Calibration of nanowatt isothermal titration calorimeters with overflow reaction vessels

Obtaining accurate results with nanowatt titration calorimeters with overflow cells requires mass calibration of the buret injection volume, chemical calibration of the reaction vessel effective volume, and chemical calibration of the calorimetric factor used to convert the measured electrical signal to heat rate. Potential errors in electrical calibration of power compensation calorimeters require validation of the calorimetric factor with chemical reactions with accurately known stoichiometries and enthalpy changes. The effective volume of the reaction vessel can be determined from the endpoint of a quantitative reaction with known stoichiometries. Methods for calibration and potential calibration errors to be avoided are described. Publication of results obtained must include data on calibrations and sufficient raw data to assess precision and accuracy of the results.     

Effects of changes in the driving forces on water quality and plankton dynamics in three Swiss lakes – long‐term simulations with BELAMO

1. With a modified version of the lake model BELAMO, we were able to describe the essential features of the dynamics of nutrients, dissolved oxygen, phyto‐ and zooplankton in three lakes of different trophic status over periods of 19–30 years, with essentially the same model parameters for all three lakes. This is remarkable, as the measured nutrient inputs decreased considerably during the simulated time period. 2. Despite having done this before for a period of 4 years with an earlier version of the model, a considerable effort was required that led to a series of model modifications without which the data could not be matched. This demonstrates that long‐term calibration of a model that combines processes in the water column with mineralisation in the sediment can be difficult. 3. Due to the necessarily simplified processes within the model, there is a bias in its output. We applied a recently developed technique for model calibration and uncertainty analysis to address bias and multiple calibration criteria. To account for the demanding long‐term simulations, a simplified numerical implementation of this technique was used. 4. Our results demonstrate good understanding of the chemical state of the lake during the calibration period but less of the biological variables. The credibility intervals used to visualise this knowledge widen substantially during the prediction period (consisting of the last 10 years of the simulation). 5. The joint calibration of the model with long‐term data from lakes of different trophic status is possible but only with considerable prediction uncertainty. Due to the explicit consideration of bias in our calibration technique, we are able to estimate quantitatively the uncertainty of our knowledge about chemical and biological variables in the lake.     

Finite element analysis of bone remodelling with piezoelectric effects using an open-source framework

Bone tissue exhibits piezoelectric properties and thus is capable of transforming mechanical stress into electrical potential. Piezoelectricity has been shown to play a vital role in bone adaptation and remodelling processes. Therefore, to better understand the interplay between mechanical and electrical stimulation during these processes, strain-adaptive bone remodelling models without and with considering the piezoelectric effect were simulated using the Python-based open-source software framework. To discretise numerical attributes, the finite element method (FEM) was used for the spatial variables and an explicit Euler scheme for the temporal derivatives. The predicted bone apparent density distributions were qualitatively and quantitatively evaluated against the radiographic scan of a human proximal femur and the bone apparent density calculated using a bone mineral density (BMD) calibration phantom, respectively. Additionally, the effect of the initial bone density on the resulting predicted density distribution was investigated globally and locally. The simulation results showed that the electrically stimulated bone surface enhanced bone deposition and these are in good agreement with previous findings from the literature. Moreover, mechanical stimuli due to daily physical activities could be supported by therapeutic electrical stimulation to reduce bone loss in case of physical impairment or osteoporosis. The bone remodelling algorithm implemented using an open-source software framework facilitates easy accessibility and reproducibility of finite element analysis made.

     

Left/right,up/down: the role of endogenous electrical fields as directional signals in development,repair and invasion

A fundamental aspect of biological systems is their spatial organization. In development, regeneration and repair, directional signals are necessary for the proper placement of the components of the organism. Likewise, pathogens that invade other organisms rely on directional signals to target vulnerable areas. It is widely understood that chemical gradients are important directional signals in living systems. Less well recognized are electrical fields, which can also provide directional information. Small, steady electrical fields can directly guide cell movement and growth and can generate chemical gradients of charged macromolecules against the leveling action of diffusion. At the site of a lesion in an ion-transporting epithelium, for example, a substantial electrical field is instantly generated and may extend over many cell diameters. There are numerous other situations in which relatively long-range electrical fields have been shown to exist naturally. Recently, there has been substantial progress in identifying specific processes that are controlled, to some extent, by these endogenous electrical fields. This review highlights these recent data and discusses possible mechanisms by which the fields might affect biological processes.     

