Institute for System Programming

Novel species of fungi described in the present study include the following from Australia: Vermiculariopsiella eucalypti, Mulderomyces natalis (incl. Mulderomyces gen. nov.), Fusicladium paraamoenum, Neotrimmatostroma paraexcentricum, and Pseudophloeospora eucalyptorum on leaves of Eucalyptus spp., Anungitea grevilleae (on leaves of Grevillea sp.), Pyrenochaeta acaciae (on leaves of Acacia sp.), and Brunneocarpos banksiae (incl. Brunneocarpos gen. nov.) on cones of Banksia attenuata. Novel foliicolous taxa from South Africa include Neosulcatispora strelitziae (on Strelitzia nicolai), Colletotrichum ledebouriae (on Ledebouria floridunda), Cylindrosympodioides brabejum (incl. Cylindrosympodioides gen. nov.) on Brabejum stellatifolium, Sclerostagonospora ericae (on Erica sp.), Setophoma cyperi (on Cyperus sphaerocephala), and Phaeosphaeria breonadiae (on Breonadia microcephala). Novelties described from Robben Island (South Africa) include Wojnowiciella cissampeli and Diaporthe cissampeli (both on Cissampelos capensis), Phaeotheca salicorniae (on Salicornia meyeriana), Paracylindrocarpon aloicola (incl. Paracylindrocarpon gen. nov.) on Aloe sp., and Libertasomyces myopori (incl. Libertasomyces gen. nov.) on Myoporum serratum. Several novelties are recorded from La Réunion (France), namely Phaeosphaeriopsis agapanthi (on Agapanthus sp.), Roussoella solani (on Solanum mauritianum), Vermiculariopsiella acaciae (on Acacia heterophylla), Dothiorella acacicola (on Acacia mearnsii), Chalara clidemiae (on Clidemia hirta), Cytospora tibouchinae (on Tibouchina semidecandra), Diaporthe ocoteae (on Ocotea obtusata), Castanediella eucalypticola, Phaeophleospora eucalypticola and Fusicladium eucalypticola (on Eucalyptus robusta), Lareunionomyces syzygii (incl. Lareunionomyces gen. nov.) and Parawiesneriomyces syzygii (incl. Parawiesneriomyces gen. nov.) on leaves of Syzygium jambos. Novel taxa from the USA include Meristemomyces arctostaphylos (on Arctostaphylos patula), Ochroconis dracaenae (on Dracaena reflexa), Rasamsonia columbiensis (air of a hotel conference room), Paecilomyces tabacinus (on Nicotiana tabacum), Toxicocladosporium hominis (from human broncoalveolar lavage fluid), Nothophoma macrospora (from respiratory secretion of a patient with pneumonia), and Penidiellopsis radicularis (incl. Penidiellopsis gen. nov.) from a human nail. Novel taxa described from Malaysia include Prosopidicola albizziae (on Albizzia falcataria), Proxipyricularia asari (on Asarum sp.), Diaporthe passifloricola (on Passiflora foetida), Paramycoleptodiscus albizziae (incl. Paramycoleptodiscus gen. nov.) on Albizzia falcataria, and Malaysiasca phaii (incl. Malaysiasca gen. nov.) on Phaius reflexipetalus. Two species are newly described from human patients in the Czech Republic, namely Microascus longicollis (from toenails of patient with suspected onychomycosis), and Chrysosporium echinulatum (from sole skin of patient). Furthermore, Alternaria quercicola is described on leaves of Quercus brantii (Iran), Stemphylium beticola on leaves of Beta vulgaris (The Netherlands), Scleroderma capeverdeanum on soil (Cape Verde Islands), Scleroderma dunensis on soil, and Blastobotrys meliponae from bee honey (Brazil), Ganoderma mbrekobenum on angiosperms (Ghana), Geoglossum raitviirii and Entoloma kruticianum on soil (Russia), Priceomyces vitoshaensis on Pterostichus melas (Carabidae) (Bulgaria) is the only one for which the family is listed, Ganoderma ecuadoriense on decaying wood (Ecuador), Thyrostroma cornicola on Cornus officinalis (Korea), Cercophora vinosa on decorticated branch of Salix sp. (France), Coprinus pinetorum, Coprinus littoralis and Xerocomellus poederi on soil (Spain). Two new genera from Colombia include Helminthosporiella and Uwemyces on leaves of Elaeis oleifera. Two species are described from India, namely Russula intervenosa (ectomycorrhizal with Shorea robusta), and Crinipellis odorata (on bark of Mytragyna parviflora). Novelties from Thailand include Cyphellophora gamsii (on leaf litter), Pisolithus aureosericeus and Corynascus citrinus (on soil). Two species are newly described from Citrus in Italy, namely Dendryphiella paravinosa on Citrus sinensis, and Ramularia citricola on Citrus floridana. Morphological and culture characteristics along with ITS nrDNA barcodes are provided for all taxa.

