Predicting the Reader's English Level From Reading Fixation Patterns Using the Siamese Convolutional Neural Network.

Among numerous functions performed by the human eye, reading is a common task that best reflects an individual's understanding and cognitive patterns. Previous studies showed that text comprehension may be determined by comprehension monitoring, a metacognitive process that evaluates and regulates the pattern of comprehension. Herein, we propose a hypothesis: an individual's cognitive pattern during reading is predictive of the level of reading comprehension. According to the criteria of the College English Test Band Six (CET-6), 80 participants (sophomore and junior) were divided into a pass group (n = 40) and a non-pass group (n = 40). Heatmaps of eye fixation counts were collected by an eye-tracker while each participant executed four reading comprehension tests. Using these heatmaps as inputs, we proposed the Siamese convolutional neural network models to predict the English level of participants. Both strategies of "Trained from scratch" and "Pretrained with fine-tuning" were employed. "Soft Voting" was applied to integrate the predictions from four tests. Results showed that the Siamese network model trained by the datasets with the cluster radius of fixation equal to 25 pixels and connection layer by L1 norm distance has a satisfactory or superior performance to other comparative experiments. The AUC values of Siamese networks trained by the two strategies reach 0.941 and 0.956, respectively. This indicates that the individual reading cognitive pattern captured by the eye-tracker can predict the level of reading comprehension through advanced deep learning models.

Risk factors for ventilator-associated events: A prospective cohort study.

BACKGROUND: In January 2013, the Centers for Disease Control and Prevention released new surveillance definitions for ventilator-associated event (VAE) to replace ventilator-associated pneumonia (VAP) in adult patients. VAEs are associated with prolonged mechanical ventilation and hospital death, but little is known about their risk factors and how best to prevent them. METHODS: We compared VAE cases with non-VAE cases with regard to demographics, comorbidities, sedative exposures, opioids exposures, paralytic exposures, routes of nutrition, blood products, gastric retention, and fluid balance. Patients mechanically ventilated for ≥4 days between January 1, 2017, and December 31, 2017, in 2 adult intensive care units of a tertiary care teaching hospital in China were included. RESULTS: On multivariable logistic regression, significant risk factors for VAEs were positive daily fluid balances of ≥ 50 mL between day of intubation and the fourth day of mechanical ventilation (relative risk [RR], 8.39; 95% confidence interval [CI], 2.99-23.50), sedative administered between the first day and the fourth day of invasive mechanical ventilation (RR, 15.69; 95% CI, 1.62-152.06), and daily gastric retention of ≥200 mL between day of intubation and the fourth day of mechanical ventilation (RR, 9.27; 95% CI, 1.89-45.47). CONCLUSIONS: Positive daily fluid balances of ≥50 mL, sedatives administered, and gastric retention of ≥200 mL are risk factors for VAEs. Intervention studies are needed to determine if targeting these risk factors can lower VAE rates.

In silico-prediction of protein-protein interactions network about MAPKs and PP2Cs reveals a novel docking site variants in Brachypodium distachyon.

Protein-protein interactions (PPIs) underlie the molecular mechanisms of most biological processes. Mitogen-activated protein kinases (MAPKs) can be dephosphorylated by MAPK-specific phosphatases such as PP2C, which are critical to transduce extracellular signals into adaptive and programmed responses. However, the experimental approaches for identifying PPIs are expensive, time-consuming, laborious and challenging. In response, many computational methods have been developed to predict PPIs. Yet, these methods have inherent disadvantages such as high false positive and negative results. Thus, it is crucial to develop in silico approaches for predicting PPIs efficiently and accurately. In this study, we identified PPIs among 16 BdMAPKs and 86 BdPP2Cs in B. distachyon using a novel docking approach. Further, we systematically investigated the docking site (D-site) of BdPP2C which plays a vital role for recognition and docking of BdMAPKs. D-site analysis revealed that there were 96 pairs of PPIs including all BdMAPKs and most BdPP2Cs, which indicated that BdPP2C may play roles in other signaling networks. Moreover, most BdPP2Cs have a D-site for BdMAPKs in our prediction results, which suggested that our method can effectively predict PPIs, as confirmed by their 3D structure. In addition, we validated this methodology with known Arabidopsis and yeast phosphatase-MAPK interactions from the STRING database. The results obtained provide a vital research resource for exploring an accurate network of PPIs between BdMAPKs and BdPP2Cs.

