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Wyniki wyszukiwania dla: PROTEIN COEVOLUTION
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Novel primosomal protein B from Clostridium pasteurianum
PublikacjaPriB is a primosomal protein that catalyzes DNA replication in Procaryota. The replication pathway starts with PriA protein - the initiator protein that binds to a DNA replication fork, unwinds double-stranded DNA and role of PriB is to stabilize PriA on the DNA. However there are many biochemical differences in replication mechanism in bacteria and only some of them use PriB proteins. A few of PriB proteins were published and...
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Construction and purification of his6-Thermus thermophilus MutS protein.
PublikacjaGen mutS z termofilnej bakterii Thermus thermophilus zamplifikowano przy użyciu PCR, sklonowano i przeprowadzono jego ekspresję w E. coli. Rekombinantowe białko MutS zawierające oligohistydynową domenę na N-końcu oczyszczono w jednoetapowej procedurze przy wykorzystaniu chromatografii powinowactwaNi(2+). Zdolność do rozpoznania niekomplementarności białka his(6)-MutS potwierdzono w eksperymentach ochrony DNA przed trawieniem...
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Conservation and diversity of MutS proteins
PublikacjaThe homologues of MutS, mismatch repair protein, exist in all prokaryotes, with the exception of Actinobacteria, Mollicutes and part of the Archaea. Multiple alignments of 316 MutS amino acid sequences from 169 species revealed conserved residues and sequence motifs distinguishing MutS homologues. All MutS homologues show high conservation within the ATPase domain. MutS1, the homologue responsible for DNA mismatch recognition,...
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Concentration of proteins in the whey stream
PublikacjaZastosowano metodę separacji pianowej do odzyskiwania białka z serwatki. Wykazano silny wpływ prędkości powietrza w kolumnie, początkowego stężenia białka w serwatce i pH roztworu na przebieg i skuteczność flotacji. Współczynnik wzbogacenia maleje ze wzrostem prędkości przepływu powietrza oraz ze wzrostem początkowego stężenia białka serwatkowego. Najwyższą wartość współczynnika wzbogacenia uzyskano dla pH naturalnej serwatki.
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Conserved motifs of MutL proteins
PublikacjatThe MutL protein is best known for its function in DNA mismatch repair (MMR). However, there isevidence to suggest that MutL is not only the linker connecting the functions of MutS and MutH in MMR,but that it also participates in other repair systems, such as Very Short Patch (VSP), Base Excision (BER)and Nucleotide Excision Repair (NER). This study set out to identify the most highly conserved aminoacid sequence motifs in MutL...
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Monocyte Chemoattractant Protein-Induced Protein 1 (MCPIP1) Enhances Angiogenic and Cardiomyogenic Potential of Murine Bone Marrow-Derived Mesenchymal Stem Cells
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Implementation of discrete convolution using polynomial residue representation
PublikacjaConvolution is one of the main algorithms performed in the digital signal processing. The algorithm is similar to polynomial multiplication and very intensive computationally. This paper presents a new convolution algorithm based on the Polynomial Residue Number System (PRNS). The use of the PRNS allows to decompose the computation problem and thereby reduce the number of multiplications. The algorithm has been implemented in Xilinx...
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Implementation of discrete convolution using polynomial residue representation
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Sign Language Recognition Using Convolution Neural Networks
PublikacjaThe objective of this work was to provide an app that can automatically recognize hand gestures from the American Sign Language (ASL) on mobile devices. The app employs a model based on Convolutional Neural Network (CNN) for gesture classification. Various CNN architectures and optimization strategies suitable for devices with limited resources were examined. InceptionV3 and VGG-19 models exhibited negligibly higher accuracy than...
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Alternative convolution approach to friction in unsteady pipe flow
PublikacjaIn the paper some aspects of the unsteady friction in pipe flow expressed by the convolution are analyzed. This additional term introduced into the motion equation involves the accelerations of fluid occurring in the past and a weighting function. The essence of such approach is to assume the appropriate form of weighting function. However, until now no fully reliable formula for this function has been found. To avoid some inconveniences...
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Computation of the convolution with use of the polynomial residue number system.
PublikacjaPrzedstawiono użycie wielomianowych systemów resztowych do obliczania splotu w cyfrowych układach dużej skali integracji VLSI.
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Dynamical Aspects of Knowledge Evolution
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Model of Rules for IT Organization Evolution
PublikacjaThe aim of this paper is to introduce the Model of Rules for IT Organization Evolution which shall be in compliance with the Generic IT Organization Evolution Model. Due to its general nature, a set of practical adjustments is proposed in order to adapt the Generic Model to the IT Service Management domain. Further, two sets of rules describing the evolution of the IT Service Management area are defined based on two types of rules...
