669 research outputs found
Improved alignment quality by combining evolutionary information, predicted secondary structure and self-organizing maps
No full textBackground Protein sequence alignment is one of the basic tools in bioinformatics. Correct alignments are required for a range of tasks including the derivation of phylogenetic trees and protein structure prediction. Numerous studies have shown that the incorporation of predicted secondary structure information into alignment algorithms improves their performance. Secondary structure predictors have to be trained on a set of somewhat arbitrarily defined states (e.g. helix, strand, coil), and it has been shown that the choice of these states has some effect on alignment quality. However, it is not unlikely that prediction of other structural features also could provide an improvement. In this study we use an unsupervised clustering method, the self-organizing map, to assign sequence profile windows to "structural states" and assess their use in sequence alignment. Results The addition of self-organizing map locations as inputs to a profile-profile scoring function improves the alignment quality of distantly related proteins slightly. The improvement is slightly smaller than that gained from the inclusion of predicted secondary structure. However, the information seems to be complementary as the two prediction schemes can be combined to improve the alignment quality by a further small but significant amount. Conclusion It has been observed in many studies that predicted secondary structure significantly improves the alignments. Here we have shown that the addition of self-organizing map locations can further improve the alignments as the self-organizing map locations seem to contain some information that is not captured by the predicted secondary structure.Naturvetenskapliga forskningsrådet (Sweden
How do variations in Urban Heat Islands in space and time influence household water use? The case of Phoenix, Arizona
No full textabstract: This paper explores how urbanization, through its role in the evolution of Urban Heat Island (UHI), affects residential water consumption. Using longitudinal data and drawing on a mesoscale atmospheric model, we examine how variations in surface temperature at the census tract level have affected water use in single family residences in Phoenix, Arizona. Results show that each Fahrenheit rise in nighttime temperature increases water consumption by 1.4%. This temperature effect is found to vary significantly with lot size and pool size. The study provides insights into the links between urban form and water use, through the dynamics of UHI.Corresponding Author:
Rimjhim M. Aggarwal
Arizona State University
[email protected]
Analog circuit optimization using evolutionary algorithms and convex optimization
No full textThesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2007.Includes bibliographical references (p. 83-88).In this thesis, we analyze state-of-art techniques for analog circuit sizing and compare them on various metrics. We ascertain that a methodology which improves the accuracy of sizing without increasing the run time or the designer effort is a contribution. We argue that the accuracy of geometric programming can be improved without adversely influencing the run time or increasing the designer's effort. This is facilitated by decomposition of geometric programming modeling into two steps, which decouples accuracy of models and run-time of geometric programming. We design a new algorithm for producing accurate posynomial models for MOS transistor parameters, which is the first step of the decomposition. The new algorithm can generate posynomial models with variable number of terms and real-valued exponents. The algorithm is a hybrid of a genetic algorithm and a convex optimization technique. We study the performance of the algorithm on artificially created benchmark problems. We show that the accuracy of posynomial models of MOS parameters is improved by a considerable amount by using the new algorithm. The new posynomial modeling algorithm can be used in any application of geometric programming and is not limited to MOS parameter modeling. In the last chapter, we discuss various ideas to improve the state-of-art in circuit sizing.by Varun Aggarwal.S.M
Caste, religion and power: an Indian case study
No full textReviews the book "Caste, Religion and Power: An Indian Case Study," by Pratap C. Aggarwal.; Reviews the book "Caste, Religion and Power: An Indian Case Study," by Pratap C. Aggarwal
Data mining : the textbook / Charu C. Aggarwal.
