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PubMed2003

Cationic comb-type copolymers for DNA analysis.

Genetic diagnoses, such as single nucleotide polymorphism (SNP) typing, allow elucidation of gene-based physiological differences, such as susceptibility to diseases and response to drugs, among individuals. Many detection technologies, including allele-specific hybridization, allele-specific primer extension and oligonucleotide ligation, are being used to discriminate SNP alleles. These methods still have many unsolved practical issues. In general they require adequate and specific hybridizations of primer or probe DNAs with target DNAs. This frequently needs optimization of the probe/primer structures and operating conditions. In nature, highly homology-sensitive hybridization is assisted by a nucleic acid chaperone that reduces the energy barrier associated with breakage and reassociation of nucleic base pairs. Here we report a simple, quick, precise but enzyme-free method for SNP analysis. The method uses cationic comb-type copolymers (CCCs) producing high nucleic acid chaperone activities. A single-base mismatch in 20-mer DNA can be detected within a few minutes at ambient temperatures (25-37 degrees C). Even without careful optimization processes, the method has the sensitivity to detect the mismatches causing subtle changes (Delta T(m) equals approximately 1 degree C) in duplex thermal stability. CCCs may have various bioanalytical applications where precise hybridization of nucleic acids is needed.

Aryl Hydrocarbon Hydroxylases↗

PubMed2006

Modelling strategies for the industrial exploitation of lactic acid bacteria.

Lactic acid bacteria (LAB) have a long tradition of use in the food industry, and the number and diversity of their applications has increased considerably over the years. Traditionally, process optimization for these applications involved both strain selection and trial and error. More recently, metabolic engineering has emerged as a discipline that focuses on the rational improvement of industrially useful strains. In the post-genomic era, metabolic engineering increasingly benefits from systems biology, an approach that combines mathematical modelling techniques with functional-genomics data to build models for biological interpretation and--ultimately--prediction. In this review, the industrial applications of LAB are mapped onto available global, genome-scale metabolic modelling techniques to evaluate the extent to which functional genomics and systems biology can live up to their industrial promise.

Biomass↗

PubMed2002

Optimization of an electrolyte conductivity detector for measuring low ion concentrations.

The optimization process of a planar interdigitated conductivity detector for measuring very low electrolyte concentrations for use in a lab-on-chip gas detection system is described. An electrical equivalent of the sensor is given, which includes the double layer capacitance dependency on the electrolyte concentration, resulting in a better description of the impedance of the sensor. The cell constant of the sensor is minimized to reduce the cell resistance in low specific conductivity solutions under the restriction of a small electrode area (> or = 0.1 cm(2)) for fast measurement, prescribed by the ammonia detection system. The small size makes it suitable for integration in micro channels. The developed sensor has a cell constant of 7.9 m(-1) resulting in a maximum resistance for deionized water of 177 k Omega at a frequency of 1 kHz.

Journal Article↗

PubMed2003

Groundwater monitoring plans at small-scale sites--an innovative spatial and temporal methodology.

An innovative methodology for improving existing groundwater monitoring plans at small-scale sites is presented. The methodology consists of three stand-alone methods: a spatial redundancy reduction method, a well-siting method for adding new sampling locations, and a sampling frequency determination method. The spatial redundancy reduction method eliminates redundant wells through an optimization process that minimizes the errors in plume delineation and the average plume concentration estimation. The well-siting method locates possible new sampling points for an inadequately delineated plume via regression analysis of plume centerline concentrations and estimation of plume dispersivity values. The sampling frequency determination method recommends the future frequency of sampling for each sampling location based on the direction, magnitude, and uncertainty of the concentration trend derived from representative historical concentration data. Although the methodology is designed for small-scale sites, it can be easily adopted for large-scale site applications. The proposed methodology is applied to a small petroleum hydrocarbon-contaminated site with a network of 12 monitoring wells to demonstrate its effectiveness and validity.

Environmental Monitoring↗

PubMed2002

A study of antifungal antibiotic production by Streptomyces chattanoogensis MTCC 3423 using full factorial design.

