The Input Signal Step Function (ISSF), a Standard Method to Encode Input Signals in SBML Models with Software Support, Applied to Circadian Clock Models

LetterThis is the final version of the article. Available from SAGE Publications via the DOI in this record.Time-dependent light input is an important feature of computational models of the circadian clock. However, publicly available models encoded in standard representations such as the Systems Biology Markup Language (SBML) either do not encode this input or use different mechanisms to do so, which hinders reproducibility of published results as well as model reuse. The authors describe here a numerically continuous function suitable for use in SBML for models of circadian rhythms forced by periodic light-dark cycles. The Input Signal Step Function (ISSF) is broadly applicable to encoding experimental manipulations, such as drug treatments, temperature changes, or inducible transgene expression, which may be transient, periodic, or mixed. It is highly configurable and is able to reproduce a wide range of waveforms. The authors have implemented this function in SBML and demonstrated its ability to modify the behavior of publicly available models to accurately reproduce published results. The implementation of ISSF allows standard simulation software to reproduce specialized circadian protocols, such as the phase-response curve. To facilitate the reuse of this function in public models, the authors have developed software to configure its behavior without any specialist knowledge of SBML. A community-standard approach to represent the inputs that entrain circadian clock models could particularly facilitate research in chronobiology.K.S. was supported by the UK BBSRC grant BB/E015263/1. SynthSys Edinburgh is a Centre for Integrative Systems Biology (CISB) funded by BBSRC and EPSRC, reference BB/D019621/1

Interacting electrons in a 2D quantum dot

The exact numerical diagonalization of the Hamiltonian of a 2D circular quantum dot is performed for 2, 3, and 4 electrons.The results are compared with those of the perturbation theory.Our numerical results agree reasonably well for small values of the dimensionles coupling constant \lambda=a\over a_B where a is the dot radius and a_B is the effective Bohr radius.Exact diagonalization results are compared with the classical predictions, and they are found to be almost coincident for large \lambda values. PACS Numbers: 73.20.Dx, 73.61.-rComment: 12 pages, 5 postscript figure

Effect of seminal plasma on functional integrity of rabbit sperm membranes during storage at 4ºC or freezing

[EN] The effect of semen plasma removal either by simple centrifugation or by separation through a Percoll gradient on the integrity of plasma membranes of rabbit spermatozoa during storage at 4°C and freezing was evaluated in two successive experiments. A modifi ed hypo-osmotic swelling test procedure combined with supravital staining was employed to evaluate simultaneously membrane integrity of head and tail membranes of sperm cells. In the first experiment, the impact of semen plasma on membrane integrity of sperm cells was examined in Tris-citric acid-glucose extender at 4°C for 96 h. The percentage of sperm cells with disintegrated tail and head membranes increased in all groups in correlation with the length of storage. After storage for 96 h, removal of semen plasma, irrespective of the method of removal, resulted in signifi cant increase (P<0.01) in the percentage of sperm cells with disintegrated plasma membranes. The adverse effect of storage and removal of semen plasma was more prominent on the tail membranes, and especially during the fi rst 24 h of the storage period. In the second experiment, the impact of semen plasma on membrane integrity of sperm cells undergoing freezing was examined. A total of three groups were arranged as described in the fi rst experiment, and semen samples were frozen in straws using an extender including acetamide and methyl cellulose. Freezing of semen drastically reduced the percentage of sperm cells with intact plasma membranes in postthaw samples. However, removal of semen plasma, irrespective of the method of removal, did not affect the proportion of sperm cells with intact plasma membranes. In conclusion, the effect of semen plasma on plasma membranes varied signifi cantly relative to the preservation temperature of sperm cells. Although it exerted a protective infl uence during storage at 4°C, no protective impact was monitored during freezing.Aksoy, M.; Cankat Lehimcioglu, N.; Akman, O. (2010). Effect of seminal plasma on functional integrity of rabbit sperm membranes during storage at 4ºC or freezing. World Rabbit Science. 16(1). doi:10.4995/wrs.2008.64216

