Six simple guidelines for introducing new genera of fungi

We formulate five guidelines for introducing new genera, plus one recommendation how to publish the results of scientific research. We recommend that reviewers and editors adhere to these guidelines. We propose that the underlying research is solid, and that the results and the final solutions are properly discussed. The six criteria are: (1) all genera that are recognized should be monophyletic; (2) the coverage of the phylogenetic tree should be wide in number of species, geographic coverage, and type species of the genera under study; (3) the branching of the phylogenetic trees has to have sufficient statistical support; (4) different options for the translation of the phylogenetic tree into a formal classification should be discussed and the final decision justified; (5) the phylogenetic evidence should be based on more than one gene; and (6) all supporting evidence and background information should be included in the publication in which the new taxa are proposed, and this publication should be peer-reviewed

Cross sections for geodesic flows and \alpha-continued fractions

We adjust Arnoux's coding, in terms of regular continued fractions, of the geodesic flow on the modular surface to give a cross section on which the return map is a double cover of the natural extension for the \alpha-continued fractions, for each $\alpha$ in (0,1]. The argument is sufficiently robust to apply to the Rosen continued fractions and their recently introduced \alpha-variants.Comment: 20 pages, 2 figure

A systematic variation of the stellar initial mass function in early-type galaxies

Much of our knowledge of galaxies comes from analysing the radiation emitted by their stars. It depends on the stellar initial mass function (IMF) describing the distribution of stellar masses when the population formed. Consequently knowledge of the IMF is critical to virtually every aspect of galaxy evolution. More than half a century after the first IMF determination, no consensus has emerged on whether it is universal in different galaxies. Previous studies indicated that the IMF and the dark matter fraction in galaxy centres cannot be both universal, but they could not break the degeneracy between the two effects. Only recently indications were found that massive elliptical galaxies may not have the same IMF as our Milky Way. Here we report unambiguous evidence for a strong systematic variation of the IMF in early-type galaxies as a function of their stellar mass-to-light ratio, producing differences up to a factor of three in mass. This was inferred from detailed dynamical models of the two-dimensional stellar kinematics for the large Atlas3D representative sample of nearby early-type galaxies spanning two orders of magnitude in stellar mass. Our finding indicates that the IMF depends intimately on a galaxy's formation history.Comment: 4 pages, 2 figures, LaTeX. Accepted for publication as a Nature Letter. More information about our Atlas3D project is available at http://purl.org/atlas3

A Search for Correlation of Ultra-High Energy Cosmic Rays with IRAS-PSCz and 2MASS-6dF Galaxies

We study the arrival directions of 69 ultra-high energy cosmic rays (UHECRs) observed at the Pierre Auger Observatory (PAO) with energies exceeding 55 EeV. We investigate whether the UHECRs exhibit the anisotropy signal expected if the primary particles are protons that originate in galaxies in the local universe, or in sources correlated with these galaxies. We cross-correlate the UHECR arrival directions with the positions of IRAS-PSCz and 2MASS-6dF galaxies taking into account particle energy losses during propagation. This is the first time that the 6dF survey is used in a search for the sources of UHECRs and the first time that the PSCz survey is used with the full 69 PAO events. The observed cross-correlation signal is larger for the PAO UHECRs than for 94% (98%) of realisations from an isotropic distribution when cross-correlated with the PSCz (6dF). On the other hand the observed cross-correlation signal is lower than that expected from 85% of realisations, had the UHECRs originated in galaxies in either survey. The observed cross-correlation signal does exceed that expected by 50% of the realisations if the UHECRs are randomly deflected by intervening magnetic fields by 5 degrees or more. We propose a new method of analysing the expected anisotropy signal, by dividing the predicted UHECR source distribution into equal predicted flux radial shells, which can help localise and constrain the properties of UHECR sources. We find that the 69 PAO events are consistent with isotropy in the nearest of three shells we define, whereas there is weak evidence for correlation with the predicted source distribution in the two more distant shells in which the galaxy distribution is less anisotropic.Comment: 23 pages, version published in JCA

Homophily and Contagion Are Generically Confounded in Observational Social Network Studies

