Inter-and Intra-Site Genetic Diversity of Natural Field Populations of Rice Tungro Bacilliform Virus in the Philippines

The genetic structure of rice tungro bacilliform virus (RTBV) populations within and between growing sites was analyzed in a collection of natural field isolates from different rice varieties grown in eight tungro-endemic sites of the Philippines. Total DNA extracts from 345 isolates were digested with EcoRV restriction enzyme and hybridized with a full-length probe of RTBV, a procedure shown in preliminary experiments capable of revealing high levels of polymorphism in RTBV field isolates. In the total population, 17 distinct EcoRV-based genome profiles (genotypes) were identified and used as indicators for virus diversity. Distinct sets of genotypes occurred in Isabela and North Cotabato provinces suggesting a geographic isolation of virus populations. However, among the sites in each province, there were few significant differences in the genotype compositions of virus populations. The number of genotypes detected at a site varied from two to nine with a few genotypes dominating. In general the isolates at a site persisted from season to season indicating a genetic stability for the local virus population. Over the sampling time, IRRI rice varieties, which have green leafhopper resistance genes, supported similar virus populations to those supported by other varieties, indicating that the variety of the host exerted no apparent selection pressures. Insect transmission experiments on selected RTBV field isolates showed that dramatic shifts in genotype and phenotype distributions can occur in response to host /environmental shifts.

Genetic Composition and Complexity of Virus Populations at Tungro-Endemic and Outbreak Rice Sites

We have recently demonstrated the geographic isolation of rice tungro bacilliform virus (RTBV) populations in the tungro-endemic provinces of Isabela and North Cotabato, Philippines. In this study, we examined the genetic structure of the virus populations at the tungro-outbreak sites of Lanao del Norte, a province adjacent to North Cotabato. We also analyzed the virus populations at the tungro-endemic sites of Subang, Indonesia, and Dien Khanh, Vietnam. Total DNA extracts from 274 isolates were digested with EcoRV restriction enzyme and hybridized with a full-length probe of RTBV. In the total population, 22 EcoRV-restricted genome profiles (genotypes) were identified. Although overlapping genotypes could be observed, the outbreak sites of Lanao del Norte had a genotype combination distinct from that of Subang or Dien Khanh but a genotype combination similar to that identified earlier from North Cotabato, the adjacent endemic province. Sequence analysis of the intergenic region and part of the ORF1 RTBV genome from randomly selected genotypes confirms the geographic clustering of RTBV genotypes and, combined with restriction analysis, the results suggest a fragmented spatial distribution of RTBV local populations in the three countries. Because RTBV depends on rice tungro spherical virus (RTSV) for transmission, the population dynamics of both tungro viruses were then examined at the endemic and outbreak sites within the Philippines. The RTBV genotypes and the coat protein RTSV genotypes were used as indicators for virus diversity. A shift in population structure of both viruses was observed at the outbreak sites with a reduced RTBV but increased RTSV gene diversity

Expected values for pedometer-determined physical activity in older populations

The purpose of this review is to update expected values for pedometer-determined physical activity in free-living healthy older populations. A search of the literature published since 2001 began with a keyword (pedometer, "step counter," "step activity monitor" or "accelerometer AND steps/day") search of PubMed, Cumulative Index to Nursing & Allied Health Literature (CINAHL), SportDiscus, and PsychInfo. An iterative process was then undertaken to abstract and verify studies of pedometer-determined physical activity (captured in terms of steps taken; distance only was not accepted) in free-living adult populations described as ≥ 50 years of age (studies that included samples which spanned this threshold were not included unless they provided at least some appropriately age-stratified data) and not specifically recruited based on any chronic disease or disability. We identified 28 studies representing at least 1,343 males and 3,098 females ranging in age from 50–94 years. Eighteen (or 64%) of the studies clearly identified using a Yamax pedometer model. Monitoring frames ranged from 3 days to 1 year; the modal length of time was 7 days (17 studies, or 61%). Mean pedometer-determined physical activity ranged from 2,015 steps/day to 8,938 steps/day. In those studies reporting such data, consistent patterns emerged: males generally took more steps/day than similarly aged females, steps/day decreased across study-specific age groupings, and BMI-defined normal weight individuals took more steps/day than overweight/obese older adults. The range of 2,000–9,000 steps/day likely reflects the true variability of physical activity behaviors in older populations. More explicit patterns, for example sex- and age-specific relationships, remain to be informed by future research endeavors.

