A tunable multivariable nonlinear robust observer for biological systems

This paper presents a robust nonlinear asymptotic observer with adjustable convergence rate with a great potential of applicability for biological systems in which the main state variables are difficult and expensive to measure or such measurements do not exist. This observer scheme is based on the classical asymptotic observer, which is modified to allow the tuning of the convergence rate. It is shown that the proposed observer provides fast and satisfactory estimates when facing load disturbances, system failures and parameter uncertainty while maintaining the excellent robustness and stability properties of the classical asymptotic observer. The implementation of the tunable observer is carried out by numerical simulations of a mathematical model of an anaerobic digestion process used for wastewater treatment. The key results are examined and further developed.     

Uniform step-by-step observer for aerobic bioreactor based on super-twisting algorithm

This paper describes a fixed-time convergent step-by-step high order sliding mode observer for a certain type of aerobic bioreactor system. The observer was developed using a hierarchical structure based on a modified super-twisting algorithm. The modification included nonlinear gains of the output error that were used to prove uniform convergence of the estimation error. An energetic function similar to a Lyapunov one was used for proving the convergence between the observer and the bioreactor variables. A nonsmooth analysis was proposed to prove the fixed-time convergence of the observer states to the bioreactor variables. The observer was tested to solve the state estimation problem of an aerobic bioreactor described by the time evolution of biomass, substrate and dissolved oxygen. This last variable was used as the output information because it is feasible to measure it online by regular sensors. Numerical simulations showed the superior behavior of this observer compared to the one having linear output error injection terms (high-gain type) and one having an output injection obtaining first-order sliding mode structure. A set of numerical simulations was developed to demonstrate how the proposed observer served to estimate real information obtained from a real aerobic process with substrate inhibition.     

The singularities of the visual mapping

In this article we treat purely metrical properties of the visual image, e.g. the time changes of the relative positions and orientations of image details. Self-induced movements of an observer relative to rigid bodies in his environment generate charactertistic motion parallax fields. The observer may regard those fields as proprioceptive and interprete the geometrical invariants of the fields as indicators of solid shape. In this way his perceptions become object-oriented, which is the normal case as the many constancy-phenomena show. Similar arguments apply to the disparity field of binocular vision. In this paper we treat the qualitative nature of such fields. [In this case the qualitative nature is basic. Compare the case of an equation with a single unknown. Often one is interested primarily in the qualitative solution (are there roots? How many?), and only slightly in the quantitative information (the numerical value of a root).] The qualitative nature of the fields is fixed if their singularities are known. It is shown that the singularities are of two types: isolated points (so-called specular points) and line-singularities (so-called folds, cusps and T-junctions). It is shown that for most vantage points that an observer can occupy, the topological structure of the set of singularities does not change if the observer performs small exploratory movements. That is most vantage points are stable. At an unstable vantage point the set of singularities changes and the observer experiences an event. Because certain properties of the set of singularities are shown to be preserved, only a few simple types of event are possible. A complete list is presented. The occurrence of an event is shown to be simply related to the solid shape of the objects of vision. Our geometrical theory enables us to understand the structure of the observer's internal models of external bodies.     

Why is the outcome of transient ischaemic attacks different in different groups of patients?

The outcomes of each of three large cohorts of patients with transient ischaemic attacks, which were studied in the same country at much the same time with the same methods, were compared and found to be quite different from each other. The differences in outcome were related not only to different strategies of treatment but also to differences in the prevalence and level of important prognostic factors (for example, case mix) and other factors such a the time delay from transient ischaemic attack to entry into the study and the play of chance. The implications for purchasers of health care are that they cannot rely solely on non-randomised comparisons of outcome of patients treated in competing units as a measure of the quality of care (which has only rather modest effects) without accounting for other factors that may influence outcome such as the nature of the illness, the case mix, observer bias, and the play of chance.     

