Showing papers by "University of São Paulo published in 2009"
TL;DR: This work has developed a code able to pack millions of atoms, grouped in arbitrarily complex molecules, inside a variety of three‐dimensional regions, which can be intersections of spheres, ellipses, cylinders, planes, or boxes.
Abstract: Adequate initial configurations for molecular dynamics simulations consist of arrangements of molecules distributed in space in such a way to approximately represent the system's overall structure. In order that the simulations are not disrupted by large van der Waals repulsive interactions, atoms from different molecules must keep safe pairwise distances. Obtaining such a molecular arrangement can be considered a packing problem: Each type molecule must satisfy spatial constraints related to the geometry of the system, and the distance between atoms of different molecules must be greater than some specified tolerance. We have developed a code able to pack millions of atoms, grouped in arbitrarily complex molecules, inside a variety of three-dimensional regions. The regions may be intersections of spheres, ellipses, cylinders, planes, or boxes. The user must provide only the structure of one molecule of each type and the geometrical constraints that each type of molecule must satisfy. Building complex mixtures, interfaces, solvating biomolecules in water, other solvents, or mixtures of solvents, is straightforward. In addition, different atoms belonging to the same molecule may also be restricted to different spatial regions, in such a way that more ordered molecular arrangements can be built, as micelles, lipid double-layers, etc. The packing time for state-of-the-art molecular dynamics systems varies from a few seconds to a few minutes in a personal computer. The input files are simple and currently compatible with PDB, Tinker, Molden, or Moldy coordinate files. The package is distributed as free software and can be downloaded from http://www.ime.unicamp.br/~martinez/packmol/.
5,322 citations
National Institutes of Health1, Imperial College London2, University of Alberta3, Boston Children's Hospital4, Royal Prince Alfred Hospital5, University of Sydney6, University of Giessen7, Amrita Institute of Medical Sciences and Research Centre8, University of Illinois at Urbana–Champaign9, Medical University of Graz10, Vanderbilt University Medical Center11, University of São Paulo12
TL;DR: In this paper, a clinical classification of pulmonary hypertension (PH) was established, categorizing PH into groups which share similar pathological and hemodynamic characteristics and therapeutic approaches, and the main change was to withdraw persistent pulmonary hypertension of the newborn (PPHN) from Group 1 because this entity carries more differences than similarities with other PAH subgroups.
4,135 citations
TL;DR: In this paper, the authors quantify how much of the Brazilian Atlantic Forest still remains, and analyze its spatial distribution, and suggest some guidelines for conservation: (i) large mature forest fragments should be a conservation priority; (ii) smaller fragments can be managed in order to maintain functionally linked mosaics; (iii) the matrix surrounding fragments, and (iv) restoration actions should be taken, particularly in certain key areas.
3,199 citations
University of Tasmania1, University of California, Santa Barbara2, Woods Hole Oceanographic Institution3, Yale University4, University of São Paulo5, University of Cape Town6, South Dakota State University7, Columbia University8, California Institute of Technology9, University of Bristol10, United States Geological Survey11, University of California, Los Angeles12, University of California, Berkeley13, Monash University14, Brown University15, Ohio State University16, Royal Holloway, University of London17, University of Arizona18, VU University Amsterdam19, Arizona State University20
TL;DR: What is known and what is needed to develop a holistic understanding of the role of fire in the Earth system are reviewed, particularly in view of the pervasive impact of fires and the likelihood that they will become increasingly difficult to control as climate changes.
Abstract: Fire is a worldwide phenomenon that appears in the geological record soon after the appearance of terrestrial plants. Fire influences global ecosystem patterns and processes, including vegetation distribution and structure, the carbon cycle, and climate. Although humans and fire have always coexisted, our capacity to manage fire remains imperfect and may become more difficult in the future as climate change alters fire regimes. This risk is difficult to assess, however, because fires are still poorly represented in global models. Here, we discuss some of the most important issues involved in developing a better understanding of the role of fire in the Earth system.
2,365 citations
TL;DR: The findings challenge the common view that humans stand out from other primates in their brain composition and indicate that, with regard to numbers of neuronal and nonneuronal cells, the human brain is an isometrically scaled‐up primate brain.
