Low complexity pre-equalization algorithms for zero-padded block transmission

The zero-padded block transmission with linear time-domain pre-equalizer is studied in this paper. A matched filter is exploited to guarantee the stability of the zero-forcing (ZF) and minimum mean square error (MMSE) pre-equalization. Then, in order to compute the pre-equalizers efficiently, an asymptotic decomposition is developed for the positive-definite Hermitian banded Toeplitz matrix. Compared to the direct matrix inverse methods or the Levinson-Durbin algorithm, the computational complexity of the proposed algorithm is significantly decreased and there is no bit error rate degradation when data block length is large. © 2010 IEEE.published_or_final_versio

Exact Outage Probability of Dual-Hop CSI-Assisted AF Relaying over Nakagami-m Fading Channels

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Non-orthogonal Opportunistic Beamforming: Performance Analysis and Implementation

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Exact performance analysis of dual-hop semi-blind AF relaying over arbitrary nakagami-m fading channels

Relay transmission is promising for future wireless systems due to its significant cooperative diversity gain. The performance of dual-hop semi-blind amplify-and-forward (AF) relaying systems was extensively investigated, for transmissions over Rayleigh fading channels or Nakagami-m fading channels with integer fading parameter. For the general Nakagami-m fading with arbitrary m values, the exact closed-form system performance analysis is more challenging. In this paper, we explicitly derive the moment generation function (MGF), probability density function (PDF) and moments of the end-to-end signal-to-noise ratio (SNR) over arbitrary Nakagami-m fading channels with semi-blind AF relay. With these results, the system performance evaluation in terms of outage probability, average symbol error probability, ergodic capacity and diversity order, is conducted. The analysis developed in this paper applies to any semi-blind AF relaying systems with fixed relay gain, and two major strategies for computing the relay gain are compared in terms of system performance. All analytical results are corroborated by simulation results and they are shown to be efficient tools to evaluate system performance. © 2011 IEEE.published_or_final_versio

Robust Tomlinson-Harashima precoding for non-regenerative multi-antenna relaying systems

Conference Theme: PHY and FundamentalsIn this paper, we consider the robust transceiver design with Tomlinson-Harashima precoding (THP) for multi-hop amplify-and-forward (AF) multiple-input multiple-output (MIMO) relaying systems. THP is adopted at the source to mitigate the spatial inter-symbol interference and then a joint Bayesian robust design of THP at source, linear forwarding matrices at relays and linear equalizer at destination is proposed. Based on the elegant characteristics of multiplicative convexity and matrix-monotone functions, the optimal structure of the nonlinear transceiver is first derived. Based on the derived structure, the optimization problem is greatly simplified and can be efficiently solved. Finally, the performance advantage of the proposed robust design is assessed by simulation results. © 2012 IEEE.published_or_final_versionThe 2012 IEEE Wireless Communications and Networking Conference (WCNC), Paris, France, 1-4 April 2012. In IEEE Wireless Communications and Networking Conference Proceedings, 2012, p. 753-75

Uplink LMMSE beamforming design for cellular networks with AF MIMO relaying

In this paper, linear beamforming design for uplink amplify-and-forward relaying cellular networks, in which multiple mobile terminals rely on one relay station to communicate with the base station, is investigated. In particular, the base station, relay station and mobile terminals are all equipped with multiple antennas. Based on linear minimum mean-square-error (LMMSE) criterion and exploiting a hidden convexity in the problem, the precoder matrices at multiple mobile terminals, forwarding matrix at relay station and equalizer matrix at base station are jointly designed. Furthermore, several existing linear beamforming designs for multi-user (MU) MIMO systems and AF MIMO relaying systems can be considered as special cases of the proposed solution. Simulation results are presented to demonstrate the performance advantage of the proposed algorithm. © 2011 IEEE.published_or_final_versionThe 2011 IEEE Global Telecommunications Conference (GLOBECOM 2011), Beijing, China, 5-9 December 2011. In Globecom. IEEE Conference and Exhibition, 2011, p. 1-

