| 1. |
- Nyberg, Lena, 1979, et al.
(författare)
-
A single-step competitive binding assay for mapping of single DNA molecules
- 2012
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Ingår i: Biochemical and Biophysical Research Communications - BBRC. - : Elsevier BV. - 0006-291X .- 1090-2104. ; 417:1, s. 404-408
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Tidskriftsartikel (refereegranskat)abstract
- Optical mapping of genomic DNA is of relevance for a plethora of applications such as scaffolding for sequencing and detection of structural variations as well as identification cif pathogens like bacteria and viruses. For future clinical applications it is desirable to have a fast and robust mapping method based on as few steps as possible. We here demonstrate a single-step method to obtain a DNA barcode that is directly visualized using nanofluidic devices and fluorescence microscopy. Using a mixture of YOYO-1, a bright DNA dye, and netropsin, a natural antibiotic with very high AT specificity, we obtain a DNA map with a fluorescence intensity profile along the DNA that reflects the underlying sequence. The netropsin binds to AT-tetrads and blocks these binding sites from YOYO-1 binding which results in lower fluorescence intensity from AT-rich regions of the DNA. We thus obtain a DNA barcode that is dark in AT-rich regions and bright in GC-rich regions with kilobasepair resolution. We demonstrate the versatility of the method by obtaining a barcode on DNA from the phage T4 that captures its circular permutation and agrees well with its known sequence.
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| 2. |
- Alizadehheidari, Mohammadreza, 1987, et al.
(författare)
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Unfolding of nanoconfined circular DNA
- 2015
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Ingår i: BIOPHYSICAL JOURNAL. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 108:2 Supplement 1
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 3. |
- Alizadehheidari, Mohammadreza, 1987, et al.
(författare)
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Nanoconfined Circular and Linear DNA: Equilibrium Conformations and Unfolding Kinetics
- 2015
-
Ingår i: Macromolecules. - : American Chemical Society (ACS). - 0024-9297 .- 1520-5835. ; 48:3, s. 871-878
-
Tidskriftsartikel (refereegranskat)abstract
- Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due to the importance of circular DNA molecules in vivo. We here observe the unfolding of confined DNA from the circular to linear configuration as a light-induced double-strand break occurs, characterize the dynamics, and compare the equilibrium conformational statistics of linear and circular configurations. This is important because it allows us to determine to what extent existing statistical theories describe the extension of confined circular DNA. We find that the ratio of the extensions of confined linear and circular DNA configurations increases as the buffer concentration decreases. The experimental results fall between theoretical predictions for the extended de Gennes regime at weaker confinement and the Odijk regime at stronger confinement. We show that it is possible to directly distinguish between circular and linear DNA molecules by measuring the emission intensity from the DNA. Finally, we determine the rate of unfolding and show that this rate is larger for more confined DNA, possibly reflecting the corresponding larger difference in entropy between the circular and linear configurations.
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| 4. |
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| 5. |
- Nyberg, Lena, 1979, et al.
(författare)
-
Heterogeneous staining: a tool for studies of how fluorescent dyes affect the physical properties of DNA
- 2013
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 41:19, s. articlenr e184-
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Tidskriftsartikel (refereegranskat)abstract
- The commonly used fluorescent dye YOYO-1 (YOYO) has, using bulk techniques, been demonstrated to stain DNA heterogeneously at substoichiometric concentrations. We here, using nanofluidic channels and fluorescence microscopy, investigate the heterogeneous staining on the single DNA molecule level and demonstrate that the dye distribution is continuous. The equilibration of YOYO on DNA is extremely slow but can be accelerated by increasing the ionic strength and/or the temperature. Furthermore, we demonstrate how to use the heterogeneous staining as a tool for detailed and time-efficient studies of how fluorescent dyes affect the physical properties of DNA. We show that the relative increase in extension of DNA with increasing amount of YOYO bound is higher at low ionic strengths and also extrapolate the extension of native DNA. Our study reveals important information on how YOYO affects the physical properties of DNA, but it also has broader applications. First, it reveals how cationic intercalators, such as potential DNA drugs, affect DNA under strong confinement. Second, the strategy of using heterogeneous staining is of general use for single molecule studies of DNA interacting with proteins or ligands.
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| 6. |
- Persson, Fredrik, 1973, et al.
(författare)
-
High-resolution array CGH analysis of salivary gland tumors reveals fusion and amplification of the FGFR1 and PLAG1 genes in ring chromosomes
- 2008
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Ingår i: Oncogene. - : Springer Science and Business Media LLC. - 0950-9232 .- 1476-5594. ; 27:21, s. 3072-3080
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Tidskriftsartikel (refereegranskat)abstract
- We have previously identified a subgroup of pleomorphic salivary gland adenomas with ring chromosomes of uncertain derivation. Here, we have used spectral karyotyping (SKY), fluorescence in situ hybridization (FISH) and high-resolution oligonucleotide array-CGH to determine the origin and content of these rings and to identify genes disrupted as a result of ring formation. Of 16 tumors with rings, 11 were derived from chromosome 8, 3 from chromosome 5 and 1 each from chromosomes 1, 6 and 9. Array-CGH revealed that 10/11 r(8) consisted of amplification of a 19 Mb pericentromeric segment with recurrent breakpoints in FGFR1 in 8p12 and in PLAG1 in 8q12.1. Molecular analyses revealed that ring formation consistently generated novel FGFR1-PLAG1 gene fusions in which the 5'-part of FGFR1 is linked to the coding sequence of PLAG1. An alternative mechanism of PLAG1 activation was found in tumors with copy number gain of an intact PLAG1 gene. Rings derived from chromosomes 1, 5, 6 or 9 did not result in gene fusions, but rather resulted in losses indicative of the involvement of putative tumor suppressor genes on 8p, 5p, 5q and/or 6q. Our findings also reveal a novel mechanism by which FGFR1 contributes to oncogenesis and further illustrate the versatility of the FGFR1 and PLAG1 genes in tumorigenesis.
