
-
Conference paper (peer-reviewed)
|
|
| 3. |
- Namjou, Bahram, et al.
(author)
-
High-density genotyping of STAT4 reveals multiple haplotypic associations with systemic lupus erythematosus in different racial groups
- 2009
-
In: Arthritis and Rheumatism. - : Wiley. - 0004-3591 .- 1529-0131. ; 60:4, s. 1085-1095
-
Journal article (peer-reviewed)abstract
- OBJECTIVE: Systemic lupus erythematosus (SLE) is the prototypical systemic autoimmune disorder, with complex etiology and a strong genetic component. Recently, gene products involved in the interferon pathway have been under intense investigation in terms of the pathogenesis of SLE. STAT-1 and STAT-4 are transcription factors that play key roles in the interferon and Th1 signaling pathways, making them attractive candidates for involvement in SLE susceptibility. METHODS: Fifty-six single-nucleotide polymorphisms (SNPs) across STAT1 and STAT4 on chromosome 2 were genotyped using the Illumina platform, as part of an extensive association study in a large collection of 9,923 lupus patients and control subjects from different racial groups. DNA samples were obtained from the peripheral blood of patients with SLE and control subjects. Principal components analyses and population-based case-control association analyses were performed, and the P values, false discovery rate q values, and odds ratios with 95% confidence intervals were calculated. RESULTS: We observed strong genetic associations with SLE and multiple SNPs located within STAT4 in different ethnic groups (Fisher's combined P = 7.02 x 10(-25)). In addition to strongly confirming the previously reported association in the third intronic region of this gene, we identified additional haplotypic association across STAT4 and, in particular, a common risk haplotype that is found in multiple racial groups. In contrast, only a relatively weak suggestive association was observed with STAT1, probably due to its proximity to STAT4. CONCLUSION: Our findings indicate that STAT4 is likely to be a crucial component in SLE pathogenesis in multiple racial groups. Knowledge of the functional effects of this association, when they are revealed, might improve our understanding of the disease and provide new therapeutic targets.
|
|
| 4. |
|
|
| 5. |
- Ström, Jacob, et al.
(author)
-
Floating-point buffer compression in a unified codec architecture
- 2008
-
In: Graphics Hardware. ; , s. 75-84
-
Conference paper (peer-reviewed)abstract
- This paper presents what we believe are the first (public) algorithms for floating-point (fp) color and fp depth buffer compression. The depth codec is also available in an integer version. The codecs are harmonized, meaning that they share basic technology, making it easier to use the same hardware unit for both types of compression. We further suggest to use these codecs in a unified codec architecture, meaning that compression/decompression units previously only used for color- and depth buffer compression can be used also during texture accesses. Finally, we investigate the bandwidth implication of using this in a unified cache architecture. The proposed fp16 color buffer codec compresses data down to 40% of the original, and the fp16 depth codec allows compression down to 4.5 bpp, compared to 5.3 for the state-of-the-art int24 depth compression method. If used in a unified codec and cache architecture, bandwidth reductions of about 50% are possible, which is significant.
|
|
| 6. |
|
|
| 7. |
|
|
| 8. |
- Agaton, Charlotta, et al.
(author)
-
Gene expression analysis by signature pyrosequencing
- 2002
-
In: Gene. - 0378-1119 .- 1879-0038. ; 289:1-2, s. 31-39
-
Journal article (peer-reviewed)abstract
- We describe a novel method for transcript profiling based on high-throughput parallel sequencing of signature tags using a non-gel-based microtiter plate format. The method relies on the identification of cDNA clones by pyrosequencing of the region corresponding to the 3'-end of the mRNA preceding the poly(A) tail. Simultaneously, the method can be used for gene discovery, since tags corresponding to unknown genes can be further characterized by extended sequencing. The protocol was validated using a model system for human atherosclerosis. Two 3'-tagged cDNA libraries, representing macrophages and foam cells, which are key components in the development of atherosclerotic plaques, were constructed using a solid phase approach. The libraries were analyzed by pyrosequencing, giving on average 25 bases. As a control, conventional expressed sequence tag (EST) sequencing using slab gel electrophoresis was performed. Homology searches were used to identify the genes corresponding to each tag. Comparisons with EST sequencing showed identical, unique matches in the majority of cases when the pyrosignature was at least 18 bases. A visualization tool was developed to facilitate differential analysis using a virtual chip format. The analysis resulted in identification of genes with possible relevance for development of atherosclerosis. The use of the method for automated massive parallel signature sequencing is discussed.
|
|
| 9. |
- Agerberth, B, et al.
(author)
-
FALL-39, a putative human peptide antibiotic, is cysteine-free and expressed in bone marrow and testis.
- 1995
-
In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 92:1, s. 195-9
-
Journal article (peer-reviewed)abstract
- PR-39, a proline/arginine-rich peptide antibiotic, has been purified from pig intestine and later shown to originate in the bone marrow. Intending to isolate a clone for a human counterpart to PR-39, we synthesized a PCR probe derived from the PR-39 gene. However, when this probe was used to screen a human bone marrow cDNA library, eight clones were obtained with information for another putative human peptide antibiotic, designated FALL-39 after the first four residues. FALL-39 is a 39-residue peptide lacking cysteine and tryptophan. All human peptide antibiotics previously isolated (or predicted) belong to the defensin family and contain three disulfide bridges. The clone for prepro-FALL-39 encodes a cathelin-like precursor protein with 170 amino acid residues. We have postulated a dibasic processing site for the mature FALL-39 and chemically synthesized the putative peptide. In basal medium E, synthetic FALL-39 was highly active against Escherichia coli and Bacillus megaterium. Residues 13-34 in FALL-39 can be predicted to form a perfect amphiphatic helix, and CD spectra showed that medium E induced 30% helix formation in FALL-39. RNA blot analyses disclosed that the gene for FALL-39 is expressed mainly in human bone marrow and testis.
|
|
| 10. |
|
|
| 11. |
- Ahmadian, Afshin, et al.
(author)
-
Genetic instability in the 9q22.3 region is a late event in the development of squamous cell carcinoma.
