| 1. |
- Abdellah, Tebani, et al.
(författare)
-
Integration of molecular profiles in a longitudinal wellness profiling cohort.
- 2020
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- An important aspect of precision medicine is to probe the stability in molecular profiles among healthy individuals over time. Here, we sample a longitudinal wellness cohort with 100 healthy individuals and analyze blood molecular profiles including proteomics, transcriptomics, lipidomics, metabolomics, autoantibodies andimmune cell profiling, complementedwith gut microbiota composition and routine clinical chemistry. Overall, our results show high variation between individuals across different molecular readouts, while the intra-individual baseline variation is low. The analyses show that each individual has a unique and stable plasma protein profile throughout the study period and that many individuals also show distinct profiles with regards to the other omics datasets, with strong underlying connections between the blood proteome and the clinical chemistry parameters. In conclusion, the results support an individual-based definition of health and show that comprehensive omics profiling in a longitudinal manner is a path forward for precision medicine.
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| 2. |
- Ericsson, Olle, et al.
(författare)
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Clinical validation of a novel automated cell-free DNA screening assay for trisomies 21, 13, and 18 in maternal plasma.
- 2019
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Ingår i: Prenatal diagnosis. - : Wiley. - 1097-0223 .- 0197-3851. ; 39:11, s. 1011-1015
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Tidskriftsartikel (refereegranskat)abstract
- To evaluate clinical performance of a new automated cell-free (cf)DNA assay in maternal plasma screening for trisomies 21, 18, and 13, and to determine fetal sex.Maternal plasma samples from 1200 singleton pregnancies were analyzed with a new non-sequencing cfDNA method, which is based on imaging and counting specific chromosome targets. Reference outcomes were determined by either cytogenetic testing, of amniotic fluid or chorionic villi, or clinical examination of neonates.The samples examined included 158 fetal aneuploidies. Sensitivity was 100% (112/112) for trisomy 21, 89% (32/36) for trisomy 18, and 100% (10/10) for trisomy 13. The respective specificities were 100%, 99.5%, and 99.9%. There were five first pass failures (0.4%), all in unaffected pregnancies. Sex classification was performed on 979 of the samples and 99.6% (975/979) provided a concordant result.The new automated cfDNA assay has high sensitivity and specificity for trisomies 21, 18, and 13 and accurate classification of fetal sex, while maintaining a low failure rate. The study demonstrated that cfDNA testing can be simplified and automated to reduce cost and thereby enabling wider population-based screening.
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| 3. |
- Karlsson, Fredrik, et al.
(författare)
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Sensor Fused Indoor Positioning Using Dual Band WiFi Signal Measurements
- 2015
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Ingår i: 2015 European Control Conference (ECC). - 9783952426937 ; , s. 1669-1672
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Konferensbidrag (refereegranskat)abstract
- In this paper, signal strengths from known WiFi access points are used together with a particle filter to perform indoor navigation. It is shown that more information is obtained by using signals of both 2.4 and 5.0 GHz, compared to using only one frequency. Thus, using both frequencies provides a more accurate positioning. The second contribution is an algorithm where WiFi measurements are combined with pedestrian dead reckoning (PDR), which is based on step counting using an accelerometer and hypotheses of the heading using a gyroscope. This was found to provide further accuracy compared to more conventional methods.
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| 4. |
- Magnusson, Peter S., et al.
(författare)
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SimICS/sun4m : A virtual workstation
- 2019
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Ingår i: USENIX 1998 Annual Technical Conference. - New Orleans, LA, USA : USENIX Association.
-
Konferensbidrag (refereegranskat)abstract
- System level simulators allow computer architects and system software designers to recreate an accurate and complete replica of the program behavior of a target system, regardless of the availability, existence, or instrumentation support of such a system. Applications include evaluation of architectural design alternatives as well as software engineering tasks such as traditional debugging and performance tuning. We present an implementation of a simulator acting as a virtual workstation fully compatible with the sun4m architecture from Sun Microsystems. Built using the system-level SPARC V8 simulator SimICS, SimICS/sun4m models one or more SPARC V8 processors, supports user-developed modules for data cache and instruction cache simulation and execution profiling of all code, and provides a symbolic and performance debugging environment for operating systems. SimICS/sun4m can boot unmodified operating systems, including Linux 2.0.30 and Solaris 2.6, directly from snapshots of disk partitions. To support essentially arbitrary code, we implemented binary-compatible simulators for several devices, including SCSI, console, interrupt, timers, EEPROM, and Ethernet. The Ethernet simulation hooks into the host and allows the virtual workstation to appear on the local network with full services available (NFS, NIS, rsh, etc). Ethernet and console traffic can be recorded for future playback. The performance of SimICS/sun4m is sufficient to run realistic workloads, such as the database benchmark TPC-D, scaling factor 1/100, or an interactive network application such as Mozilla. The slowdown in relation to native hardware is in the range of 25 to 75 (measured using SPECint95). We also demonstrate some applications, including modeling an 8-processor sun4m version (which does not exist), modeling future memory hierarchies, and debugging an operating system.
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| 5. |
- Alexeyev, Oleg, et al.
(författare)
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Association between the presence of bacterial 16S RNA in prostate specimens taken during transurethral resection of prostate and subsequent risk of prostate cancer (Sweden)
- 2006
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Ingår i: Cancer Causes and Control. - Dordrecht : Kluwer Academic Publishers. - 0957-5243 .- 1573-7225. ; 17:9, s. 1127-1133
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Tidskriftsartikel (refereegranskat)abstract
- Objective: To study bacterial 16S RNA in archival prostate samples from 352 patients with benign prostate hyperplasia (BPH) and evaluate whether the presence of bacterial DNA was different in those who later developed prostate cancer (n = 171) and in the matched controls that did not progress to cancer (n = 181).Methods: 16S DNA PCR followed by cloning and sequencing the positive samples.Results: In 96/352 (27%) of the prostate tissue specimens 16S RNA were detected. Sequence analysis revealed Propionibacterium acnes as the predominant microorganism (23% of 16S RNA positive patients). The second most frequent isolate—Escherichia coli was found in 12 (12%) patients. The other isolates included Pseudomonas sp. (3 patients), Actinomyces sp. (2), Streptococcus mutans (1), Corynebacterium sp. (2),Nocardioides sp. (1), Rhodococcus sp. (1) Veillonella sp. (2). In P. acnes positive samples 62% exhibited severe histological inflammation versus 50% in the bacteria-negative group (p = 0.602). The presence of P. acnes in the prostate was associated with prostate cancer development (OR 2.17, 95% CI 0.77–6.95).Conclusions: This study has revealed P. acnes as the most common bacteria in the prostate in BPH. Further studies are needed to clarify its role in contributing to the development of prostatic inflammation and prostate cancer.
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| 6. |
- Alvez, Maria Bueno, et al.
