Image processing based on a model of the mammalian retina

A first study in order to construct a simple model of the mammalian retina is reported. The basic elements for this model are Optical Programmable Logic Cells, OPLCs, previously employed as a functional element for Optical Computing. The same type of circuit simulates the five types of neurons present in the retina. Different responses are obtained by modifying either internal or external connections. Two types of behaviors are reported: symmetrical and non-symmetrical with respect to light position. Some other higher functions, as the possibility to differentiate between symmetric and non-symmetric light images, are performed by another simulation of the first layers of the visual cortex. The possibility to apply these models to image processing is reported.

Using Electronic Documents for Knowledge Acquisition and Model Maintenance

Knowledge acquisition and model maintenance are key problems in knowledge engineering to improve the productivity in the development of intelligent systems. Although historically a number of technical solutions have been proposed in this area, the recent experience shows that there is still an important gap between the way end-users describe their expertise and the way intelligent systems represent knowledge. In this paper we propose an original way to cope with this problem based on electronic documents. We propose the concept of intelligent document processor as a tool that allows the end-user to read/write a document explaining how an intelligent system operates in such a way that, if the user changes the content of the document, the intelligent system will react to these changes. The paper presents the structure of such a document based on knowledge categories derived from the modern knowledge modeling methodologies together with a number of requirements to be understandable by end-users and problem solvers.

Simulating potential growth and yield of oil palm (Elaeis guineensis) with PALMSIM: Model description, evaluation and application.

Reducing the gap between water-limited potential yield and actual yield in oil palm production systems through intensification is seen as an important option for sustainably increasing palm oil production. Simulation models can play an important role in quantifying water-limited potential yield, and therefore the scope for intensification, but no oil palm model exists that is both simple enough and at the same time incorporates sufficient plant physiological knowledge to be generally applicable across sites with different growing conditions. The objectives of this study therefore were to develop a model (PALMSIM) that simulates, on a monthly time step, the potential growth of oil palm as determined by solar radiation and to evaluate model performance against measured oil palm yields under optimal water and nutrient management for a range of sites across Indonesia and Malaysia. The maximum observed yield in the field matches the corresponding simulated yield for dry bunch weight with a RMSE of 1.7 Mg ha?1 year?1 against an observed yield of 18.8 Mg ha?1. Sensitivity analysis showed that PALMSIM is robust: simulated changes in yield caused by modifying the parameters by 10% are comparable to other tree crop model evaluations. While we acknowledge that, depending on the soils and climatic environment, yields may be often water limited, we suggest a relatively simple physiological approach to simulate potential yield, which can be usefully applied to high rainfall environments and is considered as a first step in developing an oil palm model that also simulates water-limited potential yield. To illustrate the application possibil- ities of the model, PALMSIM was used to create a potential yield map for Indonesia and Malaysia by sim- ulating the growth and yield at a resolution of 0.1?. This map of potential yield is considered as a first step towards a decision support tool that can identify potentially productive, but at the moment degraded sites in Indonesia and Malaysia. ?

Service Capacity Reserve under Uncertainty by Hospital’s ER Analogies: A Practical Model for Car Services

We define a capacity reserve model to dimension passenger car service installations according to the demographic distribution of the area to be serviced by using hospital?s emergency room analogies. Usually, service facilities are designed applying empirical methods, but customers arrive under uncertain conditions not included in the original estimations, and there is a gap between customer?s real demand and the service?s capacity. Our research establishes a valid methodology and covers the absence of recent researches and the lack of statistical techniques implementation, integrating demand uncertainty in a unique model built in stages by implementing ARIMA forecasting, queuing theory, and Monte Carlo simulation to optimize the service capacity and occupancy, minimizing the implicit cost of the capacity that must be reserved to service unexpected customers. Our model has proved to be a useful tool for optimal decision making under uncertainty integrating the prediction of the cost implicit in the reserve capacity to serve unexpected demand and defining a set of new process indicators, such us capacity, occupancy, and cost of capacity reserve never studied before. The new indicators are intended to optimize the service operation. This set of new indicators could be implemented in the information systems used in the passenger car services.

