Machine Learning and Graph Theory Approaches for Classification and Prediction of Protein Structure

Recently, many methods have been proposed for the classification and prediction problems in bioinformatics. One of these problems is the protein structure prediction. Machine learning approaches and new algorithms have been proposed to solve this problem. Among the machine learning approaches, Support Vector Machines (SVM) have attracted a lot of attention due to their high prediction accuracy. Since protein data consists of sequence and structural information, another most widely used approach for modeling this structured data is to use graphs. In computer science, graph theory has been widely studied; however it has only been recently applied to bioinformatics. In this work, we introduced new algorithms based on statistical methods, graph theory concepts and machine learning for the protein structure prediction problem. A new statistical method based on z-scores has been introduced for seed selection in proteins. A new method based on finding common cliques in protein data for feature selection is also introduced, which reduces noise in the data. We also introduced new binary classifiers for the prediction of structural transitions in proteins. These new binary classifiers achieve much higher accuracy results than the current traditional binary classifiers

Increased Risk of Genetic and Epigenetic Instability in Human Embryonic Stem Cells Associated with Specific Culture Conditions

The self-renewal and differentiation capacities of human pluripotent stem cells (hPSCs) make them a promising source of material for cell transplantation therapy, drug development, and studies of cellular differentiation and development. However, the large numbers of cells necessary for many of these applications require extensive expansion of hPSC cultures, a process that has been associated with genetic and epigenetic alterations. We have performed a combinatorial study on both hESCs and hiPSCs to compare the effects of enzymatic vs. mechanical passaging, and feeder-free vs. mouse embryonic fibroblast feeder substrate, on the genetic and epigenetic stability and the phenotypic characteristics of hPSCs. In extensive experiments involving over 100 continuous passages, we observed that both enzymatic passaging and feeder-free culture were associated with genetic instability, higher rates of cell proliferation, and persistence of OCT4/POU5F1-positive cells in teratomas, with enzymatic passaging having the stronger effect. In all combinations of culture conditions except for mechanical passaging on feeder layers, we noted recurrent deletions in the genomic region containing the tumor suppressor gene TP53, which was associated with decreased mRNA expression of TP53, as well as alterations in the expression of several downstream genes consistent with a decrease in the activity of the TP53 pathway. Among the hESC cultures, we also observed culture-associated variations in global gene expression and DNA methylation. The effects of enzymatic passaging and feeder-free conditions were also observed in hiPSC cultures. Our results highlight the need for careful assessment of the effects of culture conditions on cells intended for clinical therapies

Equivalence of Conventionally-Derived and Parthenote-Derived Human Embryonic Stem Cells

As human embryonic stem cell (hESC) lines can be derived via multiple means, it is important to determine particular characteristics of individual lines that may dictate the applications to which they are best suited. The objective of this work was to determine points of equivalence and differences between conventionally-derived hESC and parthenote-derived hESC lines (phESC) in the undifferentiated state and during neural differentiation.hESC and phESC were exposed to the same expansion conditions and subsequent neural and retinal pigmented epithelium (RPE) differentiation protocols. Growth rates and gross morphology were recorded during expansion. RTPCR for developmentally relevant genes and global DNA methylation profiling were used to compare gene expression and epigenetic characteristics. Parthenote lines proliferated more slowly than conventional hESC lines and yielded lower quantities of less mature differentiated cells in a neural progenitor cell (NPC) differentiation protocol. However, the cell lines performed similarly in a RPE differentiation protocol. The DNA methylation analysis showed similar general profiles, but the two cell types differed in methylation of imprinted genes. There were no major differences in gene expression between the lines before differentiation, but when differentiated into NPCs, the two cell types differed in expression of extracellular matrix (ECM) genes.These data show that hESC and phESC are similar in the undifferentiated state, and both cell types are capable of differentiation along neural lineages. The differences between the cell types, in proliferation and extent of differentiation, may be linked, in part, to the observed differences in ECM synthesis and methylation of imprinted genes