(författare)
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Next generation pan-cancer blood proteome profiling using proximity extension assay
- 2023
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- A comprehensive characterization of blood proteome profiles in cancer patients can contribute to a better understanding of the disease etiology, resulting in earlier diagnosis, risk stratification and better monitoring of the different cancer subtypes. Here, we describe the use of next generation protein profiling to explore the proteome signature in blood across patients representing many of the major cancer types. Plasma profiles of 1463 proteins from more than 1400 cancer patients are measured in minute amounts of blood collected at the time of diagnosis and before treatment. An open access Disease Blood Atlas resource allows the exploration of the individual protein profiles in blood collected from the individual cancer patients. We also present studies in which classification models based on machine learning have been used for the identification of a set of proteins associated with each of the analyzed cancers. The implication for cancer precision medicine of next generation plasma profiling is discussed.
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| 7. |
- Bengtsson, Erik L, et al.
(författare)
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A Case Study on the Influence of Multiple Users on the Effective Channel in a Massive MIMO System
- 2019
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Ingår i: IEEE Wireless Communications Letters. - 2162-2337. ; , s. 1-6
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Tidskriftsartikel (refereegranskat)abstract
- We investigate the importance of weak clusters when modeling a wireless massive MIMO channel. We do this by studying the influence of densely spaced terminals and the number of base-station antennas for a zero-forcing precoded massive MIMO system. In particular, we focus on the influence on the correlation and imbalance between the signals at the terminal antennas, the effective channel-gain, the eigenvalue distributions and the number of clusters.The study is based on measured radio-channels from terminal prototypes with integrated antennas connected to a massive MIMO testbed.We further evaluate the advantage of using block-diagonalized zero-forcing compared to conventional zero-forcing in a massive MIMO system. Unexpectedly, terminals with low antenna envelope correlation coefficient may benefit significantly from block-diagonal zero-forcing in a massive MIMO system.The main conclusion is that weaker clusters are important when modeling multi-user scenarios.
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| 8. |
- Bengtsson, Erik L., et al.
(författare)
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A Simulation Framework for Multiple-Antenna Terminals in 5G Massive MIMO Systems
- 2017
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Ingår i: IEEE Access. - 2169-3536. ; 5, s. 26819-26831
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Tidskriftsartikel (refereegranskat)abstract
- The recent interest in massive MIMO has spurred intensive work on massive MIMO channel modeling in contemporary literature. However, current models fail to take the characteristics of terminal antennas into account. There is no massive MIMO channel model available that can be used for evaluation of the influence of different antenna characteristics at the terminal side. In this paper, we provide a simulation framework that fills this gap. We evaluate the framework with antennas integrated into Sony Xperia handsets operating at 3.7 GHz as this spectrum is identified for the 5G new radio standard by 3GPP. The simulation results are compared with measured terminal performance when communicating with the Lund University’s massive MIMO testbed under the same loading conditions. Expressions are derived for comparison of the gain obtained from different diversity schemes computed from measured far-field antenna patterns. We conclude that the simulation framework yields results close to the measured ones and that the framework can be used for antenna evaluation for terminals in a practical precoded massive MIMO system.
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| 9. |
- Bengtsson, Erik L., et al.
(författare)
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Analysis of Transmission Schemes for Dual-Antenna Terminals in Massive MIMO Systems
- 2018
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Ingår i: 2018 25th International Conference on Telecommunications, ICT 2018. - 9781538623213 ; , s. 76-82
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Konferensbidrag (refereegranskat)abstract
- The overall system performance of massive MIMO is improved by equipping user terminals with multiple antennas. In this paper, we investigate transceiver designs for the case of a single downlink stream and in particular, we study the uplink pilot design. Moreover, we study the consequences of channel estimation errors at the base-station, and to what extent a dual-antenna terminal can get access to relevant channel statistics for optimization of the pilot signal. Gain expressions for comparison of different designs are derived. We verify the analytic results based on antennas integrated into Sony-Xperia handsets measured with the Lund University massive MIMO testbed. The measurements are performed at frequencies <6GHz since this part of the spectrum is a candidate for NR standard according to 3GPP.
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| 10. |
- Bengtsson, Erik L, et al.
(författare)
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Simulation of Multiple-Antenna Terminal Performance in Massive MIMO Systems based on Indoor Measurements
- 2020
-
Ingår i: IEEE Transactions on Vehicular Technology. - 0018-9545. ; 69:1, s. 418-427
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Tidskriftsartikel (refereegranskat)abstract
- In massive MIMO systems the uplink pilot signalstransmitted by a terminal define the channel seen by the basestation. This gives the terminal some degree of freedom selectingan uplink pilot transmission strategy. In this paper, we investigatethe benefit of different pilot transmission strategies when increasingthe number of antennas in the terminal. Building on previouswork on a simulation framework for Multiple-antenna terminalsin 5G massive MIMO systems, this paper presents simulatedperformance results for various transmission schemes. The resultsare calibrated to reflect a real communication situation in a largeauditorium. Emulating the measurement set-up, we show that theframework can be tuned to generate channel distributions thatmatch measured data. Under generalized conditions, we performsimulations for different terminal transmission-strategies, bothrelated to single stream and multiple streams. All evaluations arebased on terminals with four antennas integrated into real SonyXperia smartphone-chassis, tuned to 3.7 GHz. The measurementsare conducted by using the Lund University Massive MIMOtestbed with its 100 antennas. The results clearly show theadvantage of increasing the antenna-count also at the terminalside in massive MIMO systems.
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| 11. |
- Bengtsson, Erik L, et al.
(författare)
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Transmission schemes for Multiple Antenna Terminals in Real Massive MIMO systems
- 2016
-
Ingår i: 2016 IEEE Global Communications Conference (GLOBECOM). - 9781509013289 - 9781509013296
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Konferensbidrag (refereegranskat)abstract
- In massive MIMO performance evaluations it is often assumed that the terminal has a single antenna. The combination of multiple antennas in a terminal and massive MIMO precoding at the base station side can further improve overall system performance. We present measurement results for multi antenna terminals operating in different transmission schemes and how they perform under varying loading conditions. Gain expressions are derived that enable easy comparison between the transmission schemes. The evaluation is performed on realistic antennas integrated into Sony Xperia handsets tuned to 3.7~GHz and operated together with the Lund University massive MIMO (LuMaMi) test bed. It is concluded that the approach used in today's mobile systems, where up link and down link are addressed independently, will not provide the best performance. The performance can be improved by the selection of transmission schemes optimized for massive MIMO.
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| 12. |
- Bengtsson-Palme, Johan, 1985, et al.
