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Article ; Online: Critical appraisal in rapid systematic reviews of COVID-19 studies: implementation of the Quality Criteria Checklist (QCC).

Duval, Daphne / Pearce-Smith, Nicola / Palmer, Jennifer C / Sarfo-Annin, Jason Kwasi / Rudd, Paul / Clark, Rachel

2023 Volume 12, Issue 1, Page(s) 55

Abstract: In this letter, we briefly describe how we selected and implemented the quality criteria checklist (QCC) as a critical appraisal tool in rapid systematic reviews conducted to inform public health advice, guidance and policy during the COVID-19 pandemic. ... ...

Abstract	In this letter, we briefly describe how we selected and implemented the quality criteria checklist (QCC) as a critical appraisal tool in rapid systematic reviews conducted to inform public health advice, guidance and policy during the COVID-19 pandemic. As these rapid reviews usually included a range of study designs, it was key to identify a single tool that would allow for reliable critical appraisal across most experimental and observational study designs and applicable to a range of topics. After carefully considering a number of existing tools, the QCC was selected as it had good interrater agreement between three reviewers (Fleiss kappa coefficient 0.639) and was found to be easy and fast to apply once familiar with the tool. The QCC consists of 10 questions, with sub-questions to specify how it should be applied to a specific study design. Four of these questions are considered as critical (on selection bias, group comparability, intervention/exposure assessment and outcome assessment) and the rating of a study (high, moderate or low methodological quality) depends on the responses to these four critical questions. Our results suggest that the QCC is an appropriate critical appraisal tool to assess experimental and observational studies within COVID-19 rapid reviews. This study was done at pace during the COVID-19 pandemic; further reliability analyses should be conducted, and more research is needed to validate the QCC across a range of public health topics.
MeSH term(s)	Humans ; COVID-19 ; Reproducibility of Results ; Pandemics ; Checklist ; Public Health
Language	English
Publishing date	2023-03-27
Publishing country	England
Document type	Observational Study ; Letter ; Research Support, Non-U.S. Gov't
ZDB-ID	2662257-9
ISSN	2046-4053 ; 2046-4053
ISSN (online)	2046-4053
ISSN	2046-4053
DOI	10.1186/s13643-023-02219-z
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Article ; Online: Critical appraisal in rapid systematic reviews of COVID-19 studies

Daphne Duval / Nicola Pearce-Smith / Jennifer C. Palmer / Jason Kwasi Sarfo-Annin / Paul Rudd / Rachel Clark

Systematic Reviews, Vol 12, Iss 1, Pp 1-

implementation of the Quality Criteria Checklist (QCC)

2023 Volume 4

Abstract: Abstract In this letter, we briefly describe how we selected and implemented the quality criteria checklist (QCC) as a critical appraisal tool in rapid systematic reviews conducted to inform public health advice, guidance and policy during the COVID-19 ... ...

Abstract	Abstract In this letter, we briefly describe how we selected and implemented the quality criteria checklist (QCC) as a critical appraisal tool in rapid systematic reviews conducted to inform public health advice, guidance and policy during the COVID-19 pandemic. As these rapid reviews usually included a range of study designs, it was key to identify a single tool that would allow for reliable critical appraisal across most experimental and observational study designs and applicable to a range of topics. After carefully considering a number of existing tools, the QCC was selected as it had good interrater agreement between three reviewers (Fleiss kappa coefficient 0.639) and was found to be easy and fast to apply once familiar with the tool. The QCC consists of 10 questions, with sub-questions to specify how it should be applied to a specific study design. Four of these questions are considered as critical (on selection bias, group comparability, intervention/exposure assessment and outcome assessment) and the rating of a study (high, moderate or low methodological quality) depends on the responses to these four critical questions. Our results suggest that the QCC is an appropriate critical appraisal tool to assess experimental and observational studies within COVID-19 rapid reviews. This study was done at pace during the COVID-19 pandemic; further reliability analyses should be conducted, and more research is needed to validate the QCC across a range of public health topics.
Keywords	Critical appraisal ; Risk of bias tool ; Rapid systematic reviews ; Public health ; Medicine ; R
Subject code	306
Language	English
Publishing date	2023-03-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Long distance airborne transmission of SARS-CoV-2: rapid systematic review.

