Artykuły w czasopismach: „Seegage analysis”

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Strydom, K., F. Ismail, M. M. Z. Matabane, O. Onwuegbuna, S. V. Omar i N. Ismail. "Comparison of Three Commercial Molecular Assays for Detection of Rifampin and Isoniazid Resistance among Mycobacterium tuberculosis Isolates in a High-HIV-Prevalence Setting: TABLE 1". Journal of Clinical Microbiology 53, nr 9 (1.07.2015): 3032–34. http://dx.doi.org/10.1128/jcm.01691-15.

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In a head-to-head comparison of the MTBDRplusversion 2.0 (Hain Lifescience), the Xpert MTB/RIF (Cepheid), and the Anyplex MTB/NTM (Seegene) assays, we demonstrated equal sensitivity (59/61; 96.7%) and specificity (53/54; 98.1%) for detecting rifampin resistance with further analysis of discordances. The Xpert assay does not detect isoniazid resistance while the Anyplex assay showed high false positivity.

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Pavletić, Martina, Marija Mazor, Mate Lerga, Tatjana Mileta, Jelena Železnjak, Tina Ružić, Sanda Ravlić i in. "Fast, Reliable, and Simple Point-of-Care-like Adaptation of RT-qPCR for the Detection of SARS-CoV-2 for Use in Hospital Emergency Departments". Viruses 13, nr 12 (2.12.2021): 2413. http://dx.doi.org/10.3390/v13122413.

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During COVID-19 pandemics, the availability of testing has often been a limiting factor during patient admissions into the hospital. To circumvent this problem, we adapted an existing diagnostic assay, Seegene Allplex SARS-CoV-2, into a point-of-care-style direct qPCR (POC dqPCR) assay and implemented it in the Emergency Department of Clinical Hospital Center Rijeka, Croatia. In a 4-month analysis, we tested over 10,000 patients and demonstrated that POC-dqPCR is robust and reliable and can be successfully implemented in emergency departments and similar near-patient settings and can be performed by medical personnel with little prior experience in qPCR.

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Lim, Ho-Jae, Jung-Eun Park, Min-Young Park, Joo-Hwan Baek, Sunkyung Jung, Nackmoon Sung, Jae-Hyun Yang, Min-Woo Lee, Sun-Hwa Lee i Yong-Jin Yang. "Assay System for Simultaneous Detection of SARS-CoV-2 and Other Respiratory Viruses". Diagnostics 11, nr 6 (13.06.2021): 1084. http://dx.doi.org/10.3390/diagnostics11061084.

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) triggers disease with nonspecific symptoms that overlap those of infections caused by other seasonal respiratory viruses (RVs), such as the influenza virus (Flu) or respiratory syncytial virus (RSV). A molecular assay for accurate and rapid detection of RV and SARS-CoV-2 is crucial to manage these infections. Here, we compared the analytical performance and clinical reliability of Allplex™ SARS-CoV-2/FluA/FluB/RSV (SC2FabR; Seegene Inc., Seoul, South Korea) kit with those of four commercially available RV detection kits. Upon testing five target viral strains (SARS-CoV-2, FluA, FluB, RSV A, and RSV B), the analytical performance of SC2FabR was similar to that of the other kits, with no significant difference (p ≥ 0.78) in z-scores. The efficiency of SC2FabR (E-value, 81–104%) enabled reliable SARS-CoV-2 and seasonal RV detection in 888 nasopharyngeal swab specimens processed using a fully automated nucleic acid extraction platform. Bland–Altman analyses revealed an agreement value of 95.4% (SD ± 1.96) for the kits, indicating statistically similar results for all five. In conclusion, SC2FabR is a rapid and accurate diagnostic tool for both SARS-CoV-2 and seasonal RV detection, allowing for high-throughput RV analysis with efficiency comparable to that of commercially available kits. This can be used to help manage respiratory infections in patients during and after the coronavirus disease 2019 pandemic.

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Eibinger, Gerald M., Harald H. Kessler, Evelyn Stelzl, Klaus Vander, Anita Weber-Lassacher, Wilfried Renner i Markus Herrmann. "SARS-CoV-2 RNA Testing Using Different Assays—Impact on Testing Strategies in a Clinical Setting". International Journal of Molecular Sciences 23, nr 21 (25.10.2022): 12845. http://dx.doi.org/10.3390/ijms232112845.

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In order to assess SARS-CoV-2 real time quantitative polymerase chain reaction (RT-qPCR) results in a real-life setting, three independent laboratories in Graz (Austria) set up a continuous cross comparison schedule. The following test systems were used: The QIAGEN NeuMoDx SARS-CoV-2 Assay, the Allplex™ 2019-nCoV Assay (Seegene) on a MicroLab Nimbus (Hamilton) platform combined with RealStar SARS-CoV-2 RT-PCR Assay (Altona Diagnostics GmbH), and the cobas SARS-CoV-2 test on a fully automated cobas 6800 system (Roche). A total of 200 samples were analysed, 184 (92%) were found to be concordant with all testing platforms, 14 (7%) discordant. Two (1%) samples tested invalid on a single platform and were excluded from further analysis. Discordant results were distributed randomly across the assays. The Ct values from all assays correlated closely with each other. All discordant samples showed Ct values ≥ 26. SARS-CoV-2 RT-qPCR assays may show considerable variability, especially in samples with low viral RNA concentrations. Decision makers should thus balance the advantages and disadvantages of RT-qPCR for mass screening and adopt suitable strategies that ensure a rational management of positive samples with high Ct values.

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Strojan Fležar, Margareta, Neža Nedelko, Mario Poljak, Anja Oštrbenk Valenčak i Helena Gutnik. "Stratified Mucin-Producing Intraepithelial Lesion (SMILE) of the Uterine Cervix: High-Risk HPV Genotype Predominance and p40 Immunophenotype". Cells 10, nr 8 (10.08.2021): 2039. http://dx.doi.org/10.3390/cells10082039.

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Stratified mucin-producing intraepithelial lesion (SMILE) is a rare high-grade cervical precancerous lesion designated a variant of adenocarcinoma in situ (AIS) in the WHO classification. We aimed to determine HPV genotypes, immunohistochemical phenotype and mucin presence in SMILE. Between 2010 and 2018, SMILE was diagnosed in 34 out of 6958 (0.5%) cervical biopsies, in 23 patients. Twenty-six tissue samples from twenty-one patients were available for further analysis, including 13 with SMILE alone, 12 with SIL and/or AIS and one with HSIL, AIS and endocervical adenocarcinoma. HPV genotyping was performed using the Seegene Anyplex II HPV 28 assay. Of the 26 samples, a single HPV genotype was identified in the majority of cases (n = 22), including 12/13 SMILEs associated with SIL/AIS. All but one were high-risk HPV genotypes (23/24; 96.8%). We identified seven different HPV genotypes, the most common being HPV16 (n = 10; 43.5%), HPV18 (n = 8, 34.8%) and HPV 31 (n = 5, 21.7%). All SMILEs showed a strong positive reaction to p16, CK7, CK19 and high Ki67 expression comparable to adjacent HSIL and/or AIS if present. SMILE showed variable mucin presence and p40-positive squamous differentiation suggesting phenotypic diversity in cervical precancerous lesions infected by single HPV.

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Dossou, Nefert Candace, Isidore Gaubert, Elodie Maille, Remy Morello, Renaud Cassier, Cécile Schanen, Jean-Jacques Dutheil, Louis-Marie Rocque, Astrid Vabret i Meriadeg Ar Gouilh. "Use of LoopDeelab during the COVID-19 Pandemic: An Innovative Device for Field Diagnosis". Viruses 14, nr 9 (17.09.2022): 2062. http://dx.doi.org/10.3390/v14092062.

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Rapid and accurate diagnosis of SARS-CoV-2 infection is essential for the management of the COVID-19 outbreak. RT-LAMP LoopDeetect COVID-19 (LoopDeescience, France) is a rapid molecular diagnostic tool which operates with the LoopDeelab (LoopDeescience, France) device. RAPID COVID is a prospective double-blind research protocol which was conducted to evaluate the concordance between Loopdeetect COVID-19 and RT-PCR Allplex 2019 n-Cov (Seegene, Korea). Between 11 May 2020 and 14 June 2021, a total of 1122 nasopharyngeal swab specimens were collected, of which 741 were finally analysed. There were 32 “positive” and “indeterminate” RT-PCR results. The intrinsic performances of Loopdeetect COVID-19 are equivalent to other commercial RT-LAMP PCR COVID-19 kits, with a sensitivity and specificity of 69.23% [CI 95%: 48.21–85.67] and 100% [CI 95%: 99.58–100.00], respectively. To the best of our knowledge, LoopDeelab is the only LAMP PCR diagnostic device allowing such a fast and reliable analysis with low-cost equipment; this makes it a new and innovative technology, designed for field use. This device being portable, the development of other detection kits will be useful for the management of epidemics with a high attack rate and would facilitate the rapid application of health measures.

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Fattouh, Ramzi, Karel Boissinot, Esther Jeong, Andrew B. Mendlowitz, Calvin P. Sjaarda, Henry Wong, Robert Kozak, Prameet M. Sheth i Larissa M. Matukas. "Evaluation of 5 Polymerase Chain Reaction Assays for the Detection of Mpox Virus". Journal of Infectious Diseases 229, Supplement_2 (26.03.2024): S156—S162. http://dx.doi.org/10.1093/infdis/jiad464.

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Abstract Background In 2022, the global dissemination of mpox virus (MPXV) outside endemic regions prompted the expansion of diagnostic testing worldwide. This study assesses the performance characteristics of 5 real-time polymerase chain reaction (PCR) assays in detecting MPXV during the 2022 outbreak. Methods Clinical specimens collected from patients across Ontario, Canada, were tested on the following assays: RealStar Orthopoxyvirus PCR and FlexStar Monkeypox virus PCR (Altona Diagnostics), Novaplex MPXV (Seegene), VIASURE Monkeypox virus Real Time PCR Reagents (CerTest Biotec), and a laboratory-developed test. Positive percent agreement (PPA), negative percent agreement (NPA), relative limit of detection (LOD), and precision were evaluated and MPXV lineages were determined using an amplicon-based whole-genome sequencing (WGS) assay. Results Swabs were collected from various anatomic sites (65 positive and 30 negative). All assays demonstrated 100% NPA (95% confidence interval, 88.4%/88.1%–100.0%), with PPA ranging from 92.2% (82.7%–97.4%) to 96.9% (89.3%–99.6%). LOD and precision were comparable across assays, with coefficient of variations <3%. WGS analysis identified 6 lineages, all belonging to subclade IIb. Conclusions The assays exhibited excellent PPA, NPA, LOD, and precision. Ongoing performance monitoring is essential to detect assay escape mutants and ensure universal detection of evolving MPXV strains.

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Specchiarello, Eliana, Giulia Matusali, Fabrizio Carletti, Cesare Ernesto Maria Gruber, Lavinia Fabeni, Claudia Minosse, Emanuela Giombini i in. "Detection of SARS-CoV-2 Variants via Different Diagnostics Assays Based on Single-Nucleotide Polymorphism Analysis". Diagnostics 13, nr 9 (27.04.2023): 1573. http://dx.doi.org/10.3390/diagnostics13091573.

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is characterized by fast evolution with the appearance of several variants. Next-Generation Sequencing (NGS) technology is considered the gold standard for monitoring known and new SARS-CoV-2 variants. However, the complexity of this technology renders this approach impracticable in laboratories located in areas with limited resources. We analyzed the capability of the ThermoFisher TaqPath COVID-19 RT-PCR (TaqPath) and the Seegene Novaplex SARS-CoV-2 Variant assay (Novaplex) to detect Omicron variants; the Allplex VariantII (Allplex) was also evaluated for Delta variants. Sanger sequencing (SaS) was the reference method. The results obtained with n = 355 nasopharyngeal samples were: negative with TaqPath, although positive with other qualitative molecular assays (n = 35); undetermined (n = 40) with both the assays; negative for the ∆69/70 mutation and confirmed as the Delta variant via SaS (n = 100); positive for ∆69/70 and confirmed as Omicron BA.1 via SaS (n = 80); negative for ∆69/70 and typed as Omicron BA.2 via SaS (n = 80). Novaplex typed 27.5% of samples as undetermined with TaqPath, 11.4% of samples as negative with TaqPath, and confirmed 100% of samples were Omicron subtypes. In total, 99/100 samples were confirmed as the Delta variant with Allplex with a positive per cent agreement (PPA) of 98% compared to SaS. As undermined samples with Novaplex showed RdRp median Ct values (Ct = 35.4) statistically higher than those of typed samples (median Ct value = 22.0; p < 0.0001, Mann–Whitney test), the inability to establish SARS-CoV-2 variants was probably linked to the low viral load. No amplification was obtained with SaS among all 35 negative TaqPath samples. Overall, 20% of samples which were typed as negative or undetermined with TaqPath, and among them, twelve were not typed even by SaS, but they were instead correctly identified with Novaplex. Although full-genome sequencing remains the elected method to characterize new strains, our data show the high ability of a SNP-based assay to identify VOCs, also resolving samples typed as undetermined with TaqPath.

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Hint, Helen, Piia Taremaa, Maria Reile i Renate Pajusalu. "Demonstratiivpronoomenid ja -adverbid määratlejatena. Miks me oleme siin ilmas, selles olukorras?" Eesti ja soome-ugri keeleteaduse ajakiri. Journal of Estonian and Finno-Ugric Linguistics 12, nr 1 (6.09.2021): 79–111. http://dx.doi.org/10.12697/jeful.2021.12.1.03.

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Kokkuvõte. Artiklis analüüsime eesti keele demonstratiivide referentsiaalseid omadusi sellistes konstruktsioonides, kus demonstratiivid kuuluvad definiitse määratlejana nimisõnafraasi koosseisu. Otsime vastust küsimusele, mille poolest erinevad demonstratiivadverb (nt siin, seal) ning demonstratiivpronoomen (see, too), kui need esinevad määratlejana koos kohakäändes nimisõnafraasiga (vrd siin koolis ja selles koolis). Oleme püstitanud hüpoteesi, et demonstratiivadverbid seostuvad ruumitähendust väljendavate substantiividega, demonstratiivpronoomenid esinevad aga nende substantiividega, mille referent on mitteruumiline. Uurimuse andmestik pärineb 2017. aasta eesti keele ühendkorpusest, kust oleme võtnud 100 lauset iga demonstratiivi kohta igas kohakäändes, seega kokku 2400 lauset. Materjali analüüsime kvantitatiivselt (tingimuslike otsustuspuude ja juhumetsadega) ning kvalitatiivselt. Uurimuse tulemused kinnitavad, et substantiivi semantilised omadused, täpsemalt substantiivi semantiline klass ning konkreetsus, on seotud määratleja valikuga. Kohatähenduses substantiividega esineb määratlejana sagedamini demonstratiivadverb, mittekoha tähenduses substantiivide määratlejana kasutatakse aga demonstratiivpronoomenit. Mittekohta tähistavate substantiivide korral mõjutab määratleja valikut omakorda sõna konkreetsus. Seega on võimalik demonstratiivseid määratlejaid eesti keeles kasutada referenti looval viisil. Abstract. Helen Hint, Piia Taremaa, Maria Reile, Renate Pajusalu: Demonstrative pronouns and demonstrative adverbs as determiners in Estonian: why are we in “here world” in “this situation”? We investigate the variation of definite determiner constructions in Estonian: noun phrases with a demonstrative pronoun (see ‘this’, too ‘that’) or demonstrative adverb (siin ‘here’, seal ‘there’) as a determiner are contrasted. The question is what differentiates the use of a demonstrative pronoun and a demonstrative adverb if used in a determiner position in an NP. The data from Estonian National Corpus 2017 were tagged for semantic class of a noun, noun concreteness, and verb type. We collected 100 clauses for each sub-construction (six spatial cases crossed with four determiner forms), 2400 clauses in total. For statistical analysis, we used conditional random forests and inference trees. We show that nouns expressing spatial meaning prefer demonstrative adverbs as determiners, while non-spatial nouns combine with demonstrative pronouns. Spatiality-wise polysemous nouns exhibit more varied preferences. Adverbial determiners are more probably used with concrete nouns, and abstract nouns co-occur with pronominals. Overall, the frequency of demonstrative adverbs as NP attributes confirms that demonstrative adverbs are productive determiners in Estonian.

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Alkhatib, Mohammad, Maria Concetta Bellocchi, Greta Marchegiani, Sandro Grelli, Valeria Micheli, Daniele Stella, Bartolomeo Zerillo i in. "First Case of a COVID-19 Patient Infected by Delta AY.4 with a Rare Deletion Leading to a N Gene Target Failure by a Specific Real Time PCR Assay: Novel Omicron VOC Might Be Doing Similar Scenario?" Microorganisms 10, nr 2 (25.01.2022): 268. http://dx.doi.org/10.3390/microorganisms10020268.