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| 7. |
- Persson, Fredrik, 1979, et al.
(författare)
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Lipid-Based Passivation in Nanofluidics
- 2012
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Ingår i: Nano Letters. - : American Chemical Society (ACS). - 1530-6992 .- 1530-6984. ; 12:5, s. 2260-2265
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Tidskriftsartikel (refereegranskat)abstract
- Stretching DNA in nanochannels is a useful tool for direct, visual studies of genomic DNA at the single molecule level. To facilitate the study of the interaction of linear DNA with proteins in nanochannels, we have implemented a highly effective passivation scheme based on lipid bilayers. We demonstrate virtually complete long-term passivation of nanochannel surfaces to a range of relevant reagents, including streptavidin-coated quantum dots, RecA proteins, and RecA-DNA complexes. We show that the performance of the lipid bilayer is significantly better than that of standard bovine serum albumin-based passivation. Finally, we show how the passivated devices allow us to monitor single DNA cleavage events during enzymatic degradation by DNase I. We expect that our approach will open up for detailed, systematic studies of a wide range of protein-DNA interactions with high spatial and temporal resolution.
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| 8. |
- Persson, Fredrik, 1979, et al.
(författare)
-
Local conformation of confined DNA studied using emission polarization anisotropy
- 2010
-
Ingår i: Biophysical Society 54th Annual Meeting.
-
Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- When confined in nanochannels with dimensions smaller than the DNA radius of gyration, DNA will extend along the channel. We investigate long DNA confined in nanochannels, using fluorescence microscopy and intercalated dyes. Studies of the dynamics and statics of DNA in such nanoscale confinements as a function of e.g. degree of confinement and ionic strength have yielded new insights into the physical properties of DNA with relevance for applications in genomics as well as fundamental understanding of DNA packaging in vivo. Our work extends the field by not only studying the location of the emitting dyes along a confined DNA molecule but also monitoring the polarization of the emitted light. By measuring the emission polarized parallel and perpendicular to the extension axis of the stretched DNA, information on the local spatial distribution of the DNA backbone can be obtained. Comparing polarizations in two directions for DNA confined in channels of effective diameters of 85 nm and 170 nm reveals a striking difference. Whereas the DNA in the larger channels shows an isotropic polarization of the emitted light, the light is to a large extent polarized perpendicular to the elongation of the DNA in the smaller channels. We expect this technique to have a large impact on the studies of changes in DNA conformation induced by protein binding or during DNA compactation as well as in fundamental polymer physics studies of DNA in confined environments, for example in bacterial spores and viruses.
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| 9. |
- Persson, Fredrik, 1979, et al.
(författare)
-
Local conformation of confined DNA studied using emission polarization anisotropy
- 2010
-
Ingår i: NanoBioTech-Montreux 2009.
-
Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- In nanochannels with dimensions smaller than the DNA radius of gyration, DNA will extend along the channel. We investigate long DNA confined in nanochannels using fluorescence microscopy and intercalated dyes. Studies of the dynamics and statics of the DNA extension or position in such nanoscale confinements as a function of e.g. DNA contour length, degree and shape of confinement as well as ionic strength have yielded new insights in the physical properties of DNA with relevance for applications in genomics as well as fundamental understanding of DNA packaging in vivo. Our work extends the field by not only studying the location of the emitting dyes along a confined DNA molecule but also monitoring the polarization of the emitted light. We use intercalating dyes (YOYO-1) whose emission is polarized perpendicular to the DNA extension axis, and by measuring the emission polarized parallel and perpendicular to the extension axis of the stretched DNA, information on the local spatial distribution of the DNA backbone can be obtained. The results obtained are analogous to linear dichroism (LD) but on a single-molecule level, and obtained in a highly parallel fashion. We will discuss results in shallow (60 nm) and deep (180 nm) channels and describe an example of how the technique can be used to investigate non-uniform stretching of DNA on the single molecule level. Comparing polarizations in two directions for DNA confined in channels of effective diameters of 85 nm and 170 nm reveals a striking difference. Whereas the DNA in the larger channels shows an isotropic polarization of the emitted light, the light is to a large extent polarized perpendicular to the elongation of the DNA in the smaller channels. The ratio of the polarization parallel and perpendicular to the elongation direction, I|| / I⊥, is a measure of the relative local orientation of the DNA backbone. We believe that this technique will have a large impact on the studies of changes in DNA conformation induced by protein binding or during DNA compactation as well as in fundamental polymer physics studies of DNA in confined environments, for example in bacterial spores and viruses.
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| 10. |
- Persson, Marta, 1979, et al.
