A new DNA sequence entropy-based Kullback-Leibler algorithm for gene clustering

Information theory is a branch of mathematics that overlaps with communications, biology, and medical engineering. Entropy is a measure of uncertainty in the set of information. In this study, for each gene and its exons sets, the entropy was calculated in orders one to four. Based on the relative entropy of genes and exons, Kullback-Leibler divergence was calculated. After obtaining the Kullback-Leibler distance for genes and exons sets, the results were entered as input into 7 clustering algorithms: single, complete, average, weighted, centroid, median, and K-means. To aggregate the results of clustering, the AdaBoost algorithm was used. Finally, the results of the AdaBoost algorithm were investigated by GeneMANIA prediction server to explore the results from gene annotation point of view. All calculations were performed using the MATLAB Engineering Software (2015). Following our findings on investigating the results of genes metabolic pathways based on the gene annotations, it was revealed that our proposed clustering method yielded correct, logical, and fast results. This method at the same that had not had the disadvantages of aligning allowed the genes with actual length and content to be considered and also did not require high memory for large-length sequences. We believe that the performance of the proposed method could be used with other competitive gene clustering methods to group biologically relevant set of genes. Also, the proposed method can be seen as a predictive method for those genes bearing up weak genomic annotations.     

LMO1 polymorphisms and the risk of neuroblastoma: Assessment of meta‐analysis of case‐control studies

Neuroblastoma (NB), a neuroendocrine tumour, is one of the most prevalent cancers in children. The link between LMO1 polymorphisms and NB has been investigated by several groups, rendering inconclusive results. Here, with this comprehensive systematic review and up‐to‐date meta‐analysis, we aim to distinctively elucidate the possible correlation between LMO1 polymorphisms and NB susceptibility. Eligible studies were systematically researched and identified using PubMed, Web of Science and Scopus databases up to 10 February 2019. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to assess the strength of the associations. Our findings revealed that rs110419 and rs2168101 polymorphisms were significantly associated with a decreased risk of NB in all genetic models. In addition, the rs4758051 variant appeared protective against NB in homozygous, dominant and allele genetic models, whereas the rs10840002 variant markedly decreased the risk of NB in the allele model. In contrast, the rs204938 polymorphism showed a positive association with NB susceptibility in allele genetic models. In summary, our meta‐analysis is the first to provide clear evidence of an association between specific polymorphisms of LMO1 and susceptibility to NB. Of note, additional larger well‐designed studies would be helpful to further evaluate and confirm this association.     

Assessment of lncRNA DANCR,miR-145-5p and NRAS axis as biomarkers for the diagnosis of colorectal cancer

Molecular Biology Reports - Recent evidence reveals that miRNA sponges neutralize miRNAs activity by binding to miRNAs and sequester them from their relevant targets to regulate expression. The...     

Nicotinamide mononucleotide and melatonin counteract myocardial ischemia-reperfusion injury by activating SIRT3/FOXO1 and reducing apoptosis in aged male rats

Molecular Biology Reports - It has been documented that aging increases the risk of cardiovascular disease including myocardial ischemia/reperfusion (IR) injury and acute myocardial infarction. In...     

Development and fecundity of Spodoptera exigua (Hübner) (Lepidoptera: Noctuidae) on different soybean cultivars

The life history of Spodoptera exigua was studied under laboratory conditions at temperature of 25°C ± 1°C, relative humidity (RH) of 60% ± 5% and a photoperiod of 16:8 h (Light:Dark) on nine soybean (Glycine max L.) cultivars: 032, 033, Hill, M4, M7, M9, M11, TMS and Zan. Larval and pupal development times were longest on M7 cultivar (14.09 ± 0.078 and 7.78 ± 0.090 days) and shortest on 033 cultivar (11.98 ± 0.054 and 7.033 ± 0.090 days). The longest and shortest female and male longevities were observed on Hill and Zan cultivars, respectively. The results showed that the whole life span varied from 32.80 ± 0.89 to 37 ± 0.98 days for females and from 33.3 ± 0.66 to 38.74 ± 0.95 days for males. The highest daily fecundity was obtained on M9 (102. 38 eggs), and the lowest on Hill (75.87 eggs). Mean total fecundity per female during adult life was highest on 033 (1156.20 eggs) and lowest on M7 cultivars (841.68 eggs). Clustering analysis of the biological parameters of S. exigua confirmed that 033 and Hill cultivars were the susceptible and the resistant cultivars, respectively.     

