An algorithmic approach to multiple complete digest mapping.

Multiple Complete Digest (MCD) mapping is a method of determining the locations of restriction sites along a target DNA molecule. The resulting restriction map has many potential applications in DNA sequencing and genetics. In this work, we present a heuristic algorithm for fragment identification, a key step in the process of constructing an MCD map. Given measurements of the restriction fragment sizes from one or more complete digestions of each clone in a clone library covering the molecule to be mapped, the algorithm identifies groups of restriction fragments on different clones that correspond to the same region of the target DNA. Once these groups are correctly determined the desired map can be constructed by solving a system of simple linear inequalities. We demonstrate the effectiveness of our algorithm on real data provided by the Genome Center at the University of Washington.     

An algorithmic approach to modelling the retinal receptor topography

Based on published research results on the structure of the human retina and the initial assumption of tight hexagonal packing of cones, the mean cone-distance function is derived. Disorder in the cone lattice is explained as the superposition of increasing topological distortion in the hexagonal lattice (providing a possible explanation for observed systematic lattice distortions) and local jitter of neighbor-toneighbor distances, for which a simple statistical model is provided. These individual results are incorporated into a proposed algorithm for simulating the cone receptors' topography in 3D-space. Finally, possible software and hardware applications of the algorithmically defined retina model are briefly touched.     

An algorithmic and information-theoretic approach to multimetric index construction

The use of multimetric indices (MMIs), such as the widely used index of biological integrity (IBI), to measure, track, summarize and infer the overall impact of human disturbance on biological communities has been steadily growing in recent years. Initially, MMIs were developed for aquatic communities using pre-selected biological metrics as indicators of system integrity. As interest in these bioassessment tools has grown, so have the types of biological systems to which they are applied. For many ecosystem types the appropriate biological metrics to use as measures of biological integrity are not known a priori. As a result, a variety of ad hoc protocols for selecting metrics empirically has developed. However, the assumptions made by proposed protocols have not be explicitly described or justified, causing many investigators to call for a clear, repeatable methodology for developing empirically derived metrics and indices that can be applied to any biological system. An issue of particular importance that has not been sufficiently addressed is the way that individual metrics combine to produce an MMI that is a sensitive composite indicator of human disturbance. In this paper, we present and demonstrate an algorithm for constructing MMIs given a set of candidate metrics and a measure of human disturbance. The algorithm uses each metric to inform a candidate MMI, and then uses information-theoretic principles to select MMIs that capture the information in the multidimensional system response from among possible MMIs. Such an approach can be used to create purely empirical (data-based) MMIs or can, optionally, be influenced by expert opinion or biological theory through the use of a weighting vector to create value-weighted MMIs. We demonstrate the algorithm with simulated data to demonstrate the predictive capacity of the final MMIs and with real data from wetlands from Acadia and Rocky Mountain National Parks. For the Acadia wetland data, the algorithm identified 4 metrics that combined to produce a −0.88 correlation with the human disturbance index. When compared to other methods, we find this algorithmic approach resulted in MMIs that were more predictive and comprise fewer metrics.     

Rigid domains in proteins: An algorithmic approach to their identification

A rigid domain, defined here as a tertiary structure common to two or more different protein conformations, can be identified numerically from atomic coordinates by finding sets of residues, one in each conformation, such that the distance between any two residues within the set belonging to one conformation is the same as the distance between the two structurally equivalent residues within the set belonging to any other conformation. The distance between two residues is taken to be the distance between their respective α carbon atoms. With the methods of this paper we have found in the deoxy and oxy conformations of the human hemoglobin α₁β₁ dimer a rigid domain closely related to that previously identified by Baldwin and Chothia (J. Mol. Biol. 129:175–220,1979). We provide two algorithms, both using the difference-distance matrix, with which to search for rigid domains directly from atomic coordinates. The first finds all rigid domains in a protein but has storage and processing demands that become prohibitively large with increasing protein size. The second, although not necessarily finding every rigid domain, is computationally tractable for proteins of any size. Because of its efficiency we are able to search protein conformations recursively for groups of non-intersecting domains. Different protein conformations, when aligned by superimposing their respective domain structures; can be examined for structural differences in regions complementing a rigid domain. © 1995 Wiley-Liss, Inc.     

