A chemical flow system mimics waves of gene expression during segmentation

The early vertebrate developmental process of somitogenesis involves bands of gene expression that form periodically at the posterior end of the presomitic mesoderm (PSM) and traverse it with decreasing width and velocity. We have constructed a chemical flow system that, based on the novel flow-distributed oscillator (FDO) mechanism of wave pattern formation, reproduces key physical features of the PSM and observe concentration waves having similar spatio-temporal behavior. This suggests that the gene expression waves can be understood qualitatively in terms of phase dynamics in an open flow of a self-oscillating medium and that chemical flow systems can be used to mimic and model biological pattern formation during axial growth. In fact, expressions for wavelength and wave velocity derived from phase dynamics are found to be in quantitative agreement with measurements from both the biological and the chemical systems. This indicates that they, despite their significant differences, have common dynamics.     

An approach in mathematical modeling of an upflow packed-bed reactor for enzymatic hydrolysis of wheat straw

The behavior of a packed-bed reactor for enzymatic hydrolysis of pretreated wheat straw has been described by means of a mathematical model. The flow pattern has been evaluated by residence time distribution experiments. Small deviations from ideal plug flow behavior were found using the dispersion model. The kinetic model proposed for enzymatic hydrolysis of cellulosic fraction of pretreated wheat straw has been derived from batch experimental data. Variations of enzyme concentration throughout the straw bed have been approximately described using a ramp variation of adsorbed enzyme. The final explains qualitatively the experimental results.     

Pattern formation in reaction-diffusion models with nonuniform domain growth

Recent examples of biological pattern formation where a pattern changes qualitatively as the underlying domain grows have given rise to renewed interest in the reaction-diffusion (Turing) model for pattern formation. Several authors have now reported studies showing that with the addition of domain growth the Turing model can generate sequences of patterns consistent with experimental observations. These studies demonstrate the tendency for the symmetrical splitting or insertion of concentration peaks in response to domain growth. This process has also been suggested as a mechanism for reliable pattern selection. However, thus far authors have only considered the restricted case where growth is uniform throughout the domain. In this paper we generalize our recent results for reaction-diffusion pattern formation on growing domains to consider the effects of spatially nonuniform growth. The purpose is twofold: firstly to demonstrate that the addition of weak spatial heterogeneity does not significantly alter pattern selection from the uniform case, but secondly that sufficiently strong nonuniformity, for example where only a restricted part of the domain is growing, can give rise to sequences of patterns not seen for the uniform case, giving a further mechanism for controlling pattern selection. A framework for modelling is presented in which domain expansion and boundary (apical) growth are unified in a consistent manner. The results have implications for all reaction-diffusion type models subject to underlying domain growth.     

Self‐organised patchiness and scale‐dependent bio‐geomorphic feedbacks in aquatic river vegetation

Spatial self‐organisation of ecosystems is the process by which large‐scale ordered spatial patterns emerge from disordered initial conditions through local feedbacks between organisms and their environment. Such process is considered important for ecosystem functioning, providing increased productivity, resistance and resilience against environmental change. Although spatial self‐organisation has been found for an increasing number of ecosystems, it has never been shown so far for aquatic river vegetation. Here we explore the existence of spatial self‐organisation of freshwater macrophyte patches in a typical lowland river (Belgium), showing that the underlying mechanisms for pattern formation are scale‐dependent feedbacks between plant growth, water flow and local river bed erosion and sedimentation. The mapping of vegetation patches showed that the frequency distribution of patch sizes is governed by a power‐law function, suggesting that the patches are self‐organised. Scale‐dependent feedbacks, likely to lead to this self‐organised pattern, were demonstrated with a mimic experiment. Both positive and negative feedbacks on plants were confirmed by a transplantation experiment. Placing vegetation patch mimics in the river showed experimentally that on a short range (within and behind the mimics) flow reduction and increased sedimentation occurred, while on a larger range (next to patches) the flow was accelerated and decreased sedimentation took place. By transplanting macrophytes within, next to and further away from existing patches, it was proven that the conditions within the patches favoured the survival and growth of transplants (i.e. short‐range positive feedback), while the conditions just next to patches led to decreased survival and growth (i.e. long‐range negative feedback).     

