arXiv subjects

Youhua Chen

Publications and source records attributed to Youhua Chen.

4 recordsLinked to original sources

arXiv2018

3D super-resolved multi-angle TIRF via polarization modulation

Measuring the three dimension nanoscale organization of protein or cellular structures is challenging, especially when the structure is dynamic. Owing to the informative total internal reflection fluorescence (TIRF) imaging under varied illumination angles, multi-angle (MA) TIRF has been examined to offer a nanoscale axial and a sub-second temporal resolution. However, conventional MA-TIRF still performs badly in lateral resolution and fail to characterize the depth-image in densely-distributed regions, leaving a huge contrast between the nanoscale axial resolution and the diffraction limited lateral resolution. Moreover, the previous reconstructions are highly restricted by the efficiency with the increased amount of illumination angles. Here, we for the first time, emphasize the lateral super-resolution in the MA-TIRF and exampled by simply introducing polarization modulation into the illumination procedure. Equipped with a sparsity and accelerated proximal algorithm, we examine a more precise 3D sample structure compared with previous methods, enabling live cell imaging with temporal-resolution of 2 seconds, recovering high-resolution mitochondria fission and fusion process. Since the introduced vortex half wave retarder is an add-on component to the existing MA-TRIF system and the algorithm is the first open sourced and the fastest, we anticipate that the method and algorithm introduced here would be adopted rapidly by the biological community.

physics.optics↗

arXiv2014

'coexist': an R package for performing species coexistence modeling and analysis

This letter introduced a new R package 'coexist' which can perform species coexistence simulation and analysis. The package was initially developed for understanding the role of different combinations of varying species growth rates, dispersal ability, habitat heterogeneity, and competition interaction on influencing species coexistence under fluctuating environment. Further versions could introduce more coexistence models under different ecological conditions. The source package is available at the Google Code (https://code.google.com/p/coexist/) and R CRAN repository (http://cran.r-project.org/web/packages/coexist/).

q-bio.PE↗

arXiv2014

Distinguishing niche and neutral processes: issues in variation partitioning statistical methods and further perspectives

Variance partitioning methods, which are built upon multivariate statistics, have been widely applied in different taxa and habitats in community ecology. Here, I performed a literature review on the development and application of the methods, and then discussed the limitation of available methods and the difficulties involved in sampling schemes. The central goal of the work is then to propose some potential practical methods that might help to overcome different issues of traditional least-square-based regression modeling. A variety of regression models has been considered for comparison. In initial simulations, I identified that generalized additive model (GAM) has the highest accuracy to predict variation components. Therefore, I argued that other advanced regression techniques, including the GAM and related models, could be utilized in variation partitioning for better quantifying the aggregation scenarios of species distribution.

q-bio.PE↗

arXiv2014

Covariance among independent variables determines the overfitting and underfitting problems in variation partitioning methods: with a special focus on the mixed co-variation

The effectiveness and validity of applying variation partitioning methods in community ecology has been questioned. Here, using mathematical deduction and numerical simulation, we made an attempt to uncover the underlying mechanisms determining the effectiveness of variation partitioning techniques. The covariance among independent variables determines the under-fitting and over-fitting problem with the variation partitioning process. Ideally, it is assumed that the covariance among independent variables will be zero (no correlation at all), however, typically there will be some colinearities. Therefore, we analyzed the role of slight covariance on influencing species variation partitioning. We concluded that when the covariance between spatial and environmental predictors is positive, all the three components-pure environmental, spatial variations and mixed covariation were over-fitted, with the sign of the true covariation being negative. In contrast, when the covariance is negative, all the three components were under-fitted with the sign of true covariation being positive. Other factors, including extra noise levels, the strengths of variable coefficients and the patterns of landscape gradients, could reduce the fitting problems caused by the covariance of variables. The conventional calculation of mixed covariation is incorrect and misleading, as the true and estimated covariations are always sign-opposite. In conclusion, I challenge the conventional three-step procedure of variation partitioning, suggesting that a full regression model with all variables together is robust enough to correctly partition variations.

q-bio.PE↗