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Paiva Barbosa V, Bastos Silveira B, Amorim Dos Santos J, Monteiro MM, Coletta RD, De Luca Canto G, Stefani CM, Guerra ENS. Critical appraisal tools used in systematic reviews of in vitro cell culture studies: A methodological study. Res Synth Methods 2023; 14:776-793. [PMID: 37464457 DOI: 10.1002/jrsm.1657] [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: 12/21/2022] [Revised: 06/21/2023] [Accepted: 07/01/2023] [Indexed: 07/20/2023]
Abstract
Systematic reviews (SRs) of preclinical studies are marked with poor methodological quality. In vitro studies lack assessment tools to improve the quality of preclinical research. This methodological study aimed to identify, collect, and analyze SRs based on cell culture studies to highlight the current appraisal tools utilized to support the development of a validated critical appraisal tool for cell culture in vitro research. SRs, scoping reviews, and meta-analyses that included cell culture studies and used any type of critical appraisal tool were included. Electronic search, study selection, data collection and methodological quality (MQ) assessment tool were realized. Further, statistical analyses regarding possible associations and correlations between MQ and collected data were performed. After the screening process, 82 studies remained for subsequent analysis. A total of 32 different appraisal tools were identified. Approximately 60% of studies adopted pre-structured tools not designed for cell culture studies. The most frequent instruments were SYRCLE (n = 14), OHAT (n = 9), Cochrane Collaboration's tool (n = 7), GRADE (n = 6), CONSORT (n = 5), and ToxRTool (n = 5). The studies were divided into subgroups to perform statistical analyses. A significant association (OR = 5.00, 95% CI = 1.54-16.20, p = 0.008) was found between low MQ and chronic degenerative disorders as topic of SR. Several challenges in collecting information from the included studies led to some modifications related to the previously registered protocol. These results may serve as a basis for further development of a critical appraisal tool for cell culture studies capable of capturing all the essential factors related to preclinical research, therefore enhancing the practice of evidence-based.
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Affiliation(s)
- Victor Paiva Barbosa
- University of Brasília, Laboratory of Oral Histopathology, Department of Dentistry, Faculty of Health Sciences, University of Brasília, Brasília, Brazil
| | - Bruna Bastos Silveira
- University of Brasília, Laboratory of Oral Histopathology, Department of Dentistry, Faculty of Health Sciences, University of Brasília, Brasília, Brazil
| | - Juliana Amorim Dos Santos
- University of Brasília, Laboratory of Oral Histopathology, Department of Dentistry, Faculty of Health Sciences, University of Brasília, Brasília, Brazil
| | - Mylene Martins Monteiro
- University of Brasília, Laboratory of Oral Histopathology, Department of Dentistry, Faculty of Health Sciences, University of Brasília, Brasília, Brazil
| | - Ricardo D Coletta
- University of Campinas, Department of Oral Diagnosis and Graduate Program in Oral Biology, School of Dentistry, University of Campinas, Piracicaba, Brazil
| | - Graziela De Luca Canto
- Federal University of Santa Catarina, Department of Dentistry, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Cristine Miron Stefani
- University of Brasilia, Department of Dentistry, School of Health Sciences, University of Brasilia, Brasília, Brazil
| | - Eliete Neves Silva Guerra
- University of Brasília, Laboratory of Oral Histopathology, Department of Dentistry, Faculty of Health Sciences, University of Brasília, Brasília, Brazil
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Gotora PT, van der Sluis R, Williams ME. HIV-1 Tat amino acid residues that influence Tat-TAR binding affinity: a scoping review. BMC Infect Dis 2023; 23:164. [PMID: 36932337 PMCID: PMC10020771 DOI: 10.1186/s12879-023-08123-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/27/2023] [Indexed: 03/19/2023] Open
Abstract
