2,643 research outputs found

    RLZAP: Relative Lempel-Ziv with Adaptive Pointers

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    Relative Lempel-Ziv (RLZ) is a popular algorithm for compressing databases of genomes from individuals of the same species when fast random access is desired. With Kuruppu et al.'s (SPIRE 2010) original implementation, a reference genome is selected and then the other genomes are greedily parsed into phrases exactly matching substrings of the reference. Deorowicz and Grabowski (Bioinformatics, 2011) pointed out that letting each phrase end with a mismatch character usually gives better compression because many of the differences between individuals' genomes are single-nucleotide substitutions. Ferrada et al. (SPIRE 2014) then pointed out that also using relative pointers and run-length compressing them usually gives even better compression. In this paper we generalize Ferrada et al.'s idea to handle well also short insertions, deletions and multi-character substitutions. We show experimentally that our generalization achieves better compression than Ferrada et al.'s implementation with comparable random-access times

    Necrosis in grapevine buds (Vitis vinifera cv. Queen of Vineyard) I. Relation to vegetative vigor1)

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    A study on the occurrence, development and nature of necrotic buds on shoots of the Queen of Vineyard grape cultivar was carried out in the continental Jordan Valley in Israel. A vigorous vineyard having an abundance of necrotic buds and a moderately growing one with few necrotic buds were chosen.Necrosis of the central bud in the Queen of Vineyard winter buds occurred only in the vigorous vineyard. The number of necrotic dry buds was particularly high at nodes 2-3 on the shoot and decreased progressively up to the 7th node above which necrotic buds were not observed. Drying of the central bud occurred over a short period, 15-20 d after bloom. It started with the appearance of a necrotic layer at one of the basal nodes of the central bud which caused a rapid degeneration of the tissues above this layer. A negative correlation was found between the fruiting potential of winter buds and the development of a necrotic layer. The possible relation between vigor, gibberellins and bud necrosis is discussed.Knospennekrosen bei der Rebsorte Queen of Vineyard (Vitis vinifera)I. Beziehung zur vegetativen WüchsigkeitIm binnenländischen Jordantal in Israel wurde eine Untersuchung über Auftreten, Entwicklung und Art von Knospennekrosen an den Trieben der Rebsorte Queen of Vineyard durchgeführt. Hierzu wurden ein wüchsiger Weinberg, in dem nekrotische Knospen gehäuft vorkamen, und ein Weinberg von mittlerer Wüchsigkeit mit wenigen nekrotischen Knospen ausgewählt. In den Winterknospen von Queen of Vineyard trat eine Nekrose der Mittelknospe nur in der wüchsigen Rebanlage auf. Die Anzahl vertrockneter nekrotischer Knospen war besonders hoch an den Knoten 2-3 der Triebe; sie ging stetig zurück bis zum 7. Knoten; darüber wurden keine nekrotischen Knospen mehr beobachtet. Die Austrocknung der Mittelknospe erfolgte nur während einer kurzen Phase, 15-20 d nach der Blüte. Sie begann mit dem Auftreten einer nekrotischen Schicht an einem der basalen Knoten der Mittelknospe, wodurch die darüberliegenden Gewebe rasch degenerierten. Zwischen der potentiellen Fruchtbarkeit der Winterknospen und der Entwicklung einer nekrotischen Schicht wurde eine negative Korrelation gefunden. Die mögliche Beziehung zwischen Wüchsigkeit, Gibberellingehalt und Nekrosenhäufigkeit wird diskutiert

    Compressed Subsequence Matching and Packed Tree Coloring

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    We present a new algorithm for subsequence matching in grammar compressed strings. Given a grammar of size nn compressing a string of size NN and a pattern string of size mm over an alphabet of size σ\sigma, our algorithm uses O(n+nσw)O(n+\frac{n\sigma}{w}) space and O(n+nσw+mlogNlogwocc)O(n+\frac{n\sigma}{w}+m\log N\log w\cdot occ) or O(n+nσwlogw+mlogNocc)O(n+\frac{n\sigma}{w}\log w+m\log N\cdot occ) time. Here ww is the word size and occocc is the number of occurrences of the pattern. Our algorithm uses less space than previous algorithms and is also faster for occ=o(nlogN)occ=o(\frac{n}{\log N}) occurrences. The algorithm uses a new data structure that allows us to efficiently find the next occurrence of a given character after a given position in a compressed string. This data structure in turn is based on a new data structure for the tree color problem, where the node colors are packed in bit strings.Comment: To appear at CPM '1

