Noise removal from wave-forms and spectrograms derived from natural recordings of the environment

The work described in this technical report is part of an ongoing project to build practical tools for the manipulation, analysis and visualisation of recordings of the natural environment. This report describes the methods we use to remove background noise from spectrograms. It updates techniques previously described in Towsey and Planitz (2011), Technical report: acoustic analysis of the natural environment, downloadable from: http://eprints.qut.edu.au/41131/. It also describes noise removal from wave-forms, a technique not described in the above 2011 technical report.

Automated marine mammal detection from aerial imagery

This paper presents two algorithms to automate the detection of marine species in aerial imagery. An algorithm from an initial pilot study is presented in which morphology operations and colour analysis formed the basis of its working principle. A second approach is presented in which saturation channel and histogram-based shape profiling were used. We report on performance for both algorithms using datasets collected from an unmanned aerial system at an altitude of 1000 ft. Early results have demonstrated recall values of 48.57% and 51.4%, and precision values of 4.01% and 4.97%.

Climate variability over the last 35,000 years recorded in marine and terrestrial archives in the Australian region : an OZ-INTIMATE compilation

The Australian region spans some 60° of latitude and 50° of longitude and displays considerable regional climate variability both today and during the Late Quaternary. A synthesis of marine and terrestrial climate records, combining findings from the Southern Ocean, temperate, tropical and arid zones, identifies a complex response of climate proxies to a background of changing boundary conditions over the last 35,000 years. Climate drivers include the seasonal timing of insolation, greenhouse gas content of the atmosphere, sea level rise and ocean and atmospheric circulation changes. Our compilation finds few climatic events that could be used to construct a climate event stratigraphy for the entire region, limiting the usefulness of this approach. Instead we have taken a spatial approach, looking to discern the patterns of change across the continent. The data identify the clearest and most synchronous climatic response at the time of the Last Glacial Maximum (LGM) (21 ± 3 ka), with unambiguous cooling recorded in the ocean, and evidence of glaciation in the highlands of tropical New Guinea, southeast Australia and Tasmania. Many terrestrial records suggest drier conditions, but with the timing of inferred snowmelt, and changes to the rainfall/runoff relationships, driving higher river discharge at the LGM. In contrast, the deglaciation is a time of considerable south-east to north-west variation across the region. Warming was underway in all regions by 17 ka. Post-glacial sea level rise and its associated regional impacts have played an important role in determining the magnitude and timing of climate response in the north-west of the continent in contrast to the southern latitudes. No evidence for cooling during the Younger Dryas chronozone is evident in the region, but the Antarctic cold reversal clearly occurs south of Australia. The Holocene period is a time of considerable climate variability associated with an intense monsoon in the tropics early in the Holocene, giving way to a weakened monsoon and an increasingly El Niño-dominated ENSO to the present. The influence of ENSO is evident throughout the southeast of Australia, but not the southwest. This climate history provides a template from which to assess the regionality of climate events across Australia and make comparisons beyond our region. The data identify the clearest and most synchronous climatic response at the time of the Last Glacial Maximum (LGM) (21 ± 3 ka), with unambiguous cooling recorded in the ocean, and evidence of glaciation in the highlands of tropical New Guinea, southeast Australia and Tasmania. Many terrestrial records suggest drier conditions, but with the timing of inferred snowmelt, and changes to the rainfall/runoff relationships, driving higher river discharge at the LGM. In contrast, the deglaciation is a time of considerable south-east to north-west variation across the region. Warming was underway in all regions by 17 ka. Post-glacial sea level rise and its associated regional impacts have played an important role in determining the magnitude and timing of climate response in the north-west of the continent in contrast to the southern latitudes. No evidence for cooling during the Younger Dryas chronozone is evident in the region, but the Antarctic cold reversal clearly occurs south of Australia. The Holocene period is a time of considerable climate variability associated with an intense monsoon in the tropics early in the Holocene, giving way to a weakened monsoon and an increasingly El Niño-dominated ENSO to the present. The influence of ENSO is evident throughout the southeast of Australia, but not the southwest. This climate history provides a template from which to assess the regionality of climate events across Australia and make comparisons beyond our region.

