| 1. |
- Brownstein, Catherine A., et al.
(författare)
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An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
- 2014
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 15:3, s. R53-
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Tidskriftsartikel (refereegranskat)abstract
- Background: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. Results: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. Conclusions: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.
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| 2. |
- Bladen, Catherine L., et al.
(författare)
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The TREAT-NMD Duchenne Muscular Dystrophy Registries : Conception, Design, and Utilization by Industry and Academia
- 2013
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Ingår i: Human Mutation. - : Hindawi Limited. - 1059-7794 .- 1098-1004. ; 34:11, s. 1449-1457
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Tidskriftsartikel (refereegranskat)abstract
- Duchenne muscular dystrophy (DMD) is an X-linked genetic disease, caused by the absence of the dystrophin protein. Although many novel therapies are under development for DMD, there is currently no cure and affected individuals are often confined to a wheelchair by their teens and die in their twenties/thirties. DMD is a rare disease (prevalence<5/10,000). Even the largest countries do not have enough affected patients to rigorously assess novel therapies, unravel genetic complexities, and determine patient outcomes. TREAT-NMD is a worldwide network for neuromuscular diseases that provides an infrastructure to support the delivery of promising new therapies for patients. The harmonized implementation of national and ultimately global patient registries has been central to the success of TREAT-NMD. For the DMD registries within TREAT-NMD, individual countries have chosen to collect patient information in the form of standardized patient registries to increase the overall patient population on which clinical outcomes and new technologies can be assessed. The registries comprise more than 13,500 patients from 31 different countries. Here, we describe how the TREAT-NMD national patient registries for DMD were established. We look at their continued growth and assess how successful they have been at fostering collaboration between academia, patient organizations, and industry.
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| 3. |
- Holtslag, A. A. M., et al.
(författare)
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STABLE ATMOSPHERIC BOUNDARY LAYERS AND DIURNAL CYCLES : Challenges for Weather and Climate Models
- 2013
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Ingår i: Bulletin of The American Meteorological Society - (BAMS). - 0003-0007 .- 1520-0477. ; 94:11, s. 1691-1706
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Tidskriftsartikel (refereegranskat)abstract
- The representation of the atmospheric boundary layer is an important part of weather and climate models and impacts many applications such as air quality and wind energy. Over the years, the performance in modeling 2-m temperature and 10-m wind speed has improved but errors are still significant. This is in particular the case under clear skies and low wind speed conditions at night as well as during winter in stably stratified conditions over land and ice. In this paper, the authors review these issues and provide an overview of the current understanding and model performance. Results from weather forecast and climate models are used to illustrate the state of the art as well as findings and recommendations from three intercomparison studies held within the Global Energy and Water Exchanges (GEWEX) Atmospheric Boundary Layer Study (GABLS). Within GABLS, the focus has been on the examination of the representation of the stable boundary layer and the diurnal cycle over land in clear-sky conditions. For this purpose, single-column versions of weather and climate models have been compared with observations, research models, and large-eddy simulations. The intercomparison cases are based on observations taken in the Arctic, Kansas, and Cabauw in the Netherlands. From these studies, we find that even for the noncloudy boundary layer important parameterization challenges remain.
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| 4. |
- Marklund, Peter, et al.
(författare)
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Extensive inflammatory cell infiltration in human skeletal muscle in response to an ultra-endurance exercise bout in experienced athletes.
- 2013
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Ingår i: Journal of applied physiology. - : American Physiological Society. - 8750-7587 .- 1522-1601. ; 114:1, s. 66-72
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Tidskriftsartikel (refereegranskat)abstract
- The impact of a 24h ultra-endurance exercise bout on systemic and local muscle inflammatory reactions was investigated in nine experienced athletes. Blood and muscle biopsies were collected before (PRE), immediately after the exercise (POST) and after 28h of recovery (POST28). Circulating blood levels of leukocytes, CK, CRP and selected inflammatory cytokines were assessed together with the evaluation of the occurrence of inflammatory cells (CD3(+), CD8(+), CD68(+)) and the expression of major histocompatibility complex class-I (MHC class-I) in skeletal muscle. An extensive inflammatory cell infiltration occurred in all athletes and the number of CD3(+), CD8(+) and CD 68(+) cells were 2-3 fold higher at POST28 compared to PRE (P<0.05). The inflammatory cell infiltration was associated with a significant increase in the expression of MHC class-I in muscle fibers. There was a significant increase in blood leukocyte count, IL-6, IL-8, CRP and CK at POST. At POST28 total leukocytes, IL-6 and CK had declined, whereas IL-8 and CRP continued to increase. Increases in IL-1β and TNF-α were not significant. There were no significant associations between the magnitude of the systemic and local muscle inflammatory reactions. Signs of muscle degenerative and regenerative events were observed in all athletes with various degrees of severity and were not affected by the ultra-endurance exercise bout. In conclusion, a low-intensity but very prolonged single endurance exercise bout can generate a strong inflammatory cell infiltration in skeletal muscle of well-trained experienced ultra-endurance athletes, and the amplitude of the local reaction is not proportional to the systemic inflammatory response.
