scholarly journals From Delta to Omicron: analysing the SARS-CoV-2 epidemic in France using variant-specific screening tests (September 1 to December 18, 2021)

2022 ◽  
Author(s):  
Mircea T. Sofonea ◽  
Benedicte Roquebert ◽  
Vincent Foulongne ◽  
Laura Verdurme ◽  
Sabine Trombert-Paolantoni ◽  
...  
Keyword(s):  
Confidence Interval ◽  
Mathematical Modelling ◽  
Genetic Material ◽  
Screening Tests ◽  
Cycle Threshold

We analysed 131,478 SARS-CoV-2 variant screening tests performed in France from September 1st to December 18, 2021. Tests consistent with the presence of the Omicron variant exhibit significantly higher cycle threshold Ct values, which could indicate lower amounts of virus genetic material. We estimate that the transmission advantage of the Omicron variant over the Delta variant is +105% (95% confidence interval: 96-114%). Based on these data, we use mechanistic mathematical modelling to explore scenarios for early 2022.

scholarly journals Detection of Specific Antinuclear Reactivities in Patients with Negative Anti-nuclear Antibody Immunofluorescence Screening Tests

2002 ◽  
Vol 48 (12) ◽  
pp. 2171-2176 ◽  
Author(s):  
Ilse EA Hoffman ◽  
Isabelle Peene ◽  
Eric M Veys ◽  
Filip De Keyser
Keyword(s):  
Connective Tissue ◽  
Confidence Interval ◽  
Connective Tissue Disease ◽  
Indirect Immunofluorescence ◽  
Connective Tissue Diseases ◽  
Clinical Suspicion ◽  
Screening Tests ◽  
Strongly Correlated ◽  
Nuclear Antigens

Abstract Background: For detection of anti-nuclear antibodies (ANAs) and antibodies to extractable nuclear antigens (ENAs), samples frequently are screened with indirect immunofluorescence (IIF); further determination of anti-ENA antibodies is performed only when the result is positive. However, because anti-ENA reactivities are found in samples with low fluorescence intensities, we determined anti-ENA antibodies in samples with negative IIF and thus calculated the sensitivity of IIF for specific ANAs. Methods: We collected 494 samples consecutively referred by rheumatologists for routine ANA testing. IIF on HEp-2 and HEp-2000 (HEp-2 cells transfected with Ro60 cDNA) and line immunoassay (LIA) for the detection of specific ANAs were performed on all samples. Results: Fluorescence intensities and patterns on HEp-2 were strongly correlated with those on HEp-2000 [Spearman ρ = 0.852 (P <0.001) and 0.838 (P <0.001), respectively]. Sixty-eight of 494 samples were positive on LIA, of which only 72% (confidence interval, 68–76%) were detected with HEp-2 and 75% (confidence interval, 70–78%) with HEp-2000. Of 291 samples negative on both substrates, 12 were positive on LIA. Connective tissue diseases were diagnosed in four of these patients and suspected in at least three others. Conclusion: The HEp-2 and HEp-2000 substrates perform comparably for fluorescence intensities and patterns and for detecting specific ANAs, but some patients with negative IIF show reactivity on LIA. We recommend testing for fine reactivities, regardless of the IIF result, when the clinical suspicion for rheumatic connective tissue disease is high.

scholarly journals Mosaic structure of the penA gene in the oropharynx of men who have sex with men negative for gonorrhoea

2020 ◽  
Vol 31 (3) ◽  
pp. 230-235 ◽  
Author(s):  
Antonella Marangoni ◽  
Giacomo Marziali ◽  
Melissa Salvo ◽  
Antonietta D’Antuono ◽  
Valeria Gaspari ◽  
...  
Keyword(s):  
Confidence Interval ◽  
Dna Recombination ◽  
Genetic Material ◽  
Mosaic Structure ◽  
Multi Drug Resistance ◽  
Transmitted Infection ◽  
Neisseria Species ◽  
Sexually Transmitted ◽  
Pcr Products ◽  
Sex With Men

The oropharynx represents a crucial site for the emergence of multi-drug resistance in Neisseria gonorrhoeae. The mosaic penA alleles, associated with decreased susceptibility to cephalosporins, have emerged by DNA recombination with partial penA genes, particularly those from commensal pharyngeal Neisseria species. Here, we investigated the prevalence of the mosaic structure of the penA gene in the oropharynx of men who have sex with men testing negative for pharyngeal gonorrhoea. From January 2016 to June 2018, 351 gonorrhoea-negative men who have sex with men attending a sexually transmitted infection clinic in Italy were enrolled. Pharyngeal swabs underwent a real-time polymerase chain reaction (PCR) for the detection of the mosaic penA gene. In case of positivity, PCR products were sequenced and searched against several sequences of Neisseria strains. Overall, 31 patients (8.8%) were found positive for the presence of the mosaic penA gene. The positivity was significantly associated with previous cases of pharyngeal gonorrhoea (relative risk [RR]: 3.56, 95% confidence interval 1.44–8.80) and with recent exposure to beta-lactams (RR: 4.29, 95% confidence interval 2.20–8.38). All penA-positive samples showed a high relatedness (90–99%) with mosaic-positive Neisseria strains. Our data underline that commensal Neisseria species of the oropharynx may be a significant reservoir for genetic material conferring antimicrobial resistance in N. gonorrhoeae.

