Missing lithotroph identified as new planctomycete

With the increased use of chemical fertilizers in agriculture, many densely populated countries face environmental problems associated with high ammonia emissions. The process of anaerobic ammonia oxidation ('anammox') is one of the most innovative technological advances in the removal of ammonia nitrogen from waste water. This new process combines ammonia and nitrite directly into dinitrogen gas. Until now, bacteria capable of anaerobically oxidizing ammonia had never been found and were known as "lithotrophs missing from nature". Here we report the discovery of this missing lithotroph and its identification as a new, autotrophic member of the order Planctomycetales, one of the major distinct divisions of the Bacteria. The new planctomycete grows extremely slowly, dividing only once every two weeks. At present, it cannot be cultivated by conventional microbiological techniques. The identification of this bacterium as the one responsible for anaerobic oxidation of ammonia makes an important contribution to the problem of unculturability

Inside-Out Evacuation of Transitional Protoplanetary Disks by the Magneto-Rotational Instability

How do T Tauri disks accrete? The magneto-rotational instability (MRI) supplies one means, but protoplanetary disk gas is typically too poorly ionized to be magnetically active. Here we show that the MRI can, in fact, explain observed accretion rates for the sub-class of T Tauri disks known as transitional systems. Transitional disks are swept clean of dust inside rim radii of ~10 AU. Stellar coronal X-rays ionize material in the disk rim, activating the MRI there. Gas flows from the rim to the star, at a rate limited by the depth to which X-rays ionize the rim wall. The wider the rim, the larger the surface area that the rim wall exposes to X-rays, and the greater the accretion rate. Interior to the rim, the MRI continues to transport gas; the MRI is sustained even at the disk midplane by super-keV X-rays that Compton scatter down from the disk surface. Accretion is therefore steady inside the rim. Blown out by radiation pressure, dust largely fails to accrete with gas. Contrary to what is usually assumed, ambipolar diffusion, not Ohmic dissipation, limits how much gas is MRI-active. We infer values for the transport parameter alpha on the order of 0.01 for GM Aur, TW Hyd, and DM Tau. Because the MRI can only afflict a finite radial column of gas at the rim, disk properties inside the rim are insensitive to those outside. Thus our picture provides one robust setting for planet-disk interaction: a protoplanet interior to the rim will interact with gas whose density, temperature, and transport properties are definite and decoupled from uncertain initial conditions. Our study also supplies half the answer to how disks dissipate: the inner disk drains from the inside out by the MRI, while the outer disk photoevaporates by stellar ultraviolet radiation.Comment: Accepted to Nature Physics June 7, 2007. The manuscript for publication is embargoed per Nature policy. This arxiv.org version contains more technical details and discussion, and is distributed with permission from the editors. 10 pages, 4 figure

On Poincare and logarithmic Sobolev inequalities for a class of singular Gibbs measures

This note, mostly expository, is devoted to Poincar{\'e} and log-Sobolev inequalities for a class of Boltzmann-Gibbs measures with singular interaction. Such measures allow to model one-dimensional particles with confinement and singular pair interaction. The functional inequalities come from convexity. We prove and characterize optimality in the case of quadratic confinement via a factorization of the measure. This optimality phenomenon holds for all beta Hermite ensembles including the Gaussian unitary ensemble, a famous exactly solvable model of random matrix theory. We further explore exact solvability by reviewing the relation to Dyson-Ornstein-Uhlenbeck diffusion dynamics admitting the Hermite-Lassalle orthogonal polynomials as a complete set of eigenfunctions. We also discuss the consequence of the log-Sobolev inequality in terms of concentration of measure for Lipschitz functions such as maxima and linear statistics.Comment: Minor improvements. To appear in Geometric Aspects of Functional Analysis -- Israel Seminar (GAFA) 2017-2019", Lecture Notes in Mathematics 225

Photonic Analogue of Two-dimensional Topological Insulators and Helical One-Way Edge Transport in Bi-Anisotropic Metamaterials

Recent progress in understanding the topological properties of condensed matter has led to the discovery of time-reversal invariant topological insulators. Because of limitations imposed by nature, topologically non-trivial electronic order seems to be uncommon except in small-band-gap semiconductors with strong spin-orbit interactions. In this Article we show that artificial electromagnetic structures, known as metamaterials, provide an attractive platform for designing photonic analogues of topological insulators. We demonstrate that a judicious choice of the metamaterial parameters can create photonic phases that support a pair of helical edge states, and that these edge states enable one-way photonic transport that is robust against disorder.Comment: 13 pages, 3 figure

