Risk factors for the introduction and within-herd transmission of Mycobacterium avium subspecies paratuberculosis (MAP) infection in 59 Irish dairy herds

Since 1994, Irish cattle have been exposed to greater risks of acquiring Mycobacterium avium subspecies paratuberculosis (MAP) infection as a consequence of the importation of over 70,000 animals from continental Europe. In recent years, there has been an increase in the number of reported clinical cases of paratuberculosis in Ireland. This study examines the prevalence of factors that promote the introduction and within-herd transmission of Mycobacterium avium subspecies paratuberculosis (MAP) on selected Irish dairy farms in the Cork region, and the association between these factors and the results of MAP screening tests on milk sock filter residue (MFR). A total of 59 dairy farms, selected using non-random methods but apparently free of endemic paratuberculosis, were enrolled into the study. A questionnaire was used to collect data about risk factors for MAP introduction and transmission. The MFR was assessed on six occasions over 24 months for the presence of MAP, using culture and immunomagnetic separation prior to polymerase chain reaction (IMS-PCR). Furthermore, blood samples from all entire male and female animals over one year of age in 20 herds were tested by ELISA. Eighteen (31%) farms had operated as closed herds since 1994, 28 (47%) had purchased from multiple sources and 14 (24%) had either direct or indirect (progeny) contact with imported animals. Milk and colostrum were mixed on 51% of farms, while 88% of farms fed pooled milk. Thirty (51%) herds tested negative to MFR culture and IMS-PCR, 12 (20%) were MFR culture positive, 26 (44%) were IMS-PCR positive and seven (12%) were both culture and IMS-PCR positive. The probability of a positive MFR culture was significantly associated with reduced attendance at calving, and with increased use of individual calf pens and increased (but not significantly) if multiple suckling was practised. There was poor agreement between MFR culture and MFR IMS-PCR results, but moderate agreement between MFR culture and ELISA test results. This study highlights a lack of awareness among Irish dairy farmers about the effect of inadequate biosecurity on MAP introduction. Furthermore, within-herd transmission will be facilitated by traditional calf rearing and waste management practices. The findings of viable MAP in the presence of known transmission factors in non-clinically affected herds could be a prelude to long-term problems for the Irish cattle and agri-business generally.

Two-Stage Transmitter Precoding Based on Data-Driven Code Hopping and Partial Zero Forcing Beamforming for MC-DCMA Communications

This paper proposes a hybrid transmission technique based on adaptive code-to-user allocation and linear precoding for the downlink of phase shift keying (PSK) based multi-carrier code division multiple access (MC-CDMA) systems. The proposed scheme is based on the separation of the instantaneous multiple access interference (MAI) into constructive and destructive components taking into account the dependency on both the channel variation and the instantaneous symbol values of the active users. The first stage of the proposed technique is to adaptively distribute the available spreading sequences to the users on a symbol-by-symbol basis in the form of codehopping with the objective to steer the users' instantaneous crosscorrelations to yield a favourable constructive to destructive MAI ratio. The second stage is to employ a partial transmitter based zero forcing (ZF) scheme specifically designed for the exploitation of constructive MAI. The partial ZF processing decorrelates destructive interferers, while users that interfere constructively remain correlated. This results in a signal to interference-plus-noise ratio (SINR) enhancement without the need for additional power-per-user investment. It will be shown in the results section that significant bit error rate (BER) performance benefits can be achieved with this technique.

Infection-control strategies for preventing the transmission of meticillin-resistant Staphylococcus aureus (MRSA) in nursing homes for older people (Review)

Background: Nursing homes for older people provide an environment likely to promote the acquisition and spread of meticillin-resistant Staphylococcus aureus (MRSA), putting residents at increased risk of colonisation and infection. It is recognised that infection control strategies are important in preventing and controlling MRSA transmission.

Objectives: The objective of this review was to determine the effects of infection control strategies for preventing the transmission of MRSA in nursing homes for older people.

