An ensemble data assimilation modeling system for operational outdoor microalgae growth forecasting

Microalgae have received increasing attention as a potential feedstock for biofuel or biobased products. Forecasting the microalgae growth is beneficial for managers in planning pond operations and harvesting decisions. This study proposed a biomass forecasting system comprised of the Huesemann Algae Biomass Growth Model (BGM), the Modular Aquatic Simulation System in Two Dimensions (MASS2), ensemble data assimilation (DA), and numerical weather prediction Global Ensemble Forecast System (GEFS) ensemble meteorological forecasts. The novelty of this study is to seek the use of ensemble DA to improve both BGM and MASS2 model initial conditions with the assimilation of biomass and water temperature measurements and consequently improve short-term biomass forecasting skills. This study introduces the theory behind the proposed integrated biomass forecasting system, with an application undertaken in pseudo-real-time in three outdoor ponds cultured with Chlorella sorokiniana in Delhi, California, United States. Results from all three case studies demonstrate that the biomass forecasting system improved the short-term (i.e., 7-day) biomass forecasting skills by about 60% on average, comparing to forecasts without using the ensemble DA method. Given the satisfactory performances achieved in this study, it is probable that the integrated BGM-MASS2-DA forecasting system can be used operationally to inform managers in making pond operation and harvesting planning decisions.     

Uncertainty in ensemble forecasting of species distribution

Species distribution modelling has been widely applied in order to assess the potential impacts of climate change on biodiversity. Many methodological decisions, taken during the modelling process and forecasts, may, however, lead to a large variability in the assessment of future impacts. Using measures of species range change and turnover, the potential impacts of climate change on French stream fish species and assemblages were evaluated. Our main focus was to quantify the uncertainty in the projections of these impacts arising from four sources of uncertainty: initial datasets (Data), statistical methods [species distribution models (SDM)], general circulation models (GCM), and gas emission scenarios (GES). Several modalities of the aforementioned uncertainty sources were combined in an ensemble forecasting framework resulting in 8400 different projections. The variance explained by each source was then extracted from this whole ensemble of projections. Overall, SDM contributed to the largest variation in projections, followed by GCM, whose contribution increased over time equalling almost the proportion of variance explained by SDM in 2080. Data and GES had little influence on the variability in projections. Future projections of range change were more consistent for species with a large geographical extent (i.e., distribution along latitudinal or stream gradients) or with restricted environmental requirements (i.e., small thermal or elevation ranges). Variability in projections of turnover was spatially structured at the scale of France, indicating that certain particular geographical areas should be considered with care when projecting the potential impacts of climate change. The results of this study, therefore, emphasized that particular attention should be paid to the use of predictions ensembles resulting from the application of several statistical methods and climate models. Moreover, forecasted impacts of climate change should always be provided with an assessment of their uncertainty, so that management and conservation decisions can be taken in the full knowledge of their reliability.     

Alcohol-triggered signs of migraine: An animal model

We describe an animal model where characteristics of migraine can be triggered by alcohol administration. In rats chronically implanted with a cannula overlying the transverse sinus, we applied potassium chloride (KCl) (or saline) to the meninges to sensitize trigeminovascular afferents. We assessed effects of repeated KCl application on animal behavior using conditioned place avoidance paradigm. In KCl-treated rats we discovered that alcohol injections (0.2?mg/kg), but not saline, resulted in the development of extracephalic allodynia and signs of ongoing pain.     

Creatine phosphokinase elevation in a case of tick paralysis

The results of studies on a case of tick paralysis in a female child are described. The patient was paralysed by a single female specimen of Dermacentor andersoni Stiles attached to the left temporal area of the scalp. Paralysis of the lower limbs, incoordinate respiration and weakness of the arms were evident.The findings on physical examination and the results of diagnostic laboratory procedures are reported and the possible significance of the results is discussed. The only abnormal laboratory finding was an elevated level of plasma creatine phosphokinase (CPK) activity occurring during the paralytic phase and persisting for 10 days.     

