| 1. |
- Gau, Rémi, et al.
(författare)
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Brainhack : Developing a culture of open, inclusive, community-driven neuroscience
- 2021
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Ingår i: Neuron. - : Elsevier. - 0896-6273 .- 1097-4199. ; 109:11, s. 1769-1775
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Tidskriftsartikel (refereegranskat)abstract
- Brainhack is an innovative meeting format that promotes scientific collaboration and education in an open, inclusive environment. This NeuroView describes the myriad benefits for participants and the research community and how Brainhacks complement conventional formats to augment scientific progress.
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| 2. |
- Bonetti, Stefano, et al.
(författare)
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Direct observation and imaging of a spin-wave soliton with p−like symmetry
- 2015
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Ingår i: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- The prediction and realization of magnetic excitations driven by electrical currents via the spin transfer torque effect, enables novel magnetic nano-devices where spin-waves can be used to process and store information. The functional control of such devices relies on understanding the properties of non-linear spin-wave excitations. It has been demonstrated that spin waves can show both an itinerant character, but also appear as localized solitons. So far, it was assumed that localized solitons have essentially cylindrical, s−like symmetry. Using a newly developed high-sensitivity time-resolved magnetic x-ray microscopy, we instead observe the emergence of a novel localized soliton excitation with a nodal line, i.e. with p−like symmetry. Micromagnetic simulations identify the physical mechanism that controls the transition from s− to p−like solitons. Our results suggest a potential new pathway to design artificial atoms with tunable dynamical states using nanoscale magnetic devices.
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| 3. |
- Gorgolewski, Krzysztof J., et al.
(författare)
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BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods
- 2017
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Ingår i: PloS Computational Biology. - : Public Library of Science (PLoS). - 1553-734X .- 1553-7358. ; 13:3
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Tidskriftsartikel (refereegranskat)abstract
- The rate of progress in human neurosciences is limited by the inability to easily apply a wide range of analysis methods to the plethora of different datasets acquired in labs around the world. In this work, we introduce a framework for creating, testing, versioning and archiving portable applications for analyzing neuroimaging data organized and described in compliance with the Brain Imaging Data Structure (BIDS). The portability of these applications (BIDS Apps) is achieved by using container technologies that encapsulate all binary and other dependencies in one convenient package. BIDS Apps run on all three major operating systems with no need for complex setup and configuration and thanks to the comprehensiveness of the BIDS standard they require little manual user input. Previous containerized data processing solutions were limited to single user environments and not compatible with most multi-tenant High Performance Computing systems. BIDS Apps overcome this limitation by taking advantage of the Singularity container technology. As a proof of concept, this work is accompanied by 22 ready to use BIDS Apps, packaging a diverse set of commonly used neuroimaging algorithms.
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| 4. |
- Ytterberg, A Jimmy, et al.
(författare)
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Shared immunological targets in the lungs and joints of patients with rheumatoid arthritis : identification and validation
- 2015
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Ingår i: Annals of the Rheumatic Diseases. - : BMJ. - 0003-4967 .- 1468-2060. ; 74:9, s. 1772-1777
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVES: Immunological events in the lungs might trigger production of anti-citrullinated protein antibodies during early rheumatoid arthritis (RA). We investigated the presence of shared immunological citrullinated targets in joints and lungs of patients with RA.PATIENTS AND METHODS: Proteins extracted from bronchial (n=6) and synovial (n=7) biopsy specimens from patients with RA were investigated by mass spectrometry-based proteomics. One candidate peptide was synthesised and used to investigate by ELISA the presence of antibodies in patients with RA (n=393), healthy controls (n=152) and disease controls (n=236). HLA-DRB1 shared epitope (SE) alleles were detected in patients with RA.RESULTS: Ten citrullinated peptides belonging to seven proteins were identified, with two peptides shared between the synovial and bronchial biopsy samples. Further analysis, using accurate mass and retention time, enabled detection of eight citrullinated peptides in synovial and seven in bronchial biopsy specimens, with five peptides shared between the synovial and bronchial biopsy specimens. Two citrullinated vimentin (cit-vim) peptides were detected in the majority of synovial and lung tissues. Antibodies to a synthesised cit-vim peptide candidate (covering both cit-vim peptides identified in vivo) were present in 1.8% of healthy controls, 15% of patients with RA, and 3.4% of disease controls. Antibodies to cit-vim peptide were associated with the presence of the SE alleles in RA.CONCLUSIONS: Identical citrullinated peptides are present in bronchial and synovial tissues, which may be used as immunological targets for antibodies of patients with RA. The data provide further support for a link between lungs and joints in RA and identify potential targets for immunity that may mediate this link.
