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Search results for: LYME DISEASE, BORRELIA BURGDORFERI SENSU LATO, EPITOPE MAPPING, SERODIAGNOSIS, CHIMERIC PROTEINS
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Multi-agent systems registration and maintenance of address mapping without agent self-registation
PublicationMonitoring of dynamic multi-agent systems, here agents are allowed to appear and disappear, and can migrate between network nodes is a complex tasks. Applying the traditional monitoring methods is not effective, as little can be assumed in advance about such environments. It is necessary to track changes in addressing and availability of agents to create and maintain mapping between agents and their network addresses. The...
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Depth Determination Accuracy of the Modified Prony Method in a Swath Mapping Application
PublicationThis article presents the performance of the modified Prony method in a swath mapping application. Depth determination accuracy is assessed by processing raw signal acquired by an EdgeTech 6205 swath bathymetry system over flat seafloor. An updated version of the method, proposed previously by the authors, is used to determine the number of signal echoes. The number of signal echoes is essential for performing the low-rank approximation...
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Conserved motifs of MutL proteins
PublicationtThe 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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Floodsar: Automatic mapping of river flooding extent from multitemporal SAR imagery
PublicationFloodsar is an open-source tool for automatic mapping of the flood extent from a time series of synthetic aperture radar (SAR) imagery. Floodsar is unsupervised, however, it requires defining the parameters search space, geographical area of interest, and some river gauge observations (e.g. water levels or discharges) time series that overlap temporarily with the SAR imagery. Applications of Floodsar are mainly in real-time monitoring...
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Diverse Expression of Selected SMN Complex Proteins in Humans with Sporadic Amyotrophic Lateral Sclerosis and in a Transgenic Rat Model of Familial Form of the Disease
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The Development of Toxoplasma gondii Recombinant Trivalent Chimeric Proteins as an Alternative to Toxoplasma Lysate Antigen (TLA) in Enzyme-Linked Immunosorbent Assay (ELISA) for the Detection of Immunoglobulin G (IgG) in Small Ruminants
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Automatic classification and mapping of the seabed using airborne LiDAR bathymetry
PublicationShallow coastal areas are among the most inhabited areas and are valuable for biodiversity, recreation and the economy. Due to climate change and sea level rise, sustainable management of coastal areas involves extensive exploration, monitoring, and protection. Current high-resolution remote sensing methods for monitoring these areas include bathymetric LiDAR. Therefore, this study presents a novel methodological approach to assess...
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Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field
PublicationThe physics-based united-residue (UNRES) model of proteins ( www.unres.pl ) has been designed to carry out large-scale simulations of protein folding. The force field has been derived and parameterized based on the principles of statistical-mechanics, which makes it independent of structural databases and applicable to treat nonstandard situations such as, proteins that contain D-amino-acid residues. Powered by Langevin dynamics...
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A bifunctional chimeric protein consisting of MutS and beta-galactosidase
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DAF - and collagen-binding properties of chimeric Dr fimbriae
PublicationEkspozycja białek heterologicznych na powierzchni mikroorganizmów jest jedną z nowych strategii stosowanych w mikrobiologii, biotechnologii oraz projektowaniu nowoczesnych szczepionek. W niniejszej pracy zbadano możliwość wykorzystania białka podjednostkowego DraE fimbrii Dr uropatogennych szczepów Escherichia coli jako nośnika heterologicznych sekwencji. W rejon odpowiadający N-terminalnej domenie 2 białka DraE wprowadzono epitopową...
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A bifunctional chimeric protein consisting of MutS and beta-galactoside
PublicationPraca pokazuje konstrukcję DNA plazmidowego kodującego bifunkcjonalne białko chimeryczne złożone z MutS Thermus thermophilus i beta-galaktozydazy E.coli, optymalizację jego ekspresji i oczyszczania. Białko to testowano w metodzie wykrywania mutacji punktowych, wykorzystując kolorymetryczne mierzenie aktywności domeny reporterowej beta galaktozydazy.
