Processing of multi-dimensional NMR data with the new software PROSA

Summary The new program PROSA is an efficient implementation of the common data-processing steps for multi-dimensional NMR spectra. PROSA performs linear prediction, digital filtering, Fourier transformation, automatic phase correction, and baseline correction. High efficiency is achieved by avoiding disk storage of intermediate data and by the absence of any graphics display, which enables calculation in the batch mode and facilitates porting PROSA on a variety of different computer systems; including supercomputers. Furthermore, all time-consuming routines are completely vectorized. The elimination of a graphics display was made possible by the use of a new, reliable automatic phase-correction routine. CPU times for complete processing of a typical heteronuclear three-dimensional NMR data set of a protein vary between less than 1 min on a NEC SX3 supercomputer and 40 min on a Sun-4 computer system.     

Baseline sensitivity and efficacy of fluopyram against Botrytis cinerea from table grape in Italy

Succinate dehydrogenase inhibitor (SDHI) fungicides constitute a relatively recent fungicide class registered for the treatment of grey mould on grapevine in Italy. The sensitivity profile to a novel compound fluopyram was established for a set of 203 Botrytis cinerea isolates collected from Sicilian vineyards within 2009–2012 prior its introduction into market. In addition, its performances were compared in in vitro and in vivo assays with other registered SDHI fungicide boscalid, to evaluate their frequency distributions EC₅₀ values and cross‐resistance patterns. Results of the article showed that EC₅₀ values for fluopyram ranged from 0.05 to 1.98 µg mL^?1. Although EC₅₀ values of boscalid ranged from 0.01 to 89.52 µg mL^?1, no cross‐resistance relationship was observed between the two fungicides (r = 0.003; P = 0.964) within our B. cinerea population. On further confirming these data, boscalid failed in controlling grey mould infections when boscalid‐resistant isolates were inoculated on grape berries whereas fluopyram exhibited a good efficacy against the same isolates. This study represents the first report on the baseline sensitivity to fluopyram within B. cinerea population from Sicilian table grape vineyards in Italy, and it clearly shows the lack of cross‐resistance in vitro and in vivo between fluopyram and boscalid for the field pathogen isolates. These results provided useful information for managing of fungicide resistance suggesting that fluopyram could be a valid alternative to boscalid for the control of grey mould of table grape.     

Baseline susceptibility of Asian corn borer (Ostrinia furnacalis (Guenée)) populations in Vietnam to Cry1Ab insecticidal protein

Susceptibility of Asian corn borer (ACB), Ostrinia furnacalis (Guenée) to Bacillus thuringiensis (Bt) Cry1Ab protein was studied between 2015 and 2016 with 11 ACB populations, collected from various geographical regions in Vietnam. A concentration range of Cry1Ab from 0.20 to 26.10 ng/cm² of diet was evaluated against F₁ ACB neonates using diet surface-overlay bioassays. Mortality data was recorded daily until seven days after infestation. Growth inhibition was recorded at the end of seven days. The median lethal concentration (LC₅₀) varied ≈3-fold among the different populations, ranging from 0.58 to 1.83 ng/cm² of diet with an overall mean of 0.86 ng/cm² of diet. Even the lowest concentration of 0.20 ng/cm² caused 73.53% growth inhibition. >90% growth inhibition was achieved at 0.82 ng/cm² or higher concentrations. The results reflect natural variation in Bt susceptibility among ACB populations rather than variation caused by prior exposure to selection pressures. LC₉₉ value (17.26 ng/cm²) was generated by pooling mortality data across different populations. The upper fiducial limit of LC₉₉ (24.38 ng/cm²) could be a potential diagnostic dose for future resistance monitoring programs. The findings from this study suggest that ACB populations in Vietnam are highly susceptible to Cry1Ab protein. This is the first report of Cry1Ab susceptibility of different ACB populations in Vietnam and will serve as a baseline for future resistance monitoring work.     

