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Search results for: NON-PROTEIN NITROGEN
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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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Novel single-stranded DNA-binding protein from psyvhrophilic bacterium Psychrobacter arcticus
PublicationTo study the biochemical properties of SSB from Psychrobacter arcticus (ParSSB), we have cloned the ssb genes obtained by PCR and have developed Escherichia coli overexpression systems. The gene consists of an open reading frame of 642 nucleotides encoding SSB protein of 213 amino acids with a calculated molecular mass of 22.8 kDa. The amino-acid sequence of ParSSB exhibits 49% identity and 57% similarity to Escherichia coli SSB....
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Structure-based design and evaluation of novel N-phenyl-1H-indol-2-amine derivatives for fat mass and obesity-associated (FTO) protein inhibition
PublicationFat mass and obesity-associated (FTO) protein contributes to non-syndromic human obesity which refers to excessive fat accumulation in human body and results in health risk. FTO protein has become a promising target for anti-obesity medicines as there is an immense need for the rational design of potent inhibitors to treat obesity. In our study, a new scaffold N-phenyl-1H-indol-2-amine was selected as a base for FTO protein inhibitors...
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X-ray diffraction spectra of nitrogen-doped carbon in hybrid materials containing praseodymium oxide
Open Research DataX-ray powder diffraction patterns of samples were carried out by Philips X’Pert diffractometer, which was radiated by graphite monochromatized Cu Kα (l equal 1.540598). The operating voltage was maintained at 40 kV, the current was maintained at 30 mA and analyzed in the range from 20° to 90°. The data presented confirmed the presence of the PrBSCF...
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Nonlinear Excitation of the Non-Wave Perturbations by the Magnetoacoustic Waves in the Non-Isentropic Plasma
PublicationNonlinear excitation of slow modes by the planar magnetosonic perturbations in a plasma is discussed. Plasma is an open system due to radiation and external heating. This may stipulate enhancement of wave perturbations and hence the acoustical activity of plasma. Plasma is assumed to be a homogeneous ideal gas with infinite electrical conductivity. The straight magnetic field is orthogonal to the velocity of fluid’s...
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Dimeric structure of the N-terminal domain of PriB protein from Thermoanaerobacter tengcongensis solved ab initio
PublicationPriB is one of the components of the bacterial primosome, which catalyzes the reactivation of stalled replication forks at sites of DNA damage. The N-terminal domain of the PriB protein from the thermophilic bacterium Thermoanaerobacter tengcongensis (TtePriB) was expressed and its crystal structure was solved at the atomic resolution of 1.09 Å by direct methods. The protein chain, which encompasses the first 104 residues of the...
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Aqueous solutions of NMA, Na2HPO4 , and NaH2PO4 as models for interaction studies in phosphate–protein systems
PublicationPhosphate buffers are essential for many areas of studies. However, their influence on buffered systems is often ignored. The phosphate salts can interact with biologically important macromolecules (e.g. proteins) and stabilize or destabilize them. With our research, we want to answer question what kind of interactions, if any, occur between phosphate ions and a protein backbone model — N-methylacetamide (NMA). ATR-FTIR spectroscopy...
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Electrical responses of Graphene-Silicon Schottky diodes toward nitrogen dioxide and tetrahydrofuran under irradiation
Open Research DataGraphene-Silicon Schottky junctions were utilized as gas sensors toward inorganic (nitrogen dioxide) and organic (tetrahydrofuran) gas qualitative and quantitative detection. The electrical responses of the sensors were collected in the form of current-voltage characteristics and measurements of current in time domain for a selected voltage bias. The...