Search strategy: We searched the Cochrane Central Register of Controlled Trials (CENTRAL, The Cochrane Library 2009, Issue 2), the Cochrane Wounds Group Specialised Register (searched May 29th, 2009). We also searched MEDLINE (from 1950 to May Week 4 2009), Ovid EMBASE (1980 to 2009 Week 21), EBSCO CINAHL (1982 to May Week 4 2009), British Nursing Index (1985 to May 2009), DARE (1992 to May 2009), Web of Science (1981 to May 2009), and the Health Technology Assessment (HTA) website (1988 to May 2009). Research in progress was sought through Current Clinical Trials (www.controlled-trials.com), Medical Research Council Research portfolio, and HSRPRoj (current USA projects). SIGLE was also searched in order to identify atypical material which was not accessible through more conventional sources.

Selection criteria: All randomised and controlled clinical trials, controlled before and after studies and interrupted time series studies of infection control interventions in nursing homes for older people were eligible for inclusion.

Data collection and analysis: Two authors independently reviewed the results of the searches.

Main results: Since no studies met the selection criteria, neither a meta-analysis nor a narrative description of studies was possible.

Authors' conclusions: The lack of studies in this field is surprising. Nursing homes for older people provide an environment likely to promote the acquisition and spread of infection, with observational studies repeatedly reporting that being a resident of a nursing home increases the risk of MRSA colonisation. Much of the evidence for recently-issued United Kingdom guidelines for the control and prevention of MRSA in health care facilities was generated in the acute care setting. It may not be possible to transfer such strategies directly to the nursing home environment, which serves as both a healthcare setting and a resident's home. Rigorous studies should be conducted in nursing homes, to test interventions that have been specifically designed for this unique environment.

The effects of climate change on ovine parasitic gastroenteritis determined using veterinary surveillance and meteorological data for Northern Ireland over the period 1999-2009

While the influence of temperature and moisture on the free-living stages of gastrointestinal nematodes have been described in detail, and evidence for global climate change is mounting, there have been only a few attempts to relate altered incidence or seasonal patterns of disease to climate change. Studies of this type have been completed for England Scotland and Wales, but not for Northern Ireland (NI). Here we present an analysis of veterinary diagnostic data that relates three categories of gastrointestinal nematode infection in sheep to historical meteorological data for NI. The infections are: trichostrongylosis/teladorsagiosis (Teladorsagia/Trichostrongylus), strongyloidosis and nematodirosis. This study aims to provide a baseline for future climate change analyses and to provide basic information for the development of nematode control programmes. After identifying and evaluating possible sources of bias, climate change was found to be the most likely explanation for the observed patterns of change in parasite epidemiology, although other hypotheses could not be refuted. Seasonal rates of diagnosis showed a uniform year-round distribution for Teladorsagia and Trichostrongylus infections, suggesting consistent levels of larval survival throughout the year and extension of the traditionally expected seasonal transmission windows. Nematodirosis showed a higher level of autumn than Spring infection, suggesting that suitable conditions for egg and larval development occurred after the Spring infection period. Differences between regions within the Province were shown for strongyloidosis, with peaks of infection falling in the period September-November. For all three-infection categories (trichostrongylosis/teladorsagiosis, strongyloidosis and nematodirosis), significant differences in the rates of diagnosis, and in the seasonality of disease, were identified between regions. (C) 2012 Elsevier B.V. All rights reserved.

