Accurate tree density and location are important information for optimizing the management and production of forest. Combination of remote sensing techniques and local maximum (LM) filtering ...algorithm provides a feasible approach to individual tree crown detection, but still faces high error under complicate canopy structure. In this study, a revised LM (RLM) algorithm is presented and evaluated for identifying individual trees from four high spatial-resolution images. Instead of a moving window technique, the RLM algorithm finds crown center seeds by searching local maximal in the transects along row and column directions of the image. Each of final crown centers is then searched using a variable window centered at the crown center seed. Strategies for splitting and merging crowns are implemented in the RLM algorithm to reduce false detection. Result showed that accuracy of the RLM algorithm was more sensitive to its minimum crown length parameter (CLmin). The RLM algorithm driven by the CLmin estimates achieved high overall accuracies between 85% and 91% and low commission (9–14%) and omission errors (8–15%) for the four images. Splitting and merging strategies implemented in the RLM algorithm effectively reduced commission and omission errors. These results indicate that the RLM algorithm is a feasible method with well-defined parameters for automatically detecting individual trees with satisfactory detection accuracy.
•A revised local maximum (RLM) filtering for individual tree detection was proposed.•The RLM algorithm achieved high overall accuracies between 85% and 91%.•Splitting and merging strategy effectively reduced commission and omission errors.•Parameters of the RLM algorithm are easily specified by users.
The ever increasing discovery of non-coding RNAs leads to unprecedented demand for the accurate modeling of RNA folding, including the predictions of two-dimensional (base pair) and three-dimensional ...all-atom structures and folding stabilities. Accurate modeling of RNA structure and stability has far-reaching impact on our understanding of RNA functions in human health and our ability to design RNA-based therapeutic strategies.
The Vfold server offers a web interface to predict (a) RNA two-dimensional structure from the nucleotide sequence, (b) three-dimensional structure from the two-dimensional structure and the sequence, and (c) folding thermodynamics (heat capacity melting curve) from the sequence. To predict the two-dimensional structure (base pairs), the server generates an ensemble of structures, including loop structures with the different intra-loop mismatches, and evaluates the free energies using the experimental parameters for the base stacks and the loop entropy parameters given by a coarse-grained RNA folding model (the Vfold model) for the loops. To predict the three-dimensional structure, the server assembles the motif scaffolds using structure templates extracted from the known PDB structures and refines the structure using all-atom energy minimization.
The Vfold-based web server provides a user friendly tool for the prediction of RNA structure and stability. The web server and the source codes are freely accessible for public use at "http://rna.physics.missouri.edu".
The task of epitope discovery and vaccine design is increasingly reliant on bioinformatics analytic tools and access to depositories of curated data relevant to immune reactions and specific ...pathogens. The Immune Epitope Database and Analysis Resource (IEDB) was indeed created to assist biomedical researchers in the development of new vaccines, diagnostics, and therapeutics. The Analysis Resource is freely available to all researchers and provides access to a variety of epitope analysis and prediction tools. The tools include validated and benchmarked methods to predict MHC class I and class II binding. The predictions from these tools can be combined with tools predicting antigen processing, TCR recognition, and B cell epitope prediction. In addition, the resource contains a variety of secondary analysis tools that allow the researcher to calculate epitope conservation, population coverage, and other relevant analytic variables. The researcher involved in vaccine design and epitope discovery will also be interested in accessing experimental published data, relevant to the specific indication of interest. The database component of the IEDB contains a vast amount of experimentally derived epitope data that can be queried through a flexible user interface. The IEDB is linked to other pathogen-specific and immunological database resources.
Osthole is an active compound isolated from Chinese herb Cnidium monnieri (L.) Cusson, and had been reported to possess antitumor effect. However, the effect of osthole on the gastric cancer cells ...has not been investigated. In this study, the effects of osthole on the proliferation of human gastric cancer cells were tested. The data showed that osthole treatment significantly inhibited the proliferation of gastric cancer cells and resulted in the cell cycle arrest at G2/M phase in a dose-dependent manner. Western-blot study showed that the expression of cyclin B1 and cdc2 was markedly reduced by osthole. Moreover, expression of PI3K and pAKT was also significantly suppressed, and the results indicated that the inhibition of pAKT, cyclin B1, and cdc2 levels by osthole was notably enhanced by a PI3K inhibitor. These results demonstrate that osthole could inhibit gastric cancer cells proliferation via induction of cell cycle arrest at G2/M phase by the reduction of PI3K/AKT.
