Progressive tree neighborhood applied to the maximum parsimony problem

The Maximum Parsimony (MP) problem aims at reconstructing a phylogenetic tree from DNA sequences while minimizing the number of genetic transformations. To solve this NP-complete problem, heuristic methods have been developed, often based on local search. In this article, we focus on the influence of the neighborhood relations. After analyzing the advantages and drawbacks of the well-known Nearest Neighbor Interchange (NNI), Subtree Pruning Regrafting (SPR) and Tree-Bisection-Reconnection (TBR) neighborhoods, we introduce the concept of Progressive Neighborhood (PN) which consists in constraining progressively the size of the neighborhood as the search advances. We empirically show that applied to the Maximum Parsimony problem, this progressive neighborhood turns out to be more efficient and robust than the classic neighborhoods using a descent algorithm. Indeed, it allows to find better solutions with a smaller number of iterations or trees evaluated.     

A decision-making approach to the operation of flexible manufacturing systems

This paper introduces a generic decision-making framework for assigning resources of a manufacturing system to production tasks. Resources are broadly defined production units, such as machines, human operators, or material handling vehicles; and tasks are activities performed by resources. In the specific context of FMS, resources correspond to individual machines; tasks correspond to operations to be performed on parts. The framework assumes a hierarchical structure of the system and calls for the execution of four consecutive steps to make a decision for the assignment of a resource to a task. These steps are 1) establishment of decision-making criteria, 2) formation of alternative assignments, 3) estimation of the consequences of the assignments, and 4) selection of the best alternative assignment. This framework has been applied to an existing FMS as an operational policy that decides what task will be executed on which resource of this FMS. Simulation runs provide some initial results of the application of this policy. It is shown that the policy provides flexibility in terms of system performance and computational effort.     

Set-based particle swarm optimization applied to the multidimensional knapsack problem

Particle swarm optimization algorithms have been successfully applied to discrete/valued optimization problems. However, in many cases the algorithms have been tailored specifically for the problem at hand. This paper proposes a generic set-based particle swarm optimization algorithm for use in discrete-valued optimization problems that can be formulated as set-based problems. A detailed sensitivity analysis of the parameters of the algorithm is conducted. The performance of the proposed algorithm is then compared against three other discrete particle swarm optimization algorithms from literature using the multidimensional knapsack problem and is shown to statistically outperform the existing algorithms.     

Fluorescent protein biosensors applied to microphysiological systems

This mini-review discusses the evolution of fluorescence as a tool to study living cells and tissues in vitro and the present role of fluorescent protein biosensors (FPBs) in microphysiological systems (MPSs). FPBs allow the measurement of temporal and spatial dynamics of targeted cellular events involved in normal and perturbed cellular assay systems and MPSs in real time. FPBs evolved from fluorescent analog cytochemistry (FAC) that permitted the measurement of the dynamics of purified proteins covalently labeled with environmentally insensitive fluorescent dyes and then incorporated into living cells, as well as a large list of diffusible fluorescent probes engineered to measure environmental changes in living cells. In parallel, a wide range of fluorescence microscopy methods were developed to measure the chemical and molecular activities of the labeled cells, including ratio imaging, fluorescence lifetime, total internal reflection, 3D imaging, including super-resolution, as well as high-content screening. FPBs evolved from FAC by combining environmentally sensitive fluorescent dyes with proteins in order to monitor specific physiological events such as post-translational modifications, production of metabolites, changes in various ion concentrations, and the dynamic interaction of proteins with defined macromolecules in time and space within cells. Original FPBs involved the engineering of fluorescent dyes to sense specific activities when covalently attached to particular domains of the targeted protein. The subsequent development of fluorescent proteins (FPs), such as the green fluorescent protein, dramatically accelerated the adoption of studying living cells, since the genetic “labeling” of proteins became a relatively simple method that permitted the analysis of temporal–spatial dynamics of a wide range of proteins. Investigators subsequently engineered the fluorescence properties of the FPs for environmental sensitivity that, when combined with targeted proteins/peptides, created a new generation of FPBs. Examples of FPBs that are useful in MPS are presented, including the design, testing, and application in a liver MPS.     

