1,531 research outputs found
Counting, generating and sampling tree alignments
Pairwise ordered tree alignment are combinatorial objects that appear in RNA
secondary structure comparison. However, the usual representation of tree
alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce
identical sets of matches between identical pairs of trees. This ambiguity is
uninformative, and detrimental to any probabilistic analysis.In this work, we
consider tree alignments up to equivalence. Our first result is a precise
asymptotic enumeration of tree alignments, obtained from a context-free grammar
by mean of basic analytic combinatorics. Our second result focuses on
alignments between two given ordered trees and . By refining our grammar
to align specific trees, we obtain a decomposition scheme for the space of
alignments, and use it to design an efficient dynamic programming algorithm for
sampling alignments under the Gibbs-Boltzmann probability distribution. This
generalizes existing tree alignment algorithms, and opens the door for a
probabilistic analysis of the space of suboptimal RNA secondary structures
alignments.Comment: ALCOB - 3rd International Conference on Algorithms for Computational
Biology - 2016, Jun 2016, Trujillo, Spain. 201
In silico predicted epitopes from the COOH-terminal extension of cysteine proteinase B inducing distinct immune responses during Leishmania (Leishmania) amazonensis experimental murine infection
<p>Abstract</p> <p>Background</p> <p><it>Leishmania </it>parasites have been reported to interfere and even subvert their host immune responses to enhance their chances of survival and proliferation. Experimental <it>Leishmania </it>infection in mice has been widely used in the identification of specific parasite virulence factors involved in the interaction with the host immune system. Cysteine-proteinase B (CPB) is an important virulence factor in parasites from the <it>Leishmania (Leishmania) mexicana </it>complex: it inhibits lymphocytes Th1 and/or promotes Th2 responses either through proteolytic activity or through epitopes derived from its COOH-terminal extension. In the present study we analyzed the effects of <it>Leishmania (Leishmania) amazonensis </it>CPB COOH-terminal extension-derived peptides on cell cultures from murine strains with distinct levels of susceptibility to infection: BALB/c, highly susceptible, and CBA, mildly resistant.</p> <p>Results</p> <p>Predicted epitopes, obtained by <it>in silico </it>mapping, displayed the ability to induce cell proliferation and expression of cytokines related to Th1 and Th2 responses. Furthermore, we applied <it>in silico </it>simulations to investigate how the MHC/epitopes interactions could be related to the immunomodulatory effects on cytokines, finding evidence that specific interaction patterns can be related to <it>in vitro </it>activities.</p> <p>Conclusions</p> <p>Based on our results, we consider that some peptides from the CPB COOH-terminal extension may influence host immune responses in the murine infection, thus helping <it>Leishmania </it>survival.</p
Phlebotomine sand flies in the State of Piauí, Brazil (Diptera: Psychodidae: Phlebotominae)
Sandflies (Diptera: Psychodidae: Phlebotominae) collected on the banks of the Velhas River in the state of Minas Gerais, Brazil
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Arthroscopic hip surgery compared with physiotherapy and activity modification for the treatment of symptomatic femoroacetabular impingement: multicentre randomised controlled trial.
