Extrapolation of Laboratory pH Dose–Response Data to Fluctuating Environments: Comparisons with a Null Model

1989 ◽  
Vol 46 (9) ◽  
pp. 1499-1509
Author(s):  
James W. Haefner ◽  
Linda C. Abbott

A simple model was developed to extrapolate laboratory dose–response data to randomly varying conditions. We fit published data of dose–response experiments for the effects of low pH stress on survival rates of stream macro-invertebrates to a modification of the Weibull distribution. Using the resulting parameter estimates and Monte Carlo simulation, we compared the values obtained in constant laboratory conditions with the expected survival rates obtained in fluctuating environments. For each of three species, we performed 108 Monte Carlo experiments in a full factorial design that varied the mean pH, the standard deviation of pH fluctuations, the distribution from which pH values were drawn, the distributions of runs of constant pH, and the presence of episodic events. Fluctuating environments decreased the survival rates of resistant species, but increased survivorship of sensitive species. No one exposure duration under laboratory conditions could consistently be extrapolated to the suite of variable environments we examined. Probit analyses performed on the observed and simulated data indicated that LC-50s of different observed exposure durations were similar to each other and to the LC-50s of the simulated data assuming an exposure of 24 h. Based on these results, we recommend that toxicity studies incorporate temporal variability directly by using varying dose levels in laboratory tests.

1992 ◽  
Vol 11 (6) ◽  
pp. 530-534 ◽  
Author(s):  
P. Carthew ◽  
R.J. Hill ◽  
R.E. Edwards ◽  
P.N. Lee

1 The dose—response data for the induction of mesothelioma, in rats, by the intrapleural administration of the fibrous zeolite, erionite, has been compared to the published data for the crocidolite and chrysotile forms of asbestos. Erionite is more than two orders of magnitude more carcinogenic than either of the two forms of asbestos examined. 2 The relative sensitivity of the intrapleural and intraperitoneal routes of injection were also examined. The sensitivity of the intraperitoneal over the intrapleural route of administration was considerably greater for all the forms of asbestos examined but not for erionite. 3 The relationship for different fibres, between the number of fibres required to give animals mesothelioma, at the 50% or 10% observable tumour effect level (OTEL) was examined, and a ranking of relative carcinogenicity was made. 4 This showed that the data derived from the dose responses obtained by the intrapleural administration of fibres to rats ranked the relative carcinogenicity of erionite, crocidolite and chrysotile in accord with the known clinical mesothelioma induction in man after exposure to these fibres. Examination of the carcinogenicity ranking from data derived from intraperitoneal injections of fibres was not in accord with the known clinical mesothelioma induction in man for the various asbestos types examined.


2019 ◽  
Author(s):  
Joshua G. Harrison ◽  
W. John Calder ◽  
Vivaswat Shastry ◽  
C. Alex Buerkle

AbstractMolecular ecology regularly requires the analysis of count data that reflect the relative abundance of features of a composition (e.g., taxa in a community, gene transcripts in a tissue). The sampling process that generates these data can be modeled using the multinomial distribution. Replicate multinomial samples inform the relative abundances of features in an underlying Dirichlet distribution. These distributions together form a hierarchical model for relative abundances among replicates and sampling groups. This type of Dirichlet-multinomial modelling (DMM) has been described previously, but its benefits and limitations are largely untested. With simulated data, we quantified the ability of DMM to detect differences in proportions between treatment and control groups, and compared the efficacy of three computational methods to implement DMM—Hamiltonian Monte Carlo (HMC), variational inference (VI), and Gibbs Markov chain Monte Carlo. We report that DMM was better able to detect shifts in relative abundances than analogous analytical tools, while identifying an acceptably low number of false positives. Among methods for implementing DMM, HMC provided the most accurate estimates of relative abundances, and VI was the most computationally efficient. The sensitivity of DMM was exemplified through analysis of previously published data describing lung microbiomes. We report that DMM identified several potentially pathogenic, bacterial taxa as more abundant in the lungs of children who aspirated foreign material during swallowing; these differences went undetected with different statistical approaches. Our results suggest that DMM has strong potential as a statistical method to guide inference in molecular ecology.


