Search results for: MONOTONE SEQUENCES
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Rapid design optimization of antennas using variable-fidelity EM models and adjoint sensitivities
PublicationPurpose – Development of techniques for expedited design optimization of complex and numerically expensive electromagnetic (EM) simulation models of antenna structures validated both numerically and experimentally. The paper aims to discuss these issues. Design/methodology/approach – The optimization task is performed using a technique that combines gradient search with adjoint sensitivities, trust region framework, as well as...
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Some aspects of the constitutive modelling of natural fine grained soils
PublicationThe monograph deals with selected problems of the constitutive modelling of natural fine grained soils commonly known as clays. The main idea is not to propose a unified model which is capable of describing all known features of mechanical behaviour of fine grained soils. Instead, separate models are proposed describing the mechanical behaviour of heavily overconsolidated, lightly overconsolidated and normally consolidated clays....
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Molecular differences in mitochondrial DNA (mtDNA) genomes of dogs with malignant mammary tumours
Open Research DataThe aim of this study was to determine molecular defects in mitochondrial DNA with the use of large-scale genome analysis in malignant canine mammary gland tumours and indicate whether these changes were linked with the carcinogenesis process. With the use of the NGS technology, we sequenced 27 samples of mtDNA isolated from blood and tumours obtained...
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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
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...
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Organisational methods in teaching ergonomics
PublicationCivilisation generates many problems connected with job, which cannot be resolved by one field of science that deals with matters fragmentarily, only from its own point of view. Ergonomics, i.e. synthetic knowledge about job, can solve these problems by using the resources of many fields, e.g. physiology, psychology, technical science or economy. The achievements of these fields are used in ergonomics and thus problems connected...
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Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment
PublicationWe present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody–antigen complexes, and 7 large assemblies. On average 70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups...
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Computationally-Efficient Statistical Design and Yield Optimization of Resonator-Based Notch Filters Using Feature-Based Surrogates
PublicationModern microwave devices are designed to fulfill stringent requirements pertaining to electrical performance, which requires, among others, a meticulous tuning of their geometry parameters. When moving up in frequency, physical dimensions of passive microwave circuits become smaller, making the system performance increasingly susceptible to manufacturing tolerances. In particular, inherent inaccuracy of fabrication processes affect...
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DNA-damaging imidazoacridinone C-1311 induces autophagy followed by irreversible growth arrest and senescence in human lung cancer cells
PublicationImidazoacridinone 5-diethylaminoethylamino-8-hydroxyimidazoacridinone (C-1311) is an antitumor inhibitor of topoisomerase II and FMS-like tyrosine kinase 3 receptor. In this study, we describe the unique sequence of cellular responses to C-1311 in human non-small cell lung cancer (NSCLC) cell lines, A549 and H460. In A549 cells, C-1311 (IC80 = 0.08 µM) induced G1 and G2/M arrests, whereas H460 cells (IC80 = 0.051 µM) accumulated...
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Mechanisms of azole resistance among clinical isolates of Candida glabrata in Poland
PublicationCandida glabrata is currently ranked as the second most frequently isolated aetiological agent of human fungal infections, next only to Candida albicans. In comparison with C. albicans, C. glabrata shows lower susceptibility to azoles, the most common agents used in treatment of fungal infections. Interestingly, the mechanisms of resistance to azole agents in C. albicans have been much better investigated than those in C. glabrata....
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Electron collisions with methyl-substituted ethylenes: Cross section measurements and calculations for 2-methyl–2-butene and 2,3-dimethyl–2-butene
PublicationWe report electron-scattering cross sections determined for 2-methyl–2-butene [(H3C)HC==C(CH3)2] and 2,3-dimethyl–2-butene [(H3C)2C=C(CH3)2] molecules. Absolute grand-total cross sections (TCSs) were measured for incident electron energies in the 0.5–300 eV range, using a linear electron-transmission technique. The experimental TCS energy dependences for the both targets appear to be very similar with respect to the shape. In each...
