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The moisture content of combustible material on the forest floor is constantly changing due to environmental factors, which have a direct impact on the composition and emission intensity of particulate matter released during fire. In this study, an indoor biomass combustion analysis device was used to analyze the emission characteristics of fine particulate matter (PM

Automatic segmentation of abdominal organs in CT scans plays an important role in clinical practice. However, most existing benchmarks and datasets only focus on segmentation accuracy, while the model efficiency and its accuracy on the testing cases from different medical centers have not been evaluated. To comprehensively benchmark abdominal organ segmentation methods, we organized the first Fast and Low GPU memory Abdominal oRgan sEgmentation (FLARE) challenge, where the segmentation methods were encouraged to achieve high accuracy on the testing cases from different medical centers, fast inference speed, and low GPU memory consumption, simultaneously. The winning method surpassed the existing state-of-the-art method, achieving a 19× faster inference speed and reducing the GPU memory consumption by 60% with comparable accuracy. We provide a summary of the top methods, make their code and Docker containers publicly available, and give practical suggestions on building accurate and efficient abdominal organ segmentation models. The FLARE challenge remains open for future submissions through a live platform for benchmarking further methodology developments at https://flare.grand-challenge.org/.

Emission of particulate matter (PM) during forest fires is a major source of air pollution and hence purification of atmospheric pollution has gained increasing importance. Trees can absorb polluting gases and fine particles by their leaves from the atmosphere and act as a sustainable air purification filter. However, the capture efficiency varies among tree species; thus exploring the ability of forest trees to capture smoke PM released during forest fires provides a basis for assessing net emissions from forest fires and the impact of smoke on forest ecosystems. In this study, the main afforestation tree species, Cunninghamia lanceolata (Lamb.) Hook, and a fire-resistant tree species, Schima superba Gardn.et Champ, in southern China were exposed to different smoke concentrations by simulating forest fire. The amount of PM per unit leaf area, absorption of nutrient element, leaf surface characteristics and antioxidant enzyme activities were determined. The main findings were: (1) The total quantity of PM captured by unit leaf area (μg·cm

Background Carbapenem-resistant Enterobacterales (CRE) are rapidly increasing worldwide in last two decades and lead few antibiotics for treatment. The molecular epidemiology of CRE in China was investigated to provide basis for clinical rational use of antibiotics and prevent its spread. Methods All CRE isolates in this study were collected from 11 hospitals from October 2015 to July 2018. The isolates were subjected to antimicrobial susceptibility tests, PCR molecular identification, pulsed-field gel electrophoresis, and multilocus sequence typing. Results Among the 399 CRE isolates, 51.6% (206/399) harbored carbapenemase genes. Three carbapenemase genes were detected, namely blaKPC-2, blaNDM-1, and blaIMP at rates of 29.8% (119/399), 17.5% (70/399), and 4.0% (16/399), respectively. In Klebsiella pneumoniae (350) and Escherichia coli (26), blaKPC-2 (33.4%, 117/350) and blaNDM-1 (61.5%, 16/26) were the predominant genes. The most common genes in the CRE isolates were blaKPC (85.5%) and blaNDM-1 (76.5%) from adults and children, respectively. Particularly, ST11 K. pneumoniae with blaKPC-2 harbored by IncFII plasmids were distributed in both general and primary hospitals, suggesting a clonal transmission pattern at these sites. In addition, the clonal distribution of ST2407 K. pneumoniae with blaNDM-1 located on IncX3 plasmids and blaIMP-38-positive ST307 K. pneumoniae were detected in a children’s hospital. Conclusion The distribution of carbapenemase genes differed among strains and age groups. Multiple carbapenemase genes in the CRE strains were clonally disseminated in the tested regions mediated by multiple plasmids. Therefore, CRE monitoring should be increased and measures should be adopted to prevent its transmission.

The ability to remember conspecifics is critical for adaptive cognitive functioning and social communication, and impairments of this ability are hallmarks of autism spectrum disorders (ASDs). Although hippocampal ventral CA1 (vCA1) neurons are known to store social memories, how their activities are coordinated remains unclear. Here we show that vCA1 social memory neurons, characterized by enhanced activity in response to memorized individuals, were preferentially reactivated during sharp-wave ripples (SPW-Rs). Spike sequences of these social replays reflected the temporal orders of neuronal activities within theta cycles during social experiences. In ASD model Shank3 knockout mice, the proportion of social memory neurons was reduced, and neuronal ensemble spike sequences during SPW-Rs were disrupted, which correlated with impaired discriminatory social behavior. These results suggest that SPW-R-mediated sequential reactivation of neuronal ensembles is a canonical mechanism for coordinating hippocampus-dependent social memories and its disruption underlie the pathophysiology of social memory defects associated with ASD.

