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Metabolic networks are interconnected and influence diverse cellular processes. The protein-metabolite interactions that mediate these networks are frequently low affinity and challenging to systematically discover. We developed mass spectrometry integrated with equilibrium dialysis for the discovery of allostery systematically (MIDAS) to identify such interactions. Analysis of 33 enzymes from human carbohydrate metabolism identified 830 protein-metabolite interactions, including known regulators, substrates, and products as well as previously unreported interactions. We functionally validated a subset of interactions, including the isoform-specific inhibition of lactate dehydrogenase by long-chain acyl–coenzyme A. Cell treatment with fatty acids caused a loss of pyruvate-lactate interconversion dependent on lactate dehydrogenase isoform expression. These protein-metabolite interactions may contribute to the dynamic, tissue-specific metabolic flexibility that enables growth and survival in an ever-changing nutrient environment.

Simultaneous communications over parallel channels is a prominent scheme in modern wireless system. Intuitive multi-channel solution allocates one independent RF chain (including LNA, low-noise amplifier) to each separate channel, causing high implementation cost. Alternatively, low-cost RF uses one single LNA to cover all parallel channels and save implementation cost. Nevertheless, such structure introduces challenges in the control of shared LNA gain (as well as channel power allocation), especially when adapting to independent fadings across parallel channels. Under shared-LNA strucutre, and to maximize energy efficiency, this paper proposes a sub-gradient framework that optimizes both shared-LNA gain and channel power values under multiple system constraints, including Tx power, ADC saturation, baseband SNR, and LNA gain. We discuss algorithm properties including convergence performance, step size selection, and solution accuracy. Simulation results confirm that, optimized energy efficiency through our algorithm can outperform intuitive strategies by 20% to 160%. Finally, impacts of various system parameters are studied as well.

SUMMARY Multi-hop communications equipped with parallel relay nodes is an emerging network scenario visible in environments with high node density. Conventional interference-free medium access control (MAC) has little capability in utilizing such parallel relays because it essentially prohibits the existence of co-channel interference and limits the feasibility of concurrent communications. This paper aims at presenting a cooperative multi-input multi-output (MIMO) space division multiple access (SDMA) design that uses each hop's parallel relay nodes to improve multi-hop throughput performance. Specifically, we use MIMO and SDMA to enable concurrent transmissions (from multiple Tx nodes to single/multiple Rx nodes) and suppress simultaneous links' co-channel interference. As a joint physical layer (MAC/PHY) solution, our design has multiple MAC modules including load balancing that uniformly splits traffic packets at parallel relay nodes and multi-hop scheduling taking co-channel interference into consideration. Meanwhile, our PHY layer modules include distributive channel sounding that exchanges channel information in a decentralized manner and link adaptation module estimating instantaneous link rate per time frame. Simulation results validate that compared with interference-free MAC or existing Mitigating Interference using Multiple Antennas (MIMA-MAC), our proposed design can improve end-to-end throughput by around 30% to 50%. In addition, we further discuss its application on extended multi-hop topology. Copyright © 2012 John Wiley & Sons, Ltd.

Space division multiple access (SDMA)-based medium access control (MAC) protocols have been proposed to enable concurrent communications and improve link throughput in multi-input-multi-output (MIMO) ad hoc networks. For the most part, the works appearing in the literature make idealized and simplifying assumptions about the underlying physical layer and some aspects of the link adaptation protocol. The result is that the performance predicted by such works may not necessarily be a good predictor of the actual performance in a fully deployed system. In this paper, we look to introduce elements into the SDMA-MAC concept that would allow us to better predict their performance under realistic operating conditions. Using a generic SDMA MAC, we look at how the network sum throughput changes with the introduction of the following: (1) use of the more practical MMSE algorithm, instead of the zero-forcing or singular-value-decomposition-based nulling algorithms used for receive beamnulling; (2) impact of channel estimation errors; (3) introduction of link adaptation mechanism specifically designed for concurrent SDMA MACs; and (4) incorporation of TX beamforming along with RX beamnulling. Following on the transmission window during which concurrent transmissions are allowed by the MAC, we qualify the impact of each of these four elements in isolation. At the conclusion, the performance of a system that incorporates elements 1-4 is presented and compared against the baseline system, showing an improvement of up to five times in the overall network sum throughput.

