Intramural optical mapping of V(m) and Ca(i)2+ during long-duration ventricular fibrillation in canine hearts

Intramural gradients of intracellular Ca(2+) (Ca(i)(2+)) Ca(i)(2+) handling, Ca(i)(2+) oscillations, and Ca(i)(2+) transient (CaT) alternans may be important in long-duration ventricular fibrillation (LDVF). However, previous studies of Ca(i)(2+) handling have been limited to recordings from the heart surface during short-duration ventricular fibrillation. To examine whether abnormalities of intramural Ca(i)(2+) handling contribute to LDVF, we measured membrane voltage (V(m)) and Ca(i)(2+) during pacing and LDVF in six perfused canine hearts using five eight-fiber optrodes. Measurements were grouped into epicardial, midwall, and endocardial layers. We found that during pacing at 350-ms cycle length, CaT duration was slightly longer (by ?10%) in endocardial layers than in epicardial layers, whereas action potential duration (APD) exhibited no difference. Rapid pacing at 150-ms cycle length caused alternans in both APD (APD-ALT) and CaT amplitude (CaA-ALT) without significant transmural differences. For 93% of optrode recordings, CaA-ALT was transmurally concordant, whereas APD-ALT was either concordant (36%) or discordant (54%), suggesting that APD-ALT was not caused by CaA-ALT. During LDVF, V(m) and Ca(i)(2+) progressively desynchronized when not every action potential was followed by a CaT. Such desynchronization developed faster in the epicardium than in the other layers. In addition, CaT duration strongly increased (by ～240% at 5 min of LDVF), whereas APD shortened (by ～17%). CaT rises always followed V(m) upstrokes during pacing and LDVF. In conclusion, the fact that V(m) upstrokes always preceded CaTs indicates that spontaneous Ca(i)(2+) oscillations in the working myocardium were not likely the reason for LDVF maintenance. Strong V(m)-Ca(i)(2+) desynchronization and the occurrence of long CaTs during LDVF indicate severely impaired Ca(i)(2+) handling and may potentially contribute to LDVF maintenance.     

Evolution of handling time can destroy the coexistence of cycling predators

Several consumers (predators) with Holling type II functional response may robustly coexist even if they utilize the same resource (prey), provided that the population exhibits nonequilibrium dynamics and the handling time of predators is sufficiently different. We investigate the evolution of handling time and, in particular, its effect on coexistence. Longer handling time is costly in terms of lost foraging time, but allows more nutrients to be extracted from a captured prey individual. Assuming a hyperbolically saturating relationship between handling time and the number of new predators produced per prey consumed, we obtain three results: (i) There is a globally evolutionarily stable handling time; (ii) At most two predator strategies can coexist in this model; (iii) When two predators coexist, a mutant with intermediate handling time can always invade. This implies that there is no evolutionarily stable coexistence, and the evolution of handling time eventually leads to a single evolutionarily stable predator. These results are proven analytically and are valid for arbitrary (not only small) mutations; they however depend on the relationship between handling time and offspring production and on the assumption that predators differ only in their prey handling strategy.     

Flexible components of functional responses

1. The functional response of predators describes the rate at which a predator consumes prey and is an important determinant of community dynamics. Despite the importance, most empirical studies have considered a limited number of models of functional response. In addition, the models often make strong assumptions about the pattern of predation processes, even though functional responses can potentially exhibit a wide variety of patterns. 2. In addition to the limited model consideration, model selections of functional response models cannot tease apart the components of predation (i.e. capture rate and handling time) when flexible traits are considered because it is always possible that many different combinations of the capture rate and handling time can lead to the same predation rate. 3. This study directly examined the capture rate and handling time of functional response in a mite community. To avoid the model selection problem, the searching and handling behaviour data were collected. The model selection was applied directly to these two components of predation data. Commonly used functional response models and models that allow for more flexible patterns were compared. 4. The results indicated that assumptions of the commonly used models were not supported by the data, and a flexible model was selected as the best model. These results suggest the need to consider a wider variety of predation patterns when characterizing a functional response. Without making a strong assumption (e.g. static handling time), model selections on functional response models cannot be used to make reliable inferences on the predation mechanisms.     