(författare)
-
Clinically significant copy number alterations and complex rearrangements of MYB and NFIB in head and neck adenoid cystic carcinoma.
- 2012
-
Ingår i: Genes, chromosomes & cancer. - : Wiley. - 1098-2264 .- 1045-2257. ; 51:8, s. 805-17
-
Tidskriftsartikel (refereegranskat)abstract
- Adenoid cystic carcinoma (ACC) of the head and neck is a malignant tumor with poor long-term prognosis. Besides the recently identified MYB-NFIB fusion oncogene generated by a t(6;9) translocation, little is known about other genetic alterations in ACC. Using high-resolution, array-based comparative genomic hybridization, and massively paired-end sequencing, we explored genomic alterations in 40 frozen ACCs. Eighty-six percent of the tumors expressed MYB-NFIB fusion transcripts and 97% overexpressed MYB mRNA, indicating that MYB activation is a hallmark of ACC. Thirty-five recurrent copy number alterations (CNAs) were detected, including losses involving 12q, 6q, 9p, 11q, 14q, 1p, and 5q and gains involving 1q, 9p, and 22q. Grade III tumors had on average a significantly higher number of CNAs/tumor compared to Grade I and II tumors (P = 0.007). Losses of 1p, 6q, and 15q were associated with high-grade tumors, whereas losses of 14q were exclusively seen in Grade I tumors. The t(6;9) rearrangements were associated with a complex pattern of breakpoints, deletions, insertions, inversions, and for 9p also gains. Analyses of fusion-negative ACCs using high-resolution arrays and massively paired-end sequencing revealed that MYB may also be deregulated by other mechanisms in addition to gene fusion. Our studies also identified several down-regulated candidate tumor suppressor genes (CTNNBIP1, CASP9, PRDM2, and SFN) in 1p36.33-p35.3 that may be of clinical significance in high-grade tumors. Further, studies of these and other potential target genes may lead to the identification of novel driver genes in ACC.
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| 11. |
- Persson, Marta, 1979, et al.
(författare)
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Recurrent fusion of MYB and NFIB transcription factor genes in carcinomas of the breast and head and neck
- 2009
-
Ingår i: Proceedings of the National Academy of Sciences. - : Proceedings of the National Academy of Sciences. - 1091-6490 .- 0027-8424. ; 106:44, s. 18740-4
-
Tidskriftsartikel (refereegranskat)abstract
- The transcription factor gene MYB was identified recently as an oncogene that is rearranged/duplicated in some human leukemias. Here we describe a new mechanism of activation of MYB in human cancer involving gene fusion. We show that the t(6;9)(q22-23;p23-24) translocation in adenoid cystic carcinomas (ACC) of the breast and head and neck consistently results in fusions encoding chimeric transcripts predominantly consisting of MYB exon 14 linked to the last coding exon(s) of NFIB. The minimal common part of MYB deleted as the result of fusion was exon 15 including the 3'-UTR, which contains several highly conserved target sites for miR-15a/16 and miR-150 microRNAs. These microRNAs recently were shown to regulate MYB expression negatively. We suggest that deletion of these target sites may disrupt repression of MYB leading to overexpression of MYB-NFIB transcripts and protein and to activation of critical MYB targets, including genes associated with apoptosis, cell cycle control, cell growth/angiogenesis, and cell adhesion. Forced overexpression of miR-15a/16 and miR-150 in primary fusion-positive ACC cells did not significantly alter the expression of MYB as compared with leukemic cells with MYB activation/duplication. Our data indicate that the MYB-NFIB fusion is a hallmark of ACC and that deregulation of the expression of MYB and its target genes is a key oncogenic event in the pathogenesis of ACC. Our findings also suggest that the gain-of-function activity resulting from the MYB-NFIB fusion is a candidate therapeutic target.
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| 12. |
- Werner, Erik, et al.
(författare)
-
Orientational correlations in confined DNA
- 2012
-
Ingår i: Physical Review E. - 1539-3755 .- 2470-0045 .- 2470-0053. ; 86:4
-
Tidskriftsartikel (refereegranskat)abstract
- We study how the orientational correlations of DNA confined to nanochannels depend on the channel diameter D by means of Monte Carlo simulations and a mean-field theory. This theory describes DNA conformations in the experimentally relevant regime where Flory-de Gennes theory does not apply. We show how local correlations determine the dependence of the end-to-end distance of the DNA molecule upon D. Tapered nanochannels provide the necessary resolution in D to study experimentally how the extension of confined DNA molecules depends upon D. Our experimental and theoretical results are in qualitative agreement.
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| 13. |
- Westerlund, Fredrik, 1978, et al.
(författare)
-
Fluorescence Enhancement From Single DNA Molecules Confined In Si/SiO2 Nanochannels
- 2010
-
Ingår i: Biophysical Society, 54th Annual Meeting.
