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Search results for: casp, covid, ema, model accuracy, protein structure prediction, sars-cov-2
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Function and Frustration of Multi-Drug ABC Exporter Protein and Design of Model Proteins for Drug Delivery Using Protein Hydration Thermodynamics
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Effect of cyclodextrins on coupling of o-ethoxybenzenediazonium salt with pyrrole, imidazole and 2-methylimidazole
PublicationBadano wpływ B-cyklodekstryny na reakcje sprzęgania soli o-etoksybenzenodiazoniowych z pirolem, imidazolem i 2-metyloimidazolem. Porównano wydajności produktów sprzęgania wyizolowanych w poszczególnych reakcjach. W przypadku reakcji z pirolem i imidazolem prowadzonych z udziałem cyklodekstryny zaobserwowano spadek wydajności produktów sprzęgania, podczas gdy w reakcji z 2-metyloimidazolem obecność cyklodekstryny stymulowała powstawanie...
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Application of reversed-phase thin layer chromatography and QSRR modelling for prediction of protein binding of selected β-blockers
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Geometrically Nonlinear Analysis of Functionally Graded Shells Based on 2-D Cosserat Constitutive Model
PublicationIn this paper geometrically nonlinear analysis of functionally graded shells in 6-parameter shell theory is presented. It is assumed that the shell consists of two constituents: ceramic and metal. The mechanical properties are graded through the thickness and are described by power law distribution. Formulation based on 2-D Cosserat constitutive model is used to derive constitutive relation for functionally graded shells. Numerical...
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Silo music: Experimental investigations and a mechanical model
PublicationW artykule opisano zagadnienie zjawisk akustycznych oraz drgań występujących w silosach podczas przepływu materiałów granulowanych.
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Water-mediated influence of a crowded environment on internal vibrations of a protein molecule
PublicationThe influence of crowding on the protein inner dynamics is examined by putting a single protein molecule close to one or two neighboring protein molecules. The presence of additional molecules influences the amplitudes of protein fluctuations. Also, a weak dynamical coupling of collective velocities of surface atoms of proteins separated by a layer of water is detected. The possible mechanisms of these phenomena are described....
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Reliability model of two-shaft turbine combustion engine with heat regenerator
PublicationW artykule przedstawiono możliwość zastosowania teorii procesów semimarkowskich do opisu niezawodności turbinowego silnika spalinowego. Opracowano model niezawodnościowy w formie siedmiostanowego procesu semimarkowskiego, umożliwiający określenie prawdopodobieństw przebywania silnika w stanie zdatności oraz wyróżnionych stanach niezdatności.
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Balanced Spider Monkey Optimization with Bi-LSTM for Sustainable Air Quality Prediction
PublicationA reliable air quality prediction model is required for pollution control, human health monitoring, and sustainability. The existing air quality prediction models lack efficiency due to overfitting in prediction model and local optima trap in feature selection. This study proposes the Balanced Spider Monkey Optimization (BSMO) technique for effective feature selection to overcome the local optima trap and overfitting problems....
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Modified Peptide Molecules As Potential Modulators of Shelterin Protein Functions; TRF1
PublicationIn this work, we present studies on relatively new and still not well-explored potential anticancer targets which are shelterin proteins, in particular the TRF1 protein can be blocked by in silico designed "peptidomimetic" molecules. TRF1 interacts directly with the TIN2 protein, and this protein-protein interaction is crucial for the proper functioning of telomere, which could be blocked by our novel modified peptide molecules....
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Mobilenet-V2 Enhanced Parkinson's Disease Prediction with Hybrid Data Integration
PublicationThis study investigates the role of deep learning models, particularly MobileNet-v2, in Parkinson's Disease (PD) detection through handwriting spiral analysis. Handwriting difficulties often signal early signs of PD, necessitating early detection tools due to potential impacts on patients' work capacities. The study utilizes a three-fold approach, including data augmentation, algorithm development for simulated PD image datasets,...
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Assessment of the Accuracy of a Virtual Multi-Channel Temperature Measuring Instrument
PublicationThe multi-channel temperature measurement system developed works with NTC thermistors. The article presents the results of theoretical and empirical evaluation of accuracy obtained in measurement channels. The basis for the theoretical assessment is the mathematical model for each of the measurement channels and the characteristics of the system elements included in the circuits of the measurement channel. Two different methods were...
