PlantPAD: a platform for large-scale image phenomics analysis of disease in plant science.

Plant disease, a huge burden, can cause yield loss of up to 100% and thus reduce food security. Actually, smart diagnosing diseases with plant phenomics is crucial for recovering the most yield loss, which usually requires sufficient image information. Hence, phenomics is being pursued as an independent discipline to enable the development of high-throughput phenotyping for plant disease. However, we often face challenges in sharing large-scale image data due to incompatibilities in formats and descriptions provided by different communities, limiting multidisciplinary research exploration. To this end, we build a Plant Phenomics Analysis of Disease (PlantPAD) platform with large-scale information on disease. Our platform contains 421 314 images, 63 crops and 310 diseases. Compared to other databases, PlantPAD has extensive, well-annotated image data and in-depth disease information, and offers pre-trained deep-learning models for accurate plant disease diagnosis. PlantPAD supports various valuable applications across multiple disciplines, including intelligent disease diagnosis, disease education and efficient disease detection and control. Through three applications of PlantPAD, we show the easy-to-use and convenient functions. PlantPAD is mainly oriented towards biologists, computer scientists, plant pathologists, farm managers and pesticide scientists, which may easily explore multidisciplinary research to fight against plant diseases. PlantPAD is freely available at http://plantpad.samlab.cn.

XIST promotes apoptosis and the inflammatory response in CSE-stimulated cells via the miR-200c-3p/EGR3 axis.

BACKGROUND: Chronic obstructive pulmonary disease (COPD) is a disease that causes obstructed airways and abnormal inflammatory responses in the lungs. Early growth response 3 (EGR3) has been revealed to play a vital role in the regulation of the inflammatory response in certain diseases. We aimed to explore the role of EGR3 and its upstream mechanism in COPD. METHODS AND RESULT: In the present study, 16HBE cells were treated with cigarette smoke extract (CSE) to mimic the inflammatory response in vitro. RT-qPCR revealed that the expression of EGR3 was upregulated in lungs from COPD patients. EGR3 expression in 16HBE cells was increased by CSE treatment. Moreover, flow cytometry analysis and western blot analysis showed that EGR3 downregulation inhibited 16HBE cell apoptosis. EGR3 silencing decreased the protein levels of IL-6, TNF-α, IL-1ß and COX2 in CSE-stimulated 16HBE cells. In addition, EGR3 was targeted by microRNA-200c-3p (miR-200c-3p) in 16HBE cells. MiR-200c-3p expression was significantly decreased in lung tissues from COPD patients compared to that in healthy controls. Furthermore, miR-200c-3p bound to lncRNA X-inactive specific transcript (XIST) in 16HBE cells. Additionally, XIST expression was elevated in lung tissues from COPD patients. Rescue assays indicated that EGR3 overexpression counteracted the effects of XIST downregulation on apoptosis and inflammation in CSE-stimulated 16HBE cells. CONCLUSION: The XIST/miR-200c-3p/EGR3 axis facilitated apoptosis and inflammation in CSE-stimulated 16HBE cells. These findings may provide novel insight for treating COPD by alleviating lung inflammation.

CSNet: A Count-Supervised Network via Multiscale MLP-Mixer for Wheat Ear Counting.

Wheat is the most widely grown crop in the world, and its yield is closely related to global food security. The number of ears is important for wheat breeding and yield estimation. Therefore, automated wheat ear counting techniques are essential for breeding high-yield varieties and increasing grain yield. However, all existing methods require position-level annotation for training, implying that a large amount of labor is required for annotation, limiting the application and development of deep learning technology in the agricultural field. To address this problem, we propose a count-supervised multiscale perceptive wheat counting network (CSNet, count-supervised network), which aims to achieve accurate counting of wheat ears using quantity information. In particular, in the absence of location information, CSNet adopts MLP-Mixer to construct a multiscale perception module with a global receptive field that implements the learning of small target attention maps between wheat ear features. We conduct comparative experiments on a publicly available global wheat head detection dataset, showing that the proposed count-supervised strategy outperforms existing position-supervised methods in terms of mean absolute error (MAE) and root mean square error (RMSE). This superior performance indicates that the proposed approach has a positive impact on improving ear counts and reducing labeling costs, demonstrating its great potential for agricultural counting tasks. The code is available at http://csnet.samlab.cn.

Ginsenoside Rg1 Suppresses Non-Small-Cell Lung Cancer via MicroRNA-126-PI3K-AKT-mTOR Pathway.