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Herein, we report a case of an Italian male infected by Delta sublineage AY.4 harboring an atypical deletion, leading to a N gene target failure (NGTF) by a commercial molecular assay for SARS-CoV-2 diagnosis (AllplexTM SARS-CoV-2 Assay, Seegene). A 59-year-old unvaccinated patient was hospitalized for pulmonary embolism, with first negative results obtained by both molecular and antigen tests. After several days of viral negativity, he presented positive results for E and RdRP/S genes, but negative in N gene. Negativity in N gene was repeatedly confirmed in the following days. Suspecting an infection by the Omicron variant, SARS-CoV-2 genome sequencing was rapidly performed from nasopharyngeal swab by MiSeq and revealed the presence of the Delta sublineage AY.4 variant with an atypical deletion of six nucleotides, leading to G214-G215 deletion in the Nucleocapsid, thus responsible for NGTF. The analysis of GISAID sequences (N = 2,618,373 12 January 2022) showed that G214-G215 deletion is rarely occurring in most circulating Delta lineages and sublineages in the globe and Europe, with an overall prevalence never exceeding 0.2%. Hence, this study highlights the importance to perform SARS-CoV-2 sequencing and to characterize novel mutations/deletions that could jeopardize the proper interpretation of molecular diagnostic tests. Based on these assumptions, the role of deletions in the recently identified Omicron variant deserves further investigation.

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Farrar, Daniel, Julie Bettinger, Annick Audet, Aaron Campigotto, Shelley Deeks, Olivier Drouin, Joanne Embree i in. "24 Characteristics and Outcomes of Hospitalized Children by SARS-Cov-2 Lineage: An IMPACT Surveillance Network Analysis". Paediatrics & Child Health 28, Supplement_1 (1.09.2023): e11-e11. http://dx.doi.org/10.1093/pch/pxad055.024.

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Abstract Introduction/Background Changes in relative virulence of SARS-CoV-2 lineages among children remain poorly understood, yet are important considerations for vaccination and health resource management. Further evidence is needed to assess the burden of severe paediatric COVID-19 due to the Omicron variant. Objectives In this study, we aimed to compare presenting features and disease severity among hospitalized children with COVID-19 in Canada by SARS-CoV-2 lineage. Design/Methods Data were collected during two national surveillance studies: the Canadian Paediatric Surveillance Program (April 2020–May 2021) and the Canadian Immunization Monitoring Program, ACTive (June 2021–May 2022). Cases were included if children were <17 years old and hospitalized for COVID-19 (excluding incidental SARS-CoV-2) at one of thirteen sentinel paediatric hospitals. SARS-CoV-2 lineages were classified as “Ancestral”, “pre-Delta” (Alpha, Beta, or Gamma), “Delta”, or “Omicron” based on genetic sequencing or the predominant lineage across Canada at the time of hospitalization. Severe disease was defined as intensive care, ventilatory or hemodynamic support requirements, organ system complications, or death. Results We identified 1357 children hospitalized with COVID-19, including 254 (18.7%) ancestral, 105 (7.7%) pre-Delta, 175 (12.9%) Delta, and 823 (60.6%) Omicron (Table). Median age at hospitalization was highest for Delta (3.0 years, interquartile range 0.2–11.1) and lowest for Omicron (1.3 years, interquartile range 0.3–5.4; p<0.001). The proportion of children with comorbid conditions did not differ significantly by lineage, ranging from 44.9% (ancestral) to 54.3% (Delta, p=0.149). COVID-19 vaccination (≥1 doses) was received by <5 pre-Delta cases (<4.8%), six Delta cases (3.4%), and 98 Omicron cases (11.9%). Among unvaccinated patients (n=1251), severe COVID-19 was most common among Delta lineages (34.3%) versus other lineages (24.0% ancestral, 22.3 pre-Delta, 24.8% Omicron; p=0.049). Conclusion Our results show more children were hospitalized during Omicron waves than all other waves combined, though Delta was relatively more severe. These findings underscore the substantial burden of Omicron in children. Potential competing interests Jesse Papenburg received consultant fees/honoraria from Astra-Zeneca, Merck, and Seegene, and is site PI for industry trials by Astra-Zeneca, MedImmune, Merck, and Sanofi (all outside current work). Rupeena Purewal is a consultant for Verity Pharmaceuticals. Manish Sadarangani has been an investigator on projects funded by GlaxoSmithKline, Merck, Moderna, Pfizer, Sanofi-Pasteur, Seqirus, Symvivo, and VBI Vaccines (all outside current work). Fatima Kakkar received salary support from the FRQS Chercheur Boursieurs Program, and honoraria from the Association des Pédiatres du Québec. Shaun Morris has received honoraria for lectures from GlaxoSmithKline and was a member of ad hoc advisory boards for Pfizer Canada and Sanofi Pasteur (all outside current work). No other competing interests are declared.

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Lim, Ho-Jae, Hye-Soo Jung, Min-Young Park, Young-Hyun Baek, Balaji Kannappan, Jin-Young Park, Jae-Hyun Yang i in. "Evaluation of Three Automated Extraction Systems for the Detection of SARS-CoV-2 from Clinical Respiratory Specimens". Life 12, nr 1 (4.01.2022): 68. http://dx.doi.org/10.3390/life12010068.

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Severe acute respiratory syndrome coronavirus (SARS-CoV-2) is highly contagious and causes coronavirus disease 2019 (COVID-19). Reverse transcription quantitative polymerase chain reaction (RT-qPCR) is the most accurate and reliable molecular assay to detect active SARS-CoV-2 infection. However, a rapid increase in test subjects has created a global bottleneck in testing capacity. Given that efficient nucleic acid extraction greatly affects reliable and accurate testing results, we compared three extraction platforms: MagNA Pure 96 DNA and Viral NA Small Volume kit on MagNA Pure 96 (Roche, Basel, Switzerland), careGENETM Viral/Pathogen HiFi Nucleic Acid Isolation kit (WELLS BIO Inc., Seoul, Korea) on KingFisher Flex (Thermo Fisher Scientific, Rocklin, CA, USA), and SGRespiTM Pure kit (Seegene Inc., Seoul, Korea) on Maelstrom 9600 (Taiwan Advanced Nanotech Inc., Taoyuan, Taiwan). RNA was extracted from 245 residual respiratory specimens from the different types of samples (i.e., NPS, sputum, and saliva) using three different kits. The 95% limits of detection of median tissue culture infectious dose per milliliter (TCID50/mL) for the MagNA Pure 96, KingFisher Flex, and Maelstrom 9600 were 0.37–3.15 × 101, 0.41–3.62 × 101, and 0.33–1.98 × 101, respectively. The KingFisher Flex platform exhibited 99.2% sensitivity and 100% specificity, whereas Maelstrom 9600 exhibited 98.3–100% sensitivity and 100% specificity. Bland–Altman analysis revealed a 95.2% concordance between MagNA Pure 96 and KingFisher Flex and 95.4% concordance between MagNA Pure 96 and Maelstrom 9600, indicating that all three platforms provided statistically reliable results. This suggests that two modifying platforms, KingFisher Flex and Maelstrom 9600, are accurate and scalable extraction platforms for large-scale SARS-CoV-2 clinical detection and could help the management of COVID-19 patients.

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Jung, Sunkyung, Mi-Na Kim, Dongeun Yong, Miae Lee, Jongwook Lee, Hae Kyung Lee i Mi-Kyung Lee. "Prevalence of Helicobacter pylori infection and clarithromycin resistance rate from 2015 to 2018 using the laboratory information system of the Seegene Medical Foundation in Korea: a repeated cross-sectional study". Annals of Clinical Microbiology 27, nr 1 (20.03.2024): 4. http://dx.doi.org/10.5145/acm.2024.27.1.4.

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Background: Numerous studies have examined the prevalence of Helicobacter pylori infection and clarithromycin (CLA) resistance rate of H. pylori. However, in South Korea, there is a lack of research analyzing specimens from local clinics and hospitals using molecular methods. This study aimed to assess the prevalence of H. pylori infection and CLA resistance across sex and age groups, as well as to explore regional variations in CLA resistance and its characteristics. Methods: Data from a laboratory information system from 2015 to 2018 were retrospectively analyzed to determine the prevalence of H. pylori infection and CLA resistance rate. The 23S ribosomal RNA genes of H. pylori were analyzed using a dual priming oligonucleotide-based multiplex polymerase chain reaction method. Results: The overall prevalence of H. pylori infection was 50.5%(12,000/23,773), with a significantly higher prevalence among males (53.5%) than females (47.0%). The CLA resistance rate was 28.3%, with a significantly higher rate among females (34.9%) than males (23.8%). Age group analysis revealed that the highest prevalence of H. pylori infection was among individuals in their 40s, whereas the highest CLA resistance rate was observed among those in their 60s. The CLA resistance rate exhibited an upward trend and varied among patients based on their place of residence, and A2143G mutation was the most prevalent across all regions. Conclusion: The prevalence of H. pylori infection and CLA resistance rate in Korea remain high and vary according to sex, age, and region. To effectively eradicate H. pylori, it is crucial to periodically monitor regional CLA resistance patterns and conduct CLA susceptibility testing before prescription.

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Park, Young Hwan, Young Ree Kim, Sun Hyung Kim i Sung Ha Kang. "Real-Time Quantitative Polymerase Chain Reaction for Apolipoprotein E genotyping". Journal of Medicine and Life Science 12, nr 1 (1.06.2015): 30–34. http://dx.doi.org/10.22730/jmls.2015.12.1.30.

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Background : Apolipoprotein E (ApoE) is an important substance responsible for the lipoprotein metabolism and thetransportation of lipid and known to play an important role in the body's physiological and pathological processes. Recently,ApoE genotyping test has been applied to the field of diagnostic methods for predicting high risk of Alzheimer's disease,cardiovascular diseases, as well as new diseases such as immune regulation disorders. Therefore, a faster and more accurateApoE genotyping test is required for the prevention of related disease and the general public health.Methods : We evaluated 220 serum specimens using two kinds of assays: one-stop Real-Q ApoE genotyping (BioSewoom,Seoul, Korea) and Seeplex ApoE ACE genotyping (Seegene, Seoul, Korea). The results were finally confirmed using sequencingas the reference. Statistical analysis was performed for the concordance rates between each assay and sequencing and thesensitivity and specificity were calculated with their 95% confidence intervals.Results : Sequencing results of 220 DNA samples showed 1 case of E2/E2, 139 of E3/E3, 9 of E4/E4, 17 of E2/E3, 4 ofE2/E4, 50 of E3/E4. The concordance rate between One-step Real-Q ApoE genotyping and sequencing was 100% (220/220),and that between Seeplex ApoE ACE genotyping and sequencing was 99.5% (219/220). Both sensitivity and specificity of OnestepReal-Q ApoE genotyping for every genotypes was 100%. The sensitivities and specificities of Seeplex ApoE ACEgenotyping were almost 100%, with two exception: 99.3% sensitivity in E3/E3 and 99.5% specificity in E2/E2.Conclusions : The performances of One-step Real-Q ApoE genotyping and Seeplex ApoE ACE genotyping were comparableoverall. However, the former showed better sensitivity and specificity comparable with those of sequencing. Hence, One-stepApoE genotyping could be a faster and more accurate option for ApoE genotyping.

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Park, Nora Jee-Young, Claire Su-Yeon Park, Ji Yun Jeong, Moonsik Kim, Su Hyun Yoo, Gun Oh Chong, Dae Gy Hong i Ji Young Park. "Strategic Significance of Low Viral Load of Human Papillomavirus in Uterine Cervical Cytology Specimens". Diagnostics 12, nr 8 (31.07.2022): 1855. http://dx.doi.org/10.3390/diagnostics12081855.

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Infection with high-risk (HR) Human Papillomavirus (HPV) is associated with the development of precancerous lesions or invasive carcinoma of the uterine cervix. Thus, the high viral load (VL) of HR-HPV DNA currently serves as a representative quantitative marker for cervical cancer. However, the clinical significance of low HPV DNA VL remains undetermined. This study aimed to evaluate the clinical association between the low HPV DNA VL and cytology/histologic diagnosis of cervical samples. We searched the electronic medical databases for the resultant analyses of HPV genotyping among patients who underwent treatment for any cervical lesion or who had undergone gynecological examinations with any positive HPV results according to the national cancer screening service between 2015 and 2016. HPV testing with genotyping and semi-quantitative VL measurement was conducted using an AnyplexTM II H28 Detection assay (H28 assay, Seegene, Seoul, Republic of Korea). The H28 assay is a multiplex semi-quantitative real-time PCR test using the tagging of oligonucleotide cleavage and extension (TOCE) technology. The VL was semi-quantified as high (3+; positive signal before 31 PCR cycles), intermediate (2+; positive between 31 and 39 PCR cycles), or low (1+; positive after 40 PCR cycles). Out of 5940 HPV VL analyses, 356 assays (5.99%) were reported as low VL (1+) of HPV DNA. Matched cytology diagnoses were mostly negative findings (n = 347, 97.5%), except for seven cases of atypical squamous cells of undetermined significance (1.9%) and two cases of atypical glandular cells (0.6%). During the follow-up periods, abnormal cytologic diagnoses were identified, including one case of high-grade squamous intraepithelial lesion (HSIL) and two low-grade squamous intraepithelial lesions (LSILs). The matched, confirmative histologic diagnosis of HSIL cytology was compatible with chronic inflammation, wherein the two LSILs had regular check-ups. None revealed clinically concerned outcomes associated with HPV-related squamous lesions. The cytology was most likely negative for malignancy when the VL of HPV DNA was low (1+). Additional strategic monitoring and management may thus be unnecessary.

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Mboumba Bouassa, Ralph-Sydney, Serge Tonen-Wolyec, David Veyer, Hélène Péré i Laurent Bélec. "Analytical performances of the AMPLIQUICK® Respiratory Triplex assay for simultaneous detection and differentiation of SARS-CoV-2, influenza A/B and respiratory syncytial viruses in respiratory specimens". PLOS ONE 17, nr 1 (5.01.2022): e0262258. http://dx.doi.org/10.1371/journal.pone.0262258.

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Although patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A, influenza B and respiratory syncytial virus (RSV) show comparable or very similar manifestations, the therapeutic approaches of these respiratory viral infections are different, which requires an accurate diagnosis. Recently, the novel multiplex real-time reverse transcription-polymerase chain reaction assay AMPLIQUICK® Respiratory Triplex (BioSynex SA, Illkirch-Graffenstaden, France) allows simultaneous detection and differentiation of SARS-CoV-2, influenza A, influenza B, and RSV in respiratory tract samples. We herein evaluated the performance of the AMPLIQUICK® Respiratory Triplex for the detection of the four viruses in respiratory specimens, using Allplex™ Respiratory Panel 1 and 2019-nCoV assays (Seegene, Seoul, Korea) as reference comparator assays. A total of 359 archived predetermined respiratory samples, including 83, 145, 19 and 95 positive specimens for SARS-CoV-2, influenza A, influenza B and RSV respectively, were included. The AMPLIQUICK® Respiratory Triplex showed high concordance with the reference assays, with an overall agreement for SARS-CoV-2, influenza A, influenza B, and RSV at 97.6%, 98.8%, 98.3% and 100.0%, respectively, and high κ values ranging from 0.93 to 1.00, indicating an almost perfect agreement between assays. Furthermore, high correlations of cycle threshold (Ct) values were observed for positive samples of the four viruses between the AMPLIQUICK® Respiratory Triplex and comparator assays, with an overall high agreement between Ct values assessed by Bland-Altman analyses. In conclusion, these observations demonstrate that the multiplex AMPLIQUICK® Respiratory Triplex is a reliable assay for the qualitative detection and differentiation of SARS-CoV-2, influenza A, influenza B, and RSV in respiratory specimens, which may prove useful for streamlining diagnostics during the winter influenza-seasons.

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Sechi, Illari, Narcisa Muresu, Mariangela V. Puci, Laura Saderi, Arcadia Del Rio, Andrea Cossu, Maria R. Muroni i in. "Preliminary Results of Feasibility and Acceptability of Self-Collection for Cervical Screening in Italian Women". Pathogens 12, nr 9 (17.09.2023): 1169. http://dx.doi.org/10.3390/pathogens12091169.

