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Flitti D, Pandis N, Seehra J. Still to ARRIVE at adequate reporting of orthodontic studies involving animal models. Eur J Orthod 2024; 46:cjae032. [PMID: 39007674 PMCID: PMC11247523 DOI: 10.1093/ejo/cjae032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
BACKGROUND The ARRIVE 2.0 guidelines were introduced to improve the reporting of animal studies. The aim of this study was to assess the reporting adherence of orthodontic speciality animal studies in relation to ARRIVE 2.0 guidelines. Associations between the reporting and study characteristics were explored. MATERIALS AND METHOD An electronic database search was undertaken using Medline via PubMed (www.pubmed.ncbi.nlm.nih.gov) to identify studies meeting the eligibility criteria published between 1 January 2018 and 31 December 2023. Data extraction was performed in duplicate and independently. Descriptive statistics and frequency distributions for the responses to each checklist item were calculated. Mean values for adequate reporting per ARRIVE item were calculated. A sum score was calculated by adding the responses (0 = not reported, 1 = inadequate reporting, 2 = adequate reporting) per item and sub-questions. On an exploratory basis, univariable linear regression between summary score and study characteristics (year of publication, continent of authorship, type of centre, and number of authors) was performed. RESULTS Three hundred and eighty-four studies were analysed. Variability in the adequate reporting of the ARRIVE 2.0 guideline items was evident. In particular, in 32% of studies, there was a lack of reporting of the priori sample size calculation. Overall, the mean reporting score for the sample was 57.9 (SD 6.7 and range 34-74). There were no associations between score and study characteristics except for a weak association for year of publication with a small improvement over time (each additional year). CONCLUSIONS The reporting of animal studies relevant to the speciality of orthodontics is sub-optimal in relation to the ARRIVE 2.0 guidelines. There was a tendency for the non-reporting of items pertaining to study sample size, eligibility, methods to reduce bias and interpretation/scientific implications. Greater awareness and reporting adherence to the ARRIVE 2.0 guidelines are required to reduce research waste involving animal models.
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Affiliation(s)
- Dihya Flitti
- Department of Orthodontics, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, Floor 21, Guy’s Hospital, Guy’s and St Thomas NHS Foundation Trust, London, SE1 9RT, United Kingdom
| | - Nikolaos Pandis
- Department of Orthodontics and Dentofacial Orthopedics, Dental School/Medical Faculty, University of Bern, Bern, Switzerland
| | - Jadbinder Seehra
- Department of Orthodontics, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, Floor 21, Guy’s Hospital, Guy’s and St Thomas NHS Foundation Trust, London, SE1 9RT, United Kingdom
- Centre for Craniofacial Development & Regeneration, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, Floor 27, Guy’s Hospital, Guy’s and St Thomas NHS Foundation Trust, London, SE1 9RT, United Kingdom
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Safy RK, Ragab MH, Abdel-Maksoud HB. Histopathological Evaluation of Human Placental Extract as a Direct Pulp-Capping Material in Dogs' Teeth. Eur J Dent 2024. [PMID: 38942055 DOI: 10.1055/s-0044-1786841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024] Open
Abstract
OBJECTIVE The current research aimed to evaluate the histopathological pulpal alterations in dogs' teeth following direct pulp capping using either mineral trioxide aggregate (MTA) or human placenta extract (HPE). MATERIALS AND METHODS Forty-eight incisors with mature apices from four dogs were involved. The teeth were randomly allocated to three groups (n = 16) based on the material utilized for direct pulp capping: MTA, HPE, and Teflon as the negative control group. All involved teeth were capped and restored at the same session. Each group was subsequently divided into two subgroups (n = 8) based on the post treatment evaluation period: 2 and 4 weeks. The histopathologic changes in each specimen's pulp tissues, including pulp inflammation, hyperemia, necrosis, and dentin bridge development, were assessed. Then, all the data were statistically analyzed using chi-square, t-test, and one-way analysis of variance (p < 0.05). RESULTS At 2 weeks, chronic inflammation was observed in 100% of MTA and 50% of HPE subgroups with a significant difference between them whereas the remaining 50% exhibited no inflammation. In contrast to Teflon that showed acute inflammation, remission of inflammation was time-dependent at both MTA and HPE subgroups as there was a substantial difference between the 2- and 4-weeks evaluation periods within the same group. However, throughout the initially observed 2 weeks, all subgroups exhibited essentially no complete calcified bridge; at 4 weeks, all MTA and HPE subgroups developed dentin bridge formation, with a significant difference between them regarding its thickness. CONCLUSION HPE is a promising pulp-capping material inducing less intense chronic inflammation accompanied with thicker dentine bridge formation in comparison to MTA.
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Affiliation(s)
- Rehab Khalil Safy
- Department of Conservative Dentistry, Faculty of Dentistry, Suez Canal University, Ismailia Governorate, Egypt
| | - Mai Hamdy Ragab
- Department of Endodontics, Faculty of Dentistry, Suez Canal University, Ismailia Governorate, Egypt
- King Salman International University, Eltor, South Sinai, Egypt
| | - Heba Bahgat Abdel-Maksoud
- Department of Conservative Dentistry, Faculty of Dentistry, Suez Canal University, Ismailia Governorate, Egypt
- Restorative Dentistry Department, King Abdulaziz University, Jeddah, Saudi Arabia
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Sharma NK, Ayyala R, Deshpande D, Patel Y, Munteanu V, Ciorba D, Bostan V, Fiscutean A, Vahed M, Sarkar A, Guo R, Moore A, Darci-Maher N, Nogoy N, Abedalthagafi M, Mangul S. Analytical code sharing practices in biomedical research. PeerJ Comput Sci 2024; 10:e2066. [PMID: 38983240 PMCID: PMC11232620 DOI: 10.7717/peerj-cs.2066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 04/26/2024] [Indexed: 07/11/2024]
Abstract
Data-driven computational analysis is becoming increasingly important in biomedical research, as the amount of data being generated continues to grow. However, the lack of practices of sharing research outputs, such as data, source code and methods, affects transparency and reproducibility of studies, which are critical to the advancement of science. Many published studies are not reproducible due to insufficient documentation, code, and data being shared. We conducted a comprehensive analysis of 453 manuscripts published between 2016-2021 and found that 50.1% of them fail to share the analytical code. Even among those that did disclose their code, a vast majority failed to offer additional research outputs, such as data. Furthermore, only one in ten articles organized their code in a structured and reproducible manner. We discovered a significant association between the presence of code availability statements and increased code availability. Additionally, a greater proportion of studies conducting secondary analyses were inclined to share their code compared to those conducting primary analyses. In light of our findings, we propose raising awareness of code sharing practices and taking immediate steps to enhance code availability to improve reproducibility in biomedical research. By increasing transparency and reproducibility, we can promote scientific rigor, encourage collaboration, and accelerate scientific discoveries. We must prioritize open science practices, including sharing code, data, and other research products, to ensure that biomedical research can be replicated and built upon by others in the scientific community.
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Affiliation(s)
- Nitesh Kumar Sharma
- Titus Family Department of Clinical Pharmacy, University of Southern California, Los Angeles, California, United States
| | - Ram Ayyala
- Quantitative and Computational Biology Department, University of Southern California, Los Angeles, California, United States
| | - Dhrithi Deshpande
- Titus Family Department of Clinical Pharmacy, University of Southern California, Los Angeles, California, United States
| | - Yesha Patel
- Titus Family Department of Clinical Pharmacy, University of Southern California, Los Angeles, California, United States
| | - Viorel Munteanu
- Department of Computers, Informatics and Microelectronics, Technical University of Moldova, Chisinau, Moldova
| | - Dumitru Ciorba
- Department of Computers, Informatics and Microelectronics, Technical University of Moldova, Chisinau, Moldova
| | - Viorel Bostan
- Department of Computers, Informatics and Microelectronics, Technical University of Moldova, Chisinau, Moldova
| | - Andrada Fiscutean
- Faculty of Journalism and Communication Studies, University of Bucharest, Bucharest, Romania
| | - Mohammad Vahed
- Titus Family Department of Clinical Pharmacy, University of Southern California, Los Angeles, California, United States
| | - Aditya Sarkar
- School of Computing and Electrical Engineering, Indian Institute of Technology Mandi, Kamand, Himachal Pradesh, India
| | - Ruiwei Guo
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, California, United States
| | - Andrew Moore
- Daniel J. Epstein Department of Industrial and Systems Engineering, University of Southern California, Los Angeles, California, United States
| | - Nicholas Darci-Maher
- Computational and Systems Biology, University of California, Los Angeles, Los Angeles, California, United States
| | | | - Malak Abedalthagafi
- Department of Pathology & Laboratory Medicine, Emory University Hospital, Atlanta, Georgia, United States
- King Salman Center for Disability Research, Riyadh, Saudi Arabia
| | - Serghei Mangul
- Titus Family Department of Clinical Pharmacy, University of Southern California, Los Angeles, California, United States
- Quantitative and Computational Biology Department, University of Southern California, Los Angeles, California, United States
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Bisio MMC, Jurado Medina LS, García-Bournissen F, Gulin JEN. Listen to what the animals say: a systematic review and meta-analysis of sterol 14-demethylase inhibitor efficacy for in vivo models of Trypanosoma cruzi infection. Parasitol Res 2024; 123:248. [PMID: 38904688 DOI: 10.1007/s00436-024-08257-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 05/30/2024] [Indexed: 06/22/2024]
Abstract
Sterol 14-demethylase (CYP51) inhibitors, encompassing new chemical entities and repurposed drugs, have emerged as promising candidates for Chagas disease treatment, based on preclinical studies reporting anti-Trypanosoma cruzi activity. Triazoles like ravuconazole (RAV) and posaconazole (POS) progressed to clinical trials. Unexpectedly, their efficacy was transient in chronic Chagas disease patients, and their activity was not superior to benznidazole (BZ) treatment. This paper aims to summarize evidence on the global activity of CYP51 inhibitors against T. cruzi by applying systematic review strategies, risk of bias assessment, and meta-analysis from in vivo studies. PubMed and Embase databases were searched for original articles, obtaining fifty-six relevant papers meeting inclusion criteria. Characteristics of animal models, parasite strain, treatment schemes, and cure rates were extracted. Primary outcomes such as maximum parasitaemia values, survival, and parasitological cure were recorded for meta-analysis, when possible. The risk of bias was uncertain in most studies. Animals treated with itraconazole, RAV, or POS survived significantly longer than the infected non-treated groups (RR = 4.85 [3.62, 6.49], P < 0.00001), and they showed no differences with animals treated with positive control drugs (RR = 1.01 [0.98, 1.04], P = 0.54). Furthermore, the overall analysis showed that RAV or POS was not likely to achieve parasitological cure when compared with BZ or NFX treatment (OD = 0.49 [0.31, 0.77], P = 0.002). This systematic review contributes to understanding why the azoles had failed in clinical trials and, more importantly, how to improve the animal models of T. cruzi infection by filling the gaps between basic, translational, and clinical research.
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Affiliation(s)
- Margarita María Catalina Bisio
- Instituto Nacional de Parasitología (INP) 'Dr. Mario Fatala Chaben'-ANLIS 'Dr. Carlos G. Malbrán', Buenos Aires, Argentina. Av. Paseo Colón 568, C1097, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Laura Smeldy Jurado Medina
- Dipartimento Di Scienze Mediche E Chirurgiche, Alma Mater Studiorum, Università Di Bologna, Via San Giacomo 12, 2 Floor, 55. 40126, BO. Bologna, Italy
| | - Facundo García-Bournissen
- Division of Paediatric Clinical Pharmacology, Department of Paediatrics, Schulich School of Medicine & Dentistry, University of Western Ontario, 800 Commissioners Rd. E., Rm. B1-437., London, ON, Canada
| | - Julián Ernesto Nicolás Gulin
- Instituto de Biología y Medicina Experimental (IBYME), CONICET, Vuelta de Obligado 2490 (C1428ADN), Buenos Aires, Argentina.
- Instituto de Investigaciones Biomédicas (INBIOMED), UBA-CONICET, Paraguay 2155 (C1121ABG), Buenos Aires, Argentina.
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Witowski J, Sikorska D, Catar R. Reporting Practices for Animal Studies on Peritoneal Dialysis Conducted in 2021-2023 after the Introduction of the ARRIVE 2.0 Guidelines. Nephron Clin Pract 2024:1-11. [PMID: 38934165 DOI: 10.1159/000539892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
INTRODUCTION The first version of Animal Research: Reporting of in vivo Experiments (ARRIVE 1.0) guidelines was introduced to improve reporting of animal research but did not lead to major improvements in this respect. This applied also to animal studies on peritoneal dialysis (PD). Here, we examined the performance of the revised version of these guidelines (ARRIVE 2.0). METHODS Eighty-nine relevant articles published in 2018-2020 (ARRIVE 1.0 period) and 97 published in 2021-2023 (ARRIVE 2.0 period) were identified in PubMed® and analyzed for completeness and transparency of reporting. RESULTS In both periods, most studies were carried out in Asia, on rodents, and concerned the peritoneal pathophysiology. During ARRIVE 2.0, more studies were published in higher impact factor journals with the focus on pharmacology and immunology. Compared to ARRIVE 1.0, general aspects of study design and reporting improved during ARRIVE 2.0 period in studies generated in Europe and USA but did not change significantly in Asia. Detailed analysis showed no global improvement in completeness of reporting key information included in the ARRIVE 2.0 Essential 10 checklist. Articles from both periods were deficient in sample size calculations, use of blinding, recording adverse events and drop-outs, and specification of appropriate statistical methods. The level of reporting during ARRIVE 2.0 did not correspond to the journal impact factor and the presence of recommendations for the use of ARRIVE 2.0 in their instructions to authors. CONCLUSION So far, ARRIVE 2.0 has not produced significant improvements in the reporting of animal studies in PD.
