Whole Genome Sequencing Reveals Local Transmission Patterns of Mycobacterium bovis in Sympatric Cattle and Badger Populations

Whole genome sequencing (WGS) technology holds great promise as a tool for the forensic epidemiology of bacterial pathogens. It is likely to be particularly useful for studying the transmission dynamics of an observed epidemic involving a largely unsampled 'reservoir' host, as for bovine tuberculosis (bTB) in British and Irish cattle and badgers. BTB is caused by Mycobacterium bovis, a member of the M. tuberculosis complex that also includes the aetiological agent for human TB. In this study, we identified a spatio-temporally linked group of 26 cattle and 4 badgers infected with the same Variable Number Tandem Repeat (VNTR) type of M. bovis. Single-nucleotide polymorphisms (SNPs) between sequences identified differences that were consistent with bacterial lineages being persistent on or near farms for several years, despite multiple clear whole herd tests in the interim. Comparing WGS data to mathematical models showed good correlations between genetic divergence and spatial distance, but poor correspondence to the network of cattle movements or within-herd contacts. Badger isolates showed between zero and four SNP differences from the nearest cattle isolate, providing evidence for recent transmissions between the two hosts. This is the first direct genetic evidence of M. bovis persistence on farms over multiple outbreaks with a continued, ongoing interaction with local badgers. However, despite unprecedented resolution, directionality of transmission cannot be inferred at this stage. Despite the often notoriously long timescales between time of infection and time of sampling for TB, our results suggest that WGS data alone can provide insights into TB epidemiology even where detailed contact data are not available, and that more extensive sampling and analysis will allow for quantification of the extent and direction of transmission between cattle and badgers. © 2012 Biek et al.

Seasonality of Plasmodium falciparum transmission: a systematic review

Background: Although Plasmodium falciparum transmission frequently exhibits seasonal patterns, the drivers of malaria seasonality are often unclear. Given the massive variation in the landscape upon which transmission acts, intra-annual fluctuations are likely influenced by different factors in different settings. Further, the presence of potentially substantial inter-annual variation can mask seasonal patterns; it may be that a location has "strongly seasonal" transmission and yet no single season ever matches the mean, or synoptic, curve. Accurate accounting of seasonality can inform efficient malaria control and treatment strategies. In spite of the demonstrable importance of accurately capturing the seasonality of malaria, data required to describe these patterns is not universally accessible and as such localized and regional efforts at quantifying malaria seasonality are disjointed and not easily generalized. 

Methods: The purpose of this review was to audit the literature on seasonality of P. falciparum and quantitatively summarize the collective findings. Six search terms were selected to systematically compile a list of papers relevant to the seasonality of P. falciparum transmission, and a questionnaire was developed to catalogue the manuscripts. 

Results and discussion: 152 manuscripts were identified as relating to the seasonality of malaria transmission, deaths due to malaria or the population dynamics of mosquito vectors of malaria. Among these, there were 126 statistical analyses and 31 mechanistic analyses (some manuscripts did both). 

Discussion: Identified relationships between temporal patterns in malaria and climatological drivers of malaria varied greatly across the globe, with different drivers appearing important in different locations. Although commonly studied drivers of malaria such as temperature and rainfall were often found to significantly influence transmission, the lags between a weather event and a resulting change in malaria transmission also varied greatly by location. 

Conclusions: The contradicting results of studies using similar data and modelling approaches from similar locations as well as the confounding nature of climatological covariates underlines the importance of a multi-faceted modelling approach that attempts to capture seasonal patterns at both small and large spatial scales.

