A line-balancing strategy for designing flexible assembly systems

We present a rough-cut analysis tool that quickly determines a few potential cost-effective designs at the initial design stage of flexible assembly systems (FASs) prior to a detailed analysis such as simulation. It uses quantitative methods for selecting and configuring the components of an FAS suitable for medium to high volumes of several similar products. The system is organized as a series of assembly stations linked with an automated material-handling system moving parts in a unidirectional flow. Each station consists of a single machine or of identical parallel machines. The methods exploit the ability of flexible hardware to switch almost instantaneously from product to product. Our approach is particularly suitable where the product mix is expected to be stable, since we combine the hardware-configuration phase with the task-allocation phase. For the required volume of products, we use integer programming to select the number of stations and the number of machines at each station and to allocate tasks to stations. We use queueing network analysis, which takes into account the mean and variance of processing times among different products to determine the necessary capacity of the material-handling system. We iterate between the two analyses to find the combined solution with the lowest costs. Work-in-process costs are also included in the analysis. Computational results are presented.     

Performance Analysis of Flexible Manufacturing Systems with a Single Discrete Material-Handling Device

We present an analytical model for performance prediction of flexible manufacturing systems (FMSs) with a single discrete material-handling device (MHD). This configuration of FMS is significant for many reasons: it is commonly found in industry, it simplifies material-handling control, it is amenable to analytical modeling, and it forms a building block for more complex systems. Standard queueing models are inadequate to analyze this configuration because of the need to take into consideration many nontrivial issues such as state-dependent routing, interference from the MHD, and the analysis of the MHD. To account for state-dependent routing, we develop an iterative method that is built around mean value analysis. To analyze the MHD interference, we use two queueing network models. In the first, we ignore queueing at the MHD but model the interference from the MHD by inflating the station service times. The second network models the queueing for the MHD and estimates the blocking (inflation) times needed for the first model. By iterating between the two networks, we are able to predict the performance of this configuration of FMS. Our analytical estimates are validated against discrete event simulation and shown to be quite accurate for initial system design.     

eulerAPE: Drawing Area-Proportional 3-Venn Diagrams Using Ellipses

Venn diagrams with three curves are used extensively in various medical and scientific disciplines to visualize relationships between data sets and facilitate data analysis. The area of the regions formed by the overlapping curves is often directly proportional to the cardinality of the depicted set relation or any other related quantitative data. Drawing these diagrams manually is difficult and current automatic drawing methods do not always produce appropriate diagrams. Most methods depict the data sets as circles, as they perceptually pop out as complete distinct objects due to their smoothness and regularity. However, circles cannot draw accurate diagrams for most 3-set data and so the generated diagrams often have misleading region areas. Other methods use polygons to draw accurate diagrams. However, polygons are non-smooth and non-symmetric, so the curves are not easily distinguishable and the diagrams are difficult to comprehend. Ellipses are more flexible than circles and are similarly smooth, but none of the current automatic drawing methods use ellipses. We present eulerAPE as the first method and software that uses ellipses for automatically drawing accurate area-proportional Venn diagrams for 3-set data. We describe the drawing method adopted by eulerAPE and we discuss our evaluation of the effectiveness of eulerAPE and ellipses for drawing random 3-set data. We compare eulerAPE and various other methods that are currently available and we discuss differences between their generated diagrams in terms of accuracy and ease of understanding for real world data.     

The interaction networks of structured RNAs

All pairwise interactions occurring between bases which could be detected in three-dimensional structures of crystallized RNA molecules are annotated on new planar diagrams. The diagrams attempt to map the underlying complex networks of base–base interactions and, especially, they aim at conveying key relationships between helical domains: co-axial stacking, bending and all Watson–Crick as well as non-Watson–Crick base pairs. Although such wiring diagrams cannot replace full stereographic images for correct spatial understanding and representation, they reveal structural similarities as well as the conserved patterns and distances between motifs which are present within the interaction networks of folded RNAs of similar or unrelated functions. Finally, the diagrams could help devising methods for meaningfully transforming RNA structures into graphs amenable to network analysis.     

