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| 2. |
- Domingo-Almenara, Xavier, et al.
(author)
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CMS-MRM and METLIN-MRM : a cloud library and public resource for targeted analysis of small molecules
- 2018
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In: Nature Methods. - : Nature Publishing Group. - 1548-7091 .- 1548-7105. ; 15:9, s. 681-
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Journal article (peer-reviewed)abstract
- We report XCMS-MRM and METLIN-MRM (http://xcmsonline-mrm.scripps.edu/ and http://metlin.scripps.edu/), a cloud-based data-analysis platform and a public multiple-reaction monitoring (MRM) transition repository for small-molecule quantitative tandem mass spectrometry. This platform provides MRM transitions for more than 15,500 molecules and facilitates data sharing across different instruments and laboratories.
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| 3. |
- Filbee-Dexter, Karen, et al.
(author)
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Ecological surprise : concept, synthesis, and social dimensions
- 2017
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In: Ecosphere. - : Wiley. - 2150-8925 .- 2150-8925. ; 8:12
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Journal article (peer-reviewed)abstract
- As the extent and intensity of human impacts on ecosystems increase and the capacity of ecosystems to absorb these impacts dwindles, unanticipated behavior in ecological systems-or surprises-is likely to become more common. The concept of ecological surprise is broadly applied but seldom explicitly developed in ecological literature, and ecologists can employ diverging language, frameworks, and interpretations of surprise. Here, we synthesize what ecological surprise has meant to ecologists studying these events and review the development and use of the concept in ecology. We define ecological surprise as a situation where human expectations or predictions of natural system behavior deviate from observed ecosystem behavior. This can occur when people (1) fail to anticipate change in ecosystems; (2) fail to influence ecosystem behavior as intended; or (3) discover something about an ecosystem that runs counter to accepted knowledge. We develop a conceptual model that captures the interactions between social and ecological processes that lead to these events and examine two types of drivers that contribute to surprise: underlying driving forces and proximate causes. Our definition of ecological surprise inherently acknowledges that, to be surprising, there must be human observers to the ecological occurrence who have expectations about ecosystem behavior. To explore this dimension, we draw on social science perspectives to understand the ways in which human expectations of ecosystems are influenced by social networks, heuristics, and mental models. We use a case study to demonstrate how our integrated concep-tualization of ecological surprise provides a systematic way of examining these events. Our integration of these perspectives enables us to better synthesize social and ecological knowledge of these events, and encourages ecologists to critically reflect on how they, as scientists, formulate and reformulate expectations of ecosystem behavior.
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| 4. |
- Filbee-Dexter, Karen, et al.
(author)
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Quantifying ecological and social drivers of ecological surprise
- 2018
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In: Journal of Applied Ecology. - : Wiley. - 0021-8901 .- 1365-2664. ; 55:5, s. 2135-2146
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Journal article (peer-reviewed)abstract
- 1. A key challenge facing ecologists and ecosystem managers is understanding what drives unexpected shifts in ecosystems and limits the effectiveness of human interventions. Research that integrates and analyses data from natural and social systems can provide important insight for unravelling the complexity of these dynamics. It is, therefore, a critical step towards the development of evidence-based, whole-system management approaches.2. To examine our ability to influence ecosystems that are behaving in unexpected ways, we explore three prominent cases of ecological surprise. We captured the social-ecological systems (SES) using key variables and interactions from Ostrom's SES framework, which integrates broader ecosystem processes (e.g. climate, connectivity), management variables (e.g. quotas, restrictions, monitoring), resource use behaviours (e.g. harvesting) and the resource unit (e.g. trees, fish, clean water) being managed.3. Structural equation modelling revealed that management interventions often influenced resource use behaviours (e.g. rules and limits strongly affected harvest or pollution), but they did not have a significant effect on the abundance of the managed resource. Instead, most resource variability was related to ecological processes and feedbacks operating at broader spatial or temporal scales than management interventions, which locked the resource system into the degraded state.4. Synthesis and applications. Mismatch between the influence of management systems and ecosystem processes can limit the effectiveness of human interventions during periods of ecological surprise. Management strategies should shift from a conventional focus on removal or addition of a single resource towards solutions that influence the broader ecosystem. Operationalizing Ostrom’s framework to quantitatively analyse social‐ecological systems using structural equation models shows promise for testing solutions to navigate these events.
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| 5. |
- Friend, Peter, et al.
(author)
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Incidence of anemia in sirolimus-treated renal transplant recipients : the importance of preserving renal function
- 2007
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In: Transplant International. - : Frontiers Media SA. - 0934-0874 .- 1432-2277. ; 20:9, s. 754-760
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Journal article (peer-reviewed)abstract
- Sirolimus (SRL) has a concentration-related effect on hematopoiesis. In this study, 430 renal transplant recipients were randomized (1:1) 3 months post-transplantation to continue SRL-cyclosporine (CsA)-steroids (ST) or to have CsA withdrawn (SRL-ST). Over 5 years, on therapy calculated glomerular filtration rate (GFR), hematological indices, erythropoietin (EPO) use, and rates of mild, moderate, and severe anemia were determined. Longitudinal analyses using linear mixed models examined covariates predicting hemoglobin (Hgb) levels. Mean Hgb was significantly lower with SRL-ST at 6 months; but subsequently became significantly higher (at 2 years, 129 vs. 135 g/l, SRL-CsA-ST vs. SRL-ST, P<0.001). Mean corpuscular volume was low with both therapies, and significantly lower with SRL-ST. EPO use was similar in the two groups, approximately 30% during the first year and 10% thereafter. The incidence of anemia was significantly higher with SRL-CsA-ST>or=2 years. At year 5, only 39.1% of SRL-CsA-ST patients had normal Hgb vs. 68.5% of SRL-ST patients. GFR and recipient age as well as the interaction term x treatment time were significant covariates predicting Hgb. CsA withdrawal followed by SRL immunotherapy resulted in significantly less anemia than SRL-CsA-ST, despite twofold higher SRL exposure. This suggests that the improvement in GFR accompanying CsA withdrawal may mitigate the effect of SRL on hematopoiesis. (ClinicalTrials.gov number: NCT00428064).
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| 6. |
- Zody, Michael, 1968-, et al.
(author)
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Analysis of the DNA sequence and duplication history of human chromosome 15
- 2006
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 440:7084, s. 671-675
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Journal article (peer-reviewed)abstract
- Here we present a finished sequence of human chromosome 15, together with a high-quality gene catalogue. As chromosome 15 is one of seven human chromosomes with a high rate of segmental duplication, we have carried out a detailed analysis of the duplication structure of the chromosome. Segmental duplication in chromosome 15 are largely clustered in two regions, on proximal and distal 15q; the proximal region is notable because recombination among the segmental duplications can result in deletions causing Prader-Willi and Angelman syndromes. Sequence analysis shows that the proximal and distal regions of 15q share extensive ancient similarity. Using a simple approach, we have been able to reconstruct many of the events by which the current duplication structure arose. We find that most of the intrachromosomal duplications seem to share a common ancestry. Finally, we demonstrate that some remaining gaps in the genome sequence are probably due to structural polymorphisms between haplotypes; this may explain a significant fraction of the gaps remaining in the human genome.
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