ARC Centre of Excellence for Enabling Eco-Efficient Beneficiation of Minerals

Human spermatozoa are characterized by poor functionality and abundant DNA damage that collude to generate the high incidences of male infertility and miscarriage seen in our species. Although apoptosis has been suggested as a possible cause of poor sperm quality, the ability of these cells to enter an apoptotic state and the factors that might trigger such an event are unresolved. In the present study we provide evidence that the commitment of these cells to apoptosis is negatively regulated by PI3K (phosphoinositide 3-kinase)/AKT. If PI3K activity is inhibited, then spermatozoa default to an apoptotic cascade characterized by rapid motility loss, mitochondrial reactive oxygen species generation, caspase activation in the cytosol, annexin V binding to the cell surface, cytoplasmic vacuolization and oxidative DNA damage. However, the specialized physical architecture of spermatozoa subsequently prevents endonucleases activated during this process from penetrating the sperm nucleus and cleaving the DNA. As a result, DNA fragmentation does not occur as a direct result of apoptosis in spermatozoa as it does in somatic cells, even though oxidative DNA adducts can clearly be detected. We propose that this unusual truncated apoptotic cascade prepares spermatozoa for silent phagocytosis within the female tract and prevents DNA-damaged spermatozoa from participating in fertilization.

Machine learning algorithms are an important measure with which to perform landslide susceptibility assessments, but most studies use GIS-based classification methods to conduct susceptibility zonation. This study presents a machine learning approach based on the C5.0 decision tree (DT) model and the K-means cluster algorithm to produce a regional landslide susceptibility map. Yanchang County, a typical landslide-prone area located in northwestern China, was taken as the area of interest to introduce the proposed application procedure. A landslide inventory containing 82 landslides was prepared and subsequently randomly partitioned into two subsets: training data (70% landslide pixels) and validation data (30% landslide pixels). Fourteen landslide influencing factors were considered in the input dataset and were used to calculate the landslide occurrence probability based on the C5.0 decision tree model. Susceptibility zonation was implemented according to the cut-off values calculated by the K-means cluster algorithm. The validation results of the model performance analysis showed that the AUC (area under the receiver operating characteristic (ROC) curve) of the proposed model was the highest, reaching 0.88, compared with traditional models (support vector machine (SVM) = 0.85, Bayesian network (BN) = 0.81, frequency ratio (FR) = 0.75, weight of evidence (WOE) = 0.76). The landslide frequency ratio and frequency density of the high susceptibility zones were 6.76/km2 and 0.88/km2, respectively, which were much higher than those of the low susceptibility zones. The top 20% interval of landslide occurrence probability contained 89% of the historical landslides but only accounted for 10.3% of the total area. Our results indicate that the distribution of high susceptibility zones was more focused without containing more “stable” pixels. Therefore, the obtained susceptibility map is suitable for application to landslide risk management practices.

The purpose of this study was to evaluate the terminal deoxynucleotidyl transferase dUTP nick end labelling (TUNEL) assay as a method for assessing DNA damage in human spermatozoa. The conventional assay was shown to be insensitive and unresponsive to the DNA fragmentation induced in human and mouse spermatozoa on exposure to Fenton reagents (H₂O₂ and Fe(2+) ). However, both time- and dose-dependent responses could be readily detected if the chromatin was exposed to 2 mm dithiothreitol (DTT) for 45 min prior to fixation. This modified version of the assay significantly enhanced the TUNEL signals generated by subpopulations of spermatozoa isolated on discontinuous Percoll gradients as well as the responses triggered by reagents (arachidonic acid and menadione) that are known to stimulate superoxide anion production by human spermatozoa. DTT exposure also improved the signals detected with chromomycin A₃ (CMA₃), a probe designed to determine the efficacy of chromatin protamination, and enhanced the correlation observed between this criterion of sperm quality and the TUNEL assay. Finally, the output of the TUNEL assay was found to be highly correlated with sperm vitality. The TUNEL methodology was therefore further refined to incorporate a vital stain that covalently bound to intracellular amine groups in non-viable cells. This tag remained associated with the spermatozoa during fixation and processing for the TUNEL assay so that ultimately, both DNA integrity and vitality could be simultaneously assessed in the same flow cytometry assay. The methods described in this article are simple and robust and should facilitate research into the causes of DNA damage in human spermatozoa.

