Control of ��-amylase production by Bacillus subtilis

This study proposes two adaptive control algorithms for the fed-batch production of α-amylase. The first one uses online information from hardware measuring glucose. Online information of both biomass and glucose concentrations measured with different frequency is used in the second algorithm. Hardware measuring variables are inputs for software sensors of glucose concentration and (specific) glucose consumption rate. Either of the algorithms do not require any kinetic coefficients. This is a benefit, because the kinetic coefficients can vary during cultivation and between cultivations, leading to low process reproducibility and the non-stationary state of the bioprocess. The results of simulation investigations show good performance of the proposed control schemes.     

An adaptive test for a subset of coefficients in a multivariate regression model

An adaptive multivariate test is proposed for a subset of regression coefficients in a linear model. This adaptive method uses the studentized deleted residuals to calculate an appropriate weight for each observation. The weights are then used to compute Wilk's lambda for the weighted model. The adaptive test is performed by permuting the independent variables corresponding to those parameters that are assumed to equal zero in the null hypothesis. The permuted variables are then weighted to obtain a permutation test statistic that is used to estimate the p-value. An example is presented of a multivariate regression that uses systolic and diastolic blood pressure as dependent variables with age and body mass index as independent variables. The simulation results show that the adaptive test maintains its size for the three multivariate error distributions that were used in the study. For normal error models the power of the adaptive test nearly equaled that of the non-adaptive test. For models that used non-normal errors the adaptive test was considerably more powerful than the traditional non-adaptive test.     

Using Adaptive Methods to Select Variables in Case‐Control Studies

A variables selection method for case‐control studies is proposed that uses an adaptive weighting scheme along with a permutation method to determine if a variable is useful in differentiating the cases from the controls. This adaptive method is used to select exposure variables for the analysis of data from a bladder cancer case‐control study. An extensive simulation study shows that the adaptive method is nearly as effective at finding those variables that are related to case‐control status when normally distributed variables are used. The simulation also shows that the proposed variable selection procedure is much more effective than the stepwise discriminant analysis method when the variables are not normally distributed. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Piloting a social-ecological index for measuring flood resilience: A composite index approach

Global increases in the magnitude and frequency of flood events have raised concerns that traditional flood management approaches may not be sufficient to deal with future uncertainties. There is a need to move towards approaches that manage the resilience of the system to floods by understanding and managing drivers of vulnerability and adaptive capacity. Here we pilot an approach to measure the resilience of a system to a flood. A method is presented in which indicators are used to measure and map the spatial distribution of the levels of flood resilience across a landscape. Using three flood affected municipalities in South Africa, 24 resilience indicators related to floods and its relevant social, ecological, infrastructural and economic aspects are selected, and integrated into a composite index using a principal components analysis (PCA). A fifth component of institutional resilience is used to explore levels of disaster planning, mitigation and public awareness capacities and where these can be increased. The PCA transformed the 24 variables into four main components, the first of which was strongly correlated with underlying social variables, while the second and third correlated well with economic and ecological variables respectively. Distinct spatial variation of flood resilience was found across the study area, with highest flood resilience in main cities, and lowest in wards located on the periphery of cities often the location of peri-urban informal settlements. The disaggregation of underlying indicators showed wards with lowest flood resilience also had the lowest social, economic and ecological resilience. The flood resilience index was sensitive to the exclusion of all three components highlighting the importance of capturing the multidimensionality of flood resilience. The approach allows for a simple, yet robust index able to include an array of datasets generally available in flood prone areas with potential to disaggregate and trace variables for management and decision making.     