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Background: Given the diagnostic accuracy of HPV-DNA tests in terms of self-collected samples, in order to implement self-sampling in cervical screening programs, the standardization of the pre-analytical phase, including decisions concerning the choice of medium, the volume of elution, and storage conditions, are necessary, in addition to understanding the potential factors involved in acceptability by women. On this basis, we carried out a cross-sectional study to assess (i) the stability of dry vaginal self-collected samples stored at room temperature for up to 4 weeks after elution in 2 mL of eNat® (Copan) medium, and (ii) the acceptability of self-collection in enrolled women. Methods: 185 women were enrolled in the LILT (Italian League Against Tumors) regional project. A self-sampling kit, including a dry FLOQSwab® (Copan), instructions for use, and a satisfaction questionnaire, were supplied for each woman and sent by mail to the laboratory. The HPV-DNA test was carried out using the Anyplex™ II HPV HR (Seegene) kit. To evaluate the specimen’s stability, 185 dry vaginal swabs were eluted in eNat®, a lyses-based molecular medium and tested for HPV detection at two different time points (<6 days and 1 month after elution). The Cohen’s Kappa coefficients and McNemar test were used to assess the agreement of HPV-DNA at different times. Results: We found high agreement in terms of HPV-DNA results among the samples tested at two different time points (Cohen K = 0.98; p < 0.0001). Moreover, most of the women found it easy to use self-collection devices and the pictorial instructions clear to understand. Approximately half of the enrolled women declared preferring self-sampling to clinician-collected methods. Conclusion: Our results display the high reliability and accuracy of HPV-DNA tests using dry vaginal self-collection FLOQSwabs® devices eluted in 2 mL of molecular medium. The analysis of the questionnaire showed a high acceptability of self-collection among women, although a high percentage preferred standard collection devices. Overall, our preliminary results support the adoption of self-collection in screening programs, even though further analyses should be performed to optimize and standardize protocols for HPV tests on self-samples, and educational campaigns are needed to adequately inform and increase responsiveness in a target population.

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Moodley, Clinton, Hafsah Tootla, Imaan Amien i Mark E. Engel. "Evaluating the utility of the Allplex STI Essential Assay to determine the occurrence of urogenital sexually transmitted infections among symptomatic and asymptomatic patients in Cape Town, South Africa". PLOS ONE 18, nr 11 (29.11.2023): e0292534. http://dx.doi.org/10.1371/journal.pone.0292534.

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Background Sexually transmitted infections are among the most commonly occurring infections globally, with countries in sub-Saharan Africa exhibiting disproportionately higher prevalence rates. Numerous reports indicate the need for accurate detection, epidemiological characterisation, and appropriate management of these infections. This prospective observational laboratory study sought to determine the occurrence of STI, using a validated molecular assay as a diagnostic and surveillance tool in our setting. Methods Urogenital swabs from symptomatic and asymptomatic patients, submitted to the National Health Laboratory Service, at Groote Schuur Hospital, from 04 August 2021–03 February 2022, for routine microbiological investigations, were subjected to the Allplex™ STI Essential Assay (Seegene Inc, South Korea) to determine the distribution of STI pathogens in our setting. This multiplex assay includes C. trachomatis, Mycoplasma genitalium, Mycoplasma hominis, N. gonorrhoeae, Trichomonas vaginalis, Ureaplasma parvum, and Ureaplasma urealyticum. Correlations between detected organisms and participant age and clinical indications for testing were determined using Stata® software. Results A total of 148 urogenital swabs (91.2% from women) were included in the analysis, of which 56/148 (37.84%) were from symptomatic patients. Up to 83.8% of the samples tested positive for ≥1 organism, with all seven target organisms detected in at least one sample. Ureaplasma parvum was the most common organism detected, followed by N. gonorrhoeae, M. hominis, U. urealyticum, T. vaginalis, C. trachomatis, with M. genitalium being the least detected. All 25 samples submitted for routine antenatal Group B Streptococcal screening were positive for at least one STI organism, and one sample from sexual non-accidental injury tested positive for five different organisms. Conclusions STIs comprise a variety of organisms in our setting, with many patients exhibiting coinfection with multiple organisms. This suggests the need for a critical evaluation of current syndromic testing and treatment guidelines so as to stem inadvertent spread of STI organisms and the development of resistance. The use of molecular testing methods may improve detection, especially in resource limited settings, providing speedy results, and thus allowing for guided therapy in only infected patients.

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Herbst, Johanna, Vanessa Vohl, Maroje Krajina, Katharina Prieske, Anna Jaeger, Markus Leffers, Leticia Oliveira-Ferrer i in. "Abstract 6688: Development of a liquid biopsy cfDNA assay for detection of multiple HPV types in cervical neoplasias". Cancer Research 83, nr 7_Supplement (4.04.2023): 6688. http://dx.doi.org/10.1158/1538-7445.am2023-6688.

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Abstract Background: Over 95% of cervical cancers and their precancerous lesions are caused by human papillomavirus (HPV). Molecular screening approaches for HPV detection are gaining promising data over cytologic analysis. Similarly, liquid biopsy-based approaches are becoming a powerful tool for cancer detection and monitoring. Materials and Methods: An HPV panel detecting 24 HPV types was developed suitable for liquid biopsy approaches. Here, HPV measurement was performed with an iPLEX multiplex PCR-based workflow combined with mass spectrometry-based analysis (MassARRAY System, Agena Bioscience). The assay was validated on HPV positive plasmid controls and cell lines. Furthermore, 52 cervical smear samples from HSIL positive women and 40 cfDNA samples (peripheral blood) from cervical cancer patients were screened using this approach. Results: According to already published ring trial results, the HPV types HPV6, 11, 16, 18, 31, 33, 35, 39, 45, 51, 52, 58 and 59 were considered proficient with the required detection level of 50 and 5 international units (IU)/5 µl for HPV 16 and 18, and 500 and 50 HPV genome equivalents (GE)/5µl for the other HPV types (Arroyo Mühr et al., 2022). Further analyses showed a sensitivity of 0.03% for HPV16 and 0.33% HPV18 and 0.33% for the other tested HPV types. HPV DNA was detected in 94% of (49/52) smear samples analyzed. 86.5% were found positive for at least one of the high-risk HPV (hrHPV) types in the study cohort. Two of the three HPV negative samples were truly negative according to clinical data. In 15 samples, multiple HPV types were found, with positivity in up to five different HPV types. For smear samples a sensitivity of 98.14% and a positive predictive value of 0.98 (49/50) were thus obtained. The overall agreement between the MassARRAY and Seegene (from clinical records) HPV tests was 97.2% (κ=0.84). 27 of 40 (67.5%) cfDNA cervical cancer samples were tested positive for any HPV type. The distribution of HPV types showed most infections being due to hrHPV (25/27 plasma HPV positive). HPV positive samples were found in all FIGO stages, with 56.5% positivity in FIGO stage I and 87.5% in FIGO stage III and IV. Conclusions: The HPV assay showed reliable results for detecting a large number of HPV types in a multiplex mass spectrometry-based assay. A high sensitivity was achieved for both, cervical smear samples of HSIL patients as well as cfDNA from blood samples of cervical cancer patients. Citation Format: Johanna Herbst, Vanessa Vohl, Maroje Krajina, Katharina Prieske, Anna Jaeger, Markus Leffers, Leticia Oliveira-Ferrer, Yvonne Goy, Klaus Pantel, Alexander Sartori, Caren Vollmert, Linn Wölber, Katharina Effenberger, Harriet Wikman. Development of a liquid biopsy cfDNA assay for detection of multiple HPV types in cervical neoplasias [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6688.

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Cho, Young-Uk, Hyun-Sook Chi, Seongsoo Jang, Eul-Ju Seo, Jung-Hee Lee, Je-Hwan Lee, Jong-Jin Seo, Kyoo-Hyung Lee i Chan-Jeoung Park. "The Molecular Screening Using Multiplex Reverse Transcription Polymerase Chain Reaction and the Comparison with Cytogenetic Analysis in the Prognostic Stratification of Acute Leukemia". Blood 112, nr 11 (16.11.2008): 4868. http://dx.doi.org/10.1182/blood.v112.11.4868.4868.

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Abstract INTRODUCTION: The detection of chromosomal aberrations is essential for the diagnosis and prognostic stratification of acute leukemia. Classical cytogenetic analysis has the advantage of comprehensive screening of all types of abnormalities such as numerical aberrations and deletions as well as translocations. However, this technique is time-consuming and labor-intensive, and cannot detect cryptic translocations. Recently, a multiplex reverse transcription polymerase chain reaction (multiplex RT-PCR) has emerged as a tool for overcoming disadvantages of cytogenetic analysis with some degree of comprehensiveness. We designed multiplex RT-PCR system for acute leukemia based on sets of chromosomal translocations rationally selected with cost-effectiveness and clinical relevance. Herein, we tried to use molecular screening of acute leukemia with a multiplex RT-PCR system we designed, and compared with the results of cytogenetic analysis in terms of prognostic stratification. MATERIALS AND METHODS: A total of 121 consecutive patients with acute leukemia were included from November 2006 to July 2007. Multiplex RT-PCR system (Seegene, Korea) for molecular screening was carried out to detect 16 fusion transcripts: BCR-ABL, PML-RARα, PLZF-RARα, AML1-ETO, CBFβ-MYH11, DEK-CAN, E2APBX1, TEL-AML1, and MLL rearrangements (MLL-AF4, MLL-AF6, MLL-AF9, MLL-AF10, MLL-ELL, MLL-ENL, MLL-AF17, MLL-PTD). Cytogenetic analysis was performed by standard GTL-banding technique. The discordant findings were validated by fluorescence in situ hybridization (FISH) or conventional single RT-PCR. RESULTS: Eighty-nine (73.6%) adults and 32 (26.4%) children were included in this study. A total of 77 (63.6%) were diagnosed as acute myeloid leukemia (AML) and the remaining 44 (36.4%) were acute lymphoblastic leukemia (ALL) including 7 biphenotypic acute leukemia. Cytogenetic analysis was available in 118 (97.5%) of the patients. Sixty-four cases of fusion transcripts were detected in 60 patients (49.6%). Within the AML group, the following fusion transcripts were detected: 14 AML1-ETO, 8 PML-RARα, 3 CBFβ-MYH11, 1 DEK-CAN, 1 BCR-ABL, 6 MLL-PTD, 4 MLL-AF6, 3 MLL-AF9, 1 MLL-ELL. Within the ALL group, the following fusion transcripts were detected: 12 BCR-ABL, 4 TEL-AML1, 2 E2A-PBX1, 3 MLL-AF4, 1 MLL-AF9, 1 MLLPTD. The concordance rate between two tests was 88.3%. In 14 cases, the results of two methods did not agree. Seven cytogenetically unrevealed abnormalities were detected with the multiplex RT-PCR: 3 TEL-AML1, 2 MLL-AF9, 1 MLL-AF6, 1 PML-RARα. The frequency of cryptic translocation was 5.8%. MLL-PTD which is impossible to be observed by cytogenetic analysis was detected in remaining seven patients. On the other hand, the corresponding fusion transcripts were not detected by multiplex RT-PCR in three cases of inv(16), t(4;11), and MLL rearrangement suggested by FISH, respectively. Molecular screening could preferentially assign 32.5% of AML patients to favorable-risk group, and did 34.1% of ALL patients to adverse-risk group. Although the concordance rate between two methods as a prognostic factor was 89.5% in risk-determined group by multiplex RT-PCR, six patients (3 AML and 3 ALL) disclosed different risk group by molecular screening from cytogenetic analysis. CONCLUSIONS: We conclude that molecular screening using multiplex RT-PCR was useful in providing informations about genetic abnormalities more rapidly and giving appropriate therapeutic decision in acute leukemia patients. It was also useful in the detection of cytogenetically cryptic translocations. Although the multiplex RT-PCR system could not be a whole substitute for cytogenetic analysis, we expect that two methods are complementary at the time of diagnosis of acute leukemia, by which more genetic aberrations would be detected efficiently.

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Umunnakwe, Chijioke N., Zinhle N. Makatini, Mathapelo Maphanga, Anele Mdunyelwa, Khamusi M. Mlambo, Puseletso Manyaka, Monique Nijhuis, Annemarie Wensing i Hugo A. Tempelman. "Evaluation of a commercial SARS-CoV-2 multiplex PCR genotyping assay for variant identification in resource-scarce settings". PLOS ONE 17, nr 6 (24.06.2022): e0269071. http://dx.doi.org/10.1371/journal.pone.0269071.

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The rapid emergence and spread of numerous severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants across the globe underscores the crucial need for continuous SARS-CoV-2 surveillance to ensure that potentially more pathogenic variants are detected early and contained. Whole genome sequencing (WGS) is currently the gold standard for COVID-19 surveillance; however, it remains cost-prohibitive and requires specialized technical skills. To increase surveillance capacity, especially in resource-scarce settings, supplementary methods that are cost- and time-effective are needed. Real-time multiplex PCR genotyping assays offer an economical and fast solution for screening circulating and emerging variants while simultaneously complementing existing WGS approaches. In this study we evaluated the AllplexTM SARS-CoV-2 Variants II multiplex real-time PCR genotyping assay, Seegene (South Korea), and implemented it in retrospectively characterizing circulating SARS-CoV-2 variants in a rural South African setting between April and October 2021, prior to the emergence of the Omicron variant in South Africa. The AllplexTM SARS-CoV-2 Variants II real-time PCR assay demonstrated perfect concordance with whole-genome sequencing in detecting Beta and Delta variants and exhibited high specificity, sensitivity and reproducibility. Implementation of the assay in characterization of SARS-CoV-2 variants between April and October 2021 in a rural South African setting revealed a rapid shift from the Beta to the Delta variant between April and June. All specimens successfully genotyped in April were Beta variants and the Delta variant was not detected until May. By June, 78% of samples genotyped were Delta variants and in July >95% of all genotyped samples were Delta variants. The Delta variant continued to predominate through to the end of our analysis in October 2021. Taken together, a commercial SARS-CoV-2 variant genotyping assay detected the rapid rate at which the Delta variant displaced the Beta variant in Limpopo, an under-monitored province in South Africa. Such assays provide a quick and cost-effective method of monitoring circulating variants and should be used to complement genomic sequencing for COVID-19 surveillance especially in resource-scarce settings.

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Lee, H. Y., S. J. Yoon, K. A. Lee i N. H. Kim. "239IDENTIFICATION OF DIFFERENTIALLY EXPRESSED GENES IN PORCINE PARTHENOTES AT 2-CELL AND BLASTOCYST STAGES USING ANNEALING CONTROL PRIMER TECHNOLOGY". Reproduction, Fertility and Development 16, nr 2 (2004): 240. http://dx.doi.org/10.1071/rdv16n1ab239.

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Identification of embryo-specific genes will provide insight into early embryonic development. However, the current methods employed to identify genes expressed at specific stages are labor intensive and produce a high degree of false positives. In the present study we employed an accurate PCR technology controlled by an annealing control primer (ACP, SeeGene, Seoul, Korea) to identify differentially expressed genes in presumptive porcine parthenotes. In vitro-matured porcine oocytes were parthenogenetically activated by square electrical direct current pulses. After 3h of culture in North Carolina State University (NCSU) 23 medium with 0.4% BSA containing 7.5mgmL−1 cytochalasin B, embryos were washed and cultured in NCSU 23 medium with 0.4% BSA. Total RNA was prepared from a pool of 200 2-cell stage and a pool of 100 blastocyst-stage porcine parthenotes using a Dynabeads mRNA DIRECT Kit. First-strand cDNA synthesis was carried out using dT-ACP1, wherein the 3′-end core portion comprised a hybridizing sequence complementary to a poly (A) region of mRNA transcripts. Second-strand cDNAs were synthesized using PCR with an arbitrary ACP whereby the 3′-end core portion of the dT-ACP2 was prevented from annealing to the first-strand. The PCR products were electrophoresed on 2% agarose gel and stained with ethidium bromide. The differentially expressed bands were extracted and cloned into a TOPO TA cloning vector (Invitrogen, Seoul, Korea), sequenced and analyzed by BLAST search. To date we have identified 21 differentially expressed genes using 28 arbitrary ACPs. BLAST analysis revealed that most of these genes have strong homology (more than 95%) with known mouse and human genes. Differentially expressed genes in the 2-cell stage include GDP dissociation, putative translation initiation factor (SUI1) and succinate dehydrogenase iron-protein subunit. The blastocyst specific genes include rennin binding proteins, ATPase inhibitor, catenin, ribosomal protein S15a, ribosomal protein large P1, puromycin sensitive aminopeptidase, BMDP gene, arginine N-methyltrasferase p77 isoform, acylamino acid-releasing enzyme, ribosomal protein S14 and KIAA0630 protein. RT-PCR confirmed the expression of these genes in porcine parthenotes during preimplantation development. In conclusion, ACP technology is a specific and sensitive method to locate differentially expressed genes in preimplantation mammalian embryos.

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Alghounaim, Mohammad, Ahmed Abdelmoniem, Mohamed Elseadawy, Mohammad Surour, Mohamed Basuni, Jesse Papenburg i Abdulla Alfraij. "1134. The Effect of Telehealth Antimicrobial Stewardship Program on Antimicrobial Use in a Pediatric Intensive Care Unit". Open Forum Infectious Diseases 8, Supplement_1 (1.11.2021): S658. http://dx.doi.org/10.1093/ofid/ofab466.1327.