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RecA Proteins from Deinococcus geothermalis and Deinococcus murrayi - Cloning, Purification and Biochemical Characterisation
PublicationEscherichia coli RecA plays a crucial role in recombinational processes, the induction of SOS response and mutagenic lesion bypasses. It has also been demonstrated that RecA protein is indispensable when it comes to the reassembly of shattered chromosomes in gamma-irradiated Deinococcus radiodurans, one of the most radiation-resistant organisms known. Moreover, some functional differences between E. coli and D. radiodurans RecA...
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Nested Space Mapping Technology for Expedite EM-driven Design of Compact RF/microwave Components
PublicationA robust simulation-driven methodology for rapid and reliable design of RF/microwave circuits comprising compact microstrip resonant cells (CMRCs) is presented. We introduce a nested space mapping (NSM) technology, in which the inner space mapping layer is utilized to improve the generalization capabilities of the equivalent circuit model corresponding to a constitutive element of the circuit under consideration. The outer layer...
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Three-dimensional mapping for data collected using variable stereo baseline
PublicationThe paper describes a system of 3D mapping of data collected with due regard for variable baseline. This solution constitute an extension to a VisRobot sub-system developed as a subsystem, necessary for implementing the generic idea of using mobile robots to explore an indoor static environment. This subsystem is to acquire stereo images, calculate the depth in the images and construct the sought 3D map. Stereo images are obtained...
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Reliable low-cost surrogate modeling and design optimisation of antennas using implicit space mapping with substrate segmentation
PublicationAbstract: In this work, a reliable methodology for fast simulation-driven design optimisation of antenna structures is proposed. The authors’ approach exploits implicit space mapping (ISM) technology. To adopt it for handling antenna structures, they introduce substrate segmentation with separate dielectric permittivity value assigned for each segment as ISM preassigned parameters. At the same time, the coarse model for space mapping...
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Density functional theory calculations on entire proteins for free energies of binding: Application to a model polar binding site
PublicationIn drug optimization calculations, the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method can be used to compute free energies of binding of ligands to proteins. The method involves the evaluation of the energy of configurations in an implicit solvent model. One source of errors is the force field used, which can potentially lead to large errors due to the restrictions in accuracy imposed by its empirical nature....
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Fragmentomic analysis of biopeptides in silico released from milk proteins
PublicationThe fragmentomic-assisted method was employed to predict the biological potential of peptides derived from milk proteins hydrolyzed by papain and bromelain. Firstly, protein sequences were acquired from the BIOPEP-UWM database and then hydrolyzed by the above enzymes using a BIOPEP-UWM tool called “Enzyme(s) action”. The released peptides were defined as parent peptides and further analyzed for the presence of shorter peptidic...
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Nested Space Mapping Technique for Design and Optimization of Complex Microwave Structures with Enhanced Functionality
PublicationIn this work, we discuss a robust simulation-driven methodology for rapid and reliable design of complex microwave/RF circuits with enhanced functionality. Our approach exploits nested space mapping (NSM) technology, which is dedicated to expedite simulation-driven design optimization of computationally demanding microwave structures with complex topologies. The enhanced func-tionality of the developed circuits is achieved by means...
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Molecular Recognition in Complexes of TRF Proteins with Telomeric DNA
PublicationTelomeres are specialized nucleoprotein assemblies that protect the ends of linear chromosomes. In humans and many other species, telomeres consist of tandem TTAGGG repeats bound by a protein complex known as shelterin that remodels telomeric DNA into a protective loop structure and regulates telomere homeostasis. Shelterin recognizes telomeric repeats through its two major components known as Telomere Repeat-Binding Factors, TRF1...
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Active dynamic thermography method for TRAM flap blood perfusion mapping in breast reconstruction
PublicationThis paper presents the new method of the transverse rectus abdominis musculocutaneous flap blood perfusion mapping based on the active dynamic thermography. The method is aimed at aiding a surgeon during breast reconstruction procedure. A pair of dTnorm and t90_10 parameters were used as parametric image descriptors of the flap blood perfusion. The method was tested on 38 patients that were subjected to breast reconstruction procedure....
