dr4pl: A Stable Convergence Algorithm for the 4 Parameter Logistic Model

An, Hyowon; Landis, Justin T.; Bailey, Aubrey; Marron, J. S.; Dittmer, Dirk P.

doi:10.32614/rj-2019-003

Cited by 20 publications

(6 citation statements)

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“…All nauplii, dead or alive, were counted and recorded within 24 h of being placed in contact with the tested suspensions. The non-linear modeling of the concentration-lethality relationship was achieved through a four-parameter logistics model (4PL), implemented in several robust variants for estimating parameters in the R package “dr4pl” [ 78 ].…”

Section: Methodsmentioning

confidence: 99%

Insights into the Microbicidal, Antibiofilm, Antioxidant and Toxicity Profile of New O-Aryl-Carbamoyl-Oxymino-Fluorene Derivatives

Vlad

Nuță

Ancuceanu

et al. 2023

IJMS

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The unprecedented increase in microbial resistance rates to all current drugs raises an acute need for the design of more effective antimicrobial strategies. Moreover, the importance of oxidative stress due to chronic inflammation in infections with resistant bacteria represents a key factor for the development of new antibacterial agents with potential antioxidant effects. Thus, the purpose of this study was to bioevaluate new O-aryl-carbamoyl-oxymino-fluorene derivatives for their potential use against infectious diseases. With this aim, their antimicrobial effect was evaluated using quantitative assays (minimum inhibitory/bactericidal/biofilms inhibitory concentrations) (MIC/MBC/MBIC), the obtained values being 0.156–10/0.312–10/0.009–1.25 mg/mL), while some of the involved mechanisms (i.e., membrane depolarization) were investigated by flow cytometry. The antioxidant activity was evaluated by studying the scavenger capacity of DPPH and ABTS•+ radicals and the toxicity was tested in vitro on three cell lines and in vivo on the crustacean Artemia franciscana Kellog. The four compounds derived from 9H-fluoren-9-one oxime proved to exhibit promising antimicrobial features and particularly, a significant antibiofilm activity. The presence of chlorine induced an electron-withdrawing effect, favoring the anti-Staphylococcus aureus and that of the methyl group exhibited a +I effect of enhancing the anti-Candida albicans activity. The IC50 values calculated in the two toxicity assays revealed similar values and the potential of these compounds to inhibit the proliferation of tumoral cells. Taken together, all these data demonstrate the potential of the tested compounds to be further used for the development of novel antimicrobial and anticancer agents.

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Section: Methodsmentioning

confidence: 99%

Insights into the Microbicidal, Antibiofilm, Antioxidant and Toxicity Profile of New O-Aryl-Carbamoyl-Oxymino-Fluorene Derivatives

Vlad

Nuță

Ancuceanu

et al. 2023

IJMS

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“…The statistical examinations applied for each figure are stated in the legends. The half-maximal inhibitory concentration (IC 50 ) calculation was conducted in R (v.4.1.3) environment with R packages drc ( 106 ) and dr4pl ( 107 ).…”

Section: Methodsmentioning

confidence: 99%

Identification of new drugs to counteract anti-spike IgG-induced hyperinflammation in severe COVID-19

Geyer,

Chen,

Bye

et al. 2023

Life Sci. Alliance

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Previously, we and others have shown that SARS-CoV-2 spike-specific IgG antibodies play a major role in disease severity in COVID-19 by triggering macrophage hyperactivation, disrupting endothelial barrier integrity, and inducing thrombus formation. This hyperinflammation is dependent on high levels of anti-spike IgG with aberrant Fc tail glycosylation, leading to Fcγ receptor hyperactivation. For development of immune-regulatory therapeutics, drug specificity is crucial to counteract excessive inflammation whereas simultaneously minimizing the inhibition of antiviral immunity. We here developed an in vitro activation assay to screen for small molecule drugs that specifically counteract antibody-induced pathology. We identified that anti-spike-induced inflammation is specifically blocked by small molecule inhibitors against SYK and PI3K. We identified SYK inhibitor entospletinib as the most promising candidate drug, which also counteracted anti-spike-induced endothelial dysfunction and thrombus formation. Moreover, entospletinib blocked inflammation by different SARS-CoV-2 variants of concern. Combined, these data identify entospletinib as a promising treatment for severe COVID-19.

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“…We here modelled cortical thinning between childhood and adulthood using nonlinear mixed models implemented via the saemix 56 package (version 2.4) in R (version 4.1.0) and RStudio (version 1.4.1717). To capture the characteristic s-shape of cortical thinning, we fit the four-parameter logistic function 57 , as defined in the Results section. See https://github.com/df1234/HUBU_NLMMs for our analysis code.…”

Section: Methodsmentioning

confidence: 99%

The midpoint of cortical thinning between late childhood and early adulthood differs between individuals and brain regions: Evidence from longitudinal modelling in a 12-wave neuroimaging sample

Fuhrmann

Madsen

Johansen³

et al. 2022

Preprint

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Charting human brain maturation between childhood and adulthood is a fundamental prerequisite for understanding the rapid psychological changes during adolescence. Two barriers have precluded the quantification of maturational trajectories: demands on data and demands on estimation. Using high-temporal resolution neuroimaging data of up to 12-waves in the HUBU cohort (N = 90, aged 7-21 years) we investigate changes in apparent cortical thickness across childhood and adolescence. Fitting a four-parameter logistic nonlinear random effects mixed model, we quantified the characteristic, s-shaped, trajectory of cortical thinning in adolescence. This approach yields biologically meaningful parameters, including the midpoint of cortical thinning (MCT), which corresponds to the age at which the cortex shows most rapid thinning - in our sample occurring, on average, at 15 years of age. These results show that, given suitable data and models, cortical maturation can be quantified with precision for each individual and brain region.

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dr4pl: A Stable Convergence Algorithm for the 4 Parameter Logistic Model

Cited by 20 publications

References 0 publications

Insights into the Microbicidal, Antibiofilm, Antioxidant and Toxicity Profile of New O-Aryl-Carbamoyl-Oxymino-Fluorene Derivatives

Insights into the Microbicidal, Antibiofilm, Antioxidant and Toxicity Profile of New O-Aryl-Carbamoyl-Oxymino-Fluorene Derivatives

Identification of new drugs to counteract anti-spike IgG-induced hyperinflammation in severe COVID-19

The midpoint of cortical thinning between late childhood and early adulthood differs between individuals and brain regions: Evidence from longitudinal modelling in a 12-wave neuroimaging sample

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