The human liver and lymph node sinusoidal endothelial cell C-type lectin (hLSECtin), a type II integral membrane protein, containing a Ca(2+)-dependent carbohydrate recognition domain (CRD), has a well-established biological activity, yet its three-dimensional structure is unknown due to low expression yields and aggregation into inclusion bodies. Previous study has demonstrated that the HIV-1 virus-encoded Tat peptide ('YGRKKRRQRRR') can increase the yields and the solubility of heterologous proteins. However, whether the Tat peptide could promote the high-yield and soluble expression of membrane proteins in Escherichia coli is not known. Therefore, the prokaryotic expression vector pET28b-Tat-hLSECtin-CRD (using pET28b and pET28b-hLSECtin-CRD as controls) was constructed, and transformed into E. coli BL21 (DE3) cells and induced with isopropyl-β-d-thiogalactoside (IPTG) followed with identifying by SDS-PAGE and Western blot. Subsequently, the bacterial subcellular structure, in which overexpressed the heterologous proteins Tat-hLSECtin-CRD and Tat-free hLSECtin-CRD, was analyzed by transmission electron microscope (TEM) respectively, and the mannose-binding activity of Tat-hLSECtin-CRD was also determined. Expectedly, the solubility of Tat-LSECtin-CRD significantly increased compared to Tat-free LSECtin-CRD (**p < 0.01) with prolonged time, and the Tat-LSECtin-CRD had a significant mannose-binding activity. The subcellular structure analysis indicated that the bacterial cells overexpressed Tat-hLSECtin-CRD exhibited denser region compared with controls, while dot denser region aggregated in the two ends of bacterial cells overexpressed Tat-free hLSECtin-CRD. This study provided a novel method for improving the soluble expression of membrane proteins in prokaryotic systems by fusion with the Tat peptide, which may be potentially expanded to the expression of other membrane proteins.

Concurrent MIMO access is using MIMO-Beamforming vectors to mitigate interference on existing links and exploit spatial spectral opportunity. A novel distributed MIMO MAC, Net-Eigen MAC, was recently developed to (i) null interference on existing links, and (ii) maximize post-processing SNR within desired link, enjoying better throughput performance over conventional single link MAC or SPACEMAC (NullHoc). One key feature in Net-Eigen MAC, named as interference and concurrency awareness, can be utilized by network modules at MAC or higher layer as a powerful tool for network performance improvement. Inspired by such motivation, this paper will present a cooperative scheduling framework that closely utilizes the following two features in Net-Eigen MAC: (i) interference nulling on existing links; (ii) prioritized spatial concurrency among parallel links. Our design monitors all links' performance status, and accordingly schedules each time frame's prioritized concurrency/hierarchy, which naturally triggers two representative examples for practical applications: (i) max-min scheduling that optimizes fair throughput; and (ii) longest-queue-first scheduling that minimizes dropped packets. Extensive simulations show that our proposed design can help Net-Eigen MAC achieve a better performance than SPACEMAC or single link MAC in terms of throughput, delay, or loss ratio.

It is generally accepted that enabling concurrent links via the use of multi antenna techniques is an effective means of improving throughput in a MANET. Several MAC protocols (i.e. MIMA MAC, and SPACEMAC) have even been introduced in the literature specifically to increase the number of concurrent links. Recent work, however, has shown that this is not universally true. Given a MIMO enabled network, there are easily produced topologies where a single link MAC will outperform a concurrent MAC, which motivates the need for a MAC scheme that could choose between single link and concurrent link operation as the dynamics of the system changes. In this paper we present a novel MIMO MAC design that can adaptively switch between a single link scheme and a concurrent link scheme. Our design objective is to improve the link throughput by guaranteeing each link's throughput to be no less than that achievable via a single link MAC protocol. To demonstrate our design principle, we first present an idealized derivation where all network information is perfectly known at all nodes. Then as a realistic implementation, we further present a practical MAC protocol that uses distributed handshaking and imperfect channel estimation to run the adaptive switching function. Simulation results validate that our design's link throughput is greater than or equal to a single link MAC's throughput with 2% – 12% outage probabilities. Moreover, the proposed MAC's ergodic link throughput is 20%–30% higher than single link MAC and MIMA-MAC's counterparts.

