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  • 1
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    Path-integral evidence (2015)
    Oxford University Press
    Details
    Publication Date: 2015-07-16
    Description: Here we present a Bayesian formalism for the goodness of fit that is the evidence for a fixed functional form over the evidence for all functions that are a general perturbation about this form. This is done under the assumption that the statistical properties of the data can be modelled by a multivariate Gaussian distribution. We use this to show how one can optimize an experiment to find evidence for a fixed function over perturbations about this function. We apply this formalism to an illustrative problem of measuring perturbations in the dark energy equation of state about a cosmological constant.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 2
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    On scale-dependent cosmic shear systematic effects (2015)
    Oxford University Press
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    Publication Date: 2015-12-01
    Description: In this paper, we investigate the impact that realistic scale-dependent systematic effects may have on cosmic shear tomography. We model spatially varying residual galaxy ellipticity and galaxy size variations in weak lensing measurements and propagate these through to predicted changes in the uncertainty and bias of cosmological parameters. We show that the survey strategy – whether it is regular or randomized – is an important factor in determining the impact of a systematic effect: a purely randomized survey strategy produces the smallest biases, at the expense of larger parameter uncertainties, and a very regularized survey strategy produces large biases, but unaffected uncertainties. However, by removing, or modelling, the affected scales (-modes) in the regular cases the biases are reduced to negligible levels. We find that the integral of the systematic power spectrum is not a good metric for dark energy performance, and we advocate that systematic effects should be modelled accurately in real space, where they enter the measurement process, and their effect subsequently propagated into power spectrum contributions.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 3
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    Endemism and convergence across the mycobiome [Ecology] (2014)
    National Academy of Sciences
    Details
    Publication Date: 2014-04-30
    Description: Identifying the ecological processes that structure communities and the consequences for ecosystem function is a central goal of ecology. The recognition that fungi, bacteria, and viruses control key ecosystem functions has made microbial communities a major focus of this field. Because many ecological processes are apparent only at particular spatial...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 4
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    On the cross-section of dark matter using substructure infall into galaxy clusters (2014)
    Oxford University Press
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    Publication Date: 2014-04-27
    Description: We develop a statistical method to measure the interaction cross-section of dark matter, exploiting the continuous minor merger events in which small substructures fall into galaxy clusters. We find that by taking the ratio of the distances between the galaxies and dark matter, and galaxies and gas in accreting subhaloes, we form a quantity that can be statistically averaged over a large sample of systems whilst removing any inherent line-of-sight projections. To interpret this ratio as a cross-section of dark matter, we derive an analytical description of subhalo infall allowing us to constrain self-interaction models in which drag is an appropriate macroscopic treatment. We create mock observations from cosmological simulations of structure formation and find that collisionless dark matter becomes physically separated from X-ray gas by up to ~20 h –1  kpc. Adding realistic levels of noise, we are able to predict achievable constraints from observational data. Current archival data should be able to detect a difference in the dynamical behaviour of dark matter and standard model particles at 6, and measure the total interaction cross-section / m with 68 per cent confidence limits of ±1 cm 2 g –1 . We note that this method is not restricted by the limited number of major merging events and is easily extended to large samples of clusters from future surveys which could potentially push statistical errors to 〈0.1 cm 2  g –1 .
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 5
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    Construction and analysis of a human-chimpanzee comparative clone map (2002)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2002-01-05
    Description: The recently released human genome sequences provide us with reference data to conduct comparative genomic research on primates, which will be important to understand what genetic information makes us human. Here we present a first-generation human-chimpanzee comparative genome map and its initial analysis. The map was constructed through paired alignment of 77,461 chimpanzee bacterial artificial chromosome end sequences with publicly available human genome sequences. We detected candidate positions, including two clusters on human chromosome 21 that suggest large, nonrandom regions of difference between the two genomes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fujiyama, Asao -- Watanabe, Hidemi -- Toyoda, Atsushi -- Taylor, Todd D -- Itoh, Takehiko -- Tsai, Shih-Feng -- Park, Hong-Seog -- Yaspo, Marie-Laure -- Lehrach, Hans -- Chen, Zhu -- Fu, Gang -- Saitou, Naruya -- Osoegawa, Kazutoyo -- de Jong, Pieter J -- Suto, Yumiko -- Hattori, Masahira -- Sakaki, Yoshiyuki -- New York, N.Y. -- Science. 2002 Jan 4;295(5552):131-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan. afujiyam@gsc.riken.go.jp〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11778049" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Chromosomes, Artificial, Bacterial ; Chromosomes, Human, Pair 21/genetics ; Cloning, Molecular ; Contig Mapping ; Female ; Gene Library ; *Genome ; *Genome, Human ; Humans ; Male ; Pan troglodytes/*genetics ; *Physical Chromosome Mapping ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Tagged Sites ; X Chromosome/genetics ; Y Chromosome/genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 6
