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Mathematical modeling for Delta and Omicron variant of SARS-CoV-2 transmission dynamics in Greece

Infectious Disease Modelling 2023年第3期8卷 794-805页

作者： Sofia Liossi E.Tsiambas S.Maipas E.Papageorgiou A.Lazaris N.Kavantzas 1st Department of Pathology School of MedicineNational and Kapodistrian University of AthensAthens General Hospital“Laikon”AthensGreece Department of Cytopathology 417 Army Equity Fund Hospital(NIMTS)AthensGreece Master Program“Environment and Health.Management of Environmental Health Effects” School of MedicineNational and Kapodistrian University of AthensAthensGreece Department of Biomedical Sciences School of Health&Welfare SciencesUniversity of West AtticaEgaleoGreece

A compartmental,epidemiological,mathematical model was developed in order to analyze the transmission dynamics of Delta and Omicron variant,of SARS-CoV-2,in *** model was parameterized twice during the 4th and 5th wave of the *** 4th wave refers to the period during which the Delta variant was dominant(approximately July to December of 2021)and the 5th wave to the period during which the Omicron variant was dominant(approximately January to May of 2022),in accordance with the official data from the National Public Health Organization(NPHO).Fitting methods were applied to evaluate important parameters in connection with the transmission of the variants,as well as the social behavior of population during these periods of *** models revealed higher numbers of contagiousness and cases of asymptomatic disease during the Omicron variant period,but a decreased rate of hospitalization compared to the Delta ***,parameters related to the behavior of the population in Greece were also *** specifically,the use of protective masks and the abidance of social distancing *** revealed that over 5,000 deaths could have been avoided,if mask usage and social distancing were 20%more efficient,during the short period of the Delta and Omicron ***,the spread of the variants was assessed using viral load *** data were recorded from PCR tests at 417 Army Equity Fund Hospital(NIMTS),in Athens and the ct values from 746 patients with COVID-19 were processed,to explain transmission phenomena and disease severity in *** period when the Delta variant prevailed in the country,the average ct value was calculated as 25.19(range:12.32e39.29),whereas during the period when the Omicron variant prevailed,the average ct value was calculated as 28(range:14.41e39.36).In conclusion,our experimental study showed that the higher viral load,which is related to the Delta variant,may interpret the severity of the

关键词： Delta variant Omicron variant Mathematical modeling Transmission dynamics ct value Data fitting

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Comparative Evaluation of RT-PCR Kits Available in Sri Lanka for Diagnosis of COVID-19

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感染微生物与疾病(英文) 2023年第3期5卷 152-158页

作者： Kanchana P.Amarasinghe Arumugam Murugananthan Ponnuthurai T.Amalraajan Mithusha Thavaththurai Gayathri Ravindran Kalamathy Murugananthan Shakila K.Gunathilake Department of Parasitology Faculty of MedicineUniversity of JaffnaJaffnaSri Lanka Department of Microbiology Faculty of MedicineUniversity of JaffnaJaffnaSri Lanka Department of Mathematics and Statistics Faculty of ScienceUniversity of JaffnaJaffnaSri Lanka

Identification of gene targets by real-time reverse transcriptase PCR(rRT-PCR)is considered as the gold standard for diagnosis of se-vere acute respiratory syndrome coronavirus 2(SARS-CoV-2)*** many commercial rRT-PCR kits are currently used in Sri Lanka,analytical performance of these kits have not been investigated ***,the objective of the present study was to evaluate the analytical performance of rRT-PCR kits used in the laboratory of the Faculty of Medicine,University of Jaffna(five kits).Performance of the five rRT-PCR kits selected for this study was compared with the CDC 2019-Novel Coronavirus(2019-nCoV)RT-PCR Diagnostic Panel as reference *** sensitivity,specificity,positive predictive value,negative predictive value and Cohen’sκcoefficient of the five different commercial kits were ***-CoV-2 positive(62)and negative(32)respiratory sam-ples collected respectively from symptomatic individuals and asymptomatic healthy individuals were used in this *** of the cycle threshold(ct)values of the five commercial kits revealed *** them,the TaqPathTM kit showed the highest sensitivity(98.4%)and interrater reliability(0.976).The HBRT-COVID-19 kit showed the lowest sensitivity(91.9%),specificity(93.7%)and interrater reliability(0.838).Although the five RT-PCR kits exhibited varying sensitivity,specificity and ct values,all of them are suitable for the routine diagnosis of SARS-CoV-2 infections as all values were higher than 90%.

