Search

In this study, the slurry diffusion in a cavity filled with coal gangue was studied by combining experimental and numerical simulation methods. By calibrating slurry and particle materials, the grouting process in coal gangue filling area is simulated successfully, and the change of slurry diffusion flow field and particle movement and settling process in different dimensions are deeply analyzed. Both experimental and numerical simulation results show that the particle settlement presents a bell-shaped curve, which is of great significance for understanding the particle movement and settlement behavior in the filling cavity. In addition, it is found that the grouting speed has a significant effect on the particle settlement during the slurry diffusion process. When the grouting speed increases from 0.1m /s to 0.2m /s, the particle settlement and diffusion range increases about twice. In the plane flow field, it is observed that the outward diffusion trend and speed of grouting are more obvious. It is worth noting that in the whole process of grouting, it is observed that with the increase of grouting distance and depth, both the velocity of slurry and particles show a trend of rapid initial decline and gradually slow down, and the flow velocity of slurry near the grouting outlet at a flow rate of 0.2m/s is 2-4 times that of 0.1m/s. This provides important enlightenment for the porous seepage effect at different grouting speeds.

ObjectiveTo improve the accuracy of parameters used in discrete element simulation test of Chinese cabbage seeds harvesting process.MethodsFirstly, the key physical parameters of Chinese cabbage seeds were measured. According to the results, the discrete element simulation model was established and the value range of simulation test parameters was determined. Then, the actual repose angle of Chinese cabbage seeds was obtained by physical accumulation test using bottomless conical cylinder lifting method. Plackett-Burman test, steepest climb test, Box-Behnken test and parameter optimization test were carried out in sequence with the actual angle of repose as the response value. Finally, the obtained parameters are verified.Results1. The Plackett-Burman test showed that the seed-seed rolling friction coefficient, the seed-steel rolling friction coefficient, the seed-seed static friction coefficient, and the seed-steel static friction coefficient had significant effects on the repose angle of Chinese cabbage seeds (PConclusionThe study show that the discrete element simulation parameters of Chinese cabbage seeds model and calibration are reliable, which can provide reference for the discrete element simulation of Chinese cabbage seeds.

More than just a container for DNA, the nuclear envelope carries out a wide variety of critical and highly regulated cellular functions. One of these functions is nuclear import, and in this study we investigate how altering the levels of nuclear transport factors impacts developmental progression and organismal size. During early Xenopus laevis embryogenesis, the timing of a key developmental event, the midblastula transition (MBT), is sensitive to nuclear import factor levels. How might altering nuclear import factors and MBT timing in the early embryo affect downstream development of the organism? We microinjected X. laevis two-cell embryos with mRNA to increase levels of importin α or NTF2, resulting in differential amounts of nuclear import factors in the two halves of the embryo. Compared to controls, these embryos exhibited delayed gastrulation, curved neural plates, and bent tadpoles with different sized eyes. Furthermore, embryos microinjected with NTF2 developed into smaller froglets compared to control microinjected embryos. We propose that altering nuclear import factors and nuclear size affects MBT timing, cell size, and cell number, subsequently disrupting later development. Thus, altering nuclear import factors early in development can affect function and size at the organismal level.

To reduce potential oncogenic long genomic DNA in vaccines, nuclease treatment has been applied in the purification processes. However, this action increased the residue of short-fragment DNA and its effect on vaccine potency was still elusive. In this study, we found residual sf-DNA in an inactivated EV71 vaccine could enhance humoral immune response in mice. Ag stimulation in vitro and vaccine injection in vivo revealed that TLR9 transcription level was elevated, indicating that sf-DNA could activate TLR9. These new findings will help us to understand the molecular mechanism induced by vero-cell culture-derived vaccines.

Three inactivated EV71 whole-virus vaccines have completed Phase III clinical trials in mainland China, with high efficacy, satisfactory safety, and sustained immunogenicity. However, the molecular mechanisms how this new vaccine elicit potent immune response remain poorly understood. To characterize the primary and recall responses to EV71 vaccines, PBMC from 19 recipients before and after vaccination with EV71 vaccine are collected and their gene expression signatures after stimulation with EV71 antigen were compared. The results showed that primary and recall response to EV71 antigen have both activated an IRF7 regulating type I interferon and antiviral immune response network. However, up-regulated genes involved in T cell activation regulated by IRF1, inflammatory response, B-cell activation and humoral immune response were only observed in recall response. The specific secretion of IL-10 in primary response and IL-2,IP-10,CCL14a, CCL21 in recall response was consistent with the activation of immune response process found in genes. Furthermore, the expression of MX1 and secretion of IP-10 in recall response were strongly correlated with NTAb level at 180d after vaccination (r = 0.81 and 0.99). In summary, inflammatory response, adaptive immune response and a stronger antiviral response were indentified in recall response.

Hydrogen sulfide (H2S), a novel gaseous mediator, has been recognized as an important neuromodulator and neuroprotective agent in the central nervous system. The present study was undertaken to study the effects of exogenous H2S on traumatic brain injury (TBI) and the underlying mechanisms. The effects of exogenous H2S on TBI were examined by using measurement of brain edema, behavior assessment, propidium iodide (PI) staining, and Western blotting, respectively. Compared to TBI groups, H2S pretreatment had reduced brain edema, improved motor performance and ameliorated performance in Morris water maze test after TBI. Immunoblotting results showed that H2S pretreatment reversed TBI-induced cleavage of caspase-3 and decline of Bcl-2, suppressed LC3-II, Beclin-1 and Vps34 activation and maintained p62 level in injured cortex and hippocampus post TBI. The results suggest a protective effect and therapeutic potential of H2S in the treatment of brain injury and the protective effect against TBI may be associated with regulating apoptosis and autophagy.

Little is known about the role of the host defensive protein short palate, lung and nasal epithelium clone 1 (SPLUNC1) in the carcinogenesis of nasopharyngeal carcinoma (NPC). Here we report that SPLUNC1 plays a role at a very early stage of NPC carcinogenesis. SPLUNC1 regulates NPC cell proliferation, differentiation and apoptosis through miR-141, which in turn regulates PTEN and p27 expression. This signaling axis is negatively regulated by the EBV-coded gene LMP1. Therefore we propose that SPLUNC1 suppresses NPC tumor formation and its inhibition by LMP1 provides a route for NPC tumorigenesis.

Haemophilus parasuis is the etiological agent of Glässer's disease in pigs and 15 standard serovars were identified. The widespread disease causes great economic loss in the swine industry worldwide. Aiming to investigate the differences in genome composition and functions among various strains, a highly virulent strain ZJ0906 of H. parasuis serovar 12 from China was analyzed and compared with serovar 5 SH0165. Strain ZJ0906 genome is 2,324,740 base pairs with 40.06% genomic GC content. It contains 2,484 open reading frames (ORF) predicted by Glimmer 3.02, of which 2,352 (∼94.7%) were annotated by NCBI nr blast, 1,745 by COG database and 1,829 by KEGG database. 109 potential virulence factors were annotated in strain ZJ0906 and 3 of which are potentially related to antibiotic resistance. Strain ZJ0906 genome is ∼55 kilobases longer than SH0165 genome, with an extra 211 predicted ORFs. VFDB, ARDB, and PAIDB blast searches showed that ZJ0906 and SH0165 shared a nearly identical panel of potential virulence factors, drug resistant genes and four PAI-like regions which showed high homology to Enterococcus, Escherichia and Salmonella. Synteny analysis showed that gene rearrangements are frequent between the two strains, which may lead to variations in pathogenicity and cross-protection among serovars. KEGG pathway analyses showed strain ZJ0906 shared similar metabolic pathways to strain SH0165. Molecular identification of these genomic elements and potential virulence factors pave the way to the better understanding of mechanisms underlying metabolic capabilities and pathogenicity of H. parasuis and prospective vaccine targets besides the widely used method of inactivated bacteria.

