Forest above-ground biomass (AGB) can be estimated based on light detection and ranging (LiDAR) point clouds. This paper introduces an accurate and detailed quantitative structure model (AdQSM), which can estimate the AGB of large tropical trees. AdQSM is based on the reconstruction of 3D tree models from terrestrial laser scanning (TLS) point clouds. It represents a tree as a set of closed and complete convex polyhedra. We use AdQSM to model 29 trees of various species (total 18 species) scanned by TLS from three study sites (the dense tropical forests of Peru, Indonesia, and Guyana). The destructively sampled tree geometry measurement data is used as reference values to evaluate the accuracy of diameter at breast height (DBH), tree height, tree volume, branch volume, and AGB estimated from AdQSM. After AdQSM reconstructs the structure and volume of each tree, AGB is derived by combining the wood density of the specific tree species from destructive sampling. The AGB estimation from AdQSM and the post-harvest reference measurement data show a satisfying agreement. The coefficient of variation of root mean square error (CV-RMSE) and the concordance correlation coefficient (CCC) are 20.37% and 0.97, respectively. AdQSM provides accurate tree volume estimation, regardless of the characteristics of the tree structure, without major systematic deviations. We compared the accuracy of AdQSM and TreeQSM in modeling the volume of 29 trees. The tree volume from AdQSM is compared with the reference value, and the determination coefficient (R2), relative bias (rBias), and CV-RMSE of tree volume are 0.96, 6.98%, and 22.62%, respectively. The tree volume from TreeQSM is compared with the reference value, and the R2, relative Bias (rBias), and CV-RMSE of tree volume are 0.94, −9.69%, and 23.20%, respectively. The CCCs between the volume estimates based on AdQSM, TreeQSM, and the reference values are 0.97 and 0.96. AdQSM also models the branches in detail. The volume of branches from AdQSM is compared with the destructive measurement reference data. The R2, rBias, and CV-RMSE of the branches volume are 0.97, 12.38%, and 36.86%, respectively. The DBH and height of the harvested trees were used as reference values to test the accuracy of AdQSM’s estimation of DBH and tree height. The R2, rBias, and CV-RMSE of DBH are 0.94, −5.01%, and 9.06%, respectively. The R2, rBias, and CV-RMSE of the tree height were 0.95, 1.88%, and 5.79%, respectively. This paper provides not only a new QSM method for estimating AGB based on TLS point clouds but also the potential for further development and testing of allometric equations.
SZU-CHI CHUNGINSTITUTE OF STATISTICSHAO-HSUAN WANGINSTITUTE OF STATISTICPO-YAO NIUINSTITUTE OF STATISTICSU-YUN HUANGINSTITUTE OF STATISTICWEI-HAU CHANGINSTITUTE OF STATISTICI-PING TUINSTITUTE OF STATISTIC
Silver Award Paper in 2020
Annals of Mathematical Sciences and Applicaitons , 5, (2), 2020
Principal component analysis (PCA) is arguably the most widely used
dimension-reduction method for vector-type data. When applied to a
sample of images, PCA requires vectorization of the image data, which
in turn entails solving an eigenvalue problem for the sample covariance matrix. We propose herein a two-stage dimension reduction (2SDR)
method for image reconstruction from high-dimensional noisy image
data. The first stage treats the image as a matrix, which is a tensor of
order 2, and uses multilinear principal component analysis (MPCA) for
matrix rank reduction and image denoising. The second stage vectorizes
the reduced-rank matrix and achieves further dimension and noise reduction. Simulation studies demonstrate excellent performance of 2SDR, for
which we also develop an asymptotic theory that establishes consistency
of its rank selection. Applications to cryo-EM (cryogenic electronic microscopy), which has revolutionized structural biology, organic and medical chemistry, cellular and molecular physiology in the past decade, are
also provided and illustrated with benchmark cryo-EM datasets. Connections to other contemporaneous developments in image reconstruction
and high-dimensional statistical inference are also discussed.
