Dashing Growth Curves: a web application for rapid and interactive analysis of microbial growth curves.

BACKGROUND: Recording and analyzing microbial growth is a routine task in the life sciences. Microplate readers that record dozens to hundreds of growth curves simultaneously are increasingly used for this task raising the demand for their rapid and reliable analysis. RESULTS: Here, we present Dashing Growth Curves, an interactive web application ( http://dashing-growth-curves.ethz.ch/ ) that enables researchers to quickly visualize and analyze growth curves without the requirement for coding knowledge and independent of operating system. Growth curves can be fitted with parametric and non-parametric models or manually. The application extracts maximum growth rates as well as other features such as lag time, length of exponential growth phase and maximum population size among others. Furthermore, Dashing Growth Curves automatically groups replicate samples and generates downloadable summary plots for of all growth parameters. CONCLUSIONS: Dashing Growth Curves is an open-source web application that reduces the time required to analyze microbial growth curves from hours to minutes.

Compensation effect of mortality is a challenge to substantial lifespan extension of humans.

Despite frequent claims regarding radical extensions of human lifespan in the near future, many pragmatic scientists caution against excessive and baseless optimism on this front. In this study, we examine the compensation effect of mortality (CEM) as a potential challenge to substantial lifespan extension. The CEM is an empirical mortality regularity, often depicted as relative mortality convergence at advanced ages. Analysis of mortality data from 44 human populations, available in the Human Mortality Database, demonstrated that CEM can be represented as a continuous decline in relative mortality variation (assessed through the coefficient of variation and the standard deviation of the logarithm of mortality) with age, reaching a minimum corresponding to the species-specific lifespan. Through this method, the species-specific lifespan is determined to be 96-97 years, closely aligning with estimates derived from correlations between Gompertz parameters (95-98 years). Importantly, this representation of CEM can be achieved non-parametrically, eliminating the need for estimating Gompertz parameters. CEM is a challenge to lifespan extension, because it suggests that the true aging rate in humans (based on loss of vital elements, e.g., functional cells) remains stable at approximately 1% per year in the majority of human populations and is not affected by environmental or familial longevity factors. Given this rate of functional cell loss, one might anticipate that the total pool of functional cells could be entirely depleted by the age of 115-120 years creating physiological limit to human lifespan. Mortality pattern of supercentenarians (110 + years) aligns with this prediction.

Invariances in relations between aging, exposure to external hazards, and mortality reflected in life table aging rate (LAR) patterns examined through the lens of generalized Gompertz-Makeham law.

According to the Gompertz law, the age-dependent change in the logarithm of mortality (life-table aging rate, LAR) is equal to the population-averaged age-independent biological aging rate (γ), and LAR would be constant if aging were the only cause of mortality increase. However, LAR is influenced by population exposures to the external hazards. If they were constant, according to the Gompertz-Makeham law (GML), LAR would be below γ at lower ages and asymptotically and monotonically approach γ with increasing age. Actually, LAR trajectories derived from data on mortality in different countries and historical periods feature systematic undulations. In the present investigation, mortality-vs.-age trajectories were modeled based on a generalized GML (gGML). Unlike the canonical GML terms, which are population-specific constants, the respective terms of the gGML are represented with some population-specific functions of age. Invariant in gGML are the modes of translation of these functions into the dependency of mortality on age: linear for population exposure to the irresistible external hazards or exponential for population-averaged ability to withstand the resistible external and internal hazards. Modeling suggests that, at earlier ages, LAR undulations are attributable to changes in population exposures to the former hazards. However, only their unrealistically high levels can produce the transient increase in LAR at about 65 to 90 years. This pervasive undulation of LAR-vs.-age trajectory is rather caused by an increment in γ. Reasons to regard gGML as a genuine natural law, which defines relations between mortality, aging and environment, are discussed.

Two Types of Survival Curves of Different Lines of Progeric Mice.