Flash-induced kinetic infrared spectroscopy applied to biochemical systems

A flash photolysis apparatus with monitoring infrared beam is described allowing measurements of relative transmission changes of 10^–3 in times of a few milliseconds. The investigation of the photodissociation of CO-myoglobin confirms the results obtained by static infrared difference spectroscopy. The application of our method to the rhodopsin/Meta II transition reveals signals which can tentatively be ascribed to the disappearance of the C=C-band of the protonated N-retinylidene Schiff base in rhodopsin. The developed method will be compared with other existing methods of kinetic vibronic spectroscopy such as kinetic resonance Raman spectroscopy and kinetic Fourier infrared spectroscopy.     

A theory of evaluation applied to human-environment systems

1. 1. The writers present the general theory of evaluation that is being developed by their group.

2. 2. The evaluation of a human environment is a complex mental process.

3. 3. In an effort to express numerically the quality of an environment, one tends to oversimplify the complex aspects of it and the entailing problems in relation to its inhabitants.

4. 4. In this paper, some examples are taken in the evaluation of thermal environments, wherein much has been said and done in setting up numerical scales to express human comfort, and yet neither clear-cut explanations nor convincing logic seem to exist to terminate the argument over the widely scattered and sometimes seemingly contradicting experimental data.

5. 5. The writers suggest that many of the reasons for this confusion may be traced back to the oversimplified notion of evaluation.

6. 6. It is shown that there are various possibilities when looking at the scales of evaluation.

7. 7.|The nominal scale, least studied of all the four traditional scales, may be given a prominent place in evaluating a thermal environment. The pseudo-interval order scale is another example.

From social network (centralized vs. decentralized) to collective decision-making (unshared vs. shared consensus)

Relationships we have with our friends, family, or colleagues influence our personal decisions, as well as decisions we make together with others. As in human beings, despotism and egalitarian societies seem to also exist in animals. While studies have shown that social networks constrain many phenomena from amoebae to primates, we still do not know how consensus emerges from the properties of social networks in many biological systems. We created artificial social networks that represent the continuum from centralized to decentralized organization and used an agent-based model to make predictions about the patterns of consensus and collective movements we observed according to the social network. These theoretical results showed that different social networks and especially contrasted ones--star network vs. equal network--led to totally different patterns. Our model showed that, by moving from a centralized network to a decentralized one, the central individual seemed to lose its leadership in the collective movement's decisions. We, therefore, showed a link between the type of social network and the resulting consensus. By comparing our theoretical data with data on five groups of primates, we confirmed that this relationship between social network and consensus also appears to exist in animal societies.     

Technique of systems identification applied to estimating copepod production

Systems identification offers some advantages over other methodsof estimating zooplankton production. The technique involvesspecification of a dynamic population model with unknown parameters.By using least squares analysis to fit the model to data seriesthe parameters and production are estimated. Two cohort populationmodels are described and tested against data generated by asimulation model with known production. A third popular methoddeveloped by Winberg was also applied for comparison. The systems identification technique was found to be least sensitiveto varying levels of stage analysis and sampling interval. Themodels were also applied to population data from an enclosedwater column (CEPEX). Recommendations are made on the degreeof stage aggregation and sampling interval required to obtaingood estimates of production for populations with identifiablecohorts. ¹Current address: ESSA - Environmental and Social Systems AnalystsLtd., 678 West Broadway, Vancouver, B.C., Canada V5Z 1G6.     

A general solution to the time interval omission problem applied to single channel analysis.

