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  1. Article ; Online: A snapshot of statistical methods used in experimental immunoblotting

    Gosselin Romain-Daniel

    4 open, Vol 5, p

    a scoping review

    2022  Volume 9

    Abstract: Background: Among the many avenues considered to make life science more reproducible, the improvement of the quality and openness of statistical methods has taken centre stage. However, although disparities across research fields and techniques are not ... ...

    Abstract Background: Among the many avenues considered to make life science more reproducible, the improvement of the quality and openness of statistical methods has taken centre stage. However, although disparities across research fields and techniques are not unknown, they remain largely unexplored. Objectives: Provide an overview of statistical methods used in biochemical research involving immunoblotting (also referred to as western blotting), a technique frequently used to quantify proteins of interest. Source of evidence: PubMed. Eligibility criteria: Studies reporting immunoblots with quantitative interpretation (statistical inference). Charting Methods: A reverse chronological systematic sampling was implemented to analyse 2932 experimental conditions (i.e., experimental groups) from 64 articles published at the end of 2021. The statistical test (actual study size n = 67) and software (actual study size n = 61) used for each article and the sample size for each experimental condition were documented. Results: The results indicate an overhelming number of parametric tests, mostly one-way analysis of variance (ANOVA, 15/67) and Student’s t-test (13/67), but for many articles the statistical procedure was not clearly stated (23/67). GraphPad Prism was the most commonly used statistical package (36/61), but many (14/61) articles did not reveal the package used. Finally, the sample size was disclosed in only 1054/2932 conditions in which its median value was 3 (IQR = [3–6]). Conclusion: This study suggests that the transparency of reporting might be suboptimal in immunoblotting research and prompts the need for more comprehensive reviews in the future.
    Keywords biochemistry ; good practices ; meta-research ; publishing ; reporting ; reproducibility ; statistics ; western blot ; Medicine ; R ; Science ; Q
    Subject code 310
    Language English
    Publishing date 2022-01-01T00:00:00Z
    Publisher EDP Sciences
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Insufficient transparency of statistical reporting in preclinical research: a scoping review.

    Gosselin, Romain-Daniel

    Scientific reports

    2021  Volume 11, Issue 1, Page(s) 3335

    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 ... ...

    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.
    Language English
    Publishing date 2021-02-08
    Publishing country England
    Document type Journal Article
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-021-83006-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Insufficient transparency of statistical reporting in preclinical research

    Romain-Daniel Gosselin

    Scientific Reports, Vol 11, Iss 1, Pp 1-

    a scoping review

    2021  Volume 8

    Abstract: 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 ... ...

    Abstract 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.
    Keywords Medicine ; R ; Science ; Q
    Subject code 306
    Language English
    Publishing date 2021-02-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Statistical Analysis Must Improve to Address the Reproducibility Crisis: The ACcess to Transparent Statistics (ACTS) Call to Action.

    Gosselin, Romain-Daniel

    BioEssays : news and reviews in molecular, cellular and developmental biology

    2019  Volume 42, Issue 1, Page(s) e1900189

    Abstract: The ACcess to Transparent Statistics (ACTS) call to action assembles four measures that are rapidly achievable by journals and funding agencies to enhance the quality of statistical reporting. The ACTS call to action is an appeal for concrete actions ... ...

    Abstract The ACcess to Transparent Statistics (ACTS) call to action assembles four measures that are rapidly achievable by journals and funding agencies to enhance the quality of statistical reporting. The ACTS call to action is an appeal for concrete actions from institutions that should spearhead the battle for reproducibility.
    MeSH term(s) Analysis of Variance ; Data Interpretation, Statistical ; Reproducibility of Results ; Research/standards ; Research/statistics & numerical data ; Serial Publications/standards ; Serial Publications/statistics & numerical data
    Language English
    Publishing date 2019-11-21
    Publishing country United States
    Document type Journal Article
    ZDB-ID 50140-2
    ISSN 1521-1878 ; 0265-9247
    ISSN (online) 1521-1878
    ISSN 0265-9247
    DOI 10.1002/bies.201900189
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  5. Article ; Online: Guidelines on statistics for researchers using laboratory animals: the essentials.

    Gosselin, Romain-Daniel

    Laboratory animals

    2018  Volume 53, Issue 1, Page(s) 28–42

    Abstract: There is growing concern that the omnipresence of flawed statistics and the deficient reproducibility that arises therefrom results in an unethical waste of animals in research. The present review aims at providing guidelines in biostatistics for ... ...

