bluuebunny/crossref_metadata_2025 huggingface dataset:
Rational discovery of a novel interface for a coactivator in the peroxisome proliferator‐activated receptor γ: Theoretical implications of impairment in type 2 diabetes mellitus
Authors: Shiraki Takuma , Kodama Takashi S. , Jingami Hisato , Kamiya Narutoshi
Published: November 2004

The peroxisome proliferator‐activated receptor γ (PPARγ) is important to adipocyte differentiation and glucose homeostasis, and mutations in the gene have been observed in type 2 diabetes mellitus. The mutated residues, V290 and P467, bind to neither ligands nor a coactivator peptide in the reported crystal structures of the PPARγ ligand binding domain. To understand the mechanism of type 2 diabetes mellitus caused by germline mutations in the PPARγ ligand‐binding domain, theoretical models of the PPARγ–ligand–coactivator complex were built at an atomic resolution. In the models, the secondary coactivator peptide was docked next to the conventional coactivator peptide, which both contain the LXXLL motif. The secondary interface in PPARγ for the secondary coactivator peptide has not been demonstrated by experiments. Binding energy calculations of the complex, considering the solvent effect, revealed that the secondary coactivator peptide, derived from nuclear receptor box 1 of steroid receptor coactivator 1, can be favorably bound to the secondary interface. The secondary coactivator peptide forms hydrogen bonds and a hydrophobic core with PPARγ and the primary coactivator peptide. Next, we applied mutations to PPARγ in silico and found that the V290M mutation, observed in type 2 diabetes mellitus, adversely affected the binding of the secondary peptide. Thus, our model provides structural insight into the impairment of PPARγ function in type 2 diabetes mellitus. Proteins 2005. © 2004 Wiley‐Liss, Inc.
Identification of amino acids important for target recognition by the DNA:m5C methyltransferase M.NgoPII by alanine‐scanning mutagenesis of residues at the protein–DNA interface
Authors: Radlinska Monika , Kondrzycka‐Dada Aneta , Piekarowicz Andrzej , Bujnicki Janusz M.
Published: November 2004

DNA:m5C MTases comprise a catalytic domain with conserved residues of the active site and a strongly diverged TRD with variable residues involved in DNA recognition and binding. To date, crystal structures of 2 DNA:m5C MTases complexed with the substrate DNA have been obtained; however, for none of these enzymes has the importance of the whole set of DNA‐binding residues been comprehensively studied. We built a comparative model of M.NgoPII, a close homologue and isomethylomer of M.HaeIII, and systematically analyzed the effect of alanine substitutions for the complete set of amino acid residues from its TRD predicted to be important for DNA binding and target recognition. Our data demonstrate that only 1 Arg residue is indispensable for the MTase activity in vivo and in vitro, and that mutations of only a few other residues cause significant reduction of the activity in vitro, with little effect on the activity in vivo. The identification of dispensable protein–DNA contacts in the wild‐type MTase will serve as a platform for exhaustive combinatorial mutagenesis aimed at the design of new contacts, and thus construction of enzyme variants that retain the activity but exhibit potentially new substrate preferences. Proteins 2005. © 2004 Wiley‐Liss, Inc.
Analysis of pH‐dependent elements in proteins: Geometry and properties of pairs of hydrogen‐bonded carboxylic acid side‐chains
Authors: Wohlfahrt Gerd
Published: November 2004

A rather frequent but so far little discussed observation is that pairs of carboxylic acid side‐chains in proteins can share a proton in a hydrogen bond. In the present article, quantum chemical calculations of simple model systems for carboxyl–carboxylate interactions are compared with structural observations from proteins. A detailed structural analysis of the proteins deposited in the PDB revealed that, in a subset of proteins sharing less than 90% sequence identity, 19% (314) contain at least one pair of carboxylic acids with their side‐chain oxygen atoms within hydrogen‐bonding distance. As the distance between those interacting oxygen atoms is frequently very short (∼2.55 Å), many of these carboxylic acids are suggested to share a proton in a strong hydrogen bond. When situated in an appropriate structural environment (low dielectric constant), some might even form a low barrier hydrogen bond. The quantum chemical studies show that the most frequent geometric features of carboxyl–carboxylate pairs found in proteins, and no or symmetric ligation, are also the most stable arrangements at low dielectric constants, and they also suggest at medium and low pH a higher stability than for isosteric amide–carboxylate pairs. The presence of these pairs in 119 different enzymes found in the BRENDA database is set in relation to their properties and functions. This analysis shows that pH optima of enzymes with carboxyl–carboxylate pairs are shifted to lower than average values, whereas temperature optima seem to be increased. The described structural principles can be used as guidelines for rational protein design (e.g., in order to improve pH or temperature stability). Proteins 2005. © 2004 Wiley‐Liss, Inc.
First‐principles calculations on the origins of the gap bowing in BeSxSe1–x, BeSxTe1–x and BeSexTe1–x alloys
Authors: El Haj Hassan F.
Published: November 2004