As one of the most common cause of cancer death in the world, lung cancer causes approximately 1.6 million deaths annually. Among them, NSCLC accounts for approximately 85% of patients in whole lung cancer patients. Ginsenoside Rg1 has been confirmed to play an important role in various diseases including cancer. As one of miRNAs, miR-126 closely involves in pathogenesis of the several types of cancers including colorectal, prostate, bladder and gastric cancer, and so on. Thus, the present study aims to investigate effects of the Ginsenoside Rg1 on NSCLC and underlying mechanism. In the study, two lung cancer cell lines including A549 and H1650 were used. It was found that expression of miR-126 was decreased in PBMC of NSCLC patients compared to healthy control. Expression of miR-126 was decreased in cancer tissue compared to paracancerous tissues in NSCLC patients. Importantly, it was found Ginsenoside Rg1 could inhibit growth of lung cancer cells. miR-126 KD remarkably increased the expression of apoptosis genes including caspase 3 and caspase 9 and decreased cell viability in lung cancer cells including A549 and H1650 cells. Interesting, in silico analysis indicated that miR-126 could target PI3K signaling pathway, which was confirmed by WB assay. KD of PI3KR2 compromised promotion of miR-126 on cell apoptosis. Similarly, it was found that KD of mTOR compromised promotion of miR-126 on cell apoptosis. Inhibition of Ginsenoside Rg1 on growth of lung cancer cells was through miR-126 and mTOR. Thus, the present study confirmed that Ginsenoside Rg1 remarkably inhibit lung cancer, which is through microRNA-126-PI3K-AKT-mTOR pathway.

Correlation of neutrophil-lymphocyte ratio (NLR), platelet-lymphocyte ratio (PLR), and mean platelet volume (MPV) with gout activity: A monocentric and retrospective study.

To evaluate the correlation of neutrophil-lymphocyte ratio (NLR), platelet-lymphocyte ratio (PLR), and mean platelet volume (MPV) with parameters related to gout activity. The general data of the patients and healthy controls (HCs), including complete blood count, C-reactive protein (CRP), erythrocyte sedimentation rate (ESR), serum uric acid (SUA), and the presence of tophi were retrospectively analyzed. NLR, MPV, and PLR were calculated in patients with intercritical gout and gout flares. Correlation of the 3 markers with clinical features, like ESR, CRP, SUA, and the presence of tophi, were analyzed. The results revealed that NLR and PLR were elevated and MPV was markedly decreased in patients with gout compared with HCs (all P < .05). In patients with gout flares, NLR, and PLR were higher and MPV was lower than in intercritical gout patients (all P < .05). NLR and PLR were positively correlated with ESR and CRP, whereas MPV was negatively correlated with ESR. NLR, PLR, and MPV showed no obvious correlation with SUA and the presence of tophi. The receiver operating characteristic curve showed that NLR was more valuable in assessing gout disease activity. NLR, PLR, and MPV were correlated with inflammatory parameters in gout; they may be used as complementary tools to evaluate gout activity.

Downregulation of miR-499a-5p Predicts a Poor Prognosis of Patients With Non-Small Cell Lung Cancer and Restrains the Tumorigenesis by Targeting Fibroblast Growth Factor 9.

The aberrant expression of microRNA is an important regulator in the tumorigenesis of non-small cell lung cancer. In this study, we found that miR-499a-5p was notably downregulated in non-small cell lung cancer tissues and cell lines. Decreased miR-499a-5p expression was associated with larger tumor size and higher TNM stage. Non-small cell lung cancer patients with low expression of miR-499a-5p exhibited a worse overall survival rate compared with those patients with high expression of miR-499a-5p. Ectopic expression of miR-499a-5p significantly suppressed non-small cell lung cancer cell proliferation and colony formation, and hampered cell cycle at G0/G1 phase in vitro. Conversely, knockdown of miR-499a-5p promoted non-small cell lung cancer cell proliferation and colony formation, and induced cell cycle at S phase. Furthermore, in vivo experiments revealed that overexpression of miR-499a-5p inhibited the tumor formation in a nude mouse xenograft model. Mechanistic studies showed that fibroblast growth factor 9 was a direct target gene of miR-499a-5p. miR-499a-5p directly bound to fibroblast growth factor 9 mRNA 3'-UTR, therefore led to the reduction in fibroblast growth factor 9 protein expression. Finally, rescue experiments confirmed that silencing of fibroblast growth factor 9 partially reversed the phenotypes of miR-499a-5p knockdown on non-small cell lung cancer cell proliferation. In conclusion, our study demonstrates that downregulation of miR-499a-5p predicts a worse prognosis of patients with non-small cell lung cancer and restrains the tumorigenesis by targeting fibroblast growth factor 9. These findings may provide valuable clues for the future development of therapeutic strategies against this cancer.

Inflammation status of rabbit carotid artery model endothelium during intermittent hypoxia exposure and its relationship with leptin.

