New stopping criteria for segmenting DNA sequences

We propose a solution on the stopping criterion in segmenting inhomogeneous DNA sequences with complex statistical patterns. This new stopping criterion is based on Bayesian Information Criterion (BIC) in the model selection framework. When this stopping criterion is applied to a left telomere sequence of yeast Saccharomyces cerevisiae and the complete genome sequence of bacterium Escherichia coli, borders of biologically meaningful units were identified (e.g. subtelomeric units, replication origin, and replication terminus), and a more reasonable number of domains was obtained. We also introduce a measure called segmentation strength which can be used to control the delineation of large domains. The relationship between the average domain size and the threshold of segmentation strength is determined for several genome sequences.Comment: 4 pages, 4 figures, Physical Review Letters, to appea

IL-26 is overexpressed in chronically HCV-infected patients and enhances TRAIL-mediated cytotoxicity and interferon production by human NK cells

Objective Interleukin-26 (IL-26) is a member of the IL-10 cytokine family, first discovered based on its peculiar expression by virus-transformed T cells. IL-26 is overexpressed in chronic inflammation (rheumatoid arthritis and Crohn’s disease) and induces proinflammatory cytokines by myeloid cells and some epithelial cells. We thus investigated the expression and potential role of IL-26 in chronic HCV infection, a pathology associated with chronic inflammation.Design IL-26 was quantified in a cohort of chronically HCV-infected patients, naive of treatment and its expression in the liver biopsies investigated by immunohistochemistry. We also analysed the ability of IL-26 to modulate the activity of natural killer (NK) cells, which control HCV infection. Results The serum levels of IL-26 are enhanced in chronically HCV-infected patients, mainly in those with severe liver inflammation. Immunohistochemistry reveals an intense IL-26 staining in liver lesions, mainly in infiltrating CD3+ cells. We also show that NK cells from healthy subjects and from HCV-infected patients are sensitive to IL-26. IL-26 upregulates membrane tumour necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) expression on CD16− CD56bright NK cells, enabling them to kill HCV-infected hepatoma cells, with the same efficacy as interferon (IFN)-α-treated NK cells. IL-26 also induces the expression of the antiviral cytokines IFN-β and IFN-γ, and of the proinflammatory cytokines IL-1β and TNF-α by NK cells. Conclusions This study highlights IL-26 as a new player in the inflammatory and antiviral immune responses associated with chronic HCV infection

Extreme Conservation Leads to Recovery of the Virunga Mountain Gorillas

As wildlife populations are declining, conservationists are under increasing pressure to measure the effectiveness of different management strategies. Conventional conservation measures such as law enforcement and community development projects are typically designed to minimize negative human influences upon a species and its ecosystem. In contrast, we define “extreme” conservation as efforts targeted to deliberately increase positive human influences, including veterinary care and close monitoring of individual animals. Here we compare the impact of both conservation approaches upon the population growth rate of the critically endangered Virunga mountain gorillas (Gorilla beringei beringei), which increased by 50% since their nadir in 1981, from approximately 250 to nearly 400 gorillas. Using demographic data from 1967–2008, we show an annual decline of 0.7%±0.059% for unhabituated gorillas that received intensive levels of conventional conservation approaches, versus an increase 4.1%±0.088% for habituated gorillas that also received extreme conservation measures. Each group of habituated gorillas is now continuously guarded by a separate team of field staff during daylight hours and receives veterinary treatment for snares, respiratory disease, and other life-threatening conditions. These results suggest that conventional conservation efforts prevented a severe decline of the overall population, but additional extreme measures were needed to achieve positive growth. Demographic stochasticity and socioecological factors had minimal impact on variability in the growth rates. Veterinary interventions could account for up to 40% of the difference in growth rates between habituated versus unhabituated gorillas, with the remaining difference likely arising from greater protection against poachers. Thus, by increasing protection and facilitating veterinary treatment, the daily monitoring of each habituated group contributed to most of the difference in growth rates. Our results argue for wider consideration of extreme measures and offer a startling view of the enormous resources that may be needed to conserve some endangered species

