The role of galaxies and AGN in reionising the IGM -- III : IGM-galaxy cross-correlations at z~6 from 8 quasar fields with DEIMOS and MUSE

We present improved results of the measurement of the correlation between galaxies and the intergalactic medium transmission at the end of reionization. We have gathered a sample of 13 spectroscopically confirmed Lyman-break galaxies (LBGs) and 21 Lyman-α emitters (LAEs) at angular separations 20 arcsec ≲ θ ≲ 10 arcmin (∼0.1–4 pMpc at z ∼ 6) from the sightlines to eight background z ≳ 6 quasars. We report for the first time the detection of an excess of Lyman-α transmission spikes at ∼10–60 cMpc from LAEs (3.2σ) and LBGs (1.9σ). We interpret the data with an improved model of the galaxy–Lyman-α transmission and two-point cross-correlations, which includes the enhanced photoionization due to clustered faint sources, enhanced gas densities around the central bright objects and spatial variations of the mean free path. The observed LAE(LBG)–Lyman-α transmission spike two-point cross-correlation function (2PCCF) constrains the luminosity-averaged escape fraction of all galaxies contributing to reionization to ⟨fesc⟩MUV−20(2σ)⁠) is necessary to reproduce the observed 2PCCF and that reionization might be driven by different sub-populations around LBGs and LAEs at z ∼ 6

Genome-Wide Comparative Gene Family Classification

Correct classification of genes into gene families is important for understanding gene function and evolution. Although gene families of many species have been resolved both computationally and experimentally with high accuracy, gene family classification in most newly sequenced genomes has not been done with the same high standard. This project has been designed to develop a strategy to effectively and accurately classify gene families across genomes. We first examine and compare the performance of computer programs developed for automated gene family classification. We demonstrate that some programs, including the hierarchical average-linkage clustering algorithm MC-UPGMA and the popular Markov clustering algorithm TRIBE-MCL, can reconstruct manual curation of gene families accurately. However, their performance is highly sensitive to parameter setting, i.e. different gene families require different program parameters for correct resolution. To circumvent the problem of parameterization, we have developed a comparative strategy for gene family classification. This strategy takes advantage of existing curated gene families of reference species to find suitable parameters for classifying genes in related genomes. To demonstrate the effectiveness of this novel strategy, we use TRIBE-MCL to classify chemosensory and ABC transporter gene families in C. elegans and its four sister species. We conclude that fully automated programs can establish biologically accurate gene families if parameterized accordingly. Comparative gene family classification finds optimal parameters automatically, thus allowing rapid insights into gene families of newly sequenced species

Fluids in cosmology

We review the role of fluids in cosmology by first introducing them in General Relativity and then by applying them to a FRW Universe's model. We describe how relativistic and non-relativistic components evolve in the background dynamics. We also introduce scalar fields to show that they are able to yield an inflationary dynamics at very early times (inflation) and late times (quintessence). Then, we proceed to study the thermodynamical properties of the fluids and, lastly, its perturbed kinematics. We make emphasis in the constrictions of parameters by recent cosmological probes.Comment: 34 pages, 4 figures, version accepted as invited review to the book "Computational and Experimental Fluid Mechanics with Applications to Physics, Engineering and the Environment". Version 2: typos corrected and references expande

Effect of inhomogeneity of the Universe on a gravitationally bound local system: A no-go result for explaining the secular increase in the astronomical unit

We will investigate the influence of the inhomogeneity of the universe, especially that of the Lema{\^i}tre-Tolman-Bondi (LTB) model, on a gravitationally bound local system such as the solar system. We concentrate on the dynamical perturbation to the planetary motion and derive the leading order effect generated from the LTB model. It will be shown that there appear not only a well-known cosmological effect arisen from the homogeneous and isotropic model, such as the Robertson-Walker (RW) model, but also the additional terms due to the radial inhomogeneity of the LTB model. We will also apply the obtained results to the problem of secular increase in the astronomical unit, reported by Krasinsky and Brumberg (2004), and imply that the inhomogeneity of the universe cannot have a significant effect for explaining the observed $d{\rm AU}/dt = 15 \pm 4 ~{\rm [m/century]}$.Comment: 12 pages, no figure, accepted for publication in Journal of Astrophysics and Astronom

Endocrine therapy for breast cancer: a model of hormonal manipulation

Oestrogen receptor (ER) is the driving transcription factor in 70% of breast cancer. Endocrine therapies targeting the ER represent one of the most successful anticancer strategies to date. In the clinic, novel targeted agents are now being exploited in combination with established endocrine therapies to maximise efficacy. However, clinicians must balance this gain against the risk to patients of increased side effects with combination therapies. This article provides a succinct outline of the principles of hormonal manipulation in breast cancer, alongside the key evidence that underpins current clinical practice. As the role of endocrine therapy in breast cancer continues to expand, the challenge is to interpret the data and select the optimal strategy for a given clinical scenario

