Excitation of solitons in hexagonal lattices and ways of controlling electron transport

This is a post-peer-review, pre-copyedit version of an article published in Philosophical Transactions A: Mathematical, Physical and Engineering Sciences. The final authenticated version is available online at: http://dx.doi.org/10.1007/s40435-017-0383-x.We construct metastable long-living hexagonal lattices with appropriately modified Morse interactions and show that highly-energetic solitons may be excited moving along crystallographic axes. Studying the propagation, their dynamic changes and the relaxation processes it appears that lump solitons create in the lattice running local compressions. Based on the tight-binding model we investigate the possibility that electrons are trapped and guided by the electric polarization field of the compression field of one soliton or two solitons with crossing pathways. We show that electrons may jump from a bound state with the first soliton to a bound state with a second soliton and changing accordingly the direction of their path. We discuss the possibility to control by this method the path of an excess electron from a source at a boundary to a selected drain at another chosen boundary by following straight pathways on crystallographic axes.DFG, 163436311, SFB 910: Kontrolle selbstorganisierender nichtlinearer Systeme: Theoretische Methoden und Anwendungskonzept

Biodegradation of Perfluorooctanoic Acid by Pseudomonas Plecoglossicida Strain DD4

Organofluorines, as a pollutant, belongs to a group of substances which are very difficult to neutralize. They are part of many products of everyday use and for this reason they pollute the environment in large quantities. Perfluorinated carboxylic acids are entered into the list of the “Stockholm Convention on Persistent Organic Pollutants” in order to minimize the load on the environment by significantly reducing their use, up to their complete rejection. The DD4 strain was isolated from the soil by the enrichment method and identified using 16S rRNA method as Pseudomonas plecoglossicida. It is able to metabolize perfluorooctanoic acid (PFOA) as the only carbon source in Raymond nutrient medium with a concentration of 1000 mg/l with the release of 132 mg/l fluorine ions. In tests conducted on the biological decomposition of perfluorooctanoic acid, it was possible to quantify its residues using tandem LCMS-IT-TOF. The presented results characterize the Pseudomonas plecoglossicida DD4 strain actively utilized PFOA as the sole carbon source, which characterizes it as a candidate for the creation of biological products aimed at the utilization of organofluorine pollutants

Supplementary descriptions and DNA barcodes of two rarely encountered Trisetacus species (Eriophyoidea, Phytoptidae) associated with Tertiary relict conifers from the Mediterranean region

New records and supplementary morphological descriptions of two rarely encountered Trisetacus species from Pinaceae, T. abietis Postner 1968 and T. cedri (Nalepa 1920), are reported. Trisetacus abietis was found in Abkhazia under the needle epidermis of Abies nordmanniana (Steven) Spach, a conifer endemic to the mountainous Asian coast of the Black Sea. Trisetacus cedri was found in buds of introduced Cedrus deodara(Roxb. ex D. Don) G. Don in Abkhazia and South Africa. It is the only member of Trisetacus known from Cedrus spp. For the first time we provide sequences of two genes (COI and D1–D2 28S) of T. abietis(MN022221, MN025333) and T. cedri (MN022222, MN022223, MN025334, MN025335), along with microphotographs of the damage caused by these mites on their coniferous hosts. Sequences of D1–D2 28S of T. cedri from Abkhazian and South African populations are identical; COI sequences from different populations differ by only one synonymous substitution in a codon for asparagine. Females of T. abietis have long asymmetrical 8/7-rayed empodia, whereas males have shorter symmetrical 6/6-rayed empodia and shorter solenidia ω I. Similar sexual dimorphism in tarsal appendages was previously reported in Novophytoptus, representing an endoparasitic lineage of phytoptids on monocots. In T. cedri, a “long form” and a “short form” of both males and females were detected, suggesting a complex life cycle in this species. The evolution of Trisetacus is discussed within the broader context of the molecular phylogenies of Pinaceae and Eriophyoidea, including estimations of divergence times.The Russian Foundation for Basic Research; ZIN RAS (project АААА-А19-119020790133-6) and the Russian Science Foundation.https://www.biotaxa.org/saaam2019Forestry and Agricultural Biotechnology Institute (FABI

Active Brownian Particles. From Individual to Collective Stochastic Dynamics

We review theoretical models of individual motility as well as collective dynamics and pattern formation of active particles. We focus on simple models of active dynamics with a particular emphasis on nonlinear and stochastic dynamics of such self-propelled entities in the framework of statistical mechanics. Examples of such active units in complex physico-chemical and biological systems are chemically powered nano-rods, localized patterns in reaction-diffusion system, motile cells or macroscopic animals. Based on the description of individual motion of point-like active particles by stochastic differential equations, we discuss different velocity-dependent friction functions, the impact of various types of fluctuations and calculate characteristic observables such as stationary velocity distributions or diffusion coefficients. Finally, we consider not only the free and confined individual active dynamics but also different types of interaction between active particles. The resulting collective dynamical behavior of large assemblies and aggregates of active units is discussed and an overview over some recent results on spatiotemporal pattern formation in such systems is given.Comment: 161 pages, Review, Eur Phys J Special-Topics, accepte