Service capacity reserve under uncertainty by hospital's ER's analogies: a practical model for car services

El objetivo de esta investigación consiste en definir un modelo de reserva de capacidad, por analogías con emergencias hospitalarias, que pueda ser implementado en el sector de servicios. Este está específicamente enfocado a su aplicación en talleres de servicio de automóviles. Nuestra investigación incorpora la incertidumbre de la demanda en un modelo singular diseñado en etapas que agrupa técnicas ARIMA, teoría de colas y simulación Monte Carlo para definir los conceptos de capacidad y ocupación de servicio, que serán utilizados para minimizar el coste implícito de la reserva capacidad necesaria para atender a clientes que carecen de cita previa. Habitualmente, las compañías automovilísticas estiman la capacidad de sus instalaciones de servicio empíricamente, pero los clientes pueden llegar bajo condiciones de incertidumbre que no se tienen en cuenta en dichas estimaciones, por lo que existe una diferencia entre lo que el cliente realmente demanda y la capacidad que ofrece el servicio. Nuestro enfoque define una metodología válida para el sector automovilístico que cubre la ausencia genérica de investigaciones recientes y la habitual falta de aplicación de técnicas estadísticas en el sector. La equivalencia con la gestión de urgencias hospitalarias se ha validado a lo largo de la investigación en la se definen nuevos indicadores de proceso (KPIs) Tal y como hacen los hospitales, aplicamos modelos estocásticos para dimensionar las instalaciones de servicio de acuerdo con la distribución demográfica del área de influencia. El modelo final propuesto integra la predicción del coste implícito en la reserva de capacidad para atender la demanda no prevista. Asimismo, se ha desarrollado un código en Matlab que puede integrarse como un módulo adicional a los sistemas de información (DMS) que se usan actualmente en el sector, con el fin de emplear los nuevos indicadores de proceso definidos en el modelo. Los resultados principales del modelo son nuevos indicadores de servicio, tales como la capacidad, ocupación y coste de reserva de capacidad, que nunca antes han sido objeto de estudio en la industria automovilística, y que están orientados a gestionar la operativa del servicio. ABSTRACT Our aim is to define a Capacity Reserve model to be implemented in the service sector by hospital's emergency room (ER) analogies, with a practical approach to passenger car services. A stochastic model has been implemented using R and a Monte Carlo simulation code written in Matlab and has proved a very useful tool for optimal decision making under uncertainty. The research integrates demand uncertainty in a unique model which is built in stages by implementing ARIMA forecasting, Queuing Theory and a Monte Carlo simulation to define the concepts of service capacity and occupancy, minimizing the implicit cost of the capacity that must be reserved to service unexpected customers. Usually, passenger car companies estimate their service facilities capacity using empirical methods, but customers arrive under uncertain conditions not included in the estimations. Thus, there is a gap between customer’s real demand and the dealer’s capacity. This research sets a valid methodology for the passenger car industry to cover the generic absence of recent researches and the generic lack of statistical techniques implementation. The hospital’s emergency room (ER) equalization has been confirmed to be valid for the passenger car industry and new process indicators have been defined to support the study. As hospitals do, we aim to apply stochastic models to dimension installations according to the demographic distribution of the area to be serviced. The proposed model integrates the prediction of the cost implicit in the reserve capacity to serve unexpected demand. The Matlab code could be implemented as part of the existing information technology systems (ITs) to support the existing service management tools, creating a set of new process indicators. Main model outputs are new indicators, such us Capacity, Occupancy and Cost of Capacity Reserve, never studied in the passenger car service industry before, and intended to manage the service operation.

