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3. An exploration of available methods and tools to improve the efficiency of systematic review production: a scoping review

Author

Affengruber, Lisa, van der Maten, Miriam M., Spiero, Isa, Nussbaumer-Streit, Barbara, Mahmić-Kaknjo, Mersiha, Ellen, Moriah E., Goossen, Käthe, Kantorova, Lucia, Hooft, Lotty, Riva, Nicoletta, Poulentzas, Georgios, Lalagkas, Panagiotis Nikolaos, Silva, Anabela G., Sassano, Michele, Sfetcu, Raluca, Marqués, María E., Friessova, Tereza, Baladia, Eduard, Pezzullo, Angelo Maria, Martinez, Patricia, Gartlehner, Gerald, and Spijker, René

Published
2024
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4. Nodding syndrome: A scoping review

Author

Abd-Elfarag, Gasim Omer Elkhalifa, Dante Edridge, Arthur Wouter, Spijker, Rene, Sebit, Mohamed Boy, and van Hensbroek, Michael B

Published
2021

7. Explainable Drug Repurposing in Context via Deep Reinforcement Learning

Author

Stork, Lise, Tiddi, Ilaria, Spijker, René, ten Teije, Annette, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Pesquita, Catia, editor, Jimenez-Ruiz, Ernesto, editor, McCusker, Jamie, editor, Faria, Daniel, editor, Dragoni, Mauro, editor, Dimou, Anastasia, editor, Troncy, Raphael, editor, and Hertling, Sven, editor

Published
2023
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8. Training Sample Selection: Impact on Screening Automation in Diagnostic Test Accuracy Reviews

Author

Altena, Allard J., Spijker, René, Leeflang, Mariska M. G., and Olabarriaga, Sílvia Delgado

Abstract

When performing a systematic review, researchers screen the articles retrieved after a broad search strategy one by one, which is time-consuming. Computerised support of this screening process has been applied with varying success. This is partly due to the dependency on large amounts of data to develop models that predict inclusion. In this paper, we present an approach to choose which data to use in model training and compare it with established approaches. We used a dataset of 50 Cochrane diagnostic test accuracy reviews, and each was used as a target review. From the remaining 49 reviews, we selected those that most closely resembled the target review's clinical topic using the cosine similarity metric. Included and excluded studies from these selected reviews were then used to develop our prediction models. The performance of models trained on the selected reviews was compared against models trained on studies from all available reviews. The prediction models performed best with a larger number of reviews in the training set and on target reviews that had a research subject similar to other reviews in the dataset. Our approach using cosine similarity may reduce computational costs for model training and the duration of the screening process.

Published
2021
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11. Large language models, updates, and evaluation of automation tools for systematic reviews: a summary of significant discussions at the eighth meeting of the International Collaboration for the Automation of Systematic Reviews (ICASR).

Author

O'Connor, Annette M., Clark, Justin, Thomas, James, Spijker, René, Kusa, Wojciech, Walker, Vickie R., and Bond, Melissa

Subjects
LANGUAGE models, CHATGPT, LEGAL evidence, AUTOMATION, UNIVERSITIES & colleges
Abstract

The eighth meeting of the International Collaboration for the Automation of Systematic Reviews (ICASR) was held on September 7 and 8, 2023, at the University College London, London, England. ICASR is an interdisciplinary group whose goal is to maximize the use of technology for conducting rapid, accurate, and efficient evidence synthesis, e.g., systematic reviews, evidence maps, and scoping reviews of scientific evidence. In 2023, the major themes discussed were understanding the benefits and harms of automation tools that have become available in recent years, the advantages and disadvantages of large language models in evidence synthesis, and approaches to ensuring the validity of tools for the proposed task. [ABSTRACT FROM AUTHOR]

Published
2024
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12. Searching Practices and Inclusion of Unpublished Studies in Systematic Reviews of Diagnostic Accuracy

Author

Korevaar, Daniël A., Salameh, Jean-Paul, Vali, Yasaman, Cohen, Jérémie F., McInnes, Matthew D. F., Spijker, René, and Bossuyt, Patrick M.

