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PubMed2002

Characterization and implications of the cell surface reactivity of Calothrix sp. strain KC97.

The cell surface reactivity of the cyanobacterium Calothrix sp. strain KC97, an isolate from the Krisuvik hot spring, Iceland, was investigated in terms of its proton binding behavior and charge characteristics by using acid-base titrations, electrophoretic mobility analysis, and transmission electron microscopy. Analysis of titration data with the linear programming optimization method showed that intact filaments were dominated by surface proton binding sites inferred to be carboxyl groups (acid dissociation constants [pK(a)] between 5.0 and 6.2) and amine groups (mean pK(a) of 8.9). Sheath material isolated by using lysozyme and sodium dodecyl sulfate generated pK(a) spectra similarly dominated by carboxyls (pK(a) of 4.6 to 6.1) and amines (pK(a) of 8.1 to 9.2). In both intact filaments and isolated sheath material, the lower ligand concentrations at mid-pK(a) values were ascribed to phosphoryl groups. Whole filaments and isolated sheath material displayed total reactive-site densities of 80.3 x 10(-5) and 12.3 x 10(-5) mol/g (dry mass) of cyanobacteria, respectively, implying that much of the surface reactivity of this microorganism is located on the cell wall and not the sheath. This is corroborated by electrophoretic mobility measurements that showed that the sheath has a net neutral charge at mid-pHs. In contrast, unsheathed cells exhibited a stronger negative-charge characteristic. Additionally, transmission electron microscopy analysis of ultrathin sections stained with heavy metals further demonstrated that most of the reactive binding sites are located upon the cell wall. Thus, the cell surface reactivity of Calothrix sp. strain KC97 can be described as a dual layer composed of a highly reactive cell wall enclosed within a poorly reactive sheath.

Bacterial Proteins↗

PubMed2005

Metabolic engineering of Escherichia coli for enhanced production of succinic acid, based on genome comparison and in silico gene knockout simulation.

Comparative analysis of the genomes of mixed-acid-fermenting Escherichia coli and succinic acid-overproducing Mannheimia succiniciproducens was carried out to identify candidate genes to be manipulated for overproducing succinic acid in E. coli. This resulted in the identification of five genes or operons, including ptsG, pykF, sdhA, mqo, and aceBA, which may drive metabolic fluxes away from succinic acid formation in the central metabolic pathway of E. coli. However, combinatorial disruption of these rationally selected genes did not allow enhanced succinic acid production in E. coli. Therefore, in silico metabolic analysis based on linear programming was carried out to evaluate the correlation between the maximum biomass and succinic acid production for various combinatorial knockout strains. This in silico analysis predicted that disrupting the genes for three pyruvate forming enzymes, ptsG, pykF, and pykA, allows enhanced succinic acid production. Indeed, this triple mutation increased the succinic acid production by more than sevenfold and the ratio of succinic acid to fermentation products by ninefold. It could be concluded that reducing the metabolic flux to pyruvate is crucial to achieve efficient succinic acid production in E. coli. These results suggest that the comparative genome analysis combined with in silico metabolic analysis can be an efficient way of developing strategies for strain improvement.

Base Sequence↗

PubMed1979

Experience of the metabolisable energy system.

Advisory experience concerning the metabolisable energy standards for cattle and sheep introduced in 1976 is reviewed. The change appears to have proceeded smoothly, the new terminology and units being mastered and then used in discussions on dairy cow feeding. The system proposed has thrown new light on some old problems and also on established methods of feeding dairy cattle. "Feeding according to yield" and "lead feeding" need to be reinterpreted in the light of the probable dry matter intakes and live-weight changes of cows in early lactation. These parameters also affect the calculated levels of protein received in dairy compound feeds in early lactation. Group feeding of cows by stage of lactation, level of milk yield and live-weight change is readily accepted by managers of the larger dairy herds. Confidence in the accuracy of the dairy ME system has been built up, and its application to suckler cows has also proved successful. The variable net energy system for growing cattle enables ration formulation to be accomplished speedily and linear programming if desired. Published experiments have been used to confirm the accuracy of predicted live-weight gains when compared with observed gains. No sex effects are included in the system, although differences of +/- 10 per cent have been recorded in natural or hormone induced sex effect trials. The requirements for pregnant ewes have been shown to be too low and liable to reduce lamb birth-weights. In the case of growing lambs, a review of published experiments has shown that lambs grew faster than predicted, suggesting that the energy allowances are too high.