Shock tunnel studies of scramjet phenomena, supplement 5

A series of reports are presented on SCRAMjet studies, shock tunnel studies, and expansion tube studies. The SCRAMjet studies include: (1) Investigation of a Supersonic Combustion Layer; (2) Wall Injected SCRAMjet Experiments; (3) Supersonic Combustion with Transvers, Circular, Wall Jets; (4) Dissociated Test Gas Effects on SCRAMjet Combustors; (5) Use of Silane as a Fuel Additive for Hypersonic Thrust Production, (6) Pressure-length Correlations in Supersonic Combustion; (7) Hot Hydrogen Injection Technique for Shock Tunnels; (8) Heat Release - Wave Interaction Phenomena in Hypersonic Flows; (9) A Study of the Wave Drag in Hypersonic SCRAMjets; (10) Parametric Study of Thrust Production in the Two Dimensional SCRAMjet; (11) The Design of a Mass Spectrometer for use in Hypersonic Impulse Facilities; and (12) Development of a Skin Friction Gauge for use in an Impulse Facility. The shock tunnel studies include: (1) Hypervelocity flow in Axisymmetric Nozzles; (2) Shock Tunnel Development; and (3) Real Gas Efects in Hypervelocity Flows over an Inclined Cone. The expansion tube studies include: (1) Investigation of Flow Characteristics in TQ Expansion Tube; and (2) Disturbances in the Driver Gas of a Shock Tube

Functionalization of silicon nanowires with transition metal atoms

This paper investigates atomic structure, mechanical, electronic, and magnetic properties of silicon nanowires (SiNW) using first-principles plane-wave calculations within density-functional theory. We considered bare, hydrogen-terminated, and 3d -transition metal (TM) adsorbed SiNWs oriented along [001] direction. We also studied Cr interstitial impurity. Nanowires of different sizes are initially cut from the bulk Si crystal in rodlike forms, and subsequently their atomic structures are relaxed before and also after the termination of surface dangling bonds by hydrogen atoms. We first presented an extensive analysis of the atomic structure, stability, elastic, and electronic properties of bare and hydrogen-terminated SiNWs. The energetics of adsorption and resulting electronic and magnetic properties are examined for different levels of 3d -TM atom coverage. Adsorption of TM atoms generally results in magnetic ground state. The net magnetic moment increases with increasing coverage. While specific SiNWs acquire half-metallic behavior at low coverage, at high coverage ferromagnetic nanowires become metallic for both spin directions, and some of them have very high spin polarization at the Fermi level. Our results suggest that the electronic and spintronic devices with conducting interconnects between them can be fabricated on a single SiNW at a desired order. We believe that our study will initiate new research on spintronic applications of SiNWs. © 2008 The American Physical Society

Modeling of mouse experiments suggests that optimal anti-hormonal treatment for breast cancer is diet-dependent

Estrogen receptor positive breast cancer is frequently treated with anti-hormonal treatment such as aromatase inhibitors (AI). Interestingly, a high body mass index has been shown to have a negative impact on AI efficacy, most likely due to disturbances in steroid metabolism and adipokine production. Here, we propose a mathematical model based on a system of ordinary differential equations to investigate the effect of high-fat diet on tumor growth. We inform the model with data from mouse experiments, where the animals are fed with high-fat or control (normal) diet. By incorporating AI treatment with drug resistance into the model and by solving optimal control problems we found differential responses for control and high-fat diet. To the best of our knowledge, this is the first attempt to model optimal anti-hormonal treatment for breast cancer in the presence of drug resistance. Our results underline the importance of considering high-fat diet and obesity as factors influencing clinical outcomes during anti-hormonal therapies in breast cancer patients.Comment: 44 pages, 21 figure

Confined states in multiple quantum well structures of Sin Gen nanowire superlattices

Mechanical properties, atomic and energy band structures of bare and hydrogen-passivated Sin Gen nanowire superlattices have been investigated by using first-principles pseudopotential plane-wave method. Undoped, tetrahedral Si and Ge nanowire segments join pseudomorphically and can form superlattice with atomically sharp interface. We found that Sin nanowires are stiffer than Gen nanowires. Hydrogen passivation makes these nanowires and Sin Gen nanowire superlattice even more stiff. Upon heterostructure formation, superlattice electronic states form subbands in momentum space. Band lineups of Si and Ge zones result in multiple quantum wells, where specific states at the band edges and in band continua are confined. The electronic structure of the nanowire superlattice depends on the length and cross section geometry of constituent Si and Ge segments. Since bare Si and Ge nanowires are metallic and the band gaps of hydrogenated ones vary with the diameter, Sin Gen superlattices offer numerous alternatives for multiple quantum well devices with their leads made from the constituent metallic nanowires. © 2007 The American Physical Society