| 1. |
- Olson, Nathan D., et al.
(författare)
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precisionFDA Truth Challenge V2: Calling variants from short- and long-reads in difficult-to-map regions
- 2020
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The precisionFDA Truth Challenge V2 aimed to assess the state-of-the-art of variant calling in difficult-to-map regions and the Major Histocompatibility Complex (MHC). Starting with FASTQ files, 20 challenge participants applied their variant calling pipelines and submitted 64 variant callsets for one or more sequencing technologies (~35X Illumina, ~35X PacBio HiFi, and ~50X Oxford Nanopore Technologies). Submissions were evaluated following best practices for benchmarking small variants with the new GIAB benchmark sets and genome stratifications. Challenge submissions included a number of innovative methods for all three technologies, with graph-based and machine-learning methods scoring best for short-read and long-read datasets, respectively. New methods out-performed the 2016 Truth Challenge winners, and new machine-learning approaches combining multiple sequencing technologies performed particularly well. Recent developments in sequencing and variant calling have enabled benchmarking variants in challenging genomic regions, paving the way for the identification of previously unknown clinically relevant variants.
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| 2. |
- O'Shea, JN, et al.
(författare)
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Hydrogen-bond induced surface core-level shift in isonicotinic acid
- 2001
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Intermolecular hydrogen-bonding in thick films of isonicotinic acid evaporated onto rutile TiO2(110) has been investigated with X-ray photoelectron spectroscopy (XPS) and X-ray absorption spectroscopy (XAS). The rate of deposition is found to be a key fac
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| 3. |
- Fransson, Moa, 1981-, et al.
(författare)
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Engineered T regulatory cells target CNS and suppress active EAE upon intra nasal delivery
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Multiple sclerosis (MS) is an autoimmune disorder of the central nervous system (CNS). In the murine experimental autoimmune encephalomyelitis (EAE) model of MS, T regulatory (Treg) cell therapy has proven beneficial. However, systemic administration of such cells may immunologically compromise the recipient and promote infections due to general immunosuppression. We hypothesized that Tregs can be equipped with a CNS-targeting receptor and be delivered intra-nasally to avoid systemic exposure. In the current investigation, CD4+ T cells were modified with a lentiviral vector system to express a myelin oligodendrocyte (MOG)-targeting receptor in trans with the FoxP3 gene that drives Treg differentiation. The genetically engineered Tregs demonstrated suppressive capacity in vitro and were then tested in the EAE model. Engineered Tregs localized to the brain and suppressed ongoing encephalomyelitis in vivo. Cured mice were rechallenged with an EAE-inducing inoculum but remained healthy. Cytokine profile of the brain reveled lower levels of effector cytokines in TregCAR treated mice and acordingly, reduced axonal damage was seen in these mice. In conclusion, CNS-specific Tregs were able to localize to the CNS and efficiently cure mice with ongoing EAE.
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| 4. |
- Fransson, Moa, 1981-, et al.
(författare)
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Human Mesenchymal stromal cells expressing a CNS-targeting receptor can be administrated intra nasally and cure expersimental autoimmune enchphlomyelitis
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Mesenchymal stromal cells (MSCs) are a heterogeneous population of stromal cells residing in most connective tissues and have the capacity to suppress effector cells of the immune system. In experimental autoimmune encephalomyelitis (EAE), a mouse model of multiple sclerosis, systemic treatments with both murine and human MSCs have proven beneficial because of their capacity to suppress overt immune reactions. However, systemic administration of such cells may cause problems with infectious disease and low numbers of cells that reach the inflamed tissue. We hypothesized that MSCs can be accumulated and retained in the CNS using gene transfer of a CNS-targeting device and intranasal cell delivery. In the current investigation, MSCs were engineered to express a myelin oligodendrocyte glycoprotein (MOG)-specific receptor using lentiviral vectors. Genetically engineered MSCs retained their suppressive capacity in vitro and successfully targeted the brain upon both intraperitoneal and intranasal delivery. Engineered MSCs cured mice from disease symptoms and these mice were resistant to further EAE challenge. Encephalitic T cells isolated from cured mice displayed an anergic profile while peripheral T cells were still responsive to stimuli. Further, MSC treatment reduced the level of inflammatory cytokines in the brain and implyed reduced damage to axons. In conclusion, MSCs can be genetically engineered to target CNS and efficiently suppress encephalomyelitis in an active EAE model upon intranasal delivery.
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| 5. |
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| 6. |
- Höglund, Linda, et al.
(författare)
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Studies of photocurrent and dark current in quantum dots-in-a-well infrared photodetectors
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The performance of quantum dots-in-a-well infrared photodetectors (DWELL IPs) has been studied by means of interband and intersubband photocurrent measurements as well as dark current measurements. Using interband photocurrent measurements, substantial escape of electrons from lower lying states in the DWELL structure at large biases was revealed. Furthermore, a significant variation of the escape probability from energy states in the DVELL sturcture with voltage was observed. These facts could be possible explanations to the strong temperature and voltage dependence of hoth photocurrent and dark current in DWELL IPs. In a comparison between DWELL IPs and quantum well infrared photocdetectors (QWIPs), the dark current was shown to be considerably lower in DWELL IPs than in QWIPs, but alos the responsivity was low in comparison to QWIPs.
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| 7. |
- Muhammad, Riaz, et al.
(författare)
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Experimental and finite element method calculation of piezoelectric power generation from ZnO nanowire arrays grown on different substrates using high and low temperature methods
- 2008
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- In this paper we investigate the piezoelectric power generation from ZnO nanowire arrays grown using different methods. The ZnO nanowires are grown on n-SiC and n-Si substrates using both the high-temperature vapor liquid solid (VLS) and the lowtemperature aqueous chemical growth (ACG) methods. A conductive atomic force microscope (AFM) is used in contact mode to deflect the ZnO nanowire arrays. A piezoelectric potential across the nanowires is produced and then released via the rectifying behavior of the Schottky barrier at the platinum metal-ZnO interface. We do not observe any substrate effect but the growth method, crystal quality, density, length and diameter (aspect ratio) of the nanowires are found to affect the piezoelectric behavior. These parameters can significantly affect the performance manifested in the observed output voltage signal. Based on these parameters, we compare four nanogenerators under identical conditions. During the AFM scanning in contact mode without biased voltage, the ZnO nanowire arrays grown by the VLS method produce higher and larger output voltage signal of 35 mV compared to ZnO nanowires arrays grown by the ACG method, which produce smaller output voltage signal of 5 mV. We apply finite element (FE) method calculations to investigate the output voltage of ZnO nanowires based nanogenerators with different aspects ratios. From FE results we find that the output voltage of the nanogenerator is decreased above an aspect ratio 80 of ZnO nanowires.
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| 9. |
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| 10. |
- Schmidt, Bernard, 1981-, et al.
(författare)
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Integration of events and offline measurement data from a population of similar entities for condition monitoring
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- In this paper, an approach for integration of data from different sources and from a population of similar monitored entities is presented with evaluation procedure based on multiple machine learning methods that allows selection of a proper combination of methods for data integration and feature selection. It is exemplified on the real-world case from manufacturing industry with application to double ball-bar measurement from a population of machine tools. Historical data from the period of four years from a population of 29 similar multitask machine tools are analysed. Several feature selection methods are evaluated. Finally, simple economic evaluation is presented with application to proposed condition based approach. With assumed parameters, potential improvement in long term of 6 times reduced amount of unplanned stops and 40% reduced cost has been indicated with respect to optimal time based replacement policy.
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