Abstract: The human brain is often considered to be the most cognitively capable among mammalian brains and to be much larger than expected for a mammal of our body size. Although the number of neurons is generally assumed to be a determinant of computational power, and despite the widespread quotes that the human brain contains 100 billion neurons and ten times more glial cells, the absolute number of neurons and glial cells in the human brain remains unknown. Here we determine these numbers by using the isotropic fractionator and compare them with the expected values for a human-sized primate. We find that the adult male human brain contains on average 86.1 +/- 8.1 billion NeuN-positive cells ("neurons") and 84.6 +/- 9.8 billion NeuN-negative ("nonneuronal") cells. With only 19% of all neurons located in the cerebral cortex, greater cortical size (representing 82% of total brain mass) in humans compared with other primates does not reflect an increased relative number of cortical neurons. The ratios between glial cells and neurons in the human brain structures are similar to those found in other primates, and their numbers of cells match those expected for a primate of human proportions. These findings challenge the common view that humans stand out from other primates in their brain composition and indicate that, with regard to numbers of neuronal and nonneuronal cells, the human brain is an isometrically scaled-up primate brain.
1,818 citations
Uppsala University1, British Heart Foundation2, University of Erlangen-Nuremberg3, University of Oslo4, Royal Adelaide Hospital5, Bosch6, Seoul National University7, University of Helsinki8, University of São Paulo9, Innsbruck Medical University10, University of Alberta11, Aarhus University12, University of Copenhagen13, University of Gothenburg14, Akdeniz University15, Charles University in Prague16, University of Silesia in Katowice17, University of Zurich18, AstraZeneca19
TL;DR: In patients undergoing hemodialysis, the initiation of treatment with rosuvastatin lowered the LDL cholesterol level but had no significant effect on the composite primary end point of death from cardiovascular causes, nonf fatal myocardial infarction, or nonfatal stroke.
Abstract: BACKGROUND: Statins reduce the incidence of cardiovascular events in patients at high cardiovascular risk. However, a benefit of statins in such patients who are undergoing hemodialysis has not bee ...
1,789 citations
B. I. Abelev1, Madan M. Aggarwal2, Zubayer Ahammed3, A. V. Alakhverdyants4 +345 more•Institutions (49)
1,696 citations
National Institutes of Health1, Norwegian University of Science and Technology2, National Research Council3, University of São Paulo4, University of Tübingen5, University of Coimbra6, French Institute of Health and Medical Research7, University of Paris8, Chang Gung University9, Columbia University10, Mayo Clinic11, Tel Aviv University12, Technion – Israel Institute of Technology13, Rambam Health Care Campus14, Tel Aviv Sourasky Medical Center15, University of Rostock16, University Health Network17, National Taiwan Normal University18, University of Washington19, University of Tokyo20, Kobe University21, Magna Græcia University22, University of Toronto23, Duke University24, Singapore General Hospital25
TL;DR: Data collected demonstrate that there is a strong association between GBA mutations and Parkinson's disease, and those with a GBA mutation presented earlier with the disease, were more likely to have affected relatives, and were morelikely to have atypical clinical manifestations.
Abstract: Background Recent studies indicate an increased frequency of mutations in the gene encoding glucocerebrosidase (GBA), a deficiency of which causes Gaucher's disease, among patients with Parkinson's disease. We aimed to ascertain the frequency of GBA mutations in an ethnically diverse group of patients with Parkinson's disease. Methods Sixteen centers participated in our international, collaborative study: five from the Americas, six from Europe, two from Israel, and three from Asia. Each center genotyped a standard DNA panel to permit comparison of the genotyping results across centers. Genotypes and phenotypic data from a total of 5691 patients with Parkinson's disease (780 Ashkenazi Jews) and 4898 controls (387 Ashkenazi Jews) were analyzed, with multivariate logistic-regression models and the Mantel–Haenszel procedure used to estimate odds ratios across centers. Results All 16 centers could detect two GBA mutations, L444P and N370S. Among Ashkenazi Jewish subjects, either mutation was found in 15% of p...
