bluuebunny/crossref_metadata_2025 huggingface dataset:
An exponential‐function reduction method for block‐angular convex programs
Authors: Grigoriadis Michael D. , Khachiyan Leonid G.
Published: May 2007

An exponential potential‐function reduction algorithm for convex block‐angular optimization problems is described. These problems are characterized byKdisjoint convex compact sets called blocks andMnon‐negative‐valued convex block‐separable coupling inequalities with a nonempty interior. A given convex block‐separable function is to be minimized. Concurrent, minimum‐cost, and generalized multicommodity network flow problems are important special cases of this model. The method reduces the optimization problem to two resource‐sharing problems. The first of these problems is solved to obtain a feasible solution interior to the coupling constraints. Starting from this solution, The algorithm proceeds to solve the second problem on the original constraints, but with a modified exponential potential function. The method is shown to produce an ϵ‐approximate solution inO(K(InM)(ϵ−2+ inK)) iterations, provided that there is a feasible solution sufficiently interior to the coupling inequalities. Each iteration consists of solving a subset of independent block problems, followed by a simple coordination step. Computational experiments with a set of large linear concurrent and minimum‐cost multicommodity network flow problems suggest that the method can be practical for computing fast approximations to large instances.
Feedback vertex set on cocomparability graphs
Authors: Coorg Satyan R. , Rangan C. Pandu
Published: May 2007

Given an undirected graph, The feedback vertex set problem is to find a set of vertices of minimum cardinality such that removing the vertices in this set makes the graph acyclic. This problem is known to be NP‐hard on general graphs. An O(n6) algorithm for this problem on permutation graphs is known. in this paper, we give an O(n4) algorithm for this problem on cocomparability graphs. Our result improves the time complexity of the algorithm and enlarges the class of graphs on which this problem is polynomial time‐solvable.
The symmetric generalized traveling salesman polytope
Authors: Fischetti Matteo , González Juan José Salazar , Toth Paolo
Published: May 2007

The symmetric Generalized Traveling Salesman Problem (GTSP) is a variant of the classical symmetric Traveling Salesman Problem, in which the nodes are partitioned into clusters and the salesman has to visit at least one node for each cluster. A different version of the problem, called E‐GTSP, arises when exactly one node for each cluster has to be visited. Both GTSP and E‐GTSP are NP‐hard problems and find practical applications in routing, scheduling, and location‐routing. in this paper, we model GTSP and E‐GTSP as integer linear programs and study the facial structure of the corresponding polytopes. in a companion paper, Theresults described in this work have been used to design a branch‐and‐cut algorithm for the exact solution of instances up to 442 nodes.
Antepenultimate broadcasting
Authors: Bermond Jean‐Claude , Fraigniaud Pierre , Peters Joseph G.
Published: May 2007

Broadcasting is an information dissemination problem in which information originating at one node of a communication network (modeled as a graph) must be transmitted to all other nodes as quickly as possible. A broadcast graph is a graph which permits broadcasting from any originator in minimum time. in this paper, we present new methods for constructing sparse broadcast graphs. Our constructions are based on graph compounding operations which are relative to vertex sets with certain properties that depend on the broadcast protocols of the graphs. We show that many previous methods for constructing sparse broadcast graphs are special cases of our methods. We demonstrate our constructions by producing new sparse broadcast graphs and by showing how many previously constructed graphs can be obtained in a systematic way.
Hamilton cycles and paths in butterfly graphs
Authors: Wong Stephen A.
Published: May 2007

A cycle C in a graph G is a Hamilton cycle if C contains every vertex of G. Similarly, a path P in G is a Hamilton path if P contains every vertex of G. We say that G is Hamilton‐connected if for any pair of vertices, u and v of G, There exists a Hamilton path from u to v. If G is a bipartite graph with bipartition sets of equal size, and there is a Hamilton path from any vertex in one bipartition set to any vertex in the other, The n G is said to be Hamilton‐laceable. We present a proof showing that the n‐dimensional k‐ary butterfly graph, denoted BF(k, n), contains a Hamilton cycle. Then, we use this result in proving the stronger result that BF(k, n) is Hamilton‐laceable when n is even and Hamilton‐connected for odd values of n.
An approach to a problem in network design using genetic algorithms
Authors: Palmer Charles C. , Kershenbaum Aaron
Published: May 2007

This paper describes a new approach to finding solutions to the optimal communication spanning tree problem (OCSTP) using a genetic algorithm. The difficulties posed by this problem are reviewed and a genetic algorithm that consistently finds very good, if not optimal, solutions to it is presented. Finally, a comparison of the genetic algorithm's solutions to those produced by a good heuristic is given that demonstrates the genetic algorithm's ability to find solutions at least equivalent to, if not superior to, those found by the heuristic.
The intractability of the reliable assignment problem in split networks
Authors: Stivaros Constantine , Sutner Klaus
Published: May 2007

The residual network reliability concerns networks with perfect edges and nodes that fail independently. It measures the probability that the network's operating nodes remain connected. The Assignment Problem deals with allocating given operating probabilities to the nodes of the network in such a way that the resulting residual network reliability is maximized. in this paper, we show that the Assignment Problem is computationally hard even for the restricted class of split networks, a generalization of threshold networks for which the problem is solvable in polynomial time.
Computing near‐optimal solutions to the steiner problem in a graph using a genetic algorithm
Authors: Esbensen Henrik
Published: May 2007

