Finite-size scaling considerations on the ground state microcanonical temperature in entropic sampling simulations

In this work we discuss the behavior of the microcanonical temperature $\frac{\partial S(E)}{\partial E}$ obtained by means of numerical entropic sampling studies. It is observed that in almost all cases the slope of the logarithm of the density of states $S(E)$ is not infinite in the ground state, since as expected it should be directly related to the inverse temperature $\frac{1}{T}$. Here we show that these finite slopes are in fact due to finite-size effects and we propose an analytic expression $a\ln(bL)$ for the behavior of $\frac{\varDelta S}{\varDelta E}$ when $L\rightarrow\infty$. To test this idea we use three distinct two-dimensional square lattice models presenting second-order phase transitions. We calculated by exact means the parameters $a$ and $b$ for the two-states Ising model and for the $q=3$ and $4$ states Potts model and compared with the results obtained by entropic sampling simulations. We found an excellent agreement between exact and numerical values. We argue that this new set of parameters $a$ and $b$ represents an interesting novel issue of investigation in entropic sampling studies for different models

Gevrey local solvability in locally integrable structures

We consider a locally integrable real-analytic structure, and we investigate the local solvability in the category of Gevrey functions and ultradistributions of the complex d' naturally induced by the de Rham complex. We prove that the so-called condition Y(q) on the signature of the Levi form, for local solvability of d' u=f, is still necessary even if we take f in the classes of Gevrey functions and look for solutions u in the corresponding spaces of ultradistributions.Comment: 12 page

Measuring maternal mortality : an overview of opportunities and options for developing countries

Background:There is currently an unprecedented expressed need and demand for estimates of maternal mortality in developing countries. This has been stimulated in part by the creation of a Millennium Development Goal that will be judged partly on the basis of reductions in maternal mortality by 2015. Methods: Since the launch of the Safe Motherhood Initiative in 1987, new opportunities for data capture have arisen and new methods have been developed, tested and used. This paper provides a pragmatic overview of these methods and the optimal measurement strategies for different developing country contexts. Results: There are significant recent advances in the measurement of maternal mortality, yet also room for further improvement, particularly in assessing the magnitude and direction of biases and their implications for different data uses. Some of the innovations in measurement provide efficient mechanisms for gathering the requisite primary data at a reasonably low cost. No method, however, has zero costs. Investment is needed in measurement strategies for maternal mortality suited to the needs and resources of a country, and which also strengthen the technical capacity to generate and use credible estimates. Conclusion: Ownership of information is necessary for it to be acted upon: what you count is what you do. Difficulties with measurement must not be allowed to discourage efforts to reduce maternal mortality. Countries must be encouraged and enabled to count maternal deaths and act.WJG is funded partially by the University of Aberdeen. OMRC is partially funded by the London School of Hygiene and Tropical Medicine. CS and SA are partially funded by Johns Hopkins University. CAZ is funded by the Health Metrics Network at the World Health Organization. WJG, OMRC, CS and SA are also partially supported through an international research program, Immpact, funded by the Bill & Melinda Gates Foundation, the Department for International Development, the European Commission and USAID

Initial results of multilevel principal components analysis of facial shape

Traditionally, active shape models (ASMs) do not make a distinction between groups in the subject population and they rely on methods such as (single-level) principal components analysis (PCA). Multilevel principal components analysis (PCA) allows one to model between-group effects and within-group effects explicitly. Three dimensional (3D) laser scans were taken from 240 subjects (38 Croatian female, 35 Croatian male, 40 English female, 40 English male, 23 Welsh female, 27 Welsh male, 23 Finnish female, and 24 Finnish male) and 21 landmark points were created subsequently for each scan. After Procrustes transformation, eigenvalues from mPCA and from single-level PCA based on these points were examined. mPCA indicated that the first two eigenvalues of largest magnitude related to within-groups components, but that the next largest eigenvalue related to between-groups components. Eigenvalues from single-level PCA always had a larger magnitude than either within-group or between-group eigenvectors at equivalent eigenvalue number. An examination of the first mode of variation indicated possible mixing of between-group and within-group effects in single-level PCA. Component scores for mPCA indicated clustering with country and gender for the between-groups components (as ex-pected), but not for the within-group terms (also as expected). Clustering of component scores for single-level PCA was harder to resolve. In conclusion, mPCA is viable method of forming shape models that offers distinct advantages over single-level PCA when groups occur naturally in the subject population

The inevitable youthfulness of known high-redshift radio galaxies

Radio galaxies can be seen out to very high redshifts, where in principle they can serve as probes of the early evolution of the Universe. Here we show that for any model of radio-galaxy evolution in which the luminosity decreases with time after an initial rapid increase (that is, essentially all reasonable models), all observable high-redshift radio-galaxies must be seen when the lobes are less than 10^7 years old. This means that high-redshift radio galaxies can be used as a high-time-resolution probe of evolution in the early Universe. Moreover, this result helps to explain many observed trends of radio-galaxy properties with redshift [(i) the `alignment effect' of optical emission along radio-jet axes, (ii) the increased distortion in radio structure, (iii) the decrease in physical sizes, (iv) the increase in radio depolarisation, and (v) the increase in dust emission] without needing to invoke explanations based on cosmology or strong evolution of the surrounding intergalactic medium with cosmic time, thereby avoiding conflict with current theories of structure formation.Comment: To appear in Nature. 4 pages, 2 colour figures available on request. Also available at http://www-astro.physics.ox.ac.uk/~km