Implicit-explicit methods for reaction-diffusion problems in pattern formation

Reaction-diffusion mechanisms have been used to explain pattern formation in developmental biology and in experimental chemical systems. To approximate the corresponding spatially discretized models, an explicit scheme can be used for the reaction term and an implicit scheme for the diffusion term. Such implicit-explicit (IMEX) schemes have been widely used, especially in conjunction with spectral methods in fluid flow problems.In this work, we analyze the performance of several of the best known linear multistep IMEX schemes for reaction-diffusion problems in pattern formation. For the linearized two chemical system, the growth properties exhibited by IMEX schemes are examined. Schemes which accurately represent the growth of the linearized problem for large time steps are identified. Numerical experiments show that first order accurate schemes, as well as schemes which produce only a weak decay of high frequency spatial error may yield plausible results which are nonetheless qualitatively incorrect. For such schemes, computations using refinements in the time step are likely to produce essentially the same (erroneous) results. Higher order schemes which produce a strong decay of high frequency errors are proposed instead.Our findings are demonstrated on several examples.The work of the author was partially supported by an NSERC Postgraduate Scholarship     

Collective human mobility pattern from taxi trips in urban area

We analyze the passengers' traffic pattern for 1.58 million taxi trips of Shanghai, China. By employing the non-negative matrix factorization and optimization methods, we find that, people travel on workdays mainly for three purposes: commuting between home and workplace, traveling from workplace to workplace, and others such as leisure activities. Therefore, traffic flow in one area or between any pair of locations can be approximated by a linear combination of three basis flows, corresponding to the three purposes respectively. We name the coefficients in the linear combination as traffic powers, each of which indicates the strength of each basis flow. The traffic powers on different days are typically different even for the same location, due to the uncertainty of the human motion. Therefore, we provide a probability distribution function for the relative deviation of the traffic power. This distribution function is in terms of a series of functions for normalized binomial distributions. It can be well explained by statistical theories and is verified by empirical data. These findings are applicable in predicting the road traffic, tracing the traffic pattern and diagnosing the traffic related abnormal events. These results can also be used to infer land uses of urban area quite parsimoniously.     

Protein kinase C gamma expression mimics phorbol ester-induced transcriptional activation of a murine VL30 enhancer element

Protein kinase C (PKC), a critical component in the regulation of cell growth, is thought to participate in transmitting the signals of certain cell surface receptor activation events to the nucleus. We have previously shown that stable expression of the PKC gamma isoenzyme in NIH 3T3 cells causes altered growth and enhanced tumorigenicity. In this report, we show that transient expression of the PKC gamma isoenzyme can trans-activate a murine VL30 enhancer element in a pattern similar to that of the phorbol ester tumor promoter 12-O-tetradecanoylphorbol-13-acetate. In contrast, ras activation of this element is distinct both quantitatively and qualitatively from PKC gamma and 12-O-tetradecanoylphorbol-13-acetate activation. These results provide direct evidence that PKC is the cellular mediator in the activation of phorbol ester-responsive genes and suggest a mechanism by which abnormal PKC expression might lead to altered growth control by changing the pattern of cellular gene expression.     

Disturbance and diversity at two spatial scales

The spatial scale of disturbance is a factor potentially influencing the relationship between disturbance and diversity. There has been discussion on whether disturbances that affect local communities and create a mosaic of patches in different successional stages have the same effect on diversity as regional disturbances that affect the whole landscape. In a microcosm experiment with metacommunities of aquatic protists, we compared the effect of local and regional disturbances on the disturbance–diversity relationship. Local disturbances destroyed entire local communities of the metacommunity and required reimmigration from neighboring communities, while regional disturbances affected the whole metacommunity but left part of each local community intact. Both disturbance types led to a negative relationship between disturbance intensity and Shannon diversity. With strong local disturbance, this decrease in diversity was due to species loss, while strong regional disturbance had no effect on species richness but reduced the evenness of the community. Growth rate appeared to be the most important trait for survival after strong local disturbance and dominance after strong regional disturbance. The pattern of the disturbance–diversity relationship was similar for both local and regional diversity. Although local disturbances at least temporally increased beta diversity by creating a mosaic of differently disturbed patches, this high dissimilarity did not result in regional diversity being increased relative to local diversity. The disturbance–diversity relationship was negative for both scales of diversity. The flat competitive hierarchy and absence of a trade-off between competition and colonization ability are a likely explanation for this pattern.     