(författare)
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Strategies to improve usability and preserve accuracy in biological sequence databases
- 2016
-
Ingår i: Proteomics. - : Wiley. - 1615-9853 .- 1615-9861. ; 16:18, s. 2454-2460
-
Tidskriftsartikel (refereegranskat)abstract
- Biology is increasingly dependent on large-scale analysis, such as proteomics, creating a requirement for efficient bioinformatics. Bioinformatic predictions of biological functions rely upon correctly annotated database sequences, and the presence of inaccurately annotated or otherwise poorly described sequences introduces noise and bias to biological analyses. Accurate annotations are, for example, pivotal for correct identifications of polypeptide fragments. However, standards for how sequence databases are organized and presented are currently insufficient. Here, we propose five strategies to address fundamental issues in the annotation of sequence databases: (i) to clearly separate experimentally verified and unverified sequence entries; (ii) to enable a system for tracing the origins of annotations; (iii) to separate entries with high-quality, informative annotation from less useful ones; (iv) to integrate automated quality-control software whenever such tools exist; and (v) to facilitate post-submission editing of annotations and metadata associated with sequences. We believe that implementation of these strategies, for example as requirements for publication of database papers, would enable biology to better take advantage of large-scale data.
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| 13. |
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| 14. |
- Botling, Johan, et al.
(författare)
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Biomarker Discovery in Non-Small Cell Lung Cancer : Integrating Gene Expression Profiling, Meta-analysis, and Tissue Microarray Validation
- 2013
-
Ingår i: Clinical Cancer Research. - 1078-0432 .- 1557-3265. ; 19:1, s. 194-204
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: Global gene expression profiling has been widely used in lung cancer research to identify clinically relevant molecular subtypes as well as to predict prognosis and therapy response. So far, the value of these multigene signatures in clinical practice is unclear, and the biologic importance of individual genes is difficult to assess, as the published signatures virtually do not overlap.Experimental Design: Here, we describe a novel single institute cohort, including 196 non-small lung cancers (NSCLC) with clinical information and long-term follow-up. Gene expression array data were used as a training set to screen for single genes with prognostic impact. The top 450 probe sets identified using a univariate Cox regression model (significance level P < 0.01) were tested in a meta-analysis including five publicly available independent lung cancer cohorts (n = 860).Results: The meta-analysis revealed 14 genes that were significantly associated with survival (P < 0.001) with a false discovery rate < 1%. The prognostic impact of one of these genes, the cell adhesion molecule 1 (CADM1), was confirmed by use of immunohistochemistry on tissue microarrays from 2 independent NSCLC cohorts, altogether including 617 NSCLC samples. Low CADM1 protein expression was significantly associated with shorter survival, with particular influence in the adenocarcinoma patient subgroup.Conclusions: Using a novel NSCLC cohort together with a meta-analysis validation approach, we have identified a set of single genes with independent prognostic impact. One of these genes, CADM1, was further established as an immunohistochemical marker with a potential application in clinical diagnostics. Clin Cancer Res; 19(1); 194-204. (c) 2012 AACR.
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| 15. |
- Detter, Fredrik, et al.
(författare)
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A 3-year school-based exercise intervention improves muscle strength - a prospective controlled population-based study in 223 children
- 2014
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Ingår i: BMC Musculoskeletal Disorders. - : Springer Science and Business Media LLC. - 1471-2474. ; 15
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Tidskriftsartikel (refereegranskat)abstract
- Background: Intense physical activity (PA) improves muscle strength in children, but it remains uncertain whether moderately intense PA in a population-based cohort of children confers these benefits. Methods: We included children aged 6-9 years in four schools where the intervention school increased the school curriculum of PA from 60 minutes/week to 40 minutes/school day while the control schools continued with 60 minutes/week for three years. We measured muscle strength, as isokinetic Peak Torque (PT) (Nm) of the knee flexors in the right leg at speeds of 60 degrees/second and 180 degrees/second, at baseline and at follow-up, in 47 girls and 76 boys in the intervention group and 46 girls and 54 boys in the control group and then calculated annual changes in muscle strength. Data are provided as means with 95% confidence intervals. Results: Girls in the intervention group had 1.0 Nm (0.13, 1.9) and boys 1.9 Nm (0.9, 2.9) greater annual gain in knee flexor PT at 60 degrees/second, than girls and boys in the control group. Boys in the intervention group also had 1.5 Nm (0.5, 2.5) greater annual gain in knee flexors PT at 180 degrees/second than boys in the control group. Conclusion: A 3-year moderately intense PA intervention program within the school curriculum enhances muscle strength in both girls and boys.
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| 16. |
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| 17. |
- Glimelius, Bengt, et al.
(författare)
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U-CAN : a prospective longitudinal collection of biomaterials and clinical information from adult cancer patients in Sweden.
- 2018
-
Ingår i: Acta Oncologica. - : Taylor & Francis. - 0284-186X .- 1651-226X. ; 57:2, s. 187-194
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Tidskriftsartikel (refereegranskat)abstract
- Background: Progress in cancer biomarker discovery is dependent on access to high-quality biological materials and high-resolution clinical data from the same cases. To overcome current limitations, a systematic prospective longitudinal sampling of multidisciplinary clinical data, blood and tissue from cancer patients was therefore initiated in 2010 by Uppsala and Umeå Universities and involving their corresponding University Hospitals, which are referral centers for one third of the Swedish population.Material and Methods: Patients with cancer of selected types who are treated at one of the participating hospitals are eligible for inclusion. The healthcare-integrated sampling scheme encompasses clinical data, questionnaires, blood, fresh frozen and formalin-fixed paraffin-embedded tissue specimens, diagnostic slides and radiology bioimaging data.Results: In this ongoing effort, 12,265 patients with brain tumors, breast cancers, colorectal cancers, gynecological cancers, hematological malignancies, lung cancers, neuroendocrine tumors or prostate cancers have been included until the end of 2016. From the 6914 patients included during the first five years, 98% were sampled for blood at diagnosis, 83% had paraffin-embedded and 58% had fresh frozen tissues collected. For Uppsala County, 55% of all cancer patients were included in the cohort.Conclusions: Close collaboration between participating hospitals and universities enabled prospective, longitudinal biobanking of blood and tissues and collection of multidisciplinary clinical data from cancer patients in the U-CAN cohort. Here, we summarize the first five years of operations, present U-CAN as a highly valuable cohort that will contribute to enhanced cancer research and describe the procedures to access samples and data.
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| 18. |
- Gustafsson, Fredrik, et al.
(författare)
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Particle Filters for Positioning, Navigation and Tracking
- 2001
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- A framework for positioning, navigation and tracking problems using particle filters (sequential Monte Carlo methods) is developed. It consists of a class of motion models and a general non-linear measurement equation in position. A general algorithm is presented, which is parsimonious with the particle dimension. It is based on marginalization, enabling a Kalman filter to estimate all position derivatives, and the particle filter becomes low-dimensional. This is of utmost importance for high-performance real-time applications. Automotive and airborne applications illustrate numerically the advantage over classical Kalman filter based algorithms. Here the use of non-linear models and non-Gaussian noise is the main explanation for the improvement in accuracy. More specifically, we describe how the technique of map matching is used to match an aircraft's elevation profile to a digital elevation map, and a car's horizontal driven path to a street map. In both cases, real-time implementations are available, and tests have shown that the accuracy in both cases is comparable to satellite navigation (as GPS), but with higher integrity. Based on simulations, we also argue how the particle filter can be used for positioning based on cellular phone measurements, for integrated navigation in aircraft, and for target tracking in aircraft and cars. Finally, the particle filter enables a promising solution to the combined task of navigation and tracking, with possible application to airborne hunting and collision avoidance systems in cars.