scholarly journals Circulating biomarkers in renal cell carcinoma: the link between microRNAs and extracellular vesicles, where are we now?

2014 ◽  
Vol 1 (8) ◽  
pp. 84-98 ◽  
Author(s):  
Ana L Teixeira ◽  
Francisca Dias ◽  
Mónica Gomes ◽  
Mara Fernandes ◽  
Rui Medeiros
Keyword(s):  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Genetic Material ◽  
Tumor Development ◽  
Cell Communication ◽  
Bioactive Molecules ◽  
Screening Tests ◽  
Transcriptional Level ◽  
Incidence And Mortality

Renal cell carcinoma (RCC) is a lethal urological cancer, with incidence and mortality rates increasing by 2-3% per decade. The lack of   standard screening tests contributes to the fact that one-third of patients are diagnosed with locally invasive or metastatic disease. Moreover, 20-40% of RCC patients submitted to surgical nephrectomy will develop metastasis. MicroRNAs (miRNAs) are small non-coding RNAs responsible for gene regulation at a post-transcriptional level.  It is accepted that they are deregulated in cancer and can influence tumor development. Thus, miRNAs are promising RCC biomarkers, since they can be detected using non-invasive methods. They are highly stable and easier to quantify in circulating biofluids. The elevated miRNA stability in circulating samples may be the consequence of their capacity to circulate inside of extracellular microvesicles (EMVs), for example, the exosomes.  The EMVs are bilayered membrane vesicles secreted by all cell types. They can be released in the interstitial space or into circulating biofluids, which allows the travelling, binding and entrance of these vesicles in receptor cells. This type of cell communication can shuttle bioactive molecules between cells, allowing the horizontal transference of genetic material. In this review, we focus on circulating miRNAs (miR-210, miR-1233, miR-221, miR-15a, miR-451, miR-508, miR-378) in the biofluids of RCC patients and attempt to establish the diagnostic and prognostic accuracy, their synergic effects, and the pathways involved in RCC biology.

scholarly journals Some mathematical tools for modelling malaria: a subjective survey

BIOMATH ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 2110029
Author(s):  
Jacek Banasiak ◽  
Rachid Ouifki ◽  
Woldegebriel Assefa Woldegerima
Keyword(s):  
Public Health ◽  
Decision Making ◽  
Confidence Interval ◽  
Mathematical Modelling ◽  
South African ◽  
Health Interventions ◽  
Design Strategies ◽  
Public Health Interventions ◽  
The Past ◽  
Challenges And Opportunities

In this paper, we provide a brief survey of mathematical modelling of malaria and how it is used to understand the transmission and progression of the disease and design strategies for its control to support public health interventions and decision-making. We discuss some of the past and present contributions of mathematical modelling of malaria, including the recent development of modelling the transmission-blocking drugs. We also comment on the complexity of the malaria dynamics and, in particular, on its multiscale character with its challenges and opportunities. We illustrate the discussion by presenting a curve fitting using a 95% confidence interval for the South African data for malaria from the years 2001-2018$ and provide projections for the number of malaria cases and deaths up to the year 2025.

Predicting Difficult Intubation in Apparently Normal Patients

2005 ◽  
Vol 103 (2) ◽  
pp. 429-437 ◽  
Author(s):  
Toshiya Shiga ◽  
Zen’ichiro Wajima ◽  
Tetsuo Inoue ◽  
Atsuhiro Sakamoto
Keyword(s):  
Confidence Interval ◽  
Difficult Intubation ◽  
Mouth Opening ◽  
Positive Likelihood Ratio ◽  
Diagnostic Value ◽  
Screening Tests ◽  
Clinical Value ◽  
Bedside Test ◽  
Airway Pathology ◽  
Bedside Tests

