Linking transpiration reduction to rhizosphere salinity using a 3D coupled soil-plant model

Background and aims

In cold biomes, litter decomposition, which controls the nutrient availability for plants and the ecosystem carbon budget, is strongly influenced by climatic conditions. In this study, focused on the early litter decay within snowbed habitats, the magnitude of the short- and long-term influences of climate warming, the direction of the effects of warmer temperature and advanced snowmelt, and the control of microclimatic features and plant traits were compared.

Methods

Combining experimental warming and space-for-time substitution, mass loss and nutrient release of different plant functional types were estimated in different climatic treatments with the litter bag method.

Results

Plant functional types produced a larger variation in the early-decomposition compared to that produced by climatic treatments. Litter decay was not affected by warmer summer temperatures and reduced by advanced snowmelt. Structural-related plant traits exerted the major control over litter decomposition.

Conclusions

Long-term effects of climate warming, resulting from shifts in litter quality due to changes in the abundance of plant functional types, will likely have a stronger impact on plant litter decomposition than short-term variations in microclimatic features. This weaker response of litter decay to short-term climate changes may be partially due to the opposite influences of higher summer temperatures and advanced snowmelt time.     

天目山物种多样性尺度依赖及其与空间格局关系的多重分形

以浙江省天目山国家级自然保护区为例,采用多尺度分析思想,利用多重分形分析方法,研究了不同尺度下物种多样性的变化、空间分布格局以及多样性与空间格局之间的关系。研究主要得到3方面的结论：（1）物种多样性具有尺度依赖性,随着空间尺度的增大,Shannon-Wiener多样性指数Ⅳ增大,Margalef多样性指数足和均匀度指数E减小;（2）多重分形参数αmin。多重分形谱的变化范围SR等能够定量反映物种的空间分布特征,空间大尺度越大,物种越聚集,空间分布越不均匀;（3）物种多样性与空间格局存在线性或幂函数关系。研究表明多重分形分析定量描述物种空间格局是有效性的,多重分形参数与生物多样性之间的定量关系为研究物种空间格局、生态属性与尺度之间的关系奠定了基础。因此,分形结合传统方法,在生物多样性方面的研究将有很大的潜在价值。     

Development of a computational model for macroscopic predictions of device-induced thrombosis

Biomechanics and Modeling in Mechanobiology - While cardiovascular device-induced thrombosis is associated with negative patient outcomes, the convoluted nature of the processes resulting in a...     

A validated computational framework to evaluate the stiffness of 3D printed ankle foot orthoses

The purpose of this study was to create and validate a standardized framework for the evaluation of the ankle stiffness of two designs of 3D printed ankle foot orthoses (AFOs). The creation of four finite element (FE) models allowed patient-specific quantification of the stiffness and stress distribution over their specific range of motion during the second rocker of the gait. Validation was performed by comparing the model outputs with the results obtained from a dedicated experimental setup, which showed an overall good agreement with a maximum relative error of 10.38% in plantarflexion and 10.66% in dorsiflexion. The combination of advanced computer modelling algorithms and 3D printing techniques clearly shows potential to further improve the manufacturing process of AFOs.     

A computational model for cell/ECM growth on 3D surfaces using the level set method: a bone tissue engineering case study

Three-dimensional open porous scaffolds are commonly used in tissue engineering (TE) applications to provide an initial template for cell attachment and subsequent cell growth and construct development. The macroscopic geometry of the scaffold is key in determining the kinetics of cell growth and thus in vitro ‘tissue’ formation. In this study, we developed a computational framework based on the level set methodology to predict curvature-dependent growth of the cell/extracellular matrix domain within TE constructs. Scaffolds with various geometries (hexagonal, square, triangular) and pore sizes (500 and 1,000  \(\upmu \) m) were produced in-house by additive manufacturing, seeded with human periosteum-derived cells and cultured under static conditions for 14 days. Using the projected tissue area as an output measure, the comparison between the experimental and the numerical results demonstrated a good qualitative and quantitative behavior of the framework. The model in its current form is able to provide important spatio-temporal information on final shape and speed of pore-filling of tissue-engineered constructs by cells and extracellular matrix during static culture.     

Linking microvascular collapse to tissue hypoxia in a multiscale model of pressure ulcer initiation

Biomechanics and Modeling in Mechanobiology - Pressure ulcers are devastating injuries that disproportionately affect the older adult population. The initiating factor of pressure ulcers is local...     

