Network Survivability Performance Evaluation in Underwater Surveillance System Using Markov Model

Underwater Wireless Sensor Network (UWSN) is a useful technology that can be used in Underwater Surveillance System (USS). USSs are mostly used in military purposes for detecting underwater military activities. One of the most important issues in USS is mission reliability or survivability. Due to harsh underwater environment and mission critical nature of military applications, it is important to measure survivability of USS. Underwater sensor node failures can be detrimental for USS. To improve survivability in USS, we propose a fault-tolerant underwater sensor node model. To the best of our knowledge, this is the first fault-tolerant underwater sensor node model in USS that evaluates survivability of an USS.  We develop Markov models for characterizing USS survivability and MTTF (Mean Time to Failure) to facilitate USS. Performance evaluation results show the effectiveness of proposed model

Assessment and Comparison the Location of Six Universities in Tehran City Using GIS and Multi Criteria Decision Making Methods

Universities are the engine of science in any country. Thus improvement of a university led the country to development. Location of the university is one of the factors which are effective on the quality of research and educational activities at the university. Crowded or polluted areas are not proper places for the universities. There are also the other criteria such as quality of transportation system which may affect the satisfaction of the people who deal with the university. GIS has powerful tools to spatially analyze the location and produce the outputs to be considered as the indexes of properness of a location for a specific activity. In Iran most of the major universities have been constructed in the capital: Tehran. Tehran is a crowded, polluted and large metropolis which contains various neighbourhoods with various conditions. This research aims to assess and compare the spatial conditions of six important universities in Tehran. To extract the effective factors more than 500 students were interviewed. The extracted factors were categorized into two main categories of spatial and environmental and then were divided into five subcategories, namely: greenness, air pollution, noise pollution, accessibility and compatibility of surrounded land-uses. Using GIS analyzes the quantitative values extracted from the maps, satellite images and statistical data. Then Multi-Criteria Decision Making (MCDM) methods were used to combine the factors. The results revealed that Amirkabir University of Technology achieves the highest score while Allameh Tabataba'i University is ranked below among the considered six universities

Predictive Value of Absent Septal q Wave in Patients with Significant Stenosis of Proximal Left Anterior Descending Coronary Artery

Aims: There is conflicting data about the predictive value of absent septal q wave in patients with significant stenosis of proximal Left Anterior Descending coronary artery. To clarify the exact role of this simple electrocardiographic sign we conducted this prospective descriptive study. Methods: Patients who were referred for coronary angiography in Milad Hospital between December 2008 and September 2009 were chosen randomly. Standard ECG was performed and reviewed for presence or absence of septal q wave, and then the coronary angiography was done and reported by another cardiologist. Results: Of 148 patients with absent septal q wave in ECG, 85 patients (57%) had significant stenosis of proximal LAD in coronary angiography. Statistical analysis showed that significant stenosis of proximal LAD could be predicted by absence of septal q wave in ECG with sensitivity of 59% and specificity of 47%. However, Kappa statistic (Kappa = 0.36) showed low agreement between them. Conclusion: Absence of normal septal q wave in ECG could be a low value predictor of coronary artery disease mainly significant proximal LAD stenosis

characteristic Findings of primary sclerosing cholangitis on endoscopic Retrograde cholangiography: Which is the Most common Finding?

Abstract Background: Primary sclerosing cholangitis (PSC) is a chronic cholestatic liver disease and one of the most common indications for cholangiography (ERCP). We undertook this study to clarify whether there is a specific pattern of involvement of the biliary tract in patients with PSC and to evaluate features of PSC disease on ERCP in order to be able to manage this disease better. Methods: This retrospective study included 45 patients admitted to Taleghani Hospital in 2004–2010 and diagnosed to have PSC on the basis of typical cholangiographic findings in combination with clinical and laboratory data. Patients suspected to have secondary sclerosing cholangitis were excluded. Demographic and clinical data were recorded, along with cholangiographic findings and the frequency of large duct and small duct PSC. Results: Forty-five patients of mean age 34.8 (range 15–66) years were included. Twenty-nine patients (64.4%) had inflammatory bowel disease, and the frequency of large duct PSC and small duct PSC was 93.4% and 6.6%, respectively. The intrahepatic ducts alone were involved in 11 (24.4%) patients and the extrahepatic ducts were involved in 14 (31.1%), with 17 (37.7%) patients having both intrahepatic and extrahepatic PSC. Three (6.6%) patients did not have bile duct involvement on ERCP, and their disease was diagnosed by liver biopsy as small duct PSC. The most common type of cholangiographic feature of intrahepatic duct involvement was type 2, found in 15 (33.3%) patients, with type 3 being the most common type of extrahepatic duct involvement and detected in 16 (35.5%) patients. Conclusion: Our study demonstrates that the most common PSC finding on ERCP is involvement of both the extrahepatic and intrahepatic bile ducts, with small duct PSC being less common than large duct PSC

Tissue-specific transcriptional biomarkers in medicinal plants: Application of large-scale meta-analysis and computational systems biology