JNK activity has been implicated in the malignant proliferation, invasion and drug-resistance of glioma cells (GCs), but the molecular mechanisms underlying JNK activation are currently unknown. Here, we reported that MKK7, not MKK4, directly activates JNK in GCs and exerts oncogenic effects on tumor formation. Notably, MKK7 expression in glioma tissues was closely correlated with the grade of the glioma and JNK/c-Jun activation. Mechanistically, MKK7 transcription critically depends on the complexes formed by HDAC4 and the transcriptional factors SP1 and Krüppel-like factor-5 (KLF5), wherein HDAC4 directly deacetylates both SP1 and KLF5 and synergistically upregulates MKK7 transcription through two SP1 sites located on its promoter. In contrast, the increases in acetylated-SP1 and acetylated-KLF5 after HDAC4 inhibition switched to transcriptionally suppress MKK7. Selective inhibition of HDAC4 by LMK235, siRNAs or blockage of SP1 and KLF5 by the ectopic dominant-negative SP1 greatly reduced the malignant capacity of GCs. Furthermore, suppression of both MKK7 expression and JNK/c-Jun activities was involved in the tumor-growth inhibitory effects induced by LMK235 in U87-xenograft mice. Interestingly, HDAC4 is highly expressed in glioma tissues, and the rate of HDAC4 nuclear import is closely correlated with glioma grade, as well as with MKK7 expression. Collectively, these findings demonstrated that highly expressed MKK7 contributes to JNK/c-Jun signaling-mediated glioma formation. MKK7 transcription, regulated by SP1 and KLF5, critically depends on HDAC4 activity, and inhibition of HDAC4 presents a potential strategy for suppressing the oncogenic roles of MKK7/JNK/c-Jun signaling in GCs.

This work studied the effect of age at photostimulation on reproductive performance of Beijing-You Chicken (BYC) breeders. A total of 384 fourteen-week-old BYC breeder hens were randomly allocated to 4 treatments of 96 birds each, with 2 replicates per treatment. The treatments represent photostimulation at 16, 18, 20, and 22 wk of age, respectively (PS16, PS18, PS20, and PS22) by incrementally increasing day length from 8L:16D to 14L:10D and by increasing lighting intensity from 10 to 80 lx. Egg production was recorded for each replicate until 51 wk. Four birds randomly selected from each treatment were sacrificed to characterize sexual organ development at 4 time points: 1 D before photostimulation and 2, 4, and 6 wk after photostimulation. Eggshell quality at peak laying was measured. The results showed that the changes in ovary and oviduct weight in PS22 were 8.68- and 4.27-fold higher than in PS16 at 6 wk after photostimulation. PS16 had an earlier age at 5% egg production than PS20 and PS22 (P = 0.003). The interval from photostimulation to age at 5% egg production in PS20 and PS22 was shorter than in other treatments (P = 0.005). Later peak egg production was seen in PS20 (211.0 D) and PS22 (218.0 D) than in PS16 (183.0 D) and PS18 (190.0 D, P = 0.020), but the laying rate of PS20 decreased slowly after peak laying. PS20 and PS22 had higher egg weights than PS16 and PS18 at peak laying (P = 0.018). Age at photostimulation had no effect on egg number, defective egg number, or hatchability (P > 0.05). In summary, the onset of lay can be advanced by photostimulation at early ages, but there is no difference on egg production until 51 wk. Photostimulation at 20 wk improves peak of laying and laying uniformity.

Histone deacetylase 6 (HDAC6) activity contributes to the malignant proliferation, invasion, and migration of glioma cells (GCs), but the molecular mechanisms underlying the processes remains elusive. Here, we reported that HDAC6 inhibition by Ricolinostat (ACY-1215) or CAY10603 led to a remarkable decrease in the phosphorylation of c-Jun N-terminal kinase (JNK) and c-Jun, which preceded its suppressive effects on glioma cell growth. Further investigation showed that these effects resulted from HDAC6 inhibitor-induced suppression of MAPK kinase 7 (MKK7), which was identified to be critical for JNK activation and exerts the oncogenic roles in GCs. Selectively silencing HDAC6 by siRNAs had the same responses, whereas transient transfections expressing HDAC6 promoted MKK7 expression. Interestingly, by performing Q-PCR, HDAC6 inhibition did not cause a down-regulation of MKK7 mRNA level, whereas the suppressive effects on MKK7 protein can be efficiently blocked by the proteasomal inhibitor MG132. As a further test, elevating MKK7-JNK activity was sufficient to rescue HDAC6 inhibitor-mediated-suppressive effects on c-Jun activation and the malignant features. The suppression of both MKK7 expression and JNK/c-Jun activities was involved in the tumor-growth inhibitory effects induced by CAY10603 in U87-xenograft mice. Collectively, our findings provide new insights into the molecular mechanism of glioma malignancy regarding HDAC6 in the selective regulation of MKK7 expression and JNK/c-Jun activity. MKK7 protein stability critically depends on HDAC6 activity, and inhibition of HDAC6 probably presents a potential strategy for suppressing the oncogenic roles of MKK7/JNK/c-Jun axis in GCs.

