Transcriptomic Analysis of Green Leaf Plants and White-Green Leaf Mutants in Haworthia cooperi var. pilifera.

Haworthia cooperi var. pilifera is a succulent plant with ornamental value. The white-green leaf mutant (wl) showed a significant difference in leaf color from the wild-type plant (WT). In this study, we integrated the transcriptomes of wl and WT plants to screen differentially expressed genes related to leaf color variation. The results of transcriptome analysis showed that 84,163 unigenes were obtained after de novo assembly and the NR database annotated the largest number of unigenes, which accounted for 57.13%, followed by NT (43.02%), GO (39.84%), Swiss-Prot (39.25%), KEGG (36.06%), and COG (24.88%). Our finding showed that 2586 genes were differentially expressed in the two samples, including 1996 down-regulated genes and 590 up-regulated genes. GO analysis predicted that these differentially expressed genes (DEGs) participate in 12 cellular components, 20 biological processes, and 13 molecular function terms and KEGG analysis showed that metabolic pathways, plant-pathogen interaction, glycerophospholipid metabolism, endocytosis, plant hormone signal transduction, and ether lipid metabolism were enriched among all identified pathways. Through functional enrichment analysis of DEGs, we found that they were involved in chloroplast division and the biosynthesis of plant pigments, including chlorophyll, carotenoids, anthocyanin, and transcription factor families, which might be related to the formation mechanism of leaf color. Taken together, these results present insights into the difference in gene expression characteristics in leaves between WT and wl mutants and provide a new insight for breeding colorful leaf phenotypes in succulent plants.

Functional study of the soybean stamen-preferentially expressed gene GmFLA22a in regulating male fertility.

China has a high dependence on soybean imports, yield increase at a faster rate is an urgent problem that need to be solved at present. The application of heterosis is one of the effective ways to significantly increase crop yield. In recent years, the development of an intelligent male sterility system based on recessive nuclear sterile genes has provided a potential solution for rapidly harnessing the heterosis in soybean. However, research on male sterility genes in soybean has been lagged behind. Based on transcriptome data of soybean floral organs in our research group, a soybean stamen-preferentially expressed gene GmFLA22a was identified. It encodes a fasciclin-like arabinogalactan protein with the FAS1 domain, and subcellular localization studies revealed that it may play roles in the endoplasmic reticulum. Take advantage of the gene editing technology, the Gmfla22a mutant was generated in this study. However, there was a significant reduction in the seed-setting rate in the mutant plants at the reproductive growth stage. The pollen viability and germination rate of Gmfla22a mutant plants showed no apparent abnormalities. Histological staining demonstrated that the release of pollen grains in the mutant plants was delayed and incomplete, which may due to the locule wall thickening in the anther development. This could be the reason of the reduced seed-setting rate in Gmfla22a mutants. In summary, our study has preliminarily revealed that GmFLA22a may be involved in regulating soybean male fertility. It provides crucial genetic materials for further uncovering its molecular function and gene resources and theoretical basis for the utilization of heterosis in soybean.

Two new quinolinone glycoalkaloids from Chrysanthemum indicum L. and their antimicrobial activity.

Phytochemical investigation of Chrysanthemum indicum L. yielded two new quinolinone glycoalkaloids named as Chrysanthemumsides A-B (1-2). The structures of the new compounds were elucidated by analysis of their 1D- and 2D-NMR, HRESIMS and ECD calculations. Compounds 1-4 were evaluated for antimicrobial activity against the Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa and Candida albicans, and the data showed that compound 2 had significant antimicrobial effects (MIC 3.9 to 7.8 µg/mL).

The manipulation of cell suspensions from zebrafish intestinal mucosa contributes to understanding enteritis.