Methodology ◽  
2005 ◽  
Vol 1 (2) ◽  
pp. 81-85 ◽  
Author(s):  
Stefan C. Schmukle ◽  
Jochen Hardt

Abstract. Incremental fit indices (IFIs) are regularly used when assessing the fit of structural equation models. IFIs are based on the comparison of the fit of a target model with that of a null model. For maximum-likelihood estimation, IFIs are usually computed by using the χ2 statistics of the maximum-likelihood fitting function (ML-χ2). However, LISREL recently changed the computation of IFIs. Since version 8.52, IFIs reported by LISREL are based on the χ2 statistics of the reweighted least squares fitting function (RLS-χ2). Although both functions lead to the same maximum-likelihood parameter estimates, the two χ2 statistics reach different values. Because these differences are especially large for null models, IFIs are affected in particular. Consequently, RLS-χ2 based IFIs in combination with conventional cut-off values explored for ML-χ2 based IFIs may lead to a wrong acceptance of models. We demonstrate this point by a confirmatory factor analysis in a sample of 2449 subjects.


2019 ◽  
Vol 53 (5) ◽  
pp. 417-422
Author(s):  
P. De los Ríos ◽  
E. Ibáñez Arancibia

Abstract The coastal marine ecosystems in Easter Island have been poorly studied, and the main studies were isolated species records based on scientific expeditions. The aim of the present study is to apply a spatial distribution analysis and niche sharing null model in published data on intertidal marine gastropods and decapods in rocky shore in Easter Island based in field works in 2010, and published information from CIMAR cruiser in 2004. The field data revealed the presence of decapods Planes minutus (Linnaeus, 1758) and Leptograpsus variegatus (Fabricius, 1793), whereas it was observed the gastropods Nodilittorina pyramidalis pascua Rosewater, 1970 and Nerita morio (G. B. Sowerby I., 1833). The available information revealed the presence of more species in data collected in 2004 in comparison to data collected in 2010, with one species markedly dominant in comparison to the other species. The spatial distribution of species reported in field works revealed that P. minutus and N. morio have aggregated pattern and negative binomial distribution, L. variegatus had uniform pattern with binomial distribution, and finally N. pyramidalis pascua, in spite of aggregated distribution pattern, had not negative binomial distribution. Finally, the results of null model revealed that the species reported did not share ecological niche due to competition absence. The results would agree with other similar information about littoral and sub-littoral fauna for Easter Island.


2021 ◽  
Vol 80 (Suppl 1) ◽  
pp. 1132.3-1133
Author(s):  
G. Jurado Quijano ◽  
L. Fernández de la Fuente Bursón ◽  
B. Hernández-Cruz ◽  
P. Muñoz Reinoso ◽  
V. Merino Bohóquez ◽  
...  