Expected values for steps/day in special populations

Objective To assemble expected values for free-living steps/day in special populations living with chronic illnesses and disabilities. Method Studies identified since 2000 were categorized into similar illnesses and disabilities, capturing the original reference, sample descriptions, descriptions of instruments used (i.e., pedometers, piezoelectric pedometers, accelerometers), number of days worn, and mean and standard deviation of steps/day. Results Sixty unique studies represented: 1) heart and vascular diseases, 2) chronic obstructive lung disease, 3) diabetes and dialysis, 4) breast cancer, 5) neuromuscular diseases, 6) arthritis, joint replacement, and fibromyalgia, 7) disability (including mental retardation/intellectual difficulties), and 8) other special populations. A median steps/day was calculated for each category. Waist-mounted and ankle-mounted instruments were considered separately due to fundamental differences in assessment properties. For waist-mounted instruments, the lowest median values for steps/day are found in disabled older adults (1214 steps/day) followed by people living with COPD (2237 steps/day). The highest values were seen in individuals with Type 1 diabetes (8008 steps/day), mental retardation/intellectual disability (7787 steps/day), and HIV (7545 steps/day). Conclusion This review will be useful to researchers/practitioners who work with individuals living with chronic illness and disability and require such information for surveillance, screening, intervention, and program evaluation purposes. Keywords: Exercise; Walking; Ambulatory monitoring

Occurrence of iron and associated bacterial populations in soils of a forested subtropical coastal catchment

Iron (Fe) biogeochemistry is potentially of environmental significance in plantation-forested, subtropical coastal ecosystems where soil disturbance and seasonal water logging may lead to elevation of Fe mobilization and associated water quality deterioration. Using wet-chemical extraction and laboratory cultivation, we examined the occurrence of Fe forms and associated bacterial populations in diverse soils of a representative subtropical Australian coastal catchment (Poona Creek). Total reactive Fe was abundant throughout 0e30 cm soil cores, consisting primarily of crystalline forms in well-drained sand soils and water-logged loam soils, whereas in water-logged, low clay soils, over half of total reactive Fe was present in poorly-crystalline forms due to organic and inorganic complexation, respectively. Forestry practices such as plantation clear-felling and replanting, seasonal water logging and mineral soil properties significantly impacted soil organic carbon (C), potentially-bioavailable Fe pools and densities of S-, but not Fe-, bacterial populations. Bacterial Fe(III) reduction and abiotic Fe(II) oxidation, as well as chemolithotrophic S oxidation and aerobic, heterotrophic respiration were integral to catchment terrestrial FeeC cycling. This work demonstrates bacterial involvement in terrestrial Fe cycling in a subtropical coastal circumneutral-pH ecosystem.

Look before you leap : a confidence-based method for selecting species criticality while avoiding negative populations in τ-leaping

The stochastic simulation algorithm was introduced by Gillespie and in a different form by Kurtz. There have been many attempts at accelerating the algorithm without deviating from the behavior of the simulated system. The crux of the explicit τ-leaping procedure is the use of Poisson random variables to approximate the number of occurrences of each type of reaction event during a carefully selected time period, τ. This method is acceptable providing the leap condition, that no propensity function changes “significantly” during any time-step, is met. Using this method there is a possibility that species numbers can, artificially, become negative. Several recent papers have demonstrated methods that avoid this situation. One such method classifies, as critical, those reactions in danger of sending species populations negative. At most, one of these critical reactions is allowed to occur in the next time-step. We argue that the criticality of a reactant species and its dependent reaction channels should be related to the probability of the species number becoming negative. This way only reactions that, if fired, produce a high probability of driving a reactant population negative are labeled critical. The number of firings of more reaction channels can be approximated using Poisson random variables thus speeding up the simulation while maintaining the accuracy. In implementing this revised method of criticality selection we make use of the probability distribution from which the random variable describing the change in species number is drawn. We give several numerical examples to demonstrate the effectiveness of our new method.