Genome-wide identification and evolutionary analyses of the PP2C gene family with their expression profiling in response to multiple stresses in Brachypodium distachyon.

BACKGROUND: The type-2C protein phosphatases (PP2Cs), negatively regulating ABA responses and MAPK cascade pathways, play important roles in stress signal transduction in plants. Brachypodium distachyon is a new model plant for exploring the functional genomics of temperate grasses, cereals and biofuel crops. To date, genome-wide identification and analysis of the PP2C gene family in B. distachyon have not been investigated. RESULTS: In this study, 86 PP2C genes in B. distachyon were identified. Domain-based analyses of PP2C proteins showed that they all contained the phosphatase domains featured as 11 conserved signature motifs. Although not all phosphatase domains of BdPP2C members included all 11 motifs, tertiary structure analysis showed that four residues contributing to magnesium/manganese ions (Mg(2+)/Mn(2+)) coordination were conserved, except for two noncanonical members. The analysis of their chromosomal localizations showed that most of the BdPP2C genes were located within the low CpG density region. Phylogenetic tree and synteny blocks analyses among B. distachyon, Arabidopsis thaliana and Oryza sativa revealed that all PP2C members from the three species can be phylogenetically categorized into 13 subgroups (A-M) and BdPP2Cs were evolutionarily more closely related to OsPP2Cs than to AtPP2Cs. Segmental duplications contributed particularly to the expansion of the BdPP2C gene family and all duplicated BdPP2Cs evolved mainly from purifying selection. Real-time quantitative reverse transcription PCR (qRT-PCR) analysis showed that BdPP2Cs were broadly expressed in disparate tissues. We also found that almost all members displayed up-regulation in response to abiotic stresses such as cold, heat, PEG and NaCl treatments, but down-regulation to biotic stresses such as Ph14, Guy11 and F0968 infection. CONCLUSIONS: In the present study, a comprehensive analysis of genome-wide identification and characterization of protein domains, phylogenetic relationship, gene and protein structure, chromosome location and expression pattern of the PP2C gene family was carried out for the first time in a new model monocot, i.e., B. distachyon. Our results provide a reference for genome-wide identification of the PP2C gene family of other species and also provide a foundation for future functional research on PP2C genes in B. distachyon.

Genome-wide exploration of the molecular evolution and regulatory network of mitogen-activated protein kinase cascades upon multiple stresses in Brachypodium distachyon.

BACKGROUND: Brachypodium distachyon is emerging as a widely recognized model plant that has very close relations with several economically important Poaceae species. MAPK cascade is known to be an evolutionarily conserved signaling module involved in multiple stresses. Although the gene sequences of MAPK and MAPKK family have been fully identified in B. distachyon, the information related to the upstream MAPKKK gene family especially the regulatory network among MAPKs, MAPKKs and MAPKKKs upon multiple stresses remains to be understood. RESULTS: In this study, we have identified MAPKKKs which belong to the biggest gene family of MAPK cascade kinases. We have systematically investigated the evolution of whole MAPK cascade kinase gene family in terms of gene structures, protein structural organization, chromosomal localization, orthologs construction and gene duplication analysis. Our results showed that most BdMAPK cascade kinases were located at the low-CpG-density region, and the clustered members in each group shared similar structures of the genes and proteins. Synteny analysis showed that 62 or 21 pairs of duplicated orthologs were present between B. distachyon and Oryza sativa, or between B. distachyon and Arabidopsis thaliana respectively. Gene expression data revealed that BdMAPK cascade kinases were rapidly regulated by stresses and phytohormones. Importantly, we have constructed a regulation network based on co-expression patterns of the expression profiles upon multiple stresses performed in this study. CONCLUSIONS: BdMAPK cascade kinases were involved in the signaling pathways of multiple stresses in B. distachyon. The network of co-expression regulation showed the most of duplicated BdMAPK cascade kinase gene orthologs demonstrated their convergent function, whereas few of them developed divergent function in the evolutionary process. The molecular evolution analysis of identified MAPK family genes and the constructed MAPK cascade regulation network under multiple stresses provide valuable information for further investigation of the functions of BdMAPK cascade kinase genes.

