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1.
Bulanova KIa Lobanok LM 《Radiatsionnaia biologiia, radioecologiia / Rossi?skaia akademiia nauk》2004,44(1):5-14
The principles of information theory were applied for analysis of radiobiological effects. The perception of ionizing radiations as a signal enables living organism to discern their benefits or harm, to react to absolute and relatively small deviations, to keep the logic and chronicle of events, to use the former experience for reacting in presence, to forecast consequences. The systemic analysis of organism's response to ionizing radiations allows explaining the peculiarities of effects of different absorbed doses, hormesis, apoptosis, remote consequences and other post-radiation effects. 相似文献
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Urbanization induces detrimental effects on the eco-environment that are beginning to be extensively described. However, the adoption of suitable indicators and reliable methods still requires attention to provide a basis for a more accurate understanding of eco-environmental effects from urbanization. The aggregated index system representing the coupling relationships between urbanization and eco-environment was introduced and an integrated sustainable development approach (ISD) to simulate and evaluate the integrative effects was developed in this paper. The ISD consists of modules of the coupling relationship assessments, systematic analysis of potential eco-environmental changes, and sustainability evaluation. An interpretative structural modeling (ISM) and grey relative technique (GRT) are used to analyze the systematical structure and assess the coupling relationships. A system dynamics model (SD) and artificial neural network (ANN) are used to simulate the potential environmental changes and compare the sustainability, respectively. An application study of Jiangsu province in China was performed, where the general eco-environmental integrity is under significant urbanization pressure. The potential eco-environmental scenarios from 2010 to 2015 under natural, populated, economic, spatial and social urbanization patterns were simulated and analyzed. The result reveals that the urbanization sustainability may be met on condition that either populated urbanization or social urbanization pattern is adopted in Jiangsu province, China. The aggregated indexes and ISD may help local authorities better understand and address the complex coupling relationship, and develop improved regional environmental management strategies that better balance urbanization and eco-environmental conservation. 相似文献
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Systems biology approach to bioremediation 总被引:1,自引:0,他引:1
Bioremediation has historically been approached as a 'black box' in terms of our fundamental understanding. Thus it succeeds and fails, seldom without a complete understanding of why. Systems biology is an integrated research approach to study complex biological systems, by investigating interactions and networks at the molecular, cellular, community, and ecosystem level. The knowledge of these interactions within individual components is fundamental to understanding the dynamics of the ecosystem under investigation. Understanding and modeling functional microbial community structure and stress responses in environments at all levels have tremendous implications for our fundamental understanding of hydrobiogeochemical processes and the potential for making bioremediation breakthroughs and illuminating the 'black box'. 相似文献
5.
A novel approach is proposed for modeling loop regions in proteins. In this approach, a prerequisite sequence-structure alignment
is examined for regions where the target sequence is not covered by the structural template. These regions, extended with
a number of residues from adjacent stem regions, are submitted to fold recognition. The alignments produced by fold recognition
are integrated into the initial alignment to create an alignment between the target sequence and several structures, where
gaps in the main structural template are covered by local structural templates. This one-to-many (1:N) alignment is used to create a protein model by existing protein-modeling techniques. Several alternative approaches were
evaluated using a set of ten proteins. One approach was selected and evaluated using another set of 31 proteins. The most
promising result was for gap regions not located at the C-terminus or N-terminus of a protein, where the method produced an
average RMSD 12% lower than the loop modeling provided with the program MODELLER. This improvement is shown to be statistically
significant.
Figure The method derived from the training set applied to CASP target T0191 相似文献
6.
