| 1. |
- Abarenkov, Kessy, et al.
(författare)
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Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from a May 23-24, 2016 workshop (Gothenburg, Sweden)
- 2016
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Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 16, s. 1-15
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Tidskriftsartikel (refereegranskat)abstract
- Recent molecular studies have identified substantial fungal diversity in indoor environments. Fungi and fungal particles have been linked to a range of potentially unwanted effects in the built environment, including asthma, decay of building materials, and food spoilage. The study of the built mycobiome is hampered by a number of constraints, one of which is the poor state of the metadata annotation of fungal DNA sequences from the built environment in public databases. In order to enable precise interrogation of such data – for example, “retrieve all fungal sequences recovered from bathrooms” – a workshop was organized at the University of Gothenburg (May 23-24, 2016) to annotate public fungal barcode (ITS) sequences according to the MIxS-Built Environment annotation standard (http://gensc.org/mixs/). The 36 participants assembled a total of 45,488 data points from the published literature, including the addition of 8,430 instances of countries of collection from a total of 83 countries, 5,801 instances of building types, and 3,876 instances of surface-air contaminants. The results were implemented in the UNITE database for molecular identification of fungi (http://unite.ut.ee) and were shared with other online resources. Data obtained from human/animal pathogenic fungi will furthermore be verified on culture based metadata for subsequent inclusion in the ISHAM-ITS database (http://its.mycologylab.org).
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| 2. |
- Andersson, Kent, 1967-, et al.
(författare)
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Introduktion till Operationsanalys : En antologi med essäer av studerande i militärteknik 2011
- 2012
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- I ämnesplanen definieras militärteknik som ”den vetenskap som beskriver och förklarar hur tekniken inverkar på militär verksamhet på alla nivåer, strategisk, operativ och taktisk, samt hur officersprofessionen påverkar och påverkas av tekniken.”[1] En militärteknikers uppgift brukar, utgående från definitionen, uttryckas som att beskriva och förklara den militära nyttan med tekniken. För att kunna göra detta behövs verktyg. Och många av dem kommer från den vetenskapliga disciplinen Operationsanalys.Syftet med den här antologin är att introducera studerande i militärteknik på Försvarshögskolan till två av de mest refererade boktitlarna i operationsanalys – Methods for conducting military operational analysis editerad av Andrew G. Loerch och Larry B. Rainey samt Military Operations Research, quantitative decision making av N.K. Jaiswal.Kapitlen utgörs av essäer skrivna av studerande på den högre stabsofficersutbildningen med teknisk inriktning, som examinationsuppgift i en fördjupningskurs. Essäerna är till del referat av kapitel i de två böckerna ovan, men kryddade med exempel satta i svenskt sammanhang och med de studerandes egen värdering av metodernas användbarhet.[1]Försvarshögskolan, Ämnesplan militärteknik, 2007.
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| 3. |
- Andersson, Magnus, et al.
(författare)
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A structural basis for sustained bacterial adhesion : Biomechanical properties of CFA/I Pili
- 2012
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Ingår i: Journal of Molecular Biology. - : Elsevier. - 0022-2836 .- 1089-8638. ; 415:5, s. 918-928
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Tidskriftsartikel (refereegranskat)abstract
- Enterotoxigenic Escherichia coli (ETEC) are a major cause of diarrheal disease worldwide. Adhesion pili (or fimbriae), such as the CFA/I (colonization factor antigen I) organelles that enable ETEC to attach efficiently to the host intestinal tract epithelium, are critical virulence factors for initiation of infection. We characterized at single organelle level the intrinsic biomechanical properties and kinetics of individual CFA/I pili, demonstrating that weak external forces (7.5 pN) are sufficient to unwind the intact helical filament of this prototypical ETEC pilus and that it quickly regains its original structure when the force is removed. While the general relationship between exertion of force and an increase in the filament length for CFA/I pili associated with diarrheal disease is analogous to that of P-pili and type 1 pili, associated with urinary tract and other infections, the biomechanical properties of these different pili differ in key quantitative details. Unique features of CFA/I pili, including the significantly lower force required for unwinding, the higher extension speed at which the pili enter a dynamic range of unwinding, and the appearance of sudden force drops during unwinding can be attributed to morphological features of CFA/I pili including weak layer-to-layer interactions between subunits on adjacent turns of the helix, and the approximately horizontal orientation of pilin subunits with respect to the filament axis. Our results indicate that ETEC CFA/I pili are flexible organelles optimized to withstand harsh motion without breaking, resulting in continued attachment to the intestinal epithelium by the pathogenic bacteria that express these pili.
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| 4. |
- Andersson, Magnus, et al.
