An algorithm for a super-stable roommates problem

In this paper, we describe an efficient algorithm that decides if a stable matching exists for a generalized stable roommates problem, where, instead of linear preferences, agents have partial preference orders on potential partners. Furthermore, we may forbid certain partnerships, that is, we are looking for a matching such that none of the matched pairs is forbidden, and yet, no blocking pair (forbidden or not) exists. To solve the above problem, we generalize the first algorithm for the ordinary stable roommates problem

The Relative Contribution of Methanotrophs to Microbial Communities and Carbon Cycling in Soil Overlying a Coal-Bed Methane Seep

Seepage of coal-bed methane (CBM) through soils is a potential source of atmospheric CH4 and also a likely source of ancient (i.e. 14C-dead) carbon to soil microbial communities. Natural abundance 13C and 14C compositions of bacterial membrane phospholipid fatty acids (PLFAs) and soil gas CO2 and CH4 were used to assess the incorporation of CBM-derived carbon into methanotrophs and other members of the soil microbial community. Concentrations of type I and type II methanotroph PLFA biomarkers (16:1ω8c and 18:1ω8c, respectively) were elevated in CBM-impacted soils compared with a control site. Comparison of PLFA and 16s rDNA data suggested type I and II methanotroph populations were well estimated and overestimated by their PLFA biomarkers, respectively. The δ13C values of PLFAs common in type I and II methanotrophs were as negative as -67‰ and consistent with the assimilation of CBM. PLFAs more indicative of nonmethanotrophic bacteria had δ13C values that were intermediate indicating assimilation of both plantand CBM-derived carbon. Δ14C values of select PLFAs (-351 to -936‰) indicated similar patterns of CBM assimilation by methanotrophs and nonmethanotrophs and were used to estimate that 35–91% of carbon assimilated by nonmethanotrophs was derived from CBM depending on time of sampling and soil depth

Unexpected enzyme-catalysed [4+2] cycloaddition and rearrangement in polyether antibiotic biosynthesis

Enzymes that catalyse remarkable Diels–Alder-like [4+2] cyclizations have been previously implicated in the biosynthesis of spirotetronate and spirotetramate antibiotics. Biosynthesis of the polyether antibiotic tetronasin is not expected to require such steps, yet the tetronasin gene cluster encodes enzymes Tsn11 and Tsn15, which are homologous to authentic [4+2] cyclases. Here, we show that deletion of Tsn11 led to accumulation of a late-stage intermediate, in which the two central rings of tetronasin and four of its twelve asymmetric centres remain unformed. In vitro reconstitution showed that Tsn11 catalyses an apparent inverse-electron-demand hetero-Diels–Alder-like [4+2] cyclization of this species to form an unexpected oxadecalin compound that is then rearranged by Tsn15 to form tetronasin. To gain structural and mechanistic insight into the activity of Tsn15, the crystal structure of a Tsn15-substrate complex has been solved at 1.7 Å resolution

An assessment of population structure in eight breeds of cattle using a whole genome SNP panel

<p>Abstract</p> <p>Background</p> <p>Analyses of population structure and breed diversity have provided insight into the origin and evolution of cattle. Previously, these studies have used a low density of microsatellite markers, however, with the large number of single nucleotide polymorphism markers that are now available, it is possible to perform genome wide population genetic analyses in cattle. In this study, we used a high-density panel of SNP markers to examine population structure and diversity among eight cattle breeds sampled from <it>Bos indicus </it>and <it>Bos taurus</it>.</p> <p>Results</p> <p>Two thousand six hundred and forty one single nucleotide polymorphisms (SNPs) spanning all of the bovine autosomal genome were genotyped in Angus, Brahman, Charolais, Dutch Black and White Dairy, Holstein, Japanese Black, Limousin and Nelore cattle. Population structure was examined using the linkage model in the program STRUCTURE and Fst estimates were used to construct a neighbor-joining tree to represent the phylogenetic relationship among these breeds.</p> <p>Conclusion</p> <p>The whole-genome SNP panel identified several levels of population substructure in the set of examined cattle breeds. The greatest level of genetic differentiation was detected between the <it>Bos taurus </it>and <it>Bos indicus </it>breeds. When the <it>Bos indicus </it>breeds were excluded from the analysis, genetic differences among beef versus dairy and European versus Asian breeds were detected among the <it>Bos taurus </it>breeds. Exploration of the number of SNP loci required to differentiate between breeds showed that for 100 SNP loci, individuals could only be correctly clustered into breeds 50% of the time, thus a large number of SNP markers are required to replace the 30 microsatellite markers that are currently commonly used in genetic diversity studies.</p