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| 5. |
- Banuazizi, Seyed Amir Hossein, et al.
(författare)
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Control of thermal budget in nanocontact spin-torque nano-oscillators
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- We investigate the influence of the bottom Cu electrode thickness (tCu) in nanocontact spin-torque nano-oscillators (NC-STNOs) based on Si/SiO2/Pd(8)/Cu(tCu)/Co(8)/Cu(7)/NiFe(4.5)/Cu(3)/Pd(3) GMR stacks on the thermal budget of the magnetodynamically active region. Increasing tCu from 10 to 70 nm results in a ~50% reduction in Joule heating in both the Co and NiFe layers, which directly improves the microwave output stability and linewidth. Numerical simulations of the NC-STNO current distribution suggest that this improvement originates from a strongly reduced lateral current spread in the top ferromagnetic layer and a reduction in the device's resistance.
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| 6. |
- Behrens, Anders, et al.
(författare)
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A computerized neuropsychological test battery designed for idiopathic normal pressure hydrocephalus
- 2014
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Ingår i: Fluids and Barriers of the CNS. - : Springer Science and Business Media LLC. - 2045-8118. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: A tool for standardized and repeated neuropsychological assessments in patients with idiopathic normal pressure hydrocephalus (INPH) is needed. The objective of this study was to develop a computerized neuropsychological test battery designed for INPH and to evaluate its reliability, validity and patient's ability to complete the tests.METHODS: Based on a structured review of the literature on neuropsychological testing in INPH, the eight tests most sensitive to the INPH cognitive profile were implemented in a computerized format. The Geriatric Depression Scale (GDS) was also included. Tests were presented on a touch-screen monitor, with animated instructions and speaker sound. The battery was evaluated with the following cohorts: A. Test-retest reliability, 44 healthy elderly; B. Validity against standard pen and pencil testing, 28 patients with various cognitive impairments; C. Ability to complete test battery, defined as completion of at least seven of the eight tests, 40 investigated for INPH.RESULTS: A. All except the figure copy test showed good test-retest reliability, r = 0.67-0.90; B. A high correlation was seen between conventional and computerized tests (r = 0.66-0.85) except for delayed recognition and figure copy task; C. Seventy-eight percent completed the computerized battery; Patients diagnosed with INPH (n = 26) performed worse on all tests, including depression score, compared to healthy controls.CONCLUSIONS: A new computerized neuropsychological test battery designed for patients with communicating hydrocephalus and INPH was introduced. Its reliability, validity for general cognitive impairment and completion rate for INPH was promising. After exclusion of the figure copy task, the battery is ready for clinical evaluation and as a next step we suggest validation for INPH and a comparison before and after shunt surgery.TRIAL REGISTRATION: ClinicalTrials.org NCT01265251.
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| 7. |
- Chen, Tingsu, 1987-, et al.
(författare)
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Spin-Torque and Spin-Hall Nano-Oscillators
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Ingår i: Proceedings of the IEEE. - 0018-9219 .- 1558-2256.
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Tidskriftsartikel (refereegranskat)abstract
- This paper reviews the state of the art in spin-torque and spin Hall effect driven nano-oscillators. After a brief introduction to the underlying physics, the authors discuss different implementations of these oscillators, their functional properties in terms of frequency range, output power, phase noise, and modulation rates, and their inherent propensity for mutual synchronization. Finally, the potential for these oscillators in a wide range of applications, from microwave signal sources and detectors to neuromorphic computation elements, is discussed together with the specific electronic circuitry that has so far been designed to harness this potential.
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| 8. |
- Eklund, Anders, et al.
