bluuebunny/crossref_metadata_2025 huggingface dataset:
Overcoming free energy barriers using unconstrained molecular dynamics simulations
Authors: Hénin Jérôme , Chipot Christophe
Published: July 2004

Association of unconstrained molecular dynamics (MD) and the formalisms of thermodynamic integration and average force [Darve and Pohorille, J. Chem. Phys. 115, 9169 (2001)] have been employed to determine potentials of mean force. When implemented in a general MD code, the additional computational effort, compared to other standard, unconstrained simulations, is marginal. The force acting along a chosen reaction coordinate ξ is estimated from the individual forces exerted on the chemical system and accumulated as the simulation progresses. The estimated free energy derivative computed for small intervals of ξ is canceled by an adaptive bias to overcome the barriers of the free energy landscape. Evolution of the system along the reaction coordinate is, thus, limited by its sole self-diffusion properties. The illustrative examples of the reversible unfolding of deca-L-alanine, the association of acetate and guanidinium ions in water, the dimerization of methane in water, and its transfer across the water liquid-vapor interface are examined to probe the efficiency of the method.
Franck-Condon effects in collision-induced electronic energy transfer: I2(E;v=1,2)+He, Ar
Authors: Chandra Pooja P. , Stephenson Thomas A.
Published: July 2004

Collisions of I2 in the E electronic state with rare gas atoms result in electronic energy transfer to the D, β, and D′ ion-pair electronic states. Rate constants for each of these channels have been measured when I2 is initially prepared in the J=55, v=1 and 2 levels in the E state. The rate constants and effective hard sphere collision cross sections confirm the trends observed when v=0 in the E state is initially prepared: He collisions favor population of the D state, while Ar collisions favor population of the β state. Final state vibrational level distributions are determined by spectral simulation and are found to be qualitatively consistent with the trends in the Franck-Condon factors. The experimental distributions are also compared to the recent quantum scattering calculations of Tscherbul and Buchachenko.
Incoherent noise and quantum information processing
Authors: Boulant N. , Emerson J. , Havel T. F. , Cory D. G. , Furuta S.
Published: July 2004

Incoherence in the controlled Hamiltonian is an important limitation on the precision of coherent control in quantum information processing. Incoherence can typically be modeled as a distribution of unitary processes arising from slowly varying experimental parameters. We show how it introduces artifacts in quantum process tomography and we explain how the resulting estimate of the superoperator may not be completely positive. We then go on to attack the inverse problem of extracting an effective distribution of unitaries that characterizes the incoherence via a perturbation theory analysis of the superoperator eigenvalue spectra.
Nonexponential statistics of fluorescence photobleaching
Authors: Berglund Andrew J.
Published: July 2004

In this paper, I consider theoretical models of the decay via photobleaching of a sample of surface-immobilized fluorescent molecules excited by a spatially varying laser intensity profile. I show that, with mild restrictions on the photobleaching mechanism, the fluorescence decay measured in a nonuniform excitation profile is always nonexponential. Under the same conditions, the fluorescence decay can always be approximated by a discrete sum of exponentials. A particular example is given in which a homogeneous population of fluorophores with a single (intensity-dependent) photobleaching lifetime, when illuminated by a Gaussian laser, exhibits power law fluorescence decay at long times. These results indicate that the observation of multiple exponentials in single molecule or ensemble photobleaching lifetime measurements can arise solely as an artifact of a spatially varying laser profile and is not necessarily indicative of heterogeneity in molecular internal states, conformation, or local environment.
Experimental study of the impact of an ink-jet printed droplet on a solid substrate
Authors: van Dam Dirkjan B. , Le Clerc Christophe
Published: July 2004

This paper reports on an experimental study of the impact of water droplets on a solid substrate, with a droplet radius between 18 and 42 μm. We optically measured the interface shape during impact. The measured impact sequences show the impact phenomenology, droplet radius as a function of time, and oscillation behavior in the later stages of impact. The measured radius during impact is compared with existing models, and some of the deficiencies of common models are shown. The measured oscillation frequency in the later stage of impact compares well with an available analytical model. In addition, we measured the volume of the small bubble, which forms in the initial impact stage, as a function of impact velocity. The measured volume compares reasonably well with an approximate model based on air entrapment.
Grand canonical Monte Carlo simulation of a model colloid–polymer mixture: Coexistence line, critical behavior, and interfacial tension
Authors: Vink R. L. C. , Horbach J.
Published: July 2004

Grand canonical Monte Carlo simulations are used to study phase separation in a simple colloid–polymer model, the so-called Asakura–Oosawa model. To overcome the problem of small acceptance rates of the grand-canonical moves, cluster moves are introduced. Successive umbrella sampling, recently introduced by Virnau and Müller [J. Chem. Phys. 120, 10925 (2004)], is used to access the phase-separated regime. The unmixing binodal and the interfacial tension are measured and compared to theoretical predictions. By means of finite-size scaling, the behavior close to the critical point is also investigated. Close to criticality, we observe substantial deviations from mean-field behavior.
The glass-to-liquid transition of the emulsified high-density amorphous ice made by pressure-induced amorphization
Authors: Mishima Osamu
Published: July 2004