Feeding of Triportheus angulatus (Spix & Agassiz, 1829) in the Camaleão lake, Manaus, Amazonas state, Brazil

Periodical flooding cause strong modifications in Central Amazonian floodplain. Periodical rising and decreasing of the water level influences abiotic and biotic factors of the aquatic environments. During the flooding season, there is a high feed availability, in contrast with dry season in which feed availability is at the lowest level. Limnological parameters also change seasonally. Oxygen concentrations vary both daily and seasonally, sometimes even showing hypoxic conditions. Despite these alterations, floodplain lakes are inhabited by several fish species, having the most diverse and abundant fish fauna among the Amazonian environments. This study focused on Triportheus angulatus feeding in temporal distribution in order to understand the influences of hydrological changes on individual size, diet composition and feeding even in low oxygen concentrations. In rising waters season, small individuals are predominant while the decreasing and the dry seasons there are mostly larger ones. There is a seasonal change on diet composition and this is related to feed type that is more available: during the rising, fishes eat mainly insects and zooplankton; in the flood season and drying season, seeds and fruits are predominant, and at the dry season they eat mainly insects. Feed ingestion was higher in the rising waters and mostly in the flood, and it was lower in the drying season. Feeding activity was not related with oxygen concentrations.As inundações periódicas na Amazônia Central causam profundas modificações no meio ambiente. A alternância dos períodos de cheias e secas tem influência nos fatores bióticos e abióticos do meio aquático. Na enchente e na cheia é alta a oferta de alimentos, ampliando o espectro alimentar que é restrito na seca. As variáveis limnológicas também sofrem modificações. As concentrações de oxigênio têm variações sazonais e diárias, às vezes com períodos de hipoxia. Apesar dessas alterações, os lagos de várzea são habitados por muitas espécies de peixes e estão entre os ambientes de maior abundância e riqueza de peixes na Amazônia. A distribuição temporal e a alimentação de Triportheus angulatus (Spix & Agassiz, 1829) foi estudada em um lago de várzea da Amazônia Central para entender a influência das modificações hídricas sobre o tamanho dos indivíduos, a composição da dieta e a ingestão dos alimentos mesmo em condições de baixas concentrações de oxigênio. Na enchente predominam os indivíduos menores, enquanto que na cheia, vazante e seca os maiores. Houve mudança sazonal na composição da dieta que foi relacionada com a disponibilidade de alimentos no ambientena enchente os peixes ingerem principalmente insetos e zooplâncton; na cheia e vazante frutos e sementes, e na seca insetos. O consumo de alimento foi alto na enchente e cheia, decrescendo na vazante e atingindo as menores quantidades na seca. A atividade alimentar, no período estudado, não foi influenciada pelas baixas concentrações de oxigênio existentes no lago

ObjectGlobe: Open Distributed Query Processing Services on the Internet ∗

The Internet today offers access to a wide range of data sources, for example, in the area of real estate offers, geographical information, product catalogs or travel planning to name just a few. Therefore, it is often stated, that the Internet represents a huge distributed database, but at the moment we cannot use this database in the way we use a database managed by a modern DBMS. We also want to be able to pose queries over arbitrary data sources by executing data transformations, aggregate or user-defined functions or join operations. Ultimately, we strive for a query processing system which can perform an ad-hoc composition of completely unrelated query processing services which are offered on the Internet in the manner of a free market. These services could be specialized on providing data, resources for the query execution itself (CPU power, storage area) or functions which can be embedded in the execution. Such an open system could vastly ease the interaction in commercial business-to-business and business-to-customer applications like shopping portals, electronic market-places or virtual enterprises. For example, somebody could search for real estate offers which fulfill some constraints on the features of the building, its geographical position and the corresponding ambient data. The respective query should then access data from several commercial realtor databases, a geographical information system and a server with global ambient data. Additionally, the query should use a ranking function specialize