Novel species of fungi described in this study include those from various countries as follows: Antarctica: Cadophora antarctica from soil. Australia : Alfaria dandenongensis on Cyperaceae , Amphosoma persooniae on Persoonia sp., Anungitea nullicana on Eucalyptus sp., Bagadiella eucalypti on Eucalyptus globulus , Castanediella eucalyptigena on Eucalyptus sp., Cercospora dianellicola on Dianella sp., Cladoriella kinglakensis on Eucalyptus regnans , Cladoriella xanthorrhoeae (incl. Cladoriellaceae fam. nov. and Cladoriellales ord. nov.) on Xanthorrhoea sp., Cochlearomyces eucalypti (incl. Cochlearomyces gen. nov. and Cochlearomycetaceae fam. nov.) on Eucalyptus obliqua , Codinaea lambertiae on Lambertia formosa , Diaporthe obtusifoliae on Acacia obtusifolia , Didymella acaciae on Acacia melanoxylon , Dothidea eucalypti on Eucalyptus dalrympleana , Fitzroyomyces cyperi (incl. Fitzroyomyces gen. nov.) on Cyperaceae , Murramarangomyces corymbiae (incl. Murramarangomyces gen. nov., Murramarangomycetaceae fam. nov. and Murramarangomycetales ord. nov.) on Corymbia maculata , Neoanungitea eucalypti (incl. Neoanungitea gen. nov.) on Eucalyptus obliqua , Neoconiothyrium persooniae (incl. Neoconiothyrium gen. nov.) on Persoonia laurina subsp. laurina , Neocrinula lambertiae (incl. Neocrinulaceae fam. nov.) on Lambertia sp., Ochroconis podocarpi on Podocarpus grayae , Paraphysalospora eucalypti (incl. Paraphysalospora gen. nov.) on Eucalyptus sieberi , Pararamichloridium livistonae (incl. Pararamichloridium gen. nov., Pararamichloridiaceae fam. nov. and Pararamichloridiales ord. nov.) on Livistona sp., Pestalotiopsis dianellae on Dianella sp., Phaeosphaeria gahniae on Gahnia aspera , Phlogicylindrium tereticornis on Eucalyptus tereticornis , Pleopassalora acaciae on Acacia obliquinervia , Pseudodactylaria xanthorrhoeae (incl. Pseudodactylaria gen. nov., Pseudodactylariaceae fam. nov. and Pseudodactylariales ord. nov.) on Xanthorrhoea sp., Pseudosporidesmium lambertiae (incl. Pseudosporidesmiaceae fam. nov.) on Lambertia formosa , Saccharata acaciae on Acacia sp., Saccharata epacridis on Epacris sp., Saccharata hakeigena on Hakea sericea , Seiridium persooniae on Persoonia sp., Semifissispora tooloomensis on Eucalyptus dunnii , Stagonospora lomandrae on Lomandra longifolia , Stagonospora victoriana on Poaceae , Subramaniomyces podocarpi on Podocarpus elatus , Sympoventuria melaleucae on Melaleuca sp., Sympoventuria