Temporal aspects of information processing in the first two stages of the frog olfactory system: influence of stimulus intensity

To understand information processing in the first two stagesof the olfactory system, neural activities were examined froma temporal point of view. The extracellular unitary activityof receptor cells and bulb neurons in response to four odorsdelivered in a range of concentrations from 1 x 10^–6 to5.62 x 10^–2 as a fraction of saturated vapor was recorded.For each population, unitary activities were pooled by 100-msbins, according to the nature and/or to the concentration ofthe stimulus. The results provided a view of the timing of activityof cell populations and allowed a comparison of the temporalstructures of the primary afferent message with that of thebulbar output message. Temporal patterns of receptor cell populationwere characterized by late and sustained discharges; thus, theprimary input volley did not coincide with the early and briefbulbar output message. In the two cell populations, the temporalresponse patterns elicited depended on the nature of the stimulus.At receptor level, interstimulus differences could be explainedin terms of binding interactions between odorants and receptorsites. In the bulb, while the input and output messages werenot strictly synchronous, some temporal characteristics relativeto the nature of the stimulus were preserved. In receptor cells,the activity occurring within 1 s following the stimulus onsetspecified stimulus intensity. By contrast, in the bulb, theevents which seemed to be involved in intensity coding werethose occurring within the first 500 ms. The convergence ofprimary afferences onto the bulb leads to an amplification ofthe earliest peripheral events setting up a sharp, earlier outputbulb message; in the processing of the input information, theolfactory bulb seems to combine an amplifying role for the earliestevents with a shutting action on later events.     

非核糖体多肽合成酶研究进展

细菌和真菌采用非核糖体系统合成一些重要的多肽类物质.近年来的研究表明,在该系统中发挥关键作用的是一类分子巨大的非核糖体多肽合成酶.它们由顺序排列的组件构成,酶分子结构本身即蕴涵着多肽合成的信息.对非核糖体多肽合成酶结构和功能的了解,使人们期望可以通过对这类酶的修饰和重组来合成一些新的多肽类物质.     

超声波检测骨密度技术研究

人体骨密度能够体现人体的很多信息,如骨质疏松、骨折、骨龄等。研究利用超声波在固体中产生波形转换的原理,采用一种特殊角度的双晶探头。利用定量超声技术检测出胫骨中超声横波的传播速度SOS（speedofsound）,从中得到的骨密度信息,能够从一种新的角度来对估量减少,骨质疏松进行诊断和预测。分别对不同年龄层的人进行实验。得到的结果验证了系统的正确性。     

Measuring pairwise agreement among many observers

Weighted kappa is defined as a measure of pairwise inter observer agreement. A weighted intra class kappa coefficient is proposed to measure agreement on a particular response category. An interclass kappa coefficient is proposed for each pair of response categories. Simple estimation procedures are presented for the case where the observers judging one subject are not necessarily the same as those judging another subject. Large sample standard errors are derived and a numerical example is given.     

Citizen science and observer variability during American pika surveys

Within- and between-group observer variability can confound scientific discovery. If observer variability can be quantified and is addressed, data collected by participants with wide ranges of experience and training can yield more reliable inferences. The American pika (Ochotona princeps) is a mammalian sentinel of climate change that has received consideration for listing under the United States Endangered Species Act. As a result, numerous pika monitoring initiatives have been started throughout the mountains in western North America. Some initiatives employ research teams of biological science technicians (professionals), whereas many rely on networks of citizen scientists, or volunteers, for data collection. To date, few studies have quantified observer variability during pika surveys; none have explored the reliability of professional crews or volunteers. We conducted pika surveys in Glacier National Park, Montana, to quantify observer variability. We investigated observer variability 1) among a crew of professionals, 2) among volunteers, and 3) between professionals and volunteers. Professionals were more consistent at identifying pika signs and estimating potential home ranges and consistently found more pika signs than did the volunteers, with the exception of pika sightings. Estimates of pika occupancy were consistent at each site among volunteers conducting sitting surveys. We suggest that sitting surveys conducted by volunteers can reliably detect pika site occupancy. However, data on population dynamics of pikas (e.g., density) should be collected by professionals. Observer variability analyses of this nature should be common practice for wildlife-resource managers and scientists, especially with observers of varying levels of experience and motivation. © 2012 The Wildlife Society.     