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Abstract Background Inappropriate antimicrobial use is common in pediatric intensive care units (PICU). We aimed to evaluate the effect of telehealth antimicrobial stewardship program (ASP) on the rate of PICU antimicrobial use in a center without a local infectious diseases consultation service. Methods Aretrospective cohort study was performed between October 1st, 2018 and October 31st, 2020 in Farwaniyah Hospital PICU, a 20-bed unit. All pediatric patients who were admitted to PICU and received systemic antimicrobials during the study period were included and followed until hospital discharge. Patients admitted to the PICU prior to the study period but still receiving intensive care during the study period were excluded. Weekly prospective audit and feedback on antimicrobial use was provided starting October 8th, 2019 (post-ASP period) by the ASP team. A pediatric infectious diseases specialist would join ASP rounds remotely. Descriptive analyses and a pre-post intervention comparison of days of therapy (DOT) were used to assess the effectiveness of the ASP intervention Results There were 272 and 152 PICU admissions before and after initiation of ASP, respectively. Bronchiolitis and pneumonia were the most common admission diagnoses, together compromising 60.7% and 61.2% pre- and post-ASP. Requirement for respiratory support was higher post-ASP (76.5% vs 91.5%, p< 0.001). Average monthly antimicrobial use decreased from 92.2 (95% CI 74.5 to 100) to 48.5 DOT/1,000 patient-days (95% CI 24.6 to 72.2, P < 0.05) (figure). A decline in DOT was observed across all antibiotic classes, except for ceftriaxone and clarithromycin. No effect on length of PICU stay, hospital length of stay, or mortality was observed. Most (89.7%) ASP recommendations were followed fully or partially changes in antimicrobial days of therapy (DOT)/1,000 patient-days over time. The dashed line represents the start of the antimicrobial stewardship program (ASP) Conclusion In settings where infectious diseases services are not available, telehealth stewardship can be effectively implemented and associated with a significant reduction of antimicrobial use. Disclosures Jesse Papenburg, MD, AbbVie (Grant/Research Support, Other Financial or Material Support, Personal fees)Medimmune (Grant/Research Support)Sanofi Pasteur (Grant/Research Support)Seegene (Grant/Research Support, Other Financial or Material Support, Personal fees)

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Alsharrah, Danah Y., Fatemah Al-Haddad, Sarah Aljamaan, Muneera Al-Yaseen, Nahar Al-Mutairi, Mariam Ayed, Jesse Papenburg i Mohammad Alghounaim. "441. Clinical Characteristics of Pediatric SARS-CoV-2 Infection and Coronavirus Disease 2019 (COVID-19) in Kuwait". Open Forum Infectious Diseases 7, Supplement_1 (1.10.2020): S288. http://dx.doi.org/10.1093/ofid/ofaa439.634.

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Abstract Background Clinical presentation of coronavirus disease-2019 (COVID-19) ranges from asymptomatic to severe and life threatening. National-level registries found that children, generally, have less severe disease when compared to adults. However, most asymptomatically infected children will not present to hospital and may be missed. We aimed to describe the clinical characteristics in pediatric COVID-19 patients in Kuwait, and to estimate the potential duration of viral shedding. Methods A retrospective cohort study was performed in Jaber Alahmad Hospital (JAH) from Feb. 29th to Apr. 30th, 2020. During the study period and as part of the public health measures to contain COVID-19, all SARS-CoV-2 infected patients 1 month-18 years old, regardless of symptoms, were hospitalized at JAH, and were included. Demographics, clinical data, and laboratory results were collected. Polymerase chain reaction (PCR) negativity was defined as having two consecutive negative PCR results from a respiratory specimen. Descriptive statistics and multivariable regression analyses were performed. Results A total of 134 pediatric SARS-CoV-2 infections were identified. Of those, 91 patients (67.9%) were asymptomatic, the remaining cases had mild COVID-19 illness and mild pneumonia. The median age was 8.8 years (IQR: 4.7–12.4), 55.2% were males, and 89.5% were healthy. Cough and fever were the most commonly reported symptoms. The median duration to PCR negativity was 15 days (IQR: 13–19) for symptomatic patients and 15.5 days (IQR: 14–21) for asymptomatic patients. Predictors for symptoms included abnormal procalcitonin (aOR 6.6; 95% CI 1.48 -29.3), C-reactive protein (aOR 9.10; 95% CI 1.29–32.13), and X-ray finding of pneumonia (aOR 6.44; 95% CI 1.29–32.13). Conclusion Asymptomatic SARS-CoV-2 infection is very common in children. Among symptomatic patients, the disease seems to be mild. Children exhibit substantial duration of viral shedding, as measured by PCR positivity, regardless of symptoms. Disclosures Jesse Papenburg, MD, AbbVie (Consultant, Scientific Research Study Investigator, Research Grant or Support, Speaker’s Bureau)BD Diagnostics (Research Grant or Support)Cepheid (Speaker’s Bureau)MedImmune (Scientific Research Study Investigator)Sanofi Pasteur (Scientific Research Study Investigator)Seegene (Research Grant or Support, Speaker’s Bureau)

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Costa, CAGA, NLG Albuquerque, JS Mendonça, AD Loguercio, VPA Saboia i SL Santiago. "Catechin-based Dentin Pretreatment and the Clinical Performance of a Universal Adhesive: A Two-year Randomized Clinical Trial". Operative Dentistry 45, nr 5 (30.04.2020): 473–83. http://dx.doi.org/10.2341/19-088-c.

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Clinical Relevance At 24 months, the dentin pretreatment with epigallocatechin-3-gallate did not impair the clinical performance of the adhesive Single Bond Universal regardless of the bonding strategy used. SUMMARY Purpose: To evaluate the two-year effect of dentin pretreatment with epigallocatechin-3-gallate (EGCG) on the clinical performance of restorations of noncarious cervical lesions (NCCLs) with Single Bond Universal, applied in two different modes (self-etch and etch-and-rinse). Methods and Materials: In this randomized clinical trial, 33 volunteers were selected, and 156 NCCLs were assigned to four groups: ER, etch-and-rinse; ER-EGCG, 0.1% EGCG dentin pretreatment + etch-and-rinse; SE, self-etch; and SE-EGCG, 0.1% EGCG dentin pretreatment + self-etch. The NCCLs were restored with a nanofilled resin composite and evaluated at baseline and at six, 12, 18, and 24 months using FDI criteria for retention, marginal staining, marginal adaptation, caries, and postoperative sensitivity. Two evaluators were blinded to the treatments performed, and impressions were taken for resin replicas to allow indirect observations. Statistical analyses were performed with Kruskal-Wallis and McNemar tests with a significance level of 5%. Results: Six restorations (one from ER, two from SE, one from ER-EGCG, and two from SEEGCG) were lost at 24 months with no significant differences (p>0.05). The retention rates were 97.0% (ER and ER-EGCG), 94.1% (SE), and 94.2% (SE-EGCG). For marginal adaptation, a significant difference was detected between the baseline and 24 months for the SE group (p=0.0313). There were no statistical differences among all other evaluated criteria at 24 months, neither for each group at baseline nor for 24-month comparisons (p>0.05). Conclusions: The pretreatment with EGCG provided no benefit in the clinical performance of the adhesive regardless of the bonding strategy used. In addition, it adds an additional required step to the restorative procedure.

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Playford, C., Z. Asghar, S. Armstrong, R. Ngomba i A. Rochford. "P815 Diet, nutrition, and the multidisciplinary approach in adults with Inflammatory Bowel Disease". Journal of Crohn's and Colitis 17, Supplement_1 (30.01.2023): i949—i950. http://dx.doi.org/10.1093/ecco-jcc/jjac190.0945.

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Abstract Background Patients with Inflammatory Bowel Disease (IBD) may associate dietary triggers with symptoms and even relapse of the disease, yet this is rarely acknowledged and included in treatment plans. Patients often self-impose dietary restrictions and manipulate their diet which can have significant health complications including nutrient deficiencies and malnutrition1. This often leads to a worse disease state, poorer clinical outcomes, and a reduced quality of life for these patients2. Methods A self-administered survey was digitally created with Crohn’s and Colitis UK (CCUK) and advertised through the CCUK website and their social media accounts. Patients with IBD aged ≥18 years were identified through convenience sampling. Those who were three months peri-operative or had a stoma were excluded from the study as their nutritional needs and experiences were likely to be more complex. Statistical Package for Social Sciences (version 27) was used for statistical analysis. A P-value of <0.05 was considered statistically significant. Results 267 participants completed the survey, 77.5% were female, 30% of participants were aged 36-45 years and 53.9% had Crohn’s disease. 44.9% of participants had been diagnosed with IBD for >10 years. 90% of participants believed that food impacted on their disease at least some of the time. 77% reported that dietary therapy may be useful in managing their disease (P-value < 0.001). Table 1 highlights where patients with IBD source dietary information. 93% of patients report a ‘trial and error’ approach to dietary manipulation to reduce their symptoms. Access to formal dietetic advice is extremely limited and reported by only 13% of participants. The majority of participants (78.7%) reported that a multidisciplinary approach was ‘very important’ in IBD care despite 68.2% reporting no access to a multidisciplinary team (P-value = 0.006). Table 1. Sources of IBD dietary information Conclusion Diet plays an important role in the disease course for patients with IBD; however, our respondents reported poor dietary support from healthcare professionals. This may lead to unsupervised dietary restrictions based on poor sources of information that can cause or worsen nutrient deficiencies and lead to adverse health outcomes. Patients with IBD should have access to high quality dietary advice to help manage the disease. References: 1. Nazarenkov N, Seegar K, Beekan L, et al. Implementing dietary modifications and assessing nutritional adequacy of diets for Inflammatory Bowel Disease. Gastroenterology & Hepatology. 2019; 15: 133-144. 2. Balestrieri P, Ribolsi M, Guarino M, et al. Nutritional aspects in Inflammatory Bowel Disease. Nutrients. 2020; 12: 1-11.

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Cuervo-Sierra, Jorge, David Gómez-Almaguer, Jose Carlos Jaime-Pérez, Ramón Alejandro Martínez-Hernández, Ricardo David García Sepúlveda, Mónica Sánchez-Cárdenas, Rocio Ortiz-López i in. "Prevalence Of FLT3 Mutations In Acute Myeloid Leukemia: A Multicenter Latin America Study". Blood 122, nr 21 (15.11.2013): 4979. http://dx.doi.org/10.1182/blood.v122.21.4979.4979.

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Abstract In acute myeloid leukemia (AML), FLT3 mutations are associated with a poor prognosis, particularly the internal tandem duplication (ITD/FLT3). In Latin America there are few epidemiological data about these mutations.This study assessed the prevalence of FLT3 mutations in patients with AML at four reference hematology centers from Latin America. We included 138 samples of patients attending the Hematology Service of three Mexican University Hospitals (Monterrey,México D.F. and Puebla) and one Colombian center (Medellín) with a diagnosis of AML from different morphologic subgroups according to the French-American-British classification from 2006 to 2011. AML was diagnosed by morphology according to the FAB classification, by immunohistochemical staining and/or by immunophenotype according to each particular case. For sample processing DNA was extracted from peripheral blood or bone marrow with the automatic Maxwell®16 System (Promega Corporation, Madison, WI) using the principle of cellular lyses and binding nucleic acids to magnetized silice particles or the QIAAmp DNA Blood Kit (QIAGEN, Mexico City). The quality and DNA concentration was evaluated with the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE). Then internal tandem duplication and kinase domain mutations detection was performed with the GeneAmp PCR System 9700 (Applied Biosystems, Foster City, CA), through amplification of exons 14,15 with specific primers of FLT3 gen region, using the Seeplex® FLT3 Genotyping kit (Seegene, Rockville, MD, USA) or according to Kottaridis et al (1). Later, an electrophoretic analysis of the amplified products was made in a 2% agarose gel stained with ethidium bromide or in polyacrylamide gel electrophoresis (PAGE) and were observed by transilumination. In the Puebla samples the products were analyzed by capillary electrophoresis (ABI3130, Applied Biosystems, Foster City, CA). For detection of D835X mutations the exon 20 amplicom was subjected to digestion with EcoRV and analyzed by 4.5% PAGE. The patients were cytogenetically classified into three risk groups: favorable, intermediate, and adverse. Results We analyzed 138 samples of AML patients and found FLT3 mutations in 28 patients, for a prevalence of 20.3%. The median age was 47 years (5-96). Only four patients had the KD FLT3 mutation (3% of total population). The FLT3 mutation positive group was older than the negative (47 vs. 39 years), had higher WBC/mm3 (66.0 vs. 56.4 x 109/dl), higher hemoglobin values (9.3 vs. 8.6 g/dl), and lower platelet counts (72.6 vs. 92.5 x109/dl), although there were not statistically significant differences. Thirteen patients had AML M2, nine the monocytic variety, four had M3 and two M1. On cytogenetics 25% , 62.5% and 12.5% had favorable, intermediate and unfavorable risk karyotypes respectively. The rate response to standard Induction Chemotherapy was 78.3 % for the FLT3 positive group vs. 74.1 % for the non-mutated group. Nineteen of 28 patients (67.8%) with FLT3 mutations died, compared to 47 of 100 (42.72%) in those without the mutation. The median survival was 4.9 months for the FLT3 mutated group vs 20.4 months for the FLT3 negative group, P= 0.009. The cytogenetic intermediate risk group (62.5%) was further analyzed and no statistically significant difference in overall survival between FLT3 non-mutated and FLT3 mutated patients was found (P= 0.22). Younger patients (<55 years) had a higher mortality in the FLT3 positive group (P = 0.023).The presence or absence of the FLT3 mutation in patients who had the morphologic subtype M3 did not impact mortality (P = 0.28), but in non M3 subtypes, it did (P= 0.017). As conclusion, in this Latin American population the FLT3 mutation conferred a bad prognosis. References 1. Kottaridis PD, Gale RE,Frew ME et al. The presence of a FLT3 internal tandem duplication in patients with acute myeloid leukemia (AML) adds importatnt prognostic information to cytogenetic risk group and response to the first cycle of chemotherapy: analysis of 854 patients from the United Kingdom Medical Research Council AML 10 and 12 trials. Blood.2001; 98: 1752-1759 2. Emerenciano M, Meneses J, Vasquez ML et al, Brazilian Collaborative Study Groupof Infant Acute L. Clinical relevance of FLT3 gene abnormalities in Brazilian patients with infant leukemia.Leuk Lymphoma. 2008; 49 (12):2291-2297. Disclosures: No relevant conflicts of interest to declare.

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Pedachenko, Y. E., I. G. Vasilieva, N. G. Chopik, O. I. Tsiubko, N. P. Oleksenko, A. B. Dmytrenko, T. A. Makarova i I. M. Shub. "Molecular Characteristics of Blood Serum After Covid-19 Vaccination in a Remote Period". Mikrobiolohichnyi Zhurnal 86, nr 2 (28.04.2024): 75–89. http://dx.doi.org/10.15407/microbiolj86.02.075.

