Ontology learning for semantic web services

Semantic Web Services promise automatic service discovery and composition, relying heavily on domain ontology as a core component. With large Web Service repository, manual ontology development is proving a bottleneck (with associated expense and likely errors) to the realisation of a semantic Web of services. Providing the appropriate tools that assist in and automate ontology development is essential for a dynamic service vision to be realised. As a statement of research-in-progress, this paper proposes combining different ontology learning paradigms in Web Services domain, highlighting the need for further research that accommodates the variation in Web Service descriptive and operational sources. A research agenda is proposed that recognises this variation in artefacts as they are selected, pre-processed and analyzed by ontology learning techniques

Amalgamated Titanium Oxide-Carbon Hollow Sphere/Nickel-Layered Double Hydroxide as an Efficient Photocatalyst for the Degradation of Methyl Orange

Investigating efficient and selective photocatalysts for water treatment can help address the energy crisis and numerous environmental issues associated with the use of current fossil fuels. As a shell, we used nickel-layered double hydroxide nanosheets on top of an anatase TiO2-carbon core to create an integrated photocatalyst. Materials were characterized using FTIR, XRD, SEM, HRTEM, and XPS methods for their physical-chemical properties. Using N2 adsorption/desorption at −196 °C, BET-surface area and pore structure were determined. Diffuse reflectance UV–vis was used to determine the photocatalysts band gap. For the TiO2-C/NiLDH amalgam, showed the lowest band gap (3.1 eV) with an exceptional ability to degrade methyl orange as an organic pollutant. Core–shell symmetry in the TiO2-C/NiLDH amalgam provides a larger surface area (72 m2/g) for interfacial interaction and a wider base for efficient charge transfer. In subsequent tests, this photocatalyst showed a remarkable level of stability and water treatment efficacy. That the TiO2-C/NiLDH amalgam can be used to alter solar energy and protect the environment has been demonstrated by these promising results

Promotor methylation: Does it affect response to therapy in chronic hepatitis C (G4) or fibrosis?

Background and aim. DNA methylation plays a critical role in the control of important cellular processes. The present study assessed the impact of promoter methylation (PM) of some genes on the antiviral response to antiviral therapy and it’s relation to the presence of fibrosis in HCV-4 infected patients from Egypt.Material and methods. Clinical, laboratory and histopathological data of 53 HCV-4 infected patients who were subjected to combined antiviral therapy were collected; patients were classified according to their response to treatment and the fibrosis status. The methylation profiles of the studied groups were determined using the following genes: APC, P14ARF, P73, DAPK, RASSF1A, and O6MGMT in patients’ plasma.Results. O6MGMT and P73 showed the highest methylation frequencies (64.2 and 50.9%) while P14 showed the lowest frequency (34%). Sustained virological response (SVR) was 54.7%with no significant difference in clinico-pathological or laboratory features between the studied groups. PM of O6MGM was significantly higher in non-responders (p value 0.045) while DAPK showed high methylation levels in responders with no significance (p value: 0.09) andPM of RASSF1A was significantly related to mild fibrosis (p value: 0.019). No significant relations were reported between PM of any of the studied genes and patients’ features.Conclusion. PM of some Tumor Suppressor genes increases in chronic active HCV-4. However, only 06MGMT can be used as a predictor of antiviral response and RASSF1A as a marker of marked fibrosis in this small set of patients. An extended study, including more patients is required to validate the results of this preliminary study

Multigene Panel Sequencing Reveals Cancer-Specific and Common Somatic Mutations in Colorectal Cancer Patients: An Egyptian Experience

