bluuebunny/crossref_metadata_2025 huggingface dataset:
Refractive indices and linear electro-optic properties of (1−x)Pb(Mg1∕3Nb2∕3)O3−xPbTiO3 single crystals
Authors: Wan Xinming , Luo Haosu , Zhao Xiangyong , Wang D. Y. , Chan H. L. W. , Choy C. L.
Published: December 2004

The refractive indices and linear electro-optic (EO) properties of (1−x)Pb(Mg1∕3Nb2∕3)O3−xPbTiO3 single crystals were investigated over a broad composition range. The orientation and temperature effect on the EO coefficients were also examined. Large EO coefficients rc were observed near the morphotropic phase boundary (MPB). More importantly, rc of the single crystals on the tetragonal side of the MPB were nearly invariant in the experimental temperature range of 20–80°C. The calculated half-wave voltage Vπ was much lower than that of widely used EO single crystal LiNbO3. These excellent EO properties as well as being able to produce large-size and high-quality single crystals make this kind of single crystal very promising for EO modulation applications. The observed EO properties were also analyzed with the spontaneous polarization and dielectric constants.
Tunability and relaxor properties of ferroelectric barium stannate titanate ceramics
Authors: Lu S. G. , Xu Z. K. , Chen Haydn
Published: December 2004

Barium stannate titanate [Ba(SnxTi1−x)O3, x=0.1, 0.2, 0.3, and 0.4] ceramics were prepared using a conventional solid-state reaction process. Their dielectric properties were measured under direct current bias fields ranging from 0to2.5kV∕cm. A transformation from normal to relaxor ferroelectrics was observed when x⩾0.3. Broken long-range order or “dirty” ferroelectric domains and nanodomains were observed in Ba(Sn0.1Ti0.9)O3 and Ba(Sn0.4Ti0.6)O3 by transmission electron microscopy, respectively. Voltage driven tunability was found to decrease with increasing Sn content. The change from normal ferroelectric into relaxor ferroelectric had a negative impact on the tunability value of the materials.
High-power single-mode vertical-cavity surface-emitting lasers with triangular holey structure
Authors: Furukawa Akio , Sasaki Satoshi , Hoshi Mitsunari , Matsuzono Atsushi , Moritoh Kosuke , Baba Toshihiko
Published: December 2004

By the two-dimensional triangular holey structure, a high-power stable single-mode operation was demonstrated in oxide confined 850nm vertical-cavity surface-emitting lasers. For two types of hole alignments, the lasing operation was observed with different near field patterns, i.e., a single spot pattern and a floral pattern. The former showed an output power of 2mW with a high side-mode suppression ratio (SMSR) of 45–50dB, which is explained by the selective loss mechanism. The latter showed a high power of 7mW with a SMSR of 40dB. The observed lasing spectrum and far field pattern indicate that it is a deformed fundamental mode whose bright spots extending over the device are in-phase oscillating. This device structure will be effective for the enhancement of single-mode power in devices with any material system.
Regulation of flagellar dynein activity by a central pair kinesin
Authors: Yokoyama Ruth , O'Toole Eileen , Ghosh Sudipto , Mitchell David R.
Published: December 2004

The motility of cilia and flagella is powered by dynein ATPases associated with outer doublet microtubules. However, a flagellar kinesin-like protein that may function as a motor associates with the central pair complex. We determined that
Chlamydomonas reinhardtii
central pair kinesin Klp1 is a phosphoprotein and, like conventional kinesins, binds to microtubules
in vitro
in the presence of adenosine 5′-[β,γ-imido]triphosphate, but not ATP. To characterize the function of Klp1, we generated RNA interference expression constructs that reduce
in vivo
flagellar Klp1 levels. Klp1 knockdown cells have flagella that either beat very slowly or are paralyzed. EM image averages show disruption of two structures associated with the C2 central pair microtubule, C2b and C2c. Greatest density is lost from part of projection C2c, which is in a position to interact with doublet-associated radial spokes. Klp1 therefore retains properties of a motor protein and is essential for normal flagellar motility. We hypothesize that Klp1 acts as a conformational switch to signal spoke-dependent control of dynein activity.
Familiar route loyalty implies visual pilotage in the homing pigeon
Authors: Biro Dora , Meade Jessica , Guilford Tim
Published: December 2004

Wide-ranging animals, such as birds, regularly traverse large areas of the landscape efficiently in the course of their local movement patterns, which raises fundamental questions about the cognitive mechanisms involved. By using precision global-positioning-system loggers, we show that homing pigeons (
Columba livia
) not only come to rely on highly stereotyped yet surprisingly inefficient routes within the local area but are attracted directly back to their individually preferred routes even when released from novel sites off-route. This precise route loyalty demonstrates a reliance on familiar landmarks throughout the flight, which was unexpected under current models of avian navigation. We discuss how visual landmarks may be encoded as waypoints within familiar route maps.
Highly conserved upstream sequences for transcription factor genes and implications for the regulatory network
Authors: Iwama Hisakazu , Gojobori Takashi
Published: December 2004