A new genetic algorithm (GA) for the Steiner Problem in a Graph (SPG) is presented. The algorithm is based on a bitstring encoding of selected Steiner vertices and the corresponding Steiner tree is computed using a deterministic SPG heuristic. The GA is tested on all SPG instances from the OR‐Library having from 500 to 2500 vertices and up to 62,500 edges. For these graphs, The algorithm finds a global optimum in 70% of all program executions and is within 1% from the global optimum value in 90% of all executions. The performance is compared to that of two branch‐and‐cut algorithms and two of the very best deterministic heuristics: an iterated version of the Takahashi and Matsuyama heuristic (ITM) and an iterated version of the Kou, Markowsky, and Berman heuristic (IKMB). in almost all cases, even the worst result ever found by the GA is equal to or better than the best result of ITM and IKMB. Furthermore, while none of the deterministic heuristics or the branch‐and‐cut algorithms are capable of solving all problem instances within a reasonable time limit, The GA finds a near‐optimal solution to every problem in a moderate amount of time.
Reductions for the rectilinear steiner tree problem
Authors: Winter Pawel
Published: May 2007

The rectilinear Steiner tree problem asks for a shortest network connectingnterminals in the rectilinear plane (withL1‐metric). The problem can be considered as a special case of the Steiner tree problem in a grid network obtained by drawing horizontal and vertical lines through terminals. The reductions developed for the network variant of the Steiner tree problem can therefore also be used in the rectilinear case. However, computational experience indicates that they are not very powerful in the rectilinear grids. We introduce a limited number of rectilinear reductions based on the geometrical properties of terminals. Experimental results show that these reductions are extremely powerful while being quite simple to verify and easy to implement. For randomly generated problem instances with one terminal per row and column, The number of nonterminals remaining seems to be around 20‐‐25% of their original number. Furthermore, The performance of geometrical reductions improves as the density of terminals in fixed‐size grids grows.
Restricted simplicial decomposition with side constraints
Authors: Marín ÁNgel
Published: May 2007

Restricted Simplicial Decomposition with Side Constraints is a price decomposition method designed for large‐scale nonlinear problems with a set of linear constraints with special structure and an additional set of linear side constraints. The resultant algorithm iterates by solving a linear subproblem subject to the set of structured constraints and a small nonlinear master problem whose feasible region is defined by the intersection of a simplex and the set of side constraints. The number of variables of the master problem is controlled by a parameter named r. The conditions required for the parameter r and the rules for dropping extreme points of the simplex are established for global convergence of the algorithm. Computational results are presented for nonlinear network problems with side constraints.
Reliability analysis of tree‐based networks and its application to fault‐tolerant VLSI systems
Authors: Roccetti Marco
Published: May 2007

A probabilistic model is proposed that allows one to solve stochastic network reliability problems for tree‐type networks ofNnodes, takingO(logN) time. The considered networks are based on interconnection patterns consisting of complete binary trees in which spare edges are added according to different criteria. We show that the use of this probabilistic model allows one to evaluate, takingO(logN) time, Theaverage connectedness(i.e., The expected number of processing elements still functioning in the presence of random faults) of dynamically reconfigurable fault‐tolerant VLSI systems which are based on such tree‐based structures. Finally, numerical results obtained from the model are provided that show that, given a fixed chip silicon area, several of the analyzed VLSI architectures have a notably greater expected number of working processing elements w.r.t. complete binary trees, in the presence of a given fault distribution.
The pickup delivery location problem on networks
Authors: Mosheiov Gur
Published: May 2007

The Pickup Delivery Location Problem (PDLP) is a generalization of the Traveling Salesman Location Problem (TSLP) in which the daily tour involves pickup and delivery provided to customers by a vehicle of a given capacity. Two heuristics are suggested: The first is an extension of a method introduced by Simchi‐Levi and Berman for solving the TSLP. Its worst‐case relative error is shown to be bounded by 1. The second is based on a simple ranking of customers according to their probabilities for positive demand and their weighted average distances from all other locations. in addition, The fully polynomial algorithm of Berman and Simchi‐Levi is extended for solving PDLPs on tree networks. Both heuristics were tested on small‐size general networks and medium‐size tree networks. The average relative error over all test problems in the first class did not exceed 2.5% for the first heuristic and 1% for the second. in most cases, both produced the optimal solution. in about 56% of the tree network problems (with up to 80 nodes), Theoptimal home location of the server was found by at least one of the heuristics, and in about 94% of the problems, Theoptimal or an adjacent node was found by at least one of the heuristics.
Multiple message broadcasting in communication networks
Authors: Kwon Oh‐Heum , Chwa Kyung‐Yong
Published: May 2007

Broadcasting refers to the process of dissemination of a set of messages originating from one node to all other nodes in a communication network. We assume that, at any given time, a node can transmit a message along at most one incident link and simultaneously receive a message along at most one incident link. We first present an algorithm for determining the amount of time needed to broadcastkmessages in an arbitrary tree. Second, we show that, for everyn, There exists a graph withnnodes whosek‐message broadcast time matches the trivial lower bound ⌈ logn⌉ +k− 1 by designing a broadcast scheme for complete graphs. We call those graphs minimal broadcast graphs. Finally, we construct annnode minimal broadcast graph with fewer than (⌈logn⌉ + 1)2⌈ logn⌉ −1edges.
The shortest path with at most / nodes in each of the series/parallel clusters
Authors: Li Wen‐Jui , Tsao H.‐S. Jacob , Ulular Osman
Published: May 2007