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Affiliation(s)
- Janusz Witowski
- Department Pathophysiology, Poznan University of Medical Sciences, Poznan, Poland
| | - Dorota Sikorska
- Department Rheumatology, Rehabilitation and Internal Medicine, Poznan University of Medical Sciences, Poznan, Poland
| | - Rusan Catar
- Department Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany
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Ng JY, Santoro LJ, Cobey KD, Steel A, Cramer H, Moher D. Complementary, alternative, and integrative medicine researchers' practices and perceived barriers related to open science: An international, cross-sectional survey. PLoS One 2024; 19:e0301251. [PMID: 38709739 PMCID: PMC11073706 DOI: 10.1371/journal.pone.0301251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/13/2024] [Indexed: 05/08/2024] Open
Abstract
INTRODUCTION AND OBJECTIVE Open science (OS) aims to make the dissemination of knowledge and the research process transparent and accessible to everyone. With the increasing popularity of complementary, alternative, and integrative medicine (CAIM), our goal was to explore what are CAIM researchers' practices and perceived barriers related to OS. METHODS We conducted an anonymous online survey of researchers who published in journals listed in Scopus containing the words "complementary", "alternative", or "integrative" medicine in their names. We emailed 6040 researchers our purpose-built electronic survey after extracting their email address from one of their publications in our sample of journals. We questioned their familiarity with different OS concepts, along with their experiences and challenges engaging in these practices over the last 12 months. RESULTS The survey was completed by 392 researchers (6.5% response rate, 97.1% completion rate). Most respondents were CAIM researchers familiar with the overall concept of OS, indicated by those actively publishing open access (OA) (n = 244, 76.0%), registering a study protocol (n = 148, 48.0%), and using reporting guidelines (n = 181, 59.0%) in the past 12 months. Preprinting, sharing raw data, and sharing study materials were less popular. A lack of funding was reported as the greatest barrier to publishing OA by most respondents (n = 252, 79.0%), and that additional funding is the most significant incentive in applying more OS practices to their research (n = 229,72.2%). With respect to preprinting barriers, 36.3% (n = 110) participants believed there are potential harms in sharing non-peer-reviewed work and 37.0% (n = 112) feared preprinting would reduce the likelihood of their manuscript being accepted by a journal. Respondents were also concerned about intellectual property control regarding sharing data (n = 94, 31.7%) and research study materials (n = 80, 28.7%). CONCLUSIONS Although many participants were familiar with and practiced aspects of OS, many reported facing barriers relating to lack of funding to enable OS and perceived risks of revealing research ideas and data prior to publication. Future research should monitor the adoption and implementation of OS interventions in CAIM.
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Affiliation(s)
- Jeremy Y. Ng
- Ottawa Hospital Research Institute, Centre for Journalology, Ottawa, Canada
- Institute of General Practice and Interprofessional Care, University Hospital Tübingen, Tübingen, Germany
- Robert Bosch Center for Integrative Medicine and Health, Bosch Health Campus, Stuttgart, Germany
| | - Lucas J. Santoro
- Institute of General Practice and Interprofessional Care, University Hospital Tübingen, Tübingen, Germany
- Robert Bosch Center for Integrative Medicine and Health, Bosch Health Campus, Stuttgart, Germany
| | - Kelly D. Cobey
- Metaresearch and Open Science Program, University of Ottawa Heart Institute, Ottawa, Canada
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Canada
| | - Amie Steel
- Faculty of Health, Australian Research Consortium in Complementary and Integrative Medicine (ARCCIM), School of Public Health, University of Technology Sydney, Ultimo, Australia
| | - Holger Cramer
- Institute of General Practice and Interprofessional Care, University Hospital Tübingen, Tübingen, Germany
- Robert Bosch Center for Integrative Medicine and Health, Bosch Health Campus, Stuttgart, Germany
| | - David Moher
- Ottawa Hospital Research Institute, Centre for Journalology, Ottawa, Canada
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Canada
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Song J, Solmi M, Carvalho AF, Shin JI, Ioannidis JP. Twelve years after the ARRIVE guidelines: Animal research has not yet arrived at high standards. Lab Anim 2024; 58:109-115. [PMID: 37728936 DOI: 10.1177/00236772231181658] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
The reproducibility crisis across animal studies jeopardizes the credibility of the main findings derived from animal research, even though these findings are critical for informing human studies. To clarify and improve transparency among animal studies, the ARRIVE reporting guidelines were first announced in 2010 and upgraded to version 2.0 in 2020. However, compliance with and awareness of those reporting guidelines has remained suboptimal. Journal editors should encourage the authors to adhere to those guidelines. Authors, editors, referees, and reviewers should be aware of the ARRIVE guideline 2.0 when assessing and evaluating the methodology and findings of animal studies. However, we should also question whether reporting guidelines alone can change a research culture and improve the reproducibility of animal investigations. Reported research may not reflect actual research. Large segments of animal research efforts are wasted because of poor design choices and because of non-publication rather than suboptimal reporting. Better training of the scientific workforce, interventions at improving animal research at the design stage, registration practices, and alignment of the reward system with the publication of rigorous animal research may achieve more than reporting guidelines alone.
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Affiliation(s)
- Junmin Song
- Department of Medicine, Jacobi Medical Center, Albert Einstein College of Medicine, Bronx, USA
| | - Marco Solmi
- Department of Psychiatry, University of Ottawa, Ontario, Canada
- Department of Mental Health, The Ottawa Hospital, Ontario, Canada
- Ottawa Hospital Research Institute (OHRI) Clinical Epidemiology Program University of Ottawa, Ontario, Canada
- School of Epidemiology and Public Health, Faculty of Medicine, University of Ottawa, Ontario, Canada
- Department of Child and Adolescent Psychiatry, Charité Universitätsmedizin, Berlin, Germany
| | - Andre F Carvalho
- IMPACT (Innovation in Mental and Physical Health and Clinical Treatment) Strategic Research Centre, School of Medicine, Barwon Health, Deakin University, Geelong, Australia
| | - Jae Il Shin
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Republic of Korea
- The Center for Medical Education Training and Professional Development in Yonsei-Donggok Medical Education Institute, Seoul, Republic of Korea
- Severance Underwood Meta-research Center, Institute of Convergence Science, Yonsei University, Seoul, South Korea
| | - John Pa Ioannidis
- Departments of Medicine, Epidemiology and Population Health, Biomedical Data Science, and Statistics, and Meta-Research Innovation Center at Stanford (METRICS), Stanford University, USA
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Liu W, Jiang D, Schulz M, Figueiredo C, Dondossola D, Meister FA, Tihanyi DK, Mehrabi A, Tolba RH, Czigany Z, Ernst L. Machine perfusion of the liver and in vivo animal models: A systematic review of the preclinical research landscape. PLoS One 2024; 19:e0297942. [PMID: 38329986 PMCID: PMC10852327 DOI: 10.1371/journal.pone.0297942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 01/15/2024] [Indexed: 02/10/2024] Open
Abstract
Machine perfusion (MP) is often referred to as one of the most promising advancements in liver transplantation research of the last few decades, with various techniques and modalities being evaluated in preclinical studies using animal models. However, low scientific rigor and subpar reporting standards lead to limited reproducibility and translational potential, hindering progress. This pre-registered systematic review (PROSPERO: CRD42021234667) aimed to provide a thematic overview of the preclinical research landscape on MP in liver transplantation using in vivo transplantation models and to explore methodological and reporting standards, using the ARRIVE (Animal Research: Reporting of In Vivo Experiments) score. In total 56 articles were included. Studies were evenly distributed across Asia, Europe, and the Americas. Porcine models were used in 57.1% of the studies, followed by rats (39.3%) and dogs (3.6%). In terms of graft type, 55.4% of the studies used donation after cardiac death grafts, while donation after brain death grafts accounted for 37.5%. Regarding MP modalities, the distribution was as follows: 41.5% of articles utilized hypothermic MP, 21.5% normothermic MP, 13.8% subnormothermic MP, and 16.9% utilized hypothermic oxygenated MP. The stringent documentation of ARRIVE elements concerning precise experimental execution, group size and selection, the choice of statistical methods, as well as adherence to the principles of the 3Rs, was notably lacking in the majority of publications, with less than 30% providing comprehensive details. Postoperative analgesia and antibiotics treatment were not documented in 82.1% of all included studies. None of the analyzed studies fully adhered to the ARRIVE Guidelines. In conclusion, the present study emphasizes the importance of adhering to reporting standards to promote reproducibility and adequate animal welfare in preclinical studies in machine perfusion. At the same time, it highlights a clear deficiency in this field, underscoring the need for further investigations into animal welfare-related topics.
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Affiliation(s)
- Wenjia Liu
- Department of Surgery and Transplantation, Faculty of Medicine, University Hospital RWTH Aachen, Aachen, Germany
- Institute for Laboratory Animal Science and Experimental Surgery, Faculty of Medicine, RWTH, Aachen International University, Aachen, Germany
| | - Decan Jiang
- Department of Surgery and Transplantation, Faculty of Medicine, University Hospital RWTH Aachen, Aachen, Germany
| | - Mareike Schulz
- Institute for Laboratory Animal Science and Experimental Surgery, Faculty of Medicine, RWTH, Aachen International University, Aachen, Germany
| | - Constança Figueiredo
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School, Hannover, Germany
| | - Daniele Dondossola
- General and Liver Transplant Surgery Unit, Fondazione IRCCS Ca’Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Franziska Alexandra Meister
- Department of Surgery and Transplantation, Faculty of Medicine, University Hospital RWTH Aachen, Aachen, Germany
| | | | - Arianeb Mehrabi
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Rene Hany Tolba
- Institute for Laboratory Animal Science and Experimental Surgery, Faculty of Medicine, RWTH, Aachen International University, Aachen, Germany
| | - Zoltan Czigany
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Lisa Ernst
- Institute for Laboratory Animal Science and Experimental Surgery, Faculty of Medicine, RWTH, Aachen International University, Aachen, Germany
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Cobey KD, Alayche M, Saba S, Barnes NY, Ebrahimzadeh S, Alarcón E, Hibbert B, Moher D. Cardiology researchers' practices and perceived barriers to open science: an international survey. Open Heart 2024; 11:e002433. [PMID: 38233041 PMCID: PMC10806507 DOI: 10.1136/openhrt-2023-002433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024] Open
Abstract
OBJECTIVE Open science is a movement and set of practices to conduct research more transparently. Implementing open science will significantly improve public access and supports equity. It also has the potential to foster innovation and reduce duplication through data and materials sharing. Here, we survey an international group of researchers publishing in cardiovascular journals regarding their perceptions and practices related to open science. METHODS We identified the top 100 'Cardiology and Cardiovascular Medicine' subject category journals from the SCImago journal ranking platform. This is a publicly available portal that draws from Scopus. We then extracted the corresponding author's name and email from all articles published in these journals between 1 March 2021 and 1 March 2022. Participants were sent a purpose-built survey about open science. The survey contained primarily multiple choice and scale-based questions for which we report count data and percentages. For the few text-based responses we conducted thematic content analysis. RESULTS 198 participants responded to our survey. Participants had a mean response of 6.8 (N=197, SD=1.8) on a 9-point scale with endpoints, not at all familiar (1) and extremely familiar (9), when indicating how familiar they were with open science. When asked about where they obtained open science training, most participants indicated this was done on the job self-initiated while conducting research (n=103, 52%), or that they had no formal training with respect to open science (n=72, 36%). More than half of the participants indicated they would benefit from practical support from their institution on how to perform open science practices (N=106, 54%). A diversity of barriers to each of the open science practices presented to participants were acknowledged. Participants indicated that funding was the most essential incentive to adopt open science. CONCLUSIONS It is clear that policy alone will not lead to the effective implementation of open science. This survey serves as a baseline for the cardiovascular research community's open science performance and perception and can be used to inform future interventions and monitoring.
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Affiliation(s)
- Kelly D Cobey
- University of Ottawa Heart Institute, Ottawa, Ontario, Canada
- University of Ottawa, Ottawa, Ontario, Canada
| | - Mohsen Alayche
- Department of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Sara Saba
- University of Ottawa Heart Institute, Ottawa, Ontario, Canada
- University of Ottawa, Ottawa, Ontario, Canada
| | - Nana Yaa Barnes
- University of Ottawa Heart Institute, Ottawa, Ontario, Canada
- Health Sciences University of Ottawa, Ottawa, Ontario, Canada
| | | | - Emilio Alarcón
- University of Ottawa Heart Institute, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Benjamin Hibbert
- University of Ottawa Heart Institute, Ottawa, Ontario, Canada
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - David Moher
- University of Ottawa, Ottawa, Ontario, Canada
- Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
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10
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von Kortzfleisch VT, Richter SH. Systematic heterogenization revisited: Increasing variation in animal experiments to improve reproducibility? J Neurosci Methods 2024; 401:109992. [PMID: 37884081 DOI: 10.1016/j.jneumeth.2023.109992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 10/10/2023] [Accepted: 10/22/2023] [Indexed: 10/28/2023]
Abstract
Life sciences are currently facing a reproducibility crisis. Originally, the crisis was born out of single alarming failures to reproduce findings at different times and locations. Nowadays, systematic studies indicate that the prevalence of irreproducible research does in fact exceed 50%. Viewed from a rather cynical perspective, Fett's law of the lab "Never replicate a successful experiment" has thus taken on a completely new meaning. In this respect, animal research has come under particular scrutiny, as the stakes are high in terms of both research ethics and societal impact. To counteract this, it is essential to identify sources of poor reproducibility as well as to iron out these failures. We here review the current debate, briefly discuss potential reasons, and summarize steps that have already been undertaken to improve reproducibility in animal research. By the example of classical behavioural phenotyping studies, we particularly highlight the role strict standardization plays in exacerbating the crisis, and review the concept of systematic heterogenization as an alternative strategy to deal with variation in animal studies. Briefly, we argue that systematic variation rather than strict homogenization of experimental conditions benefits the robustness of research findings, and hence their reproducibility. To this end, we will present concrete examples for systematically heterogenized experiments and provide a practical guide on how to apply systematic heterogenization in experimental practice.