OBJECTIVES: To develop an intermittent hypoxia/reoxygenation (IH/ROX) rabbit carotid artery model and then investigate the inflammation status of rabbit carotid artery endothelium after IH exposure and its relationship with leptin. MATERIALS AND METHODS: After anesthetization, rabbit's right common carotid artery was cleared of surrounding tissue with anatomic microscope, cannulated to its distal part and the proximal part was ligated. Preparations were challenged by changing the PO(2) of the gas mixture equilibrating the perfusate. Alternate perfusing (2 mL/min) of equilibrated perfusate bubbled with normoxia or hypoxia gas mixtures formed IH/ROX cycles in the right carotid common artery, simulating the pattern of hypoxic episodes seen in obstructive sleep apnea (OSA), or continuous perfusing of hypoxia perfusate to form continuous hypoxia (CH) modes. Sixty adult male New Zealand White rabbits (2.5-3.0 kg) were separated into six groups, ten per group. Groups were: A, intermittent normoxia (IN) group, perfused with perfusion equilibrated with 21% O(2) [PO(2) about 141 +/- 2.87 mmHg] for 15 s and 21% O(2) for 1 min 45 s, 60 cycles; B, severe IH group, 5% O(2) [PO(2) about 35.2 +/- 1.27 mmHg] 15 s and 21% O(2) 1 min 45 s, 60 cycles; C, mild IH group, 10% O(2) [PO(2) about 54.3 +/- 3.31 mmHg] 15 s and 21% O(2) 1 min 45 s, 60 cycles; D, severe IH+Lep group, protocol was the same with severe IH group; E, CH group, IN for 1 h 45 min and then 5% O(2) for 15 min; and F, Lep group, the same with IN group. Right common carotid artery parts distal to the cannula were harvested after exposure, and endothelial cell layers were gotten from longitudinal outspread vessels. Nuclear factor kappaB (NFkappaB) DNA binding activities of partial cell layers were measured with electrophoretic mobility shift assay in the IN group, severe IH group, mild IH group, and CH group nuclear extracts. The other part of the cell layers in the IN group, severe IH group, severe IH+Lep group, and Lep group were cultured for 2 h, and during the culture procedure, recombinated human leptin solutions were added to culture dishes of severe IH+Lep group and Lep group (resulted concentration, 10 ng/mL). Enzyme-linked immunosorbent assay was used to analyze medium interleukin-6 (IL-6) concentrations, reverse transcription polymerase chain reaction was used to analyze endothelial cell Ras homology A (RhoA) mRNA expression levels. Statistical analysis was done with SPSS 11.5 software package. RESULTS: NFkappaB DNA binding activities were significantly different between groups (F = 112.428, P < 0.001). This activity in the severe IH group (4.27 +/- 0.64) was higher than that in the mild IH group (2.33 +/- 0.45, P < 0.001), IN group (1.00 +/- 0.26, P < 0.001), and CH group (1.15 +/- 0.36, P < 0.001). RhoA mRNA expression levels were different in groups (F = 26.634, P < 0.001).This level in the severe IH+Lep group (2.54 +/- 0.53) was higher than that in the severe IH group (1.57 +/- 0.44, P = 0.002), IN group (1.00 +/- 0.31, P < 0.001), and Lep group (1.31 +/- 0.30, P < 0.001). IL-6 concentrations were different in groups (F = 79.922, P < 0.001). IL-6 concentration in the severe IH+Lep group (1591.50 +/- 179.57 pg/mL) was higher than that in the severe IH group (1217.20 +/- 320.62 pg/mL, P = 0.036), IN group (325.40 +/- 85.26 pg/mL, P < 0.001), and Lep group (517.40 +/- 183.09 pg/mL, P < 0.001). CONCLUSIONS: IH/ROX activated the inflammation pathway significantly in the endothelium, which was more intensive than CH and intensity-dependent. When exposed to both IH/ROX and leptin, inflammation occurs more dramatically. It means that synergic activating roles were performed by IH/ROX and leptin. This study may have a clinical implication that IH can cause endothelial damage through activated inflammation in OSA patients, and if the OSA patients have obesity at the same time, the endothelial damage or the inflammation would be more significant because of elevated leptin level as a synergic factor.

[Carotid body inflammation and carotid sinus nerve afferent activity after intermittent hypoxia exposure of various frequencies in rabbits].