Multiple imputation and posterior simulation for multivariate missing data in longitudinal studies

This paper outlines a multiple imputation method for handling missing data in designed longitudinal studies. A random coefficients model is developed to accommodate incomplete multivariate continuous longitudinal data. Multivariate repeated measures are jointly modeled; specifically, an i.i.d. normal model is assumed for time-independent variables and a hierarchical random coefficients model is assumed for time-dependent variables in a regression model conditional on the time-independent variables and time, with heterogeneous error variances across variables and time points. Gibbs sampling is used to draw model parameters and for imputations of missing observations. An application to data from a study of startle reactions illustrates the model. A simulation study compares the multiple imputation procedure to the weighting approach of Robins, Rotnitzky, and Zhao (1995, Journal of the American Statistical Association 90, 106-121) that can be used to address similar data structures.     

A simple imputation method for longitudinal studies with non-ignorable non-responses

Missing data are a common problem in longitudinal studies in the health sciences. Motivated by data from the Muscatine Coronary Risk Factor (MCRF) study, a longitudinal study of obesity, we propose a simple imputation method for handling non-ignorable non-responses (i.e., when non-response is related to the specific values that should have been obtained) in longitudinal studies with either discrete or continuous outcomes. In the proposed approach, two regression models are specified; one for the marginal mean of the response, the other for the conditional mean of the response given non-response patterns. Statistical inference for the model parameters is based on the generalized estimating equations (GEE) approach. An appealing feature of the proposed method is that it can be readily implemented using existing, widely-available statistical software. The method is illustrated using longitudinal data on obesity from the MCRF study.     

i2dash: Creation of Flexible,Interactive, and Web-based Dashboards for Visualization of Omics Data

Data visualization and interactive data exploration are important aspects of illustrating complex concepts and results from analyses of omics data. A suitable visualization has to be intuitive and accessible. Web-based dashboards have become popular tools for the arrangement, consolidation, and display of such visualizations. However, the combination of automated data processing pipelines handling omics data and dynamically generated, interactive dashboards is poorly solved. Here, we present i2dash, an R package intended to encapsulate functionality for the programmatic creation of customized dashboards. It supports interactive and responsive (linked) visualizations across a set of predefined graphical layouts. i2dash addresses the needs of data analysts/software developers for a tool that is compatible and attachable to any R-based analysis pipeline, thereby fostering the separation of data visualization on one hand and data analysis tasks on the other hand. In addition, the generic design of i2dash enables the development of modular extensions for specific needs. As a proof of principle, we provide an extension of i2dash optimized for single-cell RNA sequencing analysis, supporting the creation of dashboards for the visualization needs of such experiments. Equipped with these features, i2dash is suitable for extensive use in large-scale sequencing/bioinformatics facilities. Along this line, we provide i2dash as a containerized solution, enabling a straightforward large-scale deployment and sharing of dashboards using cloud services. i2dash is freely available via the R package archive CRAN (https://CRAN.R-project.org/package=i2dash).     

Estimating handling times for herbivore diets: a statistical method using the gamma distribution

1. We present a statistical model for the prediction of handling times for different diet items of herbivores foraging in heterogeneous environments, based on the distribution of time intervals between bites.
2. We propose the gamma distribution as a convenient and appropriate model for foraging data and illustrate its use with field observations of foraging Nubian ibex ( Capra ibex nubiana Linnaeus 1758) in the Negev Desert of Israel.
3. Specifically, we demonstrate how to estimate handling times from skewed frequency data of intervals between bites within patches.
4. We compared two mathematically equivalent gamma models and found a pronounced difference in the numerical results in fitting empirical data.
5. Estimated handling times varied with bite size, but not with plant category or sex of the foraging animal.
6. Fitting a gamma model to foraging data allows the efficient estimation of minimum handling constraints, mean handling times and within-patch cropping rates, which should be useful for models of the herbivore foraging process.     