Identifying evolutionarily conserved blocks in orthologous genomic sequences is an effective way to detect regulatory elements. In this study, with the aim of elucidating the architecture of the regulatory network, we systematically estimated the degree of conservation of the upstream sequences of 3,750 human–mouse orthologue pairs along 8-kb stretches. We found that the genes with high upstream conservation are predominantly transcription factor (TF) genes. In particular, developmental process-related TF genes showed significantly higher conservation of the upstream sequences than other TF genes. Such extreme upstream conservation of the developmental process-related TF genes suggests that the regulatory networks involved with developmental processes have been evolutionarily well conserved in both human and mouse lineages.
Genetic networks with canalyzing Boolean rules are always stable
Authors: Kauffman Stuart , Peterson Carsten , Samuelsson Björn , Troein Carl
Published: December 2004

We determine stability and attractor properties of random Boolean genetic network models with canalyzing rules for a variety of architectures. For all power law, exponential, and flat in-degree distributions, we find that the networks are dynamically stable. Furthermore, for architectures with few inputs per node, the dynamics of the networks is close to critical. In addition, the fraction of genes that are active decreases with the number of inputs per node. These results are based upon investigating ensembles of networks using analytical methods. Also, for different in-degree distributions, the numbers of fixed points and cycles are calculated, with results intuitively consistent with stability analysis; fewer inputs per node implies more cycles, and vice versa. There are hints that genetic networks acquire broader degree distributions with evolution, and hence our results indicate that for single cells, the dynamics should become more stable with evolution. However, such an effect is very likely compensated for by multicellular dynamics, because one expects less stability when interactions among cells are included. We verify this by simulations of a simple model for interactions among cells.
Inorganic polyphosphate in
Bacillus cereus
: Motility, biofilm formation, and sporulation
Authors: Shi Xiaobing , Rao Narayana N. , Kornberg Arthur
Published: December 2004

Chains of inorganic polyphosphate (poly-P) with hundreds of P
i
residues linked by phosphoanhydride bonds, as in ATP, are found in every bacterial, fungal, plant, and animal cell, in which they perform various functions. In the spore-forming
Bacillus cereus
, we have identified three principal enzymes and genes involved in the metabolism of poly-P, namely, (
i
) poly-P kinase (PPK), which synthesizes poly-P reversibly from ATP, (
ii
) exopolyphosphatase (PPX), which hydrolyzes poly-P to P
i
, and (
iii
) poly-P/AMP phosphotransferase (PAP), which uses poly-P as a donor to convert AMP to ADP, reversibly. In the null mutant of
ppk
, poly-P levels are reduced to <5% of the WT; in the
ppx
mutant, the PPK activity is elevated 10-fold, and the accumulation of poly-P is elevated ≈1,000-fold. All of the null mutants of
ppk
,
ppx
, and
pap
showed defects in motility and biofilm formation, but sporulation efficiency was impaired only in the
ppx
mutant. These enzymes and genes in
B. cereus
are nearly identical to those in the very closely related pathogen
Bacillus anthracis
, and, thus, they may provide attractive targets for the treatment of anthrax.
Structural basis for peptidoglycan binding by peptidoglycan recognition proteins
Authors: Guan Rongjin , Roychowdhury Abhijit , Ember Brian , Kumar Sanjay , Boons Geert-Jan , Mariuzza Roy A.
Published: December 2004

Peptidoglycan (PGN) recognition proteins (PGRPs) are pattern-recognition receptors of the innate immune system that bind and, in some cases, hydrolyze bacterial PGNs. We determined the crystal structure, at 2.30-Å resolution, of the C-terminal PGN-binding domain of human PGRP-Iα in complex with a muramyl tripeptide representing the core of lysine-type PGNs from Gram-positive bacteria. The peptide stem of the ligand is buried at the deep end of a long binding groove, with
N
-acetylmuramic acid situated in the middle of the groove, whose shallow end can accommodate a linked
N
-acetylglucosamine. Although most interactions are with the peptide, the glycan moiety also seems to be essential for specific recognition by PGRPs. Conservation of key PGN-contacting residues shows that all PGRPs employ this basic PGN-binding mode. The structure pinpoints variable residues that likely mediate discrimination between lysine- and diaminopimelic acid-type PGNs. We also propose a mechanism for PGN hydrolysis by Zn
2+
-containing PGRPs.
Human cytomegalovirus immediate-early 1 protein facilitates viral replication by antagonizing histone deacetylation
Authors: Nevels Michael , Paulus Christina , Shenk Thomas
Published: December 2004

The human cytomegalovirus 72-kDa immediate-early (IE)1 and 86-kDa IE2 proteins are expressed at the start of infection, and they are believed to exert much of their function through promiscuous transcriptional activation of viral and cellular gene expression. Here, we show that the impaired growth of an IE1-deficient mutant virus in human fibroblasts is efficiently rescued by histone deacetylase (HDAC) inhibitors of three distinct chemical classes. In the absence of IE1 expression, the viral major IE and UL44 early promoters exhibited decreased
de novo
acetylation of histone H4 during the early phase of infection, and the hypoacetylation correlated with reduced transcription and accumulation of the respective gene products. Consistent with these findings, IE1 interacts specifically with HDAC3 within infected cells. We also demonstrate an interaction between IE2 and HDAC3. We propose that the ability to modify chromatin is fundamental to transcriptional activation by IE1 and, likely, IE2 as well.
Effects of Schistosoma mansoni infection on inorganic elements in the snail Biomphalaria glabrata
Authors: Ong J.H.L. , Chejlava M. , Fried B. , Koehnlein K.M. , Bosavage G.L. , Sherma J.
Published: December 2004