Development of a large-scale biocalorimeter to monitor and control bioprocesses

Calorimetry has shown real potential at bench-scale for chemical and biochemical processes. The aim of this work was therefore to scale-up the system by adaptation of a standard commercially available 300-L pilot-scale bioreactor. To achieve this, all heat flows entering or leaving the bioreactor were identified and the necessary instrumentation implemented to enable on-line monitoring and dynamic heat balance estimation. Providing that the signals are sufficiently precise, such a heat balance would enable calculation of the heat released or taken up during an operational (bio)process. Two electrical Wattmeters were developed, the first for determination of the power consumption by the stirrer motor and the second for determination of the power released by an internal calibration heater. Experiments were designed to optimize the temperature controller of the bioreactor such that it was sufficiently rapid so as to enable the heat accumulation terms to be neglected. Further calibration experiments were designed to correlate the measured stirring power to frictional heat losses of the stirrer into the reaction mass. This allows the quantitative measurement of all background heat flows and the on-line quantitative calculation of the (bio)process power. Three test fermentations were then performed with B. sphaericus 1593M, a spore-forming bacterium pathogenic to mosquitoes. A first batch culture was performed on a complex medium, to enable optimization of the calorimeter system. A second batch culture, on defined medium containing three carbon sources, was used to show the fast, accurate response of the heat signal and the ability to perfectly monitor the different growth phases associated with growth on mixed substrates, in particular when carbon sources became depleted. A maximum heat output of 1100 W was measured at the end of the log-phase. A fed-batch culture on the same defined medium was then carried out with the feed rate controlled as a function of the calorimeter signal. A maximum heat output of 2250 W was measured at the end of the first log-phase. This work demonstrates that real-time quantitative calorimetry is not only possible at pilot-scale, but could be readily applied at even larger scales. The technique requires simple, readily available devices for determination of the few necessary heat flows, making it a robust, cost-effective technique for process development and routine monitoring and control of production processes.     

PSysCal: a parallel tool for calibration of ecosystem models

The methods used for ecosystem modelling are generally based on differential equations. Nowadays, new computational models based on concurrent processing of multiple agents (multi-agents) or the simulation of biological processes with the Population Dynamic P-System models (PDPs) are gaining importance. These models have significant advantages over traditional models, such as high computational efficiency, modularity and its ability to model the interaction between different biological processes which operate concurrently. By this, they are becoming useful for simulating complex dynamic ecosystems, untreatable with classical techniques. On the other hand, the main counterpart of P-System models is the need for calibration. The model parameters represent the field measurements taken by experts. However, the exact values of some of these parameters are unknown and experts define a numerical interval of possible values. Therefore, it is necessary to perform a calibration process to fit the best value of each interval. When the number of unknown parameters increases, the calibration process becomes computationally complex and storage requirements increase significantly. In this paper, we present a parallel tool (PSysCal) for calibrating next generation PDP models. The results shown that the calibration time is reduced exponentially with the amount of computational resources. However, the complexity of the calibration process and a limitation in the number of available computational resources make the calibration process intractable for large models. To solve this, we propose a heuristic technique (PSysCal+H). The results show that this technique significantly reduces the computational cost, it being practical for solving large model instances even with limited computational resources.     

