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pepgrep:A Tool for Peptide MS/MS Pattern Matching

Genomics, Proteomics & Bioinformatics 2013年第2期11卷 127-132页

作者： igor Chernukhin School of Biological Sciences University of Essex

Typically, detection of protein sequences in collision-induced dissociation （CID） tandem MS （MS2） dataset is performed by mapping identified peptide ions back to protein sequence by using the protein database search （PDS） engine. Finding a particular peptide sequence of interest in CID MS2 records very often requires manual evaluation of the spectrum, regardless of whether the peptide-associated MS2 scan is identified by PDS algorithm or not. We have developed a com- pact cross-platform database-free command-line utility, pepgrep, which helps to find an MS2 finger- print for a selected peptide sequence by pattern-matching of modelled MS2 data using Peptide-to- MS2 scoring algorithm, pepgrep can incorporate dozens of mass offsets corresponding to a variety of post-translational modifications （PTMs） into the algorithm. Decoy peptide sequences are used with the tested peptide sequence to reduce false-positive results. The engine is capable of screening an MS2 data file at a high rate when using a cluster computing environment. The matched MS2 spectrum can be displayed by using built-in graphical application programming interface （API） or optionally recorded to file. Using this algorithm, we were able to find extra peptide sequences in studied CID spectra that were missed by PDS identification. Also we found pepgrep especially useful for examining a CID of small fractions of peptides resulting from, for example, affinity puri- fication techniques. The peptide sequences in such samples are less likely to be positively identified by using routine protein-centric algorithm implemented in PDS. The software is freely available at http：//***：8080/data/download/pepgrep- ***.

关键词： Collision-induced dissociation Tandem MSTandem MS Protein database search Peptide identification

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Risk calculators and updated tools to select and plan a repeat biopsy for prostate cancer detection

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Asian Journal of Andrology 2015年第6期17卷 864-869,I0006页

作者： igor Sorokin Badar M Mian Department of Urology Albany Medical College Albany NY USA.

Millions of men each year are faced with a clinical suspicion of prostate cancer （PCa） but the prostate biopsy fails to detect the disease. For the urologists, how to select the appropriate candidate for repeat biopsy is a significant clinical dilemma. Traditional risk-stratification tools in this setting such as prostate-specific antigen （PSA） related markers and histopathology findings have met with limited correlation with cancer diagnosis or with significant disease. Thus, an individualized approach using predictive models such as an online risk calculator （RC） or updated biomarkers is more suitable in counseling men about their risk of harboring clinically significant prostate cancer, This review will focus on the available risk-stratification tools in the population of men with prior negative biopsies and persistent suspicion of PCa. The underlying methodology and platforms of the available tools are reviewed to better understand the development and validation of these models. The index patient is then assessed with different RCs to determine the range of heterogeneity among various RCs. This should allow the urologists to better incorporate these various risk-stratification tools into their clinical practice and improve patient counseling.

关键词： biomarkers prostate cancer repeat biopsy risk calculators

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Shapes of the fastest fish and optimal underwater and floating hulls

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Theoretical & Applied Mechanics Letters 2022年第6期12卷 403-408页

作者： igor Nesteruk Institute of Hydromechanics National Academy of Sciences of UkraineNational Technical University of Ukraine“Igor Sikorsky Kyiv Polytechnic Institute”Ukraine

A streamlined shape of the best swimmers removes the boundary-layer separation and ensures a laminar flow *** fastest fish have a very sharp convex nose(rostrum),the purpose of which remains *** bodies of revolution similar to their shapes are analyzed in steady underwater and floating *** sources and sinks were located on the axis of symmetry and above the water surface to estimate the pressure on the body and the vertical velocities on the water *** was shown that the flow patterns on a special shaped body with concave nose has no stagnation points and ensure small values of the water surface *** fact allow diminishing the maximum pressure on the surface and wave *** shapes with the sharp concave nose and negative pressure gradients on their surface could be parts of the low drag underwater and floating hulls.