© 2019 Elsevier BV. This manuscript version is made available under the CC-BY-NC-ND 4.0 license: http://creativecommons.org/licenses/by-nc-nd/4.0/ This author accepted manuscript is made available following 12 month embargo from date of publication (January 2019) in accordance with the publisher’s archiving policyBiosynthesis of secondary metabolites in plant is a complex process, regulated by many genes and influenced by several factors. In recent years, the next-generation sequencing (NGS) technology and advanced statistical analysis such as meta-analysis and computational systems biology have provided novel opportunities to overcome biological complexity. Here, we performed a meta-analysis on publicly available transcriptome datasets of twelve economically significant medicinal plants to identify differentially expressed genes (DEGs) between shoot and root tissues and to find the key molecular features which may be effective in the biosynthesis of secondary metabolites. Meta-analysis identified a total of 880 genes with differential expression between two tissues. Functional enrichment and KEGG pathway analysis indicated that the functions of those DEGs are highly associated with the developmental process, starch metabolic process, response to stimulus, porphyrin and chlorophyll metabolism, biosynthesis of secondary metabolites and phenylalanine metabolism. In addition, systems biology analysis of the DEGs was applied to find protein–protein interaction network and discovery of significant modules. The detected modules were associated with hormone signal transduction, transcription repressor activity, response to light stimulus and epigenetic processes. Finally, analysis was extended to search for putative miRNAs that are associated with DEGs. A total of 31 miRNAs were detected which belonged to 16 conserved families. The present study provides a comprehensive view to better understand the tissue-specific expression of genes and mechanisms involved in secondary metabolites synthesis and may provide candidate genes for future researches to improve yield of secondary metabolites

Crosstalk between short- and long-term calorie restriction transcriptomic signatures with anxiety-like behavior, aging, and neurodegeneration: implications for drug repurposing

Calorie restriction (CR) is considered an effective intervention for anxiety, aging, and obesity. We investigated the effects of short- and long-term CR on behavior as well as transcriptome profiles in the hypothalamus, amygdala, prefrontal cortex, pituitary, and adrenal glands of Hooded Wistar and Long Evans male rats. A reduction in anxiety-like behavior, as assessed via the elevated plus maze, was observed in both short- and long-term CR. Despite this, short- and long-term CR regulated different sets of genes, leading to distinct transcriptomic signatures. The employed models were able to simultaneously analyze categorical and numerical variables, evaluating the effect of tissue type along with expression data. In all tissues, transcription factors, zinc finger protein 45-like and zinc finger BTB domain-containing two, were the top selected genes by the models in short and long-term CR treatments, respectively. Text mining identified associations between genes of the short-term CR signature and neurodegeneration, stress, and obesity and between genes of the long-term signature and the nervous system. Literature mining-based drug repurposing showed that alongside known CR mimetics such as resveratrol and rapamycin, candidates not typically associated with CR mimetics may be repurposed based on their interaction with transcriptomic signatures of CR. This study goes some way to unravelling the global effects of CR and opens new avenues for treatment for emotional disorders, neurodegeneration, and obesity

Parent–Infant Attachment in Infants with Respiratory Assist Devices Hospitalized in Intensive Care Units: A Descriptive Cross-Sectional Study

Background: Hospitalization of an infant in an intensive care unit may disrupt the normal process of parent-infant attachment. This study aimed to evaluate the quality of attachment and determine its related factors in parents of infants with respiratory assist devices.Methods: This correlational descriptive study was conducted with 180 parents of infants with respiratory assist devices hospitalized in Mofid Children Hospital in Tehran, Iran. The data gathering instrument consisted of a demographic questionnaire and the Parent-Infant Attachment Questionnaire. The data was analyzed through SPSS version 22.Results: The total score of attachment was 57.43+ and among the dimensions of the attachment questionnaire, the quality of attachment had the highest score. Also in parental and infant demographic variables, the previous history of hospitalization, father's age, and unit type were significantly correlated with attachment score. Moreover, regression results revealed that parent–pediatric attachment score of parents of infants admitted to the pediatric intensive care unit is 1.97 units less than that of the parents whose infants were admitted to NICU. And with the increase in father’s age, the rate of the parent–pediatric attachment to the child decreases by 0.19 and the history of the previous hospitalization leads to an increase in attachment to the infant by 3.76 units.Conclusion: Although the overall score of attachment in the parents of pediatrics dependent on the respiratory devices in the present study was undesirable, but the respiratory assisted device did not affect the parent-pediatric attachment score. Therefore, further studies are recommended to more accurately determine the relevant factors of the parent-pediatric attachment

Unified Transcriptomic Signature of Arbuscular Mycorrhiza Colonization in Roots of Medicago truncatula by Integration of Machine Learning, Promoter Analysis, and Direct Merging Meta-Analysis