-
Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- A large challenge in biophysics when studying single molecules using fluorescence microscopy is to obtain a signal that is clearly detectable above the background noise. Ways to improve or optimize the fluorescence signal is therefore of great interest. We here study DNA extended in 320 nm deep funnel-shaped SiO2 nanochannels with a width ranging from 40nm to 600nm. The DNA is stained with a fluorescent dye (YOYO-1) and we show that the total emission from the DNA varies significantly with the dimensions of the channels (Figure) and has a peak intensity at half the wavelength of the emitted light. Measurements at varying salt concentrations, where the same confinement leads to different extension of the DNA, confirm that it is solely the geometry of the channel that governs the enhancement effect, ruling out alternative explanations, such as self-quenching. By using polarizers on the emission side we can investigate the light polarized parallel and perpendicular to the channel separately and we see that they show vastly different behavior with the peak in emission only detected in the light polarized parallel to the channels. We will discuss how our data may be explained by cavity-resonance effects when the lateral dimensions of the channels coincide with half the wavelength of the emitted light. Our results suggest that it is possible to fine-tune the size and shape of the nanochannels to maximize the number of photons collected from the molecule under study, for example when studying DNA interacting with single DNA-binding proteins where maximizing the photon budget is paramount.
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| 14. |
- Westerlund, Fredrik, 1978, et al.
(författare)
-
Fluorescence enhancement from single DNA molecules confined in SiO 2 nanochannels
- 2010
-
Ingår i: 14th International Conference on Miniaturized Systems for Chemistry and Life Sciences 2010, MicroTAS 2010; Groningen; Netherlands; 3 October 2010 through 7 October 2010. - 9781618390622
-
Konferensbidrag (refereegranskat)abstract
- We demonstrate that the detected emission intensity from YOYO-labeled DNA molecules confined in 180 nm deep Si/SiO2 nanofunnels changes significantly and not monotonically with the width of the funnel, an emission enhancement that is only detected for emitted light polarized parallel to the channel. We explain the enhancement effect as being due to optical phenomena in the channels. The enhancement effect may be of importance for quantitative fluorescence microscopy and for experiments with a tight photon budget.
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| 15. |
- Westerlund, Fredrik, 1978, et al.
(författare)
-
Fluorescence Enhancement of Single DNA Molecules Confined in Si/SiO2 Nanochannels
- 2010
-
Ingår i: Lab on a Chip. - : Royal Society of Chemistry (RSC). - 1473-0197 .- 1473-0189. ; 10:16, s. 2049-2051
-
Tidskriftsartikel (refereegranskat)abstract
- We demonstrate that the detected emission intensity from YOYO- labeled DNA molecules confined in 180 nm deep Si/SiO2 nano- funnels changes significantly and not monotonically with the width of the funnel. This effect may be of importance for quantitative fluorescence microscopy and for experiments with a tight photon budget.
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| 16. |
- Winnes, Marta, 1979, et al.
(författare)
-
Frequent fusion of the CRTC1 and MAML2 genes in clear cell variants of cutaneous hidradenomas
- 2007
-
Ingår i: Genes Chromosomes Cancer. - : Wiley. - 1098-2264 .- 1045-2257. ; 46:6, s. 559-563
-
Tidskriftsartikel (refereegranskat)abstract
- Fusion of the CREB regulated transcription coactivator CRTC1 (a.k.a. MECT1, TORC1, or WAMTP1) to the Notch coactivator MAML2 is a characteristic feature of low-grade mucoepidermoid carcinomas of salivary and bronchial glands. The CRTC1-MAML2 fusion protein acts by inducing transcription of cAMP/CREB target genes, and this activity is crucial for the transforming properties of the protein. Here we show that the CRTC1-MAML2 gene fusion is also frequent in benign hidradenomas of the skin. FISH and RT-PCR analyses revealed that hidradenomas are genetically heterogeneous, and that 10 of the 20 tumors analyzed (50%) contained the CRTC1-MAML2 gene fusion and expressed the resulting fusion transcript. Immunohistochemical analysis demonstrated expression of the fusion protein in the majority of tumor cells, including clear cells, poroid cells, and cells with epidermoid and ductal differentiation. In addition, we could show that all fusion-positive tumors were morphologically distinguished by the presence of more or less abundant areas of clear cells whereas all fusion-negative tumors lacked clear cells. Our findings thus demonstrate that the CRTC1-MAML2 gene fusion is frequent in hidradenomas and is associated with clear cell variants of this tumor. Taken together, the present and previous observations indicate that the CRTC1-MAML2 fusion is etiologically linked to benign and low-grade malignant tumors originating from diverse exocrine glands rather than being linked to a separate tumor entity.
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| 17. |
- Alizadehheidari, Mohammadreza, 1987, et al.
(författare)
-
Nanoconfined circular DNA
- 2014
-
Ingår i: 18th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2014. - 9780979806476 ; , s. 1353-1355
-
Konferensbidrag (refereegranskat)abstract
- Studies of nanoconfined circular DNA are of interest both from a biological as well as a fundamental polymer physics perspective. We here present the use of nanofluidic channels as a tool for comparing statics and dynamics of the linear and circular configuration of the same DNA molecule.
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| 18. |
- Alizadehheidari, Mohammadreza, 1987, et al.
(författare)
-
Nanoconfined Circular DNA
- 2014
-
Konferensbidrag (övrigt vetenskapligt/konstnärligt)
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| 19. |
- Freitag, C., et al.
