Deep node clustering based on mutual information maximization

Variational Graph Autoencoders (VGAs) are generative models for unsupervised learning of node representations within graph data. While VGAs have been achieved state-of-the-art results for different predictive tasks on graph-structured data, they are susceptible to the over-pruning problem where only a small subset of the stochastic latent units are active. This can limit their modeling capacity and their ability to learn meaningful representations. In this paper, we present SOLI (Stacked auto-encoder for nOde cLusterIng), an information maximization approach for learning graph representations by leveraging maximal cliques. SOLI relies on aggregating useful representations by assigning clique-based weights to various edges in a neighborhood while maximizing mutual information. The learned representations are mindful of graph patches centered around each node, and can be used for a range of downstream tasks, and thus encouraging more active units. We demonstrate strong performance across three graph benchmark datasets.(Code is available at https://github.com/SoheilaMolaei/SOLI.

A new look at the modified Coulomb potential in a strong magnetic field

The static Coulomb potential of Quantum Electrodynamics (QED) is calculated in the presence of a strong magnetic field in the lowest Landau level (LLL) approximation using two different methods. First, the vacuum expectation value of the corresponding Wilson loop is calculated perturbatively in two different regimes of dynamical mass $m_{dyn.}$, {\it i.e.}, $|{\mathbf{q}}_{\|}^{2}|\ll m_{dyn.}^{2}\ll |eB|$ and $m_{dyn.}^{2}\ll |\mathbf{q}_{\|}^{2}|\ll|eB|$, where $\mathbf{q}_{\|}$ is the longitudinal components of the momentum relative to the external magnetic field $B$. The result is then compared with the static potential arising from Born approximation. Both results coincide. Although the arising potentials show different behavior in the aforementioned regimes, a novel dependence on the angle $\theta$ between the particle-antiparticle's axis and the direction of the magnetic field is observed. In the regime $|{\mathbf{q}}_{\|}^{2}|\ll m_{dyn.}^{2}\ll |eB|$, for strong enough magnetic field and depending on the angle $\theta$, a qualitative change occurs in the Coulomb-like potential; Whereas for $\theta=0,\pi$ the potential is repulsive, it exhibits a minimum for angles $\theta\in]0,\pi[$.Comment: V1: 26 pages, 8 figures, latex format, V2: Accepted for publication in PRD (2007

Obstacles and Challenges in the Use of Probiotics

BACKGROUND AND OBJECTIVE: Probiotics are living microorganisms whose adequate intake has shown healthful effects in the host body and have been suggested to have beneficial effects in the prevention and treatment of many diseases. This study was conducted to investigate the obstacles and challenges of probiotic products in the production process and their effects on human health. METHODS: For data collection in this review article, articles containing one of the terms “probiotic”, “lactobacillus”, “bifidobacterium”, “biogenic amine” and “antibiotic resistance” from 1990 to 2017 were searched and reviewed at Thomson Reuters, Pubmed, Scopus, Science Direct and Islamic World Science Citation Center(ISC). FINDING: Research has shown that systematic infections and chronic diseases, over-stimulation of the immune system, transfer of antibiotic resistance genes, production of biogenic amines and D-lactic acidosis, lack of survival and sustainability of microorganisms and ultimately the change in the taste and flavor of probiotic products are among the obstacles and challenges facing the production of probiotics. The use of bifidobacterium to transfer antibiotic resistance genes is safer than other microorganisms for the production of probiotic products. CONCLUSION: Based on the results of this study, probiotics are only safe in healthy people, although they are very useful for human health, but their use in children, pregnant women and people with a weakened immune system causes infection

A rare presentation of late right coronary artery spasm following aortic valve replacement

BACKGROUND: Coronary artery spasm (CAS) is defined as a reversible, sudden epicardial coronary artery stenosis that causes vessel occlusion or near occlusion. CASE REPORT: In this article, we present a clinical case of CAS in a 48-year-old woman undergoing elective aortic valve replacement surgery for aortic stenosis. On the 3rd post-operative day, the patient suffered from chest pain and dyspnea. Emergent coronary angiography demonstrated a significant spasm of the ostium portion of the right coronary artery. CONCLUSION: This case shows that delayed coronary spasm should be considered as a cause of hemodynamic instability after valvular surgery. © 2015, Isfahan University of Medical Sciences(IUMS). All rights reserved

GenoMetric Query Language: A novel approach to large-scale genomic data management

