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author:("Li, baoruco")
1.  Three-Dimensional Mapping of Soil Organic Carbon by Combining Kriging Method with Profile Depth Function 
PLoS ONE  2015;10(6):e0129038.
Understanding spatial variation of soil organic carbon (SOC) in three-dimensional direction is helpful for land use management. Due to the effect of profile depths and soil texture on vertical distribution of SOC, the stationary assumption for SOC cannot be met in the vertical direction. Therefore the three-dimensional (3D) ordinary kriging technique cannot be directly used to map the distribution of SOC at a regional scale. The objectives of this study were to map the 3D distribution of SOC at a regional scale by combining kriging method with the profile depth function of SOC (KPDF), and to explore the effects of soil texture and land use type on vertical distribution of SOC in a fluvial plain. A total of 605 samples were collected from 121 soil profiles (0.0 to 1.0 m, 0.20 m increment) in Quzhou County, China and SOC contents were determined for each soil sample. The KPDF method was used to obtain the 3D map of SOC at the county scale. The results showed that the exponential equation well described the vertical distribution of mean values of the SOC contents. The coefficients of determination, root mean squared error and mean prediction error between the measured and the predicted SOC contents were 0.52, 1.82 and -0.24 g kg-1 respectively, suggesting that the KPDF method could be used to produce a 3D map of SOC content. The surface SOC contents were high in the mid-west and south regions, and low values lay in the southeast corner. The SOC contents showed significant positive correlations between the five different depths and the correlations of SOC contents were larger in adjacent layers than in non-adjacent layers. Soil texture and land use type had significant effects on the spatial distribution of SOC. The influence of land use type was more important than that of soil texture in the surface soil, and soil texture played a more important role in influencing the SOC levels for 0.2-0.4 m layer.
PMCID: PMC4457849  PMID: 26047012
2.  Assessing the Impact of Afforestation on Soil Organic C Sequestration by Means of Sequential Density Fractionation 
PLoS ONE  2015;10(2):e0117897.
Afforestation is a prevalent practice carried out for soil recovery and carbon sequestration. Improved understanding of the effects of afforestation on soil organic carbon (SOC) content and dynamics is necessary to identify the particular processes of soil organic matter (SOM) formation and/or decomposition that result from afforestation. To elucidate these mechanisms, we have used a sequential density fractionation technique to identify the transfer mechanisms of forest derived C to soil fractions and investigate the impact of afforestation on SOC sequestration. Surface soil samples from continuous maize crop land (C4) and forest land (C3), which had been established 5, 12 and 25 yr, respectively, on the Northeast China Plain were separated into five density fractions. SOC, nitrogen (N) concentration and δ13C data from the three forests and adjacent cropland were compared. Afforestation decreased SOC concentration in the < 2.5 g cm-3 fractions from 5 yr forest sites, but increased SOC content in the < 2.0 g cm-3 fractions from 25 yr forest sites. Afforestation did not affect soil mass distribution, SOC and N proportional weight distributions across the density fractions. The < 1.8 g cm-3 fractions from 12 and 25 yr forests showed higher C/N and lower δ13C as compared to other fractions. Incorporation of forest litter-derived C occurred from low density (< 1.8 g cm-3) fractions to aggregates of higher density (1.8-2.5 g cm-3) through aggregate recombination and C transport in the pore system of the aggregates. Some forest litter-derived C could transfer from the light fractions or directly diffuse and adsorb onto mineral particles. Results from this study indicate that microaggregate protection and association between organic material and minerals provide major contribution to the SOC sequestration in the afforested soil system.
PMCID: PMC4338225  PMID: 25705896
3.  The Crucial Role of Atg5 in Cortical Neurogenesis During Early Brain Development 
Scientific Reports  2014;4:6010.
Autophagy plays an important role in the central nervous system. However, it is unknown how autophagy regulates cortical neurogenesis during early brain development. Here, we report that autophagy-related gene 5 (Atg5) expression increased with cortical development and differentiation. The suppression of Atg5 expression by knockdown led to inhibited differentiation and increased proliferation of cortical neural progenitor cells (NPCs). Additionally, Atg5 suppression impaired cortical neuronal cell morphology. We lastly observed that Atg5 was involved in the regulation of the β-Catenin signaling pathway. The β-Catenin phosphorylation level decreased when Atg5 was blocked. Atg5 cooperated with β-Catenin to modulate cortical NPCs differentiation and proliferation. Our results revealed that Atg5 has a crucial role in cortical neurogenesis during early embryonic brain development, which may contribute to the understanding of neurodevelopmental disorders caused by autophagy dysregulation.