Prostate cancer is dangerous due to its metastatic property in the advanced stage. Considerable advance has been made in unraveling the tumor-related molecular basis. Traditionally, differentially expressed genes are focused on for biomarker identification. Here, we argued that subtle gene alterations could be amplified through the biological network, those omissive non-significantly disrupted genes might be also cancer-related. To verify our hypothesis, we constructed a co-regulatory network comprised of miRNA, TF and mRNA. Then an essential score for a gene was computed by summing its neighbor expression weighted by the Jaccard similarity coefficient. The genes with the most essential score alterations (ESA) were selected for the following analyses. Although most of these genes exhibit only subtle alterations at expression levels, they are indeed informative in discriminating between tumor and normal samples. Moreover, the enrichment analysis revealed they are cancer-associated. We, therefore, debated that they could be used as cancer-related factors. Finally, feed-forward loops (FFLs) were constructed based on these genes for further investigating their potential regulation patterns associated with the prostate cancer. We found most nodes in the FFLs related to cancer. Our results suggested the subtle alterations could impact the biological system by their interaction with other elements. This observation would shed light on deep understanding the mechanism of the prostate cancer.

Introduction: Carbapenem-resistant Klebsiella pneumoniae (KP) serves as a major threat to onco-hematological patients, resulting in great morbidity and mortality. The purpose of our study was to identify the risk factors for KP bloodstream infections (BSIs) and mortality in onco-hematological patients. Methodology: A retrospective observation study was conducted on KP BSIs in the onco-hematology departments at Xiangya hospital from January 2014 to September 2018. Multivariate analysis was employed to identify the independent risk factors for carbapenem-resistant (CR) KP BSIs and related mortality. Results: A total of 89 strains of KP were analyzed in our study, in which 20 strains were CRKP. The only risk factor for CRKP BSI was carbapenem exposure within 30 days before the onset of BSIs (HR 25.122). The 30-day mortality was 24.7%. CRKP caused more mortality than carbapenem-susceptible KP (55.0% vs 15.9%, P = 0.001). In the multivariate analysis, unresolved neutropenia (HR 16.900), diarrhea (HR 3.647) and RDW > 14% (HR 6.292) were independent risk factors for mortality, and appropriate empirical therapy (HR 0.164) was protective against mortality. Conclusions: Our findings showed that carbapenem resistance was spreading in our setting, and a precise combination of antibiotics covering the common pathogen is crucial to improving patient survival.

Introduction: The aim of our study was to evaluate the epidemiology, clinical features and risk factors for shock and mortality from Escherichia coli bacteremia among children and adolescents with hematological disorders. Methodology: A retrospective observational study of E. coli bacteremia in the hematology department at Xiangya Hospital from January 2013 to June 2018 was conducted. Clinical characteristics, laboratory results and antimicrobial susceptibility were analysed. Risk factors for shock and mortality were also investigated. Results: Of the 45 strains of E. coli, 73.3% were multidrug-resistant (MDR). Septic shock was observed in 51.1% of patients, and the 30-day all-cause mortality was 22.2%. The risk factors associated with shock were an elevated red blood cell distribution (RDW) value when bloodstream infections (BSIs) occurred (> 15%, OR, 6.840; 95% CI, 1.571 – 29.788) and a lower WBC count (< 300/mm3, OR, 6.761; 95% CI, 1.383 – 33.044). Multivariate analysis showed that only an elevated D-dimer level (> 0.5 mg/L, OR 12.250, 95% CI 1.268 – 118.361) was a risk factor for 30-day mortality. Furthermore, we observed decreases for RDW changes at two time points (neutropenia and BSIs occurred) in the non-shock group and survival group. Conclusions: MDR infections from E. coli bacteremia were common in pediatric hematological patients. In our setting, the laboratory results may serve as a clue for physicians to distinguish patients at higher risk for shock and mortality. Furthermore, RDW could be used as a biomarker to elucidate potential disorders in hematological patients.

Background. Intestinal ischemia is a common clinical critical illness. Intestinal ischemia-reperfusion (IIR) leads to acute lung injury (ALI), but the causative factors of ALI are unknown. The aim of this study was to reveal the causative factors and mechanisms of IIR-induced lung injury. Methods. A mouse model of IIR was developed using C57BL/6 mice, followed by detection of lung injury status and plasma levels of inflammatory factors in sham-operated mice and model mice. Some model mice were treated with a tumor necrosis factor-α (TNF-α) inhibitor lenalidomide (10 mg/kg), followed by observation of lung injury status through hematoxylin and eosin staining and detection of neutrophil infiltration levels through naphthol esterase and Ly6G immunohistochemical staining. Additionally, peripheral blood polymorphonuclear neutrophils (PMNs) were cultured in vitro and then stimulated by TNF-α to mimic in vivo inflammatory stimuli; this TNF-α stimulation was also performed on PMNs after knockdown of FoxO3a or treatment with the c-Jun N-terminal kinase (JNK) inhibitor SP600125. PMN apoptosis after stimulation was detected using flow cytometry. Finally, the role of PMN apoptosis in IIR-induced lung injury was evaluated in vivo by detecting the ALI status in the model mice administered with ABT-199, a Bcl-2 inhibitor. Results. IIR led to pulmonary histopathological injury and increased lung water content, which were accompanied by increased plasma levels of inflammatory factors, with the TNF-α plasma level showing the most pronounced increase. Inhibition of TNF-α led to effective reduction of lung tissue injury, especially that of the damaging infiltration of PMNs in the lung. In vitro knockdown of FoxO3a or inhibition of JNK activity could inhibit TNF-α-induced PMN apoptosis. Further in vivo experiments revealed that ABT-199 effectively alleviated lung injury and decreased inflammation levels by promoting PMN apoptosis during IIR-induced lung injury. Conclusion. TNF-α activates the JNK/FoxO3a pathway to induce a delay in PMN apoptosis, which promotes IIR-induced lung injury.