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| 19. |
- Gustafsson, Fredrik, et al.
(författare)
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Particle Filters for Positioning, Navigation and Tracking
- 2002
-
Ingår i: IEEE Transactions on Signal Processing. - : Institute of Electrical and Electronics Engineers (IEEE). - 1053-587X .- 1941-0476. ; 50:2, s. 425-437
-
Tidskriftsartikel (refereegranskat)abstract
- A framework for positioning, navigation and tracking problems using particle filters (sequential Monte Carlo methods) is developed. It consists of a class of motion models and a general non-linear measurement equation in position. A general algorithm is presented, which is parsimonious with the particle dimension. It is based on marginalization, enabling a Kalman filter to estimate all position derivatives, and the particle filter becomes low-dimensional. This is of utmost importance for high-performance real-time applications. Automotive and airborne applications illustrate numerically the advantage over classical Kalman filter based algorithms. Here the use of non-linear models and non-Gaussian noise is the main explanation for the improvement in accuracy. More specifically, we describe how the technique of map matching is used to match an aircraft's elevation profile to a digital elevation map, and a car's horizontal driven path to a street map. In both cases, real-time implementations are available, and tests have shown that the accuracy in both cases is comparable to satellite navigation (as GPS), but with higher integrity. Based on simulations, we also argue how the particle filter can be used for positioning based on cellular phone measurements, for integrated navigation in aircraft, and for target tracking in aircraft and cars. Finally, the particle filter enables a promising solution to the combined task of navigation and tracking, with possible application to airborne hunting and collision avoidance systems in cars.
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| 20. |
- Hedström, Karin, 1967-, et al.
(författare)
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Challenges of introducing a professional eID card within health care
- 2016
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Ingår i: Transforming Government. - Bingley, United Kingdom : Emerald Group Publishing Limited. - 1750-6166 .- 1750-6174. ; 10:1, s. 22-46
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: The purpose of this paper is to examine the challenges that arise when introducing an electronic identification (eID) card for professional use in a health-care setting.Design/methodology/approach: This is a case study of an eID implementation project in healthcare. Data were collected through interviews with key actors in a project team and with eID end users. The authors viewed the eID card as a boundary object intersecting social worlds. For this analysis, the authors combined this with an electronic government initiative challenge framework.Findings: The findings of this paper illustrate the interpretative flexibility of eID cards and how eID cards as boundary objects intersect social worlds. The main challenges of implementing and using eID cards in healthcare are usability, user behaviour and privacy. However, the way in which these challenges are interpreted varies between different social worlds.Practical implications: One of the implications for future practice is to increase our understanding of the eID card as a socio-technical artefact, where the social and technical is intertwined, at the same time as the eID card affects the social as well as the technical. By using a socio-technical perspective, it is possible to minimise the potential problems related to the implementation and use of eID.Originality/value: Previous research has highlighted the need for more empirical research on identity management. The authors contextualise and analyse the implementation and use of eID cards within healthcare. By viewing the eID card as a boundary object, the authors have unveiled its interpretative flexibility and how it is translated across different social worlds.
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| 21. |
- Hosseini, Sara, et al.
(författare)
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Comparative proteomic analysis of hyphae and germinating cysts of Phytophthora pisi and Phytophthora sojae.
- 2015
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Ingår i: Journal of Proteomics. - : Elsevier BV. - 1874-3919 .- 1876-7737. ; 117, s. 24-40
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Tidskriftsartikel (refereegranskat)abstract
- The recently described oomycete pathogen Phytophthora pisi causes root rot on pea and faba bean, while the closely related Phytophthora sojae is the causal agent of soybean root and stem rot. Differences in the pathogenicity factor repertoires that enable the two species to have distinct host specificity towards pea and soybean, were studied using tandem mass spectrometry in a global proteome study of hyphae and germinating cysts in P. pisi and P. sojae. In total 2775 proteins from P. pisi and 2891 proteins from P. sojae were identified. Fifty-eight orthologous proteins were more abundant in germinated cysts of both pathogens and thus identified as candidate proteins for the infective stage. Several of these proteins were associated with lipid transport and metabolism, and energy production. Twenty-three orthologous proteins were more abundant in hyphae of both pathogens and thus identified as candidate proteins for vegetative growth. Proteins uniquely present in germinating cysts of either P. pisi or P. sojae were considered as candidates for species-specific pathogenicity factors that may be involved in host specificity. Among these proteins were serine proteases, membrane transporters and a berberine-like protein. These results significantly expand the knowledge of the expressed proteome in P. pisi and P. sojae.
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| 22. |
- Hägglund, Patricia, et al.
(författare)
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The Timed Water Swallow Test (TWST) : normative data on swallowing capacity for healthy people aged 60 years and older
- 2023
-
Ingår i: International Journal of Speech-Language Pathology. - : Taylor & Francis. - 1754-9507 .- 1754-9515. ; 25:4, s. 479-485
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: To provide normative data on swallowing capacity (mL/s) in people older than 60 years using the Timed Water Swallow Test (TWST), stratified by sex. Intra- and inter-rater reliability for swallowing time in TWST was further investigated.Method: A total of 165 participants, aged 60 years and above, were included in the study. The time taken to consume 150 mL of tap water and the swallowing capacity (mL/s) was observed in a clinical context using the TWST. Video recordings of the performances were collected for 118 of the 165 participants for inter-rater reliability testing, of which a random set of 25 performances were assessed for intra-rater reliability. Analysis of the agreement between TWST rated by an in-person clinician and rated from a video recording was further evaluated.Result: There were significant age and sex effects observed for swallowing capacity. The average reduction in swallowing capacity in the investigated age range (60-92 years) was 8.8 and 7.3 mL/s for women and men respectively. The results showed high inter-and intra-rater reliability and agreement between the clinical assessment and the video recording.Conclusion: The presented measurements indicate a clear effect of age on swallowing capacity and that women may be expected to have lower capacity scores than men when tested using TWST. The provided norms can be used as reference points in the clinical identification of people at risk of dysphagia in the older population.
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| 23. |
- Karlsson, Fredrik, 1974-, et al.