Emulsified high-density amorphous ice, made by pressure-induced amorphization of emulsified ice Ih, was decompressed at about 160 K. The onset of an endothermic event was observed around 0.4 GPa during the decompression. This is consistent with existence of the glass transition to a liquid state, implying the close relationship between melting and amorphization.
Evaporatively cooled M+(H2O)Ar cluster ions: Infrared spectroscopy and internal energy simulations
Authors: Vaden Timothy D. , Weinheimer Corey J. , Lisy James M.
Published: July 2004

Rotationally resolved IR spectra of M+(H2O)Ar cluster ions for M=Na, K, and Cs in the O–H stretch region were measured in a triple-quadrupole mass spectrometer. Analysis of the spectra yields O–H stretch vibrational band origins and relative IR intensities of the symmetric and asymmetric modes. The effect of the alkali-metal ions on these modes results in frequency shifts and intensity changes from the gas phase values of water. The A-rotational constants are also obtained from the rotational structure and are discussed. Experimentally, the temperatures of these species were deduced from the relative populations of the K-rotational states. The internal energies and temperatures of the cluster ions for Na and K were simulated using RRKM calculations and the evaporative ensemble formalism. With binding energies and vibrational frequencies obtained from ab initio calculations, the average predicted temperatures are qualitatively consistent with the experimental values and demonstrate the additional cooling resulting from argon evaporation.
Effective potential analytic continuation calculations of real time quantum correlation functions: Asymmetric systems
Authors: Horikoshi Atsushi , Kinugawa Kenichi
Published: July 2004

We apply the effective potential analytic continuation (EPAC) method to one-dimensional asymmetric potential systems to obtain the real time quantum correlation functions at various temperatures. Comparing the EPAC results with the exact results, we find that for an asymmetric anharmonic oscillator the EPAC results are in very good agreement with the exact ones at low temperature, while this agreement becomes worse as the temperature increases. We also show that the EPAC calculation for a certain type of asymmetric potentials can be reduced to that for the corresponding symmetric potentials.
Collisional transport in a low aspect ratio tokamak
Authors: Gates D. A. , Mynick H. E. , White R. B.
Published: July 2004

Calculations of collisional diffusivities in toroidal magnetic plasma confinement devices order the toroidal gyroradius to be small relative to the poloidal gyroradius, i.e., ρiφρiθ, where ρiφ≡mivthi/qBφ and ρiθ≡mivthi/qBθ. This ordering is central to what is usually referred to as neoclassical transport theory. This ordering is incorrect at low aspect ratio (with aspect ratio A≡R/a, where R is the major radius of the torus and a is the minor radius), where it can be the case that ρiφ>ρiθ. The correction to the test particle diffusivities is numerically calculated by comparing the diffusivities as determined by a full orbit code (which we refer to as omniclassical diffusion) with those from a gyroaveraged orbit code (neoclassical diffusion), and then corroborated by an analytic calculation. The omniclassical diffusion can be up to 2.5 times the calculated neoclassical value. The implications of this work for the analysis of collisional transport in low aspect ratio devices are discussed.
Cultural Festivals and Regional Identities in South Korea
Authors: Shin HaeRan
Published: July 2004

This paper extends the literature in cultural festivals and urban methods to consider a case where the objectives of local government in holding a cultural festival exceeded economic development. In the city of Gwangju in South Korea, authorities initiated the Biennale exhibition to replace the troubling image of its political history with the new image of a city of art. This attempted transformation faced resistance from citizens who wanted to protect and develop Gwangju's own political identity and image. From 1995 to 2002, four Biennales were held. The Biennale, initiated to remove the controversial political image of Gwangju, became a place where Gwangju's history could be reinterpreted and its identity could be negotiated and defined by its own civil society.
Making Geographies and Histories? Constructing Local Circuits of Value
Authors: Lee Roger , Leyshon Andrew , Aldridge Theresa , Tooke Jane , Williams Colin , Thrift Nigel
Published: July 2004

Reflecting on findings from research conducted in the United Kingdom, we consider some implications for an understanding of economic geographies of the emergence of local currency systems (LCSs) within developed economies. LCSs are founded on the creation of local currencies and driven by local—but contested—circuits of consumption, exchange, and production. In this paper we are concerned with three interrelated sets of issues: the intersections of social and material relations and practices in the construction of economic geographies; the possibilities—constrained by these intersections—of creating alternative economic geographies; and the consequent possibilities of contributing to economic proliferation. We distinguish between three main forms of LCS—LETSystems, LETS schemes, and Time Dollars—differentiated along a range of institutional, organisational, ethical, and moral dimensions. These LCSs reflect and illustrate the diversity of meanings, understandings, and intentions brought to bear upon economic geographies. The existence—even if only temporary—of LCSs is testament to the (limited) possibilities of local economic self-determination and organisation; but their material ineffectiveness, decline, and uneven geographical spread reflect their formative links with mainstream practices and social relations and their internal contradictions and barriers. These characteristics illustrate the vulnerabilities inherent in all economic geographies and not just in those that are locally constructed.
The kinase Grk2 regulates Nedd4/Nedd4-2-dependent control of epithelial Na
+
channels
Authors: Dinudom Anuwat , Fotia Andrew B. , Lefkowitz Robert J. , Young John A. , Kumar Sharad , Cook David I.
Published: July 2004