Animal Feed↗

PubMed2005

An optimization method for the identification of minimal sets of discriminating gene markers: application to cultivar identification in wheat.

A potentially large number of molecular markers are available for identifying genotypes in various species. For wheat, cultivar identity is an important determinant for end-use segregation and for payment of end-point royalties and grower premiums. A number of dominant DNA markers, that give either a positive or negative response, have been developed previously for wheat cultivar identification. This paper gives a method for identifying minimal marker sets for a given cultivar group, for example those grown in a specific geographical zone. It is based on an integer linear programming formulation of the problem, and can find all minimal marker sets for the group if required. The paper then describes the production of two software packages, GGDS and GGIP, that incorporate this methodology. Various practical issues are also discussed. These packages enable the rapid selection of minimal marker sets for the efficient discrimination of any sample set where the marker responses of the samples are known. They are already being used by the Australian wheat industry.

Algorithms↗

PubMed2006

Mathematical modeling of living cell metabolism using the method of steady-state stoichiometric flux balance.

This approach uses a set of algebraic linear equations for reaction rates (the method of steady-state stoichiometric flux balance) to model the purposeful metabolism of the living self-reproducing biochemical system (i.e. cell), which persists in steady-state growth. Linear programming (SIMPLEX method) is used to derive the solution for the model equations set (determining reaction rates which provide flux balance at given conditions). Here, we demonstrate the approach through the mathematical modeling of steady-state metabolism in Saccharomyces cerevisiae mitochondria.

Algorithms↗

PubMed1976

Shaping of isodose curves in intracavitary irradiation using the afterloading method. A feasibility study involving mathematical simulation.

The possibility of adjusting the irradiation scheme to shape the isodose curve around an intracavitary source arrangement was studied mathematically. The total number of millicurie hours of irradiation for each source position was derived by a linear programming approach, taking into account the shape of the tumor in three different cases. The practical isodose curves obtainable with the source arrangement chosen were compared with the shape desired.

Humans↗

PubMed1979

Information content of the multibreath nitrogen washout.

The distribution of ventilation per unit volume (Va/Vol) in the lung is often studied using the multibreath N2 washout test. Most approaches have focused on the determination of a single Va/Vol distribution (consisting of from two compartments to a continuum) compatible with the data, but because the potential number of lung units greatly exceeds the number of breaths measured, many distributions are usually compatible with a given set of washout data. Interpretation of single distributions therefore requires evaluation of the variability among all such compatible distributions. The technique of linear programing is well suited to evaluation of these compatible distributions and its application to the N2 washout is explained. Twelve examples of washout data are analyzed in this way. The results indicate that using the first 20 or so breaths of the washout, narrow distributions of Va/Vol are well specified. Distributions with up to four distinct modes are also well specified, but for broad distributions the shape cannot be adequately defined. Good resolution in the region of high Va/Vol is found to be critically dependent on measuring the first few breaths of the washout.

Computers↗

PubMed1983

A simple model of VA/Q distribution for analysis of inert gas elimination data.

A general procedure for fitting compartments models of alveolar ventilation-perfusion ratio (VA/Q) distribution to inert gas elimination data is described. The method can be applied to any model consisting of a number of compartments ventilated and perfused in parallel, each compartment of the model having a fixed predetermined VA/Q ratio. The number of compartments and their VA/Q ratios required for adequately fitting real data have been examined. A 13-compartment model consisting of a shunt, a dead space, and 11 compartments equally spaced on a logarithmic scale from VA/Q of 0.01 to 100 was found to be suitable. The fitting procedure and the 13-compartment model form the basis of a method of analysis of inert gas elimination data. Essentially the method consists of calculating a sample of 30 distributions compatible with the data analyzed taking into account experimental errors in the inert gas measurements. From this sample, the averages and standard deviations of the flows to 13 zones on the VA/Q scale are estimated. The averages are estimates of the true flows to these zones, and the standard deviations give an indication of the range of flows compatible with the data. The method has some advantages over both the enforced-smoothing approach and the Monte Carlo linear programming scheme of Evans and Wagner (J. Appl. Physiol.: Respirat. Environ. Exercise Physiol. 42: 889-898, 1977).