We propose a deep learning-based method for object detection in UAV-borne thermal images that have the capability of observing scenes in both day and night. Compared with visible images, thermal images have lower requirements for illumination conditions, but they typically have blurred edges and low contrast. Using a boundary-aware salient object detection network, we extract the saliency maps of the thermal images to improve the distinguishability. Thermal images are augmented with the corresponding saliency maps through channel replacement and pixel-level weighted fusion methods. Considering the limited computing power of UAV platforms, a lightweight combinational neural network ComNet is used as the core object detection method. The YOLOv3 model trained on the original images is used as a benchmark and compared with the proposed method. In the experiments, we analyze the detection performances of the ComNet models with different image fusion schemes. The experimental results show that the average precisions (APs) for pedestrian and vehicle detection have been improved by 2%~5% compared with the benchmark without saliency map fusion and MobileNetv2. The detection speed is increased by over 50%, while the model size is reduced by 58%. The results demonstrate that the proposed method provides a compromise model, which has application potential in UAV-borne detection tasks.
Data-based detection and quantification of causation in complex, nonlinear dynamical systems is of paramount importance to science, engineering, and beyond. Inspired by the widely used methodology in recent years, the cross-map-based techniques, we develop a general framework to advance towards a comprehensive understanding of dynamical causal mechanisms, which is consistent with the natural interpretation of causality. In particular, instead of measuring the smoothness of the cross-map as conventionally implemented, we define causation through measuring the scaling law for the continuity of the investigated dynamical system directly. The uncovered scaling law enables accurate, reliable, and efficient detection of causation and assessment of its strength in general complex dynamical systems, outperforming those existing representative methods. The continuity scaling-based framework is rigorously established and demonstrated using datasets from model complex systems and the real world.
We establish by exact, nonperturbative methods a universality for the correlation functions in Kraichnan's``rapid-change''model of a passively advected scalar field. We show that the solutions for separated points in the convective range of scales are unique and independent of the particular mechanism of the scalar dissipation. Any non-universal dependences therefore must arise from the large length-scale features. The main step in the proof is to show that solutions of the model equations are unique even in the idealized case of zero diffusivity, under a very modest regularity requirement (square-integrability). Within this regularity class the only zero-modes of the global many-body operators are shown to be trivial ones (ie constants). In a bounded domain of size L , with physical boundary conditions, the``ground-state energy''is strictly positive and scales as L with an exponent L .
Big Data bring new opportunities to modern society and challenges to data scientists. On the one hand, Big Data hold great promises for discovering subtle population patterns and heterogeneities that are not possible with small-scale data. On the other hand, the massive sample size and high dimensionality of Big Data introduce unique computational and statistical challenges, including scalability and storage bottleneck, noise accumulation, spurious correlation, incidental endogeneity and measurement errors. These challenges are distinguished and require new computational and statistical paradigm. This paper gives overviews on the salient features of Big Data and how these features impact on paradigm change on statistical and computational methods as well as computing architectures. We also provide various new perspectives on the Big Data analysis and computation. In particular, we emphasize on
Inflammatory response following central nervous system (CNS) injury contributes to progressive neuropathology and reduction in functional recovery. Axons are sensitive to mechanical injury and toxic inflammatory mediators, which may lead to demyelination. Although it is well documented that degenerated myelin triggers undesirable inflammatory responses in autoimmune diseases such as multiple sclerosis (MS) and its animal model, experimental autoimmune encephalomyelitis (EAE), there has been very little study of the direct inflammatory consequences of damaged myelin in spinal cord injury (SCI), i.e., there is no direct evidence to show that myelin debris from injured spinal cord can trigger undesirable inflammation in vitro and in vivo. Our data showed that myelin can initiate inflammatory responses in vivo, which is complement receptor 3 (CR3)-dependent via stimulating macrophages to express pro-inflammatory molecules and down-regulates expression of anti-inflammatory cytokines. Mechanism study revealed that myelin-increased cytokine expression is through activation of FAK/PI3K/Akt/NF-B signaling pathways and CR3 contributes to myelin-induced PI3K/Akt/NF-B activation and cytokine production. The myelin induced inflammatory response is myelin specific as sphingomyelin (the major lipid of myelin) and myelin basic protein (MBP, one of the major proteins of myelin) are not able to activate NF-B signaling pathway. In conclusion, our results demonstrate a crucial role of myelin as an endogenous inflammatory stimulus that induces pro-inflammatory responses and suggest that blocking myelin-CR3 interaction and
