Genome wide analysis of gene expression changes in skin from patients with type 2 diabetes

Non-healing chronic ulcers are a serious complication of diabetes and are a major healthcare problem. While a host of treatments have been explored to heal or prevent these ulcers from forming, these treatments have not been found to be consistently effective in clinical trials. An understanding of the changes in gene expression in the skin of diabetic patients may provide insight into the processes and mechanisms that precede the formation of non-healing ulcers. In this study, we investigated genome wide changes in gene expression in skin between patients with type 2 diabetes and non-diabetic patients using next generation sequencing. We compared the gene expression in skin samples taken from 27 patients (13 with type 2 diabetes and 14 non-diabetic). This information may be useful in identifying the causal factors and potential therapeutic targets for the prevention and treatment of diabetic related diseases

Factors affecting hotel selection: Greek customers' perception

Selection of hotel is of high priority and significance for tourists and entails a complicated decision-making process. The paper aims at identifying the most significant hotel selection factors taken into account by Greek customers. An empirical research study was conducted using an online survey. Ten factors identified by literature review included in the investigation. The findings indicate that Cleanliness is the most important factor in the selection of accommodation, followed by Price and Staff. Considering the priorities of tourists, hotel managers may design more effectively their segmentation, targeting and positioning strategy to ensure that their offerings match the needs and wants of their guests

Factors affecting hotel selection: Greek customers' perception

Selection of hotel is of high priority and significance for tourists and entails a complicated decision-making process. The paper aims at identifying the most significant hotel selection factors taken into account by Greek customers. An empirical research study was conducted using an online survey. Ten factors identified by literature review included in the investigation. The findings indicate that Cleanliness is the most important factor in the selection of accommodation, followed by Price and Staff. Considering the priorities of tourists, hotel managers may design more effectively their segmentation, targeting and positioning strategy to ensure that their offerings match the needs and wants of their guests

A gene expression atlas of the domestic pig

<p>Abstract</p> <p>Background</p> <p>This work describes the first genome-wide analysis of the transcriptional landscape of the pig. A new porcine Affymetrix expression array was designed in order to provide comprehensive coverage of the known pig transcriptome. The new array was used to generate a genome-wide expression atlas of pig tissues derived from 62 tissue/cell types. These data were subjected to network correlation analysis and clustering.</p> <p>Results</p> <p>The analysis presented here provides a detailed functional clustering of the pig transcriptome where transcripts are grouped according to their expression pattern, so one can infer the function of an uncharacterized gene from the company it keeps and the locations in which it is expressed. We describe the overall transcriptional signatures present in the tissue atlas, where possible assigning those signatures to specific cell populations or pathways. In particular, we discuss the expression signatures associated with the gastrointestinal tract, an organ that was sampled at 15 sites along its length and whose biology in the pig is similar to human. We identify sets of genes that define specialized cellular compartments and region-specific digestive functions. Finally, we performed a network analysis of the transcription factors expressed in the gastrointestinal tract and demonstrate how they sub-divide into functional groups that may control cellular gastrointestinal development.</p> <p>Conclusions</p> <p>As an important livestock animal with a physiology that is more similar than mouse to man, we provide a major new resource for understanding gene expression with respect to the known physiology of mammalian tissues and cells. The data and analyses are available on the websites <url>http://biogps.org and http://www.macrophages.com/pig-atlas</url>.</p

An integrated bioinformatics analysis reveals divergent evolutionary pattern of oil biosynthesis in high- and low-oil plants

Seed oils provide a renewable source of food, biofuel and industrial raw materials that is important for humans. Although many genes and pathways for acyl-lipid metabolism have been identified, little is known about whether there is a specific mechanism for high-oil content in high-oil plants. Based on the distinct differences in seed oil content between four high-oil dicots (20~50%) and three low-oil grasses (<3%), comparative genome, transcriptome and differential expression analyses were used to investigate this mechanism. Among 4,051 dicot-specific soybean genes identified from 252,443 genes in the seven species, 54 genes were shown to directly participate in acyl-lipid metabolism, and 93 genes were found to be associated with acyl-lipid metabolism. Among the 93 dicot-specific genes, 42 and 27 genes, including CBM20-like SBDs and GPT2, participate in carbohydrate degradation and transport, respectively. 40 genes highly up-regulated during seed oil rapid accumulation period are mainly involved in initial fatty acid synthesis, triacylglyceride assembly and oil-body formation, for example, ACCase, PP, DGAT1, PDAT1, OLEs and STEROs, which were also found to be differentially expressed between high- and low-oil soybean accessions. Phylogenetic analysis revealed distinct differences of oleosin in patterns of gene duplication and loss between high-oil dicots and low-oil grasses. In addition, seed-specific GmGRF5, ABI5 and GmTZF4 were predicted to be candidate regulators in seed oil accumulation. This study facilitates future research on lipid biosynthesis and potential genetic improvement of seed oil content

Water-powered, electronics-free dressings that electrically stimulate wounds for rapid wound closure

Chronic wounds affect ~2% of the U.S. population and increase risks of amputation and mortality. Unfortunately, treatments for such wounds are often expensive, complex, and only moderately effective. Electrotherapy represents a cost-effective treatment; however, its reliance on bulky equipment limits its clinical use. Here, we introduce water-powered, electronics-free dressings (WPEDs) that offer a unique solution to this issue. The WPED performs even under harsh conditions-situations wherein many present treatments fail. It uses a flexible, biocompatible magnesium-silver/silver chloride battery and a pair of stimulation electrodes; upon the addition of water, the battery creates a radial electric field. Experiments in diabetic mice confirm the WPED's ability to accelerate wound closure and promote healing by increasing epidermal thickness, modulating inflammation, and promoting angiogenesis. Across preclinical wound models, the WPED-treated group heals faster than the control with wound closure rates comparable to treatments requiring expensive biologics and/or complex electronics. The results demonstrate the WPED's potential as an effective and more practical wound treatment dressing