    Necrosis in grapevine buds (Vitis vinifera cv. Queen of Vineyard) II. Effect of gibberellic acid (GA3) application

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    The effect of gibberellic acid application on the development of necrosis in cv. Queen of Vineyard grapevine buds was studied. GA3 caused the development of a necrotic layer at the base of the central bud and promoted the development of the  axillary buds. GA3 application to leaves caused necrosis in the buds more readily than direct application to the buds. GA3 fed to the petiole was 100 times more active in inducing necrosis than leaf application. Only developing and relatively young buds were sensitive to GA3. A minimum of 6 X 10-6 mg GA3 in the bud was needed to cause bud necrosis. During the period from 1 week before to 3 weeks after bloom, the movement of GA3 in the grape shoot was acropetal. The possible involvement of gibberellins in the natural necrosis of buds on vigorous grapevines is discussed.Knospennekrosen bei der Rebsorte Queen of Vineyard (Vitis vinifera)II. Einfluß der Gibberellinsäure- (GA3)BehandlungBei der Sorte Queen of Vineyard wurde der Einfluß der GA3-Behandlung auf die Entwicklung von Knospennekrosen untersucht. GA3 bewirkte die Ausbildung einer nekrotischen Gewebeschicht an der Basis der Mittelknospe und förderte die Entwicklung der Axillarknospen. Durch GA3-Behandlung der Blätter ließen sich leichter Knospennekrosen auslösen als durch direkte Behandlung der Knospen. Wurde GA3 über den Blattstiel zugeführt, so war seine Nekrosen induzierende Wirkung 100mal stärker als bei Behandlung der Blattspreite. Nur sich entwickelnde und relativ junge Knospen waren gegen GA3 sensibel. Um eine Knospennekrose auszulösen, mußten in den Knospen mindestens 6 X 10-6 mg GA3 vorliegen. Zwischen 1 Woche vor und 3 Wochen nach der Blüte erfolgte die Bewegung des GA3in den Rebentrieben akropetal. Die mögliche Beteiligung von Gibberellinen am natürlichen Auftreten von Knospennekrosen bei wüchsigen Reben wird diskutiert

    The spatio-temporal distribution of lightning over Israel and the neighboring area and its relation to regional synoptic systems

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    The spatio-temporal distribution of lightning flashes over Israel and the neighboring area and its relation to the regional synoptic systems has been studied, based on data obtained from the Israel Lightning Location System (ILLS) operated by the Israel Electric Corporation (IEC). The system detects cloud-to-ground lightning discharges in a range of ~500 km around central Israel (32.5° N, 35° E). The study period was defined for annual activity from August through July, for 5 seasons in the period 2004–2010. <br><br> The spatial distribution of lightning flash density indicates the highest concentration over the Mediterranean Sea, attributed to the contribution of moisture as well as sensible and latent heat fluxes from the sea surface. Other centers of high density appear along the coastal plain, orographic barriers, especially in northern Israel, and downwind from the metropolitan area of Tel Aviv, Israel. The intra-annual distribution shows an absence of lightning during the summer months (JJA) due to the persistent subsidence over the region. The vast majority of lightning activity occurs during 7 months, October to April. Although over 65 % of the rainfall in Israel is obtained during the winter months (DJF), only 35 % of lightning flashes occur in these months. October is the richest month, with 40 % of total annual flashes. This is attributed both to tropical intrusions, i.e., Red Sea Troughs (RST), which are characterized by intense static instability and convection, and to Cyprus Lows (CLs) arriving from the west. <br><br> Based on daily study of the spatial distribution of lightning, three patterns have been defined; "land", "maritime" and "hybrid". CLs cause high flash density over the Mediterranean Sea, whereas some of the RST days are typified by flashes over land. The pattern defined "hybrid" is a combination of the other 2 patterns. On CL days, only the maritime pattern was noted, whereas in RST days all 3 patterns were found, including the maritime pattern. It is suggested that atmospheric processes associated with RST produce the land pattern. Hence, the occurrence of a maritime pattern in days identified as RST reflects an "apparent RST". The hybrid pattern was associated with an RST located east of Israel. This synoptic type produced the typical flash maximum over the land, but the upper-level trough together with the onshore winds it induced over the eastern coast of the Mediterranean resulted in lightning activity over the sea as well, similar to that of CLs. <br><br> It is suggested that the spatial distribution patterns of lightning may better identify the synoptic system responsible, a CL, an "active RST" or an "apparent RST". The electrical activity thus serves as a "fingerprint" for the synoptic situation responsible for its generation