(författare)
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A conceptual framework for time distortion analysis in method components
- 2014
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Ingår i: Exploring Modelling Methods for Systems Analysis and Design (EMMSAD'14). - Berlin Heidelberg : Springer Berlin/Heidelberg. - 9783662437445 ; , s. 454-463
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Konferensbidrag (refereegranskat)abstract
- The “software crisis” is still a prevailing problem to many organizations despite existence of advanced systems engineering methods, techniques for project planning and method engineering; systems engineering project still struggle to deliver on time and budget, and with sufficient quality. Existing research stresses that time leakage has a lever effect on economic outcome, which is not addressed in the abovementioned approaches. As part of an on-going research project we therefore extend existing method engineering concept to include time distortion analysis. This allows for analysis of resource use (productivity) in execution of method components. It has the potential to act as a) a tool for improving the execution of systems engineering processes, or b) criteria for selecting method parts to improve the systems engineering processes.
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| 24. |
- Karlsson, Fredrik, 1984, et al.
(författare)
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Assessing the human gut microbiota in metabolic diseases.
- 2013
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Ingår i: Diabetes. - : American Diabetes Association. - 1939-327X .- 0012-1797. ; 62:10, s. 3341-9
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Tidskriftsartikel (refereegranskat)abstract
- Recent findings have demonstrated that the gut microbiome complements our human genome with at least 100-fold more genes. In contrast to our Homo sapiens-derived genes, the microbiome is much more plastic, and its composition changes with age and diet, among other factors. An altered gut microbiota has been associated with several diseases, including obesity and diabetes, but the mechanisms involved remain elusive. Here we discuss factors that affect the gut microbiome, how the gut microbiome may contribute to metabolic diseases, and how to study the gut microbiome. Next-generation sequencing and development of software packages have led to the development of large-scale sequencing efforts to catalog the human microbiome. Furthermore, the use of genetically engineered gnotobiotic mouse models may increase our understanding of mechanisms by which the gut microbiome modulates host metabolism. A combination of classical microbiology, sequencing, and animal experiments may provide further insights into how the gut microbiota affect host metabolism and physiology.
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| 25. |
- Karlsson, Fredrik, 1984, et al.
(författare)
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Gut metagenome in European women with normal, impaired and diabetic glucose control
- 2013
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 498:7452, s. 99-103
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Tidskriftsartikel (refereegranskat)abstract
- Type 2 diabetes (T2D) is a result of complex gene-environment interactions, and several risk factors have been identified, including age, family history, diet, sedentary lifestyle and obesity. Statistical models that combine known risk factors for T2D can partly identify individuals at high risk of developing the disease. However, these studies have so far indicated that human genetics contributes little to the models, whereas socio-demographic and environmental factors have greater influence(1). Recent evidence suggests the importance of the gut microbiota as an environmental factor, and an altered gut microbiota has been linked to metabolic diseases including obesity(2,3), diabetes(4) and cardiovascular disease(5). Here we use shotgun sequencing to characterize the faecal metagenome of 145 European women with normal, impaired or diabetic glucose control. We observe compositional and functional alterations in the metagenomes of women with T2D, and develop a mathematical model based on metagenomic profiles that identified T2D with high accuracy. We applied this model to women with impaired glucose tolerance, and show that it can identify women who have a diabetes-like metabolism. Furthermore, glucose control and medication were unlikely to have major confounding effects. We also applied our model to a recently described Chinese cohort(4) and show that the discriminant metagenomicmarkers for T2D differ between the European and Chinese cohorts. Therefore, metagenomic predictive tools for T2D should be specific for the age and geographical location of the populations studied.
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| 26. |
- Karlsson, Fredrik, et al.
(författare)
-
How well does DDK task performance predict fluent speech articulation?
- 2018
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The oral diadokochinesia (DDK) task is an established tool for assessing speech motor control that has been used across a range of conditions. The predominant outcome measure reported after the patient have performed the task is the maximum syllable rate achieved by the patient. More recent reports have also highlighted stability in pace of the sequence as quantifications that may be indicative of speech impairment. While the DDK task affords quick and easy administration, concerns have been raised regarding the strength of association between DDK task performance and patients’s articulation in fluent speech. It may not be assumed that a reduced DDK rate or rate stability will cause fluent speech also to be perceived as slowed or dysrhythmic. And, patients may well improve their syllable rate at the expense of articulatory quality, which is currently not easily captured in an objective outcome measure.We report here on an effort to assess to what degree information from an expanded quantification of DDK sequences may be used identify patients with dysarthria and to model clinical assessments of fluent speech. Acoustic quantifications of the consonant and consonant-vowel relationship are combined with previously used measures, and applied to manually processed DDK sequences produced by patients with Parkinson’s disease and normal control speakers. We observe how well these quantifications may form the basis for accurate identification of patients among normal controls, and predict the outcome of blinded and randomized clinical assessments of patients’ production of fluent speech.Rapid repetition of CV syllables (oral diadochokinesis, DDK) puts pressure on the speech motor system in order to afford detection of a deteriorating articulatory ability.This study assessed how well objective quantifications of DDKsequences can be used to identify PD speakersamong age matched controls (NC), andhow well a reduced articulatory ability in PDspeakers may be predicted using quantifications of DDK sequences performed in the same recording session.The comprehensive DDK sequence quantification achieved a 93% classification accuracy for speaker group and a 79% accuracy for reduced fluent speech articulatory quality.
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| 27. |
- Karlsson, Fredrik, 1974-, et al.
(författare)
-
Information security culture : state-of-the-art review between 2000 and 2013
- 2015
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Ingår i: Information and Computer Security. - : Emerald. - 2056-4961. ; 23:3, s. 246-285
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Forskningsöversikt (refereegranskat)abstract
- Purpose – The aim of this paper is to survey existing information security culture research to scrutinise the kind of knowledge that has been developed and the way in which this knowledge has been brought about.Design/methodology/approach – Results are based on a literature review of information security culture research published between 2000 and 2013 (December).Findings – This paper can conclude that existing research has focused on a broad set of research topics, but with limited depth. It is striking that the effects of different information security cultures have not been part of that focus. Moreover, existing research has used a small repertoire of research methods, a repertoire that is more limited than in information systems research in general. Furthermore, an extensive part of the research is descriptive, philosophical or theoretical – lacking a structured use of empirical data – which means that it is quite immature.Research limitations/implications – Findings call for future research that: addresses the effects of different information security cultures; addresses the identified research topics with greater depth; focuses more on generating theories or testing theories to increase the maturity of this subfield of information security research; and uses a broader set of research methods. It would be particularly interesting to see future studies that use intervening or ethnographic approaches because, to date, these have been completely lacking in existing research.Practical implications – Findings show that existing research is, to a large extent, descriptive, philosophical or theoretical. Hence, it is difficult for practitioners to adopt these research results, such as frameworks for cultivating or assessment tools, which have not been empirically validated.Originality/value – Few state-of-the-art reviews have sought to assess the maturity of existing research on information security culture. Findings on types of research methods used in information security culture research extend beyond the existing knowledge base, which allows for a critical discussion about existing research in this sub-discipline of information security.
