DFSP: A fast and automatic distance field-based stem-leaf segmentation pipeline for point cloud of maize shoot.

The 3D point cloud data are used to analyze plant morphological structure. Organ segmentation of a single plant can be directly used to determine the accuracy and reliability of organ-level phenotypic estimation in a point-cloud study. However, it is difficult to achieve a high-precision, automatic, and fast plant point cloud segmentation. Besides, a few methods can easily integrate the global structural features and local morphological features of point clouds relatively at a reduced cost. In this paper, a distance field-based segmentation pipeline (DFSP) which could code the global spatial structure and local connection of a plant was developed to realize rapid organ location and segmentation. The terminal point clouds of different plant organs were first extracted via DFSP during the stem-leaf segmentation, followed by the identification of the low-end point cloud of maize stem based on the local geometric features. The regional growth was then combined to obtain a stem point cloud. Finally, the instance segmentation of the leaf point cloud was realized using DFSP. The segmentation method was tested on 420 maize and compared with the manually obtained ground truth. Notably, DFSP had an average processing time of 1.52 s for about 15,000 points of maize plant data. The mean precision, recall, and micro F1 score of the DFSP segmentation algorithm were 0.905, 0.899, and 0.902, respectively. These findings suggest that DFSP can accurately, rapidly, and automatically achieve maize stem-leaf segmentation tasks and could be effective in maize phenotype research. The source code can be found at https://github.com/syau-miao/DFSP.git.

Regulatory effects of bio-intensity electric field on transformation of human skin fibroblasts / 中华烧伤杂志

Objective: To investigate the regulatory effects of bio-intensity electric field on the transformation of human skin fibroblasts (HSFs). Methods: The experimental research methods were used. HSFs were collected and divided into 200 mV/mm electric field group treated with 200 mV/mm electric field for 6 h and simulated electric field group placed in the electric field device without electricity for 6 h. Changes in morphology and arrangement of cells were observed in the living cell workstation; the number of cells at 0 and 6 h of treatment was recorded, and the rate of change in cell number was calculated; the direction of cell movement, movement velocity, and trajectory velocity within 3 h were observed and calculated (the number of samples was 34 in the simulated electric field group and 30 in 200 mV/mm electric field group in the aforementioned experiments); the protein expression of α-smooth muscle actin (α-SMA) in cells after 3 h of treatment was detected by immunofluorescence method (the number of sample was 3). HSFs were collected and divided into simulated electric field group placed in the electric field device without electricity for 3 h, and 100 mV/mm electric field group, 200 mV/mm electric field group, and 400 mV/mm electric field group which were treated with electric fields of corresponding intensities for 3 h. Besides, HSFs were divided into simulated electric field group placed in the electric field device without electricity for 6 h, and electric field treatment 1 h group, electric field treatment 3 h group, and electric field treatment 6 h group treated with 200 mV/mm electric field for corresponding time. The protein expressions of α-SMA and proliferating cell nuclear antigen (PCNA) were detected by Western blotting (the number of sample was 3). Data were statistically analyzed with Mann-Whitney U test, one-way analysis of variance, independent sample t test, and least significant difference test. Results: After 6 h of treatment, compared with that in simulated electric field group, the cells in 200 mV/mm electric field group were elongated in shape and locally adhered; the cells in simulated electric field group were randomly arranged, while the cells in 200 mV/mm electric field group were arranged in a regular longitudinal direction; the change rates in the number of cells in the two groups were similar (P>0.05). Within 3 h of treatment, the cells in 200 mV/mm electric field group had an obvious tendency to move toward the positive electrode, and the cells in simulated electric field group moved around the origin; compared with those in simulated electric field group, the movement velocity and trajectory velocity of the cells in 200 mV/mm electric field group were increased significantly (with Z values of -5.33 and -5.41, respectively, P<0.01), and the directionality was significantly enhanced (Z=-4.39, P<0.01). After 3 h of treatment, the protein expression of α-SMA of cells in 200 mV/mm electric field group was significantly higher than that in simulated electric field group (t=-9.81, P<0.01). After 3 h of treatment, the protein expressions of α-SMA of cells in 100 mV/mm electric field group, 200 mV/mm electric field group, and 400 mV/mm electric field group were 1.195±0.057, 1.606±0.041, and 1.616±0.039, respectively, which were significantly more than 0.649±0.028 in simulated electric field group (P<0.01). Compared with that in 100 mV/mm electric field group, the protein expressions of α-SMA of cells in 200 mV/mm electric field group and 400 mV/mm electric field group were significantly increased (P<0.01). The protein expressions of α-SMA of cells in electric field treatment 1 h group, electric field treatment 3 h group, and electric field treatment 6 h group were 0.730±0.032, 1.561±0.031, and 1.553±0.045, respectively, significantly more than 0.464±0.020 in simulated electric field group (P<0.01). Compared with that in electric field treatment 1 h group, the protein expressions of α-SMA in electric field treatment 3 h group and electric field treatment 6 h group were significantly increased (P<0.01). After 3 h of treatment, compared with that in simulated electric field group, the protein expressions of PCNA of cells in 100 mV/mm electric field group, 200 mV/mm electric field group, and 400 mV/mm electric field group were significantly decreased (P<0.05 or P<0.01); compared with that in 100 mV/mm electric field group, the protein expressions of PCNA of cells in 200 mV/mm electric field group and 400 mV/mm electric field group were significantly decreased (P<0.05 or P<0.01); compared with that in 200 mV/mm electric field group, the protein expression of PCNA of cells in 400 mV/mm electric field group was significantly decreased (P<0.01). Compared with that in simulated electric field group, the protein expressions of PCNA of cells in electric field treatment 1 h group, electric field treatment 3 h group, and electric field treatment 6 h group were significantly decreased (P<0.01); compared with that in electric field treatment 1 h group, the protein expressions of PCNA of cells in electric field treatment 3 h group and electric field treatment 6 h group were significantly decreased (P<0.05 or P<0.01); compared with that in electric field treatment 3 h group, the protein expression of PCNA of cells in electric field treatment 6 h group was significantly decreased (P<0.01). Conclusions: The bio-intensity electric field can induce the migration of HSFs and promote the transformation of fibroblasts to myofibroblasts, and the transformation displays certain dependence on the time and intensity of electric field.