Monitoring the GAP catalyzed H-Ras GTPase reaction at atomic resolution in real time

The molecular reaction mechanism of the GTPase-activating protein (GAP)-catalyzed GTP hydrolysis by Ras was investigated by time resolved Fourier transform infrared (FTIR) difference spectroscopy using caged GTP (P3-1-(2-nitro)phenylethyl guanosine 5′-O-triphosphate) as photolabile trigger. This approach provides the complete GTPase reaction pathway with time resolution of milliseconds at the atomic level. Up to now, one structural model of the GAP⋅Ras⋅GDP⋅AlFx transition state analog is known, which represents a “snap shot” along the reaction-pathway. As now revealed, binding of GAP to Ras⋅GTP shifts negative charge from the γ to β phosphate. Such a shift was already identified by FTIR in GTP because of Ras binding and is now shown to be enhanced by GAP binding. Because the charge distribution of the GAP⋅Ras⋅GTP complex thus resembles a more dissociative-like transition state and is more like that in GDP, the activation free energy is reduced. An intermediate is observed on the reaction pathway that appears when the bond between β and γ phosphate is cleaved. In the intermediate, the released Pi is strongly bound to the protein and surprisingly shows bands typical of those seen for phosphorylated enzyme intermediates. All these results provide a mechanistic picture that is different from the intrinsic GTPase reaction of Ras. FTIR analysis reveals the release of Pi from the protein complex as the rate-limiting step for the GAP-catalyzed reaction. The approach presented allows the study not only of single proteins but of protein–protein interactions without intrinsic chromophores, in the non-crystalline state, in real time at the atomic level.

Ras-catalyzed hydrolysis of GTP: a new perspective from model studies.

Despite the biological and medical importance of signal transduction via Ras proteins and despite considerable kinetic and structural studies of wild-type and mutant Ras proteins, the mechanism of Ras-catalyzed GTP hydrolysis remains controversial. We take a different approach to this problem: the uncatalyzed hydrolysis of GTP is analyzed, and the understanding derived is applied to the Ras-catalyzed reaction. Evaluation of previous mechanistic proposals from this chemical perspective suggests that proton abstraction from the attacking water by a general base and stabilization of charge development on the gamma-phosphoryl oxygen atoms would not be catalytic. Rather, this analysis focuses attention on the GDP leaving group, including the beta-gamma bridge oxygen of GTP, the atom that undergoes the largest change in charge in going from the ground state to the transition state. This leads to a new catalytic proposal in which a hydrogen bond from the backbone amide of Gly-13 to this bridge oxygen is strengthened in the transition state relative to the ground state, within an active site that provides a template complementary to the transition state. Strengthened transition state interactions of the active site lysine, Lys-16, with the beta-nonbridging phosphoryl oxygens and a network of interactions that positions the nucleophilic water molecule and gamma-phosphoryl group with respect to one another may also contribute to catalysis. It is speculated that a significant fraction of the GAP-activated GTPase activity of Ras arises from an additional interaction of the beta-gamma bridge oxygen with an Arg side chain that is provided in trans by GAP. The conclusions for Ras and related G proteins are expected to apply more widely to other enzymes that catalyze phosphoryl (-PO(3)2-) transfer, including kinases and phosphatases.

Recombinational repair of gaps in DNA is asymmetric in Ustilago maydis and can be explained by a migrating D-loop model.

Recombinational repair of double-stranded DNA gaps was investigated in Ustilago maydis. The experimental system was designed for analysis of repair of an autonomously replicating plasmid containing a cloned gene disabled by an internal deletion. It was discovered that crossing over rarely accompanied gap repair. The strong bias against crossing over was observed in three different genes regardless of gap size. These results indicate that gap repair in U. maydis is unlikely to proceed by the mechanism envisioned in the double-stranded break repair model of recombination, which was developed to account for recombination in Saccharomyces cerevisiae. Experiments aimed at exploring processing of DNA ends were performed to gain understanding of the mechanism responsible for the observed bias. A heterologous insert placed within a gap in the coding sequence of two different marker genes strongly inhibited repair if the DNA was cleaved at the promoter-proximal junction joining the insert and coding sequence but had little effect on repair if the DNA was cleaved at the promoter-distal junction. Gene conversion of plasmid restriction fragment length polymorphism markers engineered in sequences flanking both sides of a gap accompanied repair but was directionally biased. These results are interpreted to mean that the DNA ends flanking a gap are subject to different types of processing. A model featuring a single migrating D-loop is proposed to explain the bias in gap repair outcome based on the observed asymmetry in processing the DNA ends.

Active control of waves in a cochlear model with subpartitions.