- 1998
-
In: Oncogene. - : Springer Science and Business Media LLC. - 0950-9232 .- 1476-5594. ; 17:14
-
Journal article (peer-reviewed)abstract
- Squamous cell carcinoma (SCC) of the skin represents a group of neoplasms which is associated with exposure to UV light. Recently, we obtained data suggesting that invasive skin cancer and its precursors derive from one original neoplastic clone. Here, the analysis were extended by loss of heterozygosity (LOH) analysis in the chromosome 9q22.3 region. A total of 85 samples, taken from twenty-two sections of sun-exposed sites, corresponding to normal epidermis, morphological normal cells with positive immuno-staining for the p53 protein (p53 patches), dysplasias, cancer in situ (CIS) and squamous cell carcinomas (SCC) of the skin were analysed. Overall, about 70% of p53 patches had mutations in the p53 gene but not LOH in the p53 gene or 9q22.3 region. Approximately 70% of the dysplasias showed p53 mutations of which about 40% had LOH in the p53 region but not in the 9q22.3 region. In contrast, about 65% of SCC and CIS displayed LOH in the 9q22.3 region, as well as frequent (80%) mutations and/or LOH in the p53 gene. These findings strongly suggest that alterations in the p53 gene is an early event in the progression towards SCC, whereas malignant development involves LOH and alterations in at least one (or several) tumor suppressor genes located in chromosome 9q22.3.
|
|
| 12. |
- Ahmadian, Afshin, et al.
(author)
-
Genotyping by apyrase-mediated allele-specific extension
- 2001
-
In: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 29:24
-
Journal article (peer-reviewed)abstract
- This report describes a single-step extension approach suitable for high-throughput single-nucleotide polymorphism typing applications. The method relies on extension of paired allele-specific primers and we demonstrate that the reaction kinetics were slower for mismatched configurations compared with matched configurations. In our approach we employ apyrase, a nucleotide degrading enzyme, to allow accurate discrimination between matched and mismatched primer-template configurations. This apyrase-mediated allele-specific extension (AMASE) protocol allows incorporation of nucleotides when the reaction kinetics are fast (matched 3'-end primer) but degrades the nucleotides before extension when the reaction kinetics are slow (mismatched 3'-end primer). Thus, AMASE circumvents the major limitation of previous allele-specific extension assays in which slow reaction kinetics will still give rise to extension products from mismatched 3'-end primers, hindering proper discrimination. It thus represents a significant improvement of the allele-extension method. AMASE was evaluated by a bioluminometric assay in which successful incorporation of unmodified nucleotides is monitored in real-time using an enzymatic cascade.
|
|
| 13. |
- Aidas, Kestutis, et al.
(author)
-
Gauge-origin independent magnetizabilities from hybrid quantum mechanics/molecular mechanics models: Theory and applications to liquid water
- 2007
-
In: Chemical Physics Letters. - : Elsevier BV. - 0009-2614. ; 442:4-6, s. 322-328
-
Journal article (peer-reviewed)abstract
- The theory of a hybrid quantum mechanics/molecular mechanics (QM/MM) approach for gauge-origin independent calculations of the molecular magnetizability using Hartree-Fock or Density Functional Theory is presented. The method is applied to liquid water using configurations generated from classical Molecular Dynamics simulation to calculate the statistical averaged magnetizability. Based on a comparison with experimental data, treating only one water molecule quantum mechanically appears to be insufficient, while a quantum mechanical treatment of also the first solvation shell leads to good agreement between theory and experiment. This indicates that the gas-to-liquid phase shift for the molecular magnetizability is to a large extent of non-electrostatic nature. (c) 2007 Elsevier B.V. All rights reserved.
|
|
| 14. |
- Aidas, Kestutis, et al.
(author)
-
On the performance of quantum chemical methods to predict solvatochromic effects: The case of acrolein in aqueous solution.
- 2008
-
In: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 128:19, s. 1-194503
-
Journal article (peer-reviewed)abstract
- The performance of the Hartree-Fock method and the three density functionals B3LYP, PBE0, and CAM-B3LYP is compared to results based on the coupled cluster singles and doubles model in predictions of the solvatochromic effects on the vertical n-->pi(*) and pi-->pi(*) electronic excitation energies of acrolein. All electronic structure methods employed the same solvent model, which is based on the combined quantum mechanics/molecular mechanics approach together with a dynamical averaging scheme. In addition to the predicted solvatochromic effects, we have also performed spectroscopic UV measurements of acrolein in vapor phase and aqueous solution. The gas-to-aqueous solution shift of the n-->pi(*) excitation energy is well reproduced by using all density functional methods considered. However, the B3LYP and PBE0 functionals completely fail to describe the pi-->pi(*) electronic transition in solution, whereas the recent CAM-B3LYP functional performs well also in this case. The pi-->pi(*) excitation energy of acrolein in water solution is found to be very dependent on intermolecular induction and nonelectrostatic interactions. The computed excitation energies of acrolein in vacuum and solution compare well to experimental data.
|
|
| 15. |
- Aidas, Kestutis, et al.
(author)
-
Solvent effects on NMR isotropic shielding constants. A comparison between explicit polarizable discrete and continuum approaches
- 2007
-
In: The Journal of Physical Chemistry Part A: Molecules, Spectroscopy, Kinetics, Environment and General Theory. - : American Chemical Society (ACS). - 1520-5215. ; 111:20, s. 4199-4210
-
Journal article (peer-reviewed)abstract
- The gas-to-aqueous solution shifts of the O-17 and C-13 NMR isotropic shielding constants for the carbonyl chromophore in formaldehyde and acetone are investigated. For the condensed-phase problem, we use the hybrid density functional theory/molecular mechanics approach in combination with a statistical averaging over an appropriate number of solute-solvent configurations extracted from classical molecular dynamics simulations. The PBE0 exchange-correlation functional and the 6-311++G(2d,2p) basis set are used for the calculation of the shielding constants. London atomic orbitals are employed to ensure gauge-origin independent results. The effects of the bulk solvent molecules are found to be crucial in order to calculate accurate solvation shifts of the shielding constants. Very good agreement between the computed and experimental solvation shifts is obtained for the shielding constants of acetone when a polarizable water potential is used. Supermolecular results based on geometry-optimized molecular structures are presented. We also compare the results obtained with the polarizable continuum model to the results obtained using explicit MM molecules to model the bulk solvent effect.
|
|
| 16. |
|
|
| 17. |
- Akenine-Möller, Tomas, et al.