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Affiliation(s)
| | - S Helene Richter
- Department of Behavioural Biology, University of Münster, Badestraße 13, 48149 Münster, Germany.
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11
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El-Cheikh Mohamad A, Möhrle D, Haddad FL, Rose A, Allman BL, Schmid S. Assessing the Cntnap2 knockout rat prepulse inhibition deficit through prepulse scaling of the baseline startle response curve. Transl Psychiatry 2023; 13:321. [PMID: 37852987 PMCID: PMC10584930 DOI: 10.1038/s41398-023-02629-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/27/2023] [Accepted: 10/06/2023] [Indexed: 10/20/2023] Open
Abstract
Many neurodevelopmental disorders, including autism spectrum disorder (ASD), are associated with changes in sensory processing and sensorimotor gating. The acoustic startle response and prepulse inhibition (PPI) of startle are widely used translational measures for assessing sensory processing and sensorimotor gating, respectively. The Cntnap2 knockout (KO) rat has proven to be a valid model for ASD, displaying core symptoms, including sensory processing perturbations. Here, we used a novel method to assess startle and PPI in Cntnap2 KO rats that allows for the identification of separate scaling components: startle scaling, which is a change in startle amplitude to a given sound, and sound scaling, which reflects a change in sound processing. Cntnap2 KO rats show increased startle due to both an increased overall response (startle scaling) and a left shift of the sound/response curve (sound scaling). In the presence of a prepulse, wildtype rats show a reduction of startle due to both startle scaling and sound scaling, whereas Cntnap2 KO rats show normal startle scaling, but disrupted sound scaling, resulting in the reported PPI deficit. These results validate that startle and sound scaling by a prepulse are indeed two independent processes, with only the latter being impaired in Cntnap2 KO rats. As startle scaling is likely related to motor output and sound scaling to sound processing, this novel approach reveals additional information on the possible cause of PPI disruptions in preclinical models.
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Affiliation(s)
- Alaa El-Cheikh Mohamad
- Anatomy & Cell Biology, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON, Canada
| | - Dorit Möhrle
- Anatomy & Cell Biology, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON, Canada
| | - Faraj L Haddad
- Anatomy & Cell Biology, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON, Canada
| | - Anton Rose
- Anatomy & Cell Biology, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON, Canada
| | - Brian L Allman
- Anatomy & Cell Biology, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON, Canada
| | - Susanne Schmid
- Anatomy & Cell Biology, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON, Canada.
- Department of Psychology, University of Western Ontario, London, ON, Canada.
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12
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Matos FG, Stremel ACA, Lipinski LC, Cirelli JA, Dos Santos FA. Dental implants in large animal models with experimental systemic diseases: A systematic review. Lab Anim 2023; 57:489-503. [PMID: 37021606 DOI: 10.1177/00236772221124972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
This systematic review aims to identify and discuss the most used methodologies in pre-clinical studies for the evaluation of the implementation of dental implants in systemically compromised pigs and sheep. This study provides support and guidance for future research, as well as for the prevention of unnecessary animal wastage and sacrifice. Preferred Reporting for Systematic Reviews and Meta-Analyses (PRISMA) was used as a guideline; electronic searches were performed in PubMed, Scopus, Scielo, Web of Science, Embase, Science Direct, Brazilian Bibliography of Dentistry, Latin American and Caribbean Literature in Health Sciences, Directory of Open Access Journals, Database of Abstracts of Reviews of Effects, and gray literature until January 2022 (PROSPERO/CRD42021270119). Sixty-eight articles were chosen from the 2439 results. Most studies were conducted in pigs, mainly the Göttinger and Domesticus breeds. Healthy animals with implants installed in the jaws were predominant among the pig studies. Of the studies evaluating the effect of systemic diseases on osseointegration, 42% were performed in osteoporotic sheep, 32% in diabetic sheep, and 26% in diabetic pigs. Osteoporosis was primarily induced by bilateral ovariectomy and mainly assessed by X-ray densitometry. Diabetes was induced predominantly by intravenous streptozotocin and was confirmed by blood glucose analysis. Histological and histomorphometric analyses were the most frequently employed in the evaluation of osseointegration. The animal models presented unique methodologies for each species in the studies that evaluated dental implants in the context of systemic diseases. Understanding the most commonly used techniques will help methodological choices and the performance of future studies in implantology.
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Affiliation(s)
| | | | | | - Joni Augusto Cirelli
- Department of Diagnosis and Surgery, School of Dentistry at Araraquara, State University of São Paulo (Unesp), Brazil
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13
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Gallas-Lopes M, Bastos LM, Benvenutti R, Panzenhagen AC, Piato A, Herrmann AP. Systematic review and meta-analysis of 10 years of unpredictable chronic stress in zebrafish. Lab Anim (NY) 2023; 52:229-246. [PMID: 37709998 DOI: 10.1038/s41684-023-01239-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 08/04/2023] [Indexed: 09/16/2023]
Abstract
The zebrafish (Danio rerio) is a model animal that is being increasingly used in neuroscience research. A decade ago, the first study on unpredictable chronic stress (UCS) in zebrafish was published, inspired by protocols established for rodents in the early 1980s. Since then, several studies have been published by different groups, in some cases with conflicting results. Here we conducted a systematic review to identify studies evaluating the effects of UCS in zebrafish and meta-analytically synthetized the data of neurobehavioral outcomes and relevant biomarkers. Literature searches were performed in three databases (PubMed, Scopus and Web of Science) with a two-step screening process based on inclusion/exclusion criteria. The included studies underwent extraction of qualitative and quantitative data, as well as risk-of-bias assessment. Outcomes of included studies (n = 38) were grouped into anxiety/fear-related behavior, locomotor function, social behavior or cortisol level domains. UCS increased anxiety/fear-related behavior and cortisol levels while decreasing locomotor function, but a significant summary effect was not observed for social behavior. Despite including a substantial number of studies, the high heterogeneity and the methodological and reporting problems evidenced in the risk-of-bias analysis made it difficult to assess the internal validity of most studies and the overall validity of the model. Our review thus evidences the need to conduct well-designed experiments to better evaluate the effects of UCS on diverse behavioral patterns displayed by zebrafish.
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Affiliation(s)
- Matheus Gallas-Lopes
- Brazilian Reproducibility Initiative in Preclinical Systematic Review and Meta-Analysis (BRISA) Collaboration, Rio de Janeiro, Brazil
- Laboratório de Neurobiologia e Psicofarmacologia Experimental (PsychoLab), Departamento de Farmacologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratório de Psicofarmacologia e Comportamento (LAPCOM), Departamento de Farmacologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Leonardo M Bastos
- Laboratório de Neurobiologia e Psicofarmacologia Experimental (PsychoLab), Departamento de Farmacologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratório de Psicofarmacologia e Comportamento (LAPCOM), Departamento de Farmacologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Radharani Benvenutti
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Alana C Panzenhagen
- Brazilian Reproducibility Initiative in Preclinical Systematic Review and Meta-Analysis (BRISA) Collaboration, Rio de Janeiro, Brazil
- Programa de Pós-Graduação em Ciências Biológicas: Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Angelo Piato
- Laboratório de Psicofarmacologia e Comportamento (LAPCOM), Departamento de Farmacologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Ana P Herrmann
- Brazilian Reproducibility Initiative in Preclinical Systematic Review and Meta-Analysis (BRISA) Collaboration, Rio de Janeiro, Brazil.
- Laboratório de Neurobiologia e Psicofarmacologia Experimental (PsychoLab), Departamento de Farmacologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
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Vollert J. Addressing the elephant in the T-maze: Developing experimental conduct guidelines for neuroscience. J Neurosci Methods 2023; 398:109956. [PMID: 37633649 DOI: 10.1016/j.jneumeth.2023.109956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 08/28/2023]
Abstract
Personal view - no abstract.
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Affiliation(s)
- Jan Vollert
- Pain Research, Department of Surgery and Cancer, Imperial College London, London, UK; Division of Neurological Pain Research and Therapy, Department of Neurology, University Hospital of Schleswig-Holstein, Campus Kiel, Germany; Department of Anaesthesiology, Intensive Care and Pain Medicine, University Hospital Muenster, Germany.
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15
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Kousholt BS, Præstegaard KF, Stone JC, Thomsen AF, Johansen TT, Ritskes-Hoitinga M, Wegener G. Reporting of 3Rs Approaches in Preclinical Animal Experimental Studies-A Nationwide Study. Animals (Basel) 2023; 13:3005. [PMID: 37835611 PMCID: PMC10571812 DOI: 10.3390/ani13193005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/11/2023] [Accepted: 09/13/2023] [Indexed: 10/15/2023] Open
Abstract
The 3Rs aim to refine animal welfare, reduce animal numbers, and replace animal experiments. Investigations disclose that researchers are positive towards 3Rs recommendations from peers. Communication of 3Rs approaches via primary preclinical animal experimental literature may become a fast-forward extension to learn relevant 3Rs approaches if such are reported. This study investigates 3Rs-reporting in peer-reviewed preclinical animal research with at least one author affiliated to a Danish university. Using a systematic search and random sampling, we included 500 studies from 2009 and 2018. Reporting was low and improvement over time limited. A word search for 3R retrieved zero results in 2009 and 3.2% in 2018. Reporting on 3Rs-related sentences increased from 6.4% in 2009 to 18.4% in 2018, "reduction" increased from 2.4% to 8.0%, and "refinement" from 5.2% to 14.4%. Replacement was not reported. Reporting of the methodology was missing. For "reduction", methodology was mentioned in one study in 2009 and 11 studies in 2018, and for "refinement" in 9 and 21, respectively. Twenty-one studies stated compliance with ARRIVE-guidelines or similar without disclosure of details. Reporting of 3Rs approaches in preclinical publications is currently insufficient to guide researchers. Other strategies, e.g., education, interdisciplinary collaboration, and 3Rs funding initiatives, are needed.
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Affiliation(s)
- Birgitte S. Kousholt
- Department of Clinical Medicine, AUGUST, Aarhus University, 8200 Aarhus, Denmark; (K.F.P.); (A.F.T.); (T.T.J.); (M.R.-H.); (G.W.)
| | - Kirstine F. Præstegaard
- Department of Clinical Medicine, AUGUST, Aarhus University, 8200 Aarhus, Denmark; (K.F.P.); (A.F.T.); (T.T.J.); (M.R.-H.); (G.W.)
| | - Jennifer C. Stone
- JBI, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5005, Australia;
- Department of Health Services Research and Policy, Research School of Population Health, Australian National University, Canberra, ACT 2600, Australia
| | - Anders F. Thomsen
- Department of Clinical Medicine, AUGUST, Aarhus University, 8200 Aarhus, Denmark; (K.F.P.); (A.F.T.); (T.T.J.); (M.R.-H.); (G.W.)
| | - Thea T. Johansen
- Department of Clinical Medicine, AUGUST, Aarhus University, 8200 Aarhus, Denmark; (K.F.P.); (A.F.T.); (T.T.J.); (M.R.-H.); (G.W.)
| | - Merel Ritskes-Hoitinga
- Department of Clinical Medicine, AUGUST, Aarhus University, 8200 Aarhus, Denmark; (K.F.P.); (A.F.T.); (T.T.J.); (M.R.-H.); (G.W.)
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands
| | - Gregers Wegener
- Department of Clinical Medicine, AUGUST, Aarhus University, 8200 Aarhus, Denmark; (K.F.P.); (A.F.T.); (T.T.J.); (M.R.-H.); (G.W.)
- Translational Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, 8200 Aarhus, Denmark
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16
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Tzanetakis G, Jakovljevic A, Koletsi D, Jacimovic J, Nagendrababu V, Duncan HF, Dummer PMH. Critical analysis of the reporting quality of animal studies within Endodontics using the Preferred Reporting Items for Animal Studies in Endodontics (PRIASE) 2021 quality standard checklist. Int Endod J 2023; 56:1042-1062. [PMID: 37300853 DOI: 10.1111/iej.13944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 05/07/2023] [Accepted: 06/07/2023] [Indexed: 06/12/2023]
Abstract
AIM To critically evaluate the reporting quality of a random sample of animal studies within the field of endodontics against the Preferred Reporting Items for Animal Studies in Endodontics (PRIASE) 2021 checklist and to investigate the association between the quality of reporting and several characteristics of the selected studies. METHODOLOGY Fifty animal studies related to endodontics were randomly selected from the PubMed database with publication dates from January 2017 to December 2021. For each study, a score of '1' was given when the item of the PRIASE 2021 checklist was fully reported, whereas a score of '0' was given when an item was not reported; when the item was inadequately or partially reported, a score of '0.5' was given. Based on the overall scores allocated to each manuscript, they were allocated into three categories of reporting quality: low, moderate and high. Associations between study characteristics and reporting quality scores were also analysed. Descriptive statistics and Fisher's exact tests were used to describe the data and determine associations. The probability value of .05 was selected as the level of statistical significance. RESULTS Based on the overall scores, four (8%) and 46 (92%) of the animal studies evaluated were categorized as 'High' and 'Moderate' reporting quality, respectively. A number of items were adequately reported in all studies related to background (Item 4a), relevance of methods/results (7a) and interpretation of images (11e), whereas only one item related to changes in protocol (6d) was not reported in any. No associations were confirmed between reporting quality scores and number of authors, origin of the corresponding author, journal of publication (endodontic specialty vs. non- specialty), impact factor or year of publication. CONCLUSIONS Animal studies published in the specialty of endodontics were mostly of 'moderate' quality in terms of the quality of reporting. Adherence to the PRIASE 2021 guidelines will enhance the reporting of animal studies in the expectation that all future publications will be high quality.