regnans on Eucalyptus regnans , Trichomerium eucalypti on Eucalyptus tereticornis , Vermiculariopsiella eucalypticola on Eucalyptus dalrympleana , Verrucoconiothyrium acaciae on Acacia falciformis , Xenopassalora petrophiles (incl. Xenopassalora gen. nov.) on Petrophile sp., Zasmidium dasypogonis on Dasypogon sp., Zasmidium gahniicola on Gahnia sieberiana . Brazil : Achaetomium lippiae on Lippia gracilis , Cyathus isometricus on decaying wood , Geastrum caririense on soil, Lycoperdon demoulinii (incl. Lycoperdon subg. Arenicola ) on soil, Megatomentella cristata (incl. Megatomentella gen. nov.) on unidentified plant, Mutinus verrucosus on soil, Paraopeba schefflerae (incl. Paraopeba gen. nov.) on Schefflera morototoni , Phyllosticta catimbauensis on Mandevilla catimbauensis , Pseudocercospora angularis on Prunus persica , Pseudophialophora sorghi on Sorghum bicolor , Spumula piptadeniae on Piptadenia paniculata . Bulgaria : Yarrowia parophonii from gut of Parophonus hirsutulus . Croatia : Pyrenopeziza velebitica on Lonicera borbasiana . Cyprus : Peziza halophila on coastal dunes Czech Republic : Aspergillus contaminans from human fingernail. Ecuador : Cuphophyllus yacurensis on forest soil, Ganoderma podocarpense on fallen tree trunk. England : Pilidium anglicum (incl. Chaetomellales ord. nov.) on Eucalyptus sp. France : Planamyces parisiensis (incl. Planamyces gen. nov.) on wood inside a house. French Guiana : Lactifluus ceraceus on soil. Germany : Talaromyces musae on Musa sp. India : Hyalocladosporiella cannae on Canna indica , Nothophoma raii from soil. Italy : Setophaeosphaeria citri on Citrus reticulata , Yuccamyces citri on Citrus limon . Japan : Glutinomyces brunneus (incl. Glutinomyces gen. nov.) from roots of Quercus sp. Netherlands (all from soil): Collariella hilkhuijsenii , Fusarium petersiae , Gamsia kooimaniorum , Paracremonium binnewijzendii , Phaeoisaria annesophieae , Plectosphaerella niemeijerarum , Striaticonidium deklijnearum , Talaromyces annesophieae , Umbelopsis wiegerinckiae , Vandijckella johannae (incl. Vandijckella gen. nov. and Vandijckellaceae fam. nov.), Verhulstia trisororum (incl. Verhulstia gen. nov.). New Zealand : Lasiosphaeria similisorbina on decorticated wood. Papua New Guinea : Pseudosubramaniomyces gen. nov. (based on Pseudosubramaniomyces fusisaprophyticus comb. nov.). Slovakia : Hemileucoglossum pusillum on soil. South Africa : Tygervalleyomyces podocarpi</jats:ital

