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Article ; Online: When Your Data is My Grandparents Singing. Digitisation and Access for Cultural Records, the Pacific and Regional Archive for Digital Sources in Endangered Cultures (PARADISEC)

Nick Thieberger / Amanda Harris

Data Science Journal, Vol 21, Iss

2022 Volume 1

Abstract: In this paper we discuss the Pacific and Regional Archive for Digital Sources in Endangered Cultures (PARADISEC), a research repository that explicitly aims to act as a conduit for research outputs to a range of audiences, both within and outside of ... ...

Abstract	In this paper we discuss the Pacific and Regional Archive for Digital Sources in Endangered Cultures (PARADISEC), a research repository that explicitly aims to act as a conduit for research outputs to a range of audiences, both within and outside of academia. PARADISEC has been operating for 19 years, and has grown to hold over 390,000 files currently totaling 150 terabytes and representing 1,312 languages, many of them from Papua New Guinea and the Pacific. Our focus is on recordings and transcripts in the many small languages of the world, the songs and stories that are unique cultural expressions. While this research data is created for a particular project, it has huge value beyond academic research as it is typically oral tradition recorded in places where little else has been recorded. There is an increasing focus in academia on reproducible research and research data management, and repositories are the key to successful data management. We discuss the importance for research practice of having discipline-specific repositories. The data in our work is also cultural material that has value to the people recorded and their descendants, it is their grandparents and so we, as outsider researchers, have special responsibilities to treat the materials with respect and to ensure they are accessible to the people we have worked with.
Keywords	linguistics archiving ; musicological archiving ; language documentation ; language data management ; Science (General) ; Q1-390
Subject code	020
Language	English
Publishing date	2022-04-01T00:00:00Z
Publisher	Ubiquity Press
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Understanding healthcare workers’ knowledge and attitudes regarding the coronavirus disease 2019 (COVID-19) vaccine

James Mo / Catherine J. Maples / Amanda Harris / Monica P. Meyer / Teena Chopra

Antimicrobial Stewardship & Healthcare Epidemiology, Vol

Overcoming gaps to improve public health response

2022 Volume 2

Abstract: Vaccines serve as a major tool against the coronavirus disease 2019 (COVID-19) pandemic, but vaccine hesitancy remains a major concern in the United States. Healthcare workers (HCWs) strongly influence a patient’s decision to get vaccinated. We evaluated ...

Abstract	Vaccines serve as a major tool against the coronavirus disease 2019 (COVID-19) pandemic, but vaccine hesitancy remains a major concern in the United States. Healthcare workers (HCWs) strongly influence a patient’s decision to get vaccinated. We evaluated HCW knowledge and attitudes regarding the COVID-19 vaccine.
Keywords	Infectious and parasitic diseases ; RC109-216 ; Public aspects of medicine ; RA1-1270
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Cambridge University Press
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Temporal Whole-Transcriptomic Analysis of Characterized In Vitro and Ex Vivo Primary Nasal Epithelia

Jelmer Legebeke / Katie L. Horton / Claire L. Jackson / Janice Coles / Amanda Harris / Htoo A. Wai / John W. Holloway / Gabrielle Wheway / Diana Baralle / Jane S. Lucas

Frontiers in Cell and Developmental Biology, Vol

2022 Volume 10

Abstract: Air-liquid interface (ALI) cell culture of primary airway progenitors enables the differentiation and recapitulation of a pseudostratified epithelium in vitro, providing a highly useful tool for researching respiratory health and disease. Previous ... ...

Abstract	Air-liquid interface (ALI) cell culture of primary airway progenitors enables the differentiation and recapitulation of a pseudostratified epithelium in vitro, providing a highly useful tool for researching respiratory health and disease. Previous studies into gene expression in ALI-cultures compared to ex vivo nasal brushings have been limited in the number of time-points and/or the number of genes studied. In this study physiological and global transcriptomic changes were assessed in an extended in vitro 63-day human healthy nasal epithelium ALI-culture period and compared to ex vivo nasal brushing samples. Ex vivo nasal brushing samples formed distinct transcriptome clusters to in vitro ALI-cultured nasal epithelia, with from day 14 onwards ALI samples best matching the ex vivo samples. Immune response regulation genes were not expressed in the in vitro ALI-culture compared to the ex vivo nasal brushing samples, likely because the in vitro cultures lack an airway microbiome, lack airborne particles stimulation, or did not host an immune cell component. This highlights the need for more advanced co-cultures with immune cell representation to better reflect the physiological state. During the first week of ALI-culture genes related to metabolism and proliferation were increased. By the end of week 1 epithelial cell barrier function plateaued and multiciliated cell differentiation started, although widespread ciliation was not complete until day 28. These results highlight that time-points at which ALI-cultures are harvested for research studies needs to be carefully considered to suit the purpose of investigation (transcriptomic and/or functional analysis).
Keywords	primary nasal epithelium ; air-liquid interface culture ; airway cilia ; physiological analysis ; whole transcriptome analysis ; Biology (General) ; QH301-705.5
Subject code	570
Language	English
Publishing date	2022-06-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Whole genome sequencing in the diagnosis of primary ciliary dyskinesia