Validation of a reference gene (BdFIM) for quantifying transgene copy numbers in Brachypodium distachyon by real-time PCR.

Brachypodium distachyon has been proposed as a new model system for gramineous plants with a sequenced genome and an efficient transformation system. Many transgenic B. distachyon plants have been generated in recent years. To develop a reliable fast method for detecting transgenic B. distachyon and quantifying its transgene copy numbers, a species-specific reference gene is of great priority to be validated both in qualitative PCR and quantitative real-time PCR detection. In this study, we first proved that the BdFIM (B. distachyon fimbrin-like protein) gene is a suitable reference gene in qualitative PCR and quantitative real-time PCR for B. distachyon. Fourteen different B. distachyon varieties were tested by both qualitative and quantitative PCRs, and identical amplification products of BdFIM were obtained with all of them, while no amplification products were observed with samples from 14 other plant species, suggesting that BdFIM gene was specific to B. distachyon. The results of Southern blot analysis revealed that the BdFIM gene was low copy number in seven tested B. distachyon varieties. In conclusion, the BdFIM gene can be used as a reference gene, since it had species specificity, low heterogeneity, and low copy number among the tested B. distachyon varieties. Furthermore, the copy number of inserted sequences from transgenic B. distachyon obtained by real-time PCR methods and Southern blot confirmed that the BdFIM gene was an applicable reference gene in B. distachyon.

Roles of chlorogenic Acid on regulating glucose and lipids metabolism: a review.

Intracellular glucose and lipid metabolic homeostasis is vital for maintaining basic life activities of a cell or an organism. Glucose and lipid metabolic disorders are closely related with the occurrence and progression of diabetes, obesity, hepatic steatosis, cardiovascular disease, and cancer. Chlorogenic acid (CGA), one of the most abundant polyphenol compounds in the human diet, is a group of phenolic secondary metabolites produced by certain plant species and is an important component of coffee. Accumulating evidence has demonstrated that CGA exerts many biological properties, including antibacterial, antioxidant, and anticarcinogenic activities. Recently, the roles and applications of CGA, particularly in relation to glucose and lipid metabolism, have been highlighted. This review addresses current studies investigating the roles of CGA in glucose and lipid metabolism.

Similar connotation in chronic hepatitis B and nonalcoholic Fatty liver patients with dampness-heat syndrome.

The phenomenon that the same syndrome turns up in different diseases appears in the sight of people around the world, which raises the thought for possibility of "Same Treatment for Different Diseases." Actually, treatment based on ZHENG classification in Traditional Chinese Medicine could bring revelation for the former finding. The dampness-heat syndrome in chronic hepatitis B and nonalcoholic fatty liver is regarded as the breakthrough point. We discussed the molecular mechanism of similar connotation that exists in chronic hepatitis B and nonalcoholic fatty liver by metabonomics to give the modern understanding of dampness-heat syndrome. Both urine and serum metabolic profiling revealed that obvious differences existed between dampness-heat syndrome and non-dampness-heat syndrome but the commonality was proved to appear in chronic hepatitis B and nonalcoholic fatty liver patients with dampness-heat syndrome. Furthermore, disorder of body fluid metabolism, decline in digestive capacity, and imbalance of intestinal flora were found to be the new guiding for treatment, with the hope to provide the basis for Chinese personalized medicine.