Background: Although zebrafish are commonly used to study intestinal mucosal immunity, no dedicated procedure for isolating immune cells from zebrafish intestines is currently available. A speedy and simple operating approach for preparing cell suspension from mucosa has been devised to better understanding of intestinal cellular immunity in zebrafish. Methods and results: The mucosal villi were separated away from the muscle layer by repeated blows. The complete deprivation of mucosa was done and evidenced by HE and qPCR results. Higher expression of both innate (mpeg1, mpx, and lck) and adaptive immune genes (zap70, blnk, foxp3a, and foxp3b) was revealed compared to cells obtained by typical mesh rubbing. The cytometric results also revealed that the tested operation group had a higher concentration and viability. Further, fluorescent-labelled immune cells from 3mo Tg(lyz:DsRED2), Tg(mpeg1:EGFP), Tg(Rag2:DsRED), and Tg(lck:EGFP), were isolated and evaluated for the proportion, and immune cells' type could be inferred from the expression of marker genes. The transcriptomic data demonstrated that the intestinal immune cell suspension made using the new technique was enriched in immune-related genes and pathways, including il17a/f, il22, cd59, and zap70, as well as pattern recognition receptor signaling and cytokine-cytokine receptor interaction. In addition, the low expression of DEG for the adherent and close junctions indicated less muscular contamination. Also, lower expression of gel-forming mucus-associated genes in the mucosal cell suspension was consistent with the current less viscous cell suspension. To apply and validate the developed manipulation, enteritis was induced by soybean meal diet, and immune cell suspensions were analyzed by flow cytometry and qPCR. The finding that in enteritis samples, there was inflammatory increase of neutrophils and macrophages, was in line with upregulated cytokines (il8 and il10) and cell markers (mpeg1 and mpx). Conclusion: As a result, the current work created a realistic technique for studying intestinal immune cells in zebrafish. The immune cells acquired may aid in further research and knowledge of intestinal illness at the cellular level.

A Review on Tetrabromobisphenol A: Human Biomonitoring, Toxicity, Detection and Treatment in the Environment.

Tetrabromobisphenol A (TBBPA) is a known endocrine disruptor employed in a range of consumer products and has been predominantly found in different environments through industrial processes and in human samples. In this review, we aimed to summarize published scientific evidence on human biomonitoring, toxic effects and mode of action of TBBPA in humans. Interestingly, an overview of various pretreatment methods, emerging detection methods, and treatment methods was elucidated. Studies on exposure routes in humans, a combination of detection methods, adsorbent-based treatments and degradation of TBBPA are in the preliminary phase and have several limitations. Therefore, in-depth studies on these subjects should be considered to enhance the accurate body load of non-invasive matrix, external exposure levels, optimal design of combined detection techniques, and degrading technology of TBBPA. Overall, this review will improve the scientific comprehension of TBBPA in humans as well as the environment, and the breakthrough for treating waste products containing TBBPA.

Complete chloroplast genome sequence of a bulbous flowering plant, Allium triquetrum Linnaeus, 1753 (Amaryllidaceae).

Allium triquetrum (Linnaeus, 1753) is a bulbous flowering plant of the genus Allium (Amaryllidaceae), native to the Mediterranean basin, and is now widespread and invasive in different parts of the world via ornamental horticultural trade. However, to date, the genomic study of A. triquetrum has lagged, which impedes the development of appropriate utilization and management practices for this species. Here, we report the complete chloroplast genome sequence of A. triquetrum. The chloroplast genome size of A. triquetrum was 153,298 bp, consisting of a pair of inverted repeat regions (26,547 bp), separated by a large single-copy (82,875 bp) region and a small single-copy (17,329 bp) region. Genome annotation predicted 133 genes, including 87 protein-coding genes, 38 tRNA genes, and eight rRNA genes. Phylogenetic analysis based on 60 whole chloroplast genome sequences of Allium species suggested that A. triquetrum and A. moly are sister to each other along with the clade of A. fasciculatum, A. hookeri, and A. macranthum.

The complete chloroplast genome sequence of Rhododendron oreodoxa var. fargesii (Ericaceae), an ornamental plant.

