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Spatial dynamics of TB within a highly urbanised Asian metropolis using point patterns.

ABSTRACT: Singapore is a high-income country in a region with a high prevalence of tuberculosis. The Singapore Tuberculosis (TB) Elimination Program (STEP) was set up in 1997, and the better surveillance and clinical management practices initiated under STEP led to a decade-long decline in the incidence levels. However, incidence rates started to rise again since 2008. The reasons for this rise are unclear. This study involved a spatial analysis of the epidemiology of TB among Singapore residents. More than 30 000 cases reported during 1995-2011 and their residential addresses were analysed for spatial risk and spatial clustering, using spatial point pattern methodology. The principal factor responsible for the increasing resident TB incidence in Singapore is the changing age profile of the population. In particular the burgeoning population aged above 65 years accounts for the increase in reported cases. Singapore's population has one of the world's lowest fertility and mortality rates, and the elderly population is projected to grow substantially over the next few decades. Tuberculosis rates may therefore continue to rise even with static or improving case management and surveillance.

SUBMITTER: Das S

PROVIDER: S-EPMC5428374 | biostudies-literature | 2017 Feb

REPOSITORIES: biostudies-literature

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Spatial dynamics of TB within a highly urbanised Asian metropolis using point patterns.

Das Sourav S Cook Alex R AR Wah Win W Win Khin Mar Kyi KM Chee Cynthia Bin Eng CB Wang Yee Tang YT Yang Hsu Li L

Scientific reports 20170224 1

Singapore is a high-income country in a region with a high prevalence of tuberculosis. The Singapore Tuberculosis (TB) Elimination Program (STEP) was set up in 1997, and the better surveillance and clinical management practices initiated under STEP led to a decade-long decline in the incidence levels. However, incidence rates started to rise again since 2008. The reasons for this rise are unclear. This study involved a spatial analysis of the epidemiology of TB among Singapore residents. More th ...[more]

PMID: 28232734

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Project description:BackgroundIn order to effectively combat Tuberculosis, resources to diagnose and treat TB should be allocated effectively to the areas and population that need them. Although a wealth of subnational data on TB is routinely collected to support local planning, it is often underutilized. Therefore, this study uses spatial analytical techniques and profiling to understand and identify factors underlying spatial variation in TB case notification rates (CNR) in Bangladesh, Nepal and Pakistan for better TB program planning.MethodsSpatial analytical techniques and profiling was used to identify subnational patterns of TB CNRs at the district level in Bangladesh (N = 64, 2015), Nepal (N = 75, 2014) and Pakistan (N = 142, 2015). A multivariable linear regression analysis was performed to assess the association between subnational CNR and demographic and health indicators associated with TB burden and indicators of TB programme efforts. To correct for spatial dependencies of the observations, the residuals of the multivariable models were tested for unexplained spatial autocorrelation. Spatial autocorrelation among the residuals was adjusted for by fitting a simultaneous autoregressive model (SAR).ResultsSpatial clustering of TB CNRs was observed in all three countries. In Bangladesh, TB CNR were found significantly associated with testing rate (0.06%, p < 0.001), test positivity rate (14.44%, p < 0.001), proportion of bacteriologically confirmed cases (- 1.33%, p < 0.001) and population density (4.5*10-3%, p < 0.01). In Nepal, TB CNR were associated with population sex ratio (1.54%, p < 0.01), facility density (- 0.19%, p < 0.05) and treatment success rate (- 3.68%, p < 0.001). Finally, TB CNR in Pakistan were found significantly associated with testing rate (0.08%, p < 0.001), positivity rate (4.29, p < 0.001), proportion of bacteriologically confirmed cases (- 1.45, p < 0.001), vaccination coverage (1.17%, p < 0.001) and facility density (20.41%, p < 0.001).ConclusionSubnational TB CNRs are more likely reflective of TB programme efforts and access to healthcare than TB burden. TB CNRs are better used for monitoring and evaluation of TB control efforts than the TB epidemic. Using spatial analytical techniques and profiling can help identify areas where TB is underreported. Applying these techniques routinely in the surveillance facilitates the use of TB CNRs in program planning.