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Iron–Sulfur Cluster Biogenesis Chaperones: Evidence for Emergence of Mutational Robustness of a Highly Specific Protein–Protein Interaction
PublicationBiogenesis of iron–sulfur clusters (FeS) is a highly conserved process involving Hsp70 and J-protein chaperones. However, Hsp70 specialization differs among species. In most eukaryotes, including Schizosaccharomyces pombe, FeS biogenesis involves interaction between the J-protein Jac1 and the multifunctional Hsp70 Ssc1. But, in Saccharomyces cerevisiae and closely related species, Jac1 interacts with the specialized Hsp70 Ssq1,...
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Phenotypic consequences of the LYS4 gene disruption in Candida albicans
PublicationThe main scientific purpose of our studies was to verify the hypothesis that homoaconitase (HA) from Candida albicans, an enzyme catalyzing a second step of the α-aminoadipate pathway (AAP) of L-Lys biosynthesis may become a new target for antifungal chemotherapy. Previous studies indicated that the A. fumigatus mutant lacking the functional lysF gene, encoding HA, exhibited attenuated virulence in a low-dose mouse infection model...
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Novel single-stranded DNA-binding proteins from extreme psychrophilic bacterium Psychromonas ingrahamii 37
PublicationWe report the identification and characterization of the single-stranded DNA binding protein (SSB) from extreme psychrophilic bacterium Psychromonas ingrahamii 37 (PinSSB) that grows expotentially at -12°C and may well grow at even lower temperatures. PinSSB is one of the largest known bacterial SSB protein consisting 222 amino acid residues with a calculated molecular mass of 25.1 kDa. The analysis by gel filtration chromatography...
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Synthesis, Chemical Characterization and Multiscale Biological Evaluation of a dimericcRGD Peptide for Targeted Imaging of αVβ3 Integrin Activity
PublicationCyclic peptides containing the Arg-Gly-Asp (RGD) sequence have been shown to specifically bind the angiogenesis biomarker α V β3 integrin. We report the synthesis, chemical characterization, and biological evaluation of two novel dimeric cyclic RGD-based molecular probes for the targeted imaging of α V β3 activity (a radiolabeled version, 64Cu-NOTA-PEG4-cRGD2, for PET imaging, and a fluorescent version, FITC-PEG4-cRGD2, for in...
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Potential of nanocomposites of zero valent copper and magnetite with Eleocharis dulcis biochar for packed column and batch scale removal of Congo red dye
PublicationThe current study is the first attempt to prepare nanocomposites of Eleocharis dulcis biochar (EDB) with nano zero-valent Copper (nZVCu/EDB) and magnetite nanoparticles (MNPs/EDB) for batch and column scale sequestration of Congo Red dye (CR) from synthetic and natural water. The adsorbents were characterized with advanced analytical techniques. The impact of EDB, MNPs/EDB and nZVCu/EDB dosage (1–4 g/L), pH (4–10), initial concentration...
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Potentiometric sensor with lipid-polymer membranes for quality assessment of French red wines
PublicationThe quality of wines resulting from vineyard management is important for consumers due to the taste and price of wines. In this work, the quality of red wines of three vintages has been investigated by potentiometric sensors with six all-solid-state electrodes. Two series of experiments were carried out. The first involved a qualitative analysis of wine of different vintages from freshly opened bottles. The second consisted of...
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The Influence of Microstructure on the Passive Layer Chemistry and Corrosion Resistance for Some Titanium-Based Alloys
PublicationThe effect of microstructure and chemistry on the kinetics of passive layer growth and passivity breakdown of some Ti-based alloys, namely Ti-6Al-4V, Ti-6Al-7Nb and TC21 alloys, was studied. The rate of pitting corrosion was evaluated using cyclic polarization measurements. Chronoamperometry was applied to assess the passive layer growth kinetics and breakdown. Microstructure influence on the uniform corrosion rate of these alloys...
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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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Post-comatose patients with minimal consciousness tend to preserve reading comprehension skills but neglect syntax and spelling
PublicationModern eye tracking technology provides a means for communication with patients suffering from disorders of consciousness (DoC) or remaining in locked-in-state. However, being able to use an eye tracker for controlling text-based contents by such patients requires preserved reading ability in the first place. To our knowledge, this aspect, although of great social importance, so far has seemed to be neglected. In the paper, we...
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Angular welding distortion - one sided fillet weld
Open Research DataWelding is the basic method of joining ship hull elements during its construction. However, this method of joining structural elements generates shrinks. Shrinks causes deformation of the entire welded structure, both linear and angular. In the shipbuilding industry, there is a tendency to oversize fillet welds, at the design as well as manufacturing...