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COVID-19 is a dangerous disease with long-lasting consequences. Vaccination contributes to the accumulation of neutralizing anti-S IgG antibodies, reducing the incidence of COVID-19 and its complications. However, in some individuals, the inflammatory process can persist for an indefinite period and lead to a wide range of dysfunctions. The current task is to investigate molecular markers for their detection. The aim of this study is to examine the levels of anti-S IgG antibodies, lactate, glucose, lactate dehydrogenase, and C-reactive protein in the peripheral blood of individuals who have and have not been affected by COVID-19 after vaccination. The research subject is venous blood. Among 547 employees of the Neurosurgery Institute (481 vaccinated against COVID-19 and 66 unvaccinated individuals), levels of anti-S IgG antibodies were investigated, as well as levels of lactate, lactate dehydrogenase, glucose, and C-reactive protein. At the time of the study, among 372 individuals, 16 months had passed from the first vaccination, and 12 months had passed from the second vaccination; in 21 individuals, 12 months had passed after a single vaccination, and in 88 individuals, 16 months had passed from the first vaccination, 12 months from the second, and 6 months from the third vaccination. Methods. Quantitative determination of IgG antibodies to the S protein of the SARS-CoV-2 virus. Confirmation of COVID-19 using the RT-PCR method (Allplex 2019-nCoV kit, SeeGene, Korea). Levels of lactate, lactate dehydrogenase, glucose, and C-reactive protein were determined using reagents from BioSystems (Spain). Statistical analysis of the obtained data was performed using Jamovi software (USA) and the following criteria: χ2 ‒ Kruskal-Wallis, W ‒ Dwass-Steel-Critchlow-Fligner (DSCF), χ2 ‒ Pearson, t ‒ Student, rs ‒ Spearman, τb ‒ Kendall. A statistically significant difference was considered at p < 0.05. Results. The level of anti-S IgG antibodies to the SARS-CoV-2 virus was higher in vaccinated individuals compared to unvaccinated individuals (Kruskal-Wallis χ2=14.09; p < 0.001). A higher level of antibodies to the S protein of the virus was observed when using the Comirnaty vaccine compared to vaccination with Moderna, AstraZeneca, Pfizer, and CoronaVac (Dwass-Steel-Critchlow-Fligner (DSCF): W 4.26, p=0.002; W 4.62, p=0.010; W 4.84, p=0.006, respectively). Vaccination reduces the likelihood of contracting the disease by 1.84 times (Odds Ratio (OR) 1.84; 95% Confidence Interval (CI) 1.02‒3.30; χ2=4.129; p=0.043). However, no statistically significant dependence on the prevention of COVID-19 incidence based on the type of vaccines used was found (Kruskal-Wallis χ2=2.072; p=0.72). A statistically significant difference in C-reactive protein levels is observed between groups with early mild complications and early moderate-severity complications (DSCF: W=4.193, p=0.009). A statistically significant difference in LDH levels is noted between individuals without chronic diseases and those with chronic diseases at the time of the study (Kruskal-Wallis χ2=6.08, p=0.014). In individuals vaccinated against the SARS-CoV-2 virus, a positive correlation is found between the levels of C-reactive protein and lactate dehydrogenase (Kendall's τb 0.134, p < 0.001). The mean levels of lactate among individuals with mild, moderate, and severe forms of COVID-19 are higher than the reference mean; similarly, the mean levels of glucose in these same groups are higher than the reference mean. A positive correlation exists between the levels of lactate and glucose among individuals vaccinated against the SARS-CoV-2 virus (Kendall's τb 0.082, p < 0.01). Conclusions. Vaccination contributes to an increase in antibody levels. The level of antibodies after the third vaccination exceeded the levels after the first (Dwass-Steel-Critchlow-Fligner (DSCF): W 4.42, p=0.005) and second vaccinations (W 4.24, p=0.008). Vaccination reduces the likelihood of COVID-19 infection by 1.84 times (Odds Ratio ‒ 1.84; 95% Confidence Interval 1.02‒3.30; Pearson χ2=4.129; p=0.043). The frequency of COVID-19 incidence is not dependent on the type of vaccine used: AstraZeneca, Comirnaty, CoronaVac, Moderna, Pfizer (Kruskal-Wallis χ2=2.072; p=0.723), and the level of antibodies in the vaccinated individuals' serum. In the post-COVID-19 remote period, regardless of vaccination status, various complications are observed. However, among the vaccinated, the number of individuals without complications or with minimal complications is greater than in the unvaccinated group, while the number of individuals with early and severe complications is lower (Kruskal-Wallis χ2=6.127; p=0.047). A high level of C-reactive protein (DSCF: W=4.19, p=0.009), a tendency toward increased levels of lactate dehydrogenase (DSCF: W=3.27, p=0.054), elevated levels of lactate (2.17+1.23, t=3.34; p=0.002), and glucose (6.06+0.048, t=10.54; p < 0.001) indicate that after recovering from COVID-19, regardless the type of vaccines used, in individuals with distant symptoms there are metabolic changes that are signs of a chronic inflammatory process. Individuals with chronic diseasees show an increase in the level of lactate dehydrogenase (χ2=6.08; p=0.014) and a tendency toward increased levels of C-reactive protein (χ2=3.74; p=0.053). Molecular markers of inflammation such as increased levels of lactate, glucose, C-reactive protein, and lactate dehydrogenase are informative for identifying individuals with an inflammatory process in the post-COVID-19 remote period.

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Branson, L., D. Southard, A. Jaime, W. Katrangi i R. Alturkmani. "A-268 Evaluation of a Real-Time Multiplex PCR Assay for Simultaneous Detection of Chlamydia trachomatis, Neisseria gonorrhoeae, and Trichomonas vaginalis in Urine Specimens". Clinical Chemistry 69, Supplement_1 (27.09.2023). http://dx.doi.org/10.1093/clinchem/hvad097.236.

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Abstract Background Infections with Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), and Trichomonas vaginalis (TV) are among the most prevalent and treatable sexually transmitted diseases in the US. Currently, most available testing methods require patient samples to be split between CT/NG and TV assays. Here, we evaluate performance characteristics of the Seegene Novaplex STI Essential Assay, a real-time multiplex polymerase chain reaction assay for concurrent amplification and detection of multiple pathogens including CT, NG, and TV. Methods To prepare urine samples for extraction, 1 mL of each sample was centrifuged at 13 000 rpm for 15 min. The supernatant was discarded and the pellet was rehydrated in 190 µL of saline. Nucleic acid extraction was performed on a CyBio® FeliX liquid handler (Analytik Jena, Germany) using MagMAX™ Viral/Pathogen Nucleic Acid Isolation Kit (Thermo Fisher Scientific, MA). PCR amplification and detection were performed using Seegene Novaplex STI assay (Seegene Inc, South Korea) on a CFX96™ System (Bio-Rad Laboratories, CA). The assay utilizes Seegene MuDT™ technology that allows detection of multiple targets in a single channel without melting curve analysis. For method validation, precision studies were performed within-run and over 5 days. Limits of detection were verified by spiking known negative urine samples with CT/NG standards from Exact Diagnostics (Bio-Rad Laboratories, CA) and TV standards from ZeptoMetrix® (Antylia Scientific, IL). Method comparison was carried out by extracting and analyzing split patient urine samples against cobas® CT/NG assay (Roche Diagnostics, IL) and Solana® Trichomonas assay (Quidel, CA) performed by a reference laboratory. Additional accuracy studies were performed by spiking 20 negative patient samples with variable concentrations of the three pathogens. Results Within-run and between-day precision studies demonstrated consistent and reproducible results for all pathogens. Limit of detection was established at 10 copies/mL for CT and NG and 10 cells/mL for TV. Results of the spike-and-recovery studies were consistent with expected results for all three targets across evaluated concentrations. Patient correlation studies demonstrated 100% agreement with results obtained by the reference laboratory for both NG (32 total samples, 11 positive) and TV (22 total samples, 4 positive), and 96% agreement for CT (29 total samples, 10 positive). Conclusion The Seegene Novaplex STI Essential Assay offers a rapid and reliable method for detecting CT, NG, and TV in urine samples. The capability of the assay to detect multiple targets in a single sample well improves efficiency and turnaround time.

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Haqshenas, Gholamreza, Monica Molano, Samuel Phillips, Prisha Balgovind, Suzanne M. Garland, David Hawkes, Julia ML Brotherton, Dorothy A. Machalek i Gerald Murray. "Evaluation of Seegene Anyplex II Performance for Detection of Human Papillomavirus Genotypes in Formalin-Fixed, Paraffin-Embedded Cervical Cancer Specimens". Archives of Pathology & Laboratory Medicine, 23.05.2023. http://dx.doi.org/10.5858/arpa.2022-0317-oa.

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Context.— Detection of human papillomavirus (HPV) in formalin-fixed, paraffin-embedded (FFPE) tissues may identify the cause of lesions and has value for the development of new diagnostic assays and epidemiologic studies. Seegene Anyplex II assays are widely used for HPV screening, but their performance using FFPE samples has not been fully explored. Objective.— To validate Anyplex II HPV HR Detection (Anyplex II, Seegene) using FFPE samples. Design.— We used 248 stored DNA extracts from cervical cancer FFPE samples collected during 2005–2015 and that tested HPV positive using the RHA kit HPV SPF10-LiPA25, v1 (SPF10, Labo Biomedical Products) HPV genotyping assay, manufacturer-validated for FFPE samples. Results.— Of the selected 248 samples, 243 were used in our analysis. Consistent with SPF10 genotyping results, Anyplex II detected all 12 oncogenic types and had an overall HPV detection rate of 86.4% (210 of 243 samples). Anyplex II and SPF10 showed very high agreement for the detection of the 2 most important oncogenic genotypes: HPV 16 (219 of 226; 96.9%; 95% CI, 93.7–98.75) and HPV 18 (221 of 226; 97.8%; 95% CI, 94.9–99.3). Conclusions.— Overall results showed that both platforms produced comparable HPV genotyping results, indicating the suitability of Anyplex II for FFPE samples. The Anyplex II assay has the added convenience of being an efficient, single-well semiquantitative polymerase chain reaction assay. Further optimization of Anyplex II may enhance its performance using FFPE samples by improving the detection limit.

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Pearson, Joel D., Daniel Trcka, Suying Lu, Sharon J. Hyduk, Mark Jen, Marie-Ming Aynaud, J. Javier Hernández i in. "Comparison of SARS-CoV-2 indirect and direct RT-qPCR detection methods". Virology Journal 18, nr 1 (17.05.2021). http://dx.doi.org/10.1186/s12985-021-01574-4.

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Abstract Background Sensitive, rapid, and accessible diagnostics continue to be critical to track the COVID-19 pandemic caused by the SARS-CoV-2 virus. RT-qPCR is the gold standard test, and comparison of methodologies and reagents, utilizing patient samples, is important to establish reliable diagnostic pipelines. Methods Here, we assessed indirect methods that require RNA extraction with direct RT-qPCR on patient samples. Four different RNA extraction kits (Qiagen, Invitrogen, BGI and Norgen Biotek) were compared. For detection, we assessed two recently developed Taqman-based modules (BGI and Norgen Biotek), a SYBR green-based approach (NEB Luna Universal One-Step Kit) with published and newly-developed primers, and clinical results (Seegene STARMag RNA extraction system and Allplex 2019-nCoV RT-qPCR assay). We also tested and optimized direct, extraction-free detection using these RT-qPCR systems and performed a cost analysis of the different methods evaluated here. Results Most RNA isolation procedures performed similarly, and while all RT-qPCR modules effectively detected purified viral RNA, the BGI system provided overall superior performance (lower detection limit, lower Ct values and higher sensitivity), generating comparable results to original clinical diagnostic data, and identifying samples ranging from 65 copies to 2.1 × 105 copies of viral genome/μl. However, the BGI detection system is more expensive than other options tested here. With direct RT-qPCR, simply adding an RNase inhibitor greatly improved detection, without the need for any other treatments (e.g. lysis buffers or boiling). The best direct methods detected ~ 10 fold less virus than indirect methods, but this simplified approach reduced sample handling, as well as assay time and cost. Conclusions With extracted RNA, the BGI RT-qPCR detection system exhibited superior performance over the Norgen system, matching initial clinical diagnosis with the Seegene Allplex assay. The BGI system was also suitable for direct, extraction-free analysis, providing 78.4% sensitivity. The Norgen system, however, still accurately detected samples with a clinical Ct < 33 from extracted RNA, provided significant cost savings, and was superior to SYBR green assays that exhibited reduced specificity.

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Mendonça, C. P., i D. A. Zauli. "A-303 Validation of a Quantitative and Qualitative Molecular Test for the Detection of Epstein-Barr Virus by Real-Time qPCR". Clinical Chemistry 69, Supplement_1 (27.09.2023). http://dx.doi.org/10.1093/clinchem/hvad097.268.

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Abstract Background The Epstein-Barr virus (EBV, HHV-4) is a human virus of the Herpesviridae family, mainly associated with infectious mononucleosis in adolescence, but it can also be related to other tumors. About 90% of the world's population has been infected by this virus, although the vast majority of these people are asymptomatic. In immunocompromised individuals, such as transplant recipients and HIV-infected patients, high EBV replication is a major predisposing factor to the development of a wide range of B-cell lymphoproliferative disorders such as Burkitt's lymphoma, nasopharyngeal carcinoma, Hodgkin's and non-Hodgkin lymphoma. Early detection of EBV is crucial for the effective management of patients on immunosuppressive therapy after transplantation and immunoproliferative disease. EBV-related diseases, such as in suspected cases of chronic fatigue syndrome and after transplants can be identified by EBV-DNA quantification. Molecular assays, such as Real Time qPCR, have high sensitivity and specificity and are a useful tool for the early diagnosis of EBV infection. This assay differentiates healthy carriers, with low levels of viral load, from ill carriers with a high rate of viral replication. In this way, this work aimed to validate and verify the performance of the alinity m EBV assay. Methods To evaluate the molecular detection of the EBV virus, we used the automated EBV alinity m assay (Abbott). Were evaluated 141 samples from the Molecular Genetics routine of the Pardini Group. Of those, 91 samples (63 plasma and 28 cerebrospinal fluid) were previously tested by in-house PCR for qualitative EBV detection and 50 samples (plasma) were previously tested for quantitative EBV detection by Real-Time PCR (Seegene platform). At the end of the tests, the previous qualitative and quantitative results were compared with the Alinity m EBV test results. Results The range of Alinity m EBV assay detection was <20 IU/mL or <1.30 log(IU/mL) to 200 000 000 IU/ml or 8.30 log(IU/ml). For qualitative analysis, the positive agreement was 100% in both plasma (7/7) and cerebrospinal fluid (6/6) samples, with quantification variation from 2.07 to 4.60 Log(IU/mL) and <1 .30 to 6.30 Log(IU/mL), respectively. The negative agreement was 89% (50/56) for plasma samples, with 6 discordant samples between 1.13 to 3.39 Log(IU/mL) and 91% for cerebrospinal fluid samples (21/23), with two disagreements (1.69 and 2.23 Log(IU/mL), considering the results below the detection range of the assay (<20 IU/mL or <1.30 Log (IU/mL)) as negative because they did not clinical relevance. In quantitative analysis, the negative agreement between comparative methodology (Seegene platform) was 81.0% (33/42), considering as discordant only the samples with a quantifiable detected result. Discordant samples detected by Alinity—and not detected by Seegene platform—presented quantification between 21–791 IU/mL, indicating greater sensitivity of the analyzed methodology. Positive agreement was 100% (5/5). Conclusion The Alinity m EBV Assay demonstrated good performance for molecular detection of EBV. This test can be used as an important tool for clinicians to identify patients with infection, especially in immunosuppressed cases that require a fast, accurate, and reliable diagnosis.

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Peris, M., E. Franco-Marín, B. Dehesa-García, B. García-Manrique i H. Alonso. "A-298 Performance Analysis of Three Mpox Real Time PCR Kits With Lesion Swab Clinical Samples". Clinical Chemistry 69, Supplement_1 (27.09.2023). http://dx.doi.org/10.1093/clinchem/hvad097.263.

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Abstract Background The appearance of skin lesions can be a symptom of infection or reactivation of the HSV-1, HSV-2, VZV or T. pallidum or even monkeypox virus infection. Due to the contact-bound ease of spread of these pathogens, an accurate and fast diagnosis, such as PCR-based testing, is key to a good epidemiological management. The aim of this study was to determine the clinical performance of three qPCR assays. Methods A total of 334 cutaneous swabs collected from patients attended at the Hospital Universitario Miguel Servet were analysed using the three assays under study: VIASURE Herpes virus 1, Herpes virus 2 & Varicella Zoster Virus Real Time PCR Detection Kit, VIASURE Treponema pallidum Real Time PCR Detection Kit and VIASURE Mpox Real Time PCR Detection Kit. Samples were collected between December 2021 and November 2022. These samples were requested through the Biobanco del Sistema de Salud de Aragón (BSSA) and have the approval of the Aragón Ethics Committee (PI22/409). DNA/RNA extraction was performed using the automated extraction method magLEAD® 12gC instrument with the MagDEA Dx SV kit and amplification was performed using the thermocycler CFX96™ Real-Time PCR Detection System (BioRad). The obtained results were compared with the reference assays RealStar® Orthopoxvirus PCR Kit 1.0 (Altona) and Allplex™ Genital ulcer assay (Seegene®). Results After data analysis a very good overall agreement was obtained for all the studied targets. Conclusion The assays under study demonstrated to be a good tool for differential analysis in skin lesions compatible with HSV-1, HSV-2, VZV, T. pallidum or mpox virus infection. In addition, the shared thermal protocol of the assays allowed for the simultaneous detection in the sample, creating a personalized panel option for the user, as opposed to the reference assays employed, which required two separate analyses, taking longer to reach the full assessment of the sample.

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Marling, Raili. "Authenticity and Depthiness in the Representation of Affects: Perception and Performativity in Contemporary (Auto)Fiction / Autentsus ja sügavuse illusioon afektide kujutamises: taju ja performatiivsus nüüdisaegses ilukirjanduses ja autofiktsioonis". Methis. Studia humaniora Estonica 22, nr 27/28 (15.12.2021). http://dx.doi.org/10.7592/methis.v22i27/28.18441.