Removal of phosphorus using NZVI derived from reducing natural goethite

Nano zero valent iron (NZVI) prepared by reducing natural goethite in hydrogen at 550 °C was used to remove phosphate. The effect of particle size, reaction time, NZVI dose, pH, initial phosphorus concentration, and oxygen amount in reaction system on phosphorus removal was investigated. The characterization of X-ray fluorescence (XRF), X-ray diffraction (XRD), N2 adsorption and desorption (BET analysis), transmission electron microscope (TEM), field emission scanning electron microscope with a energy dispersive X-ray detector (FESEM/EDS) and X-ray photoelectron spectroscopy (XPS) indicated that nanoscale of iron (around 80–150 nm length and 5–30 nm width) was prepared successfully with high dispersion and relative large surface area around 22 m2/g. The results of batch experiments and XPS analysis suggested that this kind of NZVI had a good performance on removal of phosphate (over 99%) despite in slightly acidic media as the initial concentration of P was 5 mg/L. The reason was ascribed to the effective corrosion of this NZVI under the function of proton and dissolved oxygen in spite of the existence of thin passive films.

NSAM-derived total surface area vs. SMPS-derived "mobility equivalent" surface area for different environmentally relevant aerosols

The surface area of inhaled particles deposited in the alveolar region, as reported by the TSI nanoparticle surface area monitor (NSAM), was compared with the corresponding value estimated by a TSI scanning mobility particle sizer (SMPS) for a range of environmentally relevant aerosols, including petrol emissions, ETS, laser printer emissions, cooking emissions and ambient aerosols. The SMPS values were based on a mobility size distribution assuming spherical particles using the appropriate size-dependent alveolar-deposition factors provided by the ICRP. In most cases, the two instruments showed good linear agreement. With petrol emissions and ETS, the linearity extended to over 103 μm2 cm-3. With printer emissions, there was good linearity up to about 300 μm2 cm-3 while the NSAM increasingly overestimated the surface area at higher concentrations. The presence of a nucleation event in ambient air caused the NSAM to over-estimate the surface area by a factor of 2. We summarize these results and conclude that the maximum number concentration up to which the NSAM is accurate clearly depends on the type of aerosol being sampled and provide guidance for the use of the instrument.

Immunosuppressive properties of mesenchymal stromal cell cultures derived from the limbus of human and rabbit corneas

Background aims Mesenchymal stromal cells (MSCs) cultivated from the corneal limbus (L-MSCs) provide a potential source of cells for corneal repair. In the present study, we investigated the immunosuppressive properties of human L-MSCs and putative rabbit L-MSCs to develop an allogeneic therapy and animal model of L-MSC transplantation. Methods MSC-like cultures were established from the limbal stroma of human and rabbit (New Zealand white) corneas using either serum-supplemented medium or a commercial serum-free MSC medium (MesenCult-XF Culture Kit; Stem Cell Technologies, Melbourne, Australia). L-MSC phenotype was examined by flow cytometry. The immunosuppressive properties of L-MSC cultures were assessed using mixed leukocyte reactions. L-MSC cultures were also tested for their ability to support colony formation by primary limbal epithelial (LE) cells. Results Human L-MSC cultures were typically CD34−, CD45− and HLA-DR− and CD73+, CD90+, CD105+ and HLA-ABC+. High levels (>80%) of CD146 expression were observed for L-MSC cultures grown in serum-supplemented medium but not cultures grown in MesenCult-XF (approximately 1%). Rabbit L-MSCs were approximately 95% positive for major histocompatibility complex class I and expressed lower levels of major histocompatibility complex class II (approximately 10%), CD45 (approximately 20%), CD105 (approximately 60%) and CD90 (<10%). Human L-MSCs and rabbit L-MSCs suppressed human T-cell proliferation by up to 75%. Conversely, L-MSCs from either species stimulated a 2-fold to 3-fold increase in LE cell colony formation. Conclusions L-MSCs display immunosuppressive qualities in addition to their established non-immunogenic profile and stimulate LE cell growth in vitro across species boundaries. These results support the potential use of allogeneic L-MSCs in the treatment of corneal disorders and suggest that the rabbit would provide a useful pre-clinical model.