For most of their lifespan, the probability of death for many animal species increases with age. Gompertz law states that this increase is exponential. In this work, we have compared previously published data on the survival kinetics of different lines of progeric mice. Visual analysis showed that in six lines of these rapidly aging mutants, the probability of death did not strictly depend on age. In contrast, ten lines of progeric mice have survival curves similar to those of the control animals, that is, in agreement with Gompertz law, similar to the shape of an exponential curve upside down. Interestingly, these ten mutations cause completely different cell malfunctions. We speculate that what these mutations have in common is a reduction in the lifespan of cells and/or an acceleration of the transition to the state of cell senescence. Thus, our analysis, similar to the conclusions of many previously published works, indicates that the aging of an organism is a consequence of the aging of individual cells.

Exploring Patterns of Human Mortality and Aging: A Reliability Theory Viewpoint.

The most important manifestation of aging is an increased risk of death with advancing age, a mortality pattern characterized by empirical regularities known as mortality laws. We highlight three significant ones: the Gompertz law, compensation effect of mortality (CEM), and late-life mortality deceleration and describe new developments in this area. It is predicted that CEM should result in declining relative variability of mortality at older ages. The quiescent phase hypothesis of negligible actuarial aging at younger adult ages is tested and refuted by analyzing mortality of the most recent birth cohorts. To comprehend the aging mechanisms, it is crucial to explain the observed empirical mortality patterns. As an illustrative example of data-directed modeling and the insights it provides, we briefly describe two different reliability models applied to human mortality patterns. The explanation of aging using a reliability theory approach aligns with evolutionary theories of aging, including idea of chronic phenoptosis. This alignment stems from their focus on elucidating the process of organismal deterioration itself, rather than addressing the reasons why organisms are not designed for perpetual existence. This article is a part of a special issue of the journal that commemorates the legacy of the eminent Russian scientist Vladimir Petrovich Skulachev (1935-2023) and his bold ideas about evolution of biological aging and phenoptosis.

Biodegradation of high molecular weight polycyclic aromatic hydrocarbons by Sarocladium terricola strain PYR-233 isolated from petrochemical contaminated sediment.

Polycyclic aromatic hydrocarbons (PAHs) were frequently found in sediment and were primarily treated through microbial degradation. Thus, efficient management of PAH pollution requires exploring the molecular degradation mechanisms of PAHs and expanding the pool of available microbial resources. A fungus (identified as Sarocladium terricola strain RCEF778) with the remarkable ability to degrade pyrene was screened from sediment near a petrochemical plant, and its growth and pyrene degradation characteristics were comprehensively investigated. The results showed that the fungus exhibited great effectiveness in pyrene degradation, with a degradation ratio of 88.97% at 21 days at the conditions: 35 °C, pH 7, 10 mg L-1 initially pyrene concentration, 3% supplementary salt, and glucose supplementation. The generation and concentration variation of the intermediate products were identified, and the results revealed that the fungus degraded pyrene through two pathways: by salicylic acid and by phthalic acid. Three sediments (M1, M2, M3), each exhibiting different levels of PAH pollution, were employed to examine the effectiveness of fungal degradation of PAHs in practical sediment samples. These data showed that with the fungus, the degradation ratios ranged from 13.64% to 23.50% for 2-3 rings PAHs, 40.93%-49.41% for 4 rings PAHs, and 39.59%-48.07% for 5-6 rings PAHs, which were significantly higher than those for the sediment without the fungus and confirmed the excellent performance of the fungal. Moreover, the Gompertz model was employed to analyze the degradation kinetics of 4-rings and 5-6 rings PAHs in these sediments, and the results demonstrated that the addition of the fungus could significantly increase the maximum degradation ratio, degradation start-up rate and maximum degradation rate of 4-rings and 5-6 rings PAHs and shorten the time required to reach the maximum degradation rate. This study not only supplied fungal materials but also established crucial theoretical foundations for the development of bioremediation technologies aimed at high molecular weight PAH-contaminated sediments.

Evaluation of the potential growth and body composition of the Cobb 700 genotype.