Macroautophagy in Immunity and Tolerance

Autophagy and proteasomal degradation constitute the two main catabolic pathways in cells. While the proteasome degrades primarily short-lived soluble proteins, macroautophagy, the main constitutive autophagic pathway, delivers cell organelles and protein aggregates for lysosomal degradation. Both the proteasome and macroautophagy are attractive effector mechanisms for the immune system because they can be used to degrade foreign substances, including pathogenic proteins, within cells. Therefore, both innate and adaptive immune responses use these pathways for intracellular clearance of pathogens as well as for presentation of pathogen fragments to the adaptive immune system. Because, however, the same mechanisms are used for the steady-state turnover of cellular self-components, the immune system has to be desensitized not to recognize these. Therefore, proteasomal degradation and macroautophagy are also involved in tolerizing the immune system prior to pathogen encounter. We will discuss recent advances in our understanding how macroautophagy selects self-structures in the steady state, how presentation of these on major histocompatibility complex class II molecules leads to tolerance and how macroautophagy assists both innate and adaptive immunity. This new knowledge on the specialized functions of the metabolic process macroautophagy in higher eukaryotes should allow us to target it for therapy development against immunopathologies and to improve vaccinations.     

Immunological Control of Fish Diseases

All metazoans possess innate immune defence system whereas parameters of the adaptive immune system make their first appearance in the gnathostomata, the jawed vertebrates. Fish are therefore the first animal phyla to possess both an innate and adaptive immune system making them very interesting as regards developmental studies of the immune system. The massive increase in aquaculture in recent decades has also put greater emphasis on studies of the fish immune system and defence against diseases commonly associated with intensive fish rearing. Some of the main components of the innate and adaptive immune system of fish are described. The innate parameters are at the forefront of immune defence in fish and are a crucial factor in disease resistance. The adaptive response of fish is commonly delayed but is essential for lasting immunity and a key factor in successful vaccination. Some of the inherent and external factors that can manipulate the immune system of fish are discussed, the main fish diseases are listed and the pathogenicity and host defence discussed. The main prophylactic measures are covered, including vaccination, probiotics and immunostimulation. A key element in the immunological control of fish diseases is the great variation in disease susceptibility and immune defence of different fish species, a reflection of the extended time the present day teleosts have been separated in evolution. Future research will probably make use of molecular and proteomic tools both to study important elements in immune defence and prophylactic measures and to assist with breeding programmes for disease resistance.     

Dynamic behavior of the adaptive control system, hypothalamus--anterior pituitary--adrenal cortex. Animal experimental study of the adequate system dynamics of the direct and indirect parameters of the adaptive control system]

The dynamic response of the adaptive closed-loop control system hypothalamus-anterior pituitary-adrenal cortex after application of short-time disturb pulses were examined experimentally in the pig. Blood sampling was performed biologically non-reactive by chronically implanted vascular catheters in the upper vena cava. A circadian biphase periodical dynamics characterizes the distrubance response of the adaptive control system, respectively, its direct and indirect parameters. After distrubance variables induced initial excess the plasma corticosteriods undershoot the basic level over a long period. Conversely, the dynamics of the eosinophils is determined through an initial eosinopenic phase and a subsequent typical overshoot. Periodical dynamic is absent in the steady state. The controller of the adaptive system does not show any spontaneous activity in the steady state without stress. The absence of an endogenic periodicity of the dependent parameters likewise gives evidence of an active oscillator. On the other hand, the controlling unit of the adaptive system constitutes a control response of circadian periodicty after activation by disturbance variables in pulse shape. The high damping of the control system terminates the transient state within 24 hours, and the corticosteriods and the eosinophils reach the steady state level. This control quality of the adaptive control system gains a high importance in the origination of the spontaneous circadian periodicity by corticosteriods and eosinophils and for the biological compensation of exogenous distrubance variables.     

Evidence for the occurrence of an oxygen limitation during soil bioremediation by solid-state fermentation

Bioremediation methods are a promising way of dealing with soil and subsoil contamination by organic substances. This biodegradation process is supported by micro-organisms which use the organic carbon from the pollutants as energy source and cells building blocks. The scope of this work is to study the main parameters of the process and the physical limiting steps. Several ground samples from an actual petroleum hydrocarbon contaminated site have been tested. Four fixed bed column reactors and one rotating fermentor are used, enabling the study of the influence of different operating variables on the biodegradation kinetics. The stoichiometric equation for bacteria growth and pollutant degradation has been established, allowing the determination of mass balances. Biodegradation monitoring is achieved by continuously measuring the emissions of carbon dioxide. Biodegradation rates and pollution load decrease in the two kinds of bioreactors are also compared.     