No full textcomputer bookfair2016Includes bibliographical references and index.xxix, 734 pages
Sensorineural hearing loss in Kawasaki disease
No full textKawasaki disease is a common nonspecific vasculitis seen in childhood. The most significant long-term sequela is coronary artery aneurysm. However, the spectrum of complications involves not only the heart, but also other organs such as the eyes, skin, kidneys, gallbladder, liver, and central nervous system. Sensorineural hearing loss (SNHL) is a relatively unrecognized complication of the disease. Although most of the complications (except coronary artery aneurysm) are self-limiting, SNHL can be persistent. It is, especially important in infants and young children who might not be able to report the hearing deficits and are most likely to have cognitive and speech delays if this hearing loss is not addressed in a timely manner. We report a child with Kawasaki disease who had SNHL during the 2 nd week of the illness. The aim of this article is to briefly review the pathophysiology behind this hearing loss and strongly emphasize the importance of universal hearing evaluation in all children diagnosed with Kawasaki disease. This screening in children with Kawasaki disease may provide some timely intervention if needed. Since most Kawasaki disease patients will be seen by cardiologists, we hope to create more awareness about this complication to the cardiology community as well
Use of modified knee-chest position for fluoroscopy-guided celiac plexus block: A novel technique in patients with discomfort in prone position
No full textCeliac plexus block (CPB) for chronic upper abdominal pain, particularly cancer pain, can be given in both supine and prone positions, using anterior and posterior approaches, respectively. Both approaches suffer from their own demerits. In ultrasonography (USG)-guided anterior approach, the needle has to pass through the liver, intestine, stomach, pancreas, and vessels, exposing the patient to the risk of infection, hemorrhage, and fistula formation. Moreover, in the presence of ascites and large lymph nodes, retroperitoneal area cannot be visualized clearly using USG. In the posterior approach, the patient lies prone with a pillow underneath the abdomen to alleviate lumbar lordosis, and the block is given under fluoroscopic or computed tomography (CT) guidance. Terminally ill patients have difficulty in tolerating prone position because of pain and discomfort due to abdominal distension. To the best of my knowledge, no position other than the supine, prone and rarely lateral, have been described for giving CPB in patients. We present three cases with carcinoma head of pancreas, where CPB was given under fluoroscopic guidance. As all three patients could not tolerate the prone position because of pain and ascites, we modified the position to a knee-chest position [Figure 1]. The patients found the position comfortable to maintain, and they were cooperative during the block. We encountered no problems in imaging the vertebral bodies in anteroposterior (AP) and lateral view. No pillow was required, as the lumbar lordosis was already abolished in this position. In each patient, bilateral block was given using 15-20 mL of 50% alcohol in 0.25% bupivacaine, on either side using a 15-cm Chiba needle. Subsequent follow-up showed successful blockade in all three patients. The use of a modified knee-chest position has not been described earlier for this procedure, but may be a suitable, convenient, and comfortable alternative for terminally ill patients who are unable to lie prone
Decoding "Public authority" under the RTI act: a comment on Subhash Chandra Aggarwal v. Indian national congress
No full textThe June, 2013 order of the Central Information Commission ("CIC") in Subhash Chandra Aggarwal v. Indian National Congress which brought political parties within the scope of the Right to Information ("RTI") Act, has highlighted some issues regarding the drafting and interpretation of the RTI Act. The CIC held that the six national political parties which were respondents
in the case, have the ingredients that qualify them as "public authorities" within the meaning of section 2(h) of the RTI Act. In this comment the author argues that the reasoning for holding what constitutes substantial financing that makes a body a "public authority" is not clear and the interpretation of the definition of "public authority" is inconsisten
Solving transcendental equations using Genetic Algorithms
No full textI. Analytical/Iterative methods to solve transcendental equations Transcendental equations are equations containing trigonometric, algebraic, exponential, logarithmic, etc. terms. Many analytical/iterative methods are used to solve transcendental equations. Though these methods are capable of solving many transcendental equations they suffer from many common disadvantages. Usually transcendental equations have many solutions in a given range, and analytical methods are not able to find all these roots in a given interval, even when they find several solutions, it is not possible to conclude that the given method has found the complete set of roots/solutions, and has not missed any particular solution. Also, these methods fail in case of misbehaved or discontinuous functions. Hence, though these methods may work very well in some situations, they are not general in nature and need a lot of homework from the Analyst. An analysis of some common methods used for solving transcendental equations, their disadvantages and cases of failures are discussed below. a) Newton Raphson method: This is a commonly used method for solvin
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