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PubMed1991

Physiological prediction of muscle forces--II. Application to isokinetic exercise.

The successful application of a physiological model of the musculoskeletal system capable of accounting for nonequilibrium dynamic loading and predicting individual muscle forces in the knee is presented. The model incorporates rigid-body mechanics and musculoskeletal physiology. Unknown muscle and joint contact forces outnumber the equilibrium equations resulting in an indeterminant problem. Mathematical optimization is utilized to resolve the indeterminacy. The model is used to estimate individual muscle forces during isokinetic exercise. Five subjects were tested at speeds of 60 degrees/s and 180 degrees/s. A newly proposed optimal criterion, minimizing muscular activation, results in muscle force predictions which have significantly higher correlations with myoelectric activity than other linear and nonlinear optimal criteria. The results demonstrate that properly constrained linear programming methods do not limit the number of active muscles and allow for uniform recruitment of the active muscles.

Adult↗
PubMed1989

An algorithm for design of beam compensators.

Beam compensators are optimally designed to give a uniform dose to any plane or midsurface that intersects a single beam, or to give a uniform dose to the volume defined by the intersection of two or more beams. The primary and scatter components are taken into account separately, as well as the patient's shape and internal heterogeneities. The design of the beam compensators is formulated as a linear programming problem and solved with a variation of the Simplex Method. Beam weighting factors are also obtained as part of the solution.

Algorithms↗
PubMed1990

Large scale optimization of beam weights under dose-volume restrictions.

The problem of choosing weights for beams in a multifield plan which maximizes tumor dose under conditions that recognize the volume dependence of organ tolerance to radiation is considered, and its solution described. Structures are modelled as collections of discrete points, and the weighting problem described as a combinatorial linear program (LP). The combinatorial LP is solved as a mixed 0/1 integer program with appropriate restrictions on normal tissue dose. The method is illustrated through the assignment of weights to a set of 10 beams incident on a pelvic target. Dose-volume restrictions are placed on surrounding bowel, bladder, and rectum, and a limit placed on tumor dose inhomogeneity. Different tolerance restrictions are examined, so that the sensitivity of the target dose to changes in the normal tissue constraints may be explored. It is shown that the distributions obtained satisfy the posed constraints. The technique permits formal solution of the optimization problem, in a time short enough to meet the needs of treatment planners.

Humans↗
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↗
PubMed1986

Fat synthesis in adipose tissue. An examination of stoichiometric constraints.

The requirement for net balance of synthesis, degradation and transport for all intermediates in the pathways from glucose to fat imposes constraints on the balance of fluxes between different pathways. Linear programming has been used to examine the interactions between these constraints on metabolism in adipocytes and the requirement for efficiency in the conversion of glucose into fat. The circumstances under which excessive ATP synthesis would accompany this conversion have been investigated.

Adipose Tissue↗
PubMed1990

Multisurface method of pattern separation for medical diagnosis applied to breast cytology.

Multisurface pattern separation is a mathematical method for distinguishing between elements of two pattern sets. Each element of the pattern sets is comprised of various scalar observations. In this paper, we use the diagnosis of breast cytology to demonstrate the applicability of this method to medical diagnosis and decision making. Each of 11 cytological characteristics of breast fine-needle aspirates reported to differ between benign and malignant samples was graded 1 to 10 at the time of sample collection. Nine characteristics were found to differ significantly between benign and malignant samples. Mathematically, these values for each sample were represented by a point in a nine-dimensional space of real variables. Benign points were separated from malignant ones by planes determined by linear programming. Correct separation was accomplished in 369 of 370 samples (201 benign and 169 malignant). In the one misclassified malignant case, the fine-needle aspirate cytology was so definitely benign and the cytology of the excised cancer so definitely malignant that we believe the tumor was missed on aspiration. Our mathematical method is applicable to other medical diagnostic and decision-making problems.

Biopsy, Needle↗
PubMed1968

The large-scale separation of peroxisomes, mitochondria, and lysosomes from the livers of rats injected with triton WR-1339. Improved isolation procedures, automated analysis, biochemical and morphological properties of fractions.