AIMS: To determine the correct levels of the three process parameters identified as the most important for maximum production of antifungal antibiotic by the newly isolated strain of Streptomyces chattanoogensis MTCC 3423. METHODS AND RESULTS: The three independent variables, namely concentration of carbon source (glucose), nitrogen source (soybean meal) and temperature of incubation, were found to be the most important for production of antifungal antibiotic by the isolate Streptomyces chattanoogensis MTCC 3423 from a one-factor-at-a-time study. These variables were varied at three levels in 27 experiments using full factorial design. The results were analysed using statistical software for social sciences, SPSS (version 6.0). They indicated that the optimum combination of the three factors for maximum yield (263.63 U) of the antibiotic was concentration of carbon source (glucose) 5%, concentration of nitrogen source (soybean meal) 1% and temperature of incubation 30 degrees C. The antifungal antibiotic activity of the isolate was estimated against Candida albicans by bioassay. CONCLUSIONS: The S. chattanoogensis MTCC 3423 isolate was found to yield a maximum of 263.63 IU Nystatin ml-1 medium by manipulating the three process parameters of glucose, soybean meal and temperature of incubation. SIGNIFICANCE AND IMPACT OF THE STUDY: As process optimization by single-dimensional search is laborious and time consuming, and does not guarantee determination of optimal conditions, an attempt was made to use a more practical full factorial method. Even though antifungal antibiotic treatment and resistance data have been analysed using SPSS software, there are no reports on antifungal antibiotic production using SPSS.

Antifungal Agents↗

PubMedDate not supplied

Racial inequity in America's ESRD program.

The end-stage renal disease (ESRD) program has a significant overrepresentation of racial and ethnic minority groups. The increased susceptibility of nonwhite populations to ESRD has not been fully explained and probably represents a complex interplay of genetic, cultural, and environmental influences. Because the program delivers care under a uniform health care payment system, it represents a unique environment in which to explore variation in health care delivery. A number of disparities in outcomes and delivery of ESRD care have been noted for racial minority participants. These include possible overdiagnosis of hypertensive nephrosclerosis, decreased provision of renal replacement therapy, limited referral for home dialysis modalities, underprescription of dialysis, increased use of synthetic grafts rather than fistulas as permanent angioaccess, and delayed wait-listing for renal transplantation. Transplantation inequities mean that black patients are likely to remain on dialysis relatively longer, so that their susceptibility to less than optimal processes of care increases disproportionately. Improved survival and quality of life (QOL) for blacks with ESRD may have encouraged provider complacency about racial disparities in the ESRD program and in particular about referral for transplantation. It is also apparent that minority ESRD patients may, similar to their non-ESRD counterparts, be referred less frequently for invasive cardiovascular (CV) procedures. Despite these observations of inequality in ESRD care, the adjusted mortality for minority participants in the ESRD program are better than for the majority population. This seeming paradox may define an opportunity to improve outcomes for minorities with ESRD even more.

Black or African American↗

PubMed2005

Modeling the morphology and mechanical properties of sheared ternary mixtures.

Through a combination of simulation techniques, we determine both the structural evolution and mechanical properties of blends formed from immiscible ternary mixtures. In this approach, we first use the lattice Boltzmann method to simulate the phase separation dynamics of A/B/C fluid mixtures for varying compositions within the spinodal region. We also investigate the effect of an imposed shear on the phase ordering of the mixture. We assume that the fluid is quenched sufficiently rapidly that the phase-separated structure is preserved in the resultant solid. Then, the output from our morphological studies serves as the input to the lattice spring model, which is used to simulate the elastic response of solids to an applied deformation. These simulations reveal how the local stress and strain fields and the global Young's modulus depend on the composition of the blend and the stiffness of the components. By comparing the results for the sheared and unsheared cases, we can isolate optimal processing conditions for enhancing the mechanical performance of the blends. Overall, the findings provide fundamental insight into the relationship between structure, processing, and properties for heterogeneous materials and can yield guidelines for formulating blends with the desired macroscopic mechanical behavior.

Journal Article↗

PubMed2005

Coexistence of 1,3-butadiene conformers in ionization energies and Dyson orbitals.