The level of neutralizing antibodies (NtAb) induced by vaccine inoculation is an important endpoint to evaluate the efficacy of EV71 vaccine. In order to evaluate the efficacy of EV71 vaccine, here, we reported the development of a novel pseudovirus system expression firefly luciferase (PVLA) for the quantitative measurement of NtAb. We first evaluated and validated the sensitivity and specificity of the PVLA method. A total of 326 serum samples from an epidemiological survey and 144 serum specimens from 3 clinical trials of EV71 vaccines were used, and the level of each specimen's neutralizing antibodies (NtAb) was measured in parallel using both the conventional CPE-based and PVLA-based assay. Against the standard neutralization assay based on the inhibition of the cytopathic effect (CPE), the sensitivity and specificity of the PVLA method are 98% and 96%, respectively. Then, we tested the potential interference of NtAb against hepatitis A virus, Polio-I, Polio-II, and Polio-III standard antisera (WHO) and goat anti-G10/CA16 serum, the PVLA based assay showed no cross-reactivity with NtAb against other specific sera. Importantly, unlike CPE based method, no live replication-competent EV71 is used during the measurement. Taken together, PVLA is a rapid and specific assay with higher sensitivity and accuracy. It could serve as a valuable tool in assessing the efficacy of EV71 vaccines in clinical trials and disease surveillance in epidemiology studies.

This study aims to develop explainable AI methods for matching patients with phase 1 oncology clinical trials using Natural Language Processing (NLP) techniques to address challenges in patient recruitment for improved efficiency in drug development. A prototype system based on modern NLP techniques has been developed to match patient records with phase 1 oncology clinical trial protocols. Four criteria are considered for the matching: cancer type, performance status, genetic mutation, and measurable disease. The system outputs a summary matching score along with explanations of the evidence. The outputs of the AI system were evaluated against the ground truth matching results provided by the domain expert on a dataset of twelve synthesized dummy patient records and six clinical trial protocols. The system achieved a precision of 73.68%, sensitivity/recall of 56%, accuracy of 77.78%, and specificity of 89.36%. Further investigation into the misclassified cases indicated that ambiguity of abbreviation and misunderstanding of context are significant contributors to errors. The system found evidence of no matching for all false positive cases. To the best of our knowledge, no system in the public domain currently deploys an explainable AI-based approach to identify optimal patients for phase 1 oncology trials. This initial attempt to develop an AI system for patients and clinical trial matching in the context of phase 1 oncology trials showed promising results that are set to increase efficiency without sacrificing quality in patient-trial matching., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Ghosh et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Since the COVID-19, cough sounds have been widely used for screening purposes. Intelligent analysis techniques have proven to be effective in detecting respiratory diseases. In 2021, there were up to 10 million TB-infected patients worldwide, with an annual growth rate of 4.5%. Most of the patients were from economically underdeveloped regions and countries. The PPD test, a common screening method in the community, has a sensitivity of as low as 77%. Although IGRA and Xpert MTB/RIF offer high specificity and sensitivity, their cost makes them less accessible. In this study, we proposed a feature fusion model-based cough sound classification method for primary TB screening in communities. Data were collected from hospitals using smart phones, including 230 cough sounds from 70 patients with TB and 226 cough sounds from 74 healthy subjects. We employed Bi-LSTM and Bi-GRU recurrent neural networks to analyze five traditional feature sets including the Mel frequency cepstrum coefficient (MFCC), zero-crossing rate (ZCR), short-time energy, root mean square, and chroma_cens. The incorporation of features extracted from the speech spectrogram by 2D convolution training into the Bi-LSTM model enhanced the classification results. With traditional futures, the best TB patient detection result was achieved with the Bi-LSTM model, with 93.99% accuracy, 93.93% specificity, and 92.39% sensitivity. When combined with a speech spectrogram, the classification results showed 96.33% accuracy, 94.99% specificity, and 98.13% sensitivity. Our findings underscore that traditional features and deep features have good complementarity when fused using Bi LSTM modelling, which outperforms existing PPD detection methods in terms of both efficiency and accuracy., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Xu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Background: Increasing evidence have elucidated that PBX3 played a crucial role in cancer initiation and progression. PBX3 was differentially expressed in many cancer types. However, PBX3 potential involvement in gliomas remains to be explored., Methods: The expression level of PBX3 in glioma tissues and glioma cells, and its correlation with clinical features were analyzed by data from TCGA, GEPIA, CGGA and CCLE. Univariable survival and Multivariate Cox analysis was used to compare several clinical characteristics with survival. We also analyzed the correlation between PBX3 expression level and survival outcome and survival time of LGG and GBM patients by using linear regression equation. GSEA was used to generate an ordered list of all genes related to PBX3 expression and screening of genes co-expressed with PBX3 mRNA by "limma" package., Results: The results showed that PBX3 was highly expressed in gliomas and its expression increased with the increase of malignancy. Survival analysis found that PBX3 is more valuable in predicting the OS and PFI of LGG patients than that of GBM. For further study, TCGA and CGGA data were downloaded for univariate Cox analysis and multivariate Cox analysis which showed that the expression of PBX3 was independent influencing factors for poor prognosis of LGG patients. Meanwhile, Receiver operating characteristic (ROC) curve showed that PBX3 was a predictor of overall survival rate and progression-free survival rate of LGG. Linear regression model analysis indicated that the higher expression of PBX3 the higher the risk of death of LGG patients, and the higher expression of PBX3 the higher the risk of disease progression of LGG patients. Next, TCGA data were downloaded for GSEA and Co-expression analyses, which was performed to study the function of PBX3., Conclusion: PBX3 may be involved in the occurrence and development of glioma, and has potential reference value for the early diagnosis and prediction of prognosis of glioma., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 pan et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

This paper presents a multi-algorithm fusion model (StackingGroup) based on the Stacking ensemble learning framework to address the variable selection problem in high-dimensional group structure data. The proposed algorithm takes into account the differences in data observation and training principles of different algorithms. It leverages the strengths of each model and incorporates Stacking ensemble learning with multiple group structure regularization methods. The main approach involves dividing the data set into K parts on average, using more than 10 algorithms as basic learning models, and selecting the base learner based on low correlation, strong prediction ability, and small model error. Finally, we selected the grSubset + grLasso, grLasso, and grSCAD algorithms as the base learners for the Stacking algorithm. The Lasso algorithm was used as the meta-learner to create a comprehensive algorithm called StackingGroup. This algorithm is designed to handle high-dimensional group structure data. Simulation experiments showed that the proposed method outperformed other R2, RMSE, and MAE prediction methods. Lastly, we applied the proposed algorithm to investigate the risk factors of low birth weight in infants and young children. The final results demonstrate that the proposed method achieves a mean absolute error (MAE) of 0.508 and a root mean square error (RMSE) of 0.668. The obtained values are smaller compared to those obtained from a single model, indicating that the proposed method surpasses other algorithms in terms of prediction accuracy., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Li et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

With a requirement of miniaturization in modern vibrating screens, the vibration synchronization method can no longer meet the process demand, so the controlled synchronization method is introduced in the vibrating screen to achieve zero phase error state and realize the purpose of increasing the amplitude. In this article, the controlled synchronization of a vibrating screen driven by two motors based on improved sliding mode controlling method is investigated. Firstly, according to the theory of mechanical dynamics, the motion state of the vibrating screen is simplified as the electromechanical coupling dynamical model of a vibrating system driven by two inductor motors. And then the synchronization conditions and stability criterion of the vibrating system are derived and numerically analyzed. Based on a master-slave controlling strategy, the controllers of two motors are respectively designed with Super-Twisting sliding mode control (ST-SMC) and backstepping second-order complementary sliding mode control (BSOCSMC), while the uncertainty is estimated by an adaptive radial basis function neural network (ARBFNN). In addition, Lyapunov stability analysis is performed on the two controllers to prove their stability theoretically. Finally, simulation analysis is conducted based on the dynamics model in this paper., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Jia et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Feed efficiency is a major constraint in the beef industry and has a significant negative correlation with residual feed intake (RFI). RFI is widely used as a measure of feed efficiency in beef cattle and is independent of economic traits such as body weight and average daily gain. However, key traits with commonality or specificity among beef cattle breeds at the same level of RFI have not been reported. Accordingly, the present study hypothesized that signatures associated with feed efficiency would have commonality or specificity in the liver of cattle breeds at the same RFI level. By comparing and integrating liver transcriptome data, we investigated the critical signatures closely associated with RFI in beef cattle using weighted co-expression network analysis, consensus module analysis, functional enrichment analysis and protein network interaction analysis. The results showed that the consensus modules in Angus and Charolais cattle were negatively correlated, and four (turquoise, red, tan, yellow) were significantly positively correlated in Angus liver, while (turquoise, red) were significantly negatively correlated in Charolais liver. These consensus modules were found to be primarily involved in biological processes such as substance metabolism, energy metabolism and gene transcription, which may be one of the possible explanations for the difference in feed efficiency between the two beef breeds. This research also identified five key candidate genes, PLA2G12B, LCAT, MTTP, LCAT, ABCA1 and FADS1, which are closely associated with hepatic lipid metabolism. The present study has identified some modules, genes and pathways that may be the major contributors to the variation in feed efficiency among different cattle breeds, providing a new perspective on the molecular mechanisms of feed efficiency in beef cattle and a research basis for investigating molecular markers associated with feed efficiency in beef cattle., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Yang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Previous studies have shown that male drivers drive faster than female drivers, but there is no agreement on whether impulsivity could induce this sex difference, nor is there a cross-sectional comparison of the effects of different road environments. The purpose of this study was to verify whether impulsivity and impulse control could explain the sex differences in driving speed. A driving simulator study (study 1, N = 41) was performed to investigate whether there were sex differences in driving speeds in two road sections of different complexity, and a questionnaire survey (study 2, N = 163) was conducted to investigate the relationship between sex, impulsivity, impulse control and driving behavior of the participants. The results showed that male drivers drove faster on simple roads, but this difference did not show on complex roads. There were no sex differences in impulsivity traits, but male participants had significant lower levels of impulse control. The results also reveal a partial mediating role of impulse control in the relationship between sex and driving speed. These results suggest that impulse control can predict dangerous driving behaviors and is an important factor in explaining sex differences in driving speed., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Pan et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

