bluuebunny/crossref_metadata_2025 huggingface dataset:
Transceive surface coil array for magnetic resonance imaging of the human brain at 4 T
Authors: Pinkerton Robert G. , Barberi Enzo A. , Menon Ravi S.
Published: July 2005

As the static magnetic field strength used in human magnetic resonance imaging increases, the wavelength of the corresponding radiofrequency field becomes comparable to the dimensions of the coil and volume of interest. The dielectric resonance effects that arise in this full wavelength regime may be partially compensated for through the use of surface coils. A novel high‐field (4 T) transceive surface coil array is presented that allows arbitrary surface coil placement and size while maintaining the ability to independently transmit and/or receive through conventional 50‐Ω power amplifiers and preamplifiers, respectively. A ninefold signal‐to‐noise ratio (SNR) increase is shown in close proximity to the transceive array and there is an overall 38% increase throughout the entire brain volume in comparison to the standard hybrid birdcage coil. Furthermore, the ability to independently transmit and receive through each surface coil within this array enables transmit and/or receive‐only fast parallel imaging techniques to be employed while maintaining the increased SNR sensitivity inherent to surface coil designs. Magn Reson Med 54:499–503, 2005. © 2005 Wiley‐Liss, Inc.
Adaptation in the rodent olfactory bulb measured by fMRI
Authors: Schafer James R. , Kida Ikuhiro , Rothman Douglas L. , Hyder Fahmeed , Xu Fuqiang
Published: July 2005

Effective evaluation of the odor environment necessitates the ability to attenuate responses to potent background odors in favor of novel and less robust stimuli. Olfactory receptor neuron studies suggest that some of this adaptation takes place in the primary sensory neurons, but the more extensive adaptation seen in higher cortical areas implies the involvement of additional neural mechanisms. At 7.0 T, high‐resolution fMRI was used to assess the response of the rodent olfactory bulb, the most peripheral cortical structure involved in olfactory processing, to a variety of odor stimuli. The results suggest that there are additional regulatory mechanisms in the olfactory bulb that result in greater adaptation in deeper areas than that seen in sensory receptors alone and that the resultant adaptation is positively affected by increasing stimulus duration and concentration and decreasing recovery time. The implications of these findings for the integration of peripheral input with perception are discussed. Magn Reson Med 54:443–448, 2005. © 2005 Wiley‐Liss, Inc.
Testing the three‐pool white matter model adapted for use with T2 relaxometry
Authors: Andrews Trevor , Lancaster Jack L. , Dodd Stephen J. , Contreras‐Sesvold Carmen , Fox Peter T.
Published: July 2005

A three‐pool model was used to improve white‐matter T2 relaxometry in low signal‐to‐noise (SNR) data. To verify the model very high SNR T2 relaxometry experiments were performed on myelinated tissue samples and three‐pool fractions were consistently found. Relaxation curves based on the in vitro results were simulated with multiple SNRs and fit using the three‐pool model and three less constraining nonnegative least squares‐based methods. All methods performed well with noiseless data. At lower SNR values the three‐pool model was superior, primarily due to the fact that the other methods often could not unambiguously calculate pool fractions. Magn Reson Med 54:449–454, 2005. © 2005 Wiley‐Liss, Inc.
Determination of dielectric and calorimetric properties in the cure reaction of two thermosets by dielectric analysis and differential scanning calorimetry
Authors: Núñez Lisardo , Gómez‐Barreiro S , Gracia‐Fernández CA
Published: July 2005

Dielectric analysis and differential scanning calorimetry were used to study the cure reaction of an epoxy resin (the diglycidyl ether of bisphenol A (DGEBA) (n = 0)) and two curing agents, ie 1,2‐diamine cyclohexane (1,2‐DCH) and m‐xylylenediamine (m‐XDA). Various dielectric properties, such as the relaxed permittivity, unrelaxed permittivity and dipole strength, were determined as a function of the curing time, temperature and conversion. The dielectric curing properties observed were related to geometric and energetic aspects of the samples. Analysis of the results shows that the relaxed permittivity and dipole strength are higher for the system DGEBA (n = 0)/1,2‐DCH than for the system DGEBA (n = 0)/m‐XDA. Copyright © 2005 Society of Chemical Industry
Effect of functional groups of modified polyolefins on the structure and properties of their composites with lamellar silicates
Authors: Passaglia Elisa , Sulcis Roberta , Ciardelli Francesco , Malvaldi Marco , Narducci Piero
Published: July 2005

The melt mixing of functionalized polyolefins with a surface‐modified layered silicate (montmorillonite) was investigated as an approach to prepare the corresponding micro/nanocomposites. The effect of the diethyl succinate groups, derived from the grafting of diethyl maleate (DEM) onto the polyolefins, on compatibility with an inorganic filler and the dispersion in a hydrophobic matrix was extensively investigated. In order to avoid possible interference by polymer multiphase morphology, the amorphous poly(propylene‐ran‐ethylene) (EPM) (70/30, wt/wt), functionalized with DEM (EPM‐graft‐DEM), was used in melt mixing with alkyl‐ammonium‐salt‐modified montmorillonite at different weight ratios by using a Brabender mixer. Materials with a nanoscale dispersion of the inorganic phase, as revealed by X‐ray diffraction (XRD) and transmission electron microscopy (TEM) analyses, were obtained. Specific interactions, involving the carbonyl groups of the polyolefin functional groups and the polar sites on the filler surface, appeared to assist intercalation and/or exfoliation of the layered system. Similar results were obtained by starting with an unfunctionalized EPM and by performing the grafting reaction with DEM during melt mixing according to a one‐step simplified procedure. Copyright © 2005 Society of Chemical Industry
Arenesulfonyl iodides: The third universal class of functional initiators for the metal‐catalyzed living radical polymerization of methacrylates and styrenes
Authors: Percec Virgil , Grigoras Cristian
Published: July 2005

