bluuebunny/crossref_metadata_2025 huggingface dataset:
New automatic system for multipass Fabry-Pérot alignment and stabilization
Authors: Salvato G. , Ponterio R. C. , Aliotta F.
Published: November 2006

We present a new automatic system for Brillouin scattering experiments employing a double pass Fabry-Pérot interferometer. The main characteristics of the system are a new procedure for reaching and maintaining mirror parallelism over time and the complete automation of most of the tasks involved in a successful Brillouin scattering experiment. The system makes use of a personal computer, a commercially available nanopositioning system with proportional-integral-derivative feedback control capability, and few commercial computer interfaces. The proposed mirror alignment method can be easily adapted to different multipass Fabry-Pérots and turned out to be reliable and practical in common experimental condition. The system does not need thermal stabilization of the surrounding environment and requires human intervention only when changing the free spectral range of the interferometer and/or scattering angle. The results from some tests under different experimental conditions are also reported.
Optical probes based on optical fibers and single-walled carbon nanotubes for hydrogen detection at cryogenic temperatures
Authors: Cusano A. , Consales M. , Cutolo A. , Penza M. , Aversa P. , Giordano M. , Guemes A.
Published: November 2006

In this letter, preliminary results on the feasibility to use optical fiber sensors coated by single-walled carbon nanotubes (SWCNTs)-based sensitive materials for hydrogen detection at cryogenic temperatures are presented. The optical probes have been realized by the Langmuir-Blodgett deposition of close-end and open-end SWCNTs on the distal end of standard optical fibers. The results obtained from hydrogen detection testing, carried out at a temperature as low as 113K, demonstrate the excellent potentiality of the proposed configuration to sense very low percentages of gaseous hydrogen (<5%), with good recovery and reversibility features as well as fast response times.
Inverse bremsstrahlung absorption and the evolution of electron distributions accounting for electron-electron collisions
Authors: Weng Su-Ming , Sheng Zheng-Ming , He Min-Qing , Wu Hui-Chun , Dong Quan-Li , Zhang Jie
Published: November 2006

Two-dimensional Fokker-Planck simulations have been conducted to investigate the inverse bremsstrahlung absorption and the evolution of the electron distribution function (EDF), where the electron-electron (e-e) collisions are taken into account, allowing for highly anisotropic electron distributions. The numerical results show that the anisotropic part of the EDF is comparable to the isotropic part even for a moderate laser field. The resulting EDF is no longer a simple super-Gaussian, but a hybrid of the super-Gaussian and Maxwellian distributions. Furthermore, the e-e collisions tend to enhance the inverse bremsstrahlung absorption; the contribution ratio of e-e collisions to the inverse bremsstrahlung absorption rate increases with increasing ion charge state Zi in the high laser frequency regime, while it decreases in the low laser frequency regime. It indicates that one cannot simply neglect the e-e collisions in high Zi cases.
Over 70% tunneling magnetoresistance at room temperature for a CoFe and AlOx based magnetic tunnel junction
Authors: Yang J. Joshua , Ji Chengxiang , Chang Y. Austin , Ke Xianglin , Rzchowski M. S.
Published: November 2006

More than 70% tunneling magnetoresistance (TMR) ratio has been observed at room temperature for a CoFe and AlOx based magnetic tunnel junction. The annealing of the epitaxial bottom electrode, Si (001)/Ag fcc (200)∕Co84Fe16 bcc (200), at 400°C prior to fabricating the tunnel barrier and the upper electrode is crucial for achieving this high TMR ratio. Moreover a high output voltage could be obtained for this magnetic tunnel junction due to its high V1∕2, the bias voltage at which the TMR ratio is reduced to half of that near the zero bias. The rationale for obtaining this high TMR ratio is discussed, and there are reasons to believe that the TMR ratio for this junction could be further improved.
Near-infrared imprinted distributed feedback lasers
Authors: Del Carro P. , Camposeo A. , Stabile R. , Mele E. , Persano L. , Cingolani R. , Pisignano D.
Published: November 2006

The authors report on the fabrication and characterization of an organic distributed feedback laser operating in the near infrared. The device, fabricated by room-temperature nanoimprint lithography, is based on an organic dye hosted by a poly(methylmethacrylate) matrix. The laser emission from an imprinted 620nm period grating is peaked at 918nm with a linewidth of 8Å and a pumping threshold of 37μJ∕cm2, and it is strongly polarized with a polarization contrast as high as 0.99. The lasing wavelength is tunable in the range of 890–930nm by adjusting the grating period, and the operational lifetime is up to 6×103 excitation pulses in vacuum environment. These results demonstrate the possibility of realizing imprinted organic-based near-infrared lasers, thus approaching spectral regions relevant for optical communication applications.
Tunable plasma wave resonant detection of optical beating in high electron mobility transistor
Authors: Torres J. , Nouvel P. , Akwoue-Ondo A. , Chusseau L. , Teppe F. , Shchepetov A. , Bollaert S.
Published: November 2006

The authors report on tunable terahertz resonant detection of two 1.55μm cw lasers beating by plasma waves in AlGaAs∕InGaAs∕InP high electron mobility transistor. The authors show that the fundamental plasma resonant frequency and its odd harmonics can be tuned with the applied gate voltage in the range of 75–490GHz. The observed frequency dependence on gate bias is found to be in good agreement with the theoretical plasma wave dispersion law.
Dense quasi-monoenergetic attosecond electron bunches from laser interaction with wire and slice targets
Authors: Ma Yan-Yun , Sheng Zheng-Ming , Li Yu-Tong , Chang Wen-Wei , Yuan Xiao-Hui , Chen Min , Wu Hui-Chun , Zheng Jun , Zhang Jie
Published: November 2006

