A unified multiscale mechanical model for soft collagenous tissues with regular fiber arrangement

In this paper the mechanical response of soft collagenous tissues with regular fiber arrangement (RSCTs) is described by means of a nanoscale model and a two-step micro–macro homogenization technique. The non-linear collagen constitutive behavior is modeled at the nanoscale by a novel approach accounting for entropic mechanisms as well as stretching effects occurring in collagen molecules. Crimped fibers are reduced to equivalent straight ones at the microscale and the constitutive response of RSCTs at the macroscale is formulated by homogenizing a fiber reinforced material. This approach has been applied to different RSCTs (tendon, periodontal ligament and aortic media), resulting effective and accurate as proved by the excellent agreement with available experimental data. The model is based on few parameters, directly related to histological and morphological evidences and whose sensitivity has been widely investigated. Applications to simulation of some physiopathological mechanisms are also proposed, providing confirmation of clinical evidences and quantitative indications helpful for clinical practice.     

Experimentelle Untersuchung,Modellierung und optimale Berechnung eines mehrstufigen Säulenfermentors II. Experimentelle Bestimmung der Parameter und Koeffizienten des mathematischen Modells

Using a system analysis for the investigation of all processes which occur in a biochemical reactor on the micro and macro level, a mathematical model was worked out. It characterizes the model of the kinetics and stoichiometry of the growth of microorganisms and the rules of hydrodynamics and mass transfer in form of blocks. Relating to the discussed mathematical total model [11], experimental data on which the calculation of the model parameters is based are described in this second part of the paper. They were determined not only directly from the cultivation process, but also from experiments with model media.     

Micro and macro Bayesian estimation of population distributions

The author describes a Bayesian probability model for estimating population distributions when either micro or macro data on population migration are available. The model is tested using data for two groups of five regions in the Federal Republic of Germany, and it is found that the macro Bayesian estimators lead to a better projection of population distribution than those using micro data.     

A mechanical model of the gating spring mechanism of stereocilia

The stereocilium is the basic sensory unit of nature's mechanotransducers, which include the cochlear and vestibular organs. In noisy environments, stereocilia display high sensitivity to miniscule stimuli, effectively dealing with a situation that is a design challenge in micro systems. The gating spring hypothesis suggests that the mechanical stiffness of stereocilia bundle is softened by tip-link gating in combination with active bundle movement, contributing to the nonlinear amplification of miniscule stimuli. To demonstrate that the amplification is induced mechanically by the gating as hypothesized, we developed a biomimetic model of stereocilia and fabricated the model at the macro scale. The model consists of an inverted pendulum array with bistable buckled springs at its tips, which represent the mechanically gated ion channel. Model simulations showed that at the moment of gating, instantaneous stiffness softening generates an increase in response magnitude, which then sequentially occurs as the number of gating increases. This amplification mechanism appeared to be robust to the change of model parameters. Experimental data from the fabricated macro model also showed a significant increase in the open probability and pendulum deflection at the region having a smaller input magnitude. The results demonstrate that the nonlinear amplification of miniscule stimuli is mechanically produced by stiffness softening from channel gating.     

Beyond the nearest-neighbor Zimm-Bragg model for helix-coil transition in peptides

The nearest-neighbor (micro = 1) variant of the Zimm and Bragg (ZB) model has been extensively used to describe the helix-coil transition in biopolymers. In this work, we investigate the helix-coil transition for a 21-residue alanine peptide (AP) with the ZB model up to fourth nearest neighbor (micro = 1, 2, 3, and 4). We use a matrix approach that takes into account combinations of any number of helical stretches of any length and therefore gives the exact statistical weight of the chain within the assumptions of the ZB model. The parameters of the model are determined by fitting the temperature-dependent circular dichroism and Fourier transform infrared experimental spectra of the AP. All variants of the model fit the experimental data, thus giving similar results in terms of the macroscopic observables, such as temperature-dependent fractional helicity. However, the resulting microscopic parameters, such as distributions of the individual residue helical probabilities and free energy surfaces, vary significantly depending on the variant of the model. Overall, the mean residue enthalpy and entropy (in the absolute value) both increase with micro, but combined yield essentially the same "effective" value of the ZB propagation parameters for all micro. Greater helical probabilities for individual residues are predicted for larger micro, in particular, near the center of the sequence. The ZB nucleation parameters increase with increasing micro, which results in a lower free energy barrier to helix nucleation and lower apparent "cooperativity" of the transition. The significance of the long-range interactions for the predictions of ZB model for helix-coil transition, the calculated model parameters and the limitations of the model are discussed.     

