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- Murray, Alison E., et al.
(author)
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Roadmap for naming uncultivated Archaea and Bacteria
- 2020
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In: Nature Microbiology. - : NATURE PUBLISHING GROUP. - 2058-5276. ; 5:8, s. 987-994
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Journal article (peer-reviewed)abstract
- The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as 'type material', thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity. In this Consensus Statement, the authors discuss the issue of naming uncultivated prokaryotic microorganisms, which currently do not have a formal nomenclature system due to a lack of type material or cultured representatives, and propose two recommendations including the recognition of DNA sequences as type material.
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- Setälä, H., et al.
(author)
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Urban and agricultural soils : Conflicts and trade-offs in the optimization of ecosystem services
- 2014
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In: Urban Ecosystems. - : Springer Science and Business Media LLC. - 1083-8155 .- 1573-1642. ; 17:1, s. 239-253
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Journal article (peer-reviewed)abstract
- On-going human population growth and changing patterns of resource consumption are increasing global demand for ecosystem services, many of which are provided by soils. Some of these ecosystem services are linearly related to the surface area of pervious soil, whereas others show non-linear relationships, making ecosystem service optimization a complex task. As limited land availability creates conflicting demands among various types of land use, a central challenge is how to weigh these conflicting interests and how to achieve the best solutions possible from a perspective of sustainable societal development. These conflicting interests become most apparent in soils that are the most heavily used by humans for specific purposes: urban soils used for green spaces, housing, and other infrastructure and agricultural soils for producing food, fibres and biofuels. We argue that, despite their seemingly divergent uses of land, agricultural and urban soils share common features with regards to interactions between ecosystem services, and that the trade-offs associated with decision-making, while scale- and context-dependent, can be surprisingly similar between the two systems. We propose that the trade-offs within land use types and their soil-related ecosystems services are often disproportional, and quantifying these will enable ecologists and soil scientists to help policy makers optimizing management decisions when confronted with demands for multiple services under limited land availability.
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- Abbott, Allan, et al.
(author)
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The effectiveness of physiotherapeutic rehabilitation and issues of outcome prediction after lumber fusion surgery.
- 2011
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In: Proceedings of the WCPT Congress, Amsterdam Netherlands.. - : World Confederation of Physical Therapy. ; , s. 20-
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Conference paper (other academic/artistic)abstract
- Purpose: The primary purpose was to analyse the short and long term effectiveness of physiotherapeutic rehabilitation programs performed during the first 3 month after lumbar fusion surgery. A secondary purpose was to analyse factors predicting long-term disability, back pain and health related quality of life (HRQOL) outcomes after lumbar fusion.Relevance: The study provides evidence for the effectiveness of early physiotherapy after lumbar fusion. Furthermore improved knowledge of predictive factors can help physiotherapist in the screening of lumbar fusion candidates and the individualised implementation of pre-surgical and post-surgical interventions.Participants: A total of 107 patients were recruited from the Karolinska University Hospital's Orthopaedic Clinic, Stockholm, Sweden. The inclusion criteria were: men and women aged between 18 and 65 years with a >12 month history of back pain and/or sciatica; a primary diagnosis of spinal stenosis, degenerative or isthmic spondylolisthesis or degenerative disc disease; selected for lumbar fusion with or without decompression; competence in the Swedish language. The criteria for exclusion were: previous lumbar fusion, rheumatoid arthritis and ankylosing spondylitis.Methods: An open book randomised controlled trial with pre-surgical and post-surgical measures at 3, 6, 12 and 24-36 months was performed to investigate the effectiveness of a psychomotor therapy focusing on cognition, behaviour and motor relearning compared to exercise therapy focusing on strength and conditioning, applied during the first 3 months after lumbar fusion. Randomisation allocated 53 patients to psychomotor therapy and 54 patients to exercise therapy. The Oswestry disability index (ODI) was the primary outcome measure. Secondary measures included the Visual analogue scale for back pain (VAS), European quality of life questionnaire (EQ5D), as well as other clinical, psychological and work related variables.Analysis: A total of 78 patients were needed assuming a power = 80%. Patient compliance was analysed and an intention to treat principle applied to data analysis. For statistical comparison between the 2 independent groups, analysis of covariance was used. Categorical regression with optimal scaling transformation, elastic net regularization and bootstrapping were used to investigate pre-surgical predictor variables and address predictive model validity.Results: Follow-up rates were 93% at 12 months and 81% at 24-36 months after surgery. Psychomotor therapy improved functional disability, self-efficacy, outcome expectancy and fear of movement/(re)injury significantly more than exercise therapy at respective follow-up occasions. Pre-surgical control over pain significantly predicted functional disability and HRQOL. Pre-surgical catastrophizing and leg pain intensity significantly predicted functional disability and back pain while the pre-surgical lasegue test significantly predicted back pain. The implementation of post-operative psychomotor therapy also significantly predicted functional disability while pre-surgical outcome expectations significantly predicted HRQOL.Conclusions: The study shows that post-operative rehabilitation can be safely implemented during the first 3 months after lumbar fusion and should include measures to modify psychological as well as motor functions. The study also demonstrates the importance of pre-surgical psychological factors, leg pain intensity, the lasegue test and post-operative psychomotor therapy in the predictions of functional disability, back pain and HRQOL related outcomes.Implications: Physiotherapist should screen patients pain, psychological factors and neuromusculoskeletal system pre-surgically and rehabilitate patients with early psychomotor therapy after lumbar fusion.