Practical applications for clay-derived zeolite N : an ammonium-selective ion exchanger for industry use

Over the past ten years, scaled-up utilisation of a previously under-exploited zeolite, Zeolite N1, has been demonstrated for selective ion exchange of ammonium and other ions in aqueous environments. As with many zeolite syntheses, the required source material should contain predictable levels of aluminium and silicon and, for full-scale industrial applications, kaolin and/or montmorillonite serve such a purpose. Field, pilot and commercial scale trials of kaolin-derived Zeolite N have focused on applications in agriculture and water treatment as these sectors are primary producers or users of ammonium. The format for the material – as fine powders, granules or extrudates – depends on the specific application albeit each has been evaluated.

Saliva-derived DNA performs well in large-scale, high-density single-nucleotide polymorphism microarray studies

As of June 2009, 361 genome-wide association studies (GWAS) had been referenced by the HuGE database. GWAS require DNA from many thousands of individuals, relying on suitable DNA collections. We recently performed a multiple sclerosis (MS) GWAS where a substantial component of the cases (24%) had DNA derived from saliva. Genotyping was done on the Illumina genotyping platform using the Infinium Hap370CNV DUO microarray. Additionally, we genotyped 10 individuals in duplicate using both saliva- and blood-derived DNA. The performance of blood- versus saliva-derived DNA was compared using genotyping call rate, which reflects both the quantity and quality of genotyping per sample and the “GCScore,” an Illumina genotyping quality score, which is a measure of DNA quality. We also compared genotype calls and GCScores for the 10 sample pairs. Call rates were assessed for each sample individually. For the GWAS samples, we compared data according to source of DNA and center of origin. We observed high concordance in genotyping quality and quantity between the paired samples and minimal loss of quality and quantity of DNA in the saliva samples in the large GWAS sample, with the blood samples showing greater variation between centers of origin. This large data set highlights the usefulness of saliva DNA for genotyping, especially in high-density single-nucleotide polymorphism microarray studies such as GWAS.

Microalgal species selection for biodiesel production based on fuel properties derived from fatty acid profiles

Physical and chemical properties of biodiesel are influenced by structural features of the fatty acids, such as chain length, degree of unsaturation and branching of the carbon chain. This study investigated if microalgal fatty acid profiles are suitable for biodiesel characterization and species selection through Preference Ranking Organisation Method for Enrichment Evaluation (PROMETHEE) and Graphical Analysis for Interactive Assistance (GAIA) analysis. Fatty acid methyl ester (FAME) profiles were used to calculate the likely key chemical and physical properties of the biodiesel [cetane number (CN), iodine value (IV), cold filter plugging point, density, kinematic viscosity, higher heating value] of nine microalgal species (this study) and twelve species from the literature, selected for their suitability for cultivation in subtropical climates. An equal-parameter weighted (PROMETHEE-GAIA) ranked Nannochloropsis oculata, Extubocellulus sp. and Biddulphia sp. highest; the only species meeting the EN14214 and ASTM D6751-02 biodiesel standards, except for the double bond limit in the EN14214. Chlorella vulgaris outranked N. oculata when the twelve microalgae were included. Culture growth phase (stationary) and, to a lesser extent, nutrient provision affected CN and IV values of N. oculata due to lower eicosapentaenoic acid (EPA) contents. Application of a polyunsaturated fatty acid (PUFA) weighting to saturation led to a lower ranking of species exceeding the double bond EN14214 thresholds. In summary, CN, IV, C18:3 and double bond limits were the strongest drivers in equal biodiesel parameter-weighted PROMETHEE analysis.

Impact of extracellular matrix derived from osteoarthritis subchondral bone osteoblasts on osteocytes : role of integrinβ1 and focal adhesion kinase signaling cues