Image-guided ToF depth upsampling: a survey

Recently, there has been remarkable growth of interest in the development and applications of time-of-flight (ToF) depth cameras. Despite the permanent improvement of their characteristics, the practical applicability of ToF cameras is still limited by low resolution and quality of depth measurements. This has motivated many researchers to combine ToF cameras with other sensors in order to enhance and upsample depth images. In this paper, we review the approaches that couple ToF depth images with high-resolution optical images. Other classes of upsampling methods are also briefly discussed. Finally, we provide an overview of performance evaluation tests presented in the related studies

Mutationism and the Dual Causation of Evolutionary Change

The rediscovery of Mendel's laws a century ago launched the science that William Bateson called "genetics," and led to a new view of evolution combining selection, particulate inheritance, and the newly characterized phenomenon of "mutation." This "mutationist" view clashed with the earlier view of Darwin, and the later "Modern Synthesis," by allowing discontinuity, and by recognizing mutation (or more properly, mutation-and-altered-development) as a source of creativity, direction, and initiative. By the mid-20th century, the opposing Modern Synthesis view was a prevailing orthodoxy: under its influence, "evolution" was redefined as "shifting gene frequencies," that is, the sorting out of pre-existing variation without new mutations; and the notion that mutation-and-altered-development can exert a predictable influence on the course of evolutionary change was seen as heretical. Nevertheless, mutationist ideas re-surfaced: the notion of mutational determinants of directionality emerged in molecular evolution by 1962, followed in the 1980s by an interest among evolutionary developmental biologists in a shaping or creative role of developmental propensities of variation, and more recently, a recognition by theoretical evolutionary geneticists of the importance of discontinuity and of new mutations in adaptive dynamics. The synthetic challenge presented by these innovations is to integrate mutation-and-altered-development into a new understanding of the dual causation of evolutionary change--a broader and more predictive understanding that already can lay claim to important empirical and theoretical results--and to develop a research program appropriately emphasizing the emergence of variation as a cause of propensities of evolutionary change

Распознавание областей текста с персональными данными на диагностических изображениях

The aim of the study is to develop a method for detecting areas of text with private data on medical diagnostic images using the Tesseract module and the modified Levenshtein distance.Materials and methods. For threshold filtering, the brightness of the points belonging to the text characters in the images is determined at the initial stage. The dynamic threshold is calculated from the histogram of the brightness of the pixels of the image. Next, the Tesseract module is used for primary text recognition. Based on the tag values from DICOM files, a set of strings was formed to search for them in the recognized text. A modified Levenshtein distance was used to search for these strings. A set of DICOM files of the “Dose Report” type was used to test the algorithm. The accuracy was assessed by experts marking up blocks of private information on images.Results. A tool has been developed with a set of metrics and optimal thresholds for choosing decisive rules in finding matches that allow detecting areas of text with private data on medical images. For this tool, the accuracy of localization of areas with personal data on a set of 1131 medical images was determined in comparison with expert markup, which is 99.86%.Conclusion. The tool developed within the framework of this study allows identifying personal data on digital medical images with high accuracy, which indicates the possibility of its practical application in the preparation of data sets.Цель исследования: разработка метода обнаружения областей текста с приватными данными на медицинских диагностических изображениях при помощи модуля Tesseract и модифицированного расстояния Левенштейна.Материал и методы. Для пороговой фильтрации на начальном этапе определяется яркость точек, принадлежащих символам текста на изображениях. Динамический порог вычисляется по гистограмме яркостей пикселей изображения. Далее для первичного распознавания текста используется модуль Tesseract. На основании значений тэгов из DICOM-файлов формировался набор строк для поиска их в распознанном тексте. Для поиска этих строк использовалось модифицированное расстояние Левенштейна. Для тестирования алгоритма применялся набор DICOM файлов типа “Dose Report” модальности CT. Оценку точности проводили эксперты, размечающие блоки приватной информации на изображениях.Результаты. Разработан инструмент с набором метрик и оптимальных порогов для выбора решающих правил в нахождении совпадений, позволяющих обнаруживать области текста с приватными данными на медицинских изображениях. Для этого инструмента определена точность локализации областей с личными данными по сравнению с экспертной разметкой, которая составляет 99,86%.Заключение. Разработанный в рамках настоящего исследования инструмент позволяет выявлять персональные данные на цифровых медицинских изображениях с высокой точностью, что указывает на возможность его практического применения при подготовке наборов данных