The amino acid derivative reactivity assay (ADRA) is an in chemico alternative assay for skin sensitization listed in OECD test guideline 442C. ADRA evaluates the reactivity of sensitizers to ...proteins, which is key event 1 in the skin sensitization adverse outcome pathway.
Although the current key event 1 evaluation method is a simple assay that evaluates nucleophile and test chemical reactivity, mixtures of unknown molecular weights cannot be evaluated because a constant molar ratio between the nucleophile and test chemical is necessary. In addition, because the nucleophile is quantified by HPLC, the frequency of co‐eluting the test chemical and nucleophile increases when measuring multi‐component mixtures. To solve these issues, test conditions have been developed using a 0.5 mg/mL test chemical solution and fluorescence‐based detection. Since the practicality of these methods has not been substantiated, a validation test to confirm reproducibility was conducted in this study.
The 10 proficiency substances listed in the ADRA guidelines were tested three times at five different laboratories. The results of both within‐ and between‐laboratory reproducibility were 100%, and the results of ultraviolet‐ and fluorescence‐based measurements were also consistent. In addition to the proficiency substances, a new positive control, squaric acid diethyl ester, was tested three times at the five laboratories. The results showed high reproducibility with N‐(2‐(1‐naphthyl)acetyl)‐l‐cysteine depletion of 37%–52% and α‐N‐(2‐(1‐naphthyl)acetyl)‐l‐lysine depletion of 99%–100%.
Thus, high reproducibility was confirmed in both evaluations of the 0.5 mg/mL test chemical and the fluorescence‐based measurements, validating the practicability of these methods.
We implemented a study to validate a new amino acid derivative reactivity assay (ADRA) using a 0.5 mg/mL test chemical solution by determining within‐laboratory and between‐laboratory reproducibility in five participating laboratories. The aim of this study was to verify reproducibility with 10 proficiency substances and 1 positive control. The results showed sufficiently high reproducibility and predictive capacity. We plan to submit this new ADRA test method to the OECD test guideline group in the near future.
A recent study of the replicability of key psychological findings is a major contribution toward understanding the human side of the scientific process. Despite the careful and nuanced analysis ...reported, the simple narrative disseminated by the mass, social, and scientific media was that in only 36% of the studies were the original results replicated. In the current study, however, we showed that 77% of the replication effect sizes reported were within a 95% prediction interval calculated using the original effect size. Our analysis suggests two critical issues in understanding replication of psychological studies. First, researchers' intuitive expectations for what a replication should show do not always match with statistical estimates of replication. Second, when the results of original studies are very imprecise, they create wide prediction intervals—and a broad range of replication effects that are consistent with the original estimates. This may lead to effects that replicate successfully, in that replication results are consistent with statistical expectations, but do not provide much information about the size (or existence) of the true effect. In this light, the results of the Reproducibility Project: Psychology can be viewed as statistically consistent with what one might expect when performing a large-scale replication experiment.
A key component of scientific communication is sufficient information for other researchers in the field to reproduce published findings. For computational and data-enabled research, this has often ...been interpreted to mean making available the raw data from which results were generated, the computer code that generated the findings, and any additional information needed such as workflows and input parameters. Many journals are revising author guidelines to include data and code availability. This work evaluates the effectiveness of journal policy that requires the data and code necessary for reproducibility be made available postpublication by the authors upon request. We assess the effectiveness of such a policy by (i) requesting data and code from authors and (ii) attempting replication of the published findings. We chose a random sample of 204 scientific papers published in the journal Science after the implementation of their policy in February 2011. We found that we were able to obtain artifacts from 44% of our sample and were able to reproduce the findings for 26%. We find this policy—author remission of data and code postpublication upon request—an improvement over no policy, but currently insufficient for reproducibility.
Replication-an important, uncommon, and misunderstood practice-is gaining appreciation in psychology. Achieving replicability is important for making research progress. If findings are not ...replicable, then prediction and theory development are stifled. If findings are replicable, then interrogation of their meaning and validity can advance knowledge. Assessing replicability can be productive for generating and testing hypotheses by actively confronting current understandings to identify weaknesses and spur innovation. For psychology, the 2010s might be characterized as a decade of active confrontation. Systematic and multi-site replication projects assessed current understandings and observed surprising failures to replicate many published findings. Replication efforts highlighted sociocultural challenges such as disincentives to conduct replications and a tendency to frame replication as a personal attack rather than a healthy scientific practice, and they raised awareness that replication contributes to self-correction. Nevertheless, innovation in doing and understanding replication and its cousins, reproducibility and robustness, has positioned psychology to improve research practices and accelerate progress.