1,629 citations
TL;DR: A detailed study on wax printing, a simple and inexpensive method for fabricating microfluidic devices in paper using a commercially available printer and hot plate, which creates complete hydrophobic barriers in paper that define hydrophilic channels, fluid reservoirs, and reaction zones.
Abstract: This technical note describes a detailed study on wax printing, a simple and inexpensive method for fabricating microfluidic devices in paper using a commercially available printer and hot plate. The printer prints patterns of solid wax on the surface of the paper, and the hot plate melts the wax so that it penetrates the full thickness of the paper. This process creates complete hydrophobic barriers in paper that define hydrophilic channels, fluid reservoirs, and reaction zones. The design of each device was based on a simple equation that accounts for the spreading of molten wax in paper.
1,403 citations
TL;DR: Some of the molecules involved in the paracrine effects of MSCs are identified with a perspective that these cells intrinsically belong to a perivascular niche in vivo, and how this knowledge could be advantageously used in clinical applications is discussed.
1,254 citations
TL;DR: In this paper, the production of mesons containing strange quarks (KS, φ) and both singly and doubly strange baryons (,, and − + +) are measured at mid-rapidity in pp collisions at √ s = 0.9 TeV with the ALICE experiment at the LHC.
A. Adare1, Serguei Afanasiev2, Christine Angela Aidala3, Christine Angela Aidala4 +601 more•Institutions (57)
Stanford University1, Prescott College2, University of Illinois at Urbana–Champaign3, Cornell University4, National Center for Atmospheric Research5, University of Bristol6, University of São Paulo7, Columbia University8, Michigan State University9, University of Colorado Boulder10, China Agricultural University11
TL;DR: Solutions to the nutrient challenges that face global agriculture can be informed by analyses of trajectories of change within, as well as across, agricultural systems.
Abstract: Nutrient cycles link agricultural systems to their societies and surroundings; inputs of nitrogen and phosphorus in particular are essential for high crop yields, but downstream and downwind losses of these same nutrients diminish environmental quality and human well-being. Agricultural nutrient balances differ substantially with economic development, from inputs that are inadequate to maintain soil fertility in parts of many developing countries, particularly those of sub-Saharan Africa, to excessive and environmentally damaging surpluses in many developed and rapidly growing economies. National and/or regional policies contribute to patterns of nutrient use and their environmental consequences in all of these situations ( 1 ). Solutions to the nutrient challenges that face global agriculture can be informed by analyses of trajectories of change within, as well as across, agricultural systems.
Christine G. Elsik1, Christine G. Elsik2, Christine G. Elsik3, Ross L. Tellam3 +325 more•Institutions (65)
TL;DR: To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage and provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
Abstract: To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
Wellcome Trust Sanger Institute1, Broad Institute2, J. Craig Venter Institute3, University of Texas Health Science Center at San Antonio4, University of York5, University of Maryland, College Park6, University of California, San Francisco7, Oswaldo Cruz Foundation8, University of Texas at San Antonio9, Universidade Federal de Minas Gerais10, University College Cork11, Iowa State University12, University of São Paulo13, University of Pittsburgh14, Kyoto University15, University of Southampton16, Natural History Museum17, Lille University of Science and Technology18, John Innes Centre19, Leiden University20, University of Göttingen21, University of Maryland, Baltimore22, Illinois State University23, Rush University Medical Center24, University at Buffalo25
TL;DR: Analysis of the 363 megabase nuclear genome of the blood fluke, the first sequenced flatworm, and a representative of the Lophotrochozoa offers insights into early events in the evolution of the animals, including the development of a body pattern with bilateral symmetry, and theDevelopment of tissues into organs.