Computers↗

PubMed1984

Sensitivity and specificity of the computational model for maximal expiratory flow.

The computational model for forced expiratory flow from human lungs of Lambert and associates (J. Appl. Physiol.: Respirat. Environ. Exercise Physiol. 52: 44-56, 1982) was used to investigate the sensitivity of maximal expiratory flow to lung properties. It was found that maximal flow is very sensitive to recoil pressure and airway areas but not very sensitive to lung volume, airway compliance, and airway length. Linear programming was used to show that a given air flow-pressure curves was compatible with a fairly wide range of airway properties. Additional data for maximal flow with a He-O2 mixture narrowed the range somewhat. It was shown that the flow-pressure curve contains more information about central than peripheral airways and that information about the latter is obtainable only from flows at recoils less than 2 cmH2O. Parameter ranges compatible with individual flow-pressure curves showed differences that demonstrated that such curves give some indication of individual central airway properties.

Airway Resistance↗

PubMed2005

Prenatal and perinatal correlates of adult mammographic breast density.

BACKGROUND: Adult mammographic percent density is one of the strongest known risk factors for breast cancer. In utero exposure to high levels of endogenous estrogens (or other pregnancy hormones) has been hypothesized to increase breast cancer risk in later life. We examined the hypothesis that those factors associated with higher levels of estrogen during pregnancy or shortly after birth are associated with higher mammographic breast density in adulthood. METHODS: We analyzed data on 1,893 women from 360 families in the Minnesota Breast Cancer Family Study who had screening mammograms, risk factor data, over age 40, and no history of breast cancer. Prenatal and perinatal risk factor data were ascertained using a mailed questionnaire. Mammographic percent density and dense area were estimated from the mediolateral oblique view using Cumulus, a computer-assisted thresholding program. Linear mixed effects models incorporating familial correlation were used to assess the association of risk factors with percent density, adjusting for age, weight, and other breast cancer risk factors, all at time of mammography. RESULTS: The mean age at mammography was 60.4 years (range, 40-91 years), and 76% were postmenopausal. Among postmenopausal women, there was a positive association of birthweight with percent density (P trend <0.01), with an adjusted mean percent density of 17.1% for <2.95 kg versus 21.0% for > or = 3.75 kg. There were suggestive positive associations with gestational age (mean percent density of 16.7% for preterm birth, 20.2% for term birth, and 23.0% for late birth; P trend = 0.07), maternal eclampsia/preeclampsia (mean percent density of 19.9% for no and 14.6% for yes; P = 0.16), and being breast-fed as an infant (mean percent density of 18.2% for never and 20.0% for ever; P = 0.08). There was no association of percent density with maternal age, birth order, maternal use of alcohol or cigarettes, or neonatal jaundice. Except for being breast-fed, these associations showed similar but attenuated trends among premenopausal women, although none were statistically significant. The results for dense area paralleled the percent density results. The associations of gestational age and being breast-fed as an infant with percent density attenuated when included in the same model as birthweight. CONCLUSIONS: Birthweight was positively associated with mammographic breast density and dense area among postmenopausal women and more weakly among premenopausal women, suggesting that it may be a marker of this early life exposure. These results offer some support to the hypothesis that pregnancy estrogens or other pregnancy changes may play a role in breast cancer etiology, and suggest that these factors may act in part through long-term effects on breast density.

Adult↗

PubMed2006

Recent issues in energy-protein malnutrition in children.

Thirty years ago, protein deficiency was perceived to be the major nutritional problem of children in developing countries. Later on increasing the energy intake of young children during the complementary feeding period became a priority. Early studies on the pathophysiology of malnutrition are now turned into strategic and practical consequences for the prevention and treatment of severe malnutrition, four of which are presented. (1) Almost half of the deaths worldwide are due to being underweight. Nowadays, well-defined preventive and curative interventions have been identified. (2) An efficient and rigorous technique based on linear programming is now available to design a diet suitable for the complementary feeding period using locally available foods with a minimum budget to cover the nutritional requirements of at least 97% of the children. (3) Managing acute malnutrition in emergencies has greatly improved by the use of a spread that a child can eat directly without the addition of water (often called Ready-to-Use Therapeutic Food) and Community Therapeutic Care that treats the majority of severely malnourished children at home. (4) Recent data strongly suggest that it is possible to avoid death due to careful and rapid rehydration despite the high purging rate even if many of the risk factors for mortality are present in these severely malnourished children. Recovery from malnutrition was achieved in 7 days.