Duval, Daphne / Palmer, Jennifer C / Tudge, Isobel / Pearce-Smith, Nicola / O'Connell, Emer / Bennett, Allan / Clark, Rachel

BMJ (Clinical research ed.)

2022 Volume 377, Page(s) e068743

Abstract: Objectives: To evaluate the potential for long distance airborne transmission of SARS-CoV-2 in indoor community settings and to investigate factors that might influence transmission.: Design: Rapid systematic review and narrative synthesis.: Data ... ...

Abstract	Objectives: To evaluate the potential for long distance airborne transmission of SARS-CoV-2 in indoor community settings and to investigate factors that might influence transmission. Design: Rapid systematic review and narrative synthesis. Data sources: Medline, Embase, medRxiv, Arxiv, and WHO COVID-19 Research Database for studies published from 27 July 2020 to 19 January 2022; existing relevant rapid systematic review for studies published from 1 January 2020 to 27 July 2020; and citation analysis in Web of Science and Cocites. Eligibility criteria for study selection: Observational studies reporting on transmission events in indoor community (non-healthcare) settings in which long distance airborne transmission of SARS-CoV-2 was the most likely route. Studies such as those of household transmission where the main transmission route was likely to be close contact or fomite transmission were excluded. Data extraction and synthesis: Data extraction was done by one reviewer and independently checked by a second reviewer. Primary outcomes were SARS-CoV-2 infections through long distance airborne transmission (>2 m) and any modifying factors. Methodological quality of included studies was rated using the quality criteria checklist, and certainty of primary outcomes was determined using the Grading of Recommendations, Assessment, Development, and Evaluation (GRADE) framework. Narrative synthesis was themed by setting. Results: 22 reports relating to 18 studies were identified (methodological quality was high in three, medium in five, and low in 10); all the studies were outbreak investigations. Long distance airborne transmission was likely to have occurred for some or all transmission events in 16 studies and was unclear in two studies (GRADE: very low certainty). In the 16 studies, one or more factors plausibly increased the likelihood of long distance airborne transmission, particularly insufficient air replacement (very low certainty), directional air flow (very low certainty), and activities associated with increased emission of aerosols, such as singing or speaking loudly (very low certainty). In 13 studies, the primary cases were reported as being asymptomatic, presymptomatic, or around symptom onset at the time of transmission. Although some of the included studies were well conducted outbreak investigations, they remain at risk of bias owing to study design and do not always provide the level of detail needed to fully assess transmission routes. Conclusion: This rapid systematic review found evidence suggesting that long distance airborne transmission of SARS-CoV-2 might occur in indoor settings such as restaurants, workplaces, and venues for choirs, and identified factors such as insufficient air replacement that probably contributed to transmission. These results strengthen the need for mitigation measures in indoor settings, particularly the use of adequate ventilation. Systematic review registration: PROSPERO CRD42021236762.
MeSH term(s)	Aerosols ; COVID-19 ; Disease Outbreaks ; Humans ; SARS-CoV-2
Chemical Substances	Aerosols
Language	English
Publishing date	2022-06-29
Publishing country	England
Document type	Journal Article ; Systematic Review
ZDB-ID	1362901-3
ISSN	1756-1833 ; 0959-8154 ; 0959-8146 ; 0959-8138 ; 0959-535X ; 1759-2151
ISSN (online)	1756-1833
ISSN	0959-8154 ; 0959-8146 ; 0959-8138 ; 0959-535X ; 1759-2151
DOI	10.1136/bmj-2021-068743
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Article ; Online: Airborne transmission of SARS-CoV-2 over distances greater than two metres: a rapid systematic review

