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5. Ten simple rules for measuring the impact of workshops

Author

Sufi, Shoaib, Duckles, Beth, Simera, Iveta, Nurmikko-Fuller, Terhi, Bellis, Louisa, Miah, Wadud, Wilde, Adriana, Nenadic, Aleksandra, Silva, Raniere, de Beyer, Jennifer A., Struthers, Caroline, Emsley, Iain, Philippe, Olivier, Balzano, Melissa, Coelho, Sara, Ford, Heather, Jones, Catherine, and Higgins, Vanessa

Subjects
Computer Science - Computers and Society
Abstract

Workshops are used to explore a specific topic, transfer knowledge, solve identified problems or create something new. In funded research projects and other research endeavours, workshops are the mechanism to gather the wider project, community or interested people together around a particular topic. However, natural questions arise: how do we measure the impact of these workshops? Do we know whether they are meeting the goals and objectives we set for them? What indicators should we use? In response to these questions, this paper will outline rules that will improve the measurement of the impact of workshops.

Published
2018
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8. Roles of the two chemotaxis clusters in Rhodobacter sphaeroides

Author

de Beyer, Jennifer Anne and Armitage, Judith P.

Subjects
579.3, Bacteriology, Chemotaxis, Microbiology, Image analysis, Biochemistry, Molecular biology, Cells--Motility, Alpha-proteobacteria, Rhodobacter sphaeroides
Abstract

Bacteria swim towards improving conditions by controlling flagellar activity via signals (CheY) sent from chemosensory protein clusters, which respond to changing stimuli. The best studied chemotactic bacterium, E. coli, has one transmembrane chemosensory protein cluster controlling flagellar behaviour. R. sphaeroides has two clusters, one transmembrane and one cytoplasmic. The roles of the two clusters in regulating swimming and chemosensory behaviour are explored here. Newly-developed software was used to measure the effect of deleting or mutating each chemotaxis protein on unstimulated swimming and on the chemosensory response to dynamic change. New behaviours were identified by using much larger sample sizes than previous studies. R. sphaeroides chemotaxis mutants were classified as (i) stoppy unresponsive; (ii) smooth unresponsive or (iii) stoppy inhibited compared to wildtype swimming and chemosensory behaviour. The data showed that the ability to stop during free-swimming is not necessarily connected to the ability to respond to a chemotaxis challenge. The data suggested a new model of connectivity between the two chemosensory pathways. CheY3 and CheY4 are phosphorylated by the transmembrane polar cluster in response to external chemoeffector concentrations. CheY6-P produced by the cytoplasmic cluster is a requirement for chemotaxis, whether or not the polar cluster is able to produce CheY6-P. CheY6-P stops the motor, whereas CheY3,4-P allow smooth swimming. When chemoeffector levels fall, the signals through CheY3,4 fall, allowing CheY6-P to bind and stop the motor. As the polar cluster adapts to the fall by the action of the adaptation proteins CheB1 and CheR2, the concentration of CheY3,4-P increases again, to compete with CheY6-P and allow periods of smooth swimming. Under aerobic conditions, the cytoplasmic cluster controls the basal stopping frequency and does not appear to respond to external chemoeffector changes. The role of the adaptation proteins in resetting the signalling state in R. sphaeroides is unclear, particularly the roles of the proteins associated with the cytoplasmic cluster, CheB2 and CheR3. Tandem mass spectrometry was used to identify glutamate and glutamine (EQ) sites on the cytoplasmic R. sphaeroides chemoreceptor TlpT that are deamidated and methylated by the R. sphaeroides adaptation homologues. In E. coli, adaptation sites are usually EQ/EQ pairs. However the sites reported in TlpT vary at the first residue in the pair. Mutation of the putative EQ adaptation sites caused changes in adaptation, suggesting that CheY6-P levels are controlled and reset by CheB2 and CheR3 controlling the adaptation state of TlpT.

