Faster and parameter-free discord search in quasi-periodic time series

Time series discord has proven to be a useful concept for time-series anomaly identification. To search for discords, various algorithms have been developed. Most of these algorithms rely on pre-building an index (such as a trie) for subsequences. Users of these algorithms are typically required to choose optimal values for word-length and/or alphabet-size parameters of the index, which are not intuitive. In this paper, we propose an algorithm to directly search for the top-K discords, without the requirement of building an index or tuning external parameters. The algorithm exploits quasi-periodicity present in many time series. For quasi-periodic time series, the algorithm gains significant speedup by reducing the number of calls to the distance function.

The global mio-pliocene climatic equability and coastal ostracod faunas of southeast Australia

This study on the Mio–Pliocene ostracod successions of southeast Australia outlines several faunal events indicative of climate warming and/or increased rainfall events. Ostracod faunas associated with a late Late Miocene sea level rise event suggest that the climate of this time in southeast Australia was similar to, or slightly warmer than that of present day southeast Australia. However, it was probably wetter and significantly warmer than immediately preceding (mid Late Miocene) palaeoclimatic conditions within the region. Evidence for a change to wetter and warmer conditions during the late Late Miocene is seen in the appearance of various extant euryhaline and semi-thermophilic ostracod species in coastal ostracod faunas. The appearance of euryhaline species, which are mostly absent from older shallow marine Cenozoic strata of the Bass Strait hinterland, suggests a major influx of fresh water into coastal marine settings, which contributed to the initial phase of development of the southeast Australian late Neogene barrier coastline and associated marginal marine palaeoenvironments.

During the time interval latest Miocene to earliest Pliocene, and during the early Late Pliocene, two subsequent global sea level rise events are also preserved in the southeast Australian coastal plain. Many of the species present in ostracod faunas associated with these two events are the same as in older local late Late Miocene faunas. In earliest (?) Pliocene faunas, there is minor evidence for the reappearance of semi-thermophilic ostracods. Faunas of early Late Pliocene age often exhibit a conspicuous faunal dominance by, or large abundance of euryhaline species, indicating the particularly strong influence of fresh water influxes into coastal marine palaeoenvironments. This may reflect the presence of especially wet local temperate palaeoclimatic conditions during a time of equable global climates.

Succeeding estuarine, lagoonal and coastal embayment ostracod faunas of late Late Pliocene age are associated with marginal marine sediments that are interbedded with coastal dune aeolianites. This suggests an overall seaward retreat of marginal marine environments that was initiated by a major global sea level fall linked to the onset of cooler Late Pliocene and Quaternary global climates.

Modelling of birds and locust-control operations in Eastern Australia

Locust outbreaks provide an abundant, but unpredictable food source for many native species in Australia. For economic reasons, locust control is unavoidable and can affect a considerable area in Eastern Australia. Depending on the pesticide applied, locust control operations may affect birds in treated areas, either directly through intoxication of the predator, or indirectly, through elimination of its prey. As a preliminary step in identifying the potential impact of these operations on native species, the co-occurrence of birds and locust control operations was assessed using GIS mapping techniques. Data from the Birds of Australia New Atlas provided information about species' distribution between latitudes 17 and 37 degree S, and longitudes 136 and 152 degree E. Of the 834 species present in this region, 292 were chosen on the basis of their geographical distribution and occurrence west of the Great Dividing Range. Sightings for each species were mapped using reporting rates and number of observations per half-degree grid cells. Birds were categorised by habitat, distribution, movement and feeding habits and those species reported to consume Orthopterans were noted. APLC locust survey (1987–2000) and spraying data (1977–2002) were analysed and overlapped with soil and vegetation maps obtained from Geoscience Australia and Environment Australia to find significant hotspots for locust occurrence. These maps were then overlayed with bird distributions to identify the species most likely to be in areas of locust presence and spraying operations.