An efficient heuristic for scheduling batches of parts in a flexible flow system

Flexible manufacturing systems (FMSs) are a class of automated systems that can be used to improve productivity in batch manufacturing. Four stages of decision making have been defined for an FMS—the design, planning, scheduling, and control stages. This research focuses on the planning stage, and specifically in the area of scheduling batches of parts through the system. The literature to date on the FMS planning stage has mostly focused on the machine grouping, tool loading, and parttype selection problems. Our research carries the literature a step further by addressing the problem of scheduling batches of parts. Due to the use of serial-access material-handling systems in many FMSs, the batch-scheduling problem is modeled for a flexible flow system (FFS). This model explicitly accounts for setup times between batches that are dependent on their processing sequence. A heuristic procedure is developed for this batch-scheduling problem—the Maximum Savings (MS) heuristic. The MS heuristic is based upon the savings in time associated with a particular sequence and selecting the one with the maximum savings. It uses a two-phase method, with the savings being calculated in phase I, while a branch-and-bound procedure is employed to seek the best heuristic solution in phase II. Extensive computational results are provided for a wide variety of problems. The results show that the MS heuristic provides good-quality solutions.     

Liquid-ordered phases induced by cholesterol: A compendium of binary phase diagrams

Mixtures of phospholipids with cholesterol are able to form liquid-ordered phases that are characterised by short-range orientational order and long-range translational disorder. These L_o-phases are distinct from the liquid-disordered, fluid L_α-phases and the solid-ordered, gel L_β-phases that are assumed by the phospholipids alone. The liquid-ordered phase can produce spatially separated in-plane fluid domains, which, in the form of lipid rafts, are thought to act as platforms for signalling and membrane sorting in cells. The areas of domain formation are defined by the regions of phase coexistence in the phase diagrams for the binary mixtures of lipid with cholesterol. In this paper, the available binary phase diagrams of lipid-cholesterol mixtures are all collected together. It is found that there is not complete agreement between different determinations of the phase diagrams for the same binary mixture. This can be attributed to the indirect methods largely used to establish the phase boundaries. Intercomparison of the various data sets allows critical assessment of which phase boundaries are rigorously established from direct evidence for phase coexistence.     

Determination of the quaternary phase diagram of the water-ethylene glycol-sucrose-NaCl system and a comparison between two theoretical methods for synthetic phase diagrams

Characterization of the thermodynamic properties of multi-solute aqueous solutions is of critical importance for biological and biochemical research. For example, the phase diagrams of aqueous systems, containing salts, saccharides, and plasma membrane permeating solutes, are indispensible in the field of cryobiology and pharmacology. However, only a few ternary phase diagrams are currently available for these systems. In this study, an auto-sampler differential scanning calorimeter (DSC) was used to determine the quaternary phase diagram of the water-ethylene glycol-sucrose-NaCl system. To improve the accuracy of melting point measurement, a “mass-redemption” method was also applied for the DSC technique. Base on the analyses of these experimental data, a comparison was made between the two practical approaches to generate phase diagrams of multi-solute solutions from those of single-solute solutions: the summation of cubic polynomial melting point equations versus the use of osmotic virial equations with cross coefficients. The calculated values of the model standard deviations suggested that both methods are satisfactory for characterizing this quaternary system.     

Species clustering and New Zealand quaternary climate

This paper uses the relative frequencies of occurrence of various types of pollen and spores to indicate the comparative temperatures under which Quaternary sediments accumulated in several locations in New Zealand. The application of association measures, and cluster and discriminant function analysis to such information is described and discussed.The analyses show that the types may be divided into groups whose members vary little with locality or with the statistical methods used to establish them. This stability suggests that anomalous dispersion effects are not a major influence. For some of these groups there is a similarity between the present-day climate of known pollen or spore sources and those of the corresponding groups at the time of deposition. The significant groups are used to summarise the results in pollen diagrams which are compared with similar diagrams for the discriminant function. It is also shown that the methods described assist in locating zone boundaries in a series of samples taken from a bore hole.The results obtained are relevant to the interpretation of samples in which southern beech (Nothofagus fusca type) is the most abundant tree pollen.     

G-quadruplex structure and stability illuminated by 2-aminopurine phasor plots

The use of time-resolved fluorescence measurements in studies of telomeric G-quadruplex folding and stability has been hampered by the complexity of fluorescence lifetime distributions in solution. The application of phasor diagrams to the analysis of time-resolved fluorescence measurements, collected from either frequency-domain or time-domain instrumentation, allows for rapid characterization of complex lifetime distributions. Phasor diagrams are model-free graphical representations of transformed time-resolved fluorescence results. Simplification of complex fluorescent decays by phasor diagrams is demonstrated here using a 2-aminopurine substituted telomeric G-quadruplex sequence. The application of phasor diagrams to complex systems is discussed with comparisons to traditional non-linear regression model fitting. Phasor diagrams allow for the folding and stability of the telomeric G-quadruplex to be monitored in the presence of either sodium or potassium. Fluorescence lifetime measurements revealed multiple transitions upon folding of the telomeric G-quadruplex through the addition of potassium. Enzymatic digestion of the telomeric G-quadruplex structure, fluorescence quenching and Förster resonance energy transfer were also monitored through phasor diagrams. This work demonstrates the sensitivity of time-resolved methods for monitoring changes to the telomeric G-quadruplex and outlines the phasor diagram approach for analysis of complex time-resolved results that can be extended to other G-quadruplex and nucleic acid systems.     