A scheme is proposed to produce high-quality quasi-monoenergetic attosecond electron bunches based on laser ponderomotive-force acceleration along the surface of wire or slice targets. Two- and three-dimensional particle-in-cell simulations demonstrate that the electron energy depends weakly on the target density. A simple analytical model shows that the electron energy scales linearly with the laser field amplitude, in good agreement with the simulation results. Electron bunches produced by this scheme are suitable for applications such as coherent x-ray radiation, radiography, and injectors in accelerators, etc.
Low threshold blue conjugated polymer lasers with first- and second-order distributed feedback
Authors: Karnutsch C. , Gýrtner C. , Haug V. , Lemmer U. , Farrell T. , Nehls B. S. , Scherf U. , Wang J. , Weimann T. , Heliotis G. , Pflumm C. , deMello J. C. , Bradley D. D. C.
Published: November 2006

We report on the fabrication of low threshold distributed feedback (DFB) polymer lasers based on a polyfluorene derivative containing statistical binaphthyl units (BN-PFO). First- and second-order feedback lasers have been realized. The emission was tuned in the wavelength range from 438to459nm by varying the grating period and the film thickness. A threshold energy of 280pJ/pulse was observed in second-order DFB structures, which could be further reduced to 160pJ/pulse by employing first-order feedback in electron beam lithographically patterned structures with a period of 140nm. In these first-order structures, laser oscillation at both edges of the photonic stop band was observed. These very low threshold values render BN-PFO a very promising material for future electrically pumped organic semiconductor laser diodes.
Two Metal Complexes of the Macrocyclic Ligand 1,4,7-Triazacyclodecane (tacd). Crystal Structures of [Zn(tacd)2](ClO4)2 and [Cu(tacd)2]Br2.4H2O
Authors: Chen XM , Yao YX , Shi KL , Mak TCW
Published: November 2006

Two metal complexes of 1,4,7-triazacyclodecane ( tacd ), [Zn( tacd )2] (ClO4)2 (1) and [Cu( tacd )2] Br2.4H2O (2), have been prepared and characterized by X-ray crystallography. Crystals of (1) are monoclinic, P21/n, a 9.506(2), b 10.279(3), c 11.505(2) Ǻ, β 91.29(2)°; crystals of (2) are orthorhombic, Pbca, a 12.035(3), b 13.673(3), c 14.248(2) Ǻ. The zinc(II) atom in (1) is surrounded in a distorted octahedral N6 environment with Zn-N bonds at 2.121(5)-2.131(4) Ǻ; the copper(II) atom in (2) adopts an elongated octahedral coordination geometry with the Cu-N bonds at 2.066(4)-2.294(5) Ǻ.
A Selective and Versatile Synthesis of Substituted Chromones via Addition of Phenols to Dimethyl Acetylenedicarboxylate
Authors: Stoermer MJ , Fairlie DP
Published: November 2006

Despite many published syntheses of chromones, none has been reported to be both selective for chromones and tolerant of ring substitution. The addition of substituted phenols to dimethyl acetylenedicarboxylate is now reported as a versatile high yield initial step in a simple three-step synthesis of chromone 2-carboxylic acids. Triethylamine being used to deprotonate the substituted phenol, the addition to dimethyl acetylenedicarboxylate proceeds under mild conditions and tolerates a wide range of functional groups on the phenol. Although not stereoselective, both fumarate and maleate aryloxy products of this addition can then be cyclized, according to a known method, to chromones without contamination by isomeric coumarins. Thus the addition reaction is a valuable component of a versatile and selective synthesis of substituted chromones.
Crystal and Molecular Structure of Cycasin, (Z)-β-D-Glucopyranosyloxy-NNO-azoxymethane
Authors: Tate ME , Delaere IM , Jones GP , Tiekink ERT
Published: November 2006

Characterization of cycasin , (Z)-β-D-glucopyranosyloxy-NNO-azoxymethane, from Cycas revoluta Thunb . is reported. A crystal structure analysis shows the azoxy substituents adopt a Z configuration. The colourless crystals are monoclinic, space group C2 with unit cell dimensions a 15.409(4), b 4.855(4), c 15.752(4) Ǻ, β 109.87(2)°, Z 4; the structure was refined to final R 0.033, 886 reflections with I ≥ 3.0σ(I) being used.
The Synthesis of Two C4 Epimers of 4,8-Dimethyl-2-oxabicyclo[3.3.1]nonan-8-ol (1-Hydroxy-2,9-cineole)
Authors: Carman RM , Garner AC
Published: November 2006

Chemical syntheses of the two 2,9-cineoles (10a) and (11a) confirm the view that such compounds may be formed during various 1,8-cineole syntheses. The n.m.r. spectra and conformations of these bicyclic compounds are discussed.
Remarkable variation in maize genome structure inferred from haplotype diversity at the
bz
locus
Authors: Wang Qinghua , Dooner Hugo K.
Published: November 2006