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| 28. |
- Karlsson, Fredrik, 1974-, et al.
(författare)
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Measuring employees’ compliance : The importance of value pluralism
- 2017
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Ingår i: Information and Computer Security. - : Emerald Group Publishing Limited. - 2056-4961. ; 25:3, s. 279-299
-
Tidskriftsartikel (refereegranskat)abstract
- Purpose: This paper aims to investigate two different types of compliance measures: the first measure is a value-monistic compliance measure, whereas the second is a value-pluralistic measure, which introduces the idea of competing organisational imperatives.Design/methodology/approach: A survey was developed using two sets of items to measure compliance. The survey was sent to 600 white-collar workers and analysed through ordinary least squares.Findings: The results suggest that when using the value-monistic measure, employees' compliance was a function of employees' intentions to comply, their self-efficacy and awareness of information security policies. In addition, compliance was not related to the occurrence of conflicts between information security and other organisational imperatives. However, when the dependent variable was changed to a value-pluralistic measure, the results suggest that employees' compliance was, to a great extent, a function of the occurrence of conflicts between information security and other organisational imperatives, indirect conflicts with other organisational values.Research limitations/implications: The results are based on small survey; yet, the findings are interesting and justify further investigation. The results suggest that relevant organisational imperatives and value systems, along with information security values, should be included in measures for employees' compliance with information security policies.Practical implications: Practitioners and researchers should be aware that there is a difference in measuring employees' compliance using value monistic and value pluralism measurements.Originality/value: Few studies exist that critically compare the two different compliance measures for the same population.
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| 29. |
- Karlsson, Fredrik, 1984, et al.
(författare)
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Symptomatic atherosclerosis is associated with an altered gut metagenome
- 2012
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 3
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Tidskriftsartikel (refereegranskat)abstract
- Recent findings have implicated the gut microbiota as a contributor of metabolic diseases through the modulation of host metabolism and inflammation. Atherosclerosis is associated with lipid accumulation and inflammation in the arterial wall, and bacteria have been suggested as a causative agent of this disease. Here we use shotgun sequencing of the gut metagenome to demonstrate that the genus Collinsella was enriched in patients with symptomatic atherosclerosis, defined as stenotic atherosclerotic plaques in the carotid artery leading to cerebrovascular events, whereas Roseburia and Eubacterium were enriched in healthy controls. Further characterization of the functional capacity of the metagenomes revealed that patient gut metagenomes were enriched in genes encoding peptidoglycan synthesis and depleted in phytoene dehydrogenase; patients also had reduced serum levels of β-carotene. Our findings suggest that the gut metagenome is associated with the inflammatory status of the host and patients with symptomatic atherosclerosis harbor characteristic changes in the gut metagenome.
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| 30. |
- Karlsson (Hillmering), Mikael, 1982-, et al.
(författare)
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High-resolution micropatterning of off-stochiometric thiol-enes (OSTE) via a novel lithography mechanism
- 2012
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Ingår i: 16th International Conference on Miniaturized Systems for Chemistry and Life Sciences (microTAS 2012). ; , s. 225-227
-
Konferensbidrag (refereegranskat)abstract
- We present an entirely novel, self-limiting photolithography mechanism in off-stoichiometry thiol-ene (OSTE) polymers enabling high-resolution and high-aspect ratio features. The OSTE polymers have previously been shown to be promising materials for fabrication of microfluidic devices with tailored surface modifications and mechanical properties. We here introduce direct lithography for micropatterning of OSTE as an alternative to mechanical machining or casting, resulting in a simple and reliable fabrication method of self-bonding photopatterned multilayer microfluidic devices.
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| 31. |
- Karlsson, Kristin E., et al.
(författare)
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Modeling Disease Progression in Acute Stroke Using Clinical Assessment Scales
- 2010
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Ingår i: AAPS Journal. - : Springer Science and Business Media LLC. - 1550-7416. ; 12:4, s. 683-691
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Tidskriftsartikel (refereegranskat)abstract
- This article demonstrates techniques for describing and predicting disease progression in acute stroke by modeling scores measured using clinical assessment scales, accommodating dropout as an additional source of information. Scores assessed using the National Institutes of Health Stroke Scale and the Barthel Index in acute stroke patients were used to model the time course of disease progression. Simultaneous continuous and probabilistic models for describing the nature and magnitude of score changes were developed, and used to model the trajectory of disease progression using scale scores. The models described the observed data well, and exhibited good simulation properties. Applications include longitudinal analysis of stroke scale data, clinical trial simulation, and prognostic forecasting. Based upon experience in other areas, it is likely that application of this modeling methodology will enable reductions in the number of patients needed to carry out clinical studies of treatments for acute stroke.
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| 32. |
- Karlsson, Max, et al.
(författare)
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A single-cell type transcriptomics map of human tissues
- 2021
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Ingår i: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 7:31
-
Tidskriftsartikel (refereegranskat)abstract
- Advances in molecular profiling have opened up the possibility to map the expression of genes in cells, tissues, and organs in the human body. Here, we combined single-cell transcriptomics analysis with spatial antibody-based protein profiling to create a high-resolution single-cell type map of human tissues. An open access atlas has been launched to allow researchers to explore the expression of human protein-coding genes in 192 individual cell type clusters. An expression specificity classification was performed to determine the number of genes elevated in each cell type, allowing comparisons with bulk transcriptomics data. The analysis highlights distinct expression clusters corresponding to cell types sharing similar functions, both within the same organs and between organs.
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| 33. |
- Karlsson, Martin, et al.
(författare)
-
Cooperative Indoor Positioning by Exchange of Bluetooth Signals and State Estimates Between Users
- 2017
-
Ingår i: 2016 European Control conference. - 9781509025916 ; , s. 1440-1444
-
Konferensbidrag (refereegranskat)abstract
- This paper presents a Bayesian indoor positioningsystem for smartphones based on the strengths of WiFi andBluetooth signals. A framework for improving the performanceof existing positioning methods with the help informationsharing between users is proposed and evaluated. Bluetoothsignals are sent between users, and the signal strengths containinformation about their relative distances, which is used toevaluate the probability distribution functions of their states.A particle filter is used for the state estimation, together withan unscented transform to propagate probability distributionsthrough nonlinearities.
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| 34. |
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| 35. |
- Karlsson, Max, et al.
(författare)
-
Genome-wide single cell annotation of the human protein-coding genes
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- An important quest for the life science community is to deliver a complete annotation of the human building-blocks of life, the genes and the proteins. Here, we report on a genome-wide effort to annotate all protein-coding genes based on single cell transcriptomics data representing all major tissues and organs in the human body, integrated with data from bulk transcriptomics and antibody-based tissue profiling. Altogether, 25 tissues have been analyzed with single cell transcriptomics resulting in genome-wide expression in 444 single cell types using a strategy involving pooling data from individual cells to obtain genome-wide expression profiles of individual cell type. We introduce a new genome-wide classification tool based on clustering of similar expression profiles across single cell types, which can be visualized using dimensional reduction maps (UMAP). The clustering classification is integrated with a new “tau” score classification for all protein-coding genes, resulting in a measure of single cell specificity across all cell types for all individual genes. The analysis has allowed us to annotate all human protein-coding genes with regards to function and spatial distribution across individual cell types across all major tissues and organs in the human body. A new version of the open access Human Protein Atlas (www.proteinatlas.org) has been launched to enable researchers to explore the new genome-wide annotation on an individual gene level.
