A model for the stability and creep of organic materials

A model is presented for the thermally assisted breaking of a number of bonds arranged in parallel and stressed by an individual soft spring each. Using a simplified potential for the bond it is shown that in equilibrium there are two definite regions of elastic behavior: one with all bonds intact, the other with a variable fraction of bonds broken, therefore with a tangent modulus steadily decreasing with applied stress. Criteria are given for the existence of these regions. Beyond these regions time-dependent creep to rupture is found, limited, in turn, by the theoretical fracture strength, the stress necessary for fracture without any thermal assistance, beyond which a bound state is impossible. The time-to-fracture for creep rupture is calculated and an example of the time evolution of the accelerating creep given. The results of the calculations are applied to experimental data on Wallaby tendons by Wang and Ker (J. Exp. Biol. 198 (1995) 831) and data estimated for the bond potential depth, the theoretical fracture strength and the number density of bonds involved as well as the elastic modulus of the ensemble. Values are derived under the assumption of one deformation mechanism being dominant--e.g., (sub-)fibril sliding or sliding of collagen molecules along one another--but the model cannot definitely distinguish between mechanisms.     

Statistical Alignment with a Sequence Evolution Model Allowing Rate Heterogeneity along the Sequence

We present a stochastic sequence evolution model to obtain alignments and estimate mutation rates between two homologous sequences. The model allows two possible evolutionary behaviors along a DNA sequence in order to determine conserved regions and take its heterogeneity into account. In our model, the sequence is divided into slow and fast evolution regions. The boundaries between these sections are not known. It is our aim to detect them. The evolution model is based on a fragment insertion and deletion process working on fast regions only and on a substitution process working on fast and slow regions with different rates. This model induces a pair hidden Markov structure at the level of alignments, thus making efficient statistical alignment algorithms possible. We propose two complementary estimation methods, namely, a Gibbs sampler for Bayesian estimation and a stochastic version of the EM algorithm for maximum likelihood estimation. Both algorithms involve the sampling of alignments. We propose a partial alignment sampler, which is computationally less expensive than the typical whole alignment sampler. We show the convergence of the two estimation algorithms when used with this partial sampler. Our algorithms provide consistent estimates for the mutation rates and plausible alignments and sequence segmentations on both simulated and real data.     

The estimation of current state of Lake Ladoga using mathematical models

This paper describes a mathematical simulation model of the transformation of organic matter and biogenic compounds. The model is validated with observations made on Lake Ladoga. Despite the approximate nature of the biogenic load data, a good agreement is obtained between the calculated substance concentrations and available observations made during individual seasons for different areas of the lake. The model was developed by the author Leonov and this paper presents new model results with accurate formulations for nitrogen and carbon components. Comparison with observational data base collected during 1976–1979 shows that the model results provide good simulation of the annual seasonal changes in material concentrations in the identified regions of the lake.     

Mechanism of Cohesin Loading onto Chromosomes: A Conformational Dynamics Study

The structure-function relationship of cohesin, an essential chromosome maintenance protein, is investigated by analyzing its collective dynamics and conformational flexibility, enhancing our understanding of the sister chromatid cohesion process. A three-dimensional model of cohesin has been constructed by homology modeling using both crystallographic and electron microscopy image data. The harmonic dynamics of the cohesin structure are calculated with a coarse-grained elastic network model. The model shows that the bending motion of the cohesin ring is able to adopt a head-to-tail conformation, in agreement with experimental data. Low-frequency conformational changes are observed to deform the highly conserved glycine residues at the interface of the cohesin heterodimer. Normal mode analysis further reveals that, near large globular structures such as nucleosome and accessory proteins docked to cohesin, the mobility of the coiled-coil regions is notably affected. Moreover, fully solvated molecular dynamics calculations, performed specifically on the hinge region, indicate that hinge opening starts from one side of the dimerization interface, and is coordinated by highly conserved glycine residues.     