On the force field optimisation of β -lactam cores using the force field Toolkit

When employing molecular dynamics (MD) simulations for computer-aided drug design, the quality of the used force fields is highly important. Here we present reparametrisations of the force fields for the core molecules from 9 different β-lactam classes, for which we utilized the force field Toolkit and Gaussian calculations. We focus on the parametrisation of the dihedral angles, with the goal of reproducing the optimised quantum geometry in MD simulations. Parameters taken from CGenFF turn out to be a good initial guess for the multiplicity of each dihedral angle, but the key to a successful parametrisation is found to lie in the phase shifts. Based on the optimised quantum geometry, we come up with a strategy for predicting the phase shifts prior to the dihedral potential fitting. This allows us to successfully parameterise 8 out of the 11 molecules studied here, while the remaining 3 molecules can also be parameterised with small adjustments. Our work highlights the importance of predicting the dihedral phase shifts in the ligand parametrisation protocol, and provides a simple yet valuable strategy for improving the process of parameterising force fields of drug-like molecules

Compromised BRCA1-PALB2 interaction is associated with breast cancer risk.

The major breast cancer suppressor proteins BRCA1 and BRCA2 play essential roles in homologous recombination (HR)-mediated DNA repair, which is thought to be critical for tumor suppression. The two BRCA proteins are linked by a third tumor suppressor, PALB2, in the HR pathway. While truncating mutations in these genes are generally pathogenic, interpretation of missense variants remains a challenge. To date, patient-derived missense variants that disrupt PALB2 binding have been identified in BRCA1 and BRCA2; however, there has not been sufficient evidence to prove their pathogenicity in humans, and no variants in PALB2 that disrupt either its BRCA1 or BRCA2 binding have been reported. Here we report on the identification of a novel PALB2 variant, c.104T>C (p.L35P), that segregates in a family with a strong history of breast cancer. Functional analyses showed that L35P abrogates the PALB2-BRCA1 interaction and completely disables its abilities to promote HR and confer resistance to platinum salts and PARP inhibitors. Whole-exome sequencing of a breast cancer from a c.104T>C carrier revealed a second, somatic, truncating mutation affecting PALB2, and the tumor displays hallmark genomic features of tumors with BRCA mutations and HR defects, cementing the pathogenicity of L35P. Parallel analyses of other germline variants in the PALB2 N-terminal BRCA1-binding domain identified multiple variants that affect HR function to varying degrees, suggesting their possible contribution to cancer development. Our findings establish L35P as the first pathogenic missense mutation in PALB2 and directly demonstrate the requirement of the PALB2-BRCA1 interaction for breast cancer suppression

Evaluation of machine-learning methods for ligand-based virtual screening

Machine-learning methods can be used for virtual screening by analysing the structural characteristics of molecules of known (in)activity, and we here discuss the use of kernel discrimination and naive Bayesian classifier (NBC) methods for this purpose. We report a kernel method that allows the processing of molecules represented by binary, integer and real-valued descriptors, and show that it is little different in screening performance from a previously described kernel that had been developed specifically for the analysis of binary fingerprint representations of molecular structure. We then evaluate the performance of an NBC when the training-set contains only a very few active molecules. In such cases, a simpler approach based on group fusion would appear to provide superior screening performance, especially when structurally heterogeneous datasets are to be processed

Measles on the Edge: Coastal Heterogeneities and Infection Dynamics

Mathematical models can help elucidate the spatio-temporal dynamics of epidemics as well as the impact of control measures. The gravity model for directly transmitted diseases is currently one of the most parsimonious models for spatial epidemic spread. This model uses distance-weighted, population size-dependent coupling to estimate host movement and disease incidence in metapopulations. The model captures overall measles dynamics in terms of underlying human movement in pre-vaccination England and Wales (previously established). In spatial models, edges often present a special challenge. Therefore, to test the model's robustness, we analyzed gravity model incidence predictions for coastal cities in England and Wales. Results show that, although predictions are accurate for inland towns, they significantly underestimate coastal persistence. We examine incidence, outbreak seasonality, and public transportation records, to show that the model's inaccuracies stem from an underestimation of total contacts per individual along the coast. We rescue this predicted ‘edge effect’ by increasing coastal contacts to approximate the number of per capita inland contacts. These results illustrate the impact of ‘edge effects’ on epidemic metapopulations in general and illustrate directions for the refinement of spatiotemporal epidemic models