An orthotropic viscoelastic material model for passive myocardium: theory and algorithmic treatment

This contribution presents a novel constitutive model in order to simulate an orthotropic rate-dependent behaviour of the passive myocardium at finite strains. The motivation for the consideration of orthotropic viscous effects in a constitutive level lies in the disagreement between theoretical predictions and experimentally observed results. In view of experimental observations, the material is deemed as nearly incompressible, hyperelastic, orthotropic and viscous. The viscoelastic response is formulated by means of a rheological model consisting of a spring coupled with a Maxwell element in parallel. In this context, the isochoric free energy function is decomposed into elastic equilibrium and viscous non-equilibrium parts. The baseline elastic response is modelled by the orthotropic model of Holzapfel and Ogden [Holzapfel GA, Ogden RW. 2009. Constitutive modelling of passive myocardium: a structurally based framework for material characterization. Philos Trans Roy Soc A Math Phys Eng Sci. 367:3445–3475]. The essential aspect of the proposed model is the account of distinct relaxation mechanisms for each orientation direction. To this end, the non-equilibrium response of the free energy function is constructed in the logarithmic strain space and additively decomposed into three anisotropic parts, denoting fibre, sheet and normal directions each accompanied by a distinct dissipation potential governing the evolution of viscous strains associated with each orientation direction. The evolution equations governing the viscous flow have an energy-activated nonlinear form. The energy storage in the Maxwell branches has a quadratic form leading to a linear stress–strain response in the logarithmic strain space. On the numerical side, the algorithmic aspects suitable for the implicit finite element method are discussed in a Lagrangian setting. The model shows excellent agreement compared to experimental data obtained from the literature. Furthermore, the finite element simulations of a heart cycle carried out with the proposed model show significant deviations in the strain field relative to the elastic solution.     

Soft-tissue sarcomas of the upper extremity: surgical treatment and outcome

The objective of this retrospective follow-up study was to evaluate the outcome of patients with soft-tissue sarcoma treated by the authors' protocol, which consists of a selective combination of conservative surgery and radiotherapy. Patients who relapsed were especially evaluated to improve treatment results. The authors examined 80 patients with local soft-tissue sarcoma in the upper extremity referred to their multidisciplinary group. Fifteen patients were referred for first or subsequent local recurrence, and 65 patients were treated for primary tumor. The goal of treatment was local control and preservation of a functional limb. Wide excision was attempted. If the margin was less than 2.5 cm, postoperative radiotherapy was administered. Eighty-five percent of the patients were treated by limb salvage. Thirty patients needed reconstructive procedures such as pedicled (20 patients) or free flaps (10 patients). No free flaps were lost. The 5-year disease-specific overall survival rate was 75 percent, the local recurrence-free survival rate was 79 percent, and the metastasis-free survival rate was 68 percent. In univariate analysis, prognostic factors for local recurrence were extracompartmental site; for development of metastases, large size and extracompartmental site; and for decreased disease-specific overall survival, large size and extracompartmental site. Intramuscular, cutaneous, and subcutaneous tumors had a 5-year local control rate of 100 percent, and extracompartmental tumors had a local control rate of 69 percent. Extracompartmental tumors clearly have the worst prognosis and should be the main target for improving treatment strategies. After exclusion of patients with inadequate treatment according to the authors' protocol, the local control rate at 5 years was 90 percent. Strict adherence to treatment protocol should be practiced.     

An algorithmic approach to constructing the on-line estimation system for the specific growth rate

The objective of this article is to propose an algorithm for the on-line estimation of the specific growth rate in a batch or a fed-batch fermentation process. The algorithm shows the practical procedure for the estimation method utilizing the macroscopic balance and the extended Kalman filter. A number of studies of the on line estimation have been presented. However, there are few studies discussing about the selection of the observed variables and for the tuning of some parameters of the extended Kalman filter, such as covariance matrix and initial values of the state.The beginning of this article is devoted to explain the selection of the observed variable. This information is very important in terms of the practical know-how for using technique. It is discovered that the condition number is a practically useful and valid criterion for number is a practically useful and valid criterion for choosing the variable to be observed.Next, when the extended Kalman filter in applied to the online estimation of the specific growth rate, which is directly unmeasurable, criteria for judging the validity of the estimated value from the observed data are proposed. Based on the proposed criterial, the system equation of the specific growth rate is selected and initial value of the state variable and covariance matrix of the system noises are adjusted. From many experiments, it is certified that the specific growth rate in the batch or fed -batch fermentation can be estimated accurately by means of the algorithm proposed here. In these experiments, that is, when the cell concentration is measured directly, the extended Kalman filter using the convariance matrix with a constant element can estimate more accurately values of the specific growth rate than the adaptive extended Kalman filter does.     