Palmer, Jennifer C / Duval, Daphne / Tudge, Isobel / Sarfo-Annin, Jason Kwasi / Pearce-Smith, Nicola / O’Connell, Emer / Bennett, Allan / Clark, Rachel

medRxiv

Abstract: Objective To evaluate the potential for long-distance (over two metres) airborne transmission of SARS-CoV-2 in indoor community settings and investigate factors which may impact this transmission. Design Systematic review and narrative synthesis. Data ... ...

Abstract	Objective To evaluate the potential for long-distance (over two metres) airborne transmission of SARS-CoV-2 in indoor community settings and investigate factors which may impact this transmission. Design Systematic review and narrative synthesis. Data source MEDLINE, Embase, medRxiv, Arxiv and WHO COVID-19 Research Database for studies published from 27 July 2020 to 21 April 2021; existing relevant rapid systematic reviews for studies published between 1 January to 27 July 2020. Eligibility criteria for study selection Observational studies that included a thorough epidemiological assessment of routes of transmission and which reported on the likelihood of airborne transmission of SARS-CoV-2 at a distance greater than two metres in indoor community settings. Data extraction and synthesis Data extraction was completed by one reviewer and independently checked by a second reviewer. Primary outcomes were COVID-19 infections via airborne transmission over distances greater than two metres and any factors that may have modified transmission risk. Included studies were rated using a quality criteria checklist (QCC) for primary research and certainty of key outcomes was determined using GRADE. Narrative synthesis was themed by setting. Results Of the 3,780 articles screened for inclusion, 15 publications reporting on 13 epidemiological investigations were included (three high, six medium and four low quality). Airborne transmission at distances greater than two metres was likely to have occurred for some or all transmission events in 12 studies and was unclear in one study (GRADE: very low certainty). In all studies, one or more factors plausibly increased the likelihood of long-distance airborne transmission occurring, particularly insufficient air replacement (GRADE: very low certainty), recirculating air flow (GRADE: very low certainty) and singing (GRADE: very low certainty). In nine studies, the primary cases were reported as being asymptomatic, presymptomatic or around symptom onset at the time of transmission. Conclusion This rapid systematic review found evidence of long-distance airborne transmission of SARS-CoV-2 in indoor community settings and identified factors that likely contributed to this transmission in all included studies. These results strengthen the need for adequate mitigation measures in indoor community settings, particularly adequate ventilation with fresh air, and caution required with the use of recirculating air flow systems. Systematic review registration PROSPERO CRD42021236762
Keywords	covid19
Language	English
Publishing date	2021-10-20
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2021.10.19.21265208
Database	COVID19

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Article ; Online: All-optical phase modulation for integrated interferometric biosensors.

Dante, Stefania / Duval, Daphné / Sepúlveda, Borja / González-Guerrero, Ana Belen / Sendra, José Ramón / Lechuga, Laura M

Optics express

2012 Volume 20, Issue 7, Page(s) 7195–7205

Abstract: We present the theoretical and the experimental implementation of an all-optical phase modulation system in integrated Mach-Zehnder Interferometers to solve the drawbacks related to the periodic nature of the interferometric signal. Sensor phase is tuned ...