Gabrielle Wheway / N. Simon Thomas / Mary Carroll / Janice Coles / Regan Doherty / Genomics England Research Consortium / Patricia Goggin / Ben Green / Amanda Harris / David Hunt / Claire L. Jackson / Jenny Lord / Vito Mennella / James Thompson / Woolf T. Walker / Jane S. Lucas

BMC Medical Genomics, Vol 14, Iss 1, Pp 1-

2021 Volume 21

Abstract: Abstract Background It is estimated that 1–13% of cases of bronchiectasis in adults globally are attributable to primary ciliary dyskinesia (PCD) but many adult patients with bronchiectasis have not been investigated for PCD. PCD is a disorder caused by ... ...

Abstract	Abstract Background It is estimated that 1–13% of cases of bronchiectasis in adults globally are attributable to primary ciliary dyskinesia (PCD) but many adult patients with bronchiectasis have not been investigated for PCD. PCD is a disorder caused by mutations in genes required for motile cilium structure or function, resulting in impaired mucociliary clearance. Symptoms appear in infancy but diagnosis is often late or missed, often due to the lack of a “gold standard” diagnostic tool and non-specific symptoms. Mutations in > 50 genes account for around 70% of cases, with additional genes, and non-coding, synonymous, missense changes or structural variants (SVs) in known genes presumed to account for the missing heritability. Methods UK patients with no identified genetic confirmation for the cause of their PCD or bronchiectasis were eligible for whole genome sequencing (WGS) in the Genomics England Ltd 100,000 Genomes Project. 21 PCD probands and 52 non-cystic fibrosis (CF) bronchiectasis probands were recruited in Wessex Genome Medicine Centre (GMC). We carried out analysis of single nucleotide variants (SNVs) and SVs in all families recruited in Wessex GMC. Results 16/21 probands in the PCD cohort received confirmed (n = 9), probable (n = 4) or possible (n = 3) diagnosis from WGS, although 13/16 of these could have been picked up by current standard of care gene panel testing. In the other cases, SVs were identified which were missed by panel testing. We identified variants in novel PCD candidate genes (IFT140 and PLK4) in 2 probands in the PCD cohort. 3/52 probands in the non-CF bronchiectasis cohort received a confirmed (n = 2) or possible (n = 1) diagnosis of PCD. We identified variants in novel PCD candidate genes (CFAP53 and CEP164) in 2 further probands in the non-CF bronchiectasis cohort. Conclusions Genetic testing is an important component of diagnosing PCD, especially in cases of atypical disease history. WGS is effective in cases where prior gene panel testing has found no variants or only heterozygous variants. In these cases it may detect SVs and is a powerful tool for novel gene discovery.
Keywords	Primary ciliary dyskinesia ; Non-CF bronchiectasis ; Whole genome sequencing ; Diagnosis ; Gene discovery ; Internal medicine ; RC31-1245 ; Genetics ; QH426-470
Subject code	610
Language	English
Publishing date	2021-09-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: COVID-PCD

Eva S.L. Pedersen / Eugénie N.R. Collaud / Rebeca Mozun / Cristina Ardura-Garcia / Yin Ting Lam / Amanda Harris / Jane S. Lucas / Fiona Copeland / Michele Manion / Bernhard Rindlisbacher / Hansruedi Silberschmidt / Myrofora Goutaki / Claudia E. Kuehni

ERJ Open Research, Vol 7, Iss

a participatory research study on the impact of COVID-19 in people with primary ciliary dyskinesia

2021 Volume 1

Abstract: COVID-PCD is a participatory study initiated by people with primary ciliary dyskinesia (PCD) who have an essential vote in all stages of the research from the design of the study to the recruitment of participants, and interpretation and communication of ...