Maize is probably the most diverse of all crop species. Unexpectedly large differences among haplotypes were first revealed in a comparison of the
bz
genomic regions of two different inbred lines, McC and B73. Retrotransposon clusters, which comprise most of the repetitive DNA in maize, varied markedly in makeup, and location relative to the genes in the region and genic sequences, later shown to be carried by two helitron transposons, also differed between the inbreds. Thus, the allelic
bz
regions of these Corn Belt inbreds shared only a minority of the total sequence. To investigate further the variation caused by retrotransposons, helitrons, and other insertions, we have analyzed the organization of the
bz
genomic region in five additional cultivars selected because of their geographic and genetic diversity: the inbreds A188, CML258, and I137TN, and the land races Coroico and NalTel. This vertical comparison has revealed the existence of several new helitrons, new retrotransposons, members of every superfamily of DNA transposons, numerous miniature elements, and novel insertions flanked at either end by TA repeats, which we call TAFTs (TA-flanked transposons). The extent of variation in the region is remarkable. In pairwise comparisons of eight
bz
haplotypes, the percentage of shared sequences ranges from 25% to 84%. Chimeric haplotypes were identified that combine retrotransposon clusters found in different haplotypes. We propose that recombination in the common gene space greatly amplifies the variability produced by the retrotransposition explosion in the maize ancestry, creating the heterogeneity in genome organization found in modern maize.
Transposon insertion site profiling chip (TIP-chip)
Authors: Wheelan Sarah J. , Scheifele Lisa Z. , Martínez-Murillo Francisco , Irizarry Rafael A. , Boeke Jef D.
Published: November 2006

Mobile elements are important components of our genomes, with diverse and significant effects on phenotype. Not only can transposons inactivate genes by direct disruption and shuffle the genome through recombination, they can also alter gene expression subtly or powerfully. Currently active transposons are highly polymorphic in host populations, including, among hundreds of others, L1 and Alu elements in humans and Ty1 elements in yeast. For this reason, we wished to develop a simple genome-wide method for identifying all transposons in any given sample. We have designed a transposon insertion site profiling chip (TIP-chip), a microarray intended for use as a high-throughput technique for mapping transposon insertions. By selectively amplifying transposon flanking regions and hybridizing them to the array, we can locate all transposons present in a sample. We have tested the TIP-chip extensively to map Ty1 retrotransposon insertions in yeast and have achieved excellent results in two laboratory strains as well as in evolved Ty1 high-copy strains. We are able to identify all of the theoretically detectable transposons in the FY2 lab strain, with essentially no false positives. In addition, we mapped many new transposon copies in the high-copy Ty1 strain and determined its Ty1 insertion pattern.
A large-scale full-length cDNA analysis to explore the budding yeast transcriptome
Authors: Miura Fumihito , Kawaguchi Noriko , Sese Jun , Toyoda Atsushi , Hattori Masahira , Morishita Shinichi , Ito Takashi
Published: November 2006

We performed a large-scale cDNA analysis to explore the transcriptome of the budding yeast
Saccharomyces cerevisiae
. We sequenced two cDNA libraries, one from the cells exponentially growing in a minimal medium and the other from meiotic cells. Both libraries were generated by using a vector-capping method that allows the accurate mapping of transcription start sites (TSSs). Consequently, we identified 11,575 TSSs associated with 3,638 annotated genomic features, including 3,599 ORFs, to suggest that most yeast genes have two or more TSSs. In addition, we identified 45 previously undescribed introns, including those affecting current ORF annotations and those spliced alternatively. Furthermore, the analysis revealed 667 transcription units in the intergenic regions and transcripts derived from antisense strands of 367 known features. We also found that 348 ORFs carry TSSs in their 3′-halves to generate sense transcripts starting from inside the ORFs. These results indicate that the budding yeast transcriptome is considerably more complex than previously thought, and it shares many recently revealed characteristics with the transcriptomes of mammals and other higher eukaryotes. Thus, the genome-wide active transcription that generates novel classes of transcripts appears to be an intrinsic feature of the eukaryotic cells. The budding yeast will serve as a versatile model for the studies on these aspects of transcriptome, and the full-length cDNA clones can function as an invaluable resource in such studies.
Crystal structure of cryptochrome 3 from
Arabidopsis thaliana
and its implications for photolyase activity
Authors: Huang Yihua , Baxter Richard , Smith Barbara S. , Partch Carrie L. , Colbert Christopher L. , Deisenhofer Johann
Published: November 2006

Cryptochromes use near-UV/blue light to regulate a variety of growth and adaptive process. Recent biochemical studies demonstrate that the Cryptochrome-
Drosophila, Arabidopsis, Synechocystis
, Human (Cry-DASH) subfamily of cryptochromes have photolyase activity exclusively for single-stranded cyclobutane pyrimidine dimer (CPD)-containing DNA substrate [Selby C, Sancar A (2006)
Proc Natl Acad Sci USA
103:17696–17700]. The crystal structure of cryptochrome 3 from
Arabidopsis thaliana
(At-Cry3), a member of the Cry-DASH proteins, at 2.1 Å resolution, reveals that both the light-harvesting cofactor 5,10-methenyl-tetrahydrofolyl-polyglutamate (MTHF) and the catalytic cofactor flavin adenine dinucleotide (FAD) are noncovalently bound to the protein. The residues responsible for binding of MTHF in At-Cry3 are not conserved in
Escherichia coli
photolyase but are strongly conserved in the Cry-DASH subfamily of cryptochromes. The distance and orientation between MTHF and flavin adenine dinucleotide in At-Cry3 is similar to that of
E. coli
photolyase, in conjunction with the presence of electron transfer chain, suggesting the conservation of redox activity in At-Cry3. Two amino acid substitutions and the penetration of three charged side chains into the CPD-binding cavity in At-Cry3 alter the hydrophobic environment that is accommodating the hydrophobic sugar ring and thymine base moieties in class I CPD photolyases. These changes most likely make CPD binding less energetically favorable and, hence, insufficient to compete with pairing and stacking interactions between the CPD and the duplex DNA substrate. Thus, Cry-DASH subfamily proteins may be unable to stabilize CPD flipped out from the duplex DNA substrate but may be able to preserve the DNA repair activity toward single-stranded CPD-containing DNA substrate.
CCN3 controls 3D spatial localization of melanocytes in the human skin through DDR1
Authors: Fukunaga-Kalabis Mizuho , Martinez Gabriela , Liu Zhao-Jun , Kalabis Jiri , Mrass Paul , Weninger Wolfgang , Firth Sue M. , Planque Nathalie , Perbal Bernard , Herlyn Meenhard
Published: November 2006