A deep memory bare-bones particle swarm optimization algorithm (DMBBPSO) for single-objective optimization problems is proposed in this paper. The DMBBPSO is able to perform high-precision local search while maintaining a large global search, thus providing a reliable solution to high-dimensional complex optimization problems. Normally, maintaining high accuracy while conducting global searches is an important challenge for single-objective optimizers. Traditional particle swarms optimizers can rapidly lose the diversity during iterations and are unable to perform global searches efficiently, and thus are more likely to be trapped by local optima. To address this problem, the DMBBPSO combines multiple memory storage mechanism (MMSM) and a layer-by-layer activation strategy (LAS). The MMSM catalyzes a set of deep memories to increase the diversity of the particle swarm. For every single particle, both of the personal best position and deep memories will be used in the evaluation process. The LAS enables the particle swarm to avoid premature convergence while enhancing local search capabilities. The collaboration between MMSM and LAS enhances the diversity of the particle swarm, which in turn enhances the robustness of the DMBBPSO. To investigate the optimization ability of the DMBBPSO for single-objective optimization problems, The CEC2017 benchmark functions are used in experiments. Five state-of-the-art evolutionary algorithms are used in the control group. Finally, experimental results demonstrate that the DMBBPSO can provide high precision results for single-objective optimization problems., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Sun et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

In the field of surface electromyography (sEMG) gesture recognition, how to improve recognition accuracy has been a research hotspot. The rapid development of deep learning provides a new solution to this problem. At present, the main applications of deep learning for sEMG gesture feature extraction are based on convolutional neural network (CNN) structures to capture spatial morphological information of the multichannel sEMG or based on long short-term memory network (LSTM) to extract time-dependent information of the single-channel sEMG. However, there are few methods to comprehensively consider the distribution area of the sEMG signal acquisition electrode sensor and the arrangement of the sEMG signal morphological features and electrode spatial features. In this paper, a novel multi-stream feature fusion network (MSFF-Net) model is proposed for sEMG gesture recognition. The model adopts a divide-and-conquer strategy to learn the relationship between different muscle regions and specific gestures. Firstly, a multi-stream convolutional neural network (Multi-stream CNN) and a convolutional block attention module integrated with a resblock (ResCBAM) are used to extract multi-dimensional spatial features from signal morphology, electrode space, and feature map space. Then the learned multi-view depth features are fused by a view aggregation network consisting of an early fusion network and a late fusion network. The results of all subjects and gesture movement validation experiments in the sEMG signal acquired from 12 sensors provided by NinaPro's DB2 and DB4 sub-databases show that the proposed model in this paper has better performance in terms of gesture recognition accuracy compared with the existing models., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2022 Peng et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

To study the difference between the fungal community compositional and fragrance components in medium- and high-Temperature Taorong-type Baijiu Daqu. The microbial communities and fragrance components of Taorong-type Baijiu Daqu were analyzed using high-throughput sequencing (HTS) and headspace-solid-phase microextraction-gas chromatography-mass spectrometry (HS-SPME-GC-MS). With an abundance at the phylum and genus levels ≥0.01% as the threshold, 3 phyla, Mucoromycota, Ascomycota, and Basidiomycota, were found in both medium- and high-temperature Daqu, but their abundances differed. At the genus level, 15 and 13 genera were recognized. Rhizopus (72.40%) and Thermomyces (53.32%) accounted for the most significant proportions in medium-temperature and high-temperature Daqu, respectively. Medium-temperature Daqu and high-temperature Daqu were found to have 40 and 29 fragrance components, respectively and contained the highest proportions of pyrazines (53.12%) and acids (32.68%). Correlation analyses between microbes and fragrance components showed that Aspergillus, Hyphopichia, Trichosporon, Alternaria were all highly and positively correlated with pyrazines, but the dominant fungal communities were highly correlated with only a few individual acid compounds but not with acid compounds overall. The unique Daqu -making process and environment lead to these differences., Competing Interests: The authors declare that they have no competing interests.

A total of 296 strains of protease-producing bacteria were isolated and purified from medium-temperature Daqu produced by ZhangGong LaoJiu Wine Co. Ltd. After calculating the ratio of transparent ring diameter to colony diameter and measuring the protease activities, a strain of high-yield protease bacteria, called DW-7, was screened out with a protease activity of 99.54 U/mL. Through morphological observation, 16S rDNA sequence analysis, and physiological and biochemical tests, the isolated bacteria DW-7 was determined to be Bacillus velezensis. In addition, whole-genome sequencing (WGS), using PacBio and the Illumina platform, was performed. Gene annotation was then conducted using the Clusters of Orthologous Groups (COG), Kyoto Encyclopedia of Genes and Genomes (KEGG), Non-Redundant Protein Sequence Database (NR), and Gene Ontology (GO) databases. The results showed that the genome of DW-7 was 3,942,829 bp long with a GC content of 46.45%. A total of 3,662 protein-encoding genes were predicted, with a total length of 3,402,822 bp. Additionally, 2,283; 2,796; and 2,127 genes were annotated in the COG, KEGG, and GO databases, respectively. A total of 196 high-yield protease genes were mainly enriched in the metabolism of alanine, aspartic acid, glutamate, glycine, serine, and threonine, as well as ABC transporter and transporter pathways., Competing Interests: The authors have declared that no competing interests exist.

With ongoing improvements in vehicle automation, research on automation trust has attracted considerable attention. In order to explore effects of automation trust on drivers' visual distraction, we designed a three-factor 2 (trust type: high trust group, low trust group) × 2 (video entertainment: variety-show videos, news videos) × 3 (measurement stage: 1-3) experiment. 48 drivers were recruited in Dalian, China for the experiment. With a driving simulator, we used detection-response tasks (DRT) to measure each driver's performance. Their eye movements were recorded, and automation-trust scale was used to divide participants into high trust group and low trust group. The results show that: (1) drivers in the high trust group has lower mental workload and paid more attention to visual non-driving-related tasks; (2) video entertainment also has an impact on distraction behavior, variety-show videos catch more attention than news videos. The findings of the present study indicate that drivers with high automation trust are more likely to be involved in non-driving-related visual tasks., Competing Interests: The authors have declared that no competing interests exist.