First‐principles calculations have been used to investigate the electronic structure and disorder effects in beryllium chalcogenides alloys (BeSxSe1–x, BeSxTe1–x and BeSexTe1–x) using the full potential‐linearized augmented‐plane wave method (FP‐LAPW) within density‐functional theory. We used the local‐density approximation within the generalized gradient correction as well as the Engel–Vosko GGA formalism to calculate the electronic structure at equilibrium volume. The ground‐state properties are determined for the bulk materials (BeS, BeSe, and BeTe) as well as for the average concentration (x = 0.5) of the alloys. Using the approach of Zunger and coworkers, the microscopic origins of compositional disorder have been detailed and explained. The disorder parameter (gap bowing) is found to be mainly caused by the chemical charge‐transfer effect, while the volume deformation and the structural relaxation contribute to the gap bowing parameter at smaller magnitude. This should be expected since there is a weak lattice mismatch between the binary compounds and a considerable electronegativity difference between Be and X (X = S, Se, Te) atoms. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Evaluation of clastogenic potential of the antimalarial plant Solanum nudum
Authors: Alvarez Gonzalo , Pabón Adriana , Carmona Jaime , Blair Silvia
Published: November 2004

Compounds isolated from Solanum nudum have shown in vitro antimalarial activity against the FCB‐2 strain of Plasmodium falciparum. Diosgenone (C27H40O3) the main component isolated from the hexane extract and an aqueous extract were evaluated to measure their clastogenic potential using the micronucleus test. Three concentrations (16, 32 and 64 g/kg of weight) of the aqueous extract were administered intraperitoneally into mice, (the highest concentration corresponded to 80% LD50) and diosgenone solubilized in olive oil was inoculated at the highest concentration possible (11.187 g/kg of weight). After administration of the compounds, no induction of micronucleus was observed either in polychromatic or normochromatic erythrocytes. Interestingly, a reduction of 51% in the young/mature erythrocytes ratio was seen in cells treated with aqueous extract. We conclude that neither diosgenone nor the aqueous extract have clastogenic activity, and that the aqueous extract showed some toxicity at the above mentioned concentrations. These results are signiﬁcant since diosgenone could be a new therapeutic alternative for the treatment of malaria. Copyright © 2004 John Wiley & Sons, Ltd.
Antioxidant availability of turmeric in relation to its medicinal and culinary uses
Authors: Tilak Jai C. , Banerjee Meenal , Mohan Hari , Devasagayam T. P. A.
Published: November 2004

Turmeric (Curcuma longa) has been used in Indian cooking, and in herbal remedies. Its possible mechanism of action was examined in terms of antioxidant availability during actual cooking conditions and in therapeutic applications using standardized extracts. The assays involve different levels of antioxidant action such as oxygen radical absorbance capacity (ORAC), radical scavenging abilities using 1,1‐diphenyl‐2‐picryl hydrazyl (DPPH), 2,2′‐azobis‐3‐ethylbenzthiazoline‐6‐sulfonic acid (ABTS), ferric reducing antioxidant power (FRAP) and protection of membranes examined by inhibition of lipid peroxidation besides the content of phenols and total ﬂavonoids. The aqueous and ethanol extracts of two major preparations of turmeric, corresponding to its use in cooking and medicine, showed signiﬁcant antioxidant abilities. In conclusion, the studies reveal that the ability of turmeric to scavenge radicals, reduce iron complex and inhibit peroxidation may explain the possible mechanisms by which turmeric exhibits its beneﬁcial effects in relation to its use in cooking and medicine. Copyright © 2004 John Wiley & Sons, Ltd.
Anticlastogenic effects of Hibiscus sabdariffa fruits against sodium arsenite‐induced micronuclei formation in erythrocytes in mouse bone marrow
Authors: Adetutu A. , Odunola O. A. , Owoade O. A. , Adeleke O. A. , Amuda O. S.
Published: November 2004

An in vivo micronucleus assay using albino mice was used to examine the anticlastogenic effects of a crude aqueous extract of Hibiscus sabdariffa fruits in bone marrow cells of mice. Various doses of freshly prepared crude extract of Hibiscus sabdariffa (50, 100 and 150 mg/kg b.w.) were given by gavaging to male laboratory bred Swiss albino mice for 7 days as a dietary supplement followed by a single dose of sodium arsenite (2.5 mg/kg b.w.) After 24 h, the animals were killed and bone marrow smears were prepared and stained in Giemsa. The results show that sodium arsenite effectively induced micronuclei in polychromatic erythrocytes (PCEs). Administration of a crude extract of Hibiscus sabdariffa led to a signiﬁcant reduction of micronuclei in PCEs. The results also show that a combination of Hibiscus sabdariffa and sodium arsenite reduced signiﬁcantly the frequencies of micronucleated PCEs induced by sodium arsenite. Copyright © 2004 John Wiley & Sons, Ltd.
Further studies on the clinical efﬁcacy of Solanum xanthocarpum and Solanum trilobatum in bronchial asthma
Authors: Govindan S. , Viswanathan S. , Vijayasekaran V. , Alagappan R.
Published: November 2004

The clinical efﬁcacy of two herbs S. xanthocarpum and S. trilobatum in a dose of 300 mg tds for 3 days was investigated in mild to moderate bronchial asthma. Their effect was compared with standard bronchodilator drugs, salbutamol (4 mg) and deriphylline (200 mg). The respiratory function was assessed by measuring the peak expiratory ﬂow rate (PEFR) using a mini peak ﬂow meter. In addition, improvement in lung function was assessed by physical examination (rhonchi and crepitation) and other symptoms such as cough, breathlessness and sputum. S. xanthocarpum and S. trilobatum produced a progressive improvement in the ventilatory function of asthmatic individuals over 3 days. The scores for rhonchi, cough, breathlessness and sputum were decreased by these drug treatments. The improvement in PEFR and the reduction in other symptom scores clearly indicate a bronchodilator effect, a decrease of oedema and secretions in the airway lumen. The response to these herbs can be considered to be equivalent to that of deriphylline but less than salbutamol. No untoward effects were reported during the study. The present study further conﬁrms the traditional use of these herbs in bronchial asthma. Copyright © 2004 John Wiley & Sons, Ltd.
A double‐blind, placebo‐controlled investigation of the effects of two doses of a valerian preparation on the sleep, cognitive and psychomotor function of sleep‐disturbed older adults
Authors: Diaper A. , Hindmarch I.
Published: November 2004