ZmCPK11 is involved in abscisic acid-induced antioxidant defence and functions upstream of ZmMPK5 in abscisic acid signalling in maize.

Calcium-dependent protein kinases (CDPKs) have been shown to be involved in abscisic acid (ABA)-mediated physiological processes, including seed germination, post-germination growth, stomatal movement, and plant stress tolerance. However, it is not clear whether CDPKs are involved in ABA-induced antioxidant defence. In the present study, the role of the maize CDPK ZmCPK11 in ABA-induced antioxidant defence and the relationship between ZmCPK11 and ZmMPK5, a maize ABA-activated mitogen-activated protein kinase (MAPK), in ABA signalling were investigated. Treatments with ABA and H(2)O(2) induced the expression of ZmCPK11 and increased the activity of ZmCPK11, while H(2)O(2) was required for the ABA-induced increases in the expression and the activity of ZmCPK11. The transient gene expression analysis and the transient RNA interference (RNAi) test in protoplasts showed that ZmCPK11 is involved in ABA-induced up-regulation of the expression and the activities of superoxide dismutase (SOD) and ascorbate peroxidase (APX), and in the production of H(2)O(2). Further, ZmCPK11 was shown to be required for the up-regulation of the expression and the activity of ZmMPK5 in ABA signalling, but ZmMPK5 had very little effect on the ABA-induced up-regulation of the expression and the activity of ZmCPK11. Moreover, the transient gene expression analysis in combination with the transient RNAi test in protoplasts showed that ZmCPK11 acts upstream of ZmMPK5 to regulate the activities of antioxidant enzymes. These results indicate that ZmCPK11 is involved in ABA-induced antioxidant defence and functions upstream of ZmMPK5 in ABA signalling in maize.

OsDMI3 is a novel component of abscisic acid signaling in the induction of antioxidant defense in leaves of rice.

Ca(2+) and calmodulin (CaM) have been shown to play an important role in abscisic acid (ABA)-induced antioxidant defense. However, it is unknown whether Ca(2+)/CaM-dependent protein kinase (CCaMK) is involved in the process. In the present study, the role of rice CCaMK, OsDMI3, in ABA-induced antioxidant defense was investigated in leaves of rice (Oryza sativa) plants. Treatments with ABA, H(2)O(2), and polyethylene glycol (PEG) induced the expression of OsDMI3 and the activity of OsDMI3, and H(2)O(2) is required for the ABA-induced increases in the expression and the activity of OsDMI3 under water stress. Subcellular localization analysis showed that OsDMI3 is located in the nucleus, the cytoplasm, and the plasma membrane. The analysis of the transient expression of OsDMI3 in rice protoplasts and the RNA interference (RNAi) silencing of OsDMI3 in rice protoplasts showed that OsDMI3 is required for ABA-induced increases in the expression and the activities of superoxide dismutase (SOD) and catalase (CAT). Further, the oxidative damage induced by higher concentrations of PEG and H(2)O(2) was aggravated in the mutant of OsDMI3. Moreover, the analysis of the RNAi silencing of OsDMI3 in protoplasts and the mutant of OsDMI3 showed that higher levels of H(2)O(2) accumulation require OsDMI3 activation in ABA signaling, but the initial H(2)O(2) production induced by ABA is not dependent on the activation of OsDMI3 in leaves of rice plants. Our data reveal that OsDMI3 is an important component in ABA-induced antioxidant defense in rice.

ZmMPK5 is required for the NADPH oxidase-mediated self-propagation of apoplastic H2O2 in brassinosteroid-induced antioxidant defence in leaves of maize.