This study aims at identifying common pathogenic somatic mutations at different stages of colorectal carcinogenesis in Egyptian patients. Our cohort included colonoscopic biopsies collected from 120 patients: 20 biopsies from patients with inflammatory bowel disease, 38 from colonic polyp patients, and 62 from patients with colorectal cancer. On top of this, the cohort included 20 biopsies from patients with non-specific mild to moderated colitis. Targeted DNA sequencing using a customized gene panel of 96 colorectal related genes running on the Ion Torrent NGS technology was used to process the samples. Our results revealed that 69% of all cases harbored at least one somatic mutation. Fifty-seven genes were found to carry 232 somatic non-synonymous variants. The most frequently pathogenic somatic mutations were localized in TP53, APC, KRAS, and PIK3CA. In total, 16 somatic mutations were detected in the CRC group and in either the IBD or CP group. In addition, our data showed that 51% of total somatic variants were CRC-specific variants. The average number of CRC-specific variants per sample is 2.4. The top genes carrying CRC-specific mutations are APC, TP53, PIK3CA, FBXW7, ATM, and SMAD4. It seems obvious that TP53 and APC genes were the most affected genes with somatic mutations in all groups. Of interest, 85% and 28% of the APC and TP53 deleterious somatic mutations were located in Exon 14 and Exon 3, respectively. Besides, 37% and 28% of the total somatic mutations identified in APC and TP53 were CRC-specific variants, respectively. Moreover, we identified that, in 29 somatic mutations in 21 genes, their association with CRC patients was unprecedented. Ten detected variants were likely to be novel: six in PIK3CA and four variants in FBXW7. The detected P53, Wnt/βcatenin, Angiogenesis, EGFR, TGF-β and Interleukin signaling pathways were the most altered pathways in 22%, 16%, 12%, 10%, 9% and 9% of the CRC patients, respectively. These results would contribute to a better understanding of the colorectal cancer and in introducing personalized therapies for Egyptian CRC patients

MicroRNA Signatures for circulating CD133-positive cells in hepatocellular carcinoma with HCV infection

<div><p>Aim</p><p>Molecular characterization of the CD133+ stem cells associated with hepatocarinogensis through identifying the expression patterns of specific microRNAs (miRNAs).</p><p>Methods</p><p>We investigated the expression pattern of 13 miRNAs in purified CD133+ cells separated from the peripheral blood of healthy volunteers, chronic hepatitis C (CHC), liver cirrhosis (LC) and hepatocellular carcinoma (HCC) patients a long with bone marrow samples from the healthy volunteers and the LC patients using custom miScript miRNA PCR array.</p><p>Results</p><p>The differential expression of the 13 studied miRNAs in CD133+ cells separated from the HCC patients' peripheral blood compared to the controls revealed that <i>miR-602</i>, <i>miR-181b</i>, <i>miR-101</i>, <i>miR-122</i>, <i>miR-192</i>, <i>miR-125a-5p</i>, and <i>miR-221</i> were significantly up regulated (fold change = 1.8, 1.7, 2, 5.4, 1.6, 2.9 & 1.5 <i>P</i> value = 0.039, 0.0019, 0.0013, 0.0370, 00024, 0.000044 &0.000007 respectively). As for the HCC group compared to the CHC group; <i>miR-602</i>, miR-122, <i>miR-181b</i>, <i>miR-125a-5p</i>, and <i>miR-192</i> were significantly up regulated (fold change = 13, 3.1, 2.8, 1.6 & 1.56, <i>P</i> value = 0.01, 0.001, 0.000004, 0.002 & 0.007 respectively). Upon comparing the HCC group to the LC group; <i>miR-199a-3p</i>, <i>miR-192</i>, <i>miR-122</i>, <i>miR-181b</i>, <i>miR-224</i>, <i>miR-125a-5p</i>, and <i>miR-885-5p</i> were significantly up regulated (fold change = 5, 6.7, 2.3, 3, 2.5, 4.2 & 39.5 <i>P</i> value = 0.001025, 0.000024, 0.000472, 0.000278, 0.000004, 0.000075 & 0.0000001 respectively) whereas <i>miR-22</i> was significantly down regulated (fold change = 0.57 <i>P</i> value = 0.00002). Only, <i>miR-192</i>, <i>miR-122</i>, <i>miR-181b</i> and <i>miR-125a-5p</i> were significant common miRNAs in CD133+ cells of the HCC group compared to the other non-malignant groups.</p><p>Conclusion</p><p>We identified a miRNA panel comprised of four miRNAs (<i>miR-192</i>, <i>miR-122</i>, <i>miR-181b</i> and <i>miR-125a-5p</i>) that may serve as a molecular tool for characterization of the CD133+ cells associated with different stages of hepatocarinogensis. This panel may aid in developing a new target therapy specific for those CD133+ cells.</p></div