关键词： Drag reduction Wave drag Ship hulls optimization Unseparated shapes Water locomotion

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Computational approaches to substrate-based cell motility

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npj Computational Materials 2016年第1期2卷 103-118页

作者： Falko Ziebert igor S Aranson Physikalisches Institut Albert-Ludwigs-Universität FreiburgFreiburgGermany Institut Charles Sadron CNRS-UPR22StrasbourgFrance Materials Science Division Argonne National LaboratoryArgonneILUSA Engineering Sciences and Applied Mathematics Northwestern UniversityEvanstonILUSA

Substrate-based crawling motility of eukaryotic cells is essential for many biological functions,both in developing and mature *** dysfunctions are involved in several life-threatening pathologies such as cancer and *** cells are also a natural realisation of active,self-propelled‘particles’,a popular research topic in nonequilibrium ***,from the materials perspective,assemblies of motile cells and evolving tissues constitute a class of adaptive self-healing materials that respond to the topography,elasticity and surface chemistry of the environment and react to external *** a comprehensive understanding of substrate-based cell motility remains elusive,progress has been achieved recently in its modelling on the whole-cell *** we survey the most recent advances in computational approaches to cell movement and demonstrate how these models improve our understanding of complex self-organised systems such as living cells.

关键词： motility healing metastasis

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On character sums with determinants

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Science China Mathematics 2023年第12期66卷 2693-2714页

作者： Etienne Fouvry igor E.Shparlinski CNRS Laboratoire de Mathématiques d'OrsayUniversité Paris-SaclayOrsay 91405France School of Mathematics and Statistics University of New South WalesSydneyNSW 2052Australia

We estimate weighted character sums with determinants ad-bc of 2×2 matrices modulo a prime p with entries a,b,c and d vary ing over the interval [1,N].Our goal is to obtain non-trivial bounds for values of N as small as *** particular,we achieve this goal,with a power saving,for N≥p^(1/8+ε) with any fixed ε>0,which is very likely to be the best possible unless the celebrated Burgess bound is improved,By other techniques,we also treat more general sums but sometimes for larger values of N.

关键词： character sum determinant Burgess bound

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Analytical model of 2D leakoff in waterflood-induced fractures

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Journal of Rock Mechanics and Geotechnical Engineering 2023年第7期15卷 1713-1733页

作者： igor Reznikov Dimitry Chuprakov Ilmir Bekerov Schlumberger Moscow Research MoscowRussia

Waterflood-induced fractures,also known as self-induced fractures,spontaneously form at injection wells during *** fractures propagate long distances through rock,allowing injected fluids to travel far away from a well,both within and outside the flooding ***,the me-chanics of waterflood-induced fracture propagation is similar to that of hydraulic fractures,which are intentionally created for reservoir *** models developed for hydraulic fractures can also be applied to waterflood-induced ***,waterflood-induced fractures are typically pumped with much larger volumes of water or brine and grow much longer in *** a result,fluid leakoff from waterflood fractures into the formation is more extensive and two-dimensional(2D),a characteristic that is often ignored in a majority of modern fracturing simulators,making their appli-cation to waterflood fractures *** this work,we revisit the problem of leakoff for long-growing waterflood-induced fractures and develop a new analytical model for fluid leakoff that provides improved predictions of fracture geometry and can be easily implemented in fracturing *** incorporate the developed solution into the classical Perkins-Kern-Nordgren(PKN)model of fracture growth,which shows that the choice of the Carter or a 2D leakoff model greatly impacts fracture ge-ometry at large *** conducted parametric study shows while a toughness-dominated regime af-fects fracture evolution,most of fracture lifetime occurs in a viscosity-and-leakoff-dominated *** also develop an asymptotic solution for a leakoff profile in the limiting case of 2D leakoff domination(~~M and~~K).Finally,we study 3D fracture growth and out-of-zone injection with three layers and a complex structure of *** study shows that ignoring the 2D leakoff during simulation results in a significant overestimation of fracture geometry *** present work,thus,plays an impor

关键词： Waterflooding Leakoff Analytical model Hydraulic fracturing Two-dimensional flow

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Dynamical behavior of a mobile system with two degrees of freedom near the resonance

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Acta Mechanica Sinica 2011年第1期27卷 7-17页

作者： Klaus Zimmermann igor Zeidis Faculty of Mechanical Engineering Technische Universitaet Ilmenau

The design of mobile robots that can move without wheels or legs is an important engineering and technological ***-propelling mechanisms consisting of a body that has contact with a rough surface and moveable internal masses are *** models of such systems are presented in this ***,a model of a vibration driven robot that moves along a rough horizontal plane with isotropic dry friction is *** is shown that by changing the off-resonance frequency detuning in sign,one can control the direction of motion of the *** addition,a locomotion system which moves in an environment with anisotropic viscous friction is *** all models,the method of averaging to obtain an algebraic equation for the steady-state＂average＂velocity of the system is used. Prototypes were constructed to compare the theoretical results with experimental ones.