Schizophrenia and the neurodevelopmental continuum:evidence from genomics

The idea that disturbances occurring early in brain development contribute to the pathogenesis of schizophrenia, often referred to as the neurodevelopmental hypothesis, has become widely accepted. Despite this, the disorder is viewed as being distinct nosologically, and by implication pathophysiologically and clinically, from syndromes such as autism spectrum disorders, attention‐deficit/hyperactivity disorder (ADHD) and intellectual disability, which typically present in childhood and are grouped together as “neurodevelopmental disorders”. An alternative view is that neurodevelopmental disorders, including schizophrenia, rather than being etiologically discrete entities, are better conceptualized as lying on an etiological and neurodevelopmental continuum, with the major clinical syndromes reflecting the severity, timing and predominant pattern of abnormal brain development and resulting functional abnormalities. It has also been suggested that, within the neurodevelopmental continuum, severe mental illnesses occupy a gradient of decreasing neurodevelopmental impairment as follows: intellectual disability, autism spectrum disorders, ADHD, schizophrenia and bipolar disorder. Recent genomic studies have identified large numbers of specific risk DNA changes and offer a direct and robust test of the predictions of the neurodevelopmental continuum model and gradient hypothesis. These findings are reviewed in detail. They not only support the view that schizophrenia is a disorder whose origins lie in disturbances of brain development, but also that it shares genetic risk and pathogenic mechanisms with the early onset neurodevelopmental disorders (intellectual disability, autism spectrum disorders and ADHD). They also support the idea that these disorders lie on a gradient of severity, implying that they differ to some extent quantitatively as well as qualitatively. These findings have important implications for nosology, clinical practice and research.     

Calibrating the radial-growth averaging method for detecting releases in old-growth forests of coastal British Columbia,Canada

Dendroecological methods that use growth releases to reconstruct the history of canopy disturbances are most useful when calibrated for specific species in specific forest types. In this study, we calibrate the radial-growth averaging method to detect growth releases of western redcedar (Thuja plicata Donn ex D. Don), western hemlock (Tsuga heterophylla (Raf.) Sarg.), and Pacific silver fir (Abies amabilis Dougl. ex J. Forbes) following fine-scale canopy disturbances in old-growth forests of coastal British Columbia, Canada. Our goal is to establish a version of the method that will capture the full range of growth increases that occur for the study species following natural, fine-scale canopy gaps, yet will account for the effects of climatic variability on radial growth and growth increases. We used traditional dendroclimatological techniques and the radial-growth averaging method to examine how climatic and regional-scale factors contributed to radial growth and growth increases. In addition, we did a sensitivity analysis, using both ring widths and basal area increments, to explore how varying the values of three parameters of the radial-growth averaging method (threshold, moving average, and window) influenced the proportion of trees that showed a release pattern following the formation of canopy gaps of known timing of origin. Although radial growth of western redcedar and western hemlock was significantly associated with climate, percent-growth change derived from residual chronologies rarely exceeded 25%, which defined our minimum threshold for a release. For the sensitivity analysis, two general trends were common to all three species: (1) as threshold increased, the proportion of trees that showed a release pattern decreased, particularly for western redcedar and (2) a higher proportion of trees showed a release pattern using a 10-year versus a 5-year window, particularly for thresholds <100%. The greatest proportion of trees showed a release pattern using a 25% threshold, 5-year moving average, and 10-year window for both ring widths and basal area increments. Overall, a higher proportion of trees showed a release pattern using basal area increments as opposed to ring widths. Therefore, basal area increments are better suited to assess releases in these old-growth stands that have large inter- and intra-species variability in tree size. By establishing these empirically-based criteria, we have achieved the first step towards quantifying attributes of growth releases of trees in the study stands, allowing future studies to capture the variability of past disturbance events and predict changes in forest structure and composition over time.     