1. The potential growth of the chemical and physical components of males and females of the Cobb 700 strain was measured from hatch to 15 weeks of age.2. A four-phase ad libitum feeding programme was used to feed 200 chicks of each sex. All birds were weighed weekly. Ten birds per sex were sampled at 0, 7, 14, 28, 42, 56, 70, 84 and 105 d of age. They were weighed before and after plucking to determine the weight of feathers. Physical parts were measured on defeathered birds, whereafter these components were combined, minced, freeze dried to measure water content, and then analysed for protein, lipid and ash content.3. Mature body weights of males and females averaged 8.38 and 6.94 kg, respectively, mature body protein weights averaged 1.48 and 1.19 kg and mature body lipid contents averaged 1.08 and 1.54 kg, respectively.4. Rates of maturing of the empty feather-free body weights of males and females averaged 0.0417 and 0.0402/d, respectively. All chemical and physical components within a sex, other than feathers, had the same rate of maturing. The rate of maturing of feathers, calculated by iteration, in males was lower than in females (0.0324 vs. 0.0357/d) and the mature weight was higher (435 vs. 372 g).5. The ratios of the chemical components to feather-free body protein at maturity for males and females were, for water, 3.80 and 3.34; for lipid, 0.73 and 1.29; and for ash, 0.13 and 0.19, respectively. Separate equations were required for males and females to describe the allometric relationship between lipid and protein in the feather-free body.6. Mature body weights of broilers in this trial were considerably higher than those measured using the same protocol 28 years ago, whereas rates of maturing have remained the same.

Comparative assessment of growth curves in Brazilian white Morada Nova hair sheep breed.

The Morada Nova sheep breed is essential for the economy of the semi-arid region of Northeast Brazil, standing out for its adaptability, resistance to parasites and reproductive ability. However, the white variant is endangered, highlighting the importance of studies on its productivity to support conservation efforts. This study focuses on the growth curve of the Morada Nova sheep breed, using nonlinear models and analyzing flock profiles. Total of 764 observations of 165 animals from four farms in Ceará and Rio Grande do Norte, Brazil, were analyzed. Canonical discriminant analysis (CDA) was used for the exploratory analysis and four nonlinear models were used to study the growth curve. Weight from birth to 270 days of age, absolute growth rate (AGR), and the impact of sex on growth curves were assessed. Sex and farm are significant discriminating variables (P < 0.05) for the studied effects (weight and age). Weight was the primary phenotypic biomarker that discriminated between the two indicators, while age was a discriminating indicator only for the core effect. The Gompertz model was the most efficient, presenting the lowest residuals and greatest convergence. The study reveals new information about the growth of Morada Nova sheep, the white variety, including weight differences between the sexes at all analyzed ages and an inflection point before 90 days of age. These discoveries contribute to the understanding of the breed's growth and help in the formulation of conservation strategies.

Application of growth models to South African Boer goat castrates and does under feedlot conditions.

Mathematical models may aid researchers in describing biological processes, like growth, in animals. This study aimed to collect the body weight data of 18 Boer goat castrates and 20 Boer goat does, from birth until maturity, to model growth and determine growth trends. This is a novel investigation as sufficient information on an age-weight database for these two Boer goat sexes from birth to maturity, is lacking. Using age-weight data, four nonlinear models, namely the Brody, Gompertz, Logistic and Von Bertalanffy growth models, were plotted and evaluated. The model parameters of each growth model were compared for differences between the two sexes. The statistical effectiveness of fit was determined for each model using AIC and RMSE, with R2 also being considered. All models except the Brody model, predicted significantly heavier mature weights for castrates. The Brody model was deemed unfit to describe Boer goat growth as the function severely over-predict weights from birth until maturity for both sexes. The Von Bertalanffy (R2 = 91.3) and Gompertz functions (R2 = 91.3) showed the best fit for Boer goat castrates, while the Gompertz model (R2 = 95.1) showed the best fit for Boer goat does. The Gompertz function is the preferred model to depict Boer goat growth overall, as it accurately characterized growth of both sexes. According to the Gompertz model the age at which the inflection point of the growth curve was reached, did not differ significantly between castrates and does (141.80 days versus 136.31 days). There was also no significant difference in maturation rate between the two sexes.

In-vitro screening of compatible synbiotics and (introducing) "prophybiotics" as a tool to improve gut health.