HIV-1 remains a global health concern and to date, nearly 38 million people are living with HIV. The complexity of HIV-1 pathogenesis and its subsequent prevalence is influenced by several factors including the HIV-1 subtype. HIV-1 subtype variation extends to sequence variation in the amino acids of the HIV-1 viral proteins. Of particular interest is the transactivation of transcription (Tat) protein due to its key function in viral transcription. The Tat protein predominantly functions by binding to the transactivation response (TAR) RNA element to activate HIV-1 transcriptional elongation. Subtype-specific Tat protein sequence variation influences Tat-TAR binding affinity. Despite several studies investigating Tat-TAR binding, it is not clear which regions of the Tat protein and/or individual Tat amino acid residues may contribute to TAR binding affinity. We, therefore, conducted a scoping review on studies investigating Tat-TAR binding. We aimed to synthesize the published data to determine (1) the regions of the Tat protein that may be involved in TAR binding, (2) key Tat amino acids involved in TAR binding and (3) if Tat subtype-specific variation influences TAR binding. A total of thirteen studies met our inclusion criteria and the key findings were that (1) both N-terminal and C-terminal amino acids outside the basic domain (47-59) may be important in increasing Tat-TAR binding affinity, (2) substitution of the amino acids Lysine and Arginine (47-59) resulted in a reduction in binding affinity to TAR, and (3) none of the included studies have investigated Tat subtype-specific substitutions and therefore no commentary could be made regarding which subtype may have a higher Tat-TAR binding affinity. Future studies investigating Tat-TAR binding should therefore use full-length Tat proteins and compare subtype-specific variations. Studies of such a nature may help explain why we see differential pathogenesis and prevalence when comparing HIV-1 subtypes.
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Visalli M, Schlich P, Mahieu B, Thomas A, Weber M, Guichard E. First steps towards FAIRization of product-focused sensory data. Food Qual Prefer 2022. [DOI: 10.1016/j.foodqual.2022.104765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Lee BM, Lee SH, Yamada T, Park S, Wang Y, Kim KB, Kwon S. Read-across approaches: current applications and regulatory acceptance in Korea, Japan, and China. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2022; 85:184-197. [PMID: 34670481 DOI: 10.1080/15287394.2021.1992323] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The aim of this paper was to investigate the current status of read-across approaches in the Republic of Korea, Japan, and China in terms of applications and regulatory acceptance. In the Republic of Korea, over the last 6 years, approximately 8% of safety data records used for chemical registrations were based upon read-across, and a guideline published on the use of read-across results in 2017. In Japan, read-across is generally accepted for screening hazard classification of toxicological endpoints according to the Chemical Substances Control Law (CSCL). In China, read-across data, along with data from other animal alternatives are accepted as a data source for chemical registrations, but could be only considered when testing is not technically feasible. At present, read-across is not widely used for chemical registrations and regulatory acceptance of read-across may differ among countries in Asia. With consideration of the advantages and limitations of read-across, it is expected that read-across may soon gradually be employed in Asian countries. Thus, regulatory agencies need to prepare for this progression.
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Affiliation(s)
- Byung-Mu Lee
- Division of Toxicology, College of Pharmacy, Sungkyunkwan University, Gyeonggi-Do, Korea
| | - Sang Hee Lee
- Chemicals Registration & Evaluation Team, Risk Assessment Research Division, National Institute of Environmental Research, Ministry of Environment, Incheon, Korea
| | - Takashi Yamada
- Division of Risk Assessment, Center for Biological Safety Research, National Institute of Health Sciences, Kawasaki, Japan
| | | | - Ying Wang
- Procter & Gamble (P&G) Technology (Beijing) Co., Ltd, Beijing, PR China
| | - Kyu-Bong Kim
- College of Pharmacy, Dankook University, Chungnam, Korea
| | - Seok Kwon
- Global Product Stewardship, Research & Development, Singapore Innovation Center, Procter & Gamble (P&G) International Operations, Singapore, Singapore
