Density-based hierarchical clustering of pyro-sequences on a large scale--the case of fungal ITS1.

MOTIVATION: Analysis of millions of pyro-sequences is currently playing a crucial role in the advance of environmental microbiology. Taxonomy-independent, i.e. unsupervised, clustering of these sequences is essential for the definition of Operational Taxonomic Units. For this application, reproducibility and robustness should be the most sought after qualities, but have thus far largely been overlooked. RESULTS: More than 1 million hyper-variable internal transcribed spacer 1 (ITS1) sequences of fungal origin have been analyzed. The ITS1 sequences were first properly extracted from 454 reads using generalized profiles. Then, otupipe, cd-hit-454, ESPRIT-Tree and DBC454, a new algorithm presented here, were used to analyze the sequences. A numerical assay was developed to measure the reproducibility and robustness of these algorithms. DBC454 was the most robust, closely followed by ESPRIT-Tree. DBC454 features density-based hierarchical clustering, which complements the other methods by providing insights into the structure of the data. AVAILABILITY: An executable is freely available for non-commercial users at ftp://ftp.vital-it.ch/tools/dbc454. It is designed to run under MPI on a cluster of 64-bit Linux machines running Red Hat 4.x, or on a multi-core OSX system. CONTACT: dbc454@vital-it.ch or nicolas.guex@isb-sib.ch.

The co-evolution of social institutions, demography, and large-scale human cooperation.

Human cooperation is typically coordinated by institutions, which determine the outcome structure of the social interactions individuals engage in. Explaining the Neolithic transition from small- to large-scale societies involves understanding how these institutions co-evolve with demography. We study this using a demographically explicit model of institution formation in a patch-structured population. Each patch supports both social and asocial niches. Social individuals create an institution, at a cost to themselves, by negotiating how much of the costly public good provided by cooperators is invested into sanctioning defectors. The remainder of their public good is invested in technology that increases carrying capacity, such as irrigation systems. We show that social individuals can invade a population of asocials, and form institutions that support high levels of cooperation. We then demonstrate conditions where the co-evolution of cooperation, institutions, and demographic carrying capacity creates a transition from small- to large-scale social groups.

The Empirical Forcing Function as a tool for the diagnosis of large-scale atmospheric anomalies

The time-mean quasi-geostrophic potential vorticity equation of the atmospheric flow on isobaric surfaces can explicitly include an atmospheric (internal) forcing term of the stationary-eddy flow. In fact, neglecting some non-linear terms in this equation, this forcing can be mathematically expressed as a single function, called Empirical Forcing Function (EFF), which is equal to the material derivative of the time-mean potential vorticity. Furthermore, the EFF can be decomposed as a sum of seven components, each one representing a forcing mechanism of different nature. These mechanisms include diabatic components associated with the radiative forcing, latent heat release and frictional dissipation, and components related to transient eddy transports of heat and momentum. All these factors quantify the role of the transient eddies in forcing the atmospheric circulation. In order to assess the relevance of the EFF in diagnosing large-scale anomalies in the atmospheric circulation, the relationship between the EFF and the occurrence of strong North Atlantic ridges over the Eastern North Atlantic is analyzed, which are often precursors of severe droughts over Western Iberia. For such events, the EFF pattern depicts a clear dipolar structure over the North Atlantic; cyclonic (anticyclonic) forcing of potential vorticity is found upstream (downstream) of the anomalously strong ridges. Results also show that the most significant components are related to the diabatic processes. Lastly, these results highlight the relevance of the EFF in diagnosing large-scale anomalies, also providing some insight into their interaction with different physical mechanisms.

