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Objective: to investigate the association between cartilage lesion-related features observed in knee osteoarthritis (OA) patients' first MRI examination and incident knee surgery within 5 years. Additionally, to assess the predictive value of these features for the incident knee surgery. Methods: We identified patients diagnosed with knee OA and treated at our institution between January 2015 and January 2018, and retrieved their baseline clinical data and first MRI examination films from the information system. Next, we proceeded to determine joint space narrowing grade, cartilage lesion size grade, cartilage full-thickness loss grade and cartilage lesion sum score for the medial and lateral compartments, respectively. Generalized linear regression models examined the association of these features with 5-year incident knee surgery. Positive and negative predictive values (PPVs and NPVs) were determined referring to 5-year incident knee surgery. Results: Totally, 878 participants (knees) were found eligible to form the study population. Within the 5 years, surgery was performed on 61 knees. None of the cartilage-related features had been found significantly associated with incident surgery. The results were similar for medial and lateral compartments. The PPVs were low for all the features. Conclusions: Among symptomatic clinically diagnosed OA knees, cartilage lesions observed in the first MRI examinations were not found to be associated with the occurrence of joint surgery within a 5-year period. All these cartilage-related features appear to have no additional value in predicting 5-year incident joint surgery. [ABSTRACT FROM AUTHOR]

Background: The purpose of this study was to design a customized fixation plate for mandibular angle fracture using topological optimization based on the biomechanical properties of the two conventional fixation systems, and compare the results of stress, strain and displacement distributions calculated by finite element analysis (FEA).Methods: A three-dimensional (3D) virtual mandible was reconstructed from CT images with a mimic angle fracture and a 1 mm gap between two bone segments, and then a FEA model, including volume mesh with inhomogeneous bone material properties, three loading conditions and constraints (muscles and condyles), was created to design a customized plate using topological optimization method, then the shape of the plate was referenced from the stress concentrated area on an initial part created from thickened bone surface for optimal calculation, and then the plate was formulated as "V" pattern according to dimensions of standard mini-plate finally. To compare the biomechanical behavior of the "V" plate and other conventional mini-plates for angle fracture fixation, two conventional fixation systems were used: type A, one standard mini-plate, and type B, two standard mini-plates, and the stress, strain and displacement distributions within the three fixation systems were compared and discussed.Results: The stress, strain and displacement distributions to the angle fractured mandible with three different fixation modalities were collected, respectively, and the maximum stress for each model emerged at the mandibular ramus or screw holes. Under the same loading conditions, the maximum stress on the customized fixation system decreased 74.3, 75.6 and 70.6% compared to type A, and 34.9, 34.1, and 39.6% compared to type B. All maximum von Mises stresses of mandible were well below the allowable stress of human bone, as well as maximum principal strain. And the displacement diagram of bony segments indicated the effect of treatment with different fixation systems.Conclusions: The customized fixation system with topological optimized structure has good biomechanical behavior for mandibular angle fracture because the stress, strain and displacement within the plate could be reduced significantly comparing to conventional "one mini-plate" or "two mini-plates" systems. The design methodology for customized fixation system could be used for other fractures in mandible or other bones to acquire better mechanical behavior of the system and improve stable environment for bone healing. And together with SLM, the customized plate with optimal structure could be designed and fabricated rapidly to satisfy the urgent time requirements for treatment. [ABSTRACT FROM AUTHOR]

Background: Sugarcane smut caused by Sporisorium scitamineum is one of the most severe fungal diseases in the sugarcane industry. Using a molecular biological technique to mine sugarcane resistance genes can provide gene resources for further genetic engineering of sugarcane disease-resistant breeding. Jasmonate ZIM (zinc-finger inflorescence meristem) domain (JAZ) proteins, which involved in the responses to plant pathogens and abiotic stresses, are important signaling molecules of the jasmonic acid (JA) pathway. Results: Seven differentially expressed sugarcane JAZ genes, ScJAZ1-ScJAZ7, were mined from the transcriptome of sugarcane after inoculation with S. scitamineum. Bioinformatic analyses revealed that these seven ScJAZ genes encoded basic proteins that contain the TIFY and CCT_2 domains. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis demonstrated that the ScJAZ1-ScJAZ7 genes were tissue specific and differentially expressed under adverse stress. During S. scitamineum infection, the transcripts of ScJAZ4 and ScJAZ5 were both upregulated in the susceptible genotype ROC22 and the resistant genotype Yacheng05-179; ScJAZ1, ScJAZ2, ScJAZ3, and ScJAZ7 were downregulated in Yacheng05-179 and upregulated in ROC22; and the expression of ScJAZ6 did not change in ROC22, but was upregulated in Yacheng05-179. The transcripts of the seven ScJAZ genes were increased by the stimuli of salicylic acid and abscisic acid, particularly methyl jasmonate. The expression of the genes ScJAZ1-ScJAZ7 was immediately upregulated by the stressors hydrogen peroxide, sodium chloride, and copper chloride, whereas slightly induced after treatment with calcium chloride and polyethylene glycol. In addition, the expression of ScJAZ6, as well as seven tobacco immunity-associated marker genes were upregulated, and antimicrobial activity against Pseudomonas solanacearum and Fusarium solani var. coeruleum was observed during the transient overexpression of ScJAZ6 in Nicotiana benthamiana, suggesting that the ScJAZ6 gene is associated with plant immunity. Conclusions: The different expression profiles of the ScJAZ1-ScJAZ7 genes during S. scitamineum infection, the positive response of ScJAZ1-ScJAZ7 to hormones and abiotic treatments, and the function analysis of the ScJAZ6 gene revealed their involvement in the defense against biotic and abiotic stresses. The findings of the present study facilitate further research on the ScJAZ gene family especially their regulatory mechanism in sugarcane. [ABSTRACT FROM AUTHOR]

Background: It is important to quantify the dose response for a drug in phase 2a clinical trials so the optimal doses can then be selected for subsequent late phase trials. In a phase 2a clinical trial of new lead drug being developed for the treatment of rheumatoid arthritis (RA), a U-shaped dose response curve was observed. In the light of this result further research was undertaken to design an efficient phase 2a proof of concept (PoC) trial for a follow-on compound using the lessons learnt from the lead compound.Methods: The planned analysis for the Phase 2a trial for GSK123456 was a Bayesian Emax model which assumes the dose-response relationship follows a monotonic sigmoid "S" shaped curve. This model was found to be suboptimal to model the U-shaped dose response observed in the data from this trial and alternatives approaches were needed to be considered for the next compound for which a Normal dynamic linear model (NDLM) is proposed. This paper compares the statistical properties of the Bayesian Emax model and NDLM model and both models are evaluated using simulation in the context of adaptive Phase 2a PoC design under a variety of assumed dose response curves: linear, Emax model, U-shaped model, and flat response.Results: It is shown that the NDLM method is flexible and can handle a wide variety of dose-responses, including monotonic and non-monotonic relationships. In comparison to the NDLM model the Emax model excelled with higher probability of selecting ED90 and smaller average sample size, when the true dose response followed Emax like curve. In addition, the type I error, probability of incorrectly concluding a drug may work when it does not, is inflated with the Bayesian NDLM model in all scenarios which would represent a development risk to pharmaceutical company. The bias, which is the difference between the estimated effect from the Emax and NDLM models and the simulated value, is comparable if the true dose response follows a placebo like curve, an Emax like curve, or log linear shape curve under fixed dose allocation, no adaptive allocation, half adaptive and adaptive scenarios. The bias though is significantly increased for the Emax model if the true dose response follows a U-shaped curve.Conclusions: In most cases the Bayesian Emax model works effectively and efficiently, with low bias and good probability of success in case of monotonic dose response. However, if there is a belief that the dose response could be non-monotonic then the NDLM is the superior model to assess the dose response. [ABSTRACT FROM AUTHOR]

Background: Video-assisted thoracoscopic surgery (VATS) has been used for many thoracic diseases as an alternate approach to thoracotomy. The aim of this study was to compare the surgical outcome of pneumonectomy using VATS with that using thoracotomy pneumonectomy in pigs. Fourteen pigs were equally divided into two groups; one group underwent VATS and the other group underwent transthoracic pneumonectomy. We monitored pre-, intra-, and post-operative physiologic parameters, along with blood cell count, serum C-reactive protein (CRP), serum amyloid A (SAA), interleukin-6 (IL-6) and cortisol. The differences between the two approaches were analyzed. Results: Mean surgical time in the VATS group (160.6 ± 16.2 min) was significantly longer than that in the thoracotomy group (123.7 ± 13.2 min). In both groups, CRP and IL-6 concentrations were significantly increased at postoperative 4 h, and then gradually decreased to preoperative levels. CRP and IL-6 at postoperative day 1 were significant lower in the VATS group compared with the thoracotomy group. SAA was significantly increased at postoperative days 1 and 3 in both groups compared with preoperative levels. Cortisol was significantly increased immediately after surgery in both groups compared with preoperative levels, and was significantly higher in the thoracotomy group than the VATS group at postoperative 4 h and 1 day. Conclusions: There was no difference between the two groups in physiologic parameters and blood cell count. However, the results indicate that VATS resulted in a smaller incision, less acute-phase reaction, less stress and less pain compared with thoracotomy pneumonectomy. [ABSTRACT FROM AUTHOR]