We established a rapid and sensitive ultra high-performance liquid chromatography tandem mass spectrometry method for the simultaneous quantification of xanthones and steroidal saponins in rat plasma. Chromatographic separation was achieved on a C18 column with a mobile phase comprising acetonitrile and 0.1% formic acid. The detection was performed by negative electrospray ionization in multiple reaction monitoring mode. The validated method showed good linearity within the tested range (r > 0.9945). The intra- and interday precision at high, medium, and low concentrations was less than 7.96%. The bias of accuracies ranged from -1.92 to 9.62%. The extraction recoveries of the compounds ranged from 84.78 to 88.69%, and the matrix effects ranged from 96.76 to 108.59%. This method was successfully applied to a pharmacokinetic comparison of crude and salt-processed Anemarrhenae Rhizoma aqueous extracts after oral administration in rats. The maximum plasma concentration and area under concentration-time curve of timosaponin BIII and timosaponin AIII increased significantly (P < 0.05 or 0.01) and those of timosaponin BII decreased significantly (P < 0.05) after processing. These results could contribute to the clinical application of crude and salt-processed Anemarrhenae Rhizoma and reveal the processing mechanism.

Biomarker discovery plays an important role in cancer diagnosis and prognosis assessments. The biomarkers that could be applied among different cancer types are highly useful. Although many traditional feature selection algorithms have shown their power on picking discriminative genes, they are incapable of identifying biologically meaningful biomarkers. Here, on the hypothesis that gene essentiality would be disrupted in cancers, we estimated the gene sets with significant essentiality alteration in six cancer types. We found that different cancer types would share some common gene essentiality alterations. Then, the variable combination population analysis (VCPA) algorithm was applied to identify the potential biomarkers from these common genes, which were used to construct prediction models and exhibited satisfactory classification ability (averaged accuracy: 0.9752) among six cancer types. Interestingly, these biomarkers would tend to cluster as a subnetwork and be characterized by high centrality values in the protein–protein interaction network. They were significantly enriched in the cell cycle and DNA replication pathway which are hallmark signatures of cancers. Several biomarkers have been even verified by the literature searching, reported having roles in chromosome instability and aberrantly expressed between cancer/normal samples. An additional comparison analysis between the VCPA and other six feature selection methods in WEKA suggested biomarkers by VCPA perform superior over those by other methods. These results suggested that our method is promising in identifying the potential multi-cancer biomarkers.

NACHT, LRR and PYD domains-containing protein 3 (NLRP3) protein is the core actor involved in inflammasome formation, and plays a pivotal role in the innate immune response. However, whether NLRP3 participates in the regulation of innate immunity in invertebrates is still unknown. In the present study, we characterized a NLRP3 ortholog in Penaeus vannamei (designated PvNLRP3-like) with 2514 bp length of open reading frame (ORF) encoding a putative protein of 837 amino acids. Sequence analysis revealed that PvNLRP3-like contained only NACHT domain and shared closely homology with other invertebrates, but the topological structure of NACHT domain of PvNLRP3-like is similar with that in human NLRP3. PvNLRP3-like was ubiquitously expressed in tissues and induced in hemocytes by Vibrio parahaemolyticus, Streptococcus iniae and White Spot Syndrome Virus (WSSV) challenge, suggesting that PvNLRP3-like participated in the immune responses to pathogens. Furthermore, silencing of PvNLRP3-like followed by V. parahaemolyticus stimulation negatively regulated the transcripts of antimicrobial peptides (AMPs) including Lysozyme (LYZ) 3, Crustin (CRU) 2, Anti-lipopolysaccharide factor (ALF) 2/3 and Penaeidins (PEN) 3/4. This study enriches our current knowledge on shrimp innate immunity, and provides novel perspective to understand the immune regulation role of PvNLRP3-like.

Increasingly attention has been paid to the active substances in grapefruit peel. In this study, insoluble bound phenolic compounds (BP) were released from grapefruit peel insoluble dietary fiber (GP-IDF) by microwave extraction (M-BP), enzymatic hydrolysis (E-BP) and combined microwave and enzymatic treatment (ME-BP). The results showed that the yield of ME-BP was the highest (148.856 ± 0.620 GAE mg/100 g), and conditions of microwave treatment (microwave power, temperature, time) were 600 W, 85 °C, and 37 min, while that of enzymatic treatment were 8% addition, 60 °C, and 2 h. Scanning electron microscopy displayed that GP-IDF became looser by ME. ME mainly resulted in the removal of lignin in IDF from X-ray diffraction, which was consistent with FT-IR. Twenty seven BP were identified by UPLC-ESI-QTOF-MS/MS. The high content of gallic acid (42.50 ± 3.21 μg/g DW), ferulic acid (18.46 ± 1.65 μg/g DW) and protocatechuic acid (6.16 ± 0.72 μg/g DW) was quantified by LC-ESI-QqQ-MS/MS. Furthermore, ME-BP showed stronger antioxidant capacities than that of others (ABTS, oxygen and DPPH free radical scavenging ability), and showed good inhibition of α-glucosidase. Our results demonstrated that combined microwave and enzymatic treatment was an effective treatment for improving the release of BP.

