Strategy for optimizing experimental settings for studying low atomic number colloidal assemblies using liquid phase scanning transmission electron microscopy

Observing processes of nanoscale materials of low atomic number is possible using liquid phase electron microscopy (LP-EM). However, the achievable spatial resolution (d) is limited by radiation damage. Here, we examine a strategy for optimizing LP-EM experiments based on an analytical model and experimental measurements, and develop a method for quantifying image quality at ultra low electron dose De using scanning transmission electron microscopy (STEM). As experimental test case we study the formation of a colloidal binary system containing 30 nm diameter SiO2 nanoparticles (SiONPs), and 100 nm diameter polystyrene microspheres (PMs). We show that annular dark field (DF) STEM is preferred over bright field (BF) STEM for practical reasons. Precise knowledge of the material's density is crucial for the calculations in order to match experimental data. To calculate the detectability of nano-objects in an image, the Rose criterion for single pixels is expanded to a model of the signal to noise ratio obtained for multiple pixels spanning the image of an object. Using optimized settings, it is possible to visualize the radiation-sensitive, hierarchical low-Z binary structures, and identify both components

Developing a Library of Shear Walls Database and the Neural Network Based Predictive Meta-Model

There is a large amount of useful information from past experimental tests, which are usually ignored in test-setup for the new ones. Variation of assumptions, materials, test procedures, and test objectives make it difficult to choose the right model for validation of the numerical models. Results from different experiments are sometimes in conflict with each other, or have minimum correlation. Furthermore, not all these information are easily accessible for researchers and engineers. Therefore, this paper presents the results of a comprehensive study on different experimental models for steel plate and reinforced concrete shear walls. A unique library of up to 13 parameters (mechanical properties and geometric characteristics) affecting the strength, stiffness and drift ratio of the shear walls are gathered including their sensitivity analysis. Next, a predictive meta-model is developed based on artificial neural network. It is capable of forecasting the responses for any desired shear wall with good accuracy. The proposed network can be used to as an alternative to the nonlinear numerical simulations or expensive experimental test.</p

Factors Affecting the Decline in Childbearing in Iran: A Systematic Review

AbstractIntroduction: The decline in fertility and childbearing tendency in Iran is due tovarious demographic, economic, social, and cultural variables. The present research wasconducted to review studies carried out on factors affecting the decline in childbearing.Methods: This systematic review searched for articles published from 2011 to 2017in all the available Iranian and foreign databases, including SID, Magiran, Irandoc,Medlib, Pubmed, Google Scholar, Science Direct, and Proquest using the followingkeywords, “childbearing”, “fertility”, “fertility decline” and “population decline”. Thesearch ultimately led to the inclusion of 53 studies.Results: The main factors affecting the decline in childbearing discussed in the 53reviewed articles were divided to three general categories: 1. Personal and familyfactors, including aging, older age at marriage, current number of children, theduration of marriage, the mean birth spacing, gender preferences, hopefulness, maritalsatisfaction, and quality of life, 2. Socioeconomic factors, including social support,education, occupation and social participation, especially of females, place of residenceand the effect of social networks, 3. Cultural factors, including modernity, urbanizationand industrialization, attitude change towards the value of children, changes in familyvalues and religion.Conclusions: To intervene in the decline in childbearing and to increase the successrate of the designed plans and strategies, policy-makers and planners should providestrategies to deal with all the three noted groups of factors affecting childbearing

In Vitro Anti Proliferative Activity, Antioxidant Potential and Total Phenolic Compounds of Black Tea Extract