INTRODUCTION: Our recent study indicated that subchondral bone pathogenesis in osteoarthritis (OA) is associated with osteocyte morphology and phenotypic abnormalities. However, the mechanism underlying this abnormality needs to be identified. In this study we investigated the effect of extracellular matrix (ECM) produced from normal and OA bone on osteocytic cells function. METHODS: De-cellularized matrices, resembling the bone provisional ECM secreted from primary human subchondral bone osteoblasts (SBOs) of normal and OA patients were used as a model to study the effect on osteocytic cells. Osteocytic cells (MLOY4 osteocyte cell line) cultured on normal and OA derived ECMs were analyzed by confocal microscopy, scanning electron microscopy (SEM), cell attachment assays, zymography, apoptosis assays, qRT-PCR and western blotting. The role of integrinβ1 and focal adhesion kinase (FAK) signaling pathways during these interactions were monitored using appropriate blocking antibodies. RESULTS: The ECM produced by OA SBOs contained less mineral content, showed altered organization of matrix proteins and matrix structure compared with the matrices produced by normal SBOs. Culture of osteocytic cells on these defective OA ECM resulted in a decrease of integrinβ1 expression and the de-activation of FAK cell signaling pathway, which subsequently affected the initial osteocytic cell's attachment and functions including morphological abnormalities of cytoskeletal structures, focal adhesions, increased apoptosis, altered osteocyte specific gene expression and increased Matrix metalloproteinases (MMP-2) and -9 expression. CONCLUSION: This study provides new insights in understanding how altered OA bone matrix can lead to the abnormal osteocyte phenotypic changes, which is typical in OA pathogenesis.

Higher harmonic large-amplitude fourier transformed alternating current voltammetry : analytical attributes derived from studies of the oxidation of ferrocenemethanol and uric acid at a glassy carbon electrode

An analytical evaluation of the higher ac harmonic components derived from large amplitude Fourier transformed voltammetry is provided for the reversible oxidation of ferrocenemethanol (FcMeOH) and oxidation of uric acid by an EEC mechanism in a pH 7.4 phosphate buffer at a glassy carbon (GC) electrode. The small background current in the analytically optimal fifth harmonic is predominantly attributed to faradaic current associated with the presence of electroactive functional groups on the GC electrode surface, rather than to capacitive current which dominates the background in the dc, and the initial three ac harmonics. The detection limits for the dc and the first to fifth harmonic ac components are 1.9, 5.89, 2.1, 2.5, 0.8, and 0.5 µM for FcMeOH, respectively, using a sine wave modulation of 100 mV at 21.46 Hz and a dc sweep rate of 111.76 mV s−1. Analytical performance then progressively deteriorates in the sixth and higher harmonics. For the determination of uric acid, the capacitive background current was enhanced and the reproducibility lowered by the presence of surface active uric acid, but the rapid overall 2e− rather than 1e– electron transfer process gives rise to a significantly enhanced fifth harmonic faradaic current which enabled a detection limit of 0.3 µM to be achieved which is similar to that reported using chemically modified electrodes. Resolution of overlapping voltammetric signals for a mixture of uric acid and dopamine is also achieved using higher fourth or fifth harmonic components, under very low background current conditions. The use of higher fourth and fifth harmonics exhibiting highly favorable faradaic to background (noise) current ratios should therefore be considered in analytical applications under circumstances where the electron transfer rate is fast.

An outbreak of salmonellosis linked to a marine turtle

In September 1998, an outbreak of gastroenteritis occurred in a coastal Aboriginal community in the Northern Territory over a seven day period. An investigation was conducted by the Center for Disease Control, Territory Health Services. Thirty-six cases were detected and 17% (n=6) were hospitalized. Salmonella chester was isolated from eight of nine stool specimens. Sixty-two percent of cases interviewed (n=28) reported consumption of a green turtle (Chelonia mydas) within a median of 24 hours prior to onset of illness. Of the remainder, all but two were contacts of other cases. Salmonella chester was isolated from a section of partially cooked turtle meat. There are no previous published reports of salmonellosis associated with consumption of sea turtles despite them being a popular food source in coastal communities in the Pacific.

COX-derived prostanoid pathways in gastrointestinal cancer development and progression : novel targets for prevention and intervention