The conservation of ground layer lichen communities in alvar grasslands and the relevance of substitution habitats

Semi-natural calcareous grasslands (alvars) are biodiversity hotspots in Northern Europe, particularly for herb layer plants. In the last century, traditional management has ceased, and the area of grasslands has declined due to extensive encroachment. We were interested in the drivers of ground layer (alias terricolous or epigeic) lichen communities. Our survey consisted of 86 habitat fragments in western Estonia, covering four types of historic alvar grasslands and three types of alvar-like habitats. We found that the ground lichen communities were primarily soil-type-specific, but were also affected by historic disturbances and land use change. In contrast to knowledge about herb layer communities, for which shrub encroachment has been shown to be main driver, the increased density of the herb layer and the reduced diversity of microhabitats were major drivers for the ground layer lichen community. These drivers caused a decrease in species richness, but only within the species of conservation value, and also led to a shift in the composition of lichen growth form from the dominance of squamulose and crustose towards fruticose lichens. We conclude that the traditional practice of restoring alvars by cutting shrubs is insufficient to maintain ground layer lichen biodiversity. Alvar maintenance practices should include grazing, which creates various small-scale ground disturbances and increases microhabitat heterogeneity. Alvar-like habitats originating from large-scale historic disturbances appeared to be suitable for calcicolous epigeic lichens, and can therefore be considered to be temporary substitution habitats, i.e. refugia for the regional species pool.     

Trickle-bed root culture bioreactor design and scale-up: growth, fluid-dynamics, and oxygen mass transfer

Trickle-bed root culture reactors are shown to achieve tissue concentrations as high as 36 g DW/L (752 g FW/L) at a scale of 14 L. Root growth rate in a 1.6-L reactor configuration with improved operational conditions is shown to be indistinguishable from the laboratory-scale benchmark, the shaker flask (mu=0.33 day(-1)). These results demonstrate that trickle-bed reactor systems can sustain tissue concentrations, growth rates and volumetric biomass productivities substantially higher than other reported bioreactor configurations. Mass transfer and fluid dynamics are characterized in trickle-bed root reactors to identify appropriate operating conditions and scale-up criteria. Root tissue respiration goes through a minimum with increasing liquid flow, which is qualitatively consistent with traditional trickle-bed performance. However, liquid hold-up is much higher than traditional trickle-beds and alternative correlations based on liquid hold-up per unit tissue mass are required to account for large changes in biomass volume fraction. Bioreactor characterization is sufficient to carry out preliminary design calculations that indicate scale-up feasibility to at least 10,000 liters.     

Linear enamel hypoplasias as indicators of systemic physiological stress: evidence from two known age-at-death and sex populations from postmedieval London