Birschwilks M Gruenberger M Adelmann C Tapio S Gerber G Schofield PN Grosche B 《Radiation research》2011,175(4):526-531
For financial and ethical reasons, the large-scale radiobiological animal studies conducted over the past 50 years are, to a large extent, unrepeatable experiments. It is therefore important to retain the primary data from these experiments to allow reanalysis, reinterpretation and re-evaluation of results from, for example, carcinogenicity studies, in the light of new knowledge in radiation biology. Consequently, there is an imperative need to keep these data available for the research community. The European Radiobiological Archives (ERA) were developed to fulfill this task. ERA has become a unique archive, including information from almost all European long-term studies carried out between the 1960s and the 1990s. The legacy database was originally developed in a manner that precluded online use. Therefore, strong efforts were made to transform it into a version that is available online through the web. This went together with quality assurance measures, including first the estimation of the rate of non-systematic errors in data entry, which at 2% proved to be very low. Second, every data set was compared against two external sources of information. Standardization of terminology and histopathology is a prerequisite for meaningful comparison of data across studies and analysis of potential carcinogenic effects. Standardization is particularly critical for the construction of a database that includes data from different studies evaluated by pathologists in different laboratories. A harmonized pathology nomenclature with modern standard pathology terms was introduced. As far as possible, references for the various studies were directly linked to the studies themselves. Further, a direct link to the JANUS database was established. ERA is now in a position where it has the potential to become a worldwide radiobiological research tool. ERA can be accessed at no cost at https://era.bfs.de. An ID and password can be obtained from the curators at era@bfs.de . 相似文献
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A multilevel approach to cancer growth modeling 总被引:1,自引:0,他引:1
Cancer growth models may be divided into macroscopic models, which describe the tumor as a single entity, and microscopic ones, which consider the tumor as a complex system whose behavior emerges from the local dynamics of its basic components, the neoplastic cells. Mesoscopic models (e.g. as based on the Local Interaction Simulation Approach [Delsanto, P.P., Mignogna, R., Scalerandi, M., Schechter, R., 1998. In: Delsanto, P.P. Saenz, A.W. (Eds.), New Perspectives on Problems in Classical and Quantum Physics, vol. 2. Gordon & Breach, New Delhi, p. 5174]), which explicitly consider the behavior of cell clusters and their interactions, may be used instead of the microscopic ones, in order to study the properties of cancer biology that strongly depend on the interactions of small groups of cells at intermediate spatial and temporal scales. All these approaches have been developed independently, which limits their usefulness, since they all include relevant features and information that should be cross-correlated for a deeper understanding of the mechanisms involved. In this contribution we consider multicellular tumor spheroids as biological reference systems and propose an intermediate model to bridge the gap between a macroscopic formulation of tumor growth and a mesoscopic one. Thus we are able to establish, as an important result of our formalism, a direct correspondence between parameters characterizing processes occurring at different scales. In particular, we analyze their dependence on an important limiting factor to tumor growth, i.e. the extra-cellular matrix pressure. Since the macro and meso-models stem from totally different roots (energy conservation and clinical observations vs. cell groups dynamics), their consistency may be used to validate both approaches. It may also be interesting to note that the proposed formalism fits well into a recently proposed conjecture of growth laws universality. 相似文献
10.
We present a “natural-constructive approach” to modeling the cognitive process, which is based on the dynamic theory of information, the technique of nonlinear differential equations, and the concept of a “dynamic formal neuron.” The version of cognitive architecture that was designed within the natural-constructive approach is presented. One important constructive feature of this architecture consists in splitting up the entire system into two similar hemi-systems (by analogy with the right and left cerebral hemispheres). One of these is responsible for the generation of information and learning, with other one being responsible for the reception and processing of well-known information. This functional specialization is provided by the presence of noise (a random factor) in the generation hemi-system; in the reception hemi-system, all the processes should proceed successively rather than stochastically. The interpretation of the concepts of intuition, logic, consciousness, and sub-consciousness is discussed. The architecture that is designed within the natural-constructive approach is compared with other theoretical approaches (graph theory and the “cognitom” concept), and with anatomical data. The concept of an experiment is proposed that could verify or disprove the main inferences of the natural-constructive approach. 相似文献
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We propose a general Bayesian approach to heteroskedastic error modeling for generalized linear mixed models (GLMM) in which linked functions of conditional means and residual variances are specified as separate linear combinations of fixed and random effects. We focus on the linear mixed model (LMM) analysis of birth weight (BW) and the cumulative probit mixed model (CPMM) analysis of calving ease (CE). The deviance information criterion (DIC) was demonstrated to be useful in correctly choosing between homoskedastic and heteroskedastic error GLMM for both traits when data was generated according to a mixed model specification for both location parameters and residual variances. Heteroskedastic error LMM and CPMM were fitted, respectively, to BW and CE data on 8847 Italian Piemontese first parity dams in which residual variances were modeled as functions of fixed calf sex and random herd effects. The posterior mean residual variance for male calves was over 40% greater than that for female calves for both traits. Also, the posterior means of the standard deviation of the herd-specific variance ratios (relative to a unitary baseline) were estimated to be 0.60 ± 0.09 for BW and 0.74 ± 0.14 for CE. For both traits, the heteroskedastic error LMM and CPMM were chosen over their homoskedastic error counterparts based on DIC values. 相似文献
