Modelling potential energy surfaces for small clusters using Shepard interpolation with Gaussian-form nodal functions.

The potential energy surface (PES) of a chemical system is an analytical function that outputs the potential energy of the system when a nuclear configuration is given as input. The PESs of small atmospheric clusters have theoretical as well as environmental significance. A common method used to generate analytical PESs is the Shepard interpolation, where the PES is a weighed sum of Taylor series expansions (nodal functions) at ab initio sample points. Based on this, in this study we present a new method based on the Shepard interpolation, where the nodal functions are composed of a symmetric Gaussian term and an asymmetric exponential term in each dimension. Corresponding sampling methods were also developed. We tested the method on several atmospheric bimolecular clusters and achieved root mean square errors (RMSE) below 0.13 kJ mol-1 in 150 samples for Ar-rigid H2O and Ne-rigid CO2, and below 0.39 kJ mol-1 in 1800 samples for rigid N2-rigid CO2.

Successful establishment of Wolbachia in Aedes populations to suppress dengue transmission.

Genetic manipulations of insect populations for pest control have been advocated for some time, but there are few cases where manipulated individuals have been released in the field and no cases where they have successfully invaded target populations. Population transformation using the intracellular bacterium Wolbachia is particularly attractive because this maternally-inherited agent provides a powerful mechanism to invade natural populations through cytoplasmic incompatibility. When Wolbachia are introduced into mosquitoes, they interfere with pathogen transmission and influence key life history traits such as lifespan. Here we describe how the wMel Wolbachia infection, introduced into the dengue vector Aedes aegypti from Drosophila melanogaster, successfully invaded two natural A. aegypti populations in Australia, reaching near-fixation in a few months following releases of wMel-infected A. aegypti adults. Models with plausible parameter values indicate that Wolbachia-infected mosquitoes suffered relatively small fitness costs, leading to an unstable equilibrium frequency <30% that must be exceeded for invasion. These findings demonstrate that Wolbachia-based strategies can be deployed as a practical approach to dengue suppression with potential for area-wide implementation.

Comparing Vibrationally Averaged Nuclear Shielding Constants by Quantum Diffusion Monte Carlo and Second-Order Perturbation Theory.

Using the method of modified Shepard's interpolation to construct potential energy surfaces of the H2O, O3, and HCOOH molecules, we compute vibrationally averaged isotropic nuclear shielding constants ⟨σ⟩ of the three molecules via quantum diffusion Monte Carlo (QDMC). The QDMC results are compared to that of second-order perturbation theory (PT), to see if second-order PT is adequate for obtaining accurate values of nuclear shielding constants of molecules with large amplitude motions. ⟨σ⟩ computed by the two approaches differ for the hydrogens and carbonyl oxygen of HCOOH, suggesting that for certain molecules such as HCOOH where big displacements away from equilibrium happen (internal OH rotation), ⟨σ⟩ of experimental quality may only be obtainable with the use of more sophisticated and accurate methods, such as quantum diffusion Monte Carlo. The approach of modified Shepard's interpolation is also extended to construct shielding constants σ surfaces of the three molecules. By using a σ surface with the equilibrium geometry as a single data point to compute isotropic nuclear shielding constants for each descendant in the QDMC ensemble representing the ground state wave function, we reproduce the results obtained through ab initio computed σ to within statistical noise. Development of such an approach could thereby alleviate the need for any future costly ab initio σ calculations.

The combined fragmentation and systematic molecular fragmentation methods.