PMCID: PMC4127499  PMID: 25109817
4.  Factors associated with the survival of prostate cancer patients with rectal involvement 
Diagnostic Pathology  2014;9:35.
Prostate cancer patients with rectal involvement are rare, and the factors associated with the survival of these patients are yet to be elucidated.
Patients and methods
We collected data on patients who were admitted to our hospital for prostate cancer in the last thirteen years and of those in studies in the literature. The associations of clinical characteristics with survival were evaluated using Cox regression models.
This study included 94 patients (5 admitted to our hospital and 89 from studies in the literature) of prostate cancer with rectal involvement. 11 patients in the group of synchronous rectal involvement at first cancer diagnosis (n = 58) and 23 patients in the group of metachronous diagnosis of rectal involvement (n = 29) died at the latest follow up. The estimated overall survival rate (% ± SE) at 1, 3, and 5 years were 68.3 ± 5.3%, 54.4 ± 7.2%, and 38.1 ± 11.1%, respectively. In the Cox univariate analysis, Asian prostate cancer (p = 0.001) was associated with better survival, while rectal bleeding (p = 0.043), metachronous presentation of development of rectal involvement (p = 0.000), prior hormonal therapy (p = 0.000) and extrarectal metastases (p = 0.054) were associated with poor survival. In multivariate analysis, prior hormone therapy (HR = 14.540, p = 0.000) and rectal bleeding (HR = 2.195, p = 0.041) retained independent poor prognostic values. There were 13 patients survived for more than 3 years, the longest survival time was 96 months. Total pelvic extenteration (TPE) combined with hormonal therapy in 12 hormone-untreated prostate cancer give us six of thirteen long-term survivors for more than 3 years in this series.
Our findings suggest that rectal involvement does not necessarily predict a worse outcome when presenting as a previously hormone-untreated disease and that the prognosis was worse when presenting as a hormone relapsed disease. Prior hormone therapy and rectal bleeding were associated independently with a significantly poor overall survival in prostate cancer patients with rectal involvement. TPE combined with hormonal therapy appears to confer better overall survival in hormonally untreated patients.
Virtual slides
The virtual slide(s) for this article can be found here:
PMCID: PMC3938032  PMID: 24555830
Prostate cancer; Rectal involvement; Total pelvic extenteration; Prognostic factors
5.  Supply and Demand Determine the Market Value of Access to Infants in the Golden Snub-Nosed Monkey (Rhinopithecus roxellana) 
PLoS ONE  2013;8(6):e65962.
According to a biological market paradigm, trading decisions between partners will be influenced by the current ‘exchange rate’ of commodities (good and services), which is affected by supply and demand, and the trader’s ability to outbid competitors. In several species of nonhuman primates, newborn infants are attractive to female group members and may become a desired commodity that can be traded for grooming within a biological market place. We investigated whether grooming was interchanged for infant handling in female golden snub-nosed monkeys (Rhinopithecus roxellana) inhabiting the Qinling Mountains of central China. R. roxellana exhibit a multilevel social organization characterized by over 100 troop members organized into 6–11 one-male units each composed one adult male and several adult females and their offspring. Behavioral data were collected over the course of 28 months on grooming patterns between mothers with infants less than 6 months old (N = 36) and other adult female troop members. Our results provide strong evidence for the interchange of grooming for access to infants. Grooming for infant access was more likely to be initiated by potential handlers (nonmothers) and less likely reciprocated by mothers. Moreover, grooming bout duration was inversely related to the number of infants per female present in each one-male unit indicating the possibility of a supply and demand market effect. The rank difference between mothers and handlers was negatively correlated with grooming duration. With increasing infant age, the duration of grooming provided by handlers was shorter suggesting that the ‘value’ of older infants had decreased. Finally, frequent grooming partners were allowed to handle and maintain access to infants longer than infrequent groomers. These results support the contention that grooming and infant handling may be traded in R. roxellana and that the price individuals paid for access to infants fluctuated with supply and demand.