Background: Tianma-Gouteng-Yin (TGY), which is common Chinese medicine formulation consisting of 11 different herbs and being used in China for the treatment of Parkinson's disease, inflammatory conditions and cardiovascular diseases, was selected for full component analysis. The aim of this study was to quantitatively analyze the chemical profiles of ten commercial TGY samples and one sample produced in our laboratory. Methods: Ultra-high performance liquid chromatography (UHPLC) coupled with quadrupole-tandem time-of-light mass spectrometry (Q-TOF-MS) was used to analyze the non-saccharide small molecule components of the different TGY samples. The established method was validated in terms of its linearity, sensitivity, precision, accuracy and stability. High performance liquid chromatography coupled with evaporative light scattering detection (HPLC-ELSD) was also used to quantify three major saccharides (fructose, glucose and sucrose). Results: The relative standard deviations for the precision, repeatability and stability of these compounds were less than 5 %, while the accuracy of the method was 95-105 %. Twenty-eight of the compounds found in TGY were successfully identified, with 20 being quantified. The macromolecules present in these samples were also identified using an ethanol precipitation method, representing 294.68-696.64 mg/g of the total material depending on the batch. Notably, the components identified using this method represented up to 78 % of the total weight of the TGY samples. Conclusions: The developed UHPLC/Q-TOF-MS and HPLC-ELSD methods successfully identified 28 of the complex compounds found in TGY. [ABSTRACT FROM AUTHOR]

Background: HOT (high-occupancy target) regions, which are bound by a surprisingly large number of transcription factors, are considered to be among the most intriguing findings of recent years. An improved understanding of the roles that HOT regions play in biology would be afforded by knowing the constellation of factors that constitute these domains and by identifying HOT regions across the spectrum of human cell types. Results: We characterised and validated HOT regions in embryonic stem cells (ESCs) and produced a catalogue of HOT regions in a broad range of human cell types. We found that HOT regions are associated with genes that control and define the developmental processes of the respective cell and tissue types. We also showed evidence of the developmental persistence of HOT regions at primitive enhancers and demonstrate unique signatures of HOT regions that distinguish them from typical enhancers and super-enhancers. Finally, we performed a dynamic analysis to reveal the dynamical regulation of HOT regions upon H1 differentiation. Conclusions: Taken together, our results provide a resource for the functional exploration of HOT regions and extend our understanding of the key roles of HOT regions in development and differentiation. [ABSTRACT FROM AUTHOR]

Objective: Stereotactic body radiotherapy (SBRT) has been shown to improve overall survival in patients with advanced hepatocellular carcinoma. This study aimed to assess the cost-effectiveness of SBRT compared to sorafenib which is the only drug for advanced hepatocellular carcinoma.Methods: A Markov decision-analytic model was performed to compare the cost-effectiveness of SBRT and sorafenib for unresectable advanced hepatocellular carcinoma. Patients transitioned between three health states: stable disease, progression disease and death. We calculated the data on cost from the perspective of our National Health Insurance Bureau. Sensitivity analyses were conducted to determine the impact of several variables.Results: The incremental cost effectiveness ratio (ICER) for sorafenib compared to SBRT was NT$3,788,238 per quality-adjusted life year gained (cost/QALY), which was higher than the willingness to pay threshold of Taiwan according to WHO's guideline. One-way sensitivity analysis revealed that the utility of progression disease for the sorafenib treatment, utility of progression free survival for SBRT, utility of progression free survival for sorafenib, utility of PFS to progression disease for SBRT and transition probability of progression disease to dead for SBRT were the most sensitive parameters in all cost scenarios. The Monte-Carlo simulation demonstrated that the probability of cost-effectiveness at a willingness to pay threshold of NT$ 2,213,145 per QALY was 100 % and 0 % chance for SBRT and sorafenib.Conclusion: This study indicated that SBRT for advanced hepatocellular carcinoma is cost-effective at a willingness to pay threshold as defined by WHO guideline in Taiwan. [ABSTRACT FROM AUTHOR]

Background: Predicting drug side effects is an important topic in the drug discovery. Although several machine learning methods have been proposed to predict side effects, there is still space for improvements. Firstly, the side effect prediction is a multi-label learning task, and we can adopt the multi-label learning techniques for it. Secondly, drug-related features are associated with side effects, and feature dimensions have specific biological meanings. Recognizing critical dimensions and reducing irrelevant dimensions may help to reveal the causes of side effects. Methods: In this paper, we propose a novel method 'feature selection-based multi-label k-nearest neighbor method' (FS-MLKNN), which can simultaneously determine critical feature dimensions and construct high-accuracy multi-label prediction models. Results: Computational experiments demonstrate that FS-MLKNN leads to good performances as well as explainable results. To achieve better performances, we further develop the ensemble learning model by integrating individual feature-based FS-MLKNN models. When compared with other state-of-the-art methods, the ensemble method produces better performances on benchmark datasets. Conclusions: In conclusion, FS-MLKNN and the ensemble method are promising tools for the side effect prediction. The source code and datasets are available in the Additional file 1. [ABSTRACT FROM AUTHOR]

Background: Endoscopic sphincterotomy (ES) is a therapeutic technique developed as an advanced application of endoscopic retrograde cholangiopancreatography (ERCP). An important adverse event associated with this procedure is hemorrhage, which may sometimes be uncontrollable. We sought to examine whether cap-assisted hemoclip application is effective in controlling ES-induced hemorrhage. Methods: In this prospective study, we investigated the outcomes in 10 patients who had uncontrolled ES-induced hemorrhage and were treated by cap-assisted application of hemoclip with a forward-viewing endoscope. Results: Nine of the 10 investigated patients were successfully treated using the cap-assisted hemoclip technique with forward-viewing endoscope, yielding a success rate of 90 %. The patient with hemorrhage non-responsive to hemoclipping required catheter embolization of the bleeding artery after its identification by digital subtraction angiography. One of the 10 patients developed mild pancreatitis after the procedure, but was successfully managed conservatively. Conclusions: Cap-assisted hemoclip application with a forward-viewing endoscope appears to be an effective therapeutic modality for achieving hemostasis in cases of ES-induced hemorrhage, without the occurrence of any severe adverse events; we believe that this method should be considered as an option in the management of ES-induced hemorrhage. [ABSTRACT FROM AUTHOR]

Background: Endoscopic sphincterotomy (ES) is a therapeutic technique developed as an advanced application of endoscopic retrograde cholangiopancreatography (ERCP). An important adverse event associated with this procedure is hemorrhage, which may sometimes be uncontrollable. We sought to examine whether cap-assisted hemoclip application is effective in controlling ES-induced hemorrhage.Methods: In this prospective study, we investigated the outcomes in 10 patients who had uncontrolled ES-induced hemorrhage and were treated by cap-assisted application of hemoclip with a forward-viewing endoscope.Results: Nine of the 10 investigated patients were successfully treated using the cap-assisted hemoclip technique with forward-viewing endoscope, yielding a success rate of 90 %. The patient with hemorrhage non-responsive to hemoclipping required catheter embolization of the bleeding artery after its identification by digital subtraction angiography. One of the 10 patients developed mild pancreatitis after the procedure, but was successfully managed conservatively.Conclusions: Cap-assisted hemoclip application with a forward-viewing endoscope appears to be an effective therapeutic modality for achieving hemostasis in cases of ES-induced hemorrhage, without the occurrence of any severe adverse events; we believe that this method should be considered as an option in the management of ES-induced hemorrhage. [ABSTRACT FROM AUTHOR]

Background: SUMOylation is an important post-translational modification of eukaryotic proteins that involves the reversible conjugation of a small ubiquitin-related modifier (SUMO) polypeptide to its specific protein substrates, thereby regulating numerous complex cellular processes. The PIAS (protein inhibitor of activated signal transducers and activators of transcription [STAT]) and SIZ (scaffold attachment factor A/B/acinus/PIAS [SAP] and MIZ) proteins are SUMO E3 ligases that modulate SUMO conjugation. The characteristic features and SUMOylation mechanisms of SIZ1 protein in monocotyledon are poorly understood. Here, we examined the functions of a homolog of Arabidopsis SIZ1, a functional SIZ/PIAS-type SUMO E3 ligase from Dendrobium. Results: In Dendrobium, the predicted DnSIZ1 protein has domains that are highly conserved among SIZ/PIAS-type proteins. DnSIZ1 is widely expressed in Dendrobium organs and has a up-regulated trend by treatment with cold, high temperature and wounding. The DnSIZ1 protein localizes to the nucleus and shows SUMO E3 ligase activity when expressed in an Escherichia coli reconstitution system. Moreover, ectopic expression of DnSIZ1 in the Arabidopsis siz1-2 mutant partially complements several phenotypes and results in enhanced levels of SUMO conjugates in plants exposed to heat shock conditions. We observed that DnSIZ1 acts as a negative regulator of flowering transition which may be via a vernalization-induced pathway. In addition, ABA-hypersensitivity of siz1-2 seed germination can be partially suppressed by DnSIZ1. Conclusions: Our results suggest that DnSIZ1 is a functional homolog of the Arabidopsis SIZ1 with SUMO E3 ligase activity and may play an important role in the regulation of Dendrobium stress responses, flowering and development. [ABSTRACT FROM AUTHOR]

