Genotyping of Hepatitis C virus by nucleotide sequencing: A robust method for a diagnostic laboratory

Abstract Hepatitis C virus (HCV) is a globally significant blood-borne agent causing liver diseases, and it has infected over 170 million people worldwide. HCV is a diverse group of RNA viruses currently divided into genotypes 1–7 as well as subtypes. HCV infection can be treated with antiviral drugs, but the HCV genotype has to be determined for optimal selection of treatment strategy. The aim of this study was to set up a sequencing-based HCV genotyping method suitable for the workflow of a diagnostic laboratory. The established method is robust and stable, and it utilizes a one-step reverse transcription and PCR amplification of the 5’ untranslated region (5’UTR) and partial Core region of the HCV genome. Amplification products are sequenced using the standard Sanger method, and the genotype is determined by using a freely accessible web-based genotyping tool. The method was validated at the Helsinki University Hospital Laboratory using 238 previously genotyped serum samples. • A new one-step RT-PCR method for the amplification of the 5’ untranslated region and partial Core region of hepatitis C virus was established. • HCV genotype is determined using Sanger sequencing and a freely accessible, easy-to-use web-based genotyping tool. • The method is robust, reproducible and suitable for diagnostic laboratory workflow, and it requires no costly instrumentation or specialized sequence analysis skills.Peer reviewe

Real-life clinical sensitivity of SARS-CoV-2 RT-PCR test in symptomatic patients

Background Understanding the false negative rates of SARS-CoV-2 RT-PCR testing is pivotal for the management of the COVID-19 pandemic and it has implications for patient management. Our aim was to determine the real-life clinical sensitivity of SARS-CoV-2 RT-PCR. Methods This population-based retrospective study was conducted in March-April 2020 in the Helsinki Capital Region, Finland. Adults who were clinically suspected of SARS-CoV-2 infection and underwent SARS-CoV-2 RT-PCR testing, with sufficient data in their medical records for grading of clinical suspicion were eligible. In addition to examining the first RT-PCR test of repeat-tested individuals, we also used high clinical suspicion for COVID-19 as the reference standard for calculating the sensitivity of SARS-CoV-2 RT-PCR. Results All 1,194 inpatients (mean [SD] age, 63.2 [18.3] years; 45.2% women) admitted to COVID-19 cohort wards during the study period were included. The outpatient cohort of 1,814 individuals (mean [SD] age, 45.4 [17.2] years; 69.1% women) was sampled from epidemiological line lists by systematic quasi-random sampling. The sensitivity (95% CI) for laboratory confirmed cases (repeat-tested patients) was 85.7% (81.5-89.1%) inpatients; 95.5% (92.2-97.5%) outpatients, 89.9% (88.2-92.1%) all. When also patients that were graded as high suspicion but never tested positive were included in the denominator, the sensitivity (95% CI) was: 67.5% (62.9-71.9%) inpatients; 34.9% (31.4-38.5%) outpatients; 47.3% (44.4-50.3%) all. Conclusions The clinical sensitivity of SARS-CoV-2 RT-PCR testing was only moderate at best. The relatively high false negative rates of SARS-CoV-2 RT-PCR testing need to be accounted for in clinical decision making, epidemiological interpretations, and when using RT-PCR as a reference for other tests.Peer reviewe

Kä-Ki-Ku-oppimistyyli yhdistää kielen ja kulttuurin opetuksen

Käsityön, kielen ja kulttuurin oppimisen yhdistäminen on harvinaista. Se tarkoittaa sitä, että opetuksen käytännöissä pedagogiikan sisältöalueeksi liitetään harkitun tietoisesti käsityön, kielen ja kulttuurin oppimista. Menetelmä maahanmuuttajien suomen kielen oppimiseksi syntyi käsityön, kielen ja kulttuurin oppimisprosessissa. Väitöstutkimukseni tuloksissa se nimeytyi Kä-Ki-Ku-oppimistyyliksi

Arts and Crafts Design in Time, Space and Place. Methods for Learning and Constructing Arts and Crafts Design, Developing the Pedagogy

The Ha-La Cu -Method developed in my thesis 2005 stands for meaning of language- and culture learning/training connected with arts and crafts design learning. For this paper I observed a group of elementary school and kindergarten teacher students to see how the method works, and how students analysed artefacts and trained to become interpreters. They navigated the course in learning with different requirements and were differently understanding realising, internalised and addressed by arts and crafts design products. We study and observe the functionally theoretical arts and crafts design and learning by means of intense reading and interpretation. Keywords: method, sloyd, arts and crafts, language and culture, learningURN:NBN:no-2996

Käsityön, kielen ja kulttuurin yhdistäminen maahanmuuttajien suomen kielen oppimisprosessissa

Kulttuurisesti sensitiiviseksi opettajaksi kasvun polkuni oli monikymmenvuotinen. Sen aikana tulin kulttuurien kohtauttajaksi ja rakensin käsityön, kielen ja kulttuurin oppimisen yhdistämisestä monikulttuurisuuspedagogisen välineen. (Lappalainen 2005.) Tästä syntyi uusi suomalainen tyyli ja menetelmä maahanmuuttajien kielenoppimisen tehostamiseksi

Kä-Ki-Ku-oppimistyyli yhdistää kielen ja kulttuurin opetuksen

Käsityön, kielen ja kulttuurin oppimisen yhdistäminen on harvinaista. Se tarkoittaa sitä, että opetuksen käytännöissä pedagogiikan sisältöalueeksi liitetään harkitun tietoisesti käsityön, kielen ja kulttuurin oppimista. Menetelmä maahanmuuttajien suomen kielen oppimiseksi syntyi käsityön, kielen ja kulttuurin oppimisprosessissa. Väitöstutkimukseni tuloksissa se nimeytyi Kä-Ki-Ku-oppimistyyliksi

Effective Multicultural Learning in Iterative Cycles; Language Learning Breaking Gender Barriers in Doing Craft

Myths prevail on craft, culture and language, and in multicultural learning environments. In multicultural education teaching, I explored the learning language in craft learning environments and in learning situation the myths’ effects on gender gap. Basic terms and conceptions are 1.) The Ha-La-Cu - method and learning style: language and textile material and color impression (craft) learning in doing, 2.) Reflecting the process, generating interpretations of textile material and color impression (design), producing and processing analysis in textile material and color impression learning and 3.) Multi-scientific and multicultural education, interactive language and craft learning in doing -pedagogy: in craft activity, the analyses contain elements that are challenging learners in an active and innovative dialogue with a cultural awareness process. This is a tool for transcending the prevailing gender gap. Gathering the material, I used the (Ashman & Conway, 1989) classroom integration model, a cognitive verbalizing method; the contextualized notes I made by partial parallel and phased coding. Analogies and associations were linked to the vocabulary, increasing it in a sensitive creative manner. This multicultural pedagogy and didactic, in various contexts, is effectively breaking the gender gap. Keywords: crafts learning in doing, content analysis, gender gap, Ha-La-Cu –method, multicultural learning 

Long-term outcome of vestibular function and hearing in children with congenital cytomegalovirus infection : a prospective cohort study

Peer reviewe