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101.
102.
JF Yuan SJ Zhang O Jafer RA Furlong OE Chausiaux CA Sargent GH Zhang NA Affara 《BMC microbiology》2009,9(1):246
Background
Pseudorabies virus (PRV) is an alphaherpesviruses whose native host is pig. PRV infection mainly causes signs of central nervous system disorder in young pigs, and respiratory system diseases in the adult. 相似文献103.
Takehiro M Fujimoto S Shimodahira M Shimono D Mukai E Nabe K Radu RG Kominato R Aramaki Y Seino Y Yamada Y 《American journal of physiology. Endocrinology and metabolism》2005,288(2):E372-E380
To investigate the effects of chronic exposure to ketone bodies on glucose-induced insulin secretion, we evaluated insulin release, intracellular Ca2+ and metabolism, and Ca2+ efficacy of the exocytotic system in rat pancreatic islets. Fifteen-hour exposure to 5 mM d-beta-hydroxybutyrate (HB) reduced high glucose-induced insulin secretion and augmented basal insulin secretion. Augmentation of basal release was derived from promoting the Ca2+-independent and ATP-independent component of insulin release, which was suppressed by the GDP analog. Chronic exposure to HB affected mostly the second phase of glucose-induced biphasic secretion. Dynamic experiments showed that insulin release and NAD(P)H fluorescence were lower, although the intracellular Ca2+ concentration ([Ca2+](i)) was not affected 10 min after exposure to high glucose. Additionally, [Ca2+](i) efficacy in exocytotic system at clamped concentrations of ATP was not affected. NADH content, ATP content, and ATP-to-ADP ratio in the HB-cultured islets in the presence of high glucose were lower, whereas glucose utilization and oxidation were not affected. Mitochondrial ATP production shows that the respiratory chain downstream of complex II is not affected by chronic exposure to HB, and that the decrease in ATP production is due to decreased NADH content in the mitochondrial matrix. Chronic exposure to HB suppresses glucose-induced insulin secretion by lowering the ATP level, at least partly by inhibiting ATP production by reducing the supply of NADH to the respiratory chain. Glucose-induced insulin release in the presence of aminooxyacetate was not reduced, which implies that chronic exposure to HB affects the malate/aspartate shuttle and thus reduces NADH supply to mitochondria. 相似文献
104.
Marc Streit Rupert C Ecker Katja Osterreicher Georg E Steiner Horst Bischof Christine Bangert Tamara Kopp Radu Rogojanu 《Cytometry. Part A》2006,69(7):601-611
BACKGROUND: Presentation of multiple interactions is of vital importance in the new field of cytomics. Quantitative analysis of multi- and polychromatic stained cells in tissue will serve as a basis for medical diagnosis and prediction of disease in forthcoming years. A major problem associated with huge interdependent data sets is visualization. Therefore, alternative and easy-to-handle strategies for data visualization as well as data meta-evaluation (population analysis, cross-correlation, co-expression analysis) were developed. METHODS: To facilitate human comprehension of complex data, 3D parallel coordinate systems have been developed and used in automated microscopy-based multicolor tissue cytometry (MMTC). Frozen sections of human skin were stained using the combination anti-CD45-PE, anti-CD14-APC, and SytoxGreen as well as the appropriate single and double negative controls. Stained sections were analyzed using automated confocal laser microscopy and semiquantitative MMTC-analysis with TissueQuest 2.0. The 3D parallel coordinate plots are generated from semiquantitative immunofluorescent data of single cells. The 2D and 3D parallel coordinate plots were produced by further processing using the Matlab environment (Mathworks, USA). RESULTS: Current techniques in data visualization primarily utilize scattergrams, where two parameters are plotted against each other on linear or logarithmic scales. However, data evaluation on cartesian x/y-scattergrams is, in general, only of limited value in multiparameter analysis. Dot plots suffer from serious problems, and in particular, do not meet the requirements of polychromatic high-context tissue cytometry of millions of cells. The 3D parallel coordinate plot replaces the vast amount of scattergrams that are usually needed for the cross-correlation analysis. As a result, the scientist is able to perform the data meta-evaluation by using one single plot. On the basis of 2D parallel coordinate systems, a density isosurface is created for representing the event population in an intuitive way. CONCLUSIONS: The proposed method opens new possibilities to represent and explore multidimensional data in the perspective of cytomics and other life sciences, e.g., DNA chip array technology. Current protocols in immunofluorescence permit simultaneous staining of up to 17 markers. Showing the cross-correlation between these markers requires 136 scattergrams, which is a prohibitively high number. The improved data visualization method allows the observation of such complex patterns in only one 3D plot and could take advantage of the latest developments in 3D imaging. 相似文献
105.
