Embarking on a research project…or research for the absolute novice

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BlogForever D5.2: Implementation of Case Studies

This document presents the internal and external testing results for the BlogForever case studies. The evaluation of the BlogForever implementation process is tabulated under the most relevant themes and aspects obtained within the testing processes. The case studies provide relevant feedback for the sustainability of the platform in terms of potential users’ needs and relevant information on the possible long term impact

BlogForever D5.3: User Questionnaires and Reports

This report presents the feedback gathered from third party users during the BlogForever Case Studies. Therefore, the research framework is defined and the case studies results are presented, followed by a summary of conclusions and remarks

It's all in the details: methods in breast development and cancer

The inaugural European Network for Breast Development and Cancer (ENBDC) meeting on 'Methods in Mammary Gland Development and Cancer' was held in Weggis, Switzerland last April. The goal was to discuss the details of techniques used to study mammary gland biology and tumourigenesis. Highlights of this meeting included the use of four-colour fluorescence for protein co-localisation in tissue microarrays, genome analysis at single cell resolution, technical issues in the isolation of normal and tumour stem cells, and the use of mouse models and mammary gland transplantations to elucidate gene function in mammary development and to study drug resistance in breast cancer

Exact and quasiexact solvability of second-order superintegrable quantum systems: I. Euclidean space preliminaries

We show that second-order superintegrable systems in two-dimensional and three-dimensional Euclidean space generate both exactly solvable (ES) and quasiexactly solvable (QES) problems in quantum mechanics via separation of variables, and demonstrate the increased insight into the structure of such problems provided by superintegrability. A principal advantage of our analysis using nondegenerate superintegrable systems is that they are multiseparable. Most past separation of variables treatments of QES problems via partial differential equations have only incorporated separability, not multiseparability. Also, we propose another definition of ES and QES. The quantum mechanical problem is called ES if the solution of Schrödinger equation can be expressed in terms of hypergeometric functions mFn and is QES if the Schrödinger equation admits polynomial solutions with coefficients necessarily satisfying a three-term or higher order of recurrence relations. In three dimensions we give an example of a system that is QES in one set of separable coordinates, but is not ES in any other separable coordinates. This example encompasses Ushveridze's tenth-order polynomial QES problem in one set of separable coordinates and also leads to a fourth-order polynomial QES problem in another separable coordinate set

BASIS: High-performance bioinformatics platform for processing of large-scale mass spectrometry imaging data in chemically augmented histology

Mass Spectrometry Imaging (MSI) holds significant promise in augmenting digital histopathologic analysis by generating highly robust big data about the metabolic, lipidomic and proteomic molecular content of the samples. In the process, a vast quantity of unrefined data, that can amount to several hundred gigabytes per tissue section, is produced. Managing, analysing and interpreting this data is a significant challenge and represents a major barrier to the translational application of MSI. Existing data analysis solutions for MSI rely on a set of heterogeneous bioinformatics packages that are not scalable for the reproducible processing of large-scale (hundreds to thousands) biological sample sets. Here, we present a computational platform (pyBASIS) capable of optimized and scalable processing of MSI data for improved information recovery and comparative analysis across tissue specimens using machine learning and related pattern recognition approaches. The proposed solution also provides a means of seamlessly integrating experimental laboratory data with downstream bioinformatics interpretation/analyses, resulting in a truly integrated system for translational MSI

Neuraminidase Inhibitor Susceptibility Testing in Human Influenza Viruses: A Laboratory Surveillance Perspective

Neuraminidase inhibitors (NAIs) are vital in managing seasonal and pandemic influenza infections. NAI susceptibilities of virus isolates (n = 5540) collected during the 2008–2009 influenza season were assessed in the chemiluminescent neuraminidase inhibition (NI) assay. Box-and-whisker plot analyses of log-transformed IC50s were performed for each virus type/subtype and NAI to identify outliers which were characterized based on a statistical cutoff of IC50 >3 interquartile ranges (IQR) from the 75th percentile. Among 1533 seasonal H1N1 viruses tested, 1431 (93.3%) were outliers for oseltamivir; they all harbored the H275Y mutation in the neuraminidase (NA) and were reported as oseltamivir-resistant. Only 15 (0.7%) of pandemic 2009 H1N1 viruses tested (n = 2259) were resistant to oseltamivir. All influenza A(H3N2) (n = 834) and B (n = 914) viruses were sensitive to oseltamivir, except for one A(H3N2) and one B virus, with D151V and D197E (D198E in N2 numbering) mutations in the NA, respectively. All viruses tested were sensitive to zanamivir, except for six seasonal A(H1N1) and several A(H3N2) outliers (n = 22) which exhibited cell culture induced mutations at residue D151 of the NA. A subset of viruses (n = 1058) tested for peramivir were sensitive to the drug, with exception of H275Y variants that exhibited reduced susceptibility to this NAI. This study summarizes baseline susceptibility patterns of seasonal and pandemic influenza viruses, and seeks to contribute towards criteria for defining NAI resistance

Canonicalizing Knowledge Base Literals

Ontology-based knowledge bases (KBs) like DBpedia are very valuable resources, but their usefulness and usability is limited by various quality issues. One such issue is the use of string literals instead of semantically typed entities. In this paper we study the automated canonicalization of such literals, i.e., replacing the literal with an existing entity from the KB or with a new entity that is typed using classes from the KB. We propose a framework that combines both reasoning and machine learning in order to predict the relevant entities and types, and we evaluate this framework against state-of-the-art baselines for both semantic typing and entity matching

Morbidity, outcomes and cost-benefit analysis of wildlife rehabilitation in Catalonia (Spain)

Background There are few studies of careful examination of wildlife casualties in Wildlife Rehabilitation Centers. These studies are essential for detecting menaces to wild species and providing objective criteria about cost-benefit of treatments in those centers. The release rate is considered the main outcome indicator, but other parameters such as length of stay at the center and a cost-benefit index expressed as number of released animals per euro and day, could be used as reliable estimators of the rehabilitation costs. Methodology A retrospective study based on 54772 admissions recorded from 1995-2013 in the database of the Wildlife Rehabilitation Center of Torreferrussa (Catalonia, NW Spain) assessed the morbidity, outcomes and cost-benefits of the rehabilitation practices. Results Three hundred and two species were included: 232 birds (n = 48633), 37 mammals (n = 3293), 20 reptiles (n = 2705) and 13 amphibians (n = 141). The most frequent causes of admission were: 39.8% confiscation of protected species (89.4% passerines), 31.8% orphaned young animals (35.3% swifts, 21.7% diurnal raptors and owls) and 17.4% trauma casualties (46.7% raptors and owls). The highest proportion of releases was found in the captivity confiscation category [87.4% passerines (median time of stay: 12 days)], followed by the orphaned category [78% owls (66 days), 76.5% diurnal birds of prey (43 days), 75.6% hedgehogs (49 days), 52.7% swifts (19 days) and 52% bats (55 days)]. For the trauma group, 46.8% of releases were hedgehogs (44 days) and 25.6% owls (103 days). As regards the cost-benefit index, the trauma casualties and infectious diseases had the worse values with 1.3 and 1.4 released animals/euro/day respectively, and were particularly low in raptors, waders, marine birds and chiroptera. On the contrary, captivity (4.6) and misplacement (4.1) had the best index, particulary in amphibian, reptiles and passerines. Conclusions/significance Cost-benefit studies including the release rate, the time of stay at the center and the costbenefit index should be implemented for improving management efficiency of the Wildlife Rehabilitation Centers