Promoting the Avoidance of High-Calorie Snacks: Priming Autonomy Moderates Message Framing Effects

The beneficial effects of gain-framed vs. loss-framed messages promoting health protective behaviors have been found to be inconsistent, and consideration of potential moderating variables is essential if framed health promotion messages are to be effective. This research aimed to determine the influence of highlighting autonomy (choice and freedom) and heteronomy (coercion) on the avoidance of high-calorie snacks following reading gain-framed or loss-framed health messages. In Study 1 (N = 152) participants completed an autonomy, neutral, or heteronomy priming task, and read a gain-framed or loss-framed health message. In Study 2 (N = 242) participants read a gain-framed or loss-framed health message with embedded autonomy or heteronomy primes. In both studies, snacking intentions and behavior were recorded after seven days. In both studies, when autonomy was highlighted, the gain-framed message (compared to the loss-framed message) resulted in stronger intentions to avoid high-calorie snacks, and lower self-reported snack consumption after seven days. Study 2 demonstrated this effect occurred only for participants to whom the information was most relevant (BMI>25). The results suggest that messages promoting healthy dietary behavior may be more persuasive if the autonomy-supportive vs. coercive nature of the health information is matched to the message frame. Further research is needed to examine potential mediating processes.     

Heart rate measures in blind cave crayfish during environmental disturbances and social interactions

Most animals continually assess the environment in which they live and alter their behavior according to various stimuli. As an observer, one looks for changes in a behavior indicating that an animal responded to a particular event. When the animal does not make significant behavioral changes as measured by bodily movements, the animal may be characterized as unresponsive to a given stimulus. This study demonstrates that when behavioral body movements can not be observed an internal physiological measure of heart rate (HR) shows dramatic changes following presentation of defined stimuli. This study used the blind cave crayfish and examined their responsiveness to the following stimuli: light (infrared, dim red, and white), water-borne vibrations, removal of water, olfactory cues, and social interaction with partners. This study demonstrates that there is substantial individual variation of HR at basal levels and with the intensity of an social interaction. We find HR is a reasonable measure of the responsiveness of blind cave crayfish to given stimuli even in the absence of observable behavioral changes. This enables the observer to determine if an individual is responsive to and making an assessment of particular cues.     

Eye contact by non-human primates toward a human observer

Eye contact by monkeys toward a staring observer is a quantifiable reliable and sensitive behavioural measure. Early social deprivation, an increase in age, a new cage, and an increase in distance all decreased the frequency of eye contact. Young female rhesus monkeys made more contact than young males. Large differences in eye contact occurred between species of non-human primates. The results are considered in relation to both an arousal theory and an attention theory.     

Can Observation Skills of Citizen Scientists Be Estimated Using Species Accumulation Curves?

Volunteers are increasingly being recruited into citizen science projects to collect observations for scientific studies. An additional goal of these projects is to engage and educate these volunteers. Thus, there are few barriers to participation resulting in volunteer observers with varying ability to complete the project’s tasks. To improve the quality of a citizen science project’s outcomes it would be useful to account for inter-observer variation, and to assess the rarely tested presumption that participating in a citizen science projects results in volunteers becoming better observers. Here we present a method for indexing observer variability based on the data routinely submitted by observers participating in the citizen science project eBird, a broad-scale monitoring project in which observers collect and submit lists of the bird species observed while birding. Our method for indexing observer variability uses species accumulation curves, lines that describe how the total number of species reported increase with increasing time spent in collecting observations. We find that differences in species accumulation curves among observers equates to higher rates of species accumulation, particularly for harder-to-identify species, and reveals increased species accumulation rates with continued participation. We suggest that these properties of our analysis provide a measure of observer skill, and that the potential to derive post-hoc data-derived measurements of participant ability should be more widely explored by analysts of data from citizen science projects. We see the potential for inferential results from analyses of citizen science data to be improved by accounting for observer skill.     