Melanocytes reside within the basal layer of the human epidermis, where they attach to the basement membrane and replicate at a rate proportionate to that of keratinocytes, maintaining a lifelong stable ratio. In this study, we report that coculturing melanocytes with keratinocytes up-regulated CCN3, a matricellular protein that we subsequently found to be critical for the spatial localization of melanocytes to the basement membrane. CCN3 knockdown cells were dissociated either upward to the suprabasal layers of the epidermis or downward into the dermis. The overexpression of CCN3 increased adhesion to collagen type IV, the major component of the basement membrane. As the receptor responsible for CCN3-mediated melanocyte localization, we identified discoidin domain receptor 1 (DDR1), a receptor tyrosine kinase that acts as a collagen IV adhesion receptor. DDR1 knockdown decreased melanocyte adhesion to collagen IV and shifted melanocyte localization in a manner similar to CCN3 knockdown. These results demonstrate an intricate and necessary communication between keratinocytes and melanocytes in maintaining normal epidermal homeostasis.
Using GOstats to test gene lists for GO term association
Authors: Falcon S. , Gentleman R.
Published: November 2006

Motivation: Functional analyses based on the association of Gene Ontology (GO) terms to genes in a selected gene list are useful bioinformatic tools and the GOstats package has been widely used to perform such computations. In this paper we report significant improvements and extensions such as support for conditional testing.

Results: We discuss the capabilities of GOstats, a Bioconductor package written in R, that allows users to test GO terms for over or under-representation using either a classical hypergeometric test or a conditional hypergeometric that uses the relationships among GO terms to decorrelate the results.

Availability: GOstats is available as an R package from the Bioconductor project:

Contact:  sfalcon@fhcrc.org
PEAKS: identification of regulatory motifs by their position in DNA sequences
Authors: Bellora Nicolás , Farré Domènec , Mar Albà M.
Published: November 2006

Summary: Many DNA functional motifs tend to accumulate or cluster at specific gene locations. These locations can be detected, in a group of gene sequences, as high frequency ‘peaks’ with respect to a reference position, such as the transcription start site (TSS). We have developed a web tool for the identification of regions containing significant motif peaks. We show, by using different yeast gene datasets, that peak regions are strongly enriched in experimentally-validated motifs and contain potentially important novel motifs.

Availability:  

Contact:  malba@imim.es

Supplementary information: Supplementary Data are available at Bioinformatics online.
Effects of nucleus basalis magnocellularis stimulation on a socially transmitted food preference and c-Fos expression
Authors: Boix-Trelis Núria , Vale-Martínez Anna , Guillazo-Blanch Gemma , Costa-Miserachs David , Martí-Nicolovius Margarita
Published: November 2006

Experiment 1 examined the effects of electrical stimulation of nucleus basalis magnocellularis (NBM) on a relational odor-association task—the social transmission of food preference (STFP). Rats were stimulated unilaterally in the NBM for 20 min (100 μA, 1 Hz) immediately before the social training. They were tested on their ability to remember preference for the trained food either immediately or following a 24-h delay. Stimulation of NBM improved retention regardless of delay, and additional behavioral measures (social interaction, motor activity, or exploration) did not account for such effects. Experiment 2 investigated brain regions activated after NBM electrical stimulation by examining the induction of c-Fos. This treatment led to bilateral increased c-Fos expression in prefrontal regions, such as orbitofrontal, prelimbic, and infralimbic cortices, and some hippocampal subregions (dorsal CA and ventral dentate gyrus). In contrast, no differences between groups in c-Fos expression were found in basolateral amygdala, dorsal dentate gyrus, ventral CA, or ventral subiculum. Present findings indicate that pretraining NBM electrical stimulation facilitates the acquisition of STFP, supporting a role of NBM in the early stages of memory formation, and suggest that the treatment might cause such effects by inducing neural changes, related to transcription factors such as c-Fos, in the prefrontal cortex or the hippocampal formation.
Spatial and nonspatial escape strategies in the Barnes maze
Authors: Harrison Fiona E. , Reiserer Randall S. , Tomarken Andrew J. , McDonald Michael P.
Published: November 2006

The Barnes maze is a spatial memory task that requires subjects to learn the position of a hole that can be used to escape the brightly lit, open surface of the maze. Two experiments assessed the relative importance of spatial (extra-maze) versus proximal visible cues in solving the maze. In Experiment 1, four groups of mice were trained either with or without a discrete visible cue marking the location of the escape hole, which was either in a fixed or variable location across trials. In Experiment 2, all mice were trained with the discrete visible cue marking the target hole location. Two groups were identical to the cued-target groups from Experiment 1, with either fixed or variable escape locations. For these mice, the discrete cue either was the sole predictor of the target location or was perfectly confounded with the spatial extra-maze cues. The third group also used a cued variable target, but a curtain was drawn around the maze to prevent the use of spatial cues to guide navigation. Probe trials with all escape holes blocked were conducted to dissociate the use of spatial and discrete proximal cues. We conclude that the Barnes maze can be solved efficiently using spatial, visual cue, or serial-search strategies. However, mice showed a strong preference for using the distal room cues, even when a discrete visible cue clearly marked the escape location. Importantly, these data show that the cued-target control version of the Barnes maze as typically conducted does not dissociate spatial from nonspatial abilities.
GIGANTEAActs in Blue Light Signaling and Has Biochemically Separable Roles in Circadian Clock and Flowering Time Regulation
Authors: Martin-Tryon Ellen L. , Kreps Joel A. , Harmer Stacey L.
Published: November 2006

