Self-Organizing Genetic Algorithm for Multiple Sequence Alignment

Genetic algorithm (GA) used to solve the optimization problem is self-organized and applied to Multiple Sequence Alignment (MSA), an essential process in molecular sequence analysis. This paper presents the first attempt in applying Self-Organizing Genetic Algorithm for MSA. Self-organizing genetic algorithm (SOGA) can be developed with the complete knowledge about the problem and its parameters. In SOGA, values of various parameters are decided based on the problem and fitness value obtained in each generation. The proposed algorithm undergoes a self-organizing crossover operation by selecting an appropriate rate or a point and a self-organizing cyclic mutation for the required number of generations. The advantages of the proposed algorithm are (i) reduce the time requirement for optimizing the parameter values (ii) prevent execution with default values (iii) avoid premature convergence by the cyclic mutation operation. To validate the efficiency, SOGA is applied to MSA, and the resulting alignment is evaluated using the column score (CS). The comparison result shows that the alignment produced by SOGA is better than the widely used tools like Dialign and Multalin. It is also evident that the proposed algorithm can produce optimal or closer-to-optimal alignment compared to tools like ClustalW, Mafft, Dialign and Multalin

A Cloud-Oriented Green Computing Architecture for E-Learning Applications

Cloud computing is a highly scalable and cost-effective infrastructure for running Web applications. E-learning or e-Learning is one of such Web application has increasingly gained popularity in the recent years, as a comprehensive medium of global education system/training systems. The development of e-Learning Application within the cloud computing environment enables users to access diverse software applications, share data, collaborate more easily, and keep their data safely in the infrastructure. However, the growing demand of Cloud infrastructure has drastically increased the energy consumption of data centers, which has become a critical issue. High energy consumption not only translates to high operational cost, which reduces the profit margin of Cloud providers, but also leads to high carbon emissions which is not environmentally friendly. Hence, energy-efficient solutions are required to minimize the impact of Cloud-Oriented E-Learning on the environment. E-learning methods have drastically changed the educational environment and also reduced the use of papers and ultimately reduce the production of carbon footprint. E-learning methodology is an example of Green computing. Thus, in this paper, it is proposed a Cloud-Oriented Green Computing Architecture for eLearning Applications (COGALA). The e-Learning Applications using COGALA can lower expenses, reduce energy consumption, and help organizations with limited IT resources to deploy and maintain needed software in a timely manner. This paper also discussed the implication of this solution for future research directions to enable Cloud-Oriented Green Computing

The taxonomy of a Pentastomid parasite from an Indian Calotes versicolor

The Class Pentastomida is ranked under the Phylum Arthropoda by most authors, but its position is questionable in view of its unusual body structure, and probably the group should be regarded as occupying an isolated place among the invertebrates. The members of the Class Pentastomida are endoparasitic in the respiratory passages and lungs of vertebrates. They are veriform with flattened cylindrical annulated body; they are unique in that the body is non-segmented, but the muscles are metamerically arranged and the integument is chitinous with numerous glands. These data alone would justify the argument that they should be assigned an isolated place among the invertebrates. Pentastomid parasites in Indian lizards are meagerly known today. Very few reports have been made on the occurrence of Raillietiella in India lizards. In view of the need for a better understanding of the taxonomy, anatomy, and biology of a common Indian pentastomid parasite the present investigation was undertaken; this paper constitutes the third in a series entitled “Parasites of Reptiles.” The studies, however, are not complete, and only the taxonomy and anatomy of the parasite are discussed in detail. The form in question is easily obtainable in the environs of the city of Madras, India, where the incidence of the infection on the lizard, Calotes versicolor, appears to be high. Besides, the parasite would form a highly suitable material for the study of pentastomids in the laboratory. In as much as the pentastomid, Raillietiella, is not known to occur in Calotes versicolor, the present paper records for the first time a new host for the genus Raillietiella. The investigator has taken an independent stand from Anantaraman (Anantaraman and Krishnaswami 1958) in naming the present pentastomid parasite as a new species

Origin of biological information: Inherent occurrence of intron-rich split genes, coding for complex extant proteins, within pre-biotic random genetic sequences

The origin of biological information is an unexplained phenomenon. Prior research in resolving the origin of proteins, based on the assumption that the first genes were contiguous prokaryotic sequences has not succeeded. Rather, it has been established that contiguous protein-coding genes do not exist in practically any amount of random genetic sequences. We found that complex eukaryotic proteins could be inherently encoded in split genes that could exist by chance within mere micrograms to milligrams of random DNA. Using protein amino acid sequence variability, codon degeneracy, and stringent exon-length restriction, we demonstrate that split genes for proteins of extant eukaryotes occur extensively in random genetic sequences. The results provide evidence that an abundance of split genes encoding advanced proteins in a small amount of prebiotic genetic material could have ignited the evolution of the eukaryotic genome

A Green Process for Starch Oleate Synthesis by Cryptococcus sp. MTCC 5455 Lipase and Its Potential as an Emulsifying Agent

Starch oleate is synthesized in an aqueous medium using lipase from the yeast Cryptococcus sp. MTCC 5455. The optimum conditions of esterification are found at 24 h and 30 �C with an oleic acid/starch molar ratio of 1:2 using 500U of lipase and the degree of substitution was 0.26. Spectral techniques confirm the presence of oleate group in the modified potato starch. Scanning electron microscopic and X-ray diffraction studies also reveal the morphological and crystallographic properties of starch which are disrupted during the esterification process. Thermogravimetric analysis indicates the decrease in thermal stability of starch oleate due to the transformed structure of starch from semi crystalline to an amorphous form. The synthesized starch oleate could impart 85% stability to emulsions and has potential as an emulsifier in food sector owing to its eco-friendly preparation

