Inferential, non-parametric statistics to assess quality of probabilistic forecast systems

Many statistical forecast systems are available to interested users. In order to be useful for decision-making, these systems must be based on evidence of underlying mechanisms. Once causal connections between the mechanism and their statistical manifestation have been firmly established, the forecasts must also provide some quantitative evidence of `quality’. However, the quality of statistical climate forecast systems (forecast quality) is an ill-defined and frequently misunderstood property. Often, providers and users of such forecast systems are unclear about what ‘quality’ entails and how to measure it, leading to confusion and misinformation. Here we present a generic framework to quantify aspects of forecast quality using an inferential approach to calculate nominal significance levels (p-values) that can be obtained either by directly applying non-parametric statistical tests such as Kruskal-Wallis (KW) or Kolmogorov-Smirnov (KS) or by using Monte-Carlo methods (in the case of forecast skill scores). Once converted to p-values, these forecast quality measures provide a means to objectively evaluate and compare temporal and spatial patterns of forecast quality across datasets and forecast systems. Our analysis demonstrates the importance of providing p-values rather than adopting some arbitrarily chosen significance levels such as p < 0.05 or p < 0.01, which is still common practice. This is illustrated by applying non-parametric tests (such as KW and KS) and skill scoring methods (LEPS and RPSS) to the 5-phase Southern Oscillation Index classification system using historical rainfall data from Australia, The Republic of South Africa and India. The selection of quality measures is solely based on their common use and does not constitute endorsement. We found that non-parametric statistical tests can be adequate proxies for skill measures such as LEPS or RPSS. The framework can be implemented anywhere, regardless of dataset, forecast system or quality measure. Eventually such inferential evidence should be complimented by descriptive statistical methods in order to fully assist in operational risk management.

Improving the quality of kikuyu by reducing the lignin content

Development of improved pasture grass via chemical mutagenesis and selection of mutations in lignin genes.

Changes in sensory quality of sterile cantaloupe dice stored in controlled atmospheres.

Diced cantaloupe flesh that was microbiologically sterile was prepared in order to study the physiological deterioration of fruit when stored under a range of controlled atmospheres at 4.5°C. Sterile fruit pieces were prepared by boiling whole melons for 3 min, then dicing aseptically. Storage atmospheres were in continuous flow and contained from 0 to 26% CO2 and 3.5 to 17% O2. Sensory assessments were carried out by a highly trained panel at 14-day intervals. Products that were acceptable for up to 28 days were obtained when the following 3 treatments were used: 6% CO2 and 6% O2; 9.5% CO2 and 3.5% O2; and 15% CO2 and 6% O2. Overall, treatment with 0, 19.5 or 26% CO2 (irrespective of O2 concn.) caused significant deterioration in sensory properties.

Effect of an Ethylene Absorbent on Quality of Tomato Slices

Ethylene production is stimulated during the slicing of fresh cut tomato slices. Experiments were conducted to investigate whether the inclusion of ethylene absorbents in packaging affects the quality of tomato slices cv. Revolution during storage at 5OC. ‘Pink’ maturity stage tomatoes were cut into 7mm thick slices and vertically stacked in closed glass containers for 12 days with or without Purafil® to remove ethylene. The ethylene removal treatment resulted in reduced ethylene, less CO2 accumulation, and firmer slices.

Exposure of Tomato Fruit to 1-MCP Improves Quality of Stored Slices

Maintenance of quality, such as firmness, is important during storage of fresh cut produce. This study compared the effects of I-MCP on the quality of tomato slices when intact tomatoes were treated with 1-MCP and then sliced, or tomatoes were sliced and the slices treated with I-MCP. In both instances the MCP treatment was 1 µL Lˉٰ at 20 ºC for 12 h. Tomato cv. 'Revolution' was harvested at the 'pink' stage of maturity, cut into 7-mm slices, and stored as vertical stacks in closed plastic containers at 5ºC for up to 7 days after the 1-MCP treatment. Exposure of intact tomatoes to I-MCP resulted in reduced ethylene production (31%) and firmer (22%) slices than when tomatoes were not I-MCP treated. The application of I-MCP prior to slicing of tomatoes appears a useful strategy to retain quality of stored tomato slices.