Background: We performed a systematic review of the efficacy of various types of acupuncture in the treatment of asthma in children. Methods: We searched the MEDLINE, Embase, and Cochrane Library databases up to October 20, 2014. Randomized controlled trials (RCTs) of children and adolescents (<18 years of age) with asthma were included. Data extraction was applied, and methodologic quality was assessed. Results: A total of 32 articles were assessed for eligibility, and seven studies comprising 410 patients were included in the systematic review. Two RCTs showed significant improvement in peak expiratory flow (PEF) variability for acupuncture (traditional and laser) vs. control, with one showing significant improvement in asthma-specific anxiety level, but no significant differences in other lung function parameters or quality of life. Another RCT reported significant benefits of laser acupuncture on lung function parameters but did not describe or report statistical analyses. One crossover RCT showed significant improvements in response to both acupuncture and placebo acupuncture, with better improvements with acupuncture compared to placebo acupuncture (forced exhaled volume in 1 s [FEV1], PEF). Two additional crossover RCTs showed no significant differences between single sessions of laser acupuncture and placebo acupuncture on baseline, postacupuncture, and postinduced bronchoconstriction values (% predicted FEV1, maximum expiratory flow). A recent study showed a significant effect of acupuncture paired with acupressure on medication use and symptoms in preschool-age children. Methodologic and reporting variability remains an issue. However, the results suggest that acupuncture may have a beneficial effect on PEF or PEF variability in children with asthma. Conclusions: The efficacy of acupuncture on other outcome measures is unclear. Large-scale RCTs are needed to further assess the efficacy of acupuncture in the treatment of asthma in children. [ABSTRACT FROM AUTHOR]

Background: With respect to information management, most of the previous studies on the acceptance of healthcare information technologies were analyzed from "positive" perspectives. However, such acceptance is always influenced by both positive and negative factors and it is necessary to validate both in order to get a complete understanding. This study aims to explore physicians' acceptance of mobile electronic medical records based on the dual-factor model, which is comprised of inhibitors and enablers, to explain an individual's technology usage. Following an earlier healthcare study in the USA, the researchers conducted a similar survey for an Eastern country (Taiwan) to validate whether perceived threat to professional autonomy acts as a critical inhibitor. In addition, perceived mobility, which is regarded as a critical feature of mobile services, was also evaluated as a common antecedent variable in the model. Methods: Physicians from three branch hospitals of a medical group were invited to participate and complete questionnaires. Partial least squares, a structural equation modeling technique, was used to evaluate the proposed model for explanatory power and hypotheses testing. Results: 158 valid questionnaires were collected, yielding a response rate of 33.40%. As expected, the inhibitor of perceived threat has a significant impact on the physicians' perceptions of usefulness as well as their intention to use. The enablers of perceived ease of use and perceived usefulness were also significant. In addition, as expected, perceived mobility was confirmed to have a significant impact on perceived ease of use, perceived usefulness and perceived threat. Conclusions: It was confirmed that the dual-factor model is a comprehensive method for exploring the acceptance of healthcare information technologies, both in Western and Eastern countries. Furthermore, perceived mobility was proven to be an effective antecedent variable in the model. The researchers believe that the results of this study will contribute to the research on the acceptance of healthcare information technologies, particularly with regards to mobile electronic medical records, based on the dual-factor viewpoints of academia and practice. [ABSTRACT FROM AUTHOR]

Background Integrating hydrogen-producing bacteria with complementary capabilities, dark-fermentative bacteria (DFB) and photo-fermentative bacteria (PFB), is a promising way to completely recover bioenergy from waste biomass. However, the current coupled models always suffer from complicated pretreatment of the effluent from dark-fermentation or imbalance between dark and photo-fermentation, respectively. In this work, an integrated dark and photofermentative reactor (IDPFR) was developed to completely convert an organic substrate into bioenergy. Results In the IDPFR, Ethanoligenens harbinese B49 and Rhodopseudomonas faecalis RLD-53 were separated by a membrane into dark and photo chambers, while the acetate produced by E. harbinese B49 in the dark chamber could freely pass through the membrane into the photo chamber and serve as a carbon source for R. faecalis RLD-53. The hydrogen yield increased with increasing working volume of the photo chamber, and reached 3.38 mol H2/mol glucose at the dark-to-photo chamber ratio of 1:4. Hydrogen production by the IDPFR was also significantly affected by phosphate buffer concentration, glucose concentration, and ratio of dark-photo bacteria. The maximum hydrogen yield (4.96 mol H2/mol glucose) was obtained at a phosphate buffer concentration of 20 mmol/L, a glucose concentration of 8 g/L, and a ratio of dark to photo bacteria of 1:20. As the glucose and acetate were used up by E. harbinese B49 and R. faecalis RLD-53, ethanol produced by E. harbinese B49 was the sole end-product in the effluent from the IDPFR, and the ethanol concentration was 36.53 mmol/L with an ethanol yield of 0.82 mol ethanol/mol glucose. Conclusions The results indicated that the IDPFR not only circumvented complex pretreatments on the effluent in the two-stage process, but also overcame the imbalance of growth and metabolic rate between DFB and PFB in the co-culture process, and effectively enhanced cooperation between E. harbinense B49 and R. faecalis RLD-53. Moreover, simultaneous hydrogen and ethanol production were achieved by coupling E. harbinese B49 and R. faecalis RLD-53 in the IDPFR. According to stoichiometry, the hydrogen and ethanol production efficiencies were 82.67% and 82.19%, respectively. Therefore, IDPFR was an effective strategy for coupling DFB and PFB to fulfill efficient energy recovery from waste biomass. [ABSTRACT FROM AUTHOR]

Background Brassinosteriods (BRs) are a group of important phytohormones that have major effects on plant growth and development. To fully elucidate the function of BRs, a sensitive BR assay is required. However, most of the previously reported methods are tedious and time-consuming due to multiple pretreatment steps. Therefore, it is of great significance to develop a method to increase the throughput and detection sensitivity of BR analysis. Results We established a novel analytical method of BRs based on magnetic solid phase extraction (MSPE) combined with in situ derivatization (ISD). TiO2-coated magnetic hollow mesoporous silica spere(TiO2/MHMSS) was served as a double identity- a microextraction sorbent and "microreactor" for the capture and derivatization of BRs in sequence. BRs were first extracted onto TiO2/MHMSS through hydrophilic interaction. The BR-adsorbed TiO2/MHMSS was then employed as a "microreactor" for the derivatization of BRs with 4-(N,N-dimethyamino)phenylboronic acid (DMAPBA). The MSPE-ISD method was simple and fast, which could be accomplished within 10 min. Furthermore, the derivatives of BRs showed better MS response because they were incorporated with tertiary amino groups. Uniquely, endogenous BRs were detected in only 100 mg fresh weight plant tissue. Conclusion Our proposed MSPE-ISD method for the determination of endogenous BRs is rapid and sensitive. It can be applied to the analysis of endogenous BRs in 100 mg fresh plant tissue (Brassica napus L. (B. napus L)). The proposed strategy for plant sample preparation may be extended to develop analytical methods for determination of a wide range of analytes with poor MS response in other complex sample matrices. [ABSTRACT FROM AUTHOR]

Background: Drug side effects are one of main concerns in the drug discovery, which gains wide attentions. Investigating drug side effects is of great importance, and the computational prediction can help to guide wet experiments. As far as we known, a great number of computational methods have been proposed for the side effect predictions. The assumption that similar drugs may induce same side effects is usually employed for modeling, and how to calculate the drug-drug similarity is critical in the side effect predictions. Results: In this paper, we present a novel measure of drug-drug similarity named "linear neighborhood similarity", which is calculated in a drug feature space by exploring linear neighborhood relationship. Then, we transfer the similarity from the feature space into the side effect space, and predict drug side effects by propagating known side effect information through a similarity-based graph. Under a unified frame based on the linear neighborhood similarity, we propose method "LNSM" and its extension "LNSM-SMI" to predict side effects of new drugs, and propose the method "LNSM-MSE" to predict unobserved side effect of approved drugs. Conclusions: We evaluate the performances of LNSM and LNSM-SMI in predicting side effects of new drugs, and evaluate the performances of LNSM-MSE in predicting missing side effects of approved drugs. The results demonstrate that the linear neighborhood similarity can improve the performances of side effect prediction, and the linear neighborhood similarity-based methods can outperform existing side effect prediction methods. More importantly, the proposed methods can predict side effects of new drugs as well as unobserved side effects of approved drugs under a unified frame. [ABSTRACT FROM AUTHOR]

Background: Cancer immunotherapy offers a promising approach in cancer treatment. The adenosine A2A receptor (A2AR) could protect cancerous tissues from immune clearance via inhibiting T cells response. To date, the role of A2AR in head and neck squamous cell carcinoma (HNSCC) has not been investigated. Here, we sought to explore the expression and immunotherapeutic value of A2AR blockade in HNSCC. Methods: The expression of A2AR was evaluated by immunostaining in 43 normal mucosae, 48 dysplasia and 165 primary HNSCC tissues. The immunotherapeutic value of A2AR blockade was assessed in vivo in genetically defined immunocompetent HNSCC mouse model. Results: Immunostaining of HNSCC tissue samples revealed that increased expression of A2AR on tumor infiltrating immune cells correlated with advanced pathological grade, larger tumor size and positive lymph node status. Elevated A2AR expression was also detected in recurrent HNSCC and HNSCC tissues with induction chemotherapy. The expression of A2AR was found to be significantly correlated with HIF-1α, CD73, CD8 and Foxp3. Furthermore, the increased population of CD4+Foxp3+ regulatory T cells (Tregs), which partially expressed A2AR, was observed in an immunocompetent mouse model that spontaneously develops HNSCC. Pharmacological blockade of A2AR by SCH58261 delayed the tumor growth in the HNSCC mouse model. Meanwhile, A2AR blockade significantly reduced the population of CD4+ Foxp3+ Tregs and enhanced the anti-tumor response of CD8+ T cells. Conclusions: These results offer a preclinical proof for the administration of A2AR inhibitor on prophylactic experimental therapy of HNSCC and suggest that A2AR blockade can be a potential novel strategy for HNSCC immunotherapy. [ABSTRACT FROM AUTHOR]

