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Sökning: WFRF:(Karlsson Johan 1984)

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  • Bengtsson-Palme, Johan, 1985, et al. (författare)
  • Strategies to improve usability and preserve accuracy in biological sequence databases
  • 2016
  • Ingår i: Proteomics. - 1615-9853 .- 1615-9861. ; 16:18
  • 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.
  • Karlsson, Fredrik H., 1984, et al. (författare)
  • Gut metagenome in European women with normal, impaired and diabetic glucose control
  • 2013
  • Ingår i: Nature. - 0028-0836 .- 1476-4687. ; 498:7452, s. 99-103
  • 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.
  • Kuzmenko, Volodymyr, 1987, et al. (författare)
  • Cellulose-derived carbon nanofibers/graphene composite electrodes for powerful compact supercapacitors
  • 2017
  • Ingår i: RSC Advances. - : Royal Society of Chemistry. - 2046-2069. ; 7:73, s. 45968-45977
  • Tidskriftsartikel (refereegranskat)abstract
    • Herein, we demonstrate a unique supercapacitor composite electrode material that is originated from a sustainable cellulosic precursor via simultaneous one-step carbonization/reduction of cellulose/graphene oxide mats at 800 degrees C. The resulting freestanding material consists of mechanically stable carbon nanofibrous (CNF, fiber diameter 50-500 nm) scaffolds tightly intertwined with highly conductive reduced graphene oxide (rGO) sheets with a thickness of 1-3 nm. The material is mesoporous and has electrical conductivity of 49 S cm(-1), attributed to the well-interconnected graphene layers. The electrochemical evaluation of the CNF/graphene composite electrodes in a supercapacitor device shows very promising volumetric values of capacitance, energy and power density (up to 46 F cm(-3), 1.46 W h L-1 and 1.09 kW L-1, respectively). Moreover, the composite electrodes retain an impressive 97% of the initial capacitance over 4000 cycles. With these superior properties, the produced composite electrodes should be the "looked-for" components in compact supercapacitors used for increasingly popular portable electronics and hybrid vehicles.
  • Galli, Silvia, et al. (författare)
  • The effect of magnesium on early osseointegration in osteoporotic bone : a histological and gene expression investigation
  • 2017
  • Ingår i: Osteoporosis International. - : Springer. - 0937-941X .- 1433-2965. ; 28:7, s. 2195-2205
  • Tidskriftsartikel (refereegranskat)abstract
    • Magnesium has a key role in osteoporosis and could enhance implant osseointegration in osteoporotic patients. Titanium implants impregnated with Mg ions were installed in the tibia of ovariectomized rats. The release of Mg induced a significant increase of bone formation and the expression of anabolic markers in the peri-implant bone. The success of endosseous implants is highly predictable in patients possessing normal bone status, but it may be impaired in patients with osteoporosis. Thus, the application of strategies that adjuvate implant healing in compromized sites is of great interest. Magnesium has a key role in osteoporosis prevention and it is an interesting candidate for this purpose. In this study, the cellular and molecular effects of magnesium release from implants were investigated at the early healing stages of implant integration. Osteoporosis was induced in 24 female rats by means of ovariectomy and low-calcium diet. Titanium mini-screws were coated with mesoporous titania films and were loaded with magnesium (test group) or left as native (control group). The implants were inserted in the tibia and femur of the rats. One, 2 and 7 days after implantation, the implants were retrieved and histologically examined. In addition, expression of genes was evaluated in the peri-implant bone tissue at day 7 by means of quantitative polymerase chain reactions with pathway-oriented arrays. The histological evaluation revealed that new bone formation started already during the first week of healing for both groups. However, around the test implants, new bone was significantly more abundant and spread along a larger surface of the implants. In addition, the release of magnesium induced a significantly higher expression of BMP6. These results provide evidence that the release of magnesium promoted rapid bone formation and the activation of osteogenic signals in the vicinity of implants placed in osteoporotic bone.
  • Karlsson, Johan, 1984, et al. (författare)
  • The effect of alendronate on biomineralization at the bone/implant interface
  • 2016
  • Ingår i: Journal of Biomedical Materials Research - Part A. - 1549-3296 .- 1552-4965. ; 104:3, s. 620-629
  • Tidskriftsartikel (refereegranskat)abstract
    • A recent approach to improve osseointegration of implants is to utilize local drug administration. The presence of an osteoporosis drug may influence both bone quantity and quality at the bone/implant interface. Despite this, the performance of bone-anchoring implants is traditionally evaluated only by quantitative measurements. In the present study, the osteoporosis drug alendronate (ALN) was administrated from mesoporous titania thin films that were coated onto titanium implants. The effect that the drug had on biomineralization was explored both in vitro using simulated body fluid (SBF) and in vivo in a rat tibia model. The SBF study showed that the apatite formation was completely hindered at a high concentration of ALN (0.1 mg/ml). However, when ALN was administrated from the mesoporous coating the surface became completely covered with apatite. Ex vivo characterization of the bone/implant interface using Raman spectroscopy demonstrated that the presence of ALN enhanced the bone mineralization, and that the chemical signature of newly formed bone in the presence of ALN had a higher resemblance to the pre-existing mature bone than to the bone formed without drug. Taken together, this study demonstrates the importance of evaluating the quality of the formed bone to better understand the performance of implants.
