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Bottom-up proteomics analyses have been proved over the last years to be a powerful tool in the characterization of the proteome and are crucial for understanding cellular and organism behaviour. Through differential proteomic analysis researchers can shed light on groups of proteins or individual proteins that play key roles in certain, normal or pathological conditions. However, several tools for the analysis of such complex datasets are powerful, but hard-to-use with steep learning curves. In addition, some other tools are easy to use, but are weak in terms of analytical power. Previously, we have introduced ProteoSign, a powerful, yet user-friendly open-source online platform for protein differential expression/abundance analysis designed with the end-proteomics user in mind. Part of Proteosigns power stems from the utilization of the well-established Linear Models For Microarray Data (LIMMA) methodology. Here, we present a substantial upgrade of this computational resource, called ProteoSign v2, where we introduce major improvements, also based on user feedback. The new version offers more plot options, supports additional experimental designs, analyzes updated input datasets and performs a gene enrichment analysis of the differentially expressed proteins. We also introduce the deployment of the Docker technology and significantly increase the speed of a full analysis. ProteoSign v2 is available at http://bioinformatics.med.uoc.gr/ProteoSign.

ObjectiveNowadays, due to the technological advances of high-throughput techniques, Systems Biology has seen a tremendous growth of data generation. With network analysis, looking at biological systems at a higher level in order to better understand a system, its topology and the relationships between its components is of a great importance. Gene expression, signal transduction, protein/chemical interactions, biomedical literature co-occurrences, are few of the examples captured in biological network representations where nodes represent certain bioentities and edges represent the connections between them. Today, many tools for network visualization and analysis are available. Nevertheless, most of them are standalone applications that often (i) burden users with computing and calculation time depending on the network's size and (ii) focus on handling, editing and exploring a network interactively. While such functionality is of great importance, limited efforts have been made towards the comparison of the topological analysis of multiple networks.ResultsNetwork Analysis Provider (NAP) is a comprehensive web tool to automate network profiling and intra/inter-network topology comparison. It is designed to bridge the gap between network analysis, statistics, graph theory and partially visualization in a user-friendly way. It is freely available and aims to become a very appealing tool for the broader community. It hosts a great plethora of topological analysis methods such as node and edge rankings. Few of its powerful characteristics are: its ability to enable easy profile comparisons across multiple networks, find their intersection and provide users with simplified, high quality plots of any of the offered topological characteristics against any other within the same network. It is written in R and Shiny, it is based on the igraph library and it is able to handle medium-scale weighted/unweighted, directed/undirected and bipartite graphs. NAP is available at http://bioinformatics.med.uoc.gr/NAP .

Profiling of proteome dynamics is crucial for understanding cellular behavior in response to intrinsic and extrinsic stimuli and maintenance of homeostasis. Over the last 20 years, mass spectrometry (MS) has emerged as the most powerful tool for large-scale identification and characterization of proteins. Bottom-up proteomics, the most common MS-based proteomics approach, has always been challenging in terms of data management, processing, analysis and visualization, with modern instruments capable of producing several gigabytes of data out of a single experiment. Here, we present ProteoSign, a freely available web application, dedicated in allowing users to perform proteomics differential expression/abundance analysis in a user-friendly and self-explanatory way. Although several non-commercial standalone tools have been developed for post-quantification statistical analysis of proteomics data, most of them are not end-user appealing as they often require very stringent installation of programming environments, third-party software packages and sometimes further scripting or computer programming. To avoid this bottleneck, we have developed a user-friendly software platform accessible via a web interface in order to enable proteomics laboratories and core facilities to statistically analyse quantitative proteomics data sets in a resource-efficient manner. ProteoSign is available at http://bioinformatics.med.uoc.gr/ProteoSign and the source code at https://github.com/yorgodillo/ProteoSign.