A comprehensive analysis of the proteins found in human spermatozoa is essential for understanding the events leading up to, and including, fertilization and development. Proteomics offers a platform for investigating this process, provided that the dynamic range is relatively low. In this report, spermatozoa from a number of human sperm ejaculates were isolated in a pure state using discontinuous Percoll gradient centrifugation. Triton X-100 soluble and insoluble proteins were recovered and separated by SDS-PAGE. The separation lanes were dissected into 96 fractions and analyzed individually by LC-MS(n) . A comprehensive protocol, involving LC-MS/MS analysis eventually down to the ninth most intense peak found in the MS-survey scan, was performed. Analysis of purified human sperm populations resulted in the identification of 1056 gene products, of which approximately 8% have not previously been characterized. The data were supported by the large number of proteins represented by expressed sequence tags in the testis. Bioinformatic analysis demonstrated that 437 of the gene products were involved in various metabolic pathways including glycolysis and oxidative phosphorylation. The inventory of proteins present in the human sperm proteome includes a number of notable discoveries including the first description of a nicotinamide adenine dinucleotide phosphate oxidase, dual-oxidase 2, finally laying to rest any doubts about the presence of such enzymes in spermatozoa. Furthermore, a number of different classes of receptor have also been detected in these cells and are potential regulators of sperm function. This list includes at least six seven-pass transmembrane receptors, six tyrosine kinase receptors, a tyrosine phosphatase receptor, glutamate-gated ion channel receptors, transient receptor potential cation channels, and a non-genomic progesterone receptor. This is the first published list of identified proteins in human spermatozoa using LC-MS/MS analysis.

Human spermatozoa generate low levels of reactive oxygen species in order to stimulate key events, such as tyrosine phosphorylation, associated with sperm capacitation. However, if the generation of these potentially pernicious oxygen metabolites becomes elevated for any reason, spermatozoa possess a limited capacity to protect themselves from oxidative stress. As a consequence, exposure of human spermatozoa to intrinsically- or extrinsically- generated reactive oxygen intermediates can result in a state of oxidative stress characterized by peroxidative damage to the sperm plasma membrane and DNA damage to the mitochondrial and nuclear genomes. Oxidative stress in the male germ line is associated with poor fertilization rates, impaired embryonic development, high levels of abortion and increased morbidity in the offspring, including childhood cancer. In this review, we consider the possible origins of oxidative damage to human spermatozoa and reflect on the important contribution such stress might make to the origins of genetic disease in our species.

Fertilization of the mammalian oocyte depends on the ability of spermatozoa to undergo a process known as capacitation as they ascend the female reproductive tract. A fundamental feature of this process is a marked increase in tyrosine phosphorylation by an unusual protein kinase A (PKA)-mediated pathway. To date, the identity of the intermediate PKA-activated tyrosine kinase driving capacitation is still unresolved. In this study, we have identified SRC as a candidate intermediate kinase centrally involved in the control of sperm capacitation. Consistent with this conclusion, the SRC kinase inhibitor SU6656 was shown to suppress both tyrosine phosphorylation and hyperactivation in murine spermatozoa. Moreover, SRC co-immunoprecipitated with PKA and this interaction was found to lead to an activating phosphorylation of SRC at position Y416. We have also used difference-in-2D-gel-electrophoresis (DIGE) in combination with mass spectrometry to identify a number of SRC substrates that become phosphorylated during capacitation including enolase, HSP90 and tubulin. Our data further suggest that the activation of SRC during capacitation is negatively controlled by C-terminal SRC kinase. The latter was localized to the acrosome and flagellum of murine spermatozoa by immunocytochemistry, whereas capacitation was associated with an inactivating serine phosphosphorylation of this inhibitory kinase.