Circadian clocks are widespread in nature. In higher plants, they confer a selective advantage, providing information regarding not only time of day but also time of year. Forward genetic screens in Arabidopsis (Arabidopsis thaliana) have led to the identification of many clock components, but the functions of most of these genes remain obscure. To identify both new constituents of the circadian clock and new alleles of known clock-associated genes, we performed a mutant screen. Using a clock-regulated luciferase reporter, we isolated new alleles of ZEITLUPE, LATE ELONGATED HYPOCOTYL, and GIGANTEA (GI). GI has previously been reported to function in red light signaling, central clock function, and flowering time regulation. Characterization of this and other GI alleles has helped us to further define GI function in the circadian system. We found that GI acts in photomorphogenic and circadian blue light signaling pathways and is differentially required for clock function in constant red versus blue light. Gene expression and epistasis analyses show that TIMING OF CHLOROPHYLL A/B BINDING PROTEIN1 (TOC1) expression is not solely dependent upon GI and that GI expression is only indirectly affected by TOC1, suggesting that GI acts both in series with and in parallel to TOC1 within the central circadian oscillator. Finally, we found that the GI-dependent promotion of CONSTANS expression and flowering is intact in a gi mutant with altered circadian regulation. Thus GI function in the regulation of a clock output can be biochemically separated from its role within the circadian clock.
Ectopic Expression of aBasic Helix-Loop-HelixGene Transactivates Parallel Pathways of Proanthocyanidin Biosynthesis. Structure, Expression Analysis, and Genetic Control ofLeucoanthocyanidin 4-ReductaseandAnthocyanidin ReductaseGenes inLotus corniculatus
Authors: Paolocci Francesco , Robbins Mark P. , Madeo Laura , Arcioni Sergio , Martens Stefan , Damiani Francesco
Published: November 2006

Proanthocyanidins (PAs) are plant secondary metabolites and are composed primarily of catechin and epicatechin units in higher plant species. Due to the ability of PAs to bind reversibly with plant proteins to improve digestion and reduce bloat, engineering this pathway in leaves is a major goal for forage breeders. Here, we report the cloning and expression analysis of anthocyanidin reductase (ANR) and leucoanthocyanidin 4-reductase (LAR), two genes encoding enzymes committed to epicatechin and catechin biosynthesis, respectively, in Lotus corniculatus. We show the presence of two LAR gene families (LAR1 and LAR2) and that the steady-state levels of ANR and LAR1 genes correlate with the levels of PAs in leaves of wild-type and transgenic plants. Interestingly, ANR and LAR1, but not LAR2, genes produced active proteins following heterologous expression in Escherichia coli and are affected by the same basic helix-loop-helix transcription factor that promotes PA accumulation in cells of palisade and spongy mesophyll. This study provides direct evidence that the same subclass of transcription factors can mediate the expression of the structural genes of both branches of PA biosynthesis.
Toward More Effective Stakeholder Dialogue: Applying Theories of Negotiation to Policy and Program Evaluation1
Authors: Campbell Bernadette , Mark Melvin M.
Published: November 2006

Borrowing from the negotiation literature, we tested 2 factors that might improve stakeholder dialogue in program and policy evaluation. Undergraduate stakeholders (61 pairs) engaged in dialogue about their universities' alcohol policies. Pairs were randomly assigned to levels of accountability audience and dialogue structure. The audience for the videotaped dialogue was described as holding either (a) views about the policy similar to the participant's, consistent across audience members (homogeneous), or (b) mixed views, on both sides of the issue (heterogeneous). Pairs approached the dialogue with either (a) problem‐solving goals or (b) no particular strategy. Dyads accountable to a heterogeneous audience and given problem‐solving instructions exhibited the most effective dialogue. Accountability to a heterogeneous audience facilitated satisfaction with and optimism about dialogue. Accountability to homogeneous audiences and adopting no particular strategy yielded the least positive perceptions of dialogue. Implications for stakeholder dialogue, and for the role of social psychology in evaluation are discussed.
Blowfly succession from possum (Trichosurus vulpecula) carrion in a sheep‐farming zone
Authors: LANG M. D. , ALLEN G. R. , HORTON B. J.
Published: November 2006