B chromosomes in Stylidium crossocephalum (Angiospermae:Stylidiaceae)

Populations of Stylidium crossocephalum contain two common types of B chromosomes, macro B chromosomes and micro B chromosomes. The macro B chromosomes are telocentric, slightly smaller than the smallest A chromosomes and mitotically unstable. They have so far been found associated with 6 of the 16 stable genomes known in S. crossocephalum, occurring in populations covering a substantial portion of the species range. Micro B chromosomes are about one third the length of the smallest A chromosome, acrocentric and show some mitotic instability. They occur associated with 3 stable genomes in populations found in the more medial regions of the species range. Both types of B chromosomes generally show regular behaviour during meiosis, although when two or more are present their pairing efficiency is reduced when compared to the A chromosomes. In addition a single very large mega chromosome was found in a single cell of one heterokaryotypic plant. Its origin although conjectural at this stage may be of relevance in understanding the origin of macro and micro B chromosomes in this species.     

The estimation of natural fertility: A micro approach

Abstract

The estimation of natural fertility has heretofore been confined to population aggregates. This paper presents a technique for estimating natural fertility at the household level for developing countries with some practice of deliberate family size limitation and applies it to micro‐level WFS data for Sri Lanka and Colombia for females aged 35–44 in intact marriages. The technique is based on a proximate determinants equation estimated as part of a model that takes account of the interdependence between use of fertility control and natural fertility. To evaluate the results, the mean and household level estimates of natural fertility for each country are first compared with actual fertility; then mean estimates for each country are compared with macro‐level estimates of natural fertility based on three other methods. Finally, the implications of the analysis for the proximate sources of intercountry and intracountry variations in natural fertility are examined. The results suggest that the present approach yields plausible quantitative estimates of natural fertility and reasonable analytical results.     

Consistent micro, macro and state-based population modelling

A population system can be modelled using a micro model focusing on the individual entities, a macro model where the entities are aggregated into compartments, or a state-based model where each possible discrete state in which the system can exist is represented. However, the concepts, building blocks, procedural mechanisms and the time handling for these approaches are very different. For the results and conclusions from studies based on micro, macro and state-based models to be consistent (contradiction-free), a number of modelling issues must be understood and appropriate modelling procedures be applied. This paper presents a uniform approach to micro, macro and state-based population modelling so that these different types of models produce consistent results and conclusions. In particular, we demonstrate the procedures (distribution, attribute and combinatorial expansions) necessary to keep these three types of models consistent. We also show that the different time handling methods usually used in micro, macro and state-based models can be regarded as different integration methods that can be applied to any of these modelling categories. The result is free choice in selecting the modelling approach and the time handling method most appropriate for the study without distorting the results and conclusions.     

Mutation Size Optimizes Speciation in an Evolutionary Model

The role of mutation rate in optimizing key features of evolutionary dynamics has recently been investigated in various computational models. Here, we address the related question of how maximum mutation size affects the formation of species in a simple computational evolutionary model. We find that the number of species is maximized for intermediate values of a mutation size parameter μ; the result is observed for evolving organisms on a randomly changing landscape as well as in a version of the model where negative feedback exists between the local population size and the fitness provided by the landscape. The same result is observed for various distributions of mutation values within the limits set by μ. When organisms with various values of μ compete against each other, those with intermediate μ values are found to survive. The surviving values of μ from these competition simulations, however, do not necessarily coincide with the values that maximize the number of species. These results suggest that various complex factors are involved in determining optimal mutation parameters for any population, and may also suggest approaches for building a computational bridge between the (micro) dynamics of mutations at the level of individual organisms and (macro) evolutionary dynamics at the species level.     

What Explains Child Malnutrition of Indigenous People of Northeast India?

Household risk factors affecting child health, particularly malnutrition, are mainly basic amenities like drinking water, toilet facility, housing and fuel used for cooking. This paper considered the collective impact of basic amenities measured by an index specially constructed as the contextual factor of child malnutrition. The contextual factor operates at both the macro and micro levels namely the state level and the household level. The importance of local contextual factors is especially important when studying the nutritional status of children of indigenous people living in remote and inaccessible regions. This study has shown the contextual factors as potential factors of malnutrition among children in northeast India, which is home to the largest number of tribes in the country. In terms of macro level contextual factor it has been found that 8.9 per cent, 3.7 per cent and 3.6 per cent of children in high, medium and low risk households respectively, are severely wasted. Lower micro level household health risks, literate household heads, and scheduled tribe households have a negating effect on child malnutrition. Children who received colostrum feeding at the time of birth and those who were vaccinated against measles are also less subject to wasting compared to other children, and these differences are statistically significant.     