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Affiliation(s)
- Giorgos Tzanetakis
- Department of Endodontics, School of Dentistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Aleksandar Jakovljevic
- Department of Pathophysiology, School of Dental Medicine, University of Belgrade, Belgrade, Serbia
| | - Despina Koletsi
- Clinic of Orthodontics and Pediatric Dentistry, Center of Dental Medicine, University of Zurich, Zurich, Switzerland
- Meta- Research Innovation Center at Stanford (METRICS), Stanford University, Stanford, California, USA
| | - Jelena Jacimovic
- Central Library, School of Dental Medicine, University of Belgrade, Belgrade, Serbia
| | - Venkateshbabu Nagendrababu
- University of Sharjah, College of Dental Medicine, Department of Preventive and Restorative Dentistry, Sharjah, UAE
| | - Henry Fergus Duncan
- Division of Restorative Dentistry & Periodontology, Dublin Dental University Hospital, Trinity College Dublin, Dublin, Ireland
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Sharma NK, Ayyala R, Deshpande D, Patel YM, Munteanu V, Ciorba D, Fiscutean A, Vahed M, Sarkar A, Guo R, Moore A, Darci-Maher N, Nogoy NA, Abedalthagafi MS, Mangul S. Analytical code sharing practices in biomedical research. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.31.551384. [PMID: 37609176 PMCID: PMC10441317 DOI: 10.1101/2023.07.31.551384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Data-driven computational analysis is becoming increasingly important in biomedical research, as the amount of data being generated continues to grow. However, the lack of practices of sharing research outputs, such as data, source code and methods, affects transparency and reproducibility of studies, which are critical to the advancement of science. Many published studies are not reproducible due to insufficient documentation, code, and data being shared. We conducted a comprehensive analysis of 453 manuscripts published between 2016-2021 and found that 50.1% of them fail to share the analytical code. Even among those that did disclose their code, a vast majority failed to offer additional research outputs, such as data. Furthermore, only one in ten papers organized their code in a structured and reproducible manner. We discovered a significant association between the presence of code availability statements and increased code availability (p=2.71×10-9). Additionally, a greater proportion of studies conducting secondary analyses were inclined to share their code compared to those conducting primary analyses (p=1.15*10-07). In light of our findings, we propose raising awareness of code sharing practices and taking immediate steps to enhance code availability to improve reproducibility in biomedical research. By increasing transparency and reproducibility, we can promote scientific rigor, encourage collaboration, and accelerate scientific discoveries. We must prioritize open science practices, including sharing code, data, and other research products, to ensure that biomedical research can be replicated and built upon by others in the scientific community.
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Affiliation(s)
- Nitesh Kumar Sharma
- Titus Family Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, 1540 Alcazar Street, Los Angeles, CA 90033, USA
| | - Ram Ayyala
- Quantitative and Computational Biology Department, USC Dana and David Dornsife College of Letters, Arts, and Sciences, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089, USA
| | - Dhrithi Deshpande
- Titus Family Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, 1540 Alcazar Street, Los Angeles, CA 90033, USA
| | - Yesha M Patel
- Titus Family Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, 1540 Alcazar Street, Los Angeles, CA 90033, USA
| | - Viorel Munteanu
- Department of Computers, Informatics and Microelectronics, Technical University of Moldova, Chisinau, 2045, Moldova
| | - Dumitru Ciorba
- Department of Computers, Informatics and Microelectronics, Technical University of Moldova, Chisinau, 2045, Moldova
| | - Andrada Fiscutean
- Faculty of Journalism and Communication Studies, University of Bucharest, Soseaua Panduri, nr. 90, Sector 5, 050663, Bucharest, Romania
| | - Mohammad Vahed
- Titus Family Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, 1540 Alcazar Street, Los Angeles, CA 90033, USA
| | - Aditya Sarkar
- School of Computing and Electrical Engineering, Indian Institute of Technology Mandi, North Campus, Kamand, Mandi, Himachal Pradesh, 175005, India
| | - Ruiwei Guo
- Department of Pharmacology and Pharmaceutical Sciences, USC Alfred E. Mann School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Room 713. Los Angeles, CA 90089-9121, USA
| | - Andrew Moore
- Daniel J. Epstein Department of Industrial and Systems Engineering, Viterbi School of Engineering, University of Southern California
| | - Nicholas Darci-Maher
- Computational and Systems Biology, University of California, Los Angeles, 580 Portola Plaza, Los Angeles, CA 90095, USA
| | - Nicole A Nogoy
- GigaScience Press, L26/F, Kings Wing Plaza 2, 1 On Kwan Street, Shek Mun, N.T., Hong Kong
| | - Malak S. Abedalthagafi
- Department of Pathology & Laboratory Medicine, Emory University Hospital, Atlanta, GA, USA
- King Salman Center for Disability Research, Riyadh, Saudi Arabia
| | - Serghei Mangul
- Titus Family Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, 1540 Alcazar Street, Los Angeles, CA 90033, USA
- Department of Quantitative and Computational Biology, University of Southern California Dornsife College of Letters, Arts, and Sciences, Los Angeles, CA 90089, USA
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Plumb AN, Lesnak JB, Berardi G, Hayashi K, Janowski AJ, Smith AF, Bailey D, Kerkman C, Kienenberger Z, Martin B, Patterson E, Van Roekel H, Vance CGT, Sluka KA. Standing on the shoulders of bias: lack of transparency and reporting of critical rigor characteristics in pain research. Pain 2023; 164:1775-1782. [PMID: 36877823 PMCID: PMC10356741 DOI: 10.1097/j.pain.0000000000002874] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/03/2023] [Indexed: 03/08/2023]
Abstract
ABSTRACT Rigorous experimental design with transparent reporting in biomedical science reduces risk of bias and allows for scientists to judge the quality of the research. Basic factors of rigor such as blinding, randomization, power analysis, and inclusion of both sexes impact the reproducibility by reducing experimental bias. We designed a systematic study to analyze basic factors of rigor, inclusion of sex, and whether data were analyzed or disaggregated by sex over the past 10 years in the journal PAIN . Studies that included humans reported randomization in 81%, blinding in 48%, and the use of a power analysis calculation in 27% over the past 10 years. Studies that included mice reported randomization in 35%, blinding in 70%, and the use of a power analysis in 9%. Studies that included rats reported randomization in 38%, blinding in 63%, and the use of power analysis in 12%. This study also found that human studies consistently included both sexes over the past decade, but less than 20% of data were disaggregated or analyzed for sex differences. Although mouse and rat studies predominately used males only, there has been a slight increase in inclusion of both sexes over the past few years. Justification for single-sex studies was below 50% in both human and rodent data. In both human and animal studies, transparency in reporting of experimental design and inclusion of both sexes should be considered standard practice and will result in improved quality and reproducibility of published research.
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Affiliation(s)
- Ashley N Plumb
- Department of Physical Therapy and Rehabilitation Science, University of Iowa, Iowa City, IA, United States
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Hall RP. Replication and Reproducibility and the Self-Correction of Science: What Can JID Innovations Do? JID INNOVATIONS 2023; 3:100188. [PMID: 37252319 PMCID: PMC10213953 DOI: 10.1016/j.xjidi.2023.100188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023] Open
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20
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Identifying barriers and enablers to rigorous conduct and reporting of preclinical laboratory studies. PLoS Biol 2023; 21:e3001932. [PMID: 36603053 PMCID: PMC9888705 DOI: 10.1371/journal.pbio.3001932] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 01/31/2023] [Accepted: 11/24/2022] [Indexed: 01/06/2023] Open
Abstract
Use of rigorous study design methods and transparent reporting in publications are 2 key strategies proposed to improve the reproducibility of preclinical research. Despite promotion of these practices by funders and journals, assessments suggest uptake is low in preclinical research. Thirty preclinical scientists were interviewed to better understand barriers and enablers to rigorous design and reporting. The interview guide was informed by the Theoretical Domains Framework, which is a framework used to understand determinants of current and desired behavior. Four global themes were identified; 2 reflecting enablers and 2 reflecting barriers. We found that basic scientists are highly motivated to apply the methods of rigorous design and reporting and perceive a number of benefits to their adoption (e.g., improved quality and reliability). However, there was varied awareness of the guidelines and in implementation of these practices. Researchers also noted that these guidelines can result in disadvantages, such as increased sample sizes, expenses, time, and can require several personnel to operationalize. Most researchers expressed additional resources such as personnel and education/training would better enable the application of some methods. Using existing guidance (Behaviour Change Wheel (BCW); Expert Recommendations for Implementing Change (ERIC) project implementation strategies), we mapped and coded our interview findings to identify potential interventions, policies, and implementation strategies to improve routine use of the guidelines by preclinical scientists. These findings will help inform specific strategies that may guide the development of programs and resources to improve experimental design and transparent reporting in preclinical research.
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21
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Reporting quality in preclinical animal experimental research in 2009 and 2018: A nationwide systematic investigation. PLoS One 2022; 17:e0275962. [PMID: 36327216 PMCID: PMC9632797 DOI: 10.1371/journal.pone.0275962] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 09/27/2022] [Indexed: 11/05/2022] Open
Abstract
Lack of translation and irreproducibility challenge preclinical animal research. Insufficient reporting methodologies to safeguard study quality is part of the reason. This nationwide study investigates the reporting prevalence of these methodologies and scrutinizes the reported information’s level of detail. Publications were from two time periods to convey any reporting progress and had at least one author affiliated to a Danish University. We retrieved all relevant animal experimental studies using a predefined research protocol and a systematic search. A random sampling of 250 studies from 2009 and 2018 led to 500 publications in total. Reporting of measures known to impact study results estimates were assessed. Part I discloses a simplified two-level scoring “yes/no” to identify the presence of reporting. Part II demonstrates an additional three-level scoring to analyze the reported information’s level of detail. Overall reporting prevalence is low, although minor improvements are noted. Reporting of randomization increased from 24.0% in 2009 to 40.8% in 2018, blinded experiment conduct from 2.4% to 4.4%, blinded outcome assessment from 23.6% to 38.0%, and sample size calculation from 3.2% to 14.0%. Poor reporting of details is striking with reporting of the random allocation method to groups being only 1.2% in 2009 and 6.0% in 2018. Reporting of sample size calculation method was 2.4% in 2009 and 7.6% in 2018. Only conflict-of-interest statements reporting increased from 37.6% in 2009 to 90.4%. Measures safeguarding study quality are poorly reported in publications affiliated with Danish research institutions. Only a modest improvement was noted during the period 2009–2018, and the lack of details urgently prompts institutional strategies to accelerate this. We suggest thorough teaching in designing, conducting and reporting animal studies. Education in systematic review methodology should be implemented in this training and will increase motivation and behavior working towards quality improvements in science.
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McDougald WA, Mannheim JG. Understanding the importance of quality control and quality assurance in preclinical PET/CT imaging. EJNMMI Phys 2022; 9:77. [PMID: 36315337 PMCID: PMC9622967 DOI: 10.1186/s40658-022-00503-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 10/20/2022] [Indexed: 11/12/2022] Open
Abstract
The fundamental principle of experimental design is to ensure efficiency and efficacy of the performed experiments. Therefore, it behoves the researcher to gain knowledge of the technological equipment to be used. This should include an understanding of the instrument quality control and assurance requirements to avoid inadequate or spurious results due to instrumentation bias whilst improving reproducibility. Here, the important role of preclinical positron emission tomography/computed tomography and the scanner's required quality control and assurance is presented along with the suggested guidelines for quality control and assurance. There are a multitude of factors impeding the continuity and reproducibility of preclinical research data within a single laboratory as well as across laboratories. A more robust experimental design incorporating validation or accreditation of the scanner performance can reduce inconsistencies. Moreover, the well-being and welfare of the laboratory animals being imaged is prime justification for refining experimental designs to include verification of instrumentation quality control and assurance. Suboptimal scanner performance is not consistent with the 3R principle (Replacement, Reduction, and Refinement) and potentially subjects animals to unnecessary harm. Thus, quality assurance and control should be of paramount interest to any scientist conducting animal studies. For this reason, through this work, we intend to raise the awareness of researchers using PET/CT regarding quality control/quality assurance (QC/QA) guidelines and instil the importance of confirming that these are routinely followed. We introduce a basic understanding of the PET/CT scanner, present the purpose of QC/QA as well as provide evidence of imaging data biases caused by lack of QC/QA. This is shown through a review of the literature, QC/QA accepted standard protocols and our research. We also want to encourage researchers to have discussions with the PET/CT facilities manager and/or technicians to develop the optimal designed PET/CT experiment for obtaining their scientific objective. Additionally, this work provides an easy gateway to multiple resources not only for PET/CT knowledge but for guidelines and assistance in preclinical experimental design to enhance scientific integrity of the data and ensure animal welfare.
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Affiliation(s)
- Wendy A. McDougald
- grid.4305.20000 0004 1936 7988BHF-Centre for Cardiovascular Science, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, UK ,grid.4305.20000 0004 1936 7988Edinburgh Preclinical Imaging (EPI), Edinburgh Imaging, University of Edinburgh, Edinburgh, UK ,grid.4305.20000 0004 1936 7988Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh BioQuarter, 47 Little France Crescent, Edinburgh, EH16 4TJ UK
| | - Julia G. Mannheim
- grid.10392.390000 0001 2190 1447Department of Preclinical Imaging and Radiopharmacy, Werner Siemens Imaging Center, Eberhard-Karls University Tübingen, Tübingen, Germany ,grid.10392.390000 0001 2190 1447Cluster of Excellence iFIT (EXC 2180) “Image Guided and Functionally Instructed Tumor Therapies”, University of Tuebingen, Tübingen, Germany
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23
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Mayer B, Tuckermann J, Muche R. Could a phase model help to improve translational animal research? Animal Model Exp Med 2022; 5:550-556. [PMID: 36266781 PMCID: PMC9773301 DOI: 10.1002/ame2.12284] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 10/03/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Animal models are widely applied in medical research for different purposes. In particular, results from translational experiments may be used for subsequent clinical development. However, transferability of these findings to the human organism is controversial. Among other factors, this may be traced back to a lack of clear differentiation of the evidence (explorative vs. confirmatory) provided by such experimental results. In general, inferential statistics (i.e. p values) should not be interpreted in as confirmatory unless crucial methodological requirements are met. METHODS Therefore, we propose a phase model which reflects the well-established process of clinical research, and we discuss its potential to improve decision making in translational research. The model aims to clarify the reliability of results derived from animal models. RESULTS The phase model proposes subdividing translational, pre-clinical research into pilot, exploration, and confirmation phases. Experiments for which there is no valid estimation of the expected effect size are designated as pilot studies. Based on these data, experiments in subsequent phases may be planned using both appropriate design and statistical methods. CONCLUSION Separating the entire process of translational animal research into three phases could contribute to improved transparency of the evidence derived from such experiments.