MALTS: A Tool to Simulate Lorentz Transmission Electron Microscopy From Micromagnetic Simulations

Here we describe the development of the MALTS software which is a generalized tool that simulates Lorentz Transmission Electron Microscopy (LTEM) contrast of magnetic nanostructures. Complex magnetic nanostructures typically have multiple stable domain structures. MALTS works in conjunction with the open access micromagnetic software Object Oriented Micromagnetic Framework or MuMax. Magnetically stable trial magnetization states of the object of interest are input into MALTS and simulated LTEM images are output. MALTS computes the magnetic and electric phases accrued by the transmitted electrons via the Aharonov-Bohm expressions. Transfer and envelope functions are used to simulate the progression of the electron wave through the microscope lenses. The final contrast image due to these effects is determined by Fourier Optics. Similar approaches have been used previously for simulations of specific cases of LTEM contrast. The novelty here is the integration with micromagnetic codes via a simple user interface enabling the computation of the contrast from any structure. The output from MALTS is in good agreement with both experimental data and published LTEM simulations. A widely-available generalized code for the analysis of Lorentz contrast is a much needed step towards the use of LTEM as a standardized laboratory technique.

Next generation femtocells: An enabler for high efficiency multimedia transmission

The first generation of femtocells is evolving to the next generation with many more capabilities in terms of better utilisation of radio resources and support of high data rates. It is thus logical to conjecture that with these abilities and their inherent suitability for home environment, they stand out as an ideal enabler for delivery of high efficiency multimedia services. This paper presents a comprehensive vision towards this objective and extends the concept of femtocells from indoor to outdoor environments, and strongly couples femtocells to emergency and safety services. It also presents and identifies relevant issues and challenges that have to be overcome in realization of this vision.

Transmission Potential of Rift Valley Fever virus over the course of the 2010 epidemic in South Africa

A Rift Valley fever (RVF) epidemic affecting animals on domestic livestock farms was reported in South Africa during January-August 2010. The first cases occurred after heavy rainfall, and the virus subsequently spread countrywide. To determine the possible effect of environmental conditions and vaccination on RVF virus transmissibility, we estimated the effective reproduction number (R) for the virus over the course of the epidemic by extending the Wallinga and Teunis algorithm with spatial information. Re reached its highest value in mid-February and fell below unity around mid-March, when vaccination coverage was 7.5%-45.7% and vector-suitable environmental conditions were maintained. The epidemic fade-out likely resulted first from the immunization of animals following natural infection or vaccination. The decline in vector-suitable environmental conditions from April onwards and further vaccination helped maintain R below unity. Increased availability of vaccine use data would enable evaluation of the effect of RVF vaccination campaigns.

Piezoelectric properties of PbTiO(3) thin films characterized with piezoresponse force and high resolution transmission electron microscopy

In this paper we investigate the piezoelectric properties of PbTiO(3) thin films grown by pulsed laser deposition with piezoresponse force microscopy and transmission electron microscopy. The as-grown films exhibit an upward polarization, inhomogeneous distribution of piezoelectric characteristics concerning local coercive fields, and piezoelectric coefficient. In fact, the data obtained reveal imprints during piezoresponse force microscopy measurements, nonlinearity in the piezoelectric deformation, and limited polarization reversal. Moreover, transmission electron microscopy shows the presence of defects near the film/substrate interface, which can be associated with the variations of piezoelectric properties.

Infection control strategies for preventing the transmission of meticillin-resistant Staphylococcus aureus (MRSA) in nursing homes for older people (Review)

Background: Nursing homes for older people provide an environment likely to promote the acquisition and spread of meticillin-resistant Staphylococcus aureus (MRSA), putting residents at increased risk of colonisation and infection. It is recognised that infection prevention and control strategies are important in preventing and controlling MRSA transmission.

Objectives: To determine the effects of infection prevention and control strategies for preventing the transmission of MRSA in nursing homes for older people.

Search methods: In August 2013, for this third update, we searched the Cochrane Wounds Group Specialised Register, the Cochrane Central Register of Controlled Trials (CENTRAL, The Cochrane Library), Database of Abstracts of Reviews of Effects (DARE, The Cochrane Library), Ovid MEDLINE, OVID MEDLINE (In-process and Other Non-Indexed Citations), Ovid EMBASE, EBSCO CINAHL, Web of Science and the Health Technology Assessment (HTA) website. Research in progress was sought through Current Clinical Trials, Gateway to Reseach, and HSRProj (Health Services Research Projects in Progress).