Epithelial Na
+
channels mediate the transport of Na across epithelia in the kidney, gut, and lungs and are required for blood pressure regulation. They are inhibited by ubiquitin protein ligases, such as Nedd4 and Nedd4-2, with loss of this inhibition leading to hypertension. Here, we report that these channels are maintained in the active state by the G protein-coupled receptor kinase, Grk2, which has been previously implicated in the development of essential hypertension. We also show that Grk2 phosphorylates the C terminus of the channel β subunit and renders the channels insensitive to inhibition by Nedd4-2. This mechanism has not been previously reported to regulate epithelial Na
+
channels and provides a potential explanation for the observed association of Grk2 overactivity with hypertension. Here, we report a G protein-coupled receptor kinase regulating a membrane protein other than a receptor and provide a paradigm for understanding how the interaction between membrane proteins and ubiquitin protein ligases is controlled.
Kinetics of regulated protein–protein interactions revealed with firefly luciferase complementation imaging in cells and living animals
Authors: Luker Kathryn E. , Smith Matthew C. P. , Luker Gary D. , Gammon Seth T. , Piwnica-Worms Helen , Piwnica-Worms David
Published: July 2004

Signaling pathways regulating proliferation, differentiation, and apoptosis are commonly mediated through protein–protein interactions as well as reversible phosphorylation of proteins. To facilitate the study of regulated protein–protein interactions in cells and living animals, we optimized firefly luciferase protein fragment complementation by screening incremental truncation libraries of N- and C-terminal fragments of luciferase. Fused to the rapamycin-binding domain (FRB) of the kinase mammalian target of rapamycin and FK506-binding protein 12 (FKBP), respectively, the optimized FRB-N-terminal luciferase fragment (NLuc)/C-terminal luciferase fragment (CLuc)-FKBP luciferase complementation imaging (LCI) pair reconstituted luciferase activity in cells upon single-site binding of rapamycin in an FK506-competitive manner. LCI was used in three independent applications. In mice bearing implants of cells expressing the FRB-NLuc/CLuc-FKBP LCI pair, dose- and time-dependent luciferase activity allowed target-specific pharmacodynamic analysis of rapamycin-induced protein–protein interactions
in vivo
. In cells expressing a Cdc25C-NLuc/CLuc-14-3-3ε LCI pair, drug-mediated disruption of cell cycle regulated protein–protein interactions was demonstrated with the protein kinase inhibitor UCN-01 in a phosphoserine-dependent manner. When applied to IFN-γ-dependent activation of Janus kinase/signal transducer and activator of transcription 1 (STAT1), LCI revealed, in the absence of ligand-induced phosphorylation, STAT1 proteins existing in live cells as preformed dimers. Thus, optimized LCI provides a platform for near real-time detection and characterization of regulated and small molecule-induced protein–protein interactions in intact cells and living animals and should enable a wide range of novel applications in drug discovery, chemical genetics, and proteomics research.
Diet composition and the risk of type 2 diabetes: epidemiological and clinical evidence
Authors: Parillo M. , Riccardi G.
Published: July 2004

In the last 10 years nutritional research on diabetes has improved dramatically in terms of both number of studies produced and quality of methodologies employed. Therefore, it is now possible to attempt to provide the evidence on which nutritional recommendations for the prevention of type 2 diabetes could be based. We therefore performed a literature search and, among the papers published in indexed journals, we selected relevant epidemiological (mostly prospective) and controlled intervention studies. Lifestyle factors that have, so far, been consistently associated with increased risk of type 2 diabetes are overweight and physical inactivity. However, recent evidence from epidemiological studies has shown that the risk of type 2 diabetes is also associated with diet composition, particularly with: (1) low fibre intake; (2) a high trans fatty acid intake and a low unsaturated:saturated fat intake ratio; (3) absence of or excess alcohol consumption. All these factors are extremely common in Western populations and therefore the potential impact of any intervention on them is large: indeed, >90% of the general population has one or more of these risk factors. The ability to correct these behaviours in the population is estimated to reduce the incidence of diabetes by as much as 87%. Recent intervention studies have shown that type 2 diabetes can be prevented by lifestyle changes aimed at body-weight reduction, increased physical activity and multiple changes in the composition of the diet. Within this context, the average amount of weight loss needed is not large, about 5% initial weight, which is much less than the weight loss traditionally considered to be clinically significant for prevention of type 2 diabetes. In conclusion, new emphasis on prevention by multiple lifestyle modifications, including moderate changes in the composition of the habitual diet, might limit the dramatic increase in incidence of type 2 diabetes envisaged worldwide.
Thiamin status during the third trimester of pregnancy and its influence on thiamin concentrations in transition and mature breast milk
Authors: Ortega Rosa M. , Martínez Rosa M. , Andrés Pedro , Marín-Arias Lilliam , López-Sobaler Ana M.
Published: July 2004

