| 31. |
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| 32. |
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| 33. |
- Afanasiev, Sergey V., et al.
(författare)
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Experimental apparatus to study crystal channeling in an external SPS beamline
- 2007
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Ingår i: Proceedings of SPIE, the International Society for Optical Engineering. - : SPIE. - 0277-786X .- 1996-756X. ; 6634
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Tidskriftsartikel (refereegranskat)abstract
- For the new generation of high intensity hadronic machines as, for instance, LHC, halo collimation is a necessary issue for the accelerator to operate at the highest possible luminosity and to prevent the damage of superconductor magnets.1 We propose an experiment aimed to systematic study of the channeling phenomenology and of the newly observed "volume reflection" effect. This experiment will be performed for an external SPS beamline and will make use of a primary proton beam with 400 GeV/c momentum and very small (∼ 3 μrad) divergence. The advantage of a proposed experiment is precise tracking of particles that interacted with a crystal, so that to determine the single-pass efficiency for all the processes involved. For this purpose, a telescope equipped with high-resolution silicon microstrip detectors will be used. New generation silicon crystals and an extra-precise goniometer are mandatory issues. Main goal of the experiment is to get the precise information on channeling of relativistic particles and, ultimately, on the feasibility of such technique for halo collimation at LHC. In this contribution we review the status of the setting-up of experimental apparatus and its future development in sight of the planned run in September 2006.
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| 34. |
- Altenhoff, Adrian M., et al.
(författare)
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Standardized benchmarking in the quest for orthologs
- 2016
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Ingår i: Nature Methods. - 1548-7091 .- 1548-7105. ; 13:5, s. 425-
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Tidskriftsartikel (refereegranskat)abstract
- Achieving high accuracy in orthology inference is essential for many comparative, evolutionary and functional genomic analyses, yet the true evolutionary history of genes is generally unknown and orthologs are used for very different applications across phyla, requiring different precision-recall trade-offs. As a result, it is difficult to assess the performance of orthology inference methods. Here, we present a community effort to establish standards and an automated web-based service to facilitate orthology benchmarking. Using this service, we characterize 15 well-established inference methods and resources on a battery of 20 different benchmarks. Standardized benchmarking provides a way for users to identify the most effective methods for the problem at hand, sets a minimum requirement for new tools and resources, and guides the development of more accurate orthology inference methods.
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| 35. |
- Altenhoff, Adrian M., et al.
(författare)
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The Quest for Orthologs benchmark service and consensus calls in 2020
- 2020
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 48:W1, s. W538-W545
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Tidskriftsartikel (refereegranskat)abstract
- The identification of orthologs-genes in different species which descended from the same gene in their last common ancestor-is a prerequisite for many analyses in comparative genomics and molecular evolution. Numerous algorithms and resources have been conceived to address this problem, but benchmarking and interpreting them is fraught with difficulties (need to compare them on a common input dataset, absence of ground truth, computational cost of calling orthologs). To address this, the Quest for Orthologs consortium maintains a reference set of proteomes and provides a web server for continuous orthology benchmarking (http://orthology.benchmarkservice.org). Furthermore, consensus ortholog calls derived from public benchmark submissions are provided on the Alliance of Genome Resources website, the joint portal of NIH-funded model organism databases.
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| 36. |
- Carro, María J., et al.
(författare)
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On restriction of maximal multipliers in weighted settings
- 2012
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Ingår i: Transactions of the American Mathematical Society. - 0002-9947 .- 1088-6850. ; 364:5, s. 2241-2260
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Tidskriftsartikel (refereegranskat)abstract
- We obtain restriction results of K. De Leeuw's type for maximal operators defined through Fourier multipliers of either strong or weak type for weighted L-p spaces with 1 <= p <= infinity. Applications to the case of Hormander-Mihlin multipliers, singular integral operators and Bochner-Riesz sums are given.
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| 37. |
- Donini, Lorenzo M., et al.
