Polypeptide models of collagen. II. Solution properties of (Pro-Gly-Phe)n

The conformation of (Pro-Gly-Phe)n in trifluoroethanol was investigated using CD, nmr and ir techniques. After making appropriate correction for the contribution of the phenylalanine chromophore to the observed CD spectra of the polytripeptide at several temperatures, it is found that (Pro-Gly-Phe)n can exist in a partially triple-helical conformation in this solvent a t low temperatures. The nmr and ir data support this conclusion. In conjunction with recent theoretical sutdies, our data offer an explanation for the preferential occurrence of the Phe residue in position 2 of the tripeptide sequence Gly-R2-R3, in collagen.

Non-industrial private forest landowners’ choices of timber management strategies and potential allowable cut.

In the study, the potential allowable cut in the district of Pohjois-Savo - based on the non-industrial private forest landowners' (NIPF) choices of timber management strategies - was clarified. Alternative timber management strategies were generated, and the choices and factors affecting the choices of timber management strategies by NIPF landowners were studied. The choices of timber management strategies were solved by maximizing the utility functions of the NIPF landowners. The parameters of the utility functions were estimated using the Analytic Hierarchy Process (AHP). The level of the potential allowable cut was compared to the cutting budgets based on the 7th and 8th National Forest Inventories (NFI7 and NFI8), to the combining of private forestry plans, and to the realized drain from non-industrial private forests. The potential allowable cut was calculated using the same MELA system as has been used in the calculation of the national cutting budget. The data consisted of the NIPF holdings (from the TASO planning system) that had been inventoried compartmentwise and had forestry plans made during the years 1984-1992. The NIPF landowners' choices of timber management strategies were clarified by a two-phase mail inquiry. The most preferred strategy obtained was "sustainability" (chosen by 62 % of landowners). The second in order of preference was "finance" (17 %) and the third was "saving" (11 %). "No cuttings", and "maximum cuttings" were the least preferred (9 % and 1 %, resp.). The factors promoting the choices of strategies with intensive cuttings were a) "farmer as forest owner" and "owning fields", b) "increase in the size of the forest holding", c) agriculture and forestry orientation in production, d) "decreasing short term stumpage earning expectations", e) "increasing intensity of future cuttings", and f) "choice of forest taxation system based on site productivity". The potential allowable cut defined in the study was 20 % higher than the average of the realized drain during the years 1988-1993, which in turn, was at the same level as the cutting budget based on the combining of forestry plans in eastern Finland. Respectively, the potential allowable cut defined in the study was 12 % lower than the NFI8-based greatest sustained allowable cut for the 1990s. Using the method presented in this study, timber management strategies can be clarified for non-industrial private forest landowners in different parts of Finland. Based on the choices of timber managemet strategies, regular cutting budgets can be calculated more realistically than before.

Putative neuroprotective compounds in in vitro models of dopaminergic neurodegeneration

Parkinson´s disease (PD) is a debilitating age-related neurological disorder that affects various motor skills and can lead to a loss of cognitive functions. The motor symptoms are the result of the progressive degeneration of dopaminergic neurons within the substantia nigra. The factors that influence the pathogenesis and the progression of the neurodegeneration remain mostly unclear. This study investigated the role of various programmed cell death (PCD) pathways, oxidative stress, and glial cells both in dopaminergic neurodegeneration and in the protective action of various drugs. To this end, we exposed dopaminergic neuroblastoma cells (SH-SY5Y cells) to 6-OHDA, which produces oxidative stress and activates various PCD modalities that result in neuronal degeneration. Additionally, to explore the role of glia, we prepared rat midbrain primary mixed-cell cultures containing both neurons and glial cell types such as microglia and astroglia and then exposed the cultures to either MPP plus or lipopolysaccharide. Our results revealed that 6-OHDA activated several PCD pathways including apoptosis, autophagic stress, lysosomal membrane permeabilization, and perhaps paraptosis in SH-SY5Y cells. Furthermore, we found that minocycline protected SH-SY5Y cells from 6-OHDA by inhibiting both apoptotic and non-apoptotic PCD modalities. We also observed an inconsistent neuroprotective effect of various dietary anti-oxidant compounds against 6-OHDA toxicity in vitro in SH-SY5Y cells. Specifically, quercetin and curcumin exerted neuroprotection only within a narrow concentration range and a limited time frame, whereas resveratrol and epigallocatechin 3-gallate provided no protection whatsoever. Lastly, we found that molecules such as amantadine may delay or even halt the neurodegeneration in primary cell cultures by inhibiting the release of neurotoxic factors from overactivated microglia and by enhancing the pro-survival actions of astroglia. Together these data suggest that the strategy of dampening oxidative species with anti-oxidants is less effective than preventing the production of toxic factors such as oxidative and pro-inflammatory molecules by pathologically activated microglia. This would subsequently prevent the activation of various PCD modalities that cause neuronal degeneration.