Exploiting Human Resource Requirements to Infer Human Movement Patterns for Use in Modelling Disease Transmission Systems: An Example from Eastern Province, Zambia

In this research, an agent-based model (ABM) was developed to generate human movement routes between homes and water resources in a rural setting, given commonly available geospatial datasets on population distribution, land cover and landscape resources. ABMs are an object-oriented computational approach to modelling a system, focusing on the interactions of autonomous agents, and aiming to assess the impact of these agents and their interactions on the system as a whole. An A* pathfinding algorithm was implemented to produce walking routes, given data on the terrain in the area. A* is an extension of Dijkstra's algorithm with an enhanced time performance through the use of heuristics. In this example, it was possible to impute daily activity movement patterns to the water resource for all villages in a 75 km long study transect across the Luangwa Valley, Zambia, and the simulated human movements were statistically similar to empirical observations on travel times to the water resource (Chi-squared, 95% confidence interval). This indicates that it is possible to produce realistic data regarding human movements without costly measurement as is commonly achieved, for example, through GPS, or retrospective or real-time diaries. The approach is transferable between different geographical locations, and the product can be useful in providing an insight into human movement patterns, and therefore has use in many human exposure-related applications, specifically epidemiological research in rural areas, where spatial heterogeneity in the disease landscape, and space-time proximity of individuals, can play a crucial role in disease spread.

Statistical Eigenmode Transmission for the MU-MIMO Downlink in Rician Fading

In this paper, we study the achievable ergodic sum-rate of multiuser multiple-input multiple-output downlink systems in Rician fading channels. We first derive a lower bound on the average signal-to-leakage-and-noise ratio by using the Mullen’s inequality, and then use it to analyze the effect of channel mean information on the achievable ergodic sum-rate. A novel statistical-eigenmode space-division multiple-access (SESDMA) downlink transmission scheme is then proposed. For this scheme, we derive an exact analytical closed-form expression for the achievable ergodic rate and present tractable tight upper and lower bounds. Based on our analysis, we gain valuable insights into the system parameters, such as the number of transmit antennas, the signal-to-noise ratio (SNR) and Rician K-factor on the system sum-rate. Results show that the sum-rate converges to a saturation value in the high SNR regime and tends to a lower limit for the low Rician K-factor case. In addition, we compare the achievable ergodic sum-rate between SE-SDMA and zeroforcing beamforming with perfect channel state information at the base station. Our results reveal that the rate gap tends to zero in the high Rician K-factor regime. Finally, numerical results are presented to validate our analysis.

Soft-core Stream Processor for Sliding Window Applications

Software-programmable `soft' processors have shown tremendous potential for efficient realisation of high performance signal processing operations on Field Programmable Gate Array (FPGA), whilst lowering the design burden by avoiding the need to design fine-grained custom circuit archi-tectures. However, the complex data access patterns, high memory bandwidth and computational requirements of sliding window applications, such as Motion Estimation (ME) and Matrix Multiplication (MM), lead to low performance, inefficient soft processor realisations. This paper resolves this issue, showing how by adding support for block data addressing and accelerators for high performance loop execution, performance and resource efficiency over four times better than current best-in-class metrics can be achieved. In addition, it demonstrates the first recorded real-time soft ME estimation realisation for H.263 systems.

Beam division multiple access transmission for massive MIMO communications

We study multicarrier multiuser multiple-input multiple-output (MU-MIMO) systems, in which the base station employs an asymptotically large number of antennas. We analyze a fully correlated channel matrix and provide a beam domain channel model, where the channel gains are independent of sub-carriers. For this model, we first derive a closed-form upper bound on the achievable ergodic sum-rate, based on which, we develop asymptotically necessary and sufficient conditions for optimal downlink transmission that require only statistical channel state information at the transmitter. Furthermore, we propose a beam division multiple access (BDMA) transmission scheme that simultaneously serves multiple users via different beams. By selecting users within non-overlapping beams, the MU-MIMO channels can be equivalently decomposed into multiple single-user MIMO channels; this scheme significantly reduces the overhead of channel estimation, as well as, the processing complexity at transceivers. For BDMA transmission, we work out an optimal pilot design criterion to minimize the mean square error (MSE) and provide optimal pilot sequences by utilizing the Zadoff-Chu sequences. Simulations demonstrate the near-optimal performance of BDMA transmission and the advantages of the proposed pilot sequences.