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JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
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Impact of the anion and chalcogen on the crystal structure and properties of 4,6-dimethyl-2-pyrimido(thio)nium halides
PublicationBy the reaction of urea or thiourea, acetylacetone and hydrogen halide (HF, HBr or HI), we have obtained seven new 4,6-dimethyl-2-pyrimido(thio)nium salts, which were characterized by single-crystal X-ray diffraction, namely, 4,6-dimethyl-2-oxo-2,3-dihydropyrimidin-1-ium bifluoride, C₆H₉N₂O⁺·HF₂⁻ or (dmpH)F₂H, 4,6-dimethyl-2-oxo-2,3-dihydropyrimidin-1-ium bromide, C₆H₉N₂O⁺·Br⁻ or (dmpH)Br, 4,6-dimethyl-2-oxo-2,3-dihydropyrimidin-1-ium...
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General Mechanism of Osmolytes’ Influence on Protein Stability Irrespective of the Type of Osmolyte Cosolvent
PublicationThe stability of proteins in an aqueous solution can be modified by the presence of osmolytes. The hydration sphere of stabilizing osmolytes is strikingly similar to the enhanced hydration sphere of a protein. This similarity leads to an increase in the protein stability. Moreover, the hydration sphere of destabilizing osmolytes is significantly different. These solutes generate in their surroundings so-called “structurally different...
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The importance of trust and altruistic social orientation for COVID-19 distress
PublicationBackground: The COVID-19 pandemic, the biggest global health crisis in decades, has been a difficult experience for nations all over the world. In the present study we wanted to assess to what extent a positive attitude towards others, expressed in altruistic social orientation and a high level of trust, would be linked to lower levels of COVID-19 distress in infected and non-infected individuals. Participants and procedure:...
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An Intelligent Approach to Short-Term Wind Power Prediction Using Deep Neural Networks
PublicationIn this paper, an intelligent approach to the Short-Term Wind Power Prediction (STWPP) problem is considered, with the use of various types of Deep Neural Networks (DNNs). The impact of the prediction time horizon length on accuracy, and the influence of temperature on prediction effectiveness have been analyzed. Three types of DNNs have been implemented and tested, including: CNN (Convolutional Neural Networks), GRU (Gated Recurrent...
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Modelling and Analysis of the Positioning Accuracy in the Loading Systems of Mobile Cranes
PublicationIn this work, the authors analyse the influence of the order and range of sequential movements of a crane's working members on the accuracy of the final cargo positioning. The analysis was conducted on the basis of a specially developed method in which the authors proposed the introduction of a geometrical indicator of positioning the load in the intermediate positions (after completing each movement sequence) and in the target...
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Tree-based homogeneous ensemble model with feature selection for diabetic retinopathy prediction
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Akaike's final prediction error criterion revisited
PublicationWhen local identification of a nonstationary ARX system is carried out, two important decisions must be taken. First, one should decide upon the number of estimated parameters, i.e., on the model order. Second, one should choose the appropriate estimation bandwidth, related to the (effective) number of input-output data samples that will be used for identification/ tracking purposes. Failure to make the right decisions results...
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Mechanism of antifreeze protein functioning and the “anchored clathrate water” concept
PublicationIn liquid water, there is a natural tendency to form aggregates that consist of water molecules linked by hydrogen bonds. Such spontaneously formed aggregates are surrounded by a "sea" of disordered water molecules, with both forms remaining in equilibrium. The process of creating water aggregates also takes place in the solvation water of proteins, but in this case the interactions of water molecules with the protein surface shift...
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Neuroeconomy and Neuromarketing: The Study of the Consumer Behaviour in the COVID-19 Context
PublicationTo address the study of consumer behavior in the post-COVID-19 era, the present Research Topic brings together a set of papers that attempt to study how different factors triggered by the pandemic have achieved a significant effect on consumers' behavioral intentions. These papers examine different subtopics related to food, health products, collaborative economy and, of course, neuroscience. Globally, the objectives of this special...