Project description:The Australian backyard mosquito, Aedes notoscriptus, is a highly urbanised pest species that has invaded New Zealand and the USA. Importantly, Ae. notoscriptus has been implicated as a vector of Ross River virus, a common and arthritogenic arbovirus in Australia, and is a laboratory vector of numerous other pathogenic viruses, including West Nile, yellow fever, and Zika viruses. To further explore live viruses harboured by field populations of Ae. notoscriptus and, more specifically, assess the genetic diversity of its virome, we processed 495 pools, comprising a total of 6,674 female Ae. notoscriptus collected across fifteen suburbs in Brisbane, Australia, between January 2018 and May 2019. Nine virus isolates were recovered and characterised by metagenomic sequencing and phylogenetics. The principal viral family represented was Flaviviridae. Known viruses belonging to the genera Flavivirus, Orbivirus, Mesonivirus, and Nelorpivirus were identified together with two novel virus species, including a divergent Thogoto-like orthomyxovirus and an insect-specific flavivirus. Among these, we recovered three Stratford virus (STRV) isolates and an isolate of Wongorr virus (WGRV), which for these viral species is unprecedented for the geographical area of Brisbane. Thus, the documented geographical distribution of STRV and WGRV, both known for their respective medical and veterinary importance, has now been expanded to include this major urban centre. Phylogenies of the remaining five viruses, namely, Casuarina, Ngewotan, the novel Thogoto-like virus, and two new flavivirus species, suggested they are insect-specific viruses. None of these viruses have been previously associated with Ae. notoscriptus or been reported in Brisbane. These findings exemplify the rich genetic diversity and viral abundance within the Ae. notoscriptus virome and further highlight this species as a vector of concern with the potential to transmit viruses impacting human or animal health. Considering it is a common pest and vector in residential areas and is expanding its global distribution, ongoing surveillance, and ecological study of Ae. notoscriptus, together with mapping of its virome and phenotypic characterisation of isolated viruses, is clearly warranted. Immanently, these initiatives are essential for future understanding of both the mosquito virome and the evolution of individual viral species.

Project description:Animal behavior is highly structured. Yet, structured behavioral patterns-or "statistical ethograms"-are not immediately apparent from the full spatiotemporal data that behavioral scientists usually collect. Here, we introduce a framework to quantitatively characterize rodent behavior during spatial (e.g., maze) navigation, in terms of movement building blocks or motor primitives. The hypothesis that we pursue is that rodent behavior is characterized by a small number of motor primitives, which are combined over time to produce open-ended movements. We assume motor primitives to be organized in terms of two sparsity principles: each movement is controlled using a limited subset of motor primitives (sparse superposition) and each primitive is active only for time-limited, time-contiguous portions of movements (sparse activity). We formalize this hypothesis using a sparse dictionary learning method, which we use to extract motor primitives from rodent position and velocity data collected during spatial navigation, and successively to reconstruct past trajectories and predict novel ones. Three main results validate our approach. First, rodent behavioral trajectories are robustly reconstructed from incomplete data, performing better than approaches based on standard dimensionality reduction methods, such as principal component analysis, or single sparsity. Second, the motor primitives extracted during one experimental session generalize and afford the accurate reconstruction of rodent behavior across successive experimental sessions in the same or in modified mazes. Third, in our approach the number of motor primitives associated with each maze correlates with independent measures of maze complexity, hence showing that our formalism is sensitive to essential aspects of task structure. The framework introduced here can be used by behavioral scientists and neuroscientists as an aid for behavioral and neural data analysis. Indeed, the extracted motor primitives enable the quantitative characterization of the complexity and similarity between different mazes and behavioral patterns across multiple trials (i.e., habit formation). We provide example uses of this computational framework, showing how it can be used to identify behavioural effects of maze complexity, analyze stereotyped behavior, classify behavioral choices and predict place and grid cell displacement in novel environments.

Project description:BackgroundUrbanisation has facilitated changes in the hydrological cycle, sediment dynamics and habitat loss and it has had a tremendous impact on river ecosystems. Moreover, the invasion of non-native species reduces the number of native species with the progress of urbanisation, thereby resulting in the homogenisation of fish fauna and significant decrease in diversity. However, the effects of urbanisation on fish fauna vary depending on the region, degree of urbanisation and number of years since the construction of the city. Hence, it is necessary to collect information on how fish fauna changes due to urbanisation in different regions. The target site of the present study is the Tsurumi River, of which approximately 85% of the basin is urbanised and many of the river channels have been affected by straightening and concrete channelling. Monitoring of biota has been conducted mainly in downstream areas; however, data on fish fauna in upstream areas and tributaries of the river, which have been substantially affected by urbanisation, are lacking.New informationSurveys were conducted at 71 sites in the Tsurumi River Basin during summers and winters, focusing on river channels that have been straightened or converted to concrete channels due to urbanisation. As a result of this investigation, 10 families, 28 species and 9,335 individuals were collected. Some of the fish collected included rare species, such as Tanakialanceolata, Lefuaechigonia and Pseudobagrustokiensis, indicating that, even in rivers that have been severely impacted by human activities, there are still rare indigenous species living there, albeit in limited numbers. In addition, Misgurnus sp. (clade B2), Micropterussalmoides, Lepomismacrochirus and Poeciliareticulata were confirmed to be non-native species. Misgurnus sp. (clade B2) was widespread; however, populations of carnivorous non-native alien species were small. The data are all accessible from the document "database_fish_urban_tsurumi" (https://ipt.pensoft.net/manage/resource?r=database_fish_urban_tsurumi).

Dataset Information

Spatial dynamics of TB within a highly urbanised Asian metropolis using point patterns.

Publications

Spatial dynamics of TB within a highly urbanised Asian metropolis using point patterns.

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