Rate constant prediction
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Here, we report the data visualization, analysis and modeling for a large set of 4830 SN 2 reactions the rate constant of which (logk) was measured at different experimental conditions (solvent, temperature). The reactions were encoded by one single molecular graph - Condensed Graph of Reactions, which allowed us to use conventional chemoinformatics techniques developed for individual molecules. Thus, Matched Reaction Pairs approach was suggested and used for the analyses of substituents effects on the substrates and nucleophiles reactivity. The data were visualized with the help of the Generative Topographic Mapping approach. Consensus Support Vector Regression (SVR) model for the rate constant was prepared. Unbiased estimation of the model's performance was made in cross-validation on reactions measured on unique structural transformations. The model's performance in cross-validation (RMSE=0.61 logk units) and on the external test set (RMSE=0.80) is close to the noise in data. Performances of the local models obtained for selected subsets of reactions proceeding in particular solvents or with particular type of nucleophiles were similar to that of the model built on the entire set. Finally, four different definitions of model's applicability domains for reactions were examined.
The pancreas, liver and hypothalamus have a regulatory function in the glucose homeostasis. As the blood glucose level changes, these compartments react and the level changes again. Subsequently to this reaction, the interstitial glucose level changes with some delay. In this paper, I propose a hypothesis that the change of the blood glucose level includes information about the estimated rate with which the hypothalamus expects the blood glucose level to return to normal range, by means of regulatory mechanisms of glucose homeostasis. As the interstitial glucose level change reflects the blood glucose level change, I propose a method to estimate the blood-to-interstitial glucose level delay. It is an important factor for glucose level prediction. Once the delay was calculated, it was possible to relate the present blood glucose level and future interstitial glucose level with such coefficients, which do not seem to change over the time of the experiment to a significant extent. Perhaps, it is a parameterization of regulatory processes of glucose homeostasis, which could be possibly encoded within hypothalamus set-points. The delays were constant per subject and ranged from 7 min up to 34 min for hereditary hypertriglyceridemic rats of 230-480 g weight, in experiments with a variable glucose infusion rate.
- MeSH
- biologické modely MeSH
- extracelulární tekutina metabolismus MeSH
- homeostáza fyziologie MeSH
- hypertriglyceridemie krev MeSH
- hypothalamus metabolismus MeSH
- játra metabolismus MeSH
- krevní glukóza metabolismus fyziologie MeSH
- krysa rodu rattus MeSH
- monitorování fyziologických funkcí MeSH
- pankreas metabolismus MeSH
- reakční čas MeSH
- zvířata MeSH
- Check Tag
- krysa rodu rattus MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
This study suggests an approach for the comparison and evaluation of particular compartments with modest experimental setup costs. A glucose level prediction model was used to evaluate the compartment's glucose transport rate across the blood capillary membrane and the glucose utilization rate by the cells. The glucose levels of the blood, subcutaneous tissue, skeletal muscle tissue, and visceral fat were obtained in experiments conducted on hereditary hypertriglyceridemic rats. After the blood glucose level had undergone a rapid change, the experimenter attempted to reach a steady blood glucose level by manually correcting the glucose infusion rate and maintaining a constant insulin infusion rate. The interstitial fluid glucose levels of subcutaneous tissue, skeletal muscle tissue, and visceral fat were evaluated to determine the reaction delay compared with the change in the blood glucose level, the interstitial fluid glucose level predictability, the blood capillary permeability, the effect of the concentration gradient, and the glucose utilization rate. Based on these data, the glucose transport rate across the capillary membrane and the utilization rate in a particular tissue were determined. The rates obtained were successfully verified against positron emission tomography experiments. The subcutaneous tissue exhibits the lowest and the most predictable glucose utilization rate, whereas the skeletal muscle tissue has the greatest glucose utilization rate. In contrast, the visceral fat is the least predictable and has the shortest reaction delay compared with the change in the blood glucose level. The reaction delays obtained for the subcutaneous tissue and skeletal muscle tissue were found to be approximately equal using a metric based on the time required to reach half of the increase in the interstitial fluid glucose level.