Label-free bacteria identification for clinical applications

We have developed a system for bacteria identification based on absorption spectroscopy in the mid-infrared spectral range. The data collected are analyzed with a deep learning algorithm. It is based on a neural-network model which takes one-dimensional signal vectors and outputs a probability score of identification of a bacterium type by extracting micro and macro scale features, using convolutions and nonlinear operations. The results are achieved in real time and do not require any offline postprocessing. The study was done on 12 of the most common bacteria usually seen in clinical microbiology laboratories. The system sensitivity is 0.94 ± 0.04, with a specificity of 0.95 ± 0.02. The system can be extended to additional bacterium types and variants with no change to its hardware or software, but only updating the model's parameters. The system's accuracy, size, ease of operation and low cost make it suitable for use in any type of clinical setting.     

Animal space use: distinguishing a two‐level superposition of scale‐specific walks from scale‐free Lévy walk

How to differentiate between scale‐free space use like Lévy walk and a two‐level scale‐specific process like composite random walk (mixture of intra‐ and inter‐patch habitat movement) is surrounded by controversy. Composite random walk may under some parameter conditions appear Lévy walk‐like from the perspective of the path’s distribution of step lengths due to superabundance of very long steps relative to the expectation from a classic (single‐level) random walk. However, a more explicit focus on the qualitative differences between studying movement at a high resolution mechanistic (behavioral) level and the more coarse‐grained statistical mechanical level may contribute to resolving both this and other issues related to scaling complexity. Specifically, a re‐sampling of a composite random walk at larger time lags than the micro‐level unit time step for the simulation makes a Lévy‐look‐alike step length distribution re‐shaping towards a Brownian motion‐like pattern. Conversely, a true Levy walk maintains its scaling characteristics upon re‐sampling. This result illustrates how a confusing pattern at the mechanistic level may be resolved by changing observational scale from the micro level to the coarser statistical mechanical meso‐ or macro‐scale. The instability of the composite random walk pattern under rescaling is a consequence of influence of the central limit theorem. I propose that a coarse‐graining test – studying simulated animal paths at a coarsened temporal scale by re‐sampling a series – should be routinely performed prior to comparing theoretical results with those patterns generated from GPS data describing animal movement paths. Fixes from terrestrial mammals are often collected at hourly intervals or larger, and such a priori coarse‐grained series may thus comply better with the statistical mechanical meso‐ or macro‐level of analysis than the behavioral mechanics observed at finer resolutions typically in the range of seconds and minutes. If fixes of real animals are collected at this high frequency, coarse graining both the simulated and real series is advised in order to bring the analysis into a temporal scale domain where analytical methods from statistical mechanics can be applied.     

Fluidic and microfluidic tools for quantitative systems biology

Understanding genes and their functions is a daunting task due to the level of complexity in biological organisms. For discovering how genotype and phenotype are linked to each other, it is essential to carry out systematic studies with maximum sensitivity and high-throughput. Recent developments in fluid-handling technologies, both at the macro and micro scale, are now allowing us to apply engineering approaches to achieve this goal. With these newly developed tools, it is now possible to identify genetic factors that are responsible for particular phenotypes, perturb and monitor cells at the single-cell level, evaluate cell-to-cell variability, detect very rare phenotypes, and construct faithful in vitro disease models.     

Sources of anomalous diffusion on cell membranes: a Monte Carlo study

A stochastic random walk model of protein molecule diffusion on a cell membrane was used to investigate the fundamental causes of anomalous diffusion in two-dimensional biological media. Three different interactions were considered: collisions with fixed obstacles, picket fence posts, and capture by, or exclusion from, lipid rafts. If motion is impeded by randomly placed, fixed obstacles, we find that diffusion can be highly anomalous, in agreement with previous studies. In contrast, collision with picket fence posts has a negligible effect on the anomalous exponent at realistic picket fence parameters. The effects of lipid rafts are more complex. If proteins partition into lipid rafts there is a small to moderate effect on the anomalous exponent, whereas if proteins are excluded from rafts there is a large effect on the anomalous exponent. In combination, these mechanisms can explain the level of anomaly in experimentally observed membrane diffusion, suggesting that anomalous diffusion is caused by multiple mechanisms whose effects are approximately additive. Finally, we show that the long-range diffusion rate, D(macro), estimated from fluorescence recovery after photobleaching studies, can be much smaller than D(micro), the small-scale diffusion rate, and is highly sensitive to obstacle densities and other impeding structures.     

Discrete event, multi-level simulation of metabolite channeling

Typically differential equations are employed to simulate cellular dynamics. To develop a valid continuous model based on differential equations requires accurate parameter estimations; an accuracy which is often difficult to achieve, due to the lack of data. In addition, processes in metabolic pathways, e.g. metabolite channeling, seem to be of a rather qualitative and discrete nature. With respect to the available data and to the perception of the underlying system, a discrete rather than a continuous approach to modeling and simulation seems more adequate. A discrete approach does not necessarily imply a more abstract view on the system. If we move from macro to micro and multi-level modeling, aspects of subsystems and their interactions, which have been only implicitly represented, become an explicit part of the model. To start exploring discrete event phenomena within metabolite channeling we choose the tryptophan synthase. Based on a continuous macro model, a discrete event, multi-level model is developed which allows us to analyze the interrelation between structural and functional characteristics of the enzymes.     