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Non-Newtonian Mathematics Instead of Non-Newtonian Physics: Dark Matter and Dark Energy from a Mismatch of Arithmetics
PublicationNewtonian physics is based on Newtonian calculus applied to Newtonian dynamics. New paradigms such as ‘modified Newtonian dynamics’ (MOND) change the dynamics, but do not alter the calculus. However, calculus is dependent on arithmetic, that is the ways we add and multiply numbers. For example, in special relativity we add and subtract velocities by means of addition β1⊕β2=tanh(tanh−1(β1)+tanh−1(β2)), although multiplication β1⊙β2=tanh(tanh−1(β1)⋅tanh−1(β2)),...
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Fatty acyl benzamido antibacterials based on inhibition of DnaK-catalyzed protein folding
PublicationWe have reported that the hsp70 chaperone DnaK from Escherichia coli might assist protein folding by catalyzing the cis/trans isomerization of secondary amide peptide bonds in unfolded or partially folded proteins. In this study a series of fatty acylated benzamido inhibitors of the cis/trans isomerase activity of DnaK was developed and tested for antibacterial effects in E. coli MC4100 cells. Nα-[Tetradecanoyl-(4-aminomethylbenzoyl)]-l-asparagine...
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Mariusz Kaczmarek dr hab. inż.
PeopleReceived M.Sc., Eng. in Electronics in 1995 from Gdansk University of Technology, Ph.D. in Medical Electronics in 2003 and habilitation in Biocybernetics and Biomedical Engineering in 2017. He was an investigator in about 13 projects receiving a number of awards, including four best papers, practical innovations (7 medals and awards) and also the Andronicos G. Kantsios Award and Siemens Award. Main research activities: the issues...
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Photoelectrochemical characterization of nitrogen-modified TiO2
PublicationTrzy próbki tlenku tytanu(IV) o różnej zawartości azotu i różnych właściwościach fotokatalitycznych zostały wybrane do charakterystyki fotoelektrochemicznej. Efektem finalnym jest określenie położenia pasma wzbronionego i pasma przewodzenia w otrzymanych półprzewodnikach.
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Toxoplasma gondii Recombinant antigen AMA1: Diagnostic Utility of Protein Fragments for the Detection of IgG and IgM Antibodies
PublicationToxoplasma gondii is an important zoonotic protozoan that infects a wide variety of vertebrates as intermediate hosts. For this reason, the diagnosis of this disease is very important and requires continuous improvement. One possibility is to use recombinant antigens in serological tests. Apical membrane antigen 1 (AMA1), a protein located in specific secretory organelles (micronemes) of T. gondii, is very interesting in regard...
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INTERNATIONAL JOURNAL OF NON-LINEAR MECHANICS
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How water mediates the long-range interactions between remote protein molecules
PublicationThe high crowding of macromolecules in the cytoplasm affects the processes that occur inside a living cell. It can, for example, promote the forming of various loosely connected structures of proteins. It also means that bulk water is, essentially, not present there. The relatively thin layer of solvent that separates macromolecules may be able to participate in the long-range interactions between them and make them respond to...
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Special Issue: “Non-Destructive Testing of Structures”
PublicationThe Special Issue “Non-Destructive Testing of Structures” has been proposed to present recent developments in the field of diagnostics of structural materials and components in civil and mechanical engineering. The papers highlighted in this editorial concern various aspects of non-invasive diagnostics, including such topics as condition assessments of civil and mechanical structures and connections of structural elements, the...
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Potential and limits of landfill leachate treatment in a multi-stage subsurface flow constructed wetland – evaluation of organics and nitrogen removal
PublicationConstructed wetlands have potential of treating wastewater of poor biodegradability. The performance of a multistage sub-surface flow wetland treating municipal landfill leachate was assessed during three years of operation. During the study three research periods with different operation conditions were established. The hydralic loads, operation mode of vertical flow beds and type of treated wastewater (raw leachate – leachate...
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Structure of solvation water around the active and inactive regions of a type III antifreeze protein and its mutants of lowered activity
PublicationWater molecules from the solvation shell of the ice-binding surface are considered important for the antifreeze proteins to perform their function properly. Herein, we discuss the problem whether the extent of changes of the mean properties of solvation water can be connected with the antifreeze activity of the protein. To this aim, the structure of solvation water of a type III antifreeze protein from Macrozoarces americanus (eel...