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Machine learning-based prediction of preplaced aggregate concrete characteristics
PublicationPreplaced-Aggregate Concrete (PAC) is a type of preplaced concrete where coarse aggregate is placed in the mold and a Portland cement-sand grout with admixtures is injected to fill the voids. Due to the complex nature of PAC, many studies were conducted to determine the effects of admixtures and the compressive and tensile strengths of PAC. Considering that a prediction tool is needed to estimate the compressive and tensile...
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Machine learning-based prediction of preplaced aggregate concrete characteristics
PublicationPreplaced-Aggregate Concrete (PAC) is a type of preplaced concrete where coarse aggregate is placed in the mold and a Portland cement-sand grout with admixtures is injected to fill the voids. Due to the complex nature of PAC, many studies were conducted to determine the effects of admixtures and the compressive and tensile strengths of PAC. Considering that a prediction tool is needed to estimate the compressive and tensile strengths...
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Numerical Estimation of Hull Hydrodynamic Derivatives in Ship Maneuvering Prediction
PublicationPrediction of the maneuvering characteristics of the ship at the design stage can be done by means of model tests, computational simulations or a combination of both. The model tests can be realized as direct simulation of the standard maneuvers with the free running model, which gives the most accurate results, but is also the least affordable as it requires very large tank or natural lake, as well as complex equipment of the...
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Accuracy and Availability of EGNOS - Results of Observations
PublicationAccording to SBAS concept the user should receive timely the correct information about the system integrity and corrections to the pseudoranges measurements, which leads to better accuracyof coordinates. In theory the whole system is permanently monitored by RIMS stations, so it is impossible to deliver the faulty information to the user. The quality of the system is guaranteed inside the border of the system coverage however in...
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(7Z,7'Z)-7,7'-(1,2,4-trithiolane-3,5-diylidene)bis[2-methylquinolin-8(7H)-one] chloroform disolvate
PublicationTytułowy związek, C22H14N2O2S3*2CHCl3 został otrzymany jako produkt reakcji pomiędzy kwasem 8-hydroksy-2-metylochinolinokarboditionowym a trifluorooctanem magnezu (lub manganu). Procesy utlenienia oraz eliminacji siarki spowodowały kondensację dwóch cząsteczek kwasu z wytworzeniem pięcioczłonowego aromatycznego pierścienia heterocyklicznego S3C2 (tritiolanu). Cząsteczka wykazuje symetrię C2. Związek ko-krystalizuje z dwoma cząsteczkami...
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Theoretical study of the structure, energetics and vibrational frequencies of water-acetone and water-2-butanone complexes
PublicationKompleksy acetonu i 2-butanonu z 0-2 cząsteczkami wody połączonymi wiązaniem wodorowym z tlenem karbonylowym zbadano z wykorzystaniem teorii funkcjonału gęstości (DFT) na poziomie B3LYP/6-311++G(d,p). Obliczenia w fazie gazowej uzupełniono o optymalizacje w otoczeniu rozpuszczalnika, symulowanego za pomocą modelu polaryzowalnego kontinuum (PCM). Częstości drgań oscylacyjnych otrzymane na podstawie zależności empirycznej sa zgodne...
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Rhamnolipid CMC Prediction
PublicationRelationships between the purity, pH, hydrophobicity (log Kow) of the carbon substrate, and the critical micelle concentration (CMC) of rhamnolipid type biosurfactants (RL) were investigated using a quantitative structure–property relationship (QSPR) approach and are presented here for the first time. Measured and literature CMC values of 97 RLs, representing biosurfactants at different stages of purification, were considered....
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Unusual structural properties of water within the hydration shell of hyperactive antifreeze protein
PublicationMany hypotheses can be encountered explaining the mechanism of action of antifreeze proteins. One widespread theory postulates that the similarity of structural properties of solvation water of antifreeze proteins to ice is crucial to the antifreeze activity of these agents. In order to investigate this problem, the structural properties of solvation water of the hyperactive antifreeze protein from Choristoneura fumiferana were...