An adaptive control algorithm for fed-batch culture

The implementation of adaptive control for a fed-batch culture in order to maximize the output of product based on a self-adjusting model is discussed in the present work. Optimization methods were applied to the generalized mathematical model of a fed-batch fermentation process to determine control algorithms that could be used for on-line process control. The efficiency of the proposed adaptive algorithms was investigated by simulating a model system. The model of amylotytic enzyme fermentation that was proposed by the authors was taken from a real process. Dynamic modelling has shown that the main problem of realization is connected with the on-line identification of the adaptive model's parameters. To avoid this problem, we have introduced special limitations on the parameters' time variations that increased the convergence of the identification algorithm. The results of the investigation have shown the efficiency of the proposed adaptive algorithms, and the results of this work should be investigated for real process control.     

Real-time optimisation of a fermentation process

An adaptive on-line sub-optimal control system for yeast fermentation was developed. The control package is described with a brief history of progress. Results show the effect of the control package on process variables, and indicate present limitations and future development.     

Latent variable models for harmonization of test scores: A case study on memory

Combining data from different studies has a long tradition within the scientific community. It requires that the same information is collected from each study to be able to pool individual data. When studies have implemented different methods or used different instruments (e.g., questionnaires) for measuring the same characteristics or constructs, the observed variables need to be harmonized in some way to obtain equivalent content information across studies. This paper formulates the main concepts for harmonizing test scores from different observational studies in terms of latent variable models. The concepts are formulated in terms of calibration, invariance, and exchangeability. Although similar ideas are present in measurement reliability and test equating, harmonization is different from measurement invariance and generalizes test equating. In addition, if a test score needs to be transformed to another test score, harmonization of variables is only possible under specific conditions. Observed test scores that connect all of the different studies, are necessary to be able to test the underlying assumptions of harmonization. The concepts of harmonization are illustrated on multiple memory test scores from three different Canadian studies.     

Developmental thermal plasticity among Drosophila melanogaster populations

Many biotic and abiotic variables influence the dispersal and distribution of organisms. Temperature has a major role in determining these patterns because it changes daily, seasonally and spatially, and these fluctuations have a significant impact on an organism's behaviour and fitness. Most ecologically relevant phenotypes that are adaptive are also complex and thus they are influenced by many underlying loci that interact with the environment. In this study, we quantified the degree of thermal phenotypic plasticity within and among populations by measuring chill‐coma recovery times of lines reared from egg to adult at two different environmental temperatures. We used sixty genotypes from six natural populations of Drosophila melanogaster sampled along a latitudinal gradient in South America. We found significant variation in thermal plasticity both within and among populations. All populations exhibit a cold acclimation response, with flies reared at lower temperatures having increased resistance to cold. We tested a series of environmental parameters against the variation in population mean thermal plasticity and discovered the mean thermal plasticity was significantly correlated with altitude of origin of the population. Pairing our data with previous experiments on viability fitness assays in the same populations in fixed and variable environments suggests an adaptive role of this thermal plasticity in variable laboratory environments. Altogether, these data demonstrate abundant variation in adaptive thermal plasticity within and among populations.     

Characteristics and detection principles of a new enzyme label producing a long-term chemiluminescent signal

A new enzyme label system is described which is superior to all existing chemiluminescence labels used in immunoassays. The system consists of the enzyme xanthine oxidase with hypoxanthine as substrate. The signal reagent contains perborate, an Fe–EDTA complex and luminol. The enzyme preparation and the signal reagent are very stable upon storage. The main features of the system are a long duration of the chemiluminescent signal (half-life time of 30 hours) and a very low limit of detection (about 3 amol). Possibilities and implications for the use of various measuring system are discussed.     