OBJECTIVE: To explore the inflammatory reactions, endothelin level and carotid sinus nerve (CSN) afferent activity of carotid body (CB) after intermittent hypoxia/reoxygenation (IH/ROX) exposure of various frequencies in rabbits. METHODS: Forty-nine male adult New Zealand white rabbits (2.5-3.0 kg) were separated into 7 groups (n = 7 each). After anesthetization, the right carotid artery and CSN were cleared of surrounding tissues without touching the right CB and the left carotid region. The CSN was unenveloped to partially expose the myelin sheath, and electrodes were placed to the "single" chemoreceptor bundle of the CSN, with CSN afferent activity carefully monitored and recorded. Then the right common carotid artery was exposed, cannulated to distal part and its proximal part was ligated. Preparations were challenged by changing the PO2 of the gas mixture equilibrating the perfusate. Alternatively perfusion (2 ml/min) of equilibrated perfusate bubbled with normoxia or hypoxia gas mixtures formed IH/ROX cycles in right carotid common artery, simulating the pattern of hypoxic episodes seen in obstructive sleep apnea, or with continuously perfusing hypoxia perfusate to form continuous hypoxia (CH) modes. Groups were defined with different frequencies, and groups were: intermittent normoxia group (IN group) (21% O2, 15 s; 21% O2, 1 min 45 s), 10/hr group (5% O2, 15 s; 21% O2, 5 min 45 s), 30/hr group (5% O2, 15 s; 21% O2, 1 min 45 s), 50/hr group (5% O2, 15 s; 21% O2, 57 s), 60/hr group (5% O2, 15 s; 21% O2, 45 s) and 90/hr group (5% O2, 15 s; 21% O2, 25 s). All the above groups were exposed to 60 treatment cycles; continuous hypoxia group (CH group), IN for 1 h 45 min and then 5% O2 for 15 min. After exposure and 30 min of static placing, CSN afferent frequencies (Charge F) were recorded from chemoreceptor bundles, and the right CB was cleared of surrounding tissues and harvested. Interleukin-6 (IL-6), endothelin-1 (ET-1), hypoxia-inducible factor-1 (HIF-1), and vascular endothelial growth factor (VEGF) concentrations of the CB lysate were measured with enzyme linked immuno sorbent assay (ELISA) kits and standardized. Data were analyzed with SPSS 12.0 software package; and after one way analysis of variance (ANOVA) for whole difference, Tamhane's T2 was used for post hoc analysis. RESULTS: IL-6, ET-1 and Charge F increased but then decreased with increasing IH frequencies (F = 25,601.39, 2390.48, 6945.84, all P values < 0.01). IL-6, ET-1 and Charge F levels in 50/hr group were the highest among groups. Charge F levels correlated significantly with IL-6 or ET-1 (with IL-6: r = 0.736, P < 0.01; with ET-1: r = 0.757, P < 0.01, respectively). IL-6, ET-1 and Charge F levels between IN group and CH group were not statistically different (all P values > 0.05). HIF-1 levels elevated gradually (F = 5241.10, P < 0.01) with increasing exposure frequencies, and the CH group had the highest value (all P values < 0.01). VEGF level in CH group was the highest in all groups (all P values < 0.01). CONCLUSIONS: After IH/ROX exposure, afferent activity of CB CSN increases, which significantly correlates with inflammation and vasomotor mechanism of CB. CB inflammation comes not from IH phases but from ROX phases. Increased CB CSN activity results in elevated SNA tension, which plays a key role in the pathogenesis of systemic hypertension. This procedure influenced by IH/ROX frequencies. CH for 15 min causes no definitely damages. However, HIF-1 and VEGF can be considered as members of adaptive pathway during IH/ROX exposure.

HMGB1 Enhances Drug Resistance and Promotes In Vivo Tumor Growth of Lung Cancer Cells.

Drug resistance is an obstacle in the chemotherapeutic treatment of lung cancers. In the present study, the effects of high-mobility group box 1 (HMGB1) protein in chemotherapeutic resistance and the relationships between HMGB1 and chemotherapy drug-induced cell apoptosis or necrosis were clarified. We used cisplatin-sensitive A549 cells and cisplatin-resistant A549/DDP cells as cell models with IC50 of 11.58 and 46.95 µM, respectively. A549/DDP had higher level of HMGB1 compared with A549 cells. Interestingly, with the increasing concentration of DDP, HMGB1 was gradually located into cytoplasm in cisplatin-sensitive A549 cells. Moreover, interference with endogenous HMGB1 sensitized the effects of chemotherapeutic drugs, including 5-Fu, DDP, and OXA. Furthermore, results from an in vivo tumorigenesis experiment demonstrated that serum concentration of HMGB1 was much lower in the group inoculated with HMGB1 shRNA-transfected A549 cells than in the N.C. shRNA-transfected A549 inoculated group, as well as the tumor volume, suggesting that serum HMGB1 contributed to tumor growth in a mouse model. In conclusion, higher levels of HMGB1 probably contributed to chemotherapy drug resistance, and higher serum concentration of HMGB1 promoted in vivo tumor growth. The study would provide new clues to overcome drug resistance in chemotherapy of human lung cancers.