Search results for: draft genome sequence
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Reliable underwater communication system for shallow coastal waters
PublicationThis paper presents a reliable and robust low data rate spread spectrum approach which is implemented in the acoustic underwater communication system for shallow coastal waters. It shows operation assumptions of spread spectrum techniques based on the wellknown Shannon equation. It describes two methods of spread spectrum: frequency hopping spread spectrum and direct sequence spread spectrum; their block diagram and their characteristics...
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Evolutionary music composition system with statistically modeled criteria
PublicationThe paper concerns an original evolutionary music composition system. On the basis of available solutions, we have selected a finite set of music features which appear to have a key impact on the quality of composed musical phrases. Evaluation criteria have been divided into rule-based and statistical sub-sets. Elements of the cost function are modeled using a Gaussian distribution defined by the expected value and variance obtained...
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Average Size of a Suffix Tree for Markov Sources
PublicationWe study a suffix tree built from a sequence generated by a Markovian source. Such sources are more realistic probabilistic models for text generation, data compression, molecular applications, and so forth. We prove that the average size of such a suffix tree is asymptotically equivalent to the average size of a trie built over n independentsequences from the same Markovian source. This equivalenceis only known for memoryless...
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Identification and cloning of C. albicans SC5314 genes encoding L-methionine biosynthetic pathway enzymes.
Open Research DataEnzymes of fungal L-methionine biosynthetic pathway: homoserine O-acetyltransferase (Met2p), O-acetylhomoserine sulfhydrylase (Met15p) and cystathionine-γ-synthase (Str2p) could be exploited as molecular targets for antifungal chemotherapy. The goal of the study was to identify and clone genes encoding mentioned above enzymes. MET2, MET15 and STR2 genes...
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Initial geometries and MD trajectories of right- and left-handed G-quadruplexes
Open Research DataDataset contains initial geometries of 12 monomeric, 2-tetrad G-quadruplexes featuring three different loop lengths (T1, T2 and T3), adapted by the sequence GGTnGGTnGGTnGG where n=(1-3). For each loop length variant two directions of strand progression (clockwise (+) and anti-clockwise (-)) and two helicities (left-handed (LH) and right-handed (RH))...
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Regularized Local Basis Function Approach to Identification of Nonstationary Processes
PublicationThe problem of identification of nonstationary stochastic processes (systems or signals) is considered and a new class of identification algorithms, combining the basis functions approach with local estimation technique, is described. Unlike the classical basis function estimation schemes, the proposed regularized local basis function estimators are not used to obtain interval approximations of the parameter trajectory, but provide...
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Epigenetic Basis of Regeneration: Analysis of Genomic DNA Methylation Profiles in the MRL/MpJ Mouse
PublicationEpigenetic regulation plays essential role in cell differentiation and dedifferentiation, which are the intrinsic processes involved in regeneration. To investigate the epigenetic basis of regeneration capacity, we choose DNA methylation as one of the most important epigenetic mechanisms and the MRL/MpJ mouse as a model of mammalian regeneration known to exhibit enhanced regeneration response in different organs. We report the...
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Extracting functional groups of ALLINI to design derivatives of FDA‐approved drugs: Inhibition of HIV‐1 integrase
PublicationHIV‐1 integrase (IN) is crucial for integration of viral DNA into the host genome and a promising target in development of antiretroviral inhibitors. In this work, six new compounds were designed by linking the structures of two different class of HIV‐1 IN inhibitors (active site binders and allosteric IN inhibitors (ALLINIs)). Among newly designed compounds, INRAT10b was found most potent HIV‐1 IN inhibitor considering different...
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Probiotic potential of Bacillus Isolates from Polish Bee Pollen and Bee Bread
PublicationThe main goal of this study was the evaluation of the probiotic potential of 10 Bacillus spp. strains isolated from 5 bee bread and 3 bee pollen samples. The antagonistic interaction with Staphylococcus aureus and Escherichia coli was a primary criterion for the preliminary selection of the isolates. Three out of ten strains—PY2.3 (isolated from pollen), BP20.15 and BB10.1 (both isolated from bee bread)—were found to be possible...