Introdução: A forma mais acessível para diagnosticar dores lombares e sacroilíacas são os testes ortopédicos. Objetivo: Apresentar confiabilidade e acurácia diagnóstica por meio dos índices de ...sensibilidade e especificidade de testes clínicos para avaliar a coluna lombar e articulações sacroilíacas. Métodos: Realizou-se revisão de literatura com palavras-chave e seus correspondentes em inglês, nas bases de dados: PubMed, Embase, SciELO e Bireme. Resultados: Encontraram-se 9.806 artigos, porém apenas sete foram incluídos no estudo. Os principais testes para avaliação da coluna lombar são: slump test, teste de Lasègue, teste de Schöber e de instabilidade segmentar. Para avaliar as disfunções sacroilíacas: teste de distração, compressão, thigh thrust, Gaenslen e teste de thrust sacral. Conclusão: O slump test e o teste de Lasègue apresentaram valores excelentes de especificidade e sensibilidade no diagnóstico de disfunções lombares. Os testes para avaliação sacroilíaca evidenciaram que dois ou mais testes positivos combinados demonstram melhores resultados nos índices estudados.
Background: We examined the intra-individual reproducibility of glucose/insulin responses to a mixed meal tolerance test (MMTT) and its physiologic determinants. Methods: During an inpatient stay, ...894 participants (574 normal glucose regulation; 267 impaired glucose regulation; 53 with type 2 diabetes (T2D)) underwent a 9-hour MMTT including breakfast and lunch meals (30% of weight maintaining kcals each; 40% carbohydrate, 40% fat, 20% protein), intravenous glucose tolerance testing for acute insulin response (AIR), and hyperinsulinemiceuglycemic clamp to assess insulin action (M). 405 participants had a follow-up MMTT (median follow-up time: 1.4 years). Glucose/ insulin responses were quantified by the total/incremental area under the curve (AUC/iAUC) and reproducibility by intraclass correlation coefficients (ICC). Results: In individuals without T2D, reproducibility of glucose/insulin AUCs for same day breakfast and lunch was moderate to high (ICCs: 0.57-0.80, all p<0.01) as were insulin iAUCs (0.64-0.71), whereas ICCs for glucose iAUC were <0.15. In the those with T2D, glucose ICCs were >0.70; insulin ICCs were poor <0.40. For repeated MMTTs, ICCs for AUCs in group without T2D were 1) glucose: 0.11-0.36 2) insulin: 0.43-0.54; iAUCs were 0.21-0.58 for glucose/insulin. In those with T2D, ICCs were moderate for glucose/insulin AUC (ICCs: 0.61-0.68, p<0.01). Breakfast glucose AUC was negatively associated with M (partial R: -0.32, p<0.01) and AIR (partial R: -0.25, p<0.01). Breakfast insulin AUC was negatively/positively associated with M (partial R: -0.51, p<0.01)/AIR (partial R: 0.24, p<0.01). Conclusions: Reproducibility of glucose and insulin responses to an MMTT ranged from weak to strong depending on subtraction of fasting values, glucose status, and timeframe. Insulin secretion and action were independent determinants of glucose/insulin responses. Our findings indicate variability that requires consideration in nutrition studies utilizing MMTTs outcomes.
Scientific progress depends on the ability of independent researchers to scrutinize the results of a research study, to reproduce the study's main results using its materials, and to build on them in ...future studies (https://www.nature.com/nature-research/editorial-policies/reporting-standards). Nuances in the computer code may have marked effects on the training and evaluation of results4, potentially leading to unintended consequences5. ...transparency in the form of the actual computer code used to train a model and arrive at its final set of parameters is essential for research reproducibility. The many software dependencies of large-scale machine learning applications require appropriate control of the software environment, which can be achieved through package managers including Conda, as well as container and virtualization systems, including Code Ocean, Gigantum, Colaboratory and Docker. Sharing the fitted model (architecture along with learned parameters) should be simple aside from privacy concerns that the model may reveal sensitive information about the set of patients used to train it.