Abstract

Introduction: Many diagnostic accuracy studies are never reported in full in a peer-reviewed journal. Searching for unpublished studies may avoid bias due to selective publication, enrich the power of systematic reviews, and thereby help to reduce research waste. We assessed searching practices among recent systematic reviews of diagnostic accuracy. Methods: We extracted data from 100 non-Cochrane systematic reviews of diagnostic accuracy indexed in MEDLINE and published between October 2017 and January 2018 and from all 100 Cochrane systematic reviews of diagnostic accuracy published by December 2018, irrespective of whether meta-analysis had been performed. Results: Non-Cochrane and Cochrane reviews searched a median of 4 (IQR 3-5) and 6 (IQR 5-9) databases, respectively; most often MEDLINE/PubMed (n = 100 and n = 100) and EMBASE (n = 81 and n = 100). Additional efforts to identify studies beyond searching bibliographic databases were performed in 76 and 98 reviews, most often through screening reference lists (n = 71 and n = 96), review/guideline articles (n = 18 and n = 52), or citing articles (n = 3 and n = 42). Specific sources of unpublished studies were searched in 22 and 68 reviews, for example, conference proceedings (n = 4 and n = 18), databases only containing conference abstracts (n = 2 and n = 33), or trial registries (n = 12 and n = 39). At least one unpublished study was included in 17 and 23 reviews. Overall, 39 of 2082 studies (1.9%) included in non-Cochrane reviews were unpublished, and 64 of 2780 studies (2.3%) in Cochrane reviews, most often conference abstracts (97/103). Conclusion: Searching practices vary considerably across systematic reviews of diagnostic accuracy. Unpublished studies are a minimal fraction of the evidence included in recent reviews.

Published
2020
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14. Prediction models for diagnosis and prognosis of covid-19 : systematic review and critical appraisal

Author

Wynants, Laure, Van Calster, Ben, Collins, Gary S, Riley, Richard D, Heinze, Georg, Schuit, Ewoud, Bonten, Marc M J, Dahly, Darren L, Damen, Johanna A, Debray, Thomas P A, de Jong, Valentijn M T, De Vos, Maarten, Dhiman, Paula, Haller, Maria C, Harhay, Michael O, Henckaerts, Liesbet, Heus, Pauline, Kammer, Michael, Kreuzberger, Nina, Lohmann, Anna, Luijken, Kim, Ma, Jie, Martin, Glen P, McLernon, David J, Navarro, Constanza L Andaur, Reitsma, Johannes B, Sergeant, Jamie C, Shi, Chunhu, Skoetz, Nicole, Smits, Luc J M, Snell, Kym I E, Sperrin, Matthew, Spijker, René, Steyerberg, Ewout W, Takada, Toshihiko, Tzoulaki, Ioanna, van Kuijk, Sander M J, van Bussel, Bas C T, van der Horst, Iwan C C, van Royen, Florien S, Verbakel, Jan Y, Wallisch, Christine, Wilkinson, Jack, Wolff, Robert, Hooft, Lotty, Moons, Karel G M, and van Smeden, Maarten

Published
2020

18. Scoping review and evidence mapping of interventions aimed at improving reproducible and replicable science: Protocol

Author

MS KNO, Brain, Dudda, Leonie A, Kozula, Magdalena, Ross-Hellauer, Tony, Kormann, Eva, Spijker, René, DeVito, Nicholas, Gopalakrishna, Gowri, Van den Eynden, Veerle, Onghena, Patrick, Naudet, Florian, Banzi, Rita, Fratelli, Maddalena, Varga, Monika, Gelsleichter, Yuri Andrei, Stegeman, Inge, Leeflang, Mariska M, MS KNO, Brain, Dudda, Leonie A, Kozula, Magdalena, Ross-Hellauer, Tony, Kormann, Eva, Spijker, René, DeVito, Nicholas, Gopalakrishna, Gowri, Van den Eynden, Veerle, Onghena, Patrick, Naudet, Florian, Banzi, Rita, Fratelli, Maddalena, Varga, Monika, Gelsleichter, Yuri Andrei, Stegeman, Inge, and Leeflang, Mariska M

Published
2024

19. An exploration of available methods and tools to improve the efficiency of systematic review production: a scoping review