Thiamin deficiency remains an important public health problem in some populations. The aim of the present investigation was to study thiamin status during the third trimester of pregnancy and its influence on the concentration of this vitamin in transition (days 13–14 of lactation) and mature breast milk (day 40 of lactation) in a group of Spanish women. The pregnancies and lactation periods of fifty-one healthy women 18–35 (mean 26·7 (sd 3·7)) years old were monitored. Vitamin intake during the third trimester was determined by recording the consumption of foods over 5 d and of the quantities provided by dietary supplements. Thiamin status during this stage of pregnancy was determined by measuring the activation coefficient of erythrocyte transketolase (α-ETK). Milk thiamin content was estimated (in 41% of the subjects) by oxidizing thiamin to thiocrome and measuring fluorescence. Subjects with thiamin intakes above that recommended (group H) had more satisfactory serum α-ETK coefficients (1·01 (sd 0·19)) than did those with lower intakes (group L) (1·21 (sd 0·30); P>0·05). Mature milk thiamin concentrations were significantly higher in group H subjects (0·59 (sd 0·44) μmol/l) than group L subjects (0·25 (sd 0·07) μmol/l). Subjects with α-ETK coefficients >1·25 in the third trimester had significantly lower mature milk thiamin concentration (0·31 (sd 0·10) μmol/l) than did subjects with more satisfactory α-ETK levels at this time (0·55 (sd 0·42) μmol/l; P>0·05). The thiamin status of women can be improved since 25·5% of subjects took less than that recommended and 13·7% showed signs of severe deficiency (α-ETK >1·25). The influence of maternal thiamin intake on α-ETK coefficients and on mature breast milk thiamin concentration is confirmed.
Dietary secoisolariciresinol diglucoside and its oligomers with 3-hydroxy-3-methyl glutaric acid decrease vitamin E levels in rats
Authors: Frank Jan , Eliasson Christina , Leroy-Nivard Diane , Budek Alicja , Lundh Torbjörn , Vessby Bengt , Åman Per , Kamal-Eldin Afaf
Published: July 2004

Secoisolariciresinol diglucoside (SDG) is an important dietary lignan that is found at very high levels in flaxseed (1–4%, w/w). Flaxseed lignans have received much research interest in recent years because of reported phyto-oestrogenic, anticarcinogenic, and anti-atherogenic effects. Previously, flaxseed feeding has been shown to decrease vitamin E concentrations in rats despite the antioxidant potential of SDGin vitro. Sesamin, a sesame lignan, on the other hand has been shown to increase vitamin E concentrations in rats. The aim of the present study was to investigate the effect of dietary SDG and its oligomers on vitamin E and cholesterol concentrations in rats. SDG was extracted from defatted flaxseed flour with a dioxane–ethanol mixture and purified by silica column chromatography. The major oligomers with 3-hydroxy-3-methyl glutaric acid, containing a high ratio of SDG top−coumaric and ferulic acid glucosides, were purified from the extracts by reversed-phase liquid chromatography. When fed to rats at 0·1% in the diet for 27%, both SDG and its oligomers had no effect on animal performance but caused an increase in liver cholesterol and a 2-fold reduction in the levels of α- and γ-tocopherols in rat plasma and liver. It is notable that a phenolic antioxidant, such as SDG, causes a vitamin E-lowering effect in rats. This cannot be explained at present, but warrants further investigations with respect to the magnitude, mechanism, and significance of the observed effect for human nutrition.
γ-Tocopherol as a possible marker for nutrition-related risk: results from four National Diet and Nutrition Surveys in Britain
Authors: Bates C. J. , Mishra G. D. , Prentice A.
Published: July 2004

Relationships between vitamin E status (α and γ-tocopherol and their ratio in plasma), anthropometric and biochemical indices, and food and nutrient intakes, were studied in four British National Diet and Nutrition Surveys: children aged 1·5–4·5 years, young people aged 4·0–18·0 years, adults 19·0–64·0 years and adults aged ≥65·0 years. γ-Tocopherol:α-tocopherol ratio declined with age. In older women γ-tocopherol and γ-tocopherol:α-tocopherol ratios were directly related to indices of obesity. In young men α- and γ-tocopherols were directly correlated with obesity, but γ-tocopherol:α-tocopherol ratio was not. For young people and toddlers, fewer obesity indices were available and relationships were weaker. Other fat- and water-soluble vitamin indices correlated directly with α-tocopherol and inversely with γ-tocopherol and γ-tocopherol:α-tocopherol ratio. Whereas α-tocopherol correlated directly with ‘healthy’ nutrient choices (such as intrinsic sugars, dietary fibre, vitamins and potassium) and inversely with ‘unhealthy’ choices (extrinsic sugars and monounsaturated fats, i.e. avoidance of polyunsaturated fat), γ-tocopherol and the γ-tocopherol:α-tocopherol ratio related inversely with ‘healthy’ choices. Food groups had analogous relationships; thus, α-tocopherol related directly to use of polyunsaturated fats, fresh fruits and fruit juices, and inversely to non-polyunsaturated fats and extrinsic sugar. The reverse was true for γ-tocopherol and γ-tocopherol:α-tocopherol ratio. Although the mechanisms underlying these relationships are obscure, the γ-tocopherol:α-tocopherol ratio may reveal poor dietary choices, status predictors and a propensity for obesity in later life, especially in women.
Phylloquinone (vitamin K1) intakes and food sources in 18–64-year-old Irish adults
Authors: Duggan Paula , Cashman Kevin D. , Flynn Albert , Bolton-Smith Caroline , Kiely Máiréad
Published: July 2004