Label3DMaize: toolkit for 3D point cloud data annotation of maize shoots.

BACKGROUND: The 3D point cloud is the most direct and effective data form for studying plant structure and morphology. In point cloud studies, the point cloud segmentation of individual plants to organs directly determines the accuracy of organ-level phenotype estimation and the reliability of the 3D plant reconstruction. However, highly accurate, automatic, and robust point cloud segmentation approaches for plants are unavailable. Thus, the high-throughput segmentation of many shoots is challenging. Although deep learning can feasibly solve this issue, software tools for 3D point cloud annotation to construct the training dataset are lacking. RESULTS: We propose a top-to-down point cloud segmentation algorithm using optimal transportation distance for maize shoots. We apply our point cloud annotation toolkit for maize shoots, Label3DMaize, to achieve semi-automatic point cloud segmentation and annotation of maize shoots at different growth stages, through a series of operations, including stem segmentation, coarse segmentation, fine segmentation, and sample-based segmentation. The toolkit takes ∼4-10 minutes to segment a maize shoot and consumes 10-20% of the total time if only coarse segmentation is required. Fine segmentation is more detailed than coarse segmentation, especially at the organ connection regions. The accuracy of coarse segmentation can reach 97.2% that of fine segmentation. CONCLUSION: Label3DMaize integrates point cloud segmentation algorithms and manual interactive operations, realizing semi-automatic point cloud segmentation of maize shoots at different growth stages. The toolkit provides a practical data annotation tool for further online segmentation research based on deep learning and is expected to promote automatic point cloud processing of various plants.

Chiral Liquid Crystalline Elastomer for Twisting Motion without Preset Alignment of Mesogens.

A chiral liquid crystalline elastomer (CLCE) actuator is demonstrated. The solution-cast polydomain film of CLCE can twist upon order-disorder phase transition without any preset alignment of mesogens. The handedness of twisting is specific to the molecular chirality of the chiral dopant in the CLCE structure, while the degree of twisting, in terms of helical pitch and diameter, is sensitive to the aspect ratio and the thickness of the CLCE strip as well as the chiral dopant content. This phenomenon appears to stem from the local twisting forces and deformations of randomly oriented helical domains, which cannot cancel each other out due to the chirality and thus result in a macroscopic "chiral" force acting on the CLCE actuator. This finding reveals a materials design for preparing twisting LCE actuators.

Conditions that promote the formation of black bloom in aquatic microcosms and its effects on sediment bacteria related to iron and sulfur cycling.

