What is the potential of p53 isoforms as a predictive biomarker in the treatment of cancer?

Introduction: For decades, p53 was researched as a single protein with alterations described as mutants. The discovery of 12 human p53 isoforms expressed from 9 transcripts changed this perception, eloquently explaining the numerous roles p53 plays, including apoptosis, senescence, and regeneration. Area covered: Here, we summarise the p53 isoforms and their relevance to cancer to establish an understanding and theorise on potential applications of the isoforms in clinical practice. Expert commentary: Pertaining to the different expression of isoforms in different tumors, it is concluded that the clinical use of isoforms as prognostic and predictive biomarkers will be different depending on the cell type, the tissue origin of the tumors, the position of the TP53 mutation and the driver-oncogene.</p

Impact of Sample Sizes on Information Theoretic Measures for Audio-Visual Signal Processing

In this paper we aim to explore what is the most appropriate number of data samples needed when measuring the temporal correspondence between a chosen set of video and audio cues in a given audio-visual sequence. Presently the optimal model that connects statistics of audio and video signals does not exist since one does not know the most appropriate features to be extracted in order to analyze their correlation. Previous approaches assumed simple parametric and non-parametric models for the joint distribution for capturing the complex signal relationships. The main problem in using the standard information theoretic quantities, such as entropy and mutual information, is the accurate estimation of the probability density function from a limited number of data. The main idea is to project the data into a statistically sufficient low-dimensional subspace, suitable for density estimation. Then using a simple parametric model based on assumption of Gaussianity, mutual information is estimated and applied as a measure of correspondence. We exploit how the choice of sample size affects the reliability of the correspondence measure (mutual information) between selected features of the two modalities, audio and video

Phenolic Profile and Antioxidant Activity of Pulp and Peel from Peach and Nectarine Fruits

Peach (Prunus persica L.) is a fruit of high nutritional and economic value. Carbohydrates, dietary fibers, minerals and organic acids are among the major constituents of peach fruit, which contribute to the nutritional quality of both fresh fruits and juice. Polyphenolic compounds found in peach may play an important role in physiological functions related to human health. Different polyphenolics may have varied biological activities including antioxidant activity. In this study antioxidant characteristics between peel and pulp of different peach cultivars (‘RadmilovÄanka’, ‘June Gold’, ‘Blake’, ‘Hale’, ‘Vesna’, ‘Adria’) and one of nectarine (‘Fantasia’) were investigated. The peel and pulp extracts showed a huge amount of total phenolics (TP), total flavonoids (TF), total hydroxycinnamates (TH) and total flavonols (TFL), ranging from 42.7-211.4, 11.1-128.5 mg GAE/100 g fresh weight (f.w.) (TP), 21.9 -94.9, 5.0-58.9 mg CE/100 g f.w. (TF), 28.4-389.2, 8.5-165.8 mg kg-1 f.w. (TH) and 17.3-54 mg kg-1 f.w. (TFL). High contents of phenolic compounds were significantly correlated with high antioxidant capacities. Peach pulp and peel differ significantly in their phenolic profiles: the pulp contains mainly chlorogenic, neochlorogenic and p-coumaric acids, whereas the peel possesses chlorogenic, neochlorogenic and p-coumaric acids together with several flavonol glycosides in huge amounts. Our results indicate that cultivar and extraction solvent play important roles in phenolic compositions and antioxidant properties of peach and nectarine extracts, which was shown using statistical analysis (ANOVA). There are high correlations between extracted phenolic compounds and peach and nectarine cultivars, and used solvent and part of the fruit (peel and pulp)

Plasticity of the Muscle Stem Cell Microenvironment

Satellite cells (SCs) are adult muscle stem cells capable of repairing damaged and creating new muscle tissue throughout life. Their functionality is tightly controlled by a microenvironment composed of a wide variety of factors, such as numerous secreted molecules and different cell types, including blood vessels, oxygen, hormones, motor neurons, immune cells, cytokines, fibroblasts, growth factors, myofibers, myofiber metabolism, the extracellular matrix and tissue stiffness. This complex niche controls SC biology-quiescence, activation, proliferation, differentiation or renewal and return to quiescence. In this review, we attempt to give a brief overview of the most important players in the niche and their mutual interaction with SCs. We address the importance of the niche to SC behavior under physiological and pathological conditions, and finally survey the significance of an artificial niche both for basic and translational research purposes

HPLC ANALYSIS OF EXTRACTS OF FRESH PETALS OF PAPAVER RHOEAS L.

