Determining gene expression on a single pair of microarrays

<p>Abstract</p> <p>Background</p> <p>In microarray experiments the numbers of replicates are often limited due to factors such as cost, availability of sample or poor hybridization. There are currently few choices for the analysis of a pair of microarrays where N = 1 in each condition. In this paper, we demonstrate the effectiveness of a new algorithm called PINC (PINC is Not Cyber-T) that can analyze Affymetrix microarray experiments.</p> <p>Results</p> <p>PINC treats each pair of probes within a probeset as an independent measure of gene expression using the Bayesian framework of the Cyber-T algorithm and then assigns a corrected p-value for each gene comparison.</p> <p>The p-values generated by PINC accurately control False Discovery rate on Affymetrix control data sets, but are small enough that family-wise error rates (such as the Holm's step down method) can be used as a conservative alternative to false discovery rate with little loss of sensitivity on control data sets.</p> <p>Conclusion</p> <p>PINC outperforms previously published methods for determining differentially expressed genes when comparing Affymetrix microarrays with N = 1 in each condition. When applied to biological samples, PINC can be used to assess the degree of variability observed among biological replicates in addition to analyzing isolated pairs of microarrays.</p

Lung macrophage scavenger receptor SR-A6 (MARCO) is an adenovirus type-specific virus entry receptor

<div><p>Macrophages are a diverse group of phagocytic cells acting in host protection against stress, injury, and pathogens. Here, we show that the scavenger receptor SR-A6 is an entry receptor for human adenoviruses in murine alveolar macrophage-like MPI cells, and important for production of type I interferon. Scavenger receptors contribute to the clearance of endogenous proteins, lipoproteins and pathogens. Knockout of SR-A6 in MPI cells, anti-SR-A6 antibody or the soluble extracellular SR-A6 domain reduced adenovirus type-C5 (HAdV-C5) binding and transduction. Expression of murine SR-A6, and to a lower extent human SR-A6 boosted virion binding to human cells and transduction. Virion clustering by soluble SR-A6 and proximity localization with SR-A6 on MPI cells suggested direct adenovirus interaction with SR-A6. Deletion of the negatively charged hypervariable region 1 (HVR1) of hexon reduced HAdV-C5 binding and transduction, implying that the viral ligand for SR-A6 is hexon. SR-A6 facilitated macrophage entry of HAdV-B35 and HAdV-D26, two important vectors for transduction of hematopoietic cells and human vaccination. The study highlights the importance of scavenger receptors in innate immunity against human viruses.</p></div

Diagnostic Value of C-reactive Protein in Determining of Gestational Diabetes Mellitus (GDM)

This study was designed to evaluate diagnostic value of C-reactive protein in determining of gestational diabetes mellitus. The present case-control study was conducted on 60 pregnant women with GDM (case group) and 120 women with normal pregnancy (control group) referred to Ayatollah Taleghani and mahdiyeh Hospitals. The serum level of qualitative and quantitative CRP was measured and diagnostic value of CRP was determined. In this study information form was completed by interview and sampling was performed by convenience method. Data were analyzed by SPSS-17 and significance level of p&lt;0.05 was considered. Serum CRP value in GDM and control groups was 3/ 59±3/2 and 1/44±3/3 mg/liter, respectively. Regarding to cut-off of 2/2 mg/liter, sensitivity, specificity, positive predictive value and negative predictive value of quantitative CRP were 71%, 60%, 47% and 81%, respectively in diagnosis of GDM. The under curve area was 0/70. Sensitivity, specificity, positive predictive value and negative predictive value of qualitative CRP in diagnosis of GDM was calculated 33/3%, 98/3%, 90% and 74%, respectively. It seems that measuring CRP in pregnant women with GDM risk factors can be used as a simple, new and reliable method to screen gestational diabetes mellitus