中国陆地经济与生态环境协调发展的空间演变

以中国2853个县(区)的GDP数据和全国1km格网土地利用数据为基础,通过构建ESV、YEEH和EEHC模型,依据ESV和GDP单位面积变化计算中国陆地经济与生态环境协调度,并借助Arc GIS 10.1平台对YEEH和EEHC栅格数据进行空间分析,以此揭示中国陆地经济发展与生态环境系统的相关关系和演变特征。研究表明:(1)中国陆地经济与生态环境协调发展度逐渐好转,呈现出东北地区好于西部地区,西部地区好于中、东部地区的空间格局,反映出当面社会经济活动与自然生态环境关系之间总体上向着可持续的方向发展;(2)中国陆地经济与生态环境协调发展的空间分布状态从1980年的低于均值聚集模式发展变化到2010年的高—低两种聚集模式共同分布;(3)中国陆地经济社会与生态环境发展协调度当前整体上趋于好转,但在区域分布上空间差异较为明显,西部地区在保护生态环境的同时需大力发展经济,而东中部地区则需在发展经济的同时注重生态保持与修复,中国的经济发展与生态环境建设工作依然任重而道远。     

Normalization references for Europe and North America for application with USEtox? characterization factors

Purpose

In life cycle impact assessment, normalization can be a very effective tool for the life cycle assessment practitioner to interpret results and put them into perspective. The paper presents normalization references for the recently developed USEtox? model, which aims at calculating globally applicable characterization factors. Normalization references for Europe and North America are determined, and guidance for expansions to other geographical regions is provided.

Materials and methods

The base years of the European and North American inventories are 2004 and 2002/2008, respectively. Emission data were extracted from two literature sources referring to each of the considered regions. The inventory for North America was adapted to avoid extrapolation of data from other regions and thus bring consistency with the emission inventory for Europe. In spite of different inventory assumptions, a similar coverage of substances was obtained for both regions with relatively high representation of metals and a number of organic compounds, mainly consisting of non-methane volatile organic compounds and pesticides. The two inventory sets were eventually characterized with the characterization factors (CFs) calculated with the version 1.0 of the USEtox? model and substance database; both interim and recommended CFs were used.

Results and discussion

Normalization references are provided for Europe and North America for the three USEtox? toxic impact categories; ratios between the normalization references for the two regions in all cases lie below a factor of 3. Causes for the observed discrepancies are found to be different inventory assumptions as well as variations in the type and intensity of actual emissions between the two regions. Additional causes are inventories that only cover a limited number of substances, and the characterization model, which can only provide interim factors for certain substances like metal compounds. Based on these causes and on a review of recent studies on normalization references, a list of substances to be prioritized when collecting emission data was built, demonstrating the importance of metals.

Conclusions

In the perspective of further refining the presented normalization references and of calculating new references for other regions, guidance is provided including a list of priority substances that should be considered when building emission inventories for normalization references.     

基于MODIS-NDVI的区域冬小麦遥感估产——以山东省济宁市为例

以黄淮海平原冬小麦主产区山东省济宁市为研究实例,利用遥感方法,采用250 m分辨率经过Savitzky-Golay滤波技术平滑处理的MODIS-NDVI遥感数据对冬小麦产量进行预测.研究选取了冬小麦关键生育期内0.2～0.8范围的旬NDVI数据,并建立了其与冬小麦产量的关系.同时,采用逐步回归方法筛选建立冬小麦关键生育期旬NDVI与冬小麦产量间关系的估产模型.利用地面实测冬小麦产量数据,对所建的估产模型进行精度检验,结果表明,估产相对误差在-3.6％～3.9％之间.表明利用Savitzky-Golay滤波技术平滑后的作物关键生育期内MODIS-NDVI遥感数据进行冬小麦估产,其方法精度较高,具有一定的可行性.     

Genes that affect morphogenesis of the murine mandible. Recombinant-inbred strain analysis

The CXB set of recombinant inbred mouse strains provided an opportunity to observe the effects of reassorted subsets of genes on the shape of the mandible. The distances between 12 landmarks in all paired combinations were calculated to evaluate genetic control in small regions. The genetic relationships between interlandmark distances revealed genes to have most of their effects in localized regions, and the greater heritabilities usually to apply to those distances between adjacent landmarks. Interrelationships between measurements are usually explicable on a developmental basis. It is proposed that genes of this sort bring about the changes seen in organ shape during evolution. A model plan for the organization of gene activation during morphogenesis is described.     

Modeling of preparative reversed-phase HPLC of insulin

The adsorption isotherms of three recombinant proteins, human insulin, porcine insulin, and Lispro, were measured by frontal analysis on a YMC-ODS C18 column with an aqueous solution at 31% acetonitrile (0.1% TFA) as the mobile phase. The retention behavior of insulin, its related molecular structure, its conformation, and its aggregation in this phase system are discussed. The experimental isotherm data were fitted to the Langmuir, the Langmuir-Freundlich, and the Toth models. The results allow for a quantitative comparison of the saturation capacities, the equilibrium constants, and the exponents that represent the heterogeneity of the stationary phase obtained for the different insulin variants studied. The Toth model provided the best fit of the experimental data. The overloaded band profiles were calculated using the lumped pore diffusion and the equilibrium-dispersive model of chromatography. An excellent agreement between calculated and experimental profiles was demonstrated.     

