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  • 1
    ISSN: 1573-4803
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract When a 1∶1 weight mixture of (2,-4-dinitrophenyl)-L-alanine (DPA) and 2-methyl-4-nitroaniline (MNA) is dissolved in a 50∶50 volume mixture of ethyl acetate and hexane, two types of crystals were observed on slow evaporation. In the first stage of crystallization, light-yellow plates of MNA measuring up to 25 mm×5 mm×1 mm were formed, which belong to the triclinic space group P1 with lattice parameters a=0.7621 (3) nm, b=0.795 2(5) nm, c=0.8200 (2) nm, α=111.84(2)°, β= 93.76(2)°, γ=116.84(3)°, Z=2. The volume of the unit cell containing two molecules is 361.9(1)×10−3 nm3. The powder SHG efficiency of the triclinic polymorph (MNA(T)) is about the same as that of the monoclinic MNA(M). The Raman spectrum of the new crystal is similar to that of MNA(M) crystallized from the vapour phase or solution, except for the change in the intensity of a few bands. The DSC data show minor differences in the melting points and specific heats for the two phases. The second stage of crystallization resulted in the formation of orange-yellow coloured crystals of the DPA:MNA complex, in the monoclinic space group P21 with lattice parameters a =0.6876(1) nm, b=0.7621(3) nm, c=1.7626(4) nm, β=96.62(2)°, V=917.5 ×10−3 nm3, Z=2 for C16H17N5O8. The Raman spectrum of DPA:MNA consists of bands from both DPA and MNA. The complex melts at 138(1)°C with a specific heat of 25.3(4) cal g−1 according to the DSC measurements. The powder SHG efficiency is nearly the same as that of methyl-(2,4-dinitriphenyl)-aminoproanoate (MAP).
    Type of Medium: Electronic Resource
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  • 2
    Publication Date: 1995-01-01
    Print ISSN: 0022-2461
    Electronic ISSN: 1573-4803
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Published by Springer
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  • 3
    Publication Date: 2016-07-06
    Description: The PSI/TM-Coffee web server performs multiple sequence alignment (MSA) of proteins by combining homology extension with a consistency based alignment approach. Homology extension is performed with Position Specific Iterative (PSI) BLAST searches against a choice of redundant and non-redundant databases. The main novelty of this server is to allow databases of reduced complexity to rapidly perform homology extension. This server also gives the possibility to use transmembrane proteins (TMPs) reference databases to allow even faster homology extension on this important category of proteins. Aside from an MSA, the server also outputs topological prediction of TMPs using the HMMTOP algorithm. Previous benchmarking of the method has shown this approach outperforms the most accurate alignment methods such as MSAProbs, Kalign, PROMALS, MAFFT, ProbCons and PRALINE™. The web server is available at http://tcoffee.crg.cat/tmcoffee .
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 4
    Publication Date: 2015-10-24
    Description: Drosophila sechellia relies exclusively on the fruits of Morinda citrifolia , which are toxic to most insects, including its sibling species Drosophila melanogaster and Drosophila simulans. Although several odorant binding protein ( Obp ) genes and olfactory receptor ( Or ) genes have been suggested to be associated with the D. sechellia host shift, a broad view of how chemosensory genes have contributed to this shift is still lacking. We therefore studied the transcriptomes of antennae, the main organ responsible for detecting food resource and oviposition, of D. sechellia and its two sibling species. We wanted to know whether gene expression, particularly chemosensory genes, has diverged between D. sechellia and its two sibling species. Using a very stringent definition of differential gene expression, we found a higher percentage of chemosensory genes differentially expressed in the D. sechellia lineage (7.8%) than in the D. simulans lineage (5.4%); for upregulated chemosensory genes, the percentages were 8.8% in D. sechellia and 5.2% in D. simulans. Interestingly, Obp50a exhibited the highest upregulation, an approximately 100-fold increase, and Or85c —previously reported to be a larva-specific gene—showed approximately 20-fold upregulation in D. sechellia. Furthermore, Ir84a ( ionotropic receptor 84a ), which has been proposed to be associated with male courtship behavior, was significantly upregulated in D. sechellia. We also found expression divergence in most of the chemosensory gene families between D. sechellia and the two sibling species. Our observations suggest that the host shift of D. sechellia was associated with the enrichment of differentially expressed, particularly upregulated, chemosensory genes.
    Electronic ISSN: 1759-6653
    Topics: Biology
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  • 5
    Publication Date: 2015-07-02
    Description: This article introduces the Transitive Consistency Score (TCS) web server; a service making it possible to estimate the local reliability of protein multiple sequence alignments (MSAs) using the TCS index. The evaluation can be used to identify the aligned positions most likely to contain structurally analogous residues and also most likely to support an accurate phylogenetic reconstruction. The TCS scoring scheme has been shown to be accurate predictor of structural alignment correctness among commonly used methods. It has also been shown to outperform common filtering schemes like Gblocks or trimAl when doing MSA post-processing prior to phylogenetic tree reconstruction. The web server is available from http://tcoffee.crg.cat/tcs .