Selection criteria: All randomised and controlled clinical trials, controlled before and after studies and interrupted time series studies of infection prevention and control interventions in nursing homes for older people were eligible for inclusion.

Data collection and analysis: Two review authors independently reviewed the results of the searches. Another review author appraised identified papers and undertook data extraction which was checked by a second review author.

Main results: For this third update only one study was identified, therefore it was not possible to undertake a meta-analysis. A cluster randomised controlled trial in 32 nursing homes evaluated the effect of an infection control education and training programme on MRSA prevalence. The primary outcome was MRSA prevalence in residents and staff, and a change in infection control audit scores which measured adherence to infection control standards. At the end of the 12 month study, there was no change in MRSA prevalence between intervention and control sites, while mean infection control audit scores were significantly higher in the intervention homes compared with control homes.

Authors' conclusions: There is a lack of research evaluating the effects on MRSA transmission of infection prevention and control strategies in nursing homes. Rigorous studies should be conducted in nursing homes, involving residents and staff to test interventions that have been specifically designed for this unique environment.

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.

Multilayer optimization in radio resource allocation for the packet transmission in wireless networks

Na última década tem-se assistido a um crescimento exponencial das redes de comunicações sem fios, nomeadamente no que se refere a taxa de penetração do serviço prestado e na implementação de novas infra-estruturas em todo o globo. É ponto assente neste momento que esta tendência irá não só continuar como se fortalecer devido à convergência que é esperada entre as redes móveis sem fio e a disponibilização de serviços de banda larga para a rede Internet fixa, numa evolução para um paradigma de uma arquitectura integrada e baseada em serviços e aplicações IP. Por este motivo, as comunicações móveis sem fios irão ter um papel fundamental no desenvolvimento da sociedade de informação a médio e longo prazos. A estratégia seguida no projecto e implementação das redes móveis celulares da actual geração (2G e 3G) foi a da estratificação da sua arquitectura protocolar numa estrutura modular em camadas estanques, onde cada camada do modelo é responsável pela implementação de um conjunto de funcionalidades. Neste modelo a comunicação dá-se apenas entre camadas adjacentes através de primitivas de comunicação pré-estabelecidas. Este modelo de arquitectura resulta numa mais fácil implementação e introdução de novas funcionalidades na rede. Entretanto, o facto das camadas inferiores do modelo protocolar não utilizarem informação disponibilizada pelas camadas superiores, e vice-versa acarreta uma degradação no desempenho do sistema. Este paradigma é particularmente importante quando sistemas de antenas múltiplas são implementados (sistemas MIMO). Sistemas de antenas múltiplas introduzem um grau adicional de liberdade no que respeita a atribuição de recursos rádio: o domínio espacial. Contrariamente a atribuição de recursos no domínio do tempo e da frequência, no domínio espacial os recursos rádio mapeados no domínio espacial não podem ser assumidos como sendo completamente ortogonais, devido a interferência resultante do facto de vários terminais transmitirem no mesmo canal e/ou slots temporais mas em feixes espaciais diferentes. Sendo assim, a disponibilidade de informação relativa ao estado dos recursos rádio às camadas superiores do modelo protocolar é de fundamental importância na satisfação dos critérios de qualidade de serviço exigidos. Uma forma eficiente de gestão dos recursos rádio exige a implementação de algoritmos de agendamento de pacotes de baixo grau de complexidade, que definem os níveis de prioridade no acesso a esses recursos por base dos utilizadores com base na informação disponibilizada quer pelas camadas inferiores quer pelas camadas superiores do modelo. Este novo paradigma de comunicação, designado por cross-layer resulta na maximização da capacidade de transporte de dados por parte do canal rádio móvel, bem como a satisfação dos requisitos de qualidade de serviço derivados a partir da camada de aplicação do modelo. Na sua elaboração, procurou-se que o standard IEEE 802.16e, conhecido por Mobile WiMAX respeitasse as especificações associadas aos sistemas móveis celulares de quarta geração. A arquitectura escalonável, o baixo custo de implementação e as elevadas taxas de transmissão de dados resultam num processo de multiplexagem de dados e valores baixos no atraso decorrente da transmissão de pacotes, os quais são atributos fundamentais para a disponibilização de serviços de banda larga. Da mesma forma a comunicação orientada à comutação de pacotes, inenente na camada de acesso ao meio, é totalmente compatível com as exigências em termos da qualidade de serviço dessas aplicações. Sendo assim, o Mobile WiMAX parece satisfazer os requisitos exigentes das redes móveis de quarta geração. Nesta tese procede-se à investigação, projecto e implementação de algoritmos de encaminhamento de pacotes tendo em vista a eficiente gestão do conjunto de recursos rádio nos domínios do tempo, frequência e espacial das redes móveis celulares, tendo como caso prático as redes móveis celulares suportadas no standard IEEE802.16e. Os algoritmos propostos combinam métricas provenientes da camada física bem como os requisitos de qualidade de serviço das camadas superiores, de acordo com a arquitectura de redes baseadas no paradigma do cross-layer. O desempenho desses algoritmos é analisado a partir de simulações efectuadas por um simulador de sistema, numa plataforma que implementa as camadas física e de acesso ao meio do standard IEEE802.16e.