Conspectus Chemistry, particularly organic chemistry, is mostly concerned with functional groups: amines, amides, alcohols, ketones, and so forth. This is because the reactivity of molecules can be categorized in terms of the reactions of these functional groups, and by the influence of other adjacent groups in the molecule. These simple truths ought to be reflected in the electronic structure and electronic energy of molecules, as reactivity is determined by electronic structure. However, sophisticated ab initio quantum calculations of the molecular electronic energy usually do not make these truths apparent. In recent years, several computational chemistry groups have discovered methods for estimating the electronic energy as a sum of the energies of small molecular fragments, or small sets of groups. By decomposing molecules into such fragments of adjacent functional groups, researchers can estimate the electronic energy to chemical accuracy; not just qualitative trends, but accurate enough to understand reactivity. In addition, this has the benefit of cutting down on both computational time and cost, as the necessary calculation time increases rapidly with an increasing number of electrons. Even with steady advances in computer technology, progress in the study of large molecules is slow. In this Account, we describe two related "fragmentation" methods for treating molecules, the combined fragmentation method (CFM) and systematic molecular fragmentation (SMF). In addition, we show how we can use the SMF approach to estimate the energy and properties of nonconducting crystals, by fragmenting the periodic crystal structure into relatively small pieces. A large part of this Account is devoted to simple overviews of how the methods work. We also discuss the application of these approaches to calculating reactivity and other useful properties, such as the NMR and vibrational spectra of molecules and crystals. These applications rely on the ability of these fragmentation methods to accurately estimate derivatives of the molecular and crystal energies. Finally, to provide some common applications of CFM and SMF, we present some specific examples of energy calculations for moderately large molecules. For computational chemists, this fragmentation approach represents an important practical advance. It reduces the computer time required to estimate the energies of molecules so dramatically, that accurate calculations of the energies and reactivity of very large organic and biological molecules become feasible.

Modelling Water: A Lifetime Enigma.

The first attempt to describe water dates back to 1933 with the Bernal-Fowler model and it would take another forty years before the first computer simulation of liquid water by Barker and Watts in 1969. Since then, over a hundred different water models have been proposed. Despite being widely studied, water remains poorly understood. Examining the evolution of water models, we identified three distinct philosophies in water modelling, namely the employment of effective point charges in pioneering empirical models, the incorporation of polarization to describe many-body inductive effects and the extensive use of ab initio calculations to describe short-range effects. In doing so, we can appraise the current understanding of water and identify attributes that a water model should possess to capture the intricate interactions between water molecules.

Ab initio NMR chemical-shift calculations based on the combined fragmentation method.

NMR chemical shift is a molecular property that can be computed from first principles. In this work we show that by utilizing our combined fragmentation method (CFM), one is able to accurately compute this property for small proteins. Without nonbonded interactions, the root mean square errors (RMSEs) compared to the full calculations for (1)H, (13)C, (15)N, (17)O and (33)S were 0.340, 0.649, 3.052, 6.928 and 0.122 ppm respectively, while with the inclusion of nonbonded interactions the RMSEs for (1)H, (13)C, (15)N, (17)O and (33)S were 0.038, 0.253, 0.681, 3.480 and 0.052 ppm respectively.

A half-century record of coral skeletal P/Ca reveals late 20th century nutrient pollution in Port Dickson, Malaysia.

Anthropogenic nutrient pollution has been identified as one of the key stressors of coastal ecosystems. However, the paucity of long-term nutrient records limits our understanding of both the extent of nutrient pollution as well as of the ecological impacts. Here, using coral skeletal phosphorus (P/Ca), we reconstructed a half-a-century record of seawater phosphate at Port Dickson, Malaysia. The P/Ca in the coral revealed an up to 8-fold increase in coral P/Ca from the late 1970s to 2000s, likely linked to increases in fertilizer use (R2 = 0.47) and variabilities in rainfall (R2 = 0.17). The rise in coral P/Ca in coincided with a contemporaneous 18 % decrease in coral skeletal density, suggesting phosphate enrichment may impact the growth and structural integrity of reef-building corals. Given the importance of both agriculture and heavy reliance on coral reefs by populations in Southeast Asia, our study highlights continue the need to develop environmental management upstream of coastal zones.

Accurately reproducing ab initio electrostatic potentials with multipoles and fragmentation.