Effects of phytophthora cinnamomi on heathland flora and fauna of the Eastern Otway Ranges

The plant pathogen, Phytophthora dnnamomi, is a cause of dieback disease observed in sclerophyll vegetation in Australia, The effects of P. dnnamomi on flora and fauna were studied at two locations in heathland vegetation near the coastal town of Anglesea, Victoria. The pathogen was isolated from soils beneath diseased heathland plants. The extent of diseased vegetation was assessed by the presence and absence of highly sensitive indicator species, Xanthorrhoea australis and hopogon ceratophyllus. The characteristics of heathland vegetation exhibiting dieback disease associated with the presence of P. dnnamomi were investigated. Plant species richness was similar between diseased and non-diseased areas however diseased areas were characterised by significant declines in the cover and frequency of susceptible species, increases in resistant species and increases in percent cover of open ground. Compared to non-diseased areas, diseased areas exhibited fewer shrub species and decreased shrub cover. The percentage cover and number of species of sedges, lilies and grasses were higher in diseased areas. Structural differences were significant between 0-0.6 m with decreased cover of vegetation in diseased areas. Differences in structure between diseased and non-diseased areas were not as great as expected due to increases in the cover of resistant species. A number of regenerating X australis were observed in post-disease areas. Cluster analysis of floristic data could clearly separate diseased and non-diseased trap stations. The population dynamics and habitat use of eight small mammal species present were compared in diseased and non-diseased areas using trapping and radio-tracking techniques. The number of small mammal species captured in post-disease areas was significantly lower than non-diseased areas. Mean captures of Antechinus stuartii and Rattus fiisdpes were significantly lower in diseased areas on Grid B. Mean captures of Rattus lutreolus were significantly lower in diseased areas on both study grids. Significant differences were not observed in every season over the two year study period. Radio tracking revealed more observations of Sminthopsis leucopus in non-diseased vegetation than in diseased. Cercartetus nanus was frequently observed to utilise the disease susceptible X. australis for nesting. At one location, the recovery of vegetation and small mammal communities in non-diseased and diseased vegetation after fuel reduction burning was monitored for three years post-fire. Return of plant species after fire in both disease classes were similar, reaching 75% of pre-fire richness after three years. Vegetation cover was slower to return after fire in diseased areas. Of the seven small mammal species captured pre-fire, five were regularly captured in the three years after fire. General linear model analysis revealed a significant influence of disease on capture rates for total small mammals before fire and a significant influence of fire on capture rates for total small mammals after fire. After three years, the influence of fire on capture rates was reduced no significant difference was detected between disease classes. Measurements of microclimate indicate that diseased, burnt heathland was likely to experience greater extremes of temperature and wind speed. Seeding of diseased heathland with X. australis resulted in the establishment of seedlings of this sensitive species. The reported distributions of the mamma] species in Victoria were analysed to determine which species were associated with the reported distribution of dieback disease. Twenty-two species have more than 20% of their known distribution in diseased areas. Five of these species, Pseudomys novaehollandiae, Pseudomys fumeust Pseudomys shortridgei, Potorous longipes and Petrogale pencillata are rare or endangered in Victoria. Four of the twenty-two species, Sminthopsis leucopus, Isoodon obesulus, Cercartetus nanus and Rottus lutreolus am observed in Victorian heathlands. Phytophthora cinnamomi changes both the structure and floristics of heathland vegetation in the eastern Qtway Ranges. Small mammals respond to these changes through decreased utilisation of diseased heathland. The pathogen threatens the diversity of species present and future research efforts should be directed towards limiting its spread and rehabilitating diseased areas.

Innovative analytical chemistry for monitoring wine production

This study monitored concentration changes in the major constituents of wine during its production, through the development of new and innovative methodologies for a range of analytical instrumentation. Chemometrics (statistical analysis) was employed to enhance data interpretation, which provided insight into the reactions occurring between the key chemical species present.