(author)
-
Graphics processing units for handhelds
- 2008
-
In: Proceedings of the IEEE. - 0018-9219. ; 96:5, s. 779-789
-
Journal article (peer-reviewed)abstract
- During the past few years, mobile phones and other handheld devices have gone from only handling dull text-based menu systems to, on an increasing number of models, being able to render high-quality three-dimensional graphics at high frame rates. This paper is a survey of the special considerations that must be taken when designing graphics processing units (GPUs) on such devices. Starting off by introducing desktop GPUs as a reference, the paper discusses how mobile GPUs are designed, often with power consumption rather than performance as the primary goal. Lowering the bus traffic between the GPU and the memory is an efficient way of reducing power consumption, and therefore some high-level algorithms for bandwidth reduction are presented. In addition, an overview of the different APIs that are used in the handheld market to handle both two-dimensional and three-dimensional graphics is provided. Finally, we present our outlook for the future and discuss directions of future research on handheld GPUs.
|
|
| 18. |
|
|
| 19. |
- Aksentijevich, Ivona, et al.
(author)
-
An Autoinflammatory Disease with Deficiency of the Interleukin-1-Receptor Antagonist
- 2009
-
In: New England Journal of Medicine. - 0028-4793. ; 360:23, s. 2426-2437
-
Journal article (peer-reviewed)abstract
- BACKGROUND Autoinflammatory diseases manifest inflammation without evidence of infection, high-titer autoantibodies, or autoreactive T cells. We report a disorder caused by mutations of IL1RN, which encodes the interleukin-1-receptor antagonist, with prominent involvement of skin and bone. METHODS We studied nine children from six families who had neonatal onset of sterile multifocal osteomyelitis, periostitis, and pustulosis. Response to empirical treatment with the recombinant interleukin-1-receptor antagonist anakinra in the first patient prompted us to test for the presence of mutations and changes in proteins and their function in interleukin-1-pathway genes including IL1RN. RESULTS We identified homozygous mutations of IL1RN in nine affected children, from one family from Newfoundland, Canada, three families from the Netherlands, and one consanguineous family from Lebanon. A nonconsanguineous patient from Puerto Rico was homozygous for a genomic deletion that includes IL1RN and five other interleukin-1-family members. At least three of the mutations are founder mutations; heterozygous carriers were asymptomatic, with no cytokine abnormalities in vitro. The IL1RN mutations resulted in a truncated protein that is not secreted, thereby rendering cells hyperresponsive to interleukin-1 beta stimulation. Patients treated with anakinra responded rapidly. CONCLUSIONS We propose the term deficiency of the interleukin-1-receptor antagonist, or DIRA, to denote this autosomal recessive autoinflammatory disease caused by mutations affecting IL1RN. The absence of interleukin-1-receptor antagonist allows unopposed action of interleukin-1, resulting in life-threatening systemic inflammation with skin and bone involvement. (ClinicalTrials.gov number, NCT00059748.)
|
|
| 20. |
|
|
| 21. |
- Andersen, Malin, 1977-, et al.
(author)
-
Alternative promoter usage of the membrane glycoprotein CD36
- 2006
-
In: BMC Molecular Biology. - : Springer Science and Business Media LLC. - 1471-2199. ; 7, s. 8-
-
Journal article (peer-reviewed)abstract
- Background: CD36 is a membrane glycoprotein involved in a variety of cellular processes such as lipid transport, immune regulation, hemostasis, adhesion, angiogenesis and atherosclerosis. It is expressed in many tissues and cell types, with a tissue specific expression pattern that is a result of a complex regulation for which the molecular mechanisms are not yet fully understood. There are several alternative mRNA isoforms described for the gene. We have investigated the expression patterns of five alternative first exons of the CD36 gene in several human tissues and cell types, to better understand the molecular details behind its regulation.Results: We have identified one novel alternative first exon of the CD36 gene, and confirmed the expression of four previously known alternative first exons of the gene. The alternative transcripts are all expressed in more than one human tissue and their expression patterns vary highly in skeletal muscle, heart, liver, adipose tissue, placenta, spinal cord, cerebrum and monocytes. All alternative first exons are upregulated in THP-1 macrophages in response to oxidized low density lipoproteins. The alternative promoters lack TATA-boxes and CpG islands. The upstream region of exon 1b contains several features common for house keeping gene and monocyte specific gene promoters.Conclusion: Tissue-specific expression patterns of the alternative first exons of CD36 suggest that the alternative first exons of the gene are regulated individually and tissue specifically. At the same time, the fact that all first exons are upregulated in THP-1 macrophages in response to oxidized low density lipoproteins may suggest that the alternative first exons are coregulated in this cell type and environmental condition. The molecular mechanisms regulating CD36 thus appear to be unusually complex, which might reflect the multifunctional role of the gene in different tissues and cellular conditions.
|
|
| 22. |
- Andersen, Malin, 1977-
(author)
-
Computational and experimental approaches to regulatory genetic variation
- 2007
-
Doctoral thesis (other academic/artistic)abstract
- Genetic variation is a strong risk factor for many human diseases, including diabetes, cancer, cardiovascular disease, depression, autoimmunity and asthma. Most of the disease genes identified so far alter the amino acid sequences of encoded proteins. However, a significant number of genetic variants affecting complex diseases may alter the regulation of gene transcription. The map of the regulatory elements in the human genome is still to a large extent unknown, and it remains a challenge to separate the functional regulatory genetic variations from linked neutral variations. The objective of this thesis was to develop methods for the identification of genetic variation with a potential to affect the transcriptional regulation of human genes, and to analyze potential regulatory polymorphisms in the CD36 glycoprotein, a candidate gene for cardiovascular disease. An in silico tool for the prediction of regulatory polymorphisms in human genes was implemented and is available at www.cisreg.ca/RAVEN. The tool was evaluated using experimentally verified regulatory single nucleotide polymorphisms (SNPs) collected from the scientific literature, and tested in combination with experimental detection of allele specific expression of target genes (allelic imbalance). Regulatory SNPs were shown to be located in evolutionary conserved regions more often than background SNPs, but predicted transcription factor binding sites were unable to enrich for regulatory SNPs unless additional information linking transcription factors with the target genes were available. The in silico tool was applied to the CD36 glycoprotein, a candidate gene for cardiovascular disease. Potential regulatory SNPs in the alternative promoters of this gene were identified and evaluated in vitro and in vivo using a clinical study for coronary artery disease. We observed association to the plasma concentrations of inflammation markers (serum amyloid A protein and C-reactive protein) in myocardial infarction patients, which highlights the need for further analyses of potential regulatory polymorphisms in this gene. Taken together, this thesis describes an in silico approach to identify putative regulatory polymorphisms which can be useful for directing limited laboratory resources to the polymorphisms most likely to have a phenotypic effect.
|
|
| 23. |
- Andersen, Malin, 1977-, et al.
(author)
-
In silico detection of sequence variations modifying transcriptional regulation
- 2008
-
In: PloS Computational Biology. - : Public Library of Science (PLoS). - 1553-734X .- 1553-7358. ; 4:1, s. e5-
-
Journal article (peer-reviewed)abstract
- Identification of functional genetic variation associated with increased susceptibility to complex diseases can elucidate genes and underlying biochemical mechanisms linked to disease onset and progression. For genes linked to genetic diseases, most identified causal mutations alter an encoded protein sequence. Technological advances for measuring RNA abundance suggest that a significant number of undiscovered causal mutations may alter the regulation of gene transcription. However, it remains a challenge to separate causal genetic variations from linked neutral variations. Here we present an in silico driven approach to identify possible genetic variation in regulatory sequences. The approach combines phylogenetic footprinting and transcription factor binding site prediction to identify variation in candidate cis-regulatory elements. The bioinformatics approach has been tested on a set of SNPs that are reported to have a regulatory function, as well as background SNPs. In the absence of additional information about an analyzed gene, the poor specificity of binding site prediction is prohibitive to its application. However, when additional data is available that can give guidance on which transcription factor is involved in the regulation of the gene, the in silico binding site prediction improves the selection of candidate regulatory polymorphisms for further analyses. The bioinformatics software generated for the analysis has been implemented as a Web-based application system entitled RAVEN ( regulatory analysis of variation in enhancers). The RAVEN system is available at http://www.cisreg.ca for all researchers interested in the detection and characterization of regulatory sequence variation.
|
|
| 24. |
- Anderson, Kristin, 1977-, et al.
(author)
-
Effects of User Adjacency in the Subset Difference Scheme for Broadcast Encryption
- 2005
-
In: Radiovetenskap och Kommunikation, RVK05,2005.
-
Conference paper (peer-reviewed)abstract
- We consider the broadcast encryption problem where one sender wishes to transmit messages securely to a selected set of receivers using a broadcast channel, as is the case in digital television for example. Specifically, we study the subset difference scheme for broadcast encryption and the number of broadcast transmissions required when using this scheme. The effects of adjacency in the user set are considered and we introduce the notion of transitions in the user set as a means to quantify the adjacency. We present upper and lower bounds for the number of transmissions based on the number of transitions between privileged and nonprivileged users in the user set. For cases where the privileged users are gathered in a few groups we derive the maximum number of transmissions.
|
|
| 25. |
- Anderson, Kristin, 1977-, et al.
(author)
-
The Algebraic Structure of a Broadcast Encryption Scheme
- 2005
-
In: Radiovetenskap och Kommunikation, RVK05,2005.
-
Conference paper (peer-reviewed)abstract
- In this paper we consider the subset difference scheme for broadcast encryption and count the number of required broadcast transmissions when using this scheme. The subset difference scheme organizes receivers in a tree structure and we note that isomorphic trees yield the same number of required broadcast transmissions. Based on the isomorphism the trees can be partitioned into classes. We suggest to use the vast amount of tools available from the theory of groups to analyze the subset difference scheme and therefore we formulate the mappings between isomorphic trees using concepts from group theory. Finally we identify some research issues for further study of the performance of the subset difference scheme using group theory.
|
|
| 26. |
- Anderson, Kristin, 1977-
(author)
-
Tree Structures in Broadcast Encryption
- 2005
-
Licentiate thesis (other academic/artistic)abstract
- The need for broadcast encryption arises when a sender wishes to securely distribute messages to varying subsets of receivers, using a broadcast channel, for instance in a pay-TV scenario. This is done by selecting subsets of users and giving all users in the same subset a common decryption key. The subsets will in general be overlapping so that each user belongs to many subsets and has several different decryption keys. When the sender wants to send a message to some users, the message is encrypted using keys that those users have. In this thesis we describe some broadcast encryption schemes that have been proposed in the literature. We focus on stateless schemes which do not require receivers to update their decryption keys after the initial keys have been received; particularly we concentrate on the Subset Difference (SD) scheme.We consider the effects that the logical placement of the receivers in the tree structure used by the SD scheme has on the number of required transmissions for each message. Bounds for the number of required transmissions are derived based on the adjacency of receivers in the tree structure. The tree structure itself is also studied, also resulting in bounds on the number of required transmissions based on the placement of the users in the tree structure.By allowing a slight discrepancy between the set of receivers that the sender intends to send to and the set of receivers that actually can decrypt the message, we can reduce the cost in number of transmissions per message. We use the concept of distortion to quantify the discrepancy and develop three simple algorithms to illustrate how the cost and distortion are related.
|
|
| 27. |
- Andersson, Greger, et al.