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Population balance approach to modeling hairy root growth 总被引:1,自引:0,他引:1
Though numerous models have been developed to describe the growth of microbial cell cultures, far fewer models are available to describe the growth of hairy root cultures. Here a population balance model is proposed to simulate the growth of hairy roots. The model accounts for the increase in biomass due to elongation of a branch by cell division as well as the formation of new branches. The model incorporates the fact that although the likelihood of the formation of a new lateral branch is a maximum at a specific age of the parent branch, lateral branches can form over a distribution of ages of the parent branch. Model parameters are estimated using the genetic algorithm based on experimental data for batch and continuous bioreactors. The model proposed here may provide a better understanding of the increase in biomass of hairy root cultures. 相似文献
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Understanding conception probabilities is important not only for helping couples to achieve pregnancy but also in identifying acute or chronic reproductive toxicants that affect the highly timed and interrelated processes underlying hormonal profiles, ovulation, libido, and conception during menstrual cycles. Currently, 2 statistical approaches are available for estimating conception probabilities depending upon the research question and extent of data collection during the menstrual cycle: a survival approach when interested in modeling time-to-pregnancy (TTP) in relation to women or couples' purported exposure(s), or a hierarchical Bayesian approach when one is interested in modeling day-specific conception probabilities during the estimated fertile window. We propose a biologically valid discrete survival model that unifies the above 2 approaches while relaxing some assumptions that may not be consistent with human reproduction or behavior. This approach combines both the survival and the hierarchical models allowing investigators to obtain the distribution of TTP and day-specific probabilities during the fertile window in a single model. Our model allows for the consideration of covariate effects at both the cycle and the daily level while accounting for daily variation in conception. We conduct extensive simulations and utilize the New York State Angler Prospective Pregnancy Cohort Study to illustrate our approach. We also provide the code to implement the model in R software in the supplemental section of the supplementary material available at Biostatistics online. 相似文献
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The most recent Recommendations (Publication 103) issued by the International Commission for Radiological Protection (ICRP) are based on the data that have been published since 1990 up to now. The basic task of the ICRP Committee 1 was to formulate the key implications of studies on radiobiological effects for the purposes of radiological protection. Presented in the paper are the new achievements in the field of biology, radiobiology and radiation epidemiology which were taken into account by the ICRP in the process of Publication 103 preparation. The Recommendations provide present-day values of weighting factors for radiation exposure and tissue weighting factors, as well as radiation detriment and radiogenic risk factors for cancer and genetic diseases. Also considered are tissue reactions to radiation exposure, consequences of in utero exposure and the risks of developing non-cancer diseases for exposed individuals. It should be noted that the key inferences and recommendations are to a considerable degree related to biological effects accounted for by acute and chronic exposure to ionizing radiation in the range of small doses (up to 100 mSv). 相似文献
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Six niche-based models proposed by Tokeshi, based on different assumptions of resource allocation by species, were fitted
on phytoplankton relative abundance distributions, and potential environmental and biotic factors supporting the applicability
of the fitted models were discussed. Overall 16 assemblages corresponding to different sampling times, various environmental
conditions, and resource regimes within a year were fitted to the models. Phytoplankton biovolume was used as a measure of
abundance, and a randomization test was applied to compare the model fit to the field data. The majority of the phytoplankton
assemblages (11 of 16) were successfully described by the Random Fraction model, which is based on the theoretical assumption
that resource is apportioned by the species in a random way. Only a few assemblages (three of 16), characterized by extremes
in resource availability or disturbance, were not fitted by any of the models. The Random Fraction model in particular was
rejected due to a steep slope during the first ranks, while the rest of the distribution remained relatively even, providing
further evidence of resilience in phytoplankton communities. Although larger cells seem to have the potential to develop higher
biomass, it seems that other factors, including the surface-to-volume ratio, counterbalance this advantage, resulting in a
random-like behaviour in resource acquisition by phytoplankton, irrespective of cell size or species identity. 相似文献
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We describe a fast ab initio method for modeling local segments in protein structures. The algorithm is based on a divide and conquer approach and uses a database of precalculated look-up tables, which represent a large set of possible conformations for loop segments of variable length. The target loop is recursively decomposed until the resulting conformations are small enough to be compiled analytically. The algorithm, which is not restricted to any specific loop length, generates a ranked set of loop conformations in 20-180 s on a desktop PC. The prediction quality is evaluated in terms of global RMSD. Depending on loop length the top prediction varies between 1.06 A RMSD for three-residue loops and 3.72 A RMSD for eight-residue loops. Due to its speed the method may also be useful to generate alternative starting conformations for complex simulations. 相似文献
18.