One of the most popular herbal remedies for the alleviation of sleep problems is valerian. However, research into valerian is sparse, and studies differ greatly with respect to design, measures, and preparations used. This clinical study used standardized sleep EEG and psychometric tests to evaluate the clinical efﬁcacy of a valerian preparation (Li 156).

A placebo‐controlled three way crossover clinical trial was completed using 16 (5 male and 11 female) sleep‐disturbed participants (aged 50 to 64 years, mean age 55.9, SD 4.68). Participants slept overnight in a sleep laboratory, following a 21:00 hours dose of valerian 300 mg, valerian 600 mg, or placebo (double‐blind). EEG sleep was recorded for each participant at 23:00 hours until 07:00 hours, when a psychometric evaluation was performed the morning after dose. Test periods were separated by six days washout period.

Results showed no signiﬁcant effect between valerian 300 mg, valerian 600 mg or placebo on any EEG parameter or psychometric measure. This suggests valerian at these doses is ineffective as an acute dose for sleep problems. However, valerian is widely used, and is traditionally sedative. Therefore, more research is required into therapeutic dose, types of valerian preparation, and the optimum period of use for therapeutic effect. Copyright © 2004 John Wiley & Sons, Ltd.
GEE estimation of a misspecified time‐varying covariate: an example with the effect of alcoholism treatment on medical utilization
Authors: Wall Melanie M. , Dai Yu , Eberly Lynn E.
Published: November 2004

The generalized estimation equation (GEE) method is widely used in longitudinal data analysis, particularly when the outcome variable is non‐Gaussian distributed. Under mild regulatory conditions, the parameter estimates are consistent and their asymptotic variances are efficient. In an observational study focusing on alcoholism patients, we applied the GEE method to longitudinal count data from medical utilization records from a large national managed care organization. The health services research question was whether there was a change in medical utilization for patients after engaging in alcoholism treatment as compared to before treatment. Thus, the main effect of interest was a time‐varying covariate indicating whether the patient had undergone treatment yet or not. GEE under five different working correlations was employed and mixed results regarding the significance of the treatment effect were found. Because of the large sample size, i.e. 8485 patients with an average of 46 repeated measurements per patient, differences across the estimates produced by the different working correlation structures was suspicious. It is shown that these differences are maybe caused by the fact that the time‐varying covariate in the marginal mean model is misspecified. A simulation study is performed to demonstrate that misspecification of the time‐varying covariate in the marginal mean structure can cause differences in GEE results across various choices of working correlation structure. Copyright © 2004 John Wiley & Sons, Ltd.
Avoidance and prohibition of brother–sister sex in humans
Authors: Aoki Kenichi
Published: November 2004

Sex between full sibs is unusual in birds, mammals, and humans. These species likely possess an innate avoidance mechanism based on early proximity (i.e., the Westermarck hypothesis), and the “rare” occurrences may be attributable to error. Alternatively, an inclusive fitness argument shows that a low rate of sib mating may be an “adaptation.” The widespread occurrence of a prohibition against brother–sister sex in human societies is often invoked as evidence against an innate avoidance mechanism, since if the latter were to exist the former would be superfluous. However, given that punishing violators is costly, a prohibition is more likely to spread through an egalitarian society when the prohibited behavior is already avoided. I describe a model of the cultural dynamics of the sibling incest taboo which we have used to investigate this possibility. The predictions derived from this model are consistent with, and add rigor to, Westermarck's theory of the origin of the incest taboo.
Factors affecting seasonal mortality of rosy bitterling (Rhodeus ocellatus kurumeus) embryos on the gills of their host mussel
Authors: Kitamura Jyun‐ichi
Published: November 2004

I investigated the seasonal change in factors affecting embryonic mortality in the rosy bitterling, Rhodeus ocellatus kurumeus, a freshwater fish that spawns on the gills of living unionid mussels. Research was conducted in a small pond during 1999 and 2001 in which bitterling were provided with Anodonta sp. mussels for spawning. Bitterling spawned between April and July, peaking mid–late May. Seasonal survival rate of bitterling embryos in their mussel hosts was unimodal, with a peak between late April and mid May (about 70% of total spawnings). In mid April, survival was about 50%. The lowest survival was from late May to July (0%). Losses of bitterling embryos from mussels were identified by ejections from the mussel host. Ejections were categorized as either ejections of live embryos, or ejections of embryos that died in the mussel and were subsequently expelled from the mussel. Ejection rates of live embryos were higher in the earlier part of the spawning period (early–mid April) and dead embryo ejections in the later period (after June). The ejection rate of live embryos was higher among younger embryos earlier in the season, probably because of the incomplete development of morphological and behavioural traits associated with maintaining the embryo inside the mussel gill chambers, and as a consequence of a more protracted developmental period at low temperatures making them more susceptible to ejection. The ejection rate of dead embryos was higher in older embryos later in the season, and in larger mussels and at high embryo densities. The survival of embryos in mussels was probably related to oxygen availability, with mortalities probably caused by asphyxiation. Increased embryo mortalities may arise through competition among embryos, between embryos and mussel, and ambient dissolved oxygen levels. The optimal period for bitterling to spawn may represent a balance between two opposing factors; with positive and negative effects of a seasonal rise in temperature directly affecting embryonic growth rate and oxygen availability.
Elevation changes of ice caps in the Canadian Arctic Archipelago
Authors: Abdalati W. , Krabill W. , Frederick E. , Manizade S. , Martin C. , Sonntag J. , Swift R. , Thomas R. , Yungel J. , Koerner R.
Published: November 2004