Identifying parent perspectives to guide active travel intervention with small populations : case study in Denver, Colorado

This paper investigates a strategy for guiding school-based active travel intervention. School-based active travel programs address the travel behaviors and perceptions of small target populations (i.e., at individual schools) so they can encourage people to walk or bike. Thus, planners need to know as much as possible about the behaviors and perceptions of their target populations. However, existing strategies for modeling travel behavior and segmenting audiences typically work with larger populations and may not capture the attitudinal diversity of smaller groups. This case study used Q technique to identify salient travel-related attitude types among parents at an elementary school in Denver, Colorado; 161 parents presented their perspectives about school travel by rank-ordering 36 statements from strongly disagree to strongly agree in a normalized distribution, single centered around no opinion. Thirty-nine respondents' cases were selected for case-wise cluster analysis in SPSS according to criteria that made them most likely to walk: proximity to school, grade, and bus service. Analysis revealed five core perspectives that were then correlated with the larger respondent pool: optimistic walkers, fair-weather walkers, drivers of necessity, determined drivers, and fence sitters. Core perspectives are presented—characterized by parents' opinions, personal characteristics, and reported travel behaviors—and recommendations are made for possible intervention approaches. The study concludes that Q technique provides a fine-grained assessment of travel behavior for small populations, which would benefit small-scale behavioral interventions

Models of collective cell motion for cell populations with different aspect ratio : diffusion, proliferation and travelling waves

Continuum, partial differential equation models are often used to describe the collective motion of cell populations, with various types of motility represented by the choice of diffusion coefficient, and cell proliferation captured by the source terms. Previously, the choice of diffusion coefficient has been largely arbitrary, with the decision to choose a particular linear or nonlinear form generally based on calibration arguments rather than making any physical connection with the underlying individual-level properties of the cell motility mechanism. In this work we provide a new link between individual-level models, which account for important cell properties such as varying cell shape and volume exclusion, and population-level partial differential equation models. We work in an exclusion process framework, considering aligned, elongated cells that may occupy more than one lattice site, in order to represent populations of agents with different sizes. Three different idealizations of the individual-level mechanism are proposed, and these are connected to three different partial differential equations, each with a different diffusion coefficient; one linear, one nonlinear and degenerate and one nonlinear and nondegenerate. We test the ability of these three models to predict the population level response of a cell spreading problem for both proliferative and nonproliferative cases. We also explore the potential of our models to predict long time travelling wave invasion rates and extend our results to two dimensional spreading and invasion. Our results show that each model can accurately predict density data for nonproliferative systems, but that only one does so for proliferative systems. Hence great care must be taken to predict density data for with varying cell shape.

How does the size and shape of local populations in China compare to general anthropometric surveys currently used for product design?

Anthropometry has long been used for a range of ergonomic applications & product design. Although products are often designed for specific cohorts, anthropometric data are typically sourced from large scale surveys representative of the general population. Additionally, few data are available for emerging markets like China and India. This study measured 80 Chinese males that were representative of a specific cohort targeted for the design of a new product. Thirteen anthropometric measurements were recorded and compared to two large databases that represented a general population, a Chinese database and a Western database. Substantial differences were identified between the Chinese males measured in this study and both databases. The subjects were substantially taller, heavier and broader than subjects in the older Chinese database. However, they were still substantially smaller, lighter and thinner than Western males. Data from current Western anthropometric surveys are unlikely to accurately represent the target population for product designers and manufacturers in emerging markets like China.