Fluorescent staining is a common tool for both quantitative and qualitative assessment of pro- and eukaryotic cells sub-population fractions by using microscopy and flow cytometry. However, direct cell counting by flow cytometry is often limited, for example when working with cells rigidly adhered either to each other or to external surfaces like bacterial biofilms or adherent cell lines and tissue samples. An alternative approach is provided by using fluorescent microscopy and confocal laser scanning microscopy (CLSM), which enables the evaluation of fractions of cells subpopulations in a given sample. For the quantitative assessment of cell fractions in microphotographs, we suggest a simple two-step algorithm that combines single cells selection and the statistical analysis. To facilitate the first step, we suggest a simple procedure that supports finding the balance between the detection threshold and the typical size of single cells based on objective cell size distribution analysis. Based on a series of experimental measurements performed on bacterial and eukaryotic cells under various conditions, we show explicitly that the suggested approach effectively accounts for the fractions of different cell sub-populations (like the live/dead staining in our samples) in all studied cases that are in good agreement with manual cell counting on microphotographs and flow cytometry data. This algorithm is implemented as a simple software tool that includes an intuitive and user-friendly graphical interface for the initial adjustment of algorithm parameters to the microphotographs analysis as well as for the sequential analysis of homogeneous series of similar microscopic images without further user intervention. The software tool entitled BioFilmAnalyzer is freely available online at https://bitbucket.org/rogex/biofilmanalyzer/downloads/.

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Understanding the physical principles that govern the complex DNA structural organization as well as its mechanical and thermodynamical properties is essential for the advancement in both life sciences and genetic engineering. Recently we have discovered that the complex DNA organization is explicitly reflected in the arrangement of nucleotides depicted by the universal power law tailed internucleotide interval distribution that is valid for complete genomes of various prokaryotic and eukaryotic organisms. Here we suggest a superstatistical model that represents a long DNA molecule by a series of consecutive ~150 bp DNA segments with the alternation of the local nucleotide composition between segments exhibiting long-range correlations. We show that the superstatistical model and the corresponding DNA generation algorithm explicitly reproduce the laws governing the empirical nucleotide arrangement properties of the DNA sequences for various global GC contents and optimal living temperatures. Finally, we discuss the relevance of our model in terms of the DNA mechanical properties. As an outlook, we focus on finding the DNA sequences that encode a given protein while simultaneously reproducing the nucleotide arrangement laws observed from empirical genomes, that may be of interest in the optimization of genetic engineering of long DNA molecules.

We consider different antenna configurations, ranging from simple X-configuration to multi-beam star geometries, for airborne scatterometric measurements of the wind vector near the ocean surface. For all geometries, track-stabilized antenna configurations, as well as horizontal transmitter and receiver polarizations, are considered. The wind vector retrieval algorithm is generalized here for an arbitrary star geometry antenna configuration and tested using the Ku-Band geophysical model function. Using Monte Carlo simulations for the fixed total measurement time, we show explicitly that the relative wind speed estimation accuracy barely depends on the chosen antenna geometry, while the maximum wind direction retrieval error reduces moderately with increasing angular resolution, although at the cost of increased retrieval algorithm computational complexity, thus, limiting online analysis options with onboard equipment. Remarkably, the simplest X-configuration, while the simplest in terms of hardware implementation and computational time, appears an outlier, yielding considerably higher maximum retrieval errors when compared to all other configurations. We believe that our results are useful for the optimization of both hardware and software design for modern airborne scatterometric measurement systems based on tunable antenna arrays especially, those requiring online data processing.

We consider sea ice and water microwave backscatter features at the C-band with vertical transmit and receive polarization and present a method for sea ice/water discrimination using a multiple fixed fan-beam satellite scatterometer. The method is based on the criterion of the minimum statistical distance of measured backscatter values to the sea ice and water (CMOD7) geophysical model functions. Implementation of the method is considered both for a typical three fan-beam geometry as well as for a potential five fan-beam geometry of a satellite scatterometer. By using computer simulations, we show explicitly that the number of looks at the same cell from different azimuthal directions needs to be increased to provide better (unambiguous) retrieval of the wind vector and sea ice/water discrimination. The algorithms for sea ice/water discrimination are described, and the results obtained are also discussed along with recommendations for the number of different azimuthal looks (beams) at the same cell from the point of view of sea ice/water discrimination as well as unambiguous wind direction retrieval during the satellite’s single pass.

Structural, localization and functional properties of unknown proteins are often being predicted from their primary polypeptide chains using sequence alignment with already characterized proteins and consequent molecular modeling. Here we suggest an approach to predict various structural and structure-associated properties of proteins directly from the mass distributions of their proteolytic cleavage fragments. For amino-acid-specific cleavages, the distributions of fragment masses are determined by the distributions of inter-amino-acid intervals in the protein, that in turn apparently reflect its structural and structure-related features. Large-scale computer simulations revealed that for transmembrane proteins, either α-helical or β -barrel secondary structure could be predicted with about 90% accuracy after thermolysin cleavage. Moreover, 3/4 intrinsically disordered proteins could be correctly distinguished from proteins with fixed three-dimensional structure belonging to all four SCOP structural classes by combining 3–4 different cleavages. Additionally, in some cases the protein cellular localization (cytosolic or membrane-associated) and its host organism (Firmicute or Proteobacteria) could be predicted with around 80% accuracy. In contrast to cytosolic proteins, for membrane-associated proteins exhibiting specific structural conformations, their monotopic or transmembrane localization and functional group (ATP-binding, transporters, sensors and so on) could be also predicted with high accuracy and particular robustness against missing cleavages.

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We suggest a universal phenomenological description for the collective access patterns in the Internet traffic dynamics both at local and wide area network levels that takes into account erratic fluctuations imposed by cooperative user behaviour. Our description is based on the superstatistical approach and leads to the q-exponential inter-session time and session size distributions that are also in perfect agreement with empirical observations. The validity of the proposed description is confirmed explicitly by the analysis of complete 10-day traffic traces from the WIDE backbone link and from the local campus area network downlink from the Internet Service Provider. Remarkably, the same functional forms have been observed in the historic access patterns from single WWW servers. The suggested approach effectively accounts for the complex interplay of both "calm" and "bursty" user access patterns within a single-model setting. It also provides average sojourn time estimates with reasonable accuracy, as indicated by the queuing system performance simulation, this way largely overcoming the failure of Poisson modelling of the Internet traffic dynamics.