Precise repeat airborne laser surveys were conducted over the major ice caps in the Canadian Arctic Archipelago in the spring of 1995 and 2000 in order to measure elevation changes in the region. Our measurements reveal thinning at lower elevations (below 1600 m) on most of the ice caps and glaciers but either very little change or thickening at higher elevations in the ice cap accumulation zones. Recent increases in precipitation in the area can account for the slight thickening where it was observed but not for the thinning at lower elevations. For the northern ice caps on the Queen Elizabeth Islands, thinning was generally <0.5 m yr−1, which is consistent with what would be expected from the warm temperature anomalies in the region for the 5 year period between surveys, and appears to be a continuation of a trend that began in the mid‐1980s. Farther south, however, on the Barnes and Penny ice caps on Baffin Island, this thinning was much more pronounced at over 1 m yr−1 in the lower elevations. Here temperature anomalies were very small, and the thinning at low elevations far exceeds any associated enhanced ablation. The observations on Barnes, and perhaps Penny, are consistent with the idea that the observed thinning is part of a much longer term deglaciation, as has been previously suggested for Barnes ice cap. On the basis of the regional relationships between elevation and elevation change in our data, the 1995–2000 mass balance for the archipelago is estimated to be −25 km3 yr−1 of ice, which corresponds to a sea level increase of 0.064 mm yr−1. This places it among the more significant sources of eustatic sea level rise, though not as substantial as the Greenland ice sheet, Alaskan glaciers, or the Patagonian ice fields.
Evidence for Cenozoic tectonic deformation in SE Ireland and near offshore
Authors: Cunningham Michael J. M. , Phillips Adrian W. E. , Densmore Alexander L.
Published: November 2004

An integrated study of topography, bathymetry, high‐resolution aeromagnetic data, and structural observations demonstrates significant Cenozoic fault activity in SE Ireland. Tectonically generated knickpoints and reddened fault breccias along topographic escarpments that are underlain by greywacke bedrock and trend oblique to the regional Caledonian strike provide evidence for fault displacement. Near‐offshore faults with similar geometry produce present‐day bathymetric scarps and localized tectonic topography in the inverted Kish Bank Basin. The integration of offshore high resolution aeromagnetic data and structural interpretation of the Kish Bank Basin provides evidence for dextral transtension on NNW trending faults and sinistral transpression on ENE trending faults bounding a lower Paleozoic to Carboniferous basement block. These faults correlate onshore with previously recognized Caledonian faults producing topographic offsets and surface uplift. To the north, offshore structures can be traced onshore and cut exposures of the Caledonian Leinster Granite. Structural analysis of these outcrops indicates post‐Variscan deformation. A major fault on the NW margin of the batholith cuts a major erosion surface developed on Carboniferous carbonate rocks, and nonmarine Miocene deposits are preserved above this surface. Fault kinematics provide evidence of two paleostress systems: (1) NW‐SE σ1, subvertical σ2 and NE‐SW σ3 followed by (2) a clockwise swing of σ1 to NNW‐SSE. Timing of deformation in both stress systems is probably post‐Oligocene age. The mechanism driving this deformation is likely ridge‐push. Much is already known about Cenozoic tectonics and exhumation from offshore basins. This study shows that onshore Ireland has also been affected by significant tectonic activity and exhumation during the Cenozoic.
Relationship of pore water freshening to accretionary processes in the Cascadia margin: Fluid sources and gas hydrate abundance
Authors: Torres M. E. , Teichert B. M. A. , Tréhu A. M. , Borowski W. , Tomaru H.
Published: November 2004

Drilling in the Cascadia accretionary complex enable us to evaluate the contribution of dehydration reactions and gas hydrate dissociation to pore water freshening. The observed freshening with depth and distance from the prism toe is consistent with enhanced conversion of smectite to illite, driven by increase in temperature and age of accreted sediments. Although they contain gas hydrate ‐as evidenced by discrete low chloride spikes‐ the westernmost sites drilled on Hydrate Ridge show no freshening trend with depth. Strontium data reveal that all the mélange samples contain deep fluids modified by reaction with the subducting oceanic crust. Thus we infer that, at the westernmost sites, accretion is too recent for the sediments to have undergone significant illitization. Our data demonstrate that a smooth decrease in dissolved chloride with depth cannot generally be used to infer the presence or to estimate the amount of gas hydrate in accretionary margins.
Estimating the sliding velocity of a Pleistocene ice sheet from plowing structures in the geologic record
Authors: Iverson Neal R. , Hooyer Thomas S.
Published: November 2004