Vibrio parahemolyticus in sea food from the south sea of Iran

Vibrio parahemolyticus is a facultative anaerobic and gram negative bacteria, which lives in salty waters. It's infection in human usually like a self-limited gastroentritis to cholera diarhea. Usually after 15 hrs incubation periods disease is manifested with severe diarhea, watery, without blood, vomiting and fever. Most people were infected due to consuming low heated fish, shrimp, lobster... So its important to control sea foods for presenting of this bacteria in food control laboratories. In this study finding the rate of isolation and effective detection method for this bacteria was main aim. 30 sea food specimens were collected. after preparing suspention inoculated to enrichment salty media polymixin and alkaline pepton water, after 7 hrs in 37°C cultured respectively to TCBS and TSAT medium then after 24 hrs in 37°C suspected colonies picked up for identification and confirmation tests. Vibrio parahemolyticus was isolated f rorn 2 specimens. Due to presence of this bacteria in sea foods, detection and training for isolation of this bacteria is suggested in food control laboratories

Intravenous administration of adenoviruses targeting transforming growth factor beta signaling inhibits established bone metastases in 4T1 mouse mammary tumor model in an immunocompetent syngeneic host

We have examined the effect of adenoviruses expressing soluble transforming growth factor receptorII-Fc (sTGFβRIIFc) in a 4T1 mouse mammary tumor bone metastasis model using syngeneic BALB/c mice. Infection of 4T1 cells with a non-replicating adenovirus, Ad(E1-).sTβRFc, or with two oncolytic adenoviruses, Ad.sTβRFc and TAd.sTβRFc, expressing sTGFβRIIFc (the human TERT promoter drives viral replication in TAd.sTβRFc) produced sTGFβRIIFc protein. Oncolytic adenoviruses produced viral replication and induced cytotoxicity in 4T1 cells. 4T1 cells were resistant to the cytotoxic effects of TGFβ-1 (up to 10 ng/ml). However, TGFβ-1 induced the phosphorylation of SMAD2 and SMAD3, which were inhibited by co-incubation with sTGFβRIIFc protein. TGFβ-1 also induced IL-11, a well-known osteolytic factor. Intracardiac injection of 4T1-luc2 cells produced bone metastases by day 4. Intravenous injection of Ad.sTβRFc (on days 5 and 7) followed by bioluminescence imaging (BLI) of mice on days 7, 11 and 14 in tumor bearing mice indicated inhibition of bone metastasis progression (p<0.05). X-ray radiography of mice on day 14 showed a significant reduction of the lesion size by Ad.sTβRFc (p<0.01) and TAd.sTβRFc (p<0.05). Replication-deficient virus Ad(E1-).sTβRFc expressing sTGFβRIIFc showed some inhibition of bone metastasis, while Ad(E1-).Null was not effective in inhibiting bone metastases. Thus, systemic administration of Ad.sTβRFc and TAd.sTβRFc can inhibit bone metastasis in the 4T1 mouse mammary tumor model, and can be developed as potential anti-tumor agents for breast cancer

A New Fuzzy Multi-criteria Decision Making Approach: Extended Hierarchical Fuzzy Axiomatic Design Approach with Risk Factors

In recent years, Axiomatic Design (AD) has been widely used as a multi criteria decision making approach. AD approach compares the design objects and system capabilities in a framework and then selects the best alternative based on these comparisons. Some researchers then include fuzziness in the AD approach which helps to evaluate alternatives in fuzzy environments. The main advantage of fuzzy AD approach is the ability to evaluate both crisp and fuzzy values at the same time during decision process. However, these approaches are not appropriate for hierarchical decision problems. Therefore, these are extended to solve the hierarchical decision problems and Hierarchical Fuzzy Axiomatic Design Approach (HFAD) is presented. In this study, HFAD is extended to include risk factors for the first time in literature and a new approach called RFAD is proposed. Moreover, the application of the new approach is shown on a real world supplier selection problem and the results are compared to the other widely used decision making approaches in literature. © Springer International Publishing Switzerland 2014