Abstract: Schistosoma mansoni is responsible for the neglected tropical disease schistosomiasis that affects 210 million people in 76 countries. Here we present analysis of the 363 megabase nuclear genome of the blood fluke. It encodes at least 11,809 genes, with an unusual intron size distribution, and new families of micro-exon genes that undergo frequent alternative splicing. As the first sequenced flatworm, and a representative of the Lophotrochozoa, it offers insights into early events in the evolution of the animals, including the development of a body pattern with bilateral symmetry, and the development of tissues into organs. Our analysis has been informed by the need to find new drug targets. The deficits in lipid metabolism that make schistosomes dependent on the host are revealed, and the identification of membrane receptors, ion channels and more than 300 proteases provide new insights into the biology of the life cycle and new targets. Bioinformatics approaches have identified metabolic chokepoints, and a chemogenomic screen has pinpointed schistosome proteins for which existing drugs may be active. The information generated provides an invaluable resource for the research community to develop much needed new control tools for the treatment and eradication of this important and neglected disease.
TL;DR: This review describes important aspects of carrageenans related to their industrial/therapeutic applications, physicochemical properties and structural analysis and indicates that these polysaccharides may offer some protection against HIV infection.
TL;DR: The sources and metabolism of ROS in this organelle are reviewed, including the conditions that regulate the production of these species, such as mild uncoupling, oxygen tension, respiratory inhibition, Ca2+ and K+ transport, and mitochondrial content and morphology.
TL;DR: It is shown that the southern Atlantic forest was climatically unstable relative to the central region, which served as a large climatic refugium for neotropical species in the late Pleistocene, and establishes a validated approach to biodiversity prediction in other understudied, species-rich regions.
Abstract: Biodiversity hotspots, representing regions with high species endemism and conservation threat, have been mapped globally. Yet, biodiversity distribution data from within hotspots are too sparse for effective conservation in the face of rapid environmental change. Using frogs as indicators, ecological niche models under paleoclimates, and simultaneous Bayesian analyses of multispecies molecular data, we compare alternative hypotheses of assemblage-scale response to late Quaternary climate change. This reveals a hotspot within the Brazilian Atlantic forest hotspot. We show that the southern Atlantic forest was climatically unstable relative to the central region, which served as a large climatic refugium for neotropical species in the late Pleistocene. This sets new priorities for conservation in Brazil and establishes a validated approach to biodiversity prediction in other understudied, species-rich regions.
TL;DR: In an effort to unify the nomenclature of Trypanosoma cruzi, the causative agent of Chagas disease, an updated system was agreed upon at the Second Satellite Meeting that T. cruzi strains should be referred to by six discrete typing units.
Abstract: In an effort to unify the nomenclature of Trypanosoma cruzi, the causative agent of Chagas disease, an updated system was agreed upon at the Second Satellite Meeting. A consensus was reached that T. cruzi strains should be referred to by six discrete typing units (T. cruzi I-VI). The goal of a unified nomenclature is to improve communication within the scientific community involved in T. cruzi research. The justification and implications will be presented in a subsequent detailed report.
TL;DR: A peak of genomic amplification on chromosome 3q26.33 found in squamous cell carcinomas of the lung and esophagus contains the transcription factor gene SOX2, which is necessary for normal esophageal squamous development, promotes differentiation and proliferation of basal tracheal cells and cooperates in induction of pluripotent stem cells.
Abstract: Lineage-survival oncogenes are activated by somatic DNA alterations in cancers arising from the cell lineages in which these genes play a role in normal development. Here we show that a peak of genomic amplification on chromosome 3q26.33 found in squamous cell carcinomas (SCCs) of the lung and esophagus contains the transcription factor gene SOX2, which is mutated in hereditary human esophageal malformations, is necessary for normal esophageal squamous development, promotes differentiation and proliferation of basal tracheal cells and cooperates in induction of pluripotent stem cells. SOX2 expression is required for proliferation and anchorage-independent growth of lung and esophageal cell lines, as shown by RNA interference experiments. Furthermore, ectopic expression of SOX2 here cooperated with FOXE1 or FGFR2 to transform immortalized tracheobronchial epithelial cells. SOX2-driven tumors show expression of markers of both squamous differentiation and pluripotency. These characteristics identify SOX2 as a lineage-survival oncogene in lung and esophageal SCC.
International Agency for Research on Cancer1, Catholic University of the Sacred Heart2, Fred Hutchinson Cancer Research Center3, Universidade Federal do Rio Grande do Sul4, University of São Paulo5, National Institutes of Health6, Brown University7, Harvard University8, Oswaldo Cruz Foundation9, University of Milan10, Pennsylvania State University11, University of Lausanne12, University of Buenos Aires13, Universidade Federal de Pelotas14, Boston University15, University of North Carolina at Chapel Hill16, University of Iowa17, University of Texas MD Anderson Cancer Center18, Nofer Institute of Occupational Medicine19, Russian Academy20, Medical University of Warsaw21, University of California, Los Angeles22
TL;DR: It is confirmed that the joint effect between tobacco and alcohol use is greater than multiplicative on head and neck cancer risk, however, a substantial proportion of head and head cancers cannot be attributed to tobacco or alcohol use, particularly for oral cavity cancer and for head andneck cancer among women and among young-onset cases.
Abstract: Background: The magnitude of risk conferred by the interaction between tobacco and alcohol use on the risk of head and neck cancers is not clear because studies have used various methods to quantify the excess head and neck cancer burden. Methods: We analyzed individual-level pooled data from 17 European and American case-control studies (11,221 cases and 16,168 controls) participating in the International Head and Neck Cancer Epidemiology consortium. We estimated the multiplicative interaction parameter ( ψ ) and population attributable risks (PAR). Results: A greater than multiplicative joint effect between ever tobacco and alcohol use was observed for head and neck cancer risk ( ψ = 2.15; 95% confidence interval, 1.53-3.04). The PAR for tobacco or alcohol was 72% (95% confidence interval, 61-79%) for head and neck cancer, of which 4% was due to alcohol alone, 33% was due to tobacco alone, and 35% was due to tobacco and alcohol combined. The total PAR differed by subsite (64% for oral cavity cancer, 72% for pharyngeal cancer, 89% for laryngeal cancer), by sex (74% for men, 57% for women), by age (33% for cases 60 years), and by region (84% in Europe, 51% in North America, 83% in Latin America). Conclusions: Our results confirm that the joint effect between tobacco and alcohol use is greater than multiplicative on head and neck cancer risk. However, a substantial proportion of head and neck cancers cannot be attributed to tobacco or alcohol use, particularly for oral cavity cancer and for head and neck cancer among women and among young-onset cases. (Cancer Epidemiol Biomarkers Prev 2009;18(2):541–50)
TL;DR: In this article, the authors measured the charged-particle spectra at the BNL Relativistic Heavy Ion Collider (RHIC) time projection chamber and reported the average transverse momenta, total particle production, particle yield ratios, strangeness, and baryon production rates as a function of collision system and centrality.
Abstract: Identified charged-particle spectra of pi(+/-), K(+/-), p, and (p) over bar at midrapidity (vertical bar y vertical bar < 0.1) measured by the dE/dx method in the STAR (solenoidal tracker at the BNL Relativistic Heavy Ion Collider) time projection chamber are reported for pp and d + Au collisions at root s(NN) = 200 GeV and for Au + Au collisions at 62.4, 130, and 200 GeV. Average transverse momenta, total particle production, particle yield ratios, strangeness, and baryon production rates are investigated as a function of the collision system and centrality. The transverse momentum spectra are found to be flatter for heavy particles than for light particles in all collision systems; the effect is more prominent for more central collisions. The extracted average transverse momentum of each particle species follows a trend determined by the total charged-particle multiplicity density. The Bjorken energy density estimate is at least several GeV/fm(3) for a formation time less than 1 fm/c. A significantly larger net-baryon density and a stronger increase of the net-baryon density with centrality are found in Au + Au collisions at 62.4 GeV than at the two higher energies. Antibaryon production relative to total particle multiplicity is found to be constant over centrality, but increases with the collision energy. Strangeness production relative to total particle multiplicity is similar at the three measured RHIC energies. Relative strangeness production increases quickly with centrality in peripheral Au + Au collisions, to a value about 50% above the pp value, and remains rather constant in more central collisions. Bulk freeze-out properties are extracted from thermal equilibrium model and hydrodynamics-motivated blast-wave model fits to the data. Resonance decays are found to have little effect on the extracted kinetic freeze-out parameters because of the transverse momentum range of our measurements. The extracted chemical freeze-out temperature is constant, independent of collision system or centrality; its value is close to the predicted phase-transition temperature, suggesting that chemical freeze-out happens in the vicinity of hadronization and the chemical freeze-out temperature is universal despite the vastly different initial conditions in the collision systems. The extracted kinetic freeze-out temperature, while similar to the chemical freeze-out temperature in pp, d + Au, and peripheral Au + Au collisions, drops significantly with centrality in Au + Au collisions, whereas the extracted transverse radial flow velocity increases rapidly with centrality. There appears to be a prolonged period of particle elastic scatterings from chemical to kinetic freeze-out in central Au + Au collisions. The bulk properties extracted at chemical and kinetic freeze-out are observed to evolve smoothly over the measured energy range, collision systems, and collision centralities.