Resistance risk assessment for fludioxonil in Stemphylium solani

An outbreak of grey leaf spot caused by Stemphylium solani was observed on tomato in Shandong Province of China in recent years and brought huge economical losses. Fludioxonil is a phenylpyrrole fungicide with strong antifungal activity against S. solani. To evaluate the risk of S. solani developing fludioxonil resistance, a total of 145 field isolates were examined for sensitivity to fludioxonil by measuring mycelial growth. The baseline sensitivity was distributed as a unimodal curve with a mean EC₅₀ value of 0.0659 (±0.0170) µg mL^?1. Five mutants with high resistance to fludioxonil (RF > 1000) were obtained by successively selecting on fludioxonil‐amended plates in the laboratory. All the resistant mutants associated with strongly reduced fitness in mycelial growth, sporulation and pathogenicity. Fludioxonil had positive cross‐resistance with procymidone and iprodione, but there was no cross‐resistance with other fungicides including boscalid, fluazinam, azoxystrobin and flusilazole. Based on the current results, resistance risk of S. solani to fludioxonil could be moderate. This is the first report of baseline sensitivity of S. solani to fludioxonil and its risk assessment. In order to delay the resistance development, it is recommended that fludioxonil can be used as one component of the mixture or fungicides with different modes of action should be alternatively used for this disease management.     

A new meta-ANOVA approach for synthesizing information under signal-heterogeneity setting with application to nuclear magnetic resonance spectroscopic data

A new synthesizing statistical methodology is proposed to resolve issues of signal-heterogeneity in data sets collected through high-resolution ¹H nuclear magnetic resonance (NMR) spectroscopy. This signal-heterogeneity is typically caused by subjective operations for processing spectral profiles and measuring peak areas, non-homogeneous biological phases of experimental subjects, and variations of systems in multi-center. All these causes are likely to simultaneously impact signals of metabolic changes and their precision in a nonlinear fashion. As a combined effect, signal-heterogeneity chiefly manifests through non-homomorphic patterns of standardized treatment mean deviations spanning all experiments, and makes most remedial statistical models with linearity structure invalid. By avoiding a huge and very complex model, we develop a simple meta-ANOVA approach to synthesize many one-way-layout ANOVA analyses from individual experiments. A scale-invariant F-ratio statistic is taken as the summarizing sufficient statistic of a non-centrality parameter that supposedly captures the information about metabolic change from each experiment. Then a joint-likelihood function of a common non-centrality is constructed as the basis for maximum likelihood estimation and Chi-square likelihood ratio testing for statistical inference. We apply the meta-ANOVA to detect metabolic changes of three metabolites identified through pattern recognition on NMR spectral profiles obtained from muscle and liver tissues. We also detect effect differences among different treatments via meta-ANOVA multiple comparison.     

The ‘shifting baseline’ phenomenon: a global perspective

In this paper we demonstrate that low level ‘artisanal’ fishing can dramatically affect populations of slow-growing, late-maturing animals and that even on remote oceanic islands, stocks have been depleted and ecosystems degraded for millennia. Industrialised fisheries have developed during different decades in different regions of the world, and this has almost always been followed by a period of massive stock decline. However, ecosystems were not pristine before the onset of industrial fishing and it is difficult to assess the ‘virgin’ state of a population given that it may have been subject to moderate or even high levels of fishing mortality for many centuries. A wide range of information is available to help define or deduce historic marine population status. These include ‘traditional’ written sources but also less conventional sources such as archaeological remains, genetic analyses or simple anecdotal evidence. Detailed information, collected specifically for the purpose of determining fish stock biomass tends to exist only for recent decades, and most fishery assessments around the world (and thus time-series of biomass estimates), are less than 30 years long. Here we advocate using a wider range of multidisciplinary data sources, although we also recognise that it can be difficult to separate natural variability associated with changing climatic conditions from human-induced changes through fishing. We consider whether or not recovery of degraded ecosystems is ever possible and discuss a series of one-way ratchet like processes that can make it extremely difficult to return to a former ecosystem state.     