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Non-destructive Testing of Wooden Elements
PublicationExamining the condition of wooden elements is crucial from the perspective of proper structure performance. If the deterioration in the internal wood condition, which displays no symptoms visible from the outside, is detected, the further spread of the deterioration can be prevented. Test results often point to the necessity of conducting repairs and, renovations, replacing the structure of wooden beams, or even substituting a...
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Integration of protein tethering in a rapid and label-free SERS screening platform for drugs of abuse
PublicationSurface enhanced Raman spectroscopy (SERS) has emerged as a promising technique for the rapid and ultrasensitive detection of molecular species such as drugs of abuse in biofluids. Yet, it remains a significant challenge to create a viable screening tool for multiple drug classes, owing to the lack of affinity of certain species for the SERS substrate and to the matrix interference in complex media. Here we report a protein tethering...
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The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields?
PublicationPreorganization of large, directionally oriented, electric fields inside protein active sites has been proposed as a crucial contributor to catalytic mechanism in many enzymes, and it may be efficiently investigated at the atomistic level with molecular dynamics simulations. Here, we evaluate the ability of the AMOEBA polarizable force field, as well as the additive Amber ff14SB and Charmm C36m models, to describe the electric...
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The Unfolded Protein Response: A Double-Edged Sword for Brain Health
PublicationEfficient 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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Discrete identification of continuous non-linear and non-stationary dynamical systems that is insensitive to noise correlation and measurement outliers
PublicationThe paper uses specific parameter estimation methods to identify the coefficients of continuous-time models represented by linear and non-linear ordinary differential equations. The necessary approximation of such systems in discrete time in the form of utility models is achieved by the use of properly tuned `integrating filters' of the FIR type. The resulting discrete-time descriptions retain the original continuous parameterization...
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Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment
PublicationThe UNited RESidue (UNRES) force field was tested in the 14th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP14), in which larger oligomeric and multimeric targets were present compared to previous editions. Three prediction modes were tested (i) ab initio (the UNRES group), (ii) contact-assisted (the UNRES- contact group), and (iii) template-assisted (the UNRES-template...
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Optical emission spectroscopy study for nitrogen–acetylene–argon and nitrogen–acetylene–helium 100 kHz and dc discharges
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Near-Infrared-Triggered Nitrogen Fixation over Upconversion Nanoparticles Assembled Carbon Nitride Nanotubes with Nitrogen Vacancies
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Combined partial denitrification/anammox process for nitrogen removal in wastewater treatment
PublicationRecently, the combined partial denitrification and anammox (PD/anammox) has received special attention as a viable alternative for N removal using organic matter present in municipal wastewater. In comparison with conventional nitrification-denitrification, PD/anammox provides enormous opportunities to achieve sustainable wastewater treatment due to the lack of dissolved oxygen (DO) demand, a smaller amount of organic carbon (C)...
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Fabrication of anti-corrosion nitrogen doped graphene oxide coatings by electrophoretic deposition
PublicationThis work assesses anti-corrosion properties of graphene and N-doped graphene coatings deposited on copper by an electrophoretic method. Graphene oxide (GO) precursor was synthesized by an improved Hummers' method, whereas N-doping was performed hydrothermally in the presence of ammonia. After nitrogenation, doped graphene oxide samples (NGO) contained a reduced amount of oxygen and about 9% w/w nitrogen as pyridinic, pyrrole,...
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Colloidal aspects of protein digestion
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Alternative and New Protein Sources
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Stabilizing agents and protein stability
PublicationBiałka są kluczowymi elementami żywych organizmów, jak również efektywnymi katalizatorami w biotechnologii i medycynie. Szybki rozwój wielu gałęzi biotechnologii wiąże się z coraz większym zapotrzebowaniem na produkty białkowe charakteryzujące się wysoką stabilnością. Jednym ze sposobów osiągnięcia większej stabilności białek jest wykorzystanie małych związków organicznych, tzw. osmolitów. Do tej grupy związków należą aminokwasy,...
