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Selected AbstractsIs improved high speed performance following frusemide administration due to diuresis-induced weight loss or reduced severity of exercise-induced pulmonary haemorrhage?EQUINE VETERINARY JOURNAL, Issue S36 2006X. A. ZAWADZKAS Summary Reasons for performing study: Prerace administration of frusemide to horses has been linked with a significant improvement in racing performance, but the basis for this improvement is unclear. Objective: To test whether improved performance with prerace administration of frusemide is due to the drug's diuresis-induced weight loss rather than its apparent alleviation of exercise-induced pulmonary haemorrhage (EIPH). Methods: Eight thoroughbred horses underwent 3 trials in a random order, 2 or 3 weeks apart: control (C), frusemide/unburdened (FU), and frusemide/burdened (FB). None of the horses were known to have exhibited post-exercise epistaxis or endoscopic evidence of EIPH. Endoscope-guided bronchoalveolar lavages (BALs) were performed before and after each horse completed a standardised exercise test (SET) on an inclined treadmill to assess semi-quantitatively the volume of EIPH. For C, horses received an i.v. saline placebo injection (5 ml) and were unburdened while performing the SET. With FU, horses received frusemide (0.5 mg/kg) and were also unburdened. For FB, horses received frusemide and were burdened with weight equal to that lost during the 4 h post frusemide injection period. Erythrocyte number in BAL fluid, mass specific VO2max, time and distance for the entire SET as well as at maximum speed were recorded. A one-way repeated measures analysis of variance was conducted on all results. Results: Mass specific VO2max was significantly higher for the FU than for FB or C. Mass specific VO2max for FB and C were not different. More RBCs were found in BAL samples after C runs than after both FU and FB trial runs. Horses with the frusemide treatment (either burdened or unburdened) produced less EIPH than in the C trial, but their mass specific VO2max values were higher on the FU trial alone. For FU, horses ran longer at 115% VO2max than under C or FB conditions. Conclusion and potential relevance: Improvement of performance in the furosemide trials was due more to the weight-loss related effects of the drug than its apparent alleviation of EIPH. Further research is warranted with the same or similar project design, but with a larger sample size and with horses known to have more severe EIPH. [source] Coping With Missing Attribute Values Based on Closest Fit in Preterm Birth Data: A Rough Set ApproachCOMPUTATIONAL INTELLIGENCE, Issue 3 2001Jerzy W. Grzymala-Busse Data mining is frequently applied to data sets with missing attribute values. A new approach to missing attribute values, called closest fit, is introduced in this paper. In this approach, for a given case (example) with a missing attribute value we search for another case that is as similar as possible to the given case. Cases can be considered as vectors of attribute values. The search is for the case that has as many as possible identical attribute values for symbolic attributes, or as the smallest possible value differences for numerical attributes. There are two possible ways to conduct a search: within the same class (concept) as the case with the missing attribute values, or for the entire set of all cases. For comparison, we also experimented with another approach to missing attribute values, where the missing values are replaced by the most common value of the attribute for symbolic attributes or by the average value for numerical attributes. All algorithms were implemented in the system OOMIS. Our experiments were performed on the preterm birth data sets provided by the Duke University Medical Center. [source] The optimization of protein secondary structure determination with infrared and circular dichroism spectraFEBS JOURNAL, Issue 14 2004Keith A. Oberg We have used the circular dichroism and infrared spectra of a specially designed 50 protein database [Oberg, K.A., Ruysschaert, J.M. & Goormaghtigh, E. (2003) Protein Sci. 12, 2015,2031] in order to optimize the accuracy of spectroscopic protein secondary structure determination using multivariate statistical analysis methods. The results demonstrate that when the proteins are carefully selected for the diversity in their structure, no smaller subset of the database contains the necessary information to describe the entire set. One conclusion of the paper is therefore that large protein databases, observing stringent selection criteria, are necessary for the prediction of unknown proteins. A second important conclusion is that only the comparison of