In this study, third-generation full-length (FL) transcriptome sequencing was performed of loquat using single-molecule real-time(SMRT) sequencing from the pooled cDNA of embryos of young loquat fruit under different low temperatures (three biological replicates for treatments of 1°C, -1°C, and -3°C, for 12 h or 24 h) and the control group(three biological replicates for treatments of room temperature), Illumina sequencing was used to correct FL transcriptome sequences. A total of 3 PacBio Iso-Seq libraries (1-2 kb, 2-3 kb and 3-6 kb) and 21 Illumina transcriptome libraries were constructed, a total of 13.41 Gb of clean reads were generated, which included 215,636 reads of insert (ROIs) and 121,654 FL, non-chimaric (FLNC) reads. Transcript clustering analysis of the FLNC reads revealed 76,586 consensus isoforms, and a total of 12,520 high-quality transcript sequences corrected with non-FL sequences were used for subsequent analysis. After the redundant reads were removed, 38,435 transcripts were obtained. A total of 27,905 coding DNA sequences (CDSs) were identified, and 407 long non-coding RNAs (lncRNAs) were ultimately predicted. Additionally, 24,832 simple sequence repeats (SSRs) were identified, and a total of 1,295 alternative splicing (AS) events were predicted. Furthermore, 37,993 transcripts were annotated in eight functional databases. This is the first study to perform SMRT sequencing of the FL transcriptome of loquat. The obtained transcriptomic data are conducive for further exploration of the mechanism of loquat freezing injury and thus serve as an important theoretical basis for generating new loquat material and for identifying new ways to improve loquat cold resistance., Competing Interests: NO authors have competing interests.

To investigate the growth, physiological changes and mechanism of drought resistance of Camellia oleifera GWu-2 under drought stress conditions, changes in the main growth and physiological indices of GWu-2 under different water gradients were studied. Factor analysis was used to study the differences between indicators under different water gradients, and correlation analysis was implemented to analyze the relationship between different factors. We observed that the growth state, enzyme secretion, stomatal morphology and leaf osmotic adjustment substances were significantly affected by drought stress. In particular, increases in leaf abscisic acid (ABA), indole acetic acid (IAA) and methyl jasmonate (MeJA) contents under drought stress were negatively correlated with the stomatal opening degree, and the ratio of ZR/GA3 was significantly correlated with the growth and physiological indicators of GWu-2, indicating that different hormones respond differently to drought stress and have different functions in the growth regulation and drought resistance of GWu-2. We concluded that the drought resistance mechanism of GWu-2 was controlled by maintaining root growth to obtain the necessary water, increasing the contents of osmotic substances of leaves to maintain water holding capacity, reducing the transpiration of water by increasing leaf ABA, IAA and MeJA content to close stomata and reducing the damage caused by drought by increasing the activity of superoxide dismutase (SOD)., Competing Interests: The authors have declared that no competing interests exist.

Large urban trees have many benefits. However, falling branches pose a serious hazard to both people and infrastructure. In several tree species, aerial roots grow down from branches to the ground. These roots are capable of thickening to support the branches, lessening the risk of tree failure. Unfortunately, in urban environments most aerial roots die before reaching the ground. Here, we report a new method for encouraging aerial roots to reach the ground, developed by the second-year botany class at UNSW Sydney. Our class tested three experimental treatments on aerial roots of Ficus rubiginosa Desf. ex Vent. (Port Jackson Fig)-PVC pipes filled with sphagnum moss, PVC pipes filled with potting mix, and PVC pipes filled with sphagnum moss and topped with funnels to catch extra rainwater. All three treatments significantly improved aerial root growth, with 26 of the 30 (87%) treatment roots reaching the ground after one year compared to 0 of the 10 control roots. Our method was successful for roots up to 3 m above the ground, suggesting the potential growth rate of aerial roots is substantial when conditions are favourable. Our novel approach is an attractive and cost-effective alternative to slings and other artificial supports. This project is an example of using undergraduate practical classes to teach science while simultaneously addressing important real-world problems., Competing Interests: The authors have declared that no competing interests exist.

Objective: This study aimed to compare the levels of plasma neutrophil gelatinase-associated lipocalin (NGAL), matrix metalloproteinase (MMP)-9, high-sensitivity C-reactive protein (hs-CRP), and interleukin (IL)-1β across different clinical presentations of coronary artery disease and to evaluate the relationship between those biomarkers and the severity of coronary artery lesions in patients without kidney disease., Methods: We examined 365 eligible patients who underwent coronary angiography. A total of 124 ST-segment elevation myocardial infarction (STEMI) patients, 117 stable angina pectoris (SAP) patients and 124 patients without atherosclerotic plaques were enrolled in the study. Plasma NGAL, MMP-9, hs-CRP, and IL-1β were measured in all patients using the enzyme-linked immunosorbent assay (ELISA) method. According to the SYNTAX score, the STEMI patients and SAP patients were divided into another set of 2 groups: a high score group (≥ 33, n = 29) and a low score group (<33, n = 212). The relationship between those biomarkers and the severity of coronary stenosis was examined by Spearman correlation analysis; the ability for NGAL to discriminate severe coronary stenosis was examined by receiver operating characteristic (ROC) curve; the influencing factors for the SYNTAX score were determined by logistic regression analysis., Results: Plasma NGAL, MMP-9, and hs-CRP levels in STEMI patients were higher than in the SAP patients and control subjects (P<0.05, respectively), and plasma NGAL and hs-CRP levels were significantly higher in the SAP patients than in control subjects (P<0.05, respectively), while plasma IL-1β was similar among the 3 groups (P>0.05, respectively). The SYNTAX score was positively related to NGAL (r = 0.363, P<0.001), MMP-9 (r = 0.377, P<0.001), and hs-CRP (r = 0.163, P<0.011); the SYNTAX score was not related to IL-1β (r = -0.043, P = 0.510). Plasma NGAL was positively related to MMP-9 (r = 0.601, P<0.001) and IL-1β (r = 0.159, P = 0.014). The area under the ROC curve for NGAL discriminating severe coronary stenosis was 0.838 (95% CI: 0.752-0.923, P<0.001), which was greater than that for MMP-9 [0.818, (95% CI: 0.724-0.912, P<0.001)], IL-1β [0.485, (95% CI: 0.369-0.601, P = 0.791)], and hs-CRP [0.607, (95% CI: 0.492-0.722, P = 0.061)]. Multivariate regression analysis showed that plasma NGAL levels were independently related to high SYNTAX scores [OR = 1.109, (95% CI: 1.104-1.114), P<0.001]., Conclusion: Plasma NGAL, MMP-9, and hs-CRP levels in STEMI patients were higher than those in the SAP patients and control subjects. NGAL had a better ability to discriminate severe coronary stenosis than MMP-9, IL-1β, and hs-CRP. NGAL may be a novel biomarker to aid in risk stratification in coronary heart disease patients., Competing Interests: The authors have declared that no competing interests exist.

Purpose: To assess the prediction accuracy of four variations of total corneal refractive power (TCRP) by the ray tracing method in determining corneal power in eyes after myopic small incision lenticule extraction (SMILE)., Methods: Forty eyes of forty patients who had undergone myopic SMILE were enrolled in this prospective study. Manifest refraction and Pentacam HR were performed preoperatively and three months or more postoperatively. Mean keratometry (Km), true net power (TNP), equivalent keratometry readings (EKR) and 4 subtypes of TCRP (pupil centered or apex centered within a ring or a zone)-TCRPpupil,ring, TCRPpupil,zone, TCRPapex,ring and TCRPapex,zone-were recorded and compared to the theoretical postoperative keratometry value using the clinical history method (CHM)., Results: The only keratometric values that showed no statistically significant differences from the CHM were 4.0 mm and 4.5 mm EKR, 6.0 mm TCRPpupil,zone and TCRPapex,zone. Pearson's correlation test revealed that 4.0 mm TCRPpupil,zone exhibited the highest correlation coefficient (r = 0.974) followed by TCRPapex,zone 4.0 mm (0.972) and EKR 4.5 mm (0.970). The 95% limits of agreement (LOA) of the 4.0 mm EKR and CHM, the 4.5 mm EKR and CHM, the 6.0 mm TCRPpupil,zone and CHM, the 6.0 mm TCRPapex,zone and CHM were (-1.27 to 1.22 D), (-1.04 to 0.98 D), (-1.39 to 1.08 D) and (-1.38 to 0.96 D), respectively, while the modified 4.0 mm TCRPpupil,zone (TCRPpuil,zone + 0.70 D) and TCRPapex,zone (TCRPapex,zone+0.70 D) yielded the narrowest 95% LOA of (-0.96 to 0.95 D) and (-0.96D, 1.05 D)., Conclusions: Total corneal refractive power using the ray tracing method could predict corrected corneal power derived from the CHM in eyes following SMILE surgery after simple modification., Competing Interests: The authors have declared that no competing interests exist.

[This corrects the article DOI: 10.1371/journal.pone.0206844.].