Instability, intermittency, and multiscaling in discrete growth models of kinetic roughening

We show by numerical simulations that discretized versions of commonly studied continuum nonlinear growth equations (such as the Kardar-Parisi-Zhangequation and the Lai-Das Sarma-Villain equation) and related atomistic models of epitaxial growth have a generic instability in which isolated pillars (or grooves) on an otherwise flat interface grow in time when their height (or depth) exceeds a critical value. Depending on the details of the model, the instability found in the discretized version may or may not be present in the truly continuum growth equation, indicating that the behavior of discretized nonlinear growth equations may be very different from that of their continuum counterparts. This instability can be controlled either by the introduction of higher-order nonlinear terms with appropriate coefficients or by restricting the growth of pillars (or grooves) by other means. A number of such ''controlled instability'' models are studied by simulation. For appropriate choice of the parameters used for controlling the instability, these models exhibit intermittent behavior, characterized by multiexponent scaling of height fluctuations, over the time interval during which the instability is active. The behavior found in this regime is very similar to the ''turbulent'' behavior observed in recent simulations of several one- and two-dimensional atomistic models of epitaxial growth.

Assessment of conditional moment closure models of turbulent autoignition using DNS data

A systematic assessment of the submodels of conditional moment closure (CMC) formalism for the autoignition problem is carried out using direct numerical simulation (DNS) data. An initially non-premixed, n-heptane/air system, subjected to a three-dimensional, homogeneous, isotropic, and decaying turbulence, is considered. Two kinetic schemes, (1) a one-step and (2) a reduced four-step reaction mechanism, are considered for chemistry An alternative formulation is developed for closure of the mean chemical source term , based on the condition that the instantaneous fluctuation of excess temperature is small. With this model, it is shown that the CMC equations describe the autoignition process all the way up to near the equilibrium limit. The effect of second-order terms (namely, conditional variance of temperature excess sigma(2) and conditional correlations of species q(ij)) in modeling is examined. Comparison with DNS data shows that sigma(2) has little effect on the predicted conditional mean temperature evolution, if the average conditional scalar dissipation rate is properly modeled. Using DNS data, a correction factor is introduced in the modeling of nonlinear terms to include the effect of species fluctuations. Computations including such a correction factor show that the species conditional correlations q(ij) have little effect on model predictions with a one-step reaction, but those q(ij) involving intermediate species are found to be crucial when four-step reduced kinetics is considered. The "most reactive mixture fraction" is found to vary with time when a four-step kinetics is considered. First-order CMC results are found to be qualitatively wrong if the conditional mean scalar dissipation rate is not modeled properly. The autoignition delay time predicted by the CMC model compares excellently with DNS results and shows a trend similar to experimental data over a range of initial temperatures.

Glassy behavior in neural network models of associative memory

Neural network models of associative memory exhibit a large number of spurious attractors of the network dynamics which are not correlated with any memory state. These spurious attractors, analogous to "glassy" local minima of the energy or free energy of a system of particles, degrade the performance of the network by trapping trajectories starting from states that are not close to one of the memory states. Different methods for reducing the adverse effects of spurious attractors are examined with emphasis on the role of synaptic asymmetry. (C) 2002 Elsevier Science B.V. All rights reserved.

Performance Evaluation of Distance-Hop Proportionality on Geometric Graph Models of Dense Sensor Networks

Wireless sensor networks can often be viewed in terms of a uniform deployment of a large number of nodes on a region in Euclidean space, e.g., the unit square. After deployment, the nodes self-organise into a mesh topology. In a dense, homogeneous deployment, a frequently used approximation is to take the hop distance between nodes to be proportional to the Euclidean distance between them. In this paper, we analyse the performance of this approximation. We show that nodes with a certain hop distance from a fixed anchor node lie within a certain annulus with probability approach- ing unity as the number of nodes n → ∞. We take a uniform, i.i.d. deployment of n nodes on a unit square, and consider the geometric graph on these nodes with radius r(n) = c q ln n n . We show that, for a given hop distance h of a node from a fixed anchor on the unit square,the Euclidean distance lies within [(1−ǫ)(h−1)r(n), hr(n)],for ǫ > 0, with probability approaching unity as n → ∞.This result shows that it is more likely to expect a node, with hop distance h from the anchor, to lie within this an- nulus centred at the anchor location, and of width roughly r(n), rather than close to a circle whose radius is exactly proportional to h. We show that if the radius r of the ge- ometric graph is fixed, the convergence of the probability is exponentially fast. Similar results hold for a randomised lattice deployment. We provide simulation results that il- lustrate the theory, and serve to show how large n needs to be for the asymptotics to be useful.