We study two related constrained shortest path problems in which the nodes are partitioned into series/parallel clusters. These and many other constrained shortest path problems occur in optimizing the layout of private networks embedded in a larger telecommunications network. The first problem deals with a situation in which, in addition to each edge being assigned a nonnegative integer weight, each node is also assigned a nonnegative integer weight, and the constraint on the path is that the total node weight incurred within each cluster should not exceed a given nonnegative integer /. The second problem considers two constraints: (i) a path cannot contain more than / nodes in one cluster and (ii) a path must traverse through at least one of a given set of special nodes in each of the traversed clusters. We propose efficient exact algorithms for solving both problems. Numerical examples are also provided.
An O(N2) heuristic for steiner minimal trees in E3
Authors: Smith J. MacGregor , Weiss Rich , Patel Minoo
Published: May 2007

Even though the problem of computing Steiner minimal trees (SMTs) in the plane is well known to be NP‐hard, There exist heuristic algorithms which run in polynomial time. Recent research results have shown that the problem in three dimensions is demonstrably more difficult. This paper approaches the development of a heuristic for the problem utilizing the Delaunay triangulation in 3‐space to compute suboptimal SMTs. Computational results are also provided.
Encoding shortest paths in spatial networks
Authors: Erwig Martin
Published: May 2007

A new data structure is presented which facilitates the search for shortest paths in spatially embedded planar networks in a worst‐case time of O(l log r), where l is the number of edges in the shortest path to be found and r is an upper bound on the number of so‐called cross edges (these are edges connecting, for any node v, different shortest path subtrees rooted at v's successors). The data structure is based on the idea to identify shortest path subtrees with the regions in the plane that they cover. in the worst case, The space requirement is O(rn), which, in general, is O(n2), but for regularly shaped networks, it is expected to be only O(n√n). A decomposition of graphs into biconnected components can be used to reduce the sizes of the trees to be encoded and to reduce the complexity of the regions for these trees. The decomposition also simplifies the algorithm for computing encoding regions, which is based on minimum link paths in polygons. Approximations for region boundaries can effectively be utilized to speed up the process of shortest path reconstruction: For a realistically constrained class of networks, i.e., networks in which the ratio of the shortest path distance between any two points to the Euclidean distance between these points is bounded by a constant, it is shown that an average searching time of O(l) can be achieved.
Decreased expression level of SH2 domain‐containing protein tyrosine phosphatase‐1 (Shp1) is associated with progression of chronic myeloid leukaemia
Authors: Amin HM , Hoshino K , Yang H , Lin Q , Lai R , Garcia‐Manero G
Published: May 2007

Chronic myeloid leukaemia (CML) is characterized by t(9;22)(q34;q11) and the aberrant expression of the fusion protein Bcr‐Abl that leads to constitutive activation of c‐Abl kinase. Bcr‐Abl plays a major role in the development and progression of CML through chronic, accelerated, and blast phases. The interaction between Bcr‐Abl and other oncogenic molecules has been extensively documented. Nonetheless, negative regulatory mechanisms of Bcr‐Abl are not completely defined. One major inhibitory pathway is mediated via the SH2 domain‐containing protein tyrosine phosphatase Shp1. In the present study, we demonstrate that Shp1 levels are markedly decreased in advanced stage CML patients compared with those in chronic phase. This process was independent of DNA methylation. Furthermore, we did not detect mutations in the Shp1 gene in CML cell lines or patient samples. These data suggest that the decrease in Shp1 in advanced stage CML patients is due to post‐transcriptional modifications. Our findings suggest that the decrease in Shp1 expression levels plays a role in the progression of CML. Also, the decrease in Shp1 and subsequently its inhibitory effect on Bcr‐Abl could provide an explanation for imatinib resistance seen in advanced stage CML patients. Copyright © 2007 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Computational study of the fluorination effect on nitrogen–boron bond
Authors: Liao Hsin‐Yi
Published: May 2007

The Lewis acid‐base H3−nFnN–BFmH3−m (n = 0–3; m = 0–3) system was examined using the density functional theory calculations. The NB bond strength can be adjusted stepwise by increasing the number of substituted fluorine atoms. The main finding of this work is the bond distances of the complexes do not correlate directly with the bond strengths. Some rationalization of this interesting observation was provided by the fluorine substitution effect on the HOMO‐LUMO gap, hybridization of bonding orbitals and electrostatic interaction. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
Poor enantioselectivity of the direct aldol reaction catalyzed by (S,S)‐proline dipeptide: A density functional study
Authors: Fan Jian‐Fen , Wu Li‐Fen , Tao Fu‐Ming
Published: May 2007

Density functional theory calculations were performed to study the stereo‐controlling step of the direct aldol reaction between acetone and 4‐nitrobenzaldehyde catalyzed by (S,S)‐proline dipeptide. Four transition state structures have been determined using B3LYP functional with the 6‐31G* basis set, corresponding to the anti and syn arrangements of the methylene moiety with respect to the carbonyl group in enamine intermediate, and to the si and re attacks to the aldehyde carbonyl carbon, respectively. Solvent effects of DMSO on the stereo‐controlling step were investigated with Onsager model. The energy results of the transition states reveal the origin of poor enantioselectivity for the reaction. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
Cross‐linked SecA dimers are not functional in protein translocation
Authors: Or Eran , Rapoport Tom
Published: May 2007

