bluuebunny/crossref_metadata_2025_split huggingface dataset:
Virtual backbone construction in multihop ad hoc wireless networks
Authors: Cheng Xiuzhen , Ding Min , Du David Hongwei , Jia Xiaohua 
Published: February 2006

AbstractRecent research points out that the flooding mechanism for topology update or route request in existing ad hoc routing protocols greatly degrades the network capacity. If we restrict the broadcast of control packets within a small subset of hosts in the network, the protocol overhead can be substantially reduced. This motivates our research of constructing a virtual backbone by computing a connected dominating set (CDS) in unit‐disk graphs. In this paper, we propose two distributed algorithms to approximate a minimum CDS. These algorithms take linear time. Their performance is verified by a complete theoretical analysis. Copyright © 2006 John Wiley & Sons, Ltd.
Approximation algorithms for conflict‐free channel assignment in wirelessad hocnetworks
Authors: Wan Peng‐Jun , Yi Chih‐Wei , Jia Xiaohua , Kim Dongsoo 
Published: February 2006

AbstractConflict‐free channel assignment is a classic and fundamental problem in wirelessad hocnetworks. It seeks an assignment of the fewest channels to a given set of radio nodes with specified transmission ranges without causing either primary collision or secondary collision. It is NP‐hard even when all nodes are located in a plane and have the same transmission radii. We observe that a prior analysis of the approximation ratio of a classic greedy heuristic, FIRST‐FIT in smallest‐last ordering, is erroneous. In this paper, we provide a rigorous and tighter analysis of this heuristic and other greedy FIRST‐FIT heuristics. We obtain an upper bound of 13 on the approximation ratios of both FIRST‐FIT in smallest‐last ordering and FIRST‐FIT in radius‐decreasing ordering. Such upper bound can be reduced to 12 if all nodes have quasi‐uniform transmission radii. When all nodes have equal transmission radii, we obtain an upper bound of 7 on the approximation ratios of FIRST‐FIT in smallest‐last ordering, FIRST‐FIT in distance‐increasing ordering, and FIRST‐FIT in lexicographic ordering. In addition, for nodes with equal transmission radii, we present a spatial divide‐and‐conquer heuristic with approximation ratios of 12. All these heuristics, except FIRST‐FIT in smallest‐last ordering, are modified to heuristics for maximum independent set with the same approximation ratios. Copyright © 2006 John Wiley & Sons, Ltd.
Channel‐relay price pair: towards arbitrating incentives in wireless ad hoc networks
Authors: Xue Yuan , Li Baochun , Nahrstedt Klara 
Published: February 2006

AbstractCooperation in wireless ad hoc networks has twofold implications. First, each wireless node does not excessively and greedily inject traffic to the shared wireless channel. Second, intermediate nodes voluntarily relay traffic for upstream nodes towards the destination at the cost of its own private resource. Such an assumption supports almost all existing research when it comes to protocol design in ad hoc networks. We believe that without appropriate incentive mechanisms, the nodes are inherently selfish (unwilling to contribute its private resource to relay traffic) and greedy (unfairly sharing the wireless channel). In this paper, we present a price pair mechanism to arbitrate resource allocation and to provide incentives simultaneously such that cooperation is promoted and the desired global optimal network operating point is reached by convergence with a fully decentralized self‐optimizing algorithm. Such desired network‐wide global optimum is characterized with the concept of Nash bargaining solution (NBS), which not only provides the Pareto optimal point for the network, but is also consistent with the fairness axioms of game theory. We simulate the price pair mechanism and report encouraging results to support and validate our theoretical claims. Copyright © 2006 John Wiley & Sons, Ltd.
Voronoi diagram and convex hull based geocasting and routing in wireless networks
Authors: Stojmenovic Ivan , Ruhil Anand Prakash , Lobiyal D. K. 
Published: February 2006