Calibrating Ellenberg indicator values for moisture,acidity, nutrient availability and salinity in the Netherlands

A general calibration of Ellenberg indicator values for moisture, acidity, nutrient availability and salinity was carried out on a large database of relevées and environmental variables from a variety of ecosystems in the Netherlands.Satisfying relationships with Ellenberg indicator values for moisture, acidity and salinity were found for mean groundwater level in spring time, soil pH and chloride concentration in groundwater. For mean groundwater level in spring and chloride concentration in groundwater subdivision of the database led to clearer relationships with indicator values. For the Ellenberg indicator value for nutrient availability satisfying calibration results were only achieved with data on standing crops and N stock in standing crop. The relationship with soil chemical variables was less clear.Although the correlation between indicator and measured values is obvious, the variation around the regression lines is considerable. However, because of the size and composition of the database, it is unlikely that our calibration results can be much improved by adding more (Dutch) data.The calibration results will be applied in the multi-stress model SMART-MOVE, developed to predict changes in species composition due to acidification, eutrophication and the effects of lowering groundwater.     

The flux-force relations across complex membranes with active transport

Equations are derived for the total material flux, and the total electric current flux, across a complex membrane system with active transport. The equations describe the fluxes as linear functions of forces across the system, and specifically of electrical potential, hydrostatic pressure, chemical potentials, and active transport rates. The equations can be simplified for experimental studies by making one or more of the forces equal to zero. The osmotic pressure difference across a membrane system is shown to be a function of the electrical potential and chemical potential differences and of the active transport rates. The transmembrane potential is shown to be the sum of a diffusion potential and an active transport potential. A simple equation is derived describing the current across a membrane as a linear function of the electrical potential and the active transport rate. Specific examples of the application of the equations to nerve membrane potentials are considered.     

Pattern-oriented modelling: a 'multi-scope' for predictive systems ecology

Modern ecology recognizes that modelling systems across scales and at multiple levels-especially to link population and ecosystem dynamics to individual adaptive behaviour-is essential for making the science predictive. 'Pattern-oriented modelling' (POM) is a strategy for doing just this. POM is the multi-criteria design, selection and calibration of models of complex systems. POM starts with identifying a set of patterns observed at multiple scales and levels that characterize a system with respect to the particular problem being modelled; a model from which the patterns emerge should contain the right mechanisms to address the problem. These patterns are then used to (i) determine what scales, entities, variables and processes the model needs, (ii) test and select submodels to represent key low-level processes such as adaptive behaviour, and (iii) find useful parameter values during calibration. Patterns are already often used in these ways, but a mini-review of applications of POM confirms that making the selection and use of patterns more explicit and rigorous can facilitate the development of models with the right level of complexity to understand ecological systems and predict their response to novel conditions.     

Development and calibration of bio-kinetic model for surfactant biodegradation with combined respirometric and titrimetric measurements

Substrate removal mechanism in aerobic activated sludge processes was lately modeled using the simultaneous storage and growth (SSAG) phenomenon. The SSAG model was further refined with titrimetric components and successfully calibrated using both respirometric and titrimetric measurements for common substrate acetate. However, the improved SSAG model calibration was not verified with other organic substrates. Furthermore, very few studies are available in the literature on surfactant bio-kinetics, which generally use off-line experimental measurements with limited model-based interpretation. Therefore, the aim of this paper is to demonstrate its applicability for surfactant biodegradation using on-line measurements. Batch experiments were conducted using sodium dodecyl sulfate (SDS) as a test surfactant. Model calibration was done successfully for three different SDS concentrations using respirometric, titrimetric and combined respirometric-titrimetric measurement approaches. The parameter estimation results from all three stated combinations were statistically evaluated and found to be very close validating the model.     

Ionic permeabilities of an Aplysia giant neuron.

In a giant neuron of Aplysia californica, permeabilities and conductances obtained by measuring net fluxes of Na+, K+ and Cl- with ion-specific microelectrodes were compared with those obtained by measuring transmembrane current and potential changes when the three ions were varied in the external solution. Net fluxes were measured with ion-specific microelectrodes, after blocking metabolic processes, thus allowing movement of ions down their electrochemical gradients. Permeabilities and conductances obtained from the "chemical" measurements (i.e., ion-specific electrodes) were generally comparable to the values obtained from "electrical" measurements. Where discrepancies occurred, they could be explained by showing that some of the assumptions necessary to use the "electrical" method were not quantitatively true in this system. The absolute magnitudes of the permeabilities are significantly less than those found in many axonal preparations. There is also a relatively high PNa/PK ratio. The selectivity of the membrane against ions such as Tris+ and MeSO3 is not good, Tris+ being nearly as permeable as Na+ and MeSO3 about one-half as permeable as Cl-. These properties may be characteristic of somal membranes.     