PMCID: PMC3680491  PMID: 23776580
6.  Handedness in Nature: First Evidence on Manual Laterality on Bimanual Coordinated Tube Task in Wild Primates 
Handedness is a defining feature of human manual skill and understanding the origin of manual specialization remains a central topic of inquiry in anthropology and other sciences. In this study, we examined hand preference in a sample of wild primates on a task that requires bimanual coordinated actions (tube task) that has been widely used in captive primates. The Sichuan snub-nosed monkey (Rhinopithecus roxellana) is an arboreal Old World monkey species that is endemic to China, and 24 adult individuals from the Qinling Mountains of China were included for the analysis of hand preference in the tube task. All subjects showed strong individual hand preferences and significant group-level left-handedness was found. There were no significant differences between males and females for either direction or strength of hand preference. Strength of hand preferences of adults was significantly greater than juveniles. Use of the index finger to extract the food was the dominant extractive-act. Our findings represent the first evidence of population-level left-handedness in wild Old World monkeys, and broaden our knowledge on evaluating primate hand preference via experimental manipulation in natural conditions.
PMCID: PMC3342595  PMID: 22410843
Bimanual coordination; Hand preference; Task complexity
7.  A Functional and Structural Mongolian Scots Pine (Pinus sylvestris var. mongolica) Model Integrating Architecture, Biomass and Effects of Precipitation 
PLoS ONE  2012;7(8):e43531.
Mongolian Scots pine (Pinus sylvestris var. mongolica) is one of the principal tree species in the network of Three-North Shelterbelt for windbreak and sand stabilisation in China. The functions of shelterbelts are highly correlated with the architecture and eco-physiological processes of individual tree. Thus, model-assisted analysis of canopy architecture and function dynamic in Mongolian Scots pine is of value for better understanding its role and behaviour within shelterbelt ecosystems in these arid and semiarid regions. We present here a single-tree functional and structural model, derived from the GreenLab model, which is adapted for young Mongolian Scots pines by incorporation of plant biomass production, allocation, allometric rules and soil water dynamics. The model is calibrated and validated based on experimental measurements taken on Mongolian Scots pines in 2007 and 2006 under local meteorological conditions. Measurements include plant biomass, topology and geometry, as well as soil attributes and standard meteorological data. After calibration, the model allows reconstruction of three-dimensional (3D) canopy architecture and biomass dynamics for trees from one- to six-year-old at the same site using meteorological data for the six years from 2001 to 2006. Sensitivity analysis indicates that rainfall variation has more influence on biomass increment than on architecture, and the internode and needle compartments and the aboveground biomass respond linearly to increases in precipitation. Sensitivity analysis also shows that the balance between internode and needle growth varies only slightly within the range of precipitations considered here. The model is expected to be used to investigate the growth of Mongolian Scots pines in other regions with different soils and climates.
PMCID: PMC3425476  PMID: 22927982
8.  Plant growth and architectural modelling and its applications 
Annals of Botany  2011;107(5):723-727.
Over the last decade, a growing number of scientists around the world have invested in research on plant growth and architectural modelling and applications (often abbreviated to plant modelling and applications, PMA). By combining physical and biological processes, spatially explicit models have shown their ability to help in understanding plant–environment interactions. This Special Issue on plant growth modelling presents new information within this topic, which are summarized in this preface. Research results for a variety of plant species growing in the field, in greenhouses and in natural environments are presented. Various models and simulation platforms are developed in this field of research, opening new features to a wider community of researchers and end users. New modelling technologies relating to the structure and function of plant shoots and root systems are explored from the cellular to the whole-plant and plant-community levels.
PMCID: PMC3077987  PMID: 21638797
Plant morphology; architecture; functional–structural plant model; FSPM; source and sink; root system; photosynthesis; simulation; plasticity; computational plants
9.  Three-dimensional distribution of vessels, passage cells and lateral roots along the root axis of winter wheat (Triticum aestivum) 
Annals of Botany  2011;107(5):843-853.
Background and Aims
The capacity of a plant to absorb and transport water and nutrients depends on anatomical structures within the roots and their co-ordination. However, most descriptions of root anatomical structure are limited to 2-D cross-sections, providing little information on 3-D spatial relationships and hardly anything on their temporal evolution. Three-dimensional reconstruction and visualization of root anatomical structures can illustrate spatial co-ordination among cells and tissues and provide new insights and understanding of the interrelation between structure and function.
Classical paraffin serial-section methods, image processing, computer-aided 3-D reconstruction and 3-D visualization techniques were combined to analyse spatial relationships among metaxylem vessels, passage cells and lateral roots in nodal roots of winter wheat (Triticum aestivum).