Rhododendron oreodoxa var. fargesii is an evergreen shrub or small tree, which has great ornamental and huge medicinal value. The complete chloroplast genome of this species has not been reported. In the present study, we obtained the chloroplast complete genome, the circular genome was 200,787 bp in total length, and 141 genes were identified, including 93 protein-coding, 40 tRNA genes, and 8 rRNA genes. The results of the phylogenetic analysis supported the idea that Rhododendron belongs to the Ericaceae family and that R. oreodoxa var. fargesii is closely related to R. griersonianum in the Ericaceae family. This study will provide useful data onto phylogeny research and genomic selective breeding of R. oreodoxa var. fargesii.

Storage method of multi-channel lidar data based on tree structure.

The multi-channel lidar has fast acquisition speed, large data volume, high dimension, and vital real-time storage, which makes it challenging to be met using the traditional lidar data storage methods. This paper presents a novel approach to storing the multi-channel lidar data based on the principle of the tree structure, the adjacency linked list, the binary data storage. In the proposed system, a tree structure is constructed by the four-dimensional structure of the multi-channel lidar data, and a data retrieval method of the multi-channel lidar data file is given. The results show that the proposed tree structure approach can save the storage capacity and improve the retrieval speed, which can meet the needs for efficient storage and retrieval of multi-channel lidar data, and improve the data storage utilization and the practicality of multi-channel lidar system.

The complete chloroplast genome of Clematis florida Thunb. (Ranunculaceae), an ornamental and medicinal plant from Henan province, China.

Clematis florida Thunb. is a herbaceous and perennial plant native to East Asia. The plant is resistant to cold but sensitive to heat. It is an ornamental and medicinal plant that has great commercial potential. Here, we assembled and characterized the complete chloroplast (cp) genome of C. florida. The cp genome of C. florida was characterized by Illumina pair-end sequencing and is 159,606 bp in total length. The genome includes a large single-copy (LSC) region of 79,467 bp, a small single-copy (SSC) region of 18,057 bp, and a pair of inverted repeats (IR) regions of 31,041 bp. The genome contains 135 genes including 91 protein-coding, 36 tRNA, and eight rRNA genes. Phylogenetic analysis based on 18 Clematis species indicates that C. florida is closely related to C. fusca in the Ranunculaceae. The phylogenetic relationships and taxonomic status of C. florida revealed by cp genome were consistent with the previous molecular studies, and can serve as a reference for future studies on molecular biology, evolution, and taxonomy in the genus Clematis.

Concurrent and lagged effects of spring greening on seasonal carbon gain and water loss across the Northern Hemisphere.

Spring greening has been widely observed across the Northern Hemisphere (NH) using a remotely sensed vegetation index (e.g., the normalized difference vegetation index, NDVI). However, there is still a debate on the ecological effects of spring greening on seasonal carbon and water budgets. This study jointly investigated the concurrent and lagged effects of spring greening on carbon gain (gross primary productivity, GPP) and water loss (evapotranspiration, ET) in the summer-active ecosystems at mid and high latitudes of NH using remote sensing and multimodel ensemble data during 1982-2013. The results showed that the collective promotion of spring greening to concurrent GPP and ET is widespread despite variations in magnitude and significance. Both beneficial and adverse lagged effects of spring greening on summer GPP commonly appear with an obvious spatial heterogeneity and difference among climate-plant types. However, the expected significant suppression of spring greening to summer GPP was rarely observed even in the areas where spring ET was significantly promoted by spring greening. Nevertheless, when drought was taken into account, the response patterns of spring water use to spring greening varied to some extent, and the adverse lagged effect of spring greening to summer GPP appeared or strengthened in some regions, especially during the years with dry summer. Given the predicted warming of the climate and more frequent climatic extremes, the adverse effect of spring greening should be given more attention.

The complete chloroplast genome of Hippeastrum vittatum (Amaryllidaceae).