P values and error bars help readers infer whether a reported difference would likely recur, with the sample size n used for statistical tests representing biological replicates, independent ...measurements of the population from separate experiments. We provide examples and practical tutorials for creating figures that communicate both the cell-level variability and the experimental reproducibility.
Abstract only Introduction A “reproducibility crisis” has afflicted the recent medical literature, affecting 75‐89% of major reported findings. An important cause of the inability to replicate ...results is hypothesizing after the results are known (HARKing): presenting a post hoc hypothesis according with findings as if it were a confirmed a priori hypothesis. Meeting abstract instructions may affect the frequency of HARKing. Methods We tested the hypothesis that, compared with abstract instructions NOT indicating a "hypothesis" should be stated, instructions indicating THAT a "hypothesis" should be stated would increase the proportion of abstracts judged by field content experts to exhibit HARKing. Hypothesis pre‐registered at AsPredicted.org (#5019). We analyzed randomly sampled abstracts from 4 International Stroke Conference (ISC) meeting years with highly forceful (2015), moderately forceful (2017), and non‐forceful (2013 and 2022) requirements for statement of a “hypothesis” in abstract preparation instructions, regardless of whether a hypothesis statement was appropriate (confirmatory science) or inappropriate (exploratory science). Results The 163 abstracts (39 to 43 in each meeting year) equally sampled the 14‐17 ISC topic categories. Explicit “hypothesis” statements were more common in the highly and moderately forceful instruction years (30% and 27%) than in the non‐forceful instruction years (9% and 13%) (p = 0.006). Among the total 32 hypothesis statements, 81% were deemed falsifiable, and 19% non‐falsifiable. None (0%) of hypotheses were stated as pre‐registered prior to study conduct. Overall, 59% (19/32) of the hypothesis statements were adjudicated by two independent content experts as likely to be hypothesizing after the results were known (HARKing). HARKing was more common in the highly and moderately forceful instruction years (20% and 15%) than the non‐forceful instruction years (9% and 3%) (p = 0.03). Conclusion Abstract preparation instructions requiring the use of a hypothesis statement promoted hypothesizing after the results are known, with HARKing present in 1 out of every 5 meeting abstracts. To improve reproducibility of neurovascular research studies, appropriate meeting abstract preparation instructions are desirable, recommending hypothesis statements only for the small proportion of stroke studies that are of confirmatory, rather than exploratory, design.
Due to a range of promising results from T cell therapy clinical trials, methods and technologies of cell selection are being explored to increase safety, reproducible high potency as well as lean ...operation. Although conventional methods such as (density gradient or counterflow) centrifugation, directed cell culture and magnetic field-based cell selection methods have long been applied successfully in cGMP-compliant manufacturing of therapeutic cells, the increasing need for manufacturing large numbers of specific subpopulations of T cells demands a new approach.
In academic research settings, accurate selection of specific subpopulations of T cells such as Regulatory T cells or CD4 Cytotoxic T cells, is performed by means of flow cytometry-based cell sorting involving identification of multiple phenotypic characteristics of a single cell type. While conventional, high-speed cell sorting has been applied to clinical-grade manufacturing in the past, it is not a sustainable method for current and future demands in clinical manufacturing.
During the last decade, significant progress has been made on flow cytometry-based, microfluidic chip cell sorting that has led to the availability of at least 3 different brands of cell sorters with acceptable features and performances for selecting specific subpopulations of T cells in cGMP-compliant manufacturing of therapeutic cells.
We report on having worked with a number of these new cell sorters to select highly purified Regulatory T cells as well as CD4 Cytotoxic T cells as a component of clinical manufacturing processes for clinical trials with specific subpopulations of T cells to treat GVHD and CLL, respectively. Most of our T cell manufacturing processes begin with PBMCs – Regulatory T cells represent 2.5 – 5 % and CD4 Cytotoxic T cells 20 – 30% of PBMCs. Cell selection strategies may involve debulking, enrichment and/or high purification steps. Manufacturing criteria such as processing time, purity, yield and complexity of the workflow, determine which strategy to use. Our report provides detailed insight into best practices to apply in clinical manufacturing procedures in order to efficiently obtain high potency therapeutic cells. We conclude that this new technology narrows the methods gap between academic research and clinical trials, clearing the path to quickly establish reproducibility at large-scale.
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