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| 36. |
- Karlsson, Martin, 1982-, et al.
(författare)
-
Organisationskulturens påverkan på informationssäkerhetsarbetet
- 2017. - 1
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Ingår i: Informationssäkerhet och organisationskultur. - Lund : Studentlitteratur AB. - 9789144121406 ; , s. 25-40
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Organisationskulturen sägs ofta vara en central del i att styra en modern organisation. I detta kapitel resonerar vi kring sambandet mellan den kultur som enligt svenska tjänstemän finns i deras organisationer och informationssäkerheten i dessa organisationer. Denna kunskap är viktig dels för att kunna använda förändring av organisationskulturen som ett sätt att åstadkomma ökad informationssäkerhet, dels för att kunna förutse konsekvenserna av att allt fler organisationer idag förändras i riktning mot vad som enligt vår studie skapar sämre förutsättningar för informationssäkerhet.
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| 37. |
- Karlsson, Martin, 1982-, et al.
(författare)
-
The effect of perceived organizational culture on employees’ information security compliance
- 2022
-
Ingår i: Information and Computer Security. - : Emerald Group Publishing Limited. - 2056-4961. ; 30:3, s. 382-401
-
Tidskriftsartikel (refereegranskat)abstract
- Purpose: This paper aims to investigate the connection between different perceived organizational cultures and information security policy compliance among white-collar workers.Design/methodology/approach: The survey using the Organizational Culture Assessment Instrument was sent to white-collar workers in Sweden (n = 674), asking about compliance with information security policies. The survey instrument is an operationalization of the Competing Values Framework that distinguishes between four different types of organizational culture: clan, adhocracy,market and bureaucracy.Findings: The results indicate that organizational cultures with an internal focus are positively related to employees’ information security policy compliance. Differences in organizational culture with regards to control and flexibility seem to have less effect. The analysis shows that a bureaucratic form of organizational culture is most fruitful for fostering employees’ information security policy compliance.Research limitations/implications: The results suggest that differences in organizational culture are important for employees’ information security policy compliance. This justifies further investigating the mechanisms linking organizational culture to information security compliance.Practical implications: Practitioners should be aware that the different organizational cultures do matter for employees’ information security compliance. In businesses and the public sector, the authors see a development toward customer orientation and marketization, i.e. the opposite an internal focus, that may have negative ramifications for the information security of organizations.Originality/value: Few information security policy compliance studies exist on the consequences of different organizational/information cultures.
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| 38. |
- Karlsson, Roger, 1975, et al.
(författare)
-
Discovery of Species-unique Peptide Biomarkers of Bacterial Pathogens by Tandem Mass Spectrometry-based Proteotyping
- 2020
-
Ingår i: Molecular & Cellular Proteomics. - 1535-9476 .- 1535-9484. ; 19:3, s. 518-528
-
Tidskriftsartikel (refereegranskat)abstract
- Mass spectrometry (MS) and proteomics offer comprehensive characterization and identification of microorganisms and discovery of protein biomarkers that are applicable for diagnostics of infectious diseases. The use of biomarkers for diagnostics is widely applied in the clinic and the use of peptide biomarkers is increasingly being investigated for applications in the clinical laboratory. Respiratory-tract infections are a predominant cause for medical treatment, although, clinical assessments and standard clinical laboratory protocols are time-consuming and often inadequate for reliable diagnoses. Novel methods, preferably applied directly to clinical samples, excluding cultivation steps, are needed to improve diagnostics of infectious diseases, provide adequate treatment and reduce the use of antibiotics and associated development of antibiotic resistance. This study applied nano-liquid chromatography (LC) coupled with tandem MS, with a bioinformatics pipeline and an in-house database of curated high-quality reference genome sequences to identify species-unique peptides as potential biomarkers for four bacterial pathogens commonly found in respiratory tract infections (RTIs): Staphylococcus aureus; Moraxella catarrhalis; Haemophilus influenzae and Streptococcus pneumoniae. The species-unique peptides were initially identified in pure cultures of bacterial reference strains, reflecting the genomic variation in the four species and, furthermore, in clinical respiratory tract samples, without prior cultivation, elucidating proteins expressed in clinical conditions of infection. For each of the four bacterial pathogens, the peptide biomarker candidates most predominantly found in clinical samples, are presented. Data are available via ProteomeXchange with identifier PXD014522. As proof-of-principle, the most promising species-unique peptides were applied in targeted tandem MS-analyses of clinical samples and their relevance for identifications of the pathogens, i.e. proteotyping, was validated, thus demonstrating their potential as peptide biomarker candidates for diagnostics of infectious diseases.
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| 39. |
- Karlsson, Rickard, 1970-, et al.
(författare)
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Particle Filtering and Cramér-Rao Lower Bound for Underwater Navigation
- 2003
-
Ingår i: Proceedings of the 2003 IEEE Conference on Acoustics, Speech and Signal Processing. - 0780376633 ; , s. 65-68 vol.6
-
Konferensbidrag (refereegranskat)abstract
- We have studied a sea navigation method relying on a digital underwater terrain map and sonar measurements. The method is applicable for both ships and underwater vessels. We have used experimental data to build an underwater map and to investigate the estimation performance. Since the problem is non-linear, due to the measurement relation, we apply a sequential Monte Carlo method, or particle filter, for the state estimation. The fundamental limitations in navigation uncertainty can be described in terms of the Cramér-Rao lower bound, which is interpreted in terms of the inertial navigation system (INS) error, the sensor accuracy and the terrain map excitation. Hence, the Cramér-Rao lower bound can be interpreted and used in design for INS systems, sensor performance or if these are given, how much terrain or depth excitation that is needed for use in positioning and navigation.
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| 40. |
- Karlsson, Rickard, et al.
(författare)
-
Particle Filtering and Cramér-Rao Lower Bound for Underwater Navigation
- 2002
-
Rapport (övrigt vetenskapligt/konstnärligt)abstract
- We have studied a sea navigation method relying on a digital underwater terrain map and sonar measurements. The method is applicable for both ships and underwater vessels. We have used experimental data to build an underwater map and to investigate the estimation performance. Since the problem is non-linear, due to the measurement relation, we apply a sequential Monte Carlo method, or particle filter, for the state estimation. The fundamental limitations in navigation uncertainty can be described in terms of the Cramér-Rao lower bound, which is interpreted in terms of the inertial navigation system (INS) error, the sensor accuracy and the terrain map excitation. Hence, the Cramér-Rao lower bound can be interpreted and used in design for INS systems, sensor performance or if these are given, how much terrain or depth excitation that is needed for use in positioning and navigation.
