SEARCH · PubMed Health

Results for “Programming, Linear”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 37 records · Page 2Linked to original sources

PubMed1978

Distribution of spinal disc pressures in the seated posture subjected to impact.

A musculoskeletal model for the human spine developed by the authors is used for this study. The model takes into account the equilibrium of the vertebral bodies, the intervertebral discs and segments of the upper extremities under the influence of all major muscle and joint forces. Linear programming techniques are used to obtain the muscle load sharing and the disc pressures, based on a preselected linear criterion. The criterion is formulated as a combination of all muscles forces (F), joint forces and ligament action (R,M) with suitable weighting factors, and a minimization is sought of U = F + k1R + k2M. The model is used to study the effect of sudden forward or backward acceleration forces, such as during the impact situation, on the distribution of disc pressures in the spinal column in the unsupported seated posture.

Biomechanical Phenomena↗

PubMed1991

Planning replacement of natural gas distribution systems under constraints on acceptable risk from explosions.

Natural gas distribution systems in the United States were developed primarily in the first half of this century, utilizing materials such as cast iron and then steel. Over time, cast iron and steel pipe sections became weak from corrosion and are subject to failure which in turn can lead to explosions and possible injury and loss of life. Gas utilities maintain system integrity through repair-replacement programs where pipe sections are prioritized for replacement in any given year through cost-benefit analysis; however, the total annual amount to be budgeted for replacement is left to engineering judgment. This approach has left some utilities vulnerable to criticism that their current replacement rate on cast iron pipe is not great enough and that public safety is being compromised. This paper addresses the problem situation by formulating a linear programming replacement decision model which augments cost-benefit analysis with explicit constraints on acceptable risk to human life from fire/explosion. The model is illustrated for a hypothetical utility.

Cost-Benefit Analysis↗

PubMed1977

High-performance liquid chromatographic analysis of methadone hydrochloride oral solution.

A direct and rapid high-performance liquid chromatographic assay for methadone hydrochloride in a flavored oral solution dosage form is described. A syrup sample, one part diluted with three parts of water, is introduced onto a column packed with octadecylsilane bonded on 10 micrometer porous silica gel (reversed phase). A formic acid-ammonium formate-buffered mobile phase is linear programmed with acetonitrile. The absorbance is monitored continuously at 280 or 254 nm, using a flow-through, UV, double-beam photometer. An aqueous methadone hydrochloride solution is used for external standardization. The relative standard deviation was not more than 1.0%. Drug recovery from a syrup base was better than 99.8%.

Administration, Oral↗

PubMed1992

Fast structure alignment for protein databank searching.

A fast method is described for searching and analyzing the protein structure databank. It uses secondary structure followed by residue matching to compare protein structures and is developed from a previous structural alignment method based on dynamic programming. Linear representations of secondary structures are derived and their features compared to identify equivalent elements in two proteins. The secondary structure alignment then constrains the residue alignment, which compares only residues within aligned secondary structures and with similar buried areas and torsional angles. The initial secondary structure alignment improves accuracy and provides a means of filtering out unrelated proteins before the slower residue alignment stage. It is possible to search or sort the protein structure databank very quickly using just secondary structure comparisons. A search through 720 structures with a probe protein of 10 secondary structures required 1.7 CPU hours on a Sun 4/280. Alternatively, combined secondary structure and residue alignments, with a cutoff on the secondary structure score to remove pairs of unrelated proteins from further analysis, took 10.1 CPU hours. The method was applied in searches on different classes of proteins and to cluster a subset of the databank into structurally related groups. Relationships were consistent with known families of protein structure.

Amino Acid Sequence↗

PubMed1992

Predicted and observed shapes of human mandibular condyles.

A mathematical model based on linear programming was used to study the directions of the joint forces used to maintain the human jaw in three-dimensional static equilibrium when producing bite forces of 100 N to a maximum of 1000 N down the long axis of a central incisor, first premolar, first molar and third molar. Seven different versions of the model were studied. The two simplest versions minimized the total muscle tension and the total joint load, respectively. Assuming that the joint force direction must be normal to some part of the articular surface of the condyle, neither version produced directions consistent with the observed shapes of human condyles. The other five versions minimized different combinations of muscle tensions and joint loads. Two of these versions produced joint force directions compatible with the shapes of condyles. Both minimized total muscle tension plus the (vertical) joint load on the back of the condyle. The results suggest that joint mechanoreceptors (probably non-directional) as well as muscle receptors contribute to the neuromuscular control of bite forces. Our results are consistent with some recent observations [Marshall and Tatton, Exp. Brain Res. 83, 137-150 (1990)] of the cat knee joint.

Biomechanical Phenomena↗

PubMed1992

Determination of doughing and manipulation times of acrylic resin denture base material and a proposal for a specification for a packing plasticity test.

