Identification of SSR and RAPD markers associated with QTLs of winter survival and related traits in Brassica napus L.

Because of importance of winter survival in winter type of Brassica napus, this study was performed to identify the QTLs controlling winter survival and related traits using SSR and RAPD markers. For this,an F2:3 population of 200 families derived from crossing between cv. ‘SLMO46’ (winter type and cold resistant) and cv. ‘Quantum’ (spring type and susceptible to low temperature) were used. Wintersurvival (WS), leaves per plant in rosette stage (L/P), crown wet weight (CWW), crown dry weight (CDW) and crown water content (CWC) were measured in F3 families. 350 SSR primer pairs and 250 RAPDprimers were used to assess the parental polymorphism. The 32 SSR primer pairs and 47 RAPD polymorphic markers between parental lines were used to screen F2 individuals. Linkage map was constructed using polymorphic markers. The markers were assigned into 14 linkage groups with total length of 1199.1 cM and an average distance of 17.13 cM between adjacent markers. The relationship between measured traits and genotypic data was analyzed using CIM method and totally 12 putative QTLs were detected for studied traits. The explained phenotypic variance by identified QTLs ranged between 0.5 and 11%. The identified QTLs had positive and negative additive effects and transferred from both parents to F2 plants and F3 families. Some of these QTLs located in the same genomic regions

Sampling-based reactive motion planning with temporal logic constraints and imperfect state information

© 2017, Springer International Publishing AG. This paper presents a method that allows mobile systems with uncertainty in motion and sensing to react to unknown environments while high-level specifications are satisfied. Although previous works have addressed the problem of synthesising controllers under uncertainty constraints and temporal logic specifications, reaction to dynamic environments has not been considered under this scenario. The method uses feedback-based information roadmaps (FIRMs) to break the curse of history associated with partially observable systems. A transition system is incrementally constructed based on the idea of FIRMs by adding nodes on the belief space. Then, a policy is found in the product Markov decision process created between the transition system and a Rabin automaton representing a linear temporal logic formula. The proposed solution allows the system to react to previously unknown elements in the environment. To achieve fast reaction time, a FIRM considering the probability of violating the specification in each transition is used to drive the system towards local targets or to avoid obstacles. The method is demonstrated with an illustrative example

Helicobacter pylori Outer Membrane Protein 18 ( Hp1125 ) Induces Dendritic Cell Maturation and Function

Background.  Dendritic cells (DCs) are potent antigen-presenting cells that initiate T-cell responses. A robust adaptive Th1 immune response is crucial to an adaptive (Th2) immune response necessary for vaccine-induced protective immunity against Helicobacter pylori. It has been shown that several outer membrane proteins (Omps) induce a robust antibody response. However, it is also known that the antibodies generated are not protective. Moreover there is great variation in the recognition of high molecular weight H. pylori proteins by sera from infected patients. In contrast to the high molecular weight proteins, serologic responses to small molecular weight proteins provide assessment of current infection with H. pylori and also of its eradication. Aim.  The goal of the study was to analyze the activation of the immune response by a specific low molecular weight Omp that is universally expressed by all H. pylori strains. Therefore, we studied interaction of H. pylori Omp18 with DCs. Methods.  Activation of murine bone marrow-derived DCs and production of cytokines by Omp18 was assessed by fluorescence-activated cell sorter (FACS) for costimulatory markers and ELISA, respectively. The ability of Omp18 stimulated DCs to induce lymphocyte proliferation was measured in a mixed leukocyte reaction. Results.  Omp18 induced higher expression of the B7 (CD80 and CD86) costimulatory molecule after 18 hours indicating processing and presentation of the antigen on the surface by bone marrow-derived DCs. The maturing DCs also secreted significant levels of IL-12, but was 4-fold less than that stimulated by whole bacteria. Omp18-primed DCs induced proliferation and release of IFNγ by syngeneic splenocytes. Conclusion.  We concluded that Omp18 is capable of activating DCs initiating a Th1 immune response.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73882/1/j.1523-5378.2005.00350.x.pd

Prevalence of Amblyopia in Iranian Children

BACKGROUND AND OBJECTIVE: Amblyopia is one of the common eye diseases in children and the risk of vision loss is possible. Therefore, the aim of this study is systematic review and meta-analysis in order to align the studies on the prevalence of amblyopia in Iranian children. METHODS: In this systematic review and meta-analysis relevant articles in scientific databases including SID, Science Direct and Medline (PubMed) and Google Scholar in March 1999- February 2017, using the Persian and English Keywords of Amblyopia, children, Iran. FINDINGS: In the review of internal and external journals and search on SID databases 22 articles, PubMed 126 articles, Science Direct 112 articles and 116 Google Scholar search engines were obtained. Then the articles that had the initial conditions for entry into the study were 162 cases based on preliminary studies, with the elimination of 214 repetitive articles. Finally, removing 120 articles unrelated to the topic of the study and removing 24 articles in the secondary studies ultimately 18 papers entered the meta-analysis process. The overall Prevalence of amblyopia in Iranian children was 5.4 % (Cl-95%: 3.1%-9.1%). CONCLUSION: According to the results of this study, the prevalence of amblyopia in Iranian children is high