In this work, we show that our energy based fragmentation method (Bettens, R. P. A.; Lee, A. M. J. Phys. Chem. A 2006, 110, 8777) accurately reproduces the electrostatic potential for a selection of peptides, both charged and uncharged, and other molecules of biological interest at the solvent accessible surface and beyond when compared with the full ab initio or density functional theory electrostatic potential. We also consider the ability of various point charge models to reproduce the full electrostatic potential and compare the results to our fragmentation electrostatic potentials with the latter being significantly superior. We demonstrate that our fragmentation approach can be readily applied to very large systems and provide the fragmentation electrostatic potential for the neuraminidase tetramer (ca. 24,000 atom system) at the MP2/6-311(+)G(2d,p) level. We also show that by using at least distributed monopoles, dipoles, and quadrupoles at atomic sites in the fragment molecules an essentially identical electrostatic potential to that given by the fragmentation electrostatic potential at and beyond the solvent accessible surface can be obtained.

Genetic structure of Aedes aegypti in Australia and Vietnam revealed by microsatellite and exon primed intron crossing markers suggests feasibility of local control options.

The distribution of Aedes aegypti (L.) in Australia is currently restricted to northern Queensland, but it has been more extensive in the past. In this study, we evaluate the genetic structure of Ae. aegypti populations in Australia and Vietnam and consider genetic differentiation between mosquitoes from these areas and those from a population in Thailand. Six microsatellites and two exon primed intron crossing markers were used to assess isolation by distance across all populations and also within the Australian sample. Investigations of founder effects, amount of molecular variation between and within regions and comparison of F(ST) values among Australian and Vietnamese populations were made to assess the scale of movement ofAe. aegypti. Genetic control methods are under development for mosquito vector populations including the dengue vector Ae. aegypti. The success of these control methods will depend on the population structure of the target species including population size and rates of movement among populations. Releases of modified mosquitoes could target local populations that show a high degree of isolation from surrounding populations, potentially allowing new variants to become established in one region with eventual dispersal to other regions.

Evaluations of mosquito age grading techniques based on morphological changes.

Evaluations were made of the accuracy and practicality of mosquito age grading methods based on changes to mosquito morphology; including the Detinova ovarian tracheation, midgut meconium, Polovodova ovariole dilatation, ovarian injection, and daily growth line methods. Laboratory maintained Aedes vigilax (Skuse) and Culex annulirostris (Skuse) females of known chronological and physiological ages were used for these assessments. Application of the Detinova technique to laboratory reared Ae. vigilax females in a blinded trial enabled the successful identification of nulliparous and parous females in 83.7-89.8% of specimens. The success rate for identifying nulliparous females increased to 87.8-98.0% when observations of ovarian tracheation were combined with observations of the presence of midgut meconium. However, application of the Polovodova method only enabled 57.5% of nulliparous, 1-parous, 2-parous, and 3-parous Ae. vigilax females to be correctly classified, and ovarian injections were found to be unfeasible. Poor correlation was observed between the number of growth lines per phragma and the calendar age of laboratory reared Ae. vigilax females. In summary, morphological age grading methods that offer simple two-category predictions (ovarian tracheation and midgut meconium methods) were found to provide high-accuracy classifications, whereas methods that offer the separation of multiple age categories (ovariolar dilatation and growth line methods) were found to be extremely difficult and of low accuracy. The usefulness of the morphology-based methods is discussed in view of the availability of new mosquito age grading techniques based on cuticular hydrocarbon and gene transcription changes.

Sublethal effects of mosquito larvicides on swimming performance of larvivorous fish Melanotaenia duboulayi (Atheriniformes: Melanotaeniidae).