Apoptosis is a critical process for regulating both the size and the quality of the male and female germ lines. In this review, we examine the importance of this process during embryonic development in establishing the pool of spermatogonial stem cells and primordial follicles that will ultimately define male and female fertility. We also consider the importance of apoptosis in controlling the number and quality of germ cells that eventually determine reproductive success. The biochemical details of the apoptotic process as it affects germ cells in the mature gonad still await resolution, as do the stimuli that persuade these cells to commit to a pathway that leads to cell death. Our ability to understand and ultimately control the reproductive potential of male and female mammals depends upon a deeper understanding of these fundamental processes.

Proteomic profiling of the mouse spermatozoon has generated a unique and valuable inventory of candidates that can be mined for potential contraceptive targets and to further our understanding of the PTMs that regulate the functionality of this highly specialized cell. Here we report the identification of 858 proteins derived from mouse spermatozoa, 23 of which demonstrated testis only expression. The list contained many proteins that are known constituents of murine spermatozoa including Izumo, Spaca 1, 3, and 5, Spam 1, Zonadhesin, Spesp1, Smcp, Spata 6, 18, and 19, Zp3r, Zpbp 1 and 2, Spa17, Spag 6, 16, and 17, CatSper4, Acr, Cylc2, Odf1 and 2, Acrbp, and Acrv1. Certain protein families were highly represented in the proteome. For example, of the 42 gene products classified as proteases, 26 belonged to the 26S-proteasome. Of the many chaperones identified in this proteome, eight proteins with a TCP-1 domain were found, as were seven Rab guanosine triphosphatases. Finally, our list yielded three putative seven-transmembrane proteins, two of which have no known tissue distribution, an extragenomic progesterone receptor and three unique testis-specific kinases all of which may have some potential in the future regulation of male fertility.

The presence of water strongly affects rock properties and would be related to a series of geological disasters. To understand water saturation effects on the mechanical behavior of different rock types and interpret the underlying mechanisms of differences in water sensitivity, three kinds of rocks, namely sandstone, granite and marble, were selected for tests. Uniaxial compression experiments were conducted on specimens under oven-dried and water-saturated conditions. Acoustic emission (AE) techniques were also applied to monitor and record AE signals during tests. Experimental results reveal that water weakens the mechanical parameters of the three tested rocks, such as uniaxial compressive strength (UCS), elastic modulus and critical strain. The sandstone undergoes the greatest weakening with the addition of pore water, the mechanical properties of the granite exhibit relatively minor reductions, while the marble is the least affected by water saturation. The water-weakening degree of rock properties depends on the porosity as well as the mineralogy, especially the proportion of quartz and swelling clays. Moreover, after water saturation, the failure pattern of the sandstone and the granite tends to transform into the shear-dominant mode from the tensile one in dry state, probably due to frictional reduction. However, the water presence does not change the failure mode of the marble.

This paper describes a comprehensive characterisation study carried out on clay from the National Soft Soil Testing Facility located at Ballina in northern New South Wales (NSW, Australia). Ballina clay represents the estuarine soft clays of high to extremely high plasticity from the Richmond river valley in NSW. They are structured and lightly overconsolidated with an average organic content around 3%. Index properties as well as mechanical parameters were estimated from laboratory tests performed on tube specimens retrieved using a fixed-piston sampler. Index characterisation tests were combined with constant rate of strain tests, incremental loading tests and stress-path triaxial testing to evaluate compressibility, stiffness, permeability and strength parameters. These deposits display very high compressibility and a low undrained shear strength which is larger in triaxial compression. Ballina clay shows a non-linear stress–strain response either in one-dimensional compression or undrained shearing. The consolidation coefficient, and consequently the water permeability, reduces dramatically with the stress level in the overconsolidated zone, mainly due to soil destructuration. A brittle response has been observed during shearing that reduces the undrained shear strength by around 50% after peak. Geotechnical profiles describing the variation of index and mechanical properties with depth are provided and compared against in situ test results. It is shown that the use of the fixed-piston sampler, in combination with non-destructive methods, to assess and select samples for laboratory testing provided good quality and reliable test results which are in agreement with data interpreted from in situ tests.