Identification of disease-causing genes using microarray data mining and gene ontology

Background: One of the best and most accurate methods for identifying disease-causing genes is monitoring gene expression values in different samples using microarray technology. One of the shortcomings of microarray data is that they provide a small quantity of samples with respect to the number of genes. This problem reduces the classification accuracy of the methods, so gene selection is essential to improve the predictive accuracy and to identify potential marker genes for a disease. Among numerous existing methods for gene selection, support vector machine-based recursive feature elimination (SVMRFE) has become one of the leading methods, but its performance can be reduced because of the small sample size, noisy data and the fact that the method does not remove redundant genes. Methods: We propose a novel framework for gene selection which uses the advantageous features of conventional methods and addresses their weaknesses. In fact, we have combined the Fisher method and SVMRFE to utilize the advantages of a filtering method as well as an embedded method. Furthermore, we have added a redundancy reduction stage to address the weakness of the Fisher method and SVMRFE. In addition to gene expression values, the proposed method uses Gene Ontology which is a reliable source of information on genes. The use of Gene Ontology can compensate, in part, for the limitations of microarrays, such as having a small number of samples and erroneous measurement results. Results: The proposed method has been applied to colon, Diffuse Large B-Cell Lymphoma (DLBCL) and prostate cancer datasets. The empirical results show that our method has improved classification performance in terms of accuracy, sensitivity and specificity. In addition, the study of the molecular function of selected genes strengthened the hypothesis that these genes are involved in the process of cancer growth. Conclusions: The proposed method addresses the weakness of conventional methods by adding a redundancy reduction stage and utilizing Gene Ontology information. It predicts marker genes for colon, DLBCL and prostate cancer with a high accuracy. The predictions made in this study can serve as a list of candidates for subsequent wet-lab verification and might help in the search for a cure for cancers

Analysing the Influential Parameters on the Monopile Foundation of an Offshore Wind Turbine

This is the final version. Available on open access from MDPI via the DOI in this recordData Availability Statement: Data sharing not applicableCountries around the world generate electricity from renewable resources to decarbonise their societies and reduce global warming. Some countries have already outlined their wishes to produce a part of their total energy consumption from renewable sources in the coming years and gradually reduce the use of nuclear energy and fossil fuel in favour of cleaner fuels. While renewable energies are significant factors in tackling climate change, the parameters that can influence their performance should be analysed in detail during the design process. One of these parameters is the foundation of an offshore wind turbine. Offshore wind turbines allow more energy to be produced than an onshore installation, and do not have any harmful effects on human beings, while their geotechnical aspects need to be clearly determined in advance. In this study, the influential parameters such as soil type, the number of bolts in the design, and the size of the structure were analysed using the finite element method for three different designs. The simulations showed that some soil properties, such as cohesion, do not influence the results, while Young’s modulus has a large influence on the designs. Additionally, the results of this study showed that the maximum stress concentrations are at the bolts and connection joints where they are too close to the steel’s yield stress. It also proves that the non-elastic behaviour of the soil does not require to be assigned for such analyses and it can be simplified only with its elastic behaviour. The embedded length affects the lateral displacement, while the number of bolts influences the structure’s resistance to external loads

The Prevalence of Nosocomial Infections in Iranian Hospitals

BACKGROUND AND OBJECTIVE: Nosocomial infections are one of the major health problems. As the length of stay in the hospital increases, the risk of mortality and morbidity increases, which ultimately increases the cost of treatment. Therefore, the present study was performed as a systematic review and meta-analysis to evaluate the prevalence of nosocomial infections in Iran. METHODS: This systematic review and meta-analysis was performed in the range of the years 2001 – 2017. Articles related to the topic were assessed using Persian keywords “nosocomial infections”, “hospital”, and “Iran”, and their English equivalent in descriptive and cross sectional studies by searching online databases of SID & Magiran, PubMed and Scopus, ScienceDirect and Google Scholar. Analytical and interventional studies were excluded from the study list. FINDINGS: 578 articles had the preliminary inclusion criteria, and with the removal of 568 unrelated or low quality articles during secondary analyses, 10 articles were finally included in the process of meta-analysis. The overall prevalence of nosocomial infections in Iranian hospitals was 4.6% (CI-95%: 2.6 – 8.1). The highest prevalence of nosocomial infections was in Sanandaj with 15.6% (CI-95%: 10.22–82.1) and the lowest prevalence was in Urmia with 0.4% (CI-95%: 0.1–1.01). CONCLUSION: The results of the study showed that nosocomial infection has a low prevalence in Iran, but more attention and control over nosocomial infections in Iranian hospitals is necessary to reach standard levels

G-CSF Prevents the Progression of Structural Disintegration of White Matter Tracts in Amyotrophic Lateral Sclerosis: A Pilot Trial