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Impedance analysis of Portevin-Le Chatelier effect on aluminium alloy
PublikacjaW niniejszej pracy przeprowadzono badania elektrochemiczne powierzchniowego efektu PLC, związanego z nierównomiernym procesem płynięcia plastycznego stopów aluminium zawierających magnez. Występujący efekt PLC w postaci serration wywołuje niehomogeniczny proces zmian zewnętrznej powierzchni rozciąganej próbki. Wykonano badania metodą Dynamicznej Spektroskopii Impedancyjnej w warunkach dynamicznych prowadzenia procesu rozciągania....
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Software tools for identification, visualization and analysis of protein tunnels and channels
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Delay induced oscillations in gene expression of Hes1 protein model
PublikacjaW pracy został omówiony model produkcji białka Hes1. Stężenie Hes1 jest kontrolowane przez ujemne sprzężenie zwrotne wbudowane w białko i jego mRNA. Przeprowadzona analiza potwierdziła znane wyniki numeryczne, że oscylacje wywołane są przez opóźnienie. Pokazaliśmy również, że jeśli współczynnik Hilla jest większy niż 1, to istnieje krytyczna wartość opóźnienia, dla której ma miejsce bifurkacja Hopfa i pojawiają się rozwiązania...
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C-reactive Protein as a Diagnostic and Prognostic Factor of Endometrial Cancer
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Assessment of chemical‐crosslink‐assisted protein structure modeling in CASP13
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C-reactive protein as a diagnostic and prognostic factor of endometrial cancer
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Structural Analysis of a Peptide Fragment of Transmembrane Transporter Protein Bilitranslocase
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Nutritional value, protein and peptide composition of edible cricket powders
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Quantitative determination of mechanical stability in the novel coronavirus spike protein
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MP3vec: A Reusable Machine-Constructed Feature Representation for Protein Sequences
Publikacja—Machine Learning (ML) methods have been used with varying degrees of success on protein prediction tasks, with two inherent limitations. First, prediction performance often depends upon the features extracted from the proteins. Second, experimental data may be insufficient to construct reliable ML models. Here we introduce MP3vec, a transferable representation for protein sequences that is designed to be used specifically for sequence-to-sequence...
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X-ray and UV Radiation Damage of dsDNA/Protein Complexes
PublikacjaRadiation and photodynamic therapies are used for cancer treatment by targeting DNA. However, efficiency is limited due to physico-chemical processes and the insensitivity of native nucleobases to damage. Thus, incorporation of radio- and photosensitizers into these therapies should increase both efficacy and the yield of DNA damage. To date, studies of sensitization processes have been performed on simple model systems, e.g.,...
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Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment
PublikacjaWe present the results for CAPRI Round 50, the 4th joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of 12 targets, including 6 dimers, 3 trimers, and 3 higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers). Eight were difficult targets for which only distantly...
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The Unfolded Protein Response: A Double-Edged Sword for Brain Health
PublikacjaEfficient brain function requires as much as 20% of the total oxygen intake to support normal neuronal cell function. This level of oxygen usage, however, leads to the generation of free radicals, and thus can lead to oxidative stress and potentially to age-related cognitive decay and even neurodegenerative diseases. The regulation of this system requires a complex monitoring network to maintain proper oxygen homeostasis. Furthermore,...
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Molecular targets for antifungals in amino acid and protein biosynthetic pathways
PublikacjaFungi cause death of over 1.5 million people every year, while cutaneous mycoses are among the most common infections in the world. Mycoses vary greatly in severity, there are long-term skin (ringworm), nail or hair infections (tinea capitis), recurrent like vaginal candidiasis or severe, life-threatening systemic, multiorgan infections. In the last few years, increasing importance is attached to the health and economic problems...
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MutL protein as a constituent of vsp, ner and mmr repair systems
PublikacjaMutS 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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Mechanism of antifreeze protein functioning and the “anchored clathrate water” concept
PublikacjaIn liquid water, there is a natural tendency to form aggregates that consist of water molecules linked by hydrogen bonds. Such spontaneously formed aggregates are surrounded by a "sea" of disordered water molecules, with both forms remaining in equilibrium. The process of creating water aggregates also takes place in the solvation water of proteins, but in this case the interactions of water molecules with the protein surface shift...
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Antioxidants and proteins in ethylene-treated kiwifruits
PublikacjaW pracy porównano właściwości przeciwutleniające i profil białek owoców kiwi poddanych działaniu etylenu i powietrza. Wysokie współczynniki korelacji między całkowitą zawartością fenoli i właściwościami przeciwutleniającymi uzyskano dla trzech metod określania właściwości przeciwutleniających: ABTS, TEAC i CUPRAC. W paśmie białek owoców kiwi rozdzielonych za pomocą elektroforezy stwierdzono różnice w paśmie siarczanu dodecylu sodu...