<i>Albugo candida</i> race diversity, ploidy and host-associated microbes revealed using DNA sequence capture on diseased plants in the field

• Physiological races of the oomycete Albugo candida are biotrophic pathogens of diverse plant species, primarily the Brassicaceae, and cause infections that suppress host immunity to other pathogens. However, A. candida race diversity and the consequences of host immunosuppression are poorly understood in the field. • We report a method that enables sequencing of DNA of plant pathogens and plant-associated microbes directly from field samples (Pathogen Enrichment Sequencing: PenSeq). We apply this method to explore race diversity in A. candida and to detect A. candida-associated microbes in the field (91 A. candida-infected plants).• We show with unprecedented resolution that each host plant species supports colonization by one of 17 distinct phylogenetic lineages, each with an unique repertoire of effector candidate alleles. These data reveal the crucial role of sexual and asexual reproduction, polyploidy and host domestication in A. candida specialization on distinct plant species. Our bait design also enabled phylogenetic assignment of DNA sequences from bacteria and fungi from plants in the field.• This paper shows that targeted sequencing has a great potential for the study of pathogen populations while they are colonizing their hosts. This method could be applied to other microbes, especially to those that cannot be cultured

Responses of marine benthic microalgae to elevated CO<inf>2</inf>

Increasing anthropogenic CO2 emissions to the atmosphere are causing a rise in pCO2 concentrations in the ocean surface and lowering pH. To predict the effects of these changes, we need to improve our understanding of the responses of marine primary producers since these drive biogeochemical cycles and profoundly affect the structure and function of benthic habitats. The effects of increasing CO2 levels on the colonisation of artificial substrata by microalgal assemblages (periphyton) were examined across a CO2 gradient off the volcanic island of Vulcano (NE Sicily). We show that periphyton communities altered significantly as CO2 concentrations increased. CO2 enrichment caused significant increases in chlorophyll a concentrations and in diatom abundance although we did not detect any changes in cyanobacteria. SEM analysis revealed major shifts in diatom assemblage composition as CO2 levels increased. The responses of benthic microalgae to rising anthropogenic CO2 emissions are likely to have significant ecological ramifications for coastal systems. © 2011 Springer-Verlag

Robust estimation of microbial diversity in theory and in practice

Quantifying diversity is of central importance for the study of structure, function and evolution of microbial communities. The estimation of microbial diversity has received renewed attention with the advent of large-scale metagenomic studies. Here, we consider what the diversity observed in a sample tells us about the diversity of the community being sampled. First, we argue that one cannot reliably estimate the absolute and relative number of microbial species present in a community without making unsupported assumptions about species abundance distributions. The reason for this is that sample data do not contain information about the number of rare species in the tail of species abundance distributions. We illustrate the difficulty in comparing species richness estimates by applying Chao's estimator of species richness to a set of in silico communities: they are ranked incorrectly in the presence of large numbers of rare species. Next, we extend our analysis to a general family of diversity metrics ("Hill diversities"), and construct lower and upper estimates of diversity values consistent with the sample data. The theory generalizes Chao's estimator, which we retrieve as the lower estimate of species richness. We show that Shannon and Simpson diversity can be robustly estimated for the in silico communities. We analyze nine metagenomic data sets from a wide range of environments, and show that our findings are relevant for empirically-sampled communities. Hence, we recommend the use of Shannon and Simpson diversity rather than species richness in efforts to quantify and compare microbial diversity.Comment: To be published in The ISME Journal. Main text: 16 pages, 5 figures. Supplement: 16 pages, 4 figure

High-throughput UHPLC/MS/MS-based metabolic profiling using a vacuum jacketed column

In UHPLC, frictional heating from the eluent flowing through the column at pressures of ca. 10–15 Kpsi causes radial diffusion via temperature differences between the center of the column and its walls. Longitudinal dispersion also occurs due to temperature gradients between the inlet and outlet. These effects cause band broadening but can be mitigated via a combination of vacuum jacketed stainless steel tubing, reduced column end nut mass, and a constant temperature in the column from heating the inlet fitting. Here, vacuum jacketed column (VJC) technology, employing a novel column housing located on the source of the mass spectrometer and minimized tubing from the column outlet to the electrospray probe, was applied to profiling metabolites in urine. For a 75 s reversed-phase gradient separation, the average peak widths for endogenous compounds in urine were 1.2 and 0.6 s for conventional LC/MS and VJC systems, respectively. The peak tailing factor was reduced from 1.25 to 1.13 when using the VJC system compared to conventional UHPLC, and the peak capacity increased from 65 to 120, with a 25% increase in features detected in urine. The increased resolving power of the VJC system reduced co-elution, simplifying MS and MS/MS spectra, providing a more confident metabolite identification. The increased LC performance also gave more intense MS peaks, with a 10–120% increase in response, improving the quality of the MS data and detection limits. Reducing the LC gradient duration to 37 s gave peak widths of ca. 0.4 s and a peak capacity of 84