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BIODIVERSITY OF YEASTS ISOLATED FROM CAVES OF THE POLISH TATRA MOUNTAINS, AND ITS BIOTECHNOLOGICAL POTENTIAL
PublicationMost of the Earth’s biosphere is permanently or periodically exposed to temperatures below 5°C. Cold habitats harbor a wide diversity of psychrophiles. For many years Antarctica has been the geographic area preferred for studying the diversity and properties of cold-adapted microorganisms. However, the non-Antarctic habitats like Himalayas or Alps are also extensively explored. The Tatra Mountains are Europe’s second-highest massif...
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Kinetics of pollutants removal in vertical and horizontal flow constructed wetlands in temperate climate
PublicationThis paper reports a comparative study on kinetics of organic matter expressed as BOD5 and nitrogen removal in constructed wetlands operated in Poland. Analyzed data were collected at eight wetland systems, composed of subsurface flow beds: horizontal flow (HF) and vertical flow (VF), in different number and sequences. The analysis involved particularly mass removal rates (MRR) and first-order removal rate coefficients of BOD5...
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Quantum structure in competing lizard communities
PublicationAlmost two decades of research on applications of the mathematical formalism of quantum theory as a modeling tool in domains different from the micro-world has given rise to many successful applications in situations related to human behavior and thought, more specifically in cognitive processes of decision-making and the ways concepts are combined into sentences. In this article, we extend this approach to animal behavior, showing...
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A new cold-adapted beta-D-galactosidase from the Antarctic Arthrobacter sp. 32c - gene cloning, overexpression, purification and properties
PublicationThe development of a new cold-active β-D-galactosidases and microorganisms that efficiently ferment lactose is of high biotechnological interest, particularly for lactose removal in milk and dairy products at low temperatures and for cheese whey bioremediation processes with simultaneous bio-ethanol production. In this article, we present a new β-D-galactosidase as a candidate to be applied in the above mentioned biotechnological...
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Fast multi-objective optimization of antenna structures by means of data-driven surrogates and dimensionality reduction
PublicationDesign of contemporary antenna structures needs to account for several and often conflicting objectives. These are pertinent to both electrical and field properties of the antenna but also its geometry (e.g., footprint minimization). For practical reasons, especially to facilitate efficient optimization, single-objective formulations are most often employed, through either a priori preference articulation, objective aggregation,...
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Transport deficiency is the molecular basis of Candida albicans resistance to antifungal oligopeptides
Publication(FMDP), an inhibitor of glucosamine-6-phosphate synthase, exhibited growth inhibitory activity against Candida albicans, with minimal inhibitory concentration values in the 0.05–50 mg/L range. Uptake by the peptide permeases was found to be the main factor limiting an anticandidal activity of these compounds. Di- and tripeptide containing FMDP (F2 and F3) were transported by Ptr2p/Ptr22p peptide transporters (PTR) and FMDP-containing...
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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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Highly Conserved Homotrimer Cavity Formed by the SARS-CoV-2 Spike Glycoprotein: A Novel Binding Site
PublicationAn important stage in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) life cycle is the binding of the spike (S) protein to the angiotensin converting enzyme-2 (ACE2) host cell receptor. Therefore, to explore conserved features in spike protein dynamics and to identify potentially novel regions for drugging, we measured spike protein variability derived from 791 viral genomes and studied its properties by molecular...
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The occurrence of heavy metals and metal-resistant bacteria in water and bottom sediments of the Straszyn reservoir (Poland)
PublicationThe aim of this study is investigate the distribution of selected heavy metals (zinc, copper, lead, cadmium) and metal-resistant bacteria in water and bottom sediments of drinking water reservoir for Gdańsk (Poland). The research area - Straszyn Lake is a dam reservoir on Radunia river, of the total volume of 3 mln m3. Sediment and water sampling took place between May and October 2013 (eight series). Regarding metal concentration...
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Anticancer Properties of Amino Acid and Peptide Derivatives of Mycophenolic Acid
PublicationBackground: Although Mycophenolic Acid (MPA) is applied as prodrugs in clinic as an immunosuppressant, it also possesses anticancer activity. MPA acts as Inosine-5’-Monophosphate Dehydrogenase (IMPDH) inhibitor, where the carboxylic group at the end of the side chain interacts with Ser 276 of the enzyme via hydrogen bonds. Therefore, MPA derivatives with other polar groups indicated high inhibition too. On the other hand, potent...