Dietary vitamin K1(phylloquinone) levels that are sufficient to maintain normal blood coagulation may be sub-optimal for bone, and habitual low dietary intakes of vitamin K may have an adverse effect on bone health. The objective of the present study was to measure the intake and adequacy of phylloquinone intake and the contribution of foods to phylloquinone intake in a nationally representative sample of Irish adults. The North/South Ireland Food Consumption Survey database was used, which contains data collected using a 7 d food diary in a randomly selected sample of Irish adults aged 18–64 years (n1379; 662 men and 717 women). Phylloquinone intakes were estimated using recently compiled food composition data for phylloquinone. The mean daily intake of phylloquinone from food sources was 79 (sd 44) μg. Intakes were significantly higher (P>0·001) in men than in women at levels of 84 and 75quest;μgsol;d. The main contributors to phylloquinone intakes were vegetables (48%), particularly green vegetables (26%). Potatoes (including chipped and fried potatoes), dairy products and fat spreads contributed 10% each and meat contributed 8%. In men, social class and smoking status influenced phylloquinone intakes. Of the population, 52% had phylloquinone intakes below 1 μg/kg body weight and only 17% of men and 27% of women met the US adequate intakes of 120 and 90 μg/d, respectively. The present study shows that habitual phylloquinone intakes in Irish adults are low, which may have implications for bone health.
A comparison of three xylanases on the nutritive value of two wheats for broiler chickens
Authors: Choct M. , Kocher A. , Waters D. L. E. , Pettersson D. , Ross G.
Published: July 2004

Three xylanase products, xylanase A derived from Thermomyces lanuginosus, xylanase B from Humicola insolens and xylanase C from Aspergillus aculeatus, were examined for their effects on the nutritive value of wheat. The study investigated the effects of enzyme addition to broiler diets based on a low-metabolisable-energy (ME) wheat and a normal-ME wheat, with the emphasis on changes in composition of the NSP along the digestive tract in broiler chickens. There were significant (P>0·01) enzyme and wheat effects on the apparent ME, but there was no wheat×enzyme interaction on apparent ME. Weight gain and feed conversion efficiency (except xylanase C for normal wheat) were also significantly (P>0·01) increased by the xylanases. The enzymes differed in their effect on a number of important nutritional parameters. Xylanase A reduced (P>0·05) the excreta moisture level from 77·1% in birds fed the normal-ME wheat control to 73·4% and from 77·4% in those fed the low-ME wheat to 73·0%. The other two enzymes did not affect excreta moisture levels. The digesta viscosity in the duodenum, jejunum and ileum of birds fed both types of wheat was reduced (P>0·01) by xylanases A and C, but was increased (P>0·01) in the jejunum and ileum by xylanase B. The digestibility of the soluble NSP was mostly negative in the small intestine. The digestibility of the insoluble NSP differed (P>0·01) between the two wheats, with those in the low-ME wheat being more digestible (14 v. 28%). When supplemented with xylanase A, the ileal digestibility of the insoluble NSP in the normal- and low-ME wheats was increased by 28 and 42?%, respectively. Xylanases B and C did not affect the digestibility of the insoluble NSP regardless of wheat type. It may be concluded that wheats with low or normal ME values vary in their responses to xylanase supplementation. Apart from having an elevated level of soluble NSP, low-ME wheat may also contain insoluble NSP, which in the present study appeared to be more easily degradable in the gut of the chicken.
Inter-relationship of microbial activity, digestion and gut health in the rabbit: effect of substituting fibre by starch in diets having a high proportion of rapidly fermentable polysaccharides
Authors: Gidenne Thierry , Jehl Nathalie , Lapanouse André , Segura Muriel
Published: July 2004

Caecal microbial activity, digestion and gut health were analysed in the young rabbit, in response to fibre substitution by starch, in diets with high proportions of rapidly fermentable polysaccharides (pectins+hemicelluloses:acid-detergent fibre (ADF) ratio of 1·7). A range of five diets corresponding to a 60% linear reduction of the ADF level (230 to 92 g ADF/kg) without changes in the fibre quality, and to a corresponding linear increase in dietary starch, was given ad libitum to young rabbits from 18 d until 70 d of age. A one half reduction of the ADF level resulted in a sharp increase in energy digestibility (+25 units), associated with a lower feed intake (−35%) and to an increase of the mean retention time (+6 h) in the whole digestive tract. Despite large variations in the fibre intake (20 to 59 g ADF/d), the fibre digestive efficiency remained similar among the five diets. Starch ileal concentrations were low after 4 weeks of age (>5%), and variations with age were significant when the dietary starch level was over 19%. A 65% lower biomass production was measured when the ADF level progressed from 230 to 165 g/kg, and no precise relationship was found with fermentative activity. Reducing the fibre intake led to a linear decrease of caecal volatile fatty acids concentrations, and to higher pH and NH3 levels. An increased occurrence of mortality by diarrhoea was registered with the lowest fibre intake. It can be concluded that a sufficient supply of fibre, with high proportions in rapidly fermentable polysaccharides, stimulates the maturation of microbial activity and reduces the occurrence of diarrhoea.
Modeling interactome: scale-free or geometric?
Authors: Pržulj N. , Corneil D. G. , Jurisica I.
Published: July 2004

Motivation: Networks have been used to model many real-world phenomena to better understand the phenomena and to guide experiments in order to predict their behavior. Since incorrect models lead to incorrect predictions, it is vital to have as accurate a model as possible. As a result, new techniques and models for analyzing and modeling real-world networks have recently been introduced.