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Abstract: This article analyses the tension between the perception and performance of affect in two contemporary texts: Heather Christle’s The Crying Book (2019) and Christine Smallwood’s The Life of the Mind (2021). Both subvert the expectation of feminine sentiment and pose questions about the authenticity of affect. Although affects are always mediated in fiction, experimental fictional texts have the potential for greater authenticity than the performative affective displays of the emotional public sphere. Üks afektiuuringute keskseid teoreetikuid Brian Massumi (2002b, 233) väidab, et tänapäeval on afekt olulisem mõiste kui ideoloogia, sest võim toimib üha enam afektide abil. Kuna üldiselt vaadeldakse afekte kehaliste intensiivsustena, mida ei saa teadlikult kontrollida, siis peetakse neid autentseiks, seda ka tänapäeval, mil autentse ja võltsi piir on üha ähmasem. Kuigi üksikisiku tasandil on afektid tõesti raskesti kontrollitavad, on eri valdkondade teadlased näidanud, et afekte on võimalik kunstlikult esile kutsuda, nt poliitiliste või turunduskampaaniate või ka kogemusturismi abil. Seega väärib afektide autentsus lähemat analüüsi. Käesolev artikkel väidab, et afektid, mida me avalikus sfääris kohtame, on performatiivsed: nad lähtuvad sotsiaalsetest normidest ja tsiteerivad varasemaid afektiivseid esitusi, mis on korduste tõttu omandanud autentsuse aura. Afektide performatiivsus ei tähenda, et nad on võltsid; lihtsalt me ei tohiks nende siirust üle hinnata. Ka performatiivsed afektid kõnetavad teisi inimesi ning tekitavad autentseid afektiivseid reaktsioone. Afektid liiguvad kehalt kehale, nagu väidab Anna Gibbs (2001, 1), aga ka teatrilavalt, kinolinalt või raamatulehekülgedelt publikuni. Seega väärib afektide kujutamine ja selle performatiivsus lähemat tähelepanu kirjanduse ja teiste kunstivormide analüüsis. Jennifer Doyle (2013, 85) väidab, et kui emotsioonist saab emotsiooni representatsioon, siis kerkivad kohe küsimused selle emotsiooni autentsuse kohta. Kuigi tekstidesse kätketud emotsioon või afekt on alati mugandus ja ehk isegi manipulatsioon, ei kaota see oma väge publikut kõnetada ja selles afekte luua. Palju on uuritud etenduskunsti, mis ründab vaatajate meeli ja ootusi ning ka lugejas tugevaid emotsioone tekitavaid traumanarratiive. Vähem on tähelepanu saanud raskesti loetavad ja näilised tundetud kirjandustekstid, mille afektiivne laeng on ambivalentsem. Aga ka sellistel tekstidel on potentsiaal pakkuda inimestele uudseid viise maailmaga suhestumiseks (Berlant ja Prosser 2011, 182). Artikkel keskendub konkreetselt ühele autentseks peetavale afektiivsele fenomenile, pisaratele. Pisarad on üks ilmsemaid afektide ilminguid, mida me ei kontrolli ning mis seega näivad autentseina. Samas juba Roland Barthes (2002) juhib tähelepanu pisarate dialoogilisusele ja suisa manipulatiivsusele. Pisarad on seega huvitav näide afektide autentsuse ja performatiivsuse analüüsimiseks, seda enam, et pisaraid kasutatakse mitmesugustes kunstilistes ja kirjanduslikes tekstides afektide tähistajana. Artikkel lähtub Eugenie Brinkema (2014, 4) soovitusest otsida tekstidest afektide tekstilisi kujutusi, et hoiduda afektiuuringutele tihti omasest subjektiivsusest ning liikuda pelgalt afektide tarbimiselt sügavama teoreetilise analüüsini. Brinkema (2014, 37) soovitab otsida afektide vormi, mis võimaldab analüüsides olla tähelepanelikum kirjandusteksti stiililise keerukuse ja nüansirikkuse suhtes. Seega vaatleb artikkel kirjandusteksti keelelisi väljendusvahendeid kui afektide esitamise ja loomise vahendeid. Artiklis analüüsitakse kaht nüüdiskirjanduse näidet, mis eksperimenteerivad pisarate kujutamisega. Esimeseks tekstiks on Heather Christle’i autobiograafia sugemetega essee „The Crying Book“ („Nuturaamat“, 2019) ja teine Christine Smallwoodi romaan „The Life of the Mind“ („Vaimuelu“, 2021). Neid tekste võiks vaadelda uussiiruse näitena, kuid artikkel väidab pigem, et mõlemad autorid küsimärgistavad naiselikkuse ja naiskogemusega seondatavat sentimentaalset siirust. Pisaraid kasutatakse ühtaegu lugeja kõnetamiseks ja samaaegselt lihtsa pinnalugemise õõnestamiseks. Pisarad on performatiivsed, kuid samas ka autentsed, signaliseerides lugejale, et teiste afektide tähendus jääb meile alati kättesaamatuks. Pisarad ei allu ühesele tõlgendusele, näidates autentse ja performatiivse vahelise piiri poorsust. Tänapäeva menukite hulgas on palju mälestusi, traumanarratiive ja pihtimisi, milles mälu on suunatud tunnete voolusängi (Shields 2010, 56). Sellised tihti kommertslikult pakendatud kogemused on muutunud piiravaiks, sest nad pakuvad liiga kergesti loetavaid ja tarbitavaid stereotüüpseid emotsioone. Artiklis analüüsitud tekstid julgevad sellele kergesti loetavuse ja tarbitavuse kiusatusele vastu hakata. Nad toovad meid näiliselt turvalisse sentimentaalse pihtimuse maailma, kuid siis eemaldavad selged teetähised ja jätavad meid omapäi autentsuse ja performatiivsuse piire kompama. Selline strateegia tekitab lõhe lugeja ja teksti vahel, kuid just selle lõhe ületamiseks tehtud jõupingutus aitab meil mõista näiliselt selgete afektide tegelikku mitmetähenduslikkust. Kuigi kirjanduslikud afektid on alati vahendatud, on eksperimentaalses kirjanduses vähemalt potentsiaal murda välja stereotüüpidele üles ehitatud emotsionaalse avaliku sfääri turvalisest tarbijasõbralikkusest ning meenutada meile elatud kogemuse vasturääkivust ja metsikust.

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Aschbacher, Richard, Francesca Romagnoli, Elisa Masi, Valentina Pasquetto, Franco Perino, Klaus Eisendle, Monica Braghetto, Sergio Messini, Serena Delbue i Elisabetta Pagani. "Molecular epidemiology of non-viral sexually transmitted infections in the central Alpine province of Bolzano, northern Italy from April 2016 to March 2017". Microbiologia Medica 33, nr 1 (19.12.2018). http://dx.doi.org/10.4081/mm.2018.7852.

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Chlamydia trachomatis, Neisseria gonorrhoeae, Trichomonas vaginalis, Ureaplasma parvum, Ureaplasma urealyticum, Mycoplasma hominis and Mycoplasma genitalium are established or presumed as (??) STI pathogens. The present study aims at ng describing the one-year molecular epidemiology of these seven pathogens in the Province of Bolzano, Northern Italy. From April 2016 to March 2017, a total of 2,949 patients, mainly females, were enrolled and 3,427 urine, vaginal, endocervical and/or urethral samples were subjected to simultaneous analysis of the seven pathogens by means of Real Time Polymerase Chain Reaction (AnyplexTM II STI-7 Detection Kit Seegene, Seoul, Korea). At least one of the seven microorganisms was detected in 40.7% of patients, with an uneven distribution: 43.1% in females (F) and 29.8% (p<0.001) in males (M). The prevalence of microorganisms was as follows: 30.3% U. parvum (F: 35.6%, M: 8.3%), 6.9% U. urealyticum (F: 6.8%, M: 7.0%), 4.9% M. hominis (F: 5.4%, M: 2.3%), 4.9% C. trachomatis (F: 3.4%, M: 11.4%), 1.1% M. genitalium (F: 1.0%, M: 1.2%), 1.2% N. gonorrhoeae (F: 0.17%, M: 5.6%) and 0.40% T. vaginalis (F: 0.38%, M: 0.53%). Mixed infections were detected in 7.4% of patients. The highest prevalence was observed for U. parvum, followed by U. urealyticum and M. hominis and a significant presence of multi-pathogen infections was registered.

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Saraiello, Angela, Federica Ferrentino, Nunzia Cuomo, Maria Grimaldi, Erasmo Falco, Marcello Raffone, Antimo Di Spirito i in. "Correlation between cycle threshold and viral load through comparison of RT-PCR qualitative <em>versus</em> quantitative assay for SARS-CoV-2". Microbiologia Medica 36, nr 2 (26.10.2021). http://dx.doi.org/10.4081/mm.2021.9999.

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Background and aims. Real-time reverse transcription polymerase chain reaction (RT-PCR) is the gold-standard assay to detect SARS-CoV-2, but it has limitations compared to viral load analysis. Quantitative detection improves surveillance, diagnosis, and prevention. We performed a comparative study of qualitative and quantitative tests for the diagnosis of COVID-19 on respiratory samples from patients screened for SARS-CoV-2 infection, and explored the correlation between viral load compared to the threshold cycle (Ct) value obtained in RT-PCR.Materials and methods. Sixty respiratory samples from patients affected by SARS-CoV-2 were subjected to both the qualitative (Allplex ™ 2019-nCoV Seegene) and the quantitative (Clonit® Quanty COVID-19) assays, and the relationship between viral load and Ct value was assessed by Spearman correlation analysis (ρ). In addition, the viral load of samples collected from a patient with symptomatic cancer was monitored. Results. The results show 100% agreement between the results obtained with quantitative assay and the reference standards, whereas 99.2% agreement was found for the qualitative test. A strong negative Spearman’s correlation between the Ct values of the N genes and RdRP gene was observed from qualitative assay values and viral loads.Conclusions. Quantitative assay has a higher sensitivity than qualitative assay, and viral load testing allows the clinicians to better orient themself in the choice of therapeutic treatment to be adopted. The constantly higher viral load of clinical cases considered, irrespective of the different therapies used, confirms that viral load monitoring could represent a great advantage in clinical practice.

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Heger, Lukas Andreas, Nils Elsen, Marina Rieder, Nadine Gauchel, Urte Sommerwerck, Christoph Bode, Daniel Duerschmied, Mark Oette i Ingo Ahrens. "Clinical analysis on diagnostic accuracy of Bosch Vivalytic SARS-CoV-2 point-of-care test and evaluation of cycle threshold at admission for COVID-19 risk assessment". BMC Infectious Diseases 22, nr 1 (23.05.2022). http://dx.doi.org/10.1186/s12879-022-07447-7.

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Abstract Background Point-of-care (POC) polymerase chain reaction (PCR) tests have the ability to improve testing efficiency in the Coronavirus disease 2019 (COVID-19) pandemic. However, real-world data on POC tests is scarce. Objective To evaluate the efficiency of a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) POC test in a clinical setting and examine the prognostic value of cycle threshold (CT) on admission on the length of hospital stay (LOS) in COVID-19 patients. Methods Patients hospitalised between January and May 2021 were included in this prospective cohort study. Patients’ nasopharyngeal swabs were tested for SARS-CoV-2 with Allplex™2019-nCoV (Seegene Inc.) real-time (RT) PCR assay as gold standard as well as a novel POC test (Bosch Vivalytic SARS-CoV-2 [Bosch]) and the SARS-CoV-2 Rapid Antigen Test (Roche) accordingly. Clinical sensitivity and specificity as well as inter- and intra-assay variability were analyzed. Results 120 patients met the inclusion criteria with 46 (38%) having a definite COVID-19 diagnosis by RT-PCR. Bosch Vivalytic SARS-CoV-2 POC had a sensitivity of 88% and specificity of 96%. The inter- and intra- assay variability was below 15%. The CT value at baseline was lower in patients with LOS ≥ 10 days when compared to patients with LOS < 10 days (27.82 (± 4.648) vs. 36.2 (25.9–39.18); p = 0.0191). There was a negative correlation of CT at admission and LOS (r[44]s = − 0.31; p = 0.038) but only age was associated with the probability of an increased LOS in a multiple logistic regression analysis (OR 1.105 [95% CI, 1.03–1.19]; p = 0.006). Conclusion Our data indicate that POC testing with Bosch Vivalytic SARS-CoV-2 is a valid strategy to identify COVID-19 patients and decrease turnaround time to definite COVID-19 diagnosis. Also, our data suggest that age at admission possibly with CT value as a combined parameter could be a promising tool for risk assessment of increased length of hospital stay and severity of disease in COVID-19 patients.

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Lee, Sun Jung, Tae Su Jang i Jae Kyung Kim. "A retrospective study on the status of sexually transmitted co-infections in university hospitals in Korea from 2017 to 2021". Therapeutic Advances in Infectious Disease 10 (styczeń 2023). http://dx.doi.org/10.1177/20499361231220154.

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Background: The prevalence of sexually transmitted infections (STIs) remains high worldwide. Despite the worldwide increase in the incidence of STIs every year, there are few reports on the frequency of STIs with different pathogens according to age and gender. Accordingly, a study was conducted to determine trends in co-infection with STIs by age and gender in Cheonan, South Korea from 2017 to 2021. Objectives: To identify trends by age or sex in co-infection of STIs in this region. Design: A retrospective study was conducted on clinical samples examined at Dankook University Hospital from January 2017 to November 2021. A total of 3297 specimens were collected from patients visiting Dankook University Hospital (Cheonan, Korea), and statistical analysis was performed on patients ranging in age from 1 day to 93 years. Methods: Multiplex polymerase chain reaction, the most efficient method to diagnose a bacterial infection, was performed using an MJ Research PTC-200 Thermal Cycler (Marshall Scientific, Richmond, VA, USA) and a Seeplex STD Detection Kit (Seegene, Seoul, Republic of Korea). The co-infection rate with STI pathogens was analyzed according to age and sex. Results: Of the 3297 clinical samples, 1017 (30.9%) tested positive for sexually transmitted pathogens, ranging from one to six co-infections. Analysis of the co-infection rate by age revealed that the average age gradually decreased as the total number of co-infection pathogens increased. The co-infection percentage and age distribution of STIs differed according to sex. Co-infection was more prevalent in female patients. Furthermore, co-infection in male patients occurred frequently in the 30–39-year-old group, while those in female patients occurred in the 20–29- and 30–39-year-old groups. Conclusion: Our statistical analysis showed that STI co-infections were more common among younger than older people. Therefore, it helps in recognizing STIs at a young age and provides possible indicator data to prevent STIs at a young age. In addition, further research is needed on co-infection in other regions.

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Buonsenso, Danilo, Annamaria Musolino, Valentina Ferro, Cristina De Rose, Rosa Morello, Chiara Ventola, Flora Marzia Liotti i in. "Role of lung ultrasound for the etiological diagnosis of acute lower respiratory tract infection (ALRTI) in children: a prospective study". Journal of Ultrasound, 19.06.2021. http://dx.doi.org/10.1007/s40477-021-00600-z.

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Abstract Objective and design Our prospective study assesses the role of detailed lung ultrasound (LUS) features to discriminate the etiological diagnosis of acute lower respiratory tract infection (ALRTI) in children. Methodology We analyzed patients aged from 1 month to 17 years admitted between March 2018 and April 2020 who were hospitalized for ALRTI. For all patients, history, clinical parameters, microbiological data, and lung ultrasound data were collected. Patients were stratified into three main groups (“bacterial”, “viral”, “atypical”) according to the presumed microbial etiology and LUS findings evaluated according to the etiological group. Nasopharyngeal swabs were obtained from all patients. A qualitative diagnostic test developed by Nurex S.r.l. was used for identification of bacterial and fungal DNA in respiratory samples. The Seegene Allplex™ Respiratory assays were used for the molecular diagnosis of viral respiratory pathogens. In addition, bacterial culture of blood and respiratory samples were performed, when indicated. Results A total of 186 children with suspected ALRTI (44% female) with an average age of 6 were enrolled in the study. We found that some ultrasound findings as size, number and distribution of consolidations, the position and motion of air bronchograms, pleural effusions and distribution of vertical artifacts significantly differ (p < 0.05) in children with bacterial, viral and atypical ALRTI. Conclusion Our study provides a detailed analysis of LUS features able to predict the ALRTI ethology in children. These findings may help the physicians to better manage a child with ALRTI and to offer personalized approach, from diagnosis to treatment and follow-up.

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Prazuck, Thierry, Philippe Lanotte, Gwénaël Le Moal, Laurent Hocqueloux, Simon Sunder, Mélanie Catroux, Magali Garcia i in. "Pooling Rectal, Pharyngeal, and Urine Samples to Detect Neisseria gonorrhoeae, Chlamydia trachomatis, and Mycoplasma genitalium Using Multiplex Polymerase Chain Reaction Is as Effective as Single-Site Testing for Men Who Have Sex With Men". Open Forum Infectious Diseases 9, nr 10 (1.10.2022). http://dx.doi.org/10.1093/ofid/ofac496.