The metal‐catalyzed living radical polymerization of methyl methacrylate and styrene initiated with freshly prepared p‐toluenesulfonyl iodide (TsI) and catalyzed with CuX/2,2′‐bipyridine (bpy), where X is Cl, Br, or I, and various self‐regulated copper‐based catalytic systems, such as copper/bpy, copper(I) oxide/bpy, copper(I) sulfide/bpy, copper(I) selenide/bpy, and copper(I) telluride/bpy, is reported. The exchange of CI into CBr and CCl takes place when the living radical polymerization of methyl methacrylate is catalyzed by copper(I) bromide/bpy and copper(I) chloride/bpy, respectively. Therefore, the use of the TsI initiator facilitates the synthesis, starting from a single initiator, of poly(methyl methacrylate) containing CI, CBr, and CCl chain ends. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 3920–3931, 2005
Resistance in the mosquito, Culex quinquefasciatus, and possible mechanisms for resistance
Authors: Xu Qiang , Liu Huqi , Zhang Lee , Liu Nannan
Published: July 2005

Two mosquito strains of Culex quinquefasciatus (Say), MAmCqG0 and HAmCqG0, were collected from Mobile and Huntsville, Alabama, respectively. MAmCqG0 and HAmCqG0 were further selected in the laboratory with permethrin for one and three generations, respectively. The levels of resistance to permethrin in MAmCqG1 (after one‐generation selection) and HAmCqG3 (after three‐generation selection) increased rapidly. Resistance to permethrin in MAmCqG1 and HAmCqG3 was partially suppressed by piperonyl butoxide (PBO), S,S,S‐tributylphosphorotrithioate (DEF) and diethyl maleate (DEM), inhibitors of cytochrome P450 monooxygenases, hydrolases and glutathione S‐transferases (GST), respectively, suggesting these three enzyme families are important in conferring permethrin resistance in both strains. A substitution of leucine to phenylalanine (L to F) resulting from a single nucleotide polymorphism (SNP), termed the kdr mutation, in the para‐homologous sodium channel gene has been reported as a very common mutation associated with pyrethroid resistance of insects. A 341‐bp sodium channel gene fragment, where the kdr mutation resides, was generated by PCR from genomic DNAs of Cx. quinquefasciatus strains. We found that the kdr mutation was present in both permethrin‐selected and unselected HAmCq and MAmCq mosquito populations, suggesting that the kdr mutation plays the role in permethrin resistance. There was no significant change in the frequency and heterozygosity of the A to T SNP for the kdr allele between permethrin‐selected and unselected MAmCq and HAmCq mosquitoes, indicating that other mechanisms are involved in the evolution of resistance in mosquitoes selected by permethrin in the laboratory. Copyright © 2005 Society of Chemical Industry
Horizontal gene transfer of atrazine‐degrading genes (atz) from Agrobacterium tumefaciens St96‐4 pADP1::Tn5 to bacteria of maize‐cultivated soil
Authors: Devers Marion , Henry Sonia , Hartmann Alain , Martin‐Laurent Fabrice
Published: July 2005

The plasmid pADP1::Tn5 derived from pADP1[Atr+] carrying a Tn5 transposon conferring kanamycin and streptomycin resistances was constructed and introduced in Agrobacterium tumefaciens St96‐4. This genetically modified strain was inoculated (∼108 cfu g−1) in potted soils planted with maize and treated or not with atrazine (1.5 mg kg−1). Bulk and maize rhizosphere soils were sampled 39 days after planting to look for soil indigenous bacteria that had acquired pADP1::Tn5. Four transconjugants were isolated from four different soil samples. The estimated transfer frequency of pADP1::Tn5 was 10−4 per donor. Maize rhizosphere and atrazine treatment had no obvious effect on pADP1::Tn5 transfer frequency. The sequencing of the 16S rDNA sequences of the transconjugants revealed that they were almost identical and highly similar to that of Variovorax spp (97%). In addition, their characterization suggested that the atzA and atzB genes had been transferred from pADP1::Tn5 to the bacterial chromosome in two of the four transconjugants. These data suggest that the atz degrading genes are horizontally transferred in soil and possibly subjected to gene rearrangement. Copyright © 2005 Society of Chemical Industry
Carbon nanowires made on diamond surface by focused ion beam
Authors: Zaitsev Alexander M.
Published: July 2005