Hippeastrum vittatum (L'Hér.) Herb. is a perennial herb in the Amaryllidaceae, which has been used as a medicinal and ornamental plant. Here, we assembled and characterized the complete chloroplast (cp) genome of H. vittatum by high throughput sequencing. As a result, the length of the complete cp genome is 158,082 bp with a canonical quadripartite structure, consists of a large single-copy region (LSC) of 86,165 bp, a small single-copy region (SSC) of 18,283 bp, and two inverted repeat (IR) regions of 26,817 bp, each. A total of 137 genes were identified, including 87 protein-coding genes, 42 tRNA genes, and 8 rRNA genes. The phylogenomic analysis was performed based on the complete cp genomes of 30 species, which revealed the closest relationship between H. vittatum and H. rutilum in the genus Hippeastrum.

Unbalanced forest displacement across the coastal urban groups of eastern China in recent decades.

The Jing-Jin-Ji urban group (JJJug), the Yangtze River Delta urban group (YRDug) and the Pearl River Delta urban group (PRDug) are major urban groups of eastern China that play crucial roles in the economy and ecology. With rapid urbanization, demand for land for urban construction has significantly increased, causing direct and indirect losses of forests. At the same time, forest protection and restoration are being promoted in the construction of forested urban groups in response to the 13th Five-Year Plan for forestry development of China in the abovementioned regions. These inevitable contradictory demands for land may inhibit regional sustainable development. However, how forest coverage changed and its ecological impacts in recent decades have rarely been systematically evaluated. To address this issue, this paper quantitatively investigated the spatial and temporal variations in forest coverage and the evolution of landscape patterns using remote sensing data across the JJJug, the YRDug and the PRDug from 1992 to 2015. The results show that forest coverage in the JJJug first increased and then decreased, while that in the YRDug and the PRDug showed a sustained decline during the study period. In the case of land displacement, on the one hand, the three urban groups exhibited a transition from forest to farmland in the forest-farm ecotone at medium and high altitudes. On the other hand, grassland and shrubland were changed into forest mainly in the outer suburbs. Furthermore, in general, the landscape fragmentation in the urban groups significantly increased because of urban expansion. Besides, that of the JJJug exhibited an obvious spatial heterogeneity with a decline in the north while an increase in the south. Overall, unbalanced forest displacement, which could lead to a negative effect on both forest-coverage quantity and landscape quality, should be given more attention in the future development of forested urban groups.

Twin scanning lidars for accurate measurement of lower tropospheric aerosols by numerical approximation.

In order to improve accuracy of aerosol measurements, a novel method using twin scanning lidars is presented; this method is able to overcome the incomplete overlap range of vertical lidar as well as provide 2D spatial distributions. The scanning lidar setups in the opposite directions are employed as remote sensing tools. Aerosol measurements are performed with cross scanning from the ground to the height of interest. Aerosol optical properties are retrieved using numerical approximation, in which differences between the measured values and the constructed values of the logarithmic range-square-corrected lidar data in the cross-scanning region are minimized. In the data retrieval, we utilize a matrix formulation, in which a Cartesian 2D range-height-indicator diagram is constructed. To verify this method, scanning measurements by ultraviolet Mie scanning lidar performed at different time intervals were taken as the cross-scanning measurements from the twin scanning lidars. With the retrieved spatial distributions of aerosol optical properties, such as aerosol backscatter, aerosol extinction, and lidar ratio, the regional aerosol studies showed that aerosol loading was relatively small and in the presence of multiple layers, which may be influenced by airflow from long-range transportation and cause a large impact on the local environment. To conclude, the presented method using twin scanning lidars is feasible for aerosol measurement in the application of horizontally atmospheric inhomogeneity.

GPU-accelerated Kernel Regression Reconstruction for Freehand 3D Ultrasound Imaging.