As an ice sheet slides over its sediment bed, some clasts partly embedded in the glacier sole plow through the bed surface. The size distribution of such clasts, if it can be characterized from structures in the geologic record, can be used to estimate the sliding velocity of a past ice sheet. By combining a theory of glacier sliding with a geotechnical theory of cone penetration, sliding velocity can be calculated in terms of clast‐size parameters, a fluidity parameter for ice, and the thermodynamic properties of ice and clasts. If frictional properties of the bed are measured, the effective normal stress on the bed and bed shear strength during glaciation can also be calculated. We used this approach to estimate the sliding velocity of an Illinoian ice sheet that left plowing structures in cemented outwash near Peoria, Illinois. Fluidity parameters for normal and basal temperate ice yielded sliding velocities of 140–168 m yr−1 and 60–72 m yr−1, respectively. These are overestimates if solutes impeded regelation of ice past clasts or if friction between debris‐laden ice and clasts retarded slip. Preconsolidation stresses determined in laboratory tests on silt from the bed agree with effective normal stresses calculated using clast‐size parameters. The high shear strength of the bed (>145 kPa) and primary structures preserved within it indicate that additional movement due to pervasive shear of the bed was unlikely. Application of this method elsewhere would provide basal velocity data that are otherwise unavailable for testing and tuning of ice sheet models.
Detecting cAMP‐induced Epac activation by fluorescence resonance energy transfer: Epac as a novel cAMP indicator
Authors: Ponsioen Bas , Zhao Jun , Riedl Jurgen , Zwartkruis Fried , van der Krogt Gerard , Zaccolo Manuela , Moolenaar Wouter H , Bos Johannes L , Jalink Kees
Published: November 2004

Epac1 is a guanine nucleotide exchange factor for Rap1 that is activated by direct binding of cAMP. In vitro studies suggest that cAMP relieves the interaction between the regulatory and catalytic domains of Epac. Here, we monitor Epac1 activation in vivo by using a CFP–Epac–YFP fusion construct. When expressed in mammalian cells, CFP–Epac–YFP shows significant fluorescence resonance energy transfer (FRET). FRET rapidly decreases in response to the cAMP‐raising agents, whereas it fully recovers after addition of cAMP‐lowering agonists. Thus, by undergoing a cAMP‐induced conformational change, CFP–Epac–YFP serves as a highly sensitive cAMP indicator in vivo. When compared with a protein kinase A (PKA)‐based sensor, Epac‐based cAMP probes show an extended dynamic range and a better signal‐to‐noise ratio; furthermore, as a single polypeptide, CFP–Epac–YFP does not suffer from the technical problems encountered with multisubunit PKA‐based sensors. These properties make Epac‐based FRET probes the preferred indicators for monitoring cAMP levels in vivo.
Replication‐independent chromatin loading of Dnmt1 during G2 and M phases
Authors: Easwaran Hariharan P , Schermelleh Lothar , Leonhardt Heinrich , Cardoso M Cristina
Published: November 2004

The major DNA methyltransferase, Dnmt1, associates with DNA replication sites in S phase maintaining the methylation pattern in the newly synthesized strand. In view of the slow kinetics of Dnmt1 in vitro versus the fast progression of the replication fork, we have tested whether Dnmt1 associates with chromatin beyond S phase. Using time‐lapse microscopy of mammalian cells expressing green‐fluorescent‐protein‐tagged Dnmt1 and DsRed‐tagged DNA Ligase I as a cell cycle progression marker, we have found that Dnmt1 associates with chromatin during G2 and M. This association is mediated by a specific targeting sequence, shows strong preference for constitutive but not facultative heterochromatin and is independent of heterochromatin‐specific histone H3 Lys 9 trimethylation, SUV39H and HP1. Moreover, photobleaching analyses showed that Dnmt1 is continuously loaded onto chromatin throughout G2 and M, indicating a replication‐independent role of Dnmt1 that could represent a novel and separate pathway to maintain DNA methylation.
On the Treves theorem for the Ablowitz–Kaup–Newell–Segur equation
Authors: Morosi Carlo , Pizzocchero Livio
Published: November 2004

According to a theorem of Treves, the conserved functionals of the Ablowitz, Kaup, Newell, and Segur (AKNS) equation vanish on all pairs of formal Laurent series (q̃,r̃) of a specified form, both of them with a pole of the first order. We propose a new and very simple proof for this statement, based on the theory of Bäcklund transformations; using the same method, we prove that the AKNS conserved functionals vanish on other pairs of Laurent series. The spirit is the same as in our previous paper on the Treves theorem for the Korteweg–de Vries hierarchy, with some nontrivial technical differences.
Nonintegrable Schrödinger discrete breathers
Authors: Gómez-Gardeñes J. , Floría L. M. , Peyrard M. , Bishop A. R.
Published: November 2004

In an extensive numerical investigation of nonintegrable translational motion of discrete breathers in nonlinear Schrödinger lattices, we have used a regularized Newton algorithm to continue these solutions from the limit of the integrable Ablowitz–Ladik lattice. These solutions are shown to be a superposition of a localized moving core and an excited extended state (background) to which the localized moving pulse is spatially asymptotic. The background is a linear combination of small amplitude nonlinear resonant plane waves and it plays an essential role in the energy balance governing the translational motion of the localized core. Perturbative collective variable theory predictions are critically analyzed in the light of the numerical results.
An approach to nonstandard quantum mechanics
Authors: Raab A.
Published: November 2004