3D spatial point patterns of bioluminescent plankton: a map of the minefield

As the open ocean environment lacks points of refuge from visualpredators, it has favored the evolution of extraordinary adaptationsfor optical concealment, such as vertical migration, transparencyand counterillumination. Bioluminescent plankton, which respondto a mechanical disturbance with a flash of light, are ubiquitousin the ocean and potentially a threat to any organism seekingdarkness as a means to evade detection. Estimating encounterprobabilities for organisms maneuvering through luminescent‘minefields’ requires characterization of the three-dimensionaldistribution patterns of the potential light emitters. In orderto measure nearest neighbor distances (NNDs) of bioluminescentbiota, we have developed a spatial plankton analysis technique(SPLAT) for 3D reconstruction and statistical analysis of thespatial point patterns of identified bioluminescent displays.Analysis of aggregations of bioluminescent biota in the Gulfof Maine (Wilkinson Basin) revealed that encounter probabilitieswere highest in the temperature minimum zone (temperature <5°C)where dinoflagellates (Protoperidineum depressum) exhibitedNNDs of 3.5–3.8 cm in a regular distribution pattern.This technique was also used to examine the internal organizationof thin layers of the bioluminescent copepod, Metridia lucens.Comparison of night-time surface (migrating) and deep (non-migrating)layers indicated complete spatial randomness in both populationsand no significant difference in spacing (NNDs: 9.5–13cm).     

Complement contributes to inflammatory tissue destruction in a mouse model of Ross River virus-induced disease

Arthritogenic alphaviruses, including Ross River virus (RRV) and chikungunya virus, are mosquito-borne viruses that cause significant human disease worldwide, including explosive epidemics that can result in thousands to millions of infected individuals. Similar to infection of humans, infection of C57BL/6 mice with RRV results in severe monocytic inflammation of bone, joint, and skeletal muscle tissues. We demonstrate here that the complement system, an important component of the innate immune response, enhances the severity of RRV-induced disease in mice. Complement activation products were detected in the inflamed tissues and in the serum of RRV-infected wild-type mice. Furthermore, mice deficient in C3 (C3^−/−), the central component of the complement system, developed much less severe disease signs than did wild-type mice. Complement-mediated chemotaxis is essential for many inflammatory arthritides; however, RRV-infected wild-type and C3^−/− mice had similar numbers and composition of inflammatory infiltrates within hind limb skeletal muscle tissue. Despite similar inflammatory infiltrates, RRV-infected C3^−/− mice exhibited far less severe destruction of skeletal muscle tissue. In addition to these studies, complement activation was also detected in synovial fluid from RRV-infected patients. Taken together, these findings indicate that complement activation occurs in the tissues of humans and mice infected with RRV and suggest that complement plays an essential role in the effector phase, but not the inductive phase, of RRV-induced arthritis and myositis.     

A computational model for previtamin D(3) production in skin

Low levels of vitamin D have been implicated in a wide variety of health issues from calcemic diseases to cancer, diabetes and cardiovascular disease. For most humans, the majority of vitamin D(3) is derived from sunlight. How much vitamin D is produced under given exposure conditions is still widely discussed. We present a computational model for the production of (pre-)vitamin D within the skin. It accounts for spectral irradiance, optical properties of the skin and concentration profile of provitamin D. Results are computed for various sets of these parameters yielding the distribution of produced previtamin D in the skin.     

Validation of a 3D computational fluid-structure interaction model simulating flow through an elastic aperture

This work presents a validation of a fluid-structure interaction computational model simulating the flow conditions in an in vitro mock heart chamber modeling mitral valve regurgitation during the ejection phase during which the trans-valvular pressure drop and valve displacement are not as large. The mock heart chamber was developed to study the use of 2D and 3D color Doppler techniques in imaging the clinically relevant complex intra-cardiac flow events associated with mitral regurgitation. Computational models are expected to play an important role in supporting, refining, and reinforcing the emerging 3D echocardiographic applications. We have developed a 3D computational fluid-structure interaction algorithm based on a semi-implicit, monolithic method, combined with an arbitrary Lagrangian-Eulerian approach to capture the fluid domain motion. The mock regurgitant mitral valve corresponding to an elastic plate with a geometric orifice, was modeled using 3D elasticity, while the blood flow was modeled using the 3D Navier-Stokes equations for an incompressible, viscous fluid. The two are coupled via the kinematic and dynamic conditions describing the two-way coupling. The pressure, the flow rate, and orifice plate displacement were measured and compared with numerical simulation results. In-line flow meter was used to measure the flow, pressure transducers were used to measure the pressure, and a Doppler method developed by one of the authors was used to measure the axial displacement of the orifice plate. The maximum recorded difference between experiment and numerical simulation for the flow rate was 4%, the pressure 3.6%, and for the orifice displacement 15%, showing excellent agreement between the two.     

Improving the spatial orientation of human teeth using a virtual 3D approach

Since teeth are resistant to decomposition processes, they provide important and at times unique sources of information about fossil humans. Fortunately, dental remains reflect significant evolutionary changes. These changes make a very important and often exclusive contribution to the definition of new taxa or the attribution of fossil specimens to existing taxa.The traditional approach to dental morphometric analyses usually focuses on the recording of several measures of the tooth with calipers, especially the two basic crown diameters (buccolingual and mesiodistal). However, since these measures do not adequately represent the complex morphology of the tooth, 2D images and 3D digital models of dental morphology have been used. For both types of analysis, the possibility of correctly comparing homologous teeth depends on the adoption of a common orientation system. The lack of such a system makes it difficult to compare the results of different studies.Here we describe a new method for orienting teeth specifically devised for the upper and lower first molar (M1). Samples of unworn maxillary (n = 15) and mandibular (n = 15) first molars of modern humans were scanned with a Roland Picza 3D digitizer. The 3D virtual models were used to compare our new orientation method with those proposed in the literature. The new orientation system, which meets a geometric criterion, is based on three points identified on the cervical line and ensures acceptable repeatability of the spatial positioning and orientation independent of the shape and wear of the first molar under investigation. This orientation system is a first step toward the creation of a virtual set of hominid and fossil human first molars, which will allow us to make comparisons via a sophisticated and noninvasive approach. This pilot study also provides guidelines to extend the new methodology to the other types of teeth.     

A new technique to gather 3‐D spatial information using a single camera

A new technique using a single camera and shadows to determine 3‐D spatial positions of fishes in the laboratory is described. The apparatus consisted of a large aquarium (2·0 × 1·5 × 0·4 m), a wide‐angle camera mounted above and two light sources to cast shadows to either side of the fish. Using image analysis and vector mathematics, aquarium objects were plotted within 1·5 cm of their actual location along the x ‐, y ‐ and z ‐axis. The technique was also successful in quantifying changes in 3‐D spatial pattern of juvenile fish, Atlantic cod Gadus morhua (7·4–8·6 cm standard length, L _S) and cohabitant piscivorous shorthorned sculpin Myoxocephalus scorpinus (12·0–25·8 cm L _S), at these same viewing fields. The new technique should have a wide application, largely because it is potentially less expensive, laborious and invasive than alternative methods for determining 3‐D positions of fishes.     

Predicting RNA 3D structure using a coarse-grain helix-centered model

A 3D model of RNA structure can provide information about its function and regulation that is not possible with just the sequence or secondary structure. Current models suffer from low accuracy and long running times and either neglect or presume knowledge of the long-range interactions which stabilize the tertiary structure. Our coarse-grained, helix-based, tertiary structure model operates with only a few degrees of freedom compared with all-atom models while preserving the ability to sample tertiary structures given a secondary structure. It strikes a balance between the precision of an all-atom tertiary structure model and the simplicity and effectiveness of a secondary structure representation. It provides a simplified tool for exploring global arrangements of helices and loops within RNA structures. We provide an example of a novel energy function relying only on the positions of stems and loops. We show that coupling our model to this energy function produces predictions as good as or better than the current state of the art tools. We propose that given the wide range of conformational space that needs to be explored, a coarse-grain approach can explore more conformations in less iterations than an all-atom model coupled to a fine-grain energy function. Finally, we emphasize the overarching theme of providing an ensemble of predicted structures, something which our tool excels at, rather than providing a handful of the lowest energy structures.     

A 3D computational simulation of fracture callus formation: influence of the stiffness of the external fixator

The stiffness of the external fixation highly influences the fracture healing pattern. In this work we study this aspect by means of a finite element model of a simple transverse mid-diaphyseal fracture of an ovine metatarsus fixed with a bilateral external fixator. In order to simulate the regenerative process, a previously developed mechanobiological model of bone fracture healing was implemented in three dimensions. This model is able to simulate tissue differentiation, bone regeneration, and callus growth. A physiological load of 500 N was applied and three different stiffnesses of the external fixator were simulated (2300, 1725, and 1150 N/mm). The interfragmentary strain and load sharing mechanism between bone and the external fixator were compared to those recorded in previous experimental works. The effects of the stiffness on the callus shape and tissue distributions in the fracture site were also analyzed. We predicted that a lower stiffness of the fixator delays fracture healing and causes a larger callus, in correspondence to well-documented clinical observations.     