Arachidonic acid metabolism through cyclooxygenase (COX) pathways leads to the generation of biologically active eicosanoids. Eicosanoid expression levels vary during development and progression of gastrointestinal (GI) malignancies. COX-2 is the major COX-isoform responsible for G.I. cancer development/progression. COX-2 expression increases during progression from a normal to cancerous state. Evidence from observational studies has demonstrated that chronic NSAID use reduces the risk of cancer development, while both incidence and risk of death due to G.I. cancers were significantly reduced by daily aspirin intake. A number of randomized controlled trials (APC trial, Prevention of Sporadic Adenomatous Polyps trial, APPROVe trial) have also shown a significant protective effect in patients receiving selective COX-2 inhibitors. However, chronic use of selective COX-2 inhibitors at high doses was associated with increased cardiovascular risk, while NSAIDs have also been associated with increased risk. More recently, downstream effectors of COX-signaling have been investigated in cancer development/progression. PGE 2, which binds to both EP and PPAR receptors, is the major prostanoid implicated in the carcinogenesis of G.I. cancers. The role of TXA 2 in G.I. cancers has also been examined, although further studies are required to uncover its role in carcinogenesis. Other prostanoids investigated include PGD 2 and its metabolite 15d-PGJ2, PGF 1α and PGI 2. Targeting these prostanoids in G.I. cancers has the promise of avoiding cardiovascular toxicity associated with chronic selective COX-2 inhibition, while maintaining anti-tumor reactivity.A progressive sequence from normal to pre-malignant to a malignant state has been identified in G.I. cancers. In this review, we will discuss the role of the COX-derived prostanoids in G.I. cancer development and progression. Targeting these downstream prostanoids for chemoprevention and/or treatment of G.I. cancers will also be discussed. Finally, we will highlight the latest pre-clinical technologies as well as avenues for future investigation in this highly topical research field. © 2011 Elsevier B.V.

Platelet-derived endothelial cell growth factor expression and angiogenesis in cervical intraepithelial neoplasia and squamous cell carcinoma of the cervix

Growth and metastatic spread of invasive carcinoma depends on angiogenesis, the formation of new blood vessels. Platelet-derived endothelial cell growth factor (PD-ECGF) is an angiogenic growth factor for a number of solid tumors, including lung, bladder, colorectal, and renal cell cancer. Cervical intraepithelial neoplasia (CIN) is the precursor to squamous cell cervical carcinoma (SCC). Mean vessel density (MVD) increases from normal cervical tissue, through low- and high-grade CIN to SCC. We evaluated PD-ECGF immunoreactivity and correlated its expression with MVD in normal, premalignant, and malignant cervical tissue. PD-ECGF expression was assessed visually within the epithelial tissues and scored on the extent and intensity of staining. MVD was calculated by counting the number of vessels positive for von Willebrand factor per unit area subtending normal or CIN epithelium or within tumor hotspots for SCC. Cytoplasmic and/or nuclear PD-ECGF immunoreactivity was seen in normal epithelium. PD-ECGF expression significantly increased with histologic grade from normal, through low- and high-grade CIN, to SCC (P < .02). A progressive significant increase in the microvessel density was also seen, ranging from a mean of 28 vessels for normal tissue to 57 for SCC (P < .0005). No correlation was found between PD-ECGF expression and MVD (P = .45). We conclude that PD-ECGF expression and MVD increase as the cervix transforms from a normal to a malignant phenotype. PD-ECGF is thymidine phosphorylase, a key enzyme in the activation of fluoropyrimidines, including 5-fluorouracil. Evaluation of PD-ECGF thymidine phosphorylase expression may be important in designing future chemotherapeutic trials in cervical cancer. Copyright (C) 2000 by W.B. Saunders Company.

Platelet-derived endothelial cell growth factor (thymidine phosphorylase) expression in lung cancer

Platelet-derived endothelial cell growth factor/thymidine phosphorylase (PD-ECGF/TP) is an enzyme with angiogenic and cell motility properties. Moreover, it is involved in the transformation of fluoropyrimidines into active cytotoxic metabolites, In the present study, the expression of PD-ECGF in normal lung and lung cancer was immunohistochemically evaluated using the P-GF.44C monoclonal antibody. Alveolar and tumoural macrophages mere invariably stained and mere used as an internal control for assessment of the staining. Alveolar epithelium was always negative, whilst bronchiolar epithelium showed occasional positive reactivity. Normal lung and tumour endothelium was occasionally positive, Positive staining in more than 50 per cent of cells was observed in 23/71 squamous carcinomas (32 per cent), 16/38 (42 per cent) adenocarcinomas, and 2/6 (33 per cent) adenosquamous carcinomas. Differentiated areas and areas of squamous metaplasia mere more strongly positive than other tumour areas. All 22 small cell carcinomas and one carcinoid tumour were negative. The present study provides a baseline for future studies in non-small cell lung cancer to correlate PD-ECGF expression with tumour vascularization, prognosis, and response to chemotherapy.