Plant root symbiosis with Arbuscular mycorrhizal (AM) fungi improves uptake of water and mineral nutrients, improving plant development under stressful conditions. Unraveling the unified transcriptomic signature of a successful colonization provides a better understanding of symbiosis. We developed a framework for finding the transcriptomic signature of Arbuscular mycorrhiza colonization and its regulating transcription factors in roots of Medicago truncatula. Expression profiles of roots in response to AM species were collected from four separate studies and were combined by direct merging meta-analysis. Batch effect, the major concern in expression meta-analysis, was reduced by three normalization steps: Robust Multi-array Average algorithm, Z-standardization, and quartiling normalization. Then, expression profile of 33685 genes in 18 root samples of Medicago as numerical features, as well as study ID and Arbuscular mycorrhiza type as categorical features, were mined by seven models: RELIEF, UNCERTAINTY, GINI INDEX, Chi Squared, RULE, INFO GAIN, and INFO GAIN RATIO. In total, 73 genes selected by machine learning models were up-regulated in response to AM (Z-value difference > 0.5). Feature weighting models also documented that this signature is independent from study (batch) effect. The AM inoculation signature obtained was able to differentiate efficiently between AM inoculated and non-inoculated samples. The AP2 domain class transcription factor, GRAS family transcription factors, and cyclin-dependent kinase were among the highly expressed meta-genes identified in the signature. We found high correspondence between the AM colonization signature obtained in this study and independent RNA-seq experiments on AM colonization, validating the repeatability of the colonization signature. Promoter analysis of upregulated genes in the transcriptomic signature led to the key regulators of AM colonization, including the essential transcription factors for endosymbiosis establishment and development such as NF-YA factors. The approach developed in this study offers three distinct novel features: (I) it improves direct merging meta-analysis by integrating supervised machine learning models and normalization steps to reduce study-specific batch effects; (II) seven attribute weighting models assessed the suitability of each gene for the transcriptomic signature which contributes to robustness of the signature (III) the approach is justifiable, easy to apply, and useful in practice. Our integrative framework of meta-analysis, promoter analysis, and machine learning provides a foundation to reveal the transcriptomic signature and regulatory circuits governing Arbuscular mycorrhizal symbiosis and is transferable to the other biological settings

Regulatory control of the symbiotic enhanced soybean bHLH transcription factor, GmSAT1.

GmSAT1 is a basic Helix-Loop-Helix (bHLH) DNA binding transcription factor expressed in soybean root nodules. GmSAT1 is a unique protein, in that it is localised on cellular membranes including the symbiosome membrane, which encircles nitrogen-fixing bacteroids in soybean nodules. Its role in the regulation of gene transcription in nodules or in other plant tissues is poorly understood. In this study, GmSAT1’s functional activity was investigated through a series of studies that investigated the link between gene activities to functional phenotypes. This analysis included the influence of symbiotic partnerships with rhizobia and AM fungi and non-symbiotic root tissues. In this context, an evaluation of changes in gene transcription with or without GmSAT1 expression (RNAi-based silencing of GmSAT1) was explored at the individual and global gene levels. The data indicates that GmSAT1;1 and a close relative GmSAT1;2, are both expressed in roots and nodules but GmSAT1;1 displayed an overall enhancement in the symbiotic root nodule. Expression of both genes was reduced with external nitrogen supply to the nodule and inoculated root. Both genes were up-regulated in root and nodule tissues when plants were supplied low levels of phosphate. Using an improved method for transgenic hairy roots, developed as part of this thesis project, GmSAT1 was silenced using a RNAi construct. Tissues (roots and nodules) were analysed for changes in global gene expression using microarray analysis, the impact on symbiotic relationships (rhizobia and AM fungi) and genetic and biochemical responses to phosphorus supply. Transcriptome analysis identified networks that GmSAT1;1 may be associated with, including a suite of putatively active circadian clock regulators operating in nodules, phosphorus responsive genes in roots, cell wall maintenance and or stress defence signaling pathways, nitrogen transport and metabolism and genes linked to auxin and gibberellin regulatory pathways. The influence of phosphorus and the AM fungal symbiosis was investigated in more detail. Loss of GmSAT1 activity altered AM colonisation, causing a reduction in root colonisation when grown at reduced external P. At higher P levels, colonisation remained unchanged. Shoot P content was significantly increased at both low and high external P supply in the GmSAT1 silenced plants, indicating a potential role of GmSAT1 in mediating P homeostasis. The impact of gibberellins (GA₃) on GmSAT1 expression and activity was also investigated. Using both qPCR and native promoter:GUS fusion constructs in transformed soybean hairy roots and nodules the expression of GmSAT1;1 in roots and nodules decreased with external supply of GA₃. In parallel experiments, RNAi SAT1-silenced plants showed similar responses with GA₃ treated plants, where nodule number and weight decreased while plant height significantly increased. Furthermore, microarray analysis indicated GmSAT1 negatively interacts with known gibberellin-responsive genes, including GASA6, GAMA-TIP, CLE2, MTO3, GIP1, TPS11, and GBF1. The overall findings of this study have shown that GmSAT1 is an important TF to soybean with a broad transcriptional imprint which influences both root nodule symbiosis and AM fungal symbioses. Its activity appears to be linked to multiple genetic signaling networks that involve phosphorus and nitrogen metabolism, hormone activity and regulation of the circadian clock.Thesis (Ph.D.) -- University of Adelaide, School of Agriculture, Food and Wine, 201