Markerauto2: A fast and robust fully automatic fiducial marker-based tilt series alignment software for electron tomography.

Cryoelectron tomography (cryo-ET) has become an indispensable technology for visualizing in situ biological ultrastructures, where the tilt series alignment is the key step to obtain a high-resolution three-dimensional reconstruction. Specifically, with the advent of high-throughput cryo-ET data collection, there is an increasing demand for high-accuracy and fully automatic tilt series alignment, to enable efficient data processing. Here, we propose Markerauto2, a fast and robust fully automatic software that enables accurate fiducial marker-based tilt series alignment.

Litter decomposition and nutrient release are faster under secondary forests than under Chinese fir plantations with forest development.

In terrestrial ecosystems, leaf litter is the main source of nutrients returning to the soil. Understanding how litter decomposition responds to stand age is critical for improving predictions of the effects of forest age structure on nutrient availability and cycling in ecosystems. However, the changes in this critical process with stand age remain poorly understood due to the complexity and diversity of litter decomposition patterns and drivers among different stand ages.

Functional identity drives tree species richness-induced increases in litterfall production and forest floor mass in young tree communities.

Forest floor accumulation is a key process that influences ecosystem carbon cycling. Despite evidence suggesting that tree diversity and soil carbon are positively correlated, most soil carbon studies typically omit the response of the forest floor carbon to tree diversity loss. Here, we evaluated how tree species richness affects forest floor mass and how this effect is mediated by litterfall production and forest floor decay rate in a tree diversity experiment in a subtropical forest.

Determining protein structures in cellular lamella at pseudo-atomic resolution by GisSPA.

Cryo-electron tomography is a major tool used to study the structure of protein complexes in situ. However, the throughput of tilt-series image data collection is still quite low. Here, we show that GisSPA, a GPU accelerated program, can translationally and rotationally localize the target protein complex in cellular lamellae, as prepared with a focused ion beam, using single cryo-electron microscopy images without tilt-series, and reconstruct the protein complex at near-atomic resolution.

Phosphorus limitation induced by nitrogen addition changed soil microbial community structure in a subtropical forest.

Soil microorganisms play an important role in the biogeochemical cycles of terrestrial ecosystems. How-ever, it is still unclear how the amount and duration of nitrogen (N) addition affect soil microbial community structure and whether there is a correlation between the changes in microbial community structure and their nutrient limi-tation status. In this study, we conducted an N addition experiment in a subtropical forest to simulate N deposition with three treatments: control (CK, 0 kg N·hm·a), low N (LN, 40 kg N·hm·a), and high N (HN, 80 kg N·hm·a).

VP-Detector: A 3D multi-scale dense convolutional neural network for macromolecule localization and classification in cryo-electron tomograms.

Background And Objective: Cryo-electron tomography (cryo-ET) with subtomogram averaging (STA) is indispensable when studying macromolecule structures and functions in their native environments. Due to the low signal-to-noise ratio, the missing wedge artifacts in tomographic reconstructions, and multiple macromolecules of varied shapes and sizes, macromolecule localization and classification remain challenging. To tackle this bottleneck problem for structural determination by STA, we design an accurate macromolecule localization and classification method named voxelwise particle detector (VP-Detector).

Noise-Transfer2Clean: denoising cryo-EM images based on noise modeling and transfer.

Motivation: Cryo-electron microscopy (cryo-EM) is a widely used technology for ultrastructure determination, which constructs the 3D structures of protein and macromolecular complex from a set of 2D micrographs. However, limited by the electron beam dose, the micrographs in cryo-EM generally suffer from the extremely low signal-to-noise ratio (SNR), which hampers the efficiency and effectiveness of downstream analysis. Especially, the noise in cryo-EM is not simple additive or multiplicative noise whose statistical characteristics are quite different from the ones in natural image, extremely shackling the performance of conventional denoising methods.

Differences in Peak Oxygen Uptake in Bicycle Exercise Test Caused by Body Positions: A Meta-Analysis.

As demand for cardiopulmonary exercise test using a supine position has increased, so have the testing options. However, it remains uncertain whether the existing evaluation criteria for the upright position are suitable for the supine position. The purpose of this meta-analysis is to compare the differences in peak oxygen uptake (VO) between upright and supine lower extremity bicycle exercise.

Multi-labelled proteins recognition for high-throughput microscopy images using deep convolutional neural networks.

Background: Proteins are of extremely vital importance in the human body, and no movement or activity can be performed without proteins. Currently, microscopy imaging technologies developed rapidly are employed to observe proteins in various cells and tissues. In addition, due to the complex and crowded cellular environments as well as various types and sizes of proteins, a considerable number of protein images are generated every day and cannot be classified manually.

[Effects of root growth on leaf litter decomposition and enzyme activity in litter layer].