The measure of similarity between objects is a very useful tool in many areas of computer science, including information retrieval. SimRank is a simple and intuitive measure of this kind, based on graph-theoretic model. SimRank is typically computed iteratively, in the spirit of PageRank. However, existing work on SimRank lacks accuracy estimation of iterative computation and has discouraging time complexity. In this paper we present a technique to estimate the accuracy of computing SimRank iteratively. This technique provides a way to find out the number of iterations required to achieve a desired accuracy when computing SimRank. We also present optimization techniques that improve the computational complexity of the iterative algorithm from O ( n 4 ) to O ( n 3 ) in the worst case. We also introduce a threshold sieving heuristic and its accuracy estimation that further improves the efficiency of the method. As a practical illustration of our techniques we computed SimRank scores on a subset of English Wikipedia corpus, consisting of the complete set of articles and category links.

Open Cirrus is a cloud computing testbed that, unlike existing alternatives, federates distributed data centers. It aims to spur innovation in systems and applications research and catalyze development of an open source service stack for the cloud.

Abstract Classical machine learning modeling demands considerable computing power for internal calculations and training with big data in a reasonable amount of time. In recent years, clouds provide services to facilitate this process, but it introduces new security threats of data breaches. Modern encryption techniques ensure security and are considered as the best option to protect stored data and data in transit from an unauthorized third-party. However, a decryption process is necessary when the data must be processed or analyzed, falling into the initial problem of data vulnerability. Fully Homomorphic Encryption (FHE) is considered the holy grail of cryptography. It allows a non-trustworthy third-party resource to process encrypted information without disclosing confidential data. In this paper, we analyze the fundamental concepts of FHE, practical implementations, state-of-the-art approaches, limitations, advantages, disadvantages, potential applications, and development tools focusing on neural networks. In recent years, FHE development demonstrates remarkable progress. However, current literature in the homomorphic neural networks is almost exclusively addressed by practitioners looking for suitable implementations. It still lacks comprehensive and more thorough reviews. We focus on the privacy-preserving homomorphic encryption cryptosystems targeted at neural networks identifying current solutions, open issues, challenges, opportunities, and potential research directions.

In this work a hybrid scheme based on the PISO-algorithm and Kurganov-Tadmor's numerical scheme is proposed. This scheme utilizes compressible PISO method for coupling between velocity and pressure and Kurganov-Tadmor scheme for formulation of non-oscillating convective fluxes. Compressible and incompressible regimes of developed model are switched with blending function depending on local Mach and CFL number. A numerical scheme is implemented by means of OpenFOAM ver. 2.3.0 as pisoCentralFoam independent solver. Investigation of the mathematical model was conducted and exemplified by test cases. Proposed scheme can be used for wide range of Mach numbers from 0.01 to 3 or higher The mesh convergence was analyzed. Comparison of the results with the experimental and analytic data was carried out. The solver was tested in a parallel mode on a computer cluster.

As the population grows, the need for higher-quality medical services increases, as well as the demand for information technology in medicine. The Smart Healthcare concept brings various approaches to address the acute problems encountered in modern healthcare. In this paper, we review the main problems of modern healthcare and analyze existing approaches and technologies in digital twins, the Internet of Things, and mobile medicine. We will also analyze the key features of modern platforms that support Mobile Health Applications. Finally, based on our analysis, we will propose the concept of Smart Healthcare Platform, focused on solving tasks related to supporting the development of Mobile Health Applications, including organizing access, management, and sharing of user data.

Applications related to domain specific text processing often use glossaries and ontologies, and the main step of such resource construction is term recognition. This paper presents a survey of existing definitions of the term and its linguistic features, formulates the task definition for term recognition, and analyzes presently-available methods for automatic term recognition, such as methods for candidates collection, methods based on statistics and contexts of term occurrences, methods using topic models, and methods based on external resources (such as text collections from other domains, ontologies, and Wikipedia). This paper also provides an overview of standard methodologies and datasets for experimental research.

We have developed a deep learning-based computer algorithm to recognize and predict retinal differentiation in stem cell-derived organoids based on the brightfield imaging. The three-dimensional, “organoid” approach for the differentiation of pluripotent stem cells into retinal and other neural tissues has become a major in-vitro strategy to recapitulate development. We decided to develop a universal, robust and non-invasive method to assess retinal differentiation that would not require chemical probes or reporter gene expression. We hypothesized that basic contrast brightfield images contain sufficient information on the tissue specification and it is possible to extract this data using convolutional neural networks (CNN). Retina-specific Rx-GFP mouse embryonic reporter stem cells have been used for all of the differentiation experiments in this work. The brightfield (BF) images of organoids have been taken on day 6 and fluorescent on day 9. To train the CNN we utilized a transfer learning approach: ImageNet pre-trained ResNet50v2, VGG19, Xception and DenseNet121 CNNs had been trained on labeled BF images of the organoids, divided into two categories (retina and non-retina), based on the fluorescent reporter gene expression. The best performing classifier with ResNet50v2 architecture showed a ROC-AUC score of 0.91 on a test dataset. A comparison of the best performing CNN with the human-based classifier showed that the CNN algorithm performs better than the expert in predicting organoid fate: 84% vs 67  6% of correct predictions respectively, confirming our original hypothesis. Overall, we have demonstrated that the computer algorithm can successfully recognize and predict retinal differentiation in organoids before the onset of reporter gene expression. This is the first demonstration of CNN ability to classify stem cell-derived tissue in-vitro.