Natural products, mainly isolated from medicinal plants, have considered as valuable sources for herbal anticancer drugs. The present study aimed to determine total phenolic and flavonoid contents, antioxidant activity, and anti proliferative activity of black tea (Camellia sinensis Kuntze) extract in vitro. Crude ethyl alcohol extract of black tea was prepared. To determine antioxidant activity, total phenol, and flavonoids content of the extract, the 2, 2-diphenyl-1-picrylhydrazyl (DPPH) assay, Folin-Ciocalteu method and aluminum chloride colorimetric method were used, respectively. The anti proliferative activity in cancerous (AGS) and normal (HDFs) cell lines was tested by MTT 3-(4, 5-dimethylthiazol-2ol) 2, 5 di phenyl tetrazolium bromide] assay. The IC50 of DPPH radical assay was 8 +/- 1.41 mu g/ml, compared with butylated hydroxytoluene (BHT) with IC50 25.41 +/- 1.89 mu g/ml. The total phenol and flavonoid contents were 341.8 +/- 4.41 mg GAE/g and 21.1 +/- 2.11 mg RUT /g, respectively. The extract showed higher anti proliferative activity against the cancer cell line than normal cell line. 48 hours after treatment, crude ethyl alcohol extract inhibited the proliferation of AGS and HDFs cells with IC50 values of 264.3 mu g/ml and 689.5 mu g/ml, respectively. This study revealed that the crude ethyl alcohol extract of black tea suppresses the proliferation of gastric carcinoma cells. It is a rich resource of natural antioxidants and can prevent a lot of diseases such as cancer

THE LACK OF CORRELATION BETWEEN TP53 MUTATIONS AND GASTRIC CANCER: A REPORT FROM A PROVINCE OF IRAN

Gastric cancer ranks second cause of cancer death worldwide after lung cancer. Its etiology is heterogeneous and genetic factors including protooncogenes and tumor suppressor genes always contribute to the progression of cancer. The TP53 tumor suppressor gene has a broad role in genomic stability and DNA repair. The aim of this study was to determine the TP53 gene mutations in gastric cancer specimens in Chaharmahal Va Bakhtiari province of Iran. In this descriptive-lab based study, we investigated the promoter and exons of TP53 gene mutations in 38 paraffin-embedded gastric cancer specimens. DNA was extracted following a standard phenol-chloroform protocol. The TP53 gene mutations were determined using PCR-SSCP & PCR-RFLP procedures. The present study revealed no TP53 gene mutation in the promoter and exons in the gastric cancer subjects studied. While TP53 gene mutations have been reported as the most frequent genetic alterations and are found in about 50% of the human malignancies, no mutation was detected in this study. This may be due to mutations in other related genes in the same pathway or epigenetic factors

Genetic linkage analysis of the DFNB48 and DFNB98 loci in families with Autosomal Recessive Non-Syndromic Hearing Loss (ARNSHL) from Khouzestan province

Background and aims: Hearing loss, a sensorineural disorder, is one of the most common congenital impairments, occurring in approximately 1 in 500 newborns. Hearing loss is a highly heterogenic disease and half of the cases of deafness are attributed to genetic causes; environmental and unknown factors account for the remainder. Non-syndromic type forms 70% of hearing loss cases. Pattern of inheritance of nearly 80% of this type of HL is recessive autosomal. Iranian population provides a valuable genetic resource to study this kind of HL because of high ratio of consanguinity. In this study, genetic linkage of DFNB48 (CIB2) and DFNB98 (TSPEAR) is investigated in families with ARNSHL impairment from Khouzestan province. Methods: In this descriptive study 300 individuals of 25 families with hearing loss were examined in order to determine type and frequency of mutation of DFNB48 and DFNB98 loci in Khouzestan province. Families' selection had some criteria. Families with healthy parents, consanguineous marriage and negative result for mutations of GJB2 gene with at least two affected individuals were selected. 3 families which were detected positive for mutations of GJB2 gene were excluded from study. Linkage analysis was done for 22 families by using six STR markers which were located in or were tightly linked to each locus. Results: None of these families inspected by linkage analysis was linked to the DFNB48 or DFNB98 loci. Conclusion: Considering these results it seems that CIB2 and TSPEAR genes mutations have not important roles in hearing loss in Khouzestan province