SYNERGY OF ADVANCED PROCESSING TECHNIQUES USING COPERNICUS SAR AND OPTICAL SATELLITE IMAGERY TO DETECT GROUND DISPLACEMENTS: THE CASE STUDIES OF PYRGOS AND PAREKKLISIA VILLAGES IN CYPRUS

Cyprus has a long history of destructive tectonic activity and related geohazards. This is mainly due to its location on the Mediterranean fault zone and the interaction of the Eurasian and African plates. To study the occurrence of land displacements on a national scale, various space-based monitoring techniques exploiting the Copernicus program’s datasets were studied using Sentinel-1 and Sentinel-2 satellite images for the period of 2016-2021. More specifically, differential spectral indices were calculated by subtracting the reference 2016 Sentinel-2 image from an image for every year until 2021, and a parallelised version of Persistent Scatterer Interferometry (PSI) was conducted using a time series of Sentinel-1 data over the same period, to identify ground displacements over time. The PSI analysis in the area around Pyrgos and Parekklisia villages, detected Line-of-Sight (LoS) uplift phenomena of a maximum rate of 8 mm/y, in ascending and descending Sentinel-1 satellite passes. Similarly, deformation was identified from optical image processing. The integration of both techniques provided qualitative and quantitative information about ground deformation events in both areas, showcasing a complementarity of results obtained, with PSI detecting displacements in urban/built-up areas, and multispectral change detection in rural environment. In terms of correlation, the two techniques showed a fit of 31.34% in ascending and 26% in descending pass, providing additional information on the size of affected areas. This synergistic approach facilitates the systematic monitoring of areas of interest, providing significant and timely information to decision-makers, to take actions and adopt protective measures when and where it is required

The mEPN scheme: an intuitive and flexible graphical system for rendering biological pathways

<p>Abstract</p> <p>Background</p> <p>There is general agreement amongst biologists about the need for good pathway diagrams and a need to formalize the way biological pathways are depicted. However, implementing and agreeing how best to do this is currently the subject of some debate.</p> <p>Results</p> <p>The modified Edinburgh Pathway Notation (mEPN) scheme is founded on a notation system originally devised a number of years ago and through use has now been refined extensively. This process has been primarily driven by the author's attempts to produce process diagrams for a diverse range of biological pathways, particularly with respect to immune signaling in mammals. Here we provide a specification of the mEPN notation, its symbols, rules for its use and a comparison to the proposed Systems Biology Graphical Notation (SBGN) scheme.</p> <p>Conclusions</p> <p>We hope this work will contribute to the on-going community effort to develop a standard for depicting pathways and will provide a coherent guide to those planning to construct pathway diagrams of their biological systems of interest.</p

Discovering hidden relationships between renal diseases and regulated genes through 3D network visualizations

Abstract Background In a recent study, two-dimensional (2D) network layouts were used to visualize and quantitatively analyze the relationship between chronic renal diseases and regulated genes. The results revealed complex relationships between disease type, gene specificity, and gene regulation type, which led to important insights about the underlying biological pathways. Here we describe an attempt to extend our understanding of these complex relationships by reanalyzing the data using three-dimensional (3D) network layouts, displayed through 2D and 3D viewing methods. Findings The 3D network layout (displayed through the 3D viewing method) revealed that genes implicated in many diseases (non-specific genes) tended to be predominantly down-regulated, whereas genes regulated in a few diseases (disease-specific genes) tended to be up-regulated. This new global relationship was quantitatively validated through comparison to 1000 random permutations of networks of the same size and distribution. Our new finding appeared to be the result of using specific features of the 3D viewing method to analyze the 3D renal network. Conclusions The global relationship between gene regulation and gene specificity is the first clue from human studies that there exist common mechanisms across several renal diseases, which suggest hypotheses for the underlying mechanisms. Furthermore, the study suggests hypotheses for why the 3D visualization helped to make salient a new regularity that was difficult to detect in 2D. Future research that tests these hypotheses should enable a more systematic understanding of when and how to use 3D network visualizations to reveal complex regularities in biological networks.http://deepblue.lib.umich.edu/bitstream/2027.42/112972/1/13104_2010_Article_700.pd

D1.15 Impact Assessment Report for RP 2

This deliverable provides the impact assessment report for RP2 (M16-M30). It provides an update on the overall and specific objectives of the EXCELSIOR project that have been achieved within RP2. This task undertakes the establishment of a methodology for the yearly monitoring of the impact of the different activities carried out by Eratosthenes Centre of Excellence (ECoE) and its partners through EXCELSIOR against a set of quantified targets. The list of Key Performance Indicators established in D1.12 has been revised based on the comments received by the EXCELSIOR project reviewers on 23 June 2021 following the first project review. This list is hereby updated to reflect the activities of RP2. By monitoring the impact for the RP2, it will provide direction of the activities needed to fulfil the KPIs for the following reporting periods. The impact assessment report will be used to assess the implementation of the work plan and adjust the activities in agreement with WP and task Leaders to ensure the achievement of the Project’s strategic objectives. WP1 provides the KPI monitoring framework and general quality processes, while the WP3 defines concrete actions affecting all other WPs for meeting the Impact KPIs. This task’s activities will be coordinated with WP3 activities on strategy definition as a continuous process, in order to update the human resources, infrastructure acquisition and overall work plan and to meet new priorities identified. The analysis outputs will update the Project Action Plan of Task 1.1. The following activities were examined and assessed according to the KPIs. These activities include proposals, dissemination events, publications, academia, networks, etc. The impact for each activity was also included