Papaver rhoeas L. (Papaveraceae) is an annual grass native to many regions of the world, which is known to possess several pharmacological properties. It is also known that represent a rich source of anthocyanins. In this study, the content of the anthocyanin was determined in the examined various extracts of fresh petals by HPLC analysis. The most represented anthocyanins in the extracts of Papaver rhoeas L. are delphinidin-3-O-glucoside, cyanidin-3-O-glucoside, cyanidin-3-O-rutinoside, peonidin-3-O-glucoside, petunidin-3-O-glucoside, petunidin-3-acetylglucoside, and delphinidin-3-p-coumaroylglucoside. Acyl derivatives of anthocyanins in the water extract have not been identified. By comparing the contents of individual anthocyanins, the glycosides (polar) are better extracted with 50% alcohol solution, and their acyl derivatives are better extracted with pure alcohol. The water solution is the least suitable for anthocyanin extraction

Global, regional, and national incidence and mortality for HIV, tuberculosis, and malaria during 1990–2013: a systematic analysis for the Global Burden of Disease Study 2013

BACKGROUND: The Millennium Declaration in 2000 brought special global attention to HIV, tuberculosis, and malaria through the formulation of Millennium Development Goal (MDG) 6. The Global Burden of Disease 2013 study provides a consistent and comprehensive approach to disease estimation for between 1990 and 2013, and an opportunity to assess whether accelerated progress has occured since the Millennium Declaration. METHODS: To estimate incidence and mortality for HIV, we used the UNAIDS Spectrum model appropriately modified based on a systematic review of available studies of mortality with and without antiretroviral therapy (ART). For concentrated epidemics, we calibrated Spectrum models to fit vital registration data corrected for misclassification of HIV deaths. In generalised epidemics, we minimised a loss function to select epidemic curves most consistent with prevalence data and demographic data for all-cause mortality. We analysed counterfactual scenarios for HIV to assess years of life saved through prevention of mother-to-child transmission (PMTCT) and ART. For tuberculosis, we analysed vital registration and verbal autopsy data to estimate mortality using cause of death ensemble modelling. We analysed data for corrected case-notifications, expert opinions on the case-detection rate, prevalence surveys, and estimated cause-specific mortality using Bayesian meta-regression to generate consistent trends in all parameters. We analysed malaria mortality and incidence using an updated cause of death database, a systematic analysis of verbal autopsy validation studies for malaria, and recent studies (2010-13) of incidence, drug resistance, and coverage of insecticide-treated bednets. FINDINGS: Globally in 2013, there were 1·8 million new HIV infections (95% uncertainty interval 1·7 million to 2·1 million), 29·2 million prevalent HIV cases (28·1 to 31·7), and 1·3 million HIV deaths (1·3 to 1·5). At the peak of the epidemic in 2005, HIV caused 1·7 million deaths (1·6 million to 1·9 million). Concentrated epidemics in Latin America and eastern Europe are substantially smaller than previously estimated. Through interventions including PMTCT and ART, 19·1 million life-years (16·6 million to 21·5 million) have been saved, 70·3% (65·4 to 76·1) in developing countries. From 2000 to 2011, the ratio of development assistance for health for HIV to years of life saved through intervention was US$4498 in developing countries. Including in HIV-positive individuals, all-form tuberculosis incidence was 7·5 million (7·4 million to 7·7 million), prevalence was 11·9 million (11·6 million to 12·2 million), and number of deaths was 1·4 million (1·3 million to 1·5 million) in 2013. In the same year and in only individuals who were HIV-negative, all-form tuberculosis incidence was 7·1 million (6·9 million to 7·3 million), prevalence was 11·2 million (10·8 million to 11·6 million), and number of deaths was 1·3 million (1·2 million to 1·4 million). Annualised rates of change (ARC) for incidence, prevalence, and death became negative after 2000. Tuberculosis in HIV-negative individuals disproportionately occurs in men and boys (versus women and girls); 64·0% of cases (63·6 to 64·3) and 64·7% of deaths (60·8 to 70·3). Globally, malaria cases and deaths grew rapidly from 1990 reaching a peak of 232 million cases (143 million to 387 million) in 2003 and 1·2 million deaths (1·1 million to 1·4 million) in 2004. Since 2004, child deaths from malaria in sub-Saharan Africa have decreased by 31·5% (15·7 to 44·1). Outside of Africa, malaria mortality has been steadily decreasing since 1990. INTERPRETATION: Our estimates of the number of people living with HIV are 18·7% smaller than UNAIDS's estimates in 2012. The number of people living with malaria is larger than estimated by WHO. The number of people living with HIV, tuberculosis, or malaria have all decreased since 2000. At the global level, upward trends for malaria and HIV deaths have been reversed and declines in tuberculosis deaths have accelerated. 101 countries (74 of which are developing) still have increasing HIV incidence. Substantial progress since the Millennium Declaration is an encouraging sign of the effect of global action. FUNDING: Bill & Melinda Gates Foundation