How to teach procedures,problem solving,and concepts in microbial genetics

Flow diagrams, algorithms, decision logic tables, and concept maps are presented as methods for teaching practical procedures, problem solving, and basic concepts in microbial genetics. For practical procedures the aim is to present the sequence of operations clearly, to diagnose and correct possible errors, and to encourage the student to design investigations efficiently. Procedures for problem solving are discussed which give a logical sequence of questions with yes/no answers leading to a finite number of possible solutions. The use of concept maps in the planning of courses and in illustrating the relationships between different aspects of microbial genetics is discussed. It is suggested that the flexible use of these methods should lead to an improved understanding of microbial genetics.     

Cause-effect modeling as a general method for describing and studying phenomena in complex hierarchical systems

A strict definition of a cause-effect model of a complex phenomenon is given, and the rules for presenting such models in the form of cause-effect diagrams are formulated. The relationship between the cause-effect modeling and conventional methods of mathematical modeling is analyzed. Examples of the cause-effect models (diagrams) of phenomena of various physical nature are presented, and the application of these models to some specific problems is shown. In particular, the mechanism of renormalizing the rate constants of chemical reactions is considered in terms of dissipative resonance. An example of renormalizing the parameters of climate sensitivity and the relaxation time of the Earth’s climatic system in terms of a two-component (CO₂ + H₂O) greenhouse effect is considered.     

GeneVenn - A web application for comparing gene lists using Venn diagrams

Numerous methods are available to compare results of multiple microarray studies. One of the simplest but most effective of these procedures is to examine the overlap of resulting gene lists in a Venn diagram. Venn diagrams are graphical ways of representing interactions among sets to display information that can be read easily. Here we propose a simple but effective web application creating Venn diagrams from two or three gene lists. Each gene in the group list has link to the related information in NCBI's Entrez Nucleotide database. AVAILABILITY: GeneVenn is available for free at http://mcbc.usm.edu/genevenn/     

Motor Oil Classification Based on Time-Resolved Fluorescence

A time-resolved fluorescence (TRF) technique is presented for classifying motor oils. The system is constructed with a third harmonic Nd:YAG laser, a spectrometer, and an intensified charge coupled device (ICCD) camera. Steady-state and time-resolved fluorescence (TRF) measurements are reported for several motor oils. It is found that steady-state fluorescence is insufficient to distinguish the motor oil samples. Then contour diagrams of TRF intensities (CDTRFIs) are acquired to serve as unique fingerprints to identify motor oils by using the distinct TRF of motor oils. CDTRFIs are preferable to steady-state fluorescence spectra for classifying different motor oils, making CDTRFIs a particularly choice for the development of fluorescence-based methods for the discrimination and characterization of motor oils. The two-dimensional fluorescence contour diagrams contain more information, not only the changing shapes of the LIF spectra but also the relative intensity. The results indicate that motor oils can be differentiated based on the new proposed method, which provides reliable methods for analyzing and classifying motor oils.     

R-CHIE: a web server and R package for visualizing RNA secondary structures

Visually examining RNA structures can greatly aid in understanding their potential functional roles and in evaluating the performance of structure prediction algorithms. As many functional roles of RNA structures can already be studied given the secondary structure of the RNA, various methods have been devised for visualizing RNA secondary structures. Most of these methods depict a given RNA secondary structure as a planar graph consisting of base-paired stems interconnected by roundish loops. In this article, we present an alternative method of depicting RNA secondary structure as arc diagrams. This is well suited for structures that are difficult or impossible to represent as planar stem-loop diagrams. Arc diagrams can intuitively display pseudo-knotted structures, as well as transient and alternative structural features. In addition, they facilitate the comparison of known and predicted RNA secondary structures. An added benefit is that structure information can be displayed in conjunction with a corresponding multiple sequence alignments, thereby highlighting structure and primary sequence conservation and variation. We have implemented the visualization algorithm as a web server R-chie as well as a corresponding R package called R4RNA, which allows users to run the software locally and across a range of common operating systems.     