AbstractIn this paper, we propose a general algorithm (based on an unified framework for both routing and geocasting problems), in which message is forwarded to exactly those neighbors which may be best choices for a possible position of destination (using the appropriate criterion). We then propose and discuss new VD‐GREEDY and CH‐MFR methods and define R‐DIR, modified version of existing directional methods. In VD‐GREEDY method, these neighbors are determined by intersecting the Voronoi diagram of neighbors with the circle (or rectangle) of possible positions of destination, while the portion of the convex hull of neighboring nodes is analogously used in the CH‐MFR method. Routing and geocasting algorithms differ only inside the circle/rectangle. The proposed methods may be also used for the destination search phase allowing the application of different routing schemes after the exact position of destination is discovered. VD‐GREEDY and CH‐MFR algorithms are loop free, and have smaller flooding rate (with similar success rate) compared to directional method. We proposed to use dominating set concept to reduce flooding ratio significantly, with a marginal impact on success rate and hop count. Simulations, involving the proposed and some known algorithms, are performed for two basic scenarios, one for geocasting and reactive routing, and the other for proactive routing, and both showed that our methods have higher success rate and lower flooding rate compared to existing methods. Copyright © 2006 John Wiley & Sons, Ltd.
Sex‐specific sibling interactions and offspring fitness in vertebrates: patterns and implications for maternal sex ratios
Authors: Uller Tobias 
Published: February 2006

ABSTRACTVertebrate sex ratios are notorious for their lack of fit to theoretical models, both with respect to the direction and the magnitude of the sex ratio adjustment. The reasons for this are likely to be linked to simplifying assumptions regarding vertebrate life histories. More specifically, if the sex ratio adjustment itself influences offspring fitness, due to sex‐specific interactions among offspring, this could affect optimal sex ratios. A review of the literature suggests that sex‐specific sibling interactions in vertebrates result from three major causes: (i) sex asymmetries in competitive ability, for example due to sexual dimorphism, (ii) sex‐specific cooperation or helping, and (iii) sex asymmetries in non‐competitive interactions, for example steroid leakage between fetuses. Incorporating sex‐specific sibling interactions into a sex ratio model shows that they will affect maternal sex ratio strategies and, under some conditions, can repress other selection pressures for sex ratio adjustment. Furthermore, sex‐specific interactions could also explain patterns of within‐brood sex ratio (e.g. in relation to laying order). Failure to take sex‐specific sibling interactions into account could partly explain the lack of sex ratio adjustment in accordance with theoretical expectations in vertebrates, and differences among taxa in sex‐specific sibling interactions generate predictions for comparative and experimental studies.
Intestinal alkaline sphingomyelinase hydrolyses and inactivates platelet-activating factor by a phospholipase C activity
Authors: Wu Jun , Nilsson Åke , Jönsson Bo A. G. , Stenstad Hanna , Agace William , Cheng Yajun , Duan Rui-Dong 
Published: March 2006

Alkaline sphingomyelinase (alk-SMase) is a new member of the NPP (nucleotide pyrophosphatase/phosphodiesterase) family that hydrolyses SM (sphingomyelin) to generate ceramide in the intestinal tract. The enzyme may protect the intestinal mucosa from inflammation and tumorigenesis. PAF (platelet-activating factor) is a pro-inflammatory phospholipid involved in pathogenesis of inflammatory bowel diseases. We examined whether alk-SMase can hydrolyse and inactivate PAF. [3H]Octadecyl-labelled PAF was incubated with purified rat intestinal alk-SMase or recombinant human alk-SMase expressed in COS-7 cells. The hydrolytic products were assayed with TLC and MS. We found that alkSMase cleaved the phosphocholine head group from PAF and generated 1-O-alkyl-2-acetyl-sn-glycerol. Differing from the activity against SM, the activity against PAF was optimal at pH 7.5, inhibited by EDTA and stimulated by 0.1–0.25 mM Zn2+. The activity was abolished by site mutation of the predicted metal-binding sites that are conserved in all NPP members. Similar to the activity against SM, the activity against PAF was dependent on bile salt, particularly taurocholate and taurochenodeoxycholate. The Vmax for PAF hydrolysis was 374 μmol·h−1·(mg of protein)−1. The hydrolysis of PAF and SM could be inhibited by the presence of SM and PAF respectively, the inhibition of PAF hydrolysis by SM being stronger. The PAF-induced MAPK (mitogen-activated protein kinase) activation and IL-8 (interleukin 8) release in HT-29 cells, and chemotaxis in leucocytes were abolished by alk-SMase treatment. In conclusion, alk-SMase hydrolyses and inactivates PAF by a phospholipase C activity. The finding reveals a novel function, by which alk-SMase may counteract the development of intestinal inflammation and colon cancer.
Functional properties and differential mode of regulation of the nitrate transporter from a plant symbiotic ascomycete
Authors: Montanini Barbara , Viscomi Arturo R. , Bolchi Angelo , Martin Yusé , Siverio José M. , Balestrini Raffaella , Bonfante Paola , Ottonello Simone 
Published: March 2006