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Mitochondrial DNA levels in Huntington disease leukocytes and dermal fibroblasts
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Rapid EM-Driven Design of Compact RF Circuits By Means of Nested Space Mapping
PublicationA methodology for rapid design of RF circuits constituted by compact microstrip resonant-cells (CMRCs) is presented. Our approach exploits nested space mapping (NSM) technology, where the inner SM layer is used to correct the equivalent circuit model at the CMRC level, whereas the outer layer enhances the coarse model of the entire structure under design. We demonstrate that NSM dramatically improves performance of surrogate-based...
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Scalable Maintenance of Address Mapping and Autodetecion in Environments Where Agents are Uncapable of Self-Registration
PublicationWhen working with multi-agent systems it is often desirable to manage the agent set. The existing methods of central monitoring stems from two different fields of application. The first has its roots in in computer network monitoring, the other in mutli-agent simulation environments. Both approaches are not general enough to cater for loosely controlled environments, where the total agent population is not known and often fluctuating,...
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Knowledge representation of motor activity of patients with Parkinson’s disease
PublicationAn approach to the knowledge representation extraction from biomedical signals analysis concerning motor activity of Parkinson disease patients is proposed in this paper. This is done utilizing accelerometers attached to their body as well as exploiting video image of their hand movements. Experiments are carried out employing artificial neural networks and support vector machine to the recognition of characteristic motor activity...
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Implicit Space Mapping for Variable-Fidelity EM-Driven Design of Compact Circuits
PublicationSpace mapping (SM) belongs to the most successful surrogate-based optimization (SBO) methods in microwave engineering. Among available SM variations, implicit SM (ISM) is particularly attractive due to its simplicity and separation of extractable surrogate model parameters and design variables of the circuit/system at hand. Unlike other SM approaches, ISM exploits a set of preassigned parameters to align the surrogate with the...
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Dynamics of Chains as a Tool to Study Thermomechanical Properties of Proteins.
PublicationPolymer dynamics can be formulated on different levels of detail. One approach eliminates microscopic degrees of freedom and a polymer molecule is represented by a simplified structure—a chain. In the simplest case monomers of ideal chain have fixed length, and their orientation is independent of the orientations and positions of neighbouring monomers. This is reason that two monomers can co-exist at the same place. Ideal chain...
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2-Methoxyestradiol and Hydrogen Peroxide as Promising Biomarkers in Parkinson’s Disease
PublicationEstrogens function in numerous physiological processes including controlling brain cell growth and differentiation. 2-Meth- oxestradiol (2-ME2), a 17β-estradiol (E2) metabolite, is known for its anticancer effects as observed both in vivo and in vitro. 2-ME2 affects all actively dividing cells, including neurons. The study aimed to determine whether 2-ME2 is a potentially cancer-protective or rather neurodegenerative agent in a...
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Gastroesophageal Reflux Disease in Children with Interstitial Lung Disease
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The Application Of A Noise Mapping Tool Deployed In Grid Infrastructure For Creating Noise Maps Of Urban Areas
PublicationThe concept and implementation of the system for creating dynamic noise maps in PL-Grid infrastructure are presented. The methodology of dynamic acoustical maps creating is introduced. The concept of noise mapping, based on noise source and propagation models, was developed and employed in the system. The details of incorporation of the system to the PL-Grid infrastructure are presented. The results of simulations performed by...
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Automatic assessment of the motor state of the Parkinson's disease patient --a case study
PublicationThis paper presents a novel methodology in which the Unified Parkinson's Disease Rating Scale (UPDRS) data processed with a rule-based decision algorithm is used to predict the state of the Parkinson's Disease patients. The research was carried out to investigate whether the advancement of the Parkinson's Disease can be automatically assessed. For this purpose, past and current UPDRS data from 47 subjects were examined. The results...
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DMI measurements impact on a position estimation with lack of GNSS signals during Mobile Mapping
PublicationNowadays, Mobile Laser Scanning is common in use in addition to geodesy measurements. The data which are provided by the system characterizes with high precision and flexibility. To precise mapping, the accuracy of the data should be maintained. In Poland, according to the minister’s dispositions, the accuracy of the data should not exceeded 10 cm. With fully operated system it is easy to uphold, but there is a situation when a...