Kansas State University1, University of Maryland Center for Environmental Science2, University of Brasília3, University of California, Berkeley4, University of New Hampshire5, University of Florida6, University of São Paulo7, United States Forest Service8, Autonomous University of Barcelona9, University of Minnesota10, Edith Cowan University11, Boston University12, Dartmouth College13, University of Alaska Fairbanks14, Macquarie University15
TL;DR: It is suggested that warm, dry ecosystems have the highest N availability, while plants with high N concentrations, on average, occupy sites with higher N availability than plants with low N concentrations.
Abstract: Ratios of nitrogen (N) isotopes in leaves could elucidate underlying patterns of N cycling across ecological gradients. To better understand global-scale patterns of N cycling, we compiled data on foliar N isotope ratios (delta(15)N), foliar N concentrations, mycorrhizal type and climate for over 11,000 plants worldwide. Arbuscular mycorrhizal, ectomycorrhizal, and ericoid mycorrhizal plants were depleted in foliar delta(15)N by 2 per thousand, 3.2 per thousand, 5.9 per thousand, respectively, relative to nonmycorrhizal plants. Foliar delta(15)N increased with decreasing mean annual precipitation and with increasing mean annual temperature (MAT) across sites with MAT >or= -0.5 degrees C, but was invariant with MAT across sites with MAT < -0.5 degrees C. In independent landscape-level to regional-level studies, foliar delta(15)N increased with increasing N availability; at the global scale, foliar delta(15)N increased with increasing foliar N concentrations and decreasing foliar phosphorus (P) concentrations. Together, these results suggest that warm, dry ecosystems have the highest N availability, while plants with high N concentrations, on average, occupy sites with higher N availability than plants with low N concentrations. Global-scale comparisons of other components of the N cycle are still required for better mechanistic understanding of the determinants of variation in foliar delta(15)N and ultimately global patterns in N cycling.
01 Mar 2009
TL;DR: An up-to-date overview that is fully devoted to evolutionary algorithms for clustering, is not limited to any particular kind of evolutionary approach, and comprises advanced topics like multiobjective and ensemble-based evolutionary clustering.
Abstract: This paper presents a survey of evolutionary algorithms designed for clustering tasks. It tries to reflect the profile of this area by focusing more on those subjects that have been given more importance in the literature. In this context, most of the paper is devoted to partitional algorithms that look for hard clusterings of data, though overlapping (i.e., soft and fuzzy) approaches are also covered in the paper. The paper is original in what concerns two main aspects. First, it provides an up-to-date overview that is fully devoted to evolutionary algorithms for clustering, is not limited to any particular kind of evolutionary approach, and comprises advanced topics like multiobjective and ensemble-based evolutionary clustering. Second, it provides a taxonomy that highlights some very important aspects in the context of evolutionary data clustering, namely, fixed or variable number of clusters, cluster-oriented or nonoriented operators, context-sensitive or context-insensitive operators, guided or unguided operators, binary, integer, or real encodings, centroid-based, medoid-based, label-based, tree-based, or graph-based representations, among others. A number of references are provided that describe applications of evolutionary algorithms for clustering in different domains, such as image processing, computer security, and bioinformatics. The paper ends by addressing some important issues and open questions that can be subject of future research.