Effects of burrow condition and seed handling time on hoarding strategies of Edward's long-tailed rat (Leopoldamys edwardsi)

Many hoarding rodents use burrows not only for dwelling and protection from natural enemies, but also for food storage. However, little is known how burrows used by scatter-hoarding animals influence their foraging behaviors. In addition, handling time for a given food item has a fundamental impact on hoarding strategies of these hoarding animals: food items with longer handling time are more likely to be hoarded due to increasing predation risk because the animals spend more time outside their burrows if they consumed such food. By providing with two types of artificial burrows (aboveground vs. underground) and two types of food items (i.e. seeds) with contrasting handling times, we investigated how burrow condition and handling time co-influence hoarding strategies of a key scatter-hoarding rodent, Edward's long-tailed rat (Leopoldamys edwardsi) in large enclosures in southwest China. We found that only a few animals larder-hoarded fewer seeds when only aboveground burrows were available, while over 80% of the animals preferred to use the underground burrows and hoard significantly more seeds in the burrows when both aboveground and underground burrows were provided simultaneously. We also found that seed handling time significantly affected hoarding strategies of the animals: they consumed and/or scatter-hoarded more Camellia oleifera seeds with shorter handling time outside the burrow, but consumed and larder-hoarded more Lithocarpus harlandii seeds with longer handling time in underground burrows. Our study indicates that both burrow types and seed handling time have important impacts on hoarding strategies of scatter-hoarding animals.     

SIMFIT: a microcomputer software-toolkit for modelistic studies in biochemistry

A software package suitable for personal computers and designedto handle simulation and fitting problems related to the studyof biomolecules under pre-steady and steady state conditionsis presented, and its overall architecture as well as the implementedalgorithms illustrated. The peculiar features of the packageare: (i) integrated capability of simulating dynamic modelsand fitting to them experimental data; (ii) handling of stiffproblems; (iii) free use of algebraic as well as differentialequations; (iv) objective comparison of models of differentcomplexity. The above features are discussed through a numberof examples taken from the direct experience of the authorsin enzyme kinetics and ligand binding. Received on May 23, 1989; accepted on August 21, 1989     

beta-Adrenergic activation reveals impaired cardiac calcium handling at early stage of diabetes

Cardiac function is known to be impaired in diabetes. Alterations in intracellular calcium handling have been suggested to play a pivotal role. This study aimed to test the hypothesis that beta-adrenergic activation can reveal the functional derangements of intracellular calcium handling of the 4-week diabetic heart. Langendorff perfused hearts of 4-week streptozotocin-induced diabetic rats were subjected to the beta-adrenoceptor agonist isoproterenol. Cyclic changes in [Ca(2+)](i) levels were measured throughout the cardiac cycle using Indo-1 fluorescent dye. Based on the computational analysis of the [Ca(2+)](i) transient the kinetic parameters of the sarcoplasmic reticulum Ca(2+)-ATPase and the ryanodine receptor were determined by minimizing the squared error between the simulated and the experimentally obtained [Ca(2+)](i) transient. Under unchallenged conditions, hemodynamic parameters were comparable between control and diabetic hearts. Isoproterenol administration stimulated hemodynamic function to a greater extent in control than in diabetic hearts, which was exemplified by more pronounced increases in rate of pressure development and decline. Under unchallenged conditions, [Ca(2+)](i) amplitude and rate of rise and decline of [Ca(2+)](i) as measured throughout the cardiac cycle were comparable between diabetic and control hearts. Differences became apparent under beta-adrenoceptor stimulation. Upon beta-activation the rate-pressure product showed a blunted response, which was accompanied by a diminished rise in [Ca(2+)](i) amplitude in diabetic hearts. Computational analysis revealed a reduced function of the sarcoplasmic reticulum Ca(2+)-ATPase and Ca(2+)-release channel in response to beta-adrenoceptor challenge. Alterations in Ca(2+)(i) handling may play a causative role in depressed hemodynamic performance of the challenged heart at an early stage of diabetes.     

