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Search results for: —TRANSFER LEARNING, DEEP LEARNING, PROTEIN STRUCTURE, FUNCTION, AND INTERACTION PREDICTION, SEQUENCE MODELLING
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Machine Learning for Control Systems Security of Industrial Robots: a Post-covid-19 Overview
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Likelihood of Transformation to Green Infrastructure Using Ensemble Machine Learning Techniques in Jinan, China
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Open source learning management systems at civil engineering and environmental department: TeleCAD and Moodle.
PublicationW rozdziale zaprezentowano dwa systemy zarządzania kształceniem, służące do przygotowania i prowadzenia e-kursów. Pierwszy z nich TeleCAD został opracowany w ramach projektu Leonardo da Vinci (1998-2001). Ostanie użycie systemu miało miejsce w roku akademickim 2003/2004 i był on wykorzystany w projekcie CURE (V Program Ramowy, 2003-2006). W roku 2003 dzięki wsparciu projektu Leonardo da Vinci EMDEL (2001-2005) Centrum Edukacji...
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Advances in Architectures, Big Data, and Machine Learning Techniques for Complex Internet of Things Systems
PublicationTe feld of Big Data is rapidly developing with a lot of ongoing research, which will likely continue to expand in the future. A crucial part of this is Knowledge Discovery from Data (KDD), also known as the Knowledge Discovery Process (KDP). Tis process is a very complex procedure, and for that reason it is essential to divide it into several steps (Figure 1). Some authors use fve steps to describe this procedure, whereas others...
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Evolution towards simplicity in bacterial small heat shock protein system
PublicationEvolution can tinker with multi-protein machines and replace them with simpler single-protein systems performing equivalent functions in an equally efficient manner. It is unclear how, on a molecular level, such simplification can arise. With ancestral reconstruction and biochemical analysis, we have traced the evolution of bacterial small heat shock proteins (sHsp), which help to refold proteins from aggregates using either two...
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Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?
PublicationThe structure of B-DNA, the physiological form of the DNA molecule, has been a central topic in biology, chemistry and physics. Far from uniform and rigid, the double helix was revealed as a flexible and structurally polymorphic molecule. Conformational changes that lead to local and global changes in the helix geometry are mediated by a complex choreography of base and backbone rearrangements affecting the ability of the B-DNA...
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Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13
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MutL protein as a constituent of vsp, ner and mmr repair systems
PublicationMutS and MutL proteins are renowned mostly for their functions in well-characterized, post-DNA replication mis- match repair system (MMR). However, there is growing evidence that MMR system is not the only field of action for these pro- teins. Moreover, the participation in MMR does not even have to be their primary function. There are some reports indicat- ing involvement of MutL in BER, NER and VSP (very short patch repair)....
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A coarse‐grained approach to NMR ‐data‐assisted modeling of protein structures
PublicationThe ESCASA algorithm for analytical estimation of proton positions from coarse-grained geometry developed in our recent work has been implemented in modeling protein structures with the highly coarse-grained UNRES model of polypeptide chains (two sites per residue) and nuclear magnetic resonance (NMR) data. A penalty function with the shape of intersecting gorges was applied to treat ambiguous distance restraints, which automatically...
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Social learning and knowledge flows in cluster initiatives, In: Sanz S.C., Blanco F.P., Urzelai B. (Eds). Human and Relational Resources (pp. 44-45). the 4th International Conference on Clusters and Industrial Districts CLUSTERING, University of Valencia, Spain, May 23–24 (ISBN: 978-84-09-11926-4).
PublicationPurpose – The purpose of the paper is to explore how learning manifests and knowledge flows in cluster initiatives (CIs) due to interactions undertaken by their members. The paper addresses the research question of how social learning occurs and knowledge flows in CIs. Design/methodology/approach – The qualitative study of four cluster initiatives helped to identify various symptoms of social learning and knowledge flows in...
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Performance of protein-structure predictions with the physics-based UNRES force field in CASP11
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Frequent Sequence Mining in Web Log Data
PublicationThe amount of information available even on a single web server can be huge. On the other hand, the amount of visitors (users) can often reach a number of at least six digits. Users vary in gender, age and education, and in consequence their information needs are different. Moreover, they subconsciously expect to get more adequate content after visiting the first few pages. The scope of this kind of problem relates to the domain...
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Two-step mechanism of J-domain action in driving Hsp70 function
PublicationJ-domain proteins (JDPs), obligatory Hsp70 cochaperones, play critical roles in protein homeostasis. They promote key allosteric transitions that stabilize Hsp70 interaction with substrate polypeptides upon hydrolysis of its bound ATP. Although a recent crystal structure revealed the physical mode of interaction between a J-domain and an Hsp70, the structural and dynamic consequences of J-domain action once bound and how Hsp70s...