Published
2013

10. Completeness of Reporting in Diet- and Nutrition-Related Randomized Controlled Trials and Systematic Reviews With Meta-Analysis : Protocol for 2 Independent Meta-Research Studies

Author

Silva, Flávia, Adegboye, Amanda Rodrigues Amorim, Lachat, Carl, Curioni, Cintia, Gomes, Fabio, Collins, Gary S., Kac, Gilberto, de Beyer, Jennifer Anne, Cook, Jonathan, Ismail, Leila Cheikh, Page, Matthew, Khandpur, Neha, Lamb, Sarah, Hopewell, Sally, Kirtley, Shona, Durão, Solange, Vorland, Colby J., Schlussel, Michael M., Silva, Flávia, Adegboye, Amanda Rodrigues Amorim, Lachat, Carl, Curioni, Cintia, Gomes, Fabio, Collins, Gary S., Kac, Gilberto, de Beyer, Jennifer Anne, Cook, Jonathan, Ismail, Leila Cheikh, Page, Matthew, Khandpur, Neha, Lamb, Sarah, Hopewell, Sally, Kirtley, Shona, Durão, Solange, Vorland, Colby J., and Schlussel, Michael M.

Abstract

Background: Journal articles describing randomized controlled trials (RCTs) and systematic reviews with meta-analysis of RCTs are not optimally reported and often miss crucial details. This poor reporting makes assessing these studies’ risk of bias or reproducing their results difficult. However, the reporting quality of diet- and nutrition-related RCTs and meta-analyses has not been explored. Objective: We aimed to assess the reporting completeness and identify the main reporting limitations of diet- and nutrition-related RCTs and meta-analyses of RCTs, estimate the frequency of reproducible research practices among these RCTs, and estimate the frequency of distorted presentation or spin among these meta-analyses. Methods: Two independent meta-research studies will be conducted using articles published in PubMed-indexed journals. The first will include a sample of diet- and nutrition-related RCTs; the second will include a sample of systematic reviews with meta-analysis of diet- and nutrition-related RCTs. A validated search strategy will be used to identify RCTs of nutritional interventions and an adapted strategy to identify meta-analyses in PubMed. We will search for RCTs and meta-analyses indexed in 1 calendar year and randomly select 100 RCTs (June 2021 to June 2022) and 100 meta-analyses (July 2021 to July 2022). Two reviewers will independently screen the titles and abstracts of records yielded by the searches, then read the full texts to confirm their eligibility. The general features of these published RCTs and meta-analyses will be extracted into a research electronic data capture database (REDCap; Vanderbilt University). The completeness of reporting of each RCT will be assessed using the items in the CONSORT (Consolidated Standards of Reporting Trials), its extensions, and the TIDieR (Template for Intervention Description and Replication) statements. Information about practices that promote research transparency and reproducibility, such as the publicat

Published
2023

13. Characteristics and Development Methods of Reporting Guidelines for Health Research in the Equator Network Database

Author

Schlussel, Michael, primary, Sharp, Melissa K., additional, de Beyer, Jennifer, additional, Kirtley, Shona, additional, Logullo, Patricia, additional, Dhiman, Paula, additional, MacCarthy, Angela, additional, Koroleva, Anna, additional, Speich, Benjamin, additional, Bullock, Garrett S., additional, Moher, David, additional, and Collins, Gary, additional

Published
2023
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14. Protocol for a meta-research study of protocols for diet or nutrition-related trials published in indexed journals: general aspects of study design, rationale and reporting limitations

Author

Silva, Flávia Moraes, primary, Adegboye, Amanda Rodrigues Amorim, additional, Curioni, Cintia, additional, Gomes, Fabio S, additional, Collins, Gary Stephen, additional, Kac, Gilberto, additional, A De Beyer, Jennifer, additional, Cook, Jonathan Alistair, additional, Cheikh Ismail, Leila, additional, Page, Matthew J, additional, Khandpur, Neha, additional, Lamb, Sarah, additional, Hopewell, Sally, additional, Kirtley, Shona, additional, Durão, Solange, additional, Vorland, Colby J, additional, and M Schlussel, Michael, additional

Published
2022
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16. Completeness of Reporting in Diet- and Nutrition-Related Randomized Controlled Trials and Systematic Reviews With Meta-Analysis: Protocol for 2 Independent Meta-Research Studies (Preprint)

Author

Silva, Flávia, primary, Rodrigues Amorim Adegboye, Amanda, additional, Lachat, Carl, additional, Curioni, Cintia, additional, Gomes, Fabio, additional, Collins, Gary S, additional, Kac, Gilberto, additional, de Beyer, Jennifer Anne, additional, Cook, Jonathan, additional, Ismail, Leila Cheikh, additional, Page, Matthew, additional, Khandpur, Neha, additional, Lamb, Sarah, additional, Hopewell, Sally, additional, Kirtley, Shona, additional, Durão, Solange, additional, Vorland, Colby J, additional, and Schlussel, Michael M, additional