Motivation: Improvement of sequencing technologies and data processing pipelines is rapidly providing sequencing data, with associated high-level features, of many individual genomes in multiple biological and clinical conditions. They allow for data-driven genomic, transcriptomic and epigenomic characterizations, but require state-of-the-art ‘big data’ computing strategies, with abstraction levels beyond available tool capabilities. Results: We propose a high-level, declarative GenoMetric Query Language (GMQL) and a toolkit for its use. GMQL operates downstream of raw data preprocessing pipelines and supports queries over thousands of heterogeneous datasets and samples; as such it is key to genomic ‘big data’ analysis. GMQL leverages a simple data model that provides both abstractions of genomic region data and associated experimental, biological and clinical metadata and interoperability between many data formats. Based on Hadoop framework and Apache Pig platform, GMQL ensures high scalability, expressivity, flexibility and simplicity of use, as demonstrated by several biological query examples on ENCODE and TCGA datasets. Availability and implementation: The GMQL toolkit is freely available for non-commercial use at http://www.bioinformatics.deib.polimi.it/GMQL/. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online

The effect of Pogostone on viability, membrane integrity, and apoptosis of liver cancer cells

OBJECTIVE: The incidence of liver cancer is still high in many countries, including Iran. Drug resistance and various side effects are the main obstacles to treating this cancer. Herbs, which are traditionally used, are now widely regarded as treatment options for cancer. Pogostone is a natural substance isolated from Indian mint (Pogostemon cablin) and has various medicinal activities. This study aimed to determine the effect of Pogostone on liver cancer cell line (viability, membrane integrity, and apoptosis). MATERIALS AND METHODS: The liver cancer cell line was prepared from Pasteur Institute of Iran and treated with appropriate concentrations of Pogostone. Cytotoxicity was determined by MTT, trypan blue, and lactate dehydrogenase assay. Apoptosis induction was evaluated by diphenylamine assay, Annexin V-FITC staining and a Real-time PCR test. Data were analyzed by SPSS statistical software using Tukey’s test one-way analysis of variance. RESULTS: After all three time periods, a significant decrease in viability was observed (p <0.05) in a concentration- and time-dependent manner. The cytotoxicity of Pogostone to liver cancer cells was in a concentration- and time-dependent manner. Pogostone significantly induced apoptosis compared to control cells (p<0.05). Treatment of liver cancer cells with Pogostone significantly reduced Bcl-2 gene expression (p<0.05). On the other hand, expression of all three Bax, p53, and caspase 3 genes showed a significant increase after treatment (p<0.05). CONCLUSIONS: Pogostone had a concentration- and time-dependent toxic effect on liver cancer cells. It induced apoptosis by increasing the Bax to Bcl-2 ratio

Original Article

本研究の目的は,健康な小児ががんや白血病といった病名からどのようなイメージを抱くのか,自分が大きな病気になったとしたら,病名や治療などについて教えて欲しいと思っているのかを明らかにすることである。千葉県内の小中高校に通っている小学校5年生から高校3年生までの児童生徒1964名から得られたアンケートの回答を,統計ソフトSPSSにて分析を行い以下の結果を得た。1.健康な小児が抱くがんのイメージは,「死ぬ・治らない」「重い・危険・苦しい」といった悲観的なのものが多く,全体の約65%を占めていた。「聞いたことがない・わからない」と答えたものもおり全体の約15%であり,どの学年でも同様の傾向であった。2.健康な小児が抱く白血病のイメージは「病態や特徴について」「原因や治療について」といったものが,全体の約38%を占めていた。「聞いたことがない・わからない」と答えたものは全体の約33%を占め,小学生では半数以上が「聞いたことがない・わからない」と答えていた。3.自分が病気になったときにされる説明については小学生の80%,中学生の85%,高校生の91%が真実を伝えられることを求めていた。その理由として自分の知る権利,治療に前向きに取り組めるといった姿勢の向上,知らないことが不安になる,残された命を有意義に悔いのないように過ごしたいといったものがあげられていた。The purposes of this study were to identify the images of healthy children on cancer and leukemia, and the way of thinking of truth telling with disease. The number of subjects were 1964. They belonged to between the fifth grade of primary school and the third year in high school. They answered someitem-questionnaire, and the answers were analyzed using SPSS. The results were as follows: 1. Sixty-five percent of the images of cancer were pessimistic, like death or incurable and serious or painful . About fifteen percent were having no images. 2. Thirty-eight percent of the images of leukemia were the feature and the cause or the treatment . About thirty-three percent were having no images. 3. Truth telling was desired by eighty percent of students of primary schools, eighty-five percent of junior high schools and ninety-one percent of a high school. The reasons were the rights to know , to be patient with treatments , to become more anxious without truth telling , and to live the remaining days without regrets