(författare)
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Critical appraisal of definitions and diagnostic criteria for sarcopenic obesity based on a systematic review
- 2020
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Ingår i: Clinical Nutrition. - : Elsevier BV. - 0261-5614 .- 1532-1983. ; 39:8, s. 2368-2388
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Forskningsöversikt (refereegranskat)abstract
- Background: Sarcopenic obesity is a clinical and functional condition characterized by the coexistence of excess fat mass and sarcopenia. Currently, different definitions of sarcopenic obesity exist and its diagnostic criteria and cut-offs are not universally established. Therefore, the prevalence and sensitivity of this condition for any disease risk prediction is affected significantly. Aim: This work was conducted under the auspices of the European Society for Clinical Nutrition and Metabolism (ESPEN) and the European Association for the Study of Obesity (EASO). An international expert panel performed a systematic review as an initial step to analyze and summarize the available scientific literature on the definitions and the diagnostic criteria for sarcopenic obesity proposed and/or applied in human studies to date.Methods: The present systematic review was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. The search was conducted in April 2018 in three databases (PubMed, Scopus, Web of Science). Human studies conducted in both sexes, irrespective of ethnicity, and published from 2007 to 2018 were included; cohorts of individuals with obesity and acute or chronic conditions and treatments reported to negatively influence skeletal muscle mass and function independently of obesity were excluded from final analyses. The quality of the studies was evaluated using the Newcastle-Ottawa Scale (NOS) adapted for cross sectional studies.Results: The electronic search retrieved 2335 papers of which 75 met the eligibility criteria. A marked heterogeneity in definitions and approaches to diagnose sarcopenic obesity was observed. This was mainly due to differences in the definitions of obesity and sarcopenia, in the methodologies used to assess body composition and physical function, and in the reference values for the variables that have been used (different cut-offs, interquartile analysis, diverse statistical stratification methods). This variability may be attributable, at least in part, to the availability of the methodologies in the different settings, to the variability in specialties and backgrounds of the researcher, and to the different settings (general population, clinical settings, etc.) where studies were performed.Conclusion: The results of the current work support the need for consensus proposals on: 1) definition of sarcopenic obesity; 2) diagnostic criteria both at the level of potential gold-standards and acceptable surrogates with wide clinical applicability, and with related cut-off values; 3) methodologies to be used in actions 1 and 2. First steps should be aimed at reaching consensus on plausible proposals that would need subsequent validation based on homogeneous studies and databases, possibly based on analyses of existing cohorts, to help define the prevalence of the condition, its clinical and functional relevance as well as most effective prevention and treatment strategies.
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| 38. |
- Jarvis, Erich D., et al.
(författare)
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Whole-genome analyses resolve early branches in the tree of life of modern birds
- 2014
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6215, s. 1320-1331
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Tidskriftsartikel (refereegranskat)abstract
- To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
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| 39. |
- Nevers, Yannis, et al.
(författare)
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The Quest for Orthologs orthology benchmark service in 2022
- 2022
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 50:W1, s. W623-W632
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Tidskriftsartikel (refereegranskat)abstract
- The Orthology Benchmark Service (https://orthology.benchmarkservice.org) is the gold standard for orthology inference evaluation, supported and maintained by the Quest for Orthologs consortium. It is an essential resource to compare existing and new methods of orthology inference (the bedrock for many comparative genomics and phylogenetic analysis) over a standard dataset and through common procedures. The Quest for Orthologs Consortium is dedicated to maintaining the resource up to date, through regular updates of the Reference Proteomes and increasingly accessible data through the OpenEBench platform. For this update, we have added a new benchmark based on curated orthology assertion from the Vertebrate Gene Nomenclature Committee, and provided an example meta-analysis of the public predictions present on the platform.
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| 40. |
- Piovesan, Damiano, et al.
(författare)
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DisProt 7.0 : a major update of the database of disordered proteins
- 2017
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 45:D1, s. d219-D227
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Tidskriftsartikel (refereegranskat)abstract
- The Database of Protein Disorder (DisProt, URL: www.disprot.org) has been significantly updated and upgraded since its last major renewal in 2007. The current release holds information on more than 800 entries of IDPs/IDRs, i.e. intrinsically disordered proteins or regions that exist and function without a well-defined three-dimensional structure. We have re-curated previous entries to purge DisProt from conflicting cases, and also upgraded the functional classification scheme to reflect continuous advance in the field in the past 10 years or so. We define IDPs as proteins that are disordered along their entire sequence, i.e. entirely lack structural elements, and IDRs as regions that are at least five consecutive residues without well-defined structure. We base our assessment of disorder strictly on experimental evidence, such as X-ray crystallography and nuclear magnetic resonance ( primary techniques) and a broad range of other experimental approaches (secondary techniques). Confident and ambiguous annotations are highlighted separately. DisProt 7.0 presents classified knowledge regarding the experimental characterization and functional annotations of IDPs/IDRs, and is intended to provide an invaluable resource for the research community for a better understanding structural disorder and for developing better computational tools for studying disordered proteins.
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