Abstract	COVID-PCD is a participatory study initiated by people with primary ciliary dyskinesia (PCD) who have an essential vote in all stages of the research from the design of the study to the recruitment of participants, and interpretation and communication of the study results. COVID-PCD aims to collect epidemiological data in real-time from people with PCD throughout the pandemic to describe incidence of coronavirus disease 2019 (COVID-19), symptoms and course of disease; identify risk factors for prognosis; and assess experiences, wishes and needs. The study is advertised through patient support groups and participants register online on the study website (www.covid19pcd.ispm.ch). The study invites persons of any age from anywhere in the world with a suspected or confirmed PCD. A baseline questionnaire assesses details on PCD diagnosis, habitual symptoms and COVID-19 episodes that occurred before study entry. Afterwards, participants receive a weekly follow-up questionnaire with questions on incident severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections, current symptoms, social contact behaviour and physical activity. Occasional thematic questionnaires are sent out focussing on emerging questions of interest chosen by people with PCD. In case of hospitalisation, patients or family members are asked to obtain a hospital report. Results are continuously analysed and summaries put online. The study started recruitment on April 30, 2020, and 556 people with PCD completed the baseline questionnaire by November 2, 2020. The COVID-PCD study is a participatory study that follows people with PCD during the COVID-19 pandemic, helps to empower affected persons, and serves as a platform for communication between patients, physicians and researchers.
Keywords	Medicine ; R
Subject code	360
Language	English
Publishing date	2021-03-01T00:00:00Z
Publisher	European Respiratory Society
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Lack of Correlation of Sinonasal and Otologic Reported Symptoms With Objective Measurements Among Patients With Primary Ciliary Dyskinesia

Yin Ting Lam / Jean-François Papon / Mihaela Alexandru / Andreas Anagiotos / Miguel Armengot / Mieke Boon / Andrea Burgess / Nathalie Caversaccio / Suzanne Crowley / Sinan Ahmed D. Dheyauldeen / Nagehan Emiralioglu / Ela Erdem / Christine van Gogh / Yasemin Gokdemir / Onder Gunaydın / Eric G. Haarman / Amanda Harris / Isolde Hayn / Hasnaa Ismail-Koch /

Bulent Karadag / Céline Kempeneers / Sookyung Kim / Natalie Lorent / Ugur Ozcelik / Charlotte Pioch / Anne-Lise ML Poirrier / Ana Reula / Jobst Roehmel / Panayiotis Yiallouros / Myrofora Goutaki

Clinical and Experimental Otorhinolaryngology, Vol 16, Iss 4, Pp 407-

An International Study

2023 Volume 412

Keywords	Medicine ; R ; Otorhinolaryngology ; RF1-547
Language	English
Publishing date	2023-11-01T00:00:00Z
Publisher	Korean Society of Otorhinolaryngology-Head and Neck Surgery
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Late Diagnosis of Infants with PCD and Neonatal Respiratory Distress

Myrofora Goutaki / Florian S. Halbeisen / Angelo Barbato / Suzanne Crowley / Amanda Harris / Robert A. Hirst / Bülent Karadag / Vendula Martinu / Lucy Morgan / Christopher O’Callaghan / Ugur Ozçelik / Sergio Scigliano / Santiago Ucros / Panayiotis Yiallouros / Sven M. Schulzke / Claudia E. Kuehni

Journal of Clinical Medicine, Vol 9, Iss 2871, p

2020 Volume 2871

Abstract: Neonatal respiratory distress (NRD) is common among infants with primary ciliary dyskinesia (PCD), but we do not know whether affected neonates receive a timely diagnosis. We used data from the international PCD cohort and assessed the proportion of ... ...

Abstract	Neonatal respiratory distress (NRD) is common among infants with primary ciliary dyskinesia (PCD), but we do not know whether affected neonates receive a timely diagnosis. We used data from the international PCD cohort and assessed the proportion of patients with PCD who had a history of NRD and their age at diagnosis, stratifying by presence of laterality defects. First we analyzed data from all participants diagnosed after 2000, followed by individuals from a subgroup diagnosed using stricter criteria. Among the 1375 patients in the study, 45% had a history of NRD and 42% had laterality defects. Out of the 476 children with definite PCD diagnosis, 55% had a history of NRD and 50% had laterality defects. Overall, 30% of children with PCD were diagnosed during the first 12 months of life. This varied from 13% in those with situs solitus and no NRD, to 21% in those with situs solitus and NRD, 33% in those with situs anomalies but no NRD, and 52% in those with both situs anomalies and NRD. Our results suggest that we need to improve our knowledge of the neonatal presentation of infants with PCD and apply it so that these patients will receive appropriate care sooner.
Keywords	primary ciliary dyskinesia ; neonatal respiratory distress ; laterality defect ; orphan diseases ; Medicine ; R
Subject code	610
Language	English
Publishing date	2020-09-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A Revised Protocol for Culture of Airway Epithelial Cells as a Diagnostic Tool for Primary Ciliary Dyskinesia

Janice L. Coles / James Thompson / Katie L. Horton / Robert A. Hirst / Paul Griffin / Gwyneth M. Williams / Patricia Goggin / Regan Doherty / Peter M. Lackie / Amanda Harris / Woolf T. Walker / Christopher O’Callaghan / Claire Hogg / Jane S. Lucas / Cornelia Blume / Claire L. Jackson

Journal of Clinical Medicine, Vol 9, Iss 3753, p

2020 Volume 3753

Abstract: Air–liquid interface (ALI) culture of nasal epithelial cells is a valuable tool in the diagnosis and research of primary ciliary dyskinesia (PCD). Ex vivo samples often display secondary dyskinesia from cell damage during sampling, infection or ... ...

