Bayesian classification of vegetation types with Gaussian mixture density fitting to indicator values

Question: Is it possible to mathematically classify relevés into vegetation types on the basis of their average indicator values, including the uncertainty of the classification? Location: The Netherlands. Method: A large relevé database was used to develop a method for predicting vegetation types based on indicator values. First, each relevé was classified into a phytosociological association on the basis of its species composition. Additionally, mean indicator values for moisture, nutrients and acidity were computed for each relevé. Thus, the position of each classified relevé was obtained in a three‐dimensional space of indicator values. Fitting the data to so called Gaussian Mixture Models yielded densities of associations as a function of indicator values. Finally, these density functions were used to predict the Bayesian occurrence probabilities of associations for known indicator values. Validation of predictions was performed by using a randomly chosen half of the database for the calibration of densities and the other half for the validation of predicted associations. Results and Conclusions: With indicator values, most reléves were classified correctly into vegetation types at the association level. This was shown using confusion matrices that relate (1) the number of relevés classified into associations based on species composition to (2) those based on indicator values. Misclassified relevés belonged to ecologically similar associations. The method seems very suitable for predictive vegetation models.     

Modeling carotid and radial artery pulse pressure waveforms by curve fitting with Gaussian functions

Modeling arterial pressure waveforms holds the potential for identifying physiological changes. There is a clinical need for a simple waveform analysis method with a high accuracy in reproducing the original waveforms. The aim of this study was to determine the accuracy of modeling carotid and radial pulses using Gaussian functions, making no physiological assumptions. Carotid and radial pulses were recorded from 20 normal volunteers. Ten consecutive beats from each volunteer were analyzed to determine beat-to-beat variability. Each pulse was decomposed using seven combinations of up to three Gaussian functions. The first function was always positive, but the second or third could be either positive or negative. Three positive Gaussian functions reproduced the original waveforms best with a mean absolute error (MAE) of 1.2% and 1.3% for the carotid and radial pulses respectively, and a maximum residual error of only 4.1% for both. This model had significantly smaller errors than any of the other six (all P < 0.001). Four positive Gaussian functions were then used to test the stability of this model. An insignificant change of the mean MAE (1.2% for both carotid and radial pulses) was obtained, showing that the stability has been reached with three positive Gaussian functions. The variability of MAE calculated as the standard deviation (SD) over the 10 beats was small at 0.2% for both pulses confirming the repeatability of using three positive Gaussian functions.     

Dissipative particle dynamics of non-spherical particles using a Gaussian density model

The Gaussian density molecular model has been adapted for dissipative particle dynamics. The model, when combined with a soft potential, is shown to be a very flexible mesoscale model exhibiting a wide range of phase behaviour. The soft potential allows relatively large time steps to be used and hence a more rapid equilibration. In addition, the model can be used to study both uniaxial and biaxial systems. We have undertaken a number of pilot studies and have demonstrated that the Gaussian model is able to identify nematic–isotropic phase transitions in liquid crystals and the formation of ordered discotic phases.     

High throughput inclusion body sizing: Nano particle tracking analysis

The expression of pharmaceutical relevant proteins in Escherichia coli frequently triggers inclusion body (IB) formation caused by protein aggregation. In the scientific literature, substantial effort has been devoted to the quantification of IB size. However, particle‐based methods used up to this point to analyze the physical properties of representative numbers of IBs lack sensitivity and/or orthogonal verification. Using high pressure freezing and automated freeze substitution for transmission electron microscopy (TEM) the cytosolic inclusion body structure was preserved within the cells. TEM imaging in combination with manual grey scale image segmentation allowed the quantification of relative areas covered by the inclusion body within the cytosol. As a high throughput method nano particle tracking analysis (NTA) enables one to derive the diameter of inclusion bodies in cell homogenate based on a measurement of the Brownian motion. The NTA analysis of fixated (glutaraldehyde) and non‐fixated IBs suggests that high pressure homogenization annihilates the native physiological shape of IBs. Nevertheless, the ratio of particle counts of non‐fixated and fixated samples could potentially serve as factor for particle stickiness. In this contribution, we establish image segmentation of TEM pictures as an orthogonal method to size biologic particles in the cytosol of cells. More importantly, NTA has been established as a particle‐based, fast and high throughput method (1000–3000 particles), thus constituting a much more accurate and representative analysis than currently available methods.     

Rational vaccine strategies against AIDS: background and rationale

New vaccine candidates exploiting the rational combination of regulatory and structural HIV gene products are being developed within the program of the AIDS Vaccine Integrated Project (AVIP) and will be tested in comparative preclinical and clinical trials with the ultimate goal of selecting proper candidates for advanced clinical testing in developing countries.     