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Understanding the interactions between protein stabilizers and the peptide bond through the analysis of the volumetric and compressibility properties for the model systems
PublicationThis work confirms our earlier supposition, that volumetric and acoustic parameters for simple model proposed by us are directly related to stabilizing/destabilizing effect of osmolytes on proteins structure. The apparent molar volumes, V and the apparent molar isentropic compressions, KS,, of glycine and N,N,N –trimethylglycine (betaine) were determined from densities and speed of sound measurements in aqueous solution of N-methylacetamide...
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Distribution of the displacement sequence of an orientation preserving circle homeomorphism
PublicationIn some applications not only the knowledge of the behaviour of trajectories of a map is important, but also their displacements. We describe in detail the distribution of elements of the displacement sequence along a trajectory of an orientation preserving circle homeomorphism ϕ with irrational rotation number ϱ(ϕ). The values of displacement are dense in a set which depends on the map γ (semi-)conjugating ϕ with the rotation...
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Evaluation and cellular responses of modulators of TRF1/TRF2 protein’s function as potential anticancer drugs interfering with telomeric shelterin’s function
PublicationA number of proteins that interact with telomeres have been identified in human cells, indicating the high plasticity of human nucleoprotein complex organization. The most important complex is the "shelterin" complex, which consists of six proteins: TRF1, TRF2, TIN2, POT1, TPP1. The TRF1 and TRF2 directly bind to telomeric double-stranded DNA and the TIN2 protein. The TIN2 protein also binds to the TPP1 protein, stabilizing the...
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Experimental and Theoretical Insights into the Intermolecular Interactions in Saturated Systems of Dapsone in Conventional and Deep Eutectic Solvents
PublicationSolubility is not only a crucial physicochemical property for laboratory practice but also provides valuable insight into the mechanism of saturated system organization, as a measure of the interplay between various intermolecular interactions. The importance of these data cannot be overstated, particularly when dealing with active pharmaceutical ingredients (APIs), such as dapsone. It is a commonly used anti-inflammatory and...
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A method to determine the tightening sequence for standing rigging of a mast
PublicationThe article proposes an alternative method to determine the sequence of generation of pre-tension forces in standing rigging of a mast. The proposed approach has been verified on both a virtual simulation experiment and laboratory tests. In this method, the desired tension values are obtained using the influence matrix which allows to calculate the effect of tension change in an individual rope on the tension distribution in the...
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Modelling of Geared Multi-Rotor System
PublicationIn the paper the method of modelling a speed-varying geared rotor system is presented. The proposed approach enables us to obtain an accurate low-order lumped parameter representation of the investigated system. The final model consists of reduced modal models of an undamped beam/torsional shaft system as well as a spatially lumped model of other linear and nonlinear phenomena including gear mesh interaction.
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Arterial structure and function in subjects with acute coronary syndrome after one-year of treatment
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Interaction Design in Agile IT Projects
PublicationIn recent years, interactive systems, such as various types of software, online services or mobile applications, have become an integral part of everyday life. Interactive systems and digital services should be easy to use and provide a positive User Experience (UX). For this reason, interaction design has recently emerged as a distinct professional area of information technology (IT). Easy interaction and user experience (UX)...
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Co-simulation strategy of transient CFD and heat transfer in building thermal envelope based on calibrated heat transfer coefficients
PublicationThe paper presents a strategy to develop a fully transient numerical model of a heat transfer in building, using a transient CFD model of indoor air and a thermal envelope model, running in a co-simulation. The strategy relies on the utilization of RANS with a high-Re turbulence model and a wall function, which enables to use a coarse computational mesh limiting the computational time. Since wall functions give invalid heat transfer...
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The Knowledge Transfer From Headquarter to Local Subsidiaries Through Expatriates - Local Employees’ Perspective
PublicationBackground. Knowledge transfer between the HQ and subsidiary has recently been targets of increasing research interest. However, the role of expatriate managers and local staff perspective on this process has not been examined enough. Research aims. This paper has two main objectives: first to develop a conceptual framework (model) of knowledge transfer between the headquarters and local subsidiary, and second to empirically evaluate...
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The hydration properties of protein stabilizer, trimethylamine-N-oxide in aqueous solutions of N-methylacetamide – The volumetric and compressibility studies between 288.15 and 308.15 K
PublicationApparent molar volumes and apparent molar isentropic compressions of the protein stabilizer, trimethylamine-N-oxide (TMAO) were determined from the densities and speed of sound measured at T = (288.15, 298.15 and 308.15) K in aqueous solutions of N-methylacetamide (NMA) at four different concentrations (2, 4, 6 and 8 mol/kg). The concentration dependencies of the calculated quantities extrapolated to the infinite dilution lead...