Parallel mutual information estimation for inferring gene regulatory networks on GPUs

<p>Abstract</p> <p>Background</p> <p>Mutual information is a measure of similarity between two variables. It has been widely used in various application domains including computational biology, machine learning, statistics, image processing, and financial computing. Previously used simple histogram based mutual information estimators lack the precision in quality compared to kernel based methods. The recently introduced B-spline function based mutual information estimation method is competitive to the kernel based methods in terms of quality but at a lower computational complexity.</p> <p>Results</p> <p>We present a new approach to accelerate the B-spline function based mutual information estimation algorithm with commodity graphics hardware. To derive an efficient mapping onto this type of architecture, we have used the Compute Unified Device Architecture (CUDA) programming model to design and implement a new parallel algorithm. Our implementation, called CUDA-MI, can achieve speedups of up to 82 using double precision on a single GPU compared to a multi-threaded implementation on a quad-core CPU for large microarray datasets. We have used the results obtained by CUDA-MI to infer gene regulatory networks (GRNs) from microarray data. The comparisons to existing methods including ARACNE and TINGe show that CUDA-MI produces GRNs of higher quality in less time.</p> <p>Conclusions</p> <p>CUDA-MI is publicly available open-source software, written in CUDA and C++ programming languages. It obtains significant speedup over sequential multi-threaded implementation by fully exploiting the compute capability of commonly used CUDA-enabled low-cost GPUs.</p

In Vivo Isolation and Characterization of Stem Cells with Diverse Phenotypes Using Growth Factor Impregnated Biomatrices

BACKGROUND: The stimulation to differentiate into specific cell types for somatic stem cells is largely due to a series of internal and external signals coming from the microenvironment that surrounds the stem cell. Even though intensive research has been made, the basic mechanisms of plasticity and/or the molecules regulating stem cells proliferation and differentiation are not completely determined. Potential answers concerning the problems could be derived from the studies of stem cells in culture. METHODOLOGY/PRINCIPLE FINDINGS: We combine a new procedure (using the matrigel biopolymer supplemented with a selected cytokine/growth factor) with classic techniques such as light, confocal and electron microscopy, immunohistochemistry and cell culture, to perform an analysis on stem cells involved in the leech (Hirudo medicinalis) repair tissues. The leech has a relative anatomical simplicity and is a reliable model for studying a variety of basic events, such as tissue repair, which has a striking similarity with vertebrate responses. Our data demonstrate that the injection of an appropriate combination of the matrigel biopolymer supplemented with a selected cytokine/growth factor in the leech Hirudo medicinalis is a remarkably effective tool for isolating a specific cell population in vivo. A comparative analysis of biopolymer in vivo sorted stem cells indicates that VEGF recruited cells of a hematopoietic/endothelial phenotype whereas MCP-1/CCL2 isolated cells that were of an early myeloid lineage. CONCLUSION: Our paper describes, for the first time, a method allowing not only the isolation of a specific cell population in relation to the cytokine utilized but also the possibility to culture a precise cell type whose isolation is otherwise quite difficult. This approach could be broadly applied to isolate stem cells of diverse origins based on the recruitment stimuli employed