Malaria diagnosis from pooled blood samples: comparative analysis of real-time PCR, nested PCR and immunoassay as a platform for the molecular and serological diagnosis of malaria on a large-scale

Malaria diagnoses has traditionally been made using thick blood smears, but more sensitive and faster techniques are required to process large numbers of samples in clinical and epidemiological studies and in blood donor screening. Here, we evaluated molecular and serological tools to build a screening platform for pooled samples aimed at reducing both the time and the cost of these diagnoses. Positive and negative samples were analysed in individual and pooled experiments using real-time polymerase chain reaction (PCR), nested PCR and an immunochromatographic test. For the individual tests, 46/49 samples were positive by real-time PCR, 46/49 were positive by nested PCR and 32/46 were positive by immunochromatographic test. For the assays performed using pooled samples, 13/15 samples were positive by real-time PCR and nested PCR and 11/15 were positive by immunochromatographic test. These molecular methods demonstrated sensitivity and specificity for both the individual and pooled samples. Due to the advantages of the real-time PCR, such as the fast processing and the closed system, this method should be indicated as the first choice for use in large-scale diagnosis and the nested PCR should be used for species differentiation. However, additional field isolates should be tested to confirm the results achieved using cultured parasites and the serological test should only be adopted as a complementary method for malaria diagnosis.

National and Gender Measurement Invariance of the Utrecht-Management of Identity Commitments Scale (U-MICS) : A 10-Nation Study With University Students

The purpose of this study was to examine the psychometric properties of the Utrecht-Management of Identity Commitments Scale (U-MICS), a self-report measure aimed at assessing identity processes of commitment, in-depth exploration, and reconsideration of commitment. We tested its factor structure in university students from a large array of cultural contexts, including 10 nations located in Europe (i.e., Italy, the Netherlands, Poland, Portugal, Romania, and Switzerland), Middle East (i.e., Turkey), and Asia (i.e., China, Japan, and Taiwan). Furthermore, we tested national and gender measurement invariance. Participants were 6,118 (63.2% females) university students aged from 18 to 25 years (Mage = 20.91 years). Results indicated that the three-factor structure of the U-MICS fitted well in the total sample, in each national group, and in gender groups. Furthermore, national and gender measurement invariance were established. Thus, the U-MICS can be fruitfully applied to study identity in university students from various Western and non-Western contexts.

Large-scale production and purification of recombinant protein from an insect cell/baculovirus system in Erlenmeyer flasks: application to the chicken poly(ADP-ribose) polymerase catalytic domain

A simple and inexpensive shaker/Erlenmeyer flask system for large-scale cultivation of insect cells is described and compared to a commercial spinner system. On the basis of maximum cell density, average population doubling time and overproduction of recombinant protein, a better result was obtained with a simpler and less expensive bioreactor consisting of Erlenmeyer flasks and an ordinary shaker waterbath. Routinely, about 90 mg of pure poly(ADP-ribose) polymerase catalytic domain was obtained for a total of 3 x 109 infected cells in three liters of culture

Factor structure of Bech's version of the Brief Psychiatric Rating Scale in Brazilian patients

The objective of the present study was to evaluate the factor structure of Bech's version of the Brief Psychiatric Rating Scale (BPRS), translated into Portuguese. The BPRS was administered to a heterogeneous group of psychiatric inpatients (N = 98) and outpatients (N = 62) in a University Hospital. Each patient was evaluated from one to eight times. The interval between consecutive interviews was one week for the inpatients and one month for the outpatients. The results were submitted to factorial analysis. The internal consistency of the total scale and of each factor was also estimated. Factorial analysis followed by normalized orthogonal rotation (Varimax) yielded four factors: Withdrawal-Retardation, Thinking Disorder, Anxious-Depression and Activation. Internal consistency measured by Cronbach's alpha coefficient ranged from 0.766 to 0.879. The data show that the factor structure of the present instrument is similar to that of the American version of the BPRS which contains 18 items, except for the absence of the fifth factor of the latter scale, Hostile-Suspiciousness.

Toward a combined seasonal weather and crop productivity forecasting system: Determination of the working spatial scale