Published
2022
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17. Completeness of reporting in diet and nutrition-related randomized clinical trials and systematic reviews with meta-analysis: protocol for two independent meta-research studies (Preprint)

Author

Silva, Flávia M, primary, Adegboye, Amanda Rodrigues Amorim, additional, Lachat, Carl, additional, Curioni, Cintia, additional, Vorland, Colby J, additional, Gomes, Fabio, additional, Collins, Gary S, additional, Kac, Gilberto, additional, de Beyer, Jennifer Anne, additional, Cook, Jonathan, additional, Ismail, Leila Cheikh, additional, Page, Matthew J, additional, Khandpur, Neha, additional, Hopewell, Sally, additional, Lamb, Sarah Sallie, additional, Kirtley, Shona, additional, Durão, Solange, additional, and Schlussel, Michael, additional

Published
2022
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19. What facilitators and barriers to researchers encounter when using reporting guidelines?

Author

Harwood, James, de Beyer, Jennifer, Schlussel, Michael, Collins, Gary, Kirtley, Shona, Duan, Yuting, Zhao, yun, and Bian, Zhaoxiang

Abstract

Here we present three approaches to identifying possible barriers and facilitators that researchers encounter when using reporting guidelines: 1. A thematic synthesis of qualitative data 2. A description of quantitative questions asked in studies that gather feedback on guidelines 3. A description of Google analytics data from the EQUATOR Network website. The themes we identify will be useful to guideline developers who want to make sure their resources are easy to use, journal editors who want to encourage guideline adherence, and will inform the features of a new website being developed by the EQUATOR Network which will help authors find, understand and apply reporting guidelines.

Published
2022
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20. Protocol for a meta-research study of protocols for diet or nutrition-related trials published in peer-reviewed journals: trends, advances, and reporting limitations

Author

Silva, Flávia, Schlussel, Michael, Kirtley, Shona, Page, Matthew, Cook, Jonathan, Lamb, Sallie, Kac, Gilberto, Curioni, Cintia, Adegboye, Amanda, Durao, Solange, Khandpur, Neha, Gomes, Fabio, de Beyer, Jennifer, Hopewell, Sally, and Ismail, Leila

Subjects
education, Medicine and Health Sciences, Dietetics and Clinical Nutrition
Abstract

The "Standard Protocol Items: Recommendations for Interventional Trials" (SPIRIT) guideline establishes a minimum set of items to be reported in any randomized controlled trial (RCT) protocol, and the TIDieR (Template for Intervention Description and Replication) was developed to improve the completeness of interventions reporting in protocols and complete RCTs. Overall, reporting completeness of RCTs protocols have improved in general since the SPIRIT's publication. However, reporting completeness in protocols for diet or nutrition-related RCTs has not been systematically investigated. The purpose of this systematic review is to identify protocols of diet or nutrition-related RCTs published in peer-reviewed medical journals over time, to assess their reporting completeness and identify the main reporting limitations remaining in this field, despite SPIRIT and TIDieR.

Published
2022
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21. Does providing authors with customized article templates including items from reporting guidelines improve completeness of reporting? A randomized trial

Author

Struthers, Caroline, de Beyer, Jennifer, Logullo, Patricia, Harwood, James, and Collins, Gary

Subjects
Publishing, Medical Education, Communication, Medicine and Health Sciences, EQUATOR Reporting Guidelines, Social and Behavioral Sciences
Abstract

There is evidence that, although most reputable medical journals endorse the use of reporting guidelines, authors still find it difficult to identify the most appropriate one and use it effectively to improve the completeness of their article. We have developed an online tool called GoodReports (www.goodreports.org) to help researchers find and use reporting guidelines. The tool currently helps researchers identify the most appropriate single reporting guideline (e.g., CONSORT, STROBE, or PRISMA) and delivers an online, editable checklist that can also be downloaded. The checklist can be annotated to indicate where in the manuscript each item has been reported, then submitted to a journal alongside an article manuscript. However, pilot data collected as part of a collaboration with a medical journal indicated that when a checklist was delivered immediately before submission, it did not lead to authors making significant additions to their manuscript. Therefore, we plan to 1. Develop the functionality of the GoodReports tool to deliver an article template to be used during writing. 2. Combine items from more than one reporting guideline into a single article template, where appropriate. 3. Conduct a randomized trial to test whether article templates delivered early in the writing process result in more complete reporting of health research articles.