Electrochemical spectroscopic investigations on the interaction of an ytterbium complex with DNA and their analytical applications such as biosensor

Metal ion-DNA interactions are important in nature, often changing the genetic material's structure and function. A new Yb complex of YbCl₃ (tris(8-hydroxyquinoline-5-sulfonic acid) ytterbium) was synthesized and utilized as an electrochemical indicator for the detection of DNA oligonucleotide based on its interaction with Yb(QS)₃. Cyclic voltammetry (CV) and fluorescence spectroscopy were used to investigate the interaction of Yb(QS)₃ with ds-DNA. It was revealed that Yb(QS)₃ presented an excellent electrochemical activity on glassy carbon electrode (GCE) and could intercalate into the double helix of double-stranded DNA (ds-DNA). The binding mechanism of interaction was elucidated on glassy carbon electrode dipped in DNA solution and DNA modified carbon paste electrode by using differential pulse voltammetry and cyclic voltammetry. The binding ratio between this complex and ds-DNA was calculated to be 1:1. The extent of hybridization was evaluated on the basis of the difference between signals of Yb(QS)₃ with probe DNA before and after hybridization with complementary DNA. With this approach, this DNA could be quantified over the range from 1 × 10⁻⁸ to 1.1 × 10⁻⁷ M. The interaction mode between Yb(QS)₃ and DNA was found to be mainly intercalative interaction. These results were confirmed with fluorescence experiments.     

Antifibrotic properties of c-Ski and its regulation of cardiac myofibroblast phenotype and contractility

Cardiac myofibroblasts are key players in chronic remodeling of the cardiac extracellular matrix, which is mediated in part by elevated transforming growth factor-β? (TGF-β?). The c-Ski proto-oncoprotein has been shown to modify TGF-β? post-receptor signaling through receptor-activated Smads (R-Smads); however, little is known about how c-Ski regulates fibroblast phenotype and function. We sought to elucidate the function of c-Ski in primary cardiac myofibroblasts using a c-Ski overexpression system. Cardiac myofibroblasts expressed three forms of c-Ski with the predominant band at 105 kDa, and adenoviral c-Ski treatment resulted in overexpression of 95-kDa c-Ski in cellular nuclei. Exogenous c-Ski led to significant inhibition of type I collagen secretion and myofibroblast contractility using two-dimensional semifloating gel contraction assay in both basal and with TGF-β? (10 ng/ml for 24 h) stimulation. Overexpressed c-Ski did not inhibit nuclear translocation of phosphorylated R-Smad2, despite their binding, as demonstrated by immunoprecipitation. Acute treatment of primary myofibroblasts with TGF-β? in vitro revealed a marked nuclear shuttling of c-Ski at 24 and 48 h following stimulation. Remarkably, overexpression of c-Ski led to a stepwise reduction of the myofibroblast marker α-smooth muscle actin with increasing multiplicity of infection, and these results indicate that 95-kDa c-Ski overexpression may effect a loss of the myofibroblastic phenotype. Furthermore, adenovirus (Ad) for hemagglutinin-tagged c-Ski infection led to a reduction in the number of myofibroblasts versus Ad-LacZ-infected and uninfected controls, due to induction of apoptosis. Finally, we observed a significant increase in 105-kDa c-Ski in the cytosolic fraction of cells of the infarct scar and adjacent remnant myocardium vs. noninfarcted controls.     

Stem cell-based therapy as a promising approach in Alzheimer's disease: current perspectives on novel treatment

Alzheimer's disease (AD) is a neuronal disorder with insidious onset and slow progression, leading to growing global concern with huge implications for individuals and society. The occurrence of AD has been increased and has become an important health issue throughout the world. In recent years, the care of more than 35 million patients with AD costs over $ 600 billion per year, it is approximately 1 percent of the global Gross Domestic Product. Currently, the therapeutic approach is not effective for neurological deficits especially after the development of these major neurological disorders. The discovery of the technique called cell-based therapy has shown promising results and made important conclusions beyond AD using the stem cells approach. Here we review recent progress on stem cell-based therapy in the context of AD.

     

Using Quality Measures for Quality Improvement: The Perspective of Hospital Staff

Research objective

This study examines the perspectives of a range of key hospital staff on the use, importance, scientific background, availability of data, feasibility of data collection, cost benefit aspects and availability of professional personnel for measurement of quality indicators among Iranian hospitals. The study aims to facilitate the use of quality indicators to improve quality of care in hospitals.

Study design

A cross-sectional study was conducted over the period 2009 to 2010. Staff at Iranian hospitals completed a self-administered questionnaire eliciting their views on organizational, clinical process, and outcome (clinical effectiveness, patient safety and patient centeredness) indicators.

Population studied

93 hospital frontline staff including hospital/nursing managers, medical doctors, nurses, and quality improvement/medical records officers in 48 general and specialized hospitals in Iran.

Principal findings

On average, only 69% of respondents reported using quality indicators in practice at their affiliated hospitals. Respondents varied significantly in their reported use of organizational, clinical process and outcome quality indicators. Overall, clinical process and effectiveness indicators were reported to be least used. The reported use of indicators corresponded with their perceived level of importance. Quality indicators were reported to be used among clinical staff significantly more than among managerial staff. In total, 74% of the respondents reported to use obligatory indicators, while this was 68% for voluntary indicators (p<0.05).

Conclusions

There is a general awareness of the importance and usability of quality indicators among hospital staff in Iran, but their use is currently mostly directed towards external accountability purposes. To increase the formative use of quality indicators, creation of a common culture and feeling of shared ownership, alongside an increased uptake of clinical process and effectiveness indicators is needed to support internal quality improvement processes at hospital level.