(författare)
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A Bayesian Heteroscedastic GLM with Application to fMRI Data with Motion Spikes
- 2017
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Ingår i: NeuroImage. - : Elsevier. - 1053-8119 .- 1095-9572. ; 155, s. 354-369
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Tidskriftsartikel (refereegranskat)abstract
- We propose a voxel-wise general linear model with autoregressive noise and heteroscedastic noise innovations (GLMH) for analyzing functional magnetic resonance imaging (fMRI) data. The model is analyzed from a Bayesian perspective and has the benefit of automatically down-weighting time points close to motion spikes in a data-driven manner. We develop a highly efficient Markov Chain Monte Carlo (MCMC) algorithm that allows for Bayesian variable selection among the regressors to model both the mean (i.e., the design matrix) and variance. This makes it possible to include a broad range of explanatory variables in both the mean and variance (e.g., time trends, activation stimuli, head motion parameters and their temporal derivatives), and to compute the posterior probability of inclusion from the MCMC output. Variable selection is also applied to the lags in the autoregressive noise process, making it possible to infer the lag order from the data simultaneously with all other model parameters. We use both simulated data and real fMRI data from OpenfMRI to illustrate the importance of proper modeling of heteroscedasticity in fMRI data analysis. Our results show that the GLMH tends to detect more brain activity, compared to its homoscedastic counterpart, by allowing the variance to change over time depending on the degree of head motion.
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| 9. |
- Eklund, Anders, et al.
(författare)
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Evaluation of applanation resonator sensors for intra-ocular pressure measurement : results from clinical and in vitro studies.
- 2003
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Ingår i: Medical and Biological Engineering and Computing. - 0140-0118 .- 1741-0444. ; 41:2, s. 190-197
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Tidskriftsartikel (refereegranskat)abstract
- Glaucoma is an eye disease that, in its most common form, is characterised by high intra-ocular pressure (IOP), reduced visual field and optic nerve damage. For diagnostic purposes and for follow-up after treatment, it is important to have simple and reliable methods for measuring IOP. Recently, an applanation resonator sensor (ARS) for measuring IOP was introduced and evaluated using an in vitro pig-eye model. In the present study, the first clinical evaluation of the same probe has been carried out, with experiments in vivo on human eyes. There was a low but significant correlation between IOP(ARS) and the IOP measured with a Goldmann applanation tonometer (r = 0.40, p = 0.001, n = 72). However, off-centre positioning of the sensor against the cornea caused a non-negligible source of error. The sensor probe was redesigned to have a spherical, instead of flat, contact surface against the eye and was evaluated in the in vitro model. The new probe showed reduced sensitivity to off-centre positioning, with a decrease in relative deviation from 89% to 11% (1 mm radius). For normalised data, linear regression between IOP(ARS) and direct IOP measurement in the vitreous chamber showed a correlation of r = 0.97 (p < 0.001, n = 108) and a standard deviation for the residuals of SD < or = 2.18 mm Hg (n = 108). It was concluded that a spherical contact surface should be preferred and that further development towards a clinical instrument should focus on probe design and signal analysis.
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| 10. |
- Eklund, Anders, et al.
(författare)
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Hydrodynamics of the CertasTM programmable valve for the treatment of hydrocephalus
- 2012
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Ingår i: Fluids and barriers of the CNS. - : Springer Science and Business Media LLC. - 2045-8118. ; 9:1, s. 12-
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: The new CertasTM shunt for the treatment of hydrocephalus has seven standard pressure settings that according to the manufacturer range from 36 to 238 mmH2O, and an additional "Virtual Off" setting with an opening pressure >400 mmH2O. Information on actual pressure response and reliability of shunt performance is important in clinical application, especially the "Virtual Off" setting as a non-surgical replacement for shunt ligation. The objective of this study was to evaluate the in-vitro hydrodynamic performance of the CertasTM shunt.METHODS: Six new CertasTM shunts with proximal and distal catheters were tested with an automated, computerized test system that raised the pressure from zero to a maximum pressure and back to zero at each valve setting. Opening pressure and flow resistance were determined.RESULTS: For settings 1-7 the measured opening pressure range was 26 to 247 mmH2O, and the mean change in opening pressure for a one-step adjustment was between 33 and 38 mmH2O. For setting 8 ("Virtual Off") the measured mean opening pressure was 494 +/- 34 mmH2O (range 451 to 556 mmH2O). The mean outflow resistance was 7.0 mmHg/ml/min (outflow conductance 17.9 ul/s/kPa).CONCLUSIONS: The six shunts had similar characteristics and closely matched the manufacturer's specifications for opening pressure at settings 1-7. The opening pressure for the "Virtual Off" setting was nearly 500 mmH2O, which is 100 mmH2O higher than the manufacturer's specification of ">400" and should be functionally off for most patients with communicating hydrocephalus. Clinical studies are needed to evaluate if the CSF dynamic profile persists after implantation in patients.
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