(författare)
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Differentiating pili expressed by enterotoxigenic and uropathogenic escherichia coli with optical tweezers
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Enterotoxigenic Escherichia coli (ETEC) attach to the host epithelium in the intestinal tract via specific adhesion organelles expressed on the cell membrane. We investigate, by force measuring optical tweezers, the intrinsic biomechanical properties and kinetics of the colonization factor I (CFA/I) at a single pilus level. The measurements indicate that CFA/I pili are helix-like structures that can both be unraveled to a linearized polymer by applying a small external force, 7.5 ± 1.5 pN but also regain its helix-like structure when the applied force is reduced. The data confirm that layer-to-layer interactions, that stabilize the helix-like structure, are much weaker than the interactions found in pili expressed by Uropathogenic Escherichia coli (UPEC). It is also found, contrary to previous results assessed from UPEC pili, that the CFA/I undergo in some cases a sudden structural change, a force drop of ~2 pN, when unraveled from the helix-like configuration to an open helical linearized fiber. These data suggest a rotation of the filament about its helical axis, followed by a region in which the force required to extend the pili further increases rapidly. During this final elongation to a super-extended fiber, CFA/I pili do not show any structural transition as seen for UPEC pili. In addition, the CFA/I pili show faster kinetics than UPEC pili that allows for a larger dynamic regime of in vivo shear forces. The unfolding and refolding possibility points toward an organelle that has evolved to allow for dynamic damping of external forces and handling of harsh motion without breaking.
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| 5. |
- Blomsterwall, Elisabeth, et al.
(författare)
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Postural disturbance in patients with normal pressure hydrocephalus.
- 2000
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Ingår i: Acta neurologica Scandinavica. - : Hindawi Limited. - 0001-6314. ; 102:5, s. 284-91
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Tidskriftsartikel (refereegranskat)abstract
- The postural function in 52 patients with normal pressure hydrocephalus (NPH) and in 19 patients with subcortical arteriosclerotic encephalopathy (SAE) was analysed bedside and in 17 of the NPH, 10 of the SAE and 23 healthy individuals (HI) also examined with a force platform. At the bedside examination, no differences in postural functions between NPH and SAE patients were found. The NPH patients improved more in the postural than in motor functions after shunt surgery. The NPH patients had a larger sway area and a higher backward directed velocity of centre of pressure than HI. The direction of the inclination in the sagittal plane was neutral or forward in the NPH and the SAE patients while it was backward in HI. The postural function was better in positions with open eyes in all 3 groups, but significantly less in the NPH patients, indicating a misinterpretation of afferent visual stimuli in the brainstem postural centre.
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| 6. |
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| 7. |
- Khademi, Seyran, 1981, et al.
(författare)
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Peak-to-Average-Power-Ratio (PAPR) reduction in WiMAX and OFDM/A systems
- 2011
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Ingår i: EURASIP Journal on Advances in Signal Processing. - : Springer Science and Business Media LLC. - 1687-6180. ; , s. Article Number: 38-
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Tidskriftsartikel (refereegranskat)abstract
- A peak to average power ratio (PAPR) reduction method is proposed that exploits the precoding or beamforming mode in WiMAX. The method is applicable to any OFDM/A systems that implements beamforming using dedicated pilots which use the same beamforming antenna weights for both pilots and data. Beamforming performance depends on the relative phase shift between antennas, but is unaffected by a phase shift common to all antennas. PAPR, on the other hand, changes with a common phase shift and this paper exploits that property. An effective optimization technique based on sequential quadratic programming is proposed to compute the common phase shift. The proposed technique has several advantages compared with traditional PAPR reduction techniques in that it does not require any side-information and has no effect on power and bit-error-rate while providing better PAPR reduction performance than most other methods.
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| 8. |
- Ridderström, Mikael, et al.