(författare)
-
Visualizing the entire DNA from a chromosome in a single frame
- 2015
-
Ingår i: Biomicrofluidics. - : AIP Publishing. - 1932-1058. ; 9:4
-
Tidskriftsartikel (refereegranskat)abstract
- The contiguity and phase of sequence information are intrinsic to obtain complete understanding of the genome and its relationship to phenotype. We report the fabrication and application of a novel nanochannel design that folds megabase lengths of genomic DNA into a systematic back-and-forth meandering path. Such meandering nanochannels enabled us to visualize the complete 5.7 Mbp (1mm) stained DNA length of a Schizosaccharomyces pombe chromosome in a single frame of a CCD. We were able to hold the DNA in situ while implementing partial denaturation to obtain a barcode pattern that we could match to a reference map using the Poland-Scheraga model for DNA melting. The facility to compose such long linear lengths of genomic DNA in one field of view enabled us to directly visualize a repeat motif, count the repeat unit number, and chart its location in the genome by reference to unique barcode motifs found at measurable distances from the repeat. Meandering nanochannel dimensions can easily be tailored to human chromosome scales, which would enable the whole genome to be visualized in seconds. (C) 2015 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 Unported License.
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| 20. |
- Frykholm, Karolin, 1977, et al.
(författare)
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Probing concentration-dependent behavior of DNA-binding proteins on a single-molecule level illustrated by Rad51
- 2013
-
Ingår i: Analytical Biochemistry. - : Elsevier BV. - 0003-2697 .- 1096-0309. ; 443:2, s. 261-268
-
Tidskriftsartikel (refereegranskat)abstract
- Low throughput is an inherent problem associated with most single-molecule biophysical techniques. We have developed a versatile tool for high-throughput analysis of DNA and DNA-binding molecules by combining microfluidic and dense DNA arrays. We use an easy-to-process microfluidic flow channel system in which dense DNA arrays are prepared for simultaneous imaging of large amounts of DNA molecules with single-molecule resolution. The Y-shaped microfluidic design, where the two inlet channels can be controlled separately and precisely, enables the creation of a concentration gradient across the microfluidic channel as well as rapid and repeated addition and removal of substances from the measurement region. A DNA array stained with the fluorescent DNA-binding dye YOYO-1 in a gradient manner illustrates the method and serves as a proof of concept. We have applied the method to studies of the repair protein Rad51 and could directly probe the concentration-dependent DNA-binding behavior of human Rad51 (HsRad51). In the low-concentration regime used (100 nM HsRad51 and below), we detected binding to double-stranded DNA (dsDNA) without positive cooperativity. (C) 2013 Elsevier Inc. All rights reserved.
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| 21. |
- Gerken, Jan, 1991, et al.
(författare)
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Equivariance versus augmentation for spherical images
- 2022
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Ingår i: Proceedings of Machine Learning Resaerch. ; , s. 7404-7421
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Konferensbidrag (refereegranskat)abstract
- We analyze the role of rotational equivariance in convolutional neural networks (CNNs) applied to spherical images. We compare the performance of the group equivariant networks known as S2CNNs and standard non-equivariant CNNs trained with an increasing amount of data augmentation. The chosen architectures can be considered baseline references for the respective design paradigms. Our models are trained and evaluated on single or multiple items from the MNIST- or FashionMNIST dataset projected onto the sphere. For the task of image classification, which is inherently rotationally invariant, we find that by considerably increasing the amount of data augmentation and the size of the networks, it is possible for the standard CNNs to reach at least the same performance as the equivariant network. In contrast, for the inherently equivariant task of semantic segmentation, the non-equivariant networks are consistently outperformed by the equivariant networks with significantly fewer parameters. We also analyze and compare the inference latency and training times of the different networks, enabling detailed tradeoff considerations between equivariant architectures and data augmentation for practical problems.
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| 22. |
- Gerken, Jan, 1991, et al.
(författare)
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Geometric deep learning and equivariant neural networks
- 2023
-
Ingår i: Artificial Intelligence Review. - : Springer Nature. - 1573-7462 .- 0269-2821. ; 56:12, s. 14605-14662
-
Tidskriftsartikel (refereegranskat)abstract
- We survey the mathematical foundations of geometric deep learning, focusing on group equivariant and gauge equivariant neural networks. We develop gauge equivariant convolutional neural networks on arbitrary manifolds M using principal bundles with structure group K and equivariant maps between sections of associated vector bundles. We also discuss group equivariant neural networks for homogeneous spaces M= G/ K , which are instead equivariant with respect to the global symmetry G on M . Group equivariant layers can be interpreted as intertwiners between induced representations of G, and we show their relation to gauge equivariant convolutional layers. We analyze several applications of this formalism, including semantic segmentation and object detection networks. We also discuss the case of spherical networks in great detail, corresponding to the case M= S2= SO (3) / SO (2) . Here we emphasize the use of Fourier analysis involving Wigner matrices, spherical harmonics and Clebsch–Gordan coefficients for G= SO (3) , illustrating the power of representation theory for deep learning.
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| 23. |
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| 24. |
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| 25. |
- Hedsten, Karin, 1964, et al.