Summary This paper describes the implementation of a numerical solver that is capable of simulating compressible flows of nonideal single‐phase fluids. The proposed method can be applied to arbitrary equations of state and is suitable for all Mach numbers. The pressure‐based solver uses the operator‐splitting technique and is based on the PISO/SIMPLE algorithm: the density, velocity, and temperature fields are predicted by solving the linearized versions of the balance equations using the convective fluxes from the previous iteration or time step. The overall mass continuity is ensured by solving the pressure equation derived from the continuity equation, the momentum equation, and the equation of state. Nonphysical oscillations of the numerical solution near discontinuities are damped using the Kurganov‐Tadmor/Kurganov‐Noelle‐Petrova (KT/KNP) scheme for convective fluxes. The solver was validated using different test cases, where analytical and/or numerical solutions are present or can be derived: (1) A convergent‐divergent nozzle with three different operating conditions; (2) the Riemann problem for the Peng‐Robinson equation of state; (3) the Riemann problem for the covolume equation of state; (4) the development of a laminar velocity profile in a circular pipe (also known as Poiseuille flow); (5) a laminar flow over a circular cylinder; (6) a subsonic flow over a backward‐facing step at low Reynolds numbers; (7) a transonic flow over the RAE 2822 airfoil; and (8) a supersonic flow around a blunt cylinder‐flare model. The spatial approximation order of the scheme is second order. The mesh convergence of the numerical solution was achieved for all cases. The accuracy order for highly compressible flows with discontinuities is close to first order and, for incompressible viscous flows, it is close to second order. The proposed solver is named rhoPimpleCentralFoam and is implemented in the open‐source CFD library OpenFOAM ® . For high speed flows, it shows a similar behavior as the KT/KNP schemes (implemented as rhoCentralFoam ‐solver, Int. J. Numer. Meth. Fluids 2010), and for flows with small Mach numbers, it behaves like solvers that are based on the PISO/SIMPLE algorithm.

In this paper, we present a Big Data analysis paradigm related to smart cities using cloud computing infrastructures. The proposed architecture follows the MapReduce parallel model implemented using the Hadoop framework. We analyse two case studies: a quality-of-service assessment of public transportation system using historical bus location data, and a passenger-mobility estimation using ticket sales data from smartcards. Both case studies use real data from the transportation system of Montevideo, Uruguay. The experimental evaluation demonstrates that the proposed model allows processing large volumes of data efficiently.

In the present paper, we combine numerical and experimental approaches to study the dynamics of stable and unstable internal wave attractors. The problem is considered in a classic trapezoidal set-up filled with a uniformly stratified fluid. Energy is injected into the system at global scale by the small-amplitude motion of a vertical wall. Wave motion in the test tank is measured with the help of conventional synthetic schlieren and particle image velocimetry techniques. The numerical set-up closely reproduces the experimental one in terms of geometry and the operational range of the Reynolds and Schmidt numbers. The spectral element method is used as a numerical tool to simulate the nonlinear dynamics of a viscous salt-stratified fluid. We show that the results of 3D calculations are in excellent qualitative and quantitative agreement with the experimental data, including the spatial and temporal parameters of the secondary waves produced by triadic resonance instability. Further, we explore experimentally and numerically the effect of lateral walls on secondary currents and spanwise distribution of velocity amplitudes in the wave beams. Finally, we test the assumption of a bidimensional flow and estimate the error made in synthetic schlieren measurements due to this assumption.

Continuous testing during development is a well-established technique for software-quality assurance. Continuous model checking from revision to revision is not yet established as a standard practice, because the enormous resource consumption makes its application impractical. Model checkers compute a large number of verification facts that are necessary for verifying if a given specification holds. We have identified a category of such intermediate results that are easy to store and efficient to reuse: abstraction precisions. The precision of an abstract domain specifies the level of abstraction that the analysis works on. Precisions are thus a precious result of the verification effort and it is a waste of resources to throw them away after each verification run. In particular, precisions are reasonably small and thus easy to store; they are easy to process and have a large impact on resource consumption. We experimentally show the impact of precision reuse on industrial verification problems created from 62 Linux kernel device drivers with 1119 revisions.