Molecular diagnosis and anti-microbial resistance patterns among Shigella spp. isolated from patients with diarrhea

Aim: This study aims to determine the serogroup distribution and molecular diagnosis, as well as antimicrobial resistance profiles among Shigella spp. isolated from patients with diarrhea in Kerman, southeast of Iran. Background: Shigella species are frequent cause of bacterial dysentery worldwide. Previous studies have been reported that S. sonnei and S. flexneri are the most prevalent serogroups in various parts of Iran. Patients and methods: A total of 624 stool samples were randomly collected from patients with diarrhea from June 2013 to August 2014. Biochemical and serological characterizations were performed for identifying Shigella spp. In addition, the multiplex PCR assay was carried out for the detection and differentiation of three pathogenic Shigella spp. Antibiotic susceptibility testing was performed according to the Clinical Laboratory Standards Institute (CLSI) guidelines. Results: Fifty six (9%) Shigella strains were isolated from stool samples. The most common species were S. flexneri 31(55.4%), followed by S. sonnei 18(32.1%) and S. boydii 7(12.5%). S. dysentery was not detected in the present study. All the isolates that identified by serological test as Shigella spp. were confirmed by the multiplex PCR method. The highest rate of resistance was observed for ampicillin and trimethoprim-sulphamethoxazole antibiotics with 52(92.9%) resistant, followed by tetracycline 44(78.6%) and cefotaxime 33(58.9%). All Shigella isolates were susceptible to ciprofloxacin. A significant relationship was found between the Shigella species and cefotaxime resistance (p<0.05). Conclusion: S. flexneri was found as the most prevalent serogroup causing shigellosis. The high rate of resistance to third-generation cephalosporins limits the treatment options available for the management of shigellosis in Kerman, Iran

Constraint-Based, Score-Based and Hybrid Algorithms to Construct Bayesian Gene Networks in the Bovine Transcriptome

SIMPLE SUMMARY: In this study, we investigated and compared six different Bayesian network algorithms from three different categories to identify hub genes critical to gene expression networks activated in response to progesterone in the bovine uterus. We observed many common hub genes identified between constraint-based algorithms (CBAs) and hybrid algorithms (HAs), while it appeared that score-based algorithm (SBA) methods led to more accurate and relevant predictions of core genes. The results revealed that the identification of hub genes was affected by the type of network reconstruction and by the subsequently used topological parameters. Two identified genes known to have roles during pregnancy are ISG15 and DGAT2. The identified hub genes are associated with biological processes such as amino acid metabolism, hormonal signaling pathways and the immune system. Our analysis revealed a role for miRNAs in the regulation of this system. The biological and physiological roles (enzymatic and hormonal effects) of unannotated identified hub genes should be functionally validated by further studies. ABSTRACT: Bayesian gene networks are powerful for modelling causal relationships and incorporating prior knowledge for making inferences about relationships. We used three algorithms to construct Bayesian gene networks around genes expressed in the bovine uterus and compared the efficacies of the algorithms. Dataset GSE33030 from the Gene Expression Omnibus (GEO) repository was analyzed using different algorithms for hub gene expression due to the effect of progesterone on bovine endometrial tissue following conception. Six different algorithms (grow-shrink, max-min parent children, tabu search, hill-climbing, max-min hill-climbing and restricted maximum) were compared in three higher categories, including constraint-based, score-based and hybrid algorithms. Gene network parameters were estimated using the bnlearn bundle, which is a Bayesian network structure learning toolbox implemented in R. The results obtained indicated the tabu search algorithm identified the highest degree between genes (390), Markov blankets (25.64), neighborhood sizes (8.76) and branching factors (4.38). The results showed that the highest number of shared hub genes (e.g., proline dehydrogenase 1 (PRODH), Sam-pointed domain containing Ets transcription factor (SPDEF), monocyte-to-macrophage differentiation associated 2 (MMD2), semaphorin 3E (SEMA3E), solute carrier family 27 member 6 (SLC27A6) and actin gamma 2 (ACTG2)) was seen between the hybrid and the constraint-based algorithms, and these genes could be recommended as central to the GSE33030 data series. Functional annotation of the hub genes in uterine tissue during progesterone treatment in the pregnancy period showed that the predicted hub genes were involved in extracellular pathways, lipid and protein metabolism, protein structure and post-translational processes. The identified hub genes obtained by the score-based algorithms had a role in 2-arachidonoylglycerol and enzyme modulation. In conclusion, different algorithms and subsequent topological parameters were used to identify hub genes to better illuminate pathways acting in response to progesterone treatment in the bovine uterus, which should help with our understanding of gene regulatory networks in complex trait expression