(författare)
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MEMS-based VCSEL beam steering using replicated polymer diffractive lens
- 2008
-
Ingår i: Sensors and Actuators, A: Physical. - : Elsevier BV. - 0924-4247 .- 1873-3069. ; 142:1, s. 336-345
-
Tidskriftsartikel (refereegranskat)abstract
- Abstract. This paper describes a fully integrated micro-optical system, in which dynamic angular control of the beam from a VCSEL (vertical cavity surface emitting laser) is realized by laterally moving a collimat¬ing diffractive lens in the light path. The lens is mounted on a translatable silicon stage, which consists of a frame with an opening for the light to traverse the lens and electro-statically driven comb actuators, by which the lateral movement is achieved. Devices implementing both 1D and 2D scanning have been fabricated and evaluated. Integration of the lens onto the translatable silicon stage is done using a newly developed fabrication process based on hot embossing of an amorphous fluorocarbon polymer. This fabrication process relies on a reversed-order protocol, where the structuring of the optical element precedes the silicon microstructuring. Assembly and packaging of the VCSEL-MOEMS system, using LTCC (low temperature cofired ceramic) technique, is also demonstrated. Optical evaluation of the system and beam steering function shows significant beam deflection for a relatively low driving voltage (~70 V).
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| 26. |
- Lin, Jun, et al.
(författare)
-
Bandpass filtering of DNA elastic modes using confinement and tension
- 2012
-
Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 102, s. 96-100
-
Tidskriftsartikel (refereegranskat)abstract
- During a variety of biological and technological processes, biopolymers are simultaneously subject to both confinement and external forces. Although significant efforts have gone into understanding the physics of polymers that are only confined, or only under tension, little work has been done to explore the effects of the interplay of force and confinement. Here, we study the combined effects of stretching and confinement on a polymer's configurational freedom. We measure the elastic response of long double-stranded DNA molecules that are partially confined to thin, nanofabricated slits. We account for the data through a model in which the DNA's short-wavelength transverse elastic modes are cut off by applied force and the DNA's bending stiffness, whereas long-wavelength modes are cut off by confinement. Thus, we show that confinement and stretching combine to permit tunable bandpass filtering of the elastic modes of long polymers. © 2012 Biophysical Society.
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| 27. |
- Magnusson, Alf, 1958, et al.
(författare)
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A Comparison of Spray Properties for Model Fuel and Diesel Using Several Optical Methods
- 2004
-
Ingår i: 19th Ilass Europe.
-
Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Many experiments are carried out using a model fuel, for instance for measurement technique reasons. These data are usually transferred to situations where standard diesel fuel is used. The objective of this work is to characterize the liquid and vapour phase penetration of two different diesel fuels, one two-component model fuel, IDEA (70% n-decane and 30% α-methylnaphthalene) and one standard diesel fuel (Swedish Environmental Class I), when injected into air with density corresponding to early injections up to self ignition conditions in diesel engines. The experimental study was carried out in the high-pressure, high-temperature (HP/HT) spray rig at Chalmers, which was pressurized in the range of 4 to 85 bar and with temperature ranging from 400 to 800 K.A common-rail injection system with a single hole nozzle was used. Several optical methods (Schlieren, Shadowgraph, LIF (Laser Induced Fluorescence) and Mie-scattering) were used together or separately which allow a comparison of the output. Phase Doppler Anemometry (PDA) was used for the two fuels as a complement to the planar methods. Results from measurements show that there are differences in liquid penetration, fuel vaporization and droplet distribution in between the fuels and relatively good agreement between the methods
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| 28. |
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| 29. |
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| 30. |
- McGinn, Steven, et al.
(författare)
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New Technologies for DNA analysis-A review of the READNA Project.
- 2016
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Ingår i: New Biotechnology. - : Elsevier BV. - 1876-4347 .- 1871-6784.
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Forskningsöversikt (refereegranskat)abstract
- The REvolutionary Approaches and Devices for Nucleic Acid analysis (READNA) project received funding from the European Commission for 4 1/2 years. The objectives of the project revolved around technological developments in nucleic acid analysis. The project partners have discovered, created and developed a huge body of insights into nucleic acid analysis, ranging from improvements and implementation of current technologies to the most promising sequencing technologies that constitute a 3(rd) and 4(th) generation of sequencing methods with nanopores and in situ sequencing, respectively.
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| 31. |
- Melin, Jonas, et al.
(författare)
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Microreplication in a Silicon Processing Compatible Material
- 2005
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Ingår i: IEEE/LEOS Optical MEMS 2005: International Conference on Optical MEMS and Their Applications, Oulu, Finland, 1-4 August 2005. - 9780780392786 ; , s. 89-90
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Konferensbidrag (refereegranskat)abstract
- We present a novel fabrication process for the integration of polymer micro-optical elements on silicon. The process relies on a reverse order protocol based on embossing in an amorphous fluorocarbon polymer, Cytop™.
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| 32. |
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| 33. |
- Nambiar, Sanjay, 1997-
(författare)
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Adaptive Automation for Customized Products
- 2024
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In today’s fast-paced industrial landscape, the drive for greater efficiency and flexibility in product development has sparked significant interest in innovative automation technologies. This thesis explores the usefulness of various automation techniques for customized products such as Knowledge-Based Engineering (KBE), Multidisciplinary Optimization (MDO) and machine learning frameworks.The research begins by establishing an automated framework for fixture design, combining design automation and MDO to streamline the design process. It then moves to optimizing gas turbines, introducing an automation framework that merges CAD templates with KBE principles.For complex and unstructured production, this thesis explores the use of Reinforcement Learning (RL) to tackle challenges in unstructured manufacturing. By utilizing lightweight physics-based engines and RL, the research advances automated assembly validation and mobile robot operations, pushing the boundaries of adaptive production automation. Furthermore, a framework is developed, which integrates smoothly with industrial robotic platforms showcases practical automation solutions and highlights the adaptability and applicability of digital twin technology in real-world situations.This thesis contributes to the field of product development by providing innovative solutions that are rooted in multidisciplinary research. It bridges the theoretical and practical aspects of automation with solutions that overcomes the obstacles to realize seamless integration between digital and physical realities in a manufacturing context.