Results: One example of large and complex networks involves protein–protein interaction (PPI) networks. We analyze PPI networks of yeast Saccharomyces cerevisiae and fruitfly Drosophila melanogaster using a newly introduced measure of local network structure as well as the standardly used measures of global network structure. We examine the fit of four different network models, including Erdös-Rényi, scale-free and geometric random network models, to these PPI networks with respect to the measures of local and global network structure. We demonstrate that the currently accepted scale-free model of PPI networks fails to fit the data in several respects and show that a random geometric model provides a much more accurate model of the PPI data. We hypothesize that only the noise in these networks is scale-free.

Conclusions: We systematically evaluate how well-different network models fit the PPI networks. We show that the structure of PPI networks is better modeled by a geometric random graph than by a scale-free model.

Supplementary information: Supplementary information is available at http://www.cs.utoronto.ca/~juris/data/ppiGRG04/
DNAFSMiner: a web-based software toolbox to recognize two types of functional sites in DNA sequences
Authors: Liu Huiqing , Han Hao , Li Jinyan , Wong Limsoon
Published: July 2004

Summary: DNAFSMiner (DNA Functional Sites Miner) is a web-based software toolbox to recognize functional sites in nucleic acid sequences. Currently in this toolbox, we provide two software: TIS Miner and Poly(A) Signal Miner. The TIS Miner can be used to predict translation initiation sites in vertebrate DNA/mRNA/cDNA sequences, and the Poly(A) Signal Miner can be used to predict polyadenylation [poly(A)] signals in human DNA sequences. The prediction results are better than those by literature methods on two benchmark applications. This good performance is mainly attributable to our unique learning method. DNAFSMiner is available free of charge for academic and non-profit organizations.

Availability:  http://research.i2r.a-star.edu.sg/DNAFSMiner/

Contact:  huiqing@i2r.a-star.edu.sg
The Baumgartner-Weiß-Schindler test for the detection of differentially expressed genes in replicated microarray experiments
Authors: Neuhäuser Markus , Senske Roswitha
Published: July 2004

Motivation: An important application of microarray experiments is to identify differentially expressed genes. Because microarray data are often not distributed according to a normal distribution nonparametric methods were suggested for their statistical analysis. Here, the Baumgartner-Weiß-Schindler test, a novel and powerful test based on ranks, is investigated and compared with the parametric t-test as well as with two other nonparametric tests (Wilcoxon rank sum test, Fisher-Pitman permutation test) recently recommended for the analysis of gene expression data.

Results: Simulation studies show that an exact permutation test based on the Baumgartner-Weiß-Schindler statistic B is preferable to the other three tests. It is less conservative than the Wilcoxon test and more powerful, in particular in case of asymmetric or heavily tailed distributions. When the underlying distribution is symmetric the differences in power between the tests are relatively small. Thus, the Baumgartner-Weiß-Schindler is recommended for the usual situation that the underlying distribution is a priori unknown.

Availability: SAS code available on request from the authors.
Discovery of meaningful associations in genomic data using partial correlation coefficients
Authors: de la Fuente Alberto , Bing Nan , Hoeschele Ina , Mendes Pedro
Published: July 2004

Motivation: A major challenge of systems biology is to infer biochemical interactions from large-scale observations, such as transcriptomics, proteomics and metabolomics. We propose to use a partial correlation analysis to construct approximate Undirected Dependency Graphs from such large-scale biochemical data. This approach enables a distinction between direct and indirect interactions of biochemical compounds, thereby inferring the underlying network topology.

Results: The method is first thoroughly evaluated with a large set of simulated data. Results indicate that the approach has good statistical power and a low False Discovery Rate even in the presence of noise in the data. We then applied the method to an existing data set of yeast gene expression. Several small gene networks were inferred and found to contain genes known to be collectively involved in particular biochemical processes. In some of these networks there are also uncharacterized ORFs present, which lead to hypotheses about their functions.

Availability: Programs running in MS-Windows and Linux for applying zeroth, first, second and third order partial correlation analysis can be downloaded at: http://mendes.vbi.vt.edu/tiki-index.php?page=Software

Supplementary information: Supplementary information can be found at: URL to be decided
Quantifying reproducibility for differential proteomics: noise analysis for protein liquid chromatography-mass spectrometry of human serum
Authors: Anderle Markus , Roy Sushmita , Lin Hua , Becker Christopher , Joho Keith
Published: July 2004

Summary: Using replicated human serum samples, we applied an error model for proteomic differential expression profiling for a high-resolution liquid chromatography-mass spectrometry (LC-MS) platform. The detailed noise analysis presented here uses an experimental design that separates variance caused by sample preparation from variance due to analytical equipment. An analytic approach based on a two-component error model was applied, and in combination with an existing data driven technique that utilizes local sample averaging, we characterized and quantified the noise variance as a function of mean peak intensity. The results indicate that for processed LC-MS data a constant coefficient of variation is dominant for high intensities, whereas a model for low intensities explains Poisson-like variations. This result leads to a quadratic variance model which is used for the estimation of sample preparation noise present in LC-MS data.
Pallidotomy: A Comparison of Responders and Nonresponders
Authors: Van Horn Gage , Hassenbusch Samuel J. , Zouridakis George , Mullani Nizar A. , Wilde Mark C. , Papanicolaou Andrew C.
Published: July 2004

OBJECTIVE

We reviewed a prospective series of 32 unilateral, large-volume, microelectrode-guided posteroventral pallidotomies to determine the differences between responsive and nonresponsive patients.