(author)
-
Musikens miljöer
- 2006
-
In: Signums svenska kulturhistoria. Frihetstiden. - 9187896788 ; , s. 345-373
-
Book chapter (pop. science, debate, etc.)
|
|
| 28. |
- Andersson, Mats, et al.
(author)
-
Road Friction Estimation
- 2007
-
Reports (other academic/artistic)abstract
- This project is part of the Swedish IVSS program. The aim of IVSS is to stimulate research and development for the road safety of the future. Road conditions with low friction have been identified as a frequent cause of traffic accidents. Therefore, technology to automaticallydetect changes in road conditions and alert the driver or take proper actions with active driver support systems would be a key contribution to increased road safety.The aim of this project was to investigate the possibilities to estimate the tire to road friction.Three different approaches have been developed and evaluated, from concept to early prototypes in test vehicles. In the first method, the estimation of the coefficient of friction is based on the forces and torques that are produced at the front tires at cornering maneuvers.The second method is based on a physical model of the tire behavior and estimates road friction from information on the forces that are produced at straight driving. The third method is based on an optical sensor that classifies the road surface ahead of the vehicle.The three methods have been successfully evaluated in proving ground and public road tests in summer and winter conditions with different tires, and have been compared with reference measurements. The conclusion is that all three methods can be used for tire to road frictionestimation and are recommended for further development and industrialization.
|
|
| 29. |
- Andersson, Niklas, et al.
(author)
-
A comparison of dynamic element matching in DACs
- 1999
-
In: Proceedings '99 : Oslo, Norway, 8-9 November 1999. - 8798263722 ; , s. 385-390
-
Conference paper (other academic/artistic)abstract
- In the field of dynamic element matching, DEM, techniques, some "new" important theoretical results have been presented during the last decade. However, no comparison between these different DEM techniques (FRDEM, PRDEM, NSDEM) used in wideband digital-to-analog converters, DACs, has been reported. A brief review of different DEM techniques and a comparison between their properties in terms of complexity, etc., are presented in this paper together with simulation results showing the impact of using different DEM techniques.
|
|
| 30. |
- Andersson, Niklas, 1975-, et al.
(author)
-
A strategy for implementing dynamic element matching in current-steering DACs
- 2000
-
In: Mixed-Signal Design, 2000. SSMSD. 2000 Southwest Symposium on. - : IEEE. - 0780359755 ; , s. 51-56
-
Conference paper (other academic/artistic)abstract
- Interesting comparisons of dynamic element matching (DEM) techniques, have been presented during the last decade. However, not many chip implementations of these DEM techniques have been presented so far. A brief review of different DEM techniques are presented in this paper together with a strategy for implementing the partial randomization DEM, PRDEM, technique in a 3.3 V supply, 14 bit CMOS current-steering wideband digital-to-analog converter (DAC)
|
|
| 31. |
- Andersson, Niklas, 1975-, et al.
(author)
-
Comparison of Different Dynamic Element Matching Techniques for Wideband CMOS DACs
- 1999
-
In: Proceedings of the 17th Norchip Conference.
-
Conference paper (other academic/artistic)abstract
- In the field of dynamic element matching, DEM, techniques, some ”new” important theoretical results have been presented during the last decade. However, no comparison between these different DEM techniques (FRDEM, PRDEM, NSDEM) used in wideband digital-to-analog converters, DACs, has been reported. A brief review of different DEM techniques and a comparison between their properties in terms of complexity, etc., are presented in this paper together with simulation results showing the impact of using different DEM techniques.
|
|
| 32. |
|
|
| 33. |
- Andersson, Niklas, et al.
(author)
-
Models and Implementation of a Dynamic Element Matching DAC
- 2003
-
In: Analog Integrated Circuits and Signal Processing. - Netherlands : Springer. - 0925-1030 .- 1573-1979. ; 34:1, s. 7-16
-
Journal article (peer-reviewed)abstract
- The dynamic element matching (DEM) techniques for digital-to-analog converters (DACs) has been suggested as a promising method to improve matching between the DAC''s reference levels. However, no work has so far taken the dynamic effects that limit the performance for higher frequenciesinto account. In this paper we present a model describing the dynamic properties of a DEM DAC and compare the simulated results with measurements of a 14-bit current-steering DEM DAC implemented in a 0.35-μm CMOS process. The measured data agrees well with the results predicted by the used model. It is also shown that the DEM technique does not necessarily increase the performance of a DAC when dynamic errors are dominating the achievable performance.
|
|
| 34. |
- Andersson, Ola, et al.
(author)
-
A 14-Bit dual current-steering DAC
- 2003
-
In: Proc. Swedish System-on-Chip Conf., SSoCC'03.
-
Conference paper (other academic/artistic)abstract
- A 14-bit dual current-steering digital-to-analog converter implemented in a 0.25 µm CMOS process is presented in this work. Both implementation issues and measurement results are presented. The measured spurious-free dynamic range is higher than 73 dB for signal frequencies up to 3 MHz, and a measured multi-tone power ratio of approximately 71 dB is reported for an ADSL-like input.
|
|
| 35. |
- Andersson, Ola, et al.
(author)
-
A differential DAC architecture with variable common-mode level
- 2002
-
In: Proc. 2002 IEEE Int. Symp. on Circuits and Systems, ISCAS'02. - 0780374487 ; , s. I-113-I-116
-
Conference paper (peer-reviewed)abstract
- A differential current-steering digital-to-analog converter (DAC) architecture allowing the common-mode level of the input signal to be varied is presented. Simulation results with models of different DAC nonlinearities indicate that the proposed architecture has a potential of improving the linearity of the converters.
|
|
| 36. |
- Andersson, Ola, et al.
(author)
-
A method of segmenting digital-to-analog converters
- 2003
-
In: Proc. IEEE Southwest Symposium on Mixed-Signal Design, SSMSD'03. - 0780377788 ; , s. 32-37
-
Conference paper (peer-reviewed)abstract
- Segmented architectures are often used in digital-to-analog converters (DACs). Here we propose a DAC structure based on recursive decomposition of an N-bit binary DAC into two (N-1) bit DACs and one 1 bit DAC. A DAC model that includes matching errors has been simulated. The simulation results indicate that by using four layers of decomposition it is possible to achieve similar performance as when using seven bits of traditional segmentation.
|
|
| 37. |
- Andersson, Ola, 1976-, et al.
