Population structure of Bactrocera dorsalis s.s., B. papayae and B. philippinensis (Diptera: Tephritidae) in southeast Asia: evidence for a single species hypothesis using mitochondrial DNA and wingshape data

Background Bactrocera dorsalis s.s. is a pestiferous tephritid fruit fly distributed from Pakistan to the Pacific, with the Thai/Malay peninsula its southern limit. Sister pest taxa, B. papayae and B. philippinensis, occur in the southeast Asian archipelago and the Philippines, respectively. The relationship among these species is unclear due to their high molecular and morphological similarity. This study analysed population structure of these three species within a southeast Asian biogeographical context to assess potential dispersal patterns and the validity of their current taxonomic status. Results Geometric morphometric results generated from 15 landmarks for wings of 169 flies revealed significant differences in wing shape between almost all sites following canonical variate analysis. For the combined data set there was a greater isolation-by-distance (IBD) effect under a ‘non-Euclidean’ scenario which used geographical distances within a biogeographical ‘Sundaland context’ (r2 = 0.772, P < 0.0001) as compared to a ‘Euclidean’ scenario for which direct geographic distances between sample sites was used (r2 = 0.217, P < 0.01). COI sequence data were obtained for 156 individuals and yielded 83 unique haplotypes with no correlation to current taxonomic designations via a minimum spanning network. BEAST analysis provided a root age and location of 540kya in northern Thailand, with migration of B. dorsalis s.l. into Malaysia 470kya and Sumatra 270kya. Two migration events into the Philippines are inferred. Sequence data revealed a weak but significant IBD effect under the ‘non-Euclidean’ scenario (r2 = 0.110, P < 0.05), with no historical migration evident between Taiwan and the Philippines. Results are consistent with those expected at the intra-specific level. Conclusions Bactrocera dorsalis s.s., B. papayae and B. philippinensis likely represent one species structured around the South China Sea, having migrated from northern Thailand into the southeast Asian archipelago and across into the Philippines. No migration is apparent between the Philippines and Taiwan. This information has implications for quarantine, trade and pest management.

Molecular dynamics studies of the effects of branching characteristics on the crystalline structure of polyethylene

Molecular dynamics simulations were carried out on single chain models of linear low-density polyethylene in vacuum to study the effects of branch length, branch content, and branch distribution on the polymer’s crystalline structure at 300 K. The trans/gauche (t/g) ratios of the backbones of the modeled molecules were calculated and utilized to characterize their degree of crystallinity. The results show that the t/g ratio decreases with increasing branch content regardless of branch length and branch distribution, indicating that branch content is the key molecular parameter that controls the degree of crystallinity. Although t/g ratios of the models with the same branch content vary, they are of secondary importance. However, our data suggests that branch distribution (regular or random) has a significant effect on the degree of crystallinity for models containing 10 hexyl branches/1,000 backbone carbons. The fractions of branches that resided in the equilibrium crystalline structures of the models were also calculated. On average, 9.8% and 2.5% of the branches were found in the crystallites of the molecules with ethyl and hexyl branches while C13 NMR experiments showed that the respective probabilities of branch inclusion for ethyl and hexyl branches are 10% and 6% [Hosoda et al., Polymer 1990, 31, 1999–2005]. However, the degree of branch inclusion seems to be insensitive to the branch content and branch distribution.

Feasibility of agent-based modelling of articular cartilage including a conceptual representation of its structure