Tracer flow, permeability, and partial conductance.

It is often not possible to evaluate a permeability coefficient for net flow P from the small flows produced by physiological gradients of concentration or electrical potential. The common use of a tracer permeability coefficient P-x for this purpose, under the assumption that P-x = P, requires that the species be transported passively, and that there be no significant coupling between its flow and that of other chemical species, and between the flows of its tracer and abundant isotopes (isotope interaction). These conditions are often not satisfied. However, for passive transport in the absence of coupling of flows of different chemical species the measurement of tracer flow at two values of electrical potential difference evaluates (P-x/P) and thus P. In the presence of coupling of flows of different chemical species, although these measurements no longer evaluate P, they evaluate the partial conductance G. A graphical method of evaluating (p-x/P), P, and G is presented.     

Glial cells of the crayfish and their relationships with neurons. An ultrastructural study

1. Glial cells of the crayfish abdominal ganglia have been studied by transmission electron microscopy. Special attention is paid to the interrelationships between neurons and glial cells. Covers and hemocyte-related elements have also been considered. 2. Glial cells are identified by a common ultrastructure and close relationships with neurons. Four glial classes are considered, depending on their morphology, the compartment of neurons they ensheathe and neuron-glia interface. 3. Four ultrastructural classes of neurons are proposed. They differ in geometry and ultrastructure, as well as in glial covers (complexity and evaginations into the neuron somata). The morphology and organization of glial covers is specific for the neuron type they ensheathe. Specific glial covers do not differ in glia-glia communicatory structures. 4. The morphological and metabolical compartments of neurons are separated from the extracellular matrix or blood by specific glial systems. A system of two cells is interposed between neuron somata and hemolymph or the extracellular matrix. 5. Glial processes are crossed by membraneous tubular systems, at neuron perikarya and axons. Frequent gap junctions of varying area, density and number of IMP are found in the covers of neuron somata. 6. Neuron-glia interface bears numerous communicatory structures for both ionic and macromolecular exchange. They include junctions and transient modifications of membranes. Some of them suggest active transport mechanisms. 7. Modified endocytotic mechanisms seem to be responsible for the glia-to-neuron transfer of macromolecules as well as for the neuron-to-glia transfer of lamellar bodies. 8. The neuropil is divided into glomeruli (electrical or chemical) by glial processes and the trabeculae of the extracellular dense matrix. Neuron-glia membrane appositions have been found in electrical glomeruli. In chemical glomeruli, dense cored vesicles can release their content at neuron-neuron or neuron-glia intercellular cleft, at non-synaptic loci. 9. Neurons of type II contain peripheral complex Golgi systems, associated to subsurface cisternae and neuron-glia gap junctions, suggesting a cooperation of glial cells in specific macromolecular synthesis.     

Microfluidic devices for studying chemotaxis and electrotaxis

Directed cell migration plays important roles in physiological processes such as host defense, wound healing, cancer metastasis and embryogenesis. Many organisms are capable of directional migration, which can be guided by diverse cellular factors including chemical and electrical cues. Recently, microfluidic devices that consist of small channels with micrometer dimensions are being developed for cell migration studies. These devices can precisely configure and flexibly manipulate chemical concentration gradients and electric fields, and thus can be used to study the complex guiding mechanisms for cell migration. In this paper we highlight recent applications of microfluidic devices for cell migration research, with a focus on electric field-directed cell migration, to provide important and timely updates of this rapidly developing research field.     