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Identification and characterization of single-stranded DNA-binding protein from the facultative psychrophilic bacteria Pseudoalteromonas haloplanktis
PublicationSingle-stranded DNA-binding protein (SSB) plays an important role in DNA metabolism such as DNAreplication, repair, and recombination, and is essential for cell survival. This study reports on the ssb-likegene cloning, gene expression and characterization of a single-stranded DNA-binding protein of Pseudoal-teromonas haloplanktis (PhaSSB) and is the first report of such a protein from psychrophilic microorganism.PhaSSB possesses...
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A new division of bacterial UvrA homologues
PublicationThe UvrA protein is a DNA-binding and damage-recognition enzyme which participates in the prokaryotic type nucleotide excision repair (NER) pathway. It has recently been noted that some bacterial genomes comprise additional uvrA genes which encode five distinct types of UvrA homologue. We investigated the sequences of over 2400 bacterial genomes and found 130 examples of bacteria containing uvrA 2 genes. The sequence analyses conducted...
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Localization of impulsive disturbances in archive audio signals using predictive matched filtering
PublicationThe problem of elimination of impulsive disturbances from archive audio signals is considered and its new solution, called predictive matched filtering, is proposed. The new approach is based on the observation that a large percentage of noise pulses corrupting archive audio recordings have highly repetitive shapes that match several typical “patterns”, called click templates. To localize noise pulses, click templates can be correlated...
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Molecular Strategy for Survival at a Critical High Temperature in Eschierichia coli
PublicationThe molecular mechanism supporting survival at a critical high temperature (CHT) in Escherichia coli was investigated. Genome-wide screening with a single-gene knockout library provided a list of genes indispensable for growth at 47°C, called thermotolerant genes. Genes for which expression was affected by exposure to CHT were identified by DNA chip analysis. Unexpectedly, the former contents did not overlap with the latter except...
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An examination of an Antarctic soil metagenomic-derivate putative methylthioadenosine phosphorylase gene as a novel reporter gene for promoter trapping
PublicationThe rsfp gene was discovered during examination ofan Antarctic soil-derived metagenome library and encodesa bacterial methylthioadenosine phosphorylase (GenBank accession number GQ202582). In a previous study, we found that E. coli colonies expressing the rsfp gene reveal strong pink fluorescence after exposure to UV light when grown on culture medium supplemented with rhodamine B (Cieśliński et al., 2009). In contrast to that,...
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Selected manufacturing difficulties encountered during setup of machining on cnc multi-axis linear automatic lathe and on cnc multi-spindle turning centers
PublicationThe article presents the observed manufacturing technology implementation difficulties in workshop practice, resulting from the construction and principles of operation on the DMG’s SPRINT 32/5 CNC linear automatic lathe and on the Mazak’s HQR 150 MSY and QTN 200 MS CNC turn - mill centers, and discusses possible rules for solving the production problems encountered. The article also discusses the principles of dividing the machining...
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A New Double Digestion Ligation Mediated Suppression PCR Method for Simultaneous Bacteria DNA-Typing and Confirmation of Species: An Acinetobacter sp. Model
PublicationWe have designed a new ddLMS PCR (double digestion Ligation Mediated Suppression PCR) method based on restriction site polymorphism upstream from the specific target sequence for the simultaneous identification and differentiation of bacterial strains. The ddLMS PCR combines a simple PCR used for species or genus identification and the LM PCR strategy for strain differentiation. The bacterial identification is confirmed in the...
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Development and evaluation of RADA-PDGF2 self-assembling peptide hydrogel for enhanced skin wound healing
PublicationBackground: Wound healing complications affect numerous patients each year, creating significant economic and medical challenges. Currently, available methods are not fully effective in the treatment of chronic or complicated wounds; thus, new methods are constantly sought. Our previous studies showed that a peptide designated as PDGF2 derived from PDGF-BB could be a promising drug candidate for wound treatment and that RADA16-I...
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3D printed ABS thermoplastic vs. steel. Dry sliding wear test in constant load & velocity ring on flat configuration. Test parameters: print layer thickness and orientation. Test symbol: 009_v_2
Open Research DataData gathered in sliding ring-on-block (flat contact) tribological experiment. Materials: alloy steel (heat treated) vs. ABS plastic.
