Prognostic nomogram for bladder cancer with brain metastases: a National Cancer Database analysis.

BACKGROUND: This study aimed to establish and validate a nomogram for predicting brain metastasis in patients with bladder cancer (BCa) and assess various treatment modalities using a primary cohort comprising 234 patients with clinicopathologically-confirmed BCa from 2004 to 2015 in the National Cancer Database. METHODS: Machine learning method and Cox model were used for nomogram construction. For BCa patients with brain metastasis, surgery of the primary site, chemotherapy, radiation therapy, palliative care, brain confinement of metastatic sites, and the Charlson/Deyo Score were predictive features identified for building the nomogram. RESULTS: For the original 169 patients considered in the model, the areas under the receiver operating characteristic curve (AUC) were 0.823 (95% CI 0.758-0.889, P \u3c 0.001) and 0.854 (95% CI 0.785-0.924, P \u3c 0.001) for 0.5- and 1-year overall survival respectively. In the validation cohort, the nomogram displayed similar AUCs of 0.838 (95% CI 0.738-0.937, P \u3c 0.001) and 0.809 (95% CI 0.680-0.939, P \u3c 0.001), respectively. The high and low risk groups had median survivals of 1.91 and 5.09 months for the training cohort and 1.68 and 8.05 months for the validation set, respectively (both P \u3c 0.0001). CONCLUSIONS: Our prognostic nomogram provides a useful tool for overall survival prediction as well as assessing the risk and optimal treatment for BCa patients with brain metastasis

Tutorial and Critical Analysis of Phishing Websites Methods

The Internet has become an essential component of our everyday social and financial activities. Internet is not important for individual users only but also for organizations, because organizations that offer online trading can achieve a competitive edge by serving worldwide clients. Internet facilitates reaching customers all over the globe without any market place restrictions and with effective use of e-commerce. As a result, the number of customers who rely on the Internet to perform procurements is increasing dramatically. Hundreds of millions of dollars are transferred through the Internet every day. This amount of money was tempting the fraudsters to carry out their fraudulent operations. Hence, Internet users may be vulnerable to different types of web threats, which may cause financial damages, identity theft, loss of private information, brand reputation damage and loss of customers’ confidence in e-commerce and online banking. Therefore, suitability of the Internet for commercial transactions becomes doubtful. Phishing is considered a form of web threats that is defined as the art of impersonating a website of an honest enterprise aiming to obtain user’s confidential credentials such as usernames, passwords and social security numbers. In this article, the phishing phenomena will be discussed in detail. In addition, we present a survey of the state of the art research on such attack. Moreover, we aim to recognize the up-to-date developments in phishing and its precautionary measures and provide a comprehensive study and evaluation of these researches to realize the gap that is still predominating in this area. This research will mostly focus on the web based phishing detection methods rather than email based detection methods

Identification, Expression and Target Gene Analyses of MicroRNAs in Spodoptera litura

MicroRNAs (miRNAs) are small RNAs widely present in animals and plants and involved in post-transcriptional regulation of gene transcripts. In this study we identified and validated 58 miRNAs from an EST dataset of Spodoptera litura based on the computational and experimental analysis of sequence conservation and secondary structure of miRNA by comparing the miRNA sequences in the miRbase. RT-PCR was conducted to examine the expression of these miRNAs and stem-loop RT-PCR assay was performed to examine expression of 11 mature miRNAs (out of the 58 putative miRNA) that showed significant changes in different tissues and stages of the insect development. One hundred twenty eight possible target genes against the 11 miRNAs were predicted by using computational methods. Binding of one miRNA (sli-miR-928b) with the three possible target mRNAs was confirmed by Southern blotting, implying its possible function in regulation of the target genes

Modification of PCR Conditions and Design of Exon-Specific Primers for the Efficient Molecular Diagnosis of PKD1 Mutations