A two-space dimensional active nonlinear nonlocal cochlear model is formulated in the time domain to capture nonlinear hearing effects such as compression, multi-tone suppression and difference tones. The micromechanics of the basilar membrane (BM) are incorporated to model active cochlear properties. An active gain parameter is constructed in the form of a nonlinear nonlocal functional of BM displacement. The model is discretized with a boundary integral method and numerically solved using an iterative second-order accurate finite difference scheme. A block matrix structure of the discrete system is exploited to simplify the numerics with no loss of accuracy. Model responses to multiple frequency stimuli are shown in agreement with hearing experiments. A nonlinear spectrum is computed from the model, and compared with FFT spectrum for noisy tonal inputs. The discretized model is efficient and accurate
The single-stranded RNA Flavivirus, Zika virus (ZIKV), has recently re-emerged and spread rapidly across the western hemispheres equatorial countries, primarily through Aedes mosquito transmission. While symptoms in adult infections appear to be self-limiting and mild, severe birth defects, such as microcephaly, have been linked to infection during early pregnancy. Recently, Tang et al. (Cell Stem Cell 2016, doi: 10.1016/j.stem.2016.02.016 ) demonstrated that ZIKV efficiently infects induced pluripotent stem cell (iPSC) derived human neural progenitor cells (hNPCs), resulting in cell cycle abnormalities and apoptosis. Consequently, hNPCs are a suggested ZIKV target. We analyzed the transcriptomic sequencing (RNA-seq) data (GEO: GSE78711) of ZIKV (Strain: MR766) infected hNPCs. For comparison to the ZIKV-infected hNPCs, the expression data from hNPCs infected with human cytomegalovirus (CMV) (Strain: AD169) was used (GEO: GSE35295). Utilizing a combination of Gene Ontology, database of human diseases, and pathway analysis, we generated a putative systemic model of infection supported by known molecular pathways of other highly related viruses. We analyzed RNA-sequencing data for transcript expression alterations in ZIKV-infected hNPCs, and then compared them to expression patterns of iPSC-derived hNPCs infected with CMV, a virus that can also induce severe congenital neurological defects in developing fetuses. We demonstrate for the first time that many of cellular pathways correlate with clinical pathologies following ZIKV infection such as microcephaly, congenital nervous
Microarray techniques have been widely used to monitor gene expression in many areas of biomedical research. They have been widely used for tumor diagnosis and classification, prediction of prognoses and treatment, and understanding of molecular mechanisms, biochemical pathways, and gene networks. Statistical methods are vital for these scientific endeavors. This article reviews recent developments of statistical methods for analyzing data from microarray experiments. Emphasis has been given to normalization of expression from multiple arrays, selecting significantly differentially expressed genes, tumor classifications, and gene expression pathways and networks.
The quantitative comparison of two or more microarrays can reveal, for example, the distinct patterns of gene expression that define different cellular phenotypes or the genes that are induced in the cellular response to certain stimulations. Normalization of the measured intensities is a prerequisite of such comparisons. However, a fundamental problem in cDNA microarray analysis is the lack of a common standard to compare the expression levels of different samples. Several normalization protocols have been proposed to overcome the variabilities inherent in this technology. We have developed a normalization procedure based on within-array replications via a semilinear in-slide model, which adjusts objectively experimental variations without making critical biological assumptions. The significant analysis of gene expressions is based on a weighted <i>t</i> statistic, which accounts for the heteroscedasticity of the
We study a class of nonlinear nonlocal cochlear models of the transmission line type, describing the motion of basilar membrane (BM) in the cochlea. They are damped dispersive partial differential equations (PDEs) driven by time dependent boundary forcing due to the input sounds. The global well-posedness in time follows from energy estimates. Uniform bounds of solutions hold in the case of bounded nonlinear damping. When the input sounds are multi-frequency tones, and the nonlinearity in the PDEs is cubic, we construct smooth quasi-periodic solutions (multi-tone solutions) in the weakly nonlinear regime, where new frequencies are generated due to nonlinear interaction. When the input consists of two tones at frequencies f 1, f 2 (f 1< f 2), and high enough intensities, numerical results illustrate the formation of combination tones at 2f 1 f 2 and 2f 2 f 1, in agreement with hearing experiments. We visualize