METHODS

Our patients underwent extensive pre- and postoperative evaluations. One year postoperatively, we correlated the outcomes of 25 patients with their histories, physical findings, neuropsychological assessments, and lesion characteristics to further understand the indications, limitations, and pitfalls of unilateral pallidotomy. Our group judged responsiveness by comparing the preoperative total Unified Parkinson's Disease Rating Scale off-state scores with those obtained 1 year postoperatively. A score indicating greater than 20% improvement at 1-year follow-up was rated a good outcome; improvement of greater than 40% was rated an excellent outcome.

RESULTS

Although most patients sustained long-term benefits, some demonstrated little or no improvement. Patient and lesion factors influenced outcome. Younger age (<60 yr), tremor, unilateral predominance, l-dopa responsiveness, motor fluctuations with dyskinesia, and good lesion placement predicted a good response to unilateral pallidotomy. Advanced age (>70 yr), absence of tremor, increased duration of disease, reduced responsiveness to l-dopa, frontal behavioral changes, prominent apraxic phenomena, and improper lesion placement predicted a poor response.

CONCLUSION

Unilateral, large-volume pallidotomy with precise lesion control provides long-lasting benefits for carefully selected patients.
Quantitative and Qualitative Outcome Measures after Thalamic Deep Brain Stimulation to Treat Disabling Tremors
Authors: Obwegeser Alois A. , Uitti Ryan J. , Witte Robert J. , Lucas John A. , Turk Margaret F. , Wharen Robert E.
Published: July 2004

OBJECTIVE

We studied outcome measures after unilateral and bilateral thalamic stimulation to treat disabling tremor resulting from essential tremor and Parkinson's disease. The surgical technique, qualitative and quantitative tremor assessments, stimulation parameters, locations of active electrodes, complications, and side effects are described and analyzed.

METHODS

Forty-one patients with essential tremor or Parkinson's disease underwent implantation of 56 thalamic stimulators. Preoperative qualitative and quantitative tremor measurements were compared with those obtained after unilateral and bilateral surgery, with activated and deactivated stimulators. Stimulation parameters and stimulation-related side effects were recorded, and outcome measures were statistically analyzed.

RESULTS

Qualitative measurements demonstrated significant improvement of contralateral upper-limb (P < 0.001), lower-limb (P < 0.01), and midline (P < 0.001) tremors after unilateral surgery. Ipsilateral arm tremor also improved (P < 0.01). No differences were observed with the Purdue pegboard task. Quantitative accelerometer measurements were correlated with qualitative assessments and confirmed improvements in contralateral resting (P < 0.001) and postural (P < 0.01) tremors and ipsilateral postural tremor (P < 0.05). Activities of daily living improved after unilateral surgery (P < 0.001) and additionally after bilateral surgery (P < 0.05). Adjustments of the pulse generator were required more frequently for tremor control than for amelioration of side effects. Bilateral thalamic stimulation caused more dysarthria and dysequilibrium than did unilateral stimulation. Stimulation-related side effects were reversible for all patients. Stimulation parameters did not change significantly with time. A significantly lower voltage and greater pulse width were used for patients with bilateral implants.

CONCLUSION

Unilateral thalamic stimulation and bilateral thalamic stimulation are safe and effective procedures that produce qualitative and quantitative improvements in resting, postural, and kinetic tremor. Thalamic stimulation-related side effects are mild and reversible.
Secretory Meningiomas: Clinical and Immunohistochemical Observations
Authors: Buhl Ralf , Hugo Heinz-Hermann , Mihajlovic Zoran , Maximilian Mehdorn H.
Published: July 2004

OBJECTIVE

Secretory meningiomas are a rare histological subtype of these benign intracranial tumors. Few reports have been published regarding their tendency to develop peritumoral edema.

METHODS

Between July 1994 and February 1999, 11 patients with secretory meningiomas underwent operations in the Department of Neurosurgery, University of Kiel, Kiel, Germany. The clinical notes and radiological data (computed tomographic and magnetic resonance imaging scans) were reviewed. Immunohistochemistry was used to examine the expression of carcinoembryonic antigen and epithelial membrane antigen as well as progesterone and estrogen receptors.

RESULTS

Secretory meningiomas were found in 11 (5%) of 214 patients with intracranial meningiomas who were operated on in that period. All 11 patients were women. These patients' mean age was 65 years (range, 51–87 yr). The localization of these tumors was at the convexity in seven patients, at the sphenoid ridge in two patients, and in the olfactory groove and petroclival region in one patient each. Two meningiomas had no edema surrounding them, two meningiomas had a small amount of edema, two had moderate edema, and five had severe edema. No recurrences were observed during the mean follow-up period of 26 months (range, 8–65 mo). Immunohistochemically, all tumors contained pseudopsammoma bodies and reacted with epithelial membrane antigen and carcinoembryonic antigen. The MIB-1 antibody staining index showed a mean of 2% (range, 0–7%).