Conductive carbon nanowires were made on the polished surface of a single crystal CVD diamond by 30 keV Ga+ ion beam focused to 20 nm. Measurements of conductance of the as‐irradiated nanowires and those annealed at temperature 1400 °C revealed the onset of the ion‐induced conductance to be of 2 × 1015 cm–2. Short nanowires (sub‐micron length) irradiated with subthreshold doses from 5 × 1014 cm–2 to 3 × 1015 cm–2 exhibited unusually high conductivity of 105 Ω–1 cm–1 well exceeding the conductivity of bulk graphite and comparable with that of metals. Tentative explanation of the effect is formation of chains of highly conductive carbon nanorods along 〈100〉 direction in diamond lattice. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The evolutionary ecology of masting: does the environmental prediction hypothesis also have a role in mesic temperate forests?
Authors: Piovesan Gianluca , Adams Jonathan M.
Published: July 2005

The evolutionary advantages of mast seeding in mesic temperate forests are reviewed with reference to the whole plant's lifecycle. The aim of this article is to give attention to the environmental prediction hypothesis as an evolutionary aspect of closed‐forest dynamics that need to be tested in field studies and modelling. It is suggested that the year after a period of water stress (or other suboptimal conditions for growth) trees respond with high seed production. Due to an understory environment favorable for prolific establishment of seedlings (i.e., more light at the forest floor) this may give rise to a pulse of regeneration. Thus, understanding masting may require a multi‐faceted approach including the study of the ecology of the trees themselves beyond pollination and seed predation, and including gap ecology and patch dynamics with special attention to patterns of forest regeneration.
Electrostatic influence of active‐site waters on the nucleophilic aromatic substitution catalyzed by 4‐chlorobenzoyl‐CoA dehalogenase
Authors: Xu Dingguo , Guo Hua
Published: July 2005

The 4‐chlorobenzoyl‐CoA dehalogenase catalyzes the hydrolytic dechlorination of 4‐chlorobenzoyl‐CoA via a two‐step mechanism, namely nucleophilic aromatic substitution and ester hydrolysis. The mutation of an active‐site Histidine residue has been shown to reduce the catalytic activity in both the substitution and subsequent hydrolysis steps. In this communication, we report a quantum mechanical/molecular mechanical simulation of the potential of mean force for the substitution step, which confirms the increased barrier height in the H90Q mutant and provides evidence on the electrostatic influence of two active‐site waters on the rate‐limiting barrier.
Urocortin 1 and Urocortin 2 induce macrophage apoptosis via CRFR2
Authors: Tsatsanis Christos , Androulidaki Ariadne , Dermitzaki Erini , Charalampopoulos Ioannis , Spiess Joachim , Gravanis Achille , Margioris Andrew N.
Published: July 2005

Macrophages undergo apoptosis as a mechanism of regulating their activation and the inflammatory reaction. Macrophages express the Corticotropin‐Releasing Factor Receptor‐2 (CRFR2) the endogenous agonists of which, the urocortins, are also present at the site of inflammation. We have found that urocortins induced macrophage apoptosis in a dose‐ and time‐dependent manner via CRFR2. In contrast to lipopolysaccharide (LPS)‐induced apoptosis, the pro‐apoptosis pathway activated by urocortins involved the pro‐apoptotic Bax and Bad proteins and not nitric oxide, JNK and p38MAPK characteristic of LPS. In conclusion, our data suggest that endogenous CRFR2 ligands exert an anti‐inflammatory effect via induction of macrophage apoptosis.
Angiotensin II augments advanced glycation end product‐induced pericyte apoptosis through RAGE overexpression
Authors: Yamagishi Sho-ichi , Takeuchi Masayoshi , Matsui Takanori , Nakamura Kazuo , Imaizumi Tsutomu , Inoue Hiroyoshi
Published: July 2005

Advanced glycation end product (AGE)‐their receptor (RAGE) and angiotensin II (AII) are implicated in diabetic retinopathy. However, a crosstalk between the two is not fully understood. In vivo, AGE injection stimulated RAGE expression in the eye of spontaneously hypertensive rats, which was blocked by an AII‐type 1 receptor blocker, telmisartan. In vitro, AII‐type 1 receptor‐mediated reactive oxygen species generation elicited RAGE gene expression in pericytes through NF‐κB activation. Further, AII augmented AGE‐induced pericyte apoptosis, the earliest hallmark of diabetic retinopathy. Our present study may implicate a crosstalk between AGE‐RAGE system and AII in diabetic retinopathy.
Involvement of HP1α protein in irreversible transcriptional inactivation by antiestrogens in breast cancer cells
Authors: Oliva Joan , Messaoudi Selma El , Pellestor Franck , Fuentes Maryse , Georget Virginie , Balaguer Patrick , Cavaillès Vincent , Vignon Françoise , Badia Eric
Published: July 2005