Laboratory studies were conducted to determine the sublethal effects of exposure to selected larvicides on the critical swimming speed (Ucrit) of crimson-spotted rainbowfish, Melanotaenia duboulayi (Castlenau). This native fish is common throughout southeastern Queensland, and it is increasingly being distributed as a biological control agent of mosquitoes. The selected larvicides included, two organophosphate (OP) compounds (temephos and pirimiphos-methyl), two microbial larvicides (Bacillus thuringiensis spp. israelensis [Bti] de Barjac and Bacillus sphaericus [Bs] Neide), and an insect growth regulator (IGR) (s-methoprene). Exposure to the OP temephos at 10 times the effective field concentration (EFC; 0.33 mg/liter), and OP pirimiphos-methyl at the EFC (0.50 mg/liter), resulted in a significant reduction in the Ucrit of M. duboulayi under controlled conditions. Conversely, exposure to the microbial (Bti and Bs) and IGR (s-methoprene) larvicides at 10 times the EFC had no effect on the Ucrit of M. duboulayi. Accordingly, these products are suitable for integrated pest management programs in Australia.

Ross River virus disease clusters and spatial relationship with mosquito biting exposure in Redland Shire, southern Queensland, Australia.

The spatial heterogeneity in the risk of Ross River virus (family Togaviridae, genus Alphavirus, RRV) disease, the most common mosquito-borne disease in Australia, was examined in Redland Shire in southern Queensland, Australia. Disease cases, complaints from residents of intense mosquito biting exposure, and human population data were mapped using a geographic information system. Surface maps of RRV disease age-sex standardized morbidity ratios and mosquito biting complaint morbidity ratios were created. To determine whether there was significant spatial variation in disease and complaint patterns, a spatial scan analysis method was used to test whether the number of cases and complaints was distributed according to underlying population at risk. Several noncontiguous areas in proximity to productive saline water habitats of Aedes vigilax (Skuse), a recognized vector of RRV, had higher than expected numbers of RRV disease cases and complaints. Disease rates in human populations in areas which had high numbers of adult Ae. vigilax in carbon dioxide- and octenol-baited light traps were up to 2.9 times those in areas that rarely had high numbers of mosquitoes. It was estimated that targeted control of adult Ae. vigilax in these high-risk areas could potentially reduce the RRV disease incidence by an average of 13.6%. Spatial correlation was found between RRV disease risk and complaints from residents of mosquito biting. Based on historical patterns of RRV transmission throughout Redland Shire and estimated future human population growth in areas with higher than average RRV disease incidence, it was estimated that RRV incidence rates will increase by 8% between 2001 and 2021. The use of arbitrary administrative areas that ranged in size from 4.6 to 318.3 km2 has the potential to mask any small scale heterogeneity in disease patterns. With the availability of georeferenced data sets and high-resolution imagery, it is becoming more feasible to undertake spatial analyses at relatively small scales.

Social niche construction and evolutionary transitions in individuality.

Social evolution theory conventionally takes an externalist explanatory stance, treating observed cooperation as explanandum and the positive assortment of cooperative behaviour as explanans. We ask how the circumstances bringing about this positive assortment arose in the first place. Rather than merely push the explanatory problem back a step, we move from an externalist to an interactionist explanatory stance, in the spirit of Lewontin and the Niche Construction theorists. We develop a theory of 'social niche construction' in which we consider biological entities to be both the subject and object of their own social evolution. Some important cases of the evolution of cooperation have the side-effect of causing changes in the hierarchical level at which the evolutionary process acts. This is because the traits (e.g. life-history bottlenecks) that act to align the fitness interests of particles (e.g. cells) in a collective can also act to diminish the extent to which those particles are bearers of heritable fitness variance, while augmenting the extent to which collectives of such particles (e.g. multicellular organisms) are bearers of heritable fitness variance. In this way, we can explain upward transitions in the hierarchical level at which the Darwinian machine operates in terms of particle-level selection, even though the outcome of the process is a collective-level selection regime. Our theory avoids the logical and metaphysical paradoxes faced by other attempts to explain evolutionary transitions.

When are Many-Body Effects Significant?