Abstract
Using global magnetohydrodynamics simulations, we have developed a three-dimensional parametric model for the Venusian bow shock based on a generalized conic section function defined by six ...parameters, with the effects of the solar wind magnetosonic Mach number (
M
MS
) and the interplanetary magnetic field (IMF) involved. The parametric model’s results reveal the following findings: (1) The size of the Venusian bow shock is primarily determined by
M
MS
. An increase in
M
MS
results in the bow shock moving closer to Venus and a reduction in its flaring angle. (2) Both the subsolar standoff distance and the bow shock’s flaring angle increase with the strength of the IMF components that are perpendicular to the solar wind flow direction (
B
Y
and
B
Z
in the Venus-centered solar orbital coordinate system), whereas the parallel IMF component (
B
X
) has a limited impact on the subsolar standoff distance but affects the flaring angle. (3) The cross section of the bow shock is elongated in the direction perpendicular to the IMF on the
Y
–
Z
plane, and the elongation degree is enhanced with increasing intensities of
B
Y
and
B
Z
. (4) The quasi-parallel bow shock locates closer to the planet as compared to the quasi-perpendicular bow shock. These findings are in alignment with prior empirical and theoretical models. The influences of
M
MS
and IMF on the bow shock’s position and geometry are attributed to the propagation of fast magnetosonic waves, showing the nature of the formation of a collisionless bow shock under the interaction of magnetized flow with an atmospheric object.
Purpose
Because the roles of striatal‐thalamo‐cortical and cerebello‐thalamo‐cortical circuits in the heterogeneous motor impairments of Parkinson's disease (PD) are becoming recognized, this study ...was designed to investigate the relationships between regional iron in the cardinal subcortical nuclei in these circuits and the different motor impairments.
Materials and Methods
Sixty‐two PD patients and 40 normal subjects were included and accepted for Enhanced T2‐Star Weighted Angiography Scanning (3.0T). According to the Unified Parkinson's Disease Rating Scale, patients were divided into tremor‐dominant (PD‐TD) and akinetic/rigid‐dominant groups (PD‐AR). The intergroup differences of magnetic susceptibility in those cardinal nuclei were measured. Correlation analyses between magnetic susceptibility and motor impairments were performed in all patients.
Results
Nigral magnetic susceptibility significantly increased for each PD group compared with controls (P < 0.001 for PD‐TD; P = 0.001 for PD‐AR). Magnetic susceptibility in the dentate nucleus (DN) and red nucleus (RN) for the PD‐TD patients were significantly increased compared with controls (P < 0.001 and P = 0.004, respectively). Magnetic susceptibility in these regions was also significantly correlated with tremor severity (r = 0.444, P = 0.001 for DN; r = 0.418, P = 0.001 for RN). Significant correlation between caudate magnetic susceptibility and akinetic/rigid severity were observed (r = –0.322, P = 0.015).
Conclusion
This study provides evidence that nigral iron accumulation is a common characteristic in PD, while iron accumulation in the DN and RN is correlated with tremor symptoms. Our data also indicate that caudate iron content may be a potential marker for akinetic/rigid progression.
Level of Evidence: 3
J. MAGN. RESON. IMAGING 2017;45:1335–1342
COVID-19 can cause different neurological symptoms in some people, including smell, inability to taste, dizziness, confusion, delirium, seizures, stroke, etc. Owing to the issue of vaccine ...effectiveness, update and coverage, we still need one or more diversified strategies as the backstop to manage illness. Characterizing the structural basis of ligand recognition in the main protease (Mpro) of SARS-CoV-2 will facilitate its rational design and development of potential drug candidates with high affinity and selectivity against COVID-19. Up to date, covalent-, non-covalent inhibitors and allosteric modulators have been reported to bind to different active sites of Mpro. In the present work, we applied the molecular dynamics (MD) simulations to systematically characterize the potential binding features of catalytic active site and allosteric binding sites in Mpro using a dataset of 163 3D structures of Mpro-inhibitor complexes, in which our results are consistent with the current studies. In addition, umbrella sampling (US) simulations were used to explore the dissociation processes of substrate pathway and allosteric pathway. All the information provided new insights into the protein features of Mpro and will facilitate its rational drug design for COVID-19.
Subtropical forests play an important role in global carbon cycle and in mitigating climate change. Knowledge on the abiotic and biotic driving factors that affect vegetation carbon stocks in ...subtropical forest ecosystems is needed to take full advantage of the carbon sequestration potential. We used a large-scale database from national forest continuous inventory in Zhejiang Province, and combined the Random Forest analysis (RF) and structural equation modeling (SEM) to quantify the contribution of biotic and abiotic driving factors on vegetation carbon stocks, and to evaluate the direct and indirect effects of the main driving factors. The RF model explained 50% of the variation in vegetation carbon stocks; canopy density accounted for 17.9%, and forest age accounted for 7.0%. Moreover, the SEM explained 52% of the variation in vegetation carbon stocks; the value of standardized total effects of canopy density and forest age were 0.469 and 0.327, respectively, suggesting that they were the most crucial driving factors of vegetation carbon stocks. Since the forests in our study were relatively young, the forests had a large potential for carbon sequestration. Overall, our study provided new insights into the sensitivity and potential response of subtropical forest ecosystems carbon cycle to climate change.
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•Random Forest analysis combined with SEM to evaluate the abiotic and biotic driving factors effects on vegetation carbon stocks.•Canopy density and forest age were the most crucial driving factors.•Provides new insights into the potential response of subtropical forest ecosystems carbon sequestration to climate change.
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