Effects of severity of threshing damage on seed quality of Gatton panic Panicum maximum)

Different degrees of severity of threshing were imposed during combine-harvesting of seed of Gatton panic, a cultivar of Panicum maximum , to determine effects of degree of threshing damage on subsequent properties of seed. Threshing cylinder peripheral speeds and concave clearances covering the normal range employed commercially were varied experimentally in the harvest of 2 crops grown in north Queensland. Harvested seed was dried and cleaned, then stored under ambient conditions. The extent of physical damage was measured, and samples were tested at intervals for viability, germination, dormancy and seedling emergence from soil in a glasshouse and in the field over the 2 seasons following harvest. Physical damage increased as peripheral rotor speed rose and (though less markedly) as concave clearance was reduced. As the level of damage increased, viability was progressively reduced, life expectancy was shortened, and dormancy was broken. When the consequences were measured as seedling emergence from soil, the adverse effects on viability tended to cancel out the benefits of dormancy-breaking, leaving few net differences attributable to the degree of threshing severity. We concluded that there would be no value in trying to manipulate the quality of seed produced for normal commercial use through choice of cylinder settings, but that deliberate light or heavy threshing could benefit special-purpose seed, destined, respectively, for long-term storage or immediate use.

Effect of defoliation interval and height on the growth and quality of Arachis pintoi cv. Amarillo

The effect of defoliation on Amarillo (Arachis pintoi cv. Amarillo) was studied in a glasshouse and in mixed swards with 2 tropical grasses. In the glasshouse, Amarillo plants grown in pots were subjected to a 30/20°C or 25/15°C temperature regime and to defoliation at 10-, 20- or 30-day intervals for 60 days. Two field plot studies were conducted on Amarillo with either irrigated kikuyu (Pennisetum clandestinum) in autumn and spring or dryland Pioneer rhodes grass (Chloris gayana) over summer and autumn. Treatments imposed were 3 defoliation intervals (7, 14 and 28 days) and 2 residual heights (5 and 10 cm for kikuyu; 3 and 10 cm for rhodes grass) with extra treatments (56 days to 3 cm for both grasses and 21 days to 5 cm for kikuyu). Defoliation interval had no significant effect on accumulated Amarillo leaf dry matter (DM) at either temperature regime. At the higher temperature, frequent defoliation reduced root dry weight (DW) and increased crude protein (CP) but had no effect on stolon DW or in vitro organic matter digestibility (OMD). On the other hand, at the lower temperature, frequent defoliation reduced stolon DW and increased OMD but had no effect on root DW or CP. Irrespective of temperaure and defoliation, water-soluble carbohydrate levels were higher in stolons than in roots (4.70 vs 3.65%), whereas for starch the reverse occured (5.37 vs 9.44%). Defoliating the Amarillo-kikuyu sward once at 56 days to 3 cm produced the highest DM yield in autumn and sprong (582 and 7121 kg/ha DM, respectively), although the Amarillo component and OMD were substantially reduced. Highest DM yields (1726 kg/ha) were also achieved in the Amarillo-rhodes grass sward when defoliated every 56 days to 3 cm, although the Amarillo component was unaffected. In a mixed sward with either kikuyu or rhodes grass, the Amarillo component in the sward was maintained up to a 28-day defoliation interval and was higher when more severely defoliated. The results show that Amarillo can tolerate frequent defoliation and that it can co-exist with tropical grasses of differing growth habits, provided the Amarillo-tropical grass sward is subject to frequent and severe defoliation.

A survey of management and economic impact of weeds in dryland cotton cropping systems of subtropical Australia