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    Genome of an endosymbiont coupling N2 fixation to cellulolysis within protist cells in termite gut (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-11-15
    Description: Termites harbor diverse symbiotic gut microorganisms, the majority of which are as yet uncultivable and their interrelationships unclear. Here, we present the complete genome sequence of the uncultured Bacteroidales endosymbiont of the cellulolytic protist Pseudotrichonympha grassii, which accounts for 70% of the bacterial cells in the gut of the termite Coptotermes formosanus. Functional annotation of the chromosome (1,114,206 base pairs) unveiled its ability to fix dinitrogen and recycle putative host nitrogen wastes for biosynthesis of diverse amino acids and cofactors, and import glucose and xylose as energy and carbon sources. Thus, nitrogen fixation and cellulolysis are coupled within the protist's cells. This highly evolved symbiotic system probably underlies the ability of the worldwide pest termites Coptotermes to use wood as their sole food.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hongoh, Yuichi -- Sharma, Vineet K -- Prakash, Tulika -- Noda, Satoko -- Toh, Hidehiro -- Taylor, Todd D -- Kudo, Toshiaki -- Sakaki, Yoshiyuki -- Toyoda, Atsushi -- Hattori, Masahira -- Ohkuma, Moriya -- New York, N.Y. -- Science. 2008 Nov 14;322(5904):1108-9. doi: 10.1126/science.1165578.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Ecomolecular Biorecycling Science Research Team, RIKEN Advanced Science Institute, Saitama 351-0198, Japan. yhongo@riken.jp〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19008447" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acids/metabolism ; Animals ; Bacteroidetes/classification/*genetics/isolation & purification/metabolism ; Cellulose/*metabolism ; Chromosomes, Bacterial/genetics ; Digestive System/metabolism/microbiology/parasitology ; Eukaryota/isolation & purification/metabolism/*microbiology ; Fermentation ; Genes, Bacterial ; *Genome, Bacterial ; Glycolysis ; Isoptera/metabolism/*microbiology/parasitology ; Metabolic Networks and Pathways ; Molecular Sequence Data ; Monosaccharides/metabolism ; *Nitrogen Fixation/genetics ; Oxidoreductases/genetics ; Phylogeny ; *Symbiosis ; Wood/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 7
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    Bifidobacteria can protect from enteropathogenic infection through production of acetate (2011)
    Nature Publishing Group (NPG)
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    Publication Date: 2011-01-29
    Description: The human gut is colonized with a wide variety of microorganisms, including species, such as those belonging to the bacterial genus Bifidobacterium, that have beneficial effects on human physiology and pathology. Among the most distinctive benefits of bifidobacteria are modulation of host defence responses and protection against infectious diseases. Nevertheless, the molecular mechanisms underlying these effects have barely been elucidated. To investigate these mechanisms, we used mice associated with certain bifidobacterial strains and a simplified model of lethal infection with enterohaemorrhagic Escherichia coli O157:H7, together with an integrated 'omics' approach. Here we show that genes encoding an ATP-binding-cassette-type carbohydrate transporter present in certain bifidobacteria contribute to protecting mice against death induced by E. coli O157:H7. We found that this effect can be attributed, at least in part, to increased production of acetate and that translocation of the E. coli O157:H7 Shiga toxin from the gut lumen to the blood was inhibited. We propose that acetate produced by protective bifidobacteria improves intestinal defence mediated by epithelial cells and thereby protects the host against lethal infection.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fukuda, Shinji -- Toh, Hidehiro -- Hase, Koji -- Oshima, Kenshiro -- Nakanishi, Yumiko -- Yoshimura, Kazutoshi -- Tobe, Toru -- Clarke, Julie M -- Topping, David L -- Suzuki, Tohru -- Taylor, Todd D -- Itoh, Kikuji -- Kikuchi, Jun -- Morita, Hidetoshi -- Hattori, Masahira -- Ohno, Hiroshi -- England -- Nature. 2011 Jan 27;469(7331):543-7. doi: 10.1038/nature09646.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory for Epithelial Immunobiology, RIKEN Research Center for Allergy and Immunology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21270894" target="_blank"〉PubMed〈/a〉
    Keywords: Acetates/*metabolism ; Animals ; Bifidobacterium/genetics/*metabolism ; Cercopithecus aethiops ; Escherichia coli Infections/microbiology/*prevention & control ; Escherichia coli O157/*physiology ; Gene Expression Profiling ; Genome, Bacterial ; Mice ; Molecular Sequence Data ; Vero Cells
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 8
    Electronic Resource
    Electronic Resource
    correction: The DNA sequence of human chromosome 21 (2000)
    [s.l.] : Macmillian Magazines Ltd.
    Nature 407 (2000), S. 110-110 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Nature 405, 311— 319; 2000. The name of one author, Y. Groner, was inadvertantly omitted from the author list but is included above. He is affiliated with the Department of Molecular Genetics and Human Genome Center, ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/35024135
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  • 9
    Electronic Resource
    Electronic Resource
    The DNA sequence of human chromosome 21 (2000)
    [s.l.] : Macmillian Magazines Ltd.
    Nature 405 (2000), S. 311-319 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Chromosome 21 is the smallest human autosome. An extra copy of chromosome 21 causes Down syndrome, the most frequent genetic cause of significant mental retardation, which affects up to 1 in 700 live births. Several anonymous loci for monogenic disorders and predispositions for common complex ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/35012518
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  • 10
    Electronic Resource
    Electronic Resource
    DNA sequence and comparative analysis of chimpanzee chromosome 22 (2004)
    [s.l.] : Macmillian Magazines Ltd.
    Nature 429 (2004), S. 382-388 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Human–chimpanzee comparative genome research is essential for narrowing down genetic changes involved in the acquisition of unique human features, such as highly developed cognitive functions, bipedalism or the use of complex language. Here, we report the high-quality DNA sequence of 33.3 ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/nature02564
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