Demand for technologies delivering renewable energy and improving energy efficiencies are set to increase with the worldwide movement towards low carbon economies. Many of these technologies are reliant on “critical metals”: metals considered both important to society and vulnerable to supply disruption. Significant concentrations of critical metals have reported to mining and processing wastes over time; thus, an opportunity exists to meet critical metal demand through re-processing of these wastes. Mining and processing wastes have significantly different properties to run of mine ores. This means that while the overall mineral processing sequence for mining and processing wastes is the same as run of mine ore, the best technologies to achieve the liberation, separation, and concentration of critical metals is different. There are a range of innovative technologies that can be used to liberate and separate critical metals from mining and processing waste. Mineral liberation can be achieved using stirred milling, which breaks up particles and removes hydrophilic surface that can prevent particle flotation. Particle separation based on size can be achieved using semi-inverted cyclones and hybrid classification technologies. Separation of minerals from gangue can be achieved using flotation, with fluidised bed reactors and reactor-separator induced air reactors being suitable for coarse and fine particles, respectively. Gravity concentration using counter flow fluidised bed separators is also suitable for separating minerals from gangue. This review provides an overview of these technologies, as well as an introduction to the sequence of events when undertaking mineral processing, for an audience not specialised in this discipline. However, extraction of any metal value from tailings is contingent on detailed mineralogical characterisation. Three case studies are presented to demonstrate the analysis that is necessary as a crucial first step towards valorisation. Ultimately, implementation of these technologies to extract critical metals from mining and processing wastes will not only aid in meeting future critical metal demand but is essential for achieving a sustainable circular mining system with near-zero waste.

Landslide susceptibility prediction (LSP) modeling is an important and challenging problem. Landslide features are generally uncorrelated or nonlinearly correlated, resulting in limited LSP performance when leveraging conventional machine learning models. In this study, a deep-learning-based model using the long short-term memory (LSTM) recurrent neural network and conditional random field (CRF) in cascade-parallel form was proposed for making LSPs based on remote sensing (RS) images and a geographic information system (GIS). The RS images are the main data sources of landslide-related environmental factors, and a GIS is used to analyze, store, and display spatial big data. The cascade-parallel LSTM-CRF consists of frequency ratio values of environmental factors in the input layers, cascade-parallel LSTM for feature extraction in the hidden layers, and cascade-parallel full connection for classification and CRF for landslide/non-landslide state modeling in the output layers. The cascade-parallel form of LSTM can extract features from different layers and merge them into concrete features. The CRF is used to calculate the energy relationship between two grid points, and the extracted features are further smoothed and optimized. As a case study, the cascade-parallel LSTM-CRF was applied to Shicheng County of Jiangxi Province in China. A total of 2709 landslide grid cells were recorded and 2709 non-landslide grid cells were randomly selected from the study area. The results show that, compared with existing main traditional machine learning algorithms, such as multilayer perception, logistic regression, and decision tree, the proposed cascade-parallel LSTM-CRF had a higher landslide prediction rate (positive predictive rate: 72.44%, negative predictive rate: 80%, total predictive rate: 75.67%). In conclusion, the proposed cascade-parallel LSTM-CRF is a novel data-driven deep learning model that overcomes the limitations of traditional machine learning algorithms and achieves promising results for making LSPs.