Abstract	Air–liquid interface (ALI) culture of nasal epithelial cells is a valuable tool in the diagnosis and research of primary ciliary dyskinesia (PCD). Ex vivo samples often display secondary dyskinesia from cell damage during sampling, infection or inflammation confounding PCD diagnostic results. ALI culture enables regeneration of healthy cilia facilitating differentiation of primary from secondary ciliary dyskinesia. We describe a revised ALI culture method adopted from April 2018 across three collaborating PCD diagnostic sites, including current University Hospital Southampton COVID-19 risk mitigation measures, and present results. Two hundred and forty nasal epithelial cell samples were seeded for ALI culture and 199 (82.9%) were ciliated. Fifty-four of 83 (63.9%) ex vivo samples which were originally equivocal or insufficient provided diagnostic information following in vitro culture. Surplus basal epithelial cells from 181 nasal brushing samples were frozen in liquid nitrogen; 39 samples were ALI-cultured after cryostorage and all ciliated. The ciliary beat patterns of ex vivo samples (by high-speed video microscopy) were recapitulated, scanning electron microscopy demonstrated excellent ciliation, and cilia could be immuno-fluorescently labelled (anti-alpha-tubulin and anti-RSPH4a) in representative cases that were ALI-cultured after cryostorage. In summary, our ALI culture protocol provides high ciliation rates across three centres, minimising patient recall for repeat brushing biopsies and improving diagnostic certainty. Cryostorage of surplus diagnostic samples was successful, facilitating PCD research.
Keywords	PCD ; ALI culture ; bio-resource ; primary nasal epithelium ; diagnostics ; Medicine ; R
Subject code	610
Language	English
Publishing date	2020-11-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Study protocol

Andreas Anagiotos / Myrofora Goutaki / André Coste / Nagehan Emiralioglu / Amanda Harris / Andrea Burgess / Mieke Boon / Philipp Latzin / Jean François Papon / Eric G Haarman / Natalie Lorent / Yin Ting Lam / Mihaela Alexandru / Miguel Armengot / Emilie Bequignon / Ela Erdem / Sara-Lynn Hool / Bulent Karadag / Sookyung Kim /

Ugur Ozcelik / Ana Reula / Jobst Roehmel / Christine van Gogh / Panayiotis Yiallouros / Soeren Marian Zappe

BMJ Open, Vol 11, Iss

the ear–nose–throat (ENT) prospective international cohort of patients with primary ciliary dyskinesia (EPIC-PCD)

2021 Volume 10

Keywords	Medicine ; R
Language	English
Publishing date	2021-10-01T00:00:00Z
Publisher	BMJ Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Standardised clinical data from patients with primary ciliary dyskinesia

ERJ Open Research, Vol 6, Iss

FOLLOW-PCD

2020 Volume 1

Abstract: Clinical data on primary ciliary dyskinesia (PCD) are limited, heterogeneous and mostly derived from retrospective chart reviews, leading to missing data and unreliable symptoms and results of physical examinations. We need standardised prospective data ... ...

Abstract	Clinical data on primary ciliary dyskinesia (PCD) are limited, heterogeneous and mostly derived from retrospective chart reviews, leading to missing data and unreliable symptoms and results of physical examinations. We need standardised prospective data collection to study phenotypes, severity and prognosis and improve standards of care. A large, international and multidisciplinary group of PCD experts developed FOLLOW-PCD, a standardised clinical PCD form and patient questionnaire. We identified existing forms for clinical data collection via the Better Experimental Approaches to Treat PCD (BEAT-PCD) COST Action network and a literature review. We selected and revised the content items with the working group and patient representatives. We then revised several drafts in an adapted Delphi process, refining the content and structure. FOLLOW-PCD has a modular structure, to allow flexible use based on local practice and research focus. It includes patient-completed versions for the modules on symptoms and lifestyle. The form allows a comprehensive standardised clinical assessment at baseline and for annual reviews and a short documentation for routine follow-up. It can either be completed using printable paper forms or using an online REDCap database. Data collected in FOLLOW-PCD version 1.0 is available in real-time for national and international monitoring and research. The form will be adapted in the future after extensive piloting in different settings and we encourage the translation of the patient questionnaires to multiple languages. FOLLOW-PCD will facilitate quality research based on prospective standardised data from routine care, which can be pooled between centres, to provide first-line and real-time evidence for clinical decision-making.
Keywords	Medicine ; R
Subject code	310
Language	English
Publishing date	2020-02-01T00:00:00Z
Publisher	European Respiratory Society
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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