Black bloom occurs frequently in eutrophic waters. We investigated the conditions promoted the formation of black bloom via in-situ measurement in two aquatic microcosms and the effects of black bloom on the bacterial community composition. Although larger changes in dissolved oxygen (DO) were detected in the Hydrilla verticillata-dominated microcosm over the 90-day simulation, black bloom occurred more readily in the phytoplankton-dominated than macrophyte-dominated microcosm under conditions of O2 depletion and temperature above 30 °C. The sediment bacterial community composition shifted after black bloom; the relative abundance of Thiobacillus and Sideroxydans, which oxidize iron (Fe) and sulfur (S), decreased by 47% and 48%, respectively, in the phytoplankton-dominated microcosm and by 18% and 20% in the macrophyte-dominated microcosm. By contrast, Desulfatiglans increased by 13% and 19%, respectively, after black bloom. Furthermore, inter-taxa correlations remarkably changed according to co-occurrence network analysis. Thirty-six different taxa from the phylum to the genus level were identified as biomarkers of sediments collected before and after the black bloom event. Most of these biomarkers are related to Fe/S cycling in aquatic ecosystems.

Depth Density Achieves a Better Result for Semantic Segmentation with the Kinect System.

Image segmentation is one of the most important methods for animal phenome research. Since the advent of deep learning, many researchers have looked at multilayer convolutional neural networks to solve the problems of image segmentation. A network simplifies the task of image segmentation with automatic feature extraction. Many networks struggle to output accurate details when dealing with pixel-level segmentation. In this paper, we propose a new concept: Depth density. Based on a depth image, produced by a Kinect system, we design a new function to calculate the depth density value of each pixel and bring this value back to the result of semantic segmentation for improving the accuracy. In the experiment, we choose Simmental cattle as the target of image segmentation and fully convolutional networks (FCN) as the verification networks. We proved that depth density can improve four metrics of semantic segmentation (pixel accuracy, mean accuracy, mean intersection over union, and frequency weight intersection over union) by 2.9%, 0.3%, 11.4%, and 5.02%, respectively. The result shows that depth information produced by Kinect can improve the accuracy of the semantic segmentation of FCN. This provides a new way of analyzing the phenotype information of animals.

Facile synthesis of metal nanoparticles decorated magnetic hierarchical carbon microtubes with polydopamine-derived carbon layer for catalytic applications.

It is highly desirable but challenging to fabricate a unique hybrid material comprising nanosized copper/cobalt/nickel nanoparticles (NPs) uniformly distributed on magnetic supports. Herein in this work, hierarchical magnetic metal silicate hollow microtubes were prepared using silica coated magnetic N-doped carbon microtubes (NCMTs@Fe3O4@SiO2) as a chemical template; then polydopamine (PDA) was employed to coat onto magnetic metal silicate carbon microtubes (NCMTs@Fe3O4@CuSNTs/CoSNTs/NiSNTs), which can be carbonized to form hierarchical hybrid composites with uniformly-dispersed metallic copper/cobalt/nickel NPs embedded in PDA-derived carbon layers (NCMTs@Fe3O4@SiO2@C/Cu-Co-Ni). Owing to its hierarchical structure, large specific surface area as well as the high density of metal NPs, the resultant NCMTs@Fe3O4@SiO2@C/Ni-Co-Cu could be applied as catalysts towards the reduction of 4-nitrophenol (4-NP). Furthermore, the NCMTs@Fe3O4@SiO2@C/Ni-Co-Cu catalysts could be easily collected and separated by applying an external magnetic field. In particular, it was found that NCMTs@Fe3O4@SiO2@C/Ni exhibited ultra-high catalytic activity on 4-NP reduction in comparison with Cu and Co supported catalysts. In addition, this unique hierarchical structure combined with magnetic recyclability make NCMTs@Fe3O4@SiO2@C/Ni a highly promising candidate for diverse applications.

Role of PI3K/Akt signal pathway in BMSCs migration induced by serum of rats with severely burn / 重庆医学

Objective To study the effects of severely burned rats serum on migration of BMSCs and mechanism.Methods Severely burned rats model was established,and the preparation of severely burned rats serum.Experimental groups:normal train-ing group(containing 10% fetal bovine serum,group C),burn serum group(containing 10% burns in the rat serum,group B),burn serum+blockers(10% burns in the rat serum+final concentration of 10 μmol/L PI3K signaling pathway inhibitor LY294002 train-ing,group B+LY).Activity of cells was examined with MTT;migration of cells was examined with Transwell chambers testing;protein expression of p-AKT/AKT was determined with Western blot;microtubule structure of cells was examined with immuno-fluorescence.Results Compared with group C,group B burn serum treatment after 24 h,BMSCs activity(P <0.01),p-AKT levels (P <0.05),increased migration quantity(P <0.001);cell microtubule structures appear rupture,after adding inhibitor,compared with group B,group B+LY BMSCs activity(P <0.01),to reduce the number of migration(P <0.001),p-lower AKT(P <0.05), cell microtubule structure similar to the normal group.Conclusion Severely burned rats serum can promote BMSCs migration,may burn serum cytokine activation of PI3K/AKT signal pathway,resulting in cell microtubule structure change,promote the migration of BMSCs.