Resistance to 4‐hydroxy‐tamoxifen (OHT), which appears in breast cancer cells after long‐term antiestrogen treatment, may involve irreversible changes of gene expression. We previously developed a MCF‐7 derived cell line (MVLN), in which OHT rapidly and irreversibly inactivates the expression of an estrogen‐regulated luciferase transgene (Vit‐tk‐luciferase). In chromatin immunoprecipitation experiments, heterochromatin protein 1 (HP1α) was found to be associated with the Vit‐tk‐luciferase transgene, only when it was inactivated by OHT treatment. Chimeras composed of either HP1α or the Krupple‐associated box (KRAB) module of KOX‐1 protein (known to repress gene expression by recruitment of HP1 proteins), fused to the estrogen receptor (ER)–DNA binding domain (DBD) and the androgen receptor (AR)–ligand binding domain (LBD) were generated and appeared as potent transcriptional repressors. In stably transfected MVLN cells, irreversible inactivation of the luciferase transgene expression obtained with HP1α–ER(DBD)–AR(LBD) was partial, whereas inactivation obtained with KRAB–ER(DBD)–AR(LBD) was comparable to that obtained with OHT, although with a slower kinetics. Altogether, these data suggest that HP1α is involved in the silencing effects associated with long‐term OHT treatments.
The N‐terminal cytokine binding domain of LIFR is required for CNTF binding and signaling
Authors: He Wei , Gong Ke , Smith David K. , Ip Nancy Y.
Published: July 2005

Ciliary neurotrophic factor (CNTF) forms a functional receptor complex containing the CNTF receptor, gp130, and the leukemia inhibitory factor receptor (LIFR). However, the nature and stoichiometry of the receptor‐mediated interactions in this complex have not yet been fully resolved. We show here that signaling by CNTF, but not by LIF or oncostatin M (OSM), was abolished in cells overexpressing a LIFR mutant with the N‐terminal cytokine binding domain deleted. Our results illustrate molecular differences between the CNTF active receptor complex and those of LIF and OSM and provide further support for the hexameric model of the CNTF receptor complex.
The structure of the Ni–Fe site in the isolated HoxC subunit of the hydrogen‐sensing hydrogenase from Ralstonia eutropha
Authors: Löscher Simone , Zebger Ingo , Andersen Lars K. , Hildebrandt Peter , Meyer-Klaucke Wolfram , Haumann Michael
Published: July 2005

The regulatory Ni–Fe hydrogenase (RH) from Ralstonia eutropha which forms a [HoxBC]2 complex functions as a hydrogen sensor under aerobic conditions. We have studied a novel Strep‐tag isolate of the RH large subunit, HoxCST, which lacks the Fe–S clusters of HoxB, allowing for structure determination of the catalytic site by X‐ray absorption spectroscopy both at the Ni and, for the first time, also at the Fe K‐edge. This technique, together with Fourier‐transform infrared spectroscopy, revealed a Ni–Fe site with [O1(CysS)2NiII(μ‐SCys)2FeII(CN)2(CO)] structure in about 50% of HoxCST and a [(CysS)2FeII(CN)2(CO)] site lacking Ni in the remainder protein. Possibly both sites may be intermediates in the maturation process of the RH.
Recognition of stable protein mutants with 3D stochastic average electrostatic potentials
Authors: González-Díaz Humberto , Molina Reinaldo , Uriarte Eugenio
Published: July 2005

As more and more proteins are applied to biochemical research there is increasing interest in studying their stability. In this study, a Markov model has been used to calculate molecular descriptors of the protein structure and these are called the average electrostatic potentials (ξ

k
). These descriptors were intended to encode indirect electrostatic pair‐wise interactions between amino acids located at Euclidean distance k within a given 3D protein backbone. The different ξ

k
values could be calculated for the protein as a whole or for specific protein regions (orbits), which include amino acids that lie within a given range of distances from the center of charge of the protein. In this work we calculated the ξ

k
values for 657 mutants of different proteins. A Linear Discriminant Analysis model correctly classified a subset of 435 out of 493 proteins according to their thermal stability – a level of predictability of 88.2%. This experiment was repeated with three additional subsets of proteins selected at random from the initial series of 657. More specifically, the model predicted 314/356 (88.2%) of mutants with higher stability than the corresponding wild‐type protein and 264/301 (86.7%) of proteins with near wild‐type stability. These results illustrate the possibilities for the average stochastic potentials ξ

k
in the study of 3D‐structure/property relationships for biochemically relevant proteins.
Endosomal proteolysis of insulin‐like growth factor‐I at its C‐terminal D‐domain by cathepsin B
Authors: Authier François , Kouach Mostafa , Briand Gilbert
Published: July 2005

IGF‐I is degraded within the endosomal apparatus as a consequence of receptor‐mediated endocytosis. However, the nature of the responsible protease and the position of the cleavage sites in the IGF‐I molecule remain undefined. In vitro proteolysis of IGF‐I using an endosomal lysate required an acidic pH and was sensitive to CA074, an inhibitor of the cathepsin B enzyme. By nondenaturing immunoprecipitation, the acidic IGF‐I‐degrading activity was attributed to the luminal species of endosomal cathepsin B with apparent molecular masses of 32‐ and 28‐kDa. The cathepsin B precursor, procathepsin B, was processed in vitro within isolated endosomes at pH 5 or at 7 in the presence of ATP, the substrate of the vacuolar H+‐ATPase. The rate of IGF‐I hydrolysis using an endosomal lysate or pure cathepsin B was found to be optimal at pH 5–6 and moderate at pH 4 and 7. Competition studies revealed that EGF and IGF‐I share a common binding site on the cathepsin B enzyme, with native IGF‐I displaying the lowest affinity for the protease (IC50
≈ 1.5 μM). Hydrolysates of IGF‐I generated at low pH by endosomal IGF‐I‐degrading activity and analyzed by reverse‐phase HPLC and mass spectrometry revealed cleavage sites at Lys68‐Ser69, Ala67‐Lys68, Pro66‐Ala67 and Lys65‐Pro66 within the C‐terminal D‐domain of IGF‐I. Treatment of human HepG2 hepatoma cells with the cathepsin B proinhibitor CA074‐Me reduced, in vivo, the intracellular degradation of internalized [125I]IGF‐I and, in vitro, the degradation of exogenous [125I]IGF‐I incubated with the cell‐lysates at pH 5. Inhibitors of cathepsin B and pro‐cathepsin B processing, which abolish endosomal proteolysis of IGF‐I and alter tumor cell growth and IGF‐I receptor signalling, merit investigation as antimetastatic drugs.
Neisseria meningitidis pili induce type‐IIA phospholipase A2 expression in alveolar macrophages
Authors: Touqui Lhousseine , Paya Miguel , Thouron Françoise , Guiyoule Annie , Zarantonelli Maria-Leticia , Leduc Dominique , Wu Yongzheng , Taha Muhamed-Kheir , Alonso Jean-Michel
Published: July 2005