analyses run on circular dichroism and infrared spectra independently is able to identify failed solutions in the absence of known structure. Interestingly, it was also found in the course of this study that the amide II band has high information content and could be used alone for secondary structure prediction in place of amide I. [source] CRS-stack-based seismic imaging considering top-surface topographyGEOPHYSICAL PROSPECTING, Issue 6 2006Z. Heilmann ABSTRACT In this case study we consider the seismic processing of a challenging land data set from the Arabian Peninsula. It suffers from rough top-surface topography, a strongly varying weathering layer, and complex near-surface geology. We aim at establishing a new seismic imaging workflow, well-suited to these specific problems of land data processing. This workflow is based on the common-reflection-surface stack for topography, a generalized high-density velocity analysis and stacking process. It is applied in a non-interactive manner and provides an entire set of physically interpretable stacking parameters that include and complement the conventional stacking velocity. The implementation introduced combines two different approaches to topography handling to minimize the computational effort: after initial values of the stacking parameters are determined for a smoothly curved floating datum using conventional elevation statics, the final stack and also the related residual static correction are applied to the original prestack data, considering the true source and receiver elevations without the assumption of nearly vertical rays. Finally, we extrapolate all results to a chosen planar reference level using the stacking parameters. This redatuming procedure removes the influence of the rough measurement surface and provides standardized input for interpretation, tomographic velocity model determination, and post-stack depth migration. The methodology of the residual static correction employed and the details of its application to this data example are discussed in a separate paper in this issue. In view of the complex near-surface conditions, the imaging workflow that is conducted, i.e. stack , residual static correction , redatuming , tomographic inversion , prestack and post-stack depth migration, leads to a significant improvement in resolution, signal-to-noise ratio and reflector continuity. [source] Inherited disorders of human Toll-like receptor signaling: immunological implicationsIMMUNOLOGICAL REVIEWS, Issue 1 2005Cheng-Lung Ku Summary:,In vitro nine of 10 known human Toll-like receptors (TLRs) are engaged by well-defined chemical agonists that mimic microbial compounds, raising the possibility that human TLRs play a critical role in protective immunity in vivo. We thus review here the recently described human primary immunodeficiencies caused by germline mutations in genes encoding molecules involved in cell signaling downstream from TLRs. Subjects with anhidrotic ectodermal dysplasia with immunodeficiency (EDA-ID) carry either X-linked recessive hypomorphic mutations in NEMO or autosomal dominant hypermorphic mutations in IKBA. Their cells show a broad defect in nuclear factor-,B (NF-,B) activation, with an impaired, but not abolished response to a large variety of stimuli including TLR agonists. EDA-ID patients show developmental anomalies of skin appendages and a broad spectrum of infectious diseases. Patients with autosomal recessive amorphic mutations in IRAK4 present a purely immunological syndrome and more restricted defects, with specific impairment of the Toll and interleukin-1 receptor (TIR),interleukin-1 receptor-associated kinase (IRAK) signaling pathway. In these subjects, the NF-,B- and mitogen-activated protein kinase-mediated induction of inflammatory cytokines in response to TIR agonists is impaired. The patients present a narrow range of pyogenic bacterial infections that become increasingly rare with age. Altogether, these data suggest that human TLRs play a critical role in host defense. However, they do not provide compelling evidence, as even the infectious phenotype of patients with mutations in IRAK4 may result from impaired signaling via receptors other than TLRs. Paradoxically, these experiments of nature raise the possibility that the entire set of human TLRs is largely redundant in protective immunity in vivo. [source] Single-layer perceptron and dynamic neuron implementing linearly non-separable Boolean functionsINTERNATIONAL JOURNAL OF CIRCUIT THEORY AND APPLICATIONS, Issue 3 2009Fangyue Chen Abstract This paper presents a single-layer perceptron (SLP) scheme with an impulse activation function (IAF) and a dynamic neuron (DN) with a trapezoidal activation function (TAF). Combining