The influence of microtubule intervention drugs on glycolytic key enzymes in myocardial cells after hypoxia / 中华烧伤杂志

<p><b>OBJECTIVE</b>To investigate the influence of microtubule intervention drugs on glycolytic key enzymes in myocardial cells after hypoxia.</p><p><b>METHODS</b>The primary passage of cultured myocardial cells from neonatal rats were divided into A group (with hypoxia), B group (with hypoxia and administration of l0 micromol/L colchicine), C group (with hypoxia and administration of 5 micromol/L taxol), D group (with hypoxia and administration of 10 micromol/L taxol), E group (with hypoxia and administration of 15 micromol/L taxol). The morphology of microtubule was observed with laser scanning microscope (LSM). The cell vitality was assayed by cell counting kit (CCK). The activities of hexokinase (HK), pyruvate kinase (PK), phosphofructokinase (PFK) and lactate dehydrogenase (LDH) were assayed with colorimetry.</p><p><b>RESULTS</b>In group B and E, the microtubule structure was damaged heavily, and the cell vitality was decreased significantly [The cell vitality was (89.99 +/- 3.47)% in B group and (84.56 +/- 6.61)% in E group, respectively, at 1.0 post hypoxia hour (PHH), and hoth values were obviously lower than that in A group (97.44 +/- 1.76)%, P < 0.01]. The HK, PK and PFK activities decreased obviously. The activities of HK, PK and PFK in group C were similar to those of the A group. Compared with that in other groups, the degree of damage of microtubule structure in D group was milden. The activities of HK, PK and PFK in D group during 0.5 - 6.0 PHH were significantly higher than those in A group. The activity of LDH in each group was increased after hypoxia.</p><p><b>CONCLUSION</b>Proper concentration of microtubule-stabilizing drugs can alleviate the damages to microtubule structure, and enhance the activity of glycolytic key enzymes of myocardial cells at early stage of hypoxia.</p>

The influence of microtubule intervention drugs on the energy metabolism of myocardial cells after hypoxia / 中华烧伤杂志

<p><b>OBJECTIVE</b>To investigate the influence of microtubule intervention drugs on the energy metabolism of myocardial cells after hypoxia.</p><p><b>METHODS</b>The primary passage of cultured myocardial cells from neonatal rats were divided into A (with hypoxia), B (with hypoxia and administration of 10 micromol/ml colchicine), C (with hypoxia and administration of 5 micromol/ml taxol), D (with hypoxia and administration of 10 micromol/ml taxol) and E (with hypoxia and administration of 15 micromol/ml taxol) groups. The creatine kinase (CK) activity and contents of ATP and ADP were assayed with colorimetry and HPLC, respectively, and the vitality of myocardial cells were determined by trypan blue method at 0.5, 1.0, 3.0, 6.0, 12.0, 24.0 post-hypoxia hours (PHH).</p><p><b>RESULTS</b>The mortality was obviously higher in B and E groups than those in A group( P < 0.05) at each time-points, but that in C and D groups were markedly lower than those in A group during 6.0 to 24.0 PHH (P < 0.01). The CK activity was significantly higher in B group than that in A group during 1.0 to 24.0 PHH, while that in E group was evidently higher, but it was lower in C and D groups than that in A group at each time-points (P < 0.05 or 0.01). The ATP contents in C group during 0.5 to 6.0 PHH were [(49.9 +/- 2.8), (40.7 +/- 2.0), (25.8 +/- 1.9), (19.1 +/- 1.2) microg/10(6) cells, respectively], which were obviously higher than those in A group [(42.9 +/- 5.8), (29.5 +/- 1.8), (18.2 +/- 0.9), (14.1 +/- 0.7) microg/10(6) cells, respectively, P < 0.05 or P < 0.01, and those in E group at each time-point were significantly lower than those in A and D groups (P < 0.01). The changes in the contents of ADP were on the contrary to the above.</p><p><b>CONCLUSION</b>Microtubule-destabilizing drugs and high concentration microtubule-stabilizing drugs can sharply decrease ATP content in myocardiocytes under hypoxic conditions, while suitable amount of microtubule-stabilizing drugs can protect myocardiocytes by promoting its energy production.</p>