关键词： COVID-19 diagnosis RT-PCR ct value sensitivity specificity

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Fracture evolution analysis of soil-rock mixture in contrast with soil by ct scanning under uniaxial compressive conditions

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Science China(Technological Sciences) 2021年第12期64卷 2771-2780页

作者： SUN XiuKuo LI Xiao MAO TianQiao ZHENG Bo WU YanFang LI GuanFang Key Laboratory of Shale Gas and Geoengineering Institute of Geology and GeophysicsChinese Academy of SciencesBeijing 100029China Innovation Academy for Earth Science Chinese Academy of SciencesBeijing 100029China College of Earth and Planetary Sciences University of Chinese Academy of SciencesBeijing 100049China

Soil-rock mixture(SRM),as a type of extremely heterogeneous geomaterial,is very common in nature and *** fracture and damage of SRM often induce severe geological ***,it is important to analyze the fracture evolution process of this *** the present research,real-time computed tomography(ct)scanning was conducted on SRM and pure soil samples under uniaxial compressive experiments to investigate the influence of rocks on fracture evolution in *** initiation of cracks,the original values of,and variations in,average density and heterogeneity in the soil matrix,the crack width evolution during loading,and the final failure modes were all *** with a width greater than 0.1 mm will not arise until over 90%of ultimate stress is *** general,in SRM,areas where the initial average density of the soil matrix is smaller and the initial heterogeneity is greater,are much easier to crack,but the results for pure soil show the opposite *** to fracturing conditions shown in ct slices,fracturing and non-fracturing areas in the soil matrix were *** average density of the soil matrix decreases in all areas under loading,except non-fracturing areas in *** the whole sample,the increase in heterogeneity in the soil matrix of SRM is greater than that of pure soil;but for the fracturing areas,this increase in pure soil is ***,the average and standard deviations of crack width both follow logarithmic distributions with high correlation coefficients.

关键词： soil-rock mixture fracture evolution real-time ct scanning ct value crack width

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Mutations in Spike Gene of SARS-CoV-2 that Are Associated with a Higher Viral Load: A Clinical Case Study

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Case Reports in Clinical Medicine 2022年第11期11卷 474-486页

作者： Ibrahim Keita Garan Dabo Lassina Doumbia Youssouf Diarra Ibrahim Traoré Mariam Traoré Lansana Sangaré Yacouba Toloba Mahamadou Alpha Diallo Djeneba Sy Andres H. Gutierrez Aliou Sissako Ibrahim Guindo Mohamed Diallo Akory Ag Iknane Anne S. De Groot Ousmane Aliou Koita Laboratoire de Biologie Moléculaire Appliquée Université des Sciences Techniques et des Technologies de Bamako Bamako Mali Hô pital du Mali Ministère de la Santé Publique et du Développement Social Bamako Mali Centre Hospitalo-Universitaire du Point G Ministère de la Santé Publique et du Développement Social Bamako Mali EpiVax Inc. Providence USA Institut National de Santé Publique Ministère de la Santé Publique et du Développement Social Bamako Mali Center for Vaccines and Immunology College of Veterinary Medicine University of Georgia Athens USA

Background: Quantitative PCR (qPCR) can be used to detect and quantify a load of a pathogen. It is a good indicator of the degree of transmissibility. While performing routine qPCR, we observed an unusually short cycle threshold (ct) value of SARS-CoV-2 for a clinical specimen obtained in Bamako, Mali. This prompted us to sequence the short-cycle SARS-CoV-2 sample to identify potential mutations in the Spike gene (S gene) gene. Methods: Post-infection, Quantitative Reverse Transcription (qRT-PCR) was performed over a defined time course to estimate the ct of the SARS-CoV-2 specimen collected from the patient. Sanger sequencing was done on the entire fragment of the S gene to identify mutations. Findings: Sanger sequencing revealed mutations in the lineage of interest, designated B.1.525 by Pango, and also known as “Eta” using the nomenclature defined by WHO. This variant was originally found in Nigeria and Italy. The four novel mutations identified in Eta (D228N, Y451N, I1172M, and C1250F) were otherwise observed with a low frequency worldwide. Although the initial ct was 10 in the case study patient, he did not exhibit severe symptoms of SARS-CoV-2, for example, pneumonia. However, we observed a longer viral clearance period than usual, of 3 weeks. We note that as compared to SARS-CoV-2 samples obtained during the first peaks of SARS-CoV-2 infection in Mali, when the infection was at its peak in March 2020 (ct = 30.4), circulating strains evaluated at the time the Eta sample was obtained demonstrated a lower mean ct (ct = 24). Conclusions: The short cycle threshold associated with this variant, and the temporal association with a decrease in the mean ct in the region of Bamako, may indicate higher levels of transmissibility due to a circulating variant. This variant is a lineage of interest designated B.1.525 by Pango or Eta by WHO.