Multiscale asymptotic methods developed previously to study macromechanical wave propagation in cochlear models are generalized here to include active control of a cochlear partition having three subpartitions, the basilar membrane, the reticular lamina, and the tectorial membrane. Activation of outer hair cells by stereocilia displacement and/or by lateral wall stretching result in a frequency-dependent force acting between the reticular lamina and basilar membrane. Wavelength-dependent fluid loads are estimated by using the unsteady Stokes' equations, except in the narrow gap between the tectorial membrane and reticular lamina, where lubrication theory is appropriate. The local wavenumber and subpartition amplitude ratios are determined from the zeroth order equations of motion. A solvability relation for the first order equations of motion determines the subpartition amplitudes. The main findings are as follows: The reticular lamina and tectorial membrane move in unison with essentially no squeezing of the gap; an active force level consistent with measurements on isolated outer hair cells can provide a 35-dB amplification and sharpening of subpartition waveforms by delaying dissipation and allowing a greater structural resonance to occur before the wave is cut off; however, previously postulated activity mechanisms for single partition models cannot achieve sharp enough tuning in subpartitioned models.

Differential replication of a single, UV-induced lesion in the leading or lagging strand by a human cell extract: fork uncoupling or gap formation.

We have constructed simian virus 40 minireplicons containing uniquely placed cis,syn-thymine dimers (T <> T) for the analysis of leading- and lagging-strand bypass replication. Assaying for replication in a human cell-free extract through the analysis of full-size labeled product molecules and restriction fragments spanning the T <> T site resulted in the following findings: (i) The primary site of synthesis blockage with T <> T in either the leading or lagging strand was one nucleotide before the lesion. (ii) Replicative bypass of T <> T was detected in both leading and lagging strands. The efficiency of synthesis past T <> T was 22% for leading-strand T <> T and 13% for lagging-strand T <> T. (iii) The lagging-strand T <> T resulted in blocked retrograde synthesis with the replication fork proceeding past the lesion, resulting in daughter molecules containing small gaps (form II' DNA). (iv) With T <> T in the leading-strand template, both the leading and lagging strands were blocked, representing a stalled replication fork. Uncoupling of the concerted synthesis of the two strands of the replication fork was observed, resulting in preferential elongation of the undamaged lagging strand. These data support a model of selective reinitiation downstream from the lesion on lagging strands due to Okazaki synthesis, with no reinitiation close to the damage site on leading strands [Meneghini, R. & Hanawalt, P.C. (1976) Biochim. Biophys. Acta 425, 428-437].

Simple model of protein folding kinetics.

A simple model of the kinetics of protein folding is presented. The reaction coordinate is the "correctness" of a configuration compared with the native state. The model has a gap in the energy spectrum, a large configurational entropy, a free energy barrier between folded and partially folded states, and a good thermodynamic folding transition. Folding kinetics is described by a master equation. The folding time is estimated by means of a local thermodynamic equilibrium assumption and then is calculated both numerically and analytically by solving the master equation. The folding time has a maximum near the folding transition temperature and can have a minimum at a lower temperature.

Mixing of connexins in gap junction membrane channels.

Gap junctions are plaque-like clusters of intercellular channels that mediate intercellular communication. Each of two adjoining cells contains a connexon unit which makes up half of the whole channel. Gap junction channels are formed from a multigene family of proteins called connexins, and different connexins may be coexpressed by a single cell type and found within the same plaque. Rodent gap junctions contain two proteins, connexins 32 and 26. Use of a scanning transmission electron microscope for mass analysis of rodent gap junction plaques and split gap junctions prvided evidence consistent with a model in which the channels may be made from (i) solely connexin 26, (ii) solely connexin 32, or (iii) mixtures of connexin 26 and connexin 32 in which the two connexons are made entirely of connexin 26 and connexin 32. The different types of channels segregate into distinct domains, implying tha connexon channels self-associate to give a non-random distribution within tissues. Since each connexin confers distinct physiological properties on its membrane channels, these results imply that the physiological properties of channels can be tailored by mixing the constituent proteins within these macromolecular structures.

Two helices plus a linker: a small model substrate for eukaryotic RNase P.

