Impact of negative feedback in metabolic noise propagation

Synthetic biology combines different branches of biology and engineering aimed at designing synthetic biological circuits able to replicate emergent properties useful for the biotechnology industry, human health and environment. The role of negative feedback in noise propagation for a basic enzymatic reaction scheme is investigated. Two feedback control schemes on enzyme expression are considered: one from the final product of the pathway activity, the other from the enzyme accumulation. Both schemes are designed to provide the same steady‐state average values of the involved players, in order to evaluate the feedback performances according to the same working mode. Computations are carried out numerically and analytically, the latter allowing to infer information on which model parameter setting leads to a more efficient noise attenuation, according to the chosen scheme. In addition to highlighting the role of the feedback in providing a substantial noise reduction, our investigation concludes that the effect of feedback is enhanced by increasing the promoter sensitivity for both schemes. A further interesting biological insight is that an increase in the promoter sensitivity provides more benefits to the feedback from the product with respect to the feedback from the enzyme, in terms of enlarging the parameter design space.Inspec keywords: biotechnology, enzymes, biological techniquesOther keywords: negative feedback impact, metabolic noise propagation, mathematical modelling, synthetic biological circuit, biotechnology industry, human health, environment, enzymatic reaction scheme, feedback control scheme, enzyme expression, enzyme accumulation, negative autoregulation, steady‐state average value, feedback performance, stochastic simulation algorithm, stochastic hybrid system modelling, noise attenuation, substantial noise reduction, feedback effect, parameter design space     

Effectiveness and issues of congestion control in 802.11g wireless LANs

The current paper presents a collection of experimental data portraying the performance achieved in the wireless setting by several TCP-friendly congestion controls recently proposed in literature. This work is partly motivated by the consideration that the majority of the analytical results in this area are validated by simulation, rather than by field tests. Examining these algorithms in real environments can help verify their actual effectiveness over the wireless Internet. To reach such goal, two representative controls among the so-called window-based TCP-friendly schemes have been implemented, namely, the General Additive Increase Multiplicative Decrease (GAIMD) strategy, and the SQuare RooT (SQRT) binomial control; the most representative algorithm among rate-based controls, the TCP Friendly Rate Control (TFRC), has also been considered. Their TCP-fairness and smoothness have been comprehensively evaluated in an IEEE 802.11g Wireless Local Area Network (WLAN). The obtained results show that the GAIMD and SQRT strategies reveal non-negligible scalability and smoothness problems, that markedly limit their performance. It is empirically demonstrated that their “optimal” increase/decrease rules, based on TCP-Reno analytical model, cannot guarantee an adequate performance when GAIMD and SQRT compete with TCP-Sack, a de facto standard for current TCP implementations. TFRC is demonstrated to occasionally behave bewildering: properly tuning one of its congestion control parameters and enhancing the algorithm with a flow-control mechanism result in a definitely fairer share of bandwidth with concurrent TCP flows. Michele Borri received the M.Sc. degree in Computer Engineering from the University of Modena and Reggio Emilia in the academic year 2001–2002 and took a specialisation in Telecommunication Engineering in 2002. His professional activity is currently balanced between researching at the University of Modena and Reggio Emilia, and consulting as a system engineer and network architect. His research interests focus on congestion control and multimedia services in next generation Internet. Michele Borri has been participating to national research projects promoted by the Italian National Research Council (CNR). Maurizio Casoni is Associate Professor in Telecommunications at the University of Modena and Reggio Emilia. He graduated with honors in Electrical Engineering at the University of Bologna in 1991, with a grant by Telecom Italia and received the Ph.D. degree also in Electrical Engineering from the University of Bologna, in 1995. In 1995 he was with the Computer Science Department at Washington University in St. Louis, MO, as a research fellow where he worked on ATM broadband switching architectures. He has studied ATM broadband switching architectures and Clos architectures for the design of large photonic switches in the framework of the European Projects ATMOS and KEOPS. He has also investigated the performance of 3rd generation UMTS systems. His current research interests deal with Optical Networking, mainly focusing on Optical Burst Switching, and Satellite Networks. He currently holds the course of Interconnection Systems for undergraduate students and the course of Switching Systems for graduate students of Telecommunications Engineering. Maria Luisa Merani is currently an associate professor of Telecommunication Networks at the University of Modena and Reggio Emilia, Department of Information Engineering. She is an IEEE Senior member and has served on the Technical Program Committees of several major communication conferences (IEEE ICC, IEEE Globecom, IEEE VTC, APCC). In 2005 she has been technical program cochair of the second IEEE International Symposium in Wireless Communication Systems. In 2007 she will be the Wireless Symposium chair of IEEE Globecom. At present she is involved in research on congestion control for next generation Internet and on multicast video streaming. Her most recent research interests are related to the area of radio communications, with emphasis on performance evaluation of mobile radio systems, 3G data networking and transport solutions for optical networks. Maria Luisa Merani received both her M.Sc. (summa cum laude) and Ph.D. in electrical engineering from the University of Bologna, Italy, in the academic years 1985/86 and 1991/92, respectively. In 1992 she spent one year at the Computer Science Department of the University of California in Los Angeles, CA, USA.     