The minimum-energy structures on the torsional potential-energy surface of 1,3-butadiene have been studied quantum mechanically using a range of models including ab initio Hartree-Fock and second-order Møller-Plesset theories, outer valence Green's function, and density-functional theory with a hybrid functional and statistical average orbital potential model in order to understand the binding-energy (ionization energy) spectra and orbital cross sections observed by experiments. The unique full geometry optimization process locates the s-trans-1,3-butadiene as the global minimum structure and the s-gauche-1,3-butadiene as the local minimum structure. The latter possesses the dihedral angle of the central carbon bond of 32.81 degrees in agreement with the range of 30 degrees-41 degrees obtained by other theoretical models. Ionization energies in the outer valence space of the conformer pair have been obtained using Hartree-Fock, outer valence Green's function, and density-functional (statistical average orbital potentials) models, respectively. The Hartree-Fock results indicate that electron correlation (and orbital relaxation) effects become more significant towards the inner shell. The spectroscopic pole strengths calculated in the Green's function model are in the range of 0.85-0.91, suggesting that the independent particle picture is a good approximation in the present study. The binding energies from the density-functional (statisticaly averaged orbital potential) model are in good agreement with photoelectron spectroscopy, and the simulated Dyson orbitals in momentum space approximated by the density-functional orbitals using plane-wave impulse approximation agree well with those from experimental electron momentum spectroscopy. The coexistence of the conformer pair under the experimental conditions is supported by the approximated experimental binding-energy spectra due to the split conformer orbital energies, as well as the orbital momentum distributions of the mixed conformer pair observed in the orbital cross sections of electron momentum spectroscopy.

Butadienes↗

PubMed2003

Least effort and the origins of scaling in human language.

The emergence of a complex language is one of the fundamental events of human evolution, and several remarkable features suggest the presence of fundamental principles of organization. These principles seem to be common to all languages. The best known is the so-called Zipf's law, which states that the frequency of a word decays as a (universal) power law of its rank. The possible origins of this law have been controversial, and its meaningfulness is still an open question. In this article, the early hypothesis of Zipf of a principle of least effort for explaining the law is shown to be sound. Simultaneous minimization in the effort of both hearer and speaker is formalized with a simple optimization process operating on a binary matrix of signal-object associations. Zipf's law is found in the transition between referentially useless systems and indexical reference systems. Our finding strongly suggests that Zipf's law is a hallmark of symbolic reference and not a meaningless feature. The implications for the evolution of language are discussed. We explain how language evolution can take advantage of a communicative phase transition.

Communication↗

PubMed2005

Thrombin inhibitors identified by computer-assisted multiparameter design.

Here, we present a series of thrombin inhibitors that were generated by using powerful computer-assisted multiparameter optimization process. The process was organized in design cycles, starting with a set of randomly chosen molecules. Each cycle combined combinatorial synthesis, multiparameter characterization of compounds in a variety of bioassays, and algorithmic processing of the data to devise a set of compounds to be synthesized in the next cycle. The identified lead compounds exhibited thrombin inhibitory constants in the lower nanomolar range. They are by far the most selective synthetic thrombin inhibitors, with selectivities of >100,000-fold toward other proteases such as Factor Xa, Factor XIIa, urokinase, plasmin, and Plasma kallikrein. Furthermore, these compounds exhibit a favorable profile, comprising nontoxicity, high metabolic stability, low serum protein binding, good solubility, high anticoagulant activity, and a slow and exclusively renal elimination from the circulation in a rat model. Finally, x-ray crystallographic analysis of a thrombin-inhibitor complex revealed a binding mode with a neutral moiety in the S1 pocket of thrombin.

Antithrombins↗

PubMed2002

Significance and statistical errors in the analysis of DNA microarray data.

DNA microarrays are important devices for high throughput measurements of gene expression, but no rational foundation has been established for understanding the sources of within-chip statistical error. We designed a specialized chip and protocol to investigate the distribution and magnitude of within-chip errors and discovered that, as expected from theoretical expectations, measurement errors follow a Lorentzian-like distribution, which explains the widely observed but unexplained ill-reproducibility in microarray data. Using this specially designed chip, we examined a data set of repeated measurements to extract estimates of the distribution and magnitude of statistical errors in DNA microarray measurements. Using the common "ratio of medians" method, we find that the measurements follow a Lorentzian-like distribution, which is problematic for subsequent analysis. We show that a method of analysis dubbed "median of ratios" yields a more Gaussian-like distribution of errors. Finally, we show that the bootstrap algorithm can be used to extract the best estimates of the error in the measurement. Quantifying the statistical error in such measurements has important applications for estimating significance levels, clustering algorithms, and process optimization.