Author

Team 5a, Epidemiology & Health Economics, JC onderzoeksprogramma Methodology, Affengruber, Lisa, van der Maten, Miriam M., Spiero, Isa, Nussbaumer-Streit, Barbara, Mahmić-Kaknjo, Mersiha, Ellen, Moriah E., Goossen, Käthe, Kantorova, Lucia, Hooft, Lotty, Riva, Nicoletta, Poulentzas, Georgios, Lalagkas, Panagiotis Nikolaos, Silva, Anabela G., Sassano, Michele, Sfetcu, Raluca, Marqués, María E., Friessova, Tereza, Baladia, Eduard, Pezzullo, Angelo Maria, Martinez, Patricia, Gartlehner, Gerald, Spijker, René, Team 5a, Epidemiology & Health Economics, JC onderzoeksprogramma Methodology, Affengruber, Lisa, van der Maten, Miriam M., Spiero, Isa, Nussbaumer-Streit, Barbara, Mahmić-Kaknjo, Mersiha, Ellen, Moriah E., Goossen, Käthe, Kantorova, Lucia, Hooft, Lotty, Riva, Nicoletta, Poulentzas, Georgios, Lalagkas, Panagiotis Nikolaos, Silva, Anabela G., Sassano, Michele, Sfetcu, Raluca, Marqués, María E., Friessova, Tereza, Baladia, Eduard, Pezzullo, Angelo Maria, Martinez, Patricia, Gartlehner, Gerald, and Spijker, René

Published
2024

20. Overview of the CLEF eHealth Evaluation Lab 2019

Author

Kelly, Liadh, Suominen, Hanna, Goeuriot, Lorraine, Neves, Mariana, Kanoulas, Evangelos, Li, Dan, Azzopardi, Leif, Spijker, Rene, Zuccon, Guido, Scells, Harrisen, Palotti, João, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Crestani, Fabio, editor, Braschler, Martin, editor, Savoy, Jacques, editor, Rauber, Andreas, editor, Müller, Henning, editor, Losada, David E., editor, Heinatz Bürki, Gundula, editor, Cappellato, Linda, editor, and Ferro, Nicola, editor

Published
2019
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21. CLEF eHealth 2019 Evaluation Lab

Author

Kelly, Liadh, Goeuriot, Lorraine, Suominen, Hanna, Neves, Mariana, Kanoulas, Evangelos, Spijker, Rene, Azzopardi, Leif, Li, Dan, Jimmy, Palotti, João, Zuccon, Guido, Hutchison, David, Editorial Board Member, Kanade, Takeo, Editorial Board Member, Kittler, Josef, Editorial Board Member, Kleinberg, Jon M., Editorial Board Member, Mattern, Friedemann, Editorial Board Member, Mitchell, John C., Editorial Board Member, Naor, Moni, Editorial Board Member, Pandu Rangan, C., Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Terzopoulos, Demetri, Editorial Board Member, Tygar, Doug, Editorial Board Member, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Azzopardi, Leif, editor, Stein, Benno, editor, Fuhr, Norbert, editor, Mayr, Philipp, editor, Hauff, Claudia, editor, and Hiemstra, Djoerd, editor

Published
2019
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24. Enhanced liver fibrosis test for the non-invasive diagnosis of fibrosis in patients with NAFLD: A systematic review and meta-analysis

Author

Pavlides, Michael, Levick, Christina, Duffin, Kevin, Hyde, Craig, Bauer, Tim, Bedossa, Pierre, Leeming, Diana, Daly, Ann, Hanf, Remy, Ortiz, Pablo, Oresic, Matej, Schuppan, Detlef, Hanauer, Guido, Chen, Yu, Shumbayawonda, Elizabeth, Bjerring, Peter Nissen, Zwinderman, Koos, Vali, Yasaman, Lee, Jenny, Boursier, Jérôme, Spijker, René, Löffler, Jürgen, Verheij, Joanne, Brosnan, M. Julia, Böcskei, Zsolt, Anstee, Quentin M., Bossuyt, Patrick M., and Zafarmand, Mohammad Hadi

Published
2020
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26. Overview of the CLEF eHealth Evaluation Lab 2018

Author

Suominen, Hanna, Kelly, Liadh, Goeuriot, Lorraine, Névéol, Aurélie, Ramadier, Lionel, Robert, Aude, Kanoulas, Evangelos, Spijker, Rene, Azzopardi, Leif, Li, Dan, Jimmy, Palotti, João, Zuccon, Guido, Hutchison, David, Series Editor, Kanade, Takeo, Series Editor, Kittler, Josef, Series Editor, Kleinberg, Jon M., Series Editor, Mattern, Friedemann, Series Editor, Mitchell, John C., Series Editor, Naor, Moni, Series Editor, Pandu Rangan, C., Series Editor, Steffen, Bernhard, Series Editor, Terzopoulos, Demetri, Series Editor, Tygar, Doug, Series Editor, Weikum, Gerhard, Series Editor, Bellot, Patrice, editor, Trabelsi, Chiraz, editor, Mothe, Josiane, editor, Murtagh, Fionn, editor, Nie, Jian Yun, editor, Soulier, Laure, editor, SanJuan, Eric, editor, Cappellato, Linda, editor, and Ferro, Nicola, editor