In dryland cotton cropping systems, the main weeds and effectiveness of management practices were identified, and the economic impact of weeds was estimated using information collected in a postal and a field survey of Southern Queensland and northern New South Wales. Forty-eight completed questionnaires were returned, and 32 paddocks were monitored in early and late summer for weed species and density. The main problem weeds were bladder ketmia (Hibiscus trionum), common sowthistle (Sonchus oleraceus), barnyard grasses (Echinochloa spp.), liverseed grass (Urochloa panicoides) and black bindweed (Fallopia convolvulus), but the relative importance of these differed with crops, fallows and crop rotations. The weed flora was diverse with 54 genera identified in the field survey. Control of weed growth in rotational crops and fallows depended largely on herbicides, particularly glyphosate in fallow and atrazine in sorghum, although effective control was not consistently achieved. Weed control in dryland cotton involved numerous combinations of selective herbicides, several non-selective herbicides, inter-row cultivation and some manual chipping. Despite this, residual weeds were found at 38-59% of initial densities in about 3-quarters of the survey paddocks. The on-farm financial costs of weeds ranged from $148 to 224/ha.year depending on the rotation, resulting in an estimated annual economic cost of $19.6 million. The approach of managing weed populations across the whole cropping system needs wider adoption to reduce the weed pressure in dryland cotton and the economic impact of weeds in the long term. Strategies that optimise herbicide performance and minimise return of weed seed to the soil are needed. Data from the surveys provide direction for research to improve weed management in this cropping system. The economic framework provides a valuable measure of evaluating likely future returns from technologies or weed management improvements.

Quality of handling and holding yard environment, and beef cattle temperament: 1. Relationships with flight speed and fear of humans.

Numerous tests have been used to measure beef cattle temperament, but limited research has addressed the relationship between such tests and whether temperament can be modified. One-hundred-and-forty-four steers were given one of three human handling and yarding experiences on six occasions during a 12-month grazing period post-weaning (backgrounding): Good handling/yarding, Poor handling/yarding and Minimal handling/yarding. At the end of this phase the cattle were lot-fed for 78 days, with no handling/yarding treatments imposed, before being transported for commercial slaughter. Temperament was assessed at the start of the experiment, during backgrounding and lot-feeding by flight speed (FS) and a fear of humans test, which measured the proximity to a stimulus person (zone average; ZA), the closest approach to the person (CA) and the amount the cattle moved around the test arena (total transitions; TT). During backgrounding, FS decreased for all treatments and at the end of backgrounding there was no difference between them. The rate of decline, however, was greatest in the Good group, smallest in the Minimal group with the Poor intermediate. In contrast, ZA was affected by treatment, with a greater reduction for the Good group than the others (P = 0.012). During lot-feeding, treatment did not affect FS, but all groups showed a decrease in ZA, with the greatest change in the Poor group, the least in the Good and the Minimal intermediate (P = 0.052). CA was positively correlated with ZA (r = 0.18 to 0.66) and negatively with TT (r = -0.180 to -0.659). FS was consistently correlated with TT only (r = 0.17 to 0.49). These findings suggest that FS and TT measure a similar characteristic, as do ZA and CA, but that these characteristics are different from one another, indicating that temperament is not a unitary trait, but has different facets. FS and TT measure one facet that we suggest is general agitation, whilst ZA and CA measure fear of people. Thus, the cattle became less agitated during backgrounding, but the effect was not permanently influenced by the quantity and quality of handling/yarding. However, Good handling/yarding reduced fearfulness of people. Fear of people was also reduced during lot-feeding, probably as a consequence of frequent exposure to humans in a situation that was neutral or positive for the cattle.

Determination of management units for grey mackerel fisheries in northern Australia.