DNA Methylation

<p><b>A</b>. X Chromosome DNA Methylation and XIST Expression. Methylation levels of genes in the X-chromosome (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0118307#pone.0118307.s009" target="_blank">S6A Table</a>) are shown on the heatmap. Hierarchical clustering was performed on the samples, as indicated by the dendrogram. The genes are ordered according to their location (from the beginning to the end of the chromosome). Samples that show loss of DNA methylation for the “Enz” cluster are highlighted in blue, those that show DNA methylation for the “Ecm” cluster are highlighted in pink, and for both clusters in mauve. Genes located in the regions of loss of DNA methylation are listed to the right of the heatmap. XIST expression is shown on the line graph, with the detection limit for the microarray indicated by the red line. <b>B</b>. DNA methylation at imprinted loci. Methylation levels for imprinted probes (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0118307#pone.0118307.s009" target="_blank">S6B Table</a>) are shown on the heatmap. Hierarchical clustering was performed on the samples, as indicated by the dendrogram. The genes are ordered according to chromosome location; genes are listed to the left. The inset at the right shows a detail of the NESP/GNAS complex locus, indicating the positions of the CpG sites that were hypermethylated (red triangle) vs. hypomethylated (green triangle) in the late passage samples relative to the NESP/GNAS and NESPAS exons. <b>C, D, E</b>. Heatmaps showing differential DNA methylation genes for early vs. late passage <b>(C)</b>, mechanical vs. enzymatic passage <b>(D)</b>, and Mef vs. Ecm substrate <b>(E)</b>. In heatmap <b>(C)</b>, the black boxes indicate genes for which the DNA methylation levels in the late passage MefMech (P103) samples was more similar to those in the early passage samples. Probes were selected by multivariate regression. Functional enrichments identified by GREAT analysis are shown to the right of the heatmaps, visualized using REVIGO [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0118307#pone.0118307.ref013" target="_blank">13</a>]. Samples were arranged according to passage and culture method, and hierarchical clustering was performed on the genes only. In the functional enrichment results, the size of the node indicated the number of contributing GO terms, and color of the nodes indicates the FDR (darker color for lower FDR), and the edge length indicates the similarity between GO terms (shorter edge for more similar terms).</p

Treatment of critically ill patients with acute hypercarbic respiratory failure by average volume-assured pressure support mode

Objectives Average volume-assured pressure support (AVAPS), a dual mode, delivers a set tidal volume (TV) per kg by adjusting the pressure between upper and lower inspiratory positive airway pressures (IPAP). Thus, ventilation is presumed to be happened effectively by sending a guaranteed TV. This study was aimed to evaluate the effectiveness of AVAPS mode in critically ill patients with acute hypercarbic respiratory failure (HRF) and compare the results with bilevel positive airway pressure-spontaneous/timed (BPAP-S/T) mode. Methods Sixty patients were assigned to BPAP-S/T (n = 29) and AVAPS modes (n = 31). Maximum IPAP was started at 20 cmH(2)O and minimum IPAP was set at 5 cmH(2)O higher than expiratory positive airway pressure (EPAP) in AVAPS mode. IPAP was started at 15 cmH(2)O in BPAP-S/T mode. IPAP levels were titrated up to 30 cmH(2)O during noninvasive mechanic ventilation (NIMV) with a targeted TV of 6-8 mL/kg. Patients were followed for 5 days. Results No differences were found in pH, paCO(2), HCO3, TV and EPAP between the two groups when compared separately by days. Maximum IPAP levels were significantly high in AVAPS mode in all times (P < 0.001). The length of stay (LOS) in intensive care unit (ICU) (P = 0.994) and hospital (P = 0.509), hours of NIMV use per day (P = 0.101) and NIMV success rate (P = 0.931) were identical between the two groups. ICU (P = 0.931), hospital (P = 0.800), 6-month (P = 0.919) and 1-year (P = 0.645) mortality rates were also not different between the both groups. Conclusions AVAPS mode had similar efficiency with BPAP-S/T mode regarding the NIMV treatment success in critically ill patients with acute HRF.Duzce University Scientific Research FundDuzce University [BAP-2015.04.03.382]This work was supported by Duzce University Scientific Research Fund (Grand number: BAP-2015.04.03.382)WOS:0006576345000012-s2.0-85107160197PubMed: 3401404