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| 34. |
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| 35. |
- Persson, Fredrik, 1979, et al.
(författare)
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DNA in nanochannels—directly visualizing genomic information
- 2010
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Ingår i: Chemical Society Reviews. - 0306-0012. ; 39, s. 985-999
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Tidskriftsartikel (refereegranskat)abstract
- The power of nanofluidic channels to analyze DNA is described along with practical experimental hints. As an introduction, a general overview is given on conventional DNA analysis tools, as well as tools under development towards the $1000 genome. The focus of this tutorial review is the stretching of DNA in nanoscale channels for coarse-grained mapping of DNA. To understand the behavior of the DNA, basic theory is discussed. Experimental details are revealed so that the reader, with the proper equipment, should be able to perform experiments. Basic approaches to the analysis of the data are discussed. Finally, potential future directions are discussed including the application of melting mapping as a simple barcode for the DNA.
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| 36. |
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| 37. |
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| 38. |
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| 39. |
- Persson, Fredrik, 1973, et al.
(författare)
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High-resolution genomic profiling of adenomas and carcinomas of the salivary glands reveals amplification, rearrangement, and fusion of HMGA2
- 2009
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Ingår i: Genes Chromosomes Cancer. - : Wiley. - 1098-2264 .- 1045-2257. ; 48:1, s. 69-82
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Tidskriftsartikel (refereegranskat)abstract
- Carcinoma ex pleomorphic adenoma (Ca-ex-PA) is an epithelial malignancy developing within a benign salivary gland pleomorphic adenoma (PA). Here we have used genome-wide, high-resolution array-CGH, and fluorescence in situ hybridization to identify genes amplified in double min chromosomes and homogeneously staining regions in PA and Ca-ex-PA and to identify additional genomic imbalances characteristic of these tumor types. Ten of the 16 tumors analyzed showed amplification/gain of a 30-kb minimal common region, consisting of the 5'-part of HMGA2 (encoding the three DNA-binding domains). Coamplification of MDM2 was found in nine tumors. Five tumors had cryptic HMGA2-WIF1 gene fusions with amplification of the fusion oncogene in four tumors. Expression analysis of eight amplified candidate genes in 12q revealed that tumors with amplification/rearrangement of HMGA2 and MDM2 had significantly higher expression levels when compared with tumors without amplification. Analysis of individual HMGA2 exons showed that the expression of exons 3-5 were substantially reduced when compared with exons 1-2 in 9 of 10 tumors with HMGA2 activation, indicating that gene fusions and rearrangements of HMGA2 are common in tumors with amplification. In addition, recurrent amplifications/gains of 1q11-q32.1, 2p16.1-p12, 8q12.1, 8q22-24.1, and 20, and losses of 1p21.3-p21.1, 5q23.2-q31.2, 8p, 10q21.3, and 15q11.2 were identified. Collectively, our results identify HMGA2 and MDM2 as amplification targets in PA and Ca-ex-PA and suggest that amplification of 12q genes (in particular MDM2), deletions of 5q23.2-q31.2, gains of 8q12.1 (PLAG1) and 8q22.1-q24.1 (MYC), and amplification of ERBB2 may be of importance for malignant transformation of benign PA.
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| 40. |
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| 41. |
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| 42. |
- Shirvany, Yazdan, 1980, et al.
(författare)
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Evaluation of a finite-element reciprocity method for epileptic EEG source localization: Accuracy, computational complexity and noise robustness
- 2013
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Ingår i: Biomedical Engineering Letters. - : Springer Science and Business Media LLC. - 2093-985X .- 2093-9868. ; 3:1, s. 8-16
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Tidskriftsartikel (refereegranskat)abstract
- PURPOSEThe aim of this paper is to evaluate the performance of an EEG source localization method that combines a finite element method (FEM) and the reciprocity theorem.METHODSThe reciprocity method is applied to solve the forward problem in a four-layer spherical head model for a large number of test dipoles. To benchmark the proposed method, the results are compared with an analytical solution and two state-of-the-art methods from the literature. Moreover, the dipole localization error resulting from utilizing the method in the inverse procedure for a realistic head model is investigated with respect to EEG signal noise and electrode misplacement.RESULTSThe results show approximately 3% relative error between numerically calculated potentials done by the reciprocity theorem and the analytical solutions. When adding EEG noise with SNR between 5 and 10, the mean localization error is approximately 4.3 mm. For the case with 10 mm electrode misplacement the localization error is 4.8 mm. The reciprocity EEG source localization speeds up the solution of the inverse problem with more than three orders of magnitude compared to the state-of-the-art methods.CONCLUSIONSThe reciprocity method has high accuracy for modeling the dipole in EEG source localization, is robust with respect to noise, and faster than alternative methods.
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| 43. |
- Skogsberg, Mikael, 1975, et al.