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| 5. |
- Eriksson, Mikael, et al.
(författare)
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The MAX IV Facility
- 2013
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Ingår i: 11th International Conference on Synchrotron Radiation Instrumentation (SRI 2012). - : IOP Publishing. - 1742-6588 .- 1742-6596. ; 425
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Konferensbidrag (refereegranskat)abstract
- The MAX IV synchrotron radiation facility is currently being constructed in Lund, Sweden. The accelerator park consists of a 3 GeV linac injector and 2 storage rings operated at 1.5 and 3 GeV respectively. The linac injector will also be used for the generation of short Xray pulses. Close to 30 straight sections will be available for IDs at the rings. The three machines mentioned above are described below with some emphasis on the effort to create a very small emittance in the 3 GeV ring. Some unconventional technical solutions imposed by the emittance minimisation are discussed.
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| 6. |
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| 7. |
- Magnusson, JP, et al.
(författare)
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A latent neurogenic program in astrocytes regulated by Notch signaling in the mouse
- 2014
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Ingår i: Science (New York, N.Y.). - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 346:6206, s. 237-241
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Tidskriftsartikel (refereegranskat)abstract
- Neurogenesis is restricted in the adult mammalian brain; most neurons are neither exchanged during normal life nor replaced in pathological situations. We report that stroke elicits a latent neurogenic program in striatal astrocytes in mice. Notch1 signaling is reduced in astrocytes after stroke, and attenuated Notch1 signaling is necessary for neurogenesis by striatal astrocytes. Blocking Notch signaling triggers astrocytes in the striatum and the medial cortex to enter a neurogenic program, even in the absence of stroke, resulting in 850 ± 210 (mean ± SEM) new neurons in a mouse striatum. Thus, under Notch signaling regulation, astrocytes in the adult mouse brain parenchyma carry a latent neurogenic program that may potentially be useful for neuronal replacement strategies.
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| 8. |
- Nader, GA, et al.
(författare)
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Resistance exercise training modulates acute gene expression during human skeletal muscle hypertrophy
- 2014
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Ingår i: Journal of applied physiology (Bethesda, Md. : 1985). - : American Physiological Society. - 1522-1601 .- 8750-7587. ; 116:6, s. 693-702
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Tidskriftsartikel (refereegranskat)abstract
- We sought to determine whether acute resistance exercise (RE)-induced gene expression is modified by RE training. We studied the expression patterns of a select group of genes following an acute bout of RE in naïve and hypertrophying muscle. Thirteen untrained subjects underwent supervised RE training for 12 wk of the nondominant arm and performed an acute bout of RE 1 wk after the last bout of the training program ( training+acute). The dominant arm was either unexercised ( control) or subjected to the same acute exercise bout as the trained arm ( acute RE). Following training, men (14.8 ± 2.8%; P < 0.05) and women (12.6 ± 2.4%; P < 0.05) underwent muscle hypertrophy with increases in dynamic strength in the trained arm (48.2 ± 5.4% and 72.1 ± 9.1%, respectively; P < 0.01). RE training resulted in attenuated anabolic signaling as reflected by a reduction in rpS6 phosphorylation following acute RE. Changes in mRNA levels of genes involved in hypertrophic growth, protein degradation, angiogenesis, and metabolism commonly expressed in both men and women was determined 4 h following acute RE. We show that RE training can modify acute RE-induced gene expression in a divergent and gene-specific manner even in genes belonging to the same ontology. Changes in gene expression following acute RE are multidimensional, and may not necessarily reflect the actual adaptive response taking place during the training process. Thus RE training can selectively modify the acute response to RE, thereby challenging the use of gene expression as a marker of exercise-induced adaptations.
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