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Magnetic field mapping along a NV-rich nanodiamond-doped fiber
PublicationIntegration of NV−-rich diamond with optical fibers enables guiding quantum information on the spin state of the NV− color center. Diamond-functionalized optical fiber sensors have been demonstrated with impressive sub-nanotesla magnetic field sensitivities over localized magnetic field sources, but their potential for distributed sensing remains unexplored. The volumetric incorporation of diamonds into the optical fiber core allows...
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A CNN based coronavirus disease prediction system for chest X-rays
PublicationCoronavirus disease (COVID-19) proliferated globally in early 2020, causing existential dread in the whole world. Radiography is crucial in the clinical staging and diagnosis of COVID-19 and offers high potential to improve healthcare plans for tackling the pandemic. However high variations in infection characteristics and low contrast between normal and infected regions pose great challenges in preparing radiological reports....
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Theoretical analysis of a new approach to order determination for a modified Prony method in swath mapping application
PublicationThis article presents a new approach to determine the model order (number of principal components) in the modified Prony method applied to swath acoustic mapping. Determination of the number of principal components is a crucial step in the modified Prony method. In the proposed approach the model order is chosen based on the underlying physical model of the underwater acoustic environment, and utilised signal processing operations....
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Two highly thermostable paralogous single-stranded DNA-binding proteins from Thermoanaerobacter tengcongensis
PublicationThe thermophilic bacterium Thermoanaerobacter tengcongensis has two single-stranded DNA-binding (SSB) proteins, designated TteSSB2 and TteSSB3. In a SSB complementation assay in Escherichia coli, only TteSSB3 took over the in vivo function of EcoSSB. We have cloned the ssb genes obtained by PCR and have developed E. coli overexpression systems. The TteSSB2 and TteSSB3 consist of 153 and 150 amino acids with a calculated molecular...
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Water-mediated long-range interactions between the internal vibrations of remote proteins
PublicationIt is generally acknowledged that the mobility of protein atoms and the mobility of water molecules in the solvation layer are connected. In this article, we answer the question whether a similar interdependence exists between the motions of atoms of proteins separated by the hydration layers of variable thickness. The system consisted of a kinesin catalytic domain and a tubulin dimer. It was studied using molecular dynamics simulations....
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Diagnostics of the Peripheral Artery Disease with use of Glucose Sensor - A Proof of Concept
PublicationIt is estimated that 13% of population over 50 years old suffer from symptomatic or asymptomatic peripheral artery disease (PAD). Ankle-brachial index (ABI) is viewed as a useful parameter in diagnostics of peripheral arterial disease, however screening tests with usage of this method are not advised. Hypoxia causes increase in lactate values and decrease in blood glucose. We hypothesize that the deficit in blood supply to the...
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Diagnostics of the Peripheral Artery Disease with use of Glucose Sensor - A Proof of Concept
PublicationIt is estimated that 13 % of population over 50 years old suffer from symptomatic or asymptomatic peripheral artery disease (PAD). Ankle-brachial index (ABI) is viewed as a useful parameter in diagnostics of peripheral arterial disease, however screening tests with usage of this method are not advised. Hypoxia causes increase in lactate values and...
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Toxoplasma gondii: Chimeric Dr fimbriae as a recombinant vaccine against toxoplasmosis
PublicationW publikacji przedstawiono protekcyjne i immunogenne właściowści chimerycznych fimbrii typu Dr zawierających sekwencje epitopowe antygenów SAG1, MAG1 oraz GRA1 Toxoplasma gondii. Uzyskane wyniki porównano z właściwościami immunogennymi antygenowych białek rekombinantowych oraz poliwalentnego antygenu natywnego. Antygeny rekombinantowe indukują silną odpowiedź immunologiczną i w 89% zapobiegają formowaniu się cyst w mózgu myszy....
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Local-Global Space Mapping for Rapid EM-Driven Design of Compact RF Structures
PublicationIn this work, we introduce a robust and efficient technique for rapid design of compact RF circuits. Our approach exploits two-level space mapping (SM) correction of an equivalent circuit model of the structure under design. The first SM layer (local correction) is utilized to ensure good matching between the equivalent circuit and the electromagnetic model at the component level. On the other hand, the global correction allows...