The objective of this study was to systematically determine the diagnostic accuracy of bedside tests for predicting difficult intubation in patients with no airway pathology. Thirty-five studies (50,760 patients) were selected from electronic databases. The overall incidence of difficult intubation was 5.8% (95% confidence interval, 4.5-7.5%). Screening tests included the Mallampati oropharyngeal classification, thyromental distance, sternomental distance, mouth opening, and Wilson risk score. Each test yielded poor to moderate sensitivity (20-62%) and moderate to fair specificity (82-97%). The most useful bedside test for prediction was found to be a combination of the Mallampati classification and thyromental distance (positive likelihood ratio, 9.9; 95% confidence interval, 3.1-31.9). Currently available screening tests for difficult intubation have only poor to moderate discriminative power when used alone. Combinations of tests add some incremental diagnostic value in comparison to the value of each test alone. The clinical value of bedside screening tests for predicting difficult intubation remains limited.

scholarly journals Microsatellite Markers within —SEA Breakpoints for Prenatal Diagnosis of HbBarts Hydrops Fetalis

2007 ◽  
Vol 53 (2) ◽  
pp. 173-179 ◽  
Author(s):  
Sherry Sze Yee Ho ◽  
Samuel S Chong ◽  
Evelyn SC Koay ◽  
Yiong Huak Chan ◽  
Ponnusamy Sukumar ◽  
...  
Keyword(s):  
Confidence Interval ◽  
Microsatellite Markers ◽  
Genetic Material ◽  
Simultaneous Detection ◽  
Hydrops Fetalis ◽  
Deletion Syndrome ◽  
Correct Identification ◽  
Fetal Dna ◽  
Cell Free Fetal Dna ◽  
Maternal Contamination

Abstract Background: We sought to develop a rapid prenatal diagnostic test for simultaneous detection of HbBarts hydrops fetalis and exclusion of maternal contamination. Methods: We developed a multiplex quantitative fluorescent PCR (QF-PCR) test that detects the presence/ absence of 2 microsatellite markers (16PTEL05/16PTEL06) located within breakpoints of the Southeast Asia (—SEA) deletion. HbBarts hydrops fetalis (—SEA/—SEA) is diagnosed by absence of both markers, and maternal contamination of fetal DNA is excluded by absence of noninherited maternal alleles. Fetal and parental DNA samples from 50 families were analyzed in a blinded clinical validation study, and QF-PCR results were compared with their respective molecular genotypes. Results: The multiplex QF-PCR results included correct diagnoses of HbBarts hydrops fetalis in 11 of the fetuses tested, correct verification as unaffected in 20 fetuses, and correct identification as either carriers (αα/—SEA) or unaffected homozygotes in 18. Misidentification as unaffected occurred for 1 carrier. Sensitivity for diagnosis of HbBarts hydrops fetalis was 100% [lower 95% confidence interval, 76.2%], and specificity was 100% (lower 95% confidence interval, 92.6%). None of the samples tested showed any traces of noninherited maternal alleles; thus false-positives because of maternal contamination were eliminated. Conclusions: In this QF-PCR method, detection of maternally and paternally inherited fetal alleles allowed diagnosis of the double-deletion syndrome, and the ability to differentiate between these alleles allowed simultaneous exclusion of maternal contamination of the fetal genetic material. This novel strategy using cell-free fetal DNA in maternal plasma could form the basis for noninvasive testing for HbBarts hydrops fetalis.

scholarly journals Inferring SARS-CoV-2 variant within-host kinetics

2021 ◽  
Author(s):  
Baptiste Elie ◽  
Emmanuel Lecorche ◽  
Mircea T. Sofonea ◽  
Sabine Trombert ◽  
Vincent Foulogne ◽  
...  
Keyword(s):  
Viral Load ◽  
General Population ◽  
Host Population ◽  
Screening Tests ◽  
Infectious Period ◽  
Wild Type ◽  
Cycle Threshold ◽  
Transmission Data ◽  
Peak Viral Load ◽  
Period Duration

SARS-CoV-2 variants are causing epidemic rebounds in many countries. By analyzing longitudinal cycle threshold (Ct) values from screening tests in the general population and hospitals, we find that infections caused by variant lineages have higher peak viral load than wild type lineages and, for the B.1.1.7 lineage, have a longer infectious period duration. Linking within-host kinetics to transmission data suggests that infections caused by variants have higher transmission potentials and that their epidemiological fitness may depend on the demography of the host population.

scholarly journals Incidence of interval cancers in faecal immunochemical test colorectal screening programmes in Italy

2017 ◽  
Vol 25 (1) ◽  
pp. 32-39 ◽  
Author(s):  
Paolo Giorgi Rossi ◽  
Elisa Carretta ◽  
Lucia Mangone ◽  
Susanna Baracco ◽  
Diego Serraino ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Confidence Interval ◽  
Cancer Registries ◽  
Screening Tests ◽  
Interval Cancers ◽  
Faecal Immunochemical Test ◽  
Immunochemical Test ◽  
Second Year ◽  
Colorectal Screening ◽  
Proportional Incidence