Articular cartilage is a complex structure with an architecture in which fluid-swollen proteoglycans constrained within a 3D network of collagen fibrils. Because of the complexity of the cartilage structure, the relationship between its mechanical behaviours at the macroscale level and its components at the micro-scale level are not completely understood. The research objective in this thesis is to create a new model of articular cartilage that can be used to simulate and obtain insight into the micro-macro-interaction and mechanisms underlying its mechanical responses during physiological function. The new model of articular cartilage has two characteristics, namely: i) not use fibre-reinforced composite material idealization ii) Provide a framework for that it does probing the micro mechanism of the fluid-solid interaction underlying the deformation of articular cartilage using simple rules of repartition instead of constitutive / physical laws and intuitive curve-fitting. Even though there are various microstructural and mechanical behaviours that can be studied, the scope of this thesis is limited to osmotic pressure formation and distribution and their influence on cartilage fluid diffusion and percolation, which in turn governs the deformation of the compression-loaded tissue. The study can be divided into two stages. In the first stage, the distributions and concentrations of proteoglycans, collagen and water were investigated using histological protocols. Based on this, the structure of cartilage was conceptualised as microscopic osmotic units that consist of these constituents that were distributed according to histological results. These units were repeated three-dimensionally to form the structural model of articular cartilage. In the second stage, cellular automata were incorporated into the resulting matrix (lattice) to simulate the osmotic pressure of the fluid and the movement of water within and out of the matrix; following the osmotic pressure gradient in accordance with the chosen rule of repartition of the pressure. The outcome of this study is the new model of articular cartilage that can be used to simulate and study the micromechanical behaviours of cartilage under different conditions of health and loading. These behaviours are illuminated at the microscale level using the socalled neighbourhood rules developed in the thesis in accordance with the typical requirements of cellular automata modelling. Using these rules and relevant Boundary Conditions to simulate pressure distribution and related fluid motion produced significant results that provided the following insight into the relationships between osmotic pressure gradient and associated fluid micromovement, and the deformation of the matrix. For example, it could be concluded that: 1. It is possible to model articular cartilage with the agent-based model of cellular automata and the Margolus neighbourhood rule. 2. The concept of 3D inter connected osmotic units is a viable structural model for the extracellular matrix of articular cartilage. 3. Different rules of osmotic pressure advection lead to different patterns of deformation in the cartilage matrix, enabling an insight into how this micromechanism influences macromechanical deformation. 4. When features such as transition coefficient were changed, permeability (representing change) is altered due to the change in concentrations of collagen, proteoglycans (i.e. degenerative conditions), the deformation process is impacted. 5. The boundary conditions also influence the relationship between osmotic pressure gradient and fluid movement at the micro-scale level. The outcomes are important to cartilage research since we can use these to study the microscale damage in the cartilage matrix. From this, we are able to monitor related diseases and their progression leading to potential insight into drug-cartilage interaction for treatment. This innovative model is an incremental progress on attempts at creating further computational modelling approaches to cartilage research and other fluid-saturated tissues and material systems.

Academic wage structure by gender : the roles of peer review, performance, and market forces

We focus on understanding the role of productivity in determining wage structure differences between men and women in academia. The data arise from a pay-equity study carried out in a single Midwestern U.S. university over the 1996–7 academic year. Econometric results confirm that external market forces exert influence over both male and female salary. But peer review ratings play a significant role in male but not female earnings determination, with similar results for objective measures of research, teaching and service.

Dots versus antidots : computational exploration of structure, magnetism, and half-metallicity in boron−nitride nanostructures

Triangle-shaped nanohole, nanodot, and lattice antidot structures in hexagonal boron-nitride (h-BN) monolayer sheets are characterized with density functional theory calculations utilizing the local spin density approximation. We find that such structures may exhibit very large magnetic moments and associated spin splitting. N-terminated nanodots and antidots show strong spin anisotropy around the Fermi level, that is, half-metallicity. While B-terminated nanodots are shown to lack magnetism due to edge reconstruction, B-terminated nanoholes can retain magnetic character due to the enhanced structural stability of the surrounding two-dimensional matrix. In spite of significant lattice contraction due to the presence of multiple holes, antidot super lattices are predicted to be stable, exhibiting amplified magnetism as well as greatly enhanced half-metallicity. Collectively, the results indicate new opportunities for designing h-BNbased nanoscale devices with potential applications in the areas of spintronics, light emission, and photocatalysis.

Footprint-based estimates of arch structure are confounded by body composition in adults

Previous research employing indirect measures of arch structure, such as those derived from footprints, have indicated that obesity results in a “flatter” foot type. In the absence of radiographic measures, however, definitive conclusions regarding the osseous alignment of the foot cannot be made. We determined the effect of body mass index (BMI) on radiographic and footprint‐based measures of arch structure. The research was a cross‐sectional study in which radiographic and footprint‐based measures of foot structure were made in 30 subjects (10 males, 20 female) in addition to standard anthropometric measures of height, weight, and BMI. Multiple (univariate) regression analysis demonstrated that both BMI ( β  = 0.39, t 26  = 2.12, p  = 0.04) and radiographic arch alignment ( β  = 0.51, t 26  = 3.32, p  < 0.01) were significant predictors of footprint‐based measures of arch height after controlling for all variables in the model ( R 2  = 0.59, F 3,26  = 12.3, p  < 0.01). In contrast, radiographic arch alignment was not significantly associated with BMI ( β  = −0.03, t 26  = −0.13, p  = 0.89) when Arch Index and age were held constant ( R 2  = 0.52, F 3,26  = 9.3, p  < 0.01). Adult obesity does not influence osseous alignment of the medial longitudinal arch, but selectively distorts footprint‐based measures of arch structure. Footprint‐based measures of arch structure should be interpreted with caution when comparing groups of varying body composition.