Abstract	We present the theoretical and the experimental implementation of an all-optical phase modulation system in integrated Mach-Zehnder Interferometers to solve the drawbacks related to the periodic nature of the interferometric signal. Sensor phase is tuned by modulating the emission wavelength of low-cost commercial laser diodes by changing their output power. FFT deconvolution of the signal allows for direct phase readout, immune to sensitivity variations and to light intensity fluctuations. This simple phase modulation scheme increases the signal-to-noise ratio of the measurements in one order of magnitude, rendering in a sensor with a detection limit of 1.9·10⁻⁷ RIU. The viability of the all-optical modulation approach is demonstrated with an immunoassay detection as a biosensing proof of concept.
MeSH term(s)	Biosensing Techniques/instrumentation ; Equipment Design ; Equipment Failure Analysis ; Immunoassay/instrumentation ; Interferometry/instrumentation ; Systems Integration
Language	English
Publishing date	2012-03-26
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1491859-6
ISSN	1094-4087 ; 1094-4087
ISSN (online)	1094-4087
ISSN	1094-4087
DOI	10.1364/OE.20.007195
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Article ; Online: Nanophotonic lab-on-a-chip platforms including novel bimodal interferometers, microfluidics and grating couplers.

Duval, Daphné / González-Guerrero, Ana Belén / Dante, Stefania / Osmond, Johann / Monge, Rosa / Fernández, Luis J / Zinoviev, Kirill E / Domínguez, Carlos / Lechuga, Laura M

Lab on a chip

2012 Volume 12, Issue 11, Page(s) 1987–1994

Abstract: One of the main limitations for achieving truly lab-on-a-chip (LOC) devices for point-of-care diagnosis is the incorporation of the "on-chip" detection. Indeed, most of the state-of-the-art LOC devices usually require complex read-out instrumentation, ... ...

Abstract	One of the main limitations for achieving truly lab-on-a-chip (LOC) devices for point-of-care diagnosis is the incorporation of the "on-chip" detection. Indeed, most of the state-of-the-art LOC devices usually require complex read-out instrumentation, losing the main advantages of portability and simplicity. In this context, we present our last advances towards the achievement of a portable and label-free LOC platform with highly sensitive "on-chip" detection by using nanophotonic biosensors. Bimodal waveguide interferometers fabricated by standard silicon processes have been integrated with sub-micronic grating couplers for efficient light in-coupling, showing a phase resolution of 6.6 × 10(-4)× 2π rad and a limit of detection of 3.3 × 10(-7) refractive index unit (RIU) in bulk. A 3D network of SU-8 polymer microfluidics monolithically assembled at the wafer-level was included, ensuring perfect sealing and compact packaging. To overcome some of the drawbacks inherent to interferometric read-outs, a novel all-optical wavelength modulation system has been implemented, providing a linear response and a direct read-out of the phase variation. Sensitivity, specificity and reproducibility of the wavelength modulated BiMW sensor has been demonstrated through the label-free immunodetection of the human hormone hTSH at picomolar level using a reliable biofunctionalization process.
MeSH term(s)	Antibodies/immunology ; Biosensing Techniques ; Humans ; Interferometry/instrumentation ; Interferometry/methods ; Lab-On-A-Chip Devices ; Microfluidic Analytical Techniques/instrumentation ; Microfluidic Analytical Techniques/methods ; Nanotechnology/instrumentation ; Nanotechnology/methods ; Optics and Photonics/instrumentation ; Optics and Photonics/methods ; Refractometry ; Thyrotropin/analysis ; Thyrotropin/immunology
Chemical Substances	Antibodies ; Thyrotropin (9002-71-5)
Language	English
Publishing date	2012-05-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2056646-3
ISSN	1473-0189 ; 1473-0197
ISSN (online)	1473-0189
ISSN	1473-0197
DOI	10.1039/c2lc40054e
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Article ; Online: Mechanisms and therapeutic implications of hypermutation in gliomas.