Lamellarity of cationic liposomes and mode of preparation of lipoplexes affect transfection efficiency.

Transfection of NIH-3T3 cells by a human growth hormone expression vector complexed with liposomes composed of N-(1-(2, 3-dioleoyloxy)propyl)-N,N,N-trimethylammonium chloride (DOTAP) with or without helper lipids was studied. The transfection efficiency was dependent on the lamellarity of the liposomes used to prepare the lipoplexes. Multilamellar vesicles (MLV) were more effective than large unilamellar vesicles (LUV) of approximately 100 nm, irrespective of lipid composition. The optimal DNA/DOTAP mole ratio for transfection was 相似文献   

Risk Assessment,Microbial Communities,and Pollution-Induced Community Tolerance

Until recently, parameters from microorganisms were generally not included in risk assessment at a comparable level to animals and plants. However, the major part of global biomass, biodiversity, and ecosystem processes is present in the microbial world and microbiological techniques applicable to risk assessment are becoming available. Two microbial indicators are described based on the usage of multiwell plates with different substrates and a redox indicator for monitoring mineralisation. With both techniques autochthonous microbial communities are analysed. Producing functional fingerprints of the microbial community gives insights into the composition of different functions. This is equivalent to observations of ecological abundance and species composition. When lack of reference sites or reference data renders risk assessment difficult, measurement of the pollution-induced community tolerance (PICT) can provide useful information.     

Ethnicity and practice in Malaysian unions

In mainland Malaysia, the tri‐ethnic schema of Malay‐Chinese‐Indian continues to have a decisive influence on macro‐level policy and micro‐level behaviour. However, other means of organizing experience are not entirely precluded. This article features the profiles of three Malaysian trade union leaders who must, in effect, feed the concept of class through an ethnic grid in order to attract and retain union members. The lives of these unionists exemplify how ethnicity and class in Malaysia, as elsewhere, are constructive processes that demand the active participation of individuals even as that participation is subject to the constraints of hegemony. However, there is certainly sufficient play in the Malaysian system to suggest that current ethnic and class concepts ‐ and, indeed, hegemony itself ‐ have great potential for change.     

Comparative analysis of micro and macro B chromosomes in the Korean field mouse Apodemus peninsulae (Rodentia, Murinae) performed by chromosome microdissection and FISH

Comparative analysis of micro B and macro B chromosomes of the Korean field mouse Apodemus peninsulae, collected in populations from Siberia and the Russian Far East, was performed with Giemsa, DAPI, Ag-NOR staining and chromosome painting with whole and partial chromosome probes generated by microdissection and DOP-PCR. DNA composition of micro B chromosomes was different from that of macro B chromosomes. All analyzed micro B chromosomes contained clusters of DNA repeats associated with regions characterized by an uncondensed state in mitosis. Giemsa and DAPI staining did not reveal these regions. Their presence in micro B chromosomes led to their special morphology and underestimation in size. DNA repeat clusters homologous to DNA of micro B chromosome arms were also revealed in telomeric regions of some macro B chromosomes of specimens captured in Siberian regions. Neither active NORs nor clusters of ribosomal DNA were found in the uncondensed regions of micro B chromosomes. Possible evolutionary pathways for the origin of macro and micro B chromosomes are discussed.     

Analysis of lung parenchyma as a parametric porous medium.

The dynamic behavior of the lung in health and disease depends on its viscoelastic properties. To better understand these properties, several mathematical models have been utilized by many investigators. In the present work, we present a new approach that characterizes the dynamics of gas flow into a viscoelastic porous medium that models the lung structure. This problem is considered in terms of the lung input impedance on a macro level and parenchymal tissue impedance on the level of an alveolar wall. We start from a basic theoretical analysis in which macroscopic tissue deformations are represented in accordance with the linearized Navier-Stokes equations. This approach has strong theoretical underpinnings in other situations but has not been applied to analyze the impedance of the inflated lung. Our analysis provides a theoretical basis for analyzing the interaction between flow into the lungs as a biophysical diffusion process and parenchymal viscoelasticity described phenomenologically, within the frameworks of standard viscoelasticity and structural damping. This lung impedance incorporates parameters of porosity, permeability, and viscoelasticity on micro and macro levels of parenchymal tissue. The analysis shows the theoretical basis of the transformation from the impedance of alveolar walls or isolated tissue strips to that of the intact parenchyma. We also show how the loading impedance at the lung boundary may have a significant impact on the dynamic behavior of whole lung viscoelasticity. Our analysis may be useful in directing specific tests of different models and for analyzing experimental measurements of viscoelastic parameters of lung material under normal and pathological conditions.