The challenge of large and empty voids in the SDSS DR7 redshift survey

We present catalogues of voids for the SDSS DR7 redshift survey and for Millennium I simulation mock data. We aim to compare the observations with simulations based on a $\Lambda$CDM model and a semi-analytic galaxy formation model. We use the void statistics as a test for these models. We assembled a mock catalogue that closely resembles the SDSS DR7 catalogue and carried out a parallel statistical analysis of the observed and simulated catalogue. We find that in the observation and the simulation, voids tend to be equally spherical. The total volume occupied by the voids and their total number are slightly larger in the simulation than in the observation. We find that large voids are less abundant in the simulation and the total luminosity of the galaxies contained in a void with a given radius is higher on average than observed by SDSS DR7 survey. We expect these discrepancies to be even more significant in reality than found here since the present value of $\sigma_8$ given by WMAP7 is lower than the value of 0.9 used in the Millennium I simulation. The reason why the simulation fails to produce enough large and dark voids might be the failure of certain semi-analytic galaxy formation models to reduce the small-scale power of $\Lambda$CDM and to produce sufficient power on large scales.Comment: Kolmogrov-Smirnov test added. version to appear in A&

Down-regulatory effects of miR-211 on long non-coding RNA SOX2OT and SOX2 genes in esophageal squamous cell carcinoma

Objective: MicroRNAs (miRNAs) are a class of non-coding RNAs (ncRNAs) that transcriptionally or post-Transcriptionally regulate gene expression through degradation of their mRNA targets and/or translational suppression. However, there are a few reports on miRNA-mediated expression regulation of long ncRNAs (lncRNAs). We have previously reported a significant upregulation of the lncRNA SOX2OT and its intronic coding gene, SOX2, in esophageal squamous cell carcinoma (ESCC) tissue samples. In this study, we aimed to evaluate the effect of induced overexpression of miR-211 on SOX2OT and SOX2 expression in vitro. Materials and Methods: In this experimental study, we performed both bioinformatic and experimental analyses to examine whether these transcripts are regulated by miRNAs. From the list of potential candidate miRNAs, miR-211 was found to have complementary sequences to SOX2OT and SOX2 transcripts. To validate our finding experimentally, we transfected the NT-2 pluripotent cell line (an embryonal carcinoma stem cell) with an expression vector overexpressing miR-211. The expression changes of miR-211, SOX2OT, and SOX2 were then quantified by a real-Time polymerase chain reaction (RT-PCR) approach. Results: Compared with mock-Transfected cells, overexpression of miR-211 caused a significant down-regulation of both genes (P<0.05). Furthermore, flow-cytometry analysis revealed a significant elevation in sub-G1 cell population following ectopic expression of miR-211 in NT-2 cells. Conclusion: We report here, for the first time, the down-regulation of SOX2OT and SOX2 genes by an miRNA. Considering the vital role of SOX2OT and SOX2 genes in pluripotency and tumorigenesis, our data suggest an important and inhibitory role for miR-211 in the aforementioned processes

The effect of microRNA-375 overexpression, an inhibitor of Helicobacter pylori-induced carcinogenesis, on lncRNA SOX2OT

Background: Helicobacter pylori is a major human pathogenic bacterium in gastric mucosa. Although the association between gastric cancer and H. pylori has been well-established, the molecular mechanisms underlying H. pylori-induced carcinogenesis are still under investigation. MicroRNAs (miRNAs) are small noncoding RNAs that modulate gene expression at the posttranscriptional level. Recently, studies have revealed that miRNAs are involved in immune response and host cell response to bacteria. Also, microRNA-375 (miR-375) is a key regulator of epithelial properties that are necessary for securing epithelium-immune system crosstalk. It has been recently reported that miR-375 acts as an inhibitor of H. pylori-induced gastric carcinogenesis. There are few reports on miRNA-mediated targeting long noncoding RNAs (lncRNAs). Objectives: This study aimed to examine the possible effect of miR-375 as an inhibitor of H. pylori-induced carcinogenesis on the expression of lncRNA SOX2 overlapping transcript (SOX2OT) and SOX2, a master regulator of pluripotency of cancer stem cells. Materials and Methods: In a model cell line, NT-2 was transfected with the constructed expression vector pEGFP-C1 contained miR- 375. The RNA isolations and cDNA synthesis were performed after 48 hours of transformation. Expression of miR-375 and SOX2OT and SOX2 were quantified using real-time polymerase chain reaction and compared with control cells transfected with pEGFP-C1-Mock clone. Cell cycle modification was also compared after transfections using the flow cytometry analysis. Results: Following ectopic expression of miR-375, SOX2OT and SOX2 expression analysis revealed a significant decrease in their expression level (P < 0.05) in NT-2 cells compared to the control. Cell cycle analysis following ectopic expression of miR-375 in the NT-2 cells using propidium iodine staining revealed significant extension in sub-G1 cell cycle. Conclusions: This is the first report to show down-regulation of SOX2OT and SOX2 following induced expression of miR-375. This findingmaysuggest expression regulation potential between different classes of ncRNAs, for example between miR-375andSOX2OT. This data not only extends our understanding of possible ncRNA interactions in cancers but also may open novel investigation lines towards elucidation of molecular mechanisms controlling H. pylori inflammation and carcinogenesis. © 2016, Ahvaz Jundishapur University of Medical Sciences