Weighted least squares in calibration: the problem with using "quality coefficients" to select weighting formulas

The quality coefficient (Q) has frequently been used to select weighting formulae in calibration, and especially so in bioanalytical work, where there has been increasing awareness of the importance of data heteroscedasticity in recent years. However, this quantity is statistically flawed and should not be used for this purpose. The quality coefficient is computed from the differences between the apparent and true concentrations of the calibration samples as obtained from the least-squares calibration fit. Q is defined as the sum of either the squares or the absolute values of these differences, taken directly or as percentage (relative) deviations. It is calculated for several different trial weighting formulae, and the lowest Q value is then deemed to identify the best weighting choice. However, these Qs are predisposed to favor data consistent with their definitions-homoscedastic data for tests employing absolute differences, and data having proportional error (constant coefficient of variance) for tests using relative differences-because the Q in each case closely resembles the quantity actually minimized by the least-squares fit of the calibration data. The problem is examined and illustrated through Monte Carlo computations on data having either constant or proportional uncertainty and subjected to both tests. A modified Q based on the results of both the absolute and relative tests is much more reliable than either test alone but is still not recommended as a solution to the weighting problem, as other, statistically sound approaches are available and readily used.     

A new method for dealing with measurement error in explanatory variables of regression models

We introduce a new method, moment reconstruction, of correcting for measurement error in covariates in regression models. The central idea is similar to regression calibration in that the values of the covariates that are measured with error are replaced by "adjusted" values. In regression calibration the adjusted value is the expectation of the true value conditional on the measured value. In moment reconstruction the adjusted value is the variance-preserving empirical Bayes estimate of the true value conditional on the outcome variable. The adjusted values thereby have the same first two moments and the same covariance with the outcome variable as the unobserved "true" covariate values. We show that moment reconstruction is equivalent to regression calibration in the case of linear regression, but leads to different results for logistic regression. For case-control studies with logistic regression and covariates that are normally distributed within cases and controls, we show that the resulting estimates of the regression coefficients are consistent. In simulations we demonstrate that for logistic regression, moment reconstruction carries less bias than regression calibration, and for case-control studies is superior in mean-square error to the standard regression calibration approach. Finally, we give an example of the use of moment reconstruction in linear discriminant analysis and a nonstandard problem where we wish to adjust a classification tree for measurement error in the explanatory variables.     

Accuracy of predicting chemical body composition of growing pigs using dual-energy X-ray absorptiometry

Studies in animal science assessing nutrient and energy efficiency or determining nutrient requirements benefit from gathering exact measurements of body composition or body nutrient contents. Those are acquired by standardized dissection or by grinding the body followed by wet chemical analysis, respectively. The two methods do not result in the same type of information, but both are destructive. Harnessing human medical imaging techniques for animal science can enable repeated measurements of individuals over time and reduce the number of individuals required for research. Among imaging techniques, dual-energy X-ray absorptiometry (DXA) is particularly promising. However, the measurements obtained with DXA do not perfectly match dissections or chemical analyses, requiring the adjustment of the DXA via calibration equations. Several calibration regressions have been published, but comparative studies of those regression equations and whether they are applicable to different data sets are pending. Thus, it is currently not clear whether existing regression equations can be directly used to convert DXA measurements into chemical values or whether each individual DXA device will require its own calibration. Our study builds prediction equations that relate body composition to the content of single nutrients in growing entire male pigs (BW range 20–100 kg) as determined by both DXA and chemical analyses, with R² ranging between 0.89 for ash and 0.99 for water and CP. Moreover, we show that the chemical composition of the empty body can be satisfactorily determined by DXA scans of carcasses, with the prediction error ranging between 4.3% for CP and 12.6% for ash. Finally, we compare existing prediction equations for pigs of a similar range of BWs with the equations derived from our DXA measurements and evaluate their fit with our chemical analysis data. We found that existing equations for absolute contents that were built using the same DXA beam technology predicted our data more precisely than equations based on different technologies and percentages of fat and lean mass. This indicates that the creation of generic regression equations that yield reliable estimates of body composition in pigs of different growth stages, sexes and genetic breeds could be achievable in the near future. DXA may be a promising tool for high-throughput phenotyping for genetic studies, because it efficiently measures body composition in a large number and wide array of animals.     