The growth of roots towards aboveground litter layer is a common phenomenon in forest ecosystems. It is of great significance to examine the effects of root presence on litter decomposition for understanding nutrient cycling in forest ecosystems. We explored the effects of root growth on leaf litter decomposition, nutrient release and enzyme activities by establishing treatments with and without root with a one year field decomposition experiment in and forests at Sanming, Fujian.

Analysis of codon usage patterns in citrus based on coding sequence data.

Background: Codon usage is an important determinant of gene expression levels that can help us understand codon biology, evolution and mRNA translation of species. The majority of previous codon usage studies have focused on single species analysis, although few studies have focused on the species within the same genus. In this study, we proposed a multispecies codon usage analysis workflow to reveal the genetic features and correlation in citrus.

[Effects of broadleaved tree species on soil microbial stoichiometry in clear-cut patches of plantation].

Investigating the response of soil microbial biomass and ecological stoichiometry to tree species transition is of great significance for understanding soil nutrient cycling and availability in forest ecosystems. We measured soil microbial biomass carbon (MBC), nitrogen (MBN), phosphorus (MBP) and their stoichiometry across 0-40 cm soil depth between and plantations by the chloroform fumigation extraction method, which were replanted after the harvest of plantation. The results showed that soil MBC in the 0-10 cm layer and soil MBN and MBP in the 0-20 cm layer under the were significantly higher than those under the .

[Soil C:N:P stoichiometry and nutrient dynamics in plantations during different growth stages].

We investigated soil C:N:P stoichiometry and nutrient dynamics of plantations at different stand ages (5, 8, 21, 27 and 40 years old) in Fujian Baisha Fores-try Farm. We measured the concentrations of soil total carbon (TC), total nitrogen (TN), total phosphorus (TP), total potassium (TK), total calcium (Ca), total magnesium (Mg), and soil C:N:P stoichiometry at 0-10, 10-20, and 20-40 cm soil layers during different growth stages. The results showed that soil TC and TN concentrations and C:N remained unchanged during stand development.

A Parallel Cerebrovascular Segmentation Algorithm Based on Focused Multi-Gaussians Model and Heterogeneous Markov Random Field.

A complete and detailed cerebrovascular image segmented from time-of-flight magnetic resonance angiography (TOF-MRA) data is essential for the diagnosis and therapy of the cerebrovascular diseases. In recent years, three-dimensional cerebrovascular segmentation algorithms based on statistical models have been widely used, but the existed methods always perform poorly on stenotic vessels and are not robust enough. In this paper, we propose a parallel cerebrovascular segmentation algorithm based on focused multi-Gaussians model and heterogeneous Markov random field.

[Effects of broadleaved tree plantation on soil phosphorus fractions and availability in diffe-rent soil layers in a logged Cunninghamia lanceolata woodland].

Phosphorus (P) limitation is one of the major issues for the management of subtropical plantations. Understanding the effects of tree species transition from conifer to broadleaved trees on soil P fraction and availability in different soil layers are of great significance for the sustainable development of subtropical forests. We compared changes in soil chemical properties, P fraction and availability across 0-100 cm soil profile between Mytilaria laosensis and Cunninghamia lanceolata plantations, which were initially reforested from C.

The Association of Serum hsCRP and Urinary Alpha1-Microglobulin in Patients with Type 2 Diabetes Mellitus.

This study aimed to investigate the association of serum hsCRP and urinary A1MG in patients with T2DM. Numerous investigations have proven that serum hypersensitive C-reactive protein (hsCRP) concentration in patients with type 2 diabetes mellitus (T2DM) is increased. Also, increased urinary alpha-1 microglobulin (A1MG) can be an early sign of renal damage, primarily on the proximal tubules in T2DM.

EGFR Cooperates with EGFRvIII to Recruit Macrophages in Glioblastoma.

: Amplification of the gene and its truncation mutant are hallmarks of glioblastoma. Although coexpression of EGFR and EGFRvIII confers a growth advantage, how EGFR and EGFRvIII influence the tumor microenvironment remains incompletely understood. Here, we show that EGFR and EGFRvIII cooperate to induce macrophage infiltration via upregulation of the chemokine CCL2.

AuTom-dualx: a toolkit for fully automatic fiducial marker-based alignment of dual-axis tilt series with simultaneous reconstruction.

Motivation: Dual-axis electron tomography is an important 3 D macro-molecular structure reconstruction technology, which can reduce artifacts and suppress the effect of missing wedge. However, the fully automatic data process for dual-axis electron tomography still remains a challenge due to three difficulties: (i) how to track the mass of fiducial markers automatically; (ii) how to integrate the information from the two different tilt series; and (iii) how to cope with the inconsistency between the two different tilt series.

Results: Here we develop a toolkit for fully automatic alignment of dual-axis electron tomography, with a simultaneous reconstruction procedure.