(author)
-
Characterization of a CMOS current-steering DAC using state-space models
- 2000
-
In: Circuits and Systems, 2000. Proceedings of the 43rd IEEE Midwest Symposium on. - : IEEE. - 0780364759 ; , s. 668-671 vol.2
-
Conference paper (peer-reviewed)abstract
- Performance limitations on current-steering digital-to-analog converters (DACs) are due to finite output impedances, nonideal switches, parasitic capacitances, matching, etc. In this work we present a dynamic state-space model of a 14-bit current-steering DAC which includes dynamic nonidealities. Simulation results are presented and compared to measurement results. The model can be used for fast performance estimation of D/A converters
|
|
| 38. |
- Andersson, Ola, et al.
(author)
-
Combining DACs for improved performance
- 2002
-
In: Proc. 4th IEE Int. Conf. on Advanced A/D and D/A Conversion Techniques and their Applications, ADDA'02.
-
Conference paper (peer-reviewed)abstract
- This work is an overview of recently proposed methods on combining DACs in order to improve performance. Some further development of these techniques are also presented. The techniques aim at reducing glitches and sensitivity towards limited output impedance in current sources.
|
|
| 39. |
- Andersson, Ola, 1976-, et al.
(author)
-
Digital-to-analog converter having error correction
- 2002
-
Patent (pop. science, debate, etc.)abstract
- The values X(n) input to a current-steering digital-to-analog converter (49) are modified (41) before the actual conversion to compensate for conversion errors of the digital-to-analog converter. The input values are modified according to a model (43) of the digital-to-analog converter in which each output value of the digital-to-analog converter Y(n) is a sum of a desired value directly proportional to the respective input value and an error. The error is a product of the settled output value, i.e. the difference between the desired value and the previous output value Y(n−1) actually provided by the digital-to-analog converter, and a relative step error that is a function only of the respective input signal and is stored in a table. The relative step error can be a function also of the previous output signal and of the previous input signal. This model has a low complexity and is suitable for on-chip implementation.
|
|
| 40. |
- Andersson, Ola, 1976-, et al.
(author)
-
Modeling of the Influence of Graded Element Matching Errors in CMOS Current-Steering DACs
- 1999
-
In: Proceedings of the 17th Norchip Conference.
-
Conference paper (other academic/artistic)abstract
- In analog and mixed-mode circuits the matching between circuit elements is crucial.For example, in binary encoded digital-to-analog converters (DACs) the matchingbetween different bit weights can set the limit on the performance. Related to earlier workmodeling the influence of stochastic matching, the influence of graded element matching errorson the performance of current-steering DACs is shown. Presented are calculated results thatcorrelate very well with simulated results. As performance measures we use both static measuresas DNL and INL as well as frequency domain parameters as SNDR and SFDR. This discussioncan also be applied to other DAC structures, for example switched-capacitor.
|
|
| 41. |
- Andersson, Ola, 1976-, et al.
(author)
-
Spectral shaping of DAC nonlinearity errors through modulation of expected errors
- 2001
-
In: Circuits and Systems, 2001. ISCAS 2001. The 2001 IEEE International Symposium on. - : IEEE. - 0780366859 ; , s. 417-420
-
Conference paper (peer-reviewed)abstract
- Traditionally, delta-sigma modulation has been used for shaping of quantization noise. We present a modified version of delta-sigma modulation which also takes into account unwanted nonlinearities by feeding back not only the quantization error, but also the expected physical error. Behavioral-level simulations of a 5th-order structure showing an improvement of up to 4 effective bits are included
|
|
| 42. |
- Andersson, T., et al.
(author)
-
Monitoring of representational difference analysis subtraction procedures by global microarrays
- 2002
-
In: BioTechniques. - : Future Science Ltd. - 0736-6205 .- 1940-9818. ; 32:6, s. 1348-
-
Journal article (peer-reviewed)abstract
- Various approaches to the study of differential gene expression are applied to compare cell lines and tissue samples in a wide range of biological contexts. The compromise between focusing on only the important genes in certain cellular processes and achieving a complete picture is critical for the selection of strategy. We demonstrate how global microarray technology can be used for the exploration of the differentially expressed genes extracted through representational difference analysis (RDA). The subtraction of ubiquitous gene fragments from the two samples was demonstrated using cDNA microarrays including more than 32 000 spotted, PCR-amplified human clones. Hybridizations indicated the expression of 9100 of the microarray elements in a macrophage/foam cell atherosclerosis model system, of which many were removed during the RDA process. The stepwise subtraction procedure was demonstrated to yield an efficient enrichment of gene fragments overrepresented in either sample (18% in the representations, 86% after the first subtraction, and 88% after the second subtraction), many of which were impossible to detect in the starting material. Interestingly, the method allowed for the observation of the differential expression of several members of the low-abundant nuclear receptor gene family. We also observed a certain background level in the difference products of nondifferentially expressed gene fragments, warranting a verification strategy for selected candidate genes. The differential expression of several genes was verified by real-time PCR.
|
|
| 43. |
- Andersson, T., et al.