Nitrogen assimilation by plant symbiotic fungi plays a central role in the mutualistic interaction established by these organisms, as well as in nitrogen flux in a variety of soils. In the present study, we report on the functional properties, structural organization and distinctive mode of regulation of TbNrt2 (Tuber borchii NRT2 family transporter), the nitrate transporter of the mycorrhizal ascomycete T. borchii. As revealed by experiments conducted in a nitrate-uptake-defective mutant of the yeast Hansenula polymorpha, TbNrt2 is a high-affinity transporter (Km=4.7 μM nitrate) that is bispecific for nitrate and nitrite. It is expressed in free-living mycelia and in mycorrhizae, where it preferentially accumulates in the plasma membrane of root-contacting hyphae. The TbNrt2 mRNA, which is transcribed from a single-copy gene clustered with the nitrate reductase gene in the T. borchii genome, was specifically up-regulated following transfer of mycelia to nitrate- (or nitrite)-containing medium. However, at variance with the strict nitrate-dependent induction commonly observed in other organisms, TbNrt2 was also up-regulated (at both the mRNA and the protein level) following transfer to a nitrogen-free medium. This unusual mode of regulation differs from that of the adjacent nitrate reductase gene, which was expressed at basal levels under nitrogen deprivation conditions and required nitrate for induction. The functional and expression properties, described in the present study, delineate TbNrt2 as a versatile transporter that may be especially suited to cope with the fluctuating (and often low) mineral nitrogen concentrations found in most natural, especially forest, soils.
Effects of peptide C corresponding to the Glu724–Pro760 region of the II–III loop of the DHP (dihydropyridine) receptor α1 subunit on the domain- switch-mediated activation of RyR1 (ryanodine receptor 1) Ca2+ channels
Authors: Bannister Mark L. , Ikemoto Noriaki 
Published: March 2006

The Leu720–Leu764 region of the II–III loop of the dihydropyridine receptor is believed to be important for both orthograde and retrograde communications with the RyR (ryanodine receptor), but its actual role has not yet been resolved. Our recent studies suggest that voltage-dependent activation of the RyR channel is mediated by a pair of interacting N-terminal and central domains, designated as the ‘domain switch’. To investigate the effect of peptide C (a peptide corresponding to residues Glu724–Pro760) on domain- switch-mediated activation of the RyR, we measured Ca2+ release induced by DP (domain peptide) 1 or DP4 (which activates the RyR by mediation of the domain switch) and followed the Ca2+ release time course using a luminal Ca2+ probe (chlortetracycline) under Ca2+-clamped conditions. Peptide C produced a significant potentiation of the domain-switch-mediated Ca2+ release, provided that the Ca2+ concentration was sufficiently low (e.g. 0.1 μM) and the Ca2+ channel was only partially activated by the domain peptide. However, at micromolar Ca2+ concentrations, peptide C inhibits activation. Covalent cross-linking of fluorescently labelled peptide C to the RyR and screening of the fluorescently labelled tryptic fragments permitted us to localize the peptide-C-binding site to residues 450–1400, which may represent the primary region involved in physical coupling. Based on the above findings, we propose that the physiological role of residues Glu724–Pro760 is to facilitate depolarization-induced and domain-switch-mediated RyR activation at sub- or near-threshold concentrations of cytoplasmic Ca2+ and to suppress activation upon an increase of cytoplasmic Ca2+.
Reconstruction of human hepatocyte glyoxylate metabolic pathways in stably transformed Chinese-hamster ovary cells
Authors: Behnam Joseph T. , Williams Emma L. , Brink Susanne , Rumsby Gill , Danpure Christopher J. 
Published: March 2006