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| 41. |
- Karlsson, Roger, 1975, et al.
(författare)
-
Proteotyping bacteria: Characterization, differentiation and identification of pneumococcus and other species within the Mitis Group of the genus Streptococcus by tandem mass spectrometry proteomics
- 2018
-
Ingår i: Plos One. - : Public Library of Science (PLoS). - 1932-6203. ; 13:12
-
Tidskriftsartikel (refereegranskat)abstract
- A range of methodologies may be used for analyzing bacteria, depending on the purpose and the level of resolution needed. The capability for recognition of species distinctions within the complex spectrum of bacterial diversity is necessary for progress in microbiological research. In clinical settings, accurate, rapid and cost-effective methods are essential for early and efficient treatment of infections. Characterization and identification of microorganisms, using, bottom-up proteomics, or "proteotyping", relies on recognition of species-unique or associated peptides, by tandem mass spectrometry analyses, dependent upon an accurate and comprehensive foundation of genome sequence data, allowing for differentiation of species, at amino acid-level resolution. In this study, the high resolution and accuracy of MS/MS-based proteotyping was demonstrated, through analyses of the three phylogenetically and taxonomically most closely-related species of the Mitis Group of the genus Streptococcus: i.e., the pathogenic species, Streptococcus pneumoniae (pneumococcus), and the commensal species, Streptococcus pseudopneumoniae and Streptococcus mitis. To achieve high accuracy, a genome sequence database used for matching peptides was created and carefully curated. Here, MS-based, bottom-up proteotyping was observed and confirmed to attain the level of resolution necessary for differentiating and identifying the most-closely related bacterial species, as demonstrated by analyses of species of the Streptococcus Mitis Group, even when S. pneumoniae were mixed with S. pseudopneumoniae and S. mitis, by matching and identifying more than 200 unique peptides for each species.
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| 42. |
- Karlsson, R., et al.
(författare)
-
Proteotyping: Proteomic characterization, classification and identification of microorganisms - A prospectus
- 2015
-
Ingår i: Systematic and Applied Microbiology. - : Elsevier BV. - 0723-2020. ; 38:4, s. 246-257
-
Forskningsöversikt (refereegranskat)abstract
- Modern microbial systematics requires a range of methodologies for the comprehensive characterization, classification and identification of microorganisms. While whole-genome sequences provide the ultimate reference for defining microbial phylogeny and taxonomy, selected biomarker-based strategies continue to provide the means for the bulk of microbial systematic studies. Proteomics, the study of the expression of genes, as well as the structure and function of the resulting proteins, offers indirect measures of genome sequence data. Recent developments in applications of proteomics for analyzing microorganisms have paralleled the growing microbial genome sequence database, as well as the evolution of mass spectrometry (MS) instrumentation and bioinformatics. MALDI-TOF MS, which generates proteomic mass patterns for 'fingerprint'-based characterizations, has provided a marked breakthrough for microbial identification. However, MALDI-TOF MS is limited in the number of targets that can be detected for strain characterization. Advanced methods of tandem mass spectrometry, in which proteins and peptides generated from proteins, are characterized and identified, using LC-MS/MS, provide the ability to detect hundreds or thousands of expressed microbial strain markers for high-resolution characterizations and identifications. Model studies demonstrate the application of proteomics-based analyses for bacterial species- and strain-level detection and identification and for characterization of environmentally relevant, metabolically diverse bacteria. Proteomics-based approaches represent an emerging complement to traditional methods of characterizing microorganisms, enabling the elucidation of the expressed biomarkers of genome sequence information, which can be applied to 'proteotyping' applications of microorganisms at all taxonomic levels. (C) 2015 Elsevier GmbH. All rights reserved.
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| 43. |
- Karlsson, Roger, et al.
(författare)
-
Proteotyping: Tandem Mass Spectrometry Shotgun Proteomic Characterization and Typing of Pathogenic Microorganisms
- 2016
-
Ingår i: MALDI‐TOF and Tandem MS for Clinical Microbiology. - Chichester, UK : John Wiley & Sons, Ltd. - 9781118960226 ; , s. 419-450
-
Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Proteotyping provides the means to identify and quantify the actual expression patterns of proteins and their associated pathways, which provides a more accurate picture of infectious agents and their pathogenic potential. Proteotyping, as an analytical method, is intimately correlated with genotypic or genomic data and offers an approach for a holistic characterization of microorganisms. Bioinformatics is vital for the analysis of the data generated by shotgun proteomics. This chapter describes the complete bioinformatics workflow necessary for proteotyping. Mass spectrometry (MS)-based shotgun proteomics analyses offer more detailed and comprehensive analyses of microorganisms. Two approaches may be applied: the so-called top-down and bottom-up proteomics. A major driver for the development and use of tandem MS and proteotyping in clinical settings will be the rapidly growing databases of whole genome reference sequences, which will refine microbial phylogeny and provide a foundation for proteomics-based identification.
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| 44. |
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| 45. |
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| 46. |
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| 47. |
- Linander, Fredrik, 1973-, et al.
(författare)
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Measuring and Visualising Projects' Collective Method Rationale
- 2016
-
Ingår i: The Practice of Enterprise Modeling. - Cham : Springer International Publishing. - 9783319483924 - 9783319483931 ; , s. 344-352
-
Konferensbidrag (refereegranskat)abstract
- Existing research provide frameworks for analysing the rationale behind engineering methods and how this rationale matches the rationale of individual project members. As methods are used in groups, this raises questions about how to study method rationale on an aggregated project level. We propose an elaboration of method rationale theory to enable this type of analysis. We introduce the concept of collective method rationale together with metrics to capture this aggregated rationale. The conceptual work is implemented in a computerized tool, which enables analyses of collective method rationale in product development projects. These are the results of an action research project and we present a pilot test of the computerized tool to demonstrate the concept.
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| 48. |
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| 49. |
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| 50. |
- Malmstrom, Mikael, et al.
(författare)
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Waveguides in polycrystalline diamond for mid-IR sensing
- 2016
-
Ingår i: Optical Materials Express. - 2159-3930 .- 2159-3930. ; 6:4, s. 1286-1295
-
Tidskriftsartikel (refereegranskat)abstract
- 8 mm long channel waveguides were manufactured in polycrystalline diamond with inductively coupled plasma etching and characterized in terms of mode-profile and propagation loss in the 1.5 - 3.4 mu m spectral region. As proof of principle, the waveguides were evaluated in an evanescent field sensing setup targeting the CH absorption peak of isopropanol at similar to 3.4 mu m, showing good agreement with numerical finite element simulations. (C) 2016 Optical Society of America
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