It has been reported that the plasma levels of VEGF in tumor patients decreased during dendritic cell (DC)-based immunotherapy, but the underlying mechanism remains unclear. Our current report demonstrates that VEGF levels were significantly decreased in the supernatants of DCs incubated with rhVEGF or tumor conditioned medium (TCM) while the intracellular VEGF in DCs was increased. The increased intracellular VEGF was not due to the <i>de novo</i> VEGF synthesis by DCs because exogenous VEGF inhibited the mRNA expression of VEGF in DCs. More direct evidence was provided to demonstrate that Cy3-labeled VEGF could be internalized by DCs specifically and efficiently. In addition, the activity of DCs to internalize VEGF was abolished by neutralizing antibody against VEGF receptor-1 (Flt-1) and inhibitors of endocytosis such as carbonyl cyanide m-chlorophenyl hydrazone (CCCP) and genistein. This
Severe acute respiratory syndrome (SARS) is a new infectious disease with a global impact. Understanding its pathogenesis and developing specific diagnostic methods for its early diagnosis are crucial for the effective management and control of this disease. By using proteomic technology, truncated forms of <sub>1</sub>antitrypsin (TF<sub>1</sub>AT) were found to increase significantly and consistently in sera of SARS patients compared to control subjects. The result showed a sensitivity of 100% for SARS patients and a specificity of 92.8% for controls. Furthermore, the levels of these proteins significantly correlated with certain clinicopathological parameters. The dramatic increase in TF<sub>1</sub>AT may be the result of degradation of <sub>1</sub>AT. As <sub>1</sub>AT plays an important role in the protection of lung function, its degradation may be an important factor in the pathogenesis of SARS. These findings indicate that increased TF<sub>1</sub>AT
Although stem cell therapy holds promise as a potential treatment in a number of diseases, the tumorigenicity of embryonic stem cells (ESC) and induced pluripotent stem cells remains a major obstacle. <i>In vitro</i> predifferentiation of ESCs can help prevent the risk of teratoma formation, yet proliferating neural progenitors can generate tumors, especially in the presence of immunosuppressive therapy. In this study, we investigated the effects of the microenvironment on stem cell growth and teratoma development using undifferentiated ESCs. Syngeneic ESC transplantation triggered an inflammatory response that involved the recruitment of bone marrow (BM)derived macrophages. These macrophages differentiated into an M2 or angiogenic phenotype that expressed multiple angiogenic growth factors and proteinases, such as macrophage migration inhibitory factor (MIF), VEGF, and matrix metalloproteinase 9
Functional linear models are useful in longitudinal data analysis. They include many classical and recently proposed statistical models for longitudinal data and other functional data. Recently, smoothing spline and kernel methods have been proposed for estimating their coefficient functions nonparametrically but these methods are either intensive in computation or inefficient in performance. To overcome these drawbacks, in this paper, a simple and powerful twostep alternative is proposed. In particular, the implementation of the proposed approach via local polynomial smoothing is discussed. Methods for estimating standard deviations of estimated coefficient functions are also proposed. Some asymptotic results for the local polynomial estimators are established. Two longitudinal data sets, one of which involves timedependent covariates, are used to demonstrate the approach proposed. Simulation studies
Estimation of genewise variance arises from two important applications in microarray data analysis: selecting significantly differentially expressed genes and validation tests for normalization of microarray data. We approach the problem by introducing a two-way nonparametric model, which is an extension of the famous Neyman-Scott model and is applicable beyond microarray data. The problem itself poses interesting challenges because the number of nuisance parameters is proportional to the sample size and it is not obvious how the variance function can be estimated when measurements are correlated. In such a high-dimensional nonparametric problem, we proposed two novel nonparametric estimators for genewise variance function and semiparametric estimators for measurement correlation, via solving a system of nonlinear equations. Their asymptotic normality is established. The finite sample property is
<b>Motivation:</b> Normalization of microarray data is essential for multiple-array analyses. Several normalization protocols have been proposed based on different biological or statistical assumptions. A fundamental problem arises whether they have effectively normalized arrays. In addition, for a given array, the question arises how to choose a method to most effectively normalize the microarray data.