Child↗

PubMed1997

Heritability analysis of lipids and three gene loci in twins link the macrophage scavenger receptor to HDL cholesterol concentrations.

We studied 100 healthy monozygotic and 72 dizygotic twin pairs (mean age, 34 +/- 14 years) to test for genetic influences on blood lipids and to examine relevant gene loci. Total cholesterol (TC), LDL cholesterol (LDL-C), HDL cholesterol (HDL-C), and triglyceride (TG) levels were determined after a 12-hour fast. Zygosity was determined with the use of microsatellite markers. Heritability estimates were conducted by using the lisrel 8 program; a sib-pair analysis was conducted by using the sibpal program. Linear regression analyses were carried out between identical-by-descent status and squared within-pair differences of TC, LDL-C, HDL-C, and TG values. Heritability estimates of the lipid serum concentrations ranged from .58 to .66. A significant linkage relationship was found for HDL-C (P = .008) and TGs (P = .05) with D8S261 on chromosome 8p. However, no linkage was found between any of the lipid variables and the lipoprotein lipase gene locus (LPL GZ14/15 and D8S282). Because D8S261 is located approximately halfway between the LPL and macrophage scavenger receptor genes, we examined the nearby markers D8S549 and D8S1731. Linkage was found for HDL-C and D8S549 (P = .001) and for HDL-C and D8S1731 (P = .04). On the other hand, we found no linkage between the LDL receptor gene locus and LDL-C serum concentrations nor between the LPL gene locus and the various other lipid fractions. Our data suggest a significant influence of the macrophage scavenger receptor gene locus on HDL-C and weak influence on TG levels. We suggest that inherited variability in the macrophage scavenger receptor gene has an influence on serum lipid concentrations.

Adult↗

PubMed2002

A global optimum approach for one-layer neural networks.

The article presents a method for learning the weights in one-layer feedforward neural networks minimizing either the sum of squared errors or the maximum absolute error, measured in the input scale. This leads to the existence of a global optimum that can be easily obtained solving linear systems of equations or linear programming problems, using much less computational power than the one associated with the standard methods. Another version of the method allows computing a large set of estimates for the weights, providing robust, mean or median, estimates for them, and the associated standard errors, which give a good measure for the quality of the fit. Later, the standard one-layer neural network algorithms are improved by learning the neural functions instead of assuming them known. A set of examples of applications is used to illustrate the methods. Finally, a comparison with other high-performance learning algorithms shows that the proposed methods are at least 10 times faster than the fastest standard algorithm used in the comparison.

Journal Article↗

PubMed2004

Analysis of sparse representation and blind source separation.

In this letter, we analyze a two-stage cluster-then-l(1)-optimization approach for sparse representation of a data matrix, which is also a promising approach for blind source separation (BSS) in which fewer sensors than sources are present. First, sparse representation (factorization) of a data matrix is discussed. For a given overcomplete basis matrix, the corresponding sparse solution (coefficient matrix) with minimum l(1) norm is unique with probability one, which can be obtained using a standard linear programming algorithm. The equivalence of the l(1)-norm solution and the l(0)-norm solution is also analyzed according to a probabilistic framework. If the obtained l(1)-norm solution is sufficiently sparse, then it is equal to the l(0)-norm solution with a high probability. Furthermore, the l(1)- norm solution is robust to noise, but the l(0)-norm solution is not, showing that the l(1)-norm is a good sparsity measure. These results can be used as a recoverability analysis of BSS, as discussed. The basis matrix in this article is estimated using a clustering algorithm followed by normalization, in which the matrix columns are the cluster centers of normalized data column vectors. Zibulevsky, Pearlmutter, Boll, and Kisilev (2000) used this kind of two-stage approach in underdetermined BSS. Our recoverability analysis shows that this approach can deal with the situation in which the sources are overlapped to some degree in the analyzed domain and with the case in which the source number is unknown. It is also robust to additive noise and estimation error in the mixing matrix. Finally, four simulation examples and an EEG data analysis example are presented to illustrate the algorithm's utility and demonstrate its performance.