Analysis of Opportunities and Challenges for R&D Management and the Role of the R&D Society for its Improvement – A Case Study in Iran

Research and Development (R&D) management in Iran is faced to many barriers and obstacles, in which R&D units are considered as the basic core of the product development and innovation. Due to structural shortcomings, a great number of organizations and industries have not been able to find their actual status. There are about different 1141 R&D units with a dispersion pattern in Iran. This paper considers and analyzes the R&D case study in one of the provinces located in the north part of Iran in order to enhance the potential R&D activities in respect with the industrialized areas and zones. In this province, there are about 2504 industrial units of which there are only 44 R&D units certified by the state government. However, there are limit numbers of these R&D units that are extensively active. This paper also addresses the current status in respect with the R&D activities to find out why there is a lack and depression of these activities in the industrial units. By considering the opportunity and challenges of these R&D units, there is a need to change these units to be active in order to quickly respond the market and demand requirements. Finally, a few alternative solutions and improvement plans are proposed, in which the Iranian R&D Society is responsible for supporting and succeeding these action plans towards the organization goals.R&D Management

Persia, the Land of Shiite Faith: The Migration of Imam Ahl al-Bayt and the Encounter between Two Belief Systems in Persia

This article attempts to trace the fundamental role of early Persian beliefs, Zoroastrians, to the decision of Ahl al-Bayt’s choice to migrate to Persia (Iran). This research is based on the fact that there are many places for pilgrimage to imams in Iran.  Specifically, this research investigates the similarity of several concepts in both religions, Zoroaster and Islam, regarding the teaching in the principle of God (Ilahiyyah), the principle of life after death (eschatology), and the principle of justice and morals of the religion embraced before Islam in Persia. Several studies have also reported on the distortions, opposition, and the consequences of encountering the two beliefs for the first time between Persian beliefs and Islamic teachings. This study employs a qualitative method with historical analysis and literature study along with relevant information of the study.  This article also uses the theory of migration and identity to see the interconnectedness of religion in the migration context. The results of this study show the factors that the Persians are interested in accepting and understanding the teachings of Islam. Those are: first, the emotional closeness of beliefs and moral values between Muslims and Zoroastrians (Magi); Second, the inclusive nature of Islam; third, the absence of racial, gender, and status discrimination in Islamic teachings. The descendants of imams Ahl al-Bayt of the Prophet Muhammad SAW continued the prophet's preaching and the Imams in expanding the spread of Islamic teachings to various regions. During this expansion process, they found Iran as the most secure, and suitable region to accept the presence and teaching of Islam especially the Shiite sect. Therefore, they decided to migrate to Iran, and until now Iran is known as a Shiite country

Evaluating the miR-302b and miR-145 expression in formalin-fixed paraffin-embedded samples of esophageal squamous cell carcinoma