Variation in leaf structure of the invasive Madeira vine (Anredera cordifolia, Basellaceae) at different light levels

Madeira vine (Anredera cordifolia (Ten.) Steenis) is a climber in the angiosperm family Basellaceae. It is native to South America and has naturalised in Australia. It is regarded as a serious environmental weed because of the structural damage it causes to native vegetation. The present study, for the first time, documents anatomical and morphological traits of the leaves of A. cordifolia and considers their implications for its ecology and physiology. Plants were grown under three different light levels, and anatomical and morphological leaf characters were compared among light levels, among cohorts, and with documented traits of the related species, Basella alba L. Stomata were present on both the adaxial and abaxial sides of the leaf, with significantly more stomata on the abaxial side and under high light. This may account for the ability of this species to fix large amounts of carbon and rapidly respond to light gaps. The leaves had very narrow veins and no sclerenchyma, suggesting a low construction cost that is associated with invasive plants. There was no significant difference in any of the traits among different cohorts, which agrees with the claim that A. cordifolia primarily propagates vegetatively. The anatomy and morphology of A. cordifolia was similar to that of B. alba.

Reconceptualizing Early Mathematics Learning : The Fundamental Role of Pattern and Structure

The Pattern and Structure Mathematics Awareness Program (PASMAP) was developed concurrently with the studies of AMPS and the development of the Pattern and Structure Assessment (PASA) interview. We summarize some early classroom-based teaching studies and describe the PASMAP that resulted. A large-scale two-year longitudinal study, Reconceptualizing Early Mathematics Learning (REML) resulted. We provide an overview of the REML study and discuss the consequences for our view of early mathematics learning. A purposive sample of four large primary schools, two in Sydney and two in Brisbane, representing 316 students from diverse socio-economic and cultural contexts, participated in an evaluation of the PASMAP intervention throughout the 2009 school year and a follow-up assessment in 2010. Two different mathematics programs were implemented: in each school, two Kindergarten teachers implemented the PASMAP and another two implemented their regular program. The study shows that both groups of students made substantial gains on the ‘I Can Do Maths’ standardized assessment and the PASA interview, but highly significant differences were found on the latter with PASMAP students outperforming the regular group on PASA scores. Qualitative analysis of students’ responses for structural development showed increased levels for the PASMAP students. Implications for pedagogy and curriculum are discussed.

High-efficiency silencing of a β-glucuronidase gene in rice is correlated with repetitive transgene structure but is independent of DNA methylation

Two transgenic callus lines of rice, stably expressing a β-glucuronidase (GUS) gene, were supertransformed with a set of constructs designed to silence the resident GUS gene. An inverted-repeat (i/r) GUS construct, designed to produce mRNA with self-complementarity, was much more effective than simple sense and antisense constructs at inducing silencing. Supertransforming rice calluses with a direct-repeat (d/r) construct, although not as effective as those with the i/r construct, was also substantially more effective in silencing the resident GUS gene than the simple sense and antisense constructs. DNA hybridisation analyses revealed that every callus line supertransformed with either simple sense or antisense constructs, and subsequently showing GUS silencing, had the silence-inducing transgenes integrated into the plant genome in inverted-repeat configurations. The silenced lines containing i/r and d/r constructs did not necessarily have inverted-repeat T-DNA insertions. There was significant methylation of the GUS sequences in most of the silenced lines but not in the unsilenced lines. However, demethylation treatment of silenced lines with 5-azacytidine did not reverse the post-transcriptional gene silencing (PTGS) of GUS. Whereas the levels of RNA specific to the resident GUS gene were uniformly low in the silenced lines, RNA specific to the inducer transgenes accumulated to a substantial level, and the majority of the i/r RNA was unpolyadenylated. Altogether, these results suggest that both sense- and antisense-mediated gene suppression share a similar molecular basis, that unpolyadenylated RNA plays an important role in PTGS, and that methylation is not essential for PTGS.

Advantages of exploiting projection structure for segmenting dense 3D point clouds

Timely and comprehensive scene segmentation is often a critical step for many high level mobile robotic tasks. This paper examines a projected area based neighbourhood lookup approach with the motivation towards faster unsupervised segmentation of dense 3D point clouds. The proposed algorithm exploits the projection geometry of a depth camera to find nearest neighbours which is time independent of the input data size. Points near depth discontinuations are also detected to reinforce object boundaries in the clustering process. The search method presented is evaluated using both indoor and outdoor dense depth images and demonstrates significant improvements in speed and precision compared to the commonly used Fast library for approximate nearest neighbour (FLANN) [Muja and Lowe, 2009].

Comparison of functionals for metal hexaboride band structure calculations

Density functional calculations of the electronic band structure for superconducting and semi-conducting metal hexaborides are compared using a consistent suite of assumptions and with emphasis on the physical implications of computed models. Spin polarization enhances mathematical accuracy of the functional approximations and adds significant physical meaning to model interpretation. For YB6 and LaB6, differences in alpha and beta projections occur near the Fermi energy. These differences are pronounced for superconducting hexaborides but do not occur for other metal hexaborides.