We use nonstandard analysis to formulate quantum mechanics in hyperfinite-dimensional spaces. Self-adjoint operators on hyperfinite-dimensional spaces have complete eigensets, and bound states and continuum states of a Hamiltonian can thus be treated on an equal footing. We show that the formalism extends the standard formulation of quantum mechanics. To this end we develop the Loeb-function calculus in nonstandard hulls. The idea is to perform calculations in a hyperfinite-dimensional space, but to interpret expectation values in the corresponding nonstandard hull. We further apply the framework to nonrelativistic quantum scattering theory. For time-dependent scattering theory, we identify the starting time and the finishing time of a scattering experiment, and we obtain a natural separation of time scales on which the preparation process, the interaction process, and the detection process take place. For time-independent scattering theory, we derive rigorously explicit formulas for the Mo/ller wave operators and the S-matrix.
Emergence of chaotic attractor and anti-synchronization for two coupled monostable neurons
Authors: Courbage M. , Kazantsev V. B. , Nekorkin V. I. , Senneret M.
Published: November 2004

The dynamics of two coupled piece-wise linear one-dimensional monostable maps is investigated. The single map is associated with Poincaré section of the FitzHugh–Nagumo neuron model. It is found that a diffusive coupling leads to the appearance of chaotic attractor. The attractor exists in an invariant region of phase space bounded by the manifolds of the saddle fixed point and the saddle periodic point. The oscillations from the chaotic attractor have a spike-burst shape with anti-phase synchronized spiking.
Competitive City-Regionalism as a Politics of Space: A Critical Reinterpretation of the New Regionalism
Authors: Ward Kevin , Jonas Andrew E G
Published: November 2004

This paper sets out a sympathetic critique of a series of writings that we refer to as new regionalist approaches to the city. We review the recent work on state restructuring/rescaling and the associated work on the new regionalism, on the one hand, and that on ‘global’ city-regions, on the other. We identify key points of overlap and divergence between these two literatures and suggest that each understates the role of class interests, political alliance formation, and conflicts around the management of collective consumption and social reproduction. We proceed to outline the framework of an alternative and complementary approach in which causal emphasis is placed on the shaping of subnational state geographies by actually existing struggles and strategies developed around particular geographies of public and private investment and collective consumption, and their associated state fiscal, electoral, and regulatory arrangements. We argue that working from this position we are better able to understand why the city-region continues to constitute a strategically vital arena for managing conflict and struggle in contemporary capitalism.
Regional Devolution and Democratic Renewal: Developing a Radical Approach to Stakeholder Involvement in the English Regions
Authors: Humphrey Lynne , Shaw Keith
Published: November 2004

In this paper we aim to assess critically the relationship between devolved government and democratic renewal through a focus on the potential for stakeholder involvement within elected regional assemblies. Drawing particularly upon evidence from North East England, we will consider how the creation of elected assemblies could reinvigorate democracy, given the constraints imposed (in regions such as the North East) by the unreformed and unrepresentative political terrain upon which any new assembly is likely to be superimposed. We conclude that existing arrangements and practices are a useful development but fall far short of the radical measures needed to overcome the exclusionary nature of traditional models of governance and government.
Recurrent evolution of herbivory in small, cold-climate lizards: Breaking the ecophysiological rules of reptilian herbivory
Authors: Espinoza Robert E. , Wiens John J. , Tracy C. Richard
Published: November 2004

Herbivory has evolved in many groups of vertebrates, but it is rare among both extinct and extant nonavian reptiles. Among squamate reptiles, (lizards, snakes, and their relatives), <2% of the >7,800 species are considered to be herbivorous, and herbivory is restricted to lizards. Here, we show that within a group of South American lizards (Liolaemidae, ≈170 species), herbivory has evolved more frequently than in all other squamates combined and at a rate estimated to be >65 times faster. Furthermore, in contrast to other herbivorous lizards and to existing theory, most herbivorous liolaemids are small bodied and live in cool climates. Herbivory is generally thought to evolve only in reptile species that are large bodied, live in warm climates, and maintain high body temperatures. These three well known “rules” of herbivory are considered to form the bases of physiological constraints that explain the paucity of herbivorous reptile species. We suggest that the recurrent and paradoxical evolution of herbivory in liolaemids is explained by a combination of environmental conditions (promoting independent origins of herbivory in isolated cool-climate regions), ecophysiological constraints (requiring small body size in cool climates, yet high body temperatures for herbivores), and phylogenetic history. More generally, our study demonstrates how integrating information from ecophysiology and phylogeny can help to explain macroevolutionary trends.
Coping with cold: An integrative, multitissue analysis of the transcriptome of a poikilothermic vertebrate
Authors: Gracey Andrew Y. , Fraser E. Jane , Li Weizhong , Fang Yongxiang , Taylor Ruth R. , Rogers Jane , Brass Andrew , Cossins Andrew R.
Published: November 2004