Background: MicroRNAs are involved in key cellular processes regulating, and their misregulation is linked to cancer. The miR-302-367 cluster is exclusively expressed in embryonic stem and carcinoma cells. This cluster also promotes cell reprogramming and stemness process. In contrast, miR-145 is mostly regarded as a tumor suppressor, where it regulates cellular functions such as cell division, differentiation, and apoptosis. By suppressing the main pluripotency factors (OCT4, SOX2, MYC and KLF4), miR-145 silences the self-renewal program in ESCs. Therefore, the main aim of this study is to find a potential link between the expression level of hsa-miR-302b and hsa-miR-145 with tumor vs. non-tumor as well as high-grade vs. low-grade states of the esophageal tissue samples. Methods: A total number of 40 formalin-fixed, paraffin-embedded (FFPE) samples of esophageal squamous-cell carcinoma (ESCC) were obtained, and the tumor and marginal non-tumor areas delineated and punched off by an expert pathologist. Total RNA was extracted with Trizol, and cDNA synthesized using the miRCURY LNA™ Universal RT microRNA PCR Kit. Real-time reverse transcription polymerase chain reaction (RT-PCR) assays were performed using specific LNA-primers and SYBR Green master mix. Results: The expression level of miR-302b failed to show any significant difference, neither between tumor and their non-tumor counterparts, nor among tumors with different grades of malignancies (P > 0.05). In contrast, miR-145 was significantly down regulated in all grades of tumor samples (P 0.05). CONCLUSION: Our data revealed a significant down-regulation of miR-145 in ESCC tissue samples. Based on our ROC curve analysis data (AUC = 0.74, P < 0.001) miR-145 could be regarded as a potential tumor marker for diagnosis of esophageal cancer. © 2015, Academy of Medical Sciences of I.R. Iran. All rights reserved

Effect of Honey on Peridural Fibrosis Formation after Laminectomy in Rats: A Novel Experimental Study

Despite progress in surgical techniques, some patients still face postoperative recurrence of pain. Recently, more attention has been focused on peridural fibrosis (PF), which may be responsible for recurrent pain after laminectomy or discectomy. Honey has been shown to exert anti-inflammatory effects on exposed tissues besides its well-known antibacterial properties. The aim of this study were to investigate the effects of honey on the prevention of postlaminectomy fibrosis formation in a rat model. A controlled blinded study was performed in 45 male adult white Sprague-Dawley rats that underwent laminectomy at the L5-L6 levels. They were divided into 3 groups (A, B, and C) of 15 rats each. Group A (sham) underwent laminectomy and group B was treated with normal saline at the laminectomy site. Rats in group C received 0.1 mL honey at the laminectomy site. All rats were killed 4 weeks after laminectomy. PF was found in 5 rats (33%) of control groups A and B, and in 2 rats (10%) in honey-treated laminectomy group C. The difference was not statistically significant. Wound healing was not affected, and there was no cerebrospinal fluid leakage. Although honey appears to be safe, it cannot cause a significant reduction of PF formation after lumbar laminectomy in rats

Expression, Tissue Distribution and Function of miR-21 in Esophageal Squamous Cell Carcinoma

Objective:MiR-21 is an oncomir expressed by malignant cells and/or tumor microenvironment components. In this study we focused on understanding the effects of stromal miR-21 on esophageal malignant cells.Design:MiR-21 expression was evaluated in formalin-fixed paraffin-embedded samples from patients with esophageal squamous-cell carcinoma (SCC) by quantitative RT-PCR. MiR-21 tissue distribution was visualized with in situ hybridization. A co-culture system of normal fibroblasts and esophageal cancer cells was used to determine the effects of fibroblasts on miR-21 expression levels, and on SCC cell migration and invasion.Results:MiR-21 was overexpressed in SCCs, when compared to the adjacent non-tumor tissues (P = 0.0007), and was mainly localized in the cytoplasm of stromal cells adjacent to malignant cells. Accordingly, miR-21 expression was increased in tumors with high versus low stromal content (P = 0.04). When co-cultured with normal fibroblasts, miR-21 expression was elevated in SCC cells (KYSE-30), while its expression was restricted to fibroblasts when co-cultured with adenocarcinoma cells (OE-33 and FLO-1). MiR-21 was detected in conditioned media of cancer cell lines, illustrating the release of this miRNA into the environment. Co-culturing with normal fibroblasts or addition of fibroblast conditioned media caused a significant increase in cell migration and invasion potency of KYSE-30 cells (P<0.0001). In addition, co-culturing cancer cells with fibroblasts and expression of miR-21 induced the expression of the cancer associated fibroblast (CAF) marker S100A4.Conclusions:MiR-21 expression is mostly confined to the SCC stroma and its release from fibroblasts influences the migration and invasion capacity of SCC cells. Moreover, miR-21 may be an important factor in "activating" fibroblasts to CAFs. These findings provide new insights into the role of CAFs and the extracellular matrix in tumor microenvironment formation and in tumor cell maintenance, and suggest miR-21 may contribute to cellular crosstalk in the tumor microenvironment. © 2013 Nouraee et al