Ecological dynamics of emerging bat virus spillover

Viruses that originate in bats may be the most notorious emerging zoonoses that spill over from wildlife into domestic animals and humans. Understanding how these infections filter through ecological systems to cause disease in humans is of profound importance to public health. Transmission of viruses from bats to humans requires a hierarchy of enabling conditions that connect the distribution of reservoir hosts, viral infection within these hosts, and exposure and susceptibility of recipient hosts. For many emerging bat viruses, spillover also requires viral shedding from bats, and survival of the virus in the environment. Focusing on Hendra virus, but also addressing Nipah virus, Ebola virus, Marburg virus and coronaviruses, we delineate this cross-species spillover dynamic from the within-host processes that drive virus excretion to land-use changes that increase interaction among species. We describe how land-use changes may affect co-occurrence and contact between bats and recipient hosts. Two hypotheses may explain temporal and spatial pulses of virus shedding in bat populations: episodic shedding from persistently infected bats or transient epidemics that occur as virus is transmitted among bat populations. Management of livestock also may affect the probability of exposure and disease. Interventions to decrease the probability of virus spillover can be implemented at multiple levels from targeting the reservoir host to managing recipient host exposure and susceptibility.

Phenotyping novel stay-green traits to capture genetic variation in senescence dynamics

Stay-green plants retain green leaves longer after anthesis and can have improved yield, particularly under water limitation. As senescence is a dynamic process, genotypes with different senescence patterns may exhibit similar final normalised difference vegetative index (NDVI). By monitoring NDVI from as early as awn emergence to maturity, we demonstrate that analysing senescence dynamics improves insight into genotypic stay-green variation. A senescence evaluation tool was developed to fit a logistic function to NDVI data and used to analyse data from three environments for a wheat (Triticum aestivum L.) population whose lines contrast for stay-green. Key stay-green traits were estimated including, maximum NDVI, senescence rate and a trait integrating NDVI variation after anthesis, as well as the timing from anthesis to onset, midpoint and conclusion of senescence. The integrative trait and the timing to onset and mid-senescence exhibited high positive correlations with yield and a high heritability in the three studied environments. Senescence rate was correlated with yield in some environments, whereas maximum NDVI was associated with yield in a drought-stressed environment. Where resources preclude frequent measurements, we found that NDVI measurements may be restricted to the period of rapid senescence, but caution is required when dealing with lines of different phenology. In contrast, regular monitoring during the whole period after flowering allows the estimation of senescence dynamics traits that may be reliably compared across genotypes and environments. We anticipate that selection for stay-green traits will enhance genetic progress towards high-yielding, stay-green germplasm.

Early-season movement dynamics of phytophagous pest and natural enemies across a native vegetation-crop ecotone

There is limited understanding about how insect movement patterns are influenced by landscape features, and how landscapes can be managed to suppress pest phytophage populations in crops. Theory suggests that the relative timing of pest and natural enemy arrival in crops may influence pest suppression. However, there is a lack of data to substantiate this claim. We investigate the movement patterns of insects from native vegetation (NV) and discuss the implications of these patterns for pest control services. Using bi-directional interception traps we quantified the number of insects crossing an NV/crop ecotone relative to a control crop/crop interface in two agricultural regions early in the growing season. We used these data to infer patterns of movement and net flux. At the community-level, insect movement patterns were influenced by ecotone in two out of three years by region combinations. At the functional-group level, pests and parasitoids showed similar movement patterns from NV very soon after crop emergence. However, movement across the control interface increased towards the end of the early-season sampling period. Predators consistently moved more often from NV into crops than vice versa, even after crop emergence. Not all species showed a significant response to ecotone, however when a response was detected, these species showed similar patterns between the two regions. Our results highlight the importance of NV for the recruitment of natural enemies for early season crop immigration that may be potentially important for pest suppression. However, NV was also associated with crop immigration by some pest species. Hence, NV offers both opportunities and risks for pest management. The development of targeted NV management may reduce the risk of crop immigration by pests, but not of natural enemies.