How do organisms respond adaptively to environmental stress? Although some gene-specific responses have been explored, others remain to be identified, and there is a very poor understanding of the system-wide integration of response, particularly in complex, multitissue animals. Here, we adopt a transcript screening approach to explore the mechanisms underpinning a major, whole-body phenotypic transition in a vertebrate animal that naturally experiences extreme environmental stress. Carp were exposed to increasing levels of cold, and responses across seven tissues were assessed by using a microarray composed of 13,440 cDNA probes. A large set of unique cDNAs (≈3,400) were affected by cold. These cDNAs included an expression signature common to all tissues of 252 up-regulated genes involved in RNA processing, translation initiation, mitochondrial metabolism, proteasomal function, and modification of higher-order structures of lipid membranes and chromosomes. Also identified were large numbers of transcripts with highly tissue-specific patterns of regulation. By unbiased profiling of gene ontologies, we have identified the distinctive functional features of each tissue's response and integrate them into a comprehensive view of the whole-body transition from one strongly adaptive phenotype to another. This approach revealed an expression signature suggestive of atrophy in cooled skeletal muscle. This environmental genomics approach by using a well studied but nongenomic species has identified a range of candidate genes endowing thermotolerance and reveals a previously unrecognized scale and complexity of responses that impacts at the level of cellular and tissue function.
Differential nitros(yl)ation of blood and tissue constituents during glyceryl trinitrate biotransformation
in vivo
Authors: Janero David R. , Bryan Nathan S. , Saijo Fumito , Dhawan Vijay , Schwalb David J. , Warren Michael C. , Feelisch Martin
Published: November 2004

Nitric oxide (NO)-derived products may modify tissue constituents, forming
S
- and
N
-nitroso adducts and metal nitrosyls implicated in NO signaling. Nitrovasodilator drugs have been in widespread use for more than a century, yet their biotransformation pathways to NO and their effects as NO donors across tissues remain ill defined. By using a metabonomics approach (termed “NObonomics”) for detailing the global NO-related metabolism of the cornerstone nitrovasodilator, glyceryl trinitrate (GTN; 0.1–100 mg/kg), in the rat
in vivo
, we find that GTN biotransformation elicits extensive tissue nitros(yl)ation throughout all major organ systems. The corresponding reaction products remained detectable hours after administration, and vascular tissue was not a major nitros(yl)ation site. Extensive heart and liver modifications involved both S- and N-nitrosation, and RBC
S
-nitrosothiol formation emerged as a sensitive indicator of organic nitrate metabolism. The dynamics of GTN-derived oxidative NO metabolites in blood did not reflect the nitros(yl)ation patterns in the circulation or in tissues, casting doubt on the usefulness of plasma nitrite/nitrate as an index of NO/NO-donor biodynamics. Target-tissue NO metabolites varied in amount and type with GTN dose, suggesting a dose-sensitive shift in the prevailing routes of GTN biotransformation (“metabolic shunting”) from thiol nitrosation to heme nitrosylation. We further demonstrate that GTN-induced nitros(yl)ation is modulated by a complex, tissue-selective interplay of enzyme-catalyzed pathways. These findings provide insight into the global
in vivo
metabolism of GTN at pharmacologically relevant doses and offer an additional experimental paradigm for the NObonomic analysis of NO-donor metabolism and signaling.
dsu
functions in a MYO5A-independent pathway to suppress the coat color of
dilute
mice
Authors: O'Sullivan T. Norene , Wu Xufeng S. , Rachel Rivka A. , Huang Jiang-Dong , Swing Deborah A. , Matesic Lydia E. , Hammer John A. , Copeland Neal G. , Jenkins Nancy A.
Published: November 2004

MYO5A is a major actin-based vesicle transport motor that binds to one of its cargos, the melanosome, by means of a RAB27A/MLPH receptor. When one of the members of this receptor–motor complex is mutated, the melanosomes clump in the perinuclear region of the melanocyte and are transferred unevenly to the developing hair, leading to a dilution of coat color. Mutation of a fourth gene,
dilute suppressor
(
dsu
), suppresses this coat color dilution. MYO5A is required for the peripheral accumulation of melanosomes in melanocytes, but its role in melanosome transfer to neighboring keratinocytes and the hair is unknown. Here, we show that MYO5A is nonessential for melanosome transfer, although pigment incorporation into the hair in MYO5A-deficient mice is uneven, probably due to the clumping of melanosomes that occurs in the perinuclear region of mutant melanocytes. We also show that
dsu
is caused by a loss-of-function mutation in a unique vertebrate-specific protein that appears to function in an MYO5A-independent pathway to alter pigment incorporation into the hair. Therefore,
dsu
identifies a unique protein involved in pigmentation of the mammalian hair.
Peer acceptance and self-perceptions of verbal and behavioural aggression and social withdrawal
Authors: Chang Lei , Li Kin Kit , Lei Li , Liu Hongyun , Guo Boliang , Wang Yan , Fung Kitty Y.
Published: November 2004

This study presents a model of maladaptive social interactions that includes both behavioural and communication correlates of peer acceptance and self-perceived social competence. Tested in a sample of 377 Hong Kong secondary school students, verbal and nonverbal aggression contributed concurrently and longitudinally to peer acceptance. Communication avoidance was predictive only of self-perceived social competence but not of peer acceptance, whereas, as observed in Western children, social withdrawal negatively predicted peer acceptance and self-perceived social competency. These findings are presented in a discussion of the verbal and nonverbal involvement in defining aggression and social withdrawal in adolescent social interactions.
What can Functional Neuroimaging Tell the Experimental Psychologist?
Authors: Henson Richard
Published: November 2004