In an event-related functional MRI data analysis, an accurate and robust extraction of the hemodynamic response function (HRF) and its associated statistics (e.g., magnitude, width, and time to peak) is critical to infer quantitative information about the relative timing of the neuronal events in different brain regions. The aim of this paper is to develop a multiscale adaptive smoothing model (MASM) to accurately estimate HRFs pertaining to each stimulus sequence across all voxels. MASM explicitly accounts for both spatial and temporal smoothness information, while incorporating such information to adaptively estimate HRFs in the frequency domain. One simulation study and a real data set are used to demonstrate the methodology and examine its finite sample performance in HRF estimation, which confirms that MASM significantly outperforms the existing methods including the smooth finite impulse
A semilinear in-slide model is introduced to remove the intensity effect in the scanning process. It is demonstrated that the intensity effect can be estimated accurately and removed effectively. This normalization step is vital for Affymetrix arrays to reveal relevant biological results when comparing gene expression in multiple arrays. The normalized expression ratios are analyzed further by a modified two-sample <i>t</i> test along with a sieved permutation scheme for computing <i>P</i> values. The improved specificity and sensitivity are demonstrated by using a study on the impact of macrophage migration inhibitory factor (MIF) reduction in neuroblastoma cells. With semilinear in-slide model analysis, expression of 166 genes was altered with a <i>P</i> value no greater than 0.001. Among those genes, 44 were altered >2-fold. MIF-regulated genes associated with tumor development including IL-8 and <i>C</i>-<i>met</i>, which are overexpressed
LPS is a main causative agent of septic shock. There is a lack of effective therapies. In vitro studies have shown that uptake of apoptotic cells actively inhibits the secretion by activated macrophages (M) of proinflammatory mediators such as TNF- and that such uptake increases the antiinflammatory and immunosuppressive cytokine TGF-. We therefore investigated the protective effect of apoptotic cells against LPS-induced endotoxic shock in mice. The current report is the first study to demonstrate that administration of apoptotic cells can protect mice from LPS-induced death, even when apoptotic cells were administered 24 h after LPS challenge. The beneficial effects of administration of apoptotic cells included 1) reduced circulating proinflammatory cytokines, 2) suppression of polymorphonuclear neutrophil infiltration in target organs, and 3) decreased serum LPS levels. LPS can quickly bind to apoptotic cells
Feedback modules, which appear ubiquitously in biological regulations, are often subject to disturbances from the input, leading to fluctuations in the output. Thus, the question becomes how a feedback system can produce a faithful response with a noisy input. We employed multiple time scale analysis, Fluctuation Dissipation Theorem, linear stability, and numerical simulations to investigate a module with one positive feedback loop driven by an external stimulus, and we obtained a critical quantity in noise attenuation, termed as signed activation time. We then studied the signed activation time for a system of two positive feedback loops, a system of one positive feedback loop and one negative feedback loop, and six other existing biological models consisting of multiple components along with positive and negative feedback loops. An inverse relationship is found between the noise amplification rate and the signed activation time, defined as the difference between the deactivation and activation time scales of the noise-free system, normalized by the frequency of noises presented in the input. Thus, the combination of fast activation and slow deactivation provides the best noise attenuation, and it can be attained in a single positive feedback loop system. An additional positive feedback loop often leads to a marked decrease in activation time, decrease or slight increase of deactivation time and allows larger kinetic rate variations for slow deactivation and fast activation. On the other hand, a negative feedback loop may increase the activation and deactivation times. The negative relationship between the noise amplification rate and the signed
Dispersive instability appears in time-domain solutions of classical cochlear models. In this letter, a derivation of optimal initial data is presented to minimize the effect of instability. A second-order accurate implicit boundary integral method is introduced. Numerical solutions of two-dimensional models show that the optimal initial conditions work successfully in time-domain steady-state computations for both the zero Neumann and zero Dirichlet fluid pressure boundary conditions at the helicotrema.
Stem cell therapies have had tremendous potential application for many diseases in recent years. However, the tumorigeneic properties of stem cells restrict their potential clinical application; therefore, strategies for reducing the tumorigenic potential of stem cells must be established prior to transplantation. We have demonstrated that syngeneic transplantation of embryonic stem cells (ESCs) provokes an inflammatory response that involves the rapid recruitment of bone marrow-derived macrophages (BMDMs). ESCs are able to prevent mature macrophages from macrophage colony-stimulating factor (M-CSF) withdrawal-induced apoptosis, and thus prolong macrophage lifespan significantly by blocking various apoptotic pathways in an M-CSF-independent manner. ESCs express and secrete IL-34 which may be responsible for ESC-promoted macrophage survival. This anti-apoptotic effect of ESCs involves activation of extracellular signal-regulated kinase (ERK)1/2 and PI3K/Akt pathways and thus, inhibition of ERK1/2 and PI3K/AKT activation decreases ESC-induced macrophage survival. Functionally, ESC-treated macrophages also showed a higher level of phagocytic activity. ESCs further serve to polarize BMDMs into M2-like macrophages that exhibit most tumor-associated macrophage (TAM) phenotypic and functional features. ESC-educated macrophages produce high levels of arginase-1, Tie-2 and TNF-, which participate in angiogenesis and contribute to teratoma progression. Our study suggests that induction of M2-like macrophage activation is an important mechanism for teratoma development. Strategies targeting macrophages to