Protective effects of Astragaloside and Quercetin on rat myocardial cells after hypoxia / 中华烧伤杂志

<p><b>OBJECTIVE</b>To investigate and compare the protective effects of Astragaloside IV (AST) and Quercetin (QUE) on rat myocardial cells after their exposure to hypoxia, and to determine their dose-effect relationship.</p><p><b>METHODS</b>Myocardial cells from fetal SD rat were cultured in vitro and divided into 7 groups: i.e. A (hypoxia), B (hypoxia and 100 mg/L of QUE), C (hypoxia and 50 mg/L of QUE), D (hypoxia and 25 mg/L of QUE), E (hypoxia and 50.0 mg/L of AST), F (hypoxia and 25.0 mg/L of AST), G (hypoxia and 12.5 mg/L AST) H(hypoxia and 10 mg/L of VitE) groups. Different doses of AST and QUE were added into the culture media cells in each group before the myocardial cells receiving hypoxia for 12 hrs. The number of viable cells (CCK-8) and the content of lactate dehydrogenase (LDH), superoxide dismutase (SOD), malondialdehyde (MDA), active oxygen (ROS, with detection only in A, C, F and H groups) were determined after hypoxia.</p><p><b>RESULTS</b>The amount of LDH, MDA, ROS (C, F groups) in group B - G decreased significantly compared with those of group A, while the number of viable cells and the SOD content increased significantly. The protective effects were better in group B - G than that of the group H. With the same dosage, levels of LDH, CCK-8 in AST-treated groups were significantly lower than those in QUE-treated group (the number of viable cells in group C, F was 0.454 +/- 0.018, 0.471 +/- 0.017, and the content of lactate dehydrogenase was 2800 +/- 9,2312 +/- 52). There were no significant differences in MDA, SOD and ROS levels between AST and QUE treated groups (ROS in C and F groups were 16.0 +/- 5.3 vs 22.4 +/- 8.7, P > 0.05).</p><p><b>CONCLUSION</b>AST and QUE might be beneficial in the protection of myocardial cells against hypoxia because of attenuation of oxidative damage. The protective effects of both AST and QUE are better than that of VitE, and that of AST is better than QUE as shown by a decrease in the amount of LDH and increase in the number of viable cells with the same dosage, but no obvious difference is shown between them in attenuating oxidative damage.</p>

Study on the influence of hypoxia induced microtubule damage on the opening of mitochondrial permeable transition pore of cardiac myocytes in rat / 中华烧伤杂志

<p><b>OBJECTIVE</b>To investigate the influence of hypoxia induced microtubule damage on the opening of mitochondrial permeable transition pore (MPTP)of cardiac myocytes and on the decrease of respiratory function in rat.</p><p><b>METHODS</b>Primary cultured myocardial cells from 30 neonatal rats were randomized as normoxic group (A), hypoxia group (B), normoxia with microtubule destabilizing agent group (C, with treatment of 8 micromol/L colchicines for 30 minutes before normoxia), and hypoxia with microtubule stabilizing agent group (D, with treatment of 10 micromol/L taxol for 30 minutes before hypoxia). beta-tubulin immunofluorescence ,the opening of mitochondria permeability transition pore, and the mitochondrial inner membrane potential were detected at 0.5, 1, 3, 6 and 12 post-treatment hours (PTH), and the mitochondrial respiratory function was determined by MTT method. The changes in these indices were also determined in A group at the corresponding time-points.</p><p><b>RESULTS</b>Obvious damage of polymerized microtubule, opening of MPTP, mitochondrial inner membrane potential loss and decrease of myocardial respiratory activity were observed in both group B and C at 0.5 PTH, and they became more and more serious afterwards. However, the changes in the above indices in D group were much better than those in B group (P < 0.05 or 0.01), and no difference was found between D (92.8 +/- 4.0)% and C [(100.0 +/- 0.0) %, P > 0.05] groups.</p><p><b>CONCLUSION</b>Hypoxia played a role in the myocardial microtubule damage as well as in the opening of MPTP. Moreover, hypoxia could also impair the mitochondrial respiratory function. Microtubule destabilizing agent could reproduce well the process of hypoxia induced microtubule damage, while the stabilizing agent exerted protective effect by improving the transition of mitochondrial permeability and the mitochondria respiratory function.</p>