A methodology is presented for the development of a combined seasonal weather and crop productivity forecasting system. The first stage of the methodology is the determination of the spatial scale(s) on which the system could operate; this determination has been made for the case of groundnut production in India. Rainfall is a dominant climatic determinant of groundnut yield in India. The relationship between yield and rainfall has been explored using data from 1966 to 1995. On the all-India scale, seasonal rainfall explains 52% of the variance in yield. On the subdivisional scale, correlations vary between variance r(2) = 0.62 (significance level p < 10(-4)) and a negative correlation with r(2) = 0.1 (p = 0.13). The spatial structure of the relationship between rainfall and groundnut yield has been explored using empirical orthogonal function (EOF) analysis. A coherent, large-scale pattern emerges for both rainfall and yield. On the subdivisional scale (similar to 300 km), the first principal component (PC) of rainfall is correlated well with the first PC of yield (r(2) = 0.53, p < 10(-4)), demonstrating that the large-scale patterns picked out by the EOFs are related. The physical significance of this result is demonstrated. Use of larger averaging areas for the EOF analysis resulted in lower and (over time) less robust correlations. Because of this loss of detail when using larger spatial scales, the subdivisional scale is suggested as an upper limit on the spatial scale for the proposed forecasting system. Further, district-level EOFs of the yield data demonstrate the validity of upscaling these data to the subdivisional scale. Similar patterns have been produced using data on both of these scales, and the first PCs are very highly correlated (r(2) = 0.96). Hence, a working spatial scale has been identified, typical of that used in seasonal weather forecasting, that can form the basis of crop modeling work for the case of groundnut production in India. Last, the change in correlation between yield and seasonal rainfall during the study period has been examined using seasonal totals and monthly EOFs. A further link between yield and subseasonal variability is demonstrated via analysis of dynamical data.

The impact of large scale atmospheric circulation patterns on wind power generation and its potential predictability: a case study over the UK

Over recent years there has been an increasing deployment of renewable energy generation technologies, particularly large-scale wind farms. As wind farm deployment increases, it is vital to gain a good understanding of how the energy produced is affected by climate variations, over a wide range of time-scales, from short (hours to weeks) to long (months to decades) periods. By relating wind speed at specific sites in the UK to a large-scale climate pattern (the North Atlantic Oscillation or "NAO"), the power generated by a modelled wind turbine under three different NAO states is calculated. It was found that the wind conditions under these NAO states may yield a difference in the mean wind power output of up to 10%. A simple model is used to demonstrate that forecasts of future NAO states can potentially be used to improve month-ahead statistical forecasts of monthly-mean wind power generation. The results confirm that the NAO has a significant impact on the hourly-, daily- and monthly-mean power output distributions from the turbine with important implications for (a) the use of meteorological data (e.g. their relationship to large scale climate patterns) in wind farm site assessment and, (b) the utilisation of seasonal-to-decadal climate forecasts to estimate future wind farm power output. This suggests that further research into the links between large-scale climate variability and wind power generation is both necessary and valuable.

The large-scale circulation change at the end of the Baiu season in Japan as seen in ERA40 data

The time evolution of the circulation change at the end of the Baiu season is investigated using ERA40 data. An end-day is defined for each of the 23 years based on the 850 hPa θe value at 40˚Nin the 130-140˚E sector exceeding 330 K. Daily time series of variables are composited with respect to this day. These composite time-series exhibit a clearer and more rapid change in the precipitation and the large-scale circulation over the whole East Asia region than those performed using calendar days. The precipitation change includes the abrupt end of the Baiu rain, the northward shift of tropical convection perhaps starting a few days before this, and the start of the heavier rain at higher latitudes. The northward migration of lower tropospheric warm, moist tropical air, a general feature of the seasonal march in the region, is fast over the continent and slow over the ocean. By mid to late July the cooler air over the Sea of Japan is surrounded on 3 sides by the tropical air. It is suggestive that the large-scale stage has been set for a jump to the post-Baiu state, i.e., for the end of the Baiu season. Two likely triggers for the actual change emerge from the analysis. The first is the northward movement of tropical convection into the Philippine region. The second is an equivalent barotropic Rossby wave-train, that over a 10-day period develops downstream across Eurasia. It appears likely that in most years one or both mechanisms can be important in triggering the actual end of the Baiu season.