Induction of type‐IIA secreted phospholipase A2 (sPLA2‐IIA) expression by bacterial components other than lipopolysaccharide has not been previously investigated. Here, we show that exposure of alveolar macrophages (AM) to Neisseria meningitidis or its lipooligosaccharide (LOS) induced sPLA2‐IIA synthesis. However, N. meningitidis mutant devoid of LOS did not abolish this effect. In addition, a pili‐defective mutant exhibited significantly lower capacity to stimulate sPLA2‐IIA synthesis than the wild‐type strain. Moreover, pili isolated from a LOS‐defective strain induced sPLA2‐IIA expression and nuclear factor kappa B (NF‐κB) activation. These data suggest that pili are potent inducers of sPLA2‐IIA expression by AM, through a NF‐κB‐dependent process.
Adenosine diphosphate moiety does not participate in structural changes for the signaling state in the sensor of blue‐light using FAD domain of AppA
Authors: Masuda Shinji , Hasegawa Koji , Ono Taka-aki
Published: July 2005

A sensor of blue light using FAD (BLUF) protein is a flavin adenine dinucleotide (FAD) based new class blue‐light sensory flavoprotein. The BLUF domain of AppA was reconstituted in vitro from apoprotein and flavin adenine dinucleotide, flavin adenine mononucleotide or riboflavin. The light‐induced FTIR spectra of the domain reconstituted from various flavins and the 13C‐labeled apoprotein showed that identical light‐induced structural changes occur in both the flavin chromophore and protein for the signaling state in all of the reconstituted holoproteins. The results showed that an adenosine 5′‐dinucleotide moiety is not required for signaling‐state formation in a BLUF domain.
Gymnemic acids inhibit rabbit glyceraldehyde‐3‐phosphate dehydrogenase and induce a smearing of its electrophoretic band and dephosphorylation
Authors: Izutani Yusuke , Murai Takuya , Imoto Toshiaki , Ohnishi Masatake , Oda Masayuki , Ishijima Sumio
Published: July 2005

Gymnemic acids (GA) inhibited rabbit muscle glyceraldehyde‐3‐phosphate dehydrogenase (GAPDH) activity. Binding of GA to GAPDH was observed by surface plasmon resonance measurement. Incubation of GAPDH with GA induced a smearing of the GAPDH band in SDS–PAGE. The GA‐induced smearing was diminished by prior incubation of GA with γ‐cyclodextrin or by GA treatment with NAD. GA treatment did not affect the electrophoretic mobility of glucose‐6‐phosphate isomerase and dehydrogenase. GA treatment diminished the GAPDH band detected by an antibody to phosphoserine, but did not affect the phosphoserine bands of glucose‐6‐phosphate isomerase and dehydrogenase. These results indicated that GA specifically induced dephosphorylation of GAPDH.
Prediction of methylated CpGs in DNA sequences using a support vector machine
Authors: Bhasin Manoj , Zhang Hong , Reinherz Ellis L. , Reche Pedro A.
Published: July 2005

DNA methylation plays a key role in the regulation of gene expression. The most common type of DNA modification consists of the methylation of cytosine in the CpG dinucleotide. At the present time, there is no method available for the prediction of DNA methylation sites. Therefore, in this study we have developed a support vector machine (SVM)‐based method for the prediction of cytosine methylation in CpG dinucleotides. Initially a SVM module was developed from human data for the prediction of human‐specific methylation sites. This module achieved a MCC and AUC of 0.501 and 0.814, respectively, when evaluated using a 5‐fold cross‐validation. The performance of this SVM‐based module was better than the classifiers built using alternative machine learning and statistical algorithms including artificial neural networks, Bayesian statistics, and decision trees. Additional SVM modules were also developed based on mammalian‐ and vertebrate‐specific methylation patterns. The SVM module based on human methylation patterns was used for genome‐wide analysis of methylation sites. This analysis demonstrated that the percentage of methylated CpGs is higher in UTRs as compared to exonic and intronic regions of human genes. This method is available on line for public use under the name of Methylator at http://bio.dfci.harvard.edu/Methylator/.
Regional variability in the trophic requirements of shelf sea fisheries in the Northeast Atlantic, 1973–2000
Authors: Heath Michael R.
Published: July 2005