The prediction of drug-target interactions plays an important role in the drug discovery process, which serves to identify new drugs or novel targets for existing drugs. However, experimental methods for predicting drug-target interactions are expensive and time-consuming. Therefore, the in silico prediction of drug-target interactions has recently attracted increasing attention. In this study, we proposed a kernel matrix dimension reduction method (KMDR) for predicting drug-target interactions, and in order to facilitate benchmark comparisons, two other representative algorithms, the Regularized Least Squares classifier (RLS) and the semi-supervised link prediction classifier (SLP), were also used to predict drug-target interactions on a same dataset. The results show that the kernel matrix reduction dimension method could improve the performance on drug-target interaction prediction; in particular, KMDR could significantly improve performance on low degree drug target interaction prediction. We further show that, in theory, the formulations of above three algorithms have a unified form, which could be seen as a kernel matrix transformation based on eigenvalue. This finding could provide us a research direction -- to design better algorithms for predicting drug-target interaction by optimize kernel matrix transformation based on eigenvalue.

Background The molecular characterization of carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) isolates is not well studied. Our goal was to investigate the molecular epidemiology of CR-hvKP strains that were isolated from a Chinese hospital. Results All clinical carbapenem-resistant K. pneumoniae (CR-KP) isolates were collected and identified from patient samples between 2014 and 2017 from a Chinese hospital. The samples were subjected to screening for CR-hvKP by string test and the detection of the aerobactin gene. CR-hvKP isolates were further confirmed through neutrophil phagocytosis and a mice lethality assay. The CR-hvKP isolates were investigated for their capsular genotyping, virulence gene profiles, and the expression of carbapenemase genes by PCR and DNA sequencing. Multilocus sequence type (MLST) and pulsed-field gel electrophoresis (PFGE) were performed to exclude the homology of these isolates. Twenty strains were identified as CR-hvKP. These strains were resistant to imipenem and several other antibiotics, however, most were susceptible to amikacin. Notably, two isolates were not susceptible to tigecycline. Capsular polysaccharide synthesis genotyping revealed that 17 of the 20 CR-hvKP strains belonged to the K2 serotype, while the others belonged to serotypes other than K1, K2, K5, K20, and K57. The strains were found to be positive for 10 types of virulence genes and a variety of these genes coexisted in the same strain. Two carbapenemase genes were identified: blaKPC-2 (13/20) and blaNDM-1 (1/20). PFGE typing revealed eight clusters comprising isolates that belonged to MLST types ST25, ST11 and ST375, respectively. PFGE cluster A was identified as the main cluster, which included 11 isolates that belong to ST25 and mainly from ICU department. Conclusions Our findings suggest that hospital-acquired infections may contribute in part to the CR-hvKP strains identified in this study. It also suggests that ST25 CR-hvKP strain has a clonal distribution in our hospital. Therefore, effective surveillance and strict infection control strategies should be implemented to prevent outbreak by CR-hvKP strains in hospitals setting.

This study was conducted to investigate the effects of replacing in-feed antibiotics with synergistic organic acids on growth performance, health, carcass, and immune and oxidative statuses of broiler chickens under Clostridium perfringens (CP) type A challenge. Two organic acid products were tested: organic acid 1 (OA1), consisting of butyrate, medium-chain fatty acids, organic acids, and phenolics; and organic acid 2 (OA2), consisting of buffered short-chain fatty acids. Six hundred 1-day-old male Arbor Acres broiler chicks were randomly assigned to one of five treatments: Control 1, basal diet, nonchallenged birds; Control 2, basal diet, with CP challenge; antimicrobial growth promoters (AGP), basal diet supplemented with Aureomycin (chlortetracycline), with CP challenge; OA1, basal diet supplemented with OA1, with CP challenge; and OA1OA2, basal diet supplemented with OA1 and OA2, with CP challenge. Each treatment had eight replicate pens of 15 birds. The experiments lasted for 29 days. The disease challenge was performed on days 15-17, with an oral gavage of 0.5 mL of CP culture (2.0 × 108 colony-forming units [CFU]/mL) for each bird. Body weights (BWs), intestinal lesion scores, immune organ indices, and serum malondialdehyde (MDA) concentrations were measured on days 19, 22, and 29, respectively, in three birds per pen. Carcass characteristics were determined on day 29. No treatment-related differences in mortality were noted before (P = 0.28) or after (P = 0.64) challenge or over the whole study period (days 0-28; P = 0.66). On day 19, the BW of Control 2 was lower than other treatments (P0.0001). On day 22, AGP, OA1, and OA1OA2 had higher BW than Control 2 (P = 0.001). The breast muscle yield of OA1 and OA1OA2 was higher than AGP (P0.05). The abdominal fat yield of OA1OA2 was lower than AGP and Control 2 (P0.05). On day 22, the birds fed OA1OA2 showed lower intestinal lesion scores than OA1 (P0.05). No treatment-related differences in immune organ (spleen, thymus, and bursa) indices were noted (P0.05). On day 29, the MDA concentration of OA1 and OA1OA2 was lower than those of Control 1 and AGP (P0.05). In conclusion, the addition of organic acids may protect broiler chickens from severe intestinal lesions and oxidative stress and may help reduce abdominal fat mass deposition. There is potential for organic acid-based products as alternatives for AGP in preventing necrotic enteritis in broilers.