Calculation of the spectrum of dielectric losses in the protein-water system

The spectrum of dielectric losses in the frequency range up to microwaves for haemoglobin solution (Hb) in water was calculated. For humidified Hb the concentration relationships of epsilon components having a break of curve with water concentration exceeding some critical value were also determined. For three water fractions in the solution to be calculated the model of confined rotators was applied. The fractions of ice-like water, H2O molecules with weak H-bonds and protein-bound water were investigated. The protein molecules considered as a rigid rotator were calculated in terms of the extended diffusion model. A qualitative agreement with the experimental data was obtained. A possibility is shown of establishing relations between the Debye times in the dispersion regions beta, delta, gamma and the model parameters. The latter characterize the microscopic motion of polar molecules during the correlation time of the rotator angular velocity.     

Joint estimation of recombination fractions and interference coefficients in multilocus linkage analysis.

Estimation of recombination fractions and interference coefficients is of importance in multilocus linkage analysis. With the development of molecular genetic technologies such as RFLP, multilocus data are readily available to researchers. Several methods have been developed to analyze such data, and each performs well under restrictive conditions. The present paper proposes a method based on a multiplicative model and maximum-likelihood estimation of recombination fractions and interference coefficients. The estimators are consistent regardless of the model assumptions and are efficient if the model is a good approximation. The estimators are tractable even when there are incomplete observations. Furthermore, the interference between nonadjacent chromosomal regions or those among three chromosomal regions can be modeled and tested by a simple Z-test. The proposed method was applied to linkage analysis of four-locus data obtained from Drosophila and that of seven-locus data obtained again from Drosophila. Reanalysis of the first example revealed that there is interference between chromosomal regions 2 and 3. Analysis of the second example suggested that there is triple interference as well as pairwise interference between nonadjacent chromosomal regions; the genetic interpretation of these findings remains to be developed.     

Lipid-cholesterol interactions in the P beta' phase. Application of a statistical mechanical model.

We describe a statistical mechanical model for lipid-cholesterol mixtures in the P beta' (ripple) phase of lipid bilayers. The model is a simple extension of an earlier model for the ripple phase in pure lipid bilayers. The extension consists of adding a degree of freedom to allow for the occupation of underlying lattice sites by cholesterol molecules, and adding a lipid-cholesterol interaction term to the model Hamiltonian. The interaction term was constructed based on numerical calculations of lipid-cholesterol energies for several different packing juxtapositions of the two molecules. Other than the lipid-cholesterol interactions, the extended model uses the same parameter set as the earlier model, so that comparison of the properties of the extended model with experimental data serves as a test of the validity of the original model. Properties of the model were calculated using the Monte Carlo method. Results are displayed as snapshots of the ripple configurations at different cholesterol concentrations. The spacing of the ripples increases with increasing cholesterol concentration and the rate of increase compares very well with experimental data. The success of this model supports the conclusion drawn earlier that frustration arising from anisotropic packing interactions is responsible for the ripple phase in lipid bilayers. In the extended model these packing interactions are responsible for the selective partitioning of cholesterol in the regions between the ripples.     

A theoretical model for the association of amphiphilic transmembrane peptides in lipid bilayers

