Dynamics of transforming growth factor
- Authors: Wu, Siqi , Luwor, Rodney , Zhu, Hong-Jian
- Date: 2023
- Type: Text , Journal article , Review
- Relation: Growth Factors Vol. 41, no. 2 (2023), p. 82-100
- Full Text: false
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- Description: Transforming growth factor
Arylpyrrole and fipronil analogues that inhibit the motility and/or development of Haemonchus contortus in vitro
- Authors: Herath, Dilrukshi , Song, Hongjian , Preston, Sarah , Jabbar, Abdul , Wang, Tao , McGee, Sean , Hofmann, Andreas , Garcia-Bustos, Jose , Chang, Bill , Koehler, Anson , Liu, Yuxiu , Ma, Qiaoqiao , Zhang, Penqxiang , Zhao, Qiqi , Wang, Qingmin , Gasser, Robin
- Date: 2018
- Type: Text , Journal article
- Relation: International Journal for Parasitology: Drugs and Drug Resistance Vol. 8, no. 3 (2018), p. 379-385
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- Description: Due to widespread drug resistance in parasitic nematodes, there is a need to develop new anthelmintics. Given the cost and time involved in developing a new drug, the repurposing of known chemicals can be a promising, alternative approach. In this context, we tested a library (n = 600) of natural product-inspired pesticide analogues against exsheathed third stage-larvae (xL3s) of Haemonchus contortus (barber's pole worm) using a whole-organism, phenotypic screening technique that measures the inhibition of motility and development in treated larvae. In the primary screen, we identified 32 active analogues derived from chemical scaffolds of arylpyrrole or fipronil. The seven most promising compounds, selected based on their anthelmintic activity and/or limited cytotoxicity, are arylpyrroles that reduced the motility of fourth-stage larvae (L4s) with significant potency (IC 50 values ranged from 0.04 ± 0.01
Soil moisture, organic carbon, and nitrogen content prediction with hyperspectral data using regression models
- Authors: Datta, Dristi , Paul, Manoranjan , Murshed, Manzur , Teng, Shyh Wei , Schmidtke, Leigh
- Date: 2022
- Type: Text , Journal article
- Relation: Sensors (Basel, Switzerland) Vol. 22, no. 20 (2022), p.
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- Description: Soil moisture, soil organic carbon, and nitrogen content prediction are considered significant fields of study as they are directly related to plant health and food production. Direct estimation of these soil properties with traditional methods, for example, the oven-drying technique and chemical analysis, is a time and resource-consuming approach and can predict only smaller areas. With the significant development of remote sensing and hyperspectral (HS) imaging technologies, soil moisture, carbon, and nitrogen can be estimated over vast areas. This paper presents a generalized approach to predicting three different essential soil contents using a comprehensive study of various machine learning (ML) models by considering the dimensional reduction in feature spaces. In this study, we have used three popular benchmark HS datasets captured in Germany and Sweden. The efficacy of different ML algorithms is evaluated to predict soil content, and significant improvement is obtained when a specific range of bands is selected. The performance of ML models is further improved by applying principal component analysis (PCA), a dimensional reduction method that works with an unsupervised learning method. The effect of soil temperature on soil moisture prediction is evaluated in this study, and the results show that when the soil temperature is considered with the HS band, the soil moisture prediction accuracy does not improve. However, the combined effect of band selection and feature transformation using PCA significantly enhances the prediction accuracy for soil moisture, carbon, and nitrogen content. This study represents a comprehensive analysis of a wide range of established ML regression models using data preprocessing, effective band selection, and data dimension reduction and attempt to understand which feature combinations provide the best accuracy. The outcomes of several ML models are verified with validation techniques and the best- and worst-case scenarios in terms of soil content are noted. The proposed approach outperforms existing estimation techniques.