Volume reconstruction method plays an important role in improving reconstructed volumetric image quality for freehand three-dimensional (3D) ultrasound imaging. By utilizing the capability of programmable graphics processing unit (GPU), we can achieve a real-time incremental volume reconstruction at a speed of 25-50 frames per second (fps). After incremental reconstruction and visualization, hole-filling is performed on GPU to fill remaining empty voxels. However, traditional pixel nearest neighbor-based hole-filling fails to reconstruct volume with high image quality. On the contrary, the kernel regression provides an accurate volume reconstruction method for 3D ultrasound imaging but with the cost of heavy computational complexity. In this paper, a GPU-based fast kernel regression method is proposed for high-quality volume after the incremental reconstruction of freehand ultrasound. The experimental results show that improved image quality for speckle reduction and details preservation can be obtained with the parameter setting of kernel window size of [Formula: see text] and kernel bandwidth of 1.0. The computational performance of the proposed GPU-based method can be over 200 times faster than that on central processing unit (CPU), and the volume with size of 50 million voxels in our experiment can be reconstructed within 10 seconds.

Common pathway signature in lung and liver fibrosis.

Fibrosis, a progressive accumulation of extracellular matrix components, encompasses a wide spectrum of distinct organs, and accounts for an increasing burden of morbidity and mortality worldwide. Despite the tremendous clinical impact, the mechanisms governing the fibrotic process are not yet understood, and to date, no clinically reliable therapies for fibrosis have been discovered. Here we applied Regeneration Intelligence, a new bioinformatics software suite for qualitative analysis of intracellular signaling pathway activation using transcriptomic data, to assess a network of molecular signaling in lung and liver fibrosis. In both tissues, our analysis detected major conserved signaling pathways strongly associated with fibrosis, suggesting that some of the pathways identified by our algorithm but not yet wet-lab validated as fibrogenesis related, may be attractive targets for future research. While the majority of significantly disrupted pathways were specific to histologically distinct organs, several pathways have been concurrently activated or downregulated among the hepatic and pulmonary fibrosis samples, providing new evidence of evolutionary conserved pathways that may be relevant as possible therapeutic targets. While future confirmatory studies are warranted to validate these observations, our platform proposes a promising new approach for detecting fibrosis-promoting pathways and tailoring the right therapy to prevent fibrogenesis.

A Fast Single Image Haze Removal Algorithm Using Color Attenuation Prior.

Single image haze removal has been a challenging problem due to its ill-posed nature. In this paper, we propose a simple but powerful color attenuation prior for haze removal from a single input hazy image. By creating a linear model for modeling the scene depth of the hazy image under this novel prior and learning the parameters of the model with a supervised learning method, the depth information can be well recovered. With the depth map of the hazy image, we can easily estimate the transmission and restore the scene radiance via the atmospheric scattering model, and thus effectively remove the haze from a single image. Experimental results show that the proposed approach outperforms state-of-the-art haze removal algorithms in terms of both efficiency and the dehazing effect.

Pathway activation strength is a novel independent prognostic biomarker for cetuximab sensitivity in colorectal cancer patients.

Cetuximab, a monoclonal antibody against epidermal growth factor receptor (EGFR), was shown to be active in colorectal cancer. Although some patients who harbor K-ras wild-type tumors benefit from cetuximab treatment, 40 to 60% of patients with wild-type K-ras tumors do not respond to cetuximab. Currently, there is no universal marker or method of clinical utility that could guide the treatment of cetuximab in colorectal cancer. Here, we demonstrate a method to predict response to cetuximab in patients with colorectal cancer using OncoFinder pathway activation strength (PAS), based on the transcriptomic data of the tumors. We first evaluated our OncoFinder pathway activation strength model in a set of transcriptomic data obtained from patient-derived xenograft (PDx) models established from colorectal cancer biopsies. Then, the approach and models were validated using a clinical trial data set. PAS could efficiently predict patients' response to cetuximab, and thus holds promise as a selection criterion for cetuximab treatment in metastatic colorectal cancer.

Targeting accurate object extraction from an image: a comprehensive study of natural image matting.