Background: microRNAs (miRNAs) are endogenous small RNAs that play important regulatory functions in plant development. Genetic variations in miRNAs sequences or their target-binding sites (microRNA-target interaction sites) can alter miRNA targets in animal and human. Whether these single nucleotide polymorphisms (SNPs) in plant are functional have not yet been determined. Results: In this study, we constructed leaf, root, and stem-derived small libraries of cucumber (Cucumis sativus) line 9930 (cultivated China-group cucumber) and C. sativus var. hardwickii (wild India group cucumber). A total of 22 conserved miRNA families, nine less-conserved miRNA families, and 49 cucumber-specific miRNAs were identified in both line 9930 and hardwickii. We employed cucumber resequencing data to perform a genome-wide scan for SNPs in cucumber miRNA-target interaction sites, including miRNA mature sequences and miRNA-target binding sites. As a result, we identified a total of 19 SNPs in mature miRNA sequences and 113 SNPs in miRNA-target binding sites with the potential to affect miRNA-target interactions. Furthermore, we experimentally confirmed that these SNPs produced 14 9930-unique targets mRNAs and 15 hardwickii-unique targets mRNA for cucumber miRNAs. This is the first experimental validation of SNPs in miRNA-target interaction sites affecting miRNA-target binding in plants. Conclusions: Our results indicate that SNPs can alter miRNA function and produce unique miRNA targets in cultivated and wild cucumbers. Therefore, miRNA-related SNPs may have played important in events that led to the agronomic differences between domestic and wild cucumber. [ABSTRACT FROM AUTHOR]

Background: Drug-drug interactions (DDIs) are one of the major concerns in drug discovery. Accurate prediction of potential DDIs can help to reduce unexpected interactions in the entire lifecycle of drugs, and are important for the drug safety surveillance. Results: Since many DDIs are not detected or observed in clinical trials, this work is aimed to predict unobserved or undetected DDIs. In this paper, we collect a variety of drug data that may influence drug-drug interactions, i.e., drug substructure data, drug target data, drug enzyme data, drug transporter data, drug pathway data, drug indication data, drug side effect data, drug off side effect data and known drug-drug interactions. We adopt three representative methods: the neighbor recommender method, the random walk method and the matrix perturbation method to build prediction models based on different data. Thus, we evaluate the usefulness of different information sources for the DDI prediction. Further, we present flexible frames of integrating different models with suitable ensemble rules, including weighted average ensemble rule and classifier ensemble rule, and develop ensemble models to achieve better performances. Conclusions: The experiments demonstrate that different data sources provide diverse information, and the DDI network based on known DDIs is one of most important information for DDI prediction. The ensemble methods can produce better performances than individual methods, and outperform existing state-of-the-art methods. The datasets and source codes are available at https://github.com/zw9977129/drug-drug-interaction/. [ABSTRACT FROM AUTHOR]

Background: Human milk banks (HMBs) are essential facilities for the selection, collection, testing, transportation,storage, and distribution of DHM for special medical needs. The aim of this analysis was to analyze the operation status and data over the last 8 years of operation of the first human milk bank (HMB) in East China. Methods: Data related to the costs, donors, donation, pasteurization, and recipients were extracted from the web-based electronic monitoring system of the HMB for the period August 1, 2013 to July 31, 2021. Results: Over the 8 years of operation, 1,555 qualified donors donated 7,396.5L of qualified milk at a cost of ¥1.94 million($306,051), with the average cost per liter of donor human milk being ¥262.3($41.4). The donors were between 25 and 30 years of age, and the majority (80.1%) were primipara. All the donated milk was pasteurized and subjected to bacteriological tests before and after pasteurization: 95.4% passed the pre-pasteurization tests, and 96.3% passed the post-pasteurization tests. A total of 9,207 newborns received 5,775.2L of pasteurized donor milk. The main reason for the prescription of donor human milk was preterm birth. As a result of continuous quality improvements, January 2016 witnessed a significant increase in the volume of qualified DHM and the number of qualified donors. However, in 2020, as a result of the restrictions related to the COVID-19 pandemic, the volume of qualified DHM and the number of qualified donors decreased. Conclusions: Over its 8 years of operation, our HMB has made steady quality improvements in its screening and information processes. Continuous quality improvement is on ongoing need, along with recruiting more qualified donors and collecting donor human milk for vulnerable newborns. [ABSTRACT FROM AUTHOR]

Background: We have already discovered 23 patients during the work of the outpatient department and operations whose unstable signs on the posterolateral ankle. The anterior drawer test demonstrated normal during the physical examinations while the spaces of the posterior tibiotalar joints increased in stress X-ray plain films. ATFL intact and posterolateral ligaments lax were found during operations too. It is important to make existence claims and illuminate the mechanism of posterolateral ankle instability.Methods: A finite element model of the ankle was established for simulating to cut off posterolateral ligaments in turn. Ankle movements with tibia rotation under load on five forefoot positions were simulated as well.Results: The difference values with tibia external rotation were negative, and the positive results occurred with tibia internal rotation. The tibia-talus difference values in some forefoot positions were 2 ~ 3 mm after PTFL together with CFL or/and PITFL were cut off. The tibula-talus difference values were 2.21 ~ 2.76 mm after both PTFL and CFL were cut off. The tibia-fibula difference values were small. The difference values increased by 2 ~ 5 mm after cutting off the PITFL.Conclusions: Posterolateral ankle ligaments, especially CFL and PITFL, play a significant role in maintaining ankle stability. The serious injuries of both CFL and PITFL would affect posterolateral ankle stabilities. PITFL was important to subtalar joint stability. [ABSTRACT FROM AUTHOR]

Background: Salmonella is a common intestinal pathogen that causes acute and chronic inflammatory response. Probiotics reduce inflammatory cytokine production and serve as beneficial commensal microorganisms in the human gastrointestinal tract. TGF-β (transforming growth factor β)/SMAD and NF-κB signaling play important roles in inflammation in intestinal cells. However, the involvement of the signaling in regulating inflammation between Salmonella and probiotics is not fully understood. Methods: L. acidophilus and prebiotic inulin were used to treat human intestinal Caco-2 cells prior to infection with Salmonella. The cells were harvested to examine the cytokines and MIR21 expression with immunoblotting and real-time PCR. NF-κB and SMAD3/4 reporter vectors were transfected into cells to monitor inflammation and TGF-β1 signaling, respectively. Results: In this study, we showed that the probiotic L. acidophilus decreased Salmonella-induced NF-κB activation in human intestinal Caco-2 cells. Expression of the inflammatory cytokines, TNF-α and IL-8, in L. acidophiluspretreated cells was also significantly lower than that in cells infected with Salmonella alone. Moreover, TGF-β1 and MIR21 expression was elevated in cells pretreated with L. acidophilus or synbiotic, a combination of inulin and L. acidophilus, compared to that in untreated cells or cells infected with S. typhimurium alone. By contrast, expression of SMAD7, a target of MIR21, was accordingly reduced in cells treated with L. acidophilus or synbiotics. Consistent with TGF-β1/MIR21 and SMAD7 expression, SMAD3/4 transcriptional activity was significantly higher in the cells treated with L. acidophilus or synbiotics. Furthermore, TGF-β1 antibody antagonized the SMAD3/4 and NF-κB transcriptional activity modulated by L. acidophilus in intestinal cells. Conclusion: Our results suggest that the TGF-β1/MIR21 signaling pathway may be involved in the suppressive effects of L. acidophilus on inflammation caused by S. typhimurium in intestinal Caco-2 cells. [ABSTRACT FROM AUTHOR]

Background: Intrauterine adhesion (IUA) is a common uterine cavity disease which can be caused by mechanical damage that may eventually lead to infertility and pregnancy abnormalities. Since the effect of therapeutic drugs appears disappointing, cell therapy has emerged as an alternative choice for endometrium regeneration. The aim of this study is to investigate whether the combination of hydrogel Pluronic F-127 (PF-127), Vitamin C (Vc), and a bone marrow stromal cell (BMSC) mixture could be a feasible strategy to improve the endometrial regeneration in a mechanical damage model of IUA in rats. Methods: Firstly, PF-127 cytotoxicity and the effect of Vc was tested in vitro using the Annexin V/propidium iodide (PI) apoptosis test, cell count kit (CCK) growth test, and enzyme-linked immunosorbent assay (ELISA). For the establishment of the rat IUA model, a 2-mm transverse incision in the uterus was prepared at the upper end, and 1.5- to 2.0-cm endometrial damage was scraped. Rats were randomly assigned to five groups to investigate the combined strategy on IUA uterine regeneration: a sham group, an IUA control group, an IUA BMSC encapsulated in PF-127 plus Vc group, an IUA BMSC plus Vc group, and an IUA PF-127 plus Vc group. A cell mixture was injected into the uterine horn while making the IUA model. Eight weeks after cell transplantation, the rats were sacrificed and the uterine was dissected for analysis. Endometrial thickness, gland number, fibrosis area, and the expression of marker proteins for endometrial membrane were examined by hematoxylin and eosin staining, Masson&'s staining, and immunohistochemistry. Results: Vc promoted the survival and health of PF-127-encapsulated BMSCs in vitro. When this combination was transplanted in vivo, the endometrium showed better restoration as the endometrium membrane became thicker and had more glands and less fibrosis areas. The expression of cytokeratin, von Willebrand Factor (vWF), was also restored. The proinflammatory cytokine interleukin-1β (IL-1β) was significantly lower compared with the control group. Conclusions: Vc alleviates the cytotoxic effect of PF-127 and promotes cell survival and growth in rat BMSC encapsulation. Thus, a cell therapy strategy containing biomaterial scaffold, BMSCs and the modulatory factor Vc promotes the restoration of damaged IUA endometrium. [ABSTRACT FROM AUTHOR]

