Comparison of two multiplex PCR tests for common pathogen detection in hospitalized children with acute respiratory infection.

INTRODUCTION: Multiplex PCR methods have significantly improved the diagnosis of acute respiratory tract infections (ARTIs) in children. The ResP-CE System coupled with capillary electrophoresis is a highly specialized, automated, and expensive technology for detecting common pathogens in ARTIs. The XYRes-MCA System, a remarkably less expensive multiplex PCR instrument, employs hybridization for the detection of ARTI pathogens. Both methods detect 9 common microorganisms in ARTIs, i.e., RSV, FLUAV, FLUBV, ADV, PIV, HMPV, HBOV, HCOV, and MP. In this study, we aimed to compare the performance of these two methods in the detection of pathogens from sputum specimens collected from children with ARTIs. METHODOLOGY: Sputum specimens were collected from 237 hospitalized children with ARTIs. Nucleic acid was extracted on an automated workstation. The ResP-CE and XYres-MCA systems were applied to detect pathogens from the samples, and the test result agreement between the two methods was evaluated using Kappa statistics. RESULTS: The ResP-CE and XYres-MCA identified pathogens, single or in combination, in 151 (63.7%) and 171 (72.1%) of 237 samples, respectively. Approximately 85% of positive samples identified by either method contained a single pathogen. Moderate to almost perfect concordance between the two methods was found in detecting the following 7 pathogens: RSV, FLUAV, FLUBV, PIV, HMPV, HBOV, and MP. CONCLUSIONS: These two methods are comparable in detecting common pathogens of ARTIs in children. As XYres-MCA analysis is more cost-effective, it could play an important role in diagnosing ARTIs in children in less economically developed regions.

Rapid and precise identification of bloodstream infections using a pre-treatment protocol combined with high-throughput multiplex genetic detection system.

BACKGROUND: Bloodstream infection (BSI) is a life-threatening condition with high morbidity and mortality rates worldwide. Early diagnosis of BSI is critical to avoid the unnecessary application of antimicrobial agents and for proper treatment. However, the current standard methods based on blood culture are time-consuming, thus failing to provide a timely etiological diagnosis of BSI, and common PCR-based detection might be inhibited by matrix components. METHODS: The current study explored an integrated pre-analytical treatment protocol for whole blood samples, wherein pathogens are enriched and purified by incubation and concentration, and inhibitors are inactivated and removed. Further, this study developed and evaluated a novel high-throughput multiplex genetic detection system (HMGS) to detect 24 of the most clinically prevalent BSI pathogens in blood culture samples and pre-treated whole blood samples. The specificity and sensitivity were evaluated using related reference strains and quantified bacterial/fungal suspensions. The clinical utility of BSI-HMGS combined with the pre-analytical treatment protocol was verified using blood cultures and whole blood samples. RESULTS: The combined pre-treatment protocol and BSI-HMGS was highly specific for target pathogens and possessed a low detection limit for clinical whole blood samples. The pre-treatment protocol could deplete the PCR inhibitors effectively. For blood culture samples, the current method showed 100.0% negative percent agreements and > 87.5% positive percent agreements compared to the reference results based on blood culture findings. For whole blood samples, the current method showed 100.0% negative percent agreements and > 80.0% positive percent agreements compared to the reference results for most pathogens. The turnaround time was ≤ 8 h, and all the procedures could be conducted in a general clinical laboratory. CONCLUSION: The BSI-HMGS combined with the pre-treatment protocol was a practical and promising method for early and precise detection of BSIs, especially for areas without access to advanced medical facilities.

Soil Heavy Metal Content and Enzyme Activity in Uncaria rhynchophylla-Producing Areas under Different Land Use Patterns.

In this study, we investigated the content of soil heavy metals, the level of heavy metal pollution and the characteristics of soil enzyme activity under three different land use patterns of Uncaria rhynchophylla base, forestland and wasteland in Jianhe County, Qiandongnan Prefecture, Guizhou Province, revealing the intrinsic correlation between heavy metal content and soil enzyme activity to reveal the relationship between soil enzyme activity and heavy metal content under different land use patterns in the Uncaria rhynchophylla production area. The results showed that soil Cd and Hg contents in Uncaria rhynchophylla base both exceeded the national soil background value. The single pollution index indicated that Cd had the greatest contribution to Pn, and the comprehensive pollution index (Pn) demonstrated no heavy metal pollution in the soil of Uncaria rhynchophylla-producing areas. Under different land use patterns, the enzyme activity was forestland > wasteland > Uncaria rhynchophylla base, and catalase and acid phosphatase activities presented significant spatial differences (p < 0.05). The correlation between soil enzyme activity and heavy metal content was uncertain due to the changes in land use patterns and heavy metal species. The proportions of positive correlation and negative correlation between soil enzyme activity and heavy metals in Uncaria rhynchophylla base were 50%, respectively. In the forestland, soil enzyme activity was positively correlated with heavy metals, while in the wasteland, soil enzyme activity was negatively correlated with heavy metals. This study revealed that the changes in heavy metal content should be focused on for the soil quality in Uncaria rhynchophylla-producing areas under different land use patterns. The results of the study provide some basic theoretical references for the improvement of soil quality in the production area of Uncaria rhynchophylla under different land use practices.

Developing a multiplex PCR-based assay kit for bloodstream infection by analyzing genomic big data.