The ATPase SecA is involved in post‐translational protein translocation through the SecY channel across the bacterial inner membrane. SecA is a dimer that can dissociate into monomers with translocation activity. Here, we have addressed whether dissociation of the SecA dimer is required for translocation. We show that a dimer in which the two subunits are cross‐linked by disulfide bridges is inactive in protein translocation, translocation ATPase, and binding to a lipid bilayer. In contrast, upon reduction of the disulfide bridges, the resulting monomers regain these activities. These data support the notion that dissociation of SecA dimers into monomers occurs during protein translocation.
Evidence for a role of glycosphingolipids in CXCR4‐dependent cell migration
Authors: Limatola Cristina , Massa Valeria , Lauro Clotilde , Catalano Myriam , Giovanetti Anna , Nuccitelli Silvia , Spinedi Angelo
Published: May 2007

Chemotaxis induction is a major effect evoked by stimulation of the chemokine receptor CXCR4 with its sole ligand CXCL12. We now report that treatment of CHP‐100 human neuroepithelioma cells with the glucosylceramide synthase (GCS) inhibitor DL‐threo‐1‐phenyl‐2‐hexadecanoylamino‐3‐pyrrolidino‐1‐propanol inhibits CXCR4‐dependent chemotaxis. We provide evidence that the phenomenon is not due to unspecific effects of the inhibitor employed and that inhibition of GCS neither affects total or plasmamembrane CXCR4 expression, nor CXCL12‐induced Ca2+ mobilization. The effects of the GCS inhibitor on impairment of CXCL12‐induced cell migration temporally correlated with a pronounced downregulation of neutral glycosphingolipids, particularly glucosylceramide, and with a delayed and more moderate downregulation of gangliosides; moreover, exogenously administered glycosphingolipids allowed resumption of CXCR4‐dependent chemotaxis. Altogether our results provide evidence, for the first time, for a role glycosphingolipids in sustaining CXCL12‐induced cell migration.
Requirements for a conservative protein translocation pathway in chloroplasts
Authors: Vojta Lea , Soll Jürgen , Bölter Bettina
Published: May 2007

The chloroplast inner envelope translocon subunit Tic110 is imported via a soluble stromal translocation intermediate. In this study an in‐organellar import system is established which allows for an accumulation of this intermediate in order to analyze its requirements for reexport. All results demonstrate that the re‐export of Tic110 from the soluble intermediate stage into the inner envelope requires ATP hydrolysis, which cannot be replaced by other NTPs. Furthermore, the molecular chaperone Hsp93 seems prominently involved in the reexport pathway of Tic110, because other stromal intermediates like that of the oxygen evolving complex subunit OE33 (iOE33) en route to the thylakoid lumen interacts preferentially with Hsp70.
dXNP, a Drosophila homolog of XNP/ATRX, induces apoptosis via Jun‐N‐terminal kinase activation
Authors: Lee Nam Gon , Hong Yoon Ki , Yu Si Young , Han Seung Yeop , Geum Dongho , Cho Kyoung Sang
Published: May 2007

XNP/ATRX, a causative gene of X‐linked α‐thalassemia/mental retardation syndrome, encodes an SNF2 family ATPase/helicase protein. To better understand the role of XNP/ATRX in development, we isolated and characterized a Drosophila XNP/ATRX homolog, dXNP, which contains highly conserved SNF2 and helicase domains. Ectopically expressed dXNP induced strong apoptosis in the developing eye and wing, but did not affect cell cycle progression or the expression of wingless and engrailed, essential regulators of development. The dXNP‐induced apoptosis was strongly suppressed by DJNKK/hemipterous mutation, and dXNP increased JNK activity. Taken together, these results suggest that dXNP regulates apoptosis via JNK activation.
Characterization of zinc finger protein 496 that interacts with Jumonji/Jarid2
Authors: Mysliwiec Matthew Robert , Kim Tae-gyun , Lee Youngsook
Published: May 2007

Jumonij (JMJ)/Jarid2 plays important roles in embryonic development and functions as a transcriptional repressor. Using yeast two‐hybrid screening, we have identified a cofactor of JMJ, the zinc finger protein 496 (Zfp496) that contains a SCAN, KRAB and zinc finger domain. Our molecular analyses indicate that Zfp496 functions as a transcriptional activator. Further, Zfp496 inhibits the transcriptional repression of JMJ and JMJ represses the transcriptional activation of Zfp496. This study demonstrates that JMJ physically and functionally interacts with Zfp496, which will provide important insights into endogenous target gene regulation by both factors.
Heme binding properties of heterologously expressed spinach cytochrome b6: Implications for transmembrane b‐type cytochrome formation
Authors: Dreher Carolin , Prodöhl Alexander , Weber Mathias , Schneider Dirk
Published: May 2007

In vivo and in vitro requirements for the formation of cytochrome b
6 were examined to analyze the mechanisms of transmembrane b‐type cytochrome formation. After heterologous expression of spinach cytochrome b
6, formation of the holo‐cytochrome was observed within the E. coli inner membrane. The transmembrane orientation of cytochrome b
6 appeared not to be critical for heme binding and holo‐cytochrome formation. Furthermore, in vitro reconstitution of cytochrome b
6 was possible under oxidizing as well as under reducing conditions. Taken together these observations strongly indicate that transmembrane b‐type cytochromes can spontaneously assemble in vitro as well as in a membrane.
Synthesis of globopentaose using a novel β1,3‐galactosyltransferase activity of the Haemophilus influenzae β1,3‐N‐acetylgalactosaminyltransferase LgtD
Authors: Randriantsoa Mialy , Drouillard Sophie , Breton Christelle , Samain Eric
Published: May 2007

We have previously described a bacterial system for the conversion of globotriaose (Gb3) into globotetraose (Gb4) by a metabolically engineered Escherichia coli strain expressing the Haemophilus influenzae lgtD gene encoding β1,3‐N‐acetylgalactosaminyltransferase [Antoine, T., Bosso, C., Heyraud, A. Samain, E. (2005) Large scale in vivo synthesis of globotriose and globotetraose by high cell density culture of metabolically engineered Escherichia coli. Biochimie 87, 197–203]. Here, we found that LgtD has an additional β1,3‐galactosyltransferase activity which allows our bacterial system to be extended to the synthesis of the carbohydrate portion of globopentaosylceramide (Galβ‐3GalNAcβ‐3Galα‐4Galβ‐4Glc) which reacts with the monoclonal antibody defining the stage‐specific embryonic antigen‐3. In vitro assays confirmed that LgtD had both β1,3‐GalT and β1,3‐GalNAcT activities and showed that differences in the affinity for Gb3 and Gb4 explain the specific and exclusive formation of globopentaose.
Phosphorylation of human microtubule‐associated protein tau by protein kinases of the AGC subfamily
Authors: Virdee Kanwar , Yoshida Hirotaka , Peak-Chew Sew , Goedert Michel
Published: May 2007

Intraneuronal inclusions made of hyperphosphorylated microtubule‐associated protein tau are a defining neuropathological characteristic of Alzheimer's disease, and of several other neurodegenerative disorders. Many phosphorylation sites in tau are S/TP sites that flank the microtubule‐binding repeats. Others are KXGS motifs in the repeats. One site upstream of the repeats lies in a consensus sequence for AGC kinases. This site (S214) is believed to play an important role in the events leading from normal, soluble to filamentous, insoluble tau. Here, we show that all AGC kinases tested phosphorylated S214. RSK1 and p70 S6 kinase also phosphorylated the neighbouring T212, a TP site that conforms weakly to the AGC kinase consensus sequence. MSK1 phosphorylated S214, as well as S262, a KXGS site in the first repeat, and S305 in the second repeat.
Afr1p has a role in regulating the localization of Mpk1p at the shmoo tip in Saccharomyces cerevisiae
Authors: Changwei Zhu , Mingyong Xiong , Ranran Wen
Published: May 2007

Afr1p functions to promote adaptation to pheromone‐induced growth arrest and morphogenesis. We show here that Afr1p regulates polarized localization of the Mpk1p MAP kinase in shmooing cells. Deletion of AFR1 results in mislocalization of Mpk1p although the scaffold protein Spa2p localizes normally at shmoo tip, and overexpression of Spa2 cannot rescue this defect, indicating Afr1p in required for Spa2p to recruit Mpk1 to the site of polarized growth during mating. Overexpression of SPA2 partially suppresses the morphogenetic defect of afr1Δ cells upon α‐factor induction, suggesting the two proteins function in the same genetic pathway with Spa2p acts downstream of Afr1p.
Nuclear export and cytoplasmic maturation of ribosomal subunits
Authors: Zemp Ivo , Kutay Ulrike
Published: May 2007

Based on the characterization of ribosome precursor particles and associated trans‐acting factors, a biogenesis pathway for the 40S and 60S subunits has emerged. After nuclear synthesis and assembly steps, pre‐ribosomal subunits are exported through the nuclear pore complex in a Crm1‐ and RanGTP‐dependent manner. Subsequent cytoplasmic biogenesis steps of pre‐60S particles include the facilitated release of several non‐ribosomal proteins, yielding fully functional 60S subunits. Cytoplasmic maturation of 40S subunit precursors includes rRNA dimethylation and pre‐rRNA cleavage, allowing 40S subunits to achieve translation competence. We review current knowledge of nuclear export and cytoplasmic maturation of ribosomal subunits.
DNA photodamage recognition by RNA polymerase II
Authors: Brueckner Florian , Cramer Patrick
Published: May 2007

During gene transcription, RNA polymerase (Pol) II encounters obstacles, including lesions in the DNA template. Here, we review a recent structure–function analysis of Pol II transcribing DNA with a bulky photo‐lesion in the template strand. The study provided the molecular basis for recognition of a damaged DNA by Pol II, which is the first step in transcription‐coupled DNA repair (TCR). The results have general implications for damage recognition and the TCR mechanism.
Prevalence of the polycystic kidney disease and renal and urinary bladder ultrasonographic abnormalities in Persian and Exotic Shorthair cats in Italy
Authors: Bonazzi Mattia , Volta Antonella , Gnudi Giacomo , Bottarelli Ezio , Gazzola Margherita , Bertoni Giorgio
Published: May 2007