  • Atefyekta, Saba, 1987, et al. (författare)
  • Antimicrobial performance of mesoporous titania thin films: role of pore size, hydrophobicity, and antibiotic release
  • 2016
  • Ingår i: International journal of nanomedicine. - 1176-9114 .- 1178-2013. ; 11, s. 977-990
  • Tidskriftsartikel (refereegranskat)abstract
    • Implant-associated infections are undesirable complications that might arise after implant surgery. If the infection is not prevented, it can lead to tremendous cost, trauma, and even life threatening conditions for the patient. Development of an implant coating loaded with antimicrobial substances would be an effective way to improve the success rate of implants. In this study, the in vitro efficacy of mesoporous titania thin films used as a novel antimicrobial release coating was evaluated. Mesoporous titania thin films with pore diameters of 4, 6, and 7 nm were synthesized using the evaporation-induced self-assembly method. The films were characterized and loaded with antimicrobial agents, including vancomycin, gentamicin, and daptomycin. Staphylococcus aureus and Pseudomonas aeruginosa were used to evaluate their effectiveness toward inhibiting bacterial colonization. Drug loading and delivery were studied using a quartz crystal microbalance with dissipation monitoring, which showed successful loading and release of the antibiotics from the surfaces. Results from counting bacterial colony-forming units showed reduced bacterial adhesion on the drug-loaded films. Interestingly, the presence of the pores alone had a desired effect on bacterial colonization, which can be attributed to the documented nanotopographical effect. In summary, this study provides significant promise for the use of mesoporous titania thin films for reducing implant infections.
  • Ayatolahi, Fatemeh, 1984, et al. (författare)
  • A Study of the Impact of Single Bit-Flip and Double Bit- Flip Errors on Program Execution
  • 2013
  • Ingår i: Computer Safety, Reliability, and Security. SAFECOMP, September 24-27..
  • Konferensbidrag (refereegranskat)abstract
    • This paper presents the results of an extensive experimental study of bit-flip errors in instruction set architecture registers and main memory locations. Comprising more than two million fault injection experiments conducted with thirteen benchmark programs, the study provides insights on whether it is necessary to consider double bit-flip errors in dependability benchmarking experiments. The results show that the proportion of silent data corruptions in the program output, is almost the same for single and double bit errors. In addition, we present detailed statistics about the error sensitivity of different target registers and memory locations, including bit positions within registers and memory words. These show that the error sensitivity varies significantly between different bit positions and registers. An important observation is that injections in certain bit positions always have the same impact regardless of when the error is injected.
  • Ayatolahi, Fatemeh, 1984, et al. (författare)
  • Sources of Variation in Error Sensitivity Measurements, Significant or Not?
  • 2018
  • Ingår i: Proceedings - 48th Annual IEEE/IFIP International Conference on Dependable Systems and Networks Workshops, DSN-W 2018. - 9781538665534 ; , s. 71-72
  • Konferensbidrag (refereegranskat)abstract
    • Measuring the error sensitivity by fault injection is an important method for assessing the dependability of computer systems. In this paper, we define error sensitivity as the conditional probability that a hardware-related error causes a silent data corruption. When measuring the error sensitivity it is important to consider how the experimental setup and the workload characteristics affect the estimated error sensitivity. We consider five such potential sources of variation (PSVs) in this paper. Three of these are related to the workload: i) input profile, ii) source code implementation, and, iii) use of compiler optimization. Two are related to the experimental setup: i) single vs. double bit-flips, and ii) inject-on-read vs. inject-on-write. The paper discusses the applicability of different statistical tests for assessing whether a PSV has a significant impact on error sensitivity.
  • Calles, Olle, 1974-, et al. (författare)
  • Success of a low-sloping rack for improving downstream passage of silver eels at a hydroelectric plant
  • 2013
  • Ingår i: Freshwater Biology. - : John Wiley & Sons. - 0046-5070 .- 1365-2427. ; 58, s. 2168-2179
  • Tidskriftsartikel (refereegranskat)abstract
    • 1. The European eel (Anguilla anguilla) is a critically endangered species, and one major threat is thesurvival of silver eels migrating downstream towards the sea from lake and river rearing areas. Duringthis migration, many eels are impinged and die on intake racks, or are injured or killed whenpassing through turbines.2. Intake racks at a hydroelectric plant were modified to avoid impingement and to collect eels withoutinjury; high mortality on both racks and in turbines was previously documented. Modificationsconsisted of reducing the rack gap width from 20 to 18 mm, decreasing the rack slope from 63 to 35degrees, increasing the rack surface area by 58% and installing six openings in the rack leading totraps.3. Downstream passage conditions for silver eels at the hydroelectric plant were significantlyimproved, reducing mortality from >70% at the old steep 20 mm racks to <10% at the modified18 mm rack collection facility. No tagged eels were impinged and killed on the racks, and 80%entered the collection facility.4. Survival can probably be improved even more, as the individuals that passed the facility mostlikely escaped through holes in the traps. Moreover, injured untagged eels were still encountered atthe modified racks, illustrating the need for rehabilitative measures to be implemented at all obstaclesbetween the main eel rearing areas and the sea.
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