Brassinosteroids (BRs) have been shown to induce hydrogen peroxide (H(2)O(2)) accumulation, and BR-induced H(2)O(2) up-regulates antioxidant defence systems in plants. However, the mechanisms by which BR-induced H(2)O(2) regulates antioxidant defence systems in plants remain to be determined. In the present study, the role of ZmMPK5, a mitogen-activated protein kinase, in BR-induced anitioxidant defence and the relationship between the activation of ZmMPK5 and H(2)O(2) production in BR signalling were investigated in leaves of maize (Zea mays) plants. BR treatment activated ZmMPK5, induced apoplastic and chloroplastic H(2)O(2) accumulation, and enhanced the total activities of antioxidant enzymes. Such enhancements were blocked by pre-treatment with mitogen-activated protein kinase kinase (MAPKK) inhibitors and H(2)O(2) inhibitors or scavengers. Pre-treatment with MAPKK inhibitors substantially arrested the BR-induced apoplastic H(2)O(2) production after 6 h of BR treatment, but did not affect the levels of apoplastic H(2)O(2) within 1 h of BR treatment. BR-induced gene expression of NADPH oxidase was also blocked by pre-treatment with MAPKK inhibitors and an apoplastic H(2)O(2) inhibitor or scavenger after 120 min of BR treatment, but was not affected within 30 min of BR treatment. These results suggest that the BR-induced initial apoplastic H(2)O(2) production activates ZmMPK5, which is involved in self-propagation of apoplastic H(2)O(2) via regulation of NADPH oxidase gene expression in BR-induced antioxidant defence systems.

A novel mitogen-activated protein kinase gene in maize (Zea mays), ZmMPK3, is involved in response to diverse environmental cues.

In search for components of mitogen-activated protein kinase (MAPK) cascades in maize (Zea mays) involved in response to abscisic acid (ABA) stimulus, a novel MAPK gene, ZmMPK3, from ABA-treated maize leaves cDNA was isolated and characterized. The full length of the ZmMPK3 gene is 1 520 bp and encodes a 376 amino acid protein with a predicted molecular mass of 43.5 kD and a pI of 5.83. ZmMPK3 contains all 11 MAPK conserved subdomains and the phosphorylation motif TEY. Amino acid sequence alignment revealed that ZmMPK3 shared high identity with group-A MAPK in plants. A time course (30-360 min) experiment using a variety of signal molecules and stresses revealed that the transcripts level of ZmMPK3 accumulated markedly and rapidly when maize seedlings were subjected to exogenous signaling molecules: ABA, H2O2, jasmonic acid and salicylic acid, various abiotic stimuli such as cold, drought, ultraviolet light, salinity, heavy metal and mechanical wounding. Its transcription was also found to be tissue-specific regulated. Here, we show that ABA and H2O2 induced a significant increase in the ZmMPK3 activity using immunoprecipitation and in-gel kinase assay. Furthermore, the results showed that the ZmMPK3 protein is localized mainly to the nucleus. These results suggest that the ZmMPK3 may play an important role in response to environmental stresses.

[Preparation of Lieber-DeCarli liquid diet induced alcoholic hepatic injury model in rats].

OBJECTIVE: Duplicating the classical alcoholic hepatic injury model, to provide an ideal animal model for research on prevention and treatment of hepatic injury. METHODS: According to the prescription of Lieber-DeCarli, the same calorie fluid animal feed, which contained ethanol or non-ethanol, was prepared. Twenty-three rats were divided into normal control group (n=5), control liquid diet group (n=9), ethanol liquid diet group (n=9). Rats in the normal control group were fed normal diet, and rats in the control liquid diet group and ethanol liquid diet group were fed the corresponding diet for eight weeks. The pathologic changes of hepatic tissue were observed. The activities of the serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST), the liver tissue gamma-glutamyltransferase (gamma-GT), the content of triglyceride (TG), and the lipid peroxidation by-products were assayed. RESULTS: Compared to the normal control and the control liquid diet groups, the activities of ALT, AST, and gamma-GT, and the lipid peroxidation by-products increased significantly in the ethanol liquid diet group. The pathological changes of cellular swelling and fatty degeneration in the ethanol liquid diet group were severe. CONCLUSION: Alcoholic hepatic injury model can be successfully duplicated by Lieber-DeCarli prescription.