关键词： SARS-CoV-2 Variant Eta ct value Mali

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Omicron Infections in Otolaryngology Practice: A Retrospective Observational Study on Testing, Symptoms and Vaccination Status

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Advances in Infectious Diseases 2023年第1期13卷 81-95页

作者： Uta Stierstorfer Bernhard Zöllner Kai Wonneberger ENT Medical Office Krefeld Germany Bioscientia MVZ Nordrhein Labor Moers Moers Germany

Background: With the appearance of the SARS-CoV-2 Omicron variant the high rate of vaccination breakthroughs showed that current vaccines against COVID-19 can no longer provide adequate protection against infection. However, it is still assumed that vaccination might have a positive effect on the course of the disease. In Germany, general practitioners and specialists are usually the first treatment providers for acute illnesses. In addition, patients with infections of the upper respiratory tract often primarily consult an ear, nose and throat specialist. Most of the Omicron-infected people have a mild course of the disease and, if necessary, receive medical care on an outpatient basis. Little is known about the effectiveness of corona vaccinations on Omicron infections in relation to the clinical symptoms. In our outpatient office, we recorded a sharp increase of corona positive Omicron-infections in the beginning of 2022, despite of vaccinations against COVID-19. In a retrospective analysis, we evaluated the data of our SARS-CoV-2 tested patients with regard to clinical symptoms reported and vaccination status. The focus was particularly on the question to what extent the vaccination status in the case of Omicron infections influences the symptoms of the disease. Methods: We retrospectively evaluated the data of all patients in the first quarter of 2022 who were suspected for COVID-19. At that time, the Omicron variant was dominant in Germany. Clinical symptoms, cycle threshold (ct) values, and the vaccination status were recorded. Symptomatic patients who tested negative for SARS-CoV-2 served as a control group. Results: Of the total cohort (n = 353), 241 (68%) patients were tested SARS-CoV-2 positive. The symptoms of the corona-positive patients were essentially similar to those of a mild to moderate cold, but compared to SARS-CoV-2-negative patients (n = 69) with a clear shift in favor of fever (35% versus 16%), cough (76% versus 52%) and increased feeling of

关键词： COVID-19 Omicron Variant Vaccination Effect ct value Clinical ENT Symptoms

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Application of Dual-Energy Computed Tomography for Breast Cancer Diagnosis

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International Journal of Medical Physics, Clinical Engineering and Radiation Oncology 2016年第4期5卷 288-297页

作者： Yukiko Okamura Nobuko Yoshizawa Masaru Yamaguchi Ikuo Kashiwakura Department of Radiological Life Sciences Hirosaki University Graduate School of Health Sciences Hirosaki Japan Department of Diagnostic Radiology and Nuclear Medicine Hamamatsu University School of Medicine Hamamatsu Japan

The present study aimed to investigate the possibility of using dual-energy computed tomography (ct) before therapy to discriminate between normal breast tissue and tumor tissue in patients with breast cancer, without the need to use a contrast medium. The following patient data were extracted by interview and from the hospital’s radiology information system: height, weight, age, menstrual cycle, ct images of normal tissue and tumors with or without contrast medium, and the histopathological diagnosis of the aspiration biopsy. The median age of the 43 participants was 56 years (range, 30 - 80 years). The ct values were evaluated using a clinical analytical program based on the three-material decomposition technique. Breast cancer was classified into ductal carcinoma in situ, invasive ductal carcinoma, invasive lobular carcinoma, fibromatosis-like metaplastic carcinoma, and apocrine carcinoma. In all conditions, regardless of contrast medium, the ct values of tumor tissues were higher than those of normal breast tissue, indicating the effectiveness of dual-energy ct (DE-ct) in the diagnosis of breast cancer. By contrast, DE-ct showed limited potential for distinguishing ductal carcinoma in situ from invasive ductal carcinoma. There have only been a few reports regarding ct examination of breast cancer, and it is expected this study encourage the development of DE-ct imaging to improve tumor detection in patients with breast cancer.

关键词： Breast Cancer Dual-Energy ct ct value Contrast Medium Oncological Imaging Ductal Carcinoma in Situ Invasive Ductal Carcinoma

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Meso-damage cracking characteristics analysis for rock and soil aggregate with ct test

Meso-damage cracking characteristics analysis for rock and s...

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中国科学院地质与地球物理研究所2014年度（第14届）...