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Semantic Analysis and Text Summarization in Socio-Technical Systems
PublicationIn this chapter the authors present the results of the development the methodology for increasing the reliability of the functioning of the Socio-Technical System. The existed methods and algorithms for processing unstructured (textual) information were studied. Taking into account noted above strengths and weaknesses of Discriminant and Probabilistic approaches of Latent Semantic Relations analysis in of the summarization projection...
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The Antimicrobial Potential of Bacteria Isolated from Honey Samples Produced in the Apiaries Located in Pomeranian Voivodeship in Northern Poland
PublicationThe principal objective of this study was to determine whether the honeys produced in apiaries located in Pomeranian Voivodeship (Northern Poland) contain bacteria producing metabolites with growth inhibition potential against important human and animal pathogens. The pathogens included Staphylococcus aurues, Staphyloccocus epidermidis, Escherichia coli, Listeria monocytogenes, Pseudomonas aeruginosa, and Candida albicans. From...
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Rhythm and Colours of the Angles
PublicationABSTRACT The game of space was and still is a crucial aspect of visual arts. The aim of this study is to examine how the arrangement of hues, rhythms and angles of various polygons can create an impression of depth and movement on a flat surface. The so-called Penrose tiling and Ulam's spiral are mathematical models that have been applied for the painting experiment. There is a vast amount of evidence gathered over the ages that...
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Results of tests on speech intelligibility in reverberant conditions
Open Research DataThe dataset contains the results of tests that aimed to provide a relationship between the rate of speech (RoS) and reverberation conditions characterized by the Speech Transmission Index (STI).
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Characterization of a single-stranded DNA-binding-like Protein from Nanoarchaeum equitans - a nucleic acid binding protein with broad substrate specificity
PublicationBackground SSB (single-stranded DNA-binding) proteins play an essential role in all living cells and viruses, as they are involved in processes connected with ssDNA metabolism. There has recently been an increasing interest in SSBs, since they can be applied in molecular biology techniques and analytical methods. Nanoarchaeum equitans, the only known representative of Archaea phylum Nanoarchaeota, is a hyperthermophilic, nanosized,...
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Molecular identification and genotyping of Staphylococci: genus, species, strains, colnes, lineages, and interspecies exchanges
PublicationStaphylococci are increasingly recognized as etiological agents of many opportunistic human and animal infections, emphasizing the need for a rapid and accurate identification, even to a genotypical level of these bacteria. In the recent years, there has been a significant progress in typing and phylogenetic study of Staphylococcus species. Here, we describe molecular methods used in taxonomy as well as staphylococci characterization....
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Multiplicative Long Short-Term Memory with Improved Mayfly Optimization for LULC Classification
PublicationLand Use and Land Cover (LULC) monitoring is crucial for global transformation, sustainable land control, urban planning, urban growth prediction, and the establishment of climate regulations for long-term development. Remote sensing images have become increasingly important in many environmental planning and land use surveys in recent times. LULC is evaluated in this research using the Sat 4, Sat 6, and Eurosat datasets. Various...
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Evaluation of Linkers’ Influence on Peptide-Based Piezoelectric Biosensors’ Sensitivity to Aldehydes in the Gas Phase
PublicationRecent findings qualified aldehydes as potential biomarkers for disease diagnosis. One of the possibilities is to use electrochemical biosensors in point-of-care (PoC), but these need further development to overcome some limitations. Currently, the primary goal is to enhance their metrological parameters in terms of sensitivity and selectivity. Previous findings indicate that peptide OBPP4 (KLLFDSLTDLKKKMSEC-NH2) is a promising...
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Fusion of Taq DNA polymerase with single-stranded DNA binding-like protein of Nanoarchaeum equitans—Expression and characterization
PublicationDNA polymerases are present in all organisms and are important enzymes that synthesise DNA molecules. They are used in various fields of science, predominantly as essential components for in vitro DNA syntheses, known as PCR. Modern diagnostics, molecular biology and genetic engineering need DNA polymerases which demonstrate improved performance. This study was aimed at obtaining a new NeqSSB-TaqS fusion DNA polymerase from the...
