The fungal literature-based occurrence database in southern West Siberia (Russia)

The abstract presents the initiative to develop the Fungal Literature-based Occurrence Database for Southern West Siberia (FuSWS), which mobilizes occurrences of fungi from published literature (literature-based occurrences, Darwin Core MaterialCitation). The FuSWS database includes 28 fields describing species name, publication source, herbarium number (if exists), date of sampling or observation, locality information, vegetation, substrate, and others. The initiative on digitization of literature-based occurrence data started in the northern part of Western Siberia two years ago (Filippova et al. 2021a). The present project extends the initiative to the south and includes eight administrative regions (Sverdlovsk, Omsk, Kurgan, Tomsk, Novosibirsk, Kemerovo, Altay, and Gorny Altay). The area occupies the central to southern part of the West Siberian Plain. It extends for about 1.5 thousand km from the west to the east from the eastern slopes of the Ural Mountains to Yenisey River, and from north to south—about 1.3 thousand km. The total area equals about 1.2 million km2.Currently, the project is actively growing in spatial, collaboration and data accumulation terms. The working group of about 30 mycologists from 16 organizations dedicated to the digitization initiative was created as part of the Siberian Mycological Society (informal organization since 2019). They have created the most complete bibliographic list of mycology-related papers for the Southern West Siberia, including over 800 publications for the last two centuries (the earliest dated 1800). At abstract submission, the database had been populated with a total of about 10K records from about 100 sources. The dataset is uploaded to GBIF, where it is available for online search of species occurrences and/or download (Filippova et al. 2021b) Fig. 1. The project's page with the introduction, templates, bibliography list, video-presentations and written instructions is available at the website of the Siberian Mycological Society (https://sibmyco.org/literaturedatabase).The following protocol describes the digitization workflow in detail:The bibliography of related publications is compiled using Zotero bibliographic manager. Only published works (peer-reviewed papers, conference proceedings, PhD theses, monographs or book chapters) are selected. If possible, the sources are digitized and added to the library as PDF files. The template of the FuSWS database is made with Google Sheets, which allows simultaneous use by several specialists, in a common data format provided. The simple Microsoft Excel template is also available for the offline databasing. The Darwin Core standard is applied to the database field structure to accommodate the relevant information extracted from the publications.From the available bibliography of publications related to the region, only works with species occurrences are selected for the databasing purpose. The main source of occurrences is annotated species lists with exact localities of the records. However, different sorts of other species citations are also extracted, provided that they had the connection to any geography. All occurrences are georeferenced, either from the coordinates provided in the paper, or from the verbatim description of the field work locality. The georeferencing of the verbatim descriptions is made using Yandex or Google map services. Depending on the quality of georeference provided in publications, the uncertainty is estimated as follows: 1) the coordinate of a fruiting structure or a plot provided in the publication gives the uncertainty about 3-30 meters; 2) the coordinate of the field work locality provided in publication gives the uncertainty about 500 m to 5 km; 3) the report of the species presence in a particular region gives the centroid of the area with the uncertainty radius to include its borders.The locality names reported in Russian are translated to English and written in the «locality» field. Russian descriptions are reserved in the field «verbatimLocality» for accuracy.When possible, the «eventDate» is extracted from the annotation data. Whenever this information is absent, the date of the publication is used instead with the remarks in the «verbatimEventDate» field.The ecological features, habitat and substrate preferences are written in the «habitat» field and reserved in Russian.The original scientific names reported in publications are filled in the «originalNameUsage» field. Correction of spelling errors is made using the GBIF Species Matching tool. This tool is also used to create the additional fields of taxonomic hierarchy from species to kingdom, to fill in the «taxonRank» field and to synonymize according to the GBIF Backbone Taxonomy.To track the digitization process, a worksheet is maintained. Each bibliographic record has a series of fields to describe the digitization process and its results: the total number of extracted occurrence records, general description of the occurrence quality, presence of the observation date, details of georeferencing and the name of a person responsible for the digitization

Lattice-Boltzmann and finite-difference simulations for the permeability for three-dimensional porous media