We describe a new assaying system for the detection and genotyping of human papillomavirus (HPV) based on linear-after-the-exponential-PCR(LATE-PCR) and melting curve analysis. The 23 most prevalent HPV strains (types 6, 11, 16, 18, 31, 33, 35, 39, 42, 45, 51, 52, 53, 56, 58, 59, 66, 68, 70, 73, 81, 82, and 83) are assayed in two sealed reaction tubes within 2 h. Good sensitivity and specificity was evaluated by testing cloned HPV DNA and clinical samples. The detection limit was 5-500 copies/reaction depending on the genotype. No cross-reactivity was observed with the other HPV types that are not covered by our method or pathogens tested which were commonly found in female genital tract. When compared with the HPV GenoArray Diagnostic kit, the results from 1104 clinical samples suggest good overall agreement between the two methods,(98.37%, 95% CI: 97.44%-98.97%) and the kappa value was 0.954. Overall, this new HPV genotyping assay system presents a simple, rapid, universally applicable, sensitive, and highly specific detection methodology that should be useful for HPV detection and genotyping, therefore, is potentially of great value in clinical application., Competing Interests: The authors have declared that no competing interests exist.

Background: Key regulators of developmental processes can be prioritized through integrated analysis of ChIP-Seq data of master transcriptional factors (TFs) such as Nanog and Oct4, active histone modifications (HMs) such as H3K4me3 and H3K27ac, and repressive HMs such as H3K27me3. Recent studies show that broad enrichment signals such as super-enhancers and broad H3K4me3 enrichment signals play more dominant roles than short enrichment signals of the master TFs and H3K4me3 in epigenetic regulatory mechanism. Besides the broad enrichment signals, up to ten thousands of short enrichment signals of these TFs and HMs exist in genome. Prioritization of these broad enrichment signals from ChIP-Seq data is a prerequisite for such integrated analysis., Results: Here, we present a method named Clustering-Local-Unique-Enriched-Signals (CLUES), which uses an adaptive-size-windows strategy to identify enriched regions (ERs) and cluster them into broad enrichment signals. Tested on 62 ENCODE ChIP-Seq datasets of Ctcf and Nrsf, CLUES performs equally well as MACS2 regarding prioritization of ERs with the TF's motif. Tested on 165 ENCODE ChIP-Seq datasets of H3K4me3, H3K27me3, and H3K36me3, CLUES performs better than existing algorithms on prioritizing broad enrichment signals implicating cell functions influenced by epigenetic regulatory mechanism in cells. Most importantly, CLUES helps to confirm several novel regulators of mouse ES cell self-renewal and pluripotency through integrated analysis of prioritized broad enrichment signals of H3K4me3, H3K27me3, Nanog and Oct4 with the support of a CRISPR/Cas9 negative selection genetic screen., Conclusions: CLUES holds promise for prioritizing broad enrichment signals from ChIP-Seq data. The download site for CLUES is https://github.com/Wuchao1984/CLUESv1., Competing Interests: We have the following interests: Jing Zhu is employed by Beijing Ming-tian Genetics Ltd. There are no patents, products in development or marketed products to declare. This does not alter our adherence to all the PLOS ONE policies on sharing data and materials.

Objective: The primary aim of this meta-analysis was to test the null hypothesis of no difference in facial nerve dysfunction in studies that compared classical antegrade facial nerve dissection (AFND) versus retrograde facial nerve dissection (RFND) during benign parotid surgery., Methods: A comprehensive search of PubMed, the Cochrane Central Register of Controlled Trials, Scopus, Google Scholar, Science Direct and relevant journals was undertaken up to June 27, 2018. Randomized controlled clinical trials (RCTs), controlled clinical trials (CCTs), and retrospective studies aimed at comparing the effect of AFND vs. RFND during parotidectomy were included. The outcome measures included facial nerve dysfunction, Frey's syndrome, recurrence, silaocele, salivary fistula, operating time length of hospital stay, and estimated blood loss. Pooled risk ratio (RR) and weighted mean differences (MD) with 95% confidence intervals were calculated using either a fixed-effects or random-effects model., Results: Ten studies; four RCTs and five retrospective studies were included. There were 570 patients (319 in RFND group and 251 in AFND group). 481 patients in 9 studies reported the incidence rate of facial nerve dysfunction. No statistical significant difference was observed between both groups concerning the occurrence of transient or permanent facial nerve paralysis (p = 0.44 and 0.11 respectively). One out 10 studies reported the incidence rate of sialocele, however no statistical difference was observed between the two techniques. There was reduction in the operative time (19.30 min), amount of blood loss (25.08 ml) and amount of healthy salivary tissues removed (12.20 mm) in RFND compared with AFND., Conclusions: According to the results of the current review there is no evidence demonstrating a significant advantage of one approach over another, therefore, well-designed standardized RCTs are required., Competing Interests: The authors have declared that no competing interests exist.

Like DIP-STR markers (deletion/insertion polymorphism-short tandem repeat combinations), SNP-STR markers (single nucleotide polymorphism-STR combinations) are also valuable in forensic DNA mixture analysis. In this study, eight SNP-STRs were selected, and a stable and sensitive multiplex polymerase chain reaction (PCR) assay was developed for amplifying these SNP-STRs and the Amelogenin gender marker according to the principle of amplification refractory mutation system (ARMS). This novel multiplex set allows detection of the minor DNA contributor in a DNA mixture of any gender and cellular origin with high resolution (beyond a DNA ratio of 1:20). In addition, SNP-STR haplotype frequencies were estimated based on a survey of 350 unrelated individuals from Chinese Han population, and the combined power of discrimination (PD) and power of exclusion (PE) of the eight SNP-STRs were calculated as 0.99999999965 and 0.9996, which were obviously higher than that of the eight STR loci: 0.9999999954 and 0.9989 respectively. The results indicated that the SNP-STR compound markers have higher application value in forensic identification compared to standard autosomal STRs, especially in the analysis of imbalanced DNA mixtures., Competing Interests: The authors have declared that no competing interests exist.

Sedation induces changes in electroencephalography (EEG) dynamics. However, the distinct EEG dynamic characteristics at comparable sedation levels have not been well studied, resulting in potential interpretation errors in EEG monitoring during sedation. We aimed to analyze the EEG dynamics of dexmedetomidine and propofol at comparable sedation levels and to explore EEG changes with increased sedation levels for each agent. We measured the Bispectral Index (BIS) and 20-channel EEG under dexmedetomidine and propofol sedation from wakefulness, moderate sedation, and deep sedation to recovery in healthy volunteers (n = 10) in a randomized, 2-day, crossover study. Observer's Assessment of Alertness and Sedation (OAA/S) score was used to assess sedation levels. Despite similar changes in increased delta oscillations, multiple differences in the EEG spatiotemporal dynamics were observed between these two agents. During moderate sedation, both dexmedetomidine and propofol induced increased spindle power; however, dexmedetomidine decreased the global alpha/beta/gamma power, whereas propofol decreased the alpha power in the occipital area and increased the global spindle/beta/gamma power. During deep sedation, dexmedetomidine was associated with increased fronto-central spindle power and decreased global alpha/beta/gamma power, but propofol was associated with increased theta/alpha/spindle/beta power, which was maximized in the frontal area. The transition of topographic alpha/spindle/beta power distribution from moderate sedation to deep sedation completely differed between these two agents. Our study demonstrated that there was a distinct hierarchy of EEG changes with increased sedation depths by propofol and dexmedetomidine. Differences in EEG dynamics at the same sedation level might account for differences in the BIS value and reflect the different sedation mechanisms. EEG-based clinical sedation monitoring should consider the effect of drug types on EEG dynamics., Competing Interests: The authors have declared that no competing interests exist.

