FrameDP: sensitive peptide detection on noisy matured sequences

Summary: Transcriptome sequencing represents a fundamental source of information for genome-wide studies and transcriptome analysis and will become increasingly important for expression analysis as new sequencing technologies takes over array technology. The identification of the protein-coding region in transcript sequences is a prerequisite for systematic amino acid-level analysis and more specifically for domain identification. In this article, we present FrameDP, a self-training integrative pipeline for predicting CDS in transcripts which can adapt itself to different levels of sequence qualities

In-flight radiometric calibration of the Airborne Visible/Infrared Imaging Spectrometer (AVIRIS)

A reflectance-based method was used to provide an analysis of the in-flight radiometric performance of AVIRIS. Field spectral reflectance measurements of the surface and extinction measurements of the atmosphere using solar radiation were used as input to atmospheric radiative transfer calculations. Five separate codes were used in the analysis. Four include multiple scattering, and the computed radiances from these for flight conditions were in good agreement. Code-generated radiances were compared with AVIRIS-predicted radiances based on two laboratory calibrations (pre- and post-season of flight) for a uniform highly reflecting natural dry lake target. For one spectrometer (C), the pre- and post-season calibration factors were found to give identical results, and to be in agreement with the atmospheric models that include multiple scattering. This positive result validates the field and laboratory calibration technique. Results for the other spectrometers (A, B and D) were widely at variance with the models no matter which calibration factors were used. Potential causes of these discrepancies are discussed

ENHANCEMENT OF MODE I FRACTURE TOUGHNESS OF ADHESIVELY BONDED SECONDARY JOINTS USING LAYUP PATTERNING OF CFRP

This work aims to analyse the influence of the CFRP layup patterning on the crack path of composite bonded joints and evaluate its effect on the mode I fracture toughness. An experimental program has been performed using Double Cantilever Beam tests with three different CFRP layup patterning and two adhesives. In addition, a finite element analysis was also implemented to further identify different damage mechanisms during the tests. The outcome shows that different substrate CFRP layup patterning results in distinct crack onsets and propagation paths during the tests, also influenced by the type of adhesive used. Furthermore, an enhancement of around 25% in the joint's onset fracture toughness was observed with the layup patterning compared to a reference joint (with unidirectional layup). Thus, the substrate's patterning morphology seems to be a promising method to increase the mode I fracture toughness of the studied secondary joints

Improved microfluidic platform for simultaneous multiple drug screening towards personalized treatment

Development of new targeted therapies is a challenge in the battle against cancer. Although a variety of treatments is currently available, there is no technique for rapidly evaluating the response of cancer patients to the drug. In this work, a microfluidic platform for the real-time simultaneous analysis of the success rate of different nanoparticle based chemotherapeutic drugs is presented. Based on a previous planar chamber and a reported sensitivity enhancing strategy, linear and cross shape microstructures were integrated into the chamber dome of the microfluidic polydimethylsiloxane and glass platform in order to provide a higher fluid mixing and treatment-cell interaction. Several methotrexate (MTX) based treatments (free MTX, MTX loaded Lecithin-PVA nanoparticles, MTX loaded Lecithin-Tween 80 nanoparticles) as well as their respective controls (cell media and both blank nanoparticles) were recirculated through the microchamber over an osteosarcoma cell monolayer. These nanovehicles reduced cell population to less than 20% (LEC-PVA nanoparticles) and 2.3% (LEC-Tween nanoparticles), demonstrating that nanoparticles are a promising target therapy for cancer treatment. Moreover, microstructured platforms demonstrated a higher efficacy in the drug-screening process: due to the liquid folding a higher amount of nanoparticles was internalized by the cells and, therefore, results were observed faster. In fact, the time required to reduce cell viability to the half was nearly a 75% faster. Furthermore, this microfluidic platform offers the capability to test up to five different drugs simultaneously, making it a powerful tool to evaluate the effect of multiple drugs and determine the most effective and personalized treatment

Formative Assessment and Professional Training: Reflections from a Mathematics course in Bioengineering