Soft tissue structures resisting anterior instability in a computational glenohumeral joint model

The glenohumeral joint is the most dislocated joint in the body due to the lack of bony constraints and the dependence on soft tissue for stability. The roles that various structures provide to joint function are important for understanding injury treatment and orthopaedic device design purposes. The goal of this study was to develop a computational model of the glenohumeral joint whereby joint behaviour was dictated by articular contact, ligamentous constraints, muscle loading and external perturbations. The bone structure of the computational model consisted of assembled computer tomographic images of the scapula, humerus and clavicle. The soft tissue elements were composed of forces and tension-only springs that represented muscles and ligaments. Validation of this model was achieved by comparing computational predictions to the results of a cadaveric experiment in which the relative contribution of muscles and ligaments to anterior joint stability was examined. The computational model predicted an anterior subluxation force that was similar to the cadaveric experimental results in humeral external rotation. The individual structure results showed the subscapularis to be critical to stabilisation in both neutral and external rotations, the biceps stabilised the joint in neutral but not in external rotation, and the inferior glenohumeral ligament resisted anterior displacement only in external rotation. The model's predictions were similar to the conclusions of the cadaveric experiment and the literature. Knowledge gained from this type of model could assist in further understanding the contribution of soft tissue stabilisers to joint function, pre-operative planning or the design of orthopaedic implants.     

Construction of 3D human distal femoral surface models using a 3D statistical deformable model

Construction of 3D geometric surface models of human knee joint is always a challenge in biomedical engineering. This study introduced an improved statistical shape model (SSM) method that only uses 2D images of a joint to predict the 3D joint surface model. The SSM was constructed using 40 distal femur models of human knees. In this paper, a series validation and parametric analysis suggested that more than 25 distal femur models are needed to construct the SSM; each distal femur should be described using at least 3000 nodes in space; and two 2D fluoroscopic images taken in 45° directions should be used for the 3D surface shape prediction. Using this SSM method, ten independent distal femurs from 10 independent living subjects were predicted using their 2D plane fluoroscopic images. The predicted models were compared to their native 3D distal femur models constructed using their 3D MR images. The results demonstrated that using two fluoroscopic images of the knee, the overall difference between the predicted distal femur surface and the MR image-based surface was 0.16±1.16 mm. These data indicated that the SSM method could be a powerful method for construction of 3D surface geometries of the distal femur.     

Linking traits of foraging animals to spatial patterns of plants: social and solitary ants generate opposing patterns of surviving seeds

Foraging traits of seed predators are expected to impact the spatial structure of plant populations, community dynamics and diversity. Yet, many of the key mechanisms governing distance- or density-dependent seed predation are poorly understood. We designed an extensive set of field experiments to test how seed predation by two harvester ant species interact with seed dispersal in shaping the spatial patterns of surviving seeds. We show that the Janzen–Connell establishment pattern can be generated by central-place foragers even if their focal point is located away from the seed source. Furthermore, we found that differences in the social behaviour of seed predators influence their sensitivity to seed density gradients and yield opposing spatial patterns of surviving seeds. Our results support the predictions of a recent theoretical framework that unifies apparently opposing plant establishment patterns, and suggest that differences in foraging traits among seed predators can drive divergent pathways of plant community dynamics.     

Exploring a biological tissue from atomic to macroscopic scale using synchrotron radiation: example of hair.

A combined approach, using synchrotron radiation-based diffraction and infrared microspectrometry, has been used to study the structure and molecular composition of hair samples. These methods allowed us to get an insight at different structural scales into the composition and structure of hair. Firstly, information about the configuration of amino-acid residues was obtained at atomic scale, secondly, a model was presented for the geometry and the packing of the microfibrils at medium scale and finally different structural zones were evidenced by microdiffraction at macroscopic scale. We also showed that the two main components of hair--proteins and lipids--are not evenly distributed within the fiber. In addition, these two components exhibit different structure, depending upon their location. Moreover, diffraction and microdiffraction data indicate that the cuticle zone is mainly composed of lipid granules, whereas the cortex and the medulla zones are composed primarily of alpha-keratin. Infrared microspectroscopy, using an enhanced lateral resolution thanks to synchrotron radiation, indicates, on one hand, that the protein structure between the cuticle and cortex are different, and on the other hand, that the concentration of lipids, inside the medulla, is much higher than everywhere else. This work emphasizes the complementarity between both techniques, and highlights the potentialities they can offer in the case of various other studies in biology.