Synbiotics have been intensively studied recently to improve gut health of humans and animals. The success of synergistic synbiotics depends on the compatibility of the prebiotic and probiotic components. Certain plant extracts possess both antimicrobial and prebiotic properties representing a potential use in combination with probiotics to improve the gut health. Here, we coined the term "prophybiotics" to describe this combined bioactivity. The current study aimed to select prebiotics that are preferred as an energy source and antimicrobial plant extracts which do not inhibit the growth, of six strains of lactic acid bacteria (LAB namely; Lactiplantibacillus plantarum, Lacticaseibacillus casei, Limosilactobacillus reuteri, Lacticaseibacillus rhamnosus, Leuconostoc mesenteroides, and Pediococcus pentosaceus) in-vitro to identify compatible combinations for potential synbiotic/prophybiotic use, respectively. Their growth kinetics were profiled in the presence of prebiotics: Inulin, Raffinose, and Saccharicterpenin with glucose, as the control, using carbohydrate free MRS broth media. Similarly, their growth kinetics in MRS broth supplemented with turmeric, green tea, and garlic extracts at varying concentrations were profiled. The results revealed the most compatible pairs of prebiotics and LAB. Turmeric and garlic had very little inhibitory effect on the growth of the LAB while green tea inhibited the growth of all LAB in a dose-dependent manner. Therefore, we conclude that turmeric and garlic have broad potential for use in prophybiotics, while the prebiotics studied here have limited use in synbiotics, with these LAB.

An underappreciated peculiarity of late-life human mortality kinetics assessed through the lens of a generalization of the Gompertz-Makeham law.

Much attention in biogerontology is paid to the deceleration of mortality rate increase with age by the end of a species-specific lifespan, e.g. after ca. 90 years in humans. Being analyzed based on the Gompertz law µ(t)=µ0e^γt with its inbuilt linearity of the dependency of lnµ on t, this is commonly assumed to reflect the heterogeneity of populations where the frailer subjects die out earlier thus increasing the proportions of those whose dying out is slower and leading to decreases in the demographic rates of aging. Using Human Mortality Database data related to France, Sweden and Japan in five periods 1920, 1950, 1980, 2018 and 2020 and to the cohorts born in 1920, it is shown by LOESS smoothing of the lnµ-vs-t plots and constructing the first derivatives of the results that the late-life deceleration of the life-table aging rate (LAR) is preceded by an acceleration. It starts at about 65 years and makes LAR at about 85 years to become 30% higher than it was before the acceleration. Thereafter, LAR decreases and reaches the pre-acceleration level at ca. 90 years. This peculiarity cannot be explained by the predominant dying out of frailer subjects at earlier ages. Its plausible explanation may be the acceleration of the biological aging in humans at ages above 65-70 years, which conspicuously coincide with retirement. The decelerated biological aging may therefore contribute to the subsequent late-life LAR deceleration. The biological implications of these findings are discussed in terms of a generalized Gompertz-Makeham law µ(t) = C(t)+µ0e^f(t).

Assessing the Preanalytical Variability of Plasma and Cerebrospinal Fluid Processing and Its Effects on Inflammation-Related Protein Biomarkers.

Proteomics studies are important for the discovery of new biomarkers as clinical tools for diagnosis and disease monitoring. However, preanalytical variations caused by differences in sample handling protocol pose challenges for assessing biomarker reliability and comparability between studies. The purpose of this study was to examine the effects of delayed centrifuging on measured protein levels in plasma and cerebrospinal fluid (CSF). Blood from healthy individuals and patients with multiple sclerosis along with CSF from patients with suspected neurological disorders were left at room temperature for different periods (blood: 1, 24, 48, 72 h; CSF: 1 and 6 h) prior to centrifuging. Ninety-one inflammation-related proteins were analyzed using a proximity extension assay, a high-sensitivity multiplex immunoassay. Additional metabolic and neurology-related markers were also investigated in CSF. In summary, many proteins, particularly in plasma, had increased levels with longer delays in processing likely due in part to intracellular leakage. Levels of caspase 8, interleukin 8, interleukin 18, sirtuin 2, and sulfotransferase 1A1 increased 2-fold to 10-fold in plasma after 24 h at room temperature. Similarly, levels of cathepsin H, ectonucleoside triphosphate diphosphohydrolase 5, and WW domain containing E3 ubiquitin protein ligase 2 differentiated in CSF with <6 h delay in processing. However, the rate of change for many proteins was relatively consistent; therefore, we were able to characterize biomarkers for detecting sample handling variability. Our findings highlight the importance of timely and consistent sample collection and the need for increased awareness of protein susceptibility to sample handling bias. In addition, suggested biomarkers may be used in certain situations to detect and correct for preanalytical variation in future studies.