Published
2022
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22. EQUATOR Library Audit

Author

Schlussel, Michael, Collins, Gary, de Beyer, Jennifer, and Kirtley, Shona

Subjects
Research Transparency, Meta-research, Medicine and Health Sciences, Reporting Guidelines, Education
Abstract

To identify true gaps and ensure that reporting guidelines remain a useful tool that is straightforward to use, we are conducting a full audit of the current reporting guidelines’ landscape. We are extracting data on general reporting guidelines characteristics (e.g., scope of guideline, journal and year of publication, length of reporting guideline), methods used to develop the reporting guidelines (e.g., details on any literature review, Delphi survey, consensus process, composition of guideline group, pilot testing), and how they were disseminated (e.g., multiple publications, explanatory document, website). We are using the data collected on development methods to update our taxonomy of reporting guidelines, currently based on their scope (specific to study design, section of the report, clinical area, or a combination of these), and whether the document describes an extension of a previous guideline.

Published
2022
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24. Additional file 1 of GoodReports: developing a website to help health researchers find and use reporting guidelines

Author

Struthers, Caroline, Harwood, James, de Beyer, Jennifer Anne, Dhiman, Paula, Logullo, Patricia, and Schlüssel, Michael

Abstract

Additional file 1 : Table S1. Themes and representative free-text responses (in italics) to the question “How could we make www.goodreports.org more useful?”. Table S2. Themes and representative comments (in italic) about changes made or reasons for not making changes. Table S3. Summary of possible reasons for inappropriate recommendations, with potential solutions

Published
2021
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26. Overinterpretation and misreporting of prognostic factor studies in oncology: a systematic review

Author

Epi Methoden, Child Health, Cancer, Circulatory Health, JC onderzoeksprogramma Methodologie, Epi Methoden Team 4, Kempf, Emmanuelle, de Beyer, Jennifer A., Cook, Jonathan, Holmes, Jane, Mohammed, Seid, Nguyên, Tri Long, Simera, Iveta, Trivella, Marialena, Altman, Douglas G., Hopewell, Sally, Moons, Karel G.M., Porcher, Raphael, Reitsma, Johannes B., Sauerbrei, Willi, Collins, Gary S., Epi Methoden, Child Health, Cancer, Circulatory Health, JC onderzoeksprogramma Methodologie, Epi Methoden Team 4, Kempf, Emmanuelle, de Beyer, Jennifer A., Cook, Jonathan, Holmes, Jane, Mohammed, Seid, Nguyên, Tri Long, Simera, Iveta, Trivella, Marialena, Altman, Douglas G., Hopewell, Sally, Moons, Karel G.M., Porcher, Raphael, Reitsma, Johannes B., Sauerbrei, Willi, and Collins, Gary S.