Schisandra chinensis (Turcz.) Baill., Schisandraceae, is a well-known traditional Chinese medicine used mainly as a recipe for hepatoprotection. Modern researches have revealed that the hepatoprotection is related to its lignans and crude polysaccharide. In this study, we examined the effect and mechanism of S. chinensis total lignans on the liver injury induced by alcoholic. S. chinensis total lignans were extracted with ethanol extraction. The liver index, alanine aminotransferase and aspartate aminotransferase levels in serum of the rat culture supernatant were examined. The malondialdehyde level and superoxide dismutase activities in serum and liver tissue, and triacylglyceride content in liver tissue were tested. Western blot was conducted to determine cytochrome P450 2E1 expression in liver tissue of rats. The results showed that S. chinensis total lignans administration significantly inhibited alcohol-induced liver injury. In exploring the underlying mechanisms of S. chinensis total lignans action, we found that it significantly decreased Alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (AKP), Glutamyl transpeptidase (γ-GT), reactive oxygen species (ROS) and malondialdehyde (MDA) level in livers/serum and inhibited the gene expression level of CYP2E1 in rat livers. The Nuclear factor erythroid-2 related factor 2 (Nrf2) gene expression and Nuclear factor erythroid-2 related factor 2 (Nrf2) protein nuclear transfer increased significantly, and significantly increased the expression of downstream target gene and protein heme oxygenase-1 (HO-1), Glutamate--cysteine ligase regulatory subunit (GCLM), NAD(P)H:quinine oxidoreductase 1 (NQO1). Moreover, S. chinensis total lignans decreased production of pro-inflammatory markers including Tumor Necrosis Factor-α (TNF-α), Interleukin-1beta (IL-1β) and Interleukin-6 (IL-6). In conclusion, these results suggested that the inhibition of alcohol-induced liver injury by S. chinensis total lignans is associated with its ability to inhibiting CYP2E1 activation and activating the Nrf2/Antioxidant response element(ARE) signaling pathway. Keywords: Lignans, SCTL, Alcoholic liver injury, CYP2E1, Nrf2/ARE

Recently, rot disease caused by bacteria has seriously affected the yield of Pleurotus eryngii in China, as well as spreading so quickly that brought enormous economy loss to the mushroom industry. Therefore, we isolated and identified the pathogen according to morphologic characteristic and 16S rDNA sequence, which demonstrated that the pathogen was Pseudomonas putida. Simultaneously, the active ingredients of twelve plants were extracted and their antimicrobial activities against the pathogen were evaluated by measuring the inhibition zone. Four better essential oils were selected for further investigation of their disease control efficiency by spraying them on the surface of the mushroom. Overall, the extract of Ginkgo biloba presented the highest efficiency in controlling the rot disease. The results from this research suggest that the extract of plants has a good potential for controlling rot disease in P. eryngii.

Benefiting from the high-throughput sequencing technologies, many single nucleotide variants (SNVs) among individuals have been detected. SNVs in gene code regions were known to possibly disrupt protein functions. For this, many efforts were devoted to sort deleterious SNVs from benign ones. In general, features in the past studies can be categorized into codon level, peptide level and protein level. While those at peptide level were in widespread use, few works have carried out a comprehensive analysis by combining three levels information. In the present work, we incorporated both codon and protein level information with peptide level information to predict disease-related SNVs. Taking the advantage of combinatory multiple level features, our method exhibited competitive performance against seven well-known classifiers. Additionally, by incorporating selective pressure score and protein–protein interaction (PPI) information, we found that the functional important proteins were protected through a pressure-resistant mechanism during the evolution. Although critical proteins were obviously related with more deleterious SNVs, these pathogenic SNVs were tend to under higher selective pressures comparing to the benign variants. These results support the ongoing researches about relation between genotype and phenotype.

In this work, ZnCr–mixed metal oxides (MMO) hybridized with functionalized carbon nanotubes (A-CNTs) have been successfully fabricated via vacuum calcination of the layered double hydroxide precursors. The structural and morphological characterization of the samples was investigated by multiple techniques such as XRD, SEM, TEM, XPS, BET, Raman and UV-vis DRS. The results showed that A-CNTs were well incorporated into the MMO nanoparticles to form a nanohybrid structure dependent upon intimate interfacial contact. As compared to pristine MMO, the obtained MMO–CNTs nanohybrids exhibited significantly enhanced photocatalytic performance for bisphenol A (BPA) degradation under simulative solar light irradiation, providing powerful evidence for the superiority of the hybridization with A-CNTs. The key role of A-CNTs played in enhancing the photocatalytic activity of the nanohybrids was probably ascribed to the larger surface area, higher visible light absorption and the more efficient restriction of charge carriers recombination.