Summary The first part of the paper presents a material point method solution for the bearing capacity of a deep foundation in purely cohesive soil, which is a widely known engineering problem. The results computed with the generalised interpolation material point method are compared to the results obtained previously with an advanced limit analysis code. The second part of the paper shows material point method simulations of collapsing piles of granular material and compares the results with experimental observations from the literature. The problems considered are problematic to solve using the displacement finite element method as they generally include very large deformations. Copyright © 2014 John Wiley & Sons, Ltd.

Difference in two-dimensional (2-D) gel electrophoresis (DIGE) is a novel method for analyzing up to three samples in one 2-D gel and using the information gained to study post-translational modifications of proteins. We describe the use of DIGE to isolate and characterize those proteins that undergo processing in spermatozoa as they transit the epididymal tract. We find up to 60 protein spots are significantly modified as sperm traverse the epididymis. In this article, we report eight unambiguous protein identifications and demonstrate that one protein, the beta-subunit of the mitochondrial F1-ATPase, is serine-phosphorylated as sperm undergo epididymal maturation. We suggest that phosphorylation of this particular protein in a cAMP-dependent manner may contribute to the mechanisms by which motility is conferred upon spermatozoa.

The spatial variability of soil properties is often assumed to be modeled as stationary or weakly stationary random fields in slope reliability analyses. However, abundant site-specific data have revealed that the mean and standard deviation of soil properties, such as the undrained shear strength of soil, change with depth. Thus, the non-stationary characteristics of soil properties need to be properly accounted for. The aim of this paper is to propose a non-stationary random field (RF) model for the characterization of the spatial variability and the depth-dependent nature of the undrained shear strength of soil. With the proposed model, the uncertainties of the trend and fluctuating components can be modeled individually. As an example, a clay slope under undrained conditions is investigated to illustrate the proposed model. A subset simulation is carried out to evaluate the slope reliability incorporating the non-stationary characteristics of soil properties. The advantages of the proposed model, relative to the existing non-stationary RF models and the commonly-used stationary RF model in the literature, are demonstrated through a series of sensitivity studies.

Abstract Proteomics represents a powerful tool for the analysis of mammalian spermatozoa, since these terminally differentiated cells are transcriptionally inactive and exhibit a limited dynamic range of protein expression. Here we report the identification of 5123 peptides, leading to 829 unambiguous and 2215 redundant gene products found to be present within rat spermatozoa derived from the cauda epididymis. Bioinformatics demonstrated that 60 proteins appeared to be specifically expressed in the genitourinary tract, including pyruvate dehydrogenase 1, ropporin, testis‐specific serine kinase 4, testis‐specific transporter, and retinol dehydrogenase 14. We also identified eight members of the ADAM family, seven of which have previously been detected in spermatozoa (ADAM2, ‐3, ‐4, ‐5, ‐6, ‐7, and ‐30) while ADAM34 has been identified in the sperm proteome for the first time. Approximately 21 gene products were found to possess isomerase activity including peptidylprolyl cis / trans isomerases that are known to be involved in germ cell differentiation and protein disulfide isomerases that have been implicated in sperm–oocyte fusion. Furthermore, 51 gene products clustered into ion‐transporter activity. This inventory of gene products, the first ever 2‐D LC‐MS/MS analysis of rat spermatozoa, will be invaluable in directing future research into the molecular mechanisms that drive these highly specialized cells.

Effects of pyrolysis pressure on char reactivity remain a poorly understood aspect of the coal gasification process. In an attempt to address this problem, effects of pyrolysis pressure on char structure and reactivity are being investigated. In this paper, chemical reactivities to O2, CO2, and H2O of chars made from three Australian black coals were measured in a pressurized thermogravimetric analyzer, under conditions where chemical processes alone controlled reaction rates. These chars were prepared at a range of pyrolysis pressures, using pressurized flow reactors and an atmospheric pressure tube furnace, to ascertain any effects of devolatilization pressure and heating rate on the chemical reactivity of the resultant coal chars. It was found that while the apparent (as measured) reaction rate can be affected by pyrolysis pressure, the rate normalized to the char surface area (intrinsic rate) is much less affected, because of large effects of pyrolysis pressure on char micropore surface area. This finding was supported by measurements of char carbon crystallite dimensions that were unaffected by pyrolysis pressure increases. These results indicate that effects of pyrolysis pressure and heating rate on char gasification rates are more likely to be due to effects of structure and surface area and (depending on reaction conditions) the consequent effects on diffusion of reactants to the char surface, rather than on the intrinsic reactivity of the coal chars.