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The role of proteins in food. Chapter 6
PublikacjaStruktura i konformacja wpływają na biologiczne oraz funkcjonalne właściwości białek i na ich rolę w tworzeniu pożądanych cech produktów żywnościowych. Właściwości funkcjonalne to rozpuszczalność w środowisku wodnym o różnej sile jonowej, wodochłonność oraz zdolność żelowania, tworzenia błon, emulgowania lipidów i pienienia się. Białka mięsa, ryb, mleka, jaj, nasion roślin strączkowych, nasion zbóż oraz drobnoustrojów różnią się...
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Molecular Dynamics Studies on Amyloidogenic Proteins
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Molecular Dynamics Studies on Amyloidogenic Proteins
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Targeting shelterin proteins for cancer therapy.
PublikacjaAs a global health challenge, cancer prompts continuous exploration for innovative therapies that are also based on new targets. One promising avenue is targeting the shelterin protein complex, a safeguard for telomeres crucial in preventing DNA damage. The role of shelterin in modulating ataxia- telangiectasia mutated (ATM) and ataxia-telangiectasia and Rad3-related (ATR) kinases, key players in the DNA damage response (DDR),...
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Comparing some convolution-based methods for creation of surround sound
PublikacjaW referacie przedstawiono eksperymenty związane z symulacją dźwięku dookólnego w sali koncertowej. W tym celu wykorzystano splot odpowiedzi impulsowej z danego wnętrza (wielokanałowe nagrania odpowiedzi impulsowej) z nagraniami z komory bezechowej. Uzyskany w ten sposób sygnał został następnie przypisany do odpowiednich kanałów w systemie dookólnym. Uzyskane w ten sposób nagrania były następnie porównywane w testach subiektywnych...
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EFFICIENT LINE DETECTION METHOD BASED ON 2D CONVOLUTION FILTER
PublikacjaThe article proposes an efficient line detection method using a 2D convolution filter. The proposed method was compared with the Hough transform, the most popular method of straight lines detection. The developed method is suitable for local detection of straight lines with a slope from -45˚ to 45˚. Also, it can be used for curve detection which shape is approximated with the short straight sections. The new method is characterized...
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Karaś P., Kochanowicz K., Pitek M., Domański P., Obuchowski I., Tomiczek B., Liberek K.: Evolution towards simplicity in bacterial small heat shock protein system// eLife -, (2023), s.1-21
PublikacjaEvolution 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...
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Neural Networks and the Evolution of Environmental Change
PublikacjaZmiany środowiskowe na Ziemii są odwieczne i liczą około 4 miliardy lat. Homo sapiens wpłynął na każdy aspekt środowiska ziemskiego w wyniku rozwoju ludzkości na przestrzeni ostatnich milionów lat. Ale nic tak nie wpłynęło na wzrost i szybkość zmian na Ziemi jak ludzka aktywność w ciągu ostatnich dwóch stuleci. Po raz pierwszy zmiany ekosystemów były tak intensywne i zachodziły na tka wielką skalę i z taką szybkością jak nigdy...
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Concept of Generic IT Organization Evolution Model
PublikacjaThe purpose of this publication is to present a generic model of the IT organization evaluation process as an attempt to systematize and describe the continuous actions and changes in the organization.
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Pressure evolution of LiBaF3:Eu2+luminescence
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Time evolution of luminescence of Sr2SiO4:Eu2+
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Introductory Chapter: Evolution of Sample Preparation
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Introductory Chapter: Evolution of Sample Preparation
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Developing Prognostic Models of Organization Evolution
PublikacjaThe work focuses on the problem of measuring evolution of IT organizations. Changes in business influence functioning of the IT organization. IT departments or companies must ensure that the needs of their parent company/customers will be met. Therefore they must constantly evolve. Following question can be raised: is it possible to support process of changes the IT organization to run it smoother, faster, easier but with reduced...
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Selected aspects of the evolution of the industry analysis
PublikacjaPorter's five forces is a significant tool of analysis of industries. It helps evaluating variables of industry profitability and assessing firm performance. Using the framework, managers can take a decision as to which industries they can effectively compete in and position their companies to reduce the adverse effects of the mentioned forces. According to the critics, the five forces model is limited to its static nature. The...
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Evolution of End-User Participation in IT Projects.
PublikacjaThis chapter is aimed at presenting a review of evolutionary design paradigms which determine the end-user’s role in IT (Information Technology) projects across recent decades. This review covers different perspectives starting from technology-oriented sequential software development lifecycles, through user-centred approaches, ending finally in contemporary service design approaches supported by e-business and social media. Finally,...
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CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures
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BALCONY: an R package for MSA and functional compartments of protein variability analysis
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DSC and electrophoretic studies on protein denaturation of Anodonta woodiana (Lea, 1834)
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Zeta potential and droplet size of n-tetradecane/ethanol (protein) emulsions
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