An ensemble model for predicting Rhopalosiphum padi abundance

A novel modeling method is proposed to predict the abundance of the main vector of barley yellow dwarf virus in autumn sown cereal crops. An ensemble model based on artificial neural networks (ANN) was developed to predict the number of Rhopalosiphum padi (L.) (Homoptera: Aphididae) caught in traps during the autumn flight period at Lincoln, Canterbury, New Zealand, over the period 1982–2003. Artificial neural networks were trained using historical weather data and aphid data collected from a suction trap. Model results were compared with those obtained using multiple regression (MR) models using the same independent variables. Both ANN and MR models were validated by leave‐one‐out validation, in other words, by sequentially jackknifing each year out of the data set, fitting a model to the remaining data, then using that model to predict the number of aphids for each jackknifed year. A linear ensemble of ANN models further improved the predictions and represented the trends in the number of aphids over the 22‐year period very well. The r² between the predicted and observed numbers of aphids for the ANN models changed from 0.68 to 0.83 using the linear ensemble model, but the ensemble approach did not change the prediction for the MR models. The absolute mean error (ABSME) of prediction was much lower for the ANN ensemble predictions compared to that for the MR models. The ABMSE for the ANN models dropped from 109 to 86 aphids compared to an ABMSE reduction from 245 to 220 aphids for the MR models. We discuss the potential for ensemble models for predicting insect abundance when long‐term historical data are available.     

An ecologist's guide to the animal model

1. Efforts to understand the links between evolutionary and ecological dynamics hinge on our ability to measure and understand how genes influence phenotypes, fitness and population dynamics. Quantitative genetics provides a range of theoretical and empirical tools with which to achieve this when the relatedness between individuals within a population is known.
2. A number of recent studies have used a type of mixed-effects model, known as the animal model, to estimate the genetic component of phenotypic variation using data collected in the field. Here, we provide a practical guide for ecologists interested in exploring the potential to apply this quantitative genetic method in their research.
3. We begin by outlining, in simple terms, key concepts in quantitative genetics and how an animal model estimates relevant quantitative genetic parameters, such as heritabilities or genetic correlations.
4. We then provide three detailed example tutorials, for implementation in a variety of software packages, for some basic applications of the animal model. We discuss several important statistical issues relating to best practice when fitting different kinds of mixed models.
5. We conclude by briefly summarizing more complex applications of the animal model, and by highlighting key pitfalls and dangers for the researcher wanting to begin using quantitative genetic tools to address ecological and evolutionary questions.     

PETscan: measuring incidence of disease phenotypes to prioritize genetic studies in companion animals

Reliable incidence measurement of diseases is necessary for identification of hereditary diseases in companion animal populations. The data collection system ‘PETscan’ was developed to facilitate standardized registration of diagnoses in veterinary practice. In the development, we attempted to counter challenges known from other primary practice data systems. PETscan includes a comprehensive list of potential diagnoses and supports the veterinary professionals in the diagnostic process. Demographics, individual data and standardized diagnostic data are collected through practice management software in a central database for epidemiological analysis. A preliminary data analysis from PETscan showed specific health issues in four canine breeds. As a real‐time prospective monitoring tool, PETscan summaries can objectively assess the incidence of disorders in companion animal populations and can be used to prioritize disease–gene identification studies and evaluate the effects of breeding strategies, for example, after implementation of a new DNA test in the breeding strategy.     

Nonlinear forecasting of hepatitis and AIDS incidence

The simplex methods of nonlinear forecasting are used to study the data sets of hepatitis A and AIDS in various regions of the United States. The results are compared with those obtained from the traditional ARIMA methods. In many regions, the simplex methods developed from nonlinear dynamical system theory give smaller errors for the data of hepatitis A. A combination of the simplex methods and the traditional ARIMA methods can produce better results for the AIDS data sets.     