Inductively coupled plasma atomic emission spectrometry (ICP-AES) was used to study element ions in whole bodies of uninfected Biomphalaria glabrata snails and those experimentally infected with larval Schistosoma mansoni trematodes. Infected snails were analysed 8 weeks post-infection. Cohort snails that were left uninfected were analysed at the same time as the infected snails. Sixteen elements (aluminum, boron, barium, calcium, cadmium, copper, iron, potassium, magnesium, manganese, sodium, nickel, lead, selenium, tin and zinc) were found to be present in infected and uninfected whole bodies at concentrations above the detection limit of the ICP-AES analysis. Of these, calcium, cadmium, manganese and sodium were present in significantly higher amounts (Student's t-test, P<0.05) in whole infected versus whole uninfected snails. Variations in the present results compared with other studies reflect intrinsic differences in the larval trematode–snail systems used.
Prevalence of Libyostrongylus douglassii in commercially reared ostriches in the highveld region of Zimbabwe
Authors: Mukaratirwa S. , Cindzi Z.M. , Maononga D.B.
Published: December 2004

A total of 435 freshly dropped faecal samples were collected from 11 randomly selected ostrich farms during September and November 2002 to determine the prevalence of Libyostrongylus douglassii (ostrich wireworm) in the highveld region of Zimbabwe. Samples, which consisted of 339 samples from breeder birds and 96 samples from pre-slaughter grower birds were screened for nematode eggs using the modified McMaster technique before being individually cultured in an incubator at 28°C. Cultures were examined for the presence of L. douglassii third stage larvae (L3). Using faecal egg counts, eight of 11 farms (72.7%) were positive for L. douglassii in breeders but no eggs were detected in the growers. The faecal culture method detected wireworm larvae in the breeding stock of all farms that were surveyed (100%) and five of the eight farms (62.5%) which had grower birds. Libyostrongylus douglassii was detected in all farms (100%) based on the faecal culture method. Libyostrongylus douglassii was detected for the first time in 7 of 11 farms (64%) surveyed. Data from questionnaires designed to assess farm management practices showed that four out of seven (57.1%) of the ostrich producers were unaware of the importance of wireworms in ostriches. The farms did not have a regular deworming programme for their birds and no faecal samples were sent routinely to the veterinary laboratory for screening of wireworms. Wireworm infections were not taken into consideration by farmers during buying and selling of birds.
Metacercariae of Clinostomum attenuatum in Ambystoma tigrinum mavortium, Bufo cognatus and Spea multiplicata from west Texas
Authors: Miller D.L. , Bursey C.R. , Gray M.J. , Smith L.M.
Published: December 2004

Tissues from barred tiger salamanders (Ambystoma tigrinum mavortium), Great Plains toads (Bufo cognatus) and New Mexico spadefoots (Spea multiplicata) collected from 16 playa wetlands in Texas during 1999 and 2000 were examined by light microscopy. Digenean cysts were primarily distributed subcutaneously throughout the specimens and occasionally coelomic invasion was noted. The parasites within the cysts were 1.5–2 mm in diameter, with a thin (c. 10 μm wide) eosinophilic-staining tegument, two suckers (oral and ventral), posteriorly located primordial genitalia and paired digestive caeca. These digeneans were identified as the metacercariae of Clinostomum attenuatum. This is the first record of Clinostomum attenuatum in these amphibian species.
Wet-days: are they better indicators of Ascaris infection levels?
Authors: Gunawardena G.S.A. , Karunaweera N.D. , Ismail M.M.
Published: December 2004

Seasonal variation in a particular area may influence the occurrence of helminth infections and determining such fluctuations may help to maximize the beneficial effects of mass treatment. This study determined the seasonal variations in infection levels of Ascaris lumbricoides between March 2000 and June 2001 in two selected low-country plantations. Four hundred and seventy seven persons aged between 2 and 74 years (median 13) participated. Stools were tested using the Kato-Katz method and the prevalence and intensity of infection determined. All persons were treated with a single dose of mebendazole. Monthly follow-ups were undertaken with similar stool examinations and treatment given if found positive. Infection and re-infection rates were calculated each month. Rainfall and temperature were recorded each day. Total rainfall, number of wet-days and mean temperature was calculated for each month. The prevalence of Ascaris infection was 53.4% and 51.0% at Maliboda and Ayr estates respectively. Highest infection and re-infection rates at Maliboda (37.7%, 37.2%) occurred in June and at Ayr (13.3%, 25.9%) in October 2000 respectively. During the study period, the mean rainfall was 28.1 cm (range 7.4–63.9 cm) and mean temperature 27.6°C (range 22.1°–34.4°C). Significant correlations (P<0.05) were found between the re-infection rate and rainfall, temperature and the number of wet-days. Similar correlations were observed with the infection rate and temperature and the number of wet-days. Ascaris infections were found to correlate significantly only with the number of wet-days in a month (P<0.01). Thus, the number of wet-days appears to be a better indicator of Ascaris infections than total rainfall or mean temperature.
Intestinal helminth parasites in flounder Platichthys flesus from the River Thames: an infracommunity analysis
Authors: Guillen-Hernandez S. , Whitfield P.J.
Published: December 2004