with some interesting properties of the offset levels, it is shown that many linearly non-separable Boolean functions can be realized by using only one SLPwIAF or one DNwTAF. In the present work, a few appropriate IAF and TAF are adopted, and the inverse offset level method is used for the design of the SLPwIAF synaptic weights and the DNwTAF templates. The XOR and NXOR Boolean operations with two inputs and all 152 non-separable Boolean functions with three inputs can be easily implemented by one SLPwIAF or one DNwTAF. Finally, the entire set of 152 DNwTAF templates associated with 152 non-separable Boolean functions of three inputs is completely listed. Copyright © 2008 John Wiley & Sons, Ltd. [source] Generalization of cluster treatment of characteristic roots for robust stability of multiple time-delayed systemsINTERNATIONAL JOURNAL OF ROBUST AND NONLINEAR CONTROL, Issue 14 2008Rifat Sipahi Abstract A new perspective is presented for studying the stability robustness of nth order systems with p rationally independent delays. It deploys a holographic mapping procedure over the delay space into a new coordinate system in order to achieve the objective. This mapping collapses the entire set of potential stability switching points on a manageably small number of hypersurfaces, which are explicitly defined in the new domain. This property considerably alleviates the problem, which is otherwise infinite dimensional, and therefore notoriously complex to handle. We further declare some unrecognized features of these switching hypersurfaces, that they are (a) encapsulated within a higher-dimensional cube with edges of length 2,, which we name the ,building block', and (b) the ,offspring' of this building block, which represent the secondary stability switchings, appear within the adjacent and identical building blocks (cubes) stacked up next to each other. The final outlook is an exclusive representation of stability for this general class of systems at any arbitrary point in the delay space. Two example case studies are also provided, which are not possible to analyze using any other methodology known to the authors. Copyright © 2007 John Wiley & Sons, Ltd. [source] Modified Gaussian-2 level investigation of the identity ion-pair SN2 reactions of lithium halide and methyl halide with inversion and retention mechanismsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 4 2004Yi Ren Abstract Identity ion-pair SN2 reactions LiX + CH3X , XCH3 + LiX (X = F, Cl, Br, and I) have been investigated in the gas phase and in solution at the level of the modified Gaussian-2 theory. Two possible reaction mechanisms, inversion and retention, are discussed. The reaction barriers relative to the complexes for the inversion mechanism [,H(inv)] are found to be much higher than the corresponding values for the gas phase anionic SN2 reactions, decreasing in the following order: F (263.6 kJ mol,1) > Cl (203.3 kJ mol,1) > Br (174.7 kJ mol,1) > I (150.7 kJ mol,1). The barrier gaps between the two mechanisms [,H (ret) , ,H (inv)] increase in the order F (,62.7 kJ mol,1) < Cl (4.4 kJ mol,1) < Br (24.9 kJ mol,1) < I (45.1 kJ mol,1). Thus, the retention mechanism is energetically favorable for fluorine and the inversion mechanism is favored for other halogens, in contrast to the anionic SN2 reactions at carbon where the inversion reaction channel is much more favorable for all of the halogens. The stabilization energies for the dipole,dipole complexes CH3X · · · LiX (,Hcomp) are found to be similar for the entire set of systems with X = F, Cl, Br, and I, ranging from 53.4 kJ mol,1 for I up to 58.9 kJ mol,1 for F. The polarizable continuum model (PCM) has been used to evaluate the direct solvent effects on the energetics of the anionic and ion-pair SN2 reactions. The energetic profiles are found to be still double-well shaped for most of the ion-pair SN2 reactions in the solution, but the potential profile for reaction LiI + CH3I is predicted to be unimodal in the protic solvent. Good correlations between central barriers [,H (inv)] with the geometric looseness of the inversion transition state %C,X,, the dissociation energies of the C,X bond (DC,X) and Li,X bond (DLi,X) are observed, respectively. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 461,467, 2004 [source] A new molecular mechanics force field for the oxidized form of blue copper proteinsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2002Peter Comba Abstract A molecular mechanics force field for blue copper proteins has been developed, based on a rigid potential energy surface scan of the CuII/His/His/Cys/Met chromophore, using DFT (B3LYP) calculations and the AMBER force field for the protein backbone. The strain,energy-minimized structures of the model chromophore alone are in excellent agreement with the DFT-optimized structure, and those of the entire set of cupredoxins (five structures are considered) are, within the experimental error limits, in good agreement with the single crystal structural data. However, the structural variation in the computed structures is much smaller than those in the experimental structures. It is shown that, due to the large error limits in the experimental data, a validation of the force field with experimental structural data is impossible because, within the error limits, all experimental structures considered are virtually identical. A validation on the basis of spectroscopic data and their correlation with experimental and computed structural data is proposed, and, as a first example, the correlation of intensity ratios of the charge transfer transitions with a specific distortion mode is presented. The quality of the correlation, using the computed structures, is higher than that with the X-ray structures, and this indicates that the computed structures are meaningful. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 697,705, 2002 [source] Organizing learning materials through hierarchical topic maps: an illustration through Chinese herb medicationJOURNAL OF COMPUTER ASSISTED LEARNING, Issue 6 2007B.-J. Shih Abstract This research aims to use hierarchical topic maps to compile digital learning material and to discuss its design and application possibilities. The system renders tremendous original assets and then embeds a self-organizing map (SOM) in the material database to produce topical learning materials, as in this case, an illustration through Chinese herb medication. It helps to demonstrate robust professional information as well as knowledge structures, and provides a customized and interactive learning dynamic to support both progressive and constructive learning styles. The paper first gives a detailed procedural description of the material construction, explains how topic map techniques were applied, and observes the implications and potentials of the technology to education. Both the technical and educational evaluations of using SOM topic maps in compilation of learning materials have resulted in positive feedback. SOM allows users to review the complete databank in structural hierarchical order, which provides comprehensive understanding of the entire set of learning materials, and also brings opportunities to users to discover knowledge related to their study area. [source] Kindergarten Predictors of Math Learning DisabilityLEARNING DISABILITIES RESEARCH & PRACTICE, Issue 3 2005Michèle M. M. Mazzocco The aim of the present study was to address how to effectively predict mathematics learning disability (MLD). Specifically, we addressed whether cognitive data obtained during kindergarten can effectively predict which children will have MLD in third grade, whether an abbreviated test battery could be as effective as a standard psychoeducational assessment at predicting MLD, and whether the abbreviated battery corresponded to the literature on MLD characteristics. Participants were 226 children who enrolled in a 4-year prospective longitudinal study during kindergarten. We administered measures of mathematics achievement, formal and informal mathematics ability, visual-spatial reasoning, and rapid automatized naming and examined which test scores and test items from kindergarten best predicted MLD at grades 2 and 3. Statistical models using standardized scores from the entire test battery correctly classified ,80,83 percent of the participants as having, or not having, MLD. Regression models using scores from only individual test items were less predictive than models containing the standard scores, except for models using a specific subset of test items that dealt with reading numerals, number constancy, magnitude judgments of one-digit numbers, or mental addition of one-digit numbers. These models were as accurate in predicting MLD as was the model including the entire set of standard scores from the battery of tests examined. Our findings indicate that it is possible to effectively predict which kindergartners are at risk for MLD, and thus the findings have implications for early screening of MLD. [source] Perspectives of ammonite paleobiology from shell abnormalities in the genus BaculitesLETHAIA, Issue 3 2002R.A. HENDERSON Many Baculites specimens from the Upper Cretaceous of the United States Western Interior show exceptional preservation of the original aragonitic shell and its fine-scale surface ornamentation. Growth lines are ubiquitous, with two orders of these structures represented on some shells, and reflect the incremental addition of