Published
2018

27. Methods for Evaluating Medical Tests and Biomarkers

Author

Gopalakrishna, Gowri, Langendam, Miranda, Scholten, Rob, Bossuyt, Patrick, Leeflang, Mariska, Noel-Storr, Anna, Thomas, James, Marshall, Iain, Wallace, Byron, Whiting, Penny, Davenport, Clare, GopalaKrishna, Gowri, de Salis, Isabel, Mallett, Sue, Wolff, Robert, Riley, Richard, Westwood, Marie, Kleinen, Jos, Collins, Gary, Reitsma, Hans, Moons, Karel, Zapf, Antonia, Hoyer, Annika, Kramer, Katharina, Kuss, Oliver, Ensor, J., Deeks, J. J., Martin, E. C., Riley, R. D., Rücker, Gerta, Steinhauser, Susanne, Schumacher, Martin, Ensor, Joie, Snell, Kym, Willis, Brian, Debray, Thomas, Deeks, Jon, di Ruffano, Lavinia Ferrante, Taylor-Phillips, Sian, Hyde, Chris, Taylor, Stuart A., Batnagar, Gauraang, Di Ruffano, Lavinia Ferrante, Seedat, Farah, Clarke, Aileen, Byron, Sarah, Nixon, Frances, Albrow, Rebecca, Walker, Thomas, Deakin, Carla, Zhelev, Zhivko, Hunt, Harriet, Yang, Yaling, Abel, Lucy, Buchanan, James, Fanshawe, Thomas, Shinkins, Bethany, Wynants, Laure, Verbakel, Jan, Van Huffel, Sabine, Timmerman, Dirk, Van Calster, Ben, Zwinderman, Aeliko, Oke, Jason, O’Sullivan, Jack, Perera, Rafael, Nicholson, Brian, Bromley, Hannah L., Roberts, Tracy E., Francis, Adele, Petrie, Denniis, Mann, G. Bruce, Malottki, Kinga, Smith, Holly, Billingham, Lucinda, Sitch, Alice, Gerke, Oke, Holm-Vilstrup, Mie, Segtnan, Eivind Antonsen, Halekoh, Ulrich, Høilund-Carlsen, Poul Flemming, Francq, Bernard G., Dinnes, Jac, Parkes, Julie, Gregory, Walter, Hewison, Jenny, Altman, Doug, Rosenberg, William, Selby, Peter, Asselineau, Julien, Perez, Paul, Paye, Aïssatou, Bessede, Emilie, Proust-Lima, Cécile, Naaktgeboren, Christiana, de Groot, Joris, Rutjes, Anne, Reitsma, Johannes, Ogundimu, Emmanuel, Cook, Jonathan, Le Manach, Yannick, Vergouwe, Yvonne, Pajouheshnia, Romin, Groenwold, Rolf, Moons, Karen, Peelen, Linda, Nieboer, Daan, De Cock, Bavo, Pencina, Micael J., Steyerberg, Ewout W., Cooper, Jennifer, Parsons, Nick, Stinton, Chris, Smith, Steve, Dickens, Andy, Jordan, Rachel, Enocson, Alexandra, Fitzmaurice, David, Adab, Peymane, Boachie, Charles, Vidmar, Gaj, Freeman, Karoline, Connock, Martin, Court, Rachel, Moons, Carl, Harris, Jessica, Mumford, Andrew, Plummer, Zoe, Lee, Kurtis, Reeves, Barnaby, Rogers, Chris, Verheyden, Veerle, Angelini, Gianni D., Murphy, Gavin J., Huddy, Jeremy, Ni, Melody, Good, Katherine, Cooke, Graham, Hanna, George, Ma, Jie, Moons, K. G. M. (Carl), de Groot, Joris A. H., Altman, Doug G., Reitsma, Johannes B., Collins, Gary S., Moons, Karel G. M., Altman, Douglas G., Kamarudin, Adina Najwa, Kolamunnage-Dona, Ruwanthi, Cox, Trevor, Borsci, Simone, Pérez, Teresa, Pardo, M.Carmen, Candela-Toha, Angel, Muriel, Alfonso, Zamora, Javier, Sanghera, Sabina, Mohiuddin, Syed, Martin, Richard, Donovan, Jenny, Coast, Joanna, Seo, Mikyung