Published
2018
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29. Scoping review and evidence mapping of interventions aimed at improving reproducible and replicable science: Protocol

Author

Dudda, Leonie A., primary, Kozula, Magdalena, additional, Ross-Hellauer, Tony, additional, Kormann, Eva, additional, Spijker, René, additional, DeVito, Nicholas, additional, Gopalakrishna, Gowri, additional, Van den Eynden, Veerle, additional, Onghena, Patrick, additional, Naudet, Florian, additional, Banzi, Rita, additional, Fratelli, Maddalena, additional, Varga, Monika, additional, Gelsleichter, Yuri Andrei, additional, Stegeman, Inge, additional, and Leeflang, Mariska M., additional

Published
2023
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31. CLEF 2017 eHealth Evaluation Lab Overview

Author

Goeuriot, Lorraine, Kelly, Liadh, Suominen, Hanna, Névéol, Aurélie, Robert, Aude, Kanoulas, Evangelos, Spijker, Rene, Palotti, João, Zuccon, Guido, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Jones, Gareth J.F., editor, Lawless, Séamus, editor, Gonzalo, Julio, editor, Kelly, Liadh, editor, Goeuriot, Lorraine, editor, Mandl, Thomas, editor, Cappellato, Linda, editor, and Ferro, Nicola, editor

Published
2017
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33. Autologous Bone Is Inferior to Alloplastic Cranioplasties: Safety of Autograft and Allograft Materials for Cranioplasties, a Systematic Review

Author

Becking, A.G., Dubois, L., Karssemakers, L.H.E., Milstein, D.M.J., van de Vijfeijken, S.E.C.M., Depauw, P.R.A.M., Hoefnagels, F.W.A., Vandertop, W.P., Kleverlaan, C.J., Münker, T.J.A.G., Maal, T.J.J., Nout, E., Riool, M., Zaat, S.A.J., van de Vijfeijken, Sophie E.C.M., Münker, Tijmen J.A.G., Spijker, Rene, Karssemakers, Luc H.E., Vandertop, William P., Becking, Alfred G., and Ubbink, Dirk T.

Published
2018
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37. The persistent underrepresentation of patients with chronic kidney disease in cardiovascular trials: a systematic review and evidence map of exclusion and outcomes

Author

Colombijn, Julia M.T., primary, Idema, Demy L., additional, van Beem, Sanne, additional, Blokland, Anna Marthe, additional, van der Braak, Kim, additional, Handoko, M. Louis, additional, Huis in't Veld, Linde F., additional, Kaul, Tabea, additional, Kolagasigil-Akdemir, Nurda, additional, Kusters, Mike P.T., additional, Meijvis, Sabine C.A., additional, Oosting, Ilse J., additional, Spijker, René, additional, Bots, Michiel, additional, Hooft, Lotty, additional, Verhaar, Marianne C., additional, and Vernooij, Robin W.M., additional

Published
2023
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39. Barriers and facilitators to the uptake of tuberculosis diagnostic and treatment services by hard-to-reach populations in countries of low and medium tuberculosis incidence: a systematic review of qualitative literature

Author

de Vries, Sophia G, Cremers, Anne L, Heuvelings, Charlotte C, Greve, Patrick F, Visser, Benjamin J, Bélard, Sabine, Janssen, Saskia, Spijker, René, Shaw, Beth, Hill, Ruaraidh A, Zumla, Alimuddin, van der Werf, Marieke J, Sandgren, Andreas, and Grobusch, Martin P

Published
2017
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43. Prognostic accuracy of imaging findings for predicting morbidity and mortality in patients with COVID-19