The role of endogenous and exogenous mechanisms in the formation of R&D networks

We develop an agent-based model of strategic link formation in Research and Development (R&D)networks. Empirical evidence has shown that the growth of these networks is driven by mechanisms whichare both endogenous to the system (that is, depending on existing alliances patterns) and exogenous (that is, driven by an exploratory search for newcomer firms). Extant research to date has not investigated both mechanisms simultaneously in a comparative manner. To overcome this limitation, we develop a general modeling framework to shed light on the relative importance of these two mechanisms. We test our model against a comprehensive dataset, listing cross-country and cross-sectoral R&D alliances from 1984 to 2009. Our results show that by fitting only three macroscopic properties of the network topology, this framework is able to reproduce a number of micro-level measures, including the distributions of degree, local clustering, path length and component size, and the emergence of network clusters. Furthermore, by estimating the link probabilities towards newcomers and established firms from the data, we find that endogenous mechanisms are predominant over the exogenous ones in the network formation, thus quantifying the importance of existing structures in selecting partner firms

Health status of the advanced elderly in six european countries: results from a representative survey using EQ-5D and SF-12

<p>Abstract</p> <p>Background</p> <p>Due to demographic change, the advanced elderly represent the fastest growing population group in Europe. Health problems tend to be frequent and increasing with age within this cohort.</p> <p>Aims of the study</p> <p>To describe and compare health status of the elderly population in six European countries and to analyze the impact of socio-demographic variables on health.</p> <p>Methods</p> <p>In the European Study of the Epidemiology of Mental Disorders (ESEMeD), representative non-institutionalized population samples completed the EQ-5D and Short Form-12 (SF-12) questionnaires as part of personal computer-based home interviews in 2001-2003. This study is based on a subsample of 1659 respondents aged ≥ 75 years from Belgium (n = 194), France (n = 168), Germany (n = 244), Italy (n = 317), the Netherlands (n = 164) and Spain (n = 572). Descriptive statistics, bivariate- (chi-square tests) and multivariate methods (linear regressions) were used to examine differences in population health.</p> <p>Results</p> <p>68.8% of respondents reported problems in one or more EQ-5D dimensions, most frequently pain/discomfort (55.2%), followed by mobility (50.0%), usual activities (36.6%), self-care (18.1%) and anxiety/depression (11.6%). The proportion of respondents reporting any problems increased significantly with age in bivariate analyses (age 75-79: 65.4%; age 80-84: 69.2%; age ≥ 85: 81.1%) and differed between countries, ranging from 58.7% in the Netherlands to 72.3% in Italy. The mean EQ VAS score was 61.9, decreasing with age (age 75-79: 64.1; age 80-84: 59.8; age ≥ 85: 56.7) and ranging from 60.0 in Italy to 72.9 in the Netherlands. SF-12 derived Physical Component Summary (PCS) and Mental Component Summary (MCS) scores varied little by age and country. Age and low educational level were associated with lower EQ VAS and PCS scores. After controlling for socio-demographic variables and reported EQ-5D health states, mean EQ VAS scores were significantly higher in the Netherlands and Belgium, and lower in Germany than the grand mean.</p> <p>Conclusions</p> <p>More than two thirds of the advanced elderly report impairment of health status. Impairment increases rapidly with age but differs considerably between countries. In all countries, health status is significantly associated with socio-demographic variables.</p

An integrated network visualization framework towards metabolic engineering applications

Background Over the last years, several methods for the phenotype simulation of microorganisms, under specified genetic and environmental conditions have been proposed, in the context of Metabolic Engineering (ME). These methods provided insight on the functioning of microbial metabolism and played a key role in the design of genetic modifications that can lead to strains of industrial interest. On the other hand, in the context of Systems Biology research, biological network visualization has reinforced its role as a core tool in understanding biological processes. However, it has been scarcely used to foster ME related methods, in spite of the acknowledged potential. Results In this work, an open-source software that aims to fill the gap between ME and metabolic network visualization is proposed, in the form of a plugin to the OptFlux ME platform. The framework is based on an abstract layer, where the network is represented as a bipartite graph containing minimal information about the underlying entities and their desired relative placement. The framework provides input/output support for networks specified in standard formats, such as XGMML, SBGN or SBML, providing a connection to genome-scale metabolic models. An user-interface makes it possible to edit, manipulate and query nodes in the network, providing tools to visualize diverse effects, including visual filters and aspect changing (e.g. colors, shapes and sizes). These tools are particularly interesting for ME, since they allow overlaying phenotype simulation results or elementary flux modes over the networks. Conclusions The framework and its source code are freely available, together with documentation and other resources, being illustrated with well documented case studies.This work is partially funded by ERDF - European Regional Development Fund through the COMPETE Programme (operational programme for competitiveness) and by National Funds through the FCT (Portuguese Foundation for Science and Technology) within project ref. COMPETE FCOMP-01-0124-FEDER-015079 and the FCT Strategic Project PEst-OE/EQB/LA0023/2013. The work of PV is funded by PhD grant ref. SFRH/BDE/51442/2011

D1R/GluN1 complexes in the striatum integrate dopamine and glutamate signalling to control synaptic plasticity and cocaine-induced responses.

