On the mechanical characterization of compact bone structure using the homogenization theory

In a previous paper (Crolet et al., 1993, J. Biomechanics 26, 677–687), a modelling of the mechanical behavior of compact bone was presented, in which the homogenization theory was the basic tool of computation. In this simulation, approximations were used for the modelling of the lamellae and the osteons: the lamella and the osteon were divided into cylindrical sectors, each sector being approximated as a parallelepiped having a periodic structure (fibrous composite for the lamella, superimposition of plates for the osteon). The present study deals with a new model without these approximations. First, it can be proved that the homogenized elasticity tensor for a lamella, which has a non-periodic structure, is obtained at each geometrical point as a homogenized tensor of a periodic problem. Similarly, for the osteonal structure, the components of the homogenized tensor are determined at each point as the result of a periodic homogenization.

The software OSTEON, which is the computational method associated with this model, allows one to obtain a better understanding of the effects of many bony parameters. The obtained results are in accordance with experimental data.     

Changes in bird communities in Swaziland savannas between 1998 and 2008 owing to shrub encroachment

Aim This study investigates changes in bird communities between 1998 and 2008 in four savanna sites in Swaziland and the extent to which shrub encroachment is responsible for these changes. Location Swaziland, southern Africa. Methods Generalized estimated equations were used to estimate changes in bird species occurrence between 1998 and 2008. Remote sensing of aerial photographs/satellite images was used to assess vegetation changes during the same period. We assessed the role of shrub encroachment for bird communities by testing the relationship between change in species occurrence and species habitat using a general linear model. We also estimated species richness, colonization and extinction and used general linear models to test the effects of vegetation changes on these parameters. Results More than half of the bird species showed a significant change in occurrence between 1998 and 2008: 32 species increased and 29 decreased. Change in species occurrence was significantly explained by species habitat. Species significantly increasing were mainly associated with wooded savanna, whereas species significantly decreasing were mainly associated with open savanna. Species richness decreased significantly, and this decrease was significantly explained by shrub cover increase at the plot scale (from 24% to 44% on average). Extinction at the plot scale was significantly influenced by the loss of grass cover, while colonization at the plot scale was influenced by tree cover increase. Main conclusions This study represents the first evidence of temporal changes in bird communities owing to shrub encroachment in southern Africa. Despite its short time frame (10 years), this study shows dramatic changes in both vegetation structure and bird community composition. This confirms the general concern for southern African bird species associated with open savanna if current trends continue.     

Influence of spatial structure on effective nutrient diffusion in bacterial biofilms

The main contribution of this paper is to use homogenization techniques to compute diffusion coefficients from experimental images of microbial biofilms. Our approach requires the analysis of several experimental spatial structures of biofilms in order to derive from them a Representative Volume Element (RVE). Then, we apply a suitable numerical procedure to the RVE to derive the diffusion coefficients. We show that diffusion coefficients significantly vary with the biofilm structure. These results suggest that microbial biofilm structures can favour nutrient access in some cases.     

Intraspecific Concerted Evolution of the rDNA ITS1 in Anopheles farauti Sensu Stricto (Diptera: Culicidae) Reveals Recent Patterns of Population Structure

We examined the intraindividual variation present in the first ribosomal internal transcribed spacer (ITS1) of Anopheles farauti to determine the level of divergence among populations for this important malarial vector. We isolated 187 clones from 70 individuals and found regional variation among four internal tandem repeats. The data were partitioned prior to analysis given the presence of a paralogous ITS2 sequence, called the 5'-subrepeat, inserted in the ITS1 of most clones. A high level of homogenization and population differentiation was observed for this repeat, which indicates a higher rate of turnover relative to the adjacent 'core' region. Bayesian analysis was performed using several substitutional models on both a combined and a partitioned data set. On the whole, the ITS1 phylogeny and geographic origin of the samples appear to be congruent. Some interesting exceptions indicate the spread of variant repeats between populations and the retention of ancestral polymorphism. Our data clearly demonstrate concerted evolution at the intraspecific level despite intraindividual variation and a complex internal repeat structure from a species that occupies a continuous coastal distribution. A high rate of genomic turnover in combination with a high level of sequence divergence appears to be a major factor leading to its concerted evolution within these populations.     

Homogenization techniques for population dynamics in strongly heterogeneous landscapes

An important problem in spatial ecology is to understand how population-scale patterns emerge from individual-level birth, death, and movement processes. These processes, which depend on local landscape characteristics, vary spatially and may exhibit sharp transitions through behavioural responses to habitat edges, leading to discontinuous population densities. Such systems can be modelled using reaction–diffusion equations with interface conditions that capture local behaviour at patch boundaries. In this work we develop a novel homogenization technique to approximate the large-scale dynamics of the system. We illustrate our approach, which also generalizes to multiple species, with an example of logistic growth within a periodic environment. We find that population persistence and the large-scale population carrying capacity is influenced by patch residence times that depend on patch preference, as well as movement rates in adjacent patches. The forms of the homogenized coefficients yield key theoretical insights into how large-scale dynamics arise from the small-scale features.     