    Abstract There is growing concern that the omnipresence of flawed statistics and the deficient reproducibility that arises therefrom results in an unethical waste of animals in research. The present review aims at providing guidelines in biostatistics for researchers, based on observed frequent mistakes, misuses and misconceptions as well as on the specificities of animal experimentation. Twelve recommendations are formulated that cover sampling, sample size optimisation, choice of statistical tests, understanding p-values and reporting results. The objective is to expose important statistical issues that one should consider for the correct design, execution and reporting of experiments.
    MeSH term(s) Animal Experimentation/statistics & numerical data ; Animals ; Laboratory Animal Science/methods ; Research Design ; Sample Size ; Statistics as Topic/methods
    Language English
    Publishing date 2018-06-28
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 391008-8
    ISSN 1758-1117 ; 0023-6772
    ISSN (online) 1758-1117
    ISSN 0023-6772
    DOI 10.1177/0023677218783223
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  6. Article: Guidelines on statistics for researchers using laboratory animals: the essentials

    Gosselin, Romain-Daniel

    Laboratory animals. 2019 Feb., v. 53, no. 1

    2019  

    Abstract: There is growing concern that the omnipresence of flawed statistics and the deficient reproducibility that arises therefrom results in an unethical waste of animals in research. The present review aims at providing guidelines in biostatistics for ... ...

    Abstract There is growing concern that the omnipresence of flawed statistics and the deficient reproducibility that arises therefrom results in an unethical waste of animals in research. The present review aims at providing guidelines in biostatistics for researchers, based on observed frequent mistakes, misuses and misconceptions as well as on the specificities of animal experimentation. Twelve recommendations are formulated that cover sampling, sample size optimisation, choice of statistical tests, understanding p-values and reporting results. The objective is to expose important statistical issues that one should consider for the correct design, execution and reporting of experiments.
    Keywords animal experimentation ; biostatistics ; guidelines ; laboratory animals ; researchers ; statistical analysis
    Language English
    Dates of publication 2019-02
    Size p. 28-42.
    Publishing place SAGE Publications
    Document type Article
    ZDB-ID 391008-8
    ISSN 1758-1117 ; 0023-6772
    ISSN (online) 1758-1117
    ISSN 0023-6772
    DOI 10.1177/0023677218783223
    Database NAL-Catalogue (AGRICOLA)

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  7. Article ; Online: Meta-analysis in a time of pandemic

    Lederer Christian / Daumer Martin / Gosselin Romain-Daniel / Jamall Ijaz S. / Brücher Björn L.D.M.

    4 open, Vol 5, p E

    2022  Volume 5

    Keywords contact tracing ; coronavirus ; covid-19 ; meta-analysis ; modeling ; pandemic ; reproduction rate ; sars-cov-2 ; statistics ; virus ; Medicine ; R ; Science ; Q
    Language English
    Publishing date 2022-01-01T00:00:00Z
    Publisher EDP Sciences
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article: La médecine de précision : au carrefour de la biologie moléculaire, des sciences de l’information et des humanités.

    Gosselin, Romain-Daniel / Redin, Claire / Ristorcelli, Élodie / Raisaro, Jean Louis / Fellay, Jacques

    Revue medicale suisse

    2020  Volume 16, Issue 704, Page(s) 1574–1578

    Abstract: Precision medicine aims to tailor prevention and treatment to individual data. Although different markers can be used (e.g. transcriptome or proteome), its rise is closely linked to that of genomics, owing to the henceforth reasonable cost of DNA ... ...

    Title translation Precision medicine : at the crossroad of molecular biology, information sciences and humanities.
    Abstract Precision medicine aims to tailor prevention and treatment to individual data. Although different markers can be used (e.g. transcriptome or proteome), its rise is closely linked to that of genomics, owing to the henceforth reasonable cost of DNA sequencing. The enormous datasets thus generated can be exploited due to remarkable advances in bioinformatics and information sciences. However, beyond the technological endeavor, humanities and social sciences also play a central role to redefine health and illness. The precision medicine unit at CHUV gathers stakeholders from these various domains in order to demonstrate the utility of precision medicine and catalyze its integration into healthcare, to the benefit of the patient.
    MeSH term(s) Genomics ; Humanities ; Humans ; Medical Informatics ; Molecular Biology ; Precision Medicine/trends
    Language French
    Publishing date 2020-07-08
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2177010-4
    ISSN 1660-9379
    ISSN 1660-9379
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Peripheral nerve injury induces a transitory microglial reaction in the rat infralimbic cortex.