Comparative dosimetric analysis of IMRT and VMAT (RapidArc) in brain, head and neck, breast and prostate malignancies

Purpose: Intensity modulated radiotherapy (IMRT) in the recent past has established itself as a gold standard for organs at risk (OAR) sparing, target coverage and dose conformity. With the advent of a rotational treatment technology such as volumetric modulated arc therapy (VMAT), an inter-comparison is warranted to address the advantages and disadvantages of each technique. Methods: Twenty patients were selected retrospectively from our patient database. Sites included were brain, head and neck, chest wall, and prostate, with five patients for each site. For all the selected patients, both the IMRT and VMAT treatment plans were generated. Plan comparison was done in terms of OAR dose, dose homogeneity index (HI), dose conformity index (CI), target coverage, low isodose volumes, monitor units (MUs), and treatment time.Results: The VMAT showed better sparing of “parotids minus planning target volume (PTV)”, spinal cord and head of femur as compared to the IMRT. The lung V40 for VMAT was lower, whereas the lung V10, contralateral lung mean dose, contralateral breast mean dose and mean body dose were lower with IMRT for chest wall cases. Both the VMAT and IMRT achieved comparable HI except for the brain site, where IMRT scored over VMAT. The CI achieved by the IMRT and VMAT were similar except for chest wall cases, whereas the VMAT achieved better dose conformity. The target coverage was comparable with both the plans. The VMAT clearly scored over IMRT in terms of average MUs (486 versus 812 respectively) and average treatment time (2.54 minutes versus 5.54 minutes) per treatment session. Conclusion: The VMAT (RapidArc) has a potential to generate treatment plans for various anatomical sites which are comparable with the corresponding IMRT plans in terms of OAR sparing and plan quality parameters. The VMAT significantly reduces treatment time as compared to the IMRT, thus VMAT can increase the throughput of a busy radiotherapy department.</p

Comparative dosimetric analysis of IMRT and VMAT (RapidArc) in brain, head and neck, breast and prostate malignancies

Purpose: Intensity modulated radiotherapy (IMRT) in the recent past has established itself as a gold standard for organs at risk (OAR) sparing, target coverage and dose conformity. With the advent of a rotational treatment technology such as volumetric modulated arc therapy (VMAT), an inter-comparison is warranted to address the advantages and disadvantages of each technique. Methods: Twenty patients were selected retrospectively from our patient database. Sites included were brain, head and neck, chest wall, and prostate, with five patients for each site. For all the selected patients, both the IMRT and VMAT treatment plans were generated. Plan comparison was done in terms of OAR dose, dose homogeneity index (HI), dose conformity index (CI), target coverage, low isodose volumes, monitor units (MUs), and treatment time.Results: The VMAT showed better sparing of “parotids minus planning target volume (PTV)”, spinal cord and head of femur as compared to the IMRT. The lung V40 for VMAT was lower, whereas the lung V10, contralateral lung mean dose, contralateral breast mean dose and mean body dose were lower with IMRT for chest wall cases. Both the VMAT and IMRT achieved comparable HI except for the brain site, where IMRT scored over VMAT. The CI achieved by the IMRT and VMAT were similar except for chest wall cases, whereas the VMAT achieved better dose conformity. The target coverage was comparable with both the plans. The VMAT clearly scored over IMRT in terms of average MUs (486 versus 812 respectively) and average treatment time (2.54 minutes versus 5.54 minutes) per treatment session. Conclusion: The VMAT (RapidArc) has a potential to generate treatment plans for various anatomical sites which are comparable with the corresponding IMRT plans in terms of OAR sparing and plan quality parameters. The VMAT significantly reduces treatment time as compared to the IMRT, thus VMAT can increase the throughput of a busy radiotherapy department

Modification of conservative treatment of heterotopic cervical pregnancy by Foley catheter balloon fixation with cerclage sutures at the level of the external cervical os: a case report

<p>Abstract</p> <p>Introduction</p> <p>Conservative treatment of a heterotopic cervical pregnancy was performed with a modification of the fixation of a Foley catheter at the level of the external cervical os, followed by the ligature of the descending cervical branches of the uterine arteries and systemic methotrexate application.</p> <p>Case presentation</p> <p>A 34-year-old Caucasian woman was diagnosed with double gestation after 6 weeks of <it>in vitro </it>fertilization treatment. A gynecological examination and color Doppler ultrasound scan revealed intra-uterine and cervical gestational sacs both containing live fetuses. A Foley catheter balloon was inserted into the cervical canal, inflated and fixed by a cerclage suture at the level of the external cervical os, followed by ligation of the descending cervical branches of the uterine arteries. Systemic methotrexate was applied. Three days after removal of the Foley catheter, an evacuation of the intra-uterine gestational sac was performed. Hemorrhage from the implantation site was controlled immediately and a pregnancy termination was successfully performed. The procedure was uneventful and our patient was discharged with a preserved uterus.</p> <p>Conclusions</p> <p>Conservative treatment of cervical pregnancy using a Foley catheter balloon is more efficacious if the Foley catheter balloon is attached in the correct position with a cerclage suture at the level of the external os, followed by ligation of the descending cervical branches of the uterine arteries, thereby exerting maximal pressure on the bleeding vessels.</p

A neural network-based mobile architecture for mobile agents

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