Touat, Mehdi / Li, Yvonne Y / Boynton, Adam N / Spurr, Liam F / Iorgulescu, J Bryan / Bohrson, Craig L / Cortes-Ciriano, Isidro / Birzu, Cristina / Geduldig, Jack E / Pelton, Kristine / Lim-Fat, Mary Jane / Pal, Sangita / Ferrer-Luna, Ruben / Ramkissoon, Shakti H / Dubois, Frank / Bellamy, Charlotte / Currimjee, Naomi / Bonardi, Juliana / Qian, Kenin /

Ho, Patricia / Malinowski, Seth / Taquet, Leon / Jones, Robert E / Shetty, Aniket / Chow, Kin-Hoe / Sharaf, Radwa / Pavlick, Dean / Albacker, Lee A / Younan, Nadia / Baldini, Capucine / Verreault, Maïté / Giry, Marine / Guillerm, Erell / Ammari, Samy / Beuvon, Frédéric / Mokhtari, Karima / Alentorn, Agusti / Dehais, Caroline / Houillier, Caroline / Laigle-Donadey, Florence / Psimaras, Dimitri / Lee, Eudocia Q / Nayak, Lakshmi / McFaline-Figueroa, J Ricardo / Carpentier, Alexandre / Cornu, Philippe / Capelle, Laurent / Mathon, Bertrand / Barnholtz-Sloan, Jill S / Chakravarti, Arnab / Bi, Wenya Linda / Chiocca, E Antonio / Fehnel, Katie Pricola / Alexandrescu, Sanda / Chi, Susan N / Haas-Kogan, Daphne / Batchelor, Tracy T / Frampton, Garrett M / Alexander, Brian M / Huang, Raymond Y / Ligon, Azra H / Coulet, Florence / Delattre, Jean-Yves / Hoang-Xuan, Khê / Meredith, David M / Santagata, Sandro / Duval, Alex / Sanson, Marc / Cherniack, Andrew D / Wen, Patrick Y / Reardon, David A / Marabelle, Aurélien / Park, Peter J / Idbaih, Ahmed / Beroukhim, Rameen / Bandopadhayay, Pratiti / Bielle, Franck / Ligon, Keith L

Nature

2020 Volume 580, Issue 7804, Page(s) 517–523

Abstract: A high tumour mutational burden (hypermutation) is observed in some ... ...

Abstract	A high tumour mutational burden (hypermutation) is observed in some gliomas
MeSH term(s)	Animals ; Antineoplastic Agents, Alkylating/pharmacology ; Antineoplastic Agents, Alkylating/therapeutic use ; Brain Neoplasms/genetics ; Brain Neoplasms/immunology ; Brain Neoplasms/therapy ; DNA Mismatch Repair/genetics ; Gene Frequency ; Genome, Human/drug effects ; Genome, Human/genetics ; Glioma/genetics ; Glioma/immunology ; Glioma/therapy ; Humans ; Male ; Mice ; Microsatellite Repeats/drug effects ; Microsatellite Repeats/genetics ; Mutagenesis/drug effects ; Mutation/drug effects ; Phenotype ; Prognosis ; Programmed Cell Death 1 Receptor/antagonists & inhibitors ; Sequence Analysis, DNA ; Temozolomide/pharmacology ; Temozolomide/therapeutic use ; Xenograft Model Antitumor Assays
Chemical Substances	Antineoplastic Agents, Alkylating ; PDCD1 protein, human ; Programmed Cell Death 1 Receptor ; Temozolomide (YF1K15M17Y)
Language	English
Publishing date	2020-04-15
Publishing country	England
Document type	Journal Article
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-020-2209-9
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Article: Analysis of a simulated microarray dataset: comparison of methods for data normalisation and detection of differential expression (open access publication).

Genetics, selection, evolution : GSE

2007 Volume 39, Issue 6, Page(s) 669–683

Abstract: Microarrays allow researchers to measure the expression of thousands of genes in a single experiment. Before statistical comparisons can be made, the data must be assessed for quality and normalisation procedures must be applied, of which many have been ... ...