Eurasian large mammal dynamics in response to changing environments during the Late Neogene

Nisäkkäiden levinneisyyteen, niiden morfologisiin ja ekologisiin piirteisiin vaikuttavat ympäristön sekä lyhyet että pitkäkestoiset muutokset, etenkin ilmaston ja kasvillisuuden vaihtelut. Työssä tutkittiin nisäkkäiden sopeutumista ilmastonmuutoksiin Euraasiassa viimeisen 24 miljoonan vuoden aikana. Tutkimuksessa keskityttiin varsinkin viimeiseen kahteen miljoonaan vuoteen, jonka aikana ilmasto muuttui voimakkaasti ja ihmisen toiminta alkoi tulla merkittäväksi. Tämän takia on usein vaikea erottaa, kummasta em. seikasta jonkin nisäkäslajin sukupuutto tai häviäminen alueelta johtui. Aineistona käytettiin laajaa venäjänkielistä kirjallisuutta, josta löytyvät tiedot ovat kääntämättöminä jääneet aiemmin länsimaisen tutkimuksen ulkopuolelle. Työssä käytettiin myös NOW-tietokantaa, jossa on fossiilisten nisäkkäiden löytöpaikat sekä niiden iät.

Weed dynamics as influenced by tillage system, sowing time and weed competition duration in dry-seeded rice

Cultural practices alter patterns of crop growth and can modify dynamics of weed-crop competition, and hence need to be investigated to evolve sustainable weed management in dry-seeded rice (DSR). Studies on weed dynamics in DSR sown at different times under two tillage systems were conducted at the Agronomic Research Farm, University of Agriculture, Faisalabad, Pakistan. A commonly grown fine rice cultivar 'Super Basmati' was sown on 15th June and 7th July of 2010 and 2011 under zero-till (ZT) and conventional tillage (CONT) and it was subjected to different durations of weed competition [10, 20, 30, 40, and 50 days after sowing (DAS) and season-long competition]. Weed-free plots were maintained under each tillage system and sowing time for comparison. Grassy weeds were higher under ZT while CONT had higher relative proportion of broad-leaved weeds in terms of density and biomass. Density of sedges was higher by 175% in the crop sown on the 7th July than on the 15th June. Delaying sowing time of DSR from mid June to the first week of July reduced weed density by 69 and 43% but their biomass remained unaffected. Tillage systems had no effect on total weed biomass. Plots subjected to season-long weed competition had mostly grasses while broad-leaved weeds were not observed at harvest. In the second year of study, dominance of grassy weeds was increased under both tillage systems and sowing times. Significantly less biomass (48%) of grassy weeds was observed under CONT than ZT in 2010; however, during 2011, this effect was non-significant. Trianthema portulacastrum and Dactyloctenium aegyptium were the dominant broad-leaved and grassy weeds, respectively. Cyperus rotundus was the dominant sedge weed, especially in the crop sown on the 7th July. Relative yield loss (RYL) ranged from 3 to 13% and 7 to16% when weeds were allowed to compete only for 20 DAS. Under season-long weed competition, RYL ranged from 68 to 77% in 2010 and 74 to80% in 2011. The sowing time of 15th June was effective in minimizing weed proliferation and rectifying yield penalty associated with the 7th July sowing. The results suggest that DSR in Pakistan should preferably be sown on 15th June under CONT systems and weeds must be controlled before 20 DAS to avoid yield losses. Successful adoption of DSR at growers' fields in Pakistan will depend on whether growers can control weeds and prevent shifts in weed population from intractable weeds to more difficult-to-control weeds as a consequence of DSR adoption.

Regularized numerical integration of multibody dynamics with the generalized alpha method*

This paper discusses the consistent regularization property of the generalized α method when applied as an integrator to an initial value high index and singular differential-algebraic equation model of a multibody system. The regularization comes from within the discretization itself and the discretization remains consistent over the range of values the regularization parameter may take. The regularization involves increase of the smallest singular values of the ill-conditioned Jacobian of the discretization and is different from Baumgarte and similar techniques which tend to be inconsistent for poor choice of regularization parameter. This regularization also helps where pre-conditioning the Jacobian by scaling is of limited effect, for example, when the scleronomic constraints contain multiple closed loops or singular configuration or when high index path constraints are present. The feed-forward control in Kane's equation models is additionally considered in the numerical examples to illustrate the effect of regularization. The discretization presented in this work is adopted to the first order DAE system (unlike the original method which is intended for second order systems) for its A-stability and same order of accuracy for positions and velocities.