Ethical considerations and animal welfare in ecological field studies

This paper addresses some of the ethical and welfare considerations implicit in the application of general techniques in common use during the course of collecting data in ecological field work. Even if they are not explicitly constructed as manipulative experiments, many field studies involve some degree of intervention during routine monitoring programmes: through disturbance caused merely by the presence of an observer or where specific sampling techniques themselves involve capture, handling and marking. Such interventive techniques may cause discomfort, distress or loss of fitness, even in the extreme may result in incidental mortality — and the ethical scientist should critically evaluate the implications of each methodology before adopting any procedure. The paper reviews by way of example the types of objective information now available for both small and larger mammals in relation to: (i) distress and mortality during capture operations; (ii) mortality or distress caused at the time by marking; (iii) longer-term consequences of handling and marking in terms of subsequent [delayed] mortality or loss of fitness, before considering a formal framework for assessment of costs and benefits of any given field programme.     

More than a decade of developmental gene expression atlases: where are we now?

To unravel regulatory networks of genes functioning during embryonic development, information on in situ gene expression is required. Enormous amounts of such data are available in literature, where each paper reports on a limited number of genes and developmental stages. The best way to make these data accessible is via spatio-temporal gene expression atlases. Eleven atlases, describing developing vertebrates and covering at least 100 genes, were reviewed. This review focuses on: (i) the used anatomical framework, (ii) the handling of input data and (iii) the retrieval of information. Our aim is to provide insights into both the possibilities of the atlases, as well as to describe what more than a decade of developmental gene expression atlases can teach us about the requirements of the design of the ‘ideal atlas’. This review shows that most ingredients needed to develop the ideal atlas are already applied to some extent in at least one of the discussed atlases. A review of these atlases shows that the ideal atlas should be based on a spatial framework, i.e. a series of 3D reference models, which is anatomically annotated using an ontology with sufficient resolution, both for relations as well as for anatomical terms.     

A method for measuring some components of foraging of certain birds in the field

A rapid method for measuring the searching speed, and the delay imposed on searching by making a peck (pecking time) and handling a prey (handling time) of certain ground-feeding birds in the field is described and discussed. The method is illustrated with data from two species of wading birds.     

The effect of capture-and-handling stress on carotenoid-based beak coloration in zebra finches

Stress can have widespread effects on animal behaviors and phenotypes, including sexually selected traits. Ornamental colors have long been studied as honest signals of condition, but few studies have been conducted on how the physiological stress response (i.e., corticosterone (CORT) elevation) impacts color expression. We used a traditional capture-and-restraint technique to examine the effect of repeated handling stress on carotenoid-dependent beak coloration in male and female zebra finches (Taeniopygia guttata). Birds subjected to daily, 10-min handling treatments, which elevated circulating CORT levels, for a four-week period displayed deeper orange/red beak coloration than did control animals. Stressed males lost body mass during the experiment and marginally decreased in circulating carotenoid concentrations. Hence, handling stress may have reduced food intake or induced mobilization of body stores (i.e., fat) of carotenoids. In contrast to males, stressed females maintained orange beak color, while control females faded in color. This study highlights sex- and pigment-specific mechanisms by which stress may temporarily enhance the expression of sexual traits, but at the expense of other key fitness traits (e.g., body mass maintenance, reproduction).     