An animal model of emotional blunting in schizophrenia

Schizophrenia is often associated with emotional blunting--the diminished ability to respond to emotionally salient stimuli--particularly those stimuli representative of negative emotional states, such as fear. This disturbance may stem from dysfunction of the amygdala, a brain region involved in fear processing. The present article describes a novel animal model of emotional blunting in schizophrenia. This model involves interfering with normal fear processing (classical conditioning) in rats by means of acute ketamine administration. We confirm, in a series of experiments comprised of cFos staining, behavioral analysis and neurochemical determinations, that ketamine interferes with the behavioral expression of fear and with normal fear processing in the amygdala and related brain regions. We further show that the atypical antipsychotic drug clozapine, but not the typical antipsychotic haloperidol nor an experimental glutamate receptor 2/3 agonist, inhibits ketamine's effects and retains normal fear processing in the amygdala at a neurochemical level, despite the observation that fear-related behavior is still inhibited due to ketamine administration. Our results suggest that the relative resistance of emotional blunting to drug treatment may be partially due to an inability of conventional therapies to target the multiple anatomical and functional brain systems involved in emotional processing. A conceptual model reconciling our findings in terms of neurochemistry and behavior is postulated and discussed.     

Impact of the economic recession on companion animal relinquishment, adoption, and euthanasia: a Chicago animal shelter's experience

This study investigated how the current economic recession (since December 2007) has affected dog and cat relinquishment, adoption, and euthanasia at the Anti-Cruelty Society animal shelter in Chicago, Illinois. The study compared temporal patterns of the investigated statistics before (2000-2007) the start of the current recession with the patterns after the start of the recession (2008-2010). The results showed that once the guardianship (ownership) of a nonhuman animal had been established, the recession did not greatly affect the owner's decision on relinquishment-except for the relinquishment of senior dogs, which may be associated with increased costs of care. However, an unfavorable economic environment may have reduced adoption of animals. The consequences of a decline in adoptions might be reflected in an increase in the proportion or number of sheltered animals euthanized. This study demonstrated how monitoring changes in temporal patterns in these shelter statistics can help guide animal shelters to better prepare for the current recession.     

BIOMOD – a platform for ensemble forecasting of species distributions

BIOMOD is a computer platform for ensemble forecasting of species distributions, enabling the treatment of a range of methodological uncertainties in models and the examination of species-environment relationships. BIOMOD includes the ability to model species distributions with several techniques, test models with a wide range of approaches, project species distributions into different environmental conditions (e.g. climate or land use change scenarios) and dispersal functions. It allows assessing species temporal turnover, plot species response curves, and test the strength of species interactions with predictor variables. BIOMOD is implemented in R and is a freeware, open source, package.     

Sex ratio characteristics in Ixodes rubicundus (Acari: Ixodidae), the Karoo paralysis tick

The sex ratio is an important parameter which characterizes the state and dynamics of natural populations of animals. Although ixodid ticks are specialized ectoparasites, most species are bisexual and are characterized by a 1:1 sex ratio for their progeny. In natural populations and even in laboratory colonies, biased sex ratios are often observed. Ixodes rubicundus, the Karoo paralysis tick, parasitizes domestic stock and wild ungulates in South Africa. Adults quest from vegetation, can mate off or on the host and males are seldom parasitic. We hypothesized that the sex ratio for I. rubicundus would be 1:1 when observed directly in the progeny but that it would be strongly biased towards females in samples of parasitic adults. The results mostly supported the hypothesis but it was also shown that unexplained and unpredictable variations can occur. On hosts, females dominated strongly, except on adult angora goats where the sex ratio was biased in favour of the males. This disparity may be related to a greater retention of males in the coarse, curly hair of angora goats compared to the other hosts. Monthly variations in the sex ratios of the tick on hosts are believed to be related to the large fluctuations in sex ratios of questing ticks.     