Abstract	Microarrays allow researchers to measure the expression of thousands of genes in a single experiment. Before statistical comparisons can be made, the data must be assessed for quality and normalisation procedures must be applied, of which many have been proposed. Methods of comparing the normalised data are also abundant, and no clear consensus has yet been reached. The purpose of this paper was to compare those methods used by the EADGENE network on a very noisy simulated data set. With the a priori knowledge of which genes are differentially expressed, it is possible to compare the success of each approach quantitatively. Use of an intensity-dependent normalisation procedure was common, as was correction for multiple testing. Most variety in performance resulted from differing approaches to data quality and the use of different statistical tests. Very few of the methods used any kind of background correction. A number of approaches achieved a success rate of 95% or above, with relatively small numbers of false positives and negatives. Applying stringent spot selection criteria and elimination of data did not improve the false positive rate and greatly increased the false negative rate. However, most approaches performed well, and it is encouraging that widely available techniques can achieve such good results on a very noisy data set.
MeSH term(s)	Animals ; Animals, Domestic/genetics ; Computer Simulation ; Data Interpretation, Statistical ; Databases, Genetic ; Europe ; Gene Expression Profiling/statistics & numerical data ; Oligonucleotide Array Sequence Analysis/statistics & numerical data ; Software
Language	English
Publishing date	2007-12-06
Publishing country	France
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1005838-2
ISSN	0999-193X
ISSN	0999-193X
DOI	10.1186/1297-9686-39-6-669
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Article ; Online: Analysis of a simulated microarray dataset

Genetics Selection Evolution, Vol 39, Iss 6, Pp 669-

Comparison of methods for data normalisation and detection of differential expression ( Open Access publication )

2007 Volume 683

Abstract: Abstract Microarrays allow researchers to measure the expression of thousands of genes in a single experiment. Before statistical comparisons can be made, the data must be assessed for quality and normalisation procedures must be applied, of which many ... ...

Abstract	Abstract Microarrays allow researchers to measure the expression of thousands of genes in a single experiment. Before statistical comparisons can be made, the data must be assessed for quality and normalisation procedures must be applied, of which many have been proposed. Methods of comparing the normalised data are also abundant, and no clear consensus has yet been reached. The purpose of this paper was to compare those methods used by the EADGENE network on a very noisy simulated data set. With the a priori knowledge of which genes are differentially expressed, it is possible to compare the success of each approach quantitatively. Use of an intensity-dependent normalisation procedure was common, as was correction for multiple testing. Most variety in performance resulted from differing approaches to data quality and the use of different statistical tests. Very few of the methods used any kind of background correction. A number of approaches achieved a success rate of 95% or above, with relatively small numbers of false positives and negatives. Applying stringent spot selection criteria and elimination of data did not improve the false positive rate and greatly increased the false negative rate. However, most approaches performed well, and it is encouraging that widely available techniques can achieve such good results on a very noisy data set.
Keywords	gene expression ; two colour microarray ; simulation ; statistical analysis ; Genetics ; QH426-470 ; Biology (General) ; QH301-705.5 ; Science ; Q ; DOAJ:Genetics ; DOAJ:Biology ; DOAJ:Biology and Life Sciences
Subject code	310
Language	English
Publishing date	2007-11-01T00:00:00Z
Publisher	BioMed Central
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: A simple ATAC-seq protocol for population epigenetics.

Wellcome open research

2021 Volume 5, Page(s) 121

Abstract: ... and can be used with small individuals such as daphnia and schistosome worms, and probably ...

Abstract	We describe here a protocol for the generation of sequence-ready libraries for population epigenomics studies, and the analysis of alignment results. We show that the protocol can be used to monitor chromatin structure changes in populations when exposed to environmental cues. The protocol is a streamlined version of the Assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq) that provides a positive display of accessible, presumably euchromatic regions. The protocol is straightforward and can be used with small individuals such as daphnia and schistosome worms, and probably many other biological samples of comparable size (~10,000 cells), and it requires little molecular biology handling expertise.
Language	English
Publishing date	2021-01-07
Publishing country	England
Document type	Journal Article
ISSN	2398-502X
ISSN	2398-502X
DOI	10.12688/wellcomeopenres.15552.2
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