Determination of bubble size distribution in gas–liquid two‐phase systems via an ultrasound‐based method

Over the past few years, ultrasonic techniques are increasingly used to determine bubble size distribution in gas–liquid two‐phase systems. However, the development of a precise and efficient measuring system is very challenging because bubbles are dynamic and unstable relative to time and space in a moving fluid, thus hindering an accurate validation of the measuring system. Therefore, this study examined the possibility of using artificial bubbles to establish an ultrasonic measuring system. The main concept for this study involved developing an ultrasound‐based measuring system with the aid of a certain type of artificial bubbles. The developed system was subsequently adapted to the bypass pipeline of a propagator to demonstrate the reliability of this concept. The results indicated that the established system could measure a microbubble size distribution with a root mean squared error of validation that corresponded to 0.1243 % v/v. Additionally, the estimates of real bubble measurement agreed well with the reference method. Thus, this study demonstrated that the developed system could be a potential method to determine bubble size distributions in gas–liquid two‐phase systems.     

Environmental features influencing Carabid beetle (Coleoptera) assemblages along a recently deglaciated area in the Alpine region

Abstract.  1. The spatio-temporal approach was used to evaluate the environmental features influencing carabid beetle assemblages along a chronosequence of an Italian Alpine glacier foreland. The influence of environmental variables on species richness, morphology (wing and body length), and distribution along the chronosequence was tested.
2. Species richness was found to be a poor indicator of habitat due to weak influences by environmental variables. It seems that the neighbouring habitats of a glacier foreland are not able to determine significant changes in carabid species richness.
3. Instead it appears that history (age since deglaciation) and habitat architecture of a glacier foreland are strongly correlated to species adaptive morphological traits, such as wing morphology and body length. Assemblages characterised by species with reduced wing size are linked to the older stages of the chronosequence, where habitat is more structured. Assemblages characterised by the largest species are linked to the younger sites near the glacier. These morphological differentiations are explained in detail.
4. Habitat age can therefore be considered the main force determining assemblage composition. On the basis of the relationship between morphological traits and environmental variables, it seems likely that age since deglaciation is the main variable influencing habitat structure (primary effect) on the Forni foreland. The strong relationship between carabid assemblages and habitat type indicates that site age has but a secondary effect on carabid assemblages. This may be utilised to interpret potential changes in assemblages linked to future glacier retreat.     

Macroevolutionary dynamics in environmental space and the latitudinal diversity gradient in New World birds

Correlations between species richness and climate suggest non-random occupation of environmental space and niche evolution through time. However, the evolutionary mechanisms involved remain unresolved. Here, we partition the occupation of environmental space into intra- and inter-clade components to differentiate a model based on pure conservation of ancestral niches with higher diversification rates in the tropics, and an adaptive radiation model based on shifts in adaptive peaks at the family level allowing occupation of temperate regions. We examined these mechanisms using within- and among-family skewness components based on centroids of 3560 New World bird species across four environmental variables. We found that the accumulation of species in the tropics is a result of both processes. The components of adaptive radiation have family level skewness of species' distributions strongly structured in space, but not phylogenetically, according to the integrated analyses of spatial filters and phylogenetic eigenvectors. Moreover, stronger radiation components were found for energy variables, which are often used to argue for direct climatic effects on diversity. Thus, the correspondence between diversity and climate may be due to the conservation of ancestral tropical niches coupled with repeated broad shifts in adaptive peaks during birds' evolutionary history more than by higher diversification rates driven by more energy in the tropics.     

Computer control of pH and DO in a laboratory fermenter using a neural network technique

In this contribution, the advantages of the artificial neural network approach to the identification and control of a laboratory-scale biochemical reactor are demonstrated. It is very important to be able to maintain the levels of two process variables, pH and dissolved oxygen (DO) concentration, over the course of fermentation in biosystems control. A PC-supported, fully automated, multi-task control system has been designed and built by the authors. Forward and inverse neural process models are used to identify and control both the pH and the DO concentration in a fermenter containing a Saccharomyces cerevisiae based-culture. The models are trained off-line, using a modified back-propagation algorithm based on conjugate gradients. The inverse neural controller is augmented by a new adaptive term that results in a system with robust performance. Experimental results have confirmed that the regulatory and tracking performances of the control system proposed are good.     