Hydrographic, plankton, benthos, fisheries landings, and fish diet data from shelf sea areas in the Northeast Atlantic have been combined into an analysis of the foodweb structure and secondary production requirements of regional fisheries. Fish landings from the Baltic and North Sea are shown to be taken from a lower trophic level and are shown to be overall more planktivorous than those from shelf edge regions. The secondary production required per unit of landed fish from the North Sea was approximately half that for landings from the southwest approaches to the UK, referred to as the Celtic Seas, where zooplankton production accounted for only a small fraction of the secondary production demands of the fisheries. In the North Sea, variability in zooplankton production seems to have exerted a bottom-up effect on fish production, which in turn has exerted a top-down effect on the benthos. Conversely, Celtic Seas benthos production has been a bottom-up driver of fish production, which seems to have been independent of variability in plankton production. Thus, climate and fishing pressures can be expected to influence these regional fisheries in very different ways. Overall, the results indicate very strong spatial patterns in the fish foodweb structure and function, which will be important considerations in the establishment of regional management plans for fisheries.
The emerging role of climate in post-smolt growth of Atlantic salmon
Authors: Friedland Kevin D. , Chaput Gerald , MacLean Julian C.
Published: July 2005

Though it is well established that mortality during the post-smolt year is critical in shaping recruitment patterns in Atlantic salmon (Salmo salar L.), the controlling mechanism for North Atlantic stocks remains elusive. The emerging paradigm is based on relationships between survival and ocean thermal conditions during the early marine phase. The survival of post-smolts from both Europe and North America has been correlated to sea surface temperature conditions during their first month at sea. In addition, data for European fish support the hypothesis that growth mediates survival during that time. Thus, the working model for a salmon recruitment mechanism is analogous to those proposed for other fish species. We present growth data for two stocks, the Girnock Burn, which is a tributary to the River Dee, Scotland, and the Margaree River, Canada. Circuli spacing data for Girnock Burn fish suggest post-smolt growth is negatively correlated with temperature in the migration corridors during the first months at sea, while post-smolt growth of Margaree fish appears to be positively correlated with temperature. Growth is either patterned by a physiological response to an optimal temperature, or is co-varying with some ecosystem effect on growth, and the growth response might affect mortality and maturation of the stocks.
Long Term Follow-Up of Composite Non-Vascularized Toe Phalanx Transfers for Aphalangia
Authors: TONKIN M. A. , DEVA A. K. , FILAN S. L.
Published: July 2005

The results of 21 non-vascularized toe phalanx transfers in 13 patients were reviewed radiologically with respect to function, physeal patency, growth and donor site morbidity at a mean follow-up of 7.4 (range 2.9–13.6) years. Physeal patency was maintained in 4 of 18 surviving transfers. The length of the transferred phalanx averaged 75% of the contralateral comparable toe phalanx and 44% of the contralateral digit proximal phalanx. Most patients had good or simple use of the hand with active joint motion. There was universal shortening of the donor toe with hypoplasia of the middle and distal phalanges. This review suggests that transfer of a non-vascularized toe phalanx provides a reliable but limited means for increasing length of a digit, stabilizing soft tissue “nubbins” and improving function. Longer follow-up has shown more modest gains in growth than in some previous reports.
Cystic Fibrosis Screening
Authors: Shulman Lee P.
Published: July 2005

The integration of universal cystic fibrosis screening in women's health has considerably altered the way we care for obstetric patients and likely will be the foundation for incorporating other genetic tests into routine women's health care. Prior to this change in the standard of care, screening for genetic disease was primarily limited to those individuals who had a personal or family history of the genetic condition or who belonged to a particular ethnic or racial group characterized by a high frequency of carrier and affected individuals. However, technological advances have resulted in facile and economic methodologies for detecting an increasing number of genetic mutations and in the realization that screening for common and uncommon disorders will likely be a not‐too‐distant‐future part of routine health care. Programs that permit clinicians to properly implement genetic protocols and allow patients to make informed decisions about genetic screening and diagnostic tests are needed. The implementation of universal cystic fibrosis screening allows clinicians to recognize the benefits and pitfalls of genetic testing of the general population and encourages the development of programs that will effectively communicate genetic information to professionals and laity.
Ethical Issues in Genetic Testing
Authors: Lea Dale Halsey , Williams Janet , Donahue M. Patricia
Published: July 2005

Genetic factors contribute to risk for disease. Information clarifying risk in an individual and his/her family members can be identified through clinical screening and genetic testing. In some circumstances, this information can be used in clinical decisions about surveillance and prevention or treatment of disease. However, use of this information is not always a straightforward process. Application of knowledge about risk of genetic disease in provision of primary health care for women requires understanding of new genetic discoveries as well as the ability to participate in resolution of ethical dilemmas that may result when genetic screening and testing are considered. These dilemmas arise not only from the current state of knowledge about genetic risk factors and utility of genetic tests but also result from conflicts that can arise when the needs of the client are not in unison with needs of others within the family or society. Ethical theories and principles provide a framework for resolving ethical dilemmas in maternal screening for genetic conditions during a pregnancy, carrier testing prior to or during a pregnancy, clinical genetic testing, and newborn metabolic screening.
Options for Down Syndrome Screening: What Will Women Choose?
Authors: Grant Stanley S.
Published: July 2005