Key Results
3-D reconstruction demonstrated that metaxylem vessels were neither parallel, nor did they run directly along the root axis from the root base to the root tip; rather they underwent substitution and transition. Most vessels were connected to pre-existent or newly formed vessels by pits on their lateral walls. The spatial distributions of both passage cells and lateral roots exhibited similar position-dependent patterns. In the transverse plane, the passage cells occurred opposite the poles of the protoxylem and the lateral roots opposite those of the protophloem. Along the axis of a young root segment, the passage cells were arranged in short and discontinuous longitudinal files, thus as the tissues mature, the sequence in which the passage cells lose their transport function is not basipetal. In older segments, passage cells decreased drastically in number and coexisted with lateral roots. The spatial distribution of lateral roots was similar to that of the passage cells, mirroring their similar functions as lateral pathways for water and nutrient transport to the stele.
With the 3-D reconstruction and visualization techniques developed here, the spatial relationships between vessels, passage cells and lateral roots and the temporal evolution of these relationships can be described. The technique helps to illustrate synchronization and spatial co-ordination among the root's radial and axial pathways for water and nutrient transport and the interdependence of structure and function in the root.
PMCID: PMC3077985  PMID: 21289027
Winter wheat; Triticum aestivum; metaxylem vessel; passage cell; lateral root; 3-D reconstruction; 3-D visualization; spatial co-ordination; positional relationship
10.  A stochastic model of tree architecture and biomass partitioning: application to Mongolian Scots pines 
Annals of Botany  2010;107(5):781-792.
Background and Aims
Mongolian Scots pine (Pinus sylvestris var. mongolica) is one of the principal species used for windbreak and sand stabilization in arid and semi-arid areas in northern China. A model-assisted analysis of its canopy architectural development and functions is valuable for better understanding its behaviour and roles in fragile ecosystems. However, due to the intrinsic complexity and variability of trees, the parametric identification of such models is currently a major obstacle to their evaluation and their validation with respect to real data. The aim of this paper was to present the mathematical framework of a stochastic functional–structural model (GL2) and its parameterization for Mongolian Scots pines, taking into account inter-plant variability in terms of topological development and biomass partitioning.
In GL2, plant organogenesis is determined by the realization of random variables representing the behaviour of axillary or apical buds. The associated probabilities are calibrated for Mongolian Scots pines using experimental data including means and variances of the numbers of organs per plant in each order-based class. The functional part of the model relies on the principles of source–sink regulation and is parameterized by direct observations of living trees and the inversion method using measured data for organ mass and dimensions.
Key Results
The final calibration accuracy satisfies both organogenetic and morphogenetic processes. Our hypothesis for the number of organs following a binomial distribution is found to be consistent with the real data. Based on the calibrated parameters, stochastic simulations of the growth of Mongolian Scots pines in plantations are generated by the Monte Carlo method, allowing analysis of the inter-individual variability of the number of organs and biomass partitioning. Three-dimensional (3D) architectures of young Mongolian Scots pines were simulated for 4-, 6- and 8-year-old trees.
This work provides a new method for characterizing tree structures and biomass allocation that can be used to build a 3D virtual Mongolian Scots pine forest. The work paves the way for bridging the gap between a single-plant model and a stand model.
PMCID: PMC3077980  PMID: 21062760
Pinus sylvestris var. mongolica; functional–structural plant model; canopy architecture; three-dimensional; forest canopy; virtual plant; GreenLab, parameterization
11.  Parameter Optimization and Field Validation of the Functional–Structural Model GREENLAB for Maize at Different Population Densities 
Annals of Botany  2007;101(8):1185-1194.
Background and Aims
Plant population density (PPD) influences plant growth greatly. Functional–structural plant models such as GREENLAB can be used to simulate plant development and growth and PPD effects on plant functioning and architectural behaviour can be investigated. This study aims to evaluate the ability of GREENLAB to predict maize growth and development at different PPDs.
Two field experiments were conducted on irrigated fields in the North China Plain with a block design of four replications. Each experiment included three PPDs: 2·8, 5·6 and 11·1 plants m−2. Detailed observations were made on the dimensions and fresh biomass of above-ground plant organs for each phytomer throughout the seasons. Growth stage-specific target files (a description of plant organ weight and dimension according to plant topological structure) were established from the measured data required for GREENLAB parameterization. Parameter optimization was conducted using a generalized least square method for the entire growth cycles for all PPDs and years. Data from in situ plant digitization were used to establish geometrical symbol files for organs that were then applied to translate model output directly into 3-D representation for each time step of the model execution.
Key Results
The analysis indicated that the parameter values of organ sink variation function, and the values of most of the relative sink strength parameters varied little among years and PPDs, but the biomass production parameter, computed plant projection surface and internode relative sink strength varied with PPD. Simulations of maize plant growth based on the fitted parameters were reasonably good as indicated by the linearity and slopes similar to unity for the comparison of simulated and observed values. Based on the parameter values fitted from different PPDs, shoot (including vegetative and reproductive parts of the plant) and cob fresh biomass for other PPDs were simulated. Three-dimensional representation of individual plant and plant stand from the model output with two contrasting PPDs were presented with which the PPD effect on plant growth can be easily recognized.
