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- Yarza, P., et al.
(author)
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Sequencing orphan species initiative (SOS): Filling the gaps in the 16S rRNA gene sequence database for all species with validly published names
- 2013
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In: Systematic and Applied Microbiology. - : Elsevier BV. - 0723-2020. ; 36:1, s. 69-73
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Journal article (peer-reviewed)abstract
- High quality 16S ribosomal RNA (rRNA) gene sequences from the type strains of all species with validly published names, as defined by the International Code of Nomenclature of Bacteria, are a prerequisite for their accurate affiliations within the global genealogical classification and for the recognition of potential new taxa. During the last few years, the Living Tree Project (LTP) has taken care to create a high quality, aligned 16S and 23S rRNA gene sequence database of all type strains. However, the manual curation of the sequence dataset and type strain information revealed that a total of 552 “orphan” species (about 5.7% of the currently classified species) had to be excluded from the reference trees. Among them, 322 type strains were not represented by an SSU entry in the public sequence repositories. The remaining 230 type strains had to be discarded due to bad sequence quality. Since 2010, the LTP team has coordinated a network of researchers and culture collections in order to improve the situation by (re)-sequencing the type strains of these “orphan” species. As a result, we can now report 351 16S rRNA gene sequences of type strains. Nevertheless, 201 species could not be sequenced because cultivable type strains were not available (121), the cultures had either been lost or were never deposited in the first place (66), or it was not possible due to other constraints (14). The International Code of Nomenclature of Bacteria provides a number of mechanisms to deal with the problem of missing type strains and we recommend that due consideration be given to the appropriate mechanisms in order to help solve some of these issues.
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- Lahesmaa, M., et al.
(author)
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Hyperthyroidism increases brown fat metabolism in humans
- 2014
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In: Journal of Clinical Endocrinology and Metabolism. - : The Endocrine Society. - 0021-972X .- 1945-7197. ; 99:1
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Journal article (peer-reviewed)abstract
- Context: Thyroid hormones are important regulators of brown adipose tissue (BAT) development and function. In rodents, BAT metabolism is up-regulated by thyroid hormones. Objective: The purpose of this article was to investigate the impact of hyperthyroidism on BAT metabolism in humans. Design: This was a follow-up study using positron emission tomography imaging. Main Outcome Measures: Glucose uptake (GU) and perfusion of BAT, white adipose tissue, skeletal muscle, and thyroid gland were measured using [18F]2-fluoro-2-deoxy-D- glucose and [15O]H2Oand positron emission tomography in 10 patients with overt hyperthyroidism and in 8 healthy participants. Five of the hyperthyroid patients were restudied after restoration of euthyroidism. Supraclavicular BAT was quantified with magnetic resonance imaging or computed tomography and energy expenditure (EE) with indirect calorimetry. Results: Compared with healthy participants, hyperthyroid participants had 3-fold higher BAT GU (2.7 ± 2.3 vs 0.9 ± 0.1 ±mol/100 g/min, P = .0013), 90% higher skeletal muscle GU (P < .005), 45% higher EE (P<.005), and a 70% higher lipid oxidation rate (P = .001). These changes were reversible after restoration of euthyroidism. During hyperthyroidism, serum free T4 and free T3 were strongly associated with EE and lipid oxidation rates (P < .001). TSH correlated inversely with BAT and skeletal muscle glucose metabolism (P < .001). Hyperthyroidism had no effect on BAT perfusion, whereas it stimulated skeletal muscle perfusion (P = .04). Thyroid gland GU did not differ between hyperthyroid and euthyroid study subjects. Conclusions: Hyperthyroidism increases GU in BAT independently of BAT perfusion. Hyperthyroid patients are characterized by increased skeletal muscle metabolism and lipid oxidation rates. (J Clin Endocrinol Metab 99: E28-E35, 2014). © Copyright 2014 by The Endocrine Society.
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- de Haan, Stefan, et al.
(author)
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Parametric imaging of myocardial viability using ¹⁵O-labelled water and PET/CT : comparison with late gadolinium-enhanced CMR
- 2012
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In: European Journal of Nuclear Medicine and Molecular Imaging. - : Springer Science and Business Media LLC. - 1619-7070 .- 1619-7089. ; 39:8, s. 1240-1245
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Journal article (peer-reviewed)abstract
- PurposeThe perfusable tissue index (PTI) is a marker of myocardial viability. Recent technological advances have made it possible to generate parametric PTI images from a single [15O]H2O PET/CT scan. The purpose of this study was to validate these parametric PTI images.MethodsThe study population comprised 46 patients with documented or suspected coronary artery disease who were studied with [15O]H2O PET and late gadolinium-enhanced (LGE) cardiac magnetic resonance imaging (CMR).ResultsOf the 736 myocardial segments included, 364 showed some degree of LGE. PTI and perfusable tissue fraction (PTF) diminished with increasing LGE. The areas under the curve of the PTI and PTF, used to predict (near) transmural LGE on CMR, were 0.86 and 0.87, respectively. Optimal sensitivity and specificity were 91 % and 73 % for PTI and 69 % and 87 % for PTF, respectively.ConclusionPTI and PTF assessed with a single [15O]H2O scan can be utilized as markers of myocardial viability in patients with coronary artery disease.
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| 6. |
- Sihver, Lembit, 1962, et al.
(author)
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Current status of the "Hybrid Kurotama model" for total reaction cross sections
- 2014
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In: Nuclear Instruments and Methods in Physics Research, Section B: Beam Interactions with Materials and Atoms. - : Elsevier BV. - 0168-583X. ; 334, s. 34-39
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Journal article (peer-reviewed)abstract
- To be able to calculate the nucleon + nucleus and nucleus + nucleus total reaction cross sections with precision is of great importance for studies of fundamental nuclear properties, e.g., the nuclear structure. This is also very important for particle and heavy ion transport calculations since in all particle and heavy ion transport codes, the probability function according to which a projectile particle will collide within a certain distance in a matter depends on the total reaction cross sections. This will also scale the calculated partial fragmentation cross sections. It is therefore crucial that accurate total reaction cross section models are used in the transport calculations. In this paper, a new general purpose total reaction cross section model/subroutine called "Hybrid Kurotama" is presented. The model has been tested against available p + He, p + nucleus, and nucleus + nucleus total reaction cross sections and an overall better agreement has been found than for earlier published models. This model is therefore very suitable to be used in any deterministic or Monte Carlo particle and heavy ion transport code.
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