Purpose: Total refractive astigmatism is usually the first consideration that guides the selection of contact lens type (e.g., spherical or toric), while the ocular source of the astigmatism is a second, but more important consideration, for the final clinical decision. This study was conducted to provide detailed data on this topic by evaluating astigmatic components in Chinese adolescents., Methods: Participants were recruited from healthy high school students undergoing an annual ocular examination at a local hospital. Total astigmatism (TA), corneal astigmatism (CA), and ocular residual astigmatism (ORA) were determined by a Hartmann-Shack wavefront analyzer system (KR-1W, Topcon) with the natural pupil. The axis relationship between CA and ORA was placed into three categories: on-axis, defined as an axis with a difference of 0 ± 10°; opposite-axis, a difference of 90 ± 10°; and the rest defined as oblique-axis., Results: The study consisted of 1,466 students (57.84% girls, age: 16.49 ± 1.05 years). ORA was present in 83.97%, 66.64%, and 45.23% of participants, according to the various criteria for astigmatism (≥ 0.50 D, ≥ 0.75 D, and ≥ 1.00 D, respectively). While with-the-rule was the most common axis orientation for both TA (76.28%) and CA (89.94%), against-the-rule predominated in ORA (93.82%; χ2 = 1688.544, p < 0.001). Opposite-axis was the major type of axis difference (90.96%) of clinical significance (i.e., ≥ 1.00 D) between CA and ORA, which also prevailed in all levels of TA (range: 56.25-82.26%)., Conclusions: ORA is common in high school students and usually demonstrates a compensation relationship with CA, which should be taken into consideration when determining the design of contact lenses to correct refractive error.

Background: The mechanism of general anesthesia (GA) has been explored for hundreds of years, but unclear. Previous studies indicated a possible correlation between NREM sleep and GA. The purpose of this study is to compare them by in vivo human brain function to probe the neuromechanism of consciousness, so as to find out a clue to GA mechanism., Methods: 24 healthy participants were equally assigned to sleep or propofol sedation group by sleeping ability. EEG and Ramsay Sedation Scale were applied to determine sleep stage and sedation depth respectively. Resting-state functional magnetic resonance imaging (RS-fMRI) was acquired at each status. Regional homogeneity (ReHo) and seed-based whole brain functional connectivity maps (WB-FC maps) were compared., Results: During sleep, ReHo primarily weakened on frontal lobe (especially preoptic area), but strengthened on brainstem. While during sedation, ReHo changed in various brain areas, including cingulate, precuneus, thalamus and cerebellum. Cingulate, fusiform and insula were concomitance of sleep and sedation. Comparing to sleep, FCs between the cortex and subcortical centers (centralized in cerebellum) were significantly attenuated under sedation. As sedation deepening, cerebellum-based FC maps were diminished, while thalamus- and brainstem-based FC maps were increased., Conclusion: There're huge distinctions in human brain function between sleep and GA. Sleep mainly rely on brainstem and frontal lobe function, while sedation is prone to affect widespread functional network. The most significant differences exist in the precuneus and cingulate, which may play important roles in mechanisms of inducing unconciousness by anesthetics., Trial Registration: Institutional Review Board (IRB) ChiCTR-IOC-15007454.

Cold environment is the main constraint for tea plants (Camellia sinensis) distribution and tea farming. We identified two tea cultivars, called var. sinensis cv. Shuchazao (SCZ) with a high cold-tolerance and var. assamica cv. Yinghong9 (YH9) with low cold-tolerance. To better understand the response mechanism of tea plants under cold stress for improving breeding, we compared physiological and biochemical responses, and associated genes expression in response to 7-day and 14-day cold acclimation, followed by 7-day de-acclimation in these two tea cultivars. We found that the low EL50, low Fv/Fm, and high sucrose and raffinose accumulation are responsible for higher cold tolerance in SCZ comparing with YH9. We then measured the expression of 14 key homologous genes, known as involved in these responses in other plants, for each stages of treatment in both cultivars using RT-qPCR. Our results suggested that the increased expression of CsCBF1 and CsDHNs coupling with the accumulation of sucrose play key roles in conferring higher cold resistance in SCZ. Our findings have revealed key genes regulation responsible for cold resistance, which help to understand the cold-resistant mechanisms and guide breeding in tea plants.

The process of cryopreservation results in over-production of reactive oxygen species, which is extremely detrimental to spermatozoa. The aim of this study was to investigate whether addition of cysteine to freezing extender would facilitate the cryosurvival of rabbit spermatozoa, and if so, how cysteine protects spermatozoa from cryodamages. Freshly ejaculated semen was diluted with Tris-citrate-glucose extender supplemented with different concentrations of cysteine. The motility, intact acrosomes, membrane integrity, mitochondrial potentials, 8-hydroxyguanosine level and sperm-zona pellucida binding capacity were examined. Furthermore, glutathione peroxidase (GPx) activity, glutathione content (GSH), and level of reactive oxygen species (ROS) and hydrogen peroxide of spermatozoa were analyzed. The values of motility, intact acrosomes, membrane integrity, mitochondrial potentials and sperm-zona pellucida binding capacity of the frozen-thawed spermatozoa in the treatment of cysteine were significantly higher than those of the control. Addition of cysteine to extenders improved the GPx activity and GSH content of spermatozoa, while lowered the ROS, DNA oxidative alterations and lipid peroxidation level, which makes spermatozoa avoid ROS to attack DNA, the plasma membrane and mitochondria. In conclusion, cysteine protects spermatozoa against ROS-induced damages during cryopreservation and post-thaw incubation. Addition of cysteine is recommended to facilitate the improvement of semen preservation for the rabbit breeding industry.

Picea Schrenkiana as one of the most important zonal vegetation was an endemic species in Middle Asia. Natural regeneration of P. Schrenkiana is a long existing problem troubling scientists. The autotoxicity of 3,4-dihydroxy-acetophenone (DHAP) was found to be a causative factor causing the failure of P. Schrenkiana natural regeneration. The effects of concentrations of DHAP treatment on the viability of root cell, activities of antioxidant enzymes and levels of P. Schrenkiana phytohormones were performed to disclose the physiological mechanism of DHAP autotoxicity. It was observed that high concentration of DHAP could inhibit the seed germination and seedling growth, but had a hormesis at low concentrations. Analyses showed that the root cells significantly lost their viability treated with high DHAP. The enzymes activities of seedlings were significantly stimulated by the treatment of 0.5 mM DHAP to give a transient increase and then decrease as DHAP concentration increased to 1.0 mM except for GR (glutathione reductase) in which DHAP treatment had little effect on its activity. Comparing with the control, an increase in the levels of phytohormones ZT (zeatin), GA3 (gibberellic acid) and IAA (indole acetic acid) was induced by the treatment of DHAP at low concentrations (0.1-0.25 mM), but the significant deficiency was found treated by high concentrations (0.5-1.0 mM). In addition, the ABA (abscisic acid) level increased in all experimental observations. These results suggested that DHAP significantly affected indices of growth and physiology, and provided some new information about different effect in P. Schrenkiana treated with DHAP.

Agropyron cristatum (L.) Gaertn. (2n = 4x = 28, PPPP), a wild relative of common wheat, possesses many potentially valuable genes for wheat breeding. To transfer these genes into wheat, a series of wheat-A. cristatum derivatives have been obtained in our laboratory. In this study, a wheat-A. cristatum derivative II-3-1 was obtained, which was proven to contain a 1P (1A) disomic substitution and 2P disomic addition line with 40 wheat chromosomes and two pairs of A. cristatum chromosomes by genomic in situ hybridization (GISH) and molecular markers analysis. By further backcrossing with the wheat parent Fukuhokomugi (Fukuho) and self-fertilization, three different lines were separated from II-3-1, including wheat-A. cristatum 1P disomic addition line II-3-1a, 2P disomic addition line II-3-1b and 1P (1A) disomic substitution line II-3-1c. Because 2P addition line had been reported before, we aimed to investigate 1P disomic addition line II-3-1a and wheat-A. cristatum 1P (1A) disomic substitution line II-3-1c. Analysis of different genetic populations demonstrated that 1P chromosome harbored multiple agronomic traits, such as elevated spike length, increased tillering ability, reduced plant height and spikelet density. Besides, bristles on the glume ridges as an important morphological marker was located on 1P chromosome. Therefore, the novel 1P addition and substitution lines will be used as important genetic materials to widen the genetic resources of wheat.

The paired box 6 (Pax6) gene encodes a transcription factor essential for eye development in a wide range of animal lineages. Here we describe the cloning and characterization of Pax6 gene from the blind hydrothermal vent tubeworm Ridgeia piscesae (RpPax6). The deduced RpPax6 protein shares extensive sequence identity with Pax6 proteins from other species and contains both the paired domain and a complete homeodomain. Phylogenetic analysis indicates that it clusters with the corresponding sequence from the closely related species Platynereis dumerilii (P. dumerilii) of Annelida. Luciferase reporter assay indicate that RpPax6 protein suppresses the transcription of sine oculis (so) in D. melanogaster, interfering with the C-terminal of RpPax6. Taking advantage of Drosophila model, we show that RpPax6 expression is not able to rescue small eye phenotype of ey2 mutant, only to cause a more severe headless phenotype. In addition, RpPax6 expression induced apoptosis and inhibition of apoptosis can partially rescue RpPax6-induced headless phenotype. We provide evidence RpPax6 plays at least two roles: it blocks the expression of later-acting transcription factors in the eye development cascade, and it promotes cell apoptosis. Our results indicate alternation of the Pax6 function may be one of the possible causes that lead the eye absence in vestimentiferan tubeworms., Competing Interests: The authors have declared that no competing interests exist.