A suggestion for computing objective function in model calibration

A parameter-optimization process (model calibration) is usually required for numerical model applications, which involves the use of an objective function to determine the model cost (model-data errors). The sum of square errors (SSR) has been widely adopted as the objective function in various optimization procedures. However, ‘square error’ calculation was found to be more sensitive to extreme or high values. Thus, we proposed that the sum of absolute errors (SAR) may be a better option than SSR for model calibration. To test this hypothesis, we used two case studies—a hydrological model calibration and a biogeochemical model calibration—to investigate the behavior of a group of potential objective functions: SSR, SAR, sum of squared relative deviation (SSRD), and sum of absolute relative deviation (SARD). Mathematical evaluation of model performance demonstrates that ‘absolute error’ (SAR and SARD) are superior to ‘square error’ (SSR and SSRD) in calculating objective function for model calibration, and SAR behaved the best (with the least error and highest efficiency). This study suggests that SSR might be overly used in real applications, and SAR may be a reasonable choice in common optimization implementations without emphasizing either high or low values (e.g., modeling for supporting resources management).     

A procedure to validate and correct the 13C chemical shift calibration of RNA datasets

Chemical shifts reflect the structural environment of a certain nucleus and can be used to extract structural and dynamic information. Proper calibration is indispensable to extract such information from chemical shifts. Whereas a variety of procedures exist to verify the chemical shift calibration for proteins, no such procedure is available for RNAs to date. We present here a procedure to analyze and correct the calibration of ¹³C NMR data of RNAs. Our procedure uses five ¹³C chemical shifts as a reference, each of them found in a narrow shift range in most datasets deposited in the Biological Magnetic Resonance Bank. In 49 datasets we could evaluate the ¹³C calibration and detect errors or inconsistencies in RNA ¹³C chemical shifts based on these chemical shift reference values. More than half of the datasets (27 out of those 49) were found to be improperly referenced or contained inconsistencies. This large inconsistency rate possibly explains that no clear structure–¹³C chemical shift relationship has emerged for RNA so far. We were able to recalibrate or correct 17 datasets resulting in 39 usable ¹³C datasets. 6 new datasets from our lab were used to verify our method increasing the database to 45 usable datasets. We can now search for structure–chemical shift relationships with this improved list of ¹³C chemical shift data. This is demonstrated by a clear relationship between ribose ¹³C shifts and the sugar pucker, which can be used to predict a C2′- or C3′-endo conformation of the ribose with high accuracy. The improved quality of the chemical shift data allows statistical analysis with the potential to facilitate assignment procedures, and the extraction of restraints for structure calculations of RNA.     

On the feasibility of obtaining multiple muscular maximal voluntary excitation levels from test exertions: A shoulder example

Currently, contrasting views exist regarding which body and arm postures are most effective for eliciting maximal voluntary exertions in the shoulder muscles. Informed exertion standardization may improve comparisons between subjects and muscle groups for normalized electromyography values. Additionally, identifying exertions that can produce equivalent maximal electrical activity values can reduce experimental setup time and reduce the likelihood of fatigue development. This research study examined twelve posture and force direction defined test exertions to identify those that elicited maximal electrical activity from the deltoid (anterior and middle fibres) and pectoralis major (clavicular and sternal heads). Further, the question of whether a single test exertion could obtain maximal electrical activity from multiple muscle fascicles was explored. Maximal activation was demonstrated for the deltoid during several exertions that incorporated an upward force exertion and the pectoralis major for multiple exertions that included an inward force direction. Finally, two test exertions produced maximal electrical activity from both muscles of interest. This research supports the notion that a range of exertions can elicit maximal electrical activity from a muscle, rather than one specific exertion. This suggests that researchers may be able to leverage a smaller set of test exertions to evaluate multiple muscles simultaneously without loss of data quality, and thereby decrease overall experimental data collection time while maintaining high fidelity data.