Failure to detoxify the intermediary metabolite glyoxylate in human hepatocytes underlies the metabolic pathology of two potentially lethal hereditary calcium oxalate kidney stone diseases, PH (primary hyperoxaluria) types 1 and 2. In order to define more clearly the roles of enzymes involved in the metabolism of glyoxylate, we have established singly, doubly and triply transformed CHO (Chinese-hamster ovary) cell lines, expressing all combinations of normal human AGT (alanine:glyoxylate aminotransferase; the enzyme deficient in PH1), GR/HPR (glyoxylate/hydroxypyruvate reductase; the enzyme deficient in PH2), and GO (glycolate oxidase). We have embarked on the preliminary metabolic analysis of these transformants by studying the indirect toxicity of glycolate as a simple measure of the net intracellular production of glyoxylate. Our results show that glycolate is toxic only to those cells expressing GO and that this toxicity is diminished when AGT and/or GR/HPR are expressed in addition to GO. This finding indicates that we have been able to reconstruct the glycolate→glyoxylate, glyoxylate→glycine, and glyoxylate→glycolate metabolic pathways, catalysed by GO, AGT, and GR/HPR respectively, in cells that do not normally express them. These results are compatible with the findings in PH1 and PH2, in which AGT and GR/HPR deficiencies lead to increased oxalate synthesis, due to the failure to detoxify its immediate precursor glyoxylate. These CHO cell transformants have a potential use as a cell-based bioassay for screening small molecules that stabilize AGT or GR/HPR and might have use in the treatment of PH1 or PH2.
Coupling of protein motions and hydrogen transfer during catalysis byEscherichia colidihydrofolate reductase
Authors: Swanwick Richard S. , Maglia Giovanni , Tey Lai-hock , Allemann Rudolf K. 
Published: March 2006

The enzyme DHFR (dihydrofolate reductase) catalyses hydride transfer from NADPH to, and protonation of, dihydrofolate. The physical basis of the hydride transfer step catalysed by DHFR from Escherichia coli has been studied through the measurement of the temperature dependence of the reaction rates and the kinetic isotope effects. Single turnover experiments at pH 7.0 revealed a strong dependence of the reaction rates on temperature. The observed relatively large difference in the activation energies for hydrogen and deuterium transfer led to a temperature dependence of the primary kinetic isotope effects from 3.0±0.2 at 5 °C to 2.2±0.2 at 40 °C and an inverse ratio of the pre-exponential factors of 0.108±0.04. These results are consistent with theoretical models for hydrogen transfer that include contributions from quantum mechanical tunnelling coupled with protein motions that actively modulate the tunnelling distance. Previous work had suggested a coupling of a remote residue, Gly121, with the kinetic events at the active site. However, pre-steady-state experiments at pH 7.0 with the mutant G121V-DHFR, in which Gly121 was replaced with valine, revealed that the chemical mechanism of DHFR catalysis was robust to this replacement. The reduced catalytic efficiency of G121V-DHFR was mainly a consequence of the significantly reduced pre-exponential factors, indicating the requirement for significant molecular reorganization during G121V-DHFR catalysis. In contrast, steady-state measurements at pH 9.5, where hydride transfer is rate limiting, revealed temperature-independent kinetic isotope effects between 15 and 35 °C and a ratio of the pre-exponential factors above the semi-classical limit, suggesting a rigid active site configuration from which hydrogen tunnelling occurs. The mechanism by which hydrogen tunnelling in DHFR is coupled with the environment appears therefore to be sensitive to pH.
Mechanism of nitrite oxidation by eosinophil peroxidase: implications for oxidant production and nitration by eosinophils
Authors: van Dalen Christine J. , Winterbourn Christine C. , Kettle Anthony J. 
Published: March 2006