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Affiliation(s)
- Benjamin Mayer
- Institute of Epidemiology and Medical BiometryUlm UniversityUlmGermany
| | - Jan Tuckermann
- Institute of Comparative Molecular EndocrinologyUlm UniversityUlmGermany
| | - Rainer Muche
- Institute of Epidemiology and Medical BiometryUlm UniversityUlmGermany
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24
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Bianchimano P, Britton GJ, Wallach DS, Smith EM, Cox LM, Liu S, Iwanowski K, Weiner HL, Faith JJ, Clemente JC, Tankou SK. Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis. MICROBIOME 2022; 10:174. [PMID: 36253847 PMCID: PMC9575236 DOI: 10.1186/s40168-022-01364-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND The gut microbiome plays an important role in autoimmunity including multiple sclerosis and its mouse model called experimental autoimmune encephalomyelitis (EAE). Prior studies have demonstrated that the multiple sclerosis gut microbiota can contribute to disease, hence making it a potential therapeutic target. In addition, antibiotic treatment has been shown to ameliorate disease in the EAE mouse model of multiple sclerosis. Yet, to this date, the mechanisms mediating these antibiotic effects are not understood. Furthermore, there is no consensus on the gut-derived bacterial strains that drive neuroinflammation in multiple sclerosis. RESULTS Here, we characterized the gut microbiome of untreated and vancomycin-treated EAE mice over time to identify bacteria with neuroimmunomodulatory potential. We observed alterations in the gut microbiota composition following EAE induction. We found that vancomycin treatment ameliorates EAE, and that this protective effect is mediated via the microbiota. Notably, we observed increased abundance of bacteria known to be strong inducers of regulatory T cells, including members of Clostridium clusters XIVa and XVIII in vancomycin-treated mice during the presymptomatic phase of EAE, as well as at disease peak. We identified 50 bacterial taxa that correlate with EAE severity. Interestingly, several of these taxa exist in the human gut, and some of them have been implicated in multiple sclerosis including Anaerotruncus colihominis, a butyrate producer, which had a positive correlation with disease severity. We found that Anaerotruncus colihominis ameliorates EAE, and this is associated with induction of RORγt+ regulatory T cells in the mesenteric lymph nodes. CONCLUSIONS We identified vancomycin as a potent modulator of the gut-brain axis by promoting the proliferation of bacterial species that induce regulatory T cells. In addition, our findings reveal 50 gut commensals as regulator of the gut-brain axis that can be used to further characterize pathogenic and beneficial host-microbiota interactions in multiple sclerosis patients. Our findings suggest that elevated Anaerotruncus colihominis in multiple sclerosis patients may represent a protective mechanism associated with recovery from the disease. Video Abstract.
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Affiliation(s)
- Paola Bianchimano
- Department of Neurology, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA
| | - Graham J Britton
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - David S Wallach
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Emma M Smith
- Department of Neurology, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA
| | - Laura M Cox
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Shirong Liu
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
- Present address: Department of Medical Oncology, Bing Center for Waldenström's Macroglobulinemia, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - Kacper Iwanowski
- Department of Neurology, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA
| | - Howard L Weiner
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Jeremiah J Faith
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jose C Clemente
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stephanie K Tankou
- Department of Neurology, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA.
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, 5E 98th Street, New York, NY, 10029, USA.
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Göpel T, Burggren WW. Insufficient reporting of experimental variables as a cause for nonreproducibility in animal physiology? A case study. Am J Physiol Regul Integr Comp Physiol 2022; 323:R363-R374. [PMID: 35816721 PMCID: PMC9467468 DOI: 10.1152/ajpregu.00026.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 07/03/2022] [Accepted: 07/06/2022] [Indexed: 11/22/2022]
Abstract
Nonreproducibility in scientific investigations has been explained by inadequately reporting methodology, honest error, and even misconduct. We hypothesized that, within the field of animal physiology, the most parsimonious explanation for nonreproducibility is inadequate reporting of key methodological details. We further hypothesized that implementation of relatively recently released reporting guidelines has positively impacted journal article quality, as measured by completeness of the methodology descriptions. We analyzed 84 research articles published in five primarily organismal animal physiology journals in 2008-2010 (generally before current guidelines) and 2018-2020. Compliance for reporting 34 variables referring to biology, experiments, and data collection was assessed. Reporting compliance was just ∼61% in 2008-2010, rising only slightly to 67.5% for 2018-2020. Only 21% of the reported variables showed significant differences across the period from 2008-2020. We conclude that, despite attempts by societies and journals to promote greater reporting compliance, such efforts have so far been relatively unsuccessful in the field of animal physiology.
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Affiliation(s)
- Torben Göpel
- Developmental Integrative Biology Research Group, Department of Biological Sciences, University of North Texas, Denton, Texas
| | - Warren W Burggren
- Developmental Integrative Biology Research Group, Department of Biological Sciences, University of North Texas, Denton, Texas
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26
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Kroon C, Breuer L, Jones L, An J, Akan A, Mohamed Ali EA, Busch F, Fislage M, Ghosh B, Hellrigel-Holderbaum M, Kazezian V, Koppold A, Moreira Restrepo CA, Riedel N, Scherschinski L, Urrutia Gonzalez FR, Weissgerber TL. Blind spots on western blots: Assessment of common problems in western blot figures and methods reporting with recommendations to improve them. PLoS Biol 2022; 20:e3001783. [PMID: 36095010 PMCID: PMC9518894 DOI: 10.1371/journal.pbio.3001783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 09/28/2022] [Accepted: 08/04/2022] [Indexed: 11/18/2022] Open
Abstract
Western blotting is a standard laboratory method used to detect proteins and assess their expression levels. Unfortunately, poor western blot image display practices and a lack of detailed methods reporting can limit a reader's ability to evaluate or reproduce western blot results. While several groups have studied the prevalence of image manipulation or provided recommendations for improving western blotting, data on the prevalence of common publication practices are scarce. We systematically examined 551 articles published in the top 25% of journals in neurosciences (n = 151) and cell biology (n = 400) that contained western blot images, focusing on practices that may omit important information. Our data show that most published western blots are cropped and blot source data are not made available to readers in the supplement. Publishing blots with visible molecular weight markers is rare, and many blots additionally lack molecular weight labels. Western blot methods sections often lack information on the amount of protein loaded on the gel, blocking steps, and antibody labeling protocol. Important antibody identifiers like company or supplier, catalog number, or RRID were omitted frequently for primary antibodies and regularly for secondary antibodies. We present detailed descriptions and visual examples to help scientists, peer reviewers, and editors to publish more informative western blot figures and methods. Additional resources include a toolbox to help scientists produce more reproducible western blot data, teaching slides in English and Spanish, and an antibody reporting template.
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Affiliation(s)
- Cristina Kroon
- Institute of Molecular Biology and Biochemistry, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Larissa Breuer
- German Center for Neurodegenerative Diseases (DZNE) within the Helmholtz Association, Berlin, Germany
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Lydia Jones
- Berlin School of Public Health, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Jeehye An
- Berlin School of Mind and Brain, Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Experimental Neurology and Center for Stroke Research, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Ayça Akan
- Berlin School of Mind and Brain, Humboldt-Universität zu Berlin, Berlin, Germany
- Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | | | - Felix Busch
- Department of Radiology, Charité–Universitätsmedizin Berlin, Berlin, Germany
- Department of Anesthesiology and Intensive Care Medicine, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Marinus Fislage
- Department of Anesthesiology and Intensive Care Medicine, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Biswajit Ghosh
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Max Hellrigel-Holderbaum
- Berlin School of Mind and Brain, Humboldt-Universität zu Berlin, Berlin, Germany
- Interdisciplinary Center of Sleep Medicine, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Vartan Kazezian
- QUEST Center for Responsible Research, Berlin Institute of Health at Charité—Universitätsmedizin Berlin, Berlin, Germany
- Department of Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Alina Koppold
- Institute for Systems Neuroscience, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Nico Riedel
- QUEST Center for Responsible Research, Berlin Institute of Health at Charité—Universitätsmedizin Berlin, Berlin, Germany
| | - Lea Scherschinski
- Department of Neurosurgery, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Fernando Raúl Urrutia Gonzalez
- Berlin School of Public Health, Charité–Universitätsmedizin Berlin, Berlin, Germany
- Institute of Public Health, Charité–Universitätsmedizin Berlin, Berlin, Germany
- Center for Stroke Research Berlin, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Tracey L. Weissgerber
- QUEST Center for Responsible Research, Berlin Institute of Health at Charité—Universitätsmedizin Berlin, Berlin, Germany
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Kihara Y, Zhu Y, Jonnalagadda D, Romanow W, Palmer C, Siddoway B, Rivera R, Dutta R, Trapp BD, Chun J. Single-Nucleus RNA-seq of Normal-Appearing Brain Regions in Relapsing-Remitting vs. Secondary Progressive Multiple Sclerosis: Implications for the Efficacy of Fingolimod. Front Cell Neurosci 2022; 16:918041. [PMID: 35783097 PMCID: PMC9247150 DOI: 10.3389/fncel.2022.918041] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/23/2022] [Indexed: 11/29/2022] Open
Abstract
Multiple sclerosis (MS) is an immune-mediated demyelinating disease that alters central nervous system (CNS) functions. Relapsing-remitting MS (RRMS) is the most common form, which can transform into secondary-progressive MS (SPMS) that is associated with progressive neurodegeneration. Single-nucleus RNA sequencing (snRNA-seq) of MS lesions identified disease-related transcriptomic alterations; however, their relationship to non-lesioned MS brain regions has not been reported and which could identify prodromal or other disease susceptibility signatures. Here, snRNA-seq was used to generate high-quality RRMS vs. SPMS datasets of 33,197 nuclei from 8 normal-appearing MS brains, which revealed divergent cell type-specific changes. Notably, SPMS brains downregulated astrocytic sphingosine kinases (SPHK1/2) – the enzymes required to phosphorylate and activate the MS drug, fingolimod. This reduction was modeled with astrocyte-specific Sphk1/2 null mice in which fingolimod lost activity, supporting functionality of observed transcriptomic changes. These data provide an initial resource for studies of single cells from non-lesioned RRMS and SPMS brains.
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Affiliation(s)
- Yasuyuki Kihara
- Translational Neuroscience Initiative, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Yunjiao Zhu
- Translational Neuroscience Initiative, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Deepa Jonnalagadda
- Translational Neuroscience Initiative, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - William Romanow
- Translational Neuroscience Initiative, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Carter Palmer
- Translational Neuroscience Initiative, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
- Biomedical Sciences Graduate Program, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Benjamin Siddoway
- Translational Neuroscience Initiative, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Richard Rivera
- Translational Neuroscience Initiative, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Ranjan Dutta
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Bruce D. Trapp
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Jerold Chun
- Translational Neuroscience Initiative, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
- *Correspondence: Jerold Chun,
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28
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Dwivedi AK. How to write statistical analysis section in medical research. J Investig Med 2022; 70:1759-1770. [PMID: 35710142 DOI: 10.1136/jim-2022-002479] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/01/2022] [Indexed: 12/15/2022]
Abstract
Reporting of statistical analysis is essential in any clinical and translational research study. However, medical research studies sometimes report statistical analysis that is either inappropriate or insufficient to attest to the accuracy and validity of findings and conclusions. Published works involving inaccurate statistical analyses and insufficient reporting influence the conduct of future scientific studies, including meta-analyses and medical decisions. Although the biostatistical practice has been improved over the years due to the involvement of statistical reviewers and collaborators in research studies, there remain areas of improvement for transparent reporting of the statistical analysis section in a study. Evidence-based biostatistics practice throughout the research is useful for generating reliable data and translating meaningful data to meaningful interpretation and decisions in medical research. Most existing research reporting guidelines do not provide guidance for reporting methods in the statistical analysis section that helps in evaluating the quality of findings and data interpretation. In this report, we highlight the global and critical steps to be reported in the statistical analysis of grants and research articles. We provide clarity and the importance of understanding study objective types, data generation process, effect size use, evidence-based biostatistical methods use, and development of statistical models through several thematic frameworks. We also provide published examples of adherence or non-adherence to methodological standards related to each step in the statistical analysis and their implications. We believe the suggestions provided in this report can have far-reaching implications for education and strengthening the quality of statistical reporting and biostatistical practice in medical research.