Assessing the anthelmintic activity of pyrazole-5-carboxamide derivatives against Haemonchus contortus
- Authors: Jiao, Yaqing , Preston, Sarah , Song, Hongjian , Jabbar, Abdul , Liu, Yuxiu , Baell, Jonathan , Hofmann, Andreas , Hutchinson, Dana , Wang, Tao , Koehler, Anson , Fisher, Gillian , Andrews, Katherine , Laleu, Benoit , Palmer, Michael , Burrows, Jeremy , Wells, Timothy , Wang, Qingmin , Gasser, Robin
- Date: 2017
- Type: Text , Journal article
- Relation: Parasites and Vectors Vol. 10, no. 1 (2017), p. 1-7
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- Description: Background: In this study, we tested five series of pyrazole-5-carboxamide compounds (n = 55) for activity against parasitic stages of the nematode Haemonchus contortus (barber’s pole worm), one of the most pathogenic parasites of ruminants. Methods: In an optimised, whole-organism screening assay, using exsheathed third-stage (xL3) and fourth-stage (L4) larvae, we measured the inhibition of larval motility and development of H. contortus. Results: Amongst the 55 compounds, we identified two compounds (designated a-15 and a-17) that reproducibly inhibit xL3 motility as well as L4 motility and development, with IC50 values ranging between ~3.4 and 55.6 μM. We studied the effect of these two ‘hit’ compounds on mitochondrial function by measuring oxygen consumption. This assessment showed that xL3s exposed to each of these compounds consumed significantly less oxygen and had less mitochondrial activity than untreated xL3s, which was consistent with specific inhibition of complex I of the respiratory electron transport chain in arthropods. Conclusions: The present findings provide a sound basis for future work, aimed at identifying the targets of compounds a-15 and a-17 and establishing the modes of action of these chemicals in H. contortus. © 2017 The Author(s).
Multivariate statistical analysis of songs of the male Common Blackbird (Turdus merula) : An example from western Victoria, Australia
- Authors: Kentish, Barry , Harvey, Jack , Roberts, Lyn , Ross, Jason
- Date: 2001
- Type: Text , Journal article
- Relation: EMU Vol. 101, no. 4 (2001), p. 335-340
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- Description: Variation in the song of the male Common Blackbird was investigated within and between two locations in western Victoria. Each of 400 phrases (100 phrases per male) was characterised by 61 measurements relating to 13 aspects of each phrase. Principal component and stepwise discriminant analyses were undertaken on these measurements. Classification of blackbird song for location and individuality was based on timing within the phrase of the loudest elements. Evidence was found for within-phrase variability, with the greatest variation in the middle of the phrase. Within- and between-site comparison found that blackbird song exhibited both individual and site-specific characteristics consistent with earlier suggestions of phrase sharing within local populations. The study demonstrated that an objective statistical approach to song analysis was able to disciminate between individual birds from different locations.
Ode to form
- Authors: Mestrom, Sanne
- Date: 2012
- Type: Text , Visual art work
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A new era of integration between multiomics and spatio-temporal analysis for the translation of EMT towards clinical applications in cancer
- Authors: Fonseca Teixeira, Adilson , Wu, Siqi , Luwor, Rodney , Zhu, Hong-Jian
- Date: 2023
- Type: Text , Journal article , Review
- Relation: Cells Vol. 12, no. 23 (2023), p.
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- Description: Epithelial-mesenchymal transition (EMT) is crucial to metastasis by increasing cancer cell migration and invasion. At the cellular level, EMT-related morphological and functional changes are well established. At the molecular level, critical signaling pathways able to drive EMT have been described. Yet, the translation of EMT into efficient diagnostic methods and anti-metastatic therapies is still missing. This highlights a gap in our understanding of the precise mechanisms governing EMT. Here, we discuss evidence suggesting that overcoming this limitation requires the integration of multiple omics, a hitherto neglected strategy in the EMT field. More specifically, this work summarizes results that were independently obtained through epigenomics/transcriptomics while comprehensively reviewing the achievements of proteomics in cancer research. Additionally, we prospect gains to be obtained by applying spatio-temporal multiomics in the investigation of EMT-driven metastasis. Along with the development of more sensitive technologies, the integration of currently available omics, and a look at dynamic alterations that regulate EMT at the subcellular level will lead to a deeper understanding of this process. Further, considering the significance of EMT to cancer progression, this integrative strategy may enable the development of new and improved biomarkers and therapeutics capable of increasing the survival and quality of life of cancer patients. © 2023 by the authors.
Instructions for an imaginary man
- Authors: Chew, Richard
- Date: 2012
- Type: Text , Performance
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A quadtree-based scaled boundary finite element method for crack propagation modelling
- Authors: Ooi, Ean Tat , Man, Hou , Natarajan, Sundararajan , Song, Chongmin , Tin-Loi, Francis
- Date: 2014
- Type: Text , Conference paper
- Relation: 23rd Australasian Conference on the Mechanics of Structures and Materials, Byron Bay, NSW, 9-12 December, Southern Cross University, Lismore, NSW, p. 813-818
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- Description: The quadtree is a hierarchical-type data structure where each parent is recursively divided into four children. This structure makes it particularly efficient for adaptive mesh refinement in regions with localised gradients. Compared with unstructured triangles, mesh generation is more efficient using quadtree decompositions. The finite number of patterns in the quadtree decomposition makes it efficient for data storage and retrieval. Motivated by these advantages, a crack propagation modelling approach using a quadtree-based scaled boundary finite element method (SBFEM) is developed. Starting from the formulation of an arbitrary n-sided polygon element, each quadrant in the quadtree mesh is treated as a polygon within the framework of the SBFEM. Special techniques to treat the hanging nodes are not necessary. Moreover, the SBFEM enables accurate calculation of the stress intensity factors directly from its solutions without local mesh refinement or asymptotic enrichment functions. When a crack propagates, it is only necessary to split each quadrant cut by the crack into two. These quadrants are polygons that can be directly modelled by the SBFEM. Changes to the mesh are minimal. The efficiency of this approach is demonstrated using numerical benchmarks.