Down syndrome screening has been offered to pregnant women since the early 1980s. Protocols have changed as research confirmed improvements that result in higher detection rates and lower false‐positive rates. Results from 2 clinical trials evaluating screening protocols that include ultrasound measurement of nuchal translucency and biochemical testing in the first and second trimester are now available. First‐trimester screening is an option if there are adequate ultrasound, diagnostic, and counseling services available. Regional variation in the availability of these services may limit the implementation of first‐trimester screening. Combining screening tests for Down syndrome from both trimesters as an integrated test offers the highest detection rate with the lowest false‐positive rate. The possibility of avoiding a positive screen will make this an attractive option for some. Timing, detection rate, false‐positive rates, and personal factors influence the decision women make regarding screening versus diagnostic testing. This article reviews the efficacy of current protocols for Down syndrome screening. Accurate information about available screening tests will facilitate informed decisions about screening and testing.
Harnessing the Power of the Pedigree
Authors: Wolpert Chantelle M. , Speer Marcy C.
Published: July 2005

Primary care providers are in an ideal position to practice genomic‐based medicine. Family history data can be used to assess reproductive risks or determine an individual's risk for developing specific diseases. The US Department of Health and Human Services has recently launched the US Surgeon General's Family History Initiative, a national public health campaign designed to encourage Americans to learn more about their family health histories. Furthermore, several national associations now recommend that primary care providers collect family history data to identify patients at risk for these diseases. Ideally, family history data should be ascertained, documented, and analyzed in a standardized manner. Graphic representation of a family history in the form of a pedigree may be preferable to a text format, but further research will clarify this issue. Family history tools are now being developed and studied to identify which methods are most beneficial in different clinical settings.
Genetic Testing and the Family
Authors: Van Riper Marcia
Published: July 2005

The family experience of genetic testing is explored in this article. Two family stories are presented to illustrate how families define and manage the ethical and social issues that emerge during 2 types of genetic testing: mutation analysis for Huntington's disease and genetic testing for breast and ovarian cancer susceptibility. These 2 families were purposefully selected because their stories exemplify the complexity of the genetic testing experience. In addition, the story of the family living with Huntington's disease shows how negative consequences can occur for the individual tested, other family members, the marital relationship, and the family system, even when the test results indicate that the individual does not carry a deleterious gene mutation. Both of the families presented in this article participated in an ongoing study, Family Experience of Genetic Testing: Ethical Dimensions, in which 118 family members from 67 families have participated. The guiding framework for this research was the family management style framework developed and refined by Knafl and colleagues.
Co‐integrating currencies and yield differentials
Authors: Inci Ahmet Can
Published: July 2005

This study investigates the relationship between currencies and interest rates of different maturity horizons. The real exchange rate is found to depend both on short‐term real domestic and foreign interest rate difference and on long‐term real domestic and foreign interest rate difference. Co‐integrating regressions of contemporaneous currency rates generate negative and significant coefficients for long‐term rate differentials, consistent with uncovered interest parity. Therefore, the expectations hypothesis holds for long horizons. On the other hand, positive coefficients for real short‐term interest rate differentials reveal the forward premium puzzle: the failure of uncovered interest parity for short‐horizons. Results are partly driven by the very different risk characteristics of short‐term bonds and foreign bonds.
Recurrent events on a Quaternary fault recorded in the mineralogy and micromorphology of a weathering profile, Yangsan Fault System, Korea
Authors: Jeong Gi Young , Cheong Chang-Sik
Published: July 2005

Recurrence characteristics of a Quaternary fault are generally investigated on the basis of field properties that are rapidly degraded by chemical weathering and erosion in warm humid climates. Here we show that in intense weathering environments, mineralogical and micromorphological investigations are valuable in paleoseismological reconstruction. A weathering profile developed in Late Quaternary marine terrace deposits along the southeastern coast of the Korean Peninsula was disturbed by tectonic movement that appears to be a simple one-time reverse faulting event based on field observations. A comparative analysis of the mineralogy, micromorphology, and chemistry of the weathering profile and fault gouge, however, reveals that both the microfissures in the deformed weathering profile and larger void spaces along the fault plane were filled with multi-stage accumulations of illuvial clay and silt minerals of detrital origin, suggesting a repetition of fissuring and subsequent sealing in the weathering profile as it underwent continuous mineralogical transformation and particle translocation. We reconstruct a sequence of multiple faulting events unrecognized in previous field surveys, which requires revision of the view that the Korean Peninsula was tectonically stable, during the Late Quaternary.
Kinematic and sedimentological evolution of the Manyara Rift in northern Tanzania, East Africa
Authors: RING UWE , SCHWARTZ HILDE L. , BROMAGE TIMOTHY G. , SANAANE CHARLES
Published: July 2005

We describe the stratigraphical/sedimentological and structural evolution of the Manyara Rift in the Tanzania Divergence Zone, East Africa. The rift-related Manyara Beds on the shoaling side of the Manyara Rift were deposited between <1.7 and 0.4 Ma and can be separated into a lacustrine lower member and a fluvial upper member. The transition from lacustrine to fluvial sedimentation at ∼ 0.7 Ma appears to be related to a southward shift of major rift faulting. Fault geometry and the kinematics of the faults are consistent with major faulting during NE/E-directed extension. There is also evidence for other extensional directions including radial extension, which might be caused by magmatic activity and/or might reflect oblate strain symmetry where the East African Rift propagated into the Archaean Tanzania Craton and associated termination of rifting caused an increase in the strained area.
Finiteness spaces
Authors: EHRHARD THOMAS
Published: July 2005

