Dirichlet Priors for MAP Inference of Protein Conformation Abundances from SAXS

Estimation of mixture coefficients of protein conformations in solution find applications in understanding protein behavior. We describe a method for maximum a posteriori (MAP) estimation of the mixture coefficients of ensemble of conformations in a protein mixture solution using measured small angle X-ray scattering (SAXS) intensities. The proposed method builds upon a model for the measurements of crystallographically determined conformations. Assuming that a priori information on the protein mixture is available, and that priori information follows a Dirichlet distribution, we develop a method to estimate the relative abundances with MAP estimator. The Dirichlet distribution depends on concentration parameters which may not be known in practice and thus need to be estimated. To estimate these unknown concentration parameters we developed an expectation-maximization (EM) method. Adenylate kinase (ADK) protein was selected as the test bed due to its known conformations Beckstein et al. (Journal of Molecular Biology, 394(1), 160 1). Known conformations are assumed to form the full vector bases that span the measurement space. In Monte Carlo simulations, mixture coefficient estimation performances of MAP and maximum likelihood (ML) (which assumes a uniform prior on the mixture coefficients) estimators are compared. MAP estimators using known and unknown concentration parameters are also compared in terms of estimation performances. The results show that prior knowledge improves estimation accuracy, but performance is sensitive to perturbations in the Dirichlet distribution’s concentration parameters. Moreover, the estimation method based on EM algorithm shows comparable results to approximately known prior parameters.     

Multi-radio diversity in wireless networks

This paper describes the Multi-Radio Diversity (MRD) wireless system, which uses path diversity to improve loss resilience in wireless local area networks (WLANs). MRD coordinates wireless receptions among multiple radios to improve loss resilience in the face of path-dependent frame corruption over the radio. MRD incorporates two techniques to recover from bit errors and lower the loss rates observed by higher layers, without consuming much extra bandwidth. The first technique is frame combining, in which multiple, possibly erroneous, copies of a given frame are combined together in an attempt to recover the frame without retransmission. The second technique is a low-overhead retransmission scheme called request-for-acknowledgment (RFA), which operates above the link layer and below the network layer to attempt to recover from frame combining failures. We present an analysis that determines how the parameters for these algorithms should be chosen. We have designed and implemented MRD as a fully functional WLAN infrastructure based on 802.11a. We evaluate the MRD system under several different physical configurations, using both UDP and TCP, and measured throughput gains up to 3× over single radio communication schemes employing 802.11’s autorate adaptation scheme. Computer and Communication Sciences, EPFL, Switzerland. Allen Miu received his Ph.D. degree at the Massachusetts Institute of Technology in 2006 and is currently a wireless systems architect at Ruckus Wireless, Inc. He received his S.M. in Computer Science from MIT and a B.Sc. with highest honors in Electrical Engineering and Computer Science from the University of California at Berkeley. He previously worked on the Cricket Indoor Location System and was a research intern at Microsoft Research, Redmond in 2000 and Hewlett-Packard Laboratories, Palo Alto in 2002. His research interests include wireless networks, location systems, mobile computing, and embedded systems. Hari Balakrishnan is an Associate Professor in the EECS Department and a member of the Computer Science and Artificial Intelligence Laboratory (CSAIL) at MIT. His research interests is in the area of networked computer systems. In addition to many widely cited papers, several systems developed as part of his research are available in the public domain. He received a Ph.D. in Computer Science from the University of California at Berkeley in 1998 and a B.Tech. from the Indian Institute of Technology (Madras) in 1993. His honors include an Alfred P. Sloan Research Fellowship (2002), an NSF CAREER Award (2000), the ACM doctoral dissertation award for his work on reliable data transport over wireless networks (1998), and seven award-winning papers at various top conferences and journals, including the IEEE Communication Society’s William R. Bennett Prize (2004). He has also received awards for excellence in teaching and research at MIT (Spira, Junior Bose, and Harold Edgerton faculty achievement awards). C. Emre Koksal received his B.S. degree in Electrical Engineering from the Middle East Technical University, Ankara in 1996. He received his S.M. and Ph.D. degrees from MIT in Electrical Engineering and Computer Science in 1998 and 2002 respectively. He was a postdoctoral fellow in the Networks and Mobile Systems Group in the Computer Science and Artificial Intelligence Laboratory at MIT until 2003. Since then he has been a senior researcher jointly in the Laboratory for Computer Communications and the Laboratory for Information Theory at EPFL, Switzerland. His general areas of interest are wireless communications, computer networks, information theory, stochastic processes and financial economics. He also has a certificate on Financial Technology from the Sloan School of Management at MIT.     