Background: The hematopoietic protein Granulocyte-colony stimulating factor (G-CSF) has neuroprotective and regenerative properties. The G-CSF receptor is expressed by motoneurons, and G-CSF protects cultured motoneuronal cells from apoptosis. It therefore appears as an attractive and feasible drug candidate for the treatment of amyotrophic lateral sclerosis (ALS). The current pilot study was performed to determine whether treatment with G-CSF in ALS patients is feasible.Methods: Ten patients with definite ALS were entered into a double-blind, placebo-controlled, randomized trial. Patients received either 10 mu g/kg BW G-CSF or placebo subcutaneously for the first 10 days and from day 20 to 25 of the study. Clinical outcome was assessed by changes in the ALS functional rating scale (ALSFRS), a comprehensive neuropsychological test battery, and by examining hand activities of daily living over the course of the study (100 days). The total number of adverse events (AE) and treatment-related AEs, discontinuation due to treatment-related AEs, laboratory parameters including leukocyte, erythrocyte, and platelet count, as well as vital signs were examined as safety endpoints. Furthermore, we explored potential effects of G-CSF on structural cerebral abnormalities on the basis of voxel-wise statistics of Diffusion Tensor Imaging (DTI), brain volumetry, and voxel-based morphometry.Results: Treatment was well-tolerated. No significant differences were found between groups in clinical tests and brain volumetry from baseline to day 100. However, DTI analysis revealed significant reductions of fractional anisotropy (FA) encompassing diffuse areas of the brain when patients were compared to controls. On longitudinal analysis, the placebo group showed significant greater and more widespread decline in FA than the ALS patients treated with G-CSF.Conclusions: Subcutaneous G-CSF treatment in ALS patients appears as feasible approach. Although exploratory analysis of clinical data showed no significant effect, DTI measurements suggest that the widespread and progressive microstructural neural damage in ALS can be modulated by G-CSF treatment. These findings may carry significant implications for further clinical trials on ALS using growth factors

Responsiveness of genes to manipulation of transcription factors in ES cells is associated with histone modifications and tissue specificity

<p>Abstract</p> <p>Background</p> <p>In addition to determining static states of gene expression (high vs. low), it is important to characterize their dynamic status. For example, genes with H3K27me3 chromatin marks are not only suppressed but also poised for activation. However, the responsiveness of genes to perturbations has never been studied systematically. To distinguish gene responses to specific factors from responsiveness in general, it is necessary to analyze gene expression profiles of cells responding to a large variety of disturbances, and such databases did not exist before.</p> <p>Results</p> <p>We estimated the responsiveness of all genes in mouse ES cells using our recently published database on expression change after controlled induction of 53 transcription factors (TFs) and other genes. Responsive genes (<it>N </it>= 4746), which were readily upregulated or downregulated depending on the kind of perturbation, mostly have regulatory functions and a propensity to become tissue-specific upon differentiation. Tissue-specific expression was evaluated on the basis of published (GNF) and our new data for 15 organs and tissues. Non-responsive genes (<it>N </it>= 9562), which did not change their expression much following any perturbation, were enriched in housekeeping functions. We found that TF-responsiveness in ES cells is the best predictor known for tissue-specificity in gene expression. Among genes with CpG islands, high responsiveness is associated with H3K27me3 chromatin marks, and low responsiveness is associated with H3K36me3 chromatin, stronger tri-methylation of H3K4, binding of E2F1, and GABP binding motifs in promoters.</p> <p>Conclusions</p> <p>We thus propose the responsiveness of expression to perturbations as a new way to define the dynamic status of genes, which brings new insights into mechanisms of regulation of gene expression and tissue specificity.</p

The role of riboflavin in decolourisation of Congo red and bioelectricity production using Shewanella oneidensis-MR1 under MFC and non-MFC conditions

Dissimilatory metal reducing bacteria can exchange electrons extracellularly and hold great promise for their use in simultaneous wastewater treatment and electricity production. This study investigated the role of riboflavin, an electron carrier, in the decolourisation of Congo red in microbial fuel cells (MFCs) using Shewanella oneidensis MR-1 as a model organism. The contribution of the membrane-bound protein MtrC to the decolourisation process was also investigated. Within the range of riboflavin concentrations tested, 20 µM was found to be the best with >95% of the dye (initial concentration 200 mg/L) decolourised in MFCs within 50 h compared to 90% in the case where no riboflavin was added. The corresponding maximum power density was 45 mW/m2. There was no significant difference in the overall decolourisation efficiencies of Shewanela oneidensis MR-1 ΔMtrC mutants compared to the wild type. However, in terms of power production the mutant produced more power (Pmax 76 mW/m2) compared to the wild type (Pmax 46 mW/m2) which was attributed to higher levels of riboflavin secreted in solution. Decolourisation efficiencies in non-MFC systems (anaerobic bottles) were similar to those under MFC systems indicating that electricity generation in MFCs does not impair dye decolourisation efficiencies. The results suggest that riboflavin enhances both decolourisation of dyes and simultaneous electricity production in MFCs