OBJECTIVE: To compare arthroscopic hip surgery with physiotherapy and activity modification for improving patient reported outcome measures in patients with symptomatic femoroacetabular impingement (FAI). DESIGN: Two group parallel, assessor blinded, pragmatic randomised controlled trial. SETTING: Secondary and tertiary care centres across seven NHS England sites. PARTICIPANTS: 222 participants aged 18 to 60 years with symptomatic FAI confirmed clinically and with imaging (radiography or magnetic resonance imaging) were randomised (1:1) to receive arthroscopic hip surgery (n=112) or a programme of physiotherapy and activity modification (n=110). Exclusion criteria included previous surgery, completion of a physiotherapy programme targeting FAI within the preceding 12 months, established osteoarthritis (Kellgren-Lawrence grade ≥2), and hip dysplasia (centre-edge angle <20 degrees). INTERVENTIONS: Participants in the physiotherapy group received a goal based programme tailored to individual patient needs, with emphasis on improving core stability and movement control. A maximum of eight physiotherapy sessions were delivered over five months. Participants in the arthroscopic surgery group received surgery to excise the bone that impinged during hip movements, followed by routine postoperative care. MAIN OUTCOME MEASURES: The primary outcome measure was the hip outcome score activities of daily living subscale (HOS ADL) at eight months post-randomisation, with a minimum clinically important difference between groups of 9 points. Secondary outcome measures included additional patient reported outcome measures and clinical assessment. RESULTS: At eight months post-randomisation, data were available for 100 patients in the arthroscopic hip surgery group (89%) and 88 patients in the physiotherapy programme group (80%). Mean HOS ADL was 78.4 (95% confidence interval 74.4 to 82.3) for patients randomised to arthroscopic hip surgery and 69.2 (65.2 to 73.3) for patients randomised to the physiotherapy programme. After adjusting for baseline HOS ADL, age, sex, and study site, the mean HOS ADL was 10.0 points higher (6.4 to 13.6) in the arthroscopic hip surgery group compared with the physiotherapy programme group (P<0.001)). No serious adverse events were reported in either group. CONCLUSIONS: Patients with symptomatic FAI referred to secondary or tertiary care achieve superior outcomes with arthroscopic hip surgery than with physiotherapy and activity modification. TRIAL REGISTRATION: ClinicalTrials.gov NCT01893034.NIHR BRC oxfor
The molecular detection of different Leishmania species within sand flies from a cutaneous and visceral leishmaniasis sympatric area in Southeastern Brazil
The AFLOW Fleet for Materials Discovery
The traditional paradigm for materials discovery has been recently expanded
to incorporate substantial data driven research. With the intent to accelerate
the development and the deployment of new technologies, the AFLOW Fleet for
computational materials design automates high-throughput first principles
calculations, and provides tools for data verification and dissemination for a
broad community of users. AFLOW incorporates different computational modules to
robustly determine thermodynamic stability, electronic band structures,
vibrational dispersions, thermo-mechanical properties and more. The AFLOW data
repository is publicly accessible online at aflow.org, with more than 1.7
million materials entries and a panoply of queryable computed properties. Tools
to programmatically search and process the data, as well as to perform online
machine learning predictions, are also available.Comment: 14 pages, 8 figure
PHLEBOTOMINE FAUNA (DIPTERA: PSYCHODIDAE) IN AN AREA OF FISHING TOURISM IN CENTRAL-WESTERN BRAZIL
Capacidade para o trabalho e saúde: o que pensam as trabalhadoras da indústria de vestuário
Environmental regulation of carbon isotope composition and crassulacean acid metabolism in three plant communities along a water availability gradient
Expression of crassulacean acid metabolism (CAM) is characterized by extreme variability within and between taxa and its sensitivity to environmental variation. In this study, we determined seasonal fluctuations in CAM photosynthesis with measurements of nocturnal tissue acidification and carbon isotopic composition (δ13C) of bulk tissue and extracted sugars in three plant communities along a precipitation gradient (500, 700, and 1,000 mm year−1) on the Yucatan Peninsula. We also related the degree of CAM to light habitat and relative abundance of species in the three sites. For all species, the greatest tissue acid accumulation occurred during the rainy season. In the 500 mm site, tissue acidification was greater for the species growing at 30% of daily total photon flux density (PFD) than species growing at 80% PFD. Whereas in the two wetter sites, the species growing at 80% total PFD had greater tissue acidification. All species had values of bulk tissue δ13C less negative than −20‰, indicating strong CAM activity. The bulk tissue δ13C values in plants from the 500 mm site were 2‰ less negative than in plants from the wetter sites, and the only species growing in the three communities, Acanthocereus tetragonus (Cactaceae), showed a significant negative relationship between both bulk tissue and sugar δ13C values and annual rainfall, consistent with greater CO2 assimilation through the CAM pathway with decreasing water availability. Overall, variation in the use of CAM photosynthesis was related to water and light availability and CAM appeared to be more ecologically important in the tropical dry forests than in the coastal dune
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