Optimal throughput performance in full-duplex relay assisted cognitive networks

Wireless Networks - In this paper, we study a full-duplex cooperative cognitive radio network with multiple full-duplex secondary users acting as potential relays for transmitting the packets of a...     

On the design considerations of solid-state power amplifiers for satellite communications: A systems perspective

Conventional solid-state power amplifier (SSPA) design approach isolates radio frequency (RF) design from communication theory. In this paper, a unified SSPA design approach is proposed, which optimizes SSPA parameters (bias voltage and input RF signal power) to minimize total DC power consumption while satisfying received SNR constraint specified by the link budget. The effect of SSPA nonlinearity is quantified by the error vector magnitude measured at its output and the corresponding received SNR degradation is analyzed. Using the quantitative metrics for received SNR, it is possible to evaluate highly nonlinear SSPA classes such as Class-B or deep-Class AB, which are normally not considered in conventional SSPA design approach to be used in satellite communication applications.     

Lithium-Ion Desolvation Induced by Nitrate Additives Reveals New Insights into High Performance Lithium Batteries

Electrolyte additives have been widely used to address critical issues in current metal (ion) battery technologies. While their functions as solid electrolyte interface forming agents are reasonably well-understood, their interactions in the liquid electrolyte environment remain rather elusive. This lack of knowledge represents a significant bottleneck that hinders the development of improved electrolyte systems. Here, the key role of additives in promoting cation (e.g., Li⁺) desolvation is unraveled. In particular, nitrate anions (NO₃⁻) are found to incorporate into the solvation shells, change the local environment of cations (e.g., Li⁺) as well as their coordination in the electrolytes. The combination of these effects leads to effective Li⁺ desolvation and enhanced battery performance. Remarkably, the inexpensive NaNO₃ can successfully substitute the widely used LiNO₃ offering superior long-term stability of Li⁺ (de-)intercalation at the graphite anode and suppressed polysulfide shuttle effect at the sulfur cathode, while enhancing the performance of lithium–sulfur full batteries (initial capacity of 1153 mAh g⁻¹ at 0.25C) with Coulombic efficiency of ≈100% over 300 cycles. This work provides important new insights into the unexplored effects of additives and paves the way to developing improved electrolytes for electrochemical energy storage applications.     

Wind turbine speed control of a contactless piezoelectric wind energy harvester

ABSTRACT

Wind turbine control is an important task to make the electricity generation secure in terms of energy demand and machine safety. It also yields to control the desired power level and optimized energy because of the assignment of turbine speed. The contactless piezoelectric wind energy harvester (CPWEH) used in this study has three piezoelectric layers located around the shaft with 120 degrees apart and they are buckled by the magnetic force without any physical contact. The superiority of this device is to generate energy for low wind speeds such as 1.5 m/s. However, for high speeds, high total harmonic distortions (THDs) govern the waveforms, thus controlling the turbine speed becomes necessary for optimizing the output power. Encouraged by this, a small low inertia dc generator is coupled with the wind turbine, and the generator terminals are connected to a resistor through a power switch to generate a braking torque that opposes to wind speed direction. By controlling the switch properly, turbine speed is ensured to remain within a certain band, which accordingly prevents the turbine from rotating very fast at damaging wind speeds. Several experiments are performed on the developed CPWEH with/without the presented control scheme which prove the existence of promising performance of our proposal.     

Microbiological,chemical and sensory assessment of mussels (<Emphasis Type="Italic">Mytilus galloprovincialis</Emphasis>) stored under modified atmosphere packaging

Wild mussels (Mytilus galloprovincialis), were packaged aerobically under vaccum packaging(VP) and modified atmosphere packaging (MAP (50%/50% CO₂/N₂: M1, 80%/20% CO₂/N₂: M2, 65%/35% CO₂/N₂: M3), and stored at 2 ± 1 °C. Quality evaluation was carried out using microbiological, chemical and sensory analyses. Microbiological results revealed that M2 and M3 delayed microbial growth compared to M1. Of the chemical indices determined, the TVB-N and TMA-N values of M2 remained lower than the proposed acceptability limits of 35 mg N/100 g and 8 mg N/100 g, respectively, up to 8 days of storage. All of the MAP and VP mussel samples exceeded these limits after 12 days of storage. All samples retained desirable sensory characteristics during the first 8 days of storage. Based on microbiological and chemical analyses along with sensory evaluation, M2 and M3 gave a longer shelf-life compared with VP and M1. M2 gas mixture was the most effective for mussel preservation.