    The role of community acceptance in planning outcomes for onshore wind and solar farms: An energy justice analysis

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    The deployment of renewable technologies as part of climate mitigation strategies have provoked a range of responses from various actors, bringing public acceptance to the forefront of energy debates. A key example is the reaction of communities when renewable projects are proposed in their local areas. This paper analyses the effect that community acceptance has had on planning applications for onshore wind and solar farms in Great Britain between 1990 and 2017. It does this by compiling a set of indicators for community acceptance and testing their association with planning outcomes using binomial logistic regression. It identifies 12 variables with statistically significant effects: 4 for onshore wind, 4 for solar farms, and 4 spanning both. For both technologies, the visibility of a project, its installed capacity, the social deprivation of the area, and the year of the application are significant. The paper draws conclusions from these results for community acceptance and energy justice, and discusses the implications for energy decision-making

    Synthetic gene brushes: a structure–function relationship

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    We present the assembly of gene brushes by means of a photolithographic approach that allows us to control the density of end-immobilized linear double-stranded DNA polymers coding for entire genes. For 2 kbp DNAs, the mean distance varies from 300 nm, where DNAs are dilute and assume relaxed conformations, down to 30 nm, where steric repulsion at dense packing forces stretching out. We investigated the gene-to-protein relationship of firefly luciferase under the T7/E.Coli-extract expression system, as well as transcription-only reactions with T7 RNA polymerase, and found both systems to be highly sensitive to brush density, conformation, and orientation. A ‘structure–function' picture emerges in which extension of genes induced by moderate packing exposes coding sequences and improves their interaction with the transcription/translation machinery. However, tighter packing impairs the penetration of the machinery into the brush. The response of expression to two-dimensional gene crowding at the nanoscale identifies gene brushes as basic controllable units en route to multicomponent synthetic systems. In turn, these brushes could deepen our understanding of biochemical reactions taking place under confinement and molecular crowding in living cells

    Dynamic Fluctuation Phenomena in Double Membrane Films

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    Dynamics of double membrane films is investigated in the long-wavelength limit including the overdamped squeezing mode. We demonstrate that thermal fluctuations essentially modify the character of the mode due to its nonlinear coupling to the transversal shear hydrodynamic mode. The corresponding Green function acquires as a function of the frequency a cut along the imaginary semi-axis. Fluctuations lead to increasing the attenuation of the squeezing mode it becomes larger than the `bare' value.Comment: 7 pages, Revte

    Numerical Observation of a Tubular Phase in Anisotropic Membranes

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    We provide the first numerical evidence for the existence of a tubular phase, predicted by Radzihovsky and Toner (RT), for anisotropic tethered membranes without self-avoidance. Incorporating anisotropy into the bending rigidity of a simple model of a tethered membrane with free boundary conditions, we show that the model indeed has two phase transitions corresponding to the flat-to-tubular and tubular-to-crumpled transitions. For the tubular phase we measure the Flory exponent νF\nu_F and the roughness exponent ζ\zeta. We find νF=0.305(14)\nu_F=0.305(14) and ζ=0.895(60)\zeta=0.895(60), which are in reasonable agreement with the theoretical predictions of RT --- νF=1/4\nu_F=1/4 and ζ=1\zeta=1.Comment: 8 pages, LaTeX, REVTEX, final published versio
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