    Chu Sin Chung, Paul / Panigada, Tania / Cardis, Romain / Decosterd, Isabelle / Gosselin, Romain-Daniel

    Neuroscience letters

    2017  Volume 655, Page(s) 14–20

    Abstract: Undeniable evidence shows that microglia in the spinal cord undergo marked reactions following peripheral injuries. However, only rare studies have investigated the possible short and long term microglial reaction in brain regions following peripheral ... ...

    Abstract Undeniable evidence shows that microglia in the spinal cord undergo marked reactions following peripheral injuries. However, only rare studies have investigated the possible short and long term microglial reaction in brain regions following peripheral nerve injury and its interspecies specificities. In the present study we examined microglia in subdivisions of the prefrontal cortex in mice and rats, 7days and 42days after spared nerve injury (SNI) of the sciatic nerve. We show that a bilateral increase of microglial density takes place in the infralimbic cortex in rats 7days post-injury (sham vs. SNI, n=5: ipsilateral 35.4% increase of the median, p=0.0317; contralateral 24.9% increase of the median, p=0.0079), without any detectable change in the other investigated regions, namely the anterior cingulate, prelimbic and agranular insular cortices. In mice, no observable difference could be found in any region at both time points, neither using Iba-1 immunostaining nor with CX3CR1-eGFP animals. Our results indicate that a transitory, species-specific and highly regionalized microglial reaction takes place in the prefrontal cortex following peripheral nerve injury.
    Language English
    Publishing date 2017-08-10
    Publishing country Ireland
    Document type Journal Article
    ZDB-ID 194929-9
    ISSN 1872-7972 ; 0304-3940
    ISSN (online) 1872-7972
    ISSN 0304-3940
    DOI 10.1016/j.neulet.2017.06.037
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  10. Article: Extracellular microvesicles from astrocytes contain functional glutamate transporters: regulation by protein kinase C and cell activation.

    Gosselin, Romain-Daniel / Meylan, Patrick / Decosterd, Isabelle

    Frontiers in cellular neuroscience

    2013  Volume 7, Page(s) 251

    Abstract: Glutamate transport through astrocytic excitatory amino-acid transporters (EAAT)-1 and EAAT-2 is paramount for neural homeostasis. EAAT-1 has been reported in secreted extracellular microvesicles (eMV, such as exosomes) and because the protein kinase C ( ... ...

    Abstract Glutamate transport through astrocytic excitatory amino-acid transporters (EAAT)-1 and EAAT-2 is paramount for neural homeostasis. EAAT-1 has been reported in secreted extracellular microvesicles (eMV, such as exosomes) and because the protein kinase C (PKC) family controls the sub-cellular distribution of EAATs, we have explored whether PKCs drive EAATs into eMV. Using rat primary astrocytes, confocal immunofluorescence and ultracentrifugation on sucrose gradient we here report that PKC activation by phorbol myristate acetate (PMA) reorganizes EAAT-1 distribution and reduces functional [(3)H]-aspartate reuptake. Western-blots show that EAAT-1 is present in eMV from astrocyte conditioned medium, together with NaK ATPase and glutamine synthetase all being further increased after PMA treatment. However, nanoparticle tracking analysis reveals that PKC activation did not change particle concentration. Functional analysis indicates that eMV have the capacity to reuptake [(3)H]-aspartate. In vivo, we demonstrate that spinal astrocytic reaction induced by peripheral nerve lesion (spared nerve injury, SNI) is associated with a phosphorylation of PKC δ together with a shift of EAAT distribution ipsilaterally. Ex vivo, spinal explants from SNI rats release eMV with an increased content of NaK ATPase, EAAT-1 and EAAT-2. These data indicate PKC and cell activation as important regulators of EAAT-1 incorporation in eMV, and raise the possibility that microvesicular EAAT-1 may exert extracellular functions. Beyond a putative role in neuropathic pain, this phenomenon may be important for understanding neural homeostasis and a wide range of neurological diseases associated with astrocytic reaction as well as non-neurological diseases linked to eMV release.
    Language English
    Publishing date 2013-12-10
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2452963-1
    ISSN 1662-5102
    ISSN 1662-5102
    DOI 10.3389/fncel.2013.00251
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