A new systemic disease mouse model for glioblastoma capable of single-tumour-cell detection
- Authors: Ware, Thomas , Luwor, Rodney , Zhu, Hong-Jian
- Date: 2024
- Type: Text , Journal article
- Relation: Cells Vol. 13, no. 2 (2024), p.
- Full Text: false
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- Description: Background: Glioblastoma is characterised by extensive infiltration into the brain parenchyma, leading to inevitable tumor recurrence and therapeutic failure. Future treatments will need to target the specific biology of tumour recurrence, but our current understanding of the underlying mechanisms is limited. Significantly, there is a lack of available methods and models that are tailored to the examination of tumour recurrence. Methods: NOD-SCID mice were orthotopically implanted with luciferase-labelled donor U87MG or MU20 glioblastoma cells. Four days later, an unlabelled recipient tumor was implanted on the contralateral side. The mice were euthanised at a humane end-point and tissue and blood samples were collected for ex vivo analyses. Results: The ex vivo analyses of the firefly-labelled MU20 tumours displayed extensive invasion at the primary tumour margins, whereas the firefly-labelled U87MG tumours exhibited expansive phenotypes with no evident invasions at the tumour margins. Luciferase signals were detected in the contralateral unlabelled recipient tumours for both the U87MG and MU20 tumours compared to the non-implanted control brain. Remarkably, tumour cells were uniformly detected in all tissue samples of the supratentorial brain region compared to the control tissue, with single tumour cells detected in some tissue samples. Circulating tumour cells were also detected in the blood samples of most of the xenografted mice. Moreover, tumour cells were detected in the lungs of all of the mice, a probable event related to haematogenous dissemination. Similar results were obtained when the U87MG cells were alternatively labelled with gaussian luciferase. Conclusions: These findings describe a systemic disease model for glioblastoma which can be used to investigate recurrence biology and therapeutic efficacy towards recurrence. © 2024 by the authors.
Adaptation of quadtree meshes in the scaled boundary finite element method for crack propagation modelling
- Authors: Ooi, Ean Tat , Man, Hou , Natarajan, Sundararajan , Song, Chongmin
- Date: 2015
- Type: Text , Journal article
- Relation: Engineering Fracture Mechanics Vol. 144, no. (2015), p. 101-117
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- Description: A crack propagation modelling technique combining the scaled boundary finite element method and quadtree meshes is developed. This technique automatically satisfies the compatibility requirement between adjacent quadtree cells irrespective of the presence of hanging nodes. The quadtree structure facilitates efficient data storage and rapid computations. Only a single cell is required to accurately model the stress field near crack tips. Crack growth is modelled by splitting the cells in the mesh into two. The resulting polygons are directly modelled by the scaled boundary formulation with minimal changes to the mesh. Four numerical examples demonstrate the salient features of the technique. © 2015.
Construction of generalized shape functions over arbitrary polytopes based on scaled boundary finite element method's solution of Poisson's equation
- Authors: Xiao, B. , Natarajan, Sundararajan , Birk, Carolin , Ooi, Ean Hin , Song, Chongmin , Ooi, Ean Tat
- Date: 2023
- Type: Text , Journal article
- Relation: International Journal for Numerical Methods in Engineering Vol. 124, no. 17 (2023), p. 3603-3636
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- Description: A general technique to develop arbitrary-sided polygonal elements based on the scaled boundary finite element method is presented. Shape functions are derived from the solution of the Poisson's equation in contrast to the well-known Laplace shape functions that are only linearly complete. The application of the Poisson shape functions can be complete up to any specific order. The shape functions retain the advantage of the scaled boundary finite element method allowing direct formulation on polygons with arbitrary number of sides and quadtree meshes. The resulting formulation is similar to the finite element method where each field variable is interpolated by the same set of shape functions in parametric space and differs only in the integration of the stiffness and mass matrices. Well-established finite element procedures can be applied with the developed shape functions, to solve a variety of engineering problems including, for example, coupled field problems, phase field fracture, and addressing volumetric locking in the near-incompressibility limit by adopting a mixed formulation. Application of the formulation is demonstrated in several engineering problems. Optimal convergence rates are observed. © 2023 The Authors. International Journal for Numerical Methods in Engineering published by John Wiley & Sons Ltd.