Algorithms↗

PubMed2005

Geometrical properties of nu support vector machines with different norms.

By employing the L1 or Linfinity norms in maximizing margins, support vector machines (SVMs) result in a linear programming problem that requires a lower computational load compared to SVMs with the L2 norm. However, how the change of norm affects the generalization ability of SVMs has not been clarified so far except for numerical experiments. In this letter, the geometrical meaning of SVMs with the Lp norm is investigated, and the SVM solutions are shown to have rather little dependency on p.

Algorithms↗

PubMed2001

Evolutionary driver scheduling with relief chains.

Public transport driver scheduling problems are well known to be NP-hard. Although some mathematically based methods are being used in the transport industry, there is room for improvement. A hybrid approach incorporating a genetic algorithm (GA) is presented. The role of the GA is to derive a small selection of good shifts to seed a greedy schedule construction heuristic. A group of shifts called a relief chain is identified and recorded. The relief chain is then inherited by the offspring and used by the GA for schedule construction. The new approach has been tested using real-life data sets, some of which represent very large problem instances. The results are generally better than those compiled by experienced schedulers and are comparable to solutions found by integer linear programming (ILP). In some cases, solutions were obtained when the ILP failed within practical computational limits.

Algorithms↗

PubMed1991

Changes in rates of unscheduled hospital readmissions and changes in efficiency following the introduction of the Medicare prospective payment system. An analysis using risk-adjusted data.

The purpose of this study was to analyze changes in rates of unscheduled readmissions and changes in technical efficiency following the introduction of the Medicare Prospective Payment System (PPS). We developed the Risk-Adjusted Readmissions Index (RARI), which allowed us to make comparisons in rates of unanticipated readmissions across hospitals and over time. Data envelopment analysis (DEA), a linear programming technique, was used to measure changes in technical efficiency by comparing the inputs used and the outputs produced across a cohort of hospitals, while adjusting for changes over time in case mix and case complexity. Rates of unscheduled readmissions and efficiency scores were computed for a sample of 245 hospitals for each year. Although both readmission rates and efficiency scores increased for most hospitals, there was no evidence that those hospitals that experienced the greatest increases in efficiency had the largest increases in their rates of unscheduled readmissions.

Abstracting and Indexing↗

PubMed2002

Waste benefits of CO2 policies in Japan.

A linear programming model REAP (Regional Environmental strategy Analysis Program) has been developed for the analysis of the consequences of a CO2 tax for petrochemical products such as plastics (CO2, carbon dioxide, is the most important greenhouse gas). Special attention has been paid to the impacts on waste management. The results suggest that a 10,000 Y t(-1) CO2 tax would result in a significant reduction of CO2 emissions in the petrochemical life cycle, ranging from 40 Mt in 2015 to 70 Mt CO2 in later decades (more than 50% emission reduction). Waste quantities will be reduced simultaneously. The CO2 tax results in an 18% reduction of plastic waste weight in 2015 (3 Mt waste). Lower tax levels that may be politically more acceptable would result in proportionally lower environmental benefits. CO2 benefits and waste benefits of a CO2 tax are of equal importance in policy terms. Apart from changes in waste volume, CO2 taxes would affect the cost-effectiveness of waste handling technologies. Energy recovery in industrial kilns may replace conventional waste incineration. Recycling constitutes half of the total waste treatment. Given these results, current investments in new incineration capacity may suffer from insufficient waste availability during the next two decades in case CO2 taxes are introduced. A third effect of a CO2 tax is a significant increase of waste transportation. The results show that this increase is concentrated in the central part of Honshu (Kinki, Chubu & Kanto). Such transportation can result in new local environmental impacts that should be analysed in more detail. Given the strong impact of CO2 taxes on waste quantities and waste treatment it is recommended to co-ordinate CO2 policies and solid waste policies.

Carbon Dioxide↗