Tumor markers in breast cancer - European Group on Tumor Markers recommendations

Recommendations are presented for the routine clinical use of serum and tissue-based markers in the diagnosis and management of patients with breast cancer. Their low sensitivity and specificity preclude the use of serum markers such as the MUC-1 mucin glycoproteins ( CA 15.3, BR 27.29) and carcinoembryonic antigen in the diagnosis of early breast cancer. However, serial measurement of these markers can result in the early detection of recurrent disease as well as indicate the efficacy of therapy. Of the tissue-based markers, measurement of estrogen and progesterone receptors is mandatory in the selection of patients for treatment with hormone therapy, while HER-2 is essential in selecting patients with advanced breast cancer for treatment with Herceptin ( trastuzumab). Urokinase plasminogen activator and plasminogen activator inhibitor 1 are recently validated prognostic markers for lymph node-negative breast cancer patients and thus may be of value in selecting node-negative patients that do not require adjuvant chemotherapy. Copyright (C) 2005 S. Karger AG, Basel

Widespread horizontal transfer of mitochondrial genes in flowering plants

Horizontal gene transfer - the exchange of genes across mating barriers - is recognized as a major force in bacterial evolution(1,2). However, in eukaryotes it is prevalent only in certain phagotrophic protists and limited largely to the ancient acquisition of bacterial genes(3-5). Although the human genome was initially reported(6) to contain over 100 genes acquired during vertebrate evolution from bacteria, this claim was immediately and repeatedly rebutted(7,8). Moreover, horizontal transfer is unknown within the evolution of animals, plants and fungi except in the special context of mobile genetic elements(9-12). Here we show, however, that standard mitochondrial genes, encoding ribosomal and respiratory proteins, are subject to evolutionarily frequent horizontal transfer between distantly related flowering plants. These transfers have created a variety of genomic outcomes, including gene duplication, recapture of genes lost through transfer to the nucleus, and chimaeric, half-monocot, half-dicot genes. These results imply the existence of mechanisms for the delivery of DNA between unrelated plants, indicate that horizontal transfer is also a force in plant nuclear genomes, and are discussed in the contexts of plant molecular phylogeny and genetically modified plants.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/62688/1/nature01743.pd

The Universal Plausibility Metric (UPM) & Principle (UPP)

<p>Abstract</p> <p>Background</p> <p>Mere possibility is not an adequate basis for asserting scientific plausibility. A precisely defined universal bound is needed beyond which the assertion of <it>plausibility</it>, particularly in life-origin models, can be considered operationally falsified. But can something so seemingly relative and subjective as plausibility ever be quantified? Amazingly, the answer is, "Yes." A method of objectively measuring the plausibility of any chance hypothesis (The Universal Plausibility Metric [UPM]) is presented. A numerical inequality is also provided whereby any chance hypothesis can be definitively falsified when its UPM metric of ξ is < 1 (The Universal Plausibility Principle [UPP]). Both UPM and UPP pre-exist and are independent of any experimental design and data set.</p> <p>Conclusion</p> <p>No low-probability hypothetical plausibility assertion should survive peer-review without subjection to the UPP inequality standard of formal falsification (ξ < 1).</p

A review of elliptical and disc galaxy structure, and modern scaling laws

A century ago, in 1911 and 1913, Plummer and then Reynolds introduced their models to describe the radial distribution of stars in `nebulae'. This article reviews the progress since then, providing both an historical perspective and a contemporary review of the stellar structure of bulges, discs and elliptical galaxies. The quantification of galaxy nuclei, such as central mass deficits and excess nuclear light, plus the structure of dark matter halos and cD galaxy envelopes, are discussed. Issues pertaining to spiral galaxies including dust, bulge-to-disc ratios, bulgeless galaxies, bars and the identification of pseudobulges are also reviewed. An array of modern scaling relations involving sizes, luminosities, surface brightnesses and stellar concentrations are presented, many of which are shown to be curved. These 'redshift zero' relations not only quantify the behavior and nature of galaxies in the Universe today, but are the modern benchmark for evolutionary studies of galaxies, whether based on observations, N-body-simulations or semi-analytical modelling. For example, it is shown that some of the recently discovered compact elliptical galaxies at 1.5 < z < 2.5 may be the bulges of modern disc galaxies.Comment: Condensed version (due to Contract) of an invited review article to appear in "Planets, Stars and Stellar Systems"(www.springer.com/astronomy/book/978-90-481-8818-5). 500+ references incl. many somewhat forgotten, pioneer papers. Original submission to Springer: 07-June-201