Improved, largely automated methods are described for the purification and analysis o peroxisomes, lysosomes, and mitochondria from the livers of rats injected with Triton WR-1339. With these new methods, it has become possible to obtain, in less than 6 hr and with reliable reproducibility, mitochondria practically free of contaminants, as well as the rarer cytoplasmic particles in amounts (about 100 mg of protein) and in a state of purity (95%) that make them suitable for detailed biochemical studies. The results obtained so far on these preparations have made more conclusive and precise previous estimates of the biochemical and morphological properties of the three groups of cytoplasmic particles. In addition, peroxisomes were found to contain essentially all the L-alpha-hydroxy acid oxidase of the liver, as well as a small, but significant fraction of its NADP-linked isocitrate dehydrogenase activity. Another small fraction of the latter enzyme is present in the mitochondria, the remainder being associated with the cell sap. The mitochondrial localization of the metabolically active cytoplasmic DNA could be verified. The relative content of the fractions in mitochondria, whole peroxisomes, peroxisome cores, lysosomes, and endoplasmic reticulum was estimated independently by direct measurements on electron micrographs, and by linear programming (based on the assumption that the particles are biochemically homogeneous) of the results of enzyme assays. The two types of estimates agreed very well, except for one fraction in which low cytochrome oxidase activity was associated with mitochondrial damage.

Acid Phosphatase↗
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↗
PubMed1986

A discrete model of bacterial metabolism.

This paper describes a computer model of the intermediary metabolism of bacteria during steady-state growth and during adaptations, e.g. to new carbon sources. Metabolic regulation is represented as a process of optimisation, in which the trend is towards improved metabolic performance. The model uses linear programming techniques for the optimisation. The implementation falls into four phases: (i) assembly of model parameters; (ii) calculations; (iii) storage of solutions and (iv) projection of solutions. The use of a commercial database and a commercial spreadsheet has proved to be of great assistance in the first and third phases. A metabolic map format, with the optional addition of conversion values, names of enzymes or co-factors has been used to project the results in a form convenient for inspection.

Algorithms↗
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↗
PubMed1986

Limits to the relationship among recombination, disequilibrium and epistasis in two-locus models.

I determine limits to the equilibrium relationship among epistasis, recombination and disequilibrium in two-locus, two-allele models using linear programming techniques. I show that when allele frequencies are one-half at each locus, the symmetric model is the fitness pattern that generates the most disequilibrium for the smallest level of epistasis. When allele frequencies deviate from one-half much larger levels of epistasis are required to generate similar levels of disequilibrium. I determine the level of epistasis required to generate observed significant levels of disequilibrium in natural populations. The overall implication is that disequilibrium will be large at equilibrium only between strongly interacting, closely linked loci.

Alleles↗
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↗
PubMed1989

Evaluating managerial efficiency of Veterans Administration medical centers using Data Envelopment Analysis.

This study applied the methodology of Data Envelopment Analysis (DEA) to the set of VA medical centers to evaluate their relative managerial efficiencies. Each VAMC was viewed as a producer of multiple outputs and a consumer of multiple inputs. DEA uses linear programming to identify resources that were underutilized and services that were inefficiently produced. Managerial strategies based on the dual variables were constructed to indicate the manner in which inefficient VAMCs may be made efficient. The analysis showed that relative inefficiency existed in about one third of the VAMCs nationwide. Elimination of this inefficiency would save the VA over $300 million annually on personnel, equipment, drugs, and supplies, without reducing the level of services provided. A subsequent analysis of co-variance revealed that VAMCs affiliated with a university were generally less efficient than those without such an affiliation. A similar finding was obtained for larger VAMCs relative to smaller medical centers. In neither case, however, should these results be construed to imply that VAMCs should terminate their university affiliations or that VAMCs should be made smaller since factors other than relative efficiency are clearly as or more important in such decisions.

Cost Control↗
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↗