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Classification of objects in the LIDAR point clouds using Deep Neural Networks based on the PointNet model
PublicationThis work attempts to meet the challenges associated with the classification of LIDAR point clouds by means of deep learning. In addition to achieving high accuracy, the designed system should allow the classification of point clouds covering an area of several dozen square kilometers within a reasonable time interval. Therefore, it must be characterized by fast processing and efficient use of memory. Thus, the most popular approaches...
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Outlier detection method by using deep neural networks
PublicationDetecting outliers in the data set is quite important for building effective predictive models. Consistent prediction can not be made through models created with data sets containing outliers, or robust models can not be created. In such cases, it may be possible to exclude observations that are determined to be outlier from the data set, or to assign less weight to these points of observation than to other points of observation....
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Modelling of wastewater treatment plant for monitoring and control purposes by state - space wavelet networks
PublicationMost of industrial processes are nonlinear, not stationary, and dynamical with at least few different time scales in their internal dynamics and hardly measured states. A biological wastewater treatment plant falls into this category. The paper considers modelling such processes for monitorning and control purposes by using State - Space Wavelet Neural Networks (SSWN). The modelling method is illustrated based on bioreactors of...
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Prediction of Thymine Dimer Repair by Electron Transfer from Photoexcited 8-Aminoguanine or Its Deprotonated Anion
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MUTL PROTEIN AS A COMMON CONSTITUENT OF VSP, BER, NER AND MMR REPAIR SYSTEMS
PublicationMutS and MutL proteins are renowned mostly for their functions in well-characterized, post-DNA replication mismatch repair system (MMR). However, there is growing evidence that MMR system is not the only field of action of these proteins. Moreover, involvement in MMR does not even have to be their primary function. There are some reports indicating involvement of MutL in BER, NER and VSP (very short patch repair). MutL protein...
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Approach Manoeuvre During Emergency Ship-to-Ship Transfer Operation with Oil Spill
PublicationOne of the major activities during Ship to Ship (STS) transfer operation at sea is to safe approach the Ship to be Lightered (SBL) which moves on a constant heading with slow speed or drifting. In the paper described the manoeuvring problem for approaching during emergency STS transfer operation with oil spill. The approach manoeuvre is considered as a sequence of navigation manoeuvres in specific navigational environment with...
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A Data Driven Model for Predicting RNA-Protein Interactions based on Gradient Boosting Machine
PublicationRNA protein interactions (RPI) play a pivotal role in the regulation of various biological processes. Experimental validation of RPI has been time-consuming, paving the way for computational prediction methods. The major limiting factor of these methods has been the accuracy and confidence of the predictions, and our in-house experiments show that they fail to accurately predict RPI involving short RNA sequences such as TERRA RNA....
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The smoothness test for a density function
PublicationThe problem of testing hypothesis that a density function has no more than μ derivatives versus it has more than μ derivatives is considered. For a solution, the L2 norms of wavelet orthogonal projections on some orthogonal ‘‘differences’’ of spaces from a multiresolution analysis is used. For the construction of the smoothness test an asymptotic distribution of a smoothness estimator is used. To analyze that asymptotic distribution,...
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Experimental tests of reinforced concrete deep-beams
PublicationThe paper presents results of experimental research of the reinforced concrete deep beam with a spatial arrangement. Tested structural elements consist of the cantilever deep beam loaded on the height and transverse deep beam with hanging on it another one. The analysis includes crack morphology, effort of steel and load distribution. The article verified effectiveness of two different kind of reinforcement in both tested deep...
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Influence of amino acid sequence on the interaction of short peptides containing 3-[2-(9-anthryl)benzoxazol-5-yl]-alanine with β-cyclodextrin
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Numerical Modelling for Prediction of Compression Index from Soil Index Properties in Jimma town, Ethiopia
PublicationIn this study, correlations are developed to predict compression index (Cc) from index parameters so that one can be able to model Jimma soils with compression index using simple laboratory tests. Undisturbed and disturbed soil samples from twelve different locations in Jimma town were collected. Laboratory tests like specific gravity, grain size analysis, Atterberg limit, and one-dimensional consolidation test for a total of twenty-four...