With the development of digital multimedia technologies, image matting has gained increasing interests from both academic and industrial communities. The purpose of image matting is to precisely extract the foreground objects with arbitrary shapes from an image or a video frame for further editing. It is generally known that image matting is inherently an ill-posed problem because we need to output three images out of only one input image. In this paper, we provide a comprehensive survey of the existing image matting algorithms and evaluate their performance. In addition to the blue screen matting, we systematically divide all existing natural image matting methods into four categories: 1) color sampling-based; 2) propagation-based; 3) combination of sampling-based and propagation-based; and 4) learning-based approaches. Sampling-based methods assume that the foreground and background colors of an unknown pixel can be explicitly estimated by examining nearby pixels. Propagation-based methods are instead based on the assumption that foreground and background colors are locally smooth. Learning-based methods treat the matting process as a supervised or semisupervised learning problem. Via the learning process, users can construct a linear or nonlinear model between the alpha mattes and the image colors using a training set to estimate the alpha matte of an unknown pixel without any assumption about the characteristics of the testing image. With three benchmark data sets, the various matting algorithms are evaluated and compared using several metrics to demonstrate the strengths and weaknesses of each method both quantitatively and qualitatively. Finally, we conclude this paper by outlining the research trends and suggesting a number of promising directions for future development.

Dynamic virtual fixture on the Euclidean group for admittance-type manipulator in deforming environments.

BACKGROUND: In a deforming anatomic environment, the motion of an instrument suffers from complex geometrical and dynamic constraints, robot assisted minimally invasive surgery therefore requires more sophisticated skills for surgeons. This paper proposes a novel dynamic virtual fixture (DVF) to enhance the surgical operation accuracy of admittance-type medical robotics in the deforming environment. METHODS: A framework for DVF on the Euclidean Group SE(3) is presented, which unites rotation and translation in a compact form. First, we constructed the holonomic/non-holonomic constraints, and then searched for the corresponded reference to make a distinction between preferred and non-preferred directions. Second, different control strategies are employed to deal with the tasks along the distinguished directions. The desired spatial compliance matrix is synthesized from an allowable motion screw set to filter out the task unrelated components from manual input, the operator has complete control over the preferred directions; while the relative motion between the surgical instrument and the anatomy structures is actively tracked and cancelled, the deviation relative to the reference is compensated jointly by the operator and DVF controllers. The operator, haptic device, admittance-type proxy and virtual deforming environment are involved in a hardware-in-the-loop experiment, human-robot cooperation with the assistance of DVF controller is carried out on a deforming sphere to simulate beating heart surgery, performance of the proposed DVF on admittance-type proxy is evaluated, and both human factors and control parameters are analyzed. RESULTS: The DVF can improve the dynamic properties of human-robot cooperation in a low-frequency (0 ~ 40 rad/sec) deforming environment, and maintain synergy of orientation and translation during the operation. Statistical analysis reveals that the operator has intuitive control over the preferred directions, human and the DVF controller jointly control the motion along the non-preferred directions, the target deformation is tracked actively. CONCLUSIONS: The proposed DVF for an admittance-type manipulator is capable of assisting the operator to deal with skilled operations in a deforming environment.

Evaluation of various speckle reduction filters on medical ultrasound images.

At present, ultrasound is one of the essential tools for noninvasive medical diagnosis. However, speckle noise is inherent in medical ultrasound images and it is the cause for decreased resolution and contrast-to-noise ratio. Low image quality is an obstacle for effective feature extraction, recognition, analysis, and edge detection; it also affects image interpretation by doctor and the accuracy of computer-assisted diagnostic techniques. Thus, speckle reduction is significant and critical step in pre-processing of ultrasound images. Many speckle reduction techniques have been studied by researchers, but to date there is no comprehensive method that takes all the constraints into consideration. In this paper we discuss seven filters, namely Lee, Frost, Median, Speckle Reduction Anisotropic Diffusion (SRAD), Perona-Malik's Anisotropic Diffusion (PMAD) filter, Speckle Reduction Bilateral Filter (SRBF) and Speckle Reduction filter based on soft thresholding in the Wavelet transform. A comparative study of these filters has been made in terms of preserving the features and edges as well as effectiveness of de-noising.We computed five established evaluation metrics in order to determine which despeckling algorithm is most effective and optimal for real-time implementation. In addition, the experimental results have been demonstrated by filtered images and statistical data table.