Abstract The significance of brushtail possum, Trichosurus vulpecula Kerr (Diprotodontia: Phalangeridae) carcasses to the succession and production of Diptera species and its relevance to fly strike management in Tasmania, Australia was examined. Calliphora stygia (Fabricius), Lucilia sericata (Meigen) and Calliphora vicina Robineau–Desvoidy (Diptera: Calliphoridae) were found to be the most abundant and Lucilia cuprina (Wiedemann) (Diptera: Calliphoridae) always the least abundant (< 1%) of the putative primary fly invading species to emerge. Carcasses that were left for up to 15 days in the field before being exposed to flies for 2 days also acted as breeding sites for large numbers of all primary fly species, with the exception of L. cuprina. Ordination analysis revealed no relationship between possum carcasses according to their length of exposure but did show significant negative associations between the number of putative secondary invaders (Chrysomya rufifacies (Macquart) (Diptera: Calliphoridae), Chrysomya varipes (Macquart) (Diptera: Calliphoridae) and putative tertiary flies (Hydrotaea rostrata Robineau–Desvoidy (Diptera: Muscidae)) to the number of C. vicina or C. stygia to emerge. There was enormous variability in the numbers of secondary/tertiary fly species to emerge from carcasses (0–11 450) that negatively correlated with the proportion of all flies to emerge that were primary, and with the mean size of adult L. sericata. Although carcass temperatures, especially those with a large larval population, were elevated, this did not appear to result in significant pre‐adult fly mortality. The most important primary fly strike species L. cuprina was only found in insignificant numbers, whereas three other members of the fly strike fauna C. stygia, L. sericata and Ch. rufifacies did use possum carrion as an important breeding resource, but left implications for fly strike management inconclusive.
Comparative phylogeography of unglaciated eastern North America
Authors: SOLTIS DOUGLAS E. , MORRIS ASHLEY B. , McLACHLAN JASON S. , MANOS PAUL S. , SOLTIS PAMELA S.
Published: November 2006

Regional phylogeographical studies involving co‐distributed animal and plant species have been conducted for several areas, most notably for Europe and the Pacific Northwest of North America. Until recently, phylogeographical studies in unglaciated eastern North America have been largely limited to animals. As more studies emerge for diverse lineages (including plants), it seems timely to assess the phylogeography across this region: (i) comparing and contrasting the patterns seen in plants and animals; (ii) assessing the extent of pseudocongruence; and (iii) discussing the potential applications of regional phylogeography to issues in ecology, such as response to climatic change. Unglaciated eastern North America is a large, geologically and topographically complex area with the species examined having diverse distributions. Nonetheless, some recurrent patterns emerge: (i) maritime — Atlantic vs. Gulf Coast; (ii) Apalachicola River discontinuity; (iii) Tombigbee River discontinuity; (iv) the Appalachian Mountain discontinuity; (v) the Mississippi River discontinuity; and (vi) the Apalachicola River and Mississippi River discontinuities. Although initially documented in animals, most of these patterns are also apparent in plants, providing support for phylogeographical generalizations. These patterns may generally be attributable to isolation and differentiation during Pleistocene glaciation, but in some cases may be older (Pliocene). Molecular studies sometimes agree with longstanding hypotheses of glacial refugia, but also suggest additional possible refugia, such as the southern Appalachian Mountains and areas close to the Laurentide Ice Sheet. Many species exhibit distinct patterns that reflect the unique, rather than the shared, aspects of species’ phylogeographical histories. Furthermore, similar modern phylogeographical patterns can result from different underlying causal factors operating at different times (i.e. pseudocongruence). One underemphasized component of pseudocongruence may result from the efforts of researchers to categorize patterns visually — similar patterns may, in fact, not fully coincide, and inferring agreement may obscure the actual patterns and lead to erroneous conclusions. Our modelling analyses indicate no clear spatial patterning and support the hypothesis that phylogeographical structure in diverse temperate taxa is complex and was not shaped by just a few barriers.
A phylogeographical study of theTurnip mosaic viruspopulation in East Asia reveals an ‘emergent’ lineage in Japan
Authors: TOMITAKA YASUHIRO , OHSHIMA KAZUSATO
Published: November 2006

The genetic structure of populations ofTurnip mosaic virus(TuMV) in East Asia was assessed by making host range and gene sequence comparisons of 118 isolates utilizing a population genetic approach. Most, but not all, isolates collected fromBrassicaplants in China infected onlyBrassicaplants, whereas those from Japan infected bothBrassicaandRaphanus(BR) plants. Analyses of the positions of recombination sites in five regions of the genomes (one third of the full sequence) of the many recombinant isolates were fully congruent with the results of phylogenetic analysis, and at least one recombination type pattern was shared between Chinese and Japanese populations. One lineage of nonrecombinant isolates from the basal‐BR lineage was found in 2000 in Kyushu, Japan but none in China, and have since been found over the whole island. The sudden expansion of this basal‐BR population was strongly supported by calculations showing the deviations from the neutral equilibrium model for the individual geographical lineages with overall lack of nucleotide diversity, and by analysis of mismatch distribution. Our study shows that the recent Chinese and Japanese TuMV isolates are part of the same population but are discrete lineages.
Population genetic structuring of the king weakfish, Macrodon ancylodon (Sciaenidae), in Atlantic coastal waters of South America: deep genetic divergence without morphological change
Authors: SANTOS SIMÔNI , HRBEK TOMAS , FARIAS IZENI P. , SCHNEIDER HORACIO , SAMPAIO IRACILDA
Published: November 2006

Phylogeographic patterns in Macrodon ancylodon sampled from 12 locations across all its range were investigated using mitochondrial DNA cytochrome b sequences, and analysed together with patterns of morphometric differentiation. Populations of the North Brazil and the Brazil currents, with warmer waters, form a clade (tropical clade) separated by 23 fixed mutations from the populations that inhabit regions of colder waters influenced by the Brazil and Malvinas currents (subtropical clade). No gene flow exists between the tropical and subtropical clades, and most likely also between the two groups of the tropical clade. Distribution of these clades and groups is correlated with flow of currents and their temperatures, and is facilitated by larval retention and low adult migration. Despite differentiation at the molecular level, fishes analysed from all these current‐influenced regions are morphometrically homogeneous. Throughout its range M. ancylodon inhabits the same, or very similar niche; thus, stabilizing selection probably promotes the retention of highly conserved morphology despite deep genetic divergence at the mitochondrial DNA cytochrome b.
Ecological factors influence population genetic structure of European grey wolves
Authors: PILOT MALGORZATA , JEDRZEJEWSKI WLODZIMIERZ , BRANICKI WOJCIECH , SIDOROVICH VADIM E. , JEDRZEJEWSKA BOGUMILA , STACHURA KRYSTYNA , FUNK STEPHAN M.
Published: November 2006