A model for change: An approach for forecasting well-being from service-based decisions

Every community decision incorporates a “forecasting” strategy (whether formal or implicit) to help visualize expected results and evaluate the potential “feelings/responses” that people living in that community may have about those results. With more communities seeking to make decisions based on sustainable alternatives, forecasting efforts that examine potential impacts of decisions on overall community well-being may prove to be valuable for not only gauging future benefits and trade-offs, but also for recognizing a community's affective response to the outcomes of those decisions. This paper describes a forecasting approach based on concepts introduced in the development of the U.S. Environmental Protection Agency's (US EPA) Human Well-Being Index (HWBI) (Smith et al., 2014, Summers et al., 2014). The approach examines the relationships among selected economic, environmental and social services that can be directly impacted by community decisions and eight domains of human well-being. Using models developed from constructed- or fixed-effect step-wise and multiple regressions and 11 years of data (2000–2010), these relationship functions may be used to characterize likely direct impacts of decisions on future well-being, as well as the possible intended and unintended secondary and tertiary effects relative to any main decision effects.     

An animal paired crossover ePTFE arteriovenous graft model

Purpose

Previously, we developed a porcine model for Arterio Venous Graft (AVG) failure to allow assessment of new access strategies. This model was limited concerning graft length. In the present technical report, we describe a modification of our model allowing the assessment of long AVGs.

Technique

In 4 pigs, AVGs of 15 cm length were created bilaterally in a cross-over fashion between the carotid artery and the contralateral jugular vein. Two days (2 pigs) and two weeks (2 pigs) after AV shunting, graft patency was evaluated by angiography, showing all four grafts to be patent, with no sign of angiographic or macroscopic narrowing at the anastomoses sites.

Conclusions

In this modified pig AVG failure model, implantation of a bilateral cross-over long AVG is a feasible approach. The present model offers a suitable tool to study local interventions or compare various long graft designs aimed at improvement of AVG patency.     

The iterative ensemble modelling approach increases the accuracy of fish distribution models

Methodological absences, i.e. when a species is not detected although it is actually present, are known to reduce the prediction accuracy of species distribution models (SDMs). To deal with this problem, we assessed whether a new iterative ensemble modelling (IEM) approach better predicts the spatial distribution of a set of 31 freshwater fish species, exhibiting a wide range of prevalence and methodological absences. Model efficiency was compared using one threshold‐independent (AUC) and three threshold‐dependent indicators of model predictive performance: the percentage of misclassified sites; the Kappa index; and the True Skill Statistic. We then reconstructed species assemblages from individual species predictions and compared observed assemblages to those predicted using EM and IEM using the Jaccard index. Compared to an EM approach, IEM improved model predictive performance for most difficult‐to‐detect species. The iterative approach outperformed EM at modelling the distribution of difficult‐to‐detect species, provided that presence data are representative of the niche of the species. At the assemblage level, the discrepancy between observed and IEM predicted assemblages was significantly lower than that between observed and EM predicted assemblages, showing that IEM can be used to predict the distribution of entire species assemblages. The IEM approach provides a way to consider difficult‐to‐detect species in species distribution models.     

Vertical migration of adult Ixodes rubicundus,the Karoo paralysis tick (Acari: Ixodidae)

Mortality due to Karoo paralysis amongst livestock is of considerable economic importance in South Africa. Indications are that the extent of vertical migration of adult ticks, to reach questing positions on grasses, is influenced by sudden climatic chages. Such influences as well as selection of questing substrates were investigated under controlled conditions. Vertical migration of adult Ixodes rubicundus on copper rods was determined in a square metal arena within a closed glass container in a room in which temperature and light could be controlled. Significantly more female and male ticks migrated vertically on 1.5 mm diameter rods than on 4.0 mm rods and on 450 mm long rods than on 100 mm rods. More ticks of both sexes migrated vertically at RH>80% than at RH<50% and at 12°C than at 21°C. More female than male and more older than younger ticks migrated vertically in all experiments. The results of this study contribute towards an understanding of the epidemiology of Karoo paralysis.