new shell at the apertural margin. Growth line interruption in the form of repair of minor shell damage at the aperture, commonplace in contemporary Nautilus, is essentially absent in Baculites, suggesting that its members fed on small prey in the water column. As typical of Mesozoic ammonites in general, and in striking contrast to contemporary Nautilus, no in vivo epizoans have been recognized on specimens of Baculites. It is inferred that the shell of Baculites was covered in periostracum to eliminate epizoic colonization. By analogy with Nautilus, a distinctive micro-ornament oriented at right angles to growth lines and visible on parts of some specimens was probably associated with periostracal attachment. A small proportion of Baculites specimens show abnormalities in shell growth categorized as v-shaped indentations of growth lines, shell grooves, fine-scale folds on the surface of growth lines and feather structures. We view this entire set of structures as due to abnormalities in mantle growth induced at the leading edge, impressed into the periostracum during its fabrication, and then in turn into the shell surface. As many of the Baculites with shell abnormalities are smooth, the proposal by Checa linking homologous structures recognized on other ammonites to the formation of comarginal ribs is rejected. A case of sutural inversion, in which the form of minor divisions of the major saddles and lobes are transposed, is recognized in a specimen of Baculites codyensis Reeside. We consider sutural pattern in ammonites, an expression of septal fluting, as replicating the genetically specified standing form of an elastic adapical visceral mass. The inverted sutural pattern, and by implication the style of septal fluting, was transcribed exactly in the three successive septa preserved on the specimen. The abnormality appears to be a case of homeotic mutation in which the plan for one body region becomes translocated to another. The conservatism of major elements of sutural (=septal) patterns for Mesozoic ammonites in their evolutionary spectrum suggests that a homeobox of conserved DNA sequence, with the transcription factors encoded in homeotic genes, is likely to have been involved. [source] Asymptotic and spectral analysis of non-selfadjoint operators generated by a filament model with a critical value of a boundary parameterMATHEMATICAL METHODS IN THE APPLIED SCIENCES, Issue 3 2003Marianna A. Shubov Abstract We consider a class of non-selfadjoint operators generated by the equation and the boundary conditions, which govern small vibrations of an ideal filament with non-conservative boundary conditions at one end and a heavy load at the other end. The filament has a non-constant density and is subject to a viscous damping with a non-constant damping coefficient. The boundary conditions contain two arbitrary complex parameters. In our previous paper (Mathematical Methods in the Applied Sciences 2001; 24(15) : 1139,1169), we have derived the asymptotic approximations for the eigenvalues and eigenfunctions of the aforementioned non-selfadjoint operators when the boundary parameters were arbitrary complex numbers except for one specific value of one of the parameters. We call this value the critical value of the boundary parameter. It has been shown (in Mathematical Methods in the Applied Sciences 2001; 24(15) : 1139,1169) that the entire set of the eigenvalues is located in a strip parallel to the real axis. The latter property is crucial for the proof of the fact that the set of the root vectors of the operator forms a Riesz basis in the state space of the system. In the present paper, we derive the asymptotics of the spectrum exactly in the case of the critical value of the boundary parameter. We show that in this case, the asymptotics of the eigenvalues is totally different, i.e. both the imaginary and real parts of eigenvalues tend to ,as the number of an eigenvalue increases. We will show in our next paper, that as an indirect consequence of such a behaviour of the eigenvalues, the set of the root vectors of the corresponding operator is not uniformly minimal (let alone the Riesz basis property). Copyright © 2003 John Wiley & Sons, Ltd. [source] Shotgun proteomic analysis of Chlamydia trachomatisPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 6 2005Paul Skipp Abstract Chlamydiae are widespread bacterial pathogens responsible for a broad range of diseases, including sexually transmitted infections, pneumonia and trachoma. To validate the existence of hitherto hypothetical proteins predicted from recent chlamydial genome sequencing projects and to examine the patterns of expression of key components at the protein level, we have surveyed the expressed proteome