Optimizing coffee cultivation and its impact on economic growth and export earnings of the producing countries: The case of Saudi Arabia

Coffee is one of the historical socioeconomic crops. It has received an increasing attention at the global level, due to its positive interlinkage with the economic growth and on the gross domestic product for most of the producing countries, particularly, developing and least developed countries. Saudi Arabia is one of the coffee producing countries that has a relative comparative advantage of coffee cultivation. Yet, coffee cultivation has not received as much attention in Saudi Arabia as that of producing countries around the world. This study aims to assess the current state of coffee cultivation in Saudi Arabia and to investigate the potential to optimize coffee cultivation in Saudi Arabia that maximizes the net national economic return and export earnings, given limitation of cultivated areas, local market activities, and international trade activities. The study statistically analyzed primary data collected from around (65) coffee farms and traders in the study regions at the south and southwest Saudi Arabia, and optimized coffee cultivation in Saudi Arabia using LINGO optimization software. Empirical results of the study revealed the great potential of Saudi Arabia to expand coffee cultivation at south and southwest regions to meet the escalating local demand and to increase its share at the world market up to 2%. Optimization of coffee cultivation in Saudi Arabia showed a high potential to meet the local demand for coffee by producing 80.07 thousand tons grown over 2861.78 hectares and to generate a net return equivalent to $395.72 million a year, which is equivalent to $138.28 thousand per hectare and $4.94 thousand per ton of coffee. Optimizing coffee cultivation will play a substantial role to increase market share of Saudi Arabia to about 1–2% of the world market by increasing its export volume, respectively, to about 69.66 and 112.56 thousand tons, the national net economic return by about $395.86 and $395.95 million a year, and the export earnings of coffee by about $219.43–354.57 million a year, which in turns, will serve the national strategic trend to diversify the economic base and lower the dependency of incomes generated from oil exportation.     

Long-Term Macroevaluation of Environmental Enrichment in Three Brown Bears (Ursus arctos) at Barcelona Zoo

The evaluation of enrichment programs is important to determine their effect on nonhuman animal welfare. The daily activity pattern and use of space of 3 brown bears (Ursus arctos) were used for long-term macroevaluation of enrichment to compare the baseline and enrichment phases. Focal sampling methods were used for data collection, and instantaneous scans were made at 2-min intervals during 15 sessions of 1 hr for each animal during the 2 study periods. The enrichment devices were categorized as feeding, occupational, and sensorial. The long-term macroevaluation in 3 bears showed statistically significant differences in some types of activity but not in others. There were also statistically significant differences for the use of space in 4 of the 8 zones in which the enclosures were divided. A more homogenous pattern in the use of space was only observed during the enrichment phase in the old female. The 3 brown bears followed different patterns concerning the enrichment program.     

Site-specific chlorophyll reference conditions for lakes in Northern and Western Europe

The Water Framework Directive (WFD) requires EU Member States to assess the “ecological status” of surface waters. As a component of ecological status, many European countries are developing a classification scheme for chlorophyll concentrations as a measure of phytoplankton biomass. The chlorophyll classification must be based on the degree of divergence of a water body from an appropriate baseline or ‘reference condition’. This article describes the development of a series of regression models for predicting reference chlorophyll concentrations on a site-specific basis. For model development, a large dataset of European lakes considered to be in reference condition, 466 lakes in total, was assembled. Data were included from 12 European countries, but lakes from Northern and Western Europe dominated and made up 92% of all reference lakes. Data have been collated on chlorophyll concentration, altitude, mean depth, alkalinity, humic type, surface area and geographical region. Regression models were developed for estimating site-specific reference chlorophyll concentrations from significant predictor ‘typology’ variables. Reference chlorophyll concentrations were found to vary along a number of environmental gradients. Concentrations increased with colour and alkalinity and decreased with lake depth and altitude. Forward selection was used to identify independent explanatory variables in regression models for predicting site-specific reference chlorophyll concentrations. Depth was selected as an explanatory variable in all models. Alkalinity was included in models for low colour and humic lakes and altitude was included in models for low colour and very humic lakes. Uncertainty in the models was quite high and arises from errors in the data used to develop the models (including natural temporal and spatial variability in data) and also from additional explanatory variables not considered in the models, particularly nutrient concentrations, retention time and grazing. Despite these uncertainties, site-specific reference conditions are still recommended in preference to type-specific reference conditions, as they use the individual characteristics of a site known to influence phytoplankton biomass, rather than adopt standards set to generally represent a large population of lakes of a particular type. For this reason, site-specific reference conditions should result in reduced error in ecological status classifications, particularly for lakes close to typology boundaries.