Background:Rituximab (RTX) is a monoclonal antibody against the CD20 B cell antigen that has been used successfully in recent years for the treatment of rheumatoid arthritis (RA). It is an effective drug that reaches survival rates of 60% at 5 years of treatment as reflected in the British experience. However, survival in Spanish patients is unknown.Objectives:To study the survival of RTX treatment and the characteristics of patients with RA treated with the drug since its commercialization in Spain.Methods:Observational, retrospective and analytical study of a cohort of patients with RA treated with at least one dose of RTX. We reviewed the medical records of all patients with RA from January 2007 to June 2017. A total of 178 previous defined variables were collected, highlighting data about treatment (use of RTX, associated conventional synthetic disease modifying drugs [FAMEsc], doses of corticosteroids [GC] used) and activity indices. Descriptive statistics were performed (median and the 25th and 75th percentiles are shown). The comparative analysis was done with χ2 and U of Mann Whitney for categorical variables and paired sign rank test or Student’s t for continuous. Survival Kaplan Mayer curves were constructed. The study was carried out in accordance with the standards of our Clinical Research Ethics Committee.Results:A total of 54 patients were analyzed. 74% (n = 40) of them were women, the age was 61.2 years (51.0 - 67.4). 74% (n = 40) presented some type of relevant comorbidity. Its RA was FR + in 96% (n = 52) and ACCP + in 78% (n = 42) of the cases, with an evolution time of 9.3 years (3.5-19, 2), and with radiographic erosions in up to 63% (n = 34). At the time of the start of the RTX, 100% of the patients (n = 54) received some FAMEsc, and 33 (61%) were treated with prednisone; the daily dose of prednisone was 9 (6-12) mg. The baseline DAS28-VSG was 5 (4.1 - 6.0). The duration of the follow-up was 56.6 (29.3-92.1) months. Patients received a mean of 5 (1-6) cycles of RTX at a dose of 1000 mg on days 0 and 15 in most cases. The final DAS28-VSG was 2.6 (2.1 - 4.0), p = 0.00001 compared to baseline. The delta between baseline and final DAS was -2.36 (-0.55 - -3.1). At the end of the RTX treatment, the EULAR response rate was good in 64% (n = 25), reaching remission in 17 (31%) of the patients, and moderate response in 21% (n = 8) of them (Figure 1). Only 2 (4%) patients were treated with GCC at the end of the follow-up, p<0,00001 compared to baseline. The daily dose of PDN at the end of follow-up was 6 mg in a case and 12 mg in the other, p=00001 compared to baseline. At the end of the follow-up 24%of the patients (n = 13) changed or discontinued the drug: 9 changed due to secondary failure, 2 suspended due to adverse events, 1 due to death due to prior neoplastic process and 1 due to complete disease remission. Survival at 1, 2, 3, 4, 5, 6 and 7 years was 92%, 92%, 82% 78%, 75%, 75% and 65% respectively; with a mean survival rate of 90 months (Figure 1).Conclusion:The results of our analysis show that patients with RA undergoing RTX treatment have adequate control of disease activity and drug survival rates, like published data. RTX treatment allowed stopped GCC treatment in 31 cases (90%).References:[1]Oldroyd AGS, et al. Rheumatology (Oxford). 2018 Jun 1;57(6):1089-1096.Disclosure of Interests:Gonzalo Jurado Quijano: None declared, Lola Fernández de la Fuente Bursón: None declared, Blanca Hernández-Cruz Speakers bureau: Sociedad Española de Reumatología, Abbvie, Roche, Bristol, MSD, Lilly, Pfizer, Amgen, Sanofi, Consultant of: Abbvie, Lilly, Sanofi, STADA, UCB, Amgen, Grant/research support from: Fundación para la Investigación Sevilla, Junta de Andalucía, Fundación Andaluza de Reumatología, Paloma Muñoz Reinoso: None declared, Vicente Merino Bohóquez: None declared, José Javier Pérez Venegas: None declared


Cancers ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1889
Author(s):  
Arthur Bongrand ◽  
Charbel Koumeir ◽  
Daphnée Villoing ◽  
Arnaud Guertin ◽  
Ferid Haddad ◽  
...  

Proton therapy (PRT) is an irradiation technique that aims at limiting normal tissue damage while maintaining the tumor response. To study its specificities, the ARRONAX cyclotron is currently developing a preclinical structure compatible with biological experiments. A prerequisite is to identify and control uncertainties on the ARRONAX beamline, which can lead to significant biases in the observed biological results and dose–response relationships, as for any facility. This paper summarizes and quantifies the impact of uncertainty on proton range, absorbed dose, and dose homogeneity in a preclinical context of cell or small animal irradiation on the Bragg curve, using Monte Carlo simulations. All possible sources of uncertainty were investigated and discussed independently. Those with a significant impact were identified, and protocols were established to reduce their consequences. Overall, the uncertainties evaluated were similar to those from clinical practice and are considered compatible with the performance of radiobiological experiments, as well as the study of dose–response relationships on this proton beam. Another conclusion of this study is that Monte Carlo simulations can be used to help build preclinical lines in other setups.