Background/Aims: Autosomal-dominant polycystic kidney disease (ADPKD) is a heterogeneous genetic disorder caused by mutations in the PKD1 and PKD2 genes. Currently, long-range PCR followed by nested PCR and sequencing (LRNS) is the gold standard approach for PKD1 testing. However, LRNS is complicated by the high structural and sequence complexity of PKD1, which makes the procedure for amplification and analysis of PKD1 difficult. Methods: Here in, we modified the PCR conditions and designed primers for efficient and specific amplification of both the long-range and individual exons of PKD1. Results: Using the modified system, seven long-range fragments were specifically amplified using two distinct sets of conditions, and all individual exon PCR assays were easily performed using a touch-down PCR method. Seven pathogenic or likely pathogenic variants, including two novel truncated frameshift indels and two novel likely pathogenic missense mutations, were identified in eight unrelated patients with or without histories of ADPKD disease (one variant was observed in two unrelated patients). Using combined bioinformatics tools, two indeterminate missense variants were identified in two sporadic patients. Conclusion: Four novel PKD1 variants were identified in this study. We demonstrated that the modified LRNS method achieves high sensitivity and specificity for detecting pathogenic variants of ADPKD

Developmental expression of the 11 selected miRNAs at different stages from eggs to adults of <i>S. litura</i>.

<p>The expression levels of the miRNA by stem-loop RT-PCR were digitized by ImageQuantTL after gel electrophoresis and the relative expression levels of the miRNAs were calculated as log10(miRNA/U6snRNA). The digital numbers were converted into image by using Cluster/Treeview. The scale bar shows the relative expression levels of the miRNAs over the control (U6snRNA) from −3 to 3 folds (0.001 to 1000 folds).</p

Southern blotting analysis of sli-miR-928b binding with the mRNA transcripts of its predicted potential target genes, CG2781 (GenBank accession number: 40943), mRpL27 (GenBank accession number: 318825), Atf-2 (GenBank accession number: 37978) and CG1776 (GenBank accession number: 36002).

<p>The 3′-UTR cDNA fragments that contained the sli-miR-928b complementary sequence of the four target genes were amplified by RACE-PCR (lower panel). Sli-miR-928b miRNA was synthesized and labeled with 32P-ATP as a probe and used for the hybridization with the 3′-UTR fragments of the genes (upper panel).</p

Defining differentially methylated regions specific for the acquisition of pluripotency and maintenance in human pluripotent stem cells via microarray.

Epigenetic regulation is critical for the maintenance of human pluripotent stem cells. It has been shown that pluripotent stem cells, such as embryonic stem cells and induced pluripotent stem cells, appear to have a hypermethylated status compared with differentiated cells. However, the epigenetic differences in genes that maintain stemness and regulate reprogramming between embryonic stem cells and induced pluripotent stem cells remain unclear. Additionally, differential methylation patterns of induced pluripotent stem cells generated using diverse methods require further study.Here, we determined the DNA methylation profiles of 10 human cell lines, including 2 ESC lines, 4 virally derived iPSC lines, 2 episomally derived iPSC lines, and the 2 parental cell lines from which the iPSCs were derived using Illumina's Infinium HumanMethylation450 BeadChip. The iPSCs exhibited a hypermethylation status similar to that of ESCs but with distinct differences from the parental cells. Genes with a common methylation pattern between iPSCs and ESCs were classified as critical factors for stemness, whereas differences between iPSCs and ESCs suggested that iPSCs partly retained the parental characteristics and gained de novo methylation aberrances during cellular reprogramming. No significant differences were identified between virally and episomally derived iPSCs. This study determined in detail the de novo differential methylation signatures of particular stem cell lines.This study describes the DNA methylation profiles of human iPSCs generated using both viral and episomal methods, the corresponding somatic cells, and hESCs. Series of ss-DMRs and ES-iPS-DMRs were defined with high resolution. Knowledge of this type of epigenetic information could be used as a signature for stemness and self-renewal and provides a potential method for selecting optimal pluripotent stem cells for human regenerative medicine

Expression of the 58 predicted miRNA detected by stem-loop RT-PCR.

<p>The expression levels of the 58 predicted miRNA of <i>S. litura</i> by stem-loop RT-PCR were digitized by ImageQuantTL after gel electrophoresis and the relative expression levels of the miRNAs were calculated as log10(miRNA/U6snRNA). The digital numbers were converted into image by using Cluster/Treeview. The scale bar shows the relative expression levels of the miRNAs over the control (U6snRNA) from −3 to 3 folds (0.001 to 1000 folds). The numbers in the figure were corresponding to those in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037730#pone-0037730-t001" target="_blank">Table 1</a>.</p