A theoretical model is proposed for the association of trans-bilayer peptides in lipid bilayers. The model is based on a lattice model for the pure lipid bilayer, which accounts accurately for the most important conformational states of the lipids and their mutual interactions and statistics. Within the lattice formulation the bilayer is formed by two independent monolayers, each represented by a triangular lattice, on which sites the lipid chains are arrayed. The peptides are represented by regular objects, with no internal flexibility, and with a projected area on the bilayer plane corresponding to a hexagon with seven lattice sites. In addition, it is assumed that each peptide surface at the interface with the lipid chains is partially hydrophilic, and therefore interacts with the surrounding lipid matrix via selective anisotropic forces. The peptides would therefore assemble in order to shield their hydrophilic residues from the hydrophobic surroundings. The model describes the self-association of peptides in lipid bilayers via lateral and rotational diffusion, anisotropic lipid-peptide interactions, and peptide-peptide interactions involving the peptide hydrophilic regions. The intent of this model study is to analyse the conditions under which the association of trans-bilayer and partially hydrophilic peptides (or their dispersion in the lipid matrix) is lipid-mediated, and to what extent it is induced by direct interactions between the hydrophilic regions of the peptides. The model properties are calculated by a Monte Carlo computer simulation technique within the canonical ensemble. The results from the model study indicate that direct interactions between the hydrophilic regions of the peptides are necessary to induce peptide association in the lipid bilayer in the fluid phase. Furthermore, peptides within each aggregate are oriented in such a way as to shield their hydrophilic regions from the hydrophobic environment. The average number of peptides present in the aggregates formed depends on the degree of mismatch between the peptide hydrophobic length and the lipid bilayer hydrophobic thickness: The lower the degree of mismatch is the higher this number is. Received: 30 December 1996 / Accepted: 9 May 1997     

Analysis of thyroid cancer data from the Ukraine after ’Chernobyl’ using a two-mutation carcinogenesis model

The thyroid cancer data of children in the northern regions of the Ukraine after the reactor accident at Chernobyl were combined with thyroid dose measurements in the same regions and analysed using a two- mutation carcinogenesis model. The best fit was obtained for radiation acting as an initiating agent, i.e. on the first mutation of the model. The observed relatively high increase of thyroid cancer incidence after 1990 in children exposed to radiation released after the reactor accident could be ascribed to the high thyroid doses and the relatively low background thyroid cancer incidence in children. The maximum annual incidence is predicted to occur fairly soon after the reactor accident, i.e. about 10 years. For adults, the predicted relative increase of annual thyroid cancers is much lower than for children younger than 20 years. The modelling results are used to derive risk estimates for radiation-induced thyroid cancer. These risk estimates are dependent on age at exposure, follow-up time and the background thyroid cancer incidence. The calculated excess absolute risk for a population of all ages is about one-third of that currently used by ICRP, but for children the calculated absolute risks are about a factor of 3 higher than derived in other epidemiological studies. The model results indicate that the excess absolute radiation risk per unit dose for children is about the same as or a little lower than that for adults. Received: 11 May 1999 / Accepted: 30 December 1999     

基于CNV区域网络识别神经胶质瘤的重要功能区域

目的：基于基因拷贝数变异（CNV）区域网络识别神经胶质瘤的重要功能区域。方法：运用独特的计算样本的共相关性值的方法,使CNV数据与基因数据产生联系;基于蛋白质互作关系,在CNV区域与基因之间搭建桥梁,构建CNV区域网络;分析网络拓扑性质,识别出神经胶质瘤的重要功能CNV区域。结果：本文共识别出了11个与神经胶质瘤相关的候选重要功能CNV区域,通过功能注释和通路分析,确认了识别到的区域与神经胶质瘤有重要联系。结论：通过基因与表型之间的联系,利用已知表型基因在同源、功能、互作、结构域上的特征将CNV区域与基因联系起来,通过基因的功能可以了解到CNV区域的功能,对于疾病的预测和诊断有重要的意义。     

基于遥感和Penman-Monteith模型的内陆河流域不同生态系统蒸散发估算

遥感数据具有很好的时空连续性,它是区域蒸散发通量估算的有效方法。引入了一个简单的具有生物物理基础的Penman-Monteith(P-M)模型,分别利用黑河流域高寒草地阿柔站和干旱区农田盈科站2008—2009年的气象数据和MODIS(Moderate Resolution Imaging Spectroradiometer)叶面积指数(LAI),实现了2008—2009年日蒸散发的估算,并同时实现了对植被蒸腾和土壤蒸发的分别估算。结果表明,利用P-M公式模拟的蒸散发与实测的蒸散发具有较好的一致性,日蒸散发模拟的决定系数(R2)超过0.8。估算的高寒草甸和干旱区农田玉米全年平均的蒸腾分别为0.78 mm/d和1.20 mm/d,分别占总蒸散发的60%和61%,土壤蒸发分别为0.53和0.77 mm/d,占总蒸发的40%和39%。可见两种生态系统的作物蒸腾均强于土壤蒸发,同时农田玉米蒸腾强于高寒草甸蒸腾。研究结果证明了基于遥感的P-M公式可以很好地实现对高寒草地和干旱区农田生态系统蒸散发的估算。通过考虑土壤水分变化对气孔导度的影响,可以提高模型对农田蒸散发的模拟精度。     