Advanced energy efficient coordinated multi-point transmission for OFDMA

The ever-growing energy consumption in mobile networks stimulated by the expected growth in data tra ffic has provided the impetus for mobile operators to refocus network design, planning and deployment towards reducing the cost per bit, whilst at the same time providing a signifi cant step towards reducing their operational expenditure. As a step towards incorporating cost-eff ective mobile system, 3GPP LTE-Advanced has adopted the coordinated multi-point (CoMP) transmission technique due to its ability to mitigate and manage inter-cell interference (ICI). Using CoMP the cell average and cell edge throughput are boosted. However, there is room for reducing energy consumption further by exploiting the inherent exibility of dynamic resource allocation protocols. To this end packet scheduler plays the central role in determining the overall performance of the 3GPP longterm evolution (LTE) based on packet-switching operation and provide a potential research playground for optimizing energy consumption in future networks. In this thesis we investigate the baseline performance for down link CoMP using traditional scheduling approaches, and subsequently go beyond and propose novel energy e fficient scheduling (EES) strategies that can achieve power-e fficient transmission to the UEs whilst enabling both system energy effi ciency gain and fairness improvement. However, ICI can still be prominent when multiple nodes use common resources with di fferent power levels inside the cell, as in the so called heterogeneous networks (Het- Net) environment. HetNets are comprised of two or more tiers of cells. The rst, or higher tier, is a traditional deployment of cell sites, often referred to in this context as macrocells. The lower tiers are termed small cells, and can appear as microcell, picocells or femtocells. The HetNet has attracted signiffi cant interest by key manufacturers as one of the enablers for high speed data at low cost. Research until now has revealed several key hurdles that must be overcome before HetNets can achieve their full potential: bottlenecks in the backhaul must be alleviated, as well as their seamless interworking with CoMP. In this thesis we explore exactly the latter hurdle, and present innovative ideas on advancing CoMP to work in synergy with HetNet deployment, complemented by a novel resource allocation policy for HetNet tighter interference management. As system level simulator has been used to analyze the proposed algorithm/protocols, and results have concluded that up to 20% energy gain can be observed.

Acoustic-oceanographic data fusion for prediction of oceanic acoustic elds

Tese de doutoramento, Engenharia Electrónica e Telecomunicações (Processamento de Sinal), Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2014