Effect of Mutation and Effective Use of Mutation in Genetic Algorithm

Author tries to analyze the effect of genetic algorithm when mutation rate is selected randomly compared to fixed mutation rates or/and adaptive mutation rates. The results shows that though it is not always possible to get comparable results using randomly selected mutation rates, it is possible to obtain the required range with less number of trials than using fixed mutation rates for this nature applications

Low-Phosphate Chromatin Dynamics Predict a Cell Wall Remodeling Network in Rice Shoots

© 2020 American Society of Plant Biologists. All Rights Reserved. Phosphorus (P) is an essential plant macronutrient vital to fundamental metabolic processes. Plant-available P is low in most soils, making it a frequent limiter of growth. Declining P reserves for fertilizer production exacerbates this agricultural challenge. Plants modulate complex responses to fluctuating P levels via global transcriptional regulatory networks. Although chromatin structure plays a substantial role in controlling gene expression, the chromatin dynamics involved in regulating P homeostasis have not been determined. Here we define distinct chromatin states across the rice (Oryza sativa) genome by integrating multiple chromatin marks, including the H2A.Z histone variant, H3K4me3 modification, and nucleosome positioning. In response to P starvation, 40% of all protein-coding genes exhibit a transition from one chromatin state to another at their transcription start site. Several of these transitions are enriched in subsets of genes differentially expressed under P deficiency. The most prominent subset supports the presence of a coordinated signaling network that targets cell wall structure and is regulated in part via a decrease of H3K4me3 at transcription start sites. The P starvation-induced chromatin dynamics and correlated genes identified here will aid in enhancing P use efficiency in crop plants, benefitting global agriculture

Classical scrapie prions in ovine blood are associated with B lymphocytes and platelet-rich plasma

<p>Abstract</p> <p>Background</p> <p>Classical scrapie is a naturally occurring transmissible spongiform encephalopathy of sheep and goats characterized by cellular accumulation of abnormal isoforms of prion protein (PrP^Sc) in the central nervous system and the follicles of peripheral lymphoid tissues. Previous studies have shown that the whole blood and buffy coat blood fraction of scrapie infected sheep harbor prion infectivity. Although PrP^Schas been detected in peripheral blood mononuclear cells (PBMCs), plasma, and more recently within a subpopulation of B lymphocytes, the infectivity status of these cells and plasma in sheep remains unknown. Therefore, the objective of this study was to determine whether circulating PBMCs, B lymphocytes and platelets from classical scrapie infected sheep harbor prion infectivity using a sheep bioassay.</p> <p>Results</p> <p>Serial rectal mucosal biopsy and immunohistochemistry were used to detect preclinical infection in lambs transfused with whole blood or blood cell fractions from preclinical or clinical scrapie infected sheep. PrP^Scimmunolabeling was detected in antemortem rectal and postmortem lymphoid tissues from recipient lambs receiving PBMCs (15/15), CD72⁺B lymphocytes (3/3), CD21⁺B lymphocytes (3/3) or platelet-rich plasma (2/3) fractions. As expected, whole blood (11/13) and buffy coat (5/5) recipients showed positive PrP^Sclabeling in lymphoid follicles. However, at 549 days post-transfusion, PrP^Scwas not detected in rectal or other lymphoid tissues in three sheep receiving platelet-poor plasma fraction.</p> <p>Conclusions</p> <p>Prion infectivity was detected in circulating PBMCs, CD72⁺pan B lymphocytes, the CD21⁺subpopulation of B lymphocytes and platelet-rich plasma of classical scrapie infected sheep using a sheep bioassay. Combining platelets with B lymphocytes might enhance PrP^Scdetection levels in blood samples.</p

Multivariate analysis reveals that BVDV field isolates do not show a close VN-based antigenic relationship to US vaccine strains

Objective Evaluate bovine viral diarrhea virus (BVDV) antigenicity by using virus neutralization titers (VNT) analyzed using the principal component analysis (PCA) from antisera generated against US-based vaccine strains against both US-origin field isolates and non-US-origin field isolates. Results Data from both independent analyses demonstrated that several US-origin and non-US-origin BVDV field isolates appear to be antigenically divergent from the US-based vaccine strains. Results from the combined analysis provided greater insight into the antigenic diversity observed among BVDV isolates. Data from this study further support genetic assignment into BVDV subgenotypes, as well as strains within subgenotypes is not representative of antigenic relatedness. PCA highlights isolates that are antigenically divergent from members of the same species and subgenotype and conversely isolates that belong to different subgenotypes have similar antigenic characteristics when using antisera from US-based vaccine isolates

In vitro method to evaluate virus competition between BVDV-1 and BVDV-2 strains using the PrimeFlow RNA assay

Bovine viral diarrhea viruses (BVDV), segregated in BVDV-1 and BVDV-2 species, lead to substantial economic losses to the cattle industry worldwide. It has been hypothesized that there could be differences in level of replication, pathogenesis and tissue tropism between BVDV-1 and BVDV-2 strains. Thus, this study developed an in vitro method to evaluate virus competition between BVDV-1 and BVDV-2 strains. To this end the competitive dynamics of BVDV-1a, BVDV-1b, and BVDV-2a strains in cell cultures was evaluated by a PrimeFlow RNA assay. Similar results were observed in this study, as was observed in an earlier in vivo transmission study. Competitive exclusion was observed as the BVDV-2a strains dominated and excluded the BVDV-1a and BVDV-1b strains. The in vitro model developed can be used to identify viral variations that result in differences in frequency of subgenotypes detected in the field, vaccine failure, pathogenesis, and strain dependent variation in immune responses

ECONOMIC FEASIBILITY OF GROWING GURICIDIA UNDER COCONUTS AS AN ENERGY SOURCE FOR DEN ORO THERMAL POWER PLANTS; AN EX-ANTE APPRAISASL