An analysis was undertaken of intestinal helminth communities in flounder Platichthys flesus from two sites on the River Thames. A comparison was made between helminth community richness and diversity from these sites at the component and infracommunity levels. At the component community level, a richer and more diverse parasite community was found in flounder from the Tilbury location (marine influence) than that from the Lots Road location (freshwater influence). At the infracommunity level, more parasite species and parasite individuals per host were found at Lots Road and the percentage of similarity values were low at both locations. Helminth species with high prevalence values in the parasite communities of the flounder are the dominant species in any individual fish, harbouring multi-specific infections. The presence of more invertebrate species, which are intermediate hosts in the helminth life cycle in the Thames, fish vagility and the high prevalence and abundance values of Pomphorhynchus laevis in the flounder, may explain the differences between the two locations.
Helminth infracommunities of a population of the Gran Canaria giant lizard Gallotia stehlini
Authors: Martin J.E. , Roca V.
Published: December 2004

A survey of gastro-intestinal helminth communities of Gallotia stehlini (Sauria: Lacertidae) from Gran Canaria island (Canary Archipelago, Spain), was conducted to determine the prevalence, abundance and species diversity of intestinal parasites in these lizards. Pharyngodonid nematodes were the most common intestinal helminths, three species being Gallotia specialists. Helminth infracommunities of G. stehlini were rich and appear to be closer to the interactive end of the continuum isolationist–interactive helminth communities, according to the high values of helminth diversity. It is the first case of a saurian reptile showing this kind of diverse helminth infracommunity, produced by a large size, a wide-ranging plant diet and exposure to helminths with direct life-cycles.
Elliptic equations with BMO coefficients in Lipschitz domains
Authors: Byun Sun-Sig
Published: December 2004

In this paper, we study inhomogeneous Dirichlet problems for elliptic equations in divergence form. Optimal regularity requirements on the coefficients and domains for theW1,p (1>p>∞)W^{1,p}\ (1>p>\infty )estimates are obtained. The principal coefficients are supposed to be in the John-Nirenberg space with small BMO semi-norms. The domain is supposed to have Lipschitz boundary with small Lipschitz constant. These conditions for theW1,pW^{1,p}theory do not just weaken the requirements on the coefficients; they also lead to a more general geometric condition on the domain.
The number of certain integral polynomials and nonrecursive sets of integers, Part 1
Authors: Erdélyi Tamás , Friedman Harvey
Published: December 2004

Given

r
>
2

r > 2

, we establish a good upper bound for the number of multivariate polynomials (with as many variables and with as large degree as we wish) with integer coefficients mapping the “cube” with real coordinates from

[
−
r
,
r
]

[-r,r]

into

[
−
t
,
t
]

[-t,t]

. This directly translates to a nice statement in logic (more specifically recursion theory) with a corresponding phase transition case of 2 being open. We think this situation will be of real interest to logicians. Other related questions are also considered. In most of these problems our main idea is to write the multivariate polynomials as a linear combination of products of scaled Chebyshev polynomials of one variable.
A role for β-actin in RNA polymerase III transcription
Authors: Hu Ping , Wu Si , Hernandez Nouria
Published: December 2004

When transcription from the human U6 snRNA gene is reconstituted with recombinant factors and purified RNA polymerase III (pol III), pol III must be treated with CK2 to be active. We show that highly purified pol III contains associated β-actin, and β-actin localizes to an active U6 promoter in vivo. Pol III immunoprecipitated from IMR90 cells treated with a genotoxic agent lacks associated β-actin and is inactive in the reconstituted assay. Transcription is regained upon treatment of pol III with CK2 and addition of β-actin. This suggests that β-actin associated with pol III is essential for basal pol III transcription.
Zipper-like interaction between proteins in adjacent daughter cells mediates protein localization
Authors: Blaylock Bill , Jiang Xin , Rubio Aileen , Moran Charles P. , Pogliano Kit
Published: December 2004

Protein localization is crucial for cellular morphogenesis and intracellular signal transduction cascades. Here we describe an interaction between two membrane proteins expressed in different cells of the Bacillus subtilis sporangium, the mother cell protein SpoIIIAH and the forespore protein SpoIIQ. We used affinity chromatography, coimmunoprecipitation, and the yeast two-hybrid system to demonstrate that the extracellular domains of these proteins interact, tethering SpoIIIAH to the sporulation septum, and directing its assembly with SpoIIQ into helical arcs and foci around the forespore. We also demonstrate that this interaction can direct proteins made in the same cell to active division sites, as when SpoIIQ is made in the mother cell, it localizes to nascent septa in a SpoIIIAH-dependent manner. Both SpoIIIAH and SpoIIQ are necessary for activation of the second forespore-specific transcription factor (σG) after engulfment, and we propose that the SpoIIIAH-SpoIIQ complex contributes to a morphological checkpoint coupling σG activation to engulfment. In keeping with this hypothesis, SpoIIIAH localization depends on the first step of engulfment, septal thinning. The SpoIIQ-SpoIIIAH complex reaches from the mother cell cytoplasm to the forespore cytoplasm and is ideally positioned to govern the activity of engulfment-dependent transcription factors.
Tissue-specific tumor suppressor activity of retinoblastoma gene homologs p107 and p130
Authors: Dannenberg Jan-Hermen , Schuijff Leontine , Dekker Marleen , van der Valk Martin , Riele Hein te
Published: December 2004