A Fast Analysis Method for the Groove Gap Waveguide Using Transmission Line Theory

The Groove Gap Waveguide (GGW) shows a behavior similar to the classical rectangular waveguide (RWG), but it is formed by two pieces which do not require metal contact. This feature suggests the GGW as a suitable alternative to the RGW for mm-wave frequencies, where ensuring the proper metal contact according to the wavelength size results challenging. Nevertheless, there is a lack of effective analysis tools for the complex GGW topology, and assuming a direct equivalence between the RGW and the GGW is too rough, so that dilatory full-wave simulations are required. This work presents a fast analysis method based on transmission line theory, which establishes the proper correspondence between the GGW and the RWG. In addition, below cutoff behavior of the GGW is studied for the first time. Several numerical tests and two manufactured prototypes validate the proposed method, which seems very adequate to optimize future GGW structures.

Passive Intermodulation of Analog and Digital Signals on Transmission Lines with Distributed Nonlinearities: Modelling and Characterization

Passive intermodulation (PIM) often limits the performance of communication systems with analog and digitally-modulated signals and especially of systems supporting multiple carriers. Since the origins of the apparently multiple physical sources of nonlinearity causing PIM are not fully understood, the behavioral models are frequently used to describe the process of PIM generation. In this paper a polynomial model of memoryless nonlinearity is deduced from PIM measurements of a microstrip line with distributed nonlinearity with two-tone CW signals. The analytical model of nonlinearity is incorporated in Keysight Technology’s ADS simulator to evaluate the metrics of signal fidelity in the receive band for analog and digitally-modulated signals. PIM-induced distortion and cross-band interference with modulated signals are compared to those with two-tone CW signals. It is shown that conventional metrics can be applied to quantify the effect of distributed nonlinearities on signal fidelity. It is found that the two-tone CW test provides a worst-case estimate of cross-band interference for two-carrier modulated signals whereas with a three-carrier signal PIM interference in the receive band is noticeably overestimated. The simulated constellation diagrams for QPSK signals demonstrate that PIM interference exhibits the distinctive signatures of correlated distortion and this indicates that there are opportunities for mitigating PIM interference and that PIM interference cannot be treated as noise. One of the interesting results is that PIM distortion on a transmission line results in asymmetrical regrowth of output PIM interference for modulated signals.

Real-Time Multiple Event Detection and Classification Using Moving Window PCA

This paper proposes a method for the detection and classification of multiple events in an electrical power system in real-time, namely; islanding, high frequency events (loss of load) and low frequency events (loss of generation). This method is based on principal component analysis of frequency measurements and employs a moving window approach to combat the time-varying nature of power systems, thereby increasing overall situational awareness of the power system. Numerical case studies using both real data, collected from the UK power system, and simulated case studies, constructed using DigSilent PowerFactory, for islanding events, as well as both loss of load and generation dip events, are used to demonstrate the reliability of the proposed method.

Power Spectral Density Side-Channel Attack Overlapping Window Method

Cryptographic algorithms have been designed to be computationally secure, however it has been shown that when they are implemented in hardware, that these devices leak side channel information that can be used to mount an attack that recovers the secret encryption key. In this paper an overlapping window power spectral density (PSD) side channel attack, targeting an FPGA device running the Advanced Encryption Standard is proposed. This improves upon previous research into PSD attacks by reducing the amount of pre-processing (effort) required. It is shown that the proposed overlapping window method requires less processing effort than that of using a sliding window approach, whilst overcoming the issues of sampling boundaries. The method is shown to be effective for both aligned and misaligned data sets and is therefore recommended as an improved approach in comparison with existing time domain based correlation attacks.

Variable Window Power Spectral Density Attack

Side channel attacks permit the recovery of the secret key held within a cryptographic device. This paper presents a new EM attack in the frequency domain, using a power spectral density analysis that permits the use of variable spectral window widths for each trace of the data set and demonstrates how this attack can therefore overcome both inter-and intra-round random insertion type countermeasures. We also propose a novel re-alignment method exploiting the minimal power markers exhibited by electromagnetic emanations. The technique can be used for the extraction and re-alignment of round data in the time domain.