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Abstract Background Screening for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) at pharyngeal, urogenital, and anorectal sites is recommended for men who have sex with men (MSM). Pooling samples is a promising technique, but no data are available when pooled screening also includes Mycoplasma genitalium (MG). The main objective of this study was to examine the sensitivity of pooled samples for detecting CT, NG, and MG in MSM using nucleic acid amplification versus single-site testing. Methods In this multicenter study, MSM with a positive result for CT, NG, or MG were recalled to the clinic for treatment and were asked to participate in this study. Separate samples were sent to a central virological department that proceeded to form the pooled samples. Testing was performed using the multiplex real-time polymerase chain reaction Allplex STI Essential Assay (Seegene, Seoul, Korea), which can simultaneously detect 7 pathogens. Results A total of 130 MSM with at least 1 positive test for CT, NG, or MG were included. A total of 25.4% had a coinfection. The sensitivities of pooled-sample testing were 94.8% for CT, 97.0% for NG, and 92.3% for MG. Pooling failed to detect 8 infections, but pooled-sample analysis missed detecting only samples with a low bacterial load (cycle threshold >35). Conclusions Pooling samples from MSM to detect CT, NG, and MG is as sensitive as individual-site testing for these 3 pathogens using the Allplex assay. Missed infections with a very low bacterial load could have a low impact on further transmission. Clinical Trials Registration. NCT03568695.

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Peris, M., A. Milagro, N. F. Martínez, O. Algara, D. Martínez-Mateos, B. Dehesa-García, B. García-Manrique i A. Rezusta. "B-273 Lymphogranuloma Venereum: Validation of a Real-Time PCR Kit for Its Rapid Diagnosis". Clinical Chemistry 69, Supplement_1 (27.09.2023). http://dx.doi.org/10.1093/clinchem/hvad097.595.

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Abstract Background Chlamydia trachomatis serovars L1, L2 and L3 are responsible for lymphogranuloma venereum (LGV), a sexually transmitted infection that causes ulcerated lesions and adenopathy. Following the procedures in Clinical Microbiology recommendations, rectal samples positive for C. trachomatis are processed to detect the LGV-producing serovars in order to provide appropriate treatment. Since European regulations require for CE and IVD certification that an in vitro diagnostic product must be validated by an external body, the aim of this study was to validate the VIASURE C. trachomatis (LGV) Real Time PCR Detection Kit from Certest Biotec SL, using DNAs characterized as positive or negative for LGV extracted from clinical samples previously analyzed in the Laboratory. Methods A total of 214 DNAs from clinical samples collected between January 2021 and November 2022 were analyzed. Based on the initial diagnosis performed with the Allplex™ Genital ulcer Assay (Seegene®), 37 samples were positive for LGV and 177 were negative. The use of all data and samples was approved by the Aragon research ethics committee (CEICA) (PI20/426). The clinical sensitivity and specificity of the kit and the positive and negative predictive values (95% CI) were calculated with MetaDisc 1.4 software. Results Results are summarized in Table 1. Conclusion The comparative analysis of the “VIASURE C. trachomatis (LGV) Real Time PCR Detection Kit” proved to be as sensitive and specific as the reference molecular assay. The main advantage is that VIASURE products feature a stabilized, ready-to-use format, reducing the number of time-consuming laboratory steps, avoiding possible contamination and allowing transport and storage at room temperature.

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Akinshipo, Abdul-Warith Olaitan, Akanbi Clement Oluwarotimi, Roosevelt Amaobichukwu Anyanwu, Ernest Ebuka Aforka, Olajumoke Ajibola Effiom i Sunday Aremu Omilabu. "Low Detection of High-risk Human Papilloma Virus in Individuals with Ameloblastoma in a Tertiary Hospital in Lagos, Nigeria". Annals of African Medicine, 24.04.2024. http://dx.doi.org/10.4103/aam.aam_102_23.

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Abstract Background: Ameloblastoma is a benign but aggressive epithelial odontogenic neoplasm of unknown etiology. The role of human papilloma virus (HPV) in the etiology of oral squamous cell carcinoma has prompted the investigation of HPV as an etiologic factor in ameloblastoma. This study aimed to determine the frequency of high-risk (HR) HPV in conventional ameloblastoma and the clinical parameters associated with infection. Materials and Methods: The study was approved by the ethical review boards of the institution. DNA was extracted from fresh tissue collected 750 μL of DNA/RNA Shield (Zymo Research, United States) using Invitrogen PureLink Viral RNA/DNA Mini Kit (Invitrogen, USA). The extracted DNA was assayed for the detection of 14 HR HPV types (16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, and 68) using Anyplex™ II HPV HR Detection kit (Cat. No. HP7E00X) (Seegene Inc., Republic of Korea) on CFX-96TM Real-Time Polymerase Chain Reaction (PCR) System (Bio-Rad). Data on gender, age of patient, site of lesion, clinicohistological types of ameloblastoma and history of smoking, alcohol consumption, and practice of oral sex were collected. Data analysis was performed using analysis program SPSS version 25 and statistical significance was set at P < 0.05. Results: Two cases of conventional ameloblastoma were positive with HPV and none of the ameloblastic carcinoma cases were positive. The HPV 16 serotype was observed in both cases. While 5 of the cases had a history of alcohol consumption, none of these cases were positive for HPV serotype. Conclusions: HPV 16 positivity was detected in two cases of conventional ameloblastomas and none in ameloblastic carcinoma using real-time PCR. There was no effect of exposure to smoking, alcohol consumption, and practice of oral sex and HPV in the etiology of ameloblastoma. Data available are suggestive of a limited role of HPV in the etiology of ameloblastoma.

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Meier, Marie-Luise. "Perceiving the Default: Navigating Choice Architecture in Video Games / Vaikesätte jälgedes: valikuarhitektuuri navigeerimine videomängudes". Methis. Studia humaniora Estonica 22, nr 27/28 (15.12.2021). http://dx.doi.org/10.7592/methis.v22i27/28.18447.

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Abstract: Using Cass Sunstein and Richard Thaler’s concept of nudge (2008), this article transforms Stuart Hall’s notion of preferred reading (1973) into the concept of preferred playing to create a new approach to textual analysis appropriate for video games as interactive media. Markers for preferred playing as an alternative to more traditional close reading are discussed together with concepts and insights from contemporary game studios and game design regarding the medium’s different layers. Käesolev artikkel loob Stuart Halli (1973) eelistatud lugemise (preferred reading) käsitluse alusel eelistatud mängimise (preferred playing) kontseptsiooni, kasutades selleks Cass Sunsteini ja Richard Thaleri (2008) nügimise (nudge) mõistet, et luua uus lähenemine tekstianalüüsile, mis oleks sobiv videomängude kui interaktiivse meediumi analüüsiks. Koos mõistete ja uuendustega nüüdisaegsest ludoloogiast ja mängudisainist arutatakse eelistatud mängimise markereid kui alternatiivi levinumale lähilugemisele videomängu meediumi eri kihistuste uurimiseks. Artikli alguses on välja toodud varasemate kvalitatiivsete ja kvantitatiivsete lähenemiste problemaatika videomänguanalüüsis, mis on eriti märgatav siis, kui käsitletakse rassi, klassi ja soo kujutamist videomängudes. Kuna varasemates lähenemistes jääb tihti puudu objektiivsusest ning tihtipeale kujutatakse videomänge, vältimatult interaktiivset meediumit, ka liiga lihtsustatult, soovitan kaheosalist lähenemist videomänguanalüüsile. Alustuseks pakun ma potentsiaalsete tegevuste ja sündmuste kaardistamise videomängudes, võttes aluseks Fernández-Vara (2015) kontseptsiooni võimalusruumist (space of possibilities). Kuigi see aitab videomänge mõista terviklikena, ei piisa sellest siiski mängusiseste vaatepunktide ja ideoloogiate analüüsiks, sest need on tihti kodeeritud eelistama üht või teist valikut. Seetõttu loon ma Halli (1973) mõiste „eelistatud lugemine“ (preferred reading) alusel, koos selle alla kuuluvate vastanduva (oppositional) ja sobitava (negotiated) lugemise mõistetega, kontseptsiooni eelistatud mängimisest (preferred playing). Sel eesmärgil kasutan ma Thaleri ja Sunsteini (2008) terminit „nügimine“ (nudge), pakkudes välja, et videomäng ise markeerib ideaalse viisi enda mängimiseks. Eelistatud mängimine on seega domineeriv mängustiil, mis on tuletatud neist nügimistest, mida mäng mängijale esitab; vastanduv mängimine on mängustiil, mis tunneb need nügimised küll ära, kuid vastandub neile tahtlikult, näiteks lõhestava või etendusliku mängimise eesmärgil. Sobitav mängimine seevastu aga kaasab tihti eelistatud mängimist, kuid muudab seda vastavalt mängija soovidele. Selleks, et mõista, millised nügimised videomängudes moodustavad eelistatud mängimise, on vaja analüüsida videomängude erinevaid aspekte ja kihistusi. Nügimine on eriti tavapärane nn visuaalsete vaikesätete puhul, kuid esineb ka paljudes mängumehhaanika detailides, näiteks tasakaalustamises, keerukuses ja väljakutsetes, aga ka eesmärkides ja auhindades. Tähendusrikas tasemedisain ja žanri- ning narratiivielementide kasutamine kujundavad täiendavalt kujutluspilti ideaalsest teekonnast läbi videomängu sündmuste, mille põhjal saavad seega tuletada videomängu eelistatud mängimise nii mängijad ise kui ka ludoloogid. Kirjeldatud metodoloogia abil saab luua lähteteksti, analüüsimaks videomänge nii soo kujutamise osas kui ka näiteks rassi kujutamises, kuna alaesindatuse probleem on mõlema aspekti puhul tavapärane (Williams jt 2009). Kuna tegemist on kohandatava töövahendiga videomängude analüüsiks, saab seda vastavalt vajadusele kasutada ka koos teiste teoreetiliste lähenemistega.

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Tchounga, Boris, Apollinaire Horo, Simon Boni, Aristophane Tanon, Madeleine Amorissani Folquet, Isabelle Garrigue, Valeriane Leroy, François Dabis, Didier Ekouevi i Antoine Jaquet. "Human papilloma viruses infection among adolescent females perinatally infected with HIV in Côte d’Ivoire". Sexually Transmitted Infections, 13.07.2020, sextrans—2019–054420. http://dx.doi.org/10.1136/sextrans-2019-054420.

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BackgroundCervical cancer prevention strategies recommend human papilloma virus (HPV) vaccination for female adolescents prior to their sexual debut. While HIV is a major risk factor for HPV infection in women of childbearing age, its prevalence among HIV-infected adolescent female is mostly unknown. This study aimed to describe the HPV prevalence and correlates among perinatally HIV-infected adolescent females prior to HPV immunisation.MethodsA cross-sectional survey was conducted from January to June 2016, in the four major paediatric HIV clinics of Abidjan, Côte d’Ivoire. All HIV-infected females aged 11–16 years were approached to participate in the study. A questionnaire assessing sexual behaviours and genital hygiene practices was administered to participants completed with a systematic vaginal swab collection. HPV genotyping was performed using the Anyplex II HPV28 Detection (Seegene). A logistic regression analysis was performed to identify factors associated with the presence of HPV infection. HPV immunisation was proposed free of charge to all participants.ResultsA total of 250 participants were included, with a median age of 13 years (IQR 11–14). Among them, 237 (94.8%) were on antiretroviral treatment with a median CD4 count of 660 (IQR 439–914) cells/mm3. The overall prevalence of at least one HPV was 3.6% (95% CI 1.6 to 6.7) and the prevalence of at least one carcinogenic HPV was 2.8% (95% CI 0.7 to 4.8). Vaginal cleansing was reported by 75 (30%) of participants, with a median age at initiation of 12 years (IQR 10–13). Sexual activity was self-reported by 12 (4.8%) participants with a median age at sexual debut of 11 years (IQR 10–14). HPV infection was associated with vaginal cleansing (adjusted OR=7.0 (95% CI 1.4 to 31.6)).ConclusionThe reported low prevalence of carcinogenic HPV infections supports the appropriateness of HPV immunisation in this population. The reported association between cleansing practices and HPV infection deserves further prospective longitudinal studies.

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Kaukonen, Elisabeth. "Cleaning aunts and police uncles in action. Unveiling gender dynamics in Estonian compound words". Eesti ja soome-ugri keeleteaduse ajakiri. Journal of Estonian and Finno-Ugric Linguistics 14, nr 3 (6.12.2023). http://dx.doi.org/10.12697/jeful.2023.14.3.05.

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This paper focuses on the use of compound words ending with tädi ‘aunt’ and onu ‘uncle’ in the 2021 Estonian Web Corpus. The aim is to determine the frequencies and semantic categories of such compounds as well as to analyze how occupational titles that incorporate these gender-specific words are used. Therefore, this paper primarily seeks to understand why terms related to kinship, like tädi and onu, are integrated into compound words denoting occupations. The data is subjected to corpus-assisted discourse analysis, revealing that compound words ending with tädi and onu express various semantic categories, and these occupational titles serve several purposes in Estonian public discourse. Additionally, the study shows that such compounds carry gender stereotypes and that titles ending with tädi are more often associated with lower prestige. Kokkuvõte. Elisabeth Kaukonen: Koristajatädid ja politseionud tegustemas. Tuvastades soodünaamikat eesti keele liitsõnadest. Artikkel keskendub tädi- ja onu-lõpuliste liitsõnade kasutusele 2021. aasta eesti keele veebikorpuses, eesmärgiga välja selgitada seesuguste sõnade esinemissagedused ja tähendusrühmad. Lähemalt on analüüsitud tädi- ja onu-lõpulisi ametisõnu. Seega püüab artikkel peamiselt vastust leida küsimustele, miks kasutatakse sugulusele osutavaid termineid, nagu tädi ja onu, ametit väljendavates liitsõnades ning millised on seesuguste sõnade kasutusmustrid. Materjali analüüsiti korpuspõhise diskursuseanalüüsi meetodiga. Tulemused näitavad, et tädi- ja onu-lõpulised liitsõnad väljendavad mitmesuguseid tähendusvaldkondi ning et sellistel ametisõnadel on eesti keele avalikus diskursuses palju kasutusvõimalusi – näiteks kasutatakse tädi- ja onu-liitsõnu nii positiivses kui ka negatiivses tähenduses. Sellele lisaks on tulemustest ilmne, et seesugused liitsõnad ja nende kasutus peegeldavad soostereotüüpe ning et tädi-lõpulised liitsõnad on sageli seotud madalama prestiižiga kui onu-lõpulised.

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Sandri, Angela, Maria Carelli, Alessandro Visentin, Alessia Savoldi, Gelinda De Grandi, Massimo Mirandola, Maria M. Lleo, Caterina Signoretto i Maddalena Cordioli. "Mycoplasma genitalium antibiotic resistance-associated mutations in genital and extragenital samples from men-who-have-sex-with-men attending a STI clinic in Verona, Italy". Frontiers in Cellular and Infection Microbiology 13 (31.03.2023). http://dx.doi.org/10.3389/fcimb.2023.1155451.

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BackgroundMycoplasma genitalium (MG) is one of the most warning emerging sexually transmitted pathogens also due to its ability in developing resistance to antibiotics. MG causes different conditions ranging from asymptomatic infections to acute mucous inflammation. Resistance-guided therapy has demonstrated the best cure rates and macrolide resistance testing is recommended in many international guidelines. However, diagnostic and resistance testing can only be based on molecular methods, and the gap between genotypic resistance and microbiological clearance has not been fully evaluated yet. This study aims at finding mutations associated with MG antibiotic resistance and investigating the relationship with microbiological clearance amongst MSM.MethodsFrom 2017 to 2021, genital (urine) and extragenital (pharyngeal and anorectal swabs) biological specimens were provided by men-who-have-sex-with-men (MSM) attending the STI clinic of the Infectious Disease Unit at the Verona University Hospital, Verona, Italy. A total of 1040 MSM were evaluated and 107 samples from 96 subjects resulted positive for MG. Among the MG-positive samples, all those available for further analysis (n=47) were considered for detection of mutations known to be associated with macrolide and quinolone resistance. 23S rRNA, gyrA and parC genes were analyzed by Sanger sequencing and Allplex™ MG and AziR Assay (Seegene).ResultsA total of 96/1040 (9.2%) subjects tested positive for MG in at least one anatomical site. MG was detected in 107 specimens: 33 urine samples, 72 rectal swabs and 2 pharyngeal swabs. Among them, 47 samples from 42 MSM were available for investigating the presence of mutations associated with macrolide and quinolone resistance: 30/47 (63.8%) showed mutations in 23S rRNA while 10/47 (21.3%) in parC or gyrA genes. All patients with positive Test of Cure (ToC) after first-line treatment with azithromycin (n=15) were infected with 23S rRNA-mutated MG strains. All patients undergoing second-line moxifloxacin treatment (n=13) resulted negative at ToC, even those carrying MG strains with mutations in parC gene (n=6).ConclusionOur observations confirm that mutations in 23S rRNA gene are associated with azithromycin treatment failure and that mutations in parC gene alone are not always associated with phenotypic resistance to moxifloxacin. This reinforces the importance of macrolide resistance testing to guide the treatment and reduce antibiotic pressure on MG strains.