BACKGROUND: In recent years, the incidence of bloodstream infections (BSI) has increased, the composition of pathogenic bacteria has changed, and drug resistance among bacteria has gradually increased due to the widespread use of interventional techniques, broad-spectrum antibacterial drugs, hormones, and immunosuppressive agents. Here, we have developed a multiplex PCR assay kit for the detection of pathogens (14 Gram-negative bacteria, 15 Gram-positive bacteria, and 4 fungi) in whole blood from patients with BSI using five-color fluorescent multiplex PCR followed by capillary electrophoresis. Our assay exhibits a diagnosis of higher quality and an improved detection rate for common pathogens. METHODS: A local genome DNA database of 33 pathogenic bacteria was constructed. Next, "Exhaustive" primer search of the full coding sequence of the reference genomes of these bacteria was performed. Panels with minimal interactions between primers and amplicons were selected by random sampling and testing by a recursive algorithm. Primers and Mg2+ concentrations and PCR reaction procedures were optimized to maximize the detection efficacy. RESULTS: The LOD of the kit was determined as 100 copies/µl. Using clinical samples, results generated by this kit and regular blood culture method were found to be 95.08% consistent. Additionally, six pathogens which were unidentifiable by blood culture were successfully detected by this kit. CONCLUSION: Our study provided a bioinformatics approach to the challenge of primer design in multiplex PCR, and combined with optimized wet lab practice, a multiplex PCR-based assay kit for BSI with higher sensitivity and accuracy than blood culture was produced.

Simultaneous detection of 9 respiratory pathogens using a newly developed multiplex real-time PCR panel based on an automatic molecular detection and analysis system.

Timely identification of respiratory pathogens guides specific treatment, reduces hospital costs and minimizes the excessive use of antibiotics. A new multiplex real-time PCR panel was developed based on an automatic molecular detection and analysis system (AutoMolec system), consisting of three separate internally controlled assays. Mycoplasma pneumoniae, Chlamydia pneumoniae, adenovirus, human metapneumovirus, influenza B virus, respiratory syncytial virus and human parainfluenza virus 1-3 may be directly detected in original samples. The system's clinical performance was evaluated by comparison with an approved commercial kit, using 517 clinical samples. The limit of detection of the AutoMolec mRT-PCR panel ranged from 4 × 10-4 ∼3.3 TCID50/mL and no cross-reaction with common respiratory pathogens was observed. The AutoMolec mRT-PCR panel had 99.09% sensitivity and 100.0% specificity and overall detection consistency was 99.61%, making it comparable to that of the commercial kit. Therefore, the AutoMolec mRT-PCR panel has great potential for routine screening of respiratory infection in China.

Lamb Wave-Based Damage Localization and Quantification in Composites Using Probabilistic Imaging Algorithm and Statistical Method.

Quantitatively and accurately monitoring the damage to composites is critical for estimating the remaining life of structures and determining whether maintenance is essential. This paper proposed an active sensing method for damage localization and quantification in composite plates. The probabilistic imaging algorithm and the statistical method were introduced to reduce the impact of composite anisotropy on the accuracy of damage detection. The matching pursuit decomposition (MPD) algorithm was utilized to extract the precise TOF for damage detection. The damage localization was realized by comprehensively evaluating the damage probability evaluation results of all sensing paths in the monitoring area. Meanwhile, the scattering source was recognized on the elliptical trajectory obtained through the TOF of each sensing path to estimate the damage size. Damage size was characterized by the Gaussian kernel probability density distribution of scattering sources. The algorithm was validated by through-thickness hole damages of various locations and sizes in composite plates. The experimental results demonstrated that the localization and quantification absolute error are within 11 mm and 2.2 mm, respectively, with a sensor spacing of 100 mm. The algorithm proposed in this paper can accurately locate and quantify damage in composite plate-like structures.

Establishment and evaluation of a quadruple quantitative real-time PCR assay for simultaneous detection of human coronavirus subtypes.

BACKGROUND: The newly discovered severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and four seasonal human coronaviruses (HCoVs) (HCoV-229E, HCoV-OC43, HCoV-NL63 and HCoV-HKU1) still circulate worldwide. The early clinical symptoms of SARS-CoV-2 and seasonal HCoV infections are similar, so rapid and accurate identification of the subtypes of HCoVs is crucial for early diagnosis, early treatment, prevention and control of these infections. However, current multiplex molecular diagnostic techniques for HCoV subtypes including SARS-CoV-2 are limited. METHODS: We designed primers and probes specific for the S and N genes of SARS-CoV-2, the N gene of severe acute respiratory syndrome coronavirus (SARS-CoV), and the ORF1ab gene of four seasonal HCoVs, as well as the human B2M gene product. We developed and optimized a quadruple quantitative real-time PCR assay (qq-PCR) for simultaneous detection of SARS-CoV-2, SARS-CoV and four seasonal HCoVs. This assay was further tested for specificity and sensitivity, and validated using 184 clinical samples. RESULTS: The limit of detection of the qq-PCR assay was in the range 2.5 × 101 to 6.5 × 101 copies/µL for each gene and no cross-reactivity with other common respiratory viruses was observed. The intra-assay and inter-assay coefficients of variation were 0.5-2%. The qq-PCR assay had a 91.9% sensitivity and 100.0% specificity for SARS-CoV-2 and a 95.7% sensitivity and 100% specificity for seasonal HCoVs, using the approved commercial kits as the reference. Compared to the commercial kits, total detection consistency was 98.4% (181/184) for SARS-CoV-2 and 98.6% (142/144) for seasonal HCoVs. CONCLUