197,053 research outputs found
Megaglena sivarubani Srinivasan & Isack 2022, sp. nov.
No full textMegaglena sivarubani sp. nov. (Figs. 1–22) Material Examined. Holotype (in ethanol): Male mature nymph (AMC /ZN/228), South India, Tamil Nadu, Theni district, Bodimettu, Puliyuthu falls, 10°03′16″N, 77°27′29″E; 1230 m; 13.x.2021, Pandiarajan Srinivasan & Rajasekaran Isack. Paratypes (also in ethanol): 2 male nymphs, 2 female nymphs (AMC /ZN/229), same data as holotype.Published as part of Srinivasan, Pandiarajan & Isack, Rajasekaran, 2022, A new species of Megaglena Peters & Edmunds, 1970 (Ephemeroptera Leptophlebiidae) from Tamil Nadu, India, pp. 83-88 in Zootaxa 5138 (1) on page 84, DOI: 10.11646/zootaxa.5138.1.8, http://zenodo.org/record/655221
Effects of single nucleotide polymorphisms on human N-acetyltransferase 2 structure and dynamics by molecular dynamics simulation.
No full textBACKGROUND: Arylamine N-acetyltransferase 2 (NAT2) is an important catalytic enzyme that metabolizes the carcinogenic arylamines, hydrazine drugs and chemicals. This enzyme is highly polymorphic in different human populations. Several polymorphisms of NAT2, including the single amino acid substitutions R64Q, I114T, D122N, L137F, Q145P, R197Q, and G286E, are classified as slow acetylators, whereas the wild-type NAT2 is classified as a fast acetylator. The slow acetylators are often associated with drug toxicity and efficacy as well as cancer susceptibility. The biological functions of these 7 mutations have previously been characterized, but the structural basis behind the reduced catalytic activity and reduced protein level is not clear. METHODOLOGY/PRINCIPAL FINDINGS: We performed multiple molecular dynamics simulations of these mutants as well as NAT2 to investigate the structural and dynamical effects throughout the protein structure, specifically the catalytic triad, cofactor binding site, and the substrate binding pocket. None of these mutations induced unfolding; instead, their effects were confined to the inter-domain, domain 3 and 17-residue insert region, where the flexibility was significantly reduced relative to the wild-type. Structural effects of these mutations propagate through space and cause a change in catalytic triad conformation, cofactor binding site, substrate binding pocket size/shape and electrostatic potential. CONCLUSIONS/SIGNIFICANCE: Our results showed that the dynamical properties of all the mutant structures, especially in inter-domain, domain 3 and 17-residue insert region were affected in the same manner. Similarly, the electrostatic potential of all the mutants were altered and also the functionally important regions such as catalytic triad, cofactor binding site, and substrate binding pocket adopted different orientation and/or conformation relative to the wild-type that may affect the functions of the mutants. Overall, our study may provide the structural basis for reduced catalytic activity and protein level, as was experimentally observed for these polymorphisms
Securing a Linux-based Multi-User Web Server
No full textA commonplace solution for putting a web site on-line at
a reasonable cost is hosting, that is placing it on a shared
server, together with other sites. Hosting providers face
significant security problems, both in terms of avoiding
misuse of their servers by “guests”, and in terms of
providing effective isolation between them; the
Discretionary Access Control model implemented by
traditional operating systems can fail to provide adequate
solutions to these problems. This work describes a system
based on the integration of the widely adopted
Apache/PHP platform with the powerful Mandatory
Access Control features offered by the Security-Enhanced
Linux project. The resulting solution combines a sound
approach to the most common security problems with a
very tolerable impact on system administration
complexity
FIGURE 1 in A new species of Clypeocaenis Soldán 1978 (Ephemeroptera: Caenidae) from Tamil Nadu, India
No full textFIGURE 1. Habitus of male larva of Clypeocaenis malzacheri sp. nov.Published as part of Srinivasan, Pandiarajan, Sivaruban, T., Barathy, S., Isack, Rajasekaran & Jacobus, Luke M., 2022, A new species of Clypeocaenis Soldán 1978 (Ephemeroptera: Caenidae) from Tamil Nadu, India, pp. 467-476 in Zootaxa 5091 (3) on page 468, DOI: 10.11646/zootaxa.5091.3.6, http://zenodo.org/record/584834
Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn graphs
Get PDFAbstract Background Assembling genomic sequences from a set of overlapping reads is one of the most fundamental problems in computational biology. Algorithms addressing the assembly problem fall into two broad categories - based on the data structures which they employ. The first class uses an overlap/string graph and the second type uses a de Bruijn graph. However with the recent advances in short read sequencing technology, de Bruijn graph based algorithms seem to play a vital role in practice. Efficient algorithms for building these massive de Bruijn graphs are very essential in large sequencing projects based on short reads. In an earlier work, an O(n/p) time parallel algorithm has been given for this problem. Here n is the size of the input and p is the number of processors. This algorithm enumerates all possible bi-directed edges which can overlap with a node and ends up generating Θ(nΣ) messages (Σ being the size of the alphabet). Results In this paper we present a Θ(n/p) time parallel algorithm with a communication complexity that is equal to that of parallel sorting and is not sensitive to Σ. The generality of our algorithm makes it very easy to extend it even to the out-of-core model and in this case it has an optimal I/O complexity of Θ(nlog(n/B)Blog(M/B)) (M being the main memory size and B being the size of the disk block). We demonstrate the scalability of our parallel algorithm on a SGI/Altix computer. A comparison of our algorithm with the previous approaches reveals that our algorithm is faster - both asymptotically and practically. We demonstrate the scalability of our sequential out-of-core algorithm by comparing it with the algorithm used by VELVET to build the bi-directed de Bruijn graph. Our experiments reveal that our algorithm can build the graph with a constant amount of memory, which clearly outperforms VELVET. We also provide efficient algorithms for the bi-directed chain compaction problem. Conclusions The bi-directed de Bruijn graph is a fundamental data structure for any sequence assembly program based on Eulerian approach. Our algorithms for constructing Bi-directed de Bruijn graphs are efficient in parallel and out of core settings. These algorithms can be used in building large scale bi-directed de Bruijn graphs. Furthermore, our algorithms do not employ any all-to-all communications in a parallel setting and perform better than the prior algorithms. Finally our out-of-core algorithm is extremely memory efficient and can replace the existing graph construction algorithm in VELVET.</p
Dr. Duane M. Jackson, Morehouse College, July 2011
No full textThis video is a conversation with Dr. Duane M. Jackson. Dr. Jackson talks about his paper, "Recall and the Serial Position Effect: The Role of Primacy and Recency on Accounting Students' Performance." Jackie Daniel, AUC Woodruff Library, is the interviewer
Organic contaminants in Ganga basin: from the Green Revolution to the emerging concerns of modern India
Get PDFThe Ganga basin includes some of the most densely populated areas in the world, in a region characterized by extremely high demographic and economic growth rates. Although anthropogenic pressure in this area is increasing, the pollution status of the Ganga is still poorly studied and understood. In the light of this, we have carried out a systematic literature review of the sources, levels and spatiotemporal distribution of organic pollutants in surface water and sediment of the Ganga basin, including for the first time emerging contaminants (ECs). We have identified 61 publications over the past thirty years, with data on a total of 271 organic compounds, including pesticides, industrial chemicals, and by-products, artificial sweeteners, pharmaceuticals, and personal care products (PPCPs). The most studied organic contaminants are pesticides, whereas knowledge of industrial compounds and PPCPs, among which some of the major ECs, is highly fragmentary. Most studies focus on the main channel of the Ganga, the Yamuna, the Gomti, and the deltaic region, while most of the Ganga's major tributaries, and the entire southern part of the catchment, have not been investigated. Hotspots of contamination coincide with major urban agglomerations, including Delhi, Kolkata, Kanpur, Varanasi, and Patna. Pesticides levels have decreased at most of the sites over recent decades, while potentially harmful concentrations of polychlorinated biphenyls (PCBs), organotin compounds (OTCs), and some PPCPs have been detected in the last ten years. Considering the limited geographical coverage of sampling and number of analyzed compounds, this review highlights the need for a more careful selection of locations, compounds and environmental matrices, prioritizing PPCPs and catchment-scale, source-to-sink studies.Earth Sciences; Environmental Science; Environmental Monitoring; Pollutio
"Reflections on the subject of Emigration from Europe with a view to Settlement in the United States" By M. Carey.
No full text"Reflections on the subject of Emigration from Europe with a view to Settlement in the United States: containing bried sketches of the moral and political character of those states.
By M. Carey, member of the American philosophical, and of the American Antiquarian Society, and author of The Olive Branch, Cindiciae Hibernicae, essays on banking, on political economy, and on internal improvement.
To which are now added the English editor's comments on the subject; together with Important Advice to Emigrants, and Cautions Against Impositions Practiced in the Outports
The histidine triad nucleotide-binding protein 2 (HINT-2) positively regulates hepatocellular energy metabolism.
No full textThe histidine triad nucleotide-binding protein 2 (HINT-2) is a mitochondrial adenosine phosphoramidase expressed in hepatocytes. The phenotype of Hint2 knockout ( Hint2) mice includes progressive hepatic steatosis and lysine hyperacetylation of mitochondrial proteins, which are features of respiratory chain malfunctions. We postulated that the absence of HINT-2 induces a defect in mitochondria bioenergetics. Isolated Hint2 hepatocytes produced less ATP and generated a lower mitochondrial membrane potential than did Hint2 hepatocytes. In extracellular flux analyses with glucose, the basal, ATP-linked, and maximum oxygen consumption rates (OCRs) were decreased in Hint2 hepatocytes and in HepG2 cells lacking HINT-2. Conversely, in HINT-2 overexpressing SNU-449 and HepG2 cells, the basal, ATP-linked, and maximum OCRs were increased. Similarly, with palmitate, basal and maximum OCRs were decreased in Hint2 hepatocytes, but they were increased in HINT-2 overexpressing HepG2 cells. When assayed with radiolabeled substrate, palmitate oxidation was reduced by 25% in Hint2 mitochondria. In respirometry assays, complex I- and II-driven, coupled and uncoupled respirations and complex IV KCN-sensitive respiration were reduced in Hint2 mitochondria. Furthermore, HINT-2 associated with cardiolipin and glucose-regulated protein 75 kDa. Our study shows decreased electron transfer and oxidative phosphorylation capacity in the absence of HINT-2. The bioenergetics deficit accumulated over time in hepatocytes lacking HINT-2 likely leads to the secondary outcome of steatosis.-Rajasekaran, R., Felser, A., Nuoffer, J.-M., Dufour, J.-F., St-Pierre, M. V. The histidine triad nucleotide-binding protein 2 (HINT-2) positively regulates hepatocellular energy metabolism
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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