To obtain the open or closed time interval distributions of patch clamp signals, several workers have used a half-amplitude minimum time interval criterion. Within this framework, no transition between states of different conductance levels is considered to have taken place if it leads to a time interval smaller than a certain critical value. This procedure modifies substantially the open or closed time interval distribution of the random signal to be analyzed, since time intervals well above the time resolution of the recording system may be interrupted by short gaps that may or may not satisfy the minimum time interval criterion. We present here a general theoretical framework by means of which the effect of time interval omission on time interval distributions can be taken into account. Based on the mathematical formalism provided by the Kolmogorov forward equation, special matrix operators are first defined. The general solution to the time omission problem in its integral form is then derived. In view of the poor computational feasibility of the resulting solution, a first-order approximation is also presented. This approximation consists essentially in neglecting the contribution of the undetected gaps to the total length of the resulting time interval. The exact and approximate solutions are then applied to two special kinetic schemes commonly found in single-channel studies, namely the O-C and C-O-C models. The applicability of the proposed formalism to the time interval distribution problem of a damped random signal is finally discussed.     

Hitch-hiking: a parallel heuristic search strategy, applied to the phylogeny problem.

The article introduces a parallel heuristic search strategy ("Hitch-hiking") which can be used in conjunction with other random-walk heuristic search strategies. It is applied to an artificial phylogeny problem, in which character sequences are evolved using pseudo-random numbers from a hypothetical ancestral sequence. The objective function to be minimized is the minimum number of character-state changes required on a binary tree that could account for the sequences observed at the tips (leaves) of the tree -- the Maximum Parsimony criterion. The Hitch-hiking strategy is shown to be useful in that it is robust and that on average the solutions found using the strategy are better than those found without. Also the strategy can dynamically provide information on the characteristics of the landscape of the problem. I argue that Hitch-hiking as a scheme for parallelization of existing heuristic search strategies is of potentially very general use, in many areas of combinatorial optimization.     

Mucous systems show a novel mechanical response to applied deformation

Mucous secretions have a wide range of biological functions that are intimately linked with their rheological properties. In addition, many mucous secretions are exposed to significant stress and deformation during physiological function. This study has examined the rheological response of three mucous systems, native pig gastric mucus, purified mucin gels, and mucin alginate gels, to increasing applied stress to a level sufficient to induce flow behavior. A novel, frequency-dependent stress hardening was observed in all three systems. This hardening behavior may play a significant role in the ability of mucous systems to resist mechanical disruption in the physiological state.     

Technique of systems identification applied to estimating copepod population parameters

System identification may offer some advantages over other methodsof estimating population parameters from time series of copepodand similar populations. The technique involves the specificationof a dynamic population model with unknown parameters. The parametersare estimated using least squares analysis to fit the modelto data series. Four simple copepod population models are describedand then tested against data generated by a simulation modelwith predefined parameters. The models were also applied topopulation data from an enclosed water column (CEPEX). Someconclusions are reached on the degree of stage aggregation andsampling interval required to estimate mortality and recruitment.,     

The Cell Collective: Toward an open and collaborative approach to systems biology

Background

The construction of customized nucleic acid sequences allows us to have greater flexibility in gene design for recombinant protein expression. Among the various parameters considered for such DNA sequence design, individual codon usage (ICU) has been implicated as one of the most crucial factors affecting mRNA translational efficiency. However, previous works have also reported the significant influence of codon pair usage, also known as codon context (CC), on the level of protein expression.

Results

In this study, we have developed novel computational procedures for evaluating the relative importance of optimizing ICU and CC for enhancing protein expression. By formulating appropriate mathematical expressions to quantify the ICU and CC fitness of a coding sequence, optimization procedures based on genetic algorithm were employed to maximize its ICU and/or CC fitness. Surprisingly, the in silico validation of the resultant optimized DNA sequences for Escherichia coli, Lactococcus lactis, Pichia pastoris and Saccharomyces cerevisiae suggests that CC is a more relevant design criterion than the commonly considered ICU.

Conclusions

The proposed CC optimization framework can complement and enhance the capabilities of current gene design tools, with potential applications to heterologous protein production and even vaccine development in synthetic biotechnology.     