The retinoblastoma gene family consists of three genes: RB, p107, and p130. While loss of pRB causes retinoblastoma in humans and pituitary gland tumors in mice, tumorigenesis in other tissues may be suppressed by p107 and p130. To test this hypothesis, we have generated chimeric mice from embryonic stem cells carrying compound loss-of-function mutations in the Rb gene family. We found that Rb/p107- and Rb/p130-deficient mice were highly cancer prone. We conclude that in a variety of tissues tumor development by loss of pRB is suppressed by its homologs p107 and p130. The redundancy of the retinoblastoma proteins in vivo is reflected by the behavior of Rb-family-defective mouse embryonic fibroblasts in vitro.
Reconstructing large regions of an ancestral mammalian genome in silico
Authors: Blanchette Mathieu , Green Eric D. , Miller Webb , Haussler David
Published: December 2004

It is believed that most modern mammalian lineages arose from a series of rapid speciation events near the Cretaceous-Tertiary boundary. It is shown that such a phylogeny makes the common ancestral genome sequence an ideal target for reconstruction. Simulations suggest that with methods currently available, we can expect to get 98% of the bases correct in reconstructing megabase-scale euchromatic regions of an eutherian ancestral genome from the genomes of ∼20 optimally chosen modern mammals. Using actual genomic sequences from 19 extant mammals, we reconstruct 1.1 Mb of ancient genome sequence around the CFTR locus. Detailed examination suggests the reconstruction is accurate and that it allows us to identify features in modern species, such as remnants of ancient transposon insertions, that were not identified by direct analysis. Tracing the predicted evolutionary history of the bases in the reconstructed region, estimates are made of the amount of DNA turnover due to insertion, deletion, and substitution in the different placental mammalian lineages since the common eutherian ancestor, showing considerable variation between lineages. In coming years, such reconstructions may help in identifying and understanding the genetic features common to eutherian mammals and may shed light on the evolution of human or primate-specific traits.
Contribution of Asian mouse subspeciesMus musculus molossinusto genomic constitution of strain C57BL/6J, as defined by BAC-end sequence–SNP analysis
Authors: Abe Kuniya , Noguchi Hideki , Tagawa Keiko , Yuzuriha Misako , Toyoda Atsushi , Kojima Toshio , Ezawa Kiyoshi , Saitou Naruya , Hattori Masahira , Sakaki Yoshiyuki , Moriwaki Kazuo , Shiroishi Toshihiko
Published: December 2004

MSM/Ms is an inbred strain derived from the Japanese wild mouse,Mus musculus molossinus. It is believed that subspeciesmolossinushas contributed substantially to the genome constitution of common laboratory strains of mice, although the majority of their genome is derived from the west EuropeanM. m. domesticus. Information on themolossinusgenome is thus essential not only for genetic studies involvingmolossinusbut also for characterization of common laboratory strains. Here, we report the construction of an arrayed bacterial artificial chromosome (BAC) library from male MSM/Ms genomic DNA, covering ∼1× genome equivalent. Both ends of 176,256 BAC clone inserts were sequenced, and 62,988 BAC-end sequence (BES) pairs were mapped onto the C57BL/6J genome (NCBI mouse Build 30), covering 2,228,164 kbp or 89% of the total genome. Taking advantage of the BES map data, we established a computer-based clone screening system. Comparison of the MSM/Ms and C57BL/6J sequences revealed 489,200 candidate single nucleotide polymorphisms (SNPs) in 51,137,941 bp sequenced. The overall nucleotide substitution rate was as high as 0.0096. The distribution of SNPs along the C57BL/6J genome was not uniform: The majority of the genome showed a high SNP rate, and only 5.2% of the genome showed an extremely low SNP rate (percentage identity = 0.9997); these sequences are likely derived from themolossinusgenome.
Novel transcription regulatory elements inCaenorhabditis elegansmuscle genes
Authors: GuhaThakurta Debraj , Schriefer Lawrence A. , Waterston Robert H. , Stormo Gary D.
Published: December 2004

We report the identification of three new transcription regulatory elements that are associated with muscle gene expression in the nematodeCaenorhabditis elegans. Starting from a subset of well-characterized nematode muscle genes, we identified conserved DNA motifs in the promoter regions using computational DNA pattern-recognition algorithms. These were considered to be putative muscle transcription regulatory motifs. Using the green-fluorescent protein (GFP) as a reporter, experiments were done to determine the biological activity of these motifs in driving muscle gene expression. Prediction accuracy of muscle expression based on the presence of these three motifs was encouraging; nine of 10 previously uncharacterized genes that were predicted to have muscle expression were shown to be expressed either specifically or selectively in the muscle tissues, whereas only one of the nine that scored low for these motifs expressed in muscle. Knockouts of putative regulatory elements in the promoter of themlc-2 andunc-89 genes show that they significantly contribute to muscle expression and act in a synergistic manner. We find that these DNA motifs are also present in the muscle promoters ofC. briggsae, indicating that they are functionally conserved in the nematodes.
Computing prokaryotic gene ubiquity: Rescuing the core from extinction
Authors: Charlebois Robert L. , Doolittle W. Ford
Published: December 2004