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Affiliation(s)
- Alok Kumar Dwivedi
- Department of Molecular and Translational Medicine, Division of Biostatistics and Epidemiology, Texas Tech University Health Sciences Center El Paso, El Paso, Texas, USA
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Karl T, Nithianantharajah J, Weber-Stadlbauer U. Editorial: Looking at the Complete Picture: Tackling Broader Factors Important for Advancing the Validity of Preclinical Models in Disease. Front Behav Neurosci 2022; 16:905327. [PMID: 35558434 PMCID: PMC9090468 DOI: 10.3389/fnbeh.2022.905327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 03/31/2022] [Indexed: 11/21/2022] Open
Affiliation(s)
- Tim Karl
- School of Medicine, Western Sydney University, Sydney, NSW, Australia
- *Correspondence: Tim Karl
| | - Jess Nithianantharajah
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, VIC, Australia
| | - Ulrike Weber-Stadlbauer
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zürich, Switzerland
- Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zürich, Switzerland
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Gao F, Wahl JA, Floyd TF. Anesthesia and neurotoxicity study design, execution, and reporting in the nonhuman primate: A systematic review. Paediatr Anaesth 2022; 32:509-521. [PMID: 35066973 DOI: 10.1111/pan.14401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 01/05/2022] [Accepted: 01/06/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Concern for a role of anesthesia in neurotoxicity in children originated from neonatal rodent and nonhuman primate (NHP) models, yet prospective clinical studies have largely not supported this concern. The goal of this study was to conduct an objective assessment of published NHP study rigor in design, execution, and reporting. METHODS A MEDLINE search from 2005 to December 2021 was performed. Inclusion criteria included full-length original studies published in English under peer-reviewed journals. We documented experimental parameters on anesthetic dosing, monitoring, vitals, and experimental outcomes. RESULTS Twenty-three manuscripts were included. Critical issues identified in study design included: lack of blinding in data acquisition (57%) and analysis (100%), supratherapeutic (4-12 fold) maintenance dosing in 22% of studies, lack of sample size justification (91%) resulting in a mean (SD) sample size of 6 (3) animals per group. Critical items identified in the conduct and reporting of studies included: documentation of anesthesia provider (0%), electrocardiogram monitoring (35%), arterial monitoring (4%), spontaneous ventilation employed (35%), failed intubations resulting in comingling ventilated and unventilated animals in data analysis, inaccurate reporting of failed intubation, and only 50% reporting on survival. Inconsistencies were noted in drug-related induction of neuroapoptosis and region of occurrence. Further, 67%-100% of behavior outcomes were not significantly different from controls. CONCLUSIONS Important deficits in study design, execution, and reporting were identified in neonatal NHP studies. These results raise concern for the validity and reliability of these studies and may explain in part the divergence from results obtained in human neonates.
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Affiliation(s)
- Feng Gao
- Department of Internal Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Joseph A Wahl
- Department of Cell and Molecular Biology, Texas Tech University, Lubbock, Texas, USA
| | - Thomas F Floyd
- Department of Anesthesiology and Pain Management, University of Texas Southwestern, Dallas, Texas, USA
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Reporting of anaesthesia and pain management in preclinical large animal models of articular cartilage repair - A long way to go. OSTEOARTHRITIS AND CARTILAGE OPEN 2022; 4:100261. [DOI: 10.1016/j.ocarto.2022.100261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/04/2022] [Indexed: 11/23/2022] Open
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32
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Ratajeski MA, Miller RS. Adapting to Changes in Publishing When Searching for Alternatives and Reporting on Animal Research: A Librarian's Perspective. Altern Lab Anim 2022; 50:57-61. [PMID: 35212234 DOI: 10.1177/02611929211072862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Since the inaugural issue of ATLA, many changes within publishing have occurred, impacting when, where, and how researchers conduct literature searches for non-animal alternatives. Such changes include increased rate of growth in scientific publications, greater number of databases and online resources available to search, opportunities for open and almost immediate dissemination of research outputs such as preprints and method protocols, and the development of reporting guidelines for animal research. Here we offer a librarian's perspective on these changes and advice on how to manage them to enable robust and diverse alternatives to be implemented in future research.
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Affiliation(s)
- Melissa A Ratajeski
- Health Sciences Library System, 6614University of Pittsburgh, Pittsburgh, PA, USA
| | - Rebekah S Miller
- Health Sciences Library System, 6614University of Pittsburgh, Pittsburgh, PA, USA
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Animal Research that Respects Animal Rights: Extending Requirements for Research with Humans to Animals. Camb Q Healthc Ethics 2022; 31:59-72. [PMID: 35049455 DOI: 10.1017/s0963180121000499] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The purpose of this article is to show that animal rights are not necessarily at odds with the use of animals for research. If animals hold basic moral rights similar to those of humans, then we should consequently extend the ethical requirements guiding research with humans to research with animals. The article spells out how this can be done in practice by applying the seven requirements for ethical research with humans proposed by Ezekiel Emanuel, David Wendler, and Christine Grady to animal research. These requirements are (1) social value, (2) scientific validity, (3) independent review, (4) fair subject selection, (5) favorable risk-benefit ratio, (6) informed consent, and (7) respect for research subjects. In practice, this means that we must reform the practice of animal research to make it more similar to research with humans, rather than completely abolish the former. Indeed, if we ban animal research altogether, then we would also deprive animals of its potential benefits-which would be ethically problematic.
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Errington TM, Denis A, Perfito N, Iorns E, Nosek BA. Challenges for assessing replicability in preclinical cancer biology. eLife 2021. [DOI: 10.10.7554/elife.67995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
We conducted the Reproducibility Project: Cancer Biology to investigate the replicability of preclinical research in cancer biology. The initial aim of the project was to repeat 193 experiments from 53 high-impact papers, using an approach in which the experimental protocols and plans for data analysis had to be peer reviewed and accepted for publication before experimental work could begin. However, the various barriers and challenges we encountered while designing and conducting the experiments meant that we were only able to repeat 50 experiments from 23 papers. Here we report these barriers and challenges. First, many original papers failed to report key descriptive and inferential statistics: the data needed to compute effect sizes and conduct power analyses was publicly accessible for just 4 of 193 experiments. Moreover, despite contacting the authors of the original papers, we were unable to obtain these data for 68% of the experiments. Second, none of the 193 experiments were described in sufficient detail in the original paper to enable us to design protocols to repeat the experiments, so we had to seek clarifications from the original authors. While authors were extremely or very helpful for 41% of experiments, they were minimally helpful for 9% of experiments, and not at all helpful (or did not respond to us) for 32% of experiments. Third, once experimental work started, 67% of the peer-reviewed protocols required modifications to complete the research and just 41% of those modifications could be implemented. Cumulatively, these three factors limited the number of experiments that could be repeated. This experience draws attention to a basic and fundamental concern about replication – it is hard to assess whether reported findings are credible.
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35
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Errington TM, Denis A, Perfito N, Iorns E, Nosek BA. Challenges for assessing replicability in preclinical cancer biology. eLife 2021; 10:67995. [PMID: 34874008 PMCID: PMC8651289 DOI: 10.7554/elife.67995] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 07/20/2021] [Indexed: 02/07/2023] Open
Abstract
We conducted the Reproducibility Project: Cancer Biology to investigate the replicability of preclinical research in cancer biology. The initial aim of the project was to repeat 193 experiments from 53 high-impact papers, using an approach in which the experimental protocols and plans for data analysis had to be peer reviewed and accepted for publication before experimental work could begin. However, the various barriers and challenges we encountered while designing and conducting the experiments meant that we were only able to repeat 50 experiments from 23 papers. Here we report these barriers and challenges. First, many original papers failed to report key descriptive and inferential statistics: the data needed to compute effect sizes and conduct power analyses was publicly accessible for just 4 of 193 experiments. Moreover, despite contacting the authors of the original papers, we were unable to obtain these data for 68% of the experiments. Second, none of the 193 experiments were described in sufficient detail in the original paper to enable us to design protocols to repeat the experiments, so we had to seek clarifications from the original authors. While authors were extremely or very helpful for 41% of experiments, they were minimally helpful for 9% of experiments, and not at all helpful (or did not respond to us) for 32% of experiments. Third, once experimental work started, 67% of the peer-reviewed protocols required modifications to complete the research and just 41% of those modifications could be implemented. Cumulatively, these three factors limited the number of experiments that could be repeated. This experience draws attention to a basic and fundamental concern about replication - it is hard to assess whether reported findings are credible.
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Affiliation(s)
| | | | | | | | - Brian A Nosek
- Center for Open Science, Charlottesville, United States.,University of Virginia, Charlottesville, United States
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36
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Loss CM, Melleu FF, Domingues K, Lino-de-Oliveira C, Viola GG. Combining Animal Welfare With Experimental Rigor to Improve Reproducibility in Behavioral Neuroscience. Front Behav Neurosci 2021; 15:763428. [PMID: 34916915 PMCID: PMC8671008 DOI: 10.3389/fnbeh.2021.763428] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 10/18/2021] [Indexed: 02/05/2023] Open
Affiliation(s)
- Cássio Morais Loss
- Molecular and Behavioral Neuroscience Laboratory, Departamento de Farmacologia, Universidade Federal de São Paulo, São Paulo, Brazil
- National Institute for Translational Medicine (INCT-TM), National Council for Scientific and Technological Development (CNPq/CAPES/FAPESP), Ribeirão Preto, Brazil
| | | | - Karolina Domingues
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Cilene Lino-de-Oliveira
- Departamento de Ciências Fisiológicas do Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, Brazil
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Hepkema WM, Horbach SPJM, Hoek JM, Halffman W. Misidentified biomedical resources: Journal guidelines are not a quick fix. Int J Cancer 2021; 150:1233-1243. [PMID: 34807460 PMCID: PMC9300184 DOI: 10.1002/ijc.33882] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 10/14/2021] [Accepted: 11/02/2021] [Indexed: 01/22/2023]
Abstract
Biomedical researchers routinely use a variety of biological models and resources, such as cultured cell lines, antibodies and laboratory animals. Unfortunately, these resources are not flawless: cell lines can be misidentified; for antibodies, problems with specificity, lot‐to‐lot consistency and sensitivity are common; and the reliability of animal models is questioned due to poor translation of animal studies to human clinical trials. In some cases, these problems can render the results of a study meaningless. As a response, some journals have implemented guidelines regarding the use and reporting of cell lines, antibodies and laboratory animals. In our study we use a portfolio of existing and newly created datasets to investigate identification and authentication information of cell lines, antibodies and organisms before and after guideline introduction, compared to journals without guidelines. We observed a general improvement of reporting quality over time, which the implementation of guidelines accelerated only in some cases. We therefore conclude that the effectiveness of journal guidelines is likely to be context dependent, affected by factors such as implementation conditions, research community support and monitoring and resource availability. Hence, journal reporting guidelines in themselves are not a quick fix to repair shortcomings in biomedical resource documentation, even though they can be part of the solution.
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Affiliation(s)
- Wytske M Hepkema
- Institute of Sociology, Technische Universität Berlin, Berlin, Germany
| | - Serge P J M Horbach
- Danish Centre for Studies in Research and Research Policy, Aarhus University, Aarhus, Denmark.,Centre for Science and Technology Studies, Leiden University, Leiden, The Netherlands
| | - Joyce M Hoek
- Department of Psychology, University of Groningen, Groningen, The Netherlands
| | - Willem Halffman
- Institute for Science in Society, Radboud University Nijmegen, Nijmegen, The Netherlands
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38
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Kasali FM, Kadima JN, Peter EL, Mtewa AG, Ajayi CO, Tusiimire J, Tolo CU, Ogwang PE, Weisheit A, Agaba AG. Antidiabetic Medicinal Plants Used in Democratic Republic of Congo: A Critical Review of Ethnopharmacology and Bioactivity Data. Front Pharmacol 2021; 12:757090. [PMID: 34776975 PMCID: PMC8579071 DOI: 10.3389/fphar.2021.757090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 10/08/2021] [Indexed: 12/14/2022] Open
Abstract
Several studies have been conducted and published on medicinal plants used to manage Diabetes Mellitus worldwide. It is of great interest to review available studies from a country or a region to resort to similarities/discrepancies and data quality. Here, we examined data related to ethnopharmacology and bioactivity of antidiabetic plants used in the Democratic Republic of Congo. Data were extracted from Google Scholar, Medline/PubMed, Scopus, ScienceDirect, the Wiley Online Library, Web of Science, and other documents focusing on ethnopharmacology, pharmacology, and phytochemistry antidiabetic plants used in the Democratic Republic of Congo from 2005 to September 2021. The Kew Botanic Royal Garden and Plants of the World Online web databases were consulted to verify the taxonomic information. CAMARADES checklist was used to assess the quality of animal studies and Jadad scores for clinical trials. In total, 213 plant species belonging to 72 botanical families were reported. Only one plant, Droogmansia munamensis, is typically native to the DRC flora; 117 species are growing in the DRC and neighboring countries; 31 species are either introduced from other regions, and 64 are not specified. Alongside the treatment of Diabetes, about 78.13% of plants have multiple therapeutic uses, depending on the study sites. Experimental studies explored the antidiabetic activity of 133 plants, mainly in mice, rats, guinea pigs, and rabbits. Several chemical classes of antidiabetic compounds isolated from 67 plant species have been documented. Rare phase II clinical trials have been conducted. Critical issues included poor quality methodological protocols, author name incorrectly written (16.16%) or absent (14.25%) or confused with a synonym (4.69%), family name revised (17.26%) or missing (1.10%), voucher number not available 336(92.05%), ecological information not reported (49.59%). Most plant species have been identified and authenticated (89.32%). Hundreds of plants are used to treat Diabetes by traditional healers in DRC. However, most plants are not exclusively native to the local flora and have multiple therapeutic uses. The analysis showed the scarcity or absence of high-quality, in-depth pharmacological studies. There is a need to conduct further studies of locally specific species to fill the gap before their introduction into the national pharmacopeia.