- MeSH
- glukosa analýza metabolismus MeSH
- hypertriglyceridemie MeSH
- kapilární permeabilita fyziologie MeSH
- kosterní svaly metabolismus MeSH
- krevní glukóza analýza metabolismus MeSH
- krysa rodu rattus MeSH
- nitrobřišní tuk metabolismus MeSH
- podkožní tuk metabolismus MeSH
- statistické modely MeSH
- zvířata MeSH
- Check Tag
- krysa rodu rattus MeSH
- mužské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
Non-invasive methods of determination of baroreflex sensitivity (BRS, ms/mmHg) are based on beat-to-beat systolic blood pressure and inter-beat interval recording. Sequential methods and spectral methods at spontaneous breathing include transient superposition of breathing and 0.1 Hz rhythms. Previously, a cross-spectral method of analysis was used, at constant breathing rate using a metronome set at 0.33 Hz, enabling separate determination of BRS at 0.1 Hz (BRS0.1Hz) and respiratory rhythms (BRS0.33Hz). The aim of the present study was to evaluate the role of breathing in the spectral method of BRS determination with respect to age and hypertension. Such information would be important in evaluation of BRS at pathological conditions associated with extremely low BRS levels. Blood pressure was recorded by Finapres (5 minutes, controlled breathing at 0.33 Hz) in 118 healthy young subjects (YS: mean age 21.0±1.3 years), 26 hypertensive patients (HT: mean age 48.6±10.3 years) with 26 age-matched controls (CHT: mean age 46.3±8.6 years). A comparison of BRS0.1Hz and BRS0.33Hz was made. Statistically significant correlations were found between BRS0.1Hz and BRS0.33Hz in all groups: YS: r=0.52, p<0.01, HT: r=0.47, p<0.05, and CHT: r=0.70, p<0.01. The regression equations indicated the existence of a breathing-dependent component unrelated to BRS (YS: BRS0.33Hz=2.63+1.14*BRS0.1Hz; HT: BRS0.33Hz=3.19+0.91*BRS0.1Hz; and CHT: BRS0.33Hz=1.88+ +1.01*BRS0.1Hz; differences between the slopes and the slope of identity line were insignificant). The ratios of BRS0.1Hz to BRS0.33Hz were significantly lower than 1 (p<0.01) in all groups (YS: 0.876±0.419, HT: 0.628±0.278, and CHT: 0.782±0.260). Thus, BRS evaluated at the breathing rate overestimates the real baroreflex sensitivity. This is more pronounced at low values of BRS, which is more important in patients with pathologic low BRS. For diagnostic purposes we recommend the evaluation of BRS at the frequency of 0.1 Hz using metronome-controlled breathing at a frequency that is substantially higher than 0.1 Hz and is not a multiple of 0.1 Hz to eliminate respiratory baroreflexnon- related influence and resonance effect on heart rate fluctuations.
- MeSH
- baroreflex MeSH
- časové faktory MeSH
- dospělí MeSH
- financování organizované MeSH
- hypertenze patofyziologie MeSH
- krevní tlak MeSH
- lidé středního věku MeSH
- lidé MeSH
- mechanika dýchání MeSH
- měření krevního tlaku metody MeSH
- mladý dospělý MeSH
- modely kardiovaskulární MeSH
- prediktivní hodnota testů MeSH
- srdeční frekvence MeSH
- věkové faktory MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mladý dospělý MeSH
- Publikační typ
- srovnávací studie MeSH
An increase in the global health burden of temperature was projected for 459 locations in 28 countries worldwide under four representative concentration pathway scenarios until 2099. We determined that the amount of temperature increase for each 100 ppm increase in global CO2 concentrations is nearly constant, regardless of climate scenarios. The overall average temperature increase during 2010-2099 is largest in Canada (1.16 °C/100 ppm) and Finland (1.14 °C/100 ppm), while it is smallest in Ireland (0.62 °C/100 ppm) and Argentina (0.63 °C/100 ppm). In addition, for each 1 °C temperature increase, the amount of excess mortality is increased largely in tropical countries such as Vietnam (10.34%p/°C) and the Philippines (8.18%p/°C), while it is decreased in Ireland (-0.92%p/°C) and Australia (-0.32%p/°C). To understand the regional variability in temperature increase and mortality, we performed a regression-based modeling. We observed that the projected temperature increase is highly correlated with daily temperature range at the location and vulnerability to temperature increase is affected by health expenditure, and proportions of obese and elderly population.
- MeSH
- celosvětové zdraví * MeSH
- globální oteplování * MeSH
- lidé MeSH
- mortalita trendy MeSH
- předpověď MeSH
- teplota MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
In epidemiology, it is very important to estimate the baseline incidence of infectious diseases, but the available data are often subject to outliers due to epidemic outbreaks. Consequently, the estimate of the baseline incidence is biased and so is the predicted epidemic threshold which is a crucial reference indicator used to suspect and detect an epidemic outbreak. Another problem is that the "usual" incidence varies in a season dependent manner, i.e. it may not be constant throughout the year, is often periodic, and may also show a trend between years. To take account of these factors, more complicated models adjusted for outliers are used. If not adjusted for outliers, the baseline incidence estimate is biased. As a result, the epidemic threshold can be overestimated and thus can make the detection of an epidemic outbreak more difficult. Classical Serfling's model is based on the sine function with a phase shift and amplitude. Multiple approaches are applied to model the long-term and seasonal trends. Nevertheless, none of them controls for the effect of epidemic outbreaks. The present article deals with the adjustment of the data biased by epidemic outbreaks. Some models adjusted for outliers, i.e. for the effect of epidemic outbreaks, are presented. A possible option is to remove the epidemic weeks from the analysis, but consequently, in some calendar weeks, data will only be available for a small number of years. Furthermore, the detection of an epidemic outbreak by experts (epidemiologists and microbiologists) will be compared with that in various models.
1. Accurately measuring the rate of spread for expanding populations is important for reliably predicting their future spread, as well as for evaluating the effect of different conditions and management activities on that rate of spread. 2. Although a number of methods have been developed for such measurement, all these are designed only for one- or two-dimensional spread. Species dispersing along rivers, however, require specific methods due to the distinctly branching structure of river networks. 3. In this study, we analyse data regarding Eurasian beavers' modern recolonization of the Czech Republic. We developed a new methodology for quantifying spread of species dispersing along streams based on representation of the river network by means of a weighted graph. 4. We defined two different network-based spread rate measures, one estimating the rate of range expansion, with the range defined as the total length of occupied streams, and the second, named range diameter, quantifying the progress along one or several main streams. In addition, we estimated the population growth rates, and, dividing the population size by the range size, we measured the density of beaver records within their overall range. Using linear regression, we compared four beaver populations under different environmental conditions in terms of each of these measures. Finally, we discuss the differences between our method and the classical approaches. 5. Our method provided substantially higher spread rate values than did the classical methods. Both population growth and range expansion were found to follow logistic growth. In cases of there being no considerable barriers in dispersal routes, the rate of progress along main streams did not differ significantly among populations. In homogeneous environments, population densities remained relatively constant over time even though overall population sizes increased. This indicates that at large spatial scales, the population growth of beavers occurs through progressive space filling rather than increasing population density.
- MeSH
- hlodavci fyziologie MeSH
- hustota populace MeSH
- populační růst MeSH
- řeky * MeSH
- rozšíření zvířat * MeSH
- zachování přírodních zdrojů * MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Česká republika MeSH
The niche-filling process predicted by the "ecological opportunity" (EO) model is an often-invoked mechanism for generating exceptional diversity in island colonizers. Whether the same process governs lineage accumulation and trait disparity during continental colonization events is less clear. Here, we test this prediction by investigating the rate dynamics and trait evolution of one of Africa's most widespread amphibian colonizers, the true toads (Bufonidae). By reconstructing the most complete molecular phylogeny of African Bufonidae to date, we find that the diversification of lineages in Africa best conforms to a constant rate model throughout time and across subclades, with little support for EO. Evolutionary rates of life-history traits have similarly been constant over time. However, an analysis of generalists and specialists showed a shift toward higher speciation rates associated with habitat specialization. The overall lack of EO signal can be interpreted in a number of ways and we propose several explanations. Firstly, methodological issues might preclude the detection of EO. Secondly, colonizers might not experience true EO conditions and due to the size, ecological heterogeneity and age of landmasses, the diversification processes might be more complex. Thirdly, lower speciation rates of habitat generalists may have affected overall proliferation of lineages.
- MeSH
- biodiverzita * MeSH
- fylogeneze * MeSH
- ovum fyziologie MeSH
- ropuchy klasifikace genetika fyziologie MeSH
- rozmnožování MeSH
- sekvenční analýza DNA MeSH
- velikost těla MeSH
- vznik druhů (genetika) * MeSH
- zvířata MeSH
- zvláštnosti životní historie * MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
Identifying the fouling degree of a membrane bioreactor (MBR) provides guidance on the determination of suitable membrane cleaning methods. There is still a lack of knowledge on the effects of powdered activated carbon (PAC) refresh ratio on the MBR fouling mechanism. Major fouling mechanisms of an MBR with constant flow rate at different PAC replenishment ratios were investigated by individual and combined mechanistic fouling models. The root mean square errors were employed to assess the prediction accuracy of the used fouling models. The combined models showed better prediction. The cake-complete model provided far better fits of the transmembrane pressure data, and provided good fits of other individual model predictions regardless of the PAC refreshment ratio. Fourier transform infrared spectroscopy, scanning electron microscopy and energy dispersive X-ray spectroscopy confirmed that the cake layer clogging was the main fouling mechanism followed by complete blockage and standard plugging. The cake-complete model may be used to predict the fouling mechanisms in PAC/MBR systems.
PURPOSE: To present a new model for describing drug dissolution. On the basis of the new model to characterize the dissolution profile by the distribution function of the random dissolution time of a drug molecule, which generalizes the classical first order model. METHODS: Instead of assuming a constant fractional dissolution rate, as in the classical model, it is considered that the fractional dissolution rate is a decreasing function of the dissolved amount controlled by the dose-solubility ratio. The differential equation derived from this assumption is solved and the distribution measures (half-dissolution time, mean dissolution time, relative dispersion of the dissolution time, dissolution time density, and fractional dissolution rate) are calculated. Finally, instead of monotonically decreasing the fractional dissolution rate, a generalization resulting in zero dissolution rate at time origin is introduced. RESULTS: The behavior of the model is divided into two regions defined by q, the ratio of the dose to the solubility level: q < 1 (complete dissolution of the dose, dissolution time) and q > 1 (saturation of the solution, saturation time). The singular case q = 1 is also treated and in this situation the mean as well as the relative dispersion of the dissolution time increase to infinity. The model was successfully fitted to data (1). CONCLUSIONS: This empirical model is descriptive without detailed physical reasoning behind its derivation. According to the model, the mean dissolution time is affected by the dose-solubility ratio. Although this prediction appears to be in accordance with preliminary application, further validation based on more suitable experimental data is required.