The doughing and manipulation times of a range of acrylic resin denture base polymers are presented in this study. The methods evaluated were: (i) probing following American Society for testing materials specification, F451-76; (ii) hole penetration following British Standard, 2487: 1989 and International Standard Organisation, 1567: 1988; (iii) probing using a penetrometer employing a 20 g load and 1 mm diameter needle; (iv) oscillating rheometer apparatus used at a fixed frequency of 1 Hz by sweeping through a programmed linear increase in strain. The results indicate that each of the methods is capable of evaluating the doughing and manipulation times of the unprocessed polymers. It is concluded that the Bohlin VOR Oscillating Rheometer is excellent for investigating the flow properties of denture base polymers but it cannot be recommended for a standards specification test because of the high cost. The penetrometer method has been shown to be superior to the current standards specification test and would be ideal for a packing plasticity standards test.

Denture Bases↗

PubMed1992

Computer-aided optimization of choice and positioning of bone plates and screws used for internal fixation of mandibular fractures.

The present study describes a biomechanical integrated model of the mandibular system in which the maxilla and mandible, the masticatory muscles, and the temporomandibular joints are regarded as one system. In this model, strains in plate-osteosynthesis devices for internal fixation of mandibular fractures can be minimized by optimizing their positions. The model evaluates maximal bite force strategies on all possible dental elements; it uses a linear programming technique and a muscle architecture model, resulting in muscle recruitment patterns. The shape of a "standard" lower jaw is digitized by means of a three-dimensional (3-D) coordinate retrieval device and drawn on a computer screen after its dimensions have been changed according to the clinical case at hand. The 3-D location of the fracture as well as the anatomic restrictions for screw placement can be indicated on the screen. Osteosynthesis devices can be indicated in terms of dimensions, number, and material properties.

Biomechanical Phenomena↗

PubMed1979

Uniform depth dose distribution for biological irradiation using negative pions.

A simple, flexible technique has been developed to generate uniform depth dose profiles for the biomedical pion beam at TRIUMF using dynamic momentum control and linear programming. Either the entrance dose or the irradiation time required for a certain dose over the uniform region can be minimised. The dynamic momentum control can operate automatically under computer control even with a highly unstable beam. Cell survival profiles have been obtained for this uniform dose distribution using the gelatin technique. The RBE increases with increasing depth through the uniform dose region.

Animals↗

PubMed1992

Using fragment lengths from incomplete digestion by multiply cleaving enzymes to map antibody binding sites on a protein.

The problem of mapping the positions of the unique binding sites of several monoclonal antibodies on a linear protein structure is considered. Data giving the incidence of binding of individual antibodies to fragments of the protein obtained from it by the incomplete chemical or enzymatic digestion are used to formulate a series of linear programming problems. The solution to these problems shows which orderings of binding sites are possible, and gives upper and lower bounds for the relative positions of the sites.

Algorithms↗

PubMed2026

Detecting and reconstructing breakage-fusion-bridge cycles from long-read sequencing using BFBArchitect.

MOTIVATION: Focal oncogene amplification is a key driver of tumor progression. Remarkably, the increased pathology depends on the context-whether the amplification is extrachromosomal (ecDNA) or intrachromosomal. EcDNA amplifications promote heterogeneity, therapy resistance, and poor prognosis. Focal intrachromosomal amplifications often arise through breakage-fusion-bridge (BFB) cycles, which produce highly rearranged but stable chromosomes. Distinguishing BFB from ecDNA remains challenging due to overlapping genomic signatures. To address this, we present BFBArchitect, a computational method leveraging long-read Oxford Nanopore data to identify BFB sequences consistent with both copy number and structural variations. RESULTS: We provide a novel combinatorial characterization of BFB, which naturally leads to an integer linear programming (ILP) optimization. The ILP optimization generates a BFB sequence that best explains experimentally observed copy numbers and foldback structural variants. We implement this idea in a tool called BFBArchitect, which achieves near-perfect accuracy in distinguishing BFB from non-BFB structures in extensive simulations as well as on 18 validated tumor samples. Moreover, it generates sequence-level BFB reconstructions that provide mechanistic insights into BFB formation, including repair mechanisms with template switching and other structural variants, and recapture of telomere for stabilization. AVAILABILITY AND IMPLEMENTATION: BFBArchitect is available at https://github.com/AmpliconSuite/BFBArchitect.

Sequence Analysis, DNA↗

PubMed1978

A simple method for the computation of first neighbour frequencies of DNAs from CD spectra.

A procedure for the computation of the first neighbour frequencies of DNA's is presented. This procedure is based on the first neighbour approximation of Gray and Tinoco. We show that the knowledge of all the ten elementary CD signals attached to the ten double stranded first neighbour configurations is not necessary. One can obtain the ten frequencies of an unknown DNA with the use of eight elementary CD signals corresponding to eight linearly independent polymer sequences. These signals can be extracted very simply from any eight or more CD spectra of double stranded DNA's of known frequencies. The ten frequencies of a DNA are obtained by least square fit of its CD spectrum with these elementary signals. One advantage of this procedure is that it does not necessitate linear programming, it can be used with CD data digitalized using a large number of wavelengths, thus permitting an accurate resolution of the CD spectra. Under favorable case, the ten frequencies of a DNA (not used as input data) can be determined with an average absolute error < 2%. We have also observed that certain satellite DNA's, those of Drosophila virilis and Callinectes sapidus have CD spectra compatible with those of DNA's of quasi random sequence; these satellite DNA's should adopt also the B-form in solution.