We investigate a new denotational model of linear logic based on the purely relational model. In this semantics, webs are equipped with a notion of ‘finitary’ subsets satisfying a closure condition and proofs are interpreted as finitary sets. In spite of a formal similarity, this model is quite different from the usual models of linear logic (coherence semantics, hypercoherence semantics, the various existing game semantics…). In particular, the standard fix-point operators used for defining the general recursive functions are not finitary, although the primitive recursion operators are. This model can be considered as a discrete analogue of the Köthe space semantics introduced in a previous paper: we show how, given a field, each finiteness space gives rise to a vector space endowed with a linear topology, a notion introduced by Lefschetz in 1942, and we study the corresponding model where morphisms are linear continuous maps (a version of Girard's quantitative semantics with coefficients in the field). In this way we obtain a new model of the recently introduced differential lambda-calculus.
Abstract hierarchical graph transformation
Authors: BUSATTO GIORGIO , KREOWSKI HANS-JÖRG , KUSKE SABINE
Published: July 2005

In this paper we introduce a new hierarchical graph model to structure large graphs into small components by distributing the nodes (and, likewise, edges) into a hierarchy of packages. In contrast to other known approaches, we do not fix the type of underlying graphs. Moreover, our model is equipped with a rule-based transformation concept such that hierarchical graphs are not restricted to being used only for the static representation of complex system states, but can also be used to describe dynamic system behaviour.
Cellular and molecular mechanisms that underlie Entamoeba histolytica pathogenesis: prospects for intervention
Authors: Laughlin Richard C. , Temesvari Lesly A.
Published: July 2005

The protozoan parasite Entamoeba histolytica is the causative agent of amoebic dysentery. It is prevalent in developing countries that cannot prevent its fecal–oral spread and ranks second in worldwide causes of morbidity by parasitic infection. Improvements in sanitation would help curb disease spread. However, a lack of significant progress in this area has resulted in the need for a better understanding of the molecular and cellular biology of pathogenesis in order to design novel methods of disease treatment and prevention. Recent insight into the cellular mechanisms regulating virulence of E. histolytica has indicated that processes such as endocytosis, secretion, host cell adhesion and encystation play major roles in the infectious process. This review focuses on components of the molecular machinery that govern these cellular processes and their role in virulence, and discusses how an understanding of this might reveal opportunities to interfere with E. histolytica infection.
Biofilm formation and modulation of luxS and rpoD expression by Helicobacter pylori
Authors: Cellini L. , Grande R. , Traini T. , Di Campli E. , Di Bartolomeo S. , Di Iorio D. , Caputi S.
Published: July 2005

Bacteria often choose a sessile biofilm lifestyle as a strategy to overcome environmental stress. In this study, we describe biofilm formation by Helicobacter pylori on a polystyrene surface, evaluating the viability and the morphological dynamics of bacterial cells during multicellular aggregate development. Moreover, we investigate expression of the luxS and rpoD genes, which are involved in biofilm formation.

Two clinically susceptible and resistant strains of H. pylori were analyzed, as well as H. pylori ATCC 43629 for reference. The dominant form of expression, clustered bacterial cells arranged in an abundant matrix, was recorded after 2 days of incubation without shaking. Coccoid (spherical) cells with a “wrinkled” aspect presented the prevalent morphology (59.26%) among cells in the biofilm structure as observed by scanning electron microscopy. In aged H. pylori cultures, death occurred in single cells or cells grouped into microcolonies in which degenerated bacteria were localized inside the aggregates. The expression of luxS and rpoD genes among the sessile bacterial population reached a maximum after 2 days, with a significant reduction at subsequent time-points. No differences in gene expression and biofilm formation were recorded in the three evaluated strains.

The morphological fickleness expressed in the life cycle by H. pylori strains emphasizes the bacterium's ability to overcome environmental stress, balancing its spread both outside and inside the host.
VTFS project: Development of the lava flow simulation code LavaSIM with a model for three‐dimensional convection, spreading, and solidification
Authors: Hidaka Masataka , Goto Akio , Umino Susumu , Fujita Eisuke
Published: July 2005

The lava flow simulation code LavaSIM has been developed to give accurate predictions of volcanic disasters and to support evacuation plans. The code uses three‐dimensional analysis with free surface evaluation, including boundary transport between the melt and the crust. It is therefore applicable to various types of lava flows and flow behaviors such as flood basalts, subaqueous lava flows, and levee formation. Heat transfer between the lava and the ground, air, and water, and between the melt and crust of the flow is calculated by using appropriate relations. The code has been verified by applying it to actual lava flows, and the simulation results have been compared with observations of the Izu‐Osima flows of 1986. The lava flow rate, temperature, and properties were assigned values based on data from existing literature. The comparisons demonstrated the code's capability for prediction of inundated areas and maximum flow lengths. The present code is expected to be useful for real‐time prediction during eruptions, in addition to assessing volcanic hazards and designing protection structures for existing installations against possible future lava flows.