I argue here that functional neuroimaging data—which I restrict to the haemodynamic techniques of fMRI and PET—can inform psychological theorizing, provided one assumes a “systematic” function–structure mapping in the brain. In this case, imaging data simply comprise another dependent variable, along with behavioural data, that can be used to test competing theories. In particular, I distinguish two types of inference: function-to-structure deduction and structure-to-function induction. With the former inference, a qualitatively different pattern of activity over the brain under two experimental conditions implies at least one different function associated with changes in the independent variable. With the second type of inference, activity of the same brain region(s) under two conditions implies a common function, possibly not predicted a priori. I illustrate these inferences with imaging studies of recognition memory, short-term memory, and repetition priming. I then consider in greater detail what is meant by a “systematic” function–structure mapping and argue that, particularly for structure-to-function induction, this entails a one-to-one mapping between functional and structural units, although the structural unit may be a network of interacting regions and care must be taken over the appropriate level of functional/structural abstraction. Nonetheless, the assumption of a systematic function–structure mapping is a “working hypothesis” that, in common with other scientific fields, cannot be proved on independent grounds and is probably best evaluated by the success of the enterprise as a whole. I also consider statistical issues such as the definition of a qualitative difference and methodological issues such as the relationship between imaging and behavioural data. I finish by reviewing various objections to neuroimaging, including neophrenology, functionalism, and equipotentiality, and by observing some criticisms of current practice in the imaging literature.
Spin Dynamics in One-Dimensional and Percolating Systems Studied under UK–Japan Collaboration Program on Neutron Scattering
Authors: Itoh Shinichi
Published: November 2004

Results on the spin dynamics in one-dimensional (1D) and percolating systems obtained under the UK–Japan Collaboration Program on Neutron Scattering are summarized.
Spin Dynamics in High-Tc Superconductor YBa2Cu3O6.9
Authors: Yokoo T. , Arai M. , Frost C.D. , Endoh Y. , Egami T. , Shiohara Y. , Tajima S.
Published: November 2004

Dynamical structures in the vicinity of Q = (π, π) of optimally-doped YBa2Cu3O6.9 were measured by means of an inelastic neutron scattering technique utilizing pulsed neutron source. Obtained incommensurability δ of energy transfer at E = 36 meV was found to be ∼0.1 [rlu] which is not the value to be expected from the formation of spin-charge stripes. In higher energy above resonance energy (42 meV), a ring structure centered at (π, π) was observed up to 54 meV. Combined with the low energy part of the dynamical structure, the obtained results provide a total picture of the dynamical aspects in the high-Tc superconductor YBa2Cu3O6.9.
Pulsed High Magnetic Fields for Neutron and X-ray Scattering Experiments
Authors: Nojiri H.
Published: November 2004

Feasibility of various types of pulsed magnetic field generators for neutron scattering and X-ray scattering is discussed. Both, a conventional single shot type pulsed field and repeating type pulsed field generators are considered. As a new approach, a miniature type generator is also proposed. The characteristics of possible magnetic fields such as time structure, intensity and interval between shots are compared by considering the requests for the spectrometer in which a high field coil is installed.
Development of 3He Polarized Neutron Spin Filters at KENS
Authors: Ino Takashi , Jones Gordon L. , Kim Guinyun , Masuda Yasuhiro , Muto Suguru , Skoy Vadim R.
Published: November 2004

We report on progress of the development of neutron spin filters based on polarized gaseous 3He at KENS (Neutron Science Laboratory, KEK). 3He polarizer cells made of quartz glass and sapphire are prepared and tested. Quartz glass cells with spin relaxation times of more than 100 h are routinely produced. A 3He polarization of 63% has been achieved with a sapphire cell of a 3He pressure of 3 atm, and with this 3He cell, a neutron polarization of about 86% was obtained at thermal energy.
Incoherent Inelastic Neutron Scattering Study of Antiferroelectric Cu(HCOO)2·4H2O Crystal
Authors: Omura T. , Itoh K. , Moriyoshi C. , Ikeda S. , Kamiyama T. , Parker S.F.
Published: November 2004

Incoherent inelastic neutron scattering spectra of antiferroelectric Cu(HCOO)2·4H2O and its isomorphous Cu(HCOO)2·4D2O were measured. Comparing the spectra between these crystals, we extracted the H2O-related modes from many other modes. We find new peaks in the energy range of the H2O librational modes. The spectra in this range become broad above the phase transition temperature indicating that the antiferroelectric dynamics are dominated by the order–disorder of the H2O molecules induced by the out-of-plane hydrogen motion.
Magnetic Correlations in CuGeO3
Authors: Kajimoto R. , Itoh S. , Bull M.J. , Kakurai K. , Harada I. , Arai M. , Fujita M. , Nishi M.
Published: November 2004

The static spin structure factor S(Q) of CuGeO3 was determined above its spin-Peierls transition temperature by inelastic neutron scattering. At 20 K, S(Q) has a Lorentzian line shape centered at the antiferromagnetic (AF) zone center. With increasing temperature, however, it splits into two peaks with their centers at incommensurate wave vectors at higher temperatures (70 and 120 K). The observed results are consistent with the prediction by recent numerical studies on the S = 1/2 Heisenberg AF chain with competing spin interactions [I. Harada and Y. Aoyama, (1999) “Static spin structure factor of CuGeO3 above spin-Peierls transition temperature”, J. Phys. Chem. Solids 60, 1105; I. Harada, Y. Nishiyama, Y. Aoyama and S. Mori, (2000) “Spin correlation in the one-dimensional Heisenberg antiferromagnet with competing interactions”, J. Phys. Soc. Jpn. 69, (Suppl. A), 339].