作者： WANG Yu LI Xiao ZHANG Bo WU YanFang Key Laboratory of Engineering Geomechanics Institute of Geology and GeophysicsChinese Academy of Sciences Graduate University of Chinese Academy of Sciences

The aim of this paper is to investigate the damage cracking characteristics of rock and soil aggregate(RSA) by X-ray computed tomography(ct) under uniaxial compressive *** mean ct value for the region of interest(ROI) is used to analyze the cracking ***,the mathematical morphology method based on the image threshold segmentation is used to obtain characteristic parameters of cracks to describe the cracking evolution of *** show that the elastic mismatch between rock blocks and soil matrix is the primary reason for RSA *** mean ct value for the RSA specimen,rock block inclusions,and their adjacent soil regions decreases with the increasing stress ***,it is more sensitive for block inclusions than soil *** the image segmentation method,length,area and mean width of cracks obey to power function *** statistical characteristics are closely related to the rock block’s distribution and *** results may be useful to reveal the mesoscopic cracking mechanism,establish meso-damage evolution equation,and constitutive relation for RSA.

关键词： rock and soil aggregate(RSA) ct test ct value meso-damage mechanism cracking mechanism

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Experimental study on meso-damage cracking characteristics of RSA by ct test

Experimental study on meso-damage cracking characteristics o...

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中国科学院地质与地球物理研究所2015年度（第15届）...

作者： Y.Wang X.Li Y.F.Wu C.Lin B.Zhang Key Laboratory of Shale Gas and Geoengineering Institute of Geology and GeophysicsChinese Academy of Sciences

This paper investigates the meso-damage mechanism and the cracking characteristics of rock and soil aggregate(RSA)by X-ray computed tomography(ct)under uniaxial compressive *** RSA specimens(50 mm diameter and 100 mm height)with rock percentage 40%were produced to perform a series of uniaxial compressive strength *** damage cracking characteristic is identified by the mean ct value,and also the meso-damage propagation law is analyzed based on the damage factor defined by the ct *** the test results,the variation of ct value for region of interest is different at the same stress level,the mean ct value for the RSA specimen,and rock block inclusions,and their adjacent soil regions decrease with the increasing stress *** is more sensitive for block inclusions than soil ***,the meso-damage evolution equation and constitutive equation for RSA are *** estimated result is in agreement with the measured ***,based on the image threshold segmentation method,length,area,and mean width of cracks obey to power function *** statistical characteristics are closely related to the rock block’s distribution and *** results confirm that the elastic mismatch of RSA is the primary reason resulting in cracking under loading,damage characteristics of RSA is progressive,cracking begins from rock-soil interfaces,and then propagate into soil matrix.

关键词： Rock and soil aggregate(RSA) X-ray tomography ct value Meso-damage mechanism Cracking evolution

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Imaging in detecting sites of pulmonary fibrosis induced by paraquat

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World Journal of Emergency Medicine 2011年第1期2卷 45-49页

作者： Xiao-li Xu Wei Wang Zu-jun Song Hong Ding Xiao-hong Duan Huan-cheng Meng Jian Chong The Medical Team in Command Academy of the Frontier Control Urumqi 830049China Emergency Medicine Department Xijing Hospital Fourth Military Medical University Xi'an 710032 China Emergency Medicine Department 309 Hospital of the People's Liberation Army Beijing 100091 China School of Stomatology Fourth Military Medical University Xi'an 710032 China

BACKGROUND:The most common cause of death from paraquat (PQ) poisoning is respiratory failure from pulmonary fibrosis, which develops through pathological overproduction of extracellular matrix proteins such as collagens. In this study, a Microct system was used to observe dynamic changes of pulmonary fibrosis in rats with PQ poisoning, and find the characteristics of interstitial lung diseases via density-based and texture-based analysis of ct images of the lung structure.;METHODS:A total of 15 male SD rats were randomly divided into a control group (n=5) and a PQ poisoning group (n=10). The rats in the poisoning group were intraperitoneally administered with 4 mg/ mL PQ at 14 mg/kg, and the rats in the control group were administered with the same volume of saline. The signs of pulmonary fibrosis observed by the Microct included ground-glass opacity, nodular pattern, subpleural interstitial thickening, consolidation honeycomb-like shadow of the lung.;RESULTS:Compared with the control group, the rats with acute PQ poisoning had different signs of pulmonary fibrosis. Ground-glass opacity and consolidation of the lung appeared at the early phase of pulmonary fibrosis, and subpleural interstitial thickening and honeycomb-like shadow developed at the middle or later stage. Microct images showed that fibrotic lung tissues were denser than normal lungs, and their density was up-regulated with pulmonary fibrosis. There was no difference in the progress of pulmonary fibrosis between the right lung and the left lung (P>0.05), but there were differences in fibrosis degree at different sites in the lung (P<0.05 or P<0.01). Pulmonary fibrosis was mainly seen in the exterior area of the middle-lower part of the lung.;CONCLUSIONS:Imaging can show the development of pulmonary fibrosis in PQ poisoning rats, and this method may help to administer drugs more reasonably in treating pulmonary fibrosis.

关键词： ct value Microct Paraquat Pulmonary fibrosis Region of interest

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