Objective In Italy, colorectal screening programmes using the faecal immunochemical test from ages 50 to 69 every two years have been in place since 2005. We aimed to measure the incidence of interval cancers in the two years after a negative faecal immunochemical test, and compare this with the pre-screening incidence of colorectal cancer. Methods Using data on colorectal cancers diagnosed in Italy from 2000 to 2008 collected by cancer registries in areas with active screening programmes, we identified cases that occurred within 24 months of negative screening tests. We used the number of tests with a negative result as a denominator, grouped by age and sex. Proportional incidence was calculated for the first and second year after screening. Results Among 579,176 and 226,738 persons with negative test results followed up at 12 and 24 months, respectively, we identified 100 interval cancers in the first year and 70 in the second year. The proportional incidence was 13% (95% confidence interval 10–15) and 23% (95% confidence interval 18–25), respectively. The estimate for the two-year incidence is 18%, which was slightly higher in females (22%; 95% confidence interval 17–26), and for proximal colon (22%; 95% confidence interval 16–28). Conclusion The incidence of interval cancers in the two years after a negative faecal immunochemical test in routine population-based colorectal cancer screening was less than one-fifth of the expected incidence. This is direct evidence that the faecal immunochemical test-based screening programme protocol has high sensitivity for cancers that will become symptomatic.

Early Development of Drug-Induced Hepatic Necrosis

1971 ◽  
Vol 29 ◽  
pp. 576-577
Author(s):  
F. G. Zaki ◽  
E. Detzi ◽  
C. H. Keysser
Keyword(s):  
Early Development ◽  
Hepatic Necrosis ◽  
Screening Tests ◽  
Dense Matrix ◽  
Sprague Dawley ◽  
Electron Microscopic ◽  
Drug Induced ◽  
Hepatocellular Damage ◽  
Sprague Dawley Rats ◽  
Microscopic Studies

This study represents the first in a series of investigations carried out to elucidate the mechanism(s) of early hepatocellular damage induced by drugs and other related compounds. During screening tests of CNS-active compounds in rats, it has been found that daily oral administration of one of these compounds at a dose level of 40 mg. per kg. of body weight induced diffuse massive hepatic necrosis within 7 weeks in Charles River Sprague Dawley rats of both sexes. Partial hepatectomy enhanced the development of this peculiar type of necrosis (3 weeks instead of 7) while treatment with phenobarbital prior to the administration of the drug delayed the appearance of necrosis but did not reduce its severity.Electron microscopic studies revealed that early development of this liver injury (2 days after the administration of the drug) appeared in the form of small dark osmiophilic vesicles located around the bile canaliculi of all hepatocytes (Fig. 1). These structures differed from the regular microbodies or the pericanalicular multivesicular bodies. They first appeared regularly rounded with electron dense matrix bound with a single membrane. After one week on the drug, these vesicles appeared vacuolated and resembled autophagosomes which soon developed whorls of concentric lamellae or cisterns characteristic of lysosomes (Fig. 2). These lysosomes were found, later on, scattered all over the hepatocytes.

Development of apical pits in chloride cells of the gills of Pimephales promelas after chronic exposure to acid water

1983 ◽  
Vol 41 ◽  
pp. 462-463
Author(s):  
Richard L. Leino ◽  
Jon G. Anderson ◽  
J. Howard McCormick
Keyword(s):  
Confidence Interval ◽  
Chronic Exposure ◽  
Lake Superior ◽  
Pimephales Promelas ◽  
Chloride Cells ◽  
Fathead Minnows ◽  
Secondary Lamellae ◽  
Untreated Water ◽  
Water Ph ◽  
Flow Through

Groups of 12 fathead minnows were exposed for 129 days to Lake Superior water acidified (pH 5.0, 5.5, 6.0 or 6.5) with reagent grade H2SO4 by means of a multichannel toxicant system for flow-through bioassays. Untreated water (pH 7.5) had the following properties: hardness 45.3 ± 0.3 (95% confidence interval) mg/1 as CaCO3; alkalinity 42.6 ± 0.2 mg/1; Cl- 0.03 meq/1; Na+ 0.05 meq/1; K+ 0.01 meq/1; Ca2+ 0.68 meq/1; Mg2+ 0.26 meq/1; dissolved O2 5.8 ± 0.3 mg/1; free CO2 3.2 ± 0.4 mg/1; T= 24.3 ± 0.1°C. The 1st, 2nd and 3rd gills were subsequently processed for LM (methacrylate), TEM and SEM respectively.Three changes involving chloride cells were correlated with increasing acidity: 1) the appearance of apical pits (figs. 2,5 as compared to figs. 1, 3,4) in chloride cells (about 22% of the chloride cells had pits at pH 5.0); 2) increases in their numbers and 3) increases in the % of these cells in the epithelium of the secondary lamellae.

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