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 6
    Publication Date: 2015-10-29
    Description: Hypercubes and star graphs are widespread topologies of interconnection networks. The class of hyper-stars was introduced as a new type of interconnection network to compete with both hypercubes and star graphs, and the class of folded hyper-stars is a strengthened variation of hyper-stars with additional links to connect nodes with complemented 0/1-strings. Constructing independent spanning trees (ISTs) has numerous applications in networks such as fault-tolerant broadcasting and secure message distribution. Recently, Yang and Chang [IST on folded hyper-stars, Networks 56 (2010), 272–281] proposed an algorithm to construct $k+1$ ISTs on folded hyper-star $FHS(2k,k)$ . For $k\geqslant 4$ , their constructions include $k$ ISTs with a height $2k-2$ and the other one with a height $k+1$ . In this paper, we refine their constructed rules on $FHS(2k,k)$ for $k\geqslant 3$ and provide a set of constructions including $k$ ISTs with a height $k+2$ and the other one with a height $k+1$ . As a by-product, we obtain an improvement on the upper bound of the fault diameter (respectively, the wide diameter) of $FHS(2k,k)$ .
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
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  • 7
    Publication Date: 2013-07-05
    Description: We detected 12 landquakes in Taiwan with collapse areas between 0.27 and 2.48 km 2 associated with rock collapse, rockslide and debris and/or rock avalanche during the passage of Typhoon Morakot in 2009. These events were recorded by seismic stations of the Broadband Array in Taiwan for Seismology. Their locations were determined by a cross-correlation technique that maximizes the coherency of horizontal envelope function among seismic stations with a mean location error of 1.92 km. We applied time-frequency analysis to estimate the bandwidth of seismic energy generated by the landquakes. The predominant frequency ranges from 0.5 to 5.0 Hz, with higher-frequency signals likely caused by block impact. We extracted signal duration ( S D ), peak ground velocity, rise time ( T R ), area of velocity envelope function ( A E ) from the closest station and estimated the collapse area ( A C ) and run-out distance ( D R ) by mapping satellite images. Based on aforementioned seismic and geometrical parameters, we defined the potential of initial impact ( P I ), the frequency of rock impact signal ( f I ) and the mean quasi-front velocity ( V f ) as indicators of landquake types, especially for events with dam formation (dam-formation-type events). We also derived an empirical linear relationship between the envelope area ( A E ) and collapse area ( A C ) with a high correlation coefficient of 0.83. Our automatic approach is very effective for rapid determination of landquake centroid location and collapse area, and for identifying dam-formation event using records from existing real-time broad-band seismic networks, thus providing an important alternative for landquake hazard mitigation.
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 8
    Publication Date: 2014-05-24
    Description: Multiple sequence alignment (MSA) is a key modeling procedure when analyzing biological sequences. Homology and evolutionary modeling are the most common applications of MSAs. Both are known to be sensitive to the underlying MSA accuracy. In this work, we show how this problem can be partly overcome using the transitive consistency score (TCS), an extended version of the T-Coffee scoring scheme. Using this local evaluation function, we show that one can identify the most reliable portions of an MSA, as judged from BAliBASE and PREFAB structure-based reference alignments. We also show how this measure can be used to improve phylogenetic tree reconstruction using both an established simulated data set and a novel empirical yeast data set. For this purpose, we describe a novel lossless alternative to site filtering that involves overweighting the trustworthy columns. Our approach relies on the T-Coffee framework; it uses libraries of pairwise alignments to evaluate any third party MSA. Pairwise projections can be produced using fast or slow methods, thus allowing a trade-off between speed and accuracy. We compared TCS with Heads-or-Tails, GUIDANCE, Gblocks, and trimAl and found it to lead to significantly better estimates of structural accuracy and more accurate phylogenetic trees. The software is available from www.tcoffee.org/Projects/tcs .
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
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  • 9
    Publication Date: 2013-10-30
    Description: A t -ary tree is a rooted tree such that every internal node has exactly t disjoint subtrees. Recently, a concise representation called right-distance sequences (RD-sequences) was introduced to represent t -ary trees and their generalization called non-regular trees. In particular, a loopless algorithm has been proposed by Wu et al. ((2010) Loopless generation of non-regular trees with a prescribed branching sequence. Comput. J. , 53, 661–666) for generating non-regular trees (and thus of t -ary trees) encoded by RD-sequences in a Gray-code order. In this paper, based on such a Gray-code order, we present efficient ranking and unranking algorithms of t -ary trees with n internal nodes. The time complexity and space requirement in both algorithms are O(max{ n 2 , tn }) and O( tn ), respectively. As a by-product, we have an improvement on ranking and unranking t -ary trees encoded by z -sequences in a Gray-code order.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
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  • 10
    Publication Date: 2013-12-27
    Description: A set of k spanning trees rooted at the same vertex r in a graph G is called independent [and the trees are called independent spanning trees (ISTs)] if, for any vertex x != r , the k paths from x to r , one path in each tree, are internally disjoint. The design of ISTs on graphs has applications to fault-tolerant broadcasting and secure message distribution in networks. It was conjectured that, for any k -connected graph, there exist k ISTs rooted at any vertex of the graph. The conjecture has been proved true for k -connected graphs with k ≤ 4, and remains open otherwise. In this paper, we deal with the problem of constructing ISTs on the Cartesian product of a sequence of hybrid graphs, including cycles and complete graphs. Consequently, this result generalizes a number of previous works. Moreover, the construction is shown to be optimal in the sense that the heights of ISTs are minimized.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
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