Cardiac‐Specific Disruption of Bin1 in Mice Enables a Model of Stress‐ and Age‐Associated Dilated Cardiomyopathy 下载免费PDF全文
106.
Christopher R. Tench Radu Tanasescu Dorothee P. Auer William J. Cottam Cris S. Constantinescu 《PloS one》2014,9(9)
Coordinate based meta-analysis (CBMA) is used to find regions of consistent activation across fMRI and PET studies selected for their functional relevance to a hypothesis. Results are clusters of foci where multiple studies report in the same spatial region, indicating functional relevance. Contrast meta-analysis finds regions where there are consistent differences in activation pattern between two groups. The activation likelihood estimate methods tackle these problems, but require a specification of uncertainty in foci location: the full width half max (FWHM). Results are sensitive to FWHM. Furthermore, contrast meta-analysis requires correction for multiple statistical tests. Consequently it is sensitive only to very significant localised differences that produce very small p-values, which remain significant after correction; subtle diffuse differences between the groups can be overlooked. In this report we redefine the FWHM parameter, by analogy with a density clustering algorithm, and provide a method to estimate it. The FWHM is modified to account for the number of studies in the analysis, and represents a substantial change to the CBMA philosophy that can be applied to the current algorithms. Consequently we observe more reliable detection of clusters when there are few studies in the CBMA, and a decreasing false positive rate with larger study numbers. By contrast the standard definition (FWHM independent of the number of studies) is demonstrated to paradoxically increase the false positive rate as the number of studies increases, while reducing ability to detect true clusters for small numbers of studies. We also provide an algorithm for contrast meta-analysis, which includes a correction for multiple correlated tests that controls for the proportion of false clusters expected under the null hypothesis. Furthermore, we detail an omnibus test of difference between groups that is more sensitive than contrast meta-analysis when differences are diffuse. This test is useful where contrast meta-analysis is unrevealing. 相似文献
107.
Nowadays, scientists and companies are confronted with multiple competing goals such as makespan in high-performance computing and economic cost in Clouds that have to be simultaneously optimised. Multi-objective scheduling of scientific applications in these systems is therefore receiving increasing research attention. Most existing approaches typically aggregate all objectives in a single function, defined a-priori without any knowledge about the problem being solved, which negatively impacts the quality of the solutions. In contrast, Pareto-based approaches having as outcome a set of (nearly) optimal solutions that represent a tradeoff among the different objectives, have been scarcely studied. In this paper, we analyse MOHEFT, a Pareto-based list scheduling heuristic that provides the user with a set of tradeoff optimal solutions from which the one that better suits the user requirements can be manually selected. We demonstrate the potential of our method for multi-objective workflow scheduling on the commercial Amazon EC2 Cloud. We compare the quality of the MOHEFT tradeoff solutions with two state-of-the-art approaches using different synthetic and real-world workflows: the classical HEFT algorithm for single-objective scheduling and the SPEA2* genetic algorithm used in multi-objective optimisation problems. The results demonstrate that our approach is able to compute solutions of higher quality than SPEA2*. In addition, we show that MOHEFT is more suitable than SPEA2* for workflow scheduling in the context of commercial Clouds, since the genetic-based approach is unable of dealing with some of the constraints imposed by these systems. 相似文献
108.