Changes in the chemistry of sedimentary organic matter within the Coorong over space and time
- Authors: Krull, Evelyn , Haynes, Deborah , Lamontagne, Sebastien , Gell, Peter , McKirdy, David , Hancock, Gary , McGowan, Janine , Smernik, Ronald
- Date: 2009
- Type: Text , Journal article
- Relation: Biogeochemistry Vol. 92, no. 1-2 (2009), p. 9-25
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- Description: Like many other coastal systems across the world, the Coorong lagoonal ecosystem (South Australia) has degraded over the last 100 years; in this case as a result of extensive regulation and diversions of water across the Murray-Darling Basin following European settlement. To evaluate whether the sources of organic matter (OM) supporting its food-web have changed since the inception of water management and barrage construction, sedimentary OM was characterised in cores spanning the Coorong’s salinity gradient at depths representative of the last 100 years over which the management alterations to river and estuarine flow were most marked. Detailed 210Pb, 137Cs and Pu dating in conjunction with palaeolimnological data (Pinus pollen) allowed for the reconstruction of the timing of substantial changes observed in the composition of the OM, most of which occur during the early 1950s, concurrent with management-related variations in water flow and salinity. Negative shifts in
The molecular epidemiology of influenza in Cambodia
- Authors: Suttie, Annika
- Date: 2019
- Type: Text , Thesis , PhD
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- Description: Avian influenza viruses (AIVs) represent a risk to the health of humans and animals. The prevalence of AIVs in live bird markets in Cambodia is among the highest in the world, being detected in 45.5% of tested poultry in 2015. To better understand the potential risk presented by AIVs, this thesis investigated the genetic characteristics of AIVs circulating in Cambodia between 2014 to 2018; focusing on subtypes that pose the greatest risk to human and animal health (H5, H7 and H9). Highly pathogenic (HP) H5N1 clade 2.3.2.1c viruses and low pathogenic H9N2 BJ/94-like h9-4.2.5 clade viruses were the most frequently detected subtypes, and circulate endemically in Cambodia’s domestic poultry. Co-infections were detected and facilitated the production of two novel reassortant H5N1 AIVs with single genes from H9N2 viruses. Additionally, numerous intrasubtypic reassortment events were detected for H5 and H9 AIVs. This is concerning as reassortment events can rapidly produce novel viruses of public health risk. Phylogenetic analyses showed some genes of the Cambodian H5, H7 and H9 AIVs clustered with zoonotic viruses, suggesting a common origin. There are parallels between H5N1 and H9N2 AIVs detected in Cambodia and Vietnam, likely facilitated through the illegal trade of live poultry and/or the migration of wild birds. Molecular analyses showed H9 AIVs have major markers associated with adaptation to mammals; though during the study period the only human AIV cases were the result of HP H5N1. Molecular markers of resistance to adamantine antivirals was observed in 3% of H5 and 41% of H9 AIVs; however, both subtypes remain susceptible to first line antiviral treatment, neuraminidase inhibitors. The data presented in this thesis demonstrates that circulation of Cambodian AIVs represents a risk for the emergence of novel viruses. Interventions are urgently needed to mitigate the threat posed to poultry and humans.
- Description: Doctor of Philosophy
Efficient data gathering in 3D linear underwater wireless sensor networks using sink mobility
- Authors: Akbar, Mariam , Javaid, Nadeem , Khan, Ayesha , Imran, Muhammad , Shoaib, Muhammad , Vasilakos, Athanasios
- Date: 2016
- Type: Text , Journal article
- Relation: Sensors (Switzerland) Vol. 16, no. 3 (2016), p.
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- Description: Due to the unpleasant and unpredictable underwater environment, designing an energy-efficient routing protocol for underwater wireless sensor networks (UWSNs) demands more accuracy and extra computations. In the proposed scheme, we introduce a mobile sink (MS), i.e., an autonomous underwater vehicle (AUV), and also courier nodes (CNs), to minimize the energy consumption of nodes. MS and CNs stop at specific stops for data gathering; later on, CNs forward the received data to the MS for further transmission. By the mobility of CNs and MS, the overall energy consumption of nodes is minimized. We perform simulations to investigate the performance of the proposed scheme and compare it to preexisting techniques. Simulation results are compared in terms of network lifetime, throughput, path loss, transmission loss and packet drop ratio. The results show that the proposed technique performs better in terms of network lifetime, throughput, path loss and scalability. © 2016 by the authors; licensee MDPI, Basel, Switzerland.