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Mixed neuroendocrine non-neuroendocrine neoplasm (MiNEN) - Male, 65 - Tissue image [3200630011576491]
Open Research DataThis is the histopathological image of STOMACH tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Mixed neuroendocrine non-neuroendocrine neoplasm (MiNEN) - Male, 65 - Tissue image [3200630011574561]
Open Research DataThis is the histopathological image of STOMACH tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Influence of hydrochloric acid concentration and type of nitrogen source on the electrochemical performance of TiO2/N-MoS2 for energy storage applications
PublicationIn this work, nitrogen-doped molybdenum sulfide was directly deposited on titanium dioxide nanotubes substrate (TiO2/N-MoS2) during hydrothermal synthesis. The study focuses on the influence of hydrochloric acid concentration used for the synthesis, with the results indicating its essential role in thioacetamide hydrolysis and thus in the effectiveness of the N-MoS2 deposition. The electrode material itself is characterized by...
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Generation and Characterization of a DNA-GCN4 Oligonucleotide-Peptide Conjugate: The Impact DNA/Protein Interactions on the Sensitization of DNA
PublicationRadiotherapy, the most common therapy for the treatment of solid tumors, exerts its effects by inducing DNA damage. To fully understand the extent and nature of this damage, DNA models that mimic the in vivo situation should be utilized. In a cellular context, genomic DNA constantly interacts with proteins and these interactions could influence both the primary radical processes (triggered by ionizing radiation) and secondary reactions,...
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Impact of influent wastewater quality on nitrogen removal rates in multistage treatment wetlands
PublicationNitrogen removal in treatment wetlands is influenced by many factors, and the presence of electron donors (biodegradable organic matter) and electron acceptors (nitrate ions) is the main limiting one; for obtaining these conditions, multistage treatment wetlands (MTWs) are required, where an extensive nitrification can be obtained in the first stages under aerobic conditions leaving then to the following anoxic/anaerobic stages...
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Mixed neuroendocrine non-neuroendocrine neoplasm (MiNEN) - Male, 65 - Tissue image [3200630011579601]
Open Research DataThis is the histopathological image of LYMPH NODES tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Mixed neuroendocrine non-neuroendocrine neoplasm (MiNEN) - Male, 65 - Tissue image [32006300115761]
Open Research DataThis is the histopathological image of LYMPH NODES tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Mixed neuroendocrine non-neuroendocrine neoplasm (MiNEN) - Male, 65 - Tissue image [3200630011575841]
Open Research DataThis is the histopathological image of LYMPH NODES tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Mixed neuroendocrine non-neuroendocrine neoplasm (MiNEN) - Male, 65 - Tissue image [3200630011571551]
Open Research DataThis is the histopathological image of LYMPH NODES tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Novel DNA-binding protein from Nanoarchaeum equitans Kin4-M binds all kinds of nucleic acids
PublicationNanoarchaeum equitans is the only known representative of Archaea phylum Nanoarchaeota and stands out as one of the tiniest known living organism. What is more it has smallest genome, which is only 490.885 base pairs long. It is also one of the most compact genomes. According to predictions about 95% of the DNA encodes proteins or stable RNA. Nanoarchaeum equitans lacks genes for most vital metabolic pathways including lipid, cofactor,...
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A study on the interaction of rhodamine B with methylthioadenosine phosphorylase protein sourced from an Antarctic soil metagenomic library.
PublicationThe presented study examines the phenomenon of the fluorescence under UV light excitation (312 nm) of E. coli cells expressing a novel metagenomic-derived putative methylthioadenosine phosphorylase gene, called rsfp, grown on LB agar supplemented with a fluorescent dye rhodamine B. For this purpose, an rsfp gene was cloned and expressed in an LMG194 E. coli strain using an arabinose promoter. The resulting RSFP protein was purified...