Anthony Stuart Gilchrist Deborah CA Shearman Marianne Frommer Kathryn A Raphael Nandan P Deshpande Marc R Wilkins William B Sherwin John A Sved 《BMC genomics》2014,15(1)
Background
The tephritid fruit flies include a number of economically important pests of horticulture, with a large accumulated body of research on their biology and control. Amongst the Tephritidae, the genus Bactrocera, containing over 400 species, presents various species groups of potential utility for genetic studies of speciation, behaviour or pest control. In Australia, there exists a triad of closely-related, sympatric Bactrocera species which do not mate in the wild but which, despite distinct morphologies and behaviours, can be force-mated in the laboratory to produce fertile hybrid offspring. To exploit the opportunities offered by genomics, such as the efficient identification of genetic loci central to pest behaviour and to the earliest stages of speciation, investigators require genomic resources for future investigations.Results
We produced a draft de novo genome assembly of Australia’s major tephritid pest species, Bactrocera tryoni. The male genome (650 -700 Mbp) includes approximately 150Mb of interspersed repetitive DNA sequences and 60Mb of satellite DNA. Assessment using conserved core eukaryotic sequences indicated 98% completeness. Over 16,000 MAKER-derived gene models showed a large degree of overlap with other Dipteran reference genomes. The sequence of the ribosomal RNA transcribed unit was also determined. Unscaffolded assemblies of B. neohumeralis and B. jarvisi were then produced; comparison with B. tryoni showed that the species are more closely related than any Drosophila species pair. The similarity of the genomes was exploited to identify 4924 potentially diagnostic indels between the species, all of which occur in non-coding regions.Conclusions
This first draft B. tryoni genome resembles other dipteran genomes in terms of size and putative coding sequences. For all three species included in this study, we have identified a comprehensive set of non-redundant repetitive sequences, including the ribosomal RNA unit, and have quantified the major satellite DNA families. These genetic resources will facilitate the further investigations of genetic mechanisms responsible for the behavioural and morphological differences between these three species and other tephritids. We have also shown how whole genome sequence data can be used to generate simple diagnostic tests between very closely-related species where only one of the species is scaffolded.Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-1153) contains supplementary material, which is available to authorized users. 相似文献109.
Radu Popa 《Origins of life and evolution of the biosphere》2010,40(2):183-190
The criteria used for defining life are influenced by various philosophical visions about life, ranging from holism to reductionism
and from mechanistic-reductionism to vitalism. Using different scenarios about the origin and evolution of life as well as
properties of energy-dissipative systems, artificial life simulations and basic tenets of xenobiology, guidelines can be established
for formulating a definition of life. A definition of life is proposed that is parametric, non-Earth-centric, quantitative
and capable of discriminating ‘living entities’ from ‘life’. Living entities are defined as self-maintained systems, capable
of adaptive evolution individually, collectively or as a line of descend. Life is a broader concept indicating that the capacity
to express these attributes is either virtual or actual. At least four major phase transitions can be recognized during the
origin of life (reflexive activity; self-regulated homeostasis; the advent of informatons and the origin of adaptive evolution);
these make the origin and evolution of early life an example of ‘punctuated gradualism’. Such phase transitions can be used
to identify a boundary in early evolution where life began. This contribution identifies the step in the evolution of a dynamic
system when digital control of the system’s state becomes dominant over analogical control, and genetic information is irreversibly
used for adaptive evolution, as the boundary between non-living and living systems. 相似文献
110.
Sulfate reduction and S-oxidation in a moorland pool sediment 总被引:1,自引:2,他引:1
In an oligotrophic moorland pool in The Netherlands, S cycling near the sediment/water boundary was investigated by measuring (1) SO4
2– reduction rates in the sediment, (2) depletion of SO4
2– in the overlying water column and (3) release of35S from the sediment into the water column. Two locations differing in sediment type (highly organic and sandy) were compared, with respect to reduction rates and depletion of SO4
2– in the overlying water.Sulfate reduction rates in sediments of an oligotrophic moorland pool were estimated by diagenetic modelling and whole core35SO4
2– injection. Rates of SO4
2– consumption in the overlying water were estimated by changes in SO4
2– concentration over time in in situ enclosures. Reduction rates ranged from 0.27–11.2 mmol m–2 d–1. Rates of SO4
2– uptake from the enclosed water column varied from –0.5, –0.3 mmol m–2 d–1 (November) to 0.43–1.81 mmol m–2 d–1 (July, August and April). Maximum rates of oxidation to SO4
2– in July 1990 estimated by combination of SO4
2– reduction rates and rates of in situ SO4
2– uptake in the enclosed water column were 10.3 and 10.5 mmol m–2 d–1 at an organic rich and at a sandy site respectively.Experiments with35S2– and35SO4
2– tracer suggested (1) a rapid formation of organically bound S from dissimilatory reduced SO4
2– and (2) the presence of mainly non SO4
2–-S derived from reduced S transported from the sediment into the overlying water. A35S2– tracer experiment showed that about 7% of35S2– injected at 1 cm depth in a sediment core was recovered in the overlying water column.Sulfate reduction rates in sediments with higher volumetric mass fraction of organic matter did not significantly differ from those in sediments with a lower mass fraction of organic matter.Corresponding author 相似文献