We consider processes on social networks that can potentially involve three factors: homophily, or the formation of social ties due to matching individual traits; social contagion, also known as social influence; and the causal effect of an individual's covariates on their behavior or other measurable responses. We show that, generically, all of these are confounded with each other. Distinguishing them from one another requires strong assumptions on the parametrization of the social process or on the adequacy of the covariates used (or both). In particular we demonstrate, with simple examples, that asymmetries in regression coefficients cannot identify causal effects, and that very simple models of imitation (a form of social contagion) can produce substantial correlations between an individual's enduring traits and their choices, even when there is no intrinsic affinity between them. We also suggest some possible constructive responses to these results.Comment: 27 pages, 9 figures. V2: Revised in response to referees. V3: Ditt

Time Dynamics of Self-Pumped Reflection Gratings in a Photorefractive Polymer

The time dynamics of self-pumped reflection gratings in a commonly used photorefractive polymer PDCST:PVK:ECZ-BBP:C60 with no additional electron sources or traps is investigated. While holes are normally the mobile charges and responsible for grating formation, our experimental observations, analyzed using multi-exponential fitting curves, show evidence of electrons in addition to holes as charge carriers, particularly above an applied field of 40 V/μm. The dependence of effective carrier mobilities on the applied electric field, deduced from experimental results, show stronger field dependence of electron mobility at high electric fields. At an applied field of 70 V/μm, electron and hole mobilities become approximately equal, and the contribution of electrons on grating formation becomes significant

Zero temperature string breaking in lattice quantum chromodynamics

The separation of a heavy quark and antiquark pair leads to the formation of a tube of flux, or "string", which should break in the presence of light quark-antiquark pairs. This expected zero-temperature phenomenon has proven elusive in simulations of lattice QCD. We study mixing between the string state and the two-meson decay channel in QCD with two flavors of dynamical sea quarks. We confirm that mixing is weak and find that it decreases at level crossing. While our study does not show direct effects of internal quark loops, our results, combined with unitarity, give clear confirmation of string breaking.Comment: 20 pages, 7 figures. With small clarifications and two additions to references. Submitted to Phys. Rev.

Neuroendocrine abnormalities in Parkinson's disease.

Neuroendocrine abnormalities are common in Parkinson's disease (PD) and include disruption of melatonin secretion, disturbances of glucose, insulin resistance and bone metabolism, and body weight changes. They have been associated with multiple non-motor symptoms in PD and have important clinical consequences, including therapeutics. Some of the underlying mechanisms have been implicated in the pathogenesis of PD and represent promising targets for the development of disease biomarkers and neuroprotective therapies. In this systems-based review, we describe clinically relevant neuroendocrine abnormalities in Parkinson's disease to highlight their role in overall phenotype. We discuss pathophysiological mechanisms, clinical implications, and pharmacological and non-pharmacological interventions based on the current evidence. We also review recent advances in the field, focusing on the potential targets for development of neuroprotective drugs in Parkinson's disease and suggest future areas for research

Definition of the σW regulon of Bacillus subtilis in the absence of stress

Bacteria employ extracytoplasmic function (ECF) sigma factors for their responses to environmental stresses. Despite intensive research, the molecular dissection of ECF sigma factor regulons has remained a major challenge due to overlaps in the ECF sigma factor-regulated genes and the stimuli that activate the different ECF sigma factors. Here we have employed tiling arrays to single out the ECF σW regulon of the Gram-positive bacterium Bacillus subtilis from the overlapping ECF σX, σY, and σM regulons. For this purpose, we profiled the transcriptome of a B. subtilis sigW mutant under non-stress conditions to select candidate genes that are strictly σW-regulated. Under these conditions, σW exhibits a basal level of activity. Subsequently, we verified the σW-dependency of candidate genes by comparing their transcript profiles to transcriptome data obtained with the parental B. subtilis strain 168 grown under 104 different conditions, including relevant stress conditions, such as salt shock. In addition, we investigated the transcriptomes of rasP or prsW mutant strains that lack the proteases involved in the degradation of the σW anti-sigma factor RsiW and subsequent activation of the σW-regulon. Taken together, our studies identify 89 genes as being strictly σW-regulated, including several genes for non-coding RNAs. The effects of rasP or prsW mutations on the expression of σW-dependent genes were relatively mild, which implies that σW-dependent transcription under non-stress conditions is not strictly related to RasP and PrsW. Lastly, we show that the pleiotropic phenotype of rasP mutant cells, which have defects in competence development, protein secretion and membrane protein production, is not mirrored in the transcript profile of these cells. This implies that RasP is not only important for transcriptional regulation via σW, but that this membrane protease also exerts other important post-transcriptional regulatory functions