Background: The light/dark cycle is one of the most important factors affecting the microalgal growth and lipid accumulation. Biomass concentration and lipid productivity could be enhanced by optimization of light/dark cycles, and this is considered an effective control strategy for microalgal cultivation. Currently, most research on effects of light/dark cycles on algae is carried out under autotrophic conditions and little information is about the effects under mixotrophic cultivation. At the same time, many studies related to mixotrophic cultivation of microalgal strains, even at large scale, have been performed to obtain satisfactory biomass and lipid production. Therefore, it is necessary to investigate cellular metabolism under autotrophic and mixotrophic conditions at different light/dark cycles. Even though microalgal lipid production under optimal environmental factors has been reported by some researchers, the light/dark cycle and temperature are regarded as separate parameters in their studies. In practical cases, light/dark cycling and temperature variation during the day occur simultaneously. Therefore, studies about the combined effects of light/dark cycles and temperature variation on microalgal lipid production are of practical value, potentially providing significant guidelines for large-scale microalgal cultivation under natural conditions. Results: In this work, cell growth and lipid accumulation of an oleaginous microalgal mutant, Scenedesmus sp. Z-4, were investigated at five light/dark cycles (0 h/24 h, 8 h/16 h, 12 h/12 h, 16 h/8 h, and 24 h/0 h) in batch culture. The results showed that the optimal light/dark cycle was 12 h/12 h, when maximum lipid productivity rates of 56.8 and 182.6 mg L-1 day-1 were obtained under autotrophic and mixotrophic cultivation, respectively. Poor microalgal growth and lipid accumulation appeared in the light/dark cycles of 0 h/24 h and 24 h/0 h under autotrophic condition. Prolonging the light duration was unfavorable to the production of chlorophyll a and b, which was mainly due to photooxidation effect. Polysaccharide was converted into lipid and protein when the light irradiation time increased from 0 to 12 h; however, further increasing irradiation time had a negative effect on lipid accumulation. Due to the dependence of autotrophically cultured cells on light energy, the light/dark cycle has a more remarkable influence on cellular metabolism under autotrophic conditions. Furthermore, the combined effects of temperature variation and light/dark cycle of 12 h/12 h on cell growth and lipid accumulation of microalgal mutant Z-4 were investigated under mixotrophic cultivation, and the results showed that biomass was mainly produced at higher temperatures during the day, and a portion of biomass was converted into lipid under dark condition. Conclusions: The extension of irradiation time was beneficial to biomass accumulation, but not in favor of lipid production. Even though effects of light/dark cycles on autotrophic and mixotrophic cells were not exactly the same, the optimal lipid productivities of Scenedesmus sp. Z-4 under both cultivation conditions were achieved at the light/dark of 12 h/12 h. This may be attributed to its long-term acclimation in natural environment. By combining temperature variation with optimal light/dark cycle of 12 h/12 h, this study will be of great significance for practical microalgaebiodiesel production in the outdoor conditions. [ABSTRACT FROM AUTHOR]

Background: Pancreatic extracorporeal shock wave lithotripsy (P-ESWL) is the first-line therapy for large pancreatic duct stones. Although it is a highly effective and safe procedure for the fragmentation of pancreatic stones, it is still not complication-free. Just like endoscopic retrograde cholangiopancreatography (ERCP), pancreatitis is the most common complication. To date, nonsteroidal anti-inflammatory drugs (NSAIDs) have proven to be the only effective prophylactic medication for post-ERCP pancreatitis and the European, American and Japanese Society for Gastrointestinal Endoscopy guidelines have recommended prophylactic rectally administered indomethacin for all patients undergoing ERCP. Given the little research about effective prevention for post P-ESWL pancreatitis, we aim to determine whether rectally administered indomethacin can reduce post-ESWL-pancreatitis.Methods/design: The RIPEP study is a prospective, randomized, double-blinded, placebo-controlled trial. One thousand three hundred and seventy patients with chronic pancreatitis and pancreatic stones (>5 mm in diameter) treated with P-ESWL at Changhai Hospital will be randomly allocated to rectally administered indomethacin or placebo therapy before the procedure. The primary endpoint is the incidence of post-ESWL pancreatitis. Secondary endpoints include the severity of pancreatitis, occurrence rate of asymptomatic hyperamylasemia and other complications.Discussion: The RIPEP trial is designed to show that rectally administered indomethacin reduces the development and severity of post-ESWL pancreatitis and benefits patients treated with P-ESWL.Trial Registration: ClinicalTrials.gov, ID: NCT02797067 . Registered on 17 November 2016. [ABSTRACT FROM AUTHOR]

Background: A popliteal cyst is a benign swelling with synovial fluid located behind the knee joint. Popliteal cysts are often asymptomatic; however, symptomatic cysts may cause pain and may need surgery interventions. Here, we performed a perspective study to compare the clinical efficacy of different surgical approaches, including traditional open excision and advanced arthroscopic treatment. Methods: A total of 76 patients with popliteal cysts were assigned into three groups by a randomized complete block design. Group A included 32 patients (15 males and 17 females, age 55.3 ± 9.8 years) who received arthroscopic internal drainage of the cysts. Group B included 19 patients (9 males and 10 females, age 55.4 ±7. 6 years) who received open excision after arthroscopic treatment. Group C included 25 patients (11 males and 14 females, age 54.2 ± 8.5 years) who received open excision. All patients were followed up for an average of 13.7 ± 2. 4 months. The following parameters were compared: the time of surgery, during surgery, the length of incision, the incision healing rate, the visual analog scale (VAS) for pain, the hospitalization time, the rate of recovery to level 0-1 cysts, the recurrence rate, and the Lysholm score. Results: Group A exhibited significant better outcomes compared to groups B and C in the length of incision (1.6 ±0.1 cm), the incision healing rate (100%), the postoperative VAS score (2.7 ± 1.2), the hospitalization time (7.8 ±2.8 days), and the Lysholm score at the last follow-up (85.8 ±5.2). The recurrence rate is significantly lower in groups A (3.1%) and B (5.2%) than group C (40%) (P <0.001). Conclusions: Arthroscopic treatment for popliteal cysts exhibited better clinical outcomes with minimal invasion and can be recommended for future clinical interventions. [ABSTRACT FROM AUTHOR]

Background: With the growing demand for fossil fuels and the severe energy crisis, lignocellulose is widely regarded as a promising cost-effective renewable resource for ethanol production, and the use of lignocellulose residues as raw material is remarkable. Polar organisms have important value in scientific research and development for their novelty, uniqueness and diversity. Results: In this study, a fungus Aspergillus sydowii MS-19, with the potential for lignocellulose degradation was screened out and isolated from an Antarctic region. The growth profile of Aspergillus sydowii MS-19 was measured, revealing that Aspergillus sydowii MS-19 could utilize lignin as a sole carbon source. Its ability to synthesize low-temperature lignin peroxidase (Lip) and manganese peroxidase (Mnp) enzymes was verified, and the properties of these enzymes were also investigated. High-throughput sequencing was employed to identify and characterize the transcriptome of Aspergillus sydowii MS-19. Carbohydrate-Active Enzymes (CAZyme)-annotated genes in Aspergillus sydowiiMS-19 were compared with those in the brown-rot fungus representative species, Postia placenta and Penicillium decumbens. There were 701CAZymes annotated in Aspergillus sydowii MS-19, including 17 cellulases and 19 feruloyl esterases related to lignocellulose-degradation. Remarkably, one sequence annotated as laccase was obtained, which can degrade lignin. Three peroxidase sequences sharing a similar structure with typical lignin peroxidase and manganese peroxidase were also found and annotated as haem-binding peroxidase, glutathione peroxidase and catalase-peroxidase. Conclusions: In this study, the fungus Aspergillus sydowii MS-19 was isolated and shown to synthesize low-temperature lignin-degrading enzymes: lignin peroxidase (Lip) and manganese peroxidase (Mnp). These findings provide useful information to improve our understanding of low-temperature lignocellulosic enzyme production by polar microorganisms and to facilitate research and applications of the novel Antarctic Aspergillus sydowii strain MS-19 as a potential lignocellulosic enzyme source. [ABSTRACT FROM AUTHOR]