The process of sperm capacitation is correlated with activation of a signal transduction pathway leading to protein tyrosine phosphorylation. Whereas phosphotyrosine expression is an essential prerequisite for fertilization, the proteins that are phosphorylated during capacitation have not yet been identified. In the present study, we observed that a major target of this signaling pathway is the molecular chaperone protein, heat shock protein (HSP)-86, a member of the HSP-90 family of HSPs. We used cross-immunoprecipitation experiments to confirm the tyrosine phosphorylation of HSP-86, a process that is not inhibited by the ansamycin antibiotic, geldanamycin. The general significance of these findings was confirmed by studies in which HSP-90 was also found to be tyrosine phosphorylated in human and rat spermatozoa when incubated under conditions that support capacitation. To our knowledge, these results represent the first report of a protein that undergoes tyrosine phosphorylation during mouse sperm capacitation and the first study implicating molecular chaperones in the processes by which mammalian spermatozoa gain the ability to fertilize the oocyte.

Accurate prediction of surface subsidence due to the extraction of underground coal seams is a significant challenge in geotechnical engineering. This task is further compounded by the growing trend for coal to be extracted from seams either above or below previously extracted coal seams, a practice known as multi-seam mining. In order to accurately predict the subsidence above single and multi-seam longwall panels using numerical methods, constitutive laws need to appropriately represent the mechanical behaviour of coal measure strata. The choice of the most appropriate model is not always straightforward. This paper compares predictions of surface subsidence obtained using the finite element method, considering a range of well-known constitutive models. The results show that more sophisticated and numerically taxing constitutive laws do not necessarily lead to more accurate predictions of subsidence when compared to field measurements. The advantages and limitations of using each particular constitutive law are discussed. A comparison of the numerical predictions and field measurements of surface subsidence is also provided.

Biochar is an emerging negative emission technology. Its ability to sequester carbon and subsequent carbon credit valuation hinge on the stability of its carbon structure. The widely used indicators of carbon stability H:Corg and O:Corg provide conservative results as these are based on limited incubation experiments and associated modeling results. The results from these accepted methods and other derived methods have not been compared as indicators of carbon stability in a variety of biochar samples. Furthermore, the influence of contrasting feedstock and production techniques on biochar carbon stability is not well explored. Therefore, to address these challenges, a comprehensive stability analysis of 21 different biochar samples with contrasting feedstocks and pyrolysis techniques was conducted using a combination of instrumental methods and derived indicators of carbon stability. Methods such as biochar carbon half-life, thermo-stable fraction, oxidation resistance (R50), and carbon sequestration potential (CS) were used. Based on the initial carbon content of the biochar, simple pyrolysis techniques have similar potential for carbon credits as biochar produced from advanced pyrolysis techniques. Results indicate that the carbon stability of a biochar product is primarily a factor of feedstock type. We found that biochar carbon stability is not related to volatile matter or fixed carbon content for biochar produced using a simple pyrolysis technique and mixed feedstock. Biochars with H:Corg < 0.4 were deemed to have lower carbon stability when compared using different methods. No correlation was observed between the carbon stability of biochar using H:Corg and other methods, however, correlations were observed between half-life, O:Corg, fixed carbon, number of aromatic peaks in FTIR spectrum, R50, and CS. Therefore, it is recommended that data from additional incubation and modeling studies need to be considered to increase the confidence in carbon stability results having major implications to carbon credits.