Bioengineering is currently considered an interdisciplinary professional field which provides solutions to different problems arising in the area of health care. Its strategic importance is widely acknowledged since its developments and proposals could help diminish the level of technological dependence in the sector. The fast pace of innovation in the area of biomedical technology gives rise to permanent reflection on the learning goals and teaching strategies proposed by educators in the different training stages of a bioengineer. In this context, learning assessment appears as a controversial issue which needs to be debated and rethought. This paper describes the reflections of teachers of a Mathematics course within a Bioengineering program around the question, What approach to assessment favors the student's participation, autonomy and training as a future bioengineer? The investigation was carried out in the framework of a Participatory Research Action project and helped us to redesign assessment activities from a different perspective.Fil: Carrere, C.. Universidad Nacional de Entre Ríos. Facultad de Ingeniería; ArgentinaFil: Milesi, S.. Universidad Nacional de Entre Ríos. Facultad de Ingeniería; ArgentinaFil: Lapyckyj, I.. Universidad Nacional de Entre Ríos. Facultad de Ingeniería; ArgentinaFil: Ravera, Emiliano Pablo. Universidad Nacional de Entre Ríos. Facultad de Ingeniería; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Escher, L.. Universidad Nacional de Entre Ríos. Facultad de Ingeniería; ArgentinaFil: Miyara, A.. Universidad Nacional de Rosario; Argentina. Universidad Nacional de Entre Ríos. Facultad de Ingeniería; ArgentinaFil: Pita, G.. Universidad Nacional de Entre Ríos. Facultad de Ingeniería; ArgentinaFil: Añino, M.. Universidad Nacional de Entre Ríos. Facultad de Ingeniería; Argentin

Did Ebola emerge in West Africa by a policy-driven phase change in agroecology? Ebola's social context

SCOPUS: no.jinfo:eu-repo/semantics/publishe

Gbrowse Moby: a Web-based browser for BioMoby Services

BACKGROUND: The BioMoby project aims to identify and deploy standards and conventions that aid in the discovery, execution, and pipelining of distributed bioinformatics Web Services. As of August, 2006, approximately 680 bioinformatics resources were available through the BioMoby interoperability platform. There are a variety of clients that can interact with BioMoby-style services. Here we describe a Web-based browser-style client – Gbrowse Moby – that allows users to discover and "surf" from one bioinformatics service to the next using a semantically-aided browsing interface. RESULTS: Gbrowse Moby is a low-throughput, exploratory tool specifically aimed at non-informaticians. It provides a straightforward, minimal interface that enables a researcher to query the BioMoby Central web service registry for data retrieval or analytical tools of interest, and then select and execute their chosen tool with a single mouse-click. The data is preserved at each step, thus allowing the researcher to manually "click" the data from one service to the next, with the Gbrowse Moby application managing all data formatting and interface interpretation on their behalf. The path of manual exploration is preserved and can be downloaded for import into automated, high-throughput tools such as Taverna. Gbrowse Moby also includes a robust data rendering system to ensure that all new data-types that appear in the BioMoby registry can be properly displayed in the Web interface. CONCLUSION: Gbrowse Moby is a robust, yet facile entry point for both newcomers to the BioMoby interoperability project who wish to manually explore what is known about their data of interest, as well as experienced users who wish to observe the functionality of their analytical workflows prior to running them in a high-throughput environment

GIVE: portable genome browsers for personal websites.

Growing popularity and diversity of genomic data demand portable and versatile genome browsers. Here, we present an open source programming library called GIVE that facilitates the creation of personalized genome browsers without requiring a system administrator. By inserting HTML tags, one can add to a personal webpage interactive visualization of multiple types of genomics data, including genome annotation, "linear" quantitative data, and genome interaction data. GIVE includes a graphical interface called HUG (HTML Universal Generator) that automatically generates HTML code for displaying user chosen data, which can be copy-pasted into user's personal website or saved and shared with collaborators. GIVE is available at: https://www.givengine.org/

The subcellular localization of the hepatitis C virus non-structural protein NS2 is regulated by an ion channel-independent function of the p7 protein

The hepatitis C virus (HCV) p7 ion channel and non-structural protein 2 (NS2) are both required for efficient assembly and release of nascent virions, yet precisely how these proteins are able to influence this process is unclear. Here, we provide both biochemical and cell biological evidence for a functional interaction between p7 and NS2. We demonstrate that in the context of a genotype 1b subgenomic replicon the localization of NS2 is affected by the presence of an upstream p7 with its cognate signal peptide derived from the C terminus of E2 (SPp7). Immunofluorescence analysis revealed that the presence of SPp7 resulted in the targeting of NS2 to sites closely associated with viral replication complexes. In addition, biochemical analysis demonstrated that, in the presence of SPp7, a significant proportion of NS2 was found in a detergent (Triton X-100)-insoluble fraction, which also contained a marker of detergent resistant rafts. In contrast, in replicons lacking p7, NS2 was entirely detergent soluble and the altered localization was lost. Furthermore, we found that serine 168 within NS2 was required for its localization adjacent to replication complexes, but not for its accumulation in the detergent-insoluble fraction. NS2 physically interacted with NS5A and this interaction was dependent on both p7 and serine 168 within NS2. Mutational and pharmacological analyses demonstrated that these effects were not a consequence of p7 ion channel function, suggesting that p7 possesses an alternative function that may influence the coordination of virus genome replication and particle assembly