Convergent dopamine and glutamate signalling onto the extracellular signal-regulated kinase (ERK) pathway in medium spiny neurons (MSNs) of the striatum controls psychostimulant-initiated adaptive processes underlying long-lasting behavioural changes. We hypothesised that the physical proximity of dopamine D1 (D1R) and glutamate NMDA (NMDAR) receptors, achieved through the formation of D1R/NMDAR complexes, may act as a molecular bridge that controls the synergistic action of dopamine and glutamate on striatal plasticity and behavioural responses to drugs of abuse. We found that concomitant stimulation of D1R and NMDAR drove complex formation between endogenous D1R and the GluN1 subunit of NMDAR. Conversely, preventing D1R/GluN1 association with a cell-permeable peptide (TAT-GluN1C1) left individual D1R and NMDAR-dependent signalling intact, but prevented D1R-mediated facilitation of NMDAR-calcium influx and subsequent ERK activation. Electrophysiological recordings in striatal slices from mice revealed that D1R/GluN1 complexes control the D1R-dependent enhancement of NMDAR currents and long-term potentiation in D1R-MSN. Finally, intra-striatal delivery of TAT-GluN1C1 did not affect acute responses to cocaine but reduced behavioural sensitization. Our findings uncover D1R/GluN1 complexes as a major substrate for the dopamine-glutamate interaction in MSN that is usurped by addictive drugs to elicit persistent behavioural alterations. They also identify D1R/GluN1 complexes as molecular targets with a therapeutic potential for the vast spectrum of psychiatric diseases associated with an imbalance between dopamine and glutamate transmission

Seroprevalence of Bordetella pertussis antibodies in adults in Hungary: results of an epidemiological cross-sectional study.

BACKGROUND: Pertussis (whooping cough) is well known to be underreported, particularly among adults, who can act as an infectious reservoir, potentially putting susceptible newborns at risk of serious illness. The purpose of this study was to estimate the seroprevalence of pertussis in adults in Hungary. METHODS: This epidemiological, cross-sectional study was conducted in adults in five general practitioners' practices in Hungary. Serum anti-pertussis toxin immunoglobulin G (anti-PT IgG) antibody levels were analyzed using enzyme-linked immunosorbent assay. Sera were classified following manufacturer's instructions as: strongly indicative of current/recent infection (>/=1.5 optical density [OD] units); indicative of current/recent infection (>/=1.0 OD units); seropositive (>0.3 OD units); or seronegative (/=60 years (odds ratio [OR], 1.97; 95% confidence interval [CI], 1.39-2.80; p = .0002) or 18-29 years (OR, 1.67; 95% CI, 1.13-2.46; p = .0094) vs. 45-59 years; former smoker (OR, 1.46; 95% CI, 1.08-1.97; p = .014) or current smoker (OR, 1.38; 95% CI, 1.01-1.89; p = .045) vs. never smoker; and male (OR, 1.30; 95% CI, 1.01-1.68; p = .041) vs. female. Also, between increased rates of probable current/recent infection and current smoker (OR, 7.50; 95% CI, 2.32-24.31; p = .0008) or former smoker (OR, 4.07; 95% CI, 1.21-13.64; p = .023) vs. never smoker. CONCLUSIONS: Approximately 85% of the adults studied were seronegative and therefore susceptible to pertussis infection. Approximately 1% had anti-PT IgG levels indicative of current/recent pertussis infection, which could potentially be transmitted to susceptible young infants. Vaccination of adults is a key way to indirectly protect infants. TRIAL REGISTRATION: Clinical Trials.gov NCT02014519 . Prospectively registered 12 December 2013

Chronic non-specific abdominal complaints in general practice: a prospective study on management, patient health status and course of complaints

BACKGROUND: While in general practice chronic non-specific abdominal complaints are common, there is insufficient data on the clinical course and the management of these complaints. Aim of this study was to present a primary care based profile of these chronic complaints including health care involvement, health status and clinical course. METHODS: Thirty general practitioners (GPs) and patients from their practices participated in a prospective follow-up study. All patients and GPs were asked to complete questionnaires at baseline and at 6, 12 and 18 months of follow-up. The GPs provided information on diagnostic and therapeutic management and on referral concerning 619 patients with chronic non-specific abdominal complaints, while 291 patients provided information about health status and clinical course of the complaints. RESULTS: When asked after 18 months of follow-up, 51,7% of the patients reported an equal or worsened severity of complaints. General health perception was impaired and patients had high scores on SCL-anxiety and SCL-depression scales. Diagnostic tests other than physical examination and laboratory tests were not frequently used. Medication was the most frequent type of treatment. The persistence of chronic non-specific abdominal complaints was quite stable. CONCLUSION: Once non-specific chronic abdominal complaints have become labelled as chronic by the attending physician, little improvement can be expected. The impact on patients' physiological and psychological well-being is large. GPs use a variety of diagnostic and therapeutic strategies. Research into the evidence base of currently applied management strategies is recommended