of Chlamydia trachomatis strain,L2. A combination of two-dimensional gel analysis, multi-dimensional protein identification (MudPIT) and nanocapillary liquid chromatography-tandem mass spectrometry allowed a total of 328,chlamydial proteins to be unambiguously assigned. Proteins identified as being expressed in the metabolically inert form, elementary body, of Chlamydia include the entire set of predicted glycolytic enzymes, indicating that metabolite flux rather than de novo synthesis of this pathway is triggered upon infection of host cells. An enzyme central to cell wall biosynthesis was also detected in the intracellular form, reticulate body, of Chlamydia, suggesting that the peptidoglycan is produced during growth within host cells. Other sets of proteins identified include 17 outer membrane-associated proteins of potential significance in vaccine studies and 67,proteins previously annotated as hypothetical or conserved hypothetical. Taken together, ,35% of the predicted proteome for C.,trachomatis has been experimentally verified, representing the most extensive survey of any chlamydial proteome to date. [source] Hierarchical analysis of large-scale two-dimensional gel electrophoresis experimentsPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 10 2003Amit Rubinfeld Abstract Large-scale two-dimensional gel experiments have the potential to identify proteins that play an important role in elucidating cell mechanisms and in various stages of drug discovery. Such experiments, typically including hundreds or even thousands of related gels, are notoriously difficult to perform, and analysis of the gel images has until recently been virtually impossible. In this paper we describe a scalable computational model that permits the organization and analysis of a large gel collection. The model is implemented in Compugen's Z4000Ô system. Gels are organized in a hierarchical, multidimensional data structure that allow the user to view a large-scale experiment as a tree of numerous simpler experiments, and carry out the analysis one step at a time. Analyzed sets of gels form processing units that can be combined into higher level units in an iterative framework. The different conditions at the core of the experiment design, termed the dimensions of the experiment, are transformed from a multidimensional structure to a single hierarchy. The higher level comparison is performed with the aid of a synthetic "adaptor" gel image, called a Raw Master Gel (RMG). The RMG allows the inclusion of data from an entire set of gels to be presented as a gel image, thereby enabling the iterative process. Our model includes a flexible experimental design approach that allows the researcher to choose the condition to be analyzed a posteriori. It also enables data reuse, the performing of several different analysis designs on the same experimental data. The stability and reproducibility of a protein can be analyzed by tracking it up or down the hierarchical dimensions of the experiment. [source] Inter-laboratory comparison of elemental analysis and gas chromatography/combustion/isotope ratio mass spectrometry.RAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 7 200915N measurements of selected compounds for the development of an isotopic Grob test An inter-laboratory exercise was carried out by a consortium of five European laboratories to establish a set of compounds, suitable for calibrating gas chromatography/combustion/isotope ratio mass spectrometry (GC-C-IRMS) devices, to be used as isotopic reference materials for hydrogen, carbon, nitrogen and oxygen stable isotope measurements. The set of compounds was chosen with the aim of developing a mixture of reference materials to be used in analytical protocols to check for food and beverage authentication. The exercise was organized in several steps to achieve the certification level: the first step consisted of the a priori selection of chemical compounds on the basis of the scientific literature and successive GC tests to set the analytical conditions for each single compound and the mixture. After elimination of the compounds that turned out to be unsuitable in a multi-compound mixture, some additional oxygen- and nitrogen-containing substances were added to complete the range of calibration isotopes. The results of ,13C determinations for the entire set of reference compounds have previously been published, while the ,D and ,18O determinations were unsuccessful and after statistical analysis of the data the results did not reach the level required for certification. In the present paper we present the results of an inter-laboratory exercise to identify and test the set of nitrogen-containing compounds present in the mixture developed