Kelly, Cairns, John, Mitchell, Elizabeth, Smith, Alison, Wright, Judy, Hall, Peter, Messenger, Michael, Calder, Nicola, Wickramasekera, Nyantara, Vinall-Collier, Karen, Lewington, Andrew, Damen, Johanna, Cairns, David, Hutchinson, Michelle, Sturgeon, Cathie, Mitchel, Liz, Kift, Rebecca, Christakoudi, Sofia, Rungall, Manohursingh, Mobillo, Paula, Montero, Rosa, Tsui, Tjir-Li, Kon, Sui Phin, Tucker, Beatriz, Sacks, Steven, Farmer, Chris, Strom, Terry, Chowdhury, Paramit, Rebollo-Mesa, Irene, Hernandez-Fuentes, Maria, Damen, Johanna A. A. G., Debray, Thomas P. A., Heus, Pauline, Hooft, Lotty, Scholten, Rob J. P. M., Schuit, Ewoud, Tzoulaki, Ioanna, Lassale, Camille M., Siontis, George C. M., Chiocchia, Virginia, Roberts, Corran, Schlüssel, Michael Maia, Gerry, Stephen, Black, James A., van der Schouw, Yvonne T., Peelen, Linda M., Spence, Graeme, McCartney, David, van den Bruel, Ann, Lasserson, Daniel, Hayward, Gail, Vach, Werner, de Jong, Antoinette, Burggraaff, Coreline, Hoekstra, Otto, Zijlstra, Josée, de Vet, Henrica, Graziadio, Sara, Allen, Joy, Johnston, Louise, O’Leary, Rachel, Power, Michael, Johnson, Louise, Waters, Ray, Simpson, John, Fanshawe, Thomas R., Phillips, Peter, Plumb, Andrew, Helbren, Emma, Halligan, Steve, Gale, Alastair, Sekula, Peggy, Sauerbrei, Willi, Forman, Julia R., Dutton, Susan J., Takwoingi, Yemisi, Hensor, Elizabeth M., Nichols, Thomas E., Kempf, Emmanuelle, Porcher, Raphael, de Beyer, Jennifer, Altman, Douglas, Hopewell, Sally, Dennis, John, Shields, Beverley, Jones, Angus, Henley, William, Pearson, Ewan, Hattersley, Andrew, Scheibler, Fueloep, Rummer, Anne, Sturtz, Sibylle, Großelfinger, Robert, Banister, Katie, Ramsay, Craig, Azuara-Blanco, Augusto, Burr, Jennifer, Kumarasamy, Manjula, Bourne, Rupert, Uchegbu, Ijeoma, Murphy, Jennifer, Carter, Alex, Murphy, Jen, Marti, Joachim, Eatock, Julie, Robotham, Julie, Dudareva, Maria, Gilchrist, Mark, Holmes, Alison, Monaghan, Phillip, Lord, Sarah, StJohn, Andrew, Sandberg, Sverre, Cobbaert, Christa, Lennartz, Lieselotte, Verhagen-Kamerbeek, Wilma, Ebert, Christoph, Horvath, Andrea, Jenniskens, Kevin, Peters, Jaime, Grigore, Bogdan, Ukoumunne, Obi, Levis, Brooke, Benedetti, Andrea, Levis, Alexander W., Ioannidis, John P. A., Shrier, Ian, Cuijpers, Pim, Gilbody, Simon, Kloda, Lorie A., McMillan, Dean, Patten, Scott B, Steele, Russell J., Ziegelstein, Roy C, Bombardier, Charles H., Osório, Flavia de Lima, Fann, Jesse R., Gjerdingen, Dwenda, Lamers, Femke, Lotrakul, Manote, Loureiro, Sonia R, Löwe, Bernd, Shaaban, Juwita, Stafford, Lesley, van Weert, Henk C. P. M., Whooley, Mary A., Williams, Linda S., Wittkampf, Karin A., Yeung, Albert S., Thombs, Brett D., Cooper, Chris, Nieto, Tom, Smith, Claire, Tucker, Olga, Dretzke, Janine, Beggs, Andrew, Rai, Nirmala, Bayliss, Sue, Stevens, Simon, Mallet, Sue, Sundar, Sudha, Hall, Emma, Porta, Nuria, Estelles, David Lorente, and de Bono, Johann