(author)
-
Novel candidate genes for atherosclerosis are identified by representational difference analysis-based transcript profiling of cholesterol-loaded macrophages
- 2001
-
In: Pathobiology (Basel). - : S. Karger AG. - 1015-2008 .- 1423-0291. ; 69:6, s. 304-314
-
Journal article (peer-reviewed)abstract
- Objectives: To analyze the early gene expression in macrophages accompanying the phenotypic changes into foam cells upon exposure to oxidized low-density lipoprotein. To identify candidate genes and markers for further studies into the pathogenesis of atherosclerosis. Methods: Cells of the monocytic cell line THP-1 were activated by PMA and exposed to oxidized low-density lipoprotein. Gene expression profiles were investigated after 24 h, using a solid phase cDNA representational difference analysis (RDA) method and shotgun sequencing. Results were verified by microarray hybridization, and analyzed in the virtual chip display of a novel software tool for transcript profile exploration. Results: By comparing transcript profiles of exposed/unexposed cells, 1,984 transcript sequences, representing a total of 921 genes with altered expression levels in response to oxidized low-density lipoprotein exposure, were identified. Genes that are central to cell cycle control and proliferation, inflammatory response, and of pathways not previously implicated in atherosclerosis were identified. The data obtained is also made available on-line at http:// biobase.biotech.kth.se/thp1a for further exploration. Conclusion: The identification of new candidate genes for atherosclerotic disease through RDA-based transcript profiling facilitates further functional genomic studies in coronary artery disease. Candidate genetic polymorphism markers of potential clinical relevance can be identified by filtering information in genome variation databases through the virtual chip analysis of the transcript profiles and subsequently tested in association studies.
|
|
| 44. |
- Andersson, T., et al.
(author)
-
Shotgun sequencing and microarray analysis of RDA transcripts
- 2003
-
In: Gene. - : Elsevier BV. - 0378-1119 .- 1879-0038. ; 310, s. 39-47
-
Journal article (peer-reviewed)abstract
- Monitoring of differential gene expression is an important step towards understanding of gene function. We describe a comparison of the representational difference analysis (RDA) subtraction process with corresponding microarray analysis. The subtraction steps are followed in a quantitative manner using a shotgun cloning and sequencing procedure that includes over 1900 gene sequences. In parallel, the enriched transcripts are spotted onto microarrays facilitating large scale hybridization analysis of the representations and the difference products. We show by the shotgun procedure that there is a high diversity of gene fragments represented in the iterative RDA products (92-67% singletons) with a low number of shared sequences (<9%) between subsequent subtraction cycles. A non redundant set of 1141 RDA clones were immobilized on glass slides and the majority of these clones (97%) gave repeated good fluorescent signals in a subsequent hybridization of the labelled and amplified original cDNA. We observed only a low number of false positives (<2%) and a more than twofold differential expression for 32% (363) of the immobilized RDA clones. In conclusion, we show that by random sequencing of the difference products we obtained an accurate transcript profile of the individual steps and that large-scale confirmation of the obtained transcripts can be achieved by microarray analysis.
|
|
| 45. |
- Andrade, Jorge, et al.
(author)
-
Applications of grid computing in genetics and proteomics
- 2007
-
In: Applied Parallel Computing. - Berlin, Heidelberg : Springer Berlin Heidelberg. - 9783540757542 ; , s. 791-798
-
Conference paper (peer-reviewed)abstract
- The potential for Grid technologies in applied bioinformatics is largely unexplored. We have developed a model for solving computationally demanding bioinformatics tasks in distributed Grid environments, designed to ease the usability for scientists unfamiliar with Grid computing. With a script-based implementation that uses a strategy of temporary installations of databases and existing executables on remote nodes at submission, we propose a generic solution that do not rely on predefined Grid runtime environments and that can easily be adapted to other bioinformatics tasks suitable for parallelization. This implementation has been successfully applied to whole proteome sequence similarity analyses and to genome-wide genotype simulations, where computation time was reduced from years to weeks. We conclude that computational Grid technology is a useful resource for solving high compute tasks in genetics and proteomics using existing algorithms.
|
|
| 46. |
- Andrade, Jorge, 1969-
(author)
-
Grid and High-Performance Computing for Applied Bioinformatics
- 2007
-
Doctoral thesis (other academic/artistic)abstract
- The beginning of the twenty-first century has been characterized by an explosion of biological information. The avalanche of data grows daily and arises as a consequence of advances in the fields of molecular biology and genomics and proteomics. The challenge for nowadays biologist lies in the de-codification of this huge and complex data, in order to achieve a better understanding of how our genes shape who we are, how our genome evolved, and how we function. Without the annotation and data mining, the information provided by for example high throughput genomic sequencing projects is not very useful. Bioinformatics is the application of computer science and technology to the management and analysis of biological data, in an effort to address biological questions. The work presented in this thesis has focused on the use of Grid and High Performance Computing for solving computationally expensive bioinformatics tasks, where, due to the very large amount of available data and the complexity of the tasks, new solutions are required for efficient data analysis and interpretation. Three major research topics are addressed; First, the use of grids for distributing the execution of sequence based proteomic analysis, its application in optimal epitope selection and in a proteome-wide effort to map the linear epitopes in the human proteome. Second, the application of grid technology in genetic association studies, which enabled the analysis of thousand of simulated genotypes, and finally the development and application of a economic based model for grid-job scheduling and resource administration. The applications of the grid based technology developed in the present investigation, results in successfully tagging and linking chromosomes regions in Alzheimer disease, proteome-wide mapping of the linear epitopes, and the development of a Market-Based Resource Allocation in Grid for Scientific Applications.
|
|
| 47. |
- Andrade, Jorge, et al.
(author)
-
The use of grid computing to drive data-intensive genetic research
- 2007
-
In: European Journal of Human Genetics. - : Springer Science and Business Media LLC. - 1018-4813 .- 1476-5438. ; 15:6, s. 694-702
-
Journal article (peer-reviewed)abstract
- In genetics, with increasing data sizes and more advanced algorithms for mining complex data, a point is reached where increased computational capacity or alternative solutions becomes unavoidable. Most contemporary methods for linkage analysis are based on the Lander-Green hidden Markov model (HMM), which scales exponentially with the number of pedigree members. In whole genome linkage analysis, genotype simulations become prohibitively time consuming to perform on single computers. We have developed 'Grid-Allegro', a Grid aware implementation of the Allegro software, by which several thousands of genotype simulations can be performed in parallel in short time. With temporary installations of the Allegro executable and datasets on remote nodes at submission, the need of predefined Grid run-time environments is circumvented. We evaluated the performance, efficiency and scalability of this implementation in a genome scan on Swedish multiplex Alzheimer's disease families. We demonstrate that 'Grid-Allegro' allows for the full exploitation of the features available in Allegro for genome-wide linkage. The implementation of existing bioinformatics applications on Grids (Distributed Computing) represent a cost-effective alternative for addressing highly resource-demanding and data-intensive bioinformatics task, compared to acquiring and setting up clusters of computational hardware in house (Parallel Computing), a resource not available to most geneticists today.
|
|
| 48. |
- Andrade, Jorge, et al.