This study showed that GREENLAB model has the ability to capture plant plasticity induced by PPD. The relatively stable parameter values strengthened the hypothesis that one set of equations can govern dynamic organ growth. With further validation, this model can be used for agronomic applications such as yield optimization.
PMCID: PMC2710275  PMID: 17921525
Functional–structural plant model; GREENLAB; plant architecture; source–sink relationship; plant population density; maize (Zea mays); model parameterization
12.  Parameter Stability of the Functional–Structural Plant Model GREENLAB as Affected by Variation within Populations, among Seasons and among Growth Stages 
Annals of Botany  2006;99(1):61-73.
Background and Aims
It is increasingly accepted that crop models, if they are to simulate genotype-specific behaviour accurately, should simulate the morphogenetic process generating plant architecture. A functional–structural plant model, GREENLAB, was previously presented and validated for maize. The model is based on a recursive mathematical process, with parameters whose values cannot be measured directly and need to be optimized statistically. This study aims at evaluating the stability of GREENLAB parameters in response to three types of phenotype variability: (1) among individuals from a common population; (2) among populations subjected to different environments (seasons); and (3) among different development stages of the same plants.
Five field experiments were conducted in the course of 4 years on irrigated fields near Beijing, China. Detailed observations were conducted throughout the seasons on the dimensions and fresh biomass of all above-ground plant organs for each metamer. Growth stage-specific target files were assembled from the data for GREENLAB parameter optimization. Optimization was conducted for specific developmental stages or the entire growth cycle, for individual plants (replicates), and for different seasons. Parameter stability was evaluated by comparing their CV with that of phenotype observation for the different sources of variability. A reduced data set was developed for easier model parameterization using one season, and validated for the four other seasons.
Key Results and Conclusions
The analysis of parameter stability among plants sharing the same environment and among populations grown in different environments indicated that the model explains some of the inter-seasonal variability of phenotype (parameters varied less than the phenotype itself), but not inter-plant variability (parameter and phenotype variability were similar). Parameter variability among developmental stages was small, indicating that parameter values were largely development-stage independent. The authors suggest that the high level of parameter stability observed in GREENLAB can be used to conduct comparisons among genotypes and, ultimately, genetic analyses.
PMCID: PMC2802986  PMID: 17158141
Plant architecture; functional–structural models; crop simulation; parameter stability; allometric relationships; sink capacity; Zea mays
13.  Parameter Optimization and Field Validation of the Functional–Structural Model GREENLAB for Maize 
Annals of Botany  2006;97(2):217-230.
• Background and Aims There are three reasons for the increasing demand for crop models that build the plant on the basis of architectural principles and organogenetic processes: (1) realistic concepts for developing new crops need to be guided by such models; (2) there is an increasing interest in crop phenotypic plasticity, based on variable architecture and morphology; and (3) engineering of mechanized cropping systems requires information on crop architecture. The functional–structural model GREENLAB was recently presented that simulates resource-dependent plasticity of plant architecture. This study introduces a new methodology for crop parameter optimization against measured data called multi-fitting, validates the calibrated model for maize with independent field data, and describes a technique for 3D visualization of outputs.
• Methods Maize was grown near Beijing during the 2000, 2001 and 2003 (two sowing dates) summer seasons in a block design with four to five replications. Detailed morphological and topological observations were made on the plant architecture throughout the development of the four crops. Data obtained in 2000 was used to establish target files for parameter optimization using the generalized least square method, and parameter accuracy was evaluated by coefficient of variance. In situ plant digitization was used to establish 3D symbol files for organs that were then used to translate model outputs directly into 3D representations for each time step of model execution.
•Key Results and Conclusions Multi-fitting against several target files obtained at different growth stages gave better parameter accuracy than single fitting at maturity only, and permitted extracting generic organ expansion kinetics from the static observations. The 2000 model gave excellent predictions of plant architecture and vegetative growth for the other three seasons having different temperature regimes, but predictions of inter-seasonal variability of biomass partitioning during grain filling were less accurate. This was probably due to insufficient consideration of processes governing cob sink size and terminal leaf senescence. Further perspectives for model improvement are discussed.
PMCID: PMC2803369  PMID: 16390847
Plant architecture; competition among sinks; source–sink relationships; functional–structural models; Zea mays; model parameterization

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