Microwave-sodium hydroxide treatment (MST), microwave-enzymatic treatment (MET) and microwave-ultrasonic treatment (MUT) were used to treat grapefruit peel, then the structural and functional properties of extracted soluble dietary fibers (SDF), named as MST-SDF, MET-SDF and MUT-SDF, were investigated. The scanning electron microscopy, molecular weight, X-ray diffraction, FT-IR, thermal properties and monosaccharide composition were used to determine the structural properties. Compared to the grapefruit peel SDF without treatment (WT-SDF) and pure microwave treatment (PMT-SDF), MST-SDF, MET-SDF and MUT-SDF showed a more complex and loose structure. Moreover, they possessed higher molecular weight, crystallinity and thermal stability, and more diverse monosaccharide composition. In addition, functional properties, including water holding capacity (WHC), oil holding capacity (OHC), cholesterol adsorption capacity (CAC), glucose adsorption capacity (GAC) and nitrite ion adsorption capacity (NIAC), were enhanced by the three different modification methods. Especially, MUT-SDF showed the highest WHC, OHC, CAC, GAC and NIAC as compared with the other samples. In summary, the present study suggested that the MUT could be used as the ideal modification method for grapefruit peel SDF, and MUT-SDF has great potential for the application in functional food industry.

In traditional Chinese medicine, both crude and processed herbs are used to treat different diseases. Therefore, suitable chemical markers are crucial for the discrimination between these crude and processed herbs. In this study, a rapid strategy which used ultra-high performance liquid chromatography combined with a triple quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MS) was coupled with multivariate statistical analyses to rapidly explore the potential chemical components as chemical markers. These proposed potential chemical markers were then validated. Schisandrae Chinensis Fructus (SCF) was selected as the research object, and batches of both crude and vinegar processed samples were determined using UPLC-Q-TOF/MS. The datasets of the tR-m/z pairs, ion intensities, and sample codes were subjected to a principal component analysis (PCA), as well as an orthogonal partial least squared discriminant analysis (OPLS-DA), in order to holistically compare the differences between the crude and processed samples. The identities of the potential markers were arrived at by comparing the mass spectra and retention times with those of the reference compounds, and/or were tentatively assigned by matching an empirical molecular formula with that of the published compounds. Using this proposed strategy, the Schisantherin D, Schisandrin A and Schisandrin B and 5-Hydroxymethylfurfural were rapidly determined to be the most characteristic chemical markers of the SCF and vinegar-processed SCF (VSCF), respectively. This newly proposed strategy can not only be potentially used to explore chemical markers, but also used to investigate the chemical transforming mechanisms underlying traditional herb processing.

Thoracolumbar fractures are usually treated by open posterior pedicle screw fixation. However, this procedure involves massive paraspinal muscle stripping, inflicting surgical trauma, and prolonged X-ray exposure. In this study, we observed 127 patients with single-segment injury thoracolumbar fractures. Thirty-six patients were treated by the modified Wiltse's paraspinal approach with minimally invasive channel system, while 91 patients were treated via traditional posterior approach. Operation time, intraoperative blood loss, intraoperative fluoroscopy frequency, screw placement accuracy, visual analogue scale score, and Cobb's angle of two groups were compared. The X-ray exposure times were notably reduced (4.2±1.6) in the new approach group (P

Background TEs pervade mammalian genomes. However, compared with mice, fewer studies have focused on the TE expression patterns in rat, particularly the comparisons across different organs, developmental stages and sexes. In addition, TEs can influence the expression of nearby genes. The temporal and spatial influences of TEs remain unclear yet. Results To evaluate the TEs transcription patterns, we profiled their transcript levels in 11 organs for both sexes across four developmental stages of rat. The results show that most short interspersed elements (SINEs) are commonly expressed in all conditions, which are also the major TE types with commonly expression patterns. In contrast, long terminal repeats (LTRs) are more likely to exhibit specific expression patterns. The expression tendency of TEs and genes are similar in most cases. For example, few specific genes and TEs are in the liver, muscle and heart. However, TEs perform superior over genes on classing organ, which imply their higher organ specificity than genes. By associating the TEs with the closest genes in genome, we find their expression levels are correlated, independent of their distance in some cases. Conclusions TEs sex-dependently associate with nearest genes. A gene would be associated with more than one TE. Our works can help to functionally annotate the genome and further understand the role of TEs in gene regulation. Electronic supplementary material The online version of this article (10.1186/s12864-017-4078-7) contains supplementary material, which is available to authorized users.