Eosinophil peroxidase is a haem enzyme of eosinophils that is implicated in oxidative tissue injury in asthma. It uses hydrogen peroxide to oxidize thiocyanate and bromide to their respective hypohalous acids. Nitrite is also a substrate for eosinophil peroxidase. We have investigated the mechanisms by which the enzyme oxidizes nitrite. Nitrite was very effective at inhibiting hypothiocyanous acid (‘cyanosulphenic acid’) and hypobromous acid production. Spectral studies showed that nitrite reduced the enzyme to its compound II form, which is a redox intermediate containing FeIV in the haem active site. Compound II does not oxidize thiocyanate or bromide. These results demonstrate that nitrite is readily oxidized by compound I, which contains FeV at the active site. However, it reacts more slowly with compound II. The observed rate constant for reduction of compound II by nitrite was determined to be 5.6×103 M−1·s−1. Eosinophils were at least 4-fold more effective at promoting nitration of a heptapeptide than neutrophils. This result is explained by our finding that nitrite reacts 10-fold faster with compound II of eosinophil peroxidase than with the analogous redox intermediate of myeloperoxidase. Nitration by eosinophils was increased 3-fold by superoxide dismutase, which indicates that superoxide interferes with nitration. We propose that at sites of eosinophilic inflammation, low concentrations of nitrite will retard oxidant production by eosinophil peroxidase, whereas at higher concentrations nitrogen dioxide will be a major oxidant formed by these cells. The efficiency of protein nitration will be decreased by the diffusion-controlled reaction of superoxide with nitrogen dioxide.
Identification and characterization of Fep15, a new selenocysteine-containing member of the Sep15 protein family
Authors: Novoselov Sergey V. , Hua Deame , Lobanov Alexey V. , Gladyshev Vadim N. 
Published: March 2006

Sec (selenocysteine) is a rare amino acid in proteins. It is co-translationally inserted into proteins at UGA codons with the help of SECIS (Sec insertion sequence) elements. A full set of selenoproteins within a genome, known as the selenoproteome, is highly variable in different organisms. However, most of the known eukaryotic selenoproteins are represented in the mammalian selenoproteome. In addition, many of these selenoproteins have cysteine orthologues. Here, we describe a new selenoprotein, designated Fep15, which is distantly related to members of the 15 kDa selenoprotein (Sep15) family. Fep15 is absent in mammals, can be detected only in fish and is present in these organisms only in the selenoprotein form. In contrast with other members of the Sep15 family, which contain a putative active site composed of Sec and cysteine, Fep15 has only Sec. When transiently expressed in mammalian cells, Fep15 incorporated Sec in an SECIS- and SBP2 (SECIS-binding protein 2)-dependent manner and was targeted to the endoplasmic reticulum by its N-terminal signal peptide. Phylogenetic analyses of Sep15 family members suggest that Fep15 evolved by gene duplication.
Porcine circovirus diseases
Authors: Segalés Joaquim , Allan Gordon M. , Domingo Mariano 
Published: February 2006

AbstractPorcine circovirus type 2 (PCV2) is a member of the familyCircoviridae, a recently established virus family composed of small, non-enveloped viruses, with a circular, single-stranded DNA genome. PCV2, which is found all over the world in the domestic pig and probably the wild boar, has been recently associated with a number of disease syndromes, which have been collectively named porcine circovirus diseases (PCVD). Postweaning multisystemic wasting syndrome (PMWS), porcine dermatitis and nephropathy syndrome (PDNS) and reproductive disorders are the most relevant ones. Among them, only PMWS is considered to have a severe impact on domestic swine production. PMWS mainly affects nursery and/or fattening pigs; wasting is considered the most representative clinical sign in this disease. Diagnosis of this disease is confirmed by histopathological examination of lymphoid tissues and detection of a moderate to high amount of PCV2 in damaged tissues. Since PMWS is considered a multifactorial disease in which other factors in addition to PCV2 are needed in most cases to trigger the clinical disease, effective control measures have focused on the understanding of the co-factors involved in individual farms and the control or elimination of these triggers. PDNS, an immuno-complex disease characterized by fibrino-necrotizing glomerulonephritis and systemic necrotizing vasculitis, has been linked to PCV2, but a definitive proof of this association is still lacking. PCV2-associated reproductive disease seems to occur very sporadically under field conditions, but it has been characterized by late-term abortions and stillbirths, extensive fibrosing and/or necrotizing myocarditis in fetuses and the presence of moderate to high amounts of PCV2 in these lesions. Taking into account that scientific information on PCV2 and its associated diseases has been markedly expanded in the last 8 years, the objective of this review is to summarize the current state of knowledge of the most relevant aspects of PCV2 biology and PCVD.