(författare)
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High prevalence of carpal tunnel syndrome in individuals with rare nerve growth factor-beta mutation
- 2020
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Ingår i: Brain Communications. - United Kingdom : Oxford University Press. - 2632-1297. ; 2:2
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Tidskriftsartikel (refereegranskat)abstract
- In Sweden, a large family with a point mutation in the nerve growth factor-beta gene has previously been identified. The carriers of this mutation have reduced small-fiber density and selective deficits in deep pain and temperature modalities. The clinical findings in this population are described as hereditary sensory and autonomic neuropathy type V. The purpose of the current study was to investigate the prevalence of carpal tunnel syndrome in hereditary sensory and autonomic neuropathy type V based on clinical examinations and electrophysiological measurements. Further, the cross-sectional area of the median nerve at the carpal tunnel inlet was measured with ultrasonography. Out of 52 known individuals heterozygous for the nerve growth factor-beta mutation in Sweden, 23 participated in the current study (12 males, 11 females; mean age, 55 years; range, 25 to 86 years). All participants answered a health questionnaire and underwent clinical examination followed by median nerve conduction study in a case-control design, and measurement of the nerve cross-sectional area with ultrasonography. The diagnosis of carpal tunnel syndrome was made based on consensus criteria using patient history and nerve conduction study. The prevalence of carpal tunnel syndrome in the hereditary sensory and autonomic neuropathy group was 35% (95% CI 19-55%) or 52% (95% CI 37-74%) depending on whether those individuals who had classic symptoms of carpal tunnel syndrome but negative nerve conduction studies were included or not. Those who had a high likelihood of carpal tunnel syndrome based on classic/probable patient history with positive nerve conduction study had a significantly larger median nerve cross-sectional area than those who had an unlikely patient history with negative nerve conduction study. The prevalence of carpal tunnel syndrome was 10 to 25 times higher in individuals heterozygous for the nerve growth factor-beta mutation than the general Swedish population. Further studies are needed to better understand the underlying pathophysiological mechanisms.
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| 9. |
- Svantesson, Mats, 1975-, et al.
(författare)
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Get a New Perspective on EEG: Convolutional Neural Network Encoders for Parametric t-SNE
- 2023
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Ingår i: Brain Sciences. - : MDPI. - 2076-3425. ; 13:3
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Tidskriftsartikel (refereegranskat)abstract
- t-distributed stochastic neighbor embedding (t-SNE) is a method for reducing high-dimensional data to a low-dimensional representation, and is mostly used for visualizing data. In parametric t-SNE, a neural network learns to reproduce this mapping. When used for EEG analysis, the data are usually first transformed into a set of features, but it is not known which features are optimal. The principle of t-SNE was used to train convolutional neural network (CNN) encoders to learn to produce both a high- and a low-dimensional representation, eliminating the need for feature engineering. To evaluate the method, the Temple University EEG Corpus was used to create three datasets with distinct EEG characters: (1) wakefulness and sleep; (2) interictal epileptiform discharges; and (3) seizure activity. The CNN encoders produced low-dimensional representations of the datasets with a structure that conformed well to the EEG characters and generalized to new data. Compared to parametric t-SNE for either a short-time Fourier transform or wavelet representation of the datasets, the developed CNN encoders performed equally well in separating categories, as assessed by support vector machines. The CNN encoders generally produced a higher degree of clustering, both visually and in the number of clusters detected by k-means clustering. The developed principle is promising and could be further developed to create general tools for exploring relations in EEG data.
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| 10. |
- Svantesson, Mats, 1975-
(författare)
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Self-supervised deep learning and EEG categorization
- 2024
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Deep learning has the potential to be used to improve and streamline EEG analysis. At the present, classifiers and supervised learning dominate the field. Supervised learning depends on target labels which most often are created by human experts manually classifying data. A problem with supervised learning is intra- and interrater agreement which in some instances are far from perfect. This can affect the training and make evaluation more difficult. This thesis includes three papers where self-supervised deep neural networks were developed. In self-supervised learning, the input data to the networks themselves contain structures that are used as targets for the training and no labeling is necessary. In paper I, deep neural networks were trained to increase the number of-, or to recreate missing EEG-channels. The performance was at least on the same level as that of spherical interpolation, but unlike in the case of interpolation, missing data does not have to be identified manually first. Papers II and III involved developing deep neural networks for clustering analysis. The networks produced two-dimensional representations of EEG data and the training strategy was based on the principle of t-distributed stochastic neighbor embedding (t-SNE). In paper II, comparisons were made to parametric t-SNE and EEG-features obtained from time-frequency methods. The deep neural networks produced more distinct clustering when tested on data annotated for epileptiform discharges, seizure activity, or sleep-wakefulness.In paper III, the newly developed method was used to compare annotations of epileptiform discharges. Two experts performed independent annotations and classifiers were trained on these, using supervised learning, which in turn produced new annotations. The agreement when comparing two sets of annotations was not larger between the two experts than between an expert and a classifier. The analysis showed that differences in the annotations by the experts influenced the training of the classifiers. However, the clustering analysis indicated that although it was not always the exact same waveforms that were assessed as epileptiform discharges, they were often similar.The work thus resulted in different methods to process and analyze EEG data, which may have practical usefulness. Traditional agreement scores only assess the exact agreement. However, they reveal nothing about the nature of disagreement. Cluster analysis can provide a means to perform this assessment.
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