The genomic core concept has found several uses in comparative and evolutionary genomics. Defined as the set of all genes common to (ubiquitous among) all genomes in a phylogenetically coherent group, core size decreases as the number and phylogenetic diversity of the relevant group increases. Here, we focus on methods for defining the size and composition of the core of all genes shared by sequenced genomes of prokaryotes (Bacteria and Archaea). There are few (almost certainly less than 50) genes shared by all of the 147 genomes compared, surely insufficient to conduct all essential functions. Sequencing and annotation errors are responsible for the apparent absence of some genes, while very limited but genuine disappearances (from just one or a few genomes) can account for several others. Core size will continue to decrease as more genome sequences appear, unless the requirement for ubiquity is relaxed. Such relaxation seems consistent with any reasonable biological purpose for seeking a core, but it renders the problem of definition more problematic. We propose an alternative approach (the phylogenetically balanced core), which preserves some of the biological utility of the core concept. Cores, however delimited, preferentially contain informational rather than operational genes; we present a new hypothesis for why this might be so.
EAnnot: A genome annotation tool using experimental evidence
Authors: Ding Li , Sabo Aniko , Berkowicz Nicolas , Meyer Rekha R. , Shotland Yoram , Johnson Mark R. , Pepin Kymberlie H. , Wilson Richard K. , Spieth John
Published: December 2004

The sequence of any genome becomes most useful for biological experimentation when a complete and accurate gene set is available. Gene prediction programs offer an efficient way to generate an automated gene set. Manual annotation, when performed by experienced annotators, is more accurate and complete than automated annotation. However, it is a laborious and expensive process, and by its nature, introduces a degree of variability not found with automated annotation. EAnnot (Electronic Annotation) is a program originally developed for manually annotating the human genome. It combines the latest bioinformatics tools to extract and analyze a wide range of publicly available data in order to achieve fast and reliable automatic gene prediction and annotation. EAnnot builds gene models based on mRNA, EST, and protein alignments to genomic sequence, attaches supporting evidence to the corresponding genes, identifies pseudogenes, and locates poly(A) sites and signals. Here, we compare manual annotation of human chromosome 6 with annotation performed by EAnnot in order to assess the latter's accuracy. EAnnot can readily be applied to manual annotation of other eukaryotic genomes and can be used to rapidly obtain an automated gene set.
Efficiency Wage and the Family: An Explanation for the Impact of the Agricultural Minimum Wage in Morocco
Authors: Azam Jean‐Paul
Published: December 2004

This paper shows two points: (1) there is a statistically significant positive relationship between the real value of the agricultural minimum wage and the level of agricultural output in Morocco, for eight important crops; (ii) the latter may be explained using a theoretical model where the productivity of the laborers depends on their consumption level, and where wage incomes are shared among family members to fund consumption. The Nash equilibrium is then inefficient.

Dieser Artikel zeigt zweierlei: a) Für acht Feldfnichte existiert eine statistisch sigrufikante Beziehung zwischen realem Mindestlohn und Produktionsniveau in der marokkanischen Landwirtschaft; b) Diese Beziehung lasst sich mit einem theoretischen Modell erklären. Darin hangt die Produktivitat der Arbeiter von ihrem Lebensstandard ab. Zur Konsumfinanzierung werden die Lohneinkunfte zwischen den Mitgliedern der Familie aufgeteilt. Das Nash‐Gleichgeèicht ist somit ineffizient.

Cet article montre deux choses: (a) il y a une relation statistiquement significative entre la valeur réelle du salaire minimum agricole et le niveau de la production agricole au Maroc, pour huit cultures importantes; (b) celle‐ci peut s'expliquer au moyen d'un modèle théorique où la productivité des travailleurs dépend de leur niveau de consommation, et où les revenus salariaux sont partagés entre les membres de la famille pour financer la consommation. L'équilibre de Nash est alors inefficient.
Review article: surgical and endoscopic therapy of gastro‐oesophageal reflux disease in Japan
Authors: Katada N.
Published: December 2004

Treatment of gastro‐oesophageal reflux disease (GERD) with lifestyle changes to avoid the conditions that make the symptoms worse and medication to lower the acid content of the refluxed material are generally very effective therapies. However, some individuals do not benefit enough from these approaches, and surgical intervention is warranted. Laparoscopic surgery is the procedure of choice among surgeons performing operations for reflux disease. This surgical technique allows for shorter hospitalization, fewer post surgical complications and less pain than open surgery while maintaining a high success rate. Data from Japan confirms that laparoscopic fundoplication is a safe and effective technique for controlling both typical and atypical symptoms of GERD. Recently, several endoscopic or luminally delivered techniques have been developed as an alternative to laparoscopic surgery. These new surgical options, currently under evaluation in Japan, may offer a valuable alternative to patients who are not responsive to, or who do not wish to persist with lifelong medical therapy for GERD.
Review article: Barrett's oesophagus and carcinoma in Japan
Authors: Hongo M.
Published: December 2004

