Windows .NET Network Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST)

BACKGROUND: BLAST is one of the most common and useful tools for Genetic Research. This paper describes a software application we have termed Windows .NET Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST), which enhances the BLAST utility by improving usability, fault recovery, and scalability in a Windows desktop environment. Our goal was to develop an easy to use, fault tolerant, high-throughput BLAST solution that incorporates a comprehensive BLAST result viewer with curation and annotation functionality. RESULTS: W.ND-BLAST is a comprehensive Windows-based software toolkit that targets researchers, including those with minimal computer skills, and provides the ability increase the performance of BLAST by distributing BLAST queries to any number of Windows based machines across local area networks (LAN). W.ND-BLAST provides intuitive Graphic User Interfaces (GUI) for BLAST database creation, BLAST execution, BLAST output evaluation and BLAST result exportation. This software also provides several layers of fault tolerance and fault recovery to prevent loss of data if nodes or master machines fail. This paper lays out the functionality of W.ND-BLAST. W.ND-BLAST displays close to 100% performance efficiency when distributing tasks to 12 remote computers of the same performance class. A high throughput BLAST job which took 662.68 minutes (11 hours) on one average machine was completed in 44.97 minutes when distributed to 17 nodes, which included lower performance class machines. Finally, there is a comprehensive high-throughput BLAST Output Viewer (BOV) and Annotation Engine components, which provides comprehensive exportation of BLAST hits to text files, annotated fasta files, tables, or association files. CONCLUSION: W.ND-BLAST provides an interactive tool that allows scientists to easily utilizing their available computing resources for high throughput and comprehensive sequence analyses. The install package for W.ND-BLAST is freely downloadable from . With registration the software is free, installation, networking, and usage instructions are provided as well as a support forum

OSL Characterisation of Two Fluvial Sequences of the River Usmacinta in its Middle Catchment (SE Mexico)

The report summarizes luminescence profiling, initially using a SUERC PPSL system in Mexico, and laboratory analysis at SUERC, used to characterise the stratigraphy and interpret sedimentary processes in terrace deposits of the Usumacinta River, SE Mexico. This was then followed, by quantitative quartz OSL SAR dating of five sediment samples, aimed at defining the chronologicalframework of two sedimentary sequences, USU13-1 and USU13-2. In the wider region, the middle catchment of the Usumacinta River, contains numerous archaeological sites dating to the Maya Classic Period, including Bonampak, Yaxchilan and Piedras Negras. The broader aim of the investigation is to assess whether the two fluvial sequences contain a proxy record of environmental change through the archaeological period of interest. Initial luminescence profiling revealed that the stratigraphy in each profile was complex, reflecting multiple cycles of deposition, with signal maxima, followed by tails to lower intensities, possibly indicating deposition during extreme flood events, interleaved with periods of slower sedimentation, and potentially better luminescence resetting. Laboratory profiling reproduced the apparent maxima/trends in the field profiling dataset, confirming that both sections record complex depositional histories. Furthermore, the variations in stored dose estimates, and luminescence sensitivities with depth, confirm that the sections do not record simple age-depth progressions. Quantitative quartz OSL SAR dating was undertaken on five sediment samples. Given the information obtained from the field- and laboratory-profiles it is not surprising that the equivalent dose distributions for each sample showed considerable scatter, particularly so for the second section, USU13-2. Nevertheless, throughstatistical analysis, individual quartz OSL SAR ages were obtained for each sample. Individual dates fall into the Mayan Post-Classical Period to early modern Period, with statistical combinations pointing to a late 15th century accumulation of USU13-1, and the 18th century accumulation of the sediment within USU13-2. Interestingly, the three samples from section USU13-2, all show some aliquots which tail to higher equivalent doses; furthermore, in each sample, the mean value determined for this component is similar, suggesting that the sediment sampled in USU13-2, may be sourced from a 15th century or older accumulation upstream

Automatización de estacionamientos privados

La Administración del Estacionamiento Privado tiene la necesidad de obtener datos precisos y detallados de los accesos y no buscar en las hojas llenadas por los usuarios o visitantes, ya que a veces la escritura es un poco entendible, no se lleva una adecuada administración del estacionamiento y además ante un posible siniestro tendría una gran pérdida de tiempo

Potential use of split-beam echosounder angular information for bivalve banks cartography: a critical evaluation

Peer Reviewe

Improving Physical Activity Levels and Psychological Variables on University Students in the Contemplation Stage