Osteoblast autonomous Pi regulation via Pit1 plays a role in bone mineralization

The complex pathogenesis of mineralization defects seen in inherited and/or acquired hypophosphatemic disorders suggests that local inorganic phosphate (P(i)) regulation by osteoblasts may be a rate-limiting step in physiological bone mineralization. To test whether an osteoblast autonomous phosphate regulatory system regulates mineralization, we manipulated well-established in vivo and in vitro models to study mineralization stages separately from cellular proliferation/differentiation stages of osteogenesis. Foscarnet, an inhibitor of NaP(i) transport, blocked mineralization of osteoid formation in osteoblast cultures and local mineralization after injection over the calvariae of newborn rats. Mineralization was also down- and upregulated, respectively, with under- and overexpression of the type III NaP(i) transporter Pit1 in osteoblast cultures. Among molecules expressed in osteoblasts and known to be related to P(i) handling, stanniocalcin 1 was identified as an early response gene after foscarnet treatment; it was also regulated by extracellular P(i), and itself increased Pit1 accumulation in both osteoblast cultures and in vivo. These results provide new insights into the functional role of osteoblast autonomous P(i) handling in normal bone mineralization and the abnormalities seen in skeletal tissue in hypophosphatemic disorders.     

Differential Host Handling Behavior between Feeding and Oviposition in the Parasitic Wasp <Emphasis Type="Italic">Haplogonatopus hernandezae</Emphasis>

Lifetime fitness is directly influenced by the decision to use resources for either current or future reproduction. Thus, females should weigh the costs and benefits of each reproductive opportunity and allocate resources accordingly. Here, we explore decision-making and the time spent handling hosts of different instars in the parasitoid Haplogonatopus hernandezae, which uses a single planthopper host to either oviposit (i.e., current reproduction) or feed (i.e., future reproduction). Our results indicate that manipulation time in attacks that led to either oviposition and feeding increased with host instar and size. Consequently, attacks were less successful on older host instars than younger ones. Similarly, attack and handling time during oviposition was greater when manipulating fifth instar nymphs compared to younger ones, but oviposition time was similar. Surprisingly, host grasping by the chelate forelegs differed between oviposition and feeding events, and the specific chelate foreleg morphology of H. hernandezae facilitates the specific grasp of the clypeus and gena of the host. We also link this previously undescribed host grasping and differential handling behavior in this species to the final decision to oviposit or feed. Given the differences in handling time and effort among different host instars, we found that older hosts were more often chosen for consumption than younger hosts, and younger hosts were chosen more often for oviposition. Our study suggests that the tradeoff between current and future benefits is influenced by the investment in handling hosts of different instars, and the assessment of host suitability for successful offspring survival.     

Evaluating Virtual Cells and Multistage Flow Shops: An Analytical Approach

The implementation of cellular manufacturing can be carried out through the creation of manufacturing cells (i.e., groups of dissimilar machines dedicated to a set of part types that are placed in close proximity to one another) or virtual cells (i.e., the dedication of specific machines within the current departments to a prespecified set of part types). Typically, the former involves the reorganization of the shop floor and provides the operational benefit of reduced materials handling. On the other hand, the latter configuration is simpler to implement and easier to reconfigure in light of product demand changes, but it may not offer the same operational benefits. In this paper, we propose and validate analytical approximations for comparing the performance of virtual cells and multistage flow shops. Using these approximations and hypothetical data, we identify some key factors that influence the implementation of virtual cells in a multistage flow shop environment. We conclude with an application of our approximations to industrial data.     

Egg limitation and the functional response of the parasitoid Campoletis grioti (Hym: Ichneumonidae)

The hypothesis that mature egg availability during a parasitoid's lifetime affects the functional response, as well as a parasitoid's handling time and searching efficiency, was tested. Campoletis grioti Blanchard (Hym: Ichneumonidae) female parasitoids and Spodoptera frugiperda Smith (Lep: Noctuidae) host larvae were used as an example. Each female of C. grioti was confined with different host densities (6, 10, 30, 50, 80, 120 and 160 larvae/day) of first and second S. frugiperda instars until the female died. We found that C. grioti showed a type II functional response, with a reduction in the number of parasitized hosts in relation to female ageing. Handling time and searching efficiency increased over time. When we standardized the data simulating unlimited egg supply, the functional response, handling time and searching efficiency became constant throughout the parasitoid's life. We discuss the relationship between egg availability and functional response and its associated parameters, and its consequence on biological control programs.