Exploring pathways and barriers for coupled ET/PT in cytochrome c oxidase: a general framework for examining energetics and mechanistic alternatives

Gaining a detailed understanding of the energetics of the proton pumping process in cytochrome c oxidase (CcO) is one of the challenges of modern biophysics. Although there are several current mechanistic proposals, most of these ideas have not been subjected to consistent structure-function considerations. In particular most works have not related the activation barriers for different mechanistic proposals to the protein structure. The present work describes a general approach for exploring the energetics of different feasible models of the action of CcO, using the observed protein structure, established simulation methods and a modified Marcus' formulation. We start by reviewing our methods for evaluation of the energy diagrams for different proton translocation paths and then present a systematic analysis of various constraints that should be imposed on any energy diagram for the pumping process. After the general analysis we turn to the actual computational study, where we construct energy diagrams for forward and backward paths, using the estimated calculated reduction potentials and pK(a) values of all the relevant sites (including internal water molecules). We then explore the relationship between the calculated energy diagrams and key experimental constraints. This comparison allows us to identify some barriers that are not fully consistent with the overall requirement for an efficient pumping. In particular we identify back leakage channels, which are hard to block without stopping the forward channels. This helps to identify open problems that will require further experimental and theoretical studies. We also consider reasonable adjustments of the calculated barriers that may lead to a working pump. Although the present analysis does not establish a unique and workable model for the mechanism of CcO, it presents what is probably the most consistent current analysis of the barriers for different feasible pathways. Perhaps more importantly, the framework developed here should provide a general way for examining any proposal for the action of CcO as well as for the analysis of further experimental findings about the action of this fascinating system.     

Exploring pathways and barriers for coupled ET/PT in cytochrome c oxidase: A general framework for examining energetics and mechanistic alternatives

Gaining a detailed understanding of the energetics of the proton pumping process in cytochrome c oxidase (CcO) is one of the challenges of modern biophysics. Although there are several current mechanistic proposals, most of these ideas have not been subjected to consistent structure-function considerations. In particular most works have not related the activation barriers for different mechanistic proposals to the protein structure. The present work describes a general approach for exploring the energetics of different feasible models of the action of CcO, using the observed protein structure, established simulation methods and a modified Marcus' formulation. We start by reviewing our methods for evaluation of the energy diagrams for different proton translocation paths and then present a systematic analysis of various constraints that should be imposed on any energy diagram for the pumping process. After the general analysis we turn to the actual computational study, where we construct energy diagrams for forward and backward paths, using the estimated calculated reduction potentials and pK_a values of all the relevant sites (including internal water molecules). We then explore the relationship between the calculated energy diagrams and key experimental constraints. This comparison allows us to identify some barriers that are not fully consistent with the overall requirement for an efficient pumping. In particular we identify back leakage channels, which are hard to block without stopping the forward channels. This helps to identify open problems that will require further experimental and theoretical studies. We also consider reasonable adjustments of the calculated barriers that may lead to a working pump. Although the present analysis does not establish a unique and workable model for the mechanism of CcO, it presents what is probably the most consistent current analysis of the barriers for different feasible pathways. Perhaps more importantly, the framework developed here should provide a general way for examining any proposal for the action of CcO as well as for the analysis of further experimental findings about the action of this fascinating system.     

A technique for the continuous recording of tick feeding electrograms and temperature by telemetry from free-ranging cattle

A biotelemetric technique is described for the continuous and simultaneous transmission of an analog signal of the feeding electrogram and of the temperature of a Hyalomma dromedarii female tick on a heifer roaming freely within a confined space beside an observation and control room. The tick was completely exposed to natural micrometeorological conditions. Circuit diagrams of a 102 MHz tick feeding electrogram transmitter and a 90 MHz tick temperature transmitter are included together with new methods used to hold and protect the instruments on the heifer.     

Science in the age of mechanical reproduction: moral and epistemic relations between diagrams and photographs

Sociologists, philosophers and historians of science are gradually recognizing the importance of visual representation. This is part of a more general movement away from a theory-centric view of science and towards an interest in practical aspects of observation and experimentation. Rather than treating science as a matter of demonstrating the logical connection between theoretical and empirical statements, an increasing number of investigations are examining how scientists compose and use diagrams, graphs, photographs, micrographs, maps, charts, and related visual displays. This paper focuses on diagrams in biology, and tries to demonstrate how diagrams are an integral part of the production of scientific knowledge. In order to disclose some of the distinctive practical and analytical uses of diagrams, the paper contrasts the way diagrams and photographs are used in biological texts. Both diagrams and photographs are shown to be “constructions” that separately and together mediate the investigation of scientific phenoman.