Hepatocellular carcinoma (HCC) is currently still a major factor leading to death, lacking of reliable biomarkers. Therefore, deep understanding the pathogenesis for HCC is of great importance. The emergence of circular RNA (circRNA) provides a new way to study the pathogenesis of human disease. Here, we employed the prediction tool to identify circRNAs based on RNA-seq data. Then, to investigate the biological function of the circRNA, the candidate circRNAs were associated with the protein-coding genes (PCGs) by GREAT. We found significant candidate circRNAs expression alterations between normal and tumor samples. Additionally, the PCGs associated with these candidate circRNAs were also found have discriminative expression patterns between normal and tumor samples. The enrichment analysis illustrated that these PCGs were predominantly enriched for liver/cardiovascular-related diseases such as atherosclerosis, myocardial ischemia and coronary heart disease, and participated in various metabolic processes. Together, a further network analysis indicated that these PCGs play important roles in the regulatory and the PPI network. Finally, we built a classification model to distinguish normal and tumor samples by using candidate circRNAs and their associated genes, respectively. Both of them obtained satisfactory results (~ 0.99 of AUC for circRNA and PCG). Our findings suggested that the circRNA could be a critical factor in HCC, providing a useful resource to explore the pathogenesis of HCC.

The rhizome of Anemarrhena asphodeloides Bge. is commonly used as an herbal medicine in China. In this study, ultra-high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UHPLC-QTOF-MS) was used, in both negative and positive ion modes, to comprehensively analyze the chemical constituents of A. asphodeloides. From the intact precursor ions, MS/MS fragmentation information, and previous reports, we identified 89 compounds. These compounds included 8 cyclic peptides, 11 flavones (9 xanthones), 45 steroidal saponins, 15 fatty acids, 3 lignans, and 7 other compounds. Dimer xanthones and cyclic peptides are reported for the first time in A. asphodeloides. The analytical method we have developed is simple, reliable, and effective. The results provide comprehensive information on the metabolite profile of A. asphodeloides, which may benefit the quality control and further utilization of A. asphodeloides.

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Genome-wide association studies (GWAS) have identified more than sixty single nucleotide polymorphisms (SNPs) associated with increased risk for type 2 diabetes (T2D). However, the identification of causal risk SNPs for T2D pathogenesis was complicated by the factor that each risk SNP is a surrogate for the hundreds of SNPs, most of which reside in non-coding regions. Here we provide a comprehensive annotation of 65 known T2D related SNPs and inspect putative functional SNPs probably causing protein dysfunction, response element disruptions of known transcription factors related to T2D genes and regulatory response element disruption of four histone marks in pancreas and pancreas islet. In new identified risk SNPs, some of them were reported as T2D related SNPs in recent studies. Further, we found that accumulation of modest effects of single sites markedly enhanced the risk prediction based on 1989 T2D samples and 3000 healthy controls. The AROC value increased from 0.58 to 0.62 by only using genotype score when putative risk SNPs were added. Besides, the net reclassification improvement is 10.03% on the addition of new risk SNPs. Taken together, functional annotation could provide a list of prioritized potential risk SNPs for the further estimation on the T2D susceptibility of individuals.

The present study was designed to systematically investigate the chemical profile differences between crude Anemarrhenae rhizoma (CAR) and salt-processed Anemarrhenae rhizoma (SAR). Ultra-high-performance liquid chromatography–quadrupole time-of-flight mass spectrometry (UHPLC–QTOF-MS), coupled with multivariate statistical analysis was used for the discrimination of chemical profiles and the identification of the differentiation of the chemical constitutions of CAR and SAR. In addition, seven main constituents of CAR and SAR were simultaneously determined by ultra-high-performance liquid chromatography–quadrupole mass spectrometry (UHPLC–MS) for analyzing the content variations. A total of 24 components were found to be the main contributors to the significant difference between CAR and SAR. The structures of the marker compounds were identified based on their chromatographic behaviors, intact precursor ions, and characteristic MS fragmentation patterns. The potential structural transformation mechanism of furostanol saponins during salt processing was explored. The results may provide a scientific foundation for deeply elucidating the processing mechanism of Anemarrhenae rhizoma.

The prediction of drug-target interactions is a key step in the drug discovery process, which serves to identify new drugs or novel targets for existing drugs. However, experimental methods for predicting drug-target interactions are expensive and time-consuming. Therefore, the in silico prediction of drug-target interactions has recently attracted increasing attention. In this study, we propose an eigenvalue transformation technique and apply this technique to two representative algorithms, the Regularized Least Squares classifier (RLS) and the semi-supervised link prediction classifier (SLP), that have been used to predict drug-target interaction. The results of computational experiments with these techniques show that algorithms including eigenvalue transformation achieved better performance on drug-target interaction prediction than did the original algorithms. These findings show that eigenvalue transformation is an efficient technique for improving the performance of methods for predicting drug-target interactions. We further show that, in theory, eigenvalue transformation can be viewed as a feature transformation on the kernel matrix. Accordingly, although we only apply this technique to two algorithms in the current study, eigenvalue transformation also has the potential to be applied to other algorithms based on kernels.

A unique thermal model supported by experimental data has been successfully developed for the study of splicing joint, which is the main weakness for >100s watt fiber laser. Surface temperature of the fiber was monitored at pumping powers up to 230W under various cooling configurations. Temperature matching using a Finite Element Modeling (FEM) software was achieved by adjusting the magnitude of the heat load. This allowed reliable characterization of heating in splice joints and led to a precise prediction of the splice point temperature at higher powers. Excellent agreement to within 2°C between modeling and experimental data was achieved. This thermal simulation methodology is extended to study the splicing joint between passive fiber and active fiber under pumping power of 1.5kW. It shows the maximum surface temperature of the active fiber is