CONCLUSION

Secretory meningiomas are rare tumors, and they are mainly localized at the frontal convexity and the sphenoid ridge. They are surrounded by more edema than usual. The preponderance of female patients with this presentation is striking. The expression of carcinoembryonic antigen and epithelial membrane antigen is a characteristic feature of secretory meningiomas. These meningiomas are also positive for progesterone receptors, which has been shown to be a good prognostic factor.
Nuances of Middle Cerebral Artery Aneurysm Microsurgery
Authors: Chyatte Douglas , Porterfield Rebecca
Published: July 2004

Middle cerebral artery aneurysms, a common source of subarachnoid hemorrhage, occur predominantly at the main bifurcation of the middle cerebral artery. Microsurgical clipping is the most effective treatment of these aneurysms because of their peripheral location, wide necks, and straightforward surgical anatomy. Despite the moderate technical requirements of this type of surgery, patients with ruptured aneurysms often have poor outcomes because of the high incidence of intracerebral hematomas. Although several different surgical approaches can be used, we favor a lateral-to-medial transsylvian approach for most aneurysms. This description of our surgical technique stresses minimizing retraction to avoid injury to the brain and preparing broad-based middle cerebral artery aneurysms for clipping. Management of outcomes when using these techniques also is presented.
Transorbital Keyhole Approach to Anterior Communicating Artery Aneurysms
Authors: Steiger Hans- J. , Schmid-Elsaesser Robert , Stummer Walter , Uhl Eberhard
Published: July 2004

OBJECTIVE

The transorbital keyhole approach to anterior communicating artery aneurysms was developed as a minimally invasive method for safe control of the anterior communicating artery complex. This approach does not necessitate resection of the gyrus rectus.

METHODS

The technique is described in detail. The transorbital keyhole approach provides more ventral access than the supraorbital approaches, and the anterior communicating artery complex can be controlled by splitting the basal aspect of the interhemispheric fissure.

RESULTS

Since late 1998, the authors have used the transorbital keyhole approach routinely. During the initial experience with 33 patients, the only observed complication specific to this approach was transient diplopia in one patient. At follow-up examinations 2 to 15 months after surgery, the cosmetic results were favorable as compared with those of standard pterional craniotomy.

CONCLUSION

We have designed a small, custom-tailored approach to the anterior communicating artery complex for routine use. The small orbitocranial approach is a step toward the ideal of purely extra-axial safe control of anterior communicating artery aneurysms. The orbitocranial keyhole approach seems to be substantially better than the craniotomy, although it requires additional effort and time.
Congenital Reactive Myofibroblastic Tumor of the Petrous Bone: Case Report
Authors: Pollack Ian F. , Hamilton Ronald L. , Fitz Charles , Kassam Amin , Snyderman Carl H.
Published: July 2004

OBJECTIVE AND IMPORTANCE

Myofibroblastic tumors are members of a diverse spectrum of neoplastic and quasineoplastic lesions that occur most commonly during childhood and typically involve soft tissues. We present a case of a congenital reactive myofibroblastic tumor of the petrous bone (i.e., cranial fasciitis) that was successfully treated with surgical excision.

CLINICAL PRESENTATION

A newborn girl with congenital right facial palsy and deafness was noted during imaging evaluation to have a large enhancing mass that was destroying the right petrous bone and extending into the posterior and middle cranial fossae.

INTERVENTION

After embolization, an open biopsy was performed, which revealed a moderately cellular, spindle cell neoplasm without mitosis or necrosis, with scattered lymphocytes, eosinophils, and multinucleated giant cells. The spindle cells demonstrated strong immunoreactivity for vimentin, muscle-specific actin, and α-smooth muscle actin, with prominent reticulin staining between individual cells. Staining for CD68, a histiocyte marker, was positive within the multinucleated giant cells and many of the spindle cells; CD34, S-100, and desmin staining was absent. On the basis of these findings, the lesion was classified as a reactive myofibroblastic tumor, consistent with a cranial variant of nodular fasciitis. Because of the large size and significant mass effect of the tumor, a resection was performed several days later, using a combined supra- and infratentorial approach. Dense adherence of the mass to the walls of the sigmoid sinus and the carotid artery precluded complete resection without sacrifice of these vessels, which was not performed because of the known potential of these tumors to remain stable or regress after extensive subtotal resection. The presumed residual tumor subsequently regressed, and the patient has exhibited no detectable residual disease in 2 years of follow-up monitoring.

CONCLUSION

Reactive myofibroblastic tumors of the calvarium are uncommon lesions that superficially resemble sarcomas. Recognition of this diagnostic entity is important, to avoid unnecessary treatment with intensive adjuvant therapy. Although the management of these tumors relies predominantly on surgical resection, surgical decision-making should take into account the fact that small areas of residual disease can regress spontaneously.
Intraoperative Reduction of Locked Facets in the Cervical Spine by Use of a Modified Interlaminar Spreader: Technical Note
Authors: Fazl Mahmood , Pirouzmand Farhad
Published: July 2004

OBJECTIVE

Facet dislocations commonly require intraoperative reduction after closed reduction with traction has failed. Reduction should be performed in a gradual, controlled fashion to prevent additional inadvertent spinal cord compromise.

METHODS

We describe a new technique for safe and simple dorsal reduction of facet dislocations by use of a modified interlaminar spreader. This technique requires only minimal controlled manipulation of the spine.

RESULTS

We have used this technique in 52 consecutive patients with no complications or failures related to its use in open reduction. This technique increases the stability of the cervical spine after reduction because it limits bone removal from the facet joints.

CONCLUSION

This technique provides a feasible and reliable approach to open reduction of cervical facet dislocations via the posterior approach.