Dynamo models of grand minima

Since a universally accepted dynamo model of grand minima does not exist at the present time, we concentrate on the physical processes which may be behind the grand minima. After summarizing the relevant observational data, we make the point that, while the usual sources of irregularities of solar cycles may be sufficient to cause a grand minimum, the solar dynamo has to operate somewhat differently from the normal to bring the Sun out of the grand minimum. We then consider three possible sources of irregularities in the solar dynamo: (i) nonlinear effects; (ii) fluctuations in the poloidal field generation process; (iii) fluctuations in the meridional circulation. We conclude that (i) is unlikely to be the cause behind grand minima, but a combination of (ii) and (iii) may cause them. If fluctuations make the poloidal field fall much below the average or make the meridional circulation significantly weaker, then the Sun may be pushed into a grand minimum.

Updating reliability models of statically loaded instrumented structures

The study extends the first order reliability method (FORM) and inverse FORM to update reliability models for existing, statically loaded structures based on measured responses. Solutions based on Bayes' theorem, Markov chain Monte Carlo simulations, and inverse reliability analysis are developed. The case of linear systems with Gaussian uncertainties and linear performance functions is shown to be exactly solvable. FORM and inverse reliability based methods are subsequently developed to deal with more general problems. The proposed procedures are implemented by combining Matlab based reliability modules with finite element models residing on the Abaqus software. Numerical illustrations on linear and nonlinear frames are presented. (c) 2012 Elsevier Ltd. All rights reserved.

Satellite Evaluation of Current status of Irrigation management in Rajolibanda diversion scheme command, Mahaboobnagar District, AP

This article presents the results of a study using satellite remote sensing techniques to evaluate the current status of canal system performance in terms of the spatial and temporal mismatch between water requirements and water releases within the command area The Rajolibanda Diversion Scheme(RDS)is the only operational major irrigation project in the drought prone district of Mahaboobnagar in Andra Pradesh. It is an inter-state project between Karnataka and Andra Pradesh which comprises of an anicut constructed in Karnataka in 1995 across river Thungabhdra and a 143 km long left bank main canel. The initial 42.6 km of the canel lies in Karnataka consisting of 12 distributaries and servers and serves an localised ayacut of 2739ha. In Andra Pradesh, the latter stretch of the main canal consists of distributaries 12A to 40, is localised to serve an ayacut of 35,410 ha.of which 14,215 ha during kharif season,19,332 ha, during rabi season and 1,863 ha.of perennial crops

Sufficient conditions for formation of a network topology by self-interested agents

Networks such as organizational network of a global company play an important role in a variety of knowledge management and information diffusion tasks. The nodes in these networks correspond to individuals who are self-interested. The topology of these networks often plays a crucial role in deciding the ease and speed with which certain tasks can be accomplished using these networks. Consequently, growing a stable network having a certain topology is of interest. Motivated by this, we study the following important problem: given a certain desired network topology, under what conditions would best response (link addition/deletion) strategies played by self-interested agents lead to formation of a pairwise stable network with only that topology. We study this interesting reverse engineering problem by proposing a natural model of recursive network formation. In this model, nodes enter the network sequentially and the utility of a node captures principal determinants of network formation, namely (1) benefits from immediate neighbors, (2) costs of maintaining links with immediate neighbors, (3) benefits from indirect neighbors, (4) bridging benefits, and (5) network entry fee. Based on this model, we analyze relevant network topologies such as star graph, complete graph, bipartite Turan graph, and multiple stars with interconnected centers, and derive a set of sufficient conditions under which these topologies emerge as pairwise stable networks. We also study the social welfare properties of the above topologies.

Comparative Evaluation of Switching and Average Models of a DC-DC Boost Converter for Real-Time Simulation

This paper presents a comparative evaluation of the average and switching models of a dc-dc boost converter from the point of view of real-time simulation. Both the models are used to simulate the converter in real-time on a Field Programmable Gate Array (FPGA) platform. The converter is considered to function over a wide range of operating conditions, and could do transition between continuous conduction mode (CCM) and discontinuous conduction mode (DCM). While the average model is known to be computationally efficient from the perspective of off-line simulation, the same is shown here to consume more logical resources than the switching model for real-time simulation of the dc-dc converter. Further, evaluation of the boundary condition between CCM and DCM is found to be the main reason for the increased consumption of resources by the average model.

Non-deterministic transducer models of retransmission protocols over noisy channels

Retransmission protocols such as HDLC and TCP are designed to ensure reliable communication over noisy channels (i.e., channels that can corrupt messages). Thakkar et al. 15] have recently presented an algorithmic verification technique for deterministic streaming string transducer (DSST) models of such protocols. The verification problem is posed as equivalence checking between the specification and protocol DSSTs. In this paper, we argue that more general models need to be obtained using non-deterministic streaming string transducers (NSSTs). However, equivalence checking is undecidable for NSSTs. We present two classes where the models belong to a sub-class of NSSTs for which it is decidable. (C) 2015 Elsevier B.V. All rights reserved.