Climate perspective on the large-scale circulation associated with the transition of the first South Atlantic hurricane

The landfall of Cyclone Catarina on the Brazilian coast in March 2004 became known as the first documented hurricane in the South Atlantic Ocean, promoting a new view oil how large-scale features can contribute to tropical transition. The aim of this paper is to put the large-scale circulation associated with Catarina`s transition in climate perspective. This is discussed in the light of a robust pattern of spatial correlations between thermodynamic and dynamic variables of importance for hurricane formation. A discussion on how transition mechanisms respond to the present-day circulation is presented. These associations help in understanding why Catarina was formed in a region previously thought to be hurricane-free. Catarina developed over a large-scale area of thermodynamically favourable air/sea temperature contrast. This aspect explains the paradox that such a rare system developed when the sea surface temperature was slightly below average. But, although thermodynamics played an important role, it is apparent that Catarina would not have formed without the key dynamic interplay triggered by a high latitude blocking. The blocking was associated with an extreme positive phase of the Southern Annular Mode (SAM) both hemispherically and locally, and the nearby area where Catarina developed is found to be more cyclonic during the positive phase of the SAM. A conceptual model is developed and a `South Atlantic index` is introduced as a useful diagnostic of potential conditions leading to tropical transition in the area, where large-scale indices indicate trends towards more favourable atmospheric conditions for tropical cyclone formation. Copyright (c) 2008 Royal Meteorological Society

Random primordial magnetic fields and the gas content of dark matter haloes

We recently predicted the existence of random primordial magnetic fields (RPMFs) in the form of randomly oriented cells with dipole-like structure with a cell size L(0) and an average magnetic field B(0). Here, we investigate models for primordial magnetic field with a similar web-like structure, and other geometries, differing perhaps in L(0) and B(0). The effect of RPMF on the formation of the first galaxies is investigated. The filtering mass, M(F), is the halo mass below which baryon accretion is severely depressed. We show that these RPMF could influence the formation of galaxies by altering the filtering mass and the baryon gas fraction of a halo, f(g). The effect is particularly strong in small galaxies. We find, for example, for a comoving B(0) = 0.1 mu G, and a reionization epoch that starts at z(s) = 11 and ends at z(e) = 8, for L(0) = 100 pc at z = 12, the f(g) becomes severely depressed for M < 10(7) M(circle dot), whereas for B(0) = 0 the f(g) becomes severely depressed only for much smaller masses, M < 10(5) M(circle dot). We suggest that the observation of M(F) and f(g) at high redshifts can give information on the intensity and structure of primordial magnetic fields.

Cosmic shear requirements on the wavelength dependence of telescope point spread functions

Cosmic shear requires high precision measurement of galaxy shapes in the presence of the observational point spread function (PSF) that smears out the image. The PSF must therefore be known for each galaxy to a high accuracy. However, for several reasons, the PSF is usually wavelength dependent; therefore, the differences between the spectral energy distribution of the observed objects introduce further complexity. In this paper, we investigate the effect of the wavelength dependence of the PSF, focusing on instruments in which the PSF size is dominated by the diffraction limit of the telescope and which use broad-band filters for shape measurement. We first calculate biases on cosmological parameter estimation from cosmic shear when the stellar PSF is used uncorrected. Using realistic galaxy and star spectral energy distributions and populations and a simple three-component circular PSF, we find that the colour dependence must be taken into account for the next generation of telescopes. We then consider two different methods for removing the effect: (i) the use of stars of the same colour as the galaxies and (ii) estimation of the galaxy spectral energy distribution using multiple colours and using a telescope model for the PSF. We find that both of these methods correct the effect to levels below the tolerances required for per cent level measurements of dark energy parameters. Comparison of the two methods favours the template-fitting method because its efficiency is less dependent on galaxy redshift than the broad-band colour method and takes full advantage of deeper photometry.

Thermodynamical description of the interaction between holographic dark energy and dark matter

We present a thermodynamical description of the interaction between holographic dark energy and dark matter. If holographic dark energy and dark matter evolve separately, each of them remains in thermodynamic equilibrium. A small interaction between them may be viewed as a stable thermal fluctuation that brings a logarithmic correction to the equilibrium entropy. From this correction we obtain a physical expression for the interaction which is consistent with phenomenological descriptions and passes reasonably well the observational tests: (c) 2008 Elsevier B.V. All rights reserved.

Population Structure and Pathotype Diversity of the Wheat Blast Pathogen Magnaporthe oryzae 25 Years After Its Emergence in Brazil

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)