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Analysis of Mapping within S-module Framework
PublicationW artykule zaprezentowano wyniki prac na podejściem konglomeratowym. Podejście to polega na semantycznym opisywaniu zawartości modułów ontologicznych z wykorzystaniem zdefiniowanej algebry modułów. Głównym osiągnięciem zaprezentowanym w pracy jest opis procesu przekształcania bazy wiedzy DDL w zbiór konglomeratów. Jako że te dwie metody prezentują różne podejścia do modularyzacja, analiza procesu stanowi podstawę do dyskusji na...
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TIME SERIES DATA FOR 3D FLOOD MAPPING
PublicationThanks to the ability to collect information about large areas and with high frequency in time areas threatened by floods can be closely monitored. The effects of flooding are socio-economic losses. In order to reduce those losses, actions related to the determination of building zones are taken. Moreover, the conditions to be met by facilities approved for implementation in such areas are determined. Therefore, satellite data...
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Characterization of exceptionally thermostable single-stranded DNA-binding proteins from Thermotoga maritima and Thermotoga neapolitana
PublicationBACKGROUND: In recent years, there has been an increasing interest in SSBs because they find numerous applications in diverse molecular biology and analytical methods.RESULTS: We report the characterization of single-stranded DNA binding proteins (SSBs) from the thermophilic bacteria Thermotoga maritima (TmaSSB) and Thermotoga neapolitana (TneSSB). They are the smallest known bacterial SSB proteins, consisting of 141 and 142 amino...
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Microbial diversity of inflamed and noninflamed gut biopsy tissues in inflammatory bowel disease.
PublicationBACKGROUND: Inflammatory bowel disease (IBD) is a chronic gastrointestinal condition without any known cause or cure. An imbalance in normal gut biota has been identified as an important factor in the inflammatory process. METHODS: Fifty-eight biopsies from Crohn's disease (CD, n = 10), ulcerative colitis (UC, n = 15), and healthy controls (n = 16) were taken from a population-based case-control study. Automated ribosomal intergenic...
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Accelerated simulation-driven design optimisation of compact couplers by means of two-level space mapping
PublicationIn this study, the authors discuss a robust and efficient technique for rapid design of compact couplers. The approach exploits two-level space mapping (SM) correction of an equivalent circuit model of the coupler structure under design. The first SM layer (local correction) is utilised to ensure good matching between the equivalent circuit and the electromagnetic model at the component level. Subsequent global correction allows...
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Efficient production of the Toxoplasma gondii GRA6, p35 and SAG2 recombinant antigens and their applications in the serodiagnosis of toxoplasmosis
PublicationSkonstruowano system ekspresji rekombinantowych białek antygenowych GRA6, p35 i SAG2 Toxoplasma gondii. Uzyskano miligramowe ilości białek fuzyjnych po zastosowaniu jednoetapowego oczyszczania z wykorzystaniem metody chromatografii metalopowinowactwa. Przydatność otrzymanych antygenów do konstrukcji serologicznego testu diagnostycznego oszacowano z wykorzystaniem testu ELISA, w którym zastosowano 99 surowic pobranych od pacjentów...
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Application of multisensoral remote sensing data in the mapping of alkaline fens Natura 2000 habitat
PublicationThe Biebrza River valley (NE Poland) is distinguished by largely intact, highly natural vegetation patterns and very good conservation status of wetland ecosystems. In 2013⿿2014, studies were conducted in the upper Biebrza River basin to develop a remote sensing method for alkaline fen classification ⿿ a protected Natura 2000 habitat (code 7230) ⿿ using remote sensing technologies. High resolution airborne true colour (RGB) and...
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Analysis of the Factors Affecting Static In Vitro Pepsinolysis of Food Proteins
PublicationIn this meta-analysis, we collected 58 publications spanning the last seven decades that reported static in vitro protein gastric digestion results. A number of descriptors of the pepsinolysis process were extracted, including protein type; pepsin activity and concentration; protein concentration; pH; additives; protein form (e.g., ‘native’, ‘emulsion’, ‘gel’, etc.); molecular weight of the protein; treatment; temperature; and...
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Concentration of proteins in the whey stream
PublicationZastosowano 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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Conservation and diversity of MutS proteins
PublicationThe 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,...