The spontaneous flora around street trees in cities—A striking example for the worldwide homogenization of the flora of urban habitats

Cities are well known as rich in vascular plant species. To evaluate the importance of this richness for global biodiversity it is necessary to know the degree of homogenization of the city flora at a continental or even worldwide scale. Therefore, we looked for a habitat type that is typical urban and which is represented in nearly all cities of the world: the area around street trees (“Baumscheiben”). The spontaneous flora of this habitat was recorded in seven West and Central European metropolises situated in six countries and in Baltimore (USA). To test for floristic homogenization, the dissimilarity among the Baumscheiben Flora in the European cities was compared with dissimilarity among relevés of the potential natural vegetation in the cities. On average 81 species were found growing on Baumscheiben in each of the European cities. 29 species (i.e. more than one third of the total) were found in every city, 59 species (i.e. 74%) were represented in at least four of the seven cities. The obvious homogenization of the flora of this habitat is confirmed by low total variation among European Baumscheiben. Furthermore, the dissimilarity among Baumscheiben was much lower than among the potential natural vegetation (forests) around these cities. There is not only low variation between the Baumscheiben flora of the seven European metropolises analyzed, but also great similarity to the Baumscheiben flora of Baltimore: 80% of the species found on Baumscheiben in Baltimore also belong to the spontaneous flora of most European cities and 26% even belong to the group of the most common species of West and Central European tree bases.     

A topology optimization based model of bone adaptation

A novel topology optimization model based on homogenization methods was developed for predicting bone density distribution and anisotropy, assuming the bone structure to be a self-optimizing biological material which maximizes its own structural stiffness. The feasibility and efficiency of this method were tested on a 2D model for a proximal femur under single and multiple loading conditions. The main aim was to compute homogenized optimal designs using an optimal laminated microstructure. The computational results showed that high bone density levels are distributed along the diaphysis and form arching struts within the femoral head. The pattern of bone density distribution and the anisotropic bone behavior predicted by the model in the multiple load case were both in good agreement with the structural architecture and bone density distribution occurring in natural femora. This approach provides a novel means of understanding the remodeling processes involved in fracture repair and the treatment of bone diseases.     

厌氧产氢颗粒污泥蛋白质组分析样品的高效制备方法

【背景】厌氧产氢颗粒污泥比絮状产氢污泥具有更高的生物量、沉降性与反应效率,对颗粒污泥进行蛋白质组学研究,有助于揭示其代谢调控的分子机制,从而对厌氧代谢过程进行优化调控。目前关于产氢颗粒污泥蛋白质组分析样品制备方法的研究尚未见文献报道。革兰氏阳性菌Ethanoligenens harbinense YUAN-3是自凝集产氢发酵细菌,在间歇和连续流培养中可形成自聚集的厌氧颗粒,由于其全基因组信息清楚,可作为模式研究材料对制备方法进行评估。【目的】针对厌氧产氢颗粒污泥的蛋白质组学研究,比较不同蛋白质提取方法进行优化。【方法】分别利用液氮研磨、超声破碎、匀浆破碎对产氢颗粒污泥破碎,比较这3种方法对总蛋白提取量的影响;通过双向电泳比较三氯乙酸(Trichloroacetic acid,TCA)-丙酮沉淀法与苯酚抽提法对总蛋白提取效果的影响;对总蛋白样品分别进行同位素标记相对和绝对定量标记(Isobarictagsforrelativeandabsolutequantification,i TRAQ)、串联质谱标签(Tandemmasstag,TMT)标记以及质谱鉴定。【结果】液氮研磨、超声破碎、匀浆破碎3种破碎方法下总蛋白的提取量分别是对照样品的2.0、3.9与5.2倍。与TCA-丙酮沉淀法相比,苯酚抽提法总蛋白样品在双向电泳图谱上的蛋白质点明显增多,分布均匀,同时其在碱性蛋白端与小分子量蛋白端的蛋白质点也明显增多。质谱分析发现,iTRAQ标记样品与TMT标记样品中分别鉴定到1797个与1644个蛋白,在分子量、等电点、亚细胞定位的各个分布范围内,这些蛋白良好地覆盖了E.harbinenseYUAN-3中各个类型的蛋白。【结论】匀浆破碎与苯酚抽提法联用的总蛋白制备方法更适用于厌氧产氢颗粒污泥,该方法有利于后续的蛋白质双向电泳和定量蛋白质组质谱分析,可作为产氢颗粒污泥以及革兰氏阳性菌总蛋白制备的方法参考。     

Inflorescence structure in Rhynchospora Vahl (Cyperaceae)

We investigated the inflorescence structure of Rhynchospora following the methodology and terminology of Troll's school, with the objective of providing a characterization of the inflorescence suitable to evaluate the processes responsible for the diversity observed. Homogenization of inflorescence structures may occur fully or partially. In the first case, all branches of the inflorescence are homogeneous, while in the later, distal and proximal parts of the inflorescence bear homogeneous branches, but in the middle portions of the inflorescence non-homogeneous branches exist. Other characters leading to different forms of inflorescences are branching degree, internode elongation along the main axis of the synflorescence, degree of epipodium elongation of distal paraclades, development of bract and prophyll, and development of prophyllar paraclades. We identified three main types of inflorescences: (1) partially homogeneous paniculodia, (2) partially homogeneous capitate heads, and (3) a fully homogeneous capitate head. Within the first type, four subtypes were also recognized. Finally, we discuss how these processes can operate to produce the variation of the inflorescence shape.