Reproducibility of MRI-based white matter tract estimation using multi-fiber probabilistic tractography: effect of user-defined parameters and regions

Objective

There is a pressing need to assess user-dependent reproducibility of multi-fibre probabilistic tractography in order to encourage clinical implementation of these advanced and relevant approaches. The goal of this study was to evaluate both intrinsic and inter-user reproducibility of corticospinal tract estimation.

Materials and methods

Six clinical datasets including motor functional and diffusion MRI were used. Three users performed an independent tractography analysis following identical instructions. Dice indices were calculated to quantify the reproducibility of seed region, fMRI-based end region, and streamline maps.

Results

The inter-user reproducibility ranged 41–93%, 29–94%, and 50–92%, for seed regions, end regions, and streamline maps, respectively. Differences in streamline maps correlated with differences in seed and end regions. Good inter-user agreement in seed and end regions, yielded inter-user reproducibility close to the intrinsic reproducibility (92–97%) and in most cases higher than 80%.

Discussion

Uncertainties related to user-dependent decisions and the probabilistic nature of the analysis should be considered when interpreting probabilistic tractography data. The standardization of the methods used to define seed and end regions is a necessary step to improve the accuracy and robustness of multi-fiber probabilistic tractography in a clinical setting. Clinical users should choose a feasible compromise between reproducibility and analysis duration.

     

Ultrashort pulse-propagation effects in a semiconductor opticalamplifier: microscopic theory and experiment

We present microscopic modeling and experimental measurements of femtosecond-pulse interactions in a semiconductor optical amplifier. Two novel nonlinear propagation effects are demonstrated: pulse break-up in the gain regime and pulse compression in the transparency regime. These propagation phenomena highlight the microscopic origin and important role of adiabatic following in semiconductor optical amplifiers. Fundamental light-matter interactions are discussed in detail and possible applications are highlighted     

Spectral hole-burning and carrier-heating dynamics in InGaAsquantum-dot amplifiers

The ultrafast gain and index dynamics in a set of InAs-InGaAs-GaAs quantum-dot (QD) amplifiers are measured at room temperature with femtosecond resolution. The role of spectral hole-burning (SHB) and carrier heating (CH) in the recovery of gain compression is investigated in detail. An ultrafast recovery of the spectral hole within ~100 fs is measured, comparable to bulk and quantum-well amplifiers, which is contradicting a carrier relaxation bottleneck in electrically pumped QD devices. The CH dynamics in the QD is quantitatively compared with results on an InGaAsP bulk amplifier. Reduced CH for both gain and refractive index dynamics of the QD devices is found, which is a promising prerequisite for high-speed applications. This reduction is attributed to reduced free-carrier absorption-induced heating caused by the small carrier density necessary to provide amplification in these low-dimensional systems     

Cyclic voltammetry simulation at microelectrode arrays with COMSOL Multiphysics®

The present paper reports the results obtained applying the general purpose software COMSOL Multiphysics^® to the finite elements simulation of Cyclic Voltammetries (CV’s) at microelectrodes arrays (MEA). CV’s at inlaid micro disk electrode arrays have been simulated benchmarking our results with those obtained by Compton with the finite difference method. Then the influence of meshing on the quality of the simulated data have been investigated showing that bad meshing may provide shapes with no physical meaning. Simulations have also been performed on recessed micro disk arrays in order to show the effect of the depth of the recess on the voltammetric wave shape. We found that COMSOL Multiphysics^® provides a flexible and straightforward route to the simulation of electrochemical systems with complex geometry.