TL;DR: In this paper, the authors reported the discovery of very shallow (ΔF/F ≈ 3.4× 10 −4 ) periodic dips in the light curve of an active V = 11.7 G9V star observed by the CoRoT satellite, which they interpret as caused by a transiting companion.
Abstract: Aims. We report the discovery of very shallow (ΔF/F ≈ 3.4× 10 −4 ), periodic dips in the light curve of an active V = 11.7 G9V star observed by the CoRoT satellite, which we interpret as caused by a transiting companion. We describe the 3-colour CoRoT data and complementary ground-based observations that support the planetary nature of the companion. Methods. We used CoRoT colours information, good angular resolution ground-based photometric observations in- and out- of transit, adaptive optics imaging, near-infrared spectroscopy, and preliminary results from radial velocity measurements, to test the diluted eclipsing binary scenarios. The parameters of the host star were derived from optical spectra, which were then combined with the CoRoT light curve to derive parameters of the companion. Results. We examined all conceivable cases of false positives carefully, and all the tests support the planetary hypothesis. Blends with separation >0.40 �� or triple systems are almost excluded with a 8 × 10 −4 risk left. We conclude that, inasmuch we have been exhaustive, we have discovered a planetary companion, named CoRoT-7b, for which we derive a period of 0.853 59 ± 3 × 10 −5 day and a radius of Rp = 1.68 ± 0.09 REarth .A nalysis of preliminary radial velocity data yields an upper limit of 21 MEarth for the companion mass, supporting the finding. Conclusions. CoRoT-7b is very likely the first Super-Earth with a measured radius. This object illustrates what will probably become a common situation with missions such as Kepler, namely the need to establish the planetary origin of transits in the absence of a firm radial velocity detection and mass measurement. The composition of CoRoT-7b remains loosely constrained without a precise mass. A very high surface temperature on its irradiated face, ≈1800–2600 K at the substellar point, and a very low one, ≈50 K, on its dark face assuming no atmosphere, have been derived.
Harvard University1, University of Otago2, Universidad Autónoma Metropolitana3, Stony Brook University4, Katholieke Universiteit Leuven5, Utrecht University6, University College Hospital, Ibadan7, Peking University8, St George's Hospital9, University of Tokyo10, University of Paris11, Mental Health Services12, Pontifical Xavierian University13, All India Institute of Medical Sciences14, New Bulgarian University15, University of São Paulo16
TL;DR: Using data from over 100,000 individuals in 21 countries participating in the WHO World Mental Health Surveys, Matthew Nock and colleagues investigate which mental health disorders increase the odds of experiencing suicidal thoughts and actual suicide attempts.
Abstract: Background: Suicide is a leading cause of death worldwide. Mental disorders are among the strongest predictors of suicide; however, little is known about which disorders are uniquely predictive of suicidal behavior, the extent to which disorders predict suicide attempts beyond their association with suicidal thoughts, and whether these associations are similar across developed and developing countries. This study was designed to test each of these questions with a focus on nonfatal suicide attempts. Methods and Findings: Data on the lifetime presence and age-of-onset of Diagnostic and Statistical Manual of Mental Disorders, 4th Edition (DSM-IV) mental disorders and nonfatal suicidal behaviors were collected via structured face-to-face interviews with 108,664 respondents from 21 countries participating in the WHO World Mental Health Surveys. The results show that each lifetime disorder examined significantly predicts the subsequent first onset of suicide attempt (odds ratios [ORs] = 2.9–8.9). After controlling for comorbidity, these associations decreased substantially (ORs = 1.5–5.6) but remained significant in most cases. Overall, mental disorders were equally predictive in developed and developing countries, with a key difference being that the strongest predictors of suicide attempts in developed countries were mood disorders, whereas in developing countries impulse-control, substance use, and post-traumatic stress disorders were most predictive. Disaggregation of the associations between mental disorders and nonfatal suicide attempts showed that these associations are largely due to disorders predicting the onset of suicidal thoughts rather than predicting progression from thoughts to attempts. In the few instances where mental disorders predicted the transition from suicidal thoughts to attempts, the significant disorders are characterized by anxiety and poor impulse-control. The limitations of this study include the use of retrospective self-reports of lifetime occurrence and age-of-onset of mental disorders and suicidal behaviors, as well as the narrow focus on mental disorders as predictors of nonfatal suicidal behaviors, each of which must be addressed in future studies. Conclusions: This study found that a wide range of mental disorders increased the odds of experiencing suicide ideation. However, after controlling for psychiatric comorbidity, only disorders characterized by anxiety and poor impulse-control predict which people with suicide ideation act on such thoughts. These findings provide a more fine-grained understanding of the associations between mental disorders and subsequent suicidal behavior than previously available and indicate that mental disorders predict suicidal behaviors similarly in both developed and developing countries. Future research is needed to delineate the mechanisms through which people come to think about suicide and subsequently progress from ideation to attempts.