In Asia, oesophageal diseases, such as Barrett's oesophagus and oesophageal carcinoma, have traditionally been less common than in America and Europe. In recent years, however, the number of reported cases of these conditions in Japan has increased. Two large prospective studies, the Sendai Barrett's Esophagus Study (S‐BEST) and the Far East Study (FEST), on the geographic prevalence of Barrett's oesophagus, have recently investigated the epidemiology of Barrett's oesophagus in Japan. Results from both studies showed that overall prevalence of the condition is lower than in the West: 0.9–1.2% in Japan compared with 1–4% in Europe and 5–12% in USA. Similar to the situation in the West, the condition was shown to be most prevalent in elderly male patients and least prevalent in patients with Helicobacter pylori. Adenocarcinoma of the oesophagus is still rare in this region, although there has been an increase in the annual death rate from 3.7 (1960) to 6.9 (1995) per 100,000 population. Risk factors for oesophageal carcinoma include a strong association with the prevalence of gastro‐oesophageal reflux disease (GERD). With the increasing prevalence of GERD in the Japanese population, continued surveillance of changes in the epidemiology of columnar‐lined oesophagus (a precursor of Barrett's oesophagus), Barrett's oesophagus and adenocarcinoma of the oesophagus is strongly recommended.
Metastatic myoepithelioma of the breast
Authors: Jennens Ross R. , Rosenthal Mark A. , Gonzales Michael
Published: December 2004

Myoepitheliomas are typically benign tumours arising from exocrine glands. There have only been five reports of malignant myoepitheliomas from breast origin previously published in the English literature. This report describes a patient with myoepithelioma arising in the breast which later metastasized despite the primary tumour having benign histological features. Impaired immune function due to end‐stage renal failure and haemodialysis may have contributed to the malignant potential of her tumour. The literature regarding myoepithelial tumours is reviewed. All breast myoepitheliomas should be managed as potentially malignant tumours with appropriate surgical clearance and staging.
Outcome of endoleak following endoluminal abdominal aortic aneurysm repair
Authors: Mandziak Daniel M. , Stanley Brendan M. , Foreman Robert K. , Walsh John A. , Burnett Jim R.
Published: December 2004

Background:  The most important complication of endoluminal abdominal aortic aneurysm repair is endoleak, in which there is persistent blood flow outside the graft but within the aneurysm sac. Depending on endoleak type, there is an ongoing potential for aneurysm expansion or rupture. Conversely, some endoleaks may resolve spontaneously. Absolute indications for interventional management of endoleaks remain elusive due to the heterogeneous nature of leaks and uncertainty in predicting their outcome.

Methods:  A retrospective review was conducted on all endoluminal graft recipients with endoleaks at Repatriation General Hospital over a 3‐year period. Data were collected via a database maintained by the Department of Vascular Surgery, and hospital casenotes.

Results:  Sixty‐six patients underwent endoluminal graft insertion in the study period. Fourteen endoleaks were observed in 11 patients, representing an endoleak rate of 21.2%. There were three type I leaks and 11 type II leaks. One type I leak resolved spontaneously, one resolved immediately following interventional management, and one resolved 6 months after interventional management. Interventional treatment was undertaken in seven cases of type II leak due to increase in aneurysm diameter by 5 mm. Two type II endoleaks resolved spontaneously. Aneurysm diameter increased in two patients following radiographic resolution of their endoleaks. There were no cases of aneurysm rupture.

Conclusions:  Initial observation is a reasonable management option in most cases of type II endoleak, because some will spontaneously resolve during follow up. Those associated with increase in aneurysm size should undergo interventional treatment. Conservative management of type I endoleaks may be undertaken in extreme isolated cases.
Oral iron therapy for anaemia after orthopaedic surgery: randomized clinical trial
Authors: Weatherall Mark , Maling Timothy J.
Published: December 2004

Background:  Oral iron therapy is often used after orthopaedic surgery to improve haemoglobin levels. The aim of the present trial was to determine if administration of oral iron after orthopaedic surgery results in a better improvement of haemoglobin levels than a control treatment.

Methods:  This was a double blind randomized controlled trial at a tertiary referral orthopaedic centre. The participants were patients undergoing elective hip or knee replacement surgery with normal iron and folic acid stores and no history of iron deficiency, and the primary outcome was the haemoglobin level 10 weeks after surgery.

Results:  At 10 weeks the mean ± SD haemoglobin in the iron group was 132.8 ± 13.4 g/L and in the control group it was 128.0 ± 10.6 g/L, a difference of 4.8 g/L with a 95% confidence interval for the difference of −1.2 to 10.7 g/l, P = 0.12.

Conclusions:  Iron taken after elective hip or knee replacement surgery does not result in higher haemoglobin 10 weeks after surgery, or a faster rate of increase in haemoglobin than a control treatment.
Clinicopathological characteristics of signet ring cell carcinoma of the stomach
Authors: Kim Dong Yi , Park Young Kyu , Joo Jae Kyoon , Ryu Seong Yeob , Kim Young Jin , Kim Shin Kon , Lee Jae Hyuk
Published: December 2004

Background:  Signet ring cell (SRC) carcinoma of the stomach is characterized by its poor prognosis and potential to infiltrate the wall of stomach, although survival studies comparing carcinomas with and without SRC features have yielded inconsistent results. This study compared the clinicopathological features and prognosis of patients with SRC carcinoma with those with non‐signet ring cell carcinoma of the stomach (NSRC).

Methods:  We reviewed the records of 2358 patients diagnosed with gastric carcinoma who were treated surgically between January 1980 and December 1999 at the Department of Surgery, Chonnam National University Hospital. There were 204 patients (8.7%) with SRC carcinoma as compared to 2154 with NSRC.