Background: Sugarcane smut caused by Sporisorium scitamineum leads to a significant reduction in cane yield and sucrose content. MicroRNAs (miRNAs) play an important role in regulating plant responses to biotic stress. The present study was the first to use two sugarcane genotypes, YA05-179 (smut-resistant) and ROC22 (smut-susceptible), to identify differentially expressed miRNAs in sugarcane challenged with S. scitamineum by using high-throughput sequencing. Results: The predicted target gene number corresponding to known differentially expressed miRNAs in YA05-179 was less than that in ROC22, however most of them were in common. Expression of differential miRNAs under S. scitamineum challenge was mostly downregulated, with similar trends in the two varieties. Gene ontology (GO) analysis showed that the target gene classification of known miRNAs was similar to that of the newly identified miRNAs. These were mainly associated with cellular processes and metabolic processes in the biological process category, as well as combination and catalytic activity in the molecular function category. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that these predicted target genes involved in a series of physiological and biochemical pathways or disease resistance-related physiological metabolism and signal transduction pathways, suggesting that the molecular interaction mechanism between sugarcane and S. scitamineum was a complex network system. These findings also showed certain predicted target genes of miR5671, miR5054, miR5783, miR5221, and miR6478 play roles in the mitogen-activated protein kinase (MAPK) signaling pathway, plant hormone signal transduction, and plant-pathogen interaction. Quantitative real-time PCR (qRT-PCR) analysis showed that majority of the known miRNAs and its predicted target genes followed a negatively regulated mode. Seven out of eight predicted target genes showed identical expression after 12 h treatment and reached the highest degree of matching at 48 h, indicating that the regulatory role of miRNAs on the target genes in sugarcane was maximized at 48 h after S. scitamineum challenge. Conclusions: Taken together, our findings serve as evidence for the association of miRNA expression with the molecular mechanism underlying the pathogenesis of sugarcane smut, particularly on the significance of miRNA levels in relation to the cultivation of smut-resistant sugarcane varieties. [ABSTRACT FROM AUTHOR]

Background: Segmental duplications (SDs) commonly exist in plant and animal genomes, playing crucial roles in genomic rearrangement, gene innovation and the formation of copy number variants. However, they have received little attention in most livestock species. Results: Aiming at characterizing SDs across the genomes of diverse livestock species, we mapped genome-wide SDs of horse, rabbit, goat, sheep and chicken, and also enhanced the existing SD maps of cattle and pig genomes based on the most updated genome assemblies. We adopted two different detection strategies, whole genome analysis comparison and whole genome shotgun sequence detection, to pursue more convincing findings. Accordingly we identified SDs for each species with the length of from 21.7 Mb to 164.1 Mb, and 807 to 4,560 genes were harboured within the SD regions across different species. More interestingly, many of these SD-related genes were involved in the process of immunity and response to external stimuli. We also found the existence of 59 common genes within SD regions in all studied species except goat. These common genes mainly consisted of both UDP glucuronosyltransferase and Interferon alpha families, implying the connection between SDs and the evolution of these gene families. Conclusions: Our findings provide insights into livestock genome evolution and offer rich genomic sources for livestock genomic research. [ABSTRACT FROM AUTHOR]

Background: Long noncoding RNAs (lncRNAs) are more than 200 nucleotides in length and lack transcriptional ability. The biological function of lncRNAs in oral squamous cell carcinoma (OSCC) remains unclear. The aim of this study was to identify the dysfunction of lncRNA in OSCC. Results: We analyzed the transcriptome profiles of human OSCC tissues and paired adjacent normal tissues from two patients through a next-generation sequencing approach. A total of 14 lncRNAs were upregulated (fold change ≥3) and 13 were downregulated (fold change ≤ -3) in OSCC tissues compared with the adjacent normal tissues. SOX21- AS1 was subjected to further analysis, revealing that the expression levels of SOX21-AS1 significantly decreased in OSCC compared with the adjacent normal tissue. The promoter activity of SOX21-AS1 was obviously suppressed by in vitro methylation. The DNA methylation status of the SOX21-AS1 promoter was analyzed using combined bisulfite restriction analysis, revealing that the aberrant promoter hypermethylation of SOX21-AS1 was observed frequently in OSCC tissues. The effects of SOX21-AS1 on cell proliferation and invasion were examined through transient transfection. Our data showed that SOX21-AS1 could significantly suppress oral cancer cell growth and invasion. Furthermore, the low expression level of SOX21-AS1 was significantly correlated with an advanced stage (P =0.047), large tumor size (P = 0.033), and poor disease-specific survival in OSCC patients (P = 0.002). Conclusions: SOX21-AS1 was identified as susceptible dysfunction correlated with promoter hypermethylation in OSCC. Low SOX21-AS1 expression may be an adverse prognostic biomarker for OSCC. [ABSTRACT FROM AUTHOR]

Background: Epidermal growth factor receptor (EGFR)-tyrosine kinase inhibitor (TKI) readministration to lung cancer patients is common owing to the few options available. Impact of clinical factors on prognosis of EGFR-mutant non-small cell lung cancer (NSCLC) patients receiving EGFR-TKI readministration after first-line EGFR-TKI failure and a period of TKI holiday remains unclear. Through this retrospective study, we aimed to understand the impact of clinical factors in such patients. Methods: Of 1386 cases diagnosed between December 2010 and December 2013, 80 EGFR-mutant NSCLC patients who were readministered TKIs after failure of first-line TKIs and intercalated with at least one cycle of cytotoxic agent were included. We evaluated clinical factors that may influence prognosis of TKI readministration as well as systemic inflammatory status in terms of neutrophil-to-lymphocyte ratio (NLR) and lymphocyte-to-monocyte ratio (LMR). Baseline NLR and LMR were estimated at the beginning of TKI readministration and trends of NLR and LMR were change amount from patients receiving first-Line TKIs to TKIs readministration. Results: Median survival time since TKI readministration was 7.0 months. In the univariable analysis, progression free survival (PFS) of first-line TKIs, baseline NLR and LMR, and trend of LMR were prognostic factors in patients receiving TKIs readministration. In the multivariate analysis, only PFS of first-line TKIs (p < 0.001), baseline NLR (p = 0.037), and trend of LMR (p = 0.004) were prognostic factors. Conclusion: Longer PFS of first-line TKIs, low baseline NLR, and high trend of LMR were good prognostic factors in EGFR-mutant NSCLC patients receiving TKI readministration. [ABSTRACT FROM AUTHOR]

Background: Immunosuppression has been described as a consequence of brain injury and infection by different mechanisms. Angiostrongylus cantonensis can cause injury to the central nervous system and eosinophilic meningitis to human. Both T cell and B cell immunity play an essential role in the resistance of the infection. However, whether brain injury caused by A. cantonensis infection can lead to immunosuppression is not clear. Therefore, the present study sought to observe the alteration of immune responses in mice infected with A. cantonensis. Methods: Mice were infected with 20 third-stage A. cantonensis larvae. The messenger RNA (mRNA) expression of inflammatory mediators in brain tissues was observed by qRT-PCR. Cell surface markers including CD3, CD4, CD8, CD19, B220, 7-AAD, annexin-V, IgM, AA4.1, and CD23 were evaluated by using flow cytometry. The immune functions of T and B lymphocytes were detected upon stimulation by ConA and antibody responses to a nonself antigen OVA, respectively. Activation of the hypothalamic-pituitary-adrenal axis was evaluated by analyzing the concentration of plasma corticosterone and levels of mRNA for corticotropin-releasing hormone, tyrosine hydroxylase, and c-fos. Results: A. cantonensis infection results in obvious immunosuppression evidenced as progressive spleen and thymus atrophy and significant decrease in the number of lymphocyte subsets including B cells, CD3+ T cells, CD4+ T cells, and CD8+ T cells, as well as reduced T cell proliferation at 21 days post-infection and antibody reaction to exogenous protein after infection. However, the sharp decrease of splenic and thymic cells was not due to cell apoptosis but to B cell genesis cessation and impairing thymocyte development. In addition, helminthicide treatment with albendazole on infected mice at 7 days post-infection could prevent immunosuppressive symptoms. Importantly, infected mice displayed hypothalamic-pituitary-adrenal axis activation, with peak responses occurring at 16 days post-infection, and glucocorticoid receptor antagonist could partially restore the infectioninduced cessation of B cell genesis. Conclusions: Brain injury caused by A. cantonensis infection, like that of brain stroke and trauma, enhanced endogenous corticosteroid activity, resulting in peripheral immunosuppression. [ABSTRACT FROM AUTHOR]