(author)
-
Using Grid Technology for Computationally Intensive Applied Bioinformatics Analyses
- 2006
-
In: In Silico Biology. - 1386-6338. ; 6:6, s. 495-504
-
Journal article (peer-reviewed)abstract
- For several applications and algorithms used in applied bioinformatics, a bottle neck in terms of computational time may arise when scaled up to facilitate analyses of large datasets and databases. Re-codification, algorithm modification or sacrifices in sensitivity and accuracy may be necessary to accommodate for limited computational capacity of single work stations. Grid computing offers an alternative model for solving massive computational problems by parallel execution of existing algorithms and software implementations. We present the implementation of a Grid-aware model for solving computationally intensive bioinformatic analyses exemplified by a blastp sliding window algorithm for whole proteome sequence similarity analysis, and evaluate the performance in comparison with a local cluster and a single workstation. Our strategy involves temporary installations of the BLAST executable and databases on remote nodes at submission, accommodating for dynamic Grid environments as it avoids the need of predefined runtime environments (preinstalled software and databases at specific Grid-nodes). Importantly, the implementation is generic where the BLAST executable can be replaced by other software tools to facilitate analyses suitable for parallelisation. This model should be of general interest in applied bioinformatics. Scripts and procedures are freely available from the authors.
|
|
| 49. |
- Ansar, Saema, et al.
(author)
-
ERK1/2 inhibition attenuates cerebral blood flow reduction and abolishes ET(B) and 5-HT(1B) receptor upregulation after subarachnoid hemorrhage in rat.
- 2006
-
In: Journal of Cerebral Blood Flow and Metabolism. - : SAGE Publications. - 1559-7016 .- 0271-678X. ; 26:Nov 2, s. 846-856
-
Journal article (peer-reviewed)abstract
- Upregulation of endothelin B (ETB) and 5-hydroxytryptamine 1B (5-HT1B) receptors via transcription has been found after experimental subarachnoid hemorrhage (SAH), and this is associated with enhanced phosphorylation of the mitogen-activated protein kinase ( MAPK) extracellular signal-regulated kinase ( ERK1/2). In the present study, we hypothesized that inhibition of ERK1/2 alters the ETB and 5-HT1B receptor upregulation and at the same time prevents the sustained cerebral blood flow (CBF) reduction associated with SAH. The ERK1/2 inhibitor SB386023-b was injected intracisternally in conjunction with and after the induced SAH in rats. At 2 days after the SAH, cerebral arteries were harvested for quantitative real-time polymerase chain reaction, immunohistochemistry and analysis of contractile responses to endothelin-1 (ET-1; ETA and ETB receptor agonist) and 5-carboxamidotryptamine (5-CT; 5-HT1 receptor agonist) in a sensitive myograph. To investigate if ERK1/2 inhibition had an influence on the local and global CBF after SAH, an autoradiographic technique was used. At 48 h after induced SAH, global and regional CBF were reduced by 50%. This reduction was prevented by treatment with SB386023-b. The ERK1/2 inhibition also decreased the maximum contraction elicited by application of ET-1 and 5-CT in cerebral arteries compared with SAH. In parallel, ERK1/2 inhibition downregulated ETB and 5-HT1B receptor messenger ribonucleic acid and protein levels compared with the SAH. Cerebral ischemia after SAH involves vasoconstriction and subsequent reduction in the CBF. The results suggest that ERK1/2 inhibition might be a potential treatment for the prevention of cerebral vasospasm and ischemia associated with SAH.
|
|
| 50. |
- Ansar, Saema, et al.
(author)
-
Protein kinase C inhibition prevents upregulation of vascular ET(B) and 5-HT(1B) receptors and reverses cerebral blood flow reduction after subarachnoid haemorrhage in rats.
- 2007
-
In: Journal of Cerebral Blood Flow and Metabolism. - : SAGE Publications. - 1559-7016 .- 0271-678X. ; 27:1, s. 21-32
-
Journal article (peer-reviewed)abstract
- The pathogenesis of cerebral ischaemia after subarachnoid haemorrhage (SAH) still remains elusive. The purpose of the present study was to examine whether specific protein kinas C (PKC) inhibition in rats could alter the transcriptional SAH induced Endothelin (ET) type B and 5-hydroxytryptamine type 1B (5-HT1B) receptor upregulation and prevent the associated cerebral blood flow (CBF) reduction. The PKC inhibitor RO-31-7549 or vehicle was injected intracisternally after the induced SAH in rats (n = 3 to 10 in each groups for each method). The involvement of the PKC isoforms was investigated with Western blot; only PKC delta and PKC alpha subtypes were increased after SAH RO-31-7549 treatment abolished this. At 2 days after the SAH basilar and middle cerebral arteries were harvested and the contractile response to endothelin-1 (ET-1; ETA and ETB receptor agonist) and 5-carboxamidotryptamine (5-CT; 5-HT1B receptor agonist) were investigated with a myograph. The contractile responses to ET-1 and 5-CT were increased (P < 0.05) after SAH compared with sham operated rats. In parallel, the ETB and 5-HT1B receptor mRNA and protein expression were significantly elevated after SAH, as analysed by quantitative real-time polymerase chain reaction and immunohistochemistry, respectively. Administration of RO-31-7549 prevented the upregulated contraction elicited by application of ET-1 and 5-CT in cerebral arteries and kept the ETB and 5-HT1B receptor mRNA and protein levels at pre-SAH levels. Regional and global CBF evaluated by an autoradiographic technique were reduced by 60% 64% after SAH (P < 0.05) and prevented by treatment with RO-31-7549. Our study suggests that PKC plays an important role in the pathogenesis of cerebral ischaemia after SAH.
|
|