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Numerical evaluation of dynamic response of an experimentally tested base-isolated and fixed-base steel structure model
PublicationSeismic isolation is recognized as one of the most popular and effective methods of protecting structures during earthquake. The present paper is focused on the comparison be-tween the dynamic responses of buildings with fixed and isolated bases exposed to seismic exci-tations. The aim of the study is to investigate the effectiveness of a simplified base isolation numerical modelling technique using the linear springs. One-storey...
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Wiktoria Wojnicz dr hab. inż.
PeopleDSc in Mechanics (in the field of Biomechanics) - Lodz Univeristy of Technology, 2019 PhD in Mechanics (in the field of Biomechanics) - Lodz Univeristy of Technology, 2009 (with distinction) List of papers (2009 - ) Wojnicz W., Wittbrodt E., Analysis of muscles' behaviour. Part I. The computational model of muscle. Acta of Bioengineering and Biomechanics, Vol. 11, No.4, 2009, p. 15-21 Wojnicz W., Wittbrodt E., Analysis of...
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Active Learning on Ensemble Machine-Learning Model to Retrofit Buildings Under Seismic Mainshock-Aftershock Sequence
PublicationThis research presents an efficient computational method for retrofitting of buildings by employing an active learning-based ensemble machine learning (AL-Ensemble ML) approach developed in OpenSees, Python and MATLAB. The results of the study shows that the AL-Ensemble ML model provides the most accurate estimations of interstory drift (ID) and residual interstory drift (RID) for steel structures using a dataset of 2-, to 9-story...
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The crystal structure of (1RS,4RS,5RS,6SR)-5-cyano-5-nitro-6-phenyl-bicyclo[2.2.1]hept-2-ene
PublicationStructure of nitronorbornene derivative C14H12N2O2 synthesized in the reaction of cyclopentadiene with E-2-phenyl-1-cyano-1-nitroethene was determined by single crystal X-ray diffraction analysis. It was found that in analyzed molecule the nitro group is in endo-position whereas phenyl group have exo-ori-entation.
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Integrated information and prediction Web Service WaterPUCK General concept
PublicationIn this paper, general concept of a new method as ‘Integrated information and prediction Web Service WaterPUCK’ for investigation influence of agricultural holdings and land-use structures on coastal waters of the southern Baltic Sea is presented. WaterPUCK Service is focused on determination of the current and future environmental status of the surface water and groundwater located in the Puck District (Poland) and its impact...
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Follow-up assessment of the microvascular function in patients with long COVID
PublicationLong COVID is a complex pathophysiological condition. However, accumulating data suggests that COVID-19 is a systemic microvascular endothelial dysfunction with different clinical manifestations. In this study, a microvascular function was assessed in long COVID patients (n = 33) and healthy controls (n = 30) using flow-mediated skin fluorescence technique (FMSF), based on measurements of nicotinamide adenine dinucleotide fluorescence...
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Anti-crisis activities and export performance in the Covid-19 pandemic: The case of Polish exporters
PublicationThe article aims to investigate the impact of anti-crisis activities undertaken by the Polish exporting firms on their export sales during the Covid-19 pandemic. We used a quantitative research design. We conducted the survey on the sample of 161 manufacturing Polish exporting firms between April 21 and June 25, 2021. To verify the assumed relationships, we used the probit regression model. The main novelty is a firm-level analysis...
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[NCh-bio] Advances in Biotechnology: Protein Folding and Assembly
e-Learning Courses{mlang pl} Dyscyplina: nauki chemiczne Zajęcia obowiązkowe dla doktorantów I i II roku z obszaru biotechnologii Prowadzący: dr hab. Gracjana Klein-Raina, prof. PG Liczba godzin: 15 Forma zajęć: wykład {mlang} {mlang en} Discipline: chemical sciences Obligatory course for 1st and 2nd-year PhD students from biotechnology area Academic teachers: dr hab. Gracjana Klein-Raina, prof. PG Total hours of training: 15 teaching...