Background: Riemerella anatipestifer infection is a contagious disease that has resulted in major economic losses in the duck industry worldwide. This study attempted to characterize CRISPR-Cas systems in the disease-causing agent, Riemerella anatipestifer (R. anatipestifer). The CRISPR-Cas system provides adaptive immunity against foreign genetic elements in prokaryotes and CRISPR-cas loci extensively exist in the genomes of archaea and bacteria. However, the structure characteristics of R. anatipestifer CRISPR-Cas systems remains to be elucidated due to the limited availability of genomic data. Results: To identify the structure and components associated with CRISPR-Cas systems in R. anatipestifer, we performed comparative genomic analysis of CRISPR-Cas systems in 25 R. anatipestifer strains using high-throughput sequencing. The results showed that most of the R. anatipestifer strains (20/25) that were analyzed have two CRISPR loci (CRISPR1 and CRISPR2). CRISPR1 was shown to be flanked on one side by cas genes, while CRISPR2 was designated as an orphan. The other analyzed strains harbored only one locus, either CRISPR1 or CRISPR2. The length and content of consensus direct repeat sequences, as well as the length of spacer sequences associated with the two loci, differed from each other. Only three cas genes (cas1, cas2 and cas9) were located upstream of CRISPR1. CRISPR1 was also shown to be flanked by a 107 bp-long putative leader sequence and a 16 nt-long anti-repeat sequence. Combined with analysis of spacer organization similarity and phylogenetic tree of the R. anatipestifer strains, CRISPR arrays can be divided into different subgroups. The diversity of spacer organization was observed in the same subgroup. In general, spacer organization in CRISPR1 was more divergent than that in CRISPR2. Additionally, only 8 % of spacers (13/153) were homologous with phage or plasmid sequences. The cas operon flanking CRISPR1 was observed to be relatively conserved based on multiple sequence alignments of Cas amino acid sequences. The phylogenetic analysis associated with Cas9 showed Cas9 sequence from R. anatipestifer was closely related to that of Bacteroides fragilis and formed part of the subtype II-C subcluster. Conclusions: Our data revealed for the first time the structural features of R. anatipestifer CRISPR-Cas systems. The illumination of structural features of CRISPR-Cas system may assist in studying the specific mechanism associated with CRISPR-mediated adaptive immunity and other biological functions in R. anatipestifer. [ABSTRACT FROM AUTHOR]

Background: Predicting piwi-interacting RNA (piRNA) is an important topic in the small non-coding RNAs, which provides clues for understanding the generation mechanism of gamete. To the best of our knowledge, several machine learning approaches have been proposed for the piRNA prediction, but there is still room for improvements. Results: In this paper, we develop a genetic algorithm-based weighted ensemble method for predicting transposon-derived piRNAs. We construct datasets for three species: Human, Mouse and Drosophila. For each species, we compile the balanced dataset and imbalanced dataset, and thus obtain six datasets to build and evaluate prediction models. In the computational experiments, the genetic algorithm-based weighted ensemble method achieves 10-fold cross validation AUC of 0.932, 0.937 and 0.995 on the balanced Human dataset, Mouse dataset and Drosophila dataset, respectively, and achieves AUC of 0.935, 0.939 and 0.996 on the imbalanced datasets of three species. Further, we use the prediction models trained on the Mouse dataset to identify piRNAs of other species, and the models demonstrate the good performances in the cross-species prediction. Conclusions: Compared with other state-of-the-art methods, our method can lead to better performances. In conclusion, the proposed method is promising for the transposon-derived piRNA prediction. [ABSTRACT FROM AUTHOR]

Background: Strains of extraintestinal pathogenic Escherichia coli (ExPEC) can invade and colonize extraintestinal sites and cause a wide range of infections. Genomic analysis of ExPEC has mainly focused on isolates of human and avian origins, with porcine ExPEC isolates yet to be sequenced. To better understand the genomic attributes underlying the pathogenicity of porcine ExPEC, we isolated two E. coli strains PCN033 and PCN061 from pigs, assessed their in vivo virulence, and completed and compared their genomes. Results: Animal experiments demonstrated that strain PCN033, but not PCN061, was pathogenic in a pig model. The chromosome of PCN033 was 384 kb larger than that of PCN061. Among the PCN033-specific sequences, genes encoding adhesins, unique lipopolysaccharide, unique capsular polysaccharide, iron acquisition and transport systems, and metabolism were identified. Additionally, a large plasmid PCN033p3 harboring many typical ExPEC virulence factors was identified in PCN033. Based on the genetic variation between PCN033 and PCN061, corresponding phenotypic differences in flagellum-dependent swarming motility and metabolism were verified. Furthermore, the comparative genomic analyses showed that the PCN033 genome shared many similarities with genomic sequences of human ExPEC strains. Additionally, comparison of PCN033 genome with other nine characteristic E. coli genomes revealed 425 PCN033-special coding sequences. Genes of this subset included those encoding type I restriction-modification (R-M) system, type VI secretion system (T6SS) and membrane-associated proteins. Conclusions: The genetic and phenotypic differences between PCN033 and PCN061 could partially explain their differences in virulence, and also provide insight towards the molecular mechanisms of porcine ExPEC infections. Additionally, the similarities between the genomes of PCN033 and human ExPEC strains suggest that some connections between porcine and human ExPEC strains exist. The first completed genomic sequence for porcine ExPEC and the genomic differences identified by comparative analyses provide a baseline understanding of porcine ExPEC genetics and lay the foundation for their further study. [ABSTRACT FROM AUTHOR]

Background: In engineered strains of Escherichia coli, bioconversion efficiency is determined by not only metabolic flux but also the turnover efficiency of relevant pathways. Methyl-D-erythritol 4-phosphate (MEP)-dependent carotenoid biosynthesis in E. coli requires efficient turnover of precursors and balanced flux among precursors, cofactors, and cellular energy. However, the imbalanced supply of glyceraldehyde 3-phosphate (G3P) and pyruvate precursors remains the major metabolic bottleneck. To address this problem, we manipulated various genetic targets related to the Entner-Doudoroff (ED)/pentose phosphate (PP) pathways. Systematic target modification was conducted to improve G3P and pyruvate use and rebalance the precursor and redox fluxes. Results: Carotenoid production was improved to different degrees by modifying various targets in the Embden-Meyerhof-Parnas (EMP) and ED pathways, which directed metabolic flux from the EMP pathway towards the ED pathway. The improvements in yield were much greater when the MEP pathway was enhanced. The coordinated modification of ED and MEP pathway targets using gene expression enhancement and protein coupling strategies in the pgi deletion background further improved carotenoid synthesis. The fine-tuning of flux at the branch point between the ED and PP pathways was important for carotenoid biosynthesis. Deletion of pfkAB instead of pgi reduced the carotenoid yield. This suggested that anaplerotic flux of G3P and pyruvate might be necessary for carotenoid biosynthesis. Improved carotenoid yields were accompanied by increased biomass and decreased acetate overflow. Therefore, efficient use of G3P and pyruvate precursors resulted in a balance among carotenoid biosynthesis, cell growth, and by-product metabolism. Conclusions: An efficient and balanced MEP-dependent carotenoid bioconversion strategy involving both the ED and PP pathways was implemented by the coordinated modification of diverse central metabolic pathway targets. In this strategy, enhancement of the ED pathway for efficient G3P and pyruvate turnover was crucial for carotenoid production. The anaplerotic role of the PP pathway was important to supply precursors for the ED pathway. A balanced metabolic flux distribution among precursor supply, NADPH generation, and by-product pathways was established. [ABSTRACT FROM AUTHOR]

Granular cell tumor is rare and accounts for approximately 0.5 % of all soft tissue tumors. The malignant granular cell tumor, especially cutaneous malignant granular cell tumor is extremely rare. The present case is the first patient of primary cutaneous malignant granular cell tumor reported from China in English. A review of the literature is performed, and the presentation, position, pathological diagnosis, treatment and prognosis of the patients with cutaneous malignant granular cell tumor of the reported cases before is analysed. [ABSTRACT FROM AUTHOR]

Maintaining the physiological pH of interstitial fluid is crucial for normal cellular functions. In disease states, tissue acidosis is a common pathologic change causing abnormal activation of acid-sensing ion channels (ASICs), which according to cumulative evidence, significantly contributes to inflammation, mitochondrial dysfunction, and other pathologic mechanisms (i.e., pain, stroke, and psychiatric conditions). Thus, it has become increasingly clear that ASICs are critical in the progression of neurologic diseases. This review is focused on the importance of ASICs as potential therapeutic targets in combating neurologic diseases. [ABSTRACT FROM AUTHOR]

Granular cell tumor is rare and accounts for approximately 0.5 % of all soft tissue tumors. The malignant granular cell tumor, especially cutaneous malignant granular cell tumor is extremely rare. The present case is the first patient of primary cutaneous malignant granular cell tumor reported from China in English. A review of the literature is performed, and the presentation, position, pathological diagnosis, treatment and prognosis of the patients with cutaneous malignant granular cell tumor of the reported cases before is analysed. [ABSTRACT FROM AUTHOR]

Background: Gossypium raimondii is a Verticillium wilt-resistant cotton species whose genome encodes numerous disease resistance genes that play important roles in the defence against pathogens. However, the characteristics of resistance gene analogues (RGAs) and Verticillium dahliae response loci (VdRLs) have not been investigated on a global scale. In this study, the characteristics of RGA genes were systematically analysed using bioinformatics-driven methods. Moreover, the potential VdRLs involved in the defence response to Verticillium wilt were identified by RNA-seq and correlations with known resistance QTLs. Results: The G. raimondii genome encodes 1004 RGA genes, and most of these genes cluster in homology groups based on high levels of similarity. Interestingly, nearly half of the RGA genes occurred in 26 RGA-gene-rich clusters (Rgrcs). The homology analysis showed that sequence exchanges and tandem duplications frequently occurred within Rgrcs, and segmental duplications took place among the different Rgrcs. An RNA-seq analysis showed that the RGA genes play roles in cotton defence responses, forming 26 VdRLs inside in the Rgrcs after being inoculated with V. dahliae. A correlation analysis found that 12 VdRLs were adjacent to the known Verticillium wilt resistance QTLs, and that 5 were rich in NB-ARC domain-containing disease resistance genes. Conclusions: The cotton genome contains numerous RGA genes, and nearly half of them are located in clusters, which evolved by sequence exchanges, tandem duplications and segmental duplications. In the Rgrcs, 26 loci were induced by the V. dahliae inoculation, and 12 are in the vicinity of known Verticillium wilt resistance QTLs. [ABSTRACT FROM AUTHOR]