A modeling approach to explain pulse design in bats 总被引:2,自引:1,他引:2
In this modeling study we wanted to find out why bats of the family Vespertilionidae (and probably also members of other families of bats) use pulses with a certain bandwidth and duration. Previous studies have only speculated on the function of bandwidth and pulse duration in bat echolocation or addressed this problem by assuming that bats optimize echolocation parameters to achieve very fine acuities in receiving single echoes. Here, we take a different approach by assuming that bats in nature rarely receive single echoes from each pulse emission, but rather many highly overlapping echoes. Some echolocation tasks require individual echoes to be separated to reconstruct reflection points in space. We used an established hearing model to investigate how the parameters bandwidth and pulse duration influence the separation of overlapping echoes. Our findings corroborate the following previously unknown or unsubstantiated facts: 1. Broadening the bandwidth improves the bat's lower resolution limit. 2. Increasing the sweep rate (defined by bandwidth and pulse duration) improves acuity of each extracted echo. 3. Decreasing the sweep rate improves the probability of frequency channels being activated. Since facts 2 and 3 affect sweep rate in an opposing fashion, an optimum sweep rate will exist, depending on the quality of the returning echoes and the requirements of the bat to improve acuity. The existence of an optimal sweep rate explains why bats are likely to use certain combinations of bandwidth and pulse duration to obtain such sweep rates. 相似文献
19.
We present a new approach to modeling languages for computational biology, which we call the layer-oriented approach. The approach stems from the observation that many diverse biological phenomena are described using a small set of mathematical formalisms (e.g. differential equations), while at the same time different domains and subdomains of computational biology require that models are structured according to the accepted terminology and classification of that domain. Our approach uses distinct semantic layers to represent the domain-specific biological concepts and the underlying mathematical formalisms. Additional functionality can be transparently added to the language by adding more layers. This approach is specifically concerned with declarative languages, and throughout the paper we note some of the limitations inherent to declarative approaches. The layer-oriented approach is a way to specify explicitly how high-level biological modeling concepts are mapped to a computational representation, while abstracting away details of particular programming languages and simulation environments. To illustrate this process, we define an example language for describing models of ionic currents, and use a general mathematical notation for semantic transformations to show how to generate model simulation code for various simulation environments. We use the example language to describe a Purkinje neuron model and demonstrate how the layer-oriented approach can be used for solving several practical issues of computational neuroscience model development. We discuss the advantages and limitations of the approach in comparison with other modeling language efforts in the domain of computational biology and outline some principles for extensible, flexible modeling language design. We conclude by describing in detail the semantic transformations defined for our language. 相似文献
20.
Michael R. Blatt Adrian Hills Zhong-Hua Chen Yizhou Wang Maria Papanatsiou Vigilio L. Lew 《Plant signaling & behavior》2013,8(1)
Much of the 70% of global water usage associated with agriculture passes through stomatal pores of plant leaves. The guard cells, which regulate these pores, thus have a profound influence on photosynthetic carbon assimilation and water use efficiency of plants. We recently demonstrated how quantitative mathematical modeling of guard cells with the OnGuard modeling software yields detail sufficient to guide phenotypic and mutational analysis. This advance represents an all-important step toward applications in directing “reverse-engineering” of guard cell function for improved water use efficiency and carbon assimilation. OnGuard is nonetheless challenging for those unfamiliar with a modeler’s way of thinking. In practice, each model construct represents a hypothesis under test, to be discarded, validated or refined by comparisons between model predictions and experimental results. The few guidelines set out here summarize the standard and logical starting points for users of the OnGuard software. 相似文献