Pattern and trends of the total and age-specific fertility rates during 1990-2018 in Pakistan.

BACKGROUND: Pakistan has an inadequate vital event registration system, leading to fewer than half of all births being registered, and this issue is further exacerbated by systematic recall errors and omission of births. This study aims to evaluate direct and indirect methods of fertility estimation to analyze the trends and patterns of fertility rates in Pakistan from 1990 to 2018. DESIGN/METHODOLOGY/APPROACH: Indirect methods are utilized in this study to evaluate the direction and extent of changes in total and age-specific fertility rates, and these findings are compared to direct estimates. The study draws data on livebirths from four waves of the Pakistan Demographic and Health Survey that took place between 1990 and 2018. To ensure the quality of data, graphical methods and Whipple and Myers indices are employed. Additionally, the Brass Relational Gompertz model was used to analyze the data. RESULTS: The Relational Gompertz model revealed that total fertility rates (TFRs) were higher than direct estimates by 0.4 children and age-specific fertility rates (ASFR) were higher for all age groups except the oldest. The difference was more significant among younger women aged 15-24, and less so for age groups 29 and above. The gap in estimated fertility between direct and indirect methods decreased with age. CONCLUSION: The indirect method is an invaluable tool in situations where direct measurement of fertility rates is challenging or impossible. By utilizing this method, policymakers can gain important insights into the fertility patterns and trends of a population, which is crucial for making informed decisions on fertility planning.

Defective 3-parameter Gompertz model with frailty term for estimating cure fraction in survival data.

In several survival data, a proportion of units is not susceptible to the event of interest, even if, accompanied by a sufficiently large time, which is so-called immune or cured. In this paper, the defective Gamma 3-parameter Gompertz model with a frailty term is proposed for estimating the cure fraction. This model does not require adding extra parameters for modeling the cure rate, and it accommodates unimodal hazard shapes as well as monotone hazards. A simulation study has been carried out to assess the performance of the maximum likelihood estimators. The model was applied to two real data sets.

Kinetics of dye decolorization using heterogeneous catalytic system with immobilized Achromobacter xylosoxidans DDB6.

Textile effluents containing toxic dyes must be treated effectively before discharge to prevent adverse environmental impacts. Traditional physical and chemical treatment methods are costly and generate secondary pollutants. In contrast, biological treatment is a more suitable, clean, versatile, eco-friendly, and cost-effective technique for treating textile effluent. It is well established that indigenous microbial populations present in effluents can effectively degrade toxic dyes. In this regard, Achromobacter xylosoxidans DDB6 was isolated from the effluent sample to decolorize crystal violet (CV), Coomassie brilliant blue (CBB), and alizarin red (AR) by 67.20%, 28.58%, and 20.41%, respectively. The growth parameters of A. xylosoxidans DDB6 in media supplemented with 100 ppm of various dyes were determined using the modified Gompertz growth model. The immobilized cells in calcium alginate beads showed apparent decolorization rate constant of 0.27, 0.18, and 0.13 h-1 for CV, CBB, and AR, respectively. The immobilized cells in a packed bed reactor with an optimum flow rate of 0.5 mL/min were used to treat 100 ppm of CV with a percentage decolorization of 79.47% after three cycles. Based on the findings, A. xylosoxidans DDB6 could be effectively used for decolorization of various dyes.

A systematic review of estimation of growth curve in goats.

Growth is an economically important trait in animal production industry and is one of the subjects that can be justified mathematically. The literature recommends different non-linear model to estimate the growth of goats. The objective of this study was to systematically review the literature published on estimation of growth using non-linear models in goats. Databases such as Google Scholar, PubMed, ScienceDirect, and Web of Science were evaluated systematically using the combination of the following key terms: Non-linear growth curve models such as Brody, Richards, Gompertz, Von Bertalanffy, Logistic models. A total of 25 eligible articles were found published between 2008 and 2022 in Bangladesh, Brazil, China, Egypt, Germany, India, Indonesia, Iran, Pakistan, South Africa, Turkey, Tunisia, and Vietnam. The results showed that out of 25 articles, Gompertz growth curve model was the most used (n = 10), followed by Logistic (n = 8), then Brody growth curve model (n = 6). The findings further indicated that Janoscheck growth curve model was the least used model (n = 1) for estimation of growth in goats. One of the limitations is that some of the reviewed articles did not indicate the sex of the animals which make it difficult to draw the conclude for sexes. The systematic review concludes that Gompertz growth curve model is the most recommended for estimation of growth parameters of goats, followed by Logistic, and then Brody. Therefore, researchers should consider using these models when studying growth parameters of goats.