Background: Gossypium raimondii is a Verticillium wilt-resistant cotton species whose genome encodes numerous disease resistance genes that play important roles in the defence against pathogens. However, the characteristics of resistance gene analogues (RGAs) and Verticillium dahliae response loci (VdRLs) have not been investigated on a global scale. In this study, the characteristics of RGA genes were systematically analysed using bioinformatics-driven methods. Moreover, the potential VdRLs involved in the defence response to Verticillium wilt were identified by RNA-seq and correlations with known resistance QTLs. Results: The G. raimondii genome encodes 1004 RGA genes, and most of these genes cluster in homology groups based on high levels of similarity. Interestingly, nearly half of the RGA genes occurred in 26 RGA-gene-rich clusters (Rgrcs). The homology analysis showed that sequence exchanges and tandem duplications frequently occurred within Rgrcs, and segmental duplications took place among the different Rgrcs. An RNA-seq analysis showed that the RGA genes play roles in cotton defence responses, forming 26 VdRLs inside in the Rgrcs after being inoculated with V. dahliae. A correlation analysis found that 12 VdRLs were adjacent to the known Verticillium wilt resistance QTLs, and that 5 were rich in NB-ARC domain-containing disease resistance genes. Conclusions: The cotton genome contains numerous RGA genes, and nearly half of them are located in clusters, which evolved by sequence exchanges, tandem duplications and segmental duplications. In the Rgrcs, 26 loci were induced by the V. dahliae inoculation, and 12 are in the vicinity of known Verticillium wilt resistance QTLs. [ABSTRACT FROM AUTHOR]

Background: Cyclin D1 (CCND1) is critical in the transition of the cell cycle from the G1 to S phases, and unbalanced cell cycle regulation is a hallmark of carcinogenesis. Numerous epidemiological studies have evaluated the association between the CCND1 A870G polymorphism and the risk of prostate cancer (PCa). However, these studies have yielded conflicting results. Methods: In the present study, the possible association above was assessed by a meta-analysis. Eligible articles were identified for the period up to July 2014. Pooled odds ratios (ORs) with 95% confidence intervals (95% CI) were appropriately derived from fixed effects or random effects models. Results: A total of ten case-control studies, which included 3,820 cases and 3,825 controls, were identified. Overall, the allelic/genotypic association between the G870A polymorphism and prostate cancer was nonsignificant (OR = 1.045, 95% CI = 0.947 to 1.153 for A versus G, P = 0.380; OR = 1.088, 95% CI = 0.896 to 1.321 for AA versus GG, P = 0.393; OR = 1.044, 95% CI = 0.941 to 1.158 for GA versus GG, P = 0.414; OR = 1.053, 95% CI = 0.955 to 1.161 for the dominant model AA + GA versus GG, P = 0.303; OR = 1.072, 95% CI = 0.881 to 1.306 for the recessive model AA versus AA + GA, P = 0.486). Moreover, subgroup analyses according to ethnicity failed to demonstrate a significant association between this polymorphism and prostate cancer. In addition, we also performed a stratified analysis of cases with PCa metastasis, and the results supported the findings of no significant association between CCND1 A870G polymorphism and metastasis risk of PCa. Conclusions: Our results suggest that the CCND1 A870G polymorphism might not be a potential candidate for predicting prostate cancer risk, including metastasis risk. [ABSTRACT FROM AUTHOR]

Background Schistosomiasis is a chronic parasitic disease that affects approximately 200 million people. In Schistosomiasis japonica and mansoni, parasite eggs were trapped in host liver and stimulated the CD4+T cell responses to regulate the formation of the granulomas. Subsequently, excessive granulomatous response in some heavily, and/or repeatedly infected individuals could result in chronic liver fibrosis and circulatory impairment. Thus, elucidation of the mechanisms of these responses will not only provide more information to better understand the mechanisms of the immunoregulation in schistosomiasis, but also help to design new therapies to control granuloma-associated immunopathology. The role of aquaporin-4 (AQP4) in water transport has been extensively investigated in the central nervous system (CNS). Recently, studies have shown that AQP4 expresses in immune system and lack of AQP4 in mice results in significantly less CD4+CD25+ T regulatory cells (Treg cells) under physiological condition, one of the subpopulations of CD4+T cells which restrains immunopathology in hosts with schistosomiasis. However, little information exists regarding the contribution of AQP4 to the immune regulation in schistosome infection. Methods The liver granulomatous response in S. japonicum-infected AQP4 knockout (KO) mice and its wild-type (WT) littermates were detected by staining liver sections with hematoxylin and eosin. The generation of various CD4+ T subsets, including Th1, Th2, Th17, and Treg cells were analyzed by flow cytometry. In addition, the levels of total IgG, IgG1, IgG2a in serum of infected mice were detected by ELISA assay. Results Our results showed an enhanced granulomatous response with increased accumulation of eosinophils and macrophages around eggs in the liver of AQP4 KO mice with Schistosomiasis japonica. In addition, our study demonstrated enhanced Th2 but reduced Th1 and Treg cells generation in AQP4 KO mice with Schistosomiasis japonica, which may, at least partly, account for the enhancement of the liver granuloma formation. Conclusion Our study for the first time provides evidences that AQP4 has an association with the immunoregulation of the liver granuloma formation, which may confer a new option for schistosomiasis treatment. [ABSTRACT FROM AUTHOR]

Background We investigated whether attenuating dipeptidyl peptidase-IV (DPP4) enzyme activity protected rat heart from ischemia-reperfusion (IR) injury (40-min left anterior descending coronary artery ligation followed by 72 h reperfusion). Methods and results Adult male Fischer 344 rats (n = 24) were equally divided into sham-control (WT-SC), WTIR, and WT-IR-Sita (oral sitagliptin 400 mg/kg/day for 3 days) groups, whereas adult male DPP4-deficiency (DPP4D) rats (n = 16) were equally divided into DPP4D-SC and DPP4D-IR groups. Animals were sacrificed at 72 h after reperfusion with collection of heart specimens. Infarct area (H&E), collagen deposition (Sirius-red stain), fibrotic area (Masson's trichrome), and fluorescent-ROS intensity (H2DCFDA-labeling myocardium) of left ventricle were significantly higher in WT-IR than those in other groups, significantly higher in WT-IR-Sita and DPP4D-IR groups than in WT-SC and DPP4D-SC groups (all p < 0.001), but there was no difference between the latter two groups. Protein expressions of oxidative stress (oxidized protein), reactive oxygen species (NOX-1, NOX-2), inflammation (TNF-α, NF-κB, MMP-9, VCAM-1), apoptosis (mitochondrial Bax, cleaved caspase-3 and PARP), myocardial damage markers (cytosolic cytochrome-C, γ-H2AX), and number of inflammatory cells (CD14+, CD68+, CD40+ cells) showed a pattern identical to that of histological changes among all groups (all p < 0.005), whereas markers of anti-apoptosis (Bcl-2) and mitochondrial integrity (mitochondrial cytochrome-C) as well as left ventricular ejection fraction showed an opposite pattern (all p < 0.001). Protein expressions of anti-oxidants (HO-1, NQO-1), angiogenesis factors (SDF-1α, CXCR4), and glycogen-like-peptide-1-receptor were significantly higher inWT-IR-Sita and DPP4D-IR than those in other groups (all p < 0.001). Conclusion Abrogation of DPP4 activity protects against myocardial IR injury and preserved heart function. [ABSTRACT FROM AUTHOR]

Background: The histidine ammonia-lyse gene (HAL) encodes the histidine ammonia-lyase, which catalyzes the first reaction of histidine catabolism. In our previous genome-wide association study in Chinese Holstein cows to identify genetic variants affecting milk production traits, a SNP (rs41647754) located 357 bp upstream of HAL, was found to be significantly associated with milk yield and milk protein yield. In addition, the HAL gene resides within the reported QTLs for milk production traits. The aims of this study were to identify genetic variants in HAL and to test the association between these variants and milk production traits. Results: Fifteen SNPs were identified within the regions under study of the HAL gene, including three coding mutations, seven intronic mutations, one promoter region mutation, and four 3′UTR mutations. Nine of these identified SNPs were chosen for subsequent genotyping and association analyses. Our results showed that five SNP markers (ss974768522, ss974768525, ss974768531, ss974768533 and ss974768534) were significantly associated with one or more milk production traits. Haplotype analysis showed that two haplotype blocks were significantly associated with milk yield and milk protein yield, providing additional support for the association between HAL variants and milk production traits in dairy cows (P < 0.05). Conclusion: Our study shows evidence of significant associations between SNPs within the HAL gene and milk production traits in Chinese Holstein cows, indicating the potential role of HAL variants in these traits. These identified SNPs may serve as genetic markers used in genomic selection schemes to accelerate the genetic gains of milk production traits in dairy cattle. [ABSTRACT FROM AUTHOR]

Primary synovial sarcoma of the prostate is an uncommon malignant tumor. There are few cases reported in the English medical literature to date. Here, we present a case of 22-year old man with primary synovial sarcoma of the prostate metastatic to the liver and lung. To our knowledge, only six reports of synovial sarcoma involving the prostate have been previously published. We also reviewed the previous treatments and prognoses in previous case reports and evaluate the proper treatment for this disease. [ABSTRACT FROM AUTHOR]