The requirement for Queensland, Northern Territory and Western Australian jurisdictions to ensure sustainable harvest of fish resources and their optimal use relies on robust information on the resource status. For grey mackerel (Scomberomorus semifasciatus) fisheries, each of these jurisdictions has their own management regime in their corresponding waters. The lack of information on stock structure of grey mackerel, however, means that the appropriate spatial scale of management is not known. As well, fishers require assurance of future sustainability to encourage investment and long-term involvement in a fishery that supplies lucrative overseas markets. These management and fisher-unfriendly circumstances must be viewed in the context of recent 3-fold increases in catches of grey mackerel along the Queensland east coast, combined with significant and increasing catches in other parts of the species' northern Australian range. Establishing the stock structure of grey mackerel would also immensely improve the relevance of resource assessments for fishery management of grey mackerel across northern Australia. This highlighted the urgent need for stock structure information for this species. The impetus for this project came from the strategic recommendations of the FRDC review by Ward and Rogers (2003), "Northern mackerel (Scombridae: Scomberomorus): current and future research needs" (Project No. 2002/096), which promoted the urgency for information on the stock structure of grey mackerel. In following these recommendations this project adopted a multi-technique and phased sampling approach as carried out by Buckworth et al (2007), who examined the stock structure of Spanish mackerel, Scomberomorus commerson, across northern Australia. The project objectives were to determine the stock structure of grey mackerel across their northern Australian range, and use this information to define management units and their appropriate spatial scales. We used multiple techniques concurrently to determine the stock structure of grey mackerel. These techniques were: genetic analyses (mitochondrial DNA and microsatellite DNA), otolith (ear bones) isotope ratios, parasite abundances, and growth parameters. The advantage of using this type of multi-technique approach was that each of the different methods is informative about the fish’s life history at different spatial and temporal scales. Genetics can inform about the evolutionary patterns as well as rates of mixing of fish from adjacent areas, while parasites and otolith microchemistry are directly influenced by the environment and so will inform about the patterns of movement during the fishes lifetime. Growth patterns are influenced by both genetic and environmental factors. Due to these differences the use of these techniques concurrently increases the likelihood of detecting different stocks where they exist. We adopted a phased sampling approach whereby sampling was carried out at broad spatial scales in the first year: east coast, eastern Gulf of Carpentaria (GoC), western GoC, and the NW Northern Territory (NW NT). By comparing the fish samples from each of these locations, and using each of the techniques, we tested the null hypothesis that grey mackerel were comprised of a single homogeneous population across northern Australia. Having rejected the null hypothesis we re-sampled the 1st year locations to test for temporal stability in stock structure, and to assess stock structure at finer spatial scales. This included increased spatial coverage on the east coast, the GoC, and WA. From genetic approaches we determined that there at least four genetic stocks of grey mackerel across northern Australia: WA, NW NT (Timor/Arafura), the GoC and the east Grey mackerel management units in northern Australia ix coast. All markers revealed concordant patterns showing WA and NW NT to be clearly divergent stocks. The mtDNA D-loop fragment appeared to have more power to resolve stock boundaries because it was able to show that the GoC and east coast QLD stocks were genetically differentiated. Patterns of stock structure on a finer scale, or where stock boundaries are located, were less clear. From otolith stable isotope analyses four major groups of S. semifasciatus were identified: WA, NT/GoC, northern east coast and central east coast. Differences in the isotopic composition of whole otoliths indicate that these groups must have spent their life history in different locations. The magnitude of the difference between the groups suggests a prolonged separation period at least equal to the fish’s life span. The parasite abundance analyses, although did not include samples from WA, suggest the existence of at least four stocks of grey mackerel in northern Australia: NW NT, the GoC, northern east coast and central east coast. Grey mackerel parasite fauna on the east coast suggests a separation somewhere between Townsville and Mackay. The NW NT region also appears to comprise a separate stock while within the GoC there exists a high degree of variability in parasite faunas among the regions sampled. This may be due to 1. natural variation within the GoC and there is one grey mackerel stock, or 2. the existence of multiple localised adult sub-stocks (metapopulations) within the GoC. Growth parameter comparisons were only possible from four major locations and identified the NW NT, the GoC, and the east coast as having different population growth characteristics. Through the use of multiple techniques, and by integrating the results from each, we were able to determine that there exist at least five stocks of grey mackerel across northern Australia, with some likelihood of additional stock structuring within the GoC. The major management units determined from this study therefore were Western Australia, NW Northern Territory (Timor/Arafura), the Gulf of Carpentaria, northern east Queensland coast and central east Queensland coast. The management implications of these results indicate the possible need for management of grey mackerel fisheries in Australia to be carried out on regional scales finer than are currently in place. In some regions the spatial scales of management might continue as is currently (e.g. WA), while in other regions, such as the GoC and the east coast, managers should at least monitor fisheries on a more local scale dictated by fishing effort and assess accordingly. Stock assessments should also consider the stock divisions identified, particularly on the east coast and for the GoC, and use life history parameters particular to each stock. We also emphasise that where we have not identified different stocks does not preclude the possibility of the occurrence of further stock division. Further, this study did not, nor did it set out to, assess the status of each of the stocks identified. This we identify as a high priority action for research and development of grey mackerel fisheries, as well as a management strategy evaluation that incorporates the conclusions of this work. Until such time that these priorities are addressed, management of grey mackerel fisheries should be cognisant of these uncertainties, particularly for the GoC and the Queensland east coast.