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In silico modelling for predicting the cationic hydrophobicity and cytotoxicity of ionic liquids towards the Leukemia rat cell line, Vibrio fischeri and Scenedesmus vacuolatus based on molecular interaction potentials of ions
PublicationIn this study we present prediction models for estimating in silico the cationic hydrophobicity and the cytotoxicity (log [1/EC50]) of ionic liquids (ILs) towards the Leukemia rat cell line (IPC-81), the marine bacterium Vibrio fischeri and the limnic green algae Scenedesmus vacuolatus using linear free energy relationship (LFER) descriptors computed by COSMO calculations. The LFER descriptors used for the prediction model (i.e....
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Perception of Pathologists in Poland of Artificial Intelligence and Machine Learning in Medical Diagnosis—A Cross-Sectional Study
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SELECTING A REPRESENTATIVE DATA SET OF THE REQUIRED SIZE USING THE AGENT-BASED POPULATION LEARNING ALGORITHM
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Errorless Learning as a method of neuropsychological rehabilitation of individuals suffering from dementia in the course of Alzheimer’s disease
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Fractional-Order PID Controller (FOPID)-Based Iterative Learning Control for a Nonlinear Boiler System
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Guest editorial: learning, scheduling, resource optimization, and evolution in smart artificial systems: challenges and support
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Diversity of Students’ Unethical Behaviors in Online Learning Amid COVID-19 Pandemic: An Exploratory Analysis
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A ROLE PLAYING GAME NAME GENERATOR LEARNING ITS CREATIVITY FROM ARKADIA MUD PLAYERS
PublicationThe paper proposes an approach to creative generation of new names for the purposes of Role Playing Games in fantasy realms. The generator based on an existing database of na mes is able to propose a set of new names with regard to demanded attributes, such as: length of the name, sex and race of the character, a given p hrase as the origin for the generated name as well as subjective evaluations from former users. The software...
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Implementing SP4CE Learning Rooms concept and AUTODESK online certification in the preparation of a new generation of engineers.
PublicationIn academia, educators do not always cope with rapidly changing technologies. Yet keeping up with new trends is essential to graduates’ success in a competitive job market. In the article, the author will answer the question of how Autodesk University Open Educational Resources and Certiport exams including GMetrix can enhance students’ academic progress and prepare them for future career. The concept of co-operation between Authorized...
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The role of water in deep eutectic solvent-base extraction
PublicationDeep eutectic solvents (DESs) are currently being used in different sectors, such as electrochemistry, electrodeposition, organic synthesis, nanoparticle preparation, bioactive compound separation, etc. Their use in analytical chemistry has only recently begun to expand. Despite the publication of a sufficient number of DES-based analytical extraction procedures, some details, such as interaction of DESwith the sample and target...
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Modified SPWM Technique with Zero-Sequence Voltage Injection for a Five-Phase, Three-Level NPC Inverter
PublicationThis article presents a modified sinusoidal pulse-width modulation (SPWM) scheme for a five-phase, three-level neutral-point-clamped inverter. The modulation scheme deploys a modified min–max function to inject the zero-sequence components into the reference modulating signals; hence enabling the effective utilization of the DC-link voltage. Balanced split-input DC-link voltages were achieved through further incorporation of adjustable...
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Comparative molecular modelling of biologically active sterols
PublicationMembrane sterols are targets for a clinically important antifungal agent – amphotericin B. The relatively specific antifungal action of the drug is based on a stronger interaction of amphotericin B with fungal ergosterol than with mammalian cholesterol. Conformational space occupied by six sterols has been defined using the molecular dynamics method to establish if the conformational features correspond to the preferential interaction...
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Magnetic deep eutectic solvents – Fundamentals and applications
PublicationMagnetic deep eutectic solvents (MDES), a relatively new subclass of conventional deep eutectic solvents (DES) containing additional paramagnetic components in their structure. MDES exhibit a strong response toward external magnetic fields, thus they can improve many industrial and analytical applications. In addition, this new group of solvents present unique physicochemical properties that can be easily tuned by selecting the...
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MODELLING OF THE VISCOSITY EFFECT OF HEAVE PLATES FOR FLOATING WIND TURBINES BY HYDRODYNAMIC COEFFICIENTS
PublicationOne of the methods of modelling the movement of floating wind turbines is the use of the diffraction method. However, this method does not take into account the influence of viscosity; therefore, in many cases, it needs to be extended with a matrix of appropriate coefficients. The effect of viscosity causes both the added mass coefficient and the damping coefficient to increase. The determined coefficients were entered into the...
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Method of Skeletal System Modelling
PublicationAn original method of skeletal system modelling is presented in detail. Using DICOM images obtained from CT and PET tests, shell models of nine bones were created (humerus, radius, ulna, scapula, clavicle, femur, tibia, fibula, pelvis). Two methods of bone behaviour are also proposed, the first method treating the bone as a solid structure and the second method treating the bone as a complex porous structure. The behaviour of model...