Whole genome linkage disequilibrium maps in cattle

<p>Abstract</p> <p>Background</p> <p>Bovine whole genome linkage disequilibrium maps were constructed for eight breeds of cattle. These data provide fundamental information concerning bovine genome organization which will allow the design of studies to associate genetic variation with economically important traits and also provides background information concerning the extent of long range linkage disequilibrium in cattle.</p> <p>Results</p> <p>Linkage disequilibrium was assessed using r²among all pairs of syntenic markers within eight breeds of cattle from the <it>Bos taurus </it>and <it>Bos indicus </it>subspecies. <it>Bos taurus </it>breeds included Angus, Charolais, Dutch Black and White Dairy, Holstein, Japanese Black and Limousin while <it>Bos indicus </it>breeds included Brahman and Nelore. Approximately 2670 markers spanning the entire bovine autosomal genome were used to estimate pairwise r²values. We found that the extent of linkage disequilibrium is no more than 0.5 Mb in these eight breeds of cattle.</p> <p>Conclusion</p> <p>Linkage disequilibrium in cattle has previously been reported to extend several tens of centimorgans. Our results, based on a much larger sample of marker loci and across eight breeds of cattle indicate that in cattle linkage disequilibrium persists over much more limited distances. Our findings suggest that 30,000–50,000 loci will be needed to conduct whole genome association studies in cattle.</p

A Field Trial of Alternative Targeted Screening Strategies for Chagas Disease in Arequipa, Peru

In the wake of emerging T. cruzi infection in children of periurban Arequipa, Peru, we conducted a prospective field trial to evaluate alternative targeted screening strategies for Chagas disease across the city. Using insect vector data that is routinely collected during Ministry of Health insecticide application campaigns in 3 periurban districts of Arequipa, we separated into 4 categories those households with 1) infected vectors; 2) high vector densities; 3) low vector densities; and 4) no vectors. Residents of all infected-vector households and a random sample of those in the other 3 categories were invited for serological screening for T. cruzi infection. Subsequently, all residents of households within a 15-meter radius of detected seropositive individuals were invited to be screened in a ring case-detection scheme. Of 923 participants, 21 (2.28%) were seropositive. There were no significant differences in prevalence across the 4 screening strategies, indicating that household entomologic factors alone could not predict the risk of infection. Indeed, the most predictive variable of infection was the number of years a person lived in a location with triatomine insects. Therefore, a simple residence history questionnaire may be a useful screening tool in large, diverse urban environments with emerging Chagas disease

Os retratos de Maria Isabel e Maria Francisca de Bragança, de Nicolas-Antoine Taunay

Nicolas-Antoine Taunay, French landscape painter, produced also several portraits during his stay at the Rio de Janeiro Court. In this city, in 1816, he paints the queen Carlota Joaquina and all her daughters. In this group, two portraits have a very special way: the paintings still today catalogued as Maria Francisca and Maria Teresa, but probably being Maria Isabel and Maria Francisca de Assis - princesses that, in this year, left Brazil to marry the Spanish King Fernando VII, and his brother Carlos Maria Isidro de Bourbon. In this article, beyond to describe these portraits (and analyse the identities of the portrayed princesses), I analyse their functions in the Court society and the mains artists of this gender in Europe. I will discuss, as well, the hypothesis about the Taunay choices. In this sense, I will analyse the possible circulation of the typologies of portrait between Italy, Portugal, Spain and France, understanding these productions by Taunay and the functions occupied by these portraits in the political relations between Brazil and Europe.Nicolas-Antoine Taunay, pintor de paisagens francês, também realizou alguns retratos durante sua estadia na corte do Rio de Janeiro. Nessa cidade, em 1816, ele pinta a rainha Carlota Joaquina e todas as suas filhas. Nesse conjunto, dois retratos sobressaem-se de modo especial: os hoje ainda inventariados como de Maria Francisca e de Maria Teresa, mas que provavelmente são o de Maria Isabel e o de Maria Francisca de Assis - princesas que, nesse ano, deixavam o Brasil para casar-se, respectivamente, com Fernando VII, o rei espanhol, e com seu irmão Carlos Isidro de Bourbon. Neste artigo, além de descrevermos os retratos (e analisarmos a questão da identidade das princesas retratadas), abordamos suas funções na sociedade das cortes e os principais artistas do gênero na Europa. Discutimos, também, as hipóteses que permeiam as escolhas de Taunay para sua execução. Nesse sentido, tratamos da possível circulação de tipologias entre Itália, Portugal, Espanha e França, buscando entender a forma como Taunay os realizou e as funções que doravante tais retratos ocupariam nas relações entre o Brasil e a Europa.Universidade Federal de São Paulo (UNIFESP)UNIFESPSciEL

Landscape dynamics and diversification of the megadiverse South American freshwater fish fauna