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Routier A, Blaizot A, Agossa K, Dubar M. What do we know about the mechanisms of action of probiotics on factors involved in the pathogenesis of periodontitis? A scoping review of in vitro studies. Arch Oral Biol 2021; 129:105196. [PMID: 34153538 DOI: 10.1016/j.archoralbio.2021.105196] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 06/03/2021] [Accepted: 06/07/2021] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Probiotics are increasingly used in oral prevention and treatment conditions, but little is known about their abilities. The aim of this review is to clarify, summarize and disseminate current knowledge about the mode of action of in vitro probiotics on factors involved in the pathogenesis of periodontitis. METHOD 2495 articles were identified in three databases (Medline, Web of Science, SpringerLink) and 26 studies included in this scoping review. RESULTS Twenty-three probiotic species were identified, the majority of which were Lactobacilli or Bifidobacteria. Lactobacillus rhamnosus (30.8 %) and Lactobacillus reuteri (42.3 %) were found to be the two predominantly studied probiotic species and three main mechanisms of action of probiotics could be classified as: (i) modulation of the immuno-inflammatory response, (ii) direct actions of probiotics on periodontopathogens by adhesion or nutritive competitions and/or the secretion of antimicrobial molecules and (iii) indirect actions through environmental modifications. A combination of several probiotic strains seems to be beneficial via synergistic action amplifying the functions of each strain used. However, heterogeneity of the methodologies and probiotic species included in studies leads us to consider the following avenues for future research: (i) implementation of standardized periodontal models as close as possible to in vivo periodontal conditions to identify the functions of each strain for appropriate medication, (ii) updating data about interactions within oral biofilms to identify new candidates and to predict then analyze their behavior within these biofilms. CONCLUSION Probiotics may have their place in the response to inter-individual variability in periodontitis, provided that the choice of the probiotic strain or combination of them will be personalized and optimal for each patient.
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Affiliation(s)
- Arthur Routier
- School of Dentistry, Lille University Hospital, Lille, France.
| | - Alessandra Blaizot
- Department of Public Health, Faculty of Dental Surgery, Lille University Hospital, Lille, France.
| | - Kevimy Agossa
- Department of Periodontology, Faculty of Dental Surgery, Lille University Hospital, Lille, France; University of Lille, Inserm, Lille University Hospital, U1008, F-59000 Lille, France.
| | - Marie Dubar
- Department of Periodontology, Faculty of Dental Surgery, Lille University Hospital, Lille, France; University of Lille, Inserm, Lille University Hospital, UMR-S 1172, F-59000 Lille, France.
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Therapeutic Applications of Stem Cells and Extracellular Vesicles in Emergency Care: Futuristic Perspectives. Stem Cell Rev Rep 2021; 17:390-410. [PMID: 32839921 PMCID: PMC7444453 DOI: 10.1007/s12015-020-10029-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Regenerative medicine (RM) is an interdisciplinary field that aims to repair, replace or regenerate damaged or missing tissue or organs to function as close as possible to its physiological architecture and functions. Stem cells, which are undifferentiated cells retaining self-renewal potential, excessive proliferation and differentiation capacity into offspring or daughter cells that form different lineage cells of an organism, are considered as an important part of the RM approaches. They have been widely investigated in preclinical and clinical studies for therapeutic purposes. Extracellular vesicles (EVs) are the vital mediators that regulate the therapeutic effects of stem cells. Besides, they carry various types of cargo between cells which make them a significant contributor of intercellular communication. Given their role in physiological and pathological conditions in living cells, EVs are considered as a new therapeutic alternative solution for a variety of diseases in which there is a high unmet clinical need. This review aims to summarize and identify therapeutic potential of stem cells and EVs in diseases requiring acute emergency care such as trauma, heart diseases, stroke, acute respiratory distress syndrome and burn injury. Diseases that affect militaries or societies including acute radiation syndrome, sepsis and viral pandemics such as novel coronavirus disease 2019 are also discussed. Additionally, featuring and problematic issues that hamper clinical translation of stem cells and EVs are debated in a comparative manner with a futuristic perspective. Graphical Abstract.