for use as reference materials for the validation of GC-C-IRMS analyses in individual laboratories. Copyright © 2009 John Wiley & Sons, Ltd. [source] Treating Words as Data with Error: Uncertainty in Text Statements of Policy PositionsAMERICAN JOURNAL OF POLITICAL SCIENCE, Issue 2 2009Kenneth Benoit Political text offers extraordinary potential as a source of information about the policy positions of political actors. Despite recent advances in computational text analysis, human interpretative coding of text remains an important source of text-based data, ultimately required to validate more automatic techniques. The profession's main source of cross-national, time-series data on party policy positions comes from the human interpretative coding of party manifestos by the Comparative Manifesto Project (CMP). Despite widespread use of these data, the uncertainty associated with each point estimate has never been available, undermining the value of the dataset as a scientific resource. We propose a remedy. First, we characterize processes by which CMP data are generated. These include inherently stochastic processes of text authorship, as well as of the parsing and coding of observed text by humans. Second, we simulate these error-generating processes by bootstrapping analyses of coded quasi-sentences. This allows us to estimate precise levels of nonsystematic error for every category and scale reported by the CMP for its entire set of 3,000-plus manifestos. Using our estimates of these errors, we show how to correct biased inferences, in recent prominently published work, derived from statistical analyses of error-contaminated CMP data. [source] Cell-free synthesis of functional proteins using transcription/translation machinery entrapped in silica sol,gel matrixBIOTECHNOLOGY & BIOENGINEERING, Issue 1 2009Kyeong-Ohn Kim Abstract Herewith we report the encapsulation of functional protein synthesis machinery in a silica sol,gel matrix. When the sol,gel reaction using alkoxysilane monomers was carried out in the presence of Escherichia coli cell extract, macromolecular protein synthesis machinery in the cell extract was successfully immobilized within a silica gel matrix, catalyzing the translation of co-immobilized DNA when supplied with small-molecular-weight substrates for protein synthesis. The efficiency of protein synthesis was affected by the pore size of the gel structure, which was controlled through the use of appropriate additives during the sol,gel reactions. To the best of our knowledge, this is the first report describing the reproduction of the entire set of complicated biological process within an inorganic gel matrix, and we expect that the developed technology will find many applications in numerous fields such as high-throughput gene expression and the development of multifunctional biosensors. Biotechnol. Bioeng. 2009;102: 303,307. © 2008 Wiley Periodicals, Inc. [source] Cumulative bondomers: A new concept in flux analysis from 2D [13C,1H] COSY NMR dataBIOTECHNOLOGY & BIOENGINEERING, Issue 7 2002Wouter A. van Winden Abstract A well-established way of determining metabolic fluxes is to measure 2D [13C,1H] COSY NMR spectra of components of biomass grown on uniformly 13C-labeled carbon sources. When using the entire set of measured data to simultaneously determine all fluxes in a proposed metabolic network model, the 13C-labeling distribution in all measured compounds has to be simulated. This requires very large sets of isotopomer or cumomer balances. This article introduces the new concept of bondomers; entities that only vary in the numbers and positions of C,C bonds that have remained intact since the medium substrate molecule entered the metabolism. Bondomers are shown to have many analogies to isotopomers. One of these is that bondomers can be transformed to cumulative bondomers, just like isotopomers can be transformed to cumomers. Similarly to cumomers, cumulative bondomers allow an analytical solution of the entire set of balances describing a metabolic network. The main difference is that cumulative bondomer models are considerably smaller than corresponding cumomer models. This saves computational time, allows easier identifiability analysis, and yields new insights in the information content of 2D [13C,1H] COSY NMR data. We illustrate the theoretical concepts by means of a realistic example of the glycolytic and pentose phosphate pathways. The combinations of 2D [13C,1H] COSY NMR data that allow identification of all metabolic fluxes in these pathways are analyzed, and it is found that the NMR data contain less information than was previously expected. © 2002 Wiley Periodicals, Inc. Biotechnol Bioeng 80: 731,745, 2002. [source] | |||||||||||||||||||