Diatrack particle tracking software: Review of applications and performance evaluation

Object tracking is an instrumental tool supporting studies of cellular trafficking. There are three challenges in object tracking: the identification of targets; the precise determination of their position and boundaries; and the assembly of correct trajectories. This last challenge is particularly relevant when dealing with densely populated images with low signal‐to‐noise ratios—conditions that are often encountered in applications such as organelle tracking, virus particle tracking or single‐molecule imaging. We have developed a set of methods that can handle a wide variety of signal complexities. They are compiled into a free software package called Diatrack. Here we review its main features and utility in a range of applications, providing a survey of the dynamic imaging field together with recommendations for effective use. The performance of our framework is shown to compare favorably to a wide selection of custom‐developed algorithms, whether in terms of localization precision, processing speed or correctness of tracks.      

Machine learning‐based automated fungal cell counting under a complicated background with ilastik and ImageJ

Measuring the concentration and viability of fungal cells is an important and fundamental procedure in scientific research and industrial fermentation. In consideration of the drawbacks of manual cell counting, large quantities of fungal cells require methods that provide easy, objective and reproducible high‐throughput calculations, especially for samples in complicated backgrounds. To answer this challenge, we explored and developed an easy‐to‐use fungal cell counting pipeline that combined the machine learning‐based ilastik tool with the freeware ImageJ, as well as a conventional photomicroscope. Briefly, learning from labels provided by the user, ilastik performs segmentation and classification automatically in batch processing mode and thus discriminates fungal cells from complex backgrounds. The files processed through ilastik can be recognized by ImageJ, which can compute the numeric results with the macro ‘Fungal Cell Counter’. Taking the yeast Cryptococccus deneoformans and the filamentous fungus Pestalotiopsis microspora as examples, we observed that the customizable software algorithm reduced inter‐operator errors significantly and achieved accurate and objective results, while manual counting with a haemocytometer exhibited some errors between repeats and required more time. In summary, a convenient, rapid, reproducible and extremely low‐cost method to count yeast cells and fungal spores is described here, which can be applied to multiple kinds of eucaryotic microorganisms in genetics, cell biology and industrial fermentation.     

Chick growth in albatrosses: curve fitting with a twist

We present a new type of equation to describe the growth patterns of procellariiform seabirds and other species whose chicks characteristically lose mass towards the end of the rearing period. Our equation is based on the Gompertz curve; our principles are also applicable to logistic and von Bertalanffy curves. From our model, five coefficients can be derived to characterise the patterns of growth. These are: growth rate, peak mass and age at which it is attained, loss rate and an index describing the overall shape of the curve. We illustrate the use of this new equation with data collected, using automated weighing platforms, on six years of chick growth of Black-browed Diomedea melanophris and Grey-headed D. chrysostoma albatrosses at Bird Island, South Georgia. In comparison with Grey-headed Albatross, Black-browed Albatross chicks grow at a faster rate and to a higher peak mass; they also reach their peak mass at an earlier age, and lose mass at a faster rate in the mass recession period. However, in both species, chicks reached peak mass when 72% of the rearing period had elapsed; within species, only this did not vary between years. This new equation not only enables the period of mass recession to be incorporated into growth analysis, but, because it does not require assumptions about asymptotic mass, greatly facilitates inter-species comparisons.     

Prevalence and tracking of weight disorders in Italian primary school students: a three-year follow-up

Obesity has been widely described as the latest epidemic, and in some areas obesity co-exists with undernutrition. The purpose of this study was to assess the variability of weight status of a cohort of 279 Italian primary school students followed longitudinally for three years. Overweight was the most common weight status disorder in both sexes and generally prevailed in females. Underweight was also more frequent in females than males, while males generally showed a higher incidence of obesity. Overweight showed the highest stability in females. In males, tracking of overweight was 62.5%, while that of normal weight was 89.36%. Overweight tracks through the three consecutive years in a high percentage of both sexes. In the whole sample (regardless of sex and weight category), overweight shows the highest increase over the three-year period. This study provides public health professionals with useful data for policy planning in regard to childhood obesity.     

Collective bacterial dynamics revealed using a three-dimensional population-scale defocused particle tracking technique

An ability to monitor bacterial locomotion and collective dynamics is crucial to our understanding of a number of well-characterized phenotypes including biofilm formation, chemotaxis, and virulence. Here, we report the tracking of multiple swimming Escherichia coli cells in three spatial dimensions and at single-cell resolution using a novel three-dimensional (3D) defocused particle tracking (DPT) method. The 3D trajectories were generated for wild-type Escherichia coli strain RP437 as well as for isogenic derivatives that display smooth swimming due to a cheA deletion (strain RP9535) or incessant tumbling behavior due to a cheZ deletion (strain RP1616). The 3D DPT method successfully differentiated these three modes of locomotion and allowed direct calculation of the diffusion coefficient for each strain. As expected, we found that the smooth swimmer diffused more readily than the wild type, and both the smooth swimmer and the wild-type cells exhibited diffusion coefficients that were at least two orders of magnitude larger than that of the tumbler. Finally, we found that the diffusion coefficient increased with increasing cell density, a phenomenon that can be attributed to the hydrodynamic disturbances caused by neighboring bacteria.     