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3D printed ABS thermoplastic vs. steel. Dry sliding wear test in constant load & velocity ring on flat configuration. Test parameters: print layer thickness and orientation. Test symbol: 009_v_3
Open Research DataData gathered in sliding ring-on-block (flat contact) tribological experiment. Materials: alloy steel (heat treated) vs. ABS plastic.
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3D printed ABS thermoplastic vs. steel. Dry sliding wear test in constant load & velocity ring on flat configuration. Test parameters: print layer thickness and orientation. Test symbol: 009_h_3
Open Research DataData gathered in sliding ring-on-block (flat contact) tribological experiment. Materials: alloy steel (heat treated) vs. ABS plastic.
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3D printed ABS thermoplastic vs. steel. Dry sliding wear test in constant load & velocity ring on flat configuration. Test parameters: print layer thickness and orientation. Test symbol: 019_v_5
Open Research DataData gathered in sliding ring-on-block (flat contact) tribological experiment. Materials: alloy steel (heat treated) vs. ABS plastic.
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3D printed ABS thermoplastic vs. steel. Dry sliding wear test in constant load & velocity ring on flat configuration. Test parameters: print layer thickness and orientation. Test symbol: 009_h_5
Open Research DataData gathered in sliding ring-on-block (flat contact) tribological experiment. Materials: alloy steel (heat treated) vs. ABS plastic.
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3D printed ABS thermoplastic vs. steel. Dry sliding wear test in constant load & velocity ring on flat configuration. Test parameters: print layer thickness and orientation. Test symbol: 009_h_4
Open Research DataData gathered in sliding ring-on-block (flat contact) tribological experiment. Materials: alloy steel (heat treated) vs. ABS plastic.
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3D printed ABS thermoplastic vs. steel. Dry sliding wear test in constant load & velocity ring on flat configuration. Test parameters: print layer thickness and orientation. Test symbol: 039_h_4
Open Research DataData gathered in sliding ring-on-block (flat contact) tribological experiment. Materials: alloy steel (heat treated) vs. ABS plastic.
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3D printed ABS thermoplastic vs. steel. Dry sliding wear test in constant load & velocity ring on flat configuration. Test parameters: print layer thickness and orientation. Test symbol: 019_v_4
Open Research DataData gathered in sliding ring-on-block (flat contact) tribological experiment. Materials: alloy steel (heat treated) vs. ABS plastic.
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3D printed ABS thermoplastic vs. steel. Dry sliding wear test in constant load & velocity ring on flat configuration. Test parameters: print layer thickness and orientation. Test symbol: 019_h_5
Open Research DataData gathered in sliding ring-on-block (flat contact) tribological experiment. Materials: alloy steel (heat treated) vs. ABS plastic.
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3D printed ABS thermoplastic vs. steel. Dry sliding wear test in constant load & velocity ring on flat configuration. Test parameters: print layer thickness and orientation. Test symbol: 039_v_4
Open Research DataData gathered in sliding ring-on-block (flat contact) tribological experiment. Materials: alloy steel (heat treated) vs. ABS plastic.
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3D printed ABS thermoplastic vs. steel. Dry sliding wear test in constant load & velocity ring on flat configuration. Test parameters: print layer thickness and orientation. Test symbol: 009_v_4
Open Research DataData gathered in sliding ring-on-block (flat contact) tribological experiment. Materials: alloy steel (heat treated) vs. ABS plastic.
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3D printed ABS thermoplastic vs. steel. Dry sliding wear test in constant load & velocity ring on flat configuration. Test parameters: print layer thickness and orientation. Test symbol: 039_v_3
Open Research DataData gathered in sliding ring-on-block (flat contact) tribological experiment. Materials: alloy steel (heat treated) vs. ABS plastic.
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3D printed ABS thermoplastic vs. steel. Dry sliding wear test in constant load & velocity ring on flat configuration. Test parameters: print layer thickness and orientation. Test symbol: 019_v_3
Open Research DataData gathered in sliding ring-on-block (flat contact) tribological experiment. Materials: alloy steel (heat treated) vs. ABS plastic.