Endotoxin Neutralization as a Biomonitor for Inflammatory Bowel Disease

Gram-negative bacterial endotoxin is a potent immunostimulant implicated in the development and/or progression of a variety of diseases. The mammalian immune system has both innate and adaptive immune responses to neutralize endotoxin. In this study, a system was developed to monitor bacterial exposure by measuring the extent and nature of endotoxin neutralization in plasma. In control patients, females had higher levels of endotoxin neutralization than males, mirroring clinical outcomes from bacterial infection and sepsis. In addition to the total amount of neutralization, we used inactivation techniques to elucidate the nature of this activity and develop a system to compare early and late immune responses. Using this method to monitor patients with inflammatory bowel disease, we found a more robust total response that relies more on long-term, adaptive components of the immune system and less on early, innate components. Our results indicate that endotoxin neutralization is a valuable method to discern inflammatory bowel disease patients from a control population. Additionally, the nature of neutralization may be valuable in monitoring disease severity and/or the role of medication.     

Multivariate analysis of infant and child mortality in Java and Bali

The data used in this analysis come from the 1976 Indonesian Fertility Survey, part of the World Fertility Survey. The data are examined 3 times, fitting them to models which include different combinations of independent variables. The dependent variables are: 1) the proportion of children born between 5 and 15 years before the survey who died before their 1st birthday, for infant mortality; and 2) among those alive on their 1st birthday, the proportions who died before reaching their 5th birthday, for child mortality. The figures indicate that the chance of dying for children who were 1st born, born shortly after a previous child, whose previous sibling had died, who lived in rural areas, or had parents who were young and with little education, was greater than for children without these characteristics. In all 3 models used, the greatest net effects are attributed to the survival of a preceding sibling or the length of the preceding interval. Birth order does not have a significant gross effect on infant mortality, but the net effects are significant because of the control on maternal age. Education of both parents has significant effects, but these are overshadowed in magnitude by the demographic variables. Maternal education has a greater influence in determining differences in child mortality than was found for infant mortality. Father's education also has a significant independent effect, but mainly for 1st births. It is uncertain whether these variables are measuring the effect of schooling as such, or other characteristics such as economic status or various social roles adopted by people with different levels of education. The variables distinguishing urban from rural status shows significant gross effects which are greatly reduced when controls for other variables are introduced in the model which includes all births. That is to say, the difference in the survival chances of a child in the city is more a function of the education of its parents, and the associated demographic variables than city residence as such. Access to medical services is quite probably the main element in these differences. The findings are weakened to some extent by the lack of satisfactory data on household economic status which might have provided a better base for indirectly discerning the effects of nutrition and sanitation on mortality at young ages.     

Spots, stripes, tail tips and dark eyes: Predicting the function of carnivore colour patterns using the comparative method

Animal colour patterns are adaptive for three reasons: camouflage, communication and physico-physiological functions. This study proposes a conceptual framework for predicting the main adaptive function of carnivore colour patterns based on three factors: visibility, shape and location on the body, as well as, their behavioural ecological correlates. Using a comparative phylogenetic approach, the colour patterns present on the body, the tail and the eyes of 200 species of mammalian carnivores were analysed. Their evolutionary history was reconstructed using MacClade and Maddison's concentrated-changes test was used to test the association between species' colour patterns and their behavioural ecology on a composite phylogeny for all the Carnivora. The results for dark spots, vertical stripes, horizontal stripes, ringed tails, black tail tips, white tail tips, dark eye contour and dark eye patches, are presented. The comparative analyses indicate that spotted, vertically striped and horizontally striped coats evolved for camouflage. Tail markings seem to have evolved for intra- and/or inter-specific communication, while dark markings near and around the eyes are associated with variables consistent with a physico-physiological function. These findings suggest that both the physical environment and animal behaviour are important selective factors driving the evolution of animal colour patterns and that both need to be taken into consideration in future studies of animal coloration.