Although the mechanisms controlling gene flow among populations are particularly important for evolutionary processes, they are still poorly understood, especially in the case of large carnivoran mammals with extensive continuous distributions. We studied the question of factors affecting population genetic structure in the grey wolf,Canis lupus, one of the most mobile terrestrial carnivores. We analysed variability in mitochondrial DNA and 14 microsatellite loci for a sample of 643 individuals from 59 localities representing most of the continuous wolf range in Eastern Europe. We tested an array of geographical, historical and ecological factors to check whether they may explain genetic differentiation among local wolf populations. We showed that wolf populations in Eastern Europe displayed nonrandom spatial genetic structure in the absence of obvious physical barriers to movement. Neither topographic barriers nor past fragmentation could explain spatial genetic structure. However, we found that the genetic differentiation among local populations was correlated with climate, habitat types, and wolf diet composition. This result shows that ecological processes may strongly influence the amount of gene flow among populations. We suggest natal‐habitat‐biased dispersal as an underlying mechanism linking population ecology with population genetic structure.
Incidence and etiology of acute non‐malignant upper gastrointestinal bleeding in northern Greece
Authors: Tsesmeli Niki E , Kotsaftis Panagiotis S , Savopoulos Christos G , Hatzitolios Apostolos I , Kaiafa Georgia D , Kounanis Andreas D , Karamitsos Dimitrios T
Published: November 2006

Aim:  To evaluate the incidence and etiology of acute non‐malignant upper gastrointestinal bleeding (ANMUGIB) in northern Greece due to increased use of non‐steroidal anti‐inflammatory drugs (NSAIDs), including low‐dose aspirin (L‐A), exposure and geographical variability of Helicobacter pylori (Hp) seroprevalence.

Methods:  A retrospective study of 110 patients admitted for hematemesis or melena during a 6‐month period. All patients had undergone a gastrointestinal (GI) endoscopy during hospitalization. The presence of Hp was identified by biopsies and a 13C‐urea breath test in the case of Hp(–) biopsy bleeding peptic ulcer (BPU). The activity of ANMUGIB was assessed according to Forrest's classification. Statistical analysis was made by the χ2‐test and Yates' correction.

Results:  Most patients were in the two medium age groups with no significant difference between them (P < 0.001). NSAID or L‐A (100 mg/day) use was reported in 42.73% of patients in a ratio 1:1 (P > 0.1) and Hp infection was found in 29.09% of patients. BPU, with approximately two‐thirds in the bulb, erosions and varices were the most frequent sources. Hp infection was found in 60.65% of BPU, 65.57% were related to NSAIDs or L‐A and 8.19% were non‐Hp non‐NSAID/L‐A BPU. Flat spots were most commonly found with a significant difference (P < 0.001) to other stigmata of recent bleeding, except for clean base.

Conclusions:  In northern Greece, persons aged over 40 years are prone to ANMUGIB with a non‐significant relationship to males. Hp infection and medication use, such as NSAIDS and L‐A, are deeply involved in its etiology. Non‐Hp non‐NSAID/L‐A BPU are a small proportion. ANMUGIB seems to have a generally good prognosis.
Recurrent mucinous cystadenoma in a 20‐year‐old woman: Was hysterectomy inevitable?
Authors: Baksu Basak , Akyol Atıf , Davas Inci , Yazgan Ali , Ozgul Jale , Tanık Canan
Published: November 2006

A recurrence of ovarian mucinous cysts is very rare. Over a period of 21 months, a 20‐year‐old patient had three laparotomies resulting initially in the removal of one ovary with a mucinous cystadenoma and two cystectomies for the same pathology, but ultimately leading to hysterectomy and salphingo‐oopherectomy. Because mucinous tumors are usually benign and most of the time multilocular, management of young patients is challenging, especially in the case of recurrence. Follow‐up of these patients is very important and transvaginal ultrasound seems to be currently the most effective diagnostic tool for the follow‐up of young patients treated with cystectomy for benign mucinous cystadenomas.
Three‐cycle fentanyl patch system significantly improves pain control in gynecologic cancer
Authors: Kanamori Chiharu , Kanamori Takanobu , Hayashi Michiharu , Yorioka Hirokazu , Kanzaki Haruhide
Published: November 2006

Pain affects many cancer patients, and in advanced stages of the disease it can significantly affect the quality of their lives. Morphine has long been the ‘gold standard’ for the treatment of cancer pain. However, its side‐effects, particularly sedation and cognitive impairment at high doses, have encouraged the use of ‘opioid rotation’. The transdermal fentanyl patch has advantages over oral morphine, with reduced side‐effects and increased convenience in practical usage. The side‐effects were reduced in patients who changed to the fentanyl patch, but rescue analgesia was often needed because of the decrease of fentanyl release from the patch, especially on the patch replacement day. We have developed a three‐cycle fentanyl patch system that provided an appropriate pain control, and this system should be considered for pain relief in cancer patients.
Ovarian sclerosing stromal tumor presenting as Meigs’ syndrome with elevated CA‐125
Authors: Jung Nan Hee , Kim Tak , Kim Hai Joong , Lee Kyu Wan , Lee Nak Woo , Lee Eung Seok
Published: November 2006