Tensile properties of a boron/nitrogen-doped carbon nanotube–graphene hybrid structure

Doping is an effective approach that allows for the intrinsic modification of the electrical and chemical properties of nanomaterials. Recently, a graphene and carbon nanotube hybrid structure (GNHS) has been reported, which extends the excellent properties of carbon-based materials to three dimensions. In this paper, we carried out a first-time investigation on the tensile properties of the hybrid structures with different dopants. It is found that with the presence of dopants, the hybrid structures usually exhibit lower yield strength, Young’s modulus, and earlier yielding compared to that of a pristine hybrid structure. For dopant concentrations below 2.5% no significant reduction of Young’s modulus or yield strength could be observed. For all considered samples, the failure is found to initiate at the region where the nanotubes and graphene sheets are connected. After failure, monatomic chains are normally observed around the failure region. Dangling graphene layers without the separation of a residual CNT wall are found to adhere to each other after failure with a distance of about 3.4 Å. This study provides a fundamental understanding of the tensile properties of the doped graphene–nanotube hybrid structures, which will benefit the design and also the applications of graphene-based hybrid materials.

The crystal structure and vibrational spectroscopy of jarosite and alunite minerals

The alunite supergroup of minerals is a large hydroxy-sulfate mineral group, which has seen renewed interest following their discovery on Mars. Numerous reviews exist concerning nomenclature, formation, and natural occurrence of this mineral group. Sulfate minerals in general are widely studied and their vibrational spectra are well characterized. However, no specific review concerning alunite and jarosite spectroscopy and crystal structure has been forthcoming. This review focuses on the controversial aspects of the crystal structure and vibrational spectroscopy of jarosite and alunite minerals. Inconsistencies regarding band assignments especially in the 1000–400 cm−1 region plague these two mineral groups and result in different band assignments among the various spectroscopic studies. There are significant crystallographic and magnetic structure ambiguities with regards to ammonium and hydronium end-members, namely, the geometry these two ions assume in the structure and the fact that hydronium jarosite is a spin glass. It was also found that the synthetic causes for the super cell in plumbojarosite, minamiite, huangite, and walthierite are not known.

Fluid-structure interaction analysis by coupled FE-SPH model based on a novel searching algorithm

Fluid–Structure Interaction (FSI) problem is significant in science and engineering, which leads to challenges for computational mechanics. The coupled model of Finite Element and Smoothed Particle Hydrodynamics (FE-SPH) is a robust technique for simulation of FSI problems. However, two important steps of neighbor searching and contact searching in the coupled FE-SPH model are extremely time-consuming. Point-In-Box (PIB) searching algorithm has been developed by Swegle to improve the efficiency of searching. However, it has a shortcoming that efficiency of searching can be significantly affected by the distribution of points (nodes in FEM and particles in SPH). In this paper, in order to improve the efficiency of searching, a novel Striped-PIB (S-PIB) searching algorithm is proposed to overcome the shortcoming of PIB algorithm that caused by points distribution, and the two time-consuming steps of neighbor searching and contact searching are integrated into one searching step. The accuracy and efficiency of the newly developed searching algorithm is studied on by efficiency test and FSI problems. It has been found that the newly developed model can significantly improve the computational efficiency and it is believed to be a powerful tool for the FSI analysis.

Intercalation of dodecylamine into kaolinite and its layering structure investigated by molecular dynamics simulation

Dodecylamine was successfully intercalated into the layer space of kaolinite by utilizing the methanol treated kaolinite–dimethyl sulfoxide (DMSO) intercalation complex as an intermediate. The basal spacing of kaolinite, measured by X-ray diffraction (XRD), increased from 0.72 nm to 4.29 nm after the intercalation of dodecylamine. Also, the significant variation observed in the Fourier Transform Infrared Spectroscopy (FTIR) spectra of kaolinite when intercalated with dodecylamine verified the feasibility of intercalation of dodecylamine into kaolinite. Isothermal-isobaric (NPT) molecular dynamics simulation with the use of Dreiding force field was performed to probe into the layering behavior and structure of nanoconfined dodecylamine in the kaolinite gallery. The concentration profiles of the nitrogen atom, methyl group and methylene group of intercalated dodecylamine molecules in the direction perpendicular to the kaolinite basal surface indicated that the alkyl chains within the interlayer space of kaolinite exhibited an obvious layering structure. However, the unified bilayer, pseudo-trilayer, or paraffin-type arrangements of alkyl chains deduced based on their chain length combined with the measured basal spacing of organoclays were not found in this study. The alkyl chains aggregated to a mixture of ordered paraffin-type-like structure and disordered gauche conformation in the middle interlayer space of kaolinite, and some alkyl chains arranged in two bilayer structures, in which one was close to the silica tetrahedron surface, and the other was close to the alumina octahedron surface with their alkyl chains parallel to the kaolinite basal surface.