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Affiliation(s)
- Félicien Mushagalusa Kasali
- Pharm-Bio Technology and Traditional Medicine Center, Mbarara University of Science and Technology, Mbarara, Uganda
- Department of Pharmacy, Faculty of Pharmaceutical Sciences and Public Health, Official University of Bukavu, Bukavu, Democratic Republic of Congo
- Department of Pharmacy, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Justin Ntokamunda Kadima
- Department of Pharmacy, Faculty of Pharmaceutical Sciences and Public Health, Official University of Bukavu, Bukavu, Democratic Republic of Congo
- Department of Pharmacology, School of Medicine and Pharmacy, University of Rwanda, Huye, Rwanda
| | - Emanuel L. Peter
- Pharm-Bio Technology and Traditional Medicine Center, Mbarara University of Science and Technology, Mbarara, Uganda
- Department of Pharmacy, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
- Department of Innovation, Technology Transfer and Commercialization, National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Andrew G. Mtewa
- Pharm-Bio Technology and Traditional Medicine Center, Mbarara University of Science and Technology, Mbarara, Uganda
- Department of Pharmacy, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
- Chemistry Section, Department of Applied Studies, Institute of Technology, Malawi University of Science and Technology, Limbe, Malawi
| | - Clement Olusoji Ajayi
- Pharm-Bio Technology and Traditional Medicine Center, Mbarara University of Science and Technology, Mbarara, Uganda
- Department of Pharmacy, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
- Department of Pharmacognosy, Faculty of Pharmacy, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Jonans Tusiimire
- Department of Pharmacy, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Casim Umba Tolo
- Pharm-Bio Technology and Traditional Medicine Center, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Patrick Engeu Ogwang
- Pharm-Bio Technology and Traditional Medicine Center, Mbarara University of Science and Technology, Mbarara, Uganda
- Department of Pharmacy, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Anke Weisheit
- Pharm-Bio Technology and Traditional Medicine Center, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Amon Ganafa Agaba
- Department of Pharmacology and Therapeutics, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
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Witt AN, Green RD, Winterborn AN. A Meta-Analysis of Rhesus Macaques ( Macaca mulatta), Cynomolgus Macaques ( Macaca fascicularis), African green monkeys ( Chlorocebus aethiops), and Ferrets ( Mustela putorius furo) as Large Animal Models for COVID-19. Comp Med 2021; 71:433-441. [PMID: 34588096 DOI: 10.30802/aalas-cm-21-000032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Animal models are at the forefront of biomedical research for studies of viral transmission, vaccines, and pathogenesis, yet the need for an ideal large animal model for COVID-19 remains. We used a meta-analysis to evaluate published data relevant to this need. Our literature survey contained 22 studies with data relevant to the incidence of common COVID-19 symptoms in rhesus macaques (Macaca mulatta), cynomolgus macaques (Macaca fascicularis), African green monkeys (Chlorocebus aethiops), and ferrets (Mustela putorius furo). Rhesus macaques had leukocytosis on Day 1 after inoculation and pneumonia on Days 7 and 14 after inoculation, in frequencies that were similar enough to humans to reject the null hypothesis of a Fisher exact test. However, the differences in overall presentation of disease were too different from that of humans to successfully identify any of these 4 species as an ideal large animal of COVID-19. The greatest limitation to the current study is a lack of standardization in experimentation and reporting. To expand our understanding of the pathology of COVID-19 and evalu- ate vaccine immunogenicity, we must extend the unprecedented collaboration that has arisen in the study of COVID-19 to include standardization of animal-based research in an effort to find the optimal animal model.
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Affiliation(s)
- Alexandra N Witt
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Rachel D Green
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Andrew N Winterborn
- Office of the University Veterinarian, Queen's University, Kingston, Ontario, Canada
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40
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Davies G. Locating the 'culture wars' in laboratory animal research: national constitutions and global competition. STUDIES IN HISTORY AND PHILOSOPHY OF SCIENCE 2021; 89:177-187. [PMID: 34455260 PMCID: PMC8513693 DOI: 10.1016/j.shpsa.2021.08.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 08/02/2021] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
The increasingly global scope of biomedical research and testing using animals is generating disagreement over the best way to regulate laboratory animal science and care. Despite many common aims, the practices through which political and epistemic authority are allocated in the regulations around animal research varies internationally, coming together in what can be identified as different national constitutions. Tensions between these periodically erupt within the laboratory animal research community as a 'cultural war' between those favouring centralised control and those advocating local flexibility. Drawing on long-term engagement with key events and actors in these policy debates, I propose these national differences in the constitution of animal research can be understood through the intersection of two key variables: i) the location of institutional responsibility to permit research projects and ii) the distribution of epistemic authority to shape research practices. These variables are used to explain the development of different policy frameworks in the UK, Europe, and the USA, and identify where there is convergence and divergence in practice. Concluding, I suggest the way these approaches are combined and enacted in different countries reflects different national civic epistemologies, which are coming into conflict in the increasingly global networks of laboratory animal science.
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Affiliation(s)
- Gail Davies
- Department of Geography, University of Exeter, Amory Building, Rennes Drive, Exeter, EX4 4RJ, UK.
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41
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Minocher R, Atmaca S, Bavero C, McElreath R, Beheim B. Estimating the reproducibility of social learning research published between 1955 and 2018. ROYAL SOCIETY OPEN SCIENCE 2021; 8:210450. [PMID: 34540248 PMCID: PMC8441137 DOI: 10.1098/rsos.210450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
Reproducibility is integral to science, but difficult to achieve. Previous research has quantified low rates of data availability and results reproducibility across the biological and behavioural sciences. Here, we surveyed 560 empirical publications, published between 1955 and 2018 in the social learning literature, a research topic that spans animal behaviour, behavioural ecology, cultural evolution and evolutionary psychology. Data were recoverable online or through direct data requests for 30% of this sample. Data recovery declines exponentially with time since publication, halving every 6 years, and up to every 9 years for human experimental data. When data for a publication can be recovered, we estimate a high probability of subsequent data usability (87%), analytical clarity (97%) and agreement of published results with reproduced findings (96%). This corresponds to an overall rate of recovering data and reproducing results of 23%, largely driven by the unavailability or incompleteness of data. We thus outline clear measures to improve the reproducibility of research on the ecology and evolution of social behaviour.
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Affiliation(s)
- Riana Minocher
- Department of Human Behaviour, Ecology and Culture, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Silke Atmaca
- Department of Human Behaviour, Ecology and Culture, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Claudia Bavero
- Department of Human Behaviour, Ecology and Culture, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Richard McElreath
- Department of Human Behaviour, Ecology and Culture, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Bret Beheim
- Department of Human Behaviour, Ecology and Culture, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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Abbas TO, Elawad A, Pullattayil S. AK, Pennisi CP. Quality of Reporting in Preclinical Urethral Tissue Engineering Studies: A Systematic Review to Assess Adherence to the ARRIVE Guidelines. Animals (Basel) 2021; 11:2456. [PMID: 34438913 PMCID: PMC8388767 DOI: 10.3390/ani11082456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 01/12/2023] Open
Abstract
Preclinical research within the area of urethral tissue engineering has not yet been successfully translated into an efficient therapeutic option for patients. This gap could be attributed, in part, to inadequate design and reporting of the studies employing laboratory animals. In this study, a systematic review was conducted to investigate the quality of reporting in preclinical studies utilizing tissue engineering approaches for urethral repair. The scope was on studies performed in rabbits, published between January 2014 and March 2020. Quality assessment of the data was conducted according to the Animal Research: Reporting of in Vivo Experiments (ARRIVE) guidelines by the scoring of a 38-item checklist in different categories. A total of 28 articles that fulfilled the eligibility criteria were included in the study. The range of ARRIVE score was from 0 to 100, taking into consideration having reported the item in question or not. The mean checklist score was 53%. The items that attained the highest scores included the number of animals utilized, the size of control and experimental groups, and the definition of experimental outcomes. The least frequently reported items included the data regarding the experimental procedure, housing and husbandry, determination and justification of the number of animals, and reporting of adverse events. Surprisingly, full disclosure about ethical guidelines and animal protocol approval was missing in 54% of the studies. No paper stated the sample size estimation. Overall, our study found that a large number of studies display inadequate reporting of fundamental information and that the quality of reporting improved marginally over the study period. We encourage a comprehensive implementation of the ARRIVE guidelines in animal studies exploring tissue engineering for urethral repair, not only to facilitate effective translation of preclinical research findings into clinical therapies, but also to ensure compliance with ethical principles and to minimize unnecessary animal studies.
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Affiliation(s)
- Tariq O. Abbas
- Regenerative Medicine Research Group, Department of Health Science and Technology, Aalborg University, 9220 Aalborg, Denmark;
- Pediatric Urology Section, Sidra Medicine, Doha 26999, Qatar;
- College of Medicine, Qatar University, Doha 2713, Qatar
- Weill Cornell Medicine Qatar, Doha 24144, Qatar
| | - Abubakr Elawad
- Pediatric Urology Section, Sidra Medicine, Doha 26999, Qatar;
| | | | - Cristian Pablo Pennisi
- Regenerative Medicine Research Group, Department of Health Science and Technology, Aalborg University, 9220 Aalborg, Denmark;
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43
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Auer S, Haeltermann NA, Weissberger TL, Erlich JC, Susilaradeya D, Julkowska M, Gazda MA, Schwessinger B, Jadavji NM. A community-led initiative for training in reproducible research. eLife 2021; 10:64719. [PMID: 34151774 PMCID: PMC8282331 DOI: 10.7554/elife.64719] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 06/18/2021] [Indexed: 12/15/2022] Open
Abstract
Open and reproducible research practices increase the reusability and impact of scientific research. The reproducibility of research results is influenced by many factors, most of which can be addressed by improved education and training. Here we describe how workshops developed by the Reproducibility for Everyone (R4E) initiative can be customized to provide researchers at all career stages and across most disciplines with education and training in reproducible research practices. The R4E initiative, which is led by volunteers, has reached more than 3000 researchers worldwide to date, and all workshop materials, including accompanying resources, are available under a CC-BY 4.0 license at https://www.repro4everyone.org/.
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Affiliation(s)
- Susann Auer
- Department of Plant Physiology, Institute of Botany, Faculty of Biology, Technische Universität Dresden, Dresden, Germany
| | - Nele A Haeltermann
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Tracey L Weissberger
- QUEST Center, Berlin Institute of Health, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Jeffrey C Erlich
- Shanghai Key Laboratory of Brain Functional Genomics, East China Normal University, Shanghai, China
| | - Damar Susilaradeya
- Medical Technology Cluster, Indonesian Medical Education and Research Institute, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | | | - Małgorzata Anna Gazda
- CIBO/InBIOO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Porto, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | | | - Nafisa M Jadavji
- Department of Biomedical Science, Midwestern University, Glendale, United States.,Department of Neuroscience, Carleton University, Ottawa, Canada
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- Reproducibility for Everyone, New York, United States
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44
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Luo YN, Tian H, Mei ZG, Feng ZT, Yang SB, Fu XY, Huang YG. Acupuncture for experimental cerebral ischemia/reperfusion injury: a systematic review of methodology and reporting quality. Acupunct Med 2021; 39:646-655. [PMID: 34049448 DOI: 10.1177/09645284211009533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
OBJECTIVES Preclinical research is essential to the advancement of science but susceptible to insufficient reporting and methodological shortcomings, which compromise internal validity. We aimed to systematically assess the methodological and reporting quality of studies conducted on acupuncture for experimental cerebral ischemia/reperfusion injury (CIRI). METHODS A comprehensive search in six databases was performed for animal research concerning acupuncture for CIRI. Two authors independently selected articles, extracted data, and assessed the methodological and reporting quality of identified articles using the Systematic Review Center for Laboratory Animal Experimentation (SYRCLE) tool, and Animal Research: Reporting In Vivo Experiments (ARRIVE) guideline, respectively. RESULTS A total of 24 studies were identified. Only 1 article (4%) achieved a decent overall rating in using SYRCLE (percentage of items with "low risk" ⩾50%). Of the 22 items on the SYRCLE tool, only 8 items (37%) were rated as "low risk" of bias in more than 50% of the included studies. Of the 39 items of ARRIVE, 20 (51%) items were rated as "low risk" in more than 50% of the included studies. CONCLUSIONS The methodological and reporting quality of included studies was generally low, which demands further improvement. These findings should inform the development of evidence-based guidelines for future preclinical research assessing the effect of acupuncture on CIRI.
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Affiliation(s)
- Ya-Nan Luo
- The Department of Traditional Chinese Medicine, Medical College, China Three Gorges University, Yichang, China
| | - Huan Tian
- The Department of Traditional Chinese Medicine, Medical College, China Three Gorges University, Yichang, China
| | - Zhi-Gang Mei
- The Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha, China
| | - Zhi-Tao Feng
- The Department of Traditional Chinese Medicine, Medical College, China Three Gorges University, Yichang, China
| | - Song-Bai Yang
- Yichang Hospital of Traditional Chinese Medicine, Clinical Medical College of Traditional Chinese Medicine, China Three Gorges University, Yichang, China
| | - Xian-Yun Fu
- The Department of Traditional Chinese Medicine, Medical College, China Three Gorges University, Yichang, China
| | - Ya-Guang Huang
- The Department of Traditional Chinese Medicine, Medical College, China Three Gorges University, Yichang, China
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45
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LaPlaca MC, Huie JR, Alam HB, Bachstetter AD, Bayir H, Bellgowan PF, Cummings D, Dixon CE, Ferguson AR, Ferland-Beckham C, Floyd CL, Friess SH, Galanopoulou AS, Hall ED, Harris NG, Hawkins BE, Hicks RR, Hulbert LE, Johnson VE, Kabitzke PA, Lafrenaye AD, Lemmon VP, Lifshitz CW, Lifshitz J, Loane DJ, Misquitta L, Nikolian VC, Noble-Haeusslein LJ, Smith DH, Taylor-Burds C, Umoh N, Vovk O, Williams AM, Young M, Zai LJ. Pre-Clinical Common Data Elements for Traumatic Brain Injury Research: Progress and Use Cases. J Neurotrauma 2021; 38:1399-1410. [PMID: 33297844 PMCID: PMC8082734 DOI: 10.1089/neu.2020.7328] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Traumatic brain injury (TBI) is an extremely complex condition due to heterogeneity in injury mechanism, underlying conditions, and secondary injury. Pre-clinical and clinical researchers face challenges with reproducibility that negatively impact translation and therapeutic development for improved TBI patient outcomes. To address this challenge, TBI Pre-clinical Working Groups expanded upon previous efforts and developed common data elements (CDEs) to describe the most frequently used experimental parameters. The working groups created 913 CDEs to describe study metadata, animal characteristics, animal history, injury models, and behavioral tests. Use cases applied a set of commonly used CDEs to address and evaluate the degree of missing data resulting from combining legacy data from different laboratories for two different outcome measures (Morris water maze [MWM]; RotorRod/Rotarod). Data were cleaned and harmonized to Form Structures containing the relevant CDEs and subjected to missing value analysis. For the MWM dataset (358 animals from five studies, 44 CDEs), 50% of the CDEs contained at least one missing value, while for the Rotarod dataset (97 animals from three studies, 48 CDEs), over 60% of CDEs contained at least one missing value. Overall, 35% of values were missing across the MWM dataset, and 33% of values were missing for the Rotarod dataset, demonstrating both the feasibility and the challenge of combining legacy datasets using CDEs. The CDEs and the associated forms created here are available to the broader pre-clinical research community to promote consistent and comprehensive data acquisition, as well as to facilitate data sharing and formation of data repositories. In addition to addressing the challenge of standardization in TBI pre-clinical studies, this effort is intended to bring attention to the discrepancies in assessment and outcome metrics among pre-clinical laboratories and ultimately accelerate translation to clinical research.