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Brief Announcement: Energy Constrained Depth First Search
PublicationDepth first search is a natural algorithmic technique for constructing a closed route that visits all vertices of a graph. The length of such route equals, in an edge-weighted tree, twice the total weight of all edges of the tree and this is asymptotically optimal over all exploration strategies. This paper considers a variant of such search strategies where the length of each route is bounded by a positive integer B (e.g. due...
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On deterministic procedures for low-cost multi-objective design optimization of miniaturized impedance matching transformers
PublicationPurpose This paper aims to investigate deterministic strategies for low-cost multi-objective design optimization of compact microwave structures, specifically, impedance matching transformers. The considered methods involve surrogate modeling techniques and variable-fidelity electromagnetic (EM) simulations. In contrary to majority of conventional approaches, they do not rely on population-based metaheuristics, which permit lowering...
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MODALITY corpus - SPEAKER 35 - COMMANDS C1
Open Research DataThe MODALITY corpus is one of the multimodal database of word recordings in English. It consists of over 30 hours of multimodal recordings. The database contains high-resolution, high-framerate stereoscopic video streams and audio signals obtained from a microphone array and a laptop microphone. The corpus can be employed to develop an AVSR system,...
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MODALITY corpus - SPEAKER 21 - COMMANDS C5
Open Research DataThe MODALITY corpus is one of the multimodal database of word recordings in English. It consists of over 30 hours of multimodal recordings. The database contains high-resolution, high-framerate stereoscopic video streams and audio signals obtained from a microphone array and a laptop microphone. The corpus can be employed to develop an AVSR system,...
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MODALITY corpus - SPEAKER 39 - COMMANDS C1
Open Research DataThe MODALITY corpus is one of the multimodal database of word recordings in English. It consists of over 30 hours of multimodal recordings. The database contains high-resolution, high-framerate stereoscopic video streams and audio signals obtained from a microphone array and a laptop microphone. The corpus can be employed to develop an AVSR system,...
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MODALITY corpus - SPEAKER 01 - COMMANDS C3
Open Research DataThe MODALITY corpus is one of the multimodal database of word recordings in English. It consists of over 30 hours of multimodal recordings. The database contains high-resolution, high-framerate stereoscopic video streams and audio signals obtained from a microphone array and a laptop microphone. The corpus can be employed to develop an AVSR system,...
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MODALITY corpus - SPEAKER 01 - COMMANDS C2
Open Research DataThe MODALITY corpus is one of the multimodal database of word recordings in English. It consists of over 30 hours of multimodal recordings. The database contains high-resolution, high-framerate stereoscopic video streams and audio signals obtained from a microphone array and a laptop microphone. The corpus can be employed to develop an AVSR system,...
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MODALITY corpus - SPEAKER 21 - COMMANDS C3
Open Research DataThe MODALITY corpus is one of the multimodal database of word recordings in English. It consists of over 30 hours of multimodal recordings. The database contains high-resolution, high-framerate stereoscopic video streams and audio signals obtained from a microphone array and a laptop microphone. The corpus can be employed to develop an AVSR system,...
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MODALITY corpus - SPEAKER 01 - COMMANDS C4
Open Research DataThe MODALITY corpus is one of the multimodal database of word recordings in English. It consists of over 30 hours of multimodal recordings. The database contains high-resolution, high-framerate stereoscopic video streams and audio signals obtained from a microphone array and a laptop microphone. The corpus can be employed to develop an AVSR system,...
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MODALITY corpus - SPEAKER 21 - COMMANDS C4
Open Research DataThe MODALITY corpus is one of the multimodal database of word recordings in English. It consists of over 30 hours of multimodal recordings. The database contains high-resolution, high-framerate stereoscopic video streams and audio signals obtained from a microphone array and a laptop microphone. The corpus can be employed to develop an AVSR system,...
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MODALITY corpus - SPEAKER 01 - COMMANDS C5
Open Research DataThe MODALITY corpus is one of the multimodal database of word recordings in English. It consists of over 30 hours of multimodal recordings. The database contains high-resolution, high-framerate stereoscopic video streams and audio signals obtained from a microphone array and a laptop microphone. The corpus can be employed to develop an AVSR system,...