Population dynamics of Thaumastocoris peregrinus in Eucalyptus plantations of South Africa

Thaumastocoris peregrinus is a sap-sucking insect that infests non-native Eucalyptus plantations in Africa, New Zealand, South America and parts of Southern Europe, in addition to street trees in parts of its native range of Australia. In South Africa, pronounced fluctuations in the population densities have been observed. To characterise spatiotemporal variability in T. peregrinus abundance and the factors that might influence it, we monitored adult population densities at six sites in the main eucalypt growing regions of South Africa. At each site, twenty yellow sticky traps were monitored weekly for 30 months, together with climatic data. We also characterised the influence of temperature on growth and survival experimentally and used this to model how temperature may influence population dynamics. T. peregrinus was present throughout the year at all sites, with annual site-specific peaks in abundance. Peaks occurred during autumn (February–April) for the Pretoria site, summer (November–January) for the Zululand site and spring (August–October) for the Tzaneen, Sabie and Piet Retief monitoring sites. Temperature (both experimental and field-collected), humidity and rainfall were mostly weakly, or not at all, associated with population fluctuations. It is clear that a complex interaction of these and other factors (e.g. host quality) influence population fluctuations in an annual, site specific cycle. The results obtained not only provide insights into the biology of T. peregrinus, but will also be important for future planning of monitoring and control programs using semiochemicals, chemical insecticides or biological control agents.

Ecological dynamics of emerging bat virus spillover

Viruses that originate in bats may be the most notorious emerging zoonoses that spill over from wildlife into domestic animals and humans. Understanding how these infections filter through ecological systems to cause disease in humans is of profound importance to public health. Transmission of viruses from bats to humans requires a hierarchy of enabling conditions that connect the distribution of reservoir hosts, viral infection within these hosts, and exposure and susceptibility of recipient hosts. For many emerging bat viruses, spillover also requires viral shedding from bats, and survival of the virus in the environment. Focusing on Hendra virus, but also addressing Nipah virus, Ebola virus, Marburg virus and coronaviruses, we delineate this cross-species spillover dynamic from the within-host processes that drive virus excretion to land-use changes that increase interaction among species. We describe how land-use changes may affect co-occurrence and contact between bats and recipient hosts. Two hypotheses may explain temporal and spatial pulses of virus shedding in bat populations: episodic shedding from persistently infected bats or transient epidemics that occur as virus is transmitted among bat populations. Management of livestock also may affect the probability of exposure and disease. Interventions to decrease the probability of virus spillover can be implemented at multiple levels from targeting the reservoir host to managing recipient host exposure and susceptibility.

Effect of water quality and season on the population dynamics of Cabomba caroliniana in subtropical Queensland, Australia

Cabomba caroliniana is a submersed aquatic macrophyte that originates from the Americas and is currently invading temperate, subtropical, and tropical freshwater habitats around the world. Despite being a nuisance in many countries, little is known about its ecology. We monitored C. caroliniana populations in three reservoirs in subtropical Queensland, Australia, over 5.5 years. Although biomass, stem length, and plant density of the C. caroliniana stands fluctuated over time, they did not exhibit clear seasonal patterns. Water depth was the most important environmental factor explaining C. caroliniana abundance. Plant biomass was greatest at depths from 2–4 m and rooted plants were not found beyond 5 m. Plant density was greatest in shallow water and decreased with depth, most likely as a function of decreasing light and increasing physical stress. We tested the effect of a range of water physico-chemical parameters. The concentration of phosphorus in the water column was the variable that explained most of the variation in C. caroliniana population parameters. We found that in subtropical Australia, C. caroliniana abundance does not appear to be affected by seasonal conditions but is influenced by other environmental variables such as water depth and nutrient loading. Therefore, further spread will more likely be governed by local habitat rather than climatic conditions.