Enamel hypoplasias are useful indicators of systemic growth disturbances during childhood, and are routinely used to investigate patterns of morbidity and mortality in past populations. This study examined the pattern of linear enamel hypoplasias in two different burial populations from 18th and 19th Century church crypts in London. Linear enamel hypoplasias on the permanent dentitions of individuals from the crypt of Christ Church, Spitalfields, were compared to enamel defects on the teeth of individuals from St. Bride's. The method used involves the identification of enamel defects at a microscopic level, and systemic perturbations are detected by matching hypoplasias among different tooth classes within each individual. The pattern of linear enamel hypoplasias was contrasted between individuals from the burial sites of Spitalfields and St. Bride's, between males and females, and between those aged less than 20 years of age and those aged over 20 years at death. Six different parameters were examined: frequency of linear enamel hypoplasias, interval between defects, duration of hypoplasias, age at first occurrence of hypoplasia, age at last occurrence of hypoplasia, and the percentage of enamel formation time taken up by growth disturbances. All individuals in the study displayed linear enamel hypoplasias, with up to 33% of total visible enamel formation time affected by growth disruptions. Multiple regression analysis indicated a number of significant differences in the pattern of enamel hypoplasias. Individuals from Spitalfields had shorter intervals between defects and greater percentages of enamel formation time affected by growth disturbances than did individuals from St. Bride's. Females had greater numbers of linear enamel hypoplasias, shorter intervals between defects, and greater percentages of enamel formation time affected by growth disturbances than males. There were also differences in the pattern of enamel hypoplasias and age at death in this study. Individuals who died younger in life had an earlier age at first occurrence of enamel hypoplasia than those who survived to an older age. The pattern of enamel hypoplasias detected in this study was influenced by tooth crown geometry and tooth wear such that most defects were found in the midcrown and cervical regions of the teeth, and greater numbers of defects were identified on the anterior teeth. Differences in sensitivity of the parameters used for the detection of enamel hypoplasias were found in this study. The percentage of visible enamel formation time affected by growth disturbances was the parameter that identified the greatest number of significant differences among the subgroups examined.     

Induction and persistence of allelochemicals in the foliage of balsam fir seedlings following simulated browsing

The intensity, pattern, and timing of browsing disturbances influence the mobilization of chemical defenses (allelochemicals) and subsequent growth of conifers such as balsam fir, an important food source for various insect and mammalian herbivores. The objective of this study was to examine the induction and persistence of allelochemicals in foliage of balsam fir seedlings as affected by the pattern and timing of browsing disturbance. We conducted a simulated browsing study in a greenhouse environment using four browsing patterns and three persistence times. Total phenols were induced shortly after simulated browsing and persisted for at least 1 month, whereas condensed tannins exhibited a delayed induction but were more persistent, remaining above background levels 2 months after simulated browsing. The chemistry of non-browsed seedlings revealed that a seasonal pattern was evident for both total phenols and condensed tannins. As the experiment progressed through the growing season, background levels of total phenols decreased while those of condensed tannins increased with the two allelochemicals groups appearing to show a negative relationship. These trends suggest that total phenols, which are assumed to have a lower biosynthetic cost and are more quickly mobilized than condensed tannins, are a first line of herbivory defense followed by condensed tannins which take longer to mobilize but have a longer persistence time or that total phenols act as a primary defense against insect herbivores which disturb plants in the early growing season while condensed tannins are mobilized in the late season to defend against mammalian browsers of balsam fir in winter.     

Spatiotemporal Context Awareness for Urban Traffic Modeling and Prediction: Sparse Representation Based Variable Selection

Spatial-temporal correlations among the data play an important role in traffic flow prediction. Correspondingly, traffic modeling and prediction based on big data analytics emerges due to the city-scale interactions among traffic flows. A new methodology based on sparse representation is proposed to reveal the spatial-temporal dependencies among traffic flows so as to simplify the correlations among traffic data for the prediction task at a given sensor. Three important findings are observed in the experiments: (1) Only traffic flows immediately prior to the present time affect the formation of current traffic flows, which implies the possibility to reduce the traditional high-order predictors into an 1-order model. (2) The spatial context relevant to a given prediction task is more complex than what is assumed to exist locally and can spread out to the whole city. (3) The spatial context varies with the target sensor undergoing prediction and enlarges with the increment of time lag for prediction. Because the scope of human mobility is subject to travel time, identifying the varying spatial context against time lag is crucial for prediction. Since sparse representation can capture the varying spatial context to adapt to the prediction task, it outperforms the traditional methods the inputs of which are confined as the data from a fixed number of nearby sensors. As the spatial-temporal context for any prediction task is fully detected from the traffic data in an automated manner, where no additional information regarding network topology is needed, it has good scalability to be applicable to large-scale networks.     