The ultrasonographic findings of kidneys, liver and urinary bladder of 288 Persian and 44 Exotic Shorthair clinically normal cats that underwent screening for polycystic kidney disease (PKD) between July 2003 and December 2005 were reviewed. Cats were divided into two groups, one including cats aged <9 months (group 1) and one cats aged ≥9 months (group 2). Cats were classified as PKD-positive when at least one renal cyst was found. One hundred and thirty-six cats (41.0%) had more than one cyst in at least one kidney. The prevalence of PKD was similar in both groups. Eight PKD-positive cats had cystic livers (5.9%). Other renal abnormalities included a pelvic calculus and a medullary rim sign (MRS). The difference in prevalence of an MRS in group 2 compared to group 1 and the difference between PKD-positive and -negative cats in group 2 were not significant. There was no difference in mean kidney length between PKD-positive and -negative cats in group 2. Urinary bladder anomalies were principally represented by urinary sediment, with prevalence significantly higher in group 2. No difference was detected in group 2 between PKD-positive and -negative cats. In conclusion feline PKD is common in Italy. The ultrasonographic findings of MRS and urinary bladder sediment did not correlate with feline PKD. Urinary bladder sediment is common in Persians and Exotic Shorthairs and more likely in adults.
Robust 24±6 ka 40Ar/39 Ar Age of a Low-Potassium Tholeiitic Basalt in the Lassen Region of NE California
Authors: Turrin Brent D. , Muffler L.J. Patrick , Clynne Michael A. , Champion Duane E.
Published: May 2007

40Ar/39Ar ages on the Hat Creek Basalt (HCB) and stratigraphically related lava flows show that latest Pleistocene tholeiitic basalt with very low K2O can be dated reliably. The HCB underlies ∼ 15 ka glacial gravel and overlies four andesite and basaltic andesite lava flows that yield 40Ar/39Ar ages of 38±7 ka (Cinder Butte; 1.65% K2O), 46±7 ka (Sugarloaf Peak; 1.85% K2O), 67±4 ka (Little Potato Butte; 1.42% K2O) and 77±11 ka (Potato Butte; 1.62% K2O). Given these firm age brackets, we then dated the HCB directly. One sample (0.19% K2O) clearly failed the criteria for plateau-age interpretation, but the inverse isochron age of 26"6 ka is seductively appealing. A second sample (0.17% K2O) yielded concordant plateau, integrated (total fusion), and inverse isochron ages of 26±18, 30±20 and 24±6 ka, all within the time bracket determined by stratigraphic relations; the inverse isochron age of 24"6 ka is preferred. As with all isotopically determined ages, confidence in the results is significantly enhanced when additional constraints imposed by other isotopic ages within a stratigraphic context are taken into account.
Sedimentary responses to the Pleistocene climatic variations recorded in the South China Sea
Authors: Boulay Sébastien , Colin Christophe , Trentesaux Alain , Clain Stéphane , Liu Zhifei , Lauer-Leredde Christine
Published: May 2007

Grain-size analyses, coupled with end-member modelling, have been performed on the terrigenous fraction of two Leg 184 Ocean Drilling Program sites (1144 and 1146) from the South China Sea. The grain-size distributions over the last 1.8 Ma enable a new interpretation of their connections to sea-level variations and East Asian monsoon strength. Previous investigations in this area have associated grain-size variability with enhanced eolian input during glacial stages. End-member modelling downgrades the importance of this eolian contribution and indicates that the sediments can be described as a mixture of three end-members: fluvial mud inputs, shelf reworking and river mouth migration. Grain-size variations in the Pleistocene section of the cores indicate a multiple-stage evolution: (i) from 1.8 to 1.25 Ma, the downcore grain-size variations are low but show a correspondence between monsoon rainfall intensity and the fine grain-sized fluvial inputs; no link with sea-level variations is noticeable; (ii) from 1.25 to 0.9 Ma, there is an increase (decrease) in the intermediate (fine) end-member (∼ 100 kyr cycle) that is associated with the onset of a stronger summer monsoon and modest shelf reworking; (iii) from 0.9 to 0 Ma the grain-size record is dominated by global sea-level variations; each glacial stage is associated with extensive shelf reworking and conveyance of coarse particles to the basin.
Bedload-to-suspended load ratio and rapid bedrock incision from Himalayan Landslide-dam lake record
Authors: Pratt-Sitaula Beth , Garde Michelle , Burbank Douglas W. , Oskin Michael , Heimsath Arjun , Gabet Emmanuel
Published: May 2007

About 5400 cal yr BP, a large landslide formed a > 400-m-tall dam in the upper Marsyandi River, central Nepal. The resulting lacustrine and deltaic deposits stretched > 7 km upstream, reaching a thickness of 120 m.14C dating of 7 wood fragments reveals that the aggradation and subsequent incision occurred remarkably quickly (∼ 500 yr). Reconstructed volumes of lacustrine (∼ 0.16 km3) and deltaic (∼ 0.09 km3) deposits indicate a bedload-to-suspended load ratio of 1:2, considerably higher than the ≤ 1:10 that is commonly assumed. At the downstream end of the landslide dam, the river incised a new channel through ≥ 70 m of Greater Himalayan gneiss, requiring a minimum bedrock incision rate of 13 mm/yr over last 5400 yr. The majority of incision presumably occurred over a fraction of this time, suggesting much higher rates. The high bedload ratio from such an energetic mountain river is a particularly significant addition to our knowledge of sediment flux in orogenic environments.
The internationalization of science in a commercial context: research and development by overseas multinationals in Britain before the mid-1970s
Authors: HORROCKS SALLY M.
Published: May 2007