Landscape dynamics are widely thought to govern the tempo and mode of continental radiations, yet the effects of river network rearrangements on dispersal and lineage diversification remain poorly understood. We integrated an unprecedented occurrence dataset of 4,967 species with a newly compiled, time-calibrated phylogeny of South American freshwater fishes—the most species-rich continental vertebrate fauna on Earth—to track the evolutionary processes associated with hydrogeographic events over 100 Ma. Net lineage diversification was heterogeneous through time, across space, and among clades. Five abrupt shifts in net diversification rates occurred during the Paleogene and Miocene (between 30 and 7 Ma) in association with major landscape evolution events. Net diversification accelerated from the Miocene to the Recent (c. 20 to 0 Ma), with Western Amazonia having the highest rates of in situ diversification, which led to it being an important source of species dispersing to other regions. All regional biotic interchanges were associated with documented hydrogeographic events and the formation of biogeographic corridors, including the Early Miocene (c. 23 to 16 Ma) uplift of the Serra do Mar and Serra da Mantiqueira and the Late Miocene (c. 10 Ma) uplift of the Northern Andes and associated formation of the modern transcontinental Amazon River. The combination of high diversification rates and extensive biotic interchange associated with Western Amazonia yielded its extraordinary contemporary richness and phylogenetic endemism. Our results support the hypothesis that landscape dynamics, which shaped the history of drainage basin connections, strongly affected the assembly and diversification of basin-wide fish fauna

Bologna process, higher education and a few considerations about the New University

O presente artigo analisa o que se convencionou chamar de Processo de Bolonha, isto é, a produção de uma “política pública de um meta-Estado para um meta-campo universitário”, constituindo-se em uma política educacional supranacional, comum aos estados-membros da União Européia, com vista à construção de um “espaço europeu de educação superior”. O processo político e de reformas institucionais, realizado por cada governo nacional, conduzirá ao estabelecimento efetivo do novo sistema europeu de educação superior até 2010, incluindo atualmente 45 países – todos os da UE e outros 18 países europeus não pertencentes a ela. Nesse sentido, por se tratar de um vastíssimo número de “subsistemas nacionais” e de instituições educativas, atribui-se um grande protagonismo às questões relativas à “garantia de qualidade”. Analisam-se, igualmente, as recentes transformações na educação superior no Brasil, em que o projeto da chamada “Universidade Nova” e o Programa de Apoio a Planos de Reestruturação e Expansão das Universidades Federais (REUNI) constituem-se nas manifestações mais claras do reordenamento desse nível de ensino (seguindo os parâmetros de Bolonha), que já experimentara grandes transformações nos governos de Fernando Henrique Cardoso (1995-2002) e teve prosseguimento nos governos de Luiz Inácio Lula da Silva (2003-2006; 2007), embora com distintos matizes.This article analyzes what is conventionally known as the Bologna Process, or the making of a “public policy of a meta-State for a University meta-field” that corresponds to a supranational educational policy for all the European Union membership States, with the goal of building a “European higher education space.” The political process and the institutional reforms of each national government intends to establish the new European higher education system until 2010, with 45 countries – the number reflects current developments, including the EU membership States and 18 non-EU countries. Given the high quantity and the myriads of “national subsystems” and educational institutions involved, “quality assurance” becomes a major task in this process. We analyze, in the same way, the recent higher education changes in Brazil, where the so-called “New University” project and the Program of Support for the Restructuring and Expansion of Brazilian Federal Universities (REUNI, in Portuguese) are the clearest expressions of the reshaping of the higher education system (in accordance with the Bologna standards) after the dramatic changes made by Fernando Henrique Cardoso´s government (1995-2002) and continued by Luiz Inácio Lula da Silva´s government (2003-2006; 2007), despite some differences between both administrations

Determinants of reef fish assemblages in tropical Oceanic islands

Diversity patterns are determined by biogeographic, energetic, and anthropogenic factors, yet few studies have combined them into a large‐scale framework in order to decouple and compare their relative effects on fish faunas. Using an empirical dataset derived from 1527 underwater visual censuses (UVC) at 18 oceanic islands (five different marine provinces), we determined the relative influence of such factors on reef fish species richness, functional dispersion, density and biomass estimated from each UVC unit. Species richness presented low variation but was high at large island sites. High functional dispersion, density, and biomass were found at islands with large local species pool and distance from nearest reef. Primary productivity positively affected fish richness, density and biomass confirming that more productive areas support larger populations, and higher biomass and richness on oceanic islands. Islands densely populated by humans had lower fish species richness and biomass reflecting anthropogenic effects. Species richness, functional dispersion, and biomass were positively related to distance from the mainland. Overall, species richness and fish density were mainly influenced by biogeographical and energetic factors, whereas functional dispersion and biomass were strongly influenced by anthropogenic factors. Our results extend previous hypotheses for different assemblage metrics estimated from empirical data and confirm the negative impact of humans on fish assemblages, highlighting the need for conservation of oceanic islands.UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigación en Ciencias del Mar y Limnología (CIMAR