Bubbles induced fluctuations of some properties of aqueous solutions

A mathematical model of the air diffusion process through the water surface taking into account the reverse flow of bubbles was proposed. The numerical solving gives self-oscillation of the dissolved air concentration. Spectral density of these oscillations has the 1/f-noise form, which explains the fluctuating nature of the observed properties of water and biological effects, which depend on the amount of dissolved air. A mechanism of spontaneous water luminescence observed after laser irradiation was suggested. The calculated luminescence self-oscillations have the form of a fractal with an infinite sequence of periods, which evolve in time and that is qualitatively consistent with the experiment.     

Microcirculation, hemodynamics and blood rheology in peritonitis during plasmapheresis

By means of biomicroscopy, electrophysiological and hemorheological techniques effect of plasmapheresis with use of various plasma -substituting solutions and their combination on microcirculation, hemodynamics and rheology of blood at peritonitis has been studied in the experiment on 329 white non-inbred rats and on 50 mature dogs. Three periods of disturbances in hemomicrocirculation of the small intestine mesentery at peritonitis have been revealed: I (3-6h)--a relative well-being and compensatory reactions in the system of hemomicrocirculation; II (9-15h)--development of disturbances in the aggregate state of blood; III (18-24h)--pronounced disturbances in hemomicrocirculation. Plasmapheresis at peritonitis facilitates: to better functioning of the microcirculatory system, namely, a sharp increasing of the blood flow rate, joining into the blood flow of capillaries that did not function previously and increasing functional capacity of the capillary bed; decreasing blood viscosity and aggregation of erythrocytes. Plasmapheresis applied at peritonitis produces a favourable effect to hemodynamics, evident as an increasing minute and stroke volume of the blood flow, cardiac index, the left ventricle activity and decrease in peripheral vascular resistance.     

Establishing a Role for the GTPase Ypt1p at the Late Golgi

GTPases of the Rab family cycle between an inactive (GDP‐bound) and active (GTP‐bound) conformation. The active form of the Rab regulates a variety of cellular functions via multiple effectors. Guanine nucleotide exchange factors (GEFs) activate Rabs by accelerating the exchange of GDP for GTP, while GTPase activating proteins (GAPs) inactivate Rabs by stimulating the hydrolysis of GTP. The GTPase Ypt1p is required for endoplasmic reticulum (ER)–Golgi and intra‐Golgi traffic in the yeast Saccharomyces cerevisiae. Recent findings, however, have shown that Ypt1p GEF, GAP and an effector are all required for traffic from the early endosome to the Golgi. Here we describe a screen for ypt1 mutants that block traffic from the early endosome to the late Golgi, but not general secretion. This screen has led to the identification of a collection of recessive and dominant mutants that block traffic from the early endosome. While it has long been known that Ypt1p regulates the flow of biosynthetic traffic into the cis side of the Golgi, these findings have established a role for Ypt1p in the regulation of early endosome–Golgi traffic. We propose that Ypt1p regulates the flow of traffic into the cis and trans side of the Golgi via multiple effectors.     

Flow disturbance measurements through a constricted tube at moderate Reynolds numbers

Instantaneous velocities in the field distal to contoured axisymmetric stenoses were measured with a laser Doppler anemometer. Upstream flow conditions were steady and spanned a range of Reynolds numbers from 500 to 2000. Autocorrelation functions and spectra of the velocity were employed to describe the nature of fluid dynamic disturbances. Depending upon the degree of stenosis and the Reynolds number, the flow field contained disturbances of a discrete oscillation frequency, of a turbulent nature, or both. If turbulence was detected in a given experiment, it was always preceded upstream by velocity oscillations at discrete frequency arising from vortex shedding. For mild degrees of stenosis (50% area reduction or less) the intensity of flow disturbances was relatively low until the Reynolds number exceeded 1000, thus highlighting difficulties to be expected in employing flow disturbance detection as a diagnostic tool in the recognition of early atherosclerosis in major arteries. In view of the relatively high noise levels inherent in noninvasive Doppler ultrasound systems employed clinically, it seems unlikely that detection of stenoses of less than 50% area reduction is feasible unless the Reynolds numbers exceed 1000 or unless pulsatility introduces new unsteady flow features beyond those studied here.