Results:  Significant differences were noted in the mean patient age, mean tumour size, depth of invasion, prevalence of hepatic and regional lymph node metastases, tumour stage, and curability between the patients with SRC histology and NSRC. There were no statistically significant differences in patient gender, location, or peritoneal dissemination between patients with SRC carcinoma and NSRC. SRC carcinoma of the stomach had a higher prevalence of early gastric carcinoma (46.1%) than NSRC (21.7%). The overall 5‐year survival of all the patients with SRC carcinoma was 60.2% as compared with 48.9% for the patients with NSRC (P < 0.01). Using Cox proportional hazards model, lymph node metastasis and curability were significant factors affecting the outcome. Signet ring cell histology itself was not an independent prognostic factor.

Conclusions:  Patients with SRC histology do not have a worse prognosis than patients with other types of gastric carcinoma.
Laparoscopic radical prostatectomy: early safety and efficacy
Authors: Wilson Liam C. , Kennett Katie M. , Gilling Peter J.
Published: December 2004

Background:  To evaluate the initial results of laparoscopic radical prostatectomy at this institution.

Methods:  Between January 2000 and September 2003, 30 patients underwent laparoscopic radical prostatectomy. Peri‐ and postoperative data were accumulated prospectively and maintained in a database. All patients have a minimum of 6 month follow up.

Results:  There were no conversions to open surgery, and there were no re‐operations. Mean operating time was 328 (195−490) min. There was one intraoperative rectal injury which was repaired laparoscopically. Three patients (10%) required blood transfusion. Postoperatively, there were two cases of respiratory depression, one case of haemoptysis and one upper gastrointestinal bleed. Two anastomotic leaks were successfully treated conservatively, one of which was the only readmission to hospital. There was one case of clot retention requiring manual irrigation of the bladder. Mean hospital stay was 2.75 (1−10) days, with six of the last 10 patients being discharged on the first postoperative day. Continence rates at 6 months are 83%. Positive surgical margins occurred in seven patients (23%). At 12 months of follow up, one patient (4.5%) has had biochemical recurrence.

Conclusions:  Our initial results are comparable to, or better than, the initial series in high volume centres. The procedure is feasible in appropriately selected cases in the Australasian environment.
Migraine Pathophysiology and its Clinical Implications
Authors: Silberstein SD
Published: December 2004

The vascular hypothesis of migraine has now been superseded by a more integrated theory that involves both vascular and neuronal components. It has been demonstrated that the visual aura experienced by some migraineurs arises from cortical spreading depression, and that this neuronal event may also activate perivascular nerve afferents, leading to vasodilation and neurogenic inflammation of the meningeal blood vessels and, thus, throbbing pain. The involvement of the parasympathetic system supplying the meninges also causes increased vasodilation and pain. As an acute attack progresses, sensory neurones in the trigeminal nucleus caudalis become sensitized, resulting in the phenomenon of cutaneous allodynia. Triptans may act at several points during the progression of a migraine attack. However, the development of central sensitization impacts upon the effectiveness of triptan therapy.
Clinical Profile and Practice Experience of Almotriptan
Authors: Gendolla A
Published: December 2004

Patients expect their acute migraine treatment to have a rapid onset of action, achieve complete pain relief that is sustained for 24 h, and to have a good tolerability profile. Almotriptan has a favourable pharmacokinetic profile that translates clinically to a rapid onset of action and consistent absorption regardless of age, sex, food intake and status of the acute migraine attack. In addition, almotriptan is not associated with any clinically relevant drug-drug interactions. Pain-free status at 2 h postdose is achieved by approximately 39% of patients receiving almotriptan in clinical trials. Recurrence of headaches within 24 h is low with almotriptan (< 22%). Almotriptan has a sustained pain-free rate of 25-27%, which in a meta-analysis of triptans was superior to sumatriptan 100 mg. Almotriptan therapy is associated with a low incidence of adverse events, including those affecting the central nervous system and chest.
Salivary secretion assay for drug efficacy for cystic fibrosis in mice
Authors: Best John Adam , Quinton P. M.
Published: December 2004

Computerized assays on cultured cells ex vivo have been used to screen thousands of compounds for their effectiveness in correcting the basic physiological defect in cystic fibrosis (CF). While a number of these compounds appear promising, their effectiveness will almost certainly need to be demonstrated in animals before therapeutic tests in humans will be possible. We show herein that the function of salivary secretion in the mouse model for CF could be used as a simple, easy and rapid in vivo assay for drug effects. We demonstrate that salivary secretory capacity stimulated with a β‐adrenergic agonist closely reflects the genotype of origin. Specifically, the mean maximal secretory rate of saliva in normal wild type (+/+) mice was about 1.5 times higher than that of the mean rate in heterozygote (+/−) mice and more than 50 times greater than in CF (−/−) mice. Total saliva secreted per stimulated period obeyed a similar phenotype–genotype segregation. The data indicate that salivary secretory rates in CF mice could be used to assay potential drugs for their effectiveness in correcting the secretory defect in cystic fibrosis.
Crossing the apnoeic threshold: causes and consequences
Authors: Dempsey Jerome A.
Published: December 2004

This brief review addresses the characteristics, lability and the mechanisms underlying the hypocapnic‐induced apnoeic threshold which is unmasked during NREM sleep. The role of carotid chemoreceptors as fast, sensitive detectors of dynamic changes in CO2 is emphasized and placed in historical context of the long‐held debate over central vs. peripheral contributions to CO2 sensing and to apnoea. Finally, evidence is presented which points to a significant role for unstable, central respiratory motor output as a significant contributor to upper airway narrowing and obstruction during sleep.