The establishment of research and development (R & D) laboratories by the UK affiliates of overseas-controlled firms was a feature of the R & D landscape throughout the twentieth century and had its origins even earlier. From their foundation they served as sites for international scientific and technological collaboration and exchange. Here I draw on both quantitative and qualitative evidence to examine the research and development activities of overseas multinational enterprises in the UK. This activity has a longer history than most previous commentators have suggested. The integration of at least some R & D facilities into international research networks was already a feature during the inter-war years. This became far more common after the early 1960s, as firms worked hard to integrate previously independent laboratories into coordinated research organizations. Far from being a ‘new collaborative mode’ in the late twentieth century, cross-border networks of industrial laboratories have long contributed to the internationalization of science.
Note from the Editors
Authors: RINGEN CATHERINE , VIKNER STEN
Published: May 2007

This is the first issue of Volume 30 of the Nordic Journal of Linguistics. The NJL is the journal of the Nordic Association of Linguists. Individuals may subscribe to the Nordic Journal of Linguistics by joining the NAL. The NAL membership form can be found on the Cambridge University Press web site of the NJL, , as well as on the NAL web site, . We are well aware that there have been problems with joining the NAL in the not so distant past, but we have reasons to hope that soon such problems will only be a distant memory.
Perfect and periphrastic passive constructions in Danish
Authors: Bjerre Anne , Bjerre Tavs
Published: May 2007

This paper gives an account of the event and argument structure of past participles, and the linking between argument structure and valence structure. It further accounts for how participles form perfect and passive constructions with auxiliaries. We assume that the same participle form is used in both types of construction. Our claim is that the valence structure of a past participle is predictable from its semantic type, and that the valence structure predicts which auxiliary a past participle combines with in perfect constructions and whether the past participle may occur in passive constructions. Our approach sets itself apart from similar approaches, cf. e.g. Heinz & Matiasek (1994), Kathol (1994), Pollard (1994) and Müller (2003), with its strong emphasis on semantics.
Blunt renal trauma: Comparison of contrast-enhanced CT and angiographic findings and the usefulness of transcatheter arterial embolization
Authors: Kitase  , Mizutani  , Tomita  , Kono  , Sugie  , Shibamoto
Published: May 2007

Background: The purpose of this study was to evaluate the role of contrast-enhanced CT and the usefulness of superselective embolization therapy in the management of arterial damage in patients with severe blunt renal trauma. Patients and methods: Nine cases of severe renal trauma were evaluated. In all cases, we compared contrast-enhanced CT findings with angiographic findings, and performed transcatheter arterial embolization (TAE) in six of them with microcoils and gelatin sponge particles. Morphological changes in the kidney and site of infarction after TAE were evaluated on follow-up CT. Chronological changes in blood biochemistry findings after injury, degree of anemia and renal function were investigated. Adverse effects or complications such as duration of hematuria, fever, abdominal pain, renovascular hypertension and abscess formation were also evaluated. Results: The CT finding of extravasation was a reliable sign of active bleeding and useful for determining the indication of TAE. In all cases, bleeding was effectively controlled with superselective embolization. There was minimal procedure-related loss of renal tissue. None of the patients developed abscess, hypertension or other complications. Conclusions: In blunt renal injury, contrast-enhanced CT was useful for diagnosing arterial hemorrhage. Arterial bleeding may produce massive hematoma and TAE was a useful treatment for such cases. By using selective TAE for a bleeding artery, it was possible to minimize renal parenchymal damage, with complications of TAE rarely seen.
Mesoscale model performance with assimilation of wind profiler data: Sensitivity to assimilation parameters and network configuration
Authors: Nielsen‐Gammon John W. , McNider Richard T. , Angevine Wayne M. , White Allen B. , Knupp Kevin
Published: May 2007

The performance of the nudging scheme in the MM5 numerical model is evaluated for a 4‐day simulation of an ozone episode during the TexAQS‐2000 field study. Quality‐controlled horizontal wind data from five boundary layer profilers spaced 30–50 km apart are used as input data for the nudging as well as for quantification of model errors. Observations from selected profilers are withheld to provide independent data to evaluate the performance of the model. A series of experiments are conducted to estimate the overall model performance as well as the dependence of the model performance on nudging parameters and on profiler network configuration. Within the profiler network, nudging generally reduces 4‐day average biases in the wind components to less than 0.3 m s−1 and yields rms errors averaging 1.75 m s−1 to 2.08 m s−1, with the best model performance at about 500–1500 m above ground level. Rms errors without data assimilation are about twice as large. Model errors, with and without assimilation, are generally largest at night. Wind fields that are more accurate in a statistical sense can be obtained by simpler analysis schemes, but the consistent dynamical evolution of all meteorological variables, such as the pattern of temperatures associated with corrected sea breeze location and intensity, are lost. Tests with a reduced profiler network showed that a single profiler in an appropriate upstream location can produce model performance equivalent to that from a four‐profiler network surrounding the validation station.
The antimalarial drugs quinine, chloroquine and mefloquine are antagonists at 5‐HT3 receptors
Authors: Thompson A J , Lochner M , Lummis S C R
Published: May 2007

Background and Purpose:

The antimalarial compounds quinine, chloroquine and mefloquine affect the electrophysiological properties of Cys‐loop receptors and have structural similarities to 5‐HT3 receptor antagonists. They may therefore act at 5‐HT3 receptors.

Experimental Approach:

The effects of quinine, chloroquine and mefloquine on electrophysiological and ligand binding properties of 5‐HT3A receptors expressed in HEK 293 cells and Xenopus oocytes were examined. The compounds were also docked into models of the binding site.