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Poppelaars F, Goicoechea de Jorge E, Jongerius I, Baeumner AJ, Steiner MS, Józsi M, Toonen EJM, Pauly D. A Family Affair: Addressing the Challenges of Factor H and the Related Proteins. Front Immunol 2021; 12:660194. [PMID: 33868311 PMCID: PMC8044877 DOI: 10.3389/fimmu.2021.660194] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/08/2021] [Indexed: 12/19/2022] Open
Abstract
Inflammation is a common denominator of diseases. The complement system, an intrinsic part of the innate immune system, is a key driver of inflammation in numerous disorders. Recently, a family of proteins has been suggested to be of vital importance in conditions characterized by complement dysregulation: the human Factor H (FH) family. This group of proteins consists of FH, Factor H-like protein 1 and five Factor H-related proteins. The FH family has been linked to infectious, vascular, eye, kidney and autoimmune diseases. In contrast to FH, the functions of the other highly homologous proteins are largely unknown and, hence, their role in the different disease-specific pathogenic mechanisms remains elusive. In this perspective review, we address the major challenges ahead in this emerging area, including 1) the controversies about the functional roles of the FH protein family, 2) the discrepancies in quantification of the FH protein family, 3) the unmet needs for validated tools and 4) limitations of animal models. Next, we also discuss the opportunities that exist for the immunology community. A strong multidisciplinary approach is required to solve these obstacles and is only possible through interdisciplinary collaboration between biologists, chemists, geneticists and physicians. We position this review in light of our own perspective, as principal investigators of the SciFiMed Consortium, a consortium aiming to create a comprehensive analytical system for the quantitative and functional assessment of the entire FH protein family.
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Affiliation(s)
- Felix Poppelaars
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Elena Goicoechea de Jorge
- Department of Immunology, Faculty of Medicine, Complutense University and Research Institute Hospital 12 de Octubre (imas12), Madrid, Spain
| | - Ilse Jongerius
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory of the Academic Medical Centre, University of Amsterdam, Amsterdam, Netherlands
- Department of Pediatric Immunology, Rheumatology, and Infectious Diseases, Emma Children’s Hospital, Amsterdam University Medical Centre, Amsterdam, Netherlands
| | - Antje J. Baeumner
- Institute of Analytical Chemistry, Chemo-and Biosensors, Faculty of Chemistry and Pharmacy, University of Regensburg, Regensburg, Germany
| | | | - Mihály Józsi
- Department of Immunology, ELTE Eötvös Loránd University, Budapest, Hungary
- MTA-ELTE Complement Research Group, Eötvös Loránd Research Network (ELKH), Department of Immunology, ELTE Eötvös Loránd University, Budapest, Hungary
| | | | - Diana Pauly
- Department of Ophthalmology, University Hospital Regensburg, Regensburg, Germany
- Experimental Ophthalmology, University Marburg, Marburg, Germany
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Gosselin RD. Insufficient transparency of statistical reporting in preclinical research: a scoping review. Sci Rep 2021; 11:3335. [PMID: 33558615 PMCID: PMC7870941 DOI: 10.1038/s41598-021-83006-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 01/26/2021] [Indexed: 12/14/2022] Open
Abstract
Non-transparent statistical reporting contributes to the reproducibility crisis in life sciences, despite guidelines and educational articles regularly published. Envisioning more effective measures for ensuring transparency requires the detailed monitoring of incomplete reporting in the literature. In this study, a systematic approach was used to sample 16 periodicals from the ISI Journal Citation Report database and to collect 233 preclinical articles (including both in vitro and animal research) from online journal content published in 2019. Statistical items related to the use of location tests were quantified. Results revealed that a large proportion of articles insufficiently describe tests (median 44.8%, IQR [33.3–62.5%], k = 16 journals), software (31%, IQR [22.3–39.6%]) or sample sizes (44.2%, IQR [35.7–55.4%]). The results further point at contradictory information as a component of poor reporting (18.3%, IQR [6.79–26.7%]). No detectable correlation was found between journal impact factor and the quality of statistical reporting of any studied item. The under-representation of open-source software (4.50% of articles) suggests that the provision of code should remain restricted to articles that use such packages. Since mounting evidence indicates that transparency is key for reproducible science, this work highlights the need for a more rigorous enforcement of existing guidelines.
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Affiliation(s)
- Romain-Daniel Gosselin
- Precision Medicine Unit, Lausanne University Hospital, Chemin des Roches 1a/1b, 1010, Lausanne, Switzerland.
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