Animals↗

PubMed1992

A weighting method for predicting protein structural class from amino acid composition.

A protein is generally classified into one of the following four structural classes: all alpha, all beta, alpha+beta and alpha/beta. In this paper, based on the weighting to the 20 constituent amino acids, a new method is proposed for predicting the structural class of a protein according to its amino acid composition. The 20 weighting parameters, which reflect the different properties of the 20 constituent amino acids, have been obtained from a training set of proteins through the linear-programming approach. The rate of correct prediction for a training set of proteins by means of the new method was 100%, whereas the highest rate of previous methods was 82.8%. Furthermore, the results showed that the more numerous training proteins, the more effective the new method.

Amino Acids↗

PubMedDate not supplied

Optimized dynamic rotation with wedges.

Dynamic rotation is a computer-controlled therapy technique utilizing an automated multileaf collimator in which the radiation beam shape changes dynamically as the treatment machine rotates about the patient so that at each instant the beam shape matches the projected shape of the target volume. In simple dynamic rotation, the dose rate remains constant during rotation. For optimized dynamic rotation, the dose rate is varied as a function of gantry angle. Optimum dose rate at each gantry angle is computed by linear programming. Wedges can be included in the optimized dynamic rotation therapy by using additional rotations. Simple and optimized dynamic rotation treatment plans, with and without wedges, for a pancreatic tumor have been compared using optimization cost function values, normal tissue complication probabilities, and positive difference statistic values. For planning purposes, a continuous rotation is approximated by static beams at a number of gantry angles equally spaced about the patient. In theory, the quality of optimized treatment planning solutions should improve as the number of static beams increases. The addition of wedges should further improve dose distributions. For the case studied, no significant improvements were seen for more than 36 beam angles. Open and wedged optimized dynamic rotations were better than simple dynamic rotation, but wedged optimized dynamic rotation showed no definitive improvement over open beam optimized dynamic rotation.

Humans↗

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↗

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↗

PubMed1975

Rumen modeling: rumen input-output balance models.

Two models of rumen fermentative relationships expressed as systems of simultaneous linear equations and based on requirements for maintenance of balances of elementary imput and output and metabolic pathways are presented in matrix format consistent with solution by linear programs. Matrix entries defining the two models were verified carefully based upon a survey of the literature, and conceptual bases of the models were validated by comparisons of model outputs with experimental data not used in model construction. The models then were used to evaluate interactions among feed composition, volatile fatty acid yields and patterns, microbial growth yields and efficiencies, and microbial metabolic pathways.

Amino Acids↗

PubMed1976

Adrenodoxin reductase-adrenodexin complex.

Adrenodoxin reductase and adrenodoxin have been shown (Chu, J.-W., and Kimura, T. (1973) J. Biol. Chem. 248, 5183-5187) to form a low dissociation constant, 1:1 complex when both proteins are in the oxidized form. We have found that when adrenodoxin: adrenodoxin reductase ratios are varied by increasing the adrenodoxin concentration, with adrenodoxin reductase held constant, an increasing rate of cytochrome c reduction, with NADPH as reductant, is seen up to a ratio of 1:1, indicating that cytochrome c reduction occurs via the protein-protein complex. Spectra observed during titration of this protein-protein complex with NADH were resolved into components by the linear programming method, using a computer program written in Fortran IV. Analysis of the data has shown that the flavoprotein is reduced prior to the iron sulfur protein, and that the midpoint oxidation-reduction potentials (pH 7.5) of the two proteins are -295 and -331 mV, respectively, when both are present in the complex. Complex formation does not alter the potential of adrenodoxin reductase, but changes that of adrenodoxin by -40 mV. Equilibrium constants derived from potential measurements show that the strength of the protein-protein interaction in the complex is unaltered by reduction of adrenodoxin reductase, but is decreased by about 1 kcal due to reduction of adrenodoxin. The low dissociation constants for both oxidized reduced forms of the adrenodoxin reductase-adrenodoxin complex indicate that the complex must remain associated throughout its catalytic cycle. Titration of the adrenodoxin reductase-adrenodoxin complex with the physiologic reductant, NADPH, was followed by EPR and visible spectra, and yielded an order of reduction of the components identical with that seen when NADH was used as reductant. Reduction of the protein-protein complex with NADPH yielded a ternary complex between NADP+, flavoprotein, and iron sulfur protein, with the two electrons located in a "charge transfer" complex between flavoprotein and pyridine nucleotide.

Adrenal Cortex↗