Effect of water quality and season on the population dynamics of Cabomba caroliniana in subtropical Queensland, Australia

Cabomba caroliniana is a submersed aquatic macrophyte that originates from the Americas and is currently invading temperate, subtropical, and tropical freshwater habitats around the world. Despite being a nuisance in many countries, little is known about its ecology. We monitored C. caroliniana populations in three reservoirs in subtropical Queensland, Australia, over 5.5 years. Although biomass, stem length, and plant density of the C. caroliniana stands fluctuated over time, they did not exhibit clear seasonal patterns. Water depth was the most important environmental factor explaining C. caroliniana abundance. Plant biomass was greatest at depths from 2–4 m and rooted plants were not found beyond 5 m. Plant density was greatest in shallow water and decreased with depth, most likely as a function of decreasing light and increasing physical stress. We tested the effect of a range of water physico-chemical parameters. The concentration of phosphorus in the water column was the variable that explained most of the variation in C. caroliniana population parameters. We found that in subtropical Australia, C. caroliniana abundance does not appear to be affected by seasonal conditions but is influenced by other environmental variables such as water depth and nutrient loading. Therefore, further spread will more likely be governed by local habitat rather than climatic conditions.

Bayesian analysis of community dynamics

Elucidating the mechanisms responsible for the patterns of species abundance, diversity, and distribution within and across ecological systems is a fundamental research focus in ecology. Species abundance patterns are shaped in a convoluted way by interplays between inter-/intra-specific interactions, environmental forcing, demographic stochasticity, and dispersal. Comprehensive models and suitable inferential and computational tools for teasing out these different factors are quite limited, even though such tools are critically needed to guide the implementation of management and conservation strategies, the efficacy of which rests on a realistic evaluation of the underlying mechanisms. This is even more so in the prevailing context of concerns over climate change progress and its potential impacts on ecosystems. This thesis utilized the flexible hierarchical Bayesian modelling framework in combination with the computer intensive methods known as Markov chain Monte Carlo, to develop methodologies for identifying and evaluating the factors that control the structure and dynamics of ecological communities. These methodologies were used to analyze data from a range of taxa: macro-moths (Lepidoptera), fish, crustaceans, birds, and rodents. Environmental stochasticity emerged as the most important driver of community dynamics, followed by density dependent regulation; the influence of inter-specific interactions on community-level variances was broadly minor. This thesis contributes to the understanding of the mechanisms underlying the structure and dynamics of ecological communities, by showing directly that environmental fluctuations rather than inter-specific competition dominate the dynamics of several systems. This finding emphasizes the need to better understand how species are affected by the environment and acknowledge species differences in their responses to environmental heterogeneity, if we are to effectively model and predict their dynamics (e.g. for management and conservation purposes). The thesis also proposes a model-based approach to integrating the niche and neutral perspectives on community structure and dynamics, making it possible for the relative importance of each category of factors to be evaluated in light of field data.

Neutron Scattering and Molecular Dynamics Evidence for Levitation Effect in Nanopores

Neutron Scattering and Molecular Dynamics Evidence for Levitation Effect in Nanopores ... Neutron scattering measurements and molecular dynamics simulations have been carried out on the three isomers of pentane (neopentane (neo), isopentane (iso), and n-pentane (n-)) adsorbed in zeolite NaY. ... In order to understand this surprising dependence, the dimensionless levitation parameter, γ, for atomic systems may be modified to suit molecular systems.

Understanding the information dynamics of medication administration in residential aged care facilities (RACFs): A prerequisite for design of effective ICT systems

Medication information is a critical part of the information required to ensure residents' safety in the highly collaborative care context of RACFs. Studies report poor medication information as a barrier to improve medication management in RACFs. Research exploring medication work practices in aged care settings remains limited. This study aimed to identify contextual and work practice factors contributing to breakdowns in medication information exchange in RACFs in relation to the medication administration process. We employed non-participant observations and semi-structured interviews to explore information practices in three Australian RACFs. Findings identified inefficiencies due to lack of information timeliness, manual stock management, multiple data transcriptions, inadequate design of essential documents such as administration sheets and a reliance on manual auditing procedures. Technological solutions such as electronic medication administration records offer opportunities to overcome some of the identified problems. However these interventions need to be designed to align with the collaborative team based processes they intend to support.