Entropy ◽  
2021 ◽  
Vol 23 (4) ◽  
pp. 384
Author(s):  
Rocío Hernández-Sanjaime ◽  
Martín González ◽  
Antonio Peñalver ◽  
Jose J. López-Espín

The presence of unaccounted heterogeneity in simultaneous equation models (SEMs) is frequently problematic in many real-life applications. Under the usual assumption of homogeneity, the model can be seriously misspecified, and it can potentially induce an important bias in the parameter estimates. This paper focuses on SEMs in which data are heterogeneous and tend to form clustering structures in the endogenous-variable dataset. Because the identification of different clusters is not straightforward, a two-step strategy that first forms groups among the endogenous observations and then uses the standard simultaneous equation scheme is provided. Methodologically, the proposed approach is based on a variational Bayes learning algorithm and does not need to be executed for varying numbers of groups in order to identify the one that adequately fits the data. We describe the statistical theory, evaluate the performance of the suggested algorithm by using simulated data, and apply the two-step method to a macroeconomic problem.


Author(s):  
Nicola Orsini

Recognizing a dose–response pattern based on heterogeneous tables of contrasts is hard. Specification of a statistical model that can consider the possible dose–response data-generating mechanism, including its variation across studies, is crucial for statistical inference. The aim of this article is to increase the understanding of mixed-effects dose–response models suitable for tables of correlated estimates. One can use the command drmeta with additive (mean difference) and multiplicative (odds ratios, hazard ratios) measures of association. The postestimation command drmeta_graph greatly facilitates the visualization of predicted average and study-specific dose–response relationships. I illustrate applications of the drmeta command with regression splines in experimental and observational data based on nonlinear and random-effects data-generation mechanisms that can be encountered in health-related sciences.


Genetics ◽  
1997 ◽  
Vol 147 (4) ◽  
pp. 1855-1861 ◽  
Author(s):  
Montgomery Slatkin ◽  
Bruce Rannala

Abstract A theory is developed that provides the sampling distribution of low frequency alleles at a single locus under the assumption that each allele is the result of a unique mutation. The numbers of copies of each allele is assumed to follow a linear birth-death process with sampling. If the population is of constant size, standard results from theory of birth-death processes show that the distribution of numbers of copies of each allele is logarithmic and that the joint distribution of numbers of copies of k alleles found in a sample of size n follows the Ewens sampling distribution. If the population from which the sample was obtained was increasing in size, if there are different selective classes of alleles, or if there are differences in penetrance among alleles, the Ewens distribution no longer applies. Likelihood functions for a given set of observations are obtained under different alternative hypotheses. These results are applied to published data from the BRCA1 locus (associated with early onset breast cancer) and the factor VIII locus (associated with hemophilia A) in humans. In both cases, the sampling distribution of alleles allows rejection of the null hypothesis, but relatively small deviations from the null model can account for the data. In particular, roughly the same population growth rate appears consistent with both data sets.


2004 ◽  
Vol 67 (9) ◽  
pp. 2024-2032 ◽  
Author(s):  
FUMIKO KASUGA ◽  
MASAMITSU HIROTA ◽  
MASAMICHI WADA ◽  
TOSHIHIKO YUNOKAWA ◽  
HAJIME TOYOFUKU ◽  
...  

The Ministry of Health, Labor and Welfare (former MHW) of Japan issued a Directive in 1997 advising restaurants and caterers to freeze portions of both raw food and cooked dishes for at least 2 weeks. This system has been useful for determining vehicle foods at outbreaks. Enumeration of bacteria in samples of stored food provide data about pathogen concentrations in the implicated food. Data on Salmonella concentrations in vehicle foods associated with salmonellosis outbreaks were collected in Japan between 1989 and 1998. The 39 outbreaks that occurred during this period were categorized by the settings where the outbreaks took place, and epidemiological data from each outbreak were summarized. Characteristics of outbreak groups were analyzed and compared. The effect of new food-storage system on determination of bacterial concentration was evaluated. Freezing and nonfreezing conditions prior to microbial examination were compared in the dose-response relationship. Data from outbreaks in which implicated foods had been kept frozen suggested apparent correlation between the Salmonella dose ingested and the disease rate. Combined with results of epidemiological investigation, quantitative data from the ingested pathogen could provide complete dose-response data sets.


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