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- Stone, D., et al.
(author)
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A method of establishing a transect for biodiversity and ecosystem function monitoring across Europe
- 2016
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In: Applied Soil Ecology. - : Elsevier BV. - 0929-1393 .- 1873-0272. ; 97, s. 3-11
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Journal article (peer-reviewed)abstract
- The establishment of the range of soil biodiversity found within European soils is needed to guide EU policy development regarding the protection of soil. Such a base-line should be collated from a wide-ranging sampling campaign to ensure that soil biodiversity from the majority of soil types, land-use or management systems, and European climatic (bio-geographical zones) were included. This paper reports the design and testing of a method to achieve the large scale sampling associated with the establishment of such a baseline, carried out within the remit of the EcoFINDERS project, and outlines points to consider when such a task is undertaken. Applying a GIS spatial selection process, a sampling campaign was undertaken by 13 EcoFINDERS partners across 11 countries providing data on the range of indicators of biodiversity and ecosystem functions including; micro and meso fauna biodiversity, extracellular enzyme activity, PLEA and community level physiological profiling (MicroResp (TM) and Biolog (TM)). Physical, chemical and bio-geographical parameters of the 81 sites sampled were used to determine whether the model predicted a wide enough range of sites to allow assessment of the biodiversity indicators tested. Discrimination between the major bio-geographical zones of Atlantic and Continental was possible for all land-use types. Boreal and Alpine zones only allowed discrimination in the most common land-use type for that area e.g. forestry and grassland sites, respectively, while the Mediterranean zone did not have enough sites sampled to draw conclusions across all land-use types. The method used allowed the inclusion of a range of land-uses in both the model prediction stage and the final sites sampled. The establishment of the range of soil biodiversity across Europe is possible, though a larger targeted campaign is recommended. The techniques applied within the EcoFINDERS sampling would be applicable to a larger campaign. (C) 2015 Elsevier B.V. All rights reserved.
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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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- Gefenas, E., et al.
(author)
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Non-equivalent stringency of ethical review in the Baltic States: a sign of a systematic problem in Europe?
- 2010
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In: Journal of Medical Ethics. - : BMJ. - 1473-4257 .- 0306-6800. ; 36:7, s. 435-439
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Journal article (peer-reviewed)abstract
- We analyse the system of ethical review of human research in the Baltic States by introducing the principle of equivalent stringency of ethical review, that is, research projects imposing equal risks and inconveniences on research participants should be subjected to equally stringent review procedures. We examine several examples of non-equivalence or asymmetry in the system of ethical review of human research: (1) the asymmetry between rather strict regulations of clinical drug trials and relatively weaker regulations of other types of clinical biomedical research and (2) gaps in ethical review in the area of non-biomedical human research where some sensitive research projects are not reviewed by research ethics committees at all. We conclude that non-equivalent stringency of ethical review is at least partly linked to the differences in scope and binding character of various international legal instruments that have been shaping the system of ethical review in the Baltic States. Therefore, the Baltic example could also serve as an object lesson to other European countries which might be experiencing similar problems.
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- Hug, S., et al.
(author)
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High-dimensional Bayesian parameter estimation: Case study for a model of JAK2/STAT5 signaling
- 2013
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In: Mathematical Biosciences. - : Elsevier. - 0025-5564 .- 1879-3134. ; 246:2, s. 293-304
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Journal article (peer-reviewed)abstract
- In this work we present results of a detailed Bayesian parameter estimation for an analysis of ordinary differential equation models. These depend on many unknown parameters that have to be inferred from experimental data. The statistical inference in a high-dimensional parameter space is however conceptually and computationally challenging. To ensure rigorous assessment of model and prediction uncertainties we take advantage of both a profile posterior approach and Markov chain Monte Carlo sampling. We analyzed a dynamical model of the JAK2/STAT5 signal transduction pathway that contains more than one hundred parameters. Using the profile posterior we found that the corresponding posterior distribution is bimodal. To guarantee efficient mixing in the presence of multimodal posterior distributions we applied a multi-chain sampling approach. The Bayesian parameter estimation enables the assessment of prediction uncertainties and the design of additional experiments that enhance the explanatory power of the model. This study represents a proof of principle that detailed statistical analysis for quantitative dynamical modeling used in systems biology is feasible also in high-dimensional parameter spaces.
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- Sadlej, J., et al.
(author)
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Properties and Spectroscopies
- 2007
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In: Continuum Solvation Models in Chemical Physics: From Theory to Applications. - Chichester, UK : John Wiley & Sons. - 9780470029381 ; , s. 125-312
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Book chapter (peer-reviewed)
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| 9. |
- Siebenmann, C, et al.
(author)
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Hemoglobin mass and intravascular volume kinetics during and after exposure to 3,454-m altitude
- 2015
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In: Journal of applied physiology. - : American Physiological Society. - 8750-7587 .- 1522-1601. ; 119:10, s. 1194-1201
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Journal article (peer-reviewed)abstract
- Siebenmann C, Cathomen A, Hug M, Keiser S, Lundby AK, Hilty MP, Goetze JP, Rasmussen P, Lundby C. Hemoglobin mass and intravascular volume kinetics during and after exposure to 3,454 m altitude. J Appl Physiol 119: 1194-1201, 2015. First published March 6, 2015; doi:10.1152/japplphysiol.01121.2014.-High altitude (HA) exposure facilitates a rapid contraction of plasma volume (PV) and a slower occurring expansion of hemoglobin mass (Hbmass). The kinetics of the Hbmass expansion has never been examined by multiple repeated measurements, and this was our primary study aim. The second aim was to investigate the mechanisms mediating the PV contraction. Nine healthy, normally trained sea-level (SL) residents (8 males, 1 female) sojourned for 28 days at 3,454 m. Hbmass was measured and PV was estimated by carbon monoxide rebreathing at SL, on every 4th day at HA, and 1 and 2 wk upon return to SL. Four weeks at HA increased Hbmass by 5.26% (range 2.5-11.1%; P < 0.001). The individual Hbmass increases commenced with up to 12 days of delay and reached a maximal rate of 4.04±1.02 g/day after 14.9±5.2 days. The probability for Hbmass to plateau increased steeply after 20-24 days. Upon return to SL Hbmass decayed by-2.46 ± 2.3 g/day, reaching values similar to baseline after 2 wk. PV, aldosterone concentration, and renin activity were reduced at HA (P < 0.001) while the total circulating protein mass remained unaffected. In summary, the Hbmass response to HA exposure followed a sigmoidal pattern with a delayed onset and a plateau after ∼3 wk. The decay rate of Hbmass upon descent to SL did not indicate major changes in the rate of erythrolysis. Moreover, our data support that PV contraction at HA is regulated by the renin-angiotensin-aldosterone axis and not by changes in oncotic pressure. © 2015 The American Physiological Society.
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