Subjects
Faecal Immunochemical Test, Chronic Obstructive Pulmonary Disorder, Circulate Tumour Cell Count, Apply Health Research, Meeting Abstracts, Faecal Immunochemical Test Result
Abstract

unKnown

Published
2017

28. Ten simple rules for measuring the impact of workshops

Author

Sufi, Shoaib, primary, Nenadic, Aleksandra, additional, Silva, Raniere, additional, Duckles, Beth, additional, Simera, Iveta, additional, de Beyer, Jennifer A., additional, Struthers, Caroline, additional, Nurmikko-Fuller, Terhi, additional, Bellis, Louisa, additional, Miah, Wadud, additional, Wilde, Adriana, additional, Emsley, Iain, additional, Philippe, Olivier, additional, Balzano, Melissa, additional, Coelho, Sara, additional, Ford, Heather, additional, Jones, Catherine, additional, and Higgins, Vanessa, additional

Published
2018
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33. Novel Methods for Analysing Bacterial Tracks Reveal Persistence in Rhodobacter sphaeroides.

Author

Rosser, Gabriel, Fletcher, Alexander G., Wilkinson, David A., de Beyer, Jennifer A., Yates, Christian A., Armitage, Judith P., Maini, Philip K., and Baker, Ruth E.

Subjects
RHODOBACTER sphaeroides, VIDEO microscopy, MOTILITY of bacteria, MARKOV processes, COMPUTATIONAL biology, ESCHERICHIA coli
Abstract

Tracking bacteria using video microscopy is a powerful experimental approach to probe their motile behaviour. The trajectories obtained contain much information relating to the complex patterns of bacterial motility. However, methods for the quantitative analysis of such data are limited. Most swimming bacteria move in approximately straight lines, interspersed with random reorientation phases. It is therefore necessary to segment observed tracks into swimming and reorientation phases to extract useful statistics. We present novel robust analysis tools to discern these two phases in tracks. Our methods comprise a simple and effective protocol for removing spurious tracks from tracking datasets, followed by analysis based on a two-state hidden Markov model, taking advantage of the availability of mutant strains that exhibit swimming-only or reorientating-only motion to generate an empirical prior distribution. Using simulated tracks with varying levels of added noise, we validate our methods and compare them with an existing heuristic method. To our knowledge this is the first example of a systematic assessment of analysis methods in this field. The new methods are substantially more robust to noise and introduce less systematic bias than the heuristic method. We apply our methods to tracks obtained from the bacterial species Rhodobacter sphaeroides and Escherichia coli. Our results demonstrate that R. sphaeroides exhibits persistence over the course of a tumbling event, which is a novel result with important implications in the study of this and similar species. [ABSTRACT FROM AUTHOR]

Published
2013
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34. Novel Methods for Analysing Bacterial Tracks Reveal Persistence in Rhodobacter sphaeroides.

Author

Rosser, Gabriel, Fletcher, Alexander G., Wilkinson, David A., de Beyer, Jennifer A., Yates, Christian A., Armitage, Judith P., Maini, Philip K., and Baker, Ruth E.

Subjects
*RHODOBACTER sphaeroides, *VIDEO microscopy, *MOTILITY of bacteria, *MARKOV processes, *COMPUTATIONAL biology, *ESCHERICHIA coli
Abstract

Tracking bacteria using video microscopy is a powerful experimental approach to probe their motile behaviour. The trajectories obtained contain much information relating to the complex patterns of bacterial motility. However, methods for the quantitative analysis of such data are limited. Most swimming bacteria move in approximately straight lines, interspersed with random reorientation phases. It is therefore necessary to segment observed tracks into swimming and reorientation phases to extract useful statistics. We present novel robust analysis tools to discern these two phases in tracks. Our methods comprise a simple and effective protocol for removing spurious tracks from tracking datasets, followed by analysis based on a two-state hidden Markov model, taking advantage of the availability of mutant strains that exhibit swimming-only or reorientating-only motion to generate an empirical prior distribution. Using simulated tracks with varying levels of added noise, we validate our methods and compare them with an existing heuristic method. To our knowledge this is the first example of a systematic assessment of analysis methods in this field. The new methods are substantially more robust to noise and introduce less systematic bias than the heuristic method. We apply our methods to tracks obtained from the bacterial species Rhodobacter sphaeroides and Escherichia coli. Our results demonstrate that R. sphaeroides exhibits persistence over the course of a tumbling event, which is a novel result with important implications in the study of this and similar species. [ABSTRACT FROM AUTHOR]

Published
2013
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35. Inducible-Expression Plasmid for Rhodobacter sphaeroides and Para coccus denitrificans.

Author

Ind, Alice C., Porter, Steven L., Brown, Mostyn T., Byles, Elaine D., de Beyer, Jennifer A., Godfrey, Scott A., and Armitage, Judith P.

Subjects
*PLASMIDS, *ESCHERICHIA coli, *PROTEINS, *OXYGEN, *NUCLEOTIDE sequence, *PHENOTYPES, *PHOSPHORYLATION, *HOST-parasite relationships, *IMMUNOBLOTTING
Abstract

We have developed a stable isopropyl-β-D-thiogalactopyranoside (IPTG)-inducible-expression plasmid, pIND4, which allows graduated levels of protein expression in the aiphaproteobacteria Rhodobacter sphaeroides and Paracoccus denitrifi cans. pIND4 confers kanamycin resistance and combines the stable replicon of pMG 160 with the lac1q gene from pYanni3 and the Iac promoter, PA1/04/03, from pJBA24. [ABSTRACT FROM AUTHOR]

Published
2009
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36. Open access journal publication in health and medical research and open science: benefits, challenges and limitations.

Author

Logullo P, de Beyer JA, Kirtley S, Schlüssel MM, and Collins GS

Subjects
Humans, Access to Information, Open Access Publishing, Periodicals as Topic, Biomedical Research
Abstract

Competing Interests: Competing interests: GC is the Editor-in-Chief of BMC Diagnostic & Prognostic Research, a Statistical Editor for the BMJ, and an Associate Editor for Research Integrity and Peer Review. PL is a member of the Editorial Board of Evidence-Based Toxicology and Cytopathology. MMS is in the Editorial Board of Operative Neurosurgery. SK is an associate member of the BJOG Editorial Board.

Published
2024
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