(författare)
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Fuel distribution visualization from an air-assisted injector in a spray chamber
- 2004
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Ingår i: Comodia 2004, Yokohama, 2-5 aug 2004.
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Konferensbidrag (refereegranskat)abstract
- Optical measurements have been performed to visualize the fuel distribution from an air-assisted GDI injector in a constant volume spray chamber. In the air-assisted injector, fuel droplet breakup occurs as the droplets are accelerated by the expanded air flow passing out through the injector nozzle. The injector design allows for two distinct modes of operation: stratified (low load) and homogenous (full load). Therefore, measurements were taken at back-pressure and temperature settings corresponding to both low and full loads, to investigate the influence of these variables on fuel distribution, droplet sizes and velocities in the two modes.Results from PDA measurements show that most of the droplet break-up occurs inside the nozzle. Downstream of the nozzle, rates of break-up and evaporation are low. The cause of the low breakup and evaporation rates downstream of the nozzle is believed to be the low relative velocity between the liquid fuel and the surrounding cold air jet.The fuel distribution has been visualized qualitatively by simultaneous MIE and LIF measurements with two intensified digital cameras in combination with a 266 nm YAG-laser.
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| 44. |
- Stenman, Lisa, et al.
(författare)
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Primary orbital precursor T-cell lymphoblastic lymphoma: Report of a unique case.
- 2016
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Ingår i: Molecular and clinical oncology. - : Spandidos Publications. - 2049-9450 .- 2049-9469. ; 5:5, s. 593-595
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Tidskriftsartikel (refereegranskat)abstract
- Primary T-cell lymphoblastic lymphoma (T-LBL) in the eye region is very rare. The present study described a unique case of T-LBL involving the extraocular muscles. A 22-year-old male patient presented with a 3-week history of headache, reduced visual acuity and edema of the left eye. Clinical examination revealed left-sided exophthalmus, periorbital edema, chemosis, and reduced motility of the left eye. A magnetic resonance imaging scan revealed thickening of the left orbital muscles and a positron emission tomography-computed tomography scan also demonstrated activity in a subclavicular lymph node. Histopathological analysis of both lesions revealed infiltration by medium-sized neoplastic lymphoid cells with a high nuclear-cytoplasmic ratio and a high mitotic index. Immunostaining revealed positivity for CD2, CD3, CD99, Tia-1, and GranzymB, and variable positivity for CD4. There was no involvement of the bone marrow. Based on the clinical and histopathological findings, a diagnosis of T-LBL was made. There was no evidence of NOTCH1 mutation or rearrangements of the ETV6 and MLL genes and high-resolution array-based comparative genomic hybridization (arrayCGH) analysis revealed a normal genomic profile. The patient received chemotherapy according to the high-risk NOPHO protocol, followed by myeloablative allogenic bone marrow transplantation. At 35 months after diagnosis, the patient remained in complete first remission, but without light perception on his left eye. To the best of our knowledge, this is the first report of a case of T-LBL involving the extraocular muscles. Although primary T-LBL in the eye region is very rare, our findings demonstrate that lymphoma should be considered in the differential diagnosis of patients with similar symptoms.
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| 45. |
- Svanedal, Ida, 1979-, et al.
(författare)
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Metal Ion Coordination, Conditional Stability Constants and Solution Behavior of Chelating Surfactant Metal Complexes
- 2014
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Ingår i: Langmuir. - : American Chemical Society (ACS). - 0743-7463 .- 1520-5827. ; 30:16, s. 4605-4612
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Tidskriftsartikel (refereegranskat)abstract
- Coordination complexes of some divalent metal ions with the DTPA (diethylenetriaminepentaacetic acid)-based chelating surfactant 2-dodecyldiethylenetriaminepentaacetic acid (4-C12-DTPA) have been examined in terms of chelation and solution behavior. The headgroup of 4-C 12-DTPA contains eight donor atoms that can participate in the coordination of a metal ion. Conditional stability constants for five transition metal complexes with 4-C12-DTPA were determined by competition measurements between 4-C12-DTPA and DTPA, using electrospray ionization mass spectrometry (ESI-MS). Small differences in the relative strength between the coordination complexes of DTPA and 4-C12-DTPA indicated that the hydrocarbon tail only affected the chelating ability of the headgroup to a limited extent. The coordination of Cu2+ ions was investigated in particular, using UV-visible spectroscopy. By constructing Job's plots, it was found that 4-C12-DTPA could coordinate up to two Cu2+ ions. Surface tension measurements and NMR diffusometry showed that the coordination of metal ions affected the solution behavior of 4-C 12-DTPA, but there were no specific trends between the studied divalent metal complexes. Generally, the effects of the metal ion coordination could be linked to the neutralization of the headgroup charge of 4-C 12-DTPA, and the resulting reduced electrostatic repulsions between adjacent surfactants in micelles and monolayers. The pH vs concentration plots, on the other hand, showed a distinct difference between 4-C12-DTPA complexes of the alkaline earth metals and the transition metals. This was explained by the difference in coordination between the two groups of metal ions, as predicted by the hard and soft acid and base (HSAB) theory.
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| 46. |
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| 47. |
- Wahlqvist, Evelina, 1979, et al.
(författare)
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Socialförsäkringar behövs
- 2009
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Ingår i: Sydsvenska dagbladet, 23 oktober.
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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