Inherited retinopathies can initially present with high refractive error in the first decade of life, before accompanying signs or symptoms are evident. A 4-year-old girl with high myopia (S-12.00 C-4.00 × 20 in the right and S-14.50 C-2.75 × 160 in the left eye), moderate visual acuity (0.3 logMAR in the right and 0.4 logMAR in the left eye), and left esotropia, presented with unremarkable past medical history and no family history of high refractive error or low vision. In optical coherence tomography imaging, macular thinning was evident, while morphology was normal. Full-field electroretinogram revealed normal implicit time recordings with reduced amplitudes in scotopic and photopic conditions. Fundus autofluorescence showed a radial pattern in both eyes. During a 5-year follow-up, significant myopia progression ensued (S-17.25 C-3.00 × 20 in the right and S-17.25 C-2.00 × 160 in the left eye), with a corresponding increase in axial length and an unchanged visual acuity. Whole-exome sequencing revealed a heterozygous termination codon variant c.212C>G (p.Ser71Ter) in RPGR, considered to be pathogenic. Segregation analysis precluded the variation in the mother and sister. A random pattern of X-chromosome inactivation was detected in the proband, without X-chromosome inactivation deviation. This is the second report associating this specific RPGR mutation with high myopia and the first report to identify it in a female proband. This case provides additional evidence on the genotypic-phenotypic correlation between RPGR c.212C>G mutation and high myopia. [ABSTRACT FROM AUTHOR]

Researchers have found that the stigma associated with seeking therapy--particularly self-stigma--can inhibit the use of psychological services. Yet, most of the research on self-stigma has been conducted in the United States. This is a considerable limitation, as the role of self-stigma in the help-seeking process may vary across cultural groups. However, to examine cross-cultural variations, researchers must first develop culturally valid scales. Therefore, this study examined scale validity and reliability of the widely used Self-Stigma of Seeking Help scale (SSOSH; Vogel, Wade, & Haake, 2006) across samples from 6 different countries (England, Greece, Israel, Taiwan, Turkey, and the United States). Specifically, we used a confirmatory factor analysis framework to conduct measurement invariance analysis and latent mean comparisons of the SSOSH across the 6 sampled countries. Overall, the results suggested that the SSOSH has a similar univariate structure across countries and is sufficiently invariant across countries to be used to explore cultural differences in the way that self-stigma relates to help-seeking behavior. (Contains 5 tables and 1 footnote.)

A stochastic model motivated by the Lagrangian transported probability density function method for turbulent reacting flows and the cellular automata approach for forest fires was put together to simulate propagation of fires in terrains with inhomogeneous composition. In contrast to the usual cellular automata models for fires where the probability of ignition is prescribed, here the ignition of cells is determined by a random walk that mimics turbulent convection and diffusion of the hot gases and firebrands from upwind and neighbouring fire fronts. Radiation is also included. The model is aimed at speed of computation while approximating the key physics through only a few terrain-related inputs and tunable parameters representing fire intensity, hot gas and ember decay timescales, cell ignition delay and local turbulence. These parameters were calibrated against controlled fire experiments and the model was then used to give reasonable predictions for fires of increasing complexity. The presented framework allows improvements for more accurate representation of the flammable material characteristics, fire-induced flow modifications, and most other phenomena present in fires, hence providing an extendable and simple yet physically-realistic novel modelling approach. [ABSTRACT FROM AUTHOR]

Background. The increased comorbidities among older people are related to the longer life expectancy and the way a condition is defined. People who live longer and remain healthy express different needs from older people of previous decades. Objective. This study aims to present the profile of the older person in contemporary society and the careworkers' humanistic training needs. Methodology. The focus group methodology was selected. Twelve focus groups consisted of 69 participants over 60 years old in total and six focus groups of 41 careworkers in total, from Italy, Portugal, Finland, Romania, UK, and Cyprus, were conducted. A content analysis was used. Results. A profile of the older person living in the above stated countries was revealed with the "New Old" being financially independent, active with a healthy lifestyle, more informed and educated in relation to the past, liking social interactions, open-minded to new relationships, volunteering for non-for-profit associations, using technology, or wanting to learn how to use. However, older people in these countries were still experiencing ageism (discrimination, ignorance, and social exclusion) and lack of respect. Care workers also expressed their views in relation to the training needs that meets this new profile of older people including basic nursing skills, daily living activities, humanistic, person-centered care, social skills, and ICT competence. Conclusions. This multicenter focus group discussions study promoted the concept of the older person in contemporary society and the importance of humanistic care. A new definition of the older person and an adaptation of the training curricula for careworkers Job certification including the person-centered approach is required. [ABSTRACT FROM AUTHOR]