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3D printed ABS thermoplastic vs. steel. Dry sliding wear test in constant load & velocity ring on flat configuration. Test parameters: print layer thickness and orientation. Test symbol: 019_h_3
Open Research DataData gathered in sliding ring-on-block (flat contact) tribological experiment. Materials: alloy steel (heat treated) vs. ABS plastic.
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3D printed ABS thermoplastic vs. steel. Dry sliding wear test in constant load & velocity ring on flat configuration. Test parameters: print layer thickness and orientation. Test symbol: 039_h_5
Open Research DataData gathered in sliding ring-on-block (flat contact) tribological experiment. Materials: alloy steel (heat treated) vs. ABS plastic.
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3D printed ABS thermoplastic vs. steel. Dry sliding wear test in constant load & velocity ring on flat configuration. Test parameters: print layer thickness and orientation. Test symbol: 019_h_4
Open Research DataData gathered in sliding ring-on-block (flat contact) tribological experiment. Materials: alloy steel (heat treated) vs. ABS plastic.
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3D printed ABS thermoplastic vs. steel. Dry sliding wear test in constant load & velocity ring on flat configuration. Test parameters: print layer thickness and orientation. Test symbol: 039_v_2
Open Research DataData gathered in sliding ring-on-block (flat contact) tribological experiment. Materials: alloy steel (heat treated) vs. ABS plastic.
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3D printed ABS thermoplastic vs. steel. Dry sliding wear test in constant load & velocity ring on flat configuration. Test parameters: print layer thickness and orientation. Test symbol: 039_h_3
Open Research DataData gathered in sliding ring-on-block (flat contact) tribological experiment. Materials: alloy steel (heat treated) vs. ABS plastic.
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Novel Interpolation Method of Multi-DFT-Bins for Frequency Estimation of Signal with Parameter Step Change
PublicationThe IpDFT(Interpolation Discrete Fourier Trans-form) method is one of the most commonly used non-parametric methods. However, when a parameter (frequency, amplitude or phase) step changes in the DFT period, the DFT coefficients will be distorted seriously, resulting in the large estimation error of the IpDFT method. Hence, it is a key challenge to find an IpDFT method, which not only can eliminate the effect of the step-changed...
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Modeling and Evaluation of Electric Treeing Phenomena in Polymeric Cable Insulation
PublicationThis paper investigates the treeing phenomenon in polymeric materials such as crosslinked polyethylene (XLPE) that is widely used in medium and high voltage power cables as primary insulation. The modeling of electrical tree growth in the insulation from its initiation to breakdown is significant research work that illustrates the discharge dynamics and its impact on aging process in polymeric insulation. This study utilizes pulse...
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Trajectory planning for Service Ship during emergency STS transfer operation
PublicationIn this paper trajectory for approaching during emergency STS transfer operation with oil spill is considered as a sequence of navigation manoeuvres in specific navigational environment. The designed way points - ship positions and speed are determined as reference values to support navigator in decision making during steering and to mitigate the risk of collision which mostly results from exceeding the speed limit of approaching....
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Homoclinics for singular strong force Lagrangian systems in R^N
PublicationWe will be concerned with the existence of homoclinics for second order Hamiltonian systems in R^N (N>2) given by Hamiltonians of the form H(t,q,p)=Φ(p)+V(t,q), where Φ is a G-function in the sense of Trudinger, V is C^2-smooth, periodic in the time variable, has a single well of infinite depth at a point ξ and a unique strict global maximum 0 at the origin. Under a strong force type condition aroud the singular point ξ, we prove...
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Novel method of lung area extraction in chest perfusion computed tomography
PublicationChest perfusion computed tomography (pCT) is a useful technique in the medical diagnosis of how organs function. Perfusion CT scans are used to calculate perfusion parameters. In the case of automated methods of lung perfusion parameters calculation, the prior extraction of the lung area is desired to avoid unnecessary calculation in an area outside the lung cross-section and to avoid wasting time on processing signals of no diagnostic...
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Neural networks and deep learning
PublicationIn this chapter we will provide the general and fundamental background related to Neural Networks and Deep Learning techniques. Specifically, we divide the fundamentals of deep learning in three parts, the first one introduces Deep Feed Forward Networks and the main training algorithms in the context of optimization. The second part covers Convolutional Neural Networks (CNN) and discusses their main advantages and shortcomings...