Using precursor tRNA molecules to study RNA-protein interactions, we have identified an RNA motif recognized by eukaryotic RNase P (EC 3.1.26.5). Analysis of circularly permuted precursors indicates that interruptions in the sugar-phosphate backbone are not tolerated in the acceptor stem, in the T stem-loop, or between residues A-9 and G-10. Prokaryotic RNase P will function with a minihelix consisting of the acceptor stem connected directly to the T stem-loop. Eukaryotic RNase P cannot use such a minimal substrate unless a linker sequence is added in the gap where the D stem and anticodon stem-loop were deleted.

Can model Hamiltonians describe the electron–electron interaction in π-conjugated systems?: PAH and graphene

Model Hamiltonians have been, and still are, a valuable tool for investigating the electronic structure of systems for which mean field theories work poorly. This review will concentrate on the application of Pariser–Parr–Pople (PPP) and Hubbard Hamiltonians to investigate some relevant properties of polycyclic aromatic hydrocarbons (PAH) and graphene. When presenting these two Hamiltonians we will resort to second quantisation which, although not the way chosen in its original proposal of the former, is much clearer. We will not attempt to be comprehensive, but rather our objective will be to try to provide the reader with information on what kinds of problems they will encounter and what tools they will need to solve them. One of the key issues concerning model Hamiltonians that will be treated in detail is the choice of model parameters. Although model Hamiltonians reduce the complexity of the original Hamiltonian, they cannot be solved in most cases exactly. So, we shall first consider the Hartree–Fock approximation, still the only tool for handling large systems, besides density functional theory (DFT) approaches. We proceed by discussing to what extent one may exactly solve model Hamiltonians and the Lanczos approach. We shall describe the configuration interaction (CI) method, a common technology in quantum chemistry but one rarely used to solve model Hamiltonians. In particular, we propose a variant of the Lanczos method, inspired by CI, that has the novelty of using as the seed of the Lanczos process a mean field (Hartree–Fock) determinant (the method will be named LCI). Two questions of interest related to model Hamiltonians will be discussed: (i) when including long-range interactions, how crucial is including in the Hamiltonian the electronic charge that compensates ion charges? (ii) Is it possible to reduce a Hamiltonian incorporating Coulomb interactions (PPP) to an 'effective' Hamiltonian including only on-site interactions (Hubbard)? The performance of CI will be checked on small molecules. The electronic structure of azulene and fused azulene will be used to illustrate several aspects of the method. As regards graphene, several questions will be considered: (i) paramagnetic versus antiferromagnetic solutions, (ii) forbidden gap versus dot size, (iii) graphene nano-ribbons, and (iv) optical properties.

Imperial legacy? The EU's Developmental Model and the Crisis of the European Periphery. CES Papers - Open Forum #19, 2013-2014

The high hopes for rapid convergence of Eastern and Southern EU member states are increasingly being disappointed. With the onset of the Eurocrisis convergence has given way to divergence in the southern members, and many Eastern members have made little headway in closing the development gap. The EU´s performance compares unfavourably with East Asian success cases as well as with Western Europe´s own rapid catch-up to the USA after 1945. Historical experience indicates that successful catch up requires that less-developed economies to some extent are allowed to free-ride on an open international economic order. However, the EU´s model is based on the principle of a level-playing field, which militates against such a form of economic integration. The EU´s developmental model thus contrasts with the various strategies that have enabled successful catch up of industrial latecomers. Instead the EU´s current approach is more and more reminiscent of the relations between the pre-1945 European empires and their dependent territories. One reason for this unfortunate historical continuity is that the EU appears to have become entangled in its own myths. In the EU´s own interpretation, European integration is a peace project designed to overcome the almost continuous warfare that characterised the Westphalian system. As the sovereign state is identified as the root cause of all evil, any project to curtail its room of manoeuvre must ultimately benefit the common good. Yet, the existence of a Westphalian system of nation states is a myth. Empires and not states were the dominant actors in the international system for at least the last three centuries. If anything, the dawn of the age of the sovereign state in Western Europe occurred after 1945 with the disintegration of the colonial empires and thus historically coincided with the birth of European integration.