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Fe local structure in Pt-free nitrogen-modified carbon based electrocatalysts: XAFS study
PublicationThe paper presents a new results on the bonding environment (coordination number and geometry) and on oxidation states of Fe in nitrogen-modified Fe/C composites used as Pt-free catalysts for oxygen reduction in Direct Hydrogen Fuel Cells. Starting from glucose or fructose, two catalysts displaying different electrochemical performance were prepared and studied in the form of pristine powder and thin catalytic layer of electrode...
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Integrating conventional nitrogen removal with anammox in wastewater treatment systems: Microbial metabolism, sustainability and challenges
PublicationThe various forms of nitrogen (N), including ammonium (NH4+), nitrite (NO2−), and nitrate (NO3−), present in wastewaters can create critical biotic stress and can lead to hazardous phenomena that cause imbalances in biological diversity. Thus, biological nitrogen removal (BNR) from wastewaters is considered to be imperatively urgent. Therefore, anammox-based systems, i.e. partial nitrification and anaerobic ammonium oxidation (PN/anammox)...
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Identification of evolutionary conserved DNA sequence and corresponding S21 ribosomal protein region for diagnostic purposes of all Borrelia spirochetes
PublicationIt is still under investigation, whether all Borrelia sp. causing Lyme borreliosis and other diseases are already identified and properly classified as human pathogens. For this reason, it is of great importance to develop a diagnostic ELISA test that detects all Borrelia sp. The aim of this study was to identify conserved DNA and protein regions present in all currently known Borrelia sp. In experimental studies 31 available Borrelia...
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Quality Control of Bacterial Extracellular Vesicles with Total Protein Content Assay, Nanoparticles Tracking Analysis, and Capillary Electrophoresis
PublicationExtracellular vesicles (EVs) were isolated from Pectobacterium zantedeschiae culturing media using direct ultracentrifugation (UC), iodixanol cushion ultracentrifugation (ICUC), and iodixanol density gradient ultracentrifugation (IDGUC) techniques. The isolates were characterized with total protein content assay (bicinchoninic acid assay, BCA), nanoparticles tracking analysis (NTA), and capillary electrophoresis (CE). A satisfactory...
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Nitrogen-incorporated boron-doped diamond films for enhanced electrochemical supercapacitor performance
PublicationThe electrochemical (EC) supercapacitor, known for its rapid charging, reliability, and versatile applications, demands optimized electrode characteristics and an understanding of their electrochemical behaviour. Although boron-doped diamond (BDD) holds promise as a supercapacitor electrode, a crucial gap exists in comprehending its material behaviour under specific growth conditions. Here, nitrogen-incorporated BDD (N-BDD) films...
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Endocrine responses following exhaustive strength exercise with and without the use of protein and protein-carbohydrate supplements
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Sequence variants of p21 gene of the MRL/MpJ mouse: a possible association with the deficit of p21 protein and regenerative phenotype.
PublicationThe MRL/MpJ mouse is known for its enhanced regeneration abilities that manifested themselves by scarless ear-hole wound closure. The deficit of p21 found in the MRL is associated with the regenerative capacity as the p21 gene knockout in a mouse strain unrelated to the MRL mouse results in an ear-hole closure effect, similar to that observed in the MRL mouse. Cdkn1a gene encodes p21 protein, a cyclin-dependent kinase inhibitor,...
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Non-Diophantine Arithmetics in Mathematics, Physics and Psychology
PublicationFor a long time, all thought there was only one geometry — Euclidean geometry. Nevertheless, in the 19th century, many non-Euclidean geometries were discovered. It took almost two millennia to do this. This was the major mathematical discovery and advancement of the 19th century, which changed understanding of mathematics and the work of mathematicians providing innovative insights and tools for mathematical research and applications...