NIRS calibrations for predicting the nutritional quality of feed

NIRS calibrations for predicting the nutritional quality of feed.

Tilapia in Australia – Development of management strategies for the control and eradication of feral tilapia populations in Australia

This report presents a culmination of different research projects on two species of tilapia (Oreochromis mossambicus and Tilapia mariae) and provides recommendations for the future management and research of these pest fish. Feral populations of O. mossambicus and T. mariae are now widely distributed in tropical northeastern Queensland, with O. mossambicus also occurring in southeastern Queensland and river systems of Western Australia. O. mossambicus is known to have existed in impoundments in southeastern Queensland, as well as urban drains and ornamental ponds in the Townsville region of north Queensland from about the late 1970s, while T. mariae became established in some easternflowing tropical streams by the early 1990s. In Australia, feral stocks of tilapia are widely regarded as pests that potentially threaten both native fish stocks and biodiversity.

DAQ00104 Sponge and dough bread quality of Australian wheat germplasm

The main grade of wheat targeted for the export sponge and dough (S&D) market is Australian prime hard (APH). By association, protein should be a key parameter relating to S&D quality, specifically loaf volume (LV). Surprisingly, the project revealed a low level of correlation between total protein content and LV. It appears that protein composition may be the key to understanding S&D quality, as the glutenin Glu D1 5+10 subunit contributed to the highest LVs. The current varieties KennedyA and SunzellA, together with several breeding lines, provided a consistently high quality over a number of seasons. These varieties performed as well as, if not better than, North American S&D varieties.

Barley genotype expressing "stay-green"-like characteristics maintains starch quality of the grain during water stress condition

The identification of "stay-green" in sorghum and its positive correlation with yield increases has encouraged attempts to incorporate "stay-green"-like traits into the genomes of other commercially important cereal crops. However, knowledge on the effects of "stay-green" expression on grain quality under extreme physiological stress is limited. This study examines impacts of "stay-green"-like expression on starch biosynthesis in barley (Hordeum vulgare L.) grain under mild, severe, and acute water stress conditions induced at anthesis. The proportions of long amylopectin branches and amylose branches in the grain of Flagship (a cultivar without "stay-green"-like characteristics) were higher at low water stress, suggesting that water stress affects starch biosynthesis in grain, probably due to early termination of grain fill. The changes in long branches can affect starch properties, such as the rates of enzymatic degradation, and hence its nutritional value. By contrast, grain from the "stay-green"-like cultivar (ND24260) did not show variation in starch molecular structure under the different water stress levels. The results indicate that the cultivar with "stay-green"-like traits has a greater potential to maintain starch biosynthesis and quality in grain during drought conditions, making the "stay-green"-like traits potentially useful in ensuring food security. (C) 2013 Elsevier Ltd. All rights reserved.

Impact of 1-methylcyclopropene treatment on the sensory quality of 'Bartlett' pear fruit

The ethylene biosynthesis inhibitor, 1-methylcyclopropene (1-MCP), has been commercially used to extend the storage life of European pear fruit and to allow shipment to distant markets. However, the influence of 1-MCP on the ability of fruit to ripen to an acceptable sensory quality has not been investigated in 'Bartlett' pear, one of the most aromatic of pear fruit. In the current study, early-, mid- and late-season 'Bartlett' pear fruit were treated with 0.6μLL-1 1-MCP at 0°C for 24h, 100μLL-1 ethylene at 20°C for 24h, or untreated before immediate transfer to 20°C for ripening until eating soft (13N firmness). Fruit from each treatment were subjected to objective and sensory quality evaluation once ripe. Sensory quality showed differences related to harvest maturity; the importance of harvest maturity depended on the treatment. Treatment with 1-MCP effectively slowed fruit ripening and therefore extended postharvest life, but also resulted in fully ripened pears with more desirable sensory traits, as compared with ethylene-treated and untreated pears. The enhanced sensory quality was related to higher sweetness, juiciness and pear aroma and reduced fermented aroma, gritty texture and tart taste. In addition, the sensory profiles of 1-MCP-treated pears were more stable among fruit from the three harvest dates than the ethylene-treated pears, which exhibited very different sensory profiles between early- and late-season fruits. © 2015 Elsevier B.V.