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Polymeric materials in medicine – structure and desing 2023/24
e-Learning Courses -
Study on the Positioning Accuracy of GNSS/INS Systems Supported by DGPS and RTK Receivers for Hydrographic Surveys
PublicationHydrographic surveys, in accordance with the International Hydrographic Organization (IHO) S-44 standard, can be carried out in the following five orders: Exclusive, Special, 1a, 1b and 2, for which minimum accuracy requirements for the applied positioning system have been set out. They are as follows, respectively: 1, 2, 5, 5 and 20 m, with a confidence level of 95% in twodimensional space. The Global Navigation Satellite System...
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Compliance with the restrictions during the COVID-19 pandemic in Poland and Sweden
Open Research DataOur study is aimed to check if the difference between Sweden and Poland in trust is related to negative affective reactions to authorities and law antipathy being manifestations of lack of trust and related to value-based legitimacy, behavioral legitimacy and prosocial justification of compliance with the restrictions put on citizens to limit the spread...
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Child-Robot Interaction Studies During COVID-19 Pandemic
PublicationThe coronavirus disease (COVID-19) pandemic affected our lives deeply, just like everyone else, the children also suffered from the restrictions due to COVID-19 affecting their education and social interactions with others, being restricted from play areas and schools for a long time. Although social robots provide a promising solution to support children in their education, healthcare, and social interaction with others, the precautions...
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Seismic response and performance prediction of steel buckling-restrained braced frames using machine-learning methods
PublicationNowadays, Buckling-Restrained Brace Frames (BRBFs) have been used as lateral force-resisting systems for low-, to mid-rise buildings. Residual Interstory Drift (RID) of BRBFs plays a key role in deciding to retrofit buildings after seismic excitation; however, existing formulas have limitations and cannot effectively help civil engineers, e.g., FEMA P-58, which is a conservative estimation method. Therefore, there is a need to...
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Rich Bifurcation Structure in a Two-Patch Vaccination Model
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Thermal analysis of copper(II) complexes of general formula [Et4N]2[CuBrnCl4-n]
PublicationBadano dekompozycję termiczną związków składających sie z anionów: [CuBrnCl4-n]2- (n=0-4) i kationów tetrametyloamoniowych. Stosowano następujące metody badawcze: TG-FTIR, TG-MS, DTA i DTG. Pomiary przeprowadzono w atmosferze argonu i powietrza w zakresie temperatur od 293 K do 1073 K. Produkty dekompozycji identyfikowano metoda spektroskopii w podczerwieni (IR i FIR) oraz metodą dyfrakcji promieniowania rentgenowskiego.
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Industry-level analysis of COVID-19’s impact in emerging markets – evidence from Pakistan
PublicationPurpose – The main purpose of this study is to evaluate COVID-19’s impact on the emerging stock markets. Design/methodology/approach – To evaluate the influence of COVID-19, this study uses a novel method of event study methodology to measure the impact of COVID-19 on emerging stock markets. The research’s sample includes a total of 79 firms from 26 industries that are included in the KSE-100 Index from the Pakistan Stock Exchange....
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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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Use of the UNRES force field in template-assisted prediction of protein structures and the refinement of server models: Test with CASP12 targets
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Using deep learning to increase accuracy of gaze controlled prosthetic arm
PublicationThis paper presents how neural networks can be utilized to improve the accuracy of reach and grab functionality of hybrid prosthetic arm with eye tracing interface. The LSTM based Autoencoder was introduced to overcome the problem of lack of accuracy of the gaze tracking modality in this hybrid interface. The gaze based interaction strongly depends on the eye tracking hardware. In this paper it was presented how the overall the...
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COVID-19 severity forecast based on machine learning and complete blood count data
PublicationProper triage of COVID-19 patients is a key factor in eective case management, especially with limited and insucient resources. In this paper, we propose a machine-aided diagnostic system to predict how badly a patient with COVID-19 will develop disease. The prognosis of this type is based on the parameters of commonly used complete blood count tests, which makes it possible to obtain data from a wide range of patients.We chose...
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COVID-19 severity forecast based on machine learning and complete blood count data
PublicationProper triage of COVID-19 patients is a key factor in eective case management, especially with limited and insucient resources. In this paper, we propose a machine-aided diagnostic system to predict how badly a patient with COVID-19 will develop disease. The prognosis of this type is based on the parameters of commonly used complete blood count tests, which makes it possible to obtain data from a wide range of patients.We chose...