Many-body effects are required for an accurate description of both structure and dynamics of large chemical systems. However, there are numerous such interactions to consider, and it is not obvious which ones are significant. We provide a general and fast method for establishing which small set of three- and four-body interactions are important. This is achieved by estimating the maximum many-body effects, ϵmax, that can arise in a given arrangement of bodies. Through careful analysis of ϵmax, we find two overall causes for significant many-body interactions. First, many-body induction propagates in nonbranching paths, that is, in a chain-like manner. Second, linear arrangements of bodies promote the alignment of the dipoles to reinforce the many-body interaction. Consequently, compact and extended linear arrangements are favored. The latter result is not intuitive as these linear arrangements can lead to significant many-body effects extending over large distances. For the first time, this study provides a rigorous explanation as to how cooperative effects provide enhanced stability in helices making them one of the most common structures in biomolecules. Not only do these helices promote linear dipole alignment, but their chain-like structure is consistent with the way many-body induction propagates. Finally, using ϵmax to screen for significant many-body interactions, we are able to reproduce the total three- and four-body interaction energies using a small number of individual many-body interactions.

Analysis of Barmah Forest virus disease activity in Queensland, Australia, 1993-2003: identification of a large, isolated outbreak of disease.

Barmah Forest virus (BFV) disease is the second most common mosquito-borne disease in Australia. Although the majority of notifications are received from Queensland, little is known about the distribution of the disease within the state, or the important mosquito vectors and nonhuman vertebrate hosts. We conducted a retrospective statistical analysis of the notifications received from Queensland residents from 1993 to 2003 to establish long-term local incidence rates and to identify disease outbreaks. In total, 4,544 notifications were received over the 10-yr period. Disease reporting peaked in autumn, although the peak transmission season encompassed both summer and autumn. Long-term standardized incidence rates for summer/autumn and winter/spring varied across the state, showing positive spatial autocorrelation in both 6-mo periods. Although 15 instances of increased disease activity were identified, only one major disease outbreak affecting eight contiguous local government areas was detected in summer/autumn 2002/2003. This outbreak contained 297 cases, 115 more than would be expected over this period. The factors important to this outbreak are unknown and require further investigation. Although the incidence rates for BFV disease are lower than Ross River virus disease, the most reported mosquito-borne disease in Australia, several factors indicate that this virus should be considered an important public health risk in Queensland. These include consistent endemic transmission, apparent underreporting of the disease, and the potential for outbreaks in major population centers.

Many-Body Basis Set Superposition Effect.

The basis set superposition effect (BSSE) arises in electronic structure calculations of molecular clusters when questions relating to interactions between monomers within the larger cluster are asked. The binding energy, or total energy, of the cluster may be broken down into many smaller subcluster calculations and the energies of these subsystems linearly combined to, hopefully, produce the desired quantity of interest. Unfortunately, BSSE can plague these smaller fragment calculations. In this work, we carefully examine the major sources of error associated with reproducing the binding energy and total energy of a molecular cluster. In order to do so, we decompose these energies in terms of a many-body expansion (MBE), where a "body" here refers to the monomers that make up the cluster. In our analysis, we found it necessary to introduce something we designate here as a many-ghost many-body expansion (MGMBE). The work presented here produces some surprising results, but perhaps the most significant of all is that BSSE effects up to the order of truncation in a MBE of the total energy cancel exactly. In the case of the binding energy, the only BSSE correction terms remaining arise from the removal of the one-body monomer total energies. Nevertheless, our earlier work indicated that BSSE effects continued to remain in the total energy of the cluster up to very high truncation order in the MBE. We show in this work that the vast majority of these high-order many-body effects arise from BSSE associated with the one-body monomer total energies. Also, we found that, remarkably, the complete basis set limit values for the three-body and four-body interactions differed very little from that at the MP2/aug-cc-pVDZ level for the respective subclusters embedded within a larger cluster.

The biochemical composition of haemodynamically stressed vascular tissue. III. The collagen composition of experimental arteriovenous fistulae.