Carrier Sense Multiple Access (CSMA) is the conventional medium access method used in wireless Ad Hoc networks. It can be enhanced as a Space-Division based CSMA (namely, SD-CSMA) by using multi-antenna techniques, which allows concurrent link communications in the network. In this paper, we present a MAC design that can adaptively switch between CSMA and SD-CSMA in multi-antenna based Ad Hoc Networks. We first investigate the CSMA mode and the SD-CSMA mode by considering several practical constraints from MIMO physical layer, which include imperfect channel estimation, modulation and coding scheme, MMSE detection, power constraint and packet length. We then propose a selection criterion that adaptively switches between CSMA and SD-CSMA based on current wireless channels among nodes. Simulation results verify that the proposed design can outperform both the CSMA mode and the SD-CSMA mode in terms of aggregate throughput

MIMO based MANET has received a great deal of attention in the past decade, resulting in a number of MAC layer protocols that aim to utilize the inherent capabilities afforded by multi-antenna enabled nodes. Many of these MAC protocols look to improve on the total number of concurrent links within the network. In this paper, we present a theoretical approach for identifying the maximum number of concurrent links (MNCL) in a MIMO enabled MANET, subject to the constraint that all links provide a minimum QoS measured in terms of signal to interference and noise ratio (SINR). We assume that each receiver uses an MMSE based detector which provides a balance between completely nulling of neighboring interference and hardware complexity. As a byproduct of the MNCL, the solution will provide the optimum power allocation for the nodes as well as the optimum concurrent link allocation. The proposed approach is readily applicable to MIMO systems using Receive Diversity, Transmit Beamforming, and Space Time Block Coding (STBC). The results show that the MNCL can be improved significantly by exploiting multi-user diversity and increasing the number of receiver antennas. But the improvement from allowing higher transmit power is not significant. The derived MNCL capacity can be used to highlight theoretical insights for practical designs.

IEEE 802.11 MAC does not use RTS/CTS exchange in multicast/broadcast mode. This may cause throughput loss and packet collision by hidden terminals. We propose a new cross-layer ad hoc multicast protocol, named MIMO-CAST, to improve efficiency of IEEE 802.11 MAC. MIMO-CAST builds a multicast tree on-demand by using control packets exchange. To reduce duplicated transmissions, MIMO-CAST employs Multi Point Relay with which only designated nodes forward packets and all nodes in the network hear those packets. It also exploits Multiple-Input Multiple-Output (MIMO) by giving different weights to its multiple antennas so that a node can receive from one neighbor while blocking the interference from other nodes. We investigate the performance improvement of MIMO-CAST through a simulation study

This paper presents a new carrier frequency offset (CFO) estimation algorithm with low-complexity for uplink OFDMA systems. Extended Kalman Filter (EKF) is employed in time domain, while the multiple access interference (MAI) cancellation strategy is combined in every recursion. In addition, an adaptive noise variance estimator is contrived for EKF, and a robust EKF method is derived for CFO estimation with data symbols. The proposed algorithm is suitable for online estimation, and can be applied to both preamble and data symbols. Simulation results show that it has a large estimation range, while approaching the Cramer-Rao Bound (CRB) closely with quite reduced complexity.

Multi-path fading and multiple access interference largely degrade the performance of carrier-frequency offset and timing offset estimations in OFDMA uplink systems. This paper proposes a robust algorithm with low complexity for joint estimation of carrier-frequency offset and timing offset. The phase differences in the received sub-carrier signals between two consecutive training symbols are employed and a robust sequential least squares algorithm is used to improve the performance of the estimation. Simulation results show that the proposed low complexity algorithm outperforms the linear least squares (LLS) estimator and approaches the performance of the iteratively reweighted least squares (IRLS) estimator