This study aimed to investigate the effects of a physical activity intervention, based on self-determination theory and the transtheoretical model, on university students in the contemplation stage. Participants: 42 students, in the contemplation stage at baseline, were randomly assigned to an experimental group (16 women, 2 men; M age = 19.1 ± 1.15) and a control group (18 women, 2 men; M age = 20.1 ± 5.7). Methods: Physical activity was measured at different moments by accelerometry. Other cognitive variables were measured by self-reported scales. Results: We did not find any significant increases in students’ physical activity in favor of the intervention group. Intragroup analyses indicate that the intervention has an effect on physical activity (moderate-to-vigorous physical activity), basic psychological needs, and intrinsic and extrinsic motivation. Conclusions: Results partially demonstrate that applying social cognitive theories seems to be effective in improving physical activity and cognitive variables in university students in the contemplation stag

Lipid Transfer Protein Sensitization: Risk of Anaphylaxis and Molecular Sensitization Profile in Pru p 3-Sensitized Patients

Background: Component-resolved diagnosis reveals the IgE response to many inhaled, food, and other allergens, improving the understanding and diagnosis of allergic diseases. Objective: The aims of the study are to study the recognition of different lipid transfer proteins (LTPs) and other allergen families in a large group of people sensitized to Pru p 3 and to analyze the relationship between the clinical entities and the allergens. Methods: This cross-sectional study included a large cohort of patients with positive skin tests to peach fruit and Pru p 3 specific IgE antibodies. Respiratory and food allergy symptoms were collected, and we performed prick tests with pollen, plant food, and other allergens plus the ImmunoCAP ISAC assay. Results: Our sample consisted of 421 people with a mean age of 33.25 years (range 16–68); 54.6% were women. Clinical entities included anaphylaxis (37.1%), urticaria (67.9%), and oral allergy syndrome (59.1%). Rhinitis, rhinoconjunctivitis, and/or asthma were diagnosed in 71.8% of the participants. The most pronounced correlation existed between sensitization to Pru p 3 and to Jug r 3, Pla a 3, Ara h 9, and Cor a 8. We found a higher incidence of anaphylaxis in people with 5 or more recognized LTPs. No association was observed between inhaled and food allergies. Conclusion: Most Pru p 3-sensitized participants were sensitized to additional allergens from the same family and, to a lesser extent, to other allergens, mainly in the profilin and PR-10 protein families. Anaphylaxis occurred in more than a third of the cases evaluated, and almost three-quarters of them had respiratory symptoms. Respiratory and food allergies involving LTPs do not seem to be associated

Capsule enlargement in Cryptococcus neoformans confers resistance to oxidative stress suggesting a mechanism for intracellular survival

Cryptococcus neoformans is a facultative intracellular pathogen. The most distinctive feature of C. neoformans is a polysaccharide capsule that enlarges depending on environmental stimuli. The mechanism by which C. neoformans avoids killing during phagocytosis is unknown. We hypothesized that capsule growth conferred resistance to microbicidal molecules produced by the host during infection, particularly during phagocytosis. We observed that capsule enlargement conferred resistance to reactive oxygen species produced by H(2)O(2) that was not associated with a higher catalase activity, suggesting a new function for the capsule as a scavenger of reactive oxidative intermediates. Soluble capsular polysaccharide protected C. neoformans and Saccharomyces cerevisiae from killing by H(2)O(2). Acapsular mutants had higher susceptibility to free radicals. Capsular polysaccharide acted as an antioxidant in the nitroblue tetrazolium (NBT) reduction coupled to beta-nicotinamide adenine dinucleotide (NADH)/phenazine methosulfate (PMS) assay. Capsule enlargement conferred resistance to antimicrobial peptides and the antifungal drug Amphotericin B. Interestingly, the capsule had no effect on susceptibility to azoles and increased susceptibility to fluconazole. Capsule enlargement reduced phagocytosis by environmental predators, although we also noticed that in this system, starvation of C. neoformans cells produced resistance to phagocytosis. Our results suggest that capsular enlargement is a mechanism that enhances C. neoformans survival when ingested by phagocytic cells.We thank Dr J.D. Nosanchuk for the use of defensins and Dr Steinman for the kind gift of A. castellanii strains. We thank Dr J.C. Arguelles and Pilar González (Universidad de Murcia, Spain) for providing protocols to measure catalase activity, and Drs Carlos and Juana Maria Gancedo (CSIC, Spain) for the permission to use their technical resources and for their helpful discussions. We are indebted to Dr F. Usera and Rosa Hidalgo for their collaboration, help and technical support in the use of the γ-irradiator from the animal facility from the National Center for Biotechnology (CSIC, Spain). We warmly thank Josefa Casas for her technical support, and all the members from the Mycology Service from the National Center for Microbiology (Instituto de Salud Carlos III) for their helpful discussions. M.V.C. is funded by a research contract from the Agencia Española de Cooperación Internacional (AECI). O.Z. is a ‘Ramón y Cajal’ fellow from the Ministerio Español de Educación y Ciencia (MEC) and is funded by Grants MPY1025/06 from the MEC and 1181/06 from el Instituto de Salud Carlos III.S