dy of P53 gene mutations in promoter and exons 2-4 and 9-11 in patient with gastric cancer by PCR-SSCP in Chaharmahal Va Bakhtiari province

Background: Gastric cancer is one of the most important diseases and after lung cancer, is the second cause of cancer death worldwide. Genetic factors including oncogenes and tumor suppressor genes are always contributed in progression of this cancer. The P53 tumor suppressor gene has a broad role in genomic stability and DNA repair. The aim of this study was to determine the P53 gene mutations in gastric cancer specimens in Chaharmahal Va Bakhtiari Province. Methods: In this descriptive-lab based study, we investigated the promoter, exons 2-4 and 9-11 of P53 gene mutations in 38 paraffin embedded gastric cancer specimens. DNA was extracted following the standard phenol chloroform protocol. The P53 gene mutations were determined using PCR-SSCP procedure. Results: Our study revealed no P53 gene mutation in promoter and exons 2-4 and 9-11 in the gastric cancer subjects studied. Conclusion: While P53 gene mutations have been reported as the most frequent genetic alterations and are found in about 50% of the human malignancies, no mutation was detected in this study. The reason may be due to small sample size or mutations on other genes or epigenetic factors

Detection of mutations in exons 5-8 of the P53 gene in gastric cancer samples using PCR-SSCP in Chaharmahal va Bakhtiari province 2006-2007

زمینه و هدف: سرطان معده دومین سرطان شایع در جهان است. فاکتورهای ژنتیکی مانند انکوژن ها و ژن های سرکوبگر تومور، همواره از جمله مهمترین عوامل در بروز این سرطان هستند. ژن P53 یک ژن سرکوبگر تومور است و نقش بسیار مهمی در فرآیند مرگ برنامه ریزی شده سلول ایفا می کند. جهش در ژن P53 موجب از بین رفتن عملکرد محافظتی آن شده که یکی ازعوامل اصلی بروز سرطان معده در انسان است. این مطالعه با هدف بررسی جهش های ژن P53 در بیماران مبتلا به سرطان معده در استان چهارمحال و بختیاری انجام شده است. روش بررسی: در این مطالعه توصیفی آزمایشگاهی به بررسی جهش ها در اگزون های شماره 8-5 ژن P53 در 38 نمونه پارافینه سرطان معده پرداخته ایم. ابتدا DNA به روش استاندارد فنل کلروفرم استخراج شد، سپس با استفاده از تکنیک PCR-SSCP جهش های این ژن بررسی شدند. یافته ها: تفاوت های آشکاری در همه نمونه های کنترل مثبت مشاهده شد. با این وجود در سایر نمونه های مربوط به بیماران هیچ تفاوت و تغییری در حرکت باندها تشخیص داده نشد. نتیجه گیری: در استان چهارمحال و بختیاری ارتباط بین سرطان معده با جهش های ژن P53 بسیار ضعیف است. البته این مطالعه فقط بر روی 38 نمونه بیمار انجام شده و مطالعات بیشتری نیاز است تا ارتباط واقعی جهش بر روی ژن P53 با سرطان معده در این استان مشخص شود