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- Bowers, Robert M., et al.
(author)
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Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
- 2017
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In: Nature Biotechnology. - : NATURE PUBLISHING GROUP. - 1087-0156 .- 1546-1696. ; 35:8, s. 725-731
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Journal article (peer-reviewed)abstract
- We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity.
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- Faber, Zachary J, et al.
(author)
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The genomic landscape of core-binding factor acute myeloid leukemias
- 2016
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In: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 48, s. 1551-1556
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Journal article (peer-reviewed)abstract
- Acute myeloid leukemia (AML) comprises a heterogeneous group of leukemias frequently defined by recurrent cytogenetic abnormalities, including rearrangements involving the core-binding factor (CBF) transcriptional complex. To better understand the genomic landscape of CBF-AMLs, we analyzed both pediatric (n = 87) and adult (n = 78) samples, including cases with RUNX1-RUNX1T1 (n = 85) or CBFB-MYH11 (n = 80) rearrangements, by whole-genome or whole-exome sequencing. In addition to known mutations in the Ras pathway, we identified recurrent stabilizing mutations in CCND2, suggesting a previously unappreciated cooperating pathway in CBF-AML. Outside of signaling alterations, RUNX1-RUNX1T1 and CBFB-MYH11 AMLs demonstrated remarkably different spectra of cooperating mutations, as RUNX1-RUNX1T1 cases harbored recurrent mutations in DHX15 and ZBTB7A, as well as an enrichment of mutations in epigenetic regulators, including ASXL2 and the cohesin complex. This detailed analysis provides insights into the pathogenesis and development of CBF-AML, while highlighting dramatic differences in the landscapes of cooperating mutations for these related AML subtypes.
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- Fritzell, Peter, et al.
(author)
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Cost-effectiveness of lumbar fusion and nonsurgical treatment for chronic low back pain in the Swedish lumbar spine study : A multicenter, randomized, controlled trial from the Swedish Lumbar Spine Study Group
- 2004
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In: Spine. - : Lippincott Williams & Wilkins. - 0362-2436 .- 1528-1159. ; 29:4, s. 421-434
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Journal article (peer-reviewed)abstract
- Study Design. A cost-effectiveness study was performed from the societal and health care perspectives. Objective. To evaluate the costs-effectiveness of lumbar fusion for chronic low back pain (CLBP) during a 2-year follow-up. Summary of Background Data. A full economic evaluation comparing costs related to treatment effects in patients with CLBP is lacking. Patients and Methods. A total of 284 of 294 patients with CLBP for at least 2 years were randomized to either lumbar fusion or a nonsurgical control group. Costs for the health care sector ( direct costs), and costs associated with production losses ( indirect costs) were calculated. Societal total costs were identified as the sum of direct and indirect costs. Treatment effects were measured using patient global assessment of improvement, back pain ( VAS), functional disability (Owestry), and return to work. Results. The societal total cost per patient ( standard deviations) in the surgical group was significantly higher than in the nonsurgical group: Swedish kroner (SEK) 704,000 ( 254,000) vs. SEK 636,000 ( 208,000). The cost per patient for the health care sector was significantly higher for the surgical group, SEK 123,000 ( 60,100) vs. 65,200 ( 38,400) for the control group. All treatment effects were significantly better after surgery. The incremental cost-effectiveness ratio ( ICER), illustrating the extra cost per extra effect unit gained by using fusion instead of nonsurgical treatment, were for improvement: SEK 2,600 ( 600 - 5,900), for back pain: SEK 5,200 ( 1,100 - 11,500), for Oswestry: SEK 11,300 ( 1,200 - 48,000), and for return to work: SEK 4,100 ( 100 21,400). Conclusion. For both the society and the health care sectors, the 2-year costs for lumbar fusion was significantly higher compared with nonsurgical treatment but all treatment effects were significantly in favor of surgery. The probability of lumbar fusion being cost-effective increased with the value put on extra effect units gained by using surgery.
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- Holmfeldt, Linda, et al.
(author)
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The genomic landscape of hypodiploid acute lymphoblastic leukemia
- 2013
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In: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 45:3, s. 242-252
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Journal article (peer-reviewed)abstract
- The genetic basis of hypodiploid acute lymphoblastic leukemia (ALL), a subtype of ALL characterized by aneuploidy and poor outcome, is unknown. Genomic profiling of 124 hypodiploid ALL cases, including whole-genome and exome sequencing of 40 cases, identified two subtypes that differ in the severity of aneuploidy, transcriptional profiles and submicroscopic genetic alterations. Near-haploid ALL with 24-31 chromosomes harbor alterations targeting receptor tyrosine kinase signaling and Ras signaling (71%) and the lymphoid transcription factor gene IKZF3 (encoding AIOLOS; 13%). In contrast, low-hypodiploid ALL with 32-39 chromosomes are characterized by alterations in TP53 (91.2%) that are commonly present in nontumor cells, IKZF2 (encoding HELIOS; 53%) and RB1 (41%). Both near-haploid and low-hypodiploid leukemic cells show activation of Ras-signaling and phosphoinositide 3-kinase (PI3K)-signaling pathways and are sensitive to PI3K inhibitors, indicating that these drugs should be explored as a new therapeutic strategy for this aggressive form of leukemia.
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