Automated topographical cell proliferation analysis

BACKGROUND: Cell proliferation is often studied using the incorporation of bromodeoxyuridine (BrdU). Immunohistochemical staining is then used to detect BrdU in the nucleus. To circumvent the observer bias and labor-intensive nature of manually counting BrdU-labeled nuclei, an automated topographical cell proliferation analysis method is developed. METHODS: Sections stained with fluorescein-labeled anti-BrdU and counterstained with To-Pro-3 are scanned using confocal laser scanning microscopy (CLSM). For every point in the image, the nucleus density of BrdU-labeled nuclei and the total nucleus density of the neighborhood of that point are calculated from the BrdU and the To-Pro-3 signal, respectively. The ratio of these densities gives an indication of the amount of cell proliferation at that point. The automated measure is validated by comparing it with the ratio of BrdU-stained nuclei to the total number of nuclei obtained from a manual count. RESULTS: A positive correlation is found between the automated measure and the ratios calculated from the manual counting (r = 0.86, P < 0.001). Calculating the topographical cell proliferation using the automated method is faster and does not suffer from interobserver variability. CONCLUSIONS: Automated topographical cell proliferation analysis is a fast method to objectively find differences in cell proliferation within a tissue. This can be visualized by a topographical map that corresponds to the tissue under study.     

On-line evaluation of fermentation broth colour

Summary A novel method for evaluating pigment production during fermentation ofMonascus ruber has been developed and consists of reflectance measurement with a 10° observer under an artificial illuminant. A spectrophotometer was adapted to measure pigmentation during culture in a bioreactor. The lightness parameter L was the most useful information delivered by this sensor. An absorbency over 30 units at 480nm on batch cultures was estimated on-line without dilution. member of the GR Automatique - SARTA - CNRS     

Observer variation in quantification of immunocytochemistry by image analysis.

This paper reports the findings of a study designed to examine observer variation as a source of inaccuracy inherent in the use of computer-assisted image analysis to measure areas of stained tissue. The rat pituitary immunostained for prolactin and galanin was used as an example to estimate patterns of immunoreactivity exhibited by different cell types. Six observers, with differing experience, selected grey level threshold values on 40 fields of images of stained tissue making three repeats of each field. The 40 fields consisted of 20 serial pairs of colocalized fields, one immunostained for prolactin, the other for galanin. The 20 pairs consisted of four pairs from each of five animals. Analysis of observer variation in the selection of threshold values showed large differences in the within- and between-observer variation. Analysis of the components of variance in the estimation of the ratios of stained tissues showed that the major source of variation was the within-observer component. An additional experiment using two observers, where half of the images were compared to the original microscope images before setting threshold levels, showed that the opportunity to make a comparison did not reduce observer variation. It is suggested that any study which uses semi-automatic methods to segment regions of a digital image can benefit from an analysis of this kind so that the sources of variation can be determined to enable maximum discriminating power in future studies.     

Measuring information-based complexity across scales using cluster analysis

Scaling of ecological data can present a challenge firstly because of the large amount of information contained in an ecological data set, and secondly because of the problem of fitting data to models that we want to use to capture structure. We present a measure of similarity between data collected at several scales using the same set of attributes. The measure is based on the concept of Kolmogorov complexity and implemented through minimal message length estimates of information content and cluster analysis (the models). The similarity represents common patterns across scales, within the model class. We thus provide a novel solution to the problem of simultaneously considering data structure, model fit and scale. The methods are illustrated in application to an ecological data set.     

Improving the analysis of movement data from marked individuals through explicit estimation of observer heterogeneity

Ring re-encounter data, in particular ring recoveries, have made a large contribution to our understanding of bird movements. However, almost every study based on ring re-encounter data has struggled with the bias caused by unequal observer distribution. Re-encounter probabilities are strongly heterogeneous in space and over time. If this heterogeneity can be measured or at least controlled for, the enormous number of ring re-encounter data collected can be used effectively to answer many questions. Here, we review four different approaches to account for heterogeneity in observer distribution in spatial analyses of ring re-encounter data. The first approach is to measure re-encounter probability directly. We suggest that variation in ring re-encounter probability could be estimated by combining data whose re-encounter probabilities are close to one (radio or satellite telemetry) with data whose re-encounter probabilities are low (ring re-encounter data). The second approach is to measure the spatial variation in re-encounter probabilities using environmental covariates. It should be possible to identify powerful predictors for ring re-encounter probabilities. A third approach consists of the comparison of the actual observations with all possible observations using randomization techniques. We encourage combining such randomisations with ring re-encounter models that we discuss as a fourth approach. Ring re-encounter models are based on the comparison of groups with equal re-encounter probabilities. Together these four approaches could improve our understanding of bird movements considerably. We discuss their advantages and limitations and give directions for future research.