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Comparative analysis of mRNA transcripts of HT-29 cell line expressed in identical quantities for pathogenic E. coli strains UM146 and UM147 with control Escherichia coli Nissle 1917
PublicationAim of study was comparative analysis of mRNA transcripts of HT-29 cell line, expressed in identical quantities for the combination of pathogenic and non-pathogenic Escherichia coli strains. HT-29 confluent monolayers infection with two pathogenic E. coli strains UM146 and UM147 resulted in two sets of mRNA transcripts that were identical with RNA transcripts obtained for non-pathogenic one strain E. coli Nissle 1917. In this study...
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Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules
PublicationSingle-particle cryogenic electron microscopy (cryo-EM) has revolutionized the field of the structural biology, providing an access to the atomic resolution structures of large biomolecular complexes in their near-native environment. Today’s cryo-EM maps can frequently reach the atomic-level resolution, while often containing a range of resolutions, with conformationally variable regions obtained at 6 Å or worse. Low resolution...
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Bortezomib induces methylation changes in neuroblastoma cells that appear to play a significant role in resistance development to this compound
PublicationThe anticancer activity of bortezomib (BTZ) has been increasingly studied in a number of indications and promising results for the use of this treatment have been shown in neuroblastoma. As BTZ treatment is usually administered in cycles, the development of resistance and side effects in patients undergoing therapy with BTZ remains a major challenge for the clinical usage of this compound. Common resistance development also means...
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Convex set of quantum states with positive partial transpose analysed by hit and run algorithm
PublicationThe convex set of quantum states of a composite K×K system with positive partial transpose is analysed. A version of the hit and run algorithm is used to generate a sequence of random points covering this set uniformly and an estimation for the convergence speed of the algorithm is derived. For K >3 or K=3 this algorithm works faster than sampling over the entire set of states and verifying whether the partial transpose is positive....
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Fusion of DNA-binding domain of Pyrococcus furiosus ligase with TaqStoffel DNA polymerase as a useful tool in PCR with difficult targets
PublicationThe DNA coding sequence of TaqStoffel polymer- ase was fused with the DNA-binding domain of Pyrococcus furiosus ligase. The resulting novel recombinant gene was cloned and expressed in E. coli. The recombinant enzyme was purified and its enzymatic features were studied. The fusion protein (PfuDBDlig-TaqS) was found to have enhanced processivity as a result of the conversion of the Taq DNA polymerase from a relatively low processive...
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Measurement of Impulse Response of Shallow Water Communication Channel by Correlation Method
PublicationPerformances of underwater acoustic communication (UAC) systems are strongly related to specific propagation conditions of the underwater channel; conditions that can additionally change in time due to the movement of the acoustic system transmitter and receiver or to reflection by underwater objects of the transmitted signal. The time-varying impulse response is a comprehensive description of dynamically changing transmission...
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Visualization of a lifeboat motion during lowering along ship’s side
PublicationThis paper presents description of a computer program for motion visualization of a lifeboat lowered along ship’s side. The program is a post-processor which reads results of numerical calculations of simulated objects’ motions. The data is used to create scene composed of 3D surfaces to visualize mutual spatial positions of a lifeboat, ship’s side and water waving surface. Since the numerical data contain description of a simulation...
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Impact of Shifting Time-Window Post-Processing on the Quality of Face Detection Algorithms
PublicationWe consider binary classification algorithms, which operate on single frames from video sequences. Such a class of algorithms is named OFA (One Frame Analyzed). Two such algorithms for facial detection are compared in terms of their susceptibility to the FSA (Frame Sequence Analysis) method. It introduces a shifting time-window improvement, which includes the temporal context of frames in a post-processing step that improves the...
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A Power-Efficient Digital Technique for Gain and Offset Correction in Slope ADCs
PublicationIn this brief, a power-efficient digital technique for gain and offset correction in slope analog-to-digital converters (ADCs) has been proposed. The technique is especially useful for imaging arrays with massively parallel image acquisition where simultaneous compensation of dark signal non-uniformity (DSNU) as well as photo-response non-uniformity (PRNU) is critical. The presented approach is based on stopping the ADC clock by...