Mapping indicator models: From intuitive problem structuring to quantified decision-making in sustainable forest management

Most commonly, sustainability indicator sets presented as lists do not take into account interactions among indicators in a systematic manner. Vice versa, existing environmental indicator systems do not provide a formalized approach for problem structuring and quantitative decision support. In this paper, techniques for considering indicator relationships are highlighted and a coupled approach between a qualitative and a quantitative method is analysed. Cognitive mapping (CM) is used for structuring indicators and three different causal maps are derived based on established sustainability concepts: (a) criteria and indicators (C&I hierarchy), (b) indicator network, and (c) Driving Force-Pressure-State-Impact-Response (DPSIR) system. These maps are transferred to the Analytic Network Process (ANP) to allow their application in multi-criteria decision analysis (MCDA).In an application example, Pan-European indicators for sustainable forest management (SFM) are utilized in an ANP-based assessment. The effects of the model structure on the overall evaluation result are demonstrated by means of three reporting periods on Austrian forestry.In a comparative analysis of CM and ANP it is tested whether their measures of indicator significance do correspond. Both centrality in CM and single limited priorities in ANP have been reported to identify key indicators that play an important role in networks. We found out that the correspondence between CM and ANP is the stronger the more rigidly cause-effect relationships are interpreted, which is the case for the DPSIR system of SFM indicators.It is demonstrated that using indicator sets without consideration of the indicator interactions will cause shortcomings for evaluation and assessment procedures in SFM. Given strict and consistent definition of causal indicator relationships, a coupled use of CM and ANP is recommendable for both enhancing the process of problem structuring as well as supporting preference-based evaluation of decision alternatives.     

Fate of virus in wastewater applied to slow-infiltration land treatment systems

The removal of seeded coliphage f2 and indigenous enteroviruses from primary and secondary wastewaters applied by spray irrigation to sandy loam and silt loam soils in field test cells was examined. The amount of f2 recovered from 170-cm-deep soil percolate samples taken over a 53-day period never exceeded 0.1% of applied virus levels and was usually below detection limits. Indigenous enterovirus levels in percolate waters also constituted only a small portion of those found in the wastewaters. At 10 days after seeding, f2 virus was present throughout the soil column but tended to accumulate around the soil core middepths. Coliphage f2 disappeared from the soil surface regions at a high rate, and by 53 days very little virus could be detected within the length of the soil columns. Sterilized soil core segments from different depths were studied to determine their virus adsorption capabilities when suspended in either wastewater, test cell percolate water, or distilled water containing divalent cations. The adsorptive capacity of Windsor and Charlton soils for poliovirus 1 and coliphage f2 increased greatly with the soil sample depth until leveling off at the midcore depths. Soil suspended in wastewater had the least virus adsorption capability for all depths studied.     

Time-dependent interfacial charging effects of electrical fields applied to biological systems

An important aspect of the interaction of a biological system with an externally produced electric field is that of charge separation and interfacial charging. This aspect has been ignored in some recent experimental and theoretical work. In the case of small regions of lower electrical resistivity imbedded in a higher resistivity medium, charge separation across the lower resistivity regions will result in charging of the interfaces between the lower and higher resistivity regions. The field produced by this charge separation will significantly affect the shape and the magnitude of the net electric field pulse within the lower resistivity regions. In particular, the field experienced by bone cells will be quite different from the externally produced field. The shape as well as the magnitude of the net electric field experienced by the cells depends on the time rate of change of the rising and falling phases of the externally produced electric field pulse.     

Parameter estimation for ligand binding systems kinetics applied to 1,25-dihydroxycholecalciferol

A mathematical analysis of the kinetics of the hormone-receptor interaction was applied to the 1,25-dihydroxycholecalciferol-intestinal receptor system. The exact analytical solution and the numerical integration of the kinetic equation were installed in a Statistical Analysis System (SAS) computer program to estimate the rate constants of the reaction. Estimates of the parameters obtained by these two methods are similar, demonstrating that the numerical integration can be combined with the nonlinear regression procedure for least-squares parameter fitting using a simple SAS program. This enables estimation of kinetics rate constants when the kinetic equation cannot be solved analytically. The ratio of the rate constants (ka/kd) found by the nonlinear procedure is close to the independently determined equilibrium (Scatchard) constant in the nonlinear analysis.