关键词： Dynamics Friction Resonance Vibrationdriven systems

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Output feedback control with disturbancecompensation in nonlinear MIMO systems undermeasurement noises

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Journal of Control and Decision 2022年第1期9卷 35-44页

作者： igor Furtat Pavel Gushchin Institute for Problems of Mechanical Engineering of the Russian Academy of Sciences(IPME RAS) St.-PetersburgRussia

A novel output feedback control law with disturbance compensation for nonlinear multiinputmulti-output (MIMO) time-invariant systems under measurement noises is proposed. Thedesigned control law, based on the noise and disturbance estimations, ensures the accuracy insteady state depending on the disturbance, only one component of noise vector and its firstderivatives. Therefore, the proposed algorithm is efficient under noises with large *** conditions in terms of linear matrix inequalities (LMIs) provide a practical exponentialstability of the closed-loop system. The simulations illustrate an efficiency of the proposedmethod compared with some existing ones.

关键词： Nonlinear system disturbance measurement noise compensation S-procedure LMI

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Development of a two-stage virtual impactor for the generation of micrometer-scale monodisperse aerosols

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Particuology 2024年第12期95卷 189-197页

作者： Jun-Hyung Lim igor Kim Se-Jin Yook School of Mechanical Engineering Hanyang UniversitySeoul04763Republic of Korea

Monodisperse particles are useful across a wide range of industrial applications,such as LCD displays,solar cells and rechargeable batteries,due to their uniformly small ***,generating high volumes of monodisperse particles remains *** this study,it was aimed to generate mono-disperse aerosols by classifying micrometer-scale solid aerosol particles within a narrow size ***,a new particle-size classification device with two virtual impactors connected in series and clean air cores was *** first-stage virtual impactor had a slightly larger cutoff size than the second-stage,and the major flow discharged from the first-stage was directed to the *** target particle size range was altered by changing the nozzle sizes in the first and second stages or by adjusting the flow ***,the classification performance of the two-stage virtual impactor was simulated and validated through an experiment using Arizona test *** implemented combi-nations of cutoff sizes for the first and second stages were 3.0 and 2.0μm,3.9 and 2.7μm,or 6.7 and 4.8μ*** a result,monodisperse aerosol particles were classified at a geometric standard deviation of 1.04-1.14 and a particle size range of 2-6.7μ*** two-stage virtual impactor developed herein may be useful for various research and performance evaluations,as it can classify micrometer-scale solid particle aerosols that exhibit high monodispersity.

关键词： Virtual impactor Clean air core Dust collection efficiency Monodispersity

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On the Features of Thermal Convection in a Compressible Gas

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Fluid Dynamics & Materials Processing 2024年第5期20卷 957-974页

作者： igor B.Palymskiy Physics Department Siberian State University of Telecommunications and Information SciencesNovosibirsk City630102Russia Physics Department Siberian State University of Geosystems and TechnologiesNovosibirsk City630108Russia

The fully nonlinear equations of gas dynamics are solved in the framework of a numerical approach in order to study the stability of the steady mode of Rayleigh-Bénard convection in compressible,viscous and heat-conducting gases encapsulated in containers with no-slip boundaries and isothermal top and bottom *** initial linear temperature profile is assumed.A map of the possible convective modes is presented assuming the height of the region and the value of the temperature gradient as influential *** a relatively small height,isobaric convection is found to take place,which is taken over by an adiabatic mode when the height exceeds the critical value,or by a super-adiabatic mode in case of a relatively high temperature *** the adiabatic mode,convective flow develops due to adiabatic processes given a stable initial *** analytic formula for the critical height of the region is derived taking into account and neglecting the dependence of the gas viscosity on the ***,an analytic formula is obtained for the upper boundary of the region of applicability of the Boussinesq approximation for incompressible *** models for compressible gases are relevant to practical situations such as the study of convective flows in spatially extended gas mixtures when dealing with safety issues related to hydrocarbons stored in gas stations.A dangerous situation arises when the tank is almost empty but some hydrocarbon is left at the bottom of the *** the presence of convective flows,the vaporized fuel is mixed with the oxidizer(air)forming a gas-vapor ***,if the volumetric concentration of fuel vapor(hydrocarbon)is in the interval between the lower and upper concentration limits of ignition,then the gas-vapor mixture becomes explosive and any accidental spark is sufficient to cause an emergency.

关键词： Rayleigh-Bénard convection gas stable stratification unstable stratification temperature gradient

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