Key Results:

5‐HT3 responses were blocked with IC50 values of 13.4 μM, 11.8 μM and 9.36 μM for quinine, chloroquine and mefloquine. Schild plots indicated quinine and chloroquine behaved competitively with pA2 values of 4.92 (KB=12.0 μM) and 4.97 (KB=16.4 μM). Mefloquine displayed weakly voltage‐dependent, non‐competitive inhibition consistent with channel block. On and off rates for quinine and chloroquine indicated a simple bimolecular reaction scheme. Quinine, chloroquine and mefloquine displaced [3H]granisetron with Ki values of 15.0, 24.2 and 35.7 μM. Docking of quinine into a homology model of the 5‐HT3 receptor binding site located the tertiary ammonium between W183 and Y234, and the quinoline ring towards the membrane, stabilised by a hydrogen bond with E129. For chloroquine, the quinoline ring was positioned between W183 and Y234 and the tertiary ammonium stabilised by interactions with F226.

Conclusions and Implications:

This study shows that quinine and chloroquine competitively inhibit 5‐HT3 receptors, while mefloquine inhibits predominantly non‐competitively. Both quinine and chloroquine can be docked into a receptor binding site model, consistent with their structural homology to 5‐HT3 receptor antagonists.

British Journal of Pharmacology (2007) 151, 666–677; doi:10.1038/sj.bjp.0707238
Augmentation of spinal morphine analgesia and inhibition of tolerance by low doses of μ‐ and δ‐opioid receptor antagonists
Authors: Abul‐Husn N S , Sutak M , Milne B , Jhamandas K
Published: May 2007

Background and purpose:

Ultralow doses of naltrexone, a non‐selective opioid antagonist, have previously been found to augment acute morphine analgesia and block the development of tolerance to this effect. Since morphine tolerance is dependent on the activity of μ and δ receptors, the present study investigated the effects of ultralow doses of antagonists selective for these receptor types on morphine analgesia and tolerance in tests of thermal and mechanical nociception.

Experimental approach:

Effects of intrathecal administration of μ‐receptor antagonists, CTOP (0.01 ng) or CTAP (0.001 ng), or a δ‐receptor antagonist, naltrindole (0.01 ng), on spinal morphine analgesia and tolerance were evaluated using the tail‐flick and paw‐pressure tests in rats.

Key results:

Both μ and δ antagonists augmented analgesia produced by a sub‐maximal (5 μg) or maximal (15 μg) dose of morphine. Administration of the antagonists with morphine (15 μg) for 5 days inhibited the progressive decline of analgesia and prevented the loss of morphine potency. In animals exhibiting tolerance to morphine, administration of the antagonists with morphine produced a recovery of the analgesic response and restored morphine potency.

Conclusions and implications:

Combining ultralow doses of μ‐ or δ‐receptor antagonists with spinal morphine augmented the acute analgesic effects, inhibited the induction of chronic tolerance and reversed established tolerance. The remarkably similar effects of μ‐ and δ‐opioid receptor antagonists on morphine analgesia and tolerance are interpreted in terms of blockade of the latent excitatory effects of the agonist that limit expression of its full activity.

British Journal of Pharmacology (2007) 151, 877–887; doi:10.1038/sj.bjp.0707277
Coupled ion temperature gradient and trapped electron mode to electron temperature gradient mode gyrokinetic simulations
Authors: Waltz R. E. , Candy J. , Fahey M.
Published: May 2007

Electron temperature gradient (ETG) transport is conventionally defined as the electron energy transport at high wave number (high-k) where ions are adiabatic and there can be no ion energy or plasma transport. Previous gyrokinetic simulations have assumed adiabatic ions (ETG-ai) and work on the small electron gyroradius scale. However such ETG-ai simulations with trapped electrons often do not have well behaved nonlinear saturation unless fully kinetic ions (ki) and proper ion scale zonal flow modes are included. Electron energy transport is separated into ETG-ki at high-k and ion temperature gradient-trapped electron mode (ITG/TEM) at low-k. Expensive (more computer-intensive), high-resolution, large-ion-scale flux-tube simulations coupling ITG/TEM and ETG-ki turbulence are presented. These require a high effective Reynolds number R≡[k(max)∕k(min)]2=μ2, where μ=[ρsi∕ρsi] is the ratio of ion to electron gyroradii. Compute times scale faster than μ3. By comparing the coupled expensive simulations with (1) much cheaper (less compute-intensive), uncoupled, high-resolution, small, flux-tube ETG-ki and with (2) uncoupled low-resolution, large, flux-tube ITG/TEM simulations, and also by artificially turning “off” the low-k or high-k drives, it appears that ITG/TEM and ETG-ki transport are not strongly coupled so long as ETG-ki can access some nonadiabatic ion scale zonal flows and both high-k and low-k are linearly unstable. However expensive coupled simulations are required for physically accurate k-spectra of the transport and turbulence. Simulations with μ⩾30 appear to represent the physical range μ>40. ETG-ki transport measured in ion gyro-Bohm units is weakly dependent on μ. For the mid-radius core tokamak plasma parameters studied, ETG-ki is about 10% of the electron energy transport, which in turn is about 30% of the total energy transport (with negligible E×B shear). However at large E×B shear sufficient to quench the low-k ITG/TEM transport, the high-k tail of the ETG-ki transport survives. Decreasing the trapping to minimize the TEM opens a stability gap between ITG and ETG. High-k ETG transport driven by low-k ITG instability in an ETG linearly stable plasma is demonstrated.