On the Kaniadakis Distributions Applied in Statistical Physics and Natural Sciences.

Constitutive relations are fundamental and essential to characterize physical systems. By utilizing the κ-deformed functions, some constitutive relations are generalized. We here show some applications of the Kaniadakis distributions, based on the inverse hyperbolic sine function, to some topics belonging to the realm of statistical physics and natural science.

Drewnowski's index to measure lifespan variation: Revisiting the Gini coefficient of the life table.

The Gini coefficient of the life table is a concentration index that provides information on lifespan variation. Originally proposed by economists to measure income and wealth inequalities, it has been widely used in population studies to investigate variation in ages at death. We focus on the complement of the Gini coefficient, Drewnowski's index, which is a measure of equality. We study its mathematical properties and analyze how changes over time relate to changes in life expectancy. Further, we identify the threshold age below which mortality improvements are translated into decreasing lifespan variation and above which these improvements translate into increasing lifespan inequality. We illustrate our theoretical findings simulating scenarios of mortality improvement in the Gompertz model, and showing an example of application to Swedish life table data. Our experiments demonstrate how Drewnowski's index can serve as an indicator of the shape of mortality patterns. These properties, along with our analytical findings, support studying lifespan variation alongside life expectancy trends in multiple species.

The curse of the plateau. Measuring confidence in human mortality estimates at extreme ages.

In recent years, the importance of describing mortality at the limits of the life span has led to a number of relevant and controversial studies. Whereas considerable efforts have been devoted to collecting data and estimating models on the oldest-old individuals, the testing of statistical confidence about the conclusions of analyses at extreme ages has been largely neglected. How certain can we be in saying that the risk of dying increases, levels out, or, paradoxically, decreases over age 105? Can we recognize particular mortality age patterns at such high ages? In this paper, it is shown that very little can be confidently asserted about mortality at extreme ages. Instead of analyzing actual data, we perform a series of simulation studies mimicking actual scenarios from controlled mechanisms. Our findings are thus robust with respect to factors such as particular observation schemes, heterogeneity, and data quality issues. Given the sample sizes currently available and the levels of mortality experienced in present populations, we show that before age 110, only a Gompertzian increase of mortality may be detected. Afterwards a plateau will be regularly recognized as the most suitable pattern, regardless of the complexity of the true underlying mortality.

Parameter identifiability and model selection for sigmoid population growth models.

Sigmoid growth models, such as the logistic, Gompertz and Richards' models, are widely used to study population dynamics ranging from microscopic populations of cancer cells, to continental-scale human populations. Fundamental questions about model selection and parameter estimation are critical if these models are to be used to make practical inferences. However, the question of parameter identifiability - whether a data set contains sufficient information to give unique or sufficiently precise parameter estimates - is often overlooked. We use a profile-likelihood approach to explore practical parameter identifiability using data describing the re-growth of hard coral. With this approach, we explore the relationship between parameter identifiability and model misspecification, finding that the logistic growth model does not suffer identifiability issues for the type of data we consider whereas the Gompertz and Richards' models encounter practical non-identifiability issues. This analysis of parameter identifiability and model selection is important because different growth models are in biological modelling without necessarily considering whether parameters are identifiable. Standard practices that do not consider parameter identifiability can lead to unreliable or imprecise parameter estimates and potentially misleading mechanistic interpretations. For example, using the Gompertz model, the estimate of the time scale of coral re-growth is 625 days when we estimate the initial density from the data, whereas it is 1429 days using a more standard approach where variability in the initial density is ignored. While tools developed here focus on three standard sigmoid growth models only, our theoretical developments are applicable to any sigmoid growth model and any appropriate data set. MATLAB implementations of all software are available on GitHub.