Site-Dependent Life-Cycle Impact Assessment of Acidification

The lack of spatial differentiation in current life-cycle impact assessment (LCIA) affects the relevance of the assessed impact. This article first describes a framework for constructing factors relating the region of emission to the acidifying impact on its deposition areas. Next, these factors are established for 44 European regions with the help of the RAINS model, an integrated assessment model that combines information on regional emission levels with information on long-range atmospheric transport to estimate patterns of deposition and concentration for comparison with critical loads and thresholds for acidification, eutrophication via air; and tropospheric ozone formation. The application of the acidification factors in LCIA is very straightforward. The only additional data required, the geographical site of the emission, is generally provided by current life-cycle inventory analysis. The acidification factors add resolving power of a factor of 1,000 difference between the highest and lowest ratings, while the combined uncertainties in the RAINS model are canceled out to a large extent in the acidification factors as a result of the large number of ecosystems they cover The framework presented is also suitable for establishing similar factors for eutrophication and tropospheric ozone formation for regions outside Europe as well.     

Interfacial conditions between a press-fit acetabular cup and bone during daily activities: implications for achieving bone in-growth

Interfacial gaps and relative micromotions during activities are widely believed to restrict the boney in-growth process of non-cemented acetabular cups. Using finite element modeling of the cup-bone system, relative micromotions and interfacial gaps are calculated for walking slow, normal and fast and for climbing upstairs, downstairs and standing up from a chair. A 2mm press-fit is simulated and interfacial conditions in the immediate postoperative period (i.e. prior to boney in-growth) calculated between paired nodes covering the whole of the interface. In regions of 'safe' micromotions and 'allowable' gaps, boney in-growth is simulated by specifying zero relative displacement between nodal pairs. The modified model is then resubjected to the loads associated with climbing upstairs, which was shown to be the worst activity. Interfacial conditions are recalculated for subsequent iterations. The procedure is repeated until no further in-growth is predicted. The final pattern of in-growth calculated with the model compares reasonably well with histological evidence from explanted canine cups (Cha et al., 1998. Transactions of the Orthopaedic Research Society, 23, p. 373). Bridging between adjacent regions of in-growth is observed. Notably, in-growth occurs at most of the periphery but not in the polar region. The lack of polar in-growth is caused by the interfacial gap assumed to exist after cup implantation. It is suggested that increasing/decreasing hip-joint loads would have little effect on this lack of polar in-growth. However, excessive micromotions as a result of high hip-joint loads cause a lack of in-growth in the anterior region of the periphery in the model. Although such results were not found in the canine study, if relevant to the general human population, the avoidance of harsh weight-bearing activities may encourage complete peripheral in-growth but is speculated to do little for polar in-growth.     

Metabolic flux analysis as a tool for the elucidation of the metabolism of neurotransmitter glutamate

A flux analysis model for the metabolism of neurotransmitter glutamate is constructed, in order to study functional aspects of its metabolism. This work is based on the potassium [K(+)] evoked neurotransmitter glutamate released, as measured in a series of experiments of superfused rat or mouse brain preparations. These measurements are combined with data reported, concerning the metabolism of glutamate and its precursors, glutamine and glucose in rat cerebral cells in vivo. The proposed stoichiometry of the specific reaction network renders the model solvable. The classification procedure establishes that the measured fluxes are all balanceable and all non-measured fluxes can be calculated. The system is well posed with a condition number of 7.8536. The results emphasize the importance of phosphate activated glutaminase and aspartate aminotransferase in the metabolism of neurotransmitter glutamate. Reported data on the rate of the malate-aspartate shuttle, as well as the anaplerotic flux of the glial pyruvate carboxylase reaction are in agreement with the estimations calculated from the proposed model.     

Detecting interaction between random region and fixed age effects in disease mapping

The purpose of this article is to draw attention to the possible need for inclusion of interaction effects between regions and age groups in mapping studies. We propose a simple model for including such an interaction in order to develop a test for its significance. The assumption of an absence of such interaction effects is a helpful simplifying one. The measure of relative risk related to a particular region becomes easily and neatly summarized. Indeed, such a test seems warranted because it is anticipated that the simple model, which ignores such interaction, as is in common use, may at times be adequate. The test proposed is a score test and hence only requires fitting the simpler model. We illustrate our approaches using mortality data from British Columbia, Canada, over the 5-year period 1985-1989. For this data, the interaction effect between age groups and regions is quite large and significant.