Algorithms↗

PubMed2003

Examination of plant performance and filter ripening with particle counters at full-scale water treatment plants.

Filter performance has traditionally been assessed using turbidity as the main water quality parameter. However interest in process optimization and the ability to accurately monitor filtration and particle removal has led to particle counting becoming increasingly more popular. The objective of this research was to evaluate filtration performance and filter ripening at four full-scale water treatment plants. Most of the plants investigated in this study were capable of achieving 2 log total particle removal as well as an effluent turbidity of 0.1 NTU. In some cases 2 log removal was achieved in the lower particle size ranges of 2-5 and 5-10 microm. Log removals in this study compare particle counts in the filtered and raw water. For water treatment plants that do not filter to waste, the ripening period following a filter backwash represents a time where the plant may be most vulnerable to breakthrough of waterborne pathogens. For the plants studied, the ripening period which was defined as the time required to reach peak particle removal and a turbidity of 0.1 NTU, were very similar in duration. The ripening period generally lasted for one hour after the backwash event had been completed. Because the times to reach 2 log total particle removal and 0.1 NTU are similar, the practice of using 0.1 NTU turbidity as a measure of filter ripening may be a useful benchmark for utilities that do not have particle counters.

Environmental Monitoring↗

PubMed2004

Application of response surface methodology for studying the product characteristics of extruded rice-cowpea-groundnut blends.

Response surface methodology (with central composite rotatable design for k=3) was used to investigate the product properties of extruded rice-cowpea-groundnut blends in a single screw extruder. The combined effect of cowpea (0-20%), groundnut (0-10%), and feed moisture (14-48%) levels were used for formulation of the products. The product moisture, expansion ratio, bulk density and total colour change were studied using standard analytical methods. Well-expanded rice-legume blend extrudates of less bulk density and lower moisture content were produced at low feed moisture. Increasing legume addition affected the various shades of colour in the product. Models developed for the indices gave R(2) values ranging from 52.8% (for the b-value) to 86.5% (for bulk density). The models developed suggested that the optimal process variables for the production of a puffed snack with an enhanced nutrition and spongy structure from a rice-cowpea-groundnut blend are low feed moisture of 14-20% and maximum additions of 20% cowpea and 10% groundnut. A lack-of-fit test showed no significance, indicating that the models adequately fitted the data.

Arachis↗

PubMed2002

Application of hazard analysis critical control points (HACCP) to organic chemical contaminants in food.

Hazard Analysis Critical Control Points (HACCP) is a systematic approach to the identification, assessment, and control of hazards that was developed as an effective alternative to conventional end-point analysis to control food safety. It has been described as the most effective means of controlling foodborne diseases, and its application to the control of microbiological hazards has been accepted internationally. By contrast, relatively little has been reported relating to the potential use of HACCP, or HACCP-like procedures, to control chemical contaminants of food. This article presents an overview of the implementation of HACCP and discusses its application to the control of organic chemical contaminants in the food chain. Although this is likely to result in many of the advantages previously identified for microbiological HACCP, that is, more effective, efficient, and economical hazard management, a number of areas are identified that require further research and development. These include: (1) a need to refine the methods of chemical contaminant identification and risk assessment employed, (2) develop more cost-effective monitoring and control methods for routine chemical contaminant surveillance of food, and (3) improve the effectiveness of process optimization for the control of chemical contaminants in food.

Consumer Product Safety↗

PubMed2005

Interactive analysis of waste recycling and energy recovery program in a small-scale incinerator.