MicroRNA Signatures for circulating CD133-positive cells in hepatocellular carcinoma with HCV infection - Fig 8

<p>A) Histogram showing the differential expression of the 13 miRNAs in CD133+ cells of the control group (BM) versus the control group (PB). B) Histogram showing the differential expression of the 13 studied miRNAs in CD133+cells of the LC group (BM) versus the LC group (PB). C) Histogram showing the differential expression of the 13 miRNAs in CD133+ cells of the LC group (BM) versus the control group (BM). "*" miRNA is significant at 0.05 level while "**" miRNA is significant at 0.01 level.</p

Functional annotation of miRNAs and their target genes in CD133+ cells of HCC.

<p>Functional annotation of miRNAs and their target genes in CD133+ cells of HCC.</p

MicroRNA Signatures for circulating CD133-positive cells in hepatocellular carcinoma with HCV infection - Fig 3

<p>A) The multi group plot provided both a bar chart and line graph representation (with optional error bars) for differential expression of the13 miRNAs in CD133+ cells of the three groups (PB) compared to control group (PB) where group 1 represented CHC group, group 2 represented LC group and group 3 represented HCC group. B) The heat map with dendrograms representing co-regulated miRNAs across all groups.</p

Circulating Serum miRNAs as Diagnostic Markers for Colorectal Cancer

<div><p>Aim</p><p>The study was designed to assess the possibility of using circulating miRNAs (serum miRNAs) as diagnostic biomarkers in colorectal cancer (CRC) and to identify their possibility as candidates for targeted therapy.</p><p>Methods</p><p>The study involved two sample sets: 1- a training set which included 90 patients with colorectal related disease (30 with CRC, 18 with inflammatory bowel disease (IBD), 18 with colonic polyps (CP) and 24 with different colonic symptoms but without any colonoscopic abnormality who were enrolled as control group) and 2- a validation set which included 100 CRC patients. Serum miRNAs were extracted from all subjects to assess the expression profiles for the following miRNAs (<i>miR-17</i>, <i>miR-18a</i>, <i>miR-19a</i>, <i>miR-19b</i>, <i>miR-20a</i>, <i>miR-21</i>, <i>miR-146a</i>, <i>miR-223</i>, <i>miR-24</i>, <i>miR-454</i>, <i>miR-183</i>, <i>miR-135a</i>, <i>miR- 135b and miR- 92a</i>) using the custom miScript miRNA PCR-based sybergreen array. The area under the receiver operating characteristic curve (AUC) was used to evaluate the diagnostic performance of the studied miRNAs for colorectal cancer diagnosis.</p><p>Results</p><p>Data analysis of miRNA from the training set showed that; compared to control group, only <b><i>miR-19b</i></b> was significantly up-regulated in patients with IBD group (fold change = 5.24, p = 0.016), whereas in patients with colonic polyps, <b><i>miR-18a</i></b> was significantly up-regulated (fold change = 3.49, p-value = 0.018). On the other hand, <i>miR-17</i>, <i>miR-19a</i>, <i>miR-20a and</i> <b><i>miR-223</i></b> were significantly up-regulated (fold change = 2.35, 3.07, 2.38 and 10.35; respectively and p-value = 0.02, 0.015, 0.017 and 0.016; respectively in CRC patients. However, the validation set showed that only <b><i>miR-223</i></b> was significantly up-regulated in CRC patients (fold change = 4.06, p-value = 0.04).</p><p>Conclusion</p><p>Aberrant miRNA expressions are highly involved in the cascade of colorectal carcinogenesis. We have found that (<i>miR-17</i>, <i>miR-19a</i>, <i>miR-20a and miR-223</i>) could be used as diagnostic biomarkers for CRC. On the other hand, <i>miR-19b</i> and <i>miR-18a</i> could be used as diagnostic biomarkers for CP and IBD respectively.</p></div