Author

Epi Methoden Team 5, HAG Infectieziekten, Epi Infectieziekten Team 1b, Infection & Immunity, JC onderzoeksprogramma Infectieziekten, Islam, Nayaar, Kashif Al-Ghita, Mohammed, Ebrahimzadeh, Sanam, Dawit, Haben, Prager, Ross, Alvarez, Gonzalo G., Cohen, Jérémie F., Korevaar, Daniël A., Deeks, Jonathan J., Verbakel, Jan Y., Damen, Johanna A.A.G., Ochodo, Eleanor A., Venugopalan Nair, Anirudh, Dinnes, Jacqueline, Dennie, Carole, Van den Bruel, Ann, van de Wijgert, Janneke, Sikora, Lindsey, Spijker, René, Hare, Samanjit S., McInnes, Matthew D.F., Epi Methoden Team 5, HAG Infectieziekten, Epi Infectieziekten Team 1b, Infection & Immunity, JC onderzoeksprogramma Infectieziekten, Islam, Nayaar, Kashif Al-Ghita, Mohammed, Ebrahimzadeh, Sanam, Dawit, Haben, Prager, Ross, Alvarez, Gonzalo G., Cohen, Jérémie F., Korevaar, Daniël A., Deeks, Jonathan J., Verbakel, Jan Y., Damen, Johanna A.A.G., Ochodo, Eleanor A., Venugopalan Nair, Anirudh, Dinnes, Jacqueline, Dennie, Carole, Van den Bruel, Ann, van de Wijgert, Janneke, Sikora, Lindsey, Spijker, René, Hare, Samanjit S., and McInnes, Matthew D.F.

Published
2023

44. Effectiveness of FeNO-guided treatment in adult asthma patients: A systematic review and meta-analysis

Author

Epi Methoden Team 5, Epidemiology & Health Economics, JC onderzoeksprogramma Methodologie, Korevaar, Daniël A., Damen, Johanna A., Heus, Pauline, Moen, Maaike J., Spijker, René, van Veen, Ilonka H., Weersink, Els J., van Kemenade, Geert Jan, van Hal, Peter Th W., Hooft, Lotty, Epi Methoden Team 5, Epidemiology & Health Economics, JC onderzoeksprogramma Methodologie, Korevaar, Daniël A., Damen, Johanna A., Heus, Pauline, Moen, Maaike J., Spijker, René, van Veen, Ilonka H., Weersink, Els J., van Kemenade, Geert Jan, van Hal, Peter Th W., and Hooft, Lotty

Published
2023

45. Laboratory biomarkers of delayed cerebral ischemia following subarachnoid hemorrhage: A systematic review

Author

Tjerkstra, Maud, Labib, Homeyra, Coert, Bert A., Spijker, René, Coutinho, Jonathan M., Vandertop, W. Peter, Verbaan, Dagmar, Tjerkstra, Maud, Labib, Homeyra, Coert, Bert A., Spijker, René, Coutinho, Jonathan M., Vandertop, W. Peter, and Verbaan, Dagmar

Abstract

Delayed cerebral ischemia (DCI) substantially contributes to disability and death in subarachnoid hemorrhage (SAH) patients; however, its pathophysiology is incompletely understood and diagnostic and therapeutic strategies are lacking. Biomarkers may help to elucidate the pathophysiology, optimize early diagnosis, or provide treatment targets. We systematically searched PubMed and Embase on October 13, 2021, for studies that evaluated at least one laboratory biomarker in patients with DCI, using the most up-to-date definition of DCI as proposed by a panel of experts in 2010. Quality of studies was assessed using the Newcastle-Ottawa Scale or Cochrane Collaboration’s risk of bias assessment tool. Biomarkers of clinical and radiological DCI were analyzed separately. Results were meta-analyzed if possible, otherwise narratively reviewed. Biomarkers were classified as significant, inconclusive, or nonsignificant. We defined validated biomarkers as those with significant results in meta-analyses, or in at least two studies using similar methodologies within the same time interval after SAH. The search yielded 209 articles with 724 different biomarkers; 166 studies evaluated 646 biomarkers of clinical DCI, of which 141 were significant and 7 were validated biomarkers (haptoglobulin 2-1 and 2-2, ADAMTS13, vWF, NLR, P-selectin, F2-isoprostane); 78 studies evaluated 165 biomarkers of radiological DCI, of which 63 were significant and 1 was a validated biomarker (LPR). Hence, this review provides a selection of seven biomarkers of clinical DCI and one biomarker of radiological DCI as most promising biomarkers of DCI. Future research should focus on determining the exact predictive, diagnostic, and therapeutic potentials of these biomarkers.

Published
2023

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