Conflicting goals affecting solid waste management are explored in this paper to find the best implementation of resource recovery with a small-scale waste-to-energy process. Recycling paper and plastic material often leaves a shortage of thermal energy to support incineration that forces operators to supplement the process with auxiliary fuels. Although there are considerable profits to be made from material recovery, the increase of fuel usage causes conflict given that it is cost prohibitive. A series of trials performed on a small-scale 1.5-t/day incineration plant with a cyclone heat recovery system found that material recycling can impede performance. Experimental results are expressed as empirical regression formulas with regard to combustion temperature, energy transfer, and heat recovery. Process optimization is possible if the waste moisture content remains <30%. To test the robustness of the optimization analysis, a series of sensitivity analyses clarify the extent of material recycling needed with regard to plastic, paper, and metal. The experiments also test whether the moisture in the waste would decrease when recycling paper because of its exceptional capacity to absorb moisture. Results show that recycling paper is strongly recommended when the moisture content is >20%, whereas plastic recycling is not necessary at that moisture condition. Notably, plastic recovery reduces the heat needed to vaporize the water content of the solid waste, thus it is recommended only when the moisture content is <10%. For above-normal incineration temperatures, plastic recycling is encouraged, because it removes excess energy. Metal is confirmed as an overall priority in material recycling regardless of the moisture content of the incoming waste.

Conservation of Energy Resources↗

PubMed2006

Minimax regret analysis for municipal solid waste management: an interval-stochastic programming approach.

In this study, an interval minimax regret programming (IMMRP) method is developed for the planning of municipal solid waste (MSW) management under uncertainty. It improves on the existing interval programming and minimax regret analysis methods by allowing uncertainties presented as both intervals and random variables to be effectively communicated into the optimization process. The IMMRP can account for economic consequences under all possible scenarios without any assumption on their probabilities. The developed method is applied to a case study of long-term MSW management planning under uncertainty. Multiple scenarios associated with different cost and risk levels are analyzed. Reasonable solutions are generated, demonstrating complex tradeoffs among system cost, regret level, and system-failure risk. The method can also facilitate examination of the difference between the cost incurred with identified strategy and the least cost under an ideal condition. The results can help determine desired plans and policies for waste management under a variety of uncertainties.

Costs and Cost Analysis↗

PubMed2001

Microwave-assisted extraction of phenolic compounds from grape seed.

A microwave-assisted extraction technique was developed to optimize the extraction of phenolic compounds from grape seeds. The microwave power (300-150W) and time of extraction (20-200s) were varied during the optimization process. The polyphenol content of the resulting extracts were measured as mg of tannic acid equivalent per gram of crude extract (mg TAE/g of crude extract), using a Folin-Ciocalteau reagent. In general, neither the time nor the power had a significant effect on the overall % yield (average of 13.5%) and on the polyphenol content (392 mg TAE/g of crude extract) of the extracts. However, when the solvent polarity was changed by the addition of 10% water, the yield increased to 15.2% and the polyphenol content increased to 429 mg TAE/g of crude extract.

Antioxidants↗

PubMed2005

Preventing tobacco use among lesbian, gay, bisexual, and transgender youths.

A paucity of information regarding tobacco use among lesbian, gay, bisexual, and transgender (LGBT) youths impedes prevention programs. The aim of the present study was to conduct formative qualitative research regarding subpopulations at risk for tobacco use, protective factors, patterns of use, and approaches to prevention. This report focuses on participants' recommendations for the development of preventive intervention. Purposive sampling and maximum variation sampling were used to select 30 LGBT youths and 30 interactors for face-to-face interviews. NUD*IST6 text software was used for the indexing and thematic analysis of qualitative data, based on a grounded theory approach. All participants offered suggestions for tobacco prevention pertaining to the optimal process of prevention and cessation programs, specific strategies to promote tobacco prevention and cessation, and general strategies to foster nonsmoking. Several key themes regarding prevention emerged: LGBT youth should be involved in the design and implementation of interventions; prevention programs should support positive identity formation as well as nonsmoking; the general approach to prevention should be entertaining, supportive, and interactive; and the public might not distinguish primary prevention from cessation activities. All but one young smoker had attempted to quit at least once; but only one individual had succeeded. By way of implications, prevention programs should involve young people in enjoyable and engaging activities, address the psychosocial and cultural underpinnings of tobacco use, support healthy psychosocial development, and consider offering pharmacological smoking cessation aids.

Adolescent↗