Numerical micropermeametry is performed on three dimensional porous samples having a linear size of approximately 3 mm and a resolution of 7.5 $\mu$m. One of the samples is a microtomographic image of Fontainebleau sandstone. Two of the samples are stochastic reconstructions with the same porosity, specific surface area, and two-point correlation function as the Fontainebleau sample. The fourth sample is a physical model which mimics the processes of sedimentation, compaction and diagenesis of Fontainebleau sandstone. The permeabilities of these samples are determined by numerically solving at low Reynolds numbers the appropriate Stokes equations in the pore spaces of the samples. The physical diagenesis model appears to reproduce the permeability of the real sandstone sample quite accurately, while the permeabilities of the stochastic reconstructions deviate from the latter by at least an order of magnitude. This finding confirms earlier qualitative predictions based on local porosity theory. Two numerical algorithms were used in these simulations. One is based on the lattice-Boltzmann method, and the other on conventional finite-difference techniques. The accuracy of these two methods is discussed and compared, also with experiment.Comment: to appear in: Phys.Rev.E (2002), 32 pages, Latex, 1 Figur

The fungal literature-based occurrence database for southern West Siberia (Russia)

The paper presents the initiative on literature-based occurrence data mobilisation of fungi and fungi-related organisms (literature-based occurrences, Darwin Core MaterialCitation) to develop the Fungal literature-based occurrence database for the southern West Siberia (FuSWS). The initiative on mobilisation of literature-based occurrence data started in the northern part of West Siberia in 2016. The present project extends the initiative to the southern regions and includes ten administrative territories (Tyumen Region, Sverdlovsk Region, Chelyabinsk Region, Omsk Region, Kurgan Region, Tomsk Region, Novosibirsk Region, Kemerovo Region, Altai Territory and Republic of Altai). The area occupies the central to southern part of the West Siberian Plain and extends for about 1.5 K km from the west to the east from the eastern slopes of the Ural Mountains to Yenisey River and from north to south—about 1.3 K km. The total area equals about 1.4 million km . The initiative is actively growing in spatial, collaboration and data accumulation terms. The working group of about 30 mycologists from eight organisations dedicated to the data mobilisation was created as part of the Siberian Mycological Society (informal organisation since 2019). They have compiled the almost complete bibliographic list of mycology-related papers for the southern West Siberia, including over 900 publications for the last two centuries (the earliest dated 1800). All literature sources were digitised and an online library was created to integrate bibliography metadata and digitised papers using Zotero bibliography manager. The analysis of published sources showed that about two-thirds of works contain occurrences of fungi for the scope of mobilisation. At the time of the paper submission, the database had been populated with a total of about 8 K records from 93 sources. The dataset is uploaded to GBIF, where it is available for online search of species occurrences and/or download. The project's page with the introduction, templates, bibliography list, video-presentations and written instructions is available (in Russian) at the web site of the Siberian Mycological Society. The initiative will be continued in the following years to extract the records from all published sources. New information The paper presents the first project with the aim of literature-based occurrence data mobilisation of fungi and fungi-related organisms in the southern West Siberia. The full bibliography and a digital library of all regional mycological publications created for the first time includes about 900 published works. By the time of paper submission, nearly 8 K occurrence records were extracted from about 90 literature sources and integrated into the FuSWS database published in GBIF

Modelling effects of phytobiotic administration on coherent responses to Salmonella infection in laying hens

Practice of layer poultry farming and commercial egg production relies on the optimal use and improvement of the welfare and genetically determined functional abilities of laying hens, their efficient intake of feed and its components, adaptation to housing conditions and resistance to infectious diseases including salmonellosis. Previous studies were focussed on relationships of chicken performance and resistance with the expression profiles of individual genes involved in metabolic processes and immune system, or with genetic markers that can be closely associated with these processes in chickens. In this study, mathematical models of coherent changes in laying hens were developed for the expression of eight genes involved in immunity and metabolism, on the one hand, and biochemical and immunological blood parameters, on the other hand, in response to Salmonella infection and administration of a phytobiotic Intebio. The proposed modelling approach can be a further basis for an in-depth research of the relationship between the gene expression, functional state and welfare of poultry, impact of pathogenic microorganisms and use of immunomodulatory drugs

4U 0115+63 from RXTE and INTEGRAL Data: Pulse Profile and Cyclotron Line Energy

We analyze the observations of the transient X-ray pulsar 4U 0115+63 with the RXTE and INTEGRAL observatories in a wide X-ray (3-100 keV) energy band during its intense outbursts in 1999 and 2004. The energy of the fundamental harmonic of the cyclotron resonance absorption line near the maximum of the X-ray flux from the source (luminosity range 5x10^{37} - 2x10^{38} erg/s) is ~11 keV. When the pulsar luminosity falls below ~5x10^{37} erg/s, the energy of the fundamental harmonic is displaced sharply toward the high energies, up to ~16 keV. Under the assumption of a dipole magnetic field configuration, this change in cyclotron harmonic energy corresponds to a decrease in the height of the emitting region by ~2 km, while other spectral parameters, in particular, the cutoff energy, remain essentially constant. At a luminosity ~7x10^{37} erg/s, four almost equidistant cyclotron line harmonics are clearly seen in the spectrum. This suggests that either the region where the emission originates is compact or the emergent spectrum from different (in height) segments of the accretion column is uniform. We have found significant pulse profile variations with energy, luminosity, and time. In particular, we show that the profile variations from pulse to pulse are not reduced to a simple modulation of the accretion rate specified by external conditions.Comment: 30 pages, 13 figures, Astronomy Letters, 33, 368 (2007

Emerging landscape of oncogenic signatures across human cancers.