University of Manchester1, University of Leeds2, University of Washington3, Leeds Teaching Hospitals NHS Trust4, Université libre de Bruxelles5, Mater Dei Hospital6, Boston Children's Hospital7, University of Paris8, University of Göttingen9, Mount Sinai St. Luke's and Mount Sinai Roosevelt10, University of Barcelona11, Radboud University Nijmegen12, University of Oslo13, Royal Children's Hospital14, VU University Amsterdam15, Katholieke Universiteit Leuven16, University of São Paulo17, Rabin Medical Center18, University of British Columbia19, Technion – Israel Institute of Technology20, Baylor College of Medicine21, University of Melbourne22, Children's National Medical Center23, Ealing Hospital24, Imperial College London25
TL;DR: Mutations in SAMHD1 are described as the cause of Aicardi-Goutières syndrome at the AGS5 locus and data is presented to show that SAM HD1 may act as a negative regulator of the cell-intrinsic antiviral response.
Abstract: Aicardi-Goutieres syndrome is a mendelian mimic of congenital infection and also shows overlap with systemic lupus erythematosus at both a clinical and biochemical level The recent identification of mutations in TREX1 and genes encoding the RNASEH2 complex and studies of the function of TREX1 in DNA metabolism have defined a previously unknown mechanism for the initiation of autoimmunity by interferon-stimulatory nucleic acid Here we describe mutations in SAMHD1 as the cause of AGS at the AGS5 locus and present data to show that SAMHD1 may act as a negative regulator of the cell-intrinsic antiviral response
TL;DR: It is concluded that the average density of proteins is not a constant as often assumed and a simple molecular‐weight‐depending function is proposed that provides a more accurate estimate of the average protein density.
Abstract: The mass density of proteins is a relevant basic biophysical quantity. It is also a useful input parameter, for example, for three-dimensional structure determination by protein crystallography and studies of protein oligomers in solution by analytic ultracentrifugation. We have performed a critical analysis of published, theoretical, and experimental investigations about this issue and concluded that the average density of proteins is not a constant as often assumed. For proteins with a molecular weight below 20 kDa, the average density exhibits a positive deviation that increases for decreasing molecular weight. A simple molecular-weight-depending function is proposed that provides a more accurate estimate of the average protein density.
TL;DR: A review of more than 30 years of ecological restoration in the Brazilian part of the Atlantic Forest is presented in this paper, which summarizes the main findings and challenges for restoration in this highly threatened forest biome.
TL;DR: Direct and indirect effects of possible land-use changes from an expanded global cellulosic bioenergy program on greenhouse gas emissions over the 21st century are examined using linked economic and terrestrial biogeochemistry models.
Abstract: A global biofuels program will lead to intense pressures on land supply and can increase greenhouse gas emissions from land-use changes. Using linked economic and terrestrial biogeochemistry models, we examined direct and indirect effects of possible land-use changes from an expanded global cellulosic bioenergy program on greenhouse gas emissions over the 21st century. Our model predicts that indirect land use will be responsible for substantially more carbon loss (up to twice as much) than direct land use; however, because of predicted increases in fertilizer use, nitrous oxide emissions will be more important than carbon losses themselves in terms of warming potential. A global greenhouse gas emissions policy that protects forests and encourages best practices for nitrogen fertilizer use can dramatically reduce emissions associated with biofuels production.