Finite element computations over quadtree meshes : Strain smoothing and semi-analytical formulation
- Authors: Natarajan, Sundararajan , Ooi, Ean Tat , Song, Chongmin
- Date: 2013
- Type: Text , Journal article
- Relation: International Journal of Advances in Engineering Sciences and Applied Mathematics Vol. 7, no. 3 (2013), p. 124-133
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- Description: In this paper, we discuss two alternate techniques to treat hanging nodes in a quadtree mesh. Both the techniques share similarities, in that, they require only boundary information. Moreover, they do not require an explicit form of the shape functions, unlike the conventional approaches, for example, as in the work of Gupta (Int J Numer Methods Eng 12:35, 1978) or Tabarraei and Sukumar (Finite Elem Anal Des 41:686, 2005). Hence, no special numerical integration technique is required. One of the techniques relies on the strain projection procedure, whilst the other is based on the scaled boundary finite element method. Numerical examples are presented to demonstrate the accuracy and the convergence properties of the two techniques.
'And for harmony most ardently we long' : Musical life in Ballarat, 1851-1871
- Authors: Doggett, Anne
- Date: 2006
- Type: Text , Thesis , PhD
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- Description: "The study examines two decades in the musical life of Ballarat, a regional city in south-eastern Australia. Beginning at the time of the 1851 gold rush, it covers the period in which Ballarat grew from a rough mining camp to an established city with a socially and ethnically diverse population of over 40,000 people. The thesis pursues the aim of looking at the music practices of the community in ways that will further our understanding of the significance of music in the lives of the people."--Abstract.
- Description: Doctor of Philosphy
Conical averagedness and convergence analysis of fixed point algorithms
- Authors: Bartz, Sedi , Dao, Minh , Phan, Hung
- Date: 2022
- Type: Text , Journal article
- Relation: Journal of Global Optimization Vol. 82, no. 2 (2022), p. 351-373
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- Description: We study a conical extension of averaged nonexpansive operators and the role it plays in convergence analysis of fixed point algorithms. Various properties of conically averaged operators are systematically investigated, in particular, the stability under relaxations, convex combinations and compositions. We derive conical averagedness properties of resolvents of generalized monotone operators. These properties are then utilized in order to analyze the convergence of the proximal point algorithm, the forward–backward algorithm, and the adaptive Douglas–Rachford algorithm. Our study unifies, improves and casts new light on recent studies of these topics. © 2021, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.
A scaled boundary finite element formulation with bubble functions for elasto-static analyses of functionally graded materials
- Authors: Ooi, Ean Tat , Song, Chongmin , Natarajan, Sundararajan
- Date: 2017
- Type: Text , Journal article
- Relation: Computational Mechanics Vol. 60, no. 6 (2017), p. 943-967
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- Description: This manuscript presents an extension of the recently-developed high order complete scaled boundary shape functions to model elasto-static problems in functionally graded materials. Both isotropic and orthotropic functionally graded materials are modelled. The high order complete properties of the shape functions are realized through the introduction of bubble-like functions derived from the equilibrium condition of a polygon subjected to body loads. The bubble functions preserve the displacement compatibility between the elements in the mesh. The heterogeneity resulting from the material gradient introduces additional terms in the polygon stiffness matrix that are integrated analytically. Few numerical benchmarks were used to validate the developed formulation. The high order completeness property of the bubble functions result in superior accuracy and convergence rates for generic elasto-static and fracture problems involving functionally graded materials. © 2017, Springer-Verlag GmbH Germany.
Magic and antimagic labeling of graphs
- Authors: Sugeng, Kiki Ariyanti
- Date: 2005
- Type: Text , Thesis , PhD
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- Description: "A bijection mapping that assigns natural numbers to vertices and/or edges of a graph is called a labeling. In this thesis, we consider graph labelings that have weights associated with each edge and/or vertex. If all the vertex weights (respectively, edge weights) have the same value then the labeling is called magic. If the weight is different for every vertex (respectively, every edge) then we called the labeling antimagic. In this thesis we introduce some variations of magic and antimagic labelings and discuss their properties and provide corresponding labeling schemes. There are two main parts in this thesis. One main part is on vertex labeling and the other main part is on edge labeling."
- Description: Doctor of Philosophy