Cancer therapy is challenged by the diversity of molecular implementations of oncogenic processes and by the resulting variation in therapeutic responses. Projects such as The Cancer Genome Atlas (TCGA) provide molecular tumor maps in unprecedented detail. The interpretation of these maps remains a major challenge. Here we distilled thousands of genetic and epigenetic features altered in cancers to ∼500 selected functional events (SFEs). Using this simplified description, we derived a hierarchical classification of 3,299 TCGA tumors from 12 cancer types. The top classes are dominated by either mutations (M class) or copy number changes (C class). This distinction is clearest at the extremes of genomic instability, indicating the presence of different oncogenic processes. The full hierarchy shows functional event patterns characteristic of multiple cross-tissue groups of tumors, termed oncogenic signature classes. Targetable functional events in a tumor class are suggestive of class-specific combination therapy. These results may assist in the definition of clinical trials to match actionable oncogenic signatures with personalized therapies

Перспектива использования жидкостной биопсии в диагностике и лечении опухолей невыявленной первичной локализации

Background. The search and use of new molecular prognostic and predictive markers of efficacy detected by liquid biopsy are aimed at understanding the biology of Carcinomas of Unknown Primary (CUP) and improving results of patient treatment. The review is devoted to advances in scientific and clinical research on this issue.Materials and methods. In order to assess the current state of the problem, a search and analysis of relevant data of the scientific databases PubMed, Medline, RISC was carried out.Results. The scientific rationale for the use of liquid biopsy in clinical practice to improve the treatment of cancer patients with CUP is presented. The results of the use of modern approaches to the analysis of fluid biopsy samples in CUP are presented. In particular, the features of using circulating free DNA, circulating tumor DNA, circulating tumor cells in the analysis are considered. The modern possibilities of determining tissue specificity using liquid biopsy in CUP are discussed. The prospects for the development of liquid biopsy for improving diagnostics, determining the prognosis of the disease, and choosing a strategy for treating CUP and the treatment monitoring have been determined.Conclusion. A review of the literature confirms that modern methods of molecular profiling of tumor cells obtained both as a result of liquid biopsy and tissue biopsies will make a significant contribution to the determination of tissue specificity, molecular characteristics of CUP for a personalized approach in order to improve strategies and treatment outcomes for patients with CUP.Введение. Поиск и использование новых молекулярных прогностических и предиктивных маркеров, выявляемых методом жидкостной биопсии, направлены на определение молекулярно-биологических особенностей опухолей невыявленной первичной локализации (ОНПЛ), что должно способствовать более активному внедрению персонализированного подхода в терапии злокачественных новообразований и улучшению результатов лечения. Обзор посвящен системному анализу достижений в научных и клинических исследованиях по данной тематике.Материалы и методы. В целях оценки современного состояния проблемы были осуществлены поиск и анализ актуальных данных по научным базам PubMed, Medline, РИНЦ и др.Результаты. Представлено научное обоснование использования в клинической практике жидкостной биопсии для совершенствования лечения пациентов с ОНПЛ. Приведены результаты применения современных подходов к анализу образцов жидкостной биопсии при ОНПЛ. В частности, рассмотрены особенности использования в анализе циркулирующей свободной ДНК, циркулирующей опухолевой ДНК, циркулирующих опухолевых клеток. Обсуждены современные возможности определения тканевой специфичности с использованием жидкостной биопсии при ОНПЛ. Определены перспективы развития жидкостной биопсии для совершенствования диагностики, оценки прогноза заболевания, выбора стратегии лечения ОНПЛ.Заключение. Обзор литературы подтверждает, что современные методы молекулярного профилирования опухолевых клеток, полученных как при жидкостной биопсии, так и в результате биопсии ткани, внесут значимый вклад в определение тканевой специфичности, молекулярных характеристик ОНПЛ для персонализированного подхода в целях совершенствования стратегии и улучшения результатов лечения пациентов с ОНПЛ