Cerebrospinal fluid cell preparation methods. An evaluation.

Although the cells from cerebrospinal fluid are widely used for diagnostic purposes, the cell yield on the microscopic slide is only rarely considered and mostly unsatisfactory. A reevaluation of several preparatory methods showed a very low yield with the Sayk-type chamber, a modest yield with the cytocentrifuge and the best yield with a simple, self-adhering chamber on slides coated with a polycation.     

Two-point discrimination distances in the normal hand and forearm: application to various methods of fingertip reconstruction.

Two-point discrimination in the hand and forearm is best during the third decade of life. In the fingertips, the ulnar digits are more discriminating than the radial digits. Males and females have equal two-point discrimination during each age decade. Fingertips are twice as discriminating as the thenar and hypothenar areas, and the thenar and hypothenar areas are twice as discriminating as the volar side of the wrist; the wrist is twice as discriminating as the forearm. The Kleinert and Kutler flaps demonstrated the best two-point discrimination among the repaired fingertips.     

An evaluation of some complexing methods for the histochemistry of calcium.

A selection of reagents capable of complexing with calcium in various ways was compared by applying them to tissue sections known to contain calcium in a variety of physiochemical states. Their histochemical potential was evaluated according to their sensitivity, specificity, accuracy of localisation and intensity of staining. Murexide, for light microscopy, and 8-hydroxyquinoline, for fluorescence microscopy proved to be the best overall reagents. They failed to demonstrate calcium oxalate, which was well shown by naphthalhydroxamic acid.     

Flexible manufacturing systems evaluation: An alternative approach

The purpose of this article is to integrate the von Neumann-Morgenstern theory of utility functions and the mean-variance approach of portfolio analysis within the computational framework of selecting a production technology to replace an existing one. A stochastic, static one-period problem is formulated, and a measure that takes into account both the capital costs of implementing the new technology and the random monetary value of its output is identified to solve the problem. The properties of this measure are discussed particularly with reference to the optimal selection decision. An example is described to illustrate the methodology.     

An evaluation of beta-turn prediction methods

MOTIVATION: beta-turn is an important element of protein structure. In the past three decades, numerous beta-turn prediction methods have been developed based on various strategies. For a detailed discussion about the importance of beta-turns and a systematic introduction of the existing prediction algorithms for beta-turns and their types, please see a recent review (Chou, Analytical Biochemistry, 286, 1-16, 2000). However at present, it is still difficult to say which method is better than the other. This is because of the fact that these methods were developed on different sets of data. Thus, it is important to evaluate the performance of beta-turn prediction methods. RESULTS: We have evaluated the performance of six methods of beta-turn prediction. All the methods have been tested on a set of 426 non-homologous protein chains. It has been observed that the performance of the neural network based method, BTPRED, is significantly better than the statistical methods. One of the reasons for its better performance is that it utilizes the predicted secondary structure information. We have also trained, tested and evaluated the performance of all methods except BTPRED and GORBTURN, on new data set using a 7-fold cross-validation technique. There is a significant improvement in performance of all the methods when secondary structure information is incorporated. Moreover, after incorporating secondary structure information, the Sequence Coupled Model has yielded better results in predicting beta-turns as compared with other methods. In this study, both threshold dependent and independent (ROC) measures have been used for evaluation.     

Treating the abdominotorso region of the massive weight loss patient: an algorithmic approach

There has been tremendous growth in the number of patients seeking body contouring procedures after massive weight loss. Most patients desire improvement of the abdominotorso region first. After massive weight loss, there is enormous variability of body proportions, and therefore there have been many surgical options proposed based on the quality of the skin, subcutaneous fat component, and location of the lax tissue. Each area needs to be assessed to see whether there is a significant lower abdominal component, an upper midline abdominal component, or contributions from the buttocks and flanks. An algorithm for treatment is presented to simplify the decision-making process. Patient examples are also shown to demonstrate the usefulness of the algorithm.