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Choo, Eun Ju. "2325. Five-day quarantine of patients exposed to SARS-CoV-2 within hospitals in the Omicron variant era". Open Forum Infectious Diseases 10, Supplement_2 (27.11.2023). http://dx.doi.org/10.1093/ofid/ofad500.1947.

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Abstract Background Since severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can be transmitted even in the absence of symptoms, it can be difficult to prevent its transmission within healthcare facilities. This study aimed to investigate whether initial screening tests and quarantine are still necessary for in-hospital close contact patients in the Omicron-dominant era. Methods This retrospective, observational study was performed at a tertiary hospital in South Korea, comprising mostly multi-bed rooms, with four or five beds each. Real-time reverse transcriptase polymerase chain reaction (RT-PCR) for SARS-CoV-2 was performed on the first and fourth day of quarantine, using a PowerChekTM 2019-nCoV Real-time PCR Kit (Kogenebiotech, Seoul, Korea) or an Allplex 2019-nCoV Assay (Seegene, Seoul, Korea). If relevant symptoms developed during quarantine, testing was promptly performed, regardless of the established schedule. Results Between June 15, 2022 and December 29, 2022, there were 179 events of COVID-19 within the hospital. Eighteen exposed patients were excluded because they were discharged during quarantine, and 705 patients were included in the final analysis. The median number of exposed inpatients was 4 (interquartile range, 2 – 5) for each event. Fifty-six (7.9%; 95% confidence interval [95%CI], 6.0 – 10.3%) exposed patients had positive initial screening tests. Among those with an initially negative test, positive conversion was identified in 31 patients (4.8%; 95%CI, 3.2 – 6.8%) during quarantine. In correlation with the number of confirmed COVID-19 cases in South Korea at that time, the number of in-hospital events and exposed patients peaked in August 2022. However, positive test rates at initial testing or during quarantine did not differ significantly according to the month (P = 0.095 and P = 0.104, respectively). This study showed that 12.3% of exposed patients had a positive PCR test, either at initial screening or during quarantine. Conclusion This study suggests that screening and quarantine are still necessary for close contact inpatients in the Omicron variant era. Testing intervals and the duration of quarantine may need adjustment considering the current shortage of isolation rooms, testing capacity, and healthcare personnel. Disclosures All Authors: No reported disclosures

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Hansen, Julie. "Self-Translation Enacted in Theodor Kallifatides’ Language Memoir Ännu ett liv (Another Life) / Jõustatud enesetõlge Theodor Kallifatidese keelememuaaris „Veel üks elu“ („Ännu ett liv“)". Methis. Studia humaniora Estonica 25, nr 31-32 (15.12.2023). http://dx.doi.org/10.7592/methis.v25i31-32.23322.

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Abstract: This article examines the significance of self-translation in the Swedish version of the language memoir Ännu ett liv (2017) by the translingual Greek-Swedish writer Theodor Kallifatides. A survey of definitions of self-translation is followed by an analysis of how self-translation is enacted in Kallifatides’ text. The article discusses implications of self-translation, in various senses, for a reading of Ännu ett liv, concluding that it serves to highlight ethical issues of relevance to the Swedish target audience. Jõustatud enesetõlge Theodor Kallifatidese keelememuaaris „Veel üks elu“ („Ännu ett liv“) Terminit enesetõlge defineeritakse praegu tõlkeuuringutes ning mitmekeelse kirjanduse käsitlemisel kahel moel: üks definitsioonidest on sõnasõnaline, teine metafoorne. Käesolevas artiklis vaadeldakse enesetõlkimise implikatsioonide mõlemat tähendust tuntud keeleülese kreeka-rootsi nüüdiskirjaniku Theodor Kallifatidese (s. 1938) keelememuaari „Veel üks elu“ („Ännu ett liv“) rootsikeelse versiooni lugemisel. Kallifatides emigreerus Kreekast Rootsi 1964. aastal ning debüteeris rootsi keeles kirjutava kirjanikuna viis aastat hiljem. Tema keelememuaar ilmus kreeka keeles („Mia zoi akoma“) ning seejärel 2017. aastal rootsi tõlkes. Autori enese poolt kreeka keelest rootsi keelde tõlgituna tähistab see pöördepunkti Kallifatidese viljakas kirjanduskarjääris ning annab alust huvitavale kirjanduslikku enesetõlget käsitlevale juhtumiuuringule. Pärast lühikest ülevaadet enesetõlke definitsioonidest ning keelememuaari žanrist analüüsitakse artiklis enesetõlkimise kirjeldamist „Veel ühes elus“. Kallifatidese keelememuaar vaatleb keele, elu, surelikkuse ja demokraatia teemasid, pakkudes mõtisklusi eksistentsiaalsete ja eetiliste küsimuste üle. Artiklis käsitletakse mitmesuguste kriiside kirjeldamist selles narratiivis, alates autori isiklikust kriisist, mida põhjustasid kirjutamistõrge ning vananemise tundemärgid, kuni majanduskriisini Kreekas ning kasvava võõraviha märkideni Euroopas. Kallifatidese tekstiga seoses läbi viidud enesetõlkeanalüüsist ilmneb, kuidas seda sooritatakse kahes etapis: esimene neist kirjeldab Vana-Kreeka näidendi lavastamist ja teine jutustajat „Veel ühte elu“ sissejuhatava lausega algava teksti kirjutamis- ja enesetõlkeprotsessi vältel. Edasi vaadeldakse enesetõlke toimet lugemisprotsessile, väites, et narratiivi lõpu lähenedes toimuv avalikustamine, et rootsikeelne tekst on enesetõlge, käivitab lugejapoolse ümberkalibreerimise, mis haarab lugeja keelevahetuse ja enesetõlkega kaasneva perspektiivikehtestamise tegevusse. „Veel ühe elu“ lugejaid võib seega pidada osalisteks Kallifatidese poolt sooritatud tõlkeaktis. Artikli lõpuosas näidatakse, kuidas selle teksti enesetõlge aitab kaasa eetilisele hoiakule, mis väljendub jutustaja mõtiskluses ühiskondlike kriiside üle ning Rootsi ühiskonnas avalduva ksenofoobia temapoolses kriitikas. Seda võib omakorda seostada Lawrence Venuti ideega võõrapärastavatest tõlkestrateegiatest kui demokraatlikust projektist. Läbi kogu Kallifatidese keelememuaari toimib enesetõlge kirjandusliku võttena, mis pakub jutustajale võimalust rääkida Rootsi lugejatega Rootsist ühtaegu nii seespool kui ka väljaspool viibija positsioonist, kõneldes ühiskonnas osaleva kodaniku kogemuse pinnalt, aga ka võõramaalase pilgu läbi. Sel moel toimib enesetõlge läätsena, mis toob fookusesse rahvusülese kogemuse eetilised aspektid, kutsudes lugejat tänapäeva ühiskondlikes probleemides kaasa rääkima.

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Saro, Anneli. "Poetics and Perception of Interartistic Performance / Kunstidevahelise etenduse poeetika ja taju". Methis. Studia humaniora Estonica 22, nr 27/28 (15.12.2021). http://dx.doi.org/10.7592/methis.v22i27/28.18446.

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Abstract: The article investigates the poetics and perception of interartistic performances, using two theatre productions – NO47 A Girl That Was Looking for Her Brothers (2014) and NO33 Hysteria (2017) – by Estonian performance artist and scenographer Ene-Liis Semper at the Theatre NO99 as case studies. A theoretical and methodological framework will be developed for the purpose of the analysis, based on Erving Goffman’s notion of the frame and on transformative aesthetics elaborated in art research and psychology. Artiklis uuritakse kunstidevaheliste etenduste poeetikat ja taju, tuginedes kahele juhtumiuuringule – etenduskunstniku ja stsenograafina tuntud Ene-Liis Semperi lavastustele „NO47 Tüdruk, kes otsis oma vendi“ (2014) ja „NO33 Hüsteeria“ (2017) Teatris NO99. Selleks arendati välja spetsiaalne teoreetiline ja metodoloogiline raamistik, lähtudes Ameerika sotsioloogi Erving Goffmani terminist raam ning filosoofias (Dewey 1958), psühholoogias (Pelowski ja Akiba 2011) ja teatriteaduses (Fischer-Lichte 2008) tuntud transformatiivse esteetika käsitlustest. Kunstidevahelise etenduse defineerimisel on tuginetud Patrice Pavisile, kes termini kunstidevaheline (interartistic) puhul on eristanud viit tähendusvälja, millest viimane ja kõige kitsam tähistab ühe kunstiliigi printsiipide projektsiooni ühele või mitmele teisele kunstiliigile. Ta on toonud kunstidevaheliste teoste näiteks etenduskunsti ja installatsiooni, mis tsiteerivad ja adapteerivad teiste kunstiliikide tehnikaid ja aspekte. (Pavis 2016, 103) Kuid kuidas mõista performatiivse pöörde järgses kultuurisituatsioonis, kus etenduslikkus on tunginud peaaegu kõikidesse kunstiliikidesse, kunstidevahelist etendust? Väidan, et etenduses kui heterogeenses ja laialivalguvas nähtuses on siiski säilinud või tekkinud teatud sisemised konventsioonid, mis loovad vastuvõtul kindlaid ootusi. Artiklis vaadeldakse Semperi kunstidevahelisi teoseid, kus etendus- ja installatsioonikunst on projitseeritud teatrilavastustele. Analüüsitud lavastustel on palju sarnasusi Semperi videotega: fookuses on inimkeha, situatsioonid (tegevused, kostüümid ja lavakujundus) ning kommunikatsiooniraam on teatraalsed ning kontsentreeritud meeleseisundid (Härm 2003, 26) domineerivad narratiivsuse üle. Semper otsib oma teostes teadlikult eri materjalide, meediumite ja kunstikonventsioonide kombineerimisel tekkivaid uusi ja üllatavaid kokkupuutepindasid ning nendest tekkivaid mõjuallikaid. Tema loomemeetodit võib seega nimetada kunstidevahelise esteetika poeetikaks. Metodoloogiliselt on etendusanalüüsi kombineeritud retseptsiooniuuringutega, täpsemalt enesekohase interpretatiivse fenomenoloogilise analüüsiga. Uurisin kahe lavastuse näitel, kas ja kuidas töötab psühholoogide Matthew Pelowski ja Fuminori Akiba (2011) transformatiivse esteetilise kogemuse mudel, kus nad eristavad metakognitiivse taju viit faasi: 1) eelootused ja enesekuvand, 2) kognitiivsed oskused ja lahknevuse ilmnemine, 3) sekundaarne kontroll ja põgenemine, 4) metakognitiivne ümberhindamine ning 5) esteetiline tulemus ja uued oskused. Kokkuvõtteks võib öelda, et see mudel osutus küll kasulikuks analüüsivahendiks, kuid nagu mudelid ikka, on liiga lihtsustav ja jäik. Esiteks on keeruline, kui mitte võimatu eristada vastuvõtuprotsessis eri faase, sest mõned neist näivad toimuvat paralleelselt. Teiseks, kuna see mudel näib põhinevat selliste visuaalsete objektide vastuvõtul, mida saab haarata tervikuna ja ühe pilguga, siis ajalise kestusega teoste puhul on uue info pealevoog pidev ja see sunnib vastuvõtjat alustama mudeldatud protsessiga ühe uuesti ja uuesti, liikudes pidevalt faasist 1 faasini 4. Kunstidevahelised ja teised hübriidsed teosed loovad uusi eneseväljenduse võimalusi, võimaldades kunstnikel ületada eri kunstiliikide ning kunsti ja mitte-kunsti vahelisi piire. Kuid olulisem on see, et kunstidevahelised teosed värskendavad vastuvõtja tajusid ja tähendusloome mehhanisme ning lõhuvad harjumuslikke tajuraame, valgustades nii läbi subjekti käsutuses olevate tajuraamide loogika, ning juhivad kunsti, ühiskonna ja vastuvõtja metakognitiivse analüüsi juurde. Kunstidevahelised etendused, mis suudavad endasse akumuleerida peaaegu kõikide teiste kunstiliikide väljendusvahendid ja isegi mitte-kunstilised valdkonnad, on eriti tugevad performatiivid, sest oma stiimulite rikkuse, etenduste keskmise kestvuse ja oodatava(te) tajuraami(de) tõttu on neil suur potentsiaal vastuvõtjat tugevasti mõjutada – transformeerida ning võibolla isegi häirida kogukonna või ühiskonna traditsioone ja norme.

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Plath, Ulrike, i Kaarel Vanamölder. "Põrkuvad „ilmamaad“ 17. sajandi Liivimaal / Clashing “Weatherlands” in 17th-century Livonia". Methis. Studia humaniora Estonica 24, nr 30 (13.12.2022). http://dx.doi.org/10.7592/methis.v24i30.22101.

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Johannes Gutslaffi 1644. aastal ilmunud teos „Lühike teade ja õpetus“ ja selles sisalduv „pikse palve“ kuuluvad Eesti varauusaegsete tüvitekstide hulka. Lugedes seda keskkonnahumanitaaria vaatenurgast, saavad ilmsiks seni tähelepanuta jäänud kliimaajaloolised kihistused ja seosed. Artikkel väidab, et „Lühike teade ja õpetus“ on üks varasemaid siinmail ilmunud teoloogilisi käsitlusi ekstreemsetest ilmastikutingimustest 17. sajandil. Raamatus on kirjeldatud esimest teadaolevat ilmastikutingimustest põhjustatud mässu Balti ajaloos. Artikkel pakub seega esimesi tõlgendusi Balti nn „ilmamaade“ sügavamatest kihtidest ning analüüsib „kliimamässu“ tekkimise probleeme, kasutades selleks keskkonnahumanitaaria ja kliimaajaloo metoodikat. Summary Johannes Gutslaff’s Kurtzer Bericht und Unterricht Von der Falsch-heilig genandten Bäche in Lieffland Wöhhanda ('Short Report and Lesson on the Võhandu River, Wrongly Regarded as Sacred in Livonia') that was printed in 1644, and the “Thunder prayer” included in it belong to the main corpus of Early Modern texts in Estonia. Hitherto, this material has been interpreted mostly from the perspective of cultural history. Reading the text from an environmental humanities perspective, we claim that so far unrecognised layers and connections to climate history can be found in it: the book and can be read as a scholarly piece about changing climate conditions and their different interpretations. Kurtzer Bericht belongs among Baltic theological reflections written in German about the extreme weather in the 17th century, which was marked globally by rapidly worsening climatic conditions and social unrest caused by these. In Gutslaff’s book we can also find a detailed description of the first climate-caused uprising in Baltic history known so far. In the Early Modern period, or during the peak of the “Little Ice Age”, the Baltic region, similarly to the rest of the world, was affected by a wider trend of cooling, with extreme fluctuations of temperature and precipitation proving to be the biggest problem for peasants growing crops. A look at climate history, however, makes it clear that cultural or social reactions need not be linked to particularly extreme weather phenomena, as they can culminate and explode at a favourable later moment. Climate does not dictate cultural behaviour, but the latter’s interweaving with climate needs to be studied more broadly on the basis of the existing regional sources. When looking for traces concerning climate in Baltic German religious literature, we can contextualise Gutslaff’s text as belonging to Early Modern “weatherlands” (Tim Ingold) that transgress cultural and regional borders. The article offers first interpretations of the clashing Baltic early modern “weatherlands”, combining methods deriving from literary scholarship, environmental humanities and climate history. The interconnectedness of climate and culture makes it possible to see the challenges climate change poses to culture and social order. Thus weather can be a mirror of relationships and a “moral barometer” of society that can measure not only the state of relations between God and people or society, but also the tensions between people. According to such an interpretation, weather plays almost as significant a role in religious thinking as do measuring instruments in secular science. As weather phenomena are loaded with different societal and religious meanings, explosive conflicts can emerge in climatically extreme times, showing the tension between different layers of society. Conflicts around weather and climate can therefore be seen as inevitable in periods of climatic challenges. Johann Gutslaff's Kurzer Bericht is placed among the theological-meteorological literature that had spread across Europe and can be traced back to the Antiquity and the Bible. As phenomena related to vernacular religion are of a cross-ethnic nature and with migratory motivations, it is no wonder that the rebellion by the Võhandu was not limited to ethnically Estonian peasants, but linked representatives of different linguistic and social layers. It can be noticed that in interpreting the events Gutslaff attempted to attribute the power and competence to change the weather only to God, and the ability to react to the weather changes only to upper classes – the agency of peasants in reacting to climatic extremes was not taken seriously. They were left alone with their concerns caused by climate change due to the lack of a societal process of addressing climate fears. It was from here that the potential for the conflict that exploded on the banks of the Võhandu derived. The article shows that combined analysis of historical, cultural and natural sources that was started in Estonia about half a century ago, but has been forgotten due to the complexity of the phenomenon and for ideological reasons, is needed to explain the connection between climate and culture.

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