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Affiliation(s)
- Michelle C. LaPlaca
- Department of Biomedical Engineering, Georgia Institute of Technology/Emory University, Atlanta, Georgia, USA
- San Francisco Veterans Affairs Health Care System, San Francisco, California, USA
| | - J. Russell Huie
- Brain and Spinal Injury Center, Department of Neurological Surgery, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California, USA
| | - Hasan B. Alam
- Department of Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Adam D. Bachstetter
- Department of Neuroscience, University of Kentucky, Lexington, Kentucky, USA
| | - Hűlya Bayir
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | | | - C. Edward Dixon
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Adam R. Ferguson
- Brain and Spinal Injury Center, Department of Neurological Surgery, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California, USA
| | | | - Candace L. Floyd
- Department of Physical Medicine and Rehabilitation, University of Utah, Salt Lake City, Utah, USA
| | - Stuart H. Friess
- Division of Critical Care Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
| | | | - Edward D. Hall
- Department of Neuroscience, University of Kentucky, Lexington, Kentucky, USA
| | - Neil G. Harris
- Department of Neurosurgery, University of California, Los Angeles, Los Angeles, California, USA
| | - Bridget E. Hawkins
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, Texas, USA
| | | | - Lindsey E. Hulbert
- Department of Animal Sciences and Industry, Kansas State University, Manhattan, Kansas, USA
| | - Victoria E. Johnson
- Department of Neurosurgery, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Audrey D. Lafrenaye
- Department of Anatomy and Neurobiology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Vance P. Lemmon
- Department of Neurological Surgery, University of Miami, Miami, Florida, USA
| | - Carrie W. Lifshitz
- Department of Child Health, University of Arizona College of Medicine Phoenix, Phoenix, Arizona, USA
| | - Jonathan Lifshitz
- Department of Child Health, University of Arizona College of Medicine Phoenix, Phoenix, Arizona, USA
| | - David J. Loane
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | | | | | | | - Douglas H. Smith
- Department of Neurosurgery, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Nsini Umoh
- Department of Defense, U.S. Army Medical Research and Materiel Command, Fort Detrick, Frederick, Maryland, USA
| | - Olga Vovk
- National Institutes of Health, Bethesda, Maryland, USA
| | - Aaron M. Williams
- Department of Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Margaret Young
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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Abstract
ABSTRACT The ARRIVE (Animals in Research: Reporting In Vivo Experiments) guidelines were endorsed by the Shock Society in 2012, but to date there has been no systematic evaluation of research reporting quality for Shock. We systematically assessed 100 randomly selected animal-based research articles published between 2014 and 2018 for reporting quality and statistical practice, compared with 40 pre-ARRIVE studies. More than half of surveyed papers omitted verifiable ethical oversight information and basic animal descriptive information. Few papers reported best-practice methods, such as sample size justification (10%), randomization (43%), randomization method (7%), blinding (23%). Only one paper reported effect sizes to interpret study results. Most troubling was inadequate reporting of welfare-related information (anesthesia, analgesia, humane endpoints, euthanasia). Almost a decade after ARRIVE endorsement, our findings show that reporting deficiencies have persisted with little sign of correction. There is a clear need for investigators to increase transparency of research methods reporting, and drastically improve skills in experimental design. Improvement in standards and greater attention paid to reporting will lead to improvement in reproducibility, replicability, and research quality. It is incumbent upon the research community to improve reporting practices; accurate and transparent reporting is integral to producing rigorous and ethical science.
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Affiliation(s)
- Penny S Reynolds
- Department of Anesthesiology, Statistics in Anesthesiology Research (STAR) Core, College of Medicine, University of Florida, Gainesville, Florida
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47
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Liang HY, Zhang PP, Zhang XL, Zheng YY, Huang YR, Zheng GQ, Lin Y. Preclinical systematic review of ginsenoside Rg1 for cognitive impairment in Alzheimer's disease. Aging (Albany NY) 2021; 13:7549-7569. [PMID: 33686024 PMCID: PMC7993717 DOI: 10.18632/aging.202619] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 10/01/2020] [Indexed: 05/02/2023]
Abstract
Ginseng has been used for the treatment of aging and memory impairment for thousands of years. Several studies have found that ginsenoside Rg1, as one of the main active components of ginseng, could potentially improve cognitive function in several different animal models. A preclinical systematic review to evaluate the efficacy and mechanisms of ginsenoside Rg1 for ameliorating cognitive impairments in Alzheimer's disease is reported here. We searched six databases from their inceptions to January 2019. Thirty-two studies were selected, which included a total of 1,643 animals. According to various cognitive behavioral tests, the results of the meta-analyses showed that ginsenoside Rg1 significantly improved cognitive behavioral impairments in most Alzheimer's disease models (P < 0.05), but there were no significant effects in animals with neuronal degeneration induced by chronic stress or in SAMP8 transgenic mice. The potential mechanisms included antioxidant and anti-inflammatory effects, amelioration of Alzheimer's disease-related pathology, synapse protection, and up-regulation of nerve cells via multiple signaling pathways.
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Affiliation(s)
- Hai-Yong Liang
- Department of Neurology, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Pei-Pei Zhang
- Department of Neurology, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Xi-Le Zhang
- Department of Neurology, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Yan-Yan Zheng
- Department of Neurology, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Yan-Ran Huang
- Department of Neurology, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Guo-Qing Zheng
- Department of Neurology, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Yan Lin
- Department of Neurology, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou 325000, China
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48
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Jasińska-Stroschein M, Orszulak-Michalak D. Reporting experimental studies on animals - The problems with translating of outcomes to clinical benefits. Methodological and statistical considerations: The example of pulmonary hypertension. Eur J Pharmacol 2021; 897:173952. [PMID: 33617827 DOI: 10.1016/j.ejphar.2021.173952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/09/2021] [Accepted: 02/15/2021] [Indexed: 11/27/2022]
Abstract
The variability inherent in animal models and the methods used to define drug response can lead to highly divergent results when evaluating new drug candidates. Several guidelines exist for high-quality and comprehensive reporting of experiments with animals. The present survey makes a quantitative demonstration of whether compliance with good preclinical practice guidelines can affect the results and reduce risk of over- or underestimation of treatment benefit. This meta-analysis was performed on more than 400 animal studies concerning pulmonary hypertension, where a wide range of potential therapeutic agents have been recently positively assessed in preclinical experiments. The experiments were reviewed according to the selected methodological and statistical items being recommended to report in papers. A quantitative evaluation was performed of their impact on effect size, which defined the efficacy of particular drug candidates. In addition, the paper also examines whether the quality score calculated for the papers included in the analysis changed over the previous 25 years. In conclusion, some information in experimental studies is often missed or incomplete, which complicates the correct evaluation and comprehension of obtained results. This in turn could subsequently increase the potential hazards involved in translating positive experimental outcomes to possible clinical benefits in patients.
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Affiliation(s)
| | - Daria Orszulak-Michalak
- Department of Biopharmacy, Medical University of Łódź, Ul. Muszyńskiego 1, 90-151, Lodz, Poland
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49
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Dangond F, Donnelly A, Hohlfeld R, Lubetzki C, Kohlhaas S, Leocani L, Ciccarelli O, Stankoff B, Sormani MP, Chataway J, Bozzoli F, Cucca F, Melton L, Coetzee T, Salvetti M. Facing the urgency of therapies for progressive MS - a Progressive MS Alliance proposal. Nat Rev Neurol 2021; 17:185-192. [PMID: 33483719 DOI: 10.1038/s41582-020-00446-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2020] [Indexed: 12/20/2022]
Abstract
Therapies for infiltrative inflammation in multiple sclerosis (MS) have advanced greatly, but neurodegeneration and compartmentalized inflammation remain virtually untargeted as in other diseases of the nervous system. Consequently, many therapies are available for the relapsing-remitting form of MS, but the progressive forms remain essentially untreated. The objective of the International Progressive MS Alliance is to expedite the development of effective therapies for progressive MS through new initiatives that foster innovative thinking and concrete advancements. Based on these principles, the Alliance is developing a new funding programme that will focus on experimental medicine trials. Here, we discuss the reasons behind the focus on experimental medicine trials, the strengths and weaknesses of these approaches and of the programme, and why we hope to advance therapies while improving the understanding of progression in MS. We are soliciting public and academic feedback, which will help shape the programme and future strategies of the Alliance.
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Affiliation(s)
| | - Alexis Donnelly
- Department of Computer Science, O'Reilly Institute, Trinity College, Dublin, Ireland
| | - Reinhard Hohlfeld
- Institute of Clinical Neuroimmunology, Biomedical Center and Hospital of the Ludwig Maximilians Universität München, Munich, Germany.,Munich Cluster for Systems Neurology (Synergy), Munich, Germany
| | - Catherine Lubetzki
- Neurology Department, Sorbonne University, Pitié-Salpêtrière Hospital, Paris, France
| | | | - Letizia Leocani
- Vita-Salute San Raffaele University, Milan, Italy.,Neurorehabilitation Department and Experimental Neurophysiology Unit, INSPE, Scientific Institute Hospital San Raffaele, Milan, Italy
| | - Olga Ciccarelli
- Queen Square Multiple Sclerosis Centre, Department of Neuroinflammation, UCL Institute of Neurology, Faculty of Brain Sciences, University College London, London, UK.,National Institute for Health Research University College London Hospitals Biomedical Research Centre, London, UK
| | - Bruno Stankoff
- Sorbonne University, Brain and Spine Institute, ICM, Pitié-Salpêtrière Hospital, Paris, France
| | - Maria Pia Sormani
- Department of Health Sciences (DISSAL), University of Genova, Genova, Italy.,IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Jeremy Chataway
- Queen Square Multiple Sclerosis Centre, Department of Neuroinflammation, UCL Institute of Neurology, Faculty of Brain Sciences, University College London, London, UK.,National Institute for Health Research University College London Hospitals Biomedical Research Centre, London, UK
| | | | - Francesco Cucca
- Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
| | - Lisa Melton
- MS Research Australia, North Sydney, New South Wales, Australia
| | | | - Marco Salvetti
- Department of Neurosciences, Mental Health and Sensory Organs, Centre for Experimental Neurological Therapies (CENTERS), Faculty of Medicine and Psychology, Sapienza University, Rome, Italy. .,IRCCS Istituto Neurologico Mediterraneo (INM) Neuromed, Pozzilli, Italy.
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50
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Inadequate awareness of adherence to ARRIVE guidelines, regarding reporting quality of hernia models repaired with meshes: a systematic review. Hernia 2021; 26:389-400. [PMID: 33394255 DOI: 10.1007/s10029-020-02351-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 11/16/2020] [Indexed: 10/22/2022]
Abstract
PURPOSE Research papers involving animal studies often display poor reporting standards, leading to lower study reproducibility. We aim to determine the difference in reporting animal studies regarding abdominal wall hernia repair with mesh placement, before and after the publication of ARRIVE-2010 (Animal Research: Reporting of In Vivo Experiments) guidelines. Furthermore, we aim to present the most up-to-date reporting quality using the updated ARRIVE-2020 as criteria. METHODS All animal studies concerning hernia repair with meshes were systematically searched. Articles published in the 5 years leading up to the ARRIVE-2010 (pre-ARRIVE) and articles within the last 5 years until the updated ARRIVE 2.0 (post-ARRIVE) were compared for overall species and specific species separately. Articles published last year were evaluated for presenting fully reported (sub)items. RESULTS The number of fully reported (sub)items per article was on average significantly higher for pre-ARRIVE than post-ARRIVE for overall species (mean (SD) = 14.0 (2.8) vs. 12.6 (2.5), P < 0.001). The same applies to rabbit (mean (SD) = 14.8 (2.6) vs. 12.6 (2.6), P = 0.001) and pig studies (mean (SD) = 14.5 (2.7) vs. 11.6 (2.6), P = 0.004), with no significance in rat studies (mean (SD) = 13.6 (2.9) vs. 12.9 (2.3), P = 0.076). Significance was found in several (sub)items between pre-ARRIVE and post-ARRIVE (n = 7, 3, 8, and 3 for overall species, rat, rabbit, and pig studies, respectively). CONCLUSION General reporting quality of animal experiments has been improved markedly by ARRIVE guidelines. However, more improvements are required considering the arrival of ARRIVE 2.0 guidelines.
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