Growth of the demand for electricity intimately follows the growth of theeconomy of Sri Lanka. Since the hydro resources. the major source of electricityare insufficient to meet the growing demand for electricity, alternative powersources have to be employed. Gliricidia proves to be a promising source ofbiomass energy. Firms generating dendro-thermal power express theirwillingness to establish dendro-thermal power plants at the Coconut ResearchInstitute of Sri Lanka on build-operate and transfer (BOT) basis, and to purchaseGliricidia dry wood delivered at the power plant at Rs. 1250/MT. This studyexamines whether the farmers can supply Gliricidia at the above price with areasonable margin for them. The break-even price of a MT of dry wood deliveredat the power plant located 10 km from the coconut estate was computedemploying discounted cash now method. This was Rs.977, implying a margin ofsome 28(10 for growers. The analysis further demonstrated that the break-evenprice was more sensiti ve to variations in wood yield than the variations intransporting distances. The ex-ante appraisal concludes that the raising ofGliricidia under coconuts as an energy source for dendro-therrnal power plants isan economically viable proposition. However, other socio-economic factorsinlluencing the adoption of new technologies may be worth investigating.

Rice H2A.Z negatively regulates genes responsive to nutrient starvation but promotes expression of key housekeeping genes

© The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Experimental Biology. The H2A.Z histone variant plays a role in the modulation of environmental responses, but the nature of the associated mechanisms remains enigmatic. We investigated global H2A.Z deposition and transcriptomic changes in rice (Oryza sativa) upon exposure to phosphate (Pi) deficiency and in response to RNAi knockdown of OsARP6, which encodes a key component of the H2A.Z exchange complex. Both Pi deficiency and OsARP6-knockdown resulted in similar, profound effects on global H2A.Z distribution. H2A.Z in the gene body of stress-responsive genes was negatively correlated with gene expression, and this was more apparent in response to Pi deficiency. In contrast, the role of H2A.Z at the transcription start site (TSS) was more context dependent, acting as a repressor of some stress-responsive genes, but an activator of some genes with housekeeping functions. This was especially evident upon OsARP6-knockdown, which resulted in down-regulation of a number of genes linked to chloroplast function that contained decreases in H2A.Z at the TSS. Consistently, OsARP6-RNAi plants exhibited lower chlorophyll content relative to the wild-type. Our results demonstrate that gene body-localized H2A.Z plays a prominent role in repressing stress-responsive genes under non-inductive conditions, whereas H2A.Z at the TSS functions as a positive or negative regulator of transcription

Staging of lung cancer in a tertiary care setting in Sri Lanka, using TNM 7th edition. A comparison against TNM6

<p>Abstract</p> <p>Background</p> <p>Lung cancer is a leading cause of cancer-related mortality in Sri Lanka and throughout the world. The latest staging system for lung cancer is the tumor node metastasis (TNM) 7^thedition in which there are major changes to the previous version. The objective of our study was to find out the implications of TNM7^thedition on lung cancer staging in a resource limited setting, and to compare it with the previous TNM 6^thedition.</p> <p>Methods</p> <p>Patients with histologically proven lung cancer consecutively presented to respiratory unit of Teaching Hospital Kandy, Sri Lanka were recruited to the study over a period of one year from April 2010 to March 2011. They were staged using CT, ultrasound scan of abdomen, bronchoscopy and CT spine and brain when necessary. Staging was done using TNM 7 as well as TNM6. Surgical or non-surgical treatment arms were decided on staging and the number of patients in each treatment arm was compared between the two staging systems.</p> <p>Results</p> <p>Out of 62 patients, thirty four patients (54%) had metastatic disease and 19 (30%) of them had pleural effusions (M1a), while 15 (24%) had distant metastasis (M1b). When compared to TNM6 there was no difference in the number of patients in T1 category, but the number in T2 was higher in TNM7 (25 Vs 20). Similarly the number in T3 group was higher in TNM7 (11 Vs 5) and the number in M category was doubled (34 Vs 17 [Chi-6.46, <it>p </it>= 0.011]) compared to TNM 6. The number of patients suitable for surgery were 17(27.5%) in TNM 7 and 18(29%) [Chi-0.02, <it>p </it>= 0.88] in TNM6.</p> <p>Conclusions</p> <p>This study shows that a significant proportion of patients were having advanced disease with distant metastasis on presentation. The number of patients falling to stage IV is significantly higher when staged with TNM7 but there was no significant difference in the number of patients undergoing surgery when TNM 7 was used compared to TNM6.</p

A Deep Learning based Explainable Control System for Reconfigurable Networks of Edge Devices

Edge devices that operate in real-world environments are subjected to unpredictable conditions caused by environmental forces such as wind and uneven surfaces. Since most edge systems exhibit dynamic properties, reinforcement learning can be a powerful tool for improving system accuracy. Successful maintenance of the position of a vehicle in such environments can be achieved with the aid of Deep Reinforcement Learning (DRL) that dynamically adjusts the Reconfigurable Wireless Network (RWN) response. Deep Neural Networks (DNNs) is often seen as black boxes, as neither the acquired knowledge nor the decision rationale can be explained. In this paper, we explain the process of a DNN on an autonomous dynamic positioning system by gauging reactions of the DNN to predefined constraints. We introduce a novel digitisation technique that reduces interesting patterns of time series data into single digits to obtain a cross comparable view of the conditions. By analysing the clusters formed on this cross comparable view, we discovered multiple intensities of environmental conditions spanning across 44\% of moderate conditions and 33\% and 23\% of harsh and mild conditions, respectively. Our analysis showed that the proposed system can provide stable responses to uncertain conditions by predicting randomness