Meigs’ syndrome caused by sclerosing stromal tumor is extremely rare and only two cases have been reported to date. An elevated serum level of CA‐125 is also unusual and it has been thought that it is the consequence of physical irritation and inflammation. In this report, we present the case of a 50‐year‐old postmenopausal woman with a sclerosing stromal tumor presenting with Meigs’ syndrome and an elevated CA‐125 level (1476.8 IU/mL). This case highlights the difficulty in discerning the diagnosis of Meigs’ syndrome from that of an ovarian malignancy and it should be considered in the differential diagnosis in postmenopausal patients with pelvic mass, ascites, pleural effusions and elevated serum CA‐125.
Comparisons of maternal and perinatal outcomes in Taiwanese women with complete and partial HELLP syndrome and women with severe pre‐eclampsia without HELLP
Authors: Liu Ching‐Ming , Chang Shuenn‐Dyh , Cheng Po‐Jen , Chao An‐Shine
Published: November 2006

Aim:  To analyze the variations between maternal complications and perinatal outcome among women with complete hemolysis, elevated liver enzyme levels, and low platelet count (HELLP) syndrome, partial HELLP syndrome, and women with severe pre‐eclampsia and normal laboratory tests. We also examine the effect of corticosteroid therapy for treatment of HELLP.

Methods:  In this retrospective study, six patients with complete HELLP syndrome and 46 with partial HELLP syndrome, were compared and contrasted with 212 patients with severe pre‐eclampsia but without HELLP syndrome.

Results:  In Protocol 1, multiple organ dysfunction syndrome (MODS) was the strongest morbidity factor associated with patients among complete HELLP, partial HELLP, and severe pre‐eclampsia. After post‐hoc analysis, disseminated intravascular coagulation (DIC) was the significant outcome variable between complete and partial HELLP. In Protocol 2, after adjustment, we found that MODS (adjusted OR, 15.2, 95% CI, 6.18–35.53; P < 0.001); Apgar score less than 5 at 1 minute (adjusted OR, 2.17, 95% CI, 0.94–5.01; P = 0.069) and DIC (adjusted OR, 9.51, 95% CI, 1.68–53.7, P = 0.011) remained significantly associated with HELLP syndrome. There was a favorable outcome found in the complete HELLP group. Neither the dexamethasone group nor the aggressive therapy group could benefit from the treatment protocol.

Conclusion:  The different categories of HELLP syndrome, the protocol 1 and protocol 2 have been noted as differential effects on pregnancy outcome. MODS and DIC would be two significant outcome variables and corticosteroid therapy may not benefit HELLP patients.
Administration of myostatin does not alter fat mass in adult mice
Authors: Stolz L. E. , Li D. , Qadri A. , Jalenak M. , Klaman L. D. , Tobin J. F.
Published: November 2006

Aim:  Myostatin, a member of the TGF‐beta superfamily, is produced by skeletal muscle and acts as a negative regulator of muscle mass. It has also been suggested that low‐dose administration of myostatin (2 μg/day) in rodents can reduce fat mass without altering muscle mass. In the current study, we attempted to further explore the effects of myostatin on adipocytes and its potential to reduce fat mass, since myostatin administration could potentially be a useful strategy to treat obesity and its complications in humans.

Methods:  Purified myostatin protein was examined for its effects on adipogenesis and lipolysis in differentiated 3T3‐L1 adipocytes as well as for effects on fat mass in wild‐type, myostatin null and obese mice.

Results:  While myostatin was capable of inhibiting adipogenesis in 3T3‐L1 cells, it did not alter lipolysis in fully differentiated adipocytes. Importantly, pharmacological administration of myostatin over a range of doses (2–120 μg/day) did not affect fat mass in wild‐type or genetically obese (ob/ob, db/db) mice, although muscle mass was significantly reduced at the highest myostatin dose.

Conclusions:  Our results suggest that myostatin does not reduce adipose stores in adult animals. Contrary to prior indications, pharmacological administration of myostatin does not appear to be an effective strategy to treat obesity in vivo.
Reification and the Dictatorship of the Water Meter
Authors: Loftus Alex
Published: November 2006

In this paper, I seek to gain an understanding of the power that water meters are able to acquire in regulating the daily rhythms of life in the South African city of Durban. In doing so, I put Georg Lukács's writings on reification to work. Lukács's theorisation of the phenomenon of reification captures the twin processes of encroaching formal rationalisation and commodity fetishism. Charting the history of the introduction of water meters and the rise in power of associated infrastructures, I seek to put a historical geographical materialist imagination to work. Thus, I develop a relational ontology of the urban waterscape before seeking to identify lines of struggle that might challenge the dictatorship of the water meter and move towards radically democratic technologies for a more equitable distribution of water.
Moving Toward a Grand Theory of Development: In Memory of Esther Thelen
Authors: Spencer John P. , Clearfield Melissa , Corbetta Daniela , Ulrich Beverly , Buchanan Patricia , Schöner Gregor
Published: November 2006

This paper is in memory of Esther Thelen, who passed away while President of the Society for Research in Child Development. A survey of Esther Thelen's career reveals a trajectory from early work on simple movements like stepping, to the study of goal‐directed reaching, to work on the embodiment of cognition, and, ultimately, to a grand theory of development—dynamic systems theory. Four central concepts emerged during her career: (1) a new emphasis on time; (2) the proposal that behavior is softly assembled from the interaction of multiple subsystems; (3) the embodiment of perception, action, and cognition; and (4) a new respect for individuality. Esther Thelen communicated these ideas to scientists and practitioners alike, so the ultimate benefactors of her work were children.