Random graph (RG) models play a central role in complex networks analysis. They help us to understand, control, and predict phenomena occurring, for instance, in social networks, biological networks, the Internet, and so on. Despite a large number of RG models presented in the literature, there are few concepts underlying them. Instead of trying to classify a wide variety of very dispersed models, we capture and describe concepts they exploit considering preferential attachment, copying principle, hyperbolic geometry, recursively defined structure, edge switching, Monte Carlo sampling, and so on. We analyze RG models, extract their basic principles, and build a taxonomy of concepts they are based on. We also discuss how these concepts are combined in RG models and how they work in typical applications like benchmarks, null models, and data anonymization.

Internet-of-Things (IoT) environment has a dynamic nature with high risks of confidentiality, integrity, and availability violations. The loss of information, denial of access, information leakage, collusion, technical failures, and data security breaches are difficult to predict and anticipate in advance. These types of nonstationarity are one of the main issues in the design of the reliable IoT infrastructure capable of mitigating their consequences. It is not sufficient to propose solutions for a given scenario, but mechanisms to adapt the current solution to changes in the environment. In this article, we present a multicloud storage architecture called WA-MRC-RRNS that combines the weighted access scheme, threshold secret sharing, and redundant residue number system with multiple failure detection/recovery mechanisms and homomorphic ciphers. We provide a theoretical analysis of the probability of information loss, data redundancy, speed of encoding/decoding, and show how to dynamically configure parameters to cope with different objective preferences, workloads, and cloud properties. We propose a multiobjective optimization mechanism to adjust redundancy, encryption-decryption speed, and data loss probability. Comprehensive experimental analysis with real data shows that our approach provides a secure way to mitigate the uncertainty of the use of untrusted and not reliable IoT infrastructure.

The paper describes the basic components of ISPRAS technology stack for social network data analysis. Particular attention is given to tasks, methods, and applications of network (social connections between users) and textual (user messages and profiles) data analysis: demographic attribute detection, event detection in messages corpora, user identity resolution, community detection, and influence measurement. Means for input data acquisition are also considered: collecting real data through web-interfaces of social services and generating random social graphs. For each of the developed tools we describe its functionality, use cases, basic steps of the underlying algorithms, and experimental results.

The paper presents a survey of methods for constructing covering arrays used in generation of tests for interfaces with a great number of parameters. The application domain of these methods and algorithms used in them are analyzed. Specific characteristics of the methods, including time complexity and estimates of the required memory, are presented. Various—direct, recursive, optimization, genetic, and backtracking—algorithms used for constructing covering arrays are presented. Heuristics are presented that allow one to reduce arrays without loss of completeness, and application domains of these heuristics are outlined.

A large number of available computational fluid dynamics codes include tools for analysis of computational aeroacoustics problems. Such tools are proprietary as well as the codes themselves. Actually, the level of development of such codes as OpenFOAM makes it possible to implement enough opportunities for complication of physical models and increasing the scale of the issues described. In our paper, we develop a dynamic library libAcoustics which may be compiled independently of any modules of the main OpenFOAM package and the type of solvers being used in the model. The implemented Curle's analogy in library makes it possible to obtain acoustic spectra under the conditions of turbulent flows around arbitrary solids in a medium moving at a low velocity of flow. Calculation of the acoustic field was made for 3D test case of Cylinder – NACA 0012 Wing Profile configuration. The analogy allows user to define solvers settings through standard user I/O dictionaries of the OpenFOAM. A complete implementation of the analogy is capable of producing parallel computation. The libAcoustics library is free and is available for download on demand.

This paper describes Svace, a tool for static program analysis developed at the Institute for Systems Programming, Russian Academy of Sciences. This tool allows one to find defects and potential vulnerabilities in the source program code written in C/C++ languages. The main features of the tool are simplicity of use, wide variety of supported types of warnings, scalability up to programs of millions of code lines, and acceptable quality of analysis (30–80% of true positive warnings).

This paper describes Svace, a tool for static program analysis developed in ISP RAS. This tool allows to find defects and potential vulnerabilities in source code of programs written in C/C++ languages. Main features of the tool are simplicity of usage, wide variety of supported warning types, scalability up to programs of millions lines of code and acceptable quality of analysis (30-80% of true positive warnings).