The external jugular vein and the common carotid artery were anastomosed in 8 sheep. Morphological changes similar to those observed in human atherosclerosis are produced particularly in the venous tissue. There is a significant increase in the collagen content of the dilated mid-segment of the experimental vein. Also there is a positive correlation between post-operative age and the amount of collagen, especially in the distal region of the artery and in the proximal and middle regions of the vein. In both the control and experimental veins the amino acid composition of collagen was very similar. However, the arterial preparations did not exhibit the same degree of purity. Most of the collagen was the type I variant (approx. 80% in arteries and 70% in veins). In the sham-operated veins about 30% of the collagen was type III but it was nearer 17% in the control arteries. Whilst experimental and control arteries had similar proportions of type III collagen, there was a 30% reduction in the experimental veins. Although there was no significant correlation between the proportion of any of the genetic types of collagen and the post-operative age of the animals, there was a strong correlation for the increment in type I in all regions of the experimental vein as a function of time.

Characteristics of acquired immunodeficiency syndrome in older adults.

OBJECTIVE: To examine demographic and clinical features of older AIDS patients in comparison with younger individuals. DESIGN: Data base review. SETTING: Maryland AIDS Registry from 1981 through the end of 1994. PARTICIPANTS: All registered Maryland AIDS cases greater than or equal to 60 years of age at diagnosis and all Maryland AIDS cases aged 20 to 39. MAIN OUTCOME MEASURES: Demographic features, mode of transmission and change in mode over time, clinical presentations, CD4+ counts, and survival time. RESULTS: A total of 321 (2.7%) AIDS cases diagnosed in Maryland were people 60 years of age or older compared with 7511 cases (63.9%) in people aged 20 to 39 years. The proportion of whites was higher in the older group, but the gender distribution was similar to younger counterparts. Transfusion was the primary cause of exposure of 32% of the older people with AIDS; however, during the last few years, sexual transmission and drug abuse have been implicated more frequently. Twelve percent of older patients had no reported risk factors compared with 4% of younger AIDS patients. The most common presenting AIDS indicator disease in older cases was Pneumocystis carinii pneumonia. Wasting syndrome, candidiasis, and HIV encephalopathy also occurred frequently. Median life span was 9 months compared with 22 months in the young. CONCLUSION: Our study demonstrates that transfusion is no longer the leading cause of AIDS in older people in Maryland. The relatively increased prominence of transmission by other modes in this age group raises the importance of preventive and educational measures. Older patients generally have a shorter survival than younger individuals.

Investigation of gray-headed flying foxes (Pteropus poliocephalus) (Megachiroptera: Pteropodidae) and mosquitoes in the ecology of Ross River virus in Australia.

Entomologic and virologic factors were investigated to determine whether gray-headed flying foxes (Pteropus poliocephalus) from Indooroopilly Island, Brisbane, Australia could be vertebrate hosts of Ross River (RR) virus. Aedes funereus was the most abundant mosquito species with 6,300-38,700 females per light trap night in the flying fox camp containing gray-headed, black (P. alecto), and little red (P. scapulatus) flying foxes. Sixteen Ae. funereus blood meals from this collection were analyzed by hemoglobin electrophoresis and were found to be from P. alecto. From pledget feeding with RR virus, the infectious dose required to infect 50% of wild caught Ae. funereus was log10 4.2 50% tissue culture infectious doses per mosquito, with a transmission rate to mice of 17% at 9-10 days post infection. Experimental infection of 10 juvenile P. poliocephalus produced viremias of low titer in five animals, with a duration of 1-4 days and a mean of two days. Three percent of colonized Ae. vigilax that fed on the 10 animals during this period became infected. One of the five viremic flying foxes and two of the five aviremic animals produced a detectable immune response by either neutralization or hemagglutination-inhibition tests. Based on the low to moderate vector competence of Ae. funereus for RR virus, and evidence that P. poliocephalus is a poor vertebrate host of RR virus, it is unlikely that RR virus transmission would be maintained between these two species, but it could be maintained by other more competent vector/host pairs.