Ion association and molar conductivity in polyether electrolytes

The ion association behaviour observed in our earlier studies of a polyether electrolyte system at elevated temperatures, was reminiscent of the molar conductivity behaviour typical of low dielectric constant systems. Further investigation of this relationship has led to some suggestions about the types of ionic species present in the polymer electrolyte systems. FT-IR spectroscopy has been used in this work to contrast ion association in an amorphous polyether electrolyte with two liquid electrolytes, N,N-dimethyl-formamide and tetraethylenegylcol dimethylether, containing lithium trifluoromethan sulfonate.

Palaeo-geomorphological significance of miocene and pliocene euryhaline ostracoda in the Nepean 1 borehole, Port Phillip Basin, SE Australia

Ostracoda able to tolerate significant fluctuations in salinity occur as fossils in latest Late Miocene and earliest Late Pliocene strata of the Nepean 1 borehole within the Port Phillip Basin. The main euryhaline species present are Osticythere baragwanathi (Chapman & Crespin), Leptocythere hartmanni (McKenzie), Xestoleberis cedunaensis Hartmann and Tanella gracilis Kingma. Euryhaline ostracods occur in both high diversity, high abundance fossil ostracod assemblages and in low diversity, high abundance  assemblages. These latest Late Miocene and earliest Late Pliocene fossil ostracod assemblages accumulated close to the maximum point of flooding during respective marine transgressions onto the northern Bass Strait hinterland. The presence of euryhaline Ostracoda in these assemblages  is reminiscent of ostracod occurrences associated with modern day SE Australian barrier coastlines. Euryhaline ostracods are not common in earlier Cenozoic sediments of SE Australia and Osticythere baragwanathi makes its first appearance in the latest Late Miocene beds of the Nepean 1 borehole. This latter occurrence is interpreted to reflect the initial phase of development for the modern SE Australian barrier coastline and in particular, the initial formation of Port Phillip Bay as a coastal geomorphological feature.

High performance liquid chromatography with two simultaneous on-line antioxidant assays : evaluation and comparison of espresso coffees

The antioxidant profiles of various espresso coffees were established using HPLC with UV-absorbance detection and two rapid, simultaneous, on-line chemical assays that enabled the relative reactivity of sample components to be screened. The assays were based on (i) the colour change associated with reduction of the 2,2´-diphenyl-1-picrylhydrazyl radical (DPPH•); and (ii) the emission of light (chemiluminescence) upon reaction with acidic potassium permanganate. Results from the two approaches were similar and reflected the complex array of antioxidant species present in the samples. However, some differences in selectivity were observed. Chromatograms generated with the chemiluminescence assay contained more peaks, which was ascribed to the greater sensitivity of the reagent towards minor, readily oxidisable sample components. The three coffee samples produced closely related profiles, signifying their fundamentally similar chemical compositions and origin. Nevertheless, the overall intensity and complexity of the samples in both UV absorption and antioxidant assay chromatograms were aligned with the manufacturers description of flavour intensity and character.

Mycoplasmas in Australian fur seals (Arctocephalus pusillus doriferus) : identification and association with abortion

Bacteria from the genus Mycoplasma are common inhabitants of the respiratory, gastrointestinal, and genital tracts of mammals. The understanding of the pathological significance of mycoplasmas in seals is poor, as few studies have utilized the specific culture techniques required to isolate these bacteria. The current study surveyed for the Mycoplasma species present in Australian fur seals (Arctocephalus pusillus doriferus) and investigated the association between infection and pathology. Mycoplasmas were found in the nasal cavities of 55/80 (69%) of apparently healthy individuals. Isolates from 18 individuals were investigated through 16S ribosomal RNA sequencing, and 3 species were identified: M. zalophi, M. phocae, and Mycoplasma sp. (GenBank no. EU714238.1), all of which had previously been isolated from Northern Hemisphere pinnipeds. In addition, mycoplasmas were isolated from the lungs of 4 out of 16 juveniles and 1 out of 5 adults sampled at necropsy. Isolates obtained were M. zalophi, Mycoplasma sp. EU714238.1, and M. phocicerebrale, but infection was not associated with lung pathology in these age classes. Inflammatory disease processes of the heart and/or lungs were present in 12 out of 32 (38%) aborted fetuses on microscopic examination. Predominant findings were interstitial pneumonia, pericarditis, and myocarditis. Mycoplasma phocicerebrale was isolated from the thymus of an aborted fetus, and 3 out of 11 (27%) fetuses with inflammatory heart or lung lesions were PCR-positive for Mycoplasma. In conclusion, several species of Mycoplasma are part of the normal flora of the nasal cavity of Australian fur seals, and some mycoplasmas may be associated with abortion in this species of seal.