ATP binding cassette (ABC) transporters utilize the energy of ATP hydrolysis to uni-directionally transport substrates across cell membrane. ATP hydrolysis occurs at the nucleotide-binding domain (NBD) dimer interface of ABC transporters, whereas substrate translocation takes place at the translocation pathway between the transmembrane domains (TMDs), which is more than 30 angstroms away from the NBD dimer interface. This raises the question of how the hydrolysis energy released at NBDs is "transmitted" to trigger the conformational changes at TMDs. Using molecular dynamics (MD) simulations, we studied the post-hydrolysis state of the vitamin B12 importer BtuCD. Totally 3-μs MD trajectories demonstrate a predominantly asymmetric arrangement of the NBD dimer interface, with the ADP-bound site disrupted and the ATP-bound site preserved in most of the trajectories. TMDs response to ATP hydrolysis by separation of the L-loops and opening of the cytoplasmic gate II, indicating that hydrolysis of one ATP could facilitate substrate translocation by opening the cytoplasmic end of translocation pathway. It was also found that motions of the L-loops and the cytoplasmic gate II are coupled with each other through a contiguous interaction network involving a conserved Asn83 on the extended stretch preceding TM3 helix plus the cytoplasmic end of TM2/6/7 helix bundle. These findings entail a TMD-NBD communication mechanism for type II ABC importers., Competing Interests: The authors have declared that no competing interests exist.

Creation of wheat-alien disomic addition lines and localization of desirable genes on alien chromosomes are important for utilization of these genes in genetic improvement of common wheat. In this study, wheat-Agropyron cristatum derivative line 5113 was characterized by genomic in situ hybridization (GISH) and specific-locus amplified fragment sequencing (SLAF-seq), and was demonstrated to be a novel wheat-A. cristatum disomic 6P addition line. Compared with its parent Fukuhokomugi (Fukuho), 5113 displayed multiple elite agronomic traits, including higher uppermost internode/plant height ratio, larger flag leaf, longer spike length, elevated grain number per spike and spikelet number per spike, more kernel number in the middle spikelet, more fertile tiller number per plant, and enhanced resistance to powdery mildew and leaf rust. Genes conferring these elite traits were localized on the A. cristatum 6P chromosome by using SLAF-seq markers and biparental populations (F1, BC1F1 and BC1F2 populations) produced from the crosses between Fukuho and 5113. Taken together, chromosomal localization of these desirable genes will facilitate transferring of high-yield and high-resistance genes from A. cristatum into common wheat, and serve as the foundation for the utilization of 5113 in wheat breeding., Competing Interests: The authors have declared that no competing interests exist.

Ocular albinism type 1 (OA), caused by mutations in the OA1 gene, encodes a G-protein coupled receptor, OA1, localized in melanosomal membranes of the retinal pigment epithelium (RPE). This disorder is characterized by both RPE macro-melanosomes and abnormal decussation of ganglion cell axons at the brain's optic chiasm. We demonstrated previously that Oa1 specifically activates Gαi3, which also signals in the Oa1 transduction pathway that regulates melanosomal biogenesis. In this study, we screened the human Gαi3 gene, GNAI3, in DNA samples from 26 patients who had all clinical characteristics of OA but in whom a specific mutation in the OA1 gene had not been found, and in 6 normal control individuals. Using the Agilent HaloPlex Target Enrichment System and next-generation sequencing (NGS) on the Illumina MiSeq platform, we identified 518 variants after rigorous filtering. Many of these variants were corroborated by Sanger sequencing. Overall, 98.8% coverage of the GNAI3 gene was obtained by the HaloPlex amplicons. Of all variants, 6 non-synonymous and 3 synonymous were in exons, 41 in a non-coding exon embedded in the 3' untranslated region (UTR), 6 in the 5' UTR, and 462 in introns. These variants included novel SNVs, insertions, deletions, and a frameshift mutation. All were found in at least one patient but none in control samples. Using computational methods, we modeled the GNAI3 protein and its non-synonymous exonic mutations and determined that several of these may be the cause of disease in the patients studied. Thus, we have identified GNAI3 as a second gene possibly responsible for X-linked ocular albinism., Competing Interests: The authors have declared that no competing interests exist.

Wheat-Agropyron cristatum 7P disomic addition line Ⅱ-5-1, derived from the distant hybridization between A. cristatum (2n = 4x = 28, PPPP) and the common wheat cv. Fukuhokomugi (Fukuho), displays numerous desirable agronomic traits, including enhanced thousand-grain weight, smaller flag leaf, and enhanced tolerance to drought. In order to transfer these traits into common wheat, Ⅱ-5-1 was induced by 60Co-γ ray, leading to the creation of 18 translocation lines and three deletion lines. Genomic in situ hybridization (GISH) and fluorescence in situ hybridization (FISH) indicated that multiple wheat chromosomes were involved in the translocation events, including chromosome 2A, 3A, 5A, 7A, 3B, 5B, 7B, 3D and 7D. A. cristatum 7P chromosome was divided into 15 chromosomal bins with fifty-five sequence-tagged site (STS) markers specific to A. cristatum 7P chromosome. Seven and eight chromosomal bins were located on 7PS and 7PL, respectively. The above-mentioned translocation and deletion lines each contained different, yet overlapping 7P chromosomal fragments, covering the entire A. cristatum 7P chromosome. Three translocation lines (7PT-13, 7PT-14 and 7PT-17) and three deletion lines (del-1, del-2 and del-3), which contained the common chromosomal bins 7PS1-3, displayed higher thousand-grain weigh than Fukuho, suggesting that potential genes conferring high thousand-grain weigh might be located on these chromosomal bins. Therefore, wheat-A. cristatum 7P translocation lines with elite traits will be useful as novel germplasms for wheat genetic improvement.

Doxorubicin (DOX) is one of the most commonly used anticancer drugs in the treatment of hepatoma. However, acquired drug resistance is one of the major challenges for the chemotherapy. In this study, a down-regulation of miR-122 was observed in doxorubicin-resistant Huh7 (Huh7/R) cells compared with its parental Huh7 cells, suggesting miR-122 is associated with the chemoresistance. Meanwhile, luciferase reporter assay proved that the PKM2 is the target of miR-122, and we reported that the glucose metabolism is significantly up-regulated in Huh7/R cells. Importantly, overexpression of miR-122 in Huh7/R cells reversed the doxorubicin-resistance through the inhibition of PKM2, inducing the apoptosis in doxorubicin-resistant cancer cells. Thus, this study revealed that the dysregulated glucose metabolism contributes to doxorubicin resistance, and the inhibition of glycolysis induced by miR-122 might be a promising therapeutic strategy to overcome doxorubicin resistance in hepatocellular carcinoma.

Purpose: To assess the repeatability of Equivalent Keratometry Readings (EKRs) obtained by the Pentacam HR (high resolution) in untreated and post-LASIK eyes, and to compare them with the keratometry (K) values obtained by other algorithms., Methods: In this prospective study, 100 untreated eyes and 71 post-LASIK eyes were included. In the untreated group, each eye received 3 consecutive scans using the Pentacam HR, and EKR values in all central corneal zone, the true net power (Knet) and the simulated K (SimK) were obtained for each scan. In the post-LASIK group, each eye received subjective refraction and 3 consecutive scans with the Pentacam HR preoperatively. During the 3-month post-surgery exam, the same examinations and the use of an IOLMaster were conducted for each eye. The EKRs in all zone, the Knet, the mean K (Km) by IOLMaster and the K values by clinical history method (KCHM) were obtained. The repeatability of the EKRs was assessed by the within-subject standard deviation (Sw), 2.77Sw, coefficient of variation (CVw) and intraclass correlation coefficient (ICC). The bonferroni corrected multiple comparisons were performed to analyze the differences among the EKRs and K values calculated by other algorithms within the 2 groups. The 95% limits of agreement (LoA) were calculated., Results: The EKR values in all central corneal zone were repeatable in both the untreated group (Sw≦0.19 D, 2.77Sw≦0.52 D, CVw≦1%, ICC≧0.978) and the post-LASIK group (Sw≦0.22 D, 2.77Sw≦0.62 D, CVw≦1%, ICC≧0.980). In the untreated group, the EKR in 4mm zone was close to SimK (P = 1.000), and the 95% LoA was (-0.13 to 0.15 D). The difference between Knet and SimK was -1.30±0.13 D (95% LoA -1.55 to -1.55 D, P<0.001). In the post-LASIK group, all the EKRs were significantly higher than KCHM (all P<0.001). The differences between the EKR in 4mm zone and KCHM, the EKR in 7mm zone and KCHM, Knet and KCHM, Km and KCHM, SimK and Knet were 0.64±0.50 D (95% LoA, -0.33 to 1.62 D), 1.77±0.88 D (95% LoA, 0.04 to 3.51 D), -0.98±0.48 D (95% LoA, -1.92 to -0.04 D), 0.64±0.53 D (95% LoA, -0.40 to 1.68 D), and 1.73±0.20 D (95% LoA, 1.33 to 2.13 D), respectively., Conclusions: The EKRs obtained by the Pentacam HR were repeatable in both untreated eyes and post-LASIK eyes. Compared to the total corneal power obtained by the clinical history method, the EKR values generally overestimated the total corneal power in post-LASIK eyes. So, further calibrations for the EKR values should be conducted, before they were used for the total corneal power assessment in post-LASIK eyes.

Background: There are few data on the prevalence of obesity and its influence on achieving blood glucose, blood pressure, and blood lipid (3B) goals in Chinese type 2 diabetes outpatients., Methods: Patient demographic data, anthropometric measurements, medications, and blood glucose and lipid profiles of 24,512 type 2 diabetes patients from a large, geographically diverse study (CCMR-3B) were analyzed. Using cut-points for body mass index (BMI) and waist circumference (WC) recommended by the Working Group on Obesity in China, overweight and obesity were defined as BMIs of 24-27.9 kg/m2 and ≥28.0 kg/m2. Central obesity was defined as a waist circumference ≥80 cm in women and ≥85 cm in men. The 3B therapeutic goals were HbA1c<7.0%, BP<140/90 mmHg and LDL-C<2.6 mmol/L., Results: Overall, 43.0% of type 2 diabetes patients were overweight and 16.7% were obese; 13.3% of overweight and and 10.1% of obese patients achieved all the 3B target goals. Overweight or obese patients were less likely to achieve 3B goals than those with normal BMIs. More than a half the overweight or obese patients (69.6%) were centrally obese. Patients with abdominal obesity were less likely to achieve cardiometabolic targets than those without abdominal obesity. In multivariate logistic regression analysis, female, higher BMI and waist circumference, smoking, drinking, sedentary lifestyle, and longer diabetes duration were significantly correlated with failure to achieve 3B control goals., Conclusions: Obesity is highly prevalent and associated with poor 3B control in Chinese type 2 diabetes patients. In clinical practice, more attention and resources should focus on weight loss for such patients.

Objective: This study used con-beam computed tomography (CBCT) to investigate the prevalence and severity of alveolar bone loss in middle-aged (40-59 years) Chinese with chronic periodontitis., Materials and Methods: The study group comprised 145 dentate individuals aged 40 to 59 years residing in China who suffered from chronic periodontitis. CBCT and the application of NNT software were used to examine the level and location of alveolar bone loss., Results: The study revealed that 40-59 year old patients with chronic periodontitis had severe bone loss. At 5,286 sites (34.7%), alveolar bone loss was mild; severe alveolar bone loss was found at 5,978 sites (39.2%). A comparison of bone loss in different jaws revealed that the area with the highest degree of bone loss was on the lingual side of the maxillary molar (56.3 ± 7.2%), and that the area with the lowest degree was primarily on the lingual side of the mandibular canine (27.5 ± 6.3%). There was a lower degree of alveolar bone loss in males than females. Differences were observed when comparing the incidence of bone loss between males and females (P < 0.05). Menopause in females and smoking in both genders may affect the level of bone loss. Male smokers experienced a greater degree of bone loss (41.67 ± 5.76%) than male non-smokers (32.95 ± 4.31%). A 42.23 ± 6.34% bone loss was found in menopausal females versus 31.35 ± 3.62% in non-menopausal females., Conclusions: The study revealed that different sites and teeth exhibited a diverse degree of bone loss. In middle-aged patients with chronic periodontitis, the highest degrees of bone loss in the incisors, premolars, and molars were on the lingual side, mesial side and lingual side, respectively. Menopause in females and smoking may affect the level of bone loss.

Apoptosis is a known regulator of morphogenetic events. In mammals, the critical role of oxidative stress-induced apoptosis has been well-studied; however, in insects the role of oxidative stress in apoptosis is not clear. In a previous study, we showed that apoptosis-related genes are present in the silkworm Bombyx mori, an important lepidopteran insect model. In this study, we evaluated the effect of H2O2-induced oxidative stress on apoptosis, reactive oxygen species (ROS) levels, mitochondrial response, cytochrome c release and apoptosis-related gene expression in the BmN-SWU1 cell line from B. mori ovaries. Our results showed that BmN-SWU1 cells exposed to H2O2 showed cell protuberances, cytoplasmic condensation, apoptotic bodies, DNA ladder formation and caspase activities indicating apoptosis. H2O2-induced apoptosis also increased intracellular ROS level, changed mitochondrial distribution, reduced mitochondrial membrane potential and increased the release of cytochrome c from mitochondria. Furthermore, western blot analysis revealed a significant increase in p53 and cytochrome c expression, and a decrease in Bcl-2 expression compared to the controls. Moreover, quantitative real-time PCR (qRT-PCR) showed an increase in the transcript levels of BmICE, Bmapaf-1 and BmEndoG by 439.5%, 423.9% and 42.2%, respectively, after treatment with 1 μM H2O2 for 24 h. However, the transcript levels of Bmbuffy declined by 41.4% after 24 h of exposure to 1 μM H2O2. These results show that H2O2 treatment induced apoptosis in BmN-SWU1 cells via the mitochondrial apoptotic pathway. Further, it appears that oxidative stress induced by H2O2 activates both caspase-dependent and caspase-independent mitochondrial apoptotic pathways in silkworm cells. Taken together, these findings improve our knowledge of apoptosis in silkworm and the apoptotic pathways in insects.

Rice blast caused by Magnaporthe oryzae is the most devastating disease of rice and poses a serious threat to world food security. In this study, the distribution and effectiveness of 18 R genes in 277 accessions were investigated based on pathogenicity assays and molecular markers. The results showed that most of the accessions exhibited some degree of resistance (resistance frequency, RF >50%). Accordingly, most of the accessions were observed to harbor two or more R genes, and the number of R genes harbored in accessions was significantly positively correlated with RF. Some R genes were demonstrated to be specifically distributed in the genomes of rice sub-species, such as Pigm, Pi9, Pi5 and Pi1, which were only detected in indica-type accessions, and Pik and Piz, which were just harbored in japonica-type accessions. By analyzing the relationship between R genes and RF using a multiple stepwise regression model, the R genes Pid3, Pi5, Pi9, Pi54, Pigm and Pit were found to show the main effects against M. oryzae in indica-type accessions, while Pita, Pb1, Pik, Pizt and Pia were indicated to exhibit the main effects against M. oryzae in japonica-type accessions. Principal component analysis (PCA) and cluster analysis revealed that combination patterns of major R genes were the main factors determining the resistance of rice varieties to M. oryzae, such as 'Pi9+Pi54', 'Pid3+Pigm', 'Pi5+Pid3+Pigm', 'Pi5+Pi54+Pid3+Pigm', 'Pi5+Pid3' and 'Pi5+Pit+Pid3' in indica-type accessions and 'Pik+Pib', 'Pik+Pita', 'Pik+Pb1', 'Pizt+Pia' and 'Pizt+Pita' in japonica-type accessions, which were able to confer effective resistance against M. oryzae. The above results provide good theoretical support for the rational utilization of combinations of major R genes in developing rice cultivars with broad-spectrum resistance.