A multiplexed magnetic tweezer with precision particle tracking and bi-directional force control

Background

In the past two decades, methods have been developed to measure the mechanical properties of single biomolecules. One of these methods, Magnetic tweezers, is amenable to acquisition of data on many single molecules simultaneously, but to take full advantage of this "multiplexing" ability, it is necessary to simultaneously incorporate many capabilities that have been only demonstrated separately.

Methods

Our custom built magnetic tweezer combines high multiplexing, precision bead tracking, and bi-directional force control into a flexible and stable platform for examining single molecule behavior. This was accomplished using electromagnets, which provide high temporal control of force while achieving force levels similar to permanent magnets via large paramagnetic beads.

Results

Here we describe the instrument and its ability to apply 2–260 pN of force on up to 120 beads simultaneously, with a maximum spatial precision of 12 nm using a variety of bead sizes and experimental techniques. We also demonstrate a novel method for increasing the precision of force estimations on heterogeneous paramagnetic beads using a combination of density separation and bi-directional force correlation which reduces the coefficient of variation of force from 27% to 6%. We then use the instrument to examine the force dependence of uncoiling and recoiling velocity of type 1 fimbriae from Eschericia coli (E. coli) bacteria, and see similar results to previous studies.

Conclusion

This platform provides a simple, effective, and flexible method for efficiently gathering single molecule force spectroscopy measurements.

     

Simultaneous fitting of real-time PCR data with efficiency of amplification modeled as Gaussian function of target fluorescence

Background  

In real-time PCR, it is necessary to consider the efficiency of amplification (EA) of amplicons in order to determine initial target levels properly. EAs can be deduced from standard curves, but these involve extra effort and cost and may yield invalid EAs. Alternatively, EA can be extracted from individual fluorescence curves. Unfortunately, this is not reliable enough.     

Factors associated with tracking of BMI: a meta-regression analysis on BMI tracking

Stable tracking of body composition is a prerequisite for the long-term effect of preventive measures against obesity and its harmful effects. As BMI tracking estimates reported by individual studies vary considerably, we performed a meta-regression analysis to provide a summary estimate and to assess determinants of BMI tracking. Using the Medline and EMBASE databases, a systematic review was conducted to identify publications reporting correlation coefficients as tracking estimates between BMI at baseline and follow-up measurements and the time interval between these measurements. Additional information recorded included age at baseline measurement, gender, and origin of the studied population. Based on the extracted data, a meta-regression analysis was performed using mixed effects models to account for multiple measurements of the same cohorts. Data on 55,072 individuals (797,094 person-years) extracted from 48 publications with follow-up times between 0.5 and 44 years entered the analysis. The overall estimates for the 1-year tracking correlation coefficient were strong (r = 0.78-0.86 depending on age at baseline measurement) and gradually decreasing over time (0.67-0.78 after 10 years, and 0.27-0.47 after 30 years). Study origin classified by continent was another significant predictor of BMI tracking whereas gender was not. In conclusion, this meta-regression analysis showed a high degree of BMI tracking across all age groups investigated and independent of BMI. Successful prevention in weight control is likely to have long term effects at any age, thereby being beneficial with respect to the associated risks of over- and underweight.     

Immuno- and erythropoiesis in mice with graft vs host disease against a background of immunodeficiency

In BALB/c mice immunodeficiency was induced by the transfer of lymphocytes immune to alloantigen. This model is one of experimental models of AIDS. The work was aimed at the study of disturbances in the immuno--and erythropoiesis in immunodeficient mice. The state of erythropoiesis was evaluated by the level of level of hemoglobin, hematocrit and the content of reticulocytes in peripheral blood, by the number of erythroid bursitis-forming units and the percentage of erythrokaryocytes in the marrow, as well as by the number of colony-forming units in the spleen by days 5 and 8. The study revealed that in BALB/c mice hypoplastic anemia, accompanied by the decreased phagocytic activity of macrophages and the reduced production of interleukin 1 and tumor necrosis factor, developed on months 5-6 of the disease. Macrophagal dysfunction was supposed to be one of the causes of hypoplastic anemia in immunodeficient mice.     

Indices of acute inflammation against a background of lithium oxybutyrate action

The experiments on rats have shown that intraperitoneal administration of silver nitrate solution induces peritonitis while subplantar histamine, serotonin and prostaglandin E2 administration leads to an acute paw edema. Preliminary subcutaneous injection of lithium hydroxybutyrate prevents the development of inflammation.