Asymmetric impact of piscivorous birds on size-structured fish populations

Fish are frequently considered the top predator in freshwater food web models despite evidence that predatory birds can impact fish populations. In this study, we quantified bird predation rates on experimental populations of rainbow trout (Oncorhynchus mykiss (Walbaum, 1792)) created by stocking nine small lakes in British Columbia, Canada. Combining estimates of fish mortality with estimated bird predation rates allowed us to partition fish mortality into that due to birds versus cannibalism. Our results indicated that bird predators had significant impacts on age-1 trout populations, but little impact on age-0 trout. Common loons (Gavia immer Brunnich, 1764) were the principle predator among eight predatory bird species present, apparently consuming nearly 50% of all stocked age-1 trout and explaining almost 50% of variation in mortality rates. Age-1 trout mortality did not differ significantly from zero in lakes without loons. Birds consumed a small proportion of age-0 trout, and estimated consumption explained none of the variation in age-0 trout mortality among lakes. We conclude that birds affect fish populations by asymmetric predation on different age (size) classes and can be important top predators that should not be ignored when characterizing freshwater food webs in lakes.

Predicting avian distributions to evaluate spatiotemporal overlap with locust control operations in eastern Australia.

Locusts and grasshoppers cause considerable economic damage to agriculture worldwide. The Australian Plague Locust Commission uses multiple pesticides to control locusts in eastern Australia. Avian exposure to agricultural pesticides is of conservation concern, especially in the case of rare and threatened species. The aim of this study was to evaluate the probability of pesticide exposure of native avian species during operational locust control based on knowledge of species occurrence in areas and times of application. Using presence-absence data provided by the Birds Australia Atlas for 1998 to 2002, we developed a series of generalized linear models to predict avian occurrences on a monthly basis in 0.5 degrees grid cells for 280 species over 2 million km2 in eastern Australia. We constructed species-specific models relating occupancy patterns to survey date and location, rainfall, and derived habitat preference. Model complexity depended on the number of observations available. Model output was the probability of occurrence for each species at times and locations of past locust control operations within the 5-year study period. Given the high spatiotemporal variability of locust control events, the variability in predicted bird species presence was high, with 108 of the total 280 species being included at least once in the top 20 predicted species for individual space-time events. The models were evaluated using field surveys collected between 2000 and 2005, at sites with and without locust outbreaks. Model strength varied among species. Some species were under- or over-predicted as times and locations of interest typically did not correspond to those in the prediction data set and certain species were likely attracted to locusts as a food source. Field surveys demonstrated the utility of the spatially explicit species lists derived from the models but also identified the presence of a number of previously unanticipated species. These results also emphasize the need for special consideration of rare and threatened species that are poorly predicted by presence-absence models. This modeling exercise was a useful a priori approach in species risk assessments to identify species present at times and locations of locust control applications, and to discover gaps in our knowledge and need for further focused data collection.

Changes in lipid class content and composition of Isochrysis sp. (T-Iso) grown in batch culture

© 2015, Springer International Publishing Switzerland. For decades, the microalgae Isochrysis spp. have been widely utilised as a live feed in aquaculture practices. This species possesses a number of favourable characteristics, notably its long-chain omega-3 polyunsaturated fatty acid (LC n-3 PUFA) content; primarily docosahexaenoic acid (DHA, 22:6n-3). This article describes the lipid class content and composition of this microalga grown in batch culture, covering the entirety of lag, log and stationary growth phases. The total lipid was highest in the lag phase (27 pg/cell). Total lipid significantly decreased in the exponential growth (7 pg/cell), then steadily increasing for the remainder of growth. The increase in total lipid was due to the accumulation of neutral lipid in the form of triacylglycerides. The DHA content (pg/cell) of the neutral lipid remained relatively unchanged for the duration of growth, with the influx of fatty acids being primarily myristic and palmitic acids. DHA (pg/cell) was found at relatively uniform amounts across all lipid classes. However, the DHA content as a percentage differed greatly between classes. The polar lipid class had a significantly higher DHA content, which peaked at 38 % of all polar lipid in log growth. The primary PUFA species present in the glycolipid class was stearidonic acid (18:4n-3). This work gives an overview of the lipid content and composition of Isochrysis sp. (T-Iso) over the entirety of its growth under batch culture. The lipid profile for this species at different stages of culture provides a basal data set that is useful for comparative studies using this organism.

At the crossroads: does the configuration of roadside vegetation affect woodland bird communities in rural landscapes?

In agricultural regions worldwide, linear networks of vegetation such as hedges, fencerows and live fences provide habitat for plant and animal species in heavily modified landscapes. In Australia, networks of remnant native vegetation along roadsides are a distinctive feature of many rural landscapes. Here, we investigated the richness and composition of woodland-dependent bird communities in networks of eucalypt woodland vegetation along roadsides, in an agricultural region in which >80% of native woodland and forest vegetation has been cleared. We stratified sites in a) cross sections and b) linear strips of roadside vegetation, to test the influence on woodland birds of site location and configuration in the linear network (the 'intersection effect'). We also examined the influence of tree size at the site, the amount of wooded vegetation surrounding the site, and the abundance of an aggressive native species, the noisy miner Manorina melanocephala. Birds were surveyed at 26 pairs of sites (cross section or linear strip) on four occasions. A total of 66 species was recorded, including 35 woodland species. The richness of woodland bird species was influenced by site configuration, with more species present at cross sections, particularly those with larger trees (>30 cm diameter). However, the strongest influence on species richness was the relative abundance of the noisy miner. The richness of woodland birds at sites where noisy miners were abundant was ~20% of that where miners were absent. These results recognise the value of networks of roadside vegetation as habitat for woodland birds in depleted agricultural landscapes; but highlight that this value is not realised for much of this vast vegetation network because of the dominance of the noisy miner. Nevertheless, roadside vegetation is particularly important where the configuration of networks create nodes that facilitate movement. Globally, the protection, conservation and restoration of such linear networks has an important influence on the persistence of biota within human-dominated landscapes.

The characterisation of polycyclic aromatic hydrocarbons emissions from burning of different firewood species in Australia

Four kinds of woods used for residential heating in Australia were selected and burned under two burning conditions in a domestic wood heater installed in a laboratory. The selected wood species included pine (Pinus radiata), red gum (Eucalyptus camaldulensis), sugar gum (Eucalyptus cladocalyx) and yellow box (Eucalyptus melliodora). The two different burning conditions represented fast burning and slow burning, with the air inlet of the combustion chamber respectively ‘full open’ and ‘half open’. By sampling and analysing particulate and gaseous emissions from the burning of each load of wood under defined experimental conditions, PAHs emissions and their profiles in the particulate and gaseous phases were obtained. 16 species out of the 18 selected PAHs were detected. Of these, seven species were detected in the gaseous phase and most were lower molecular weight compounds. Similarly, more than 10 species of PAHs were detected in the particulate phase and these were mostly heavier molecular weight compounds. Under both burning conditions, emission levels for total PAHs and total genotoxic PAHs were the highest for pine and lowest for sugar gum, with red gum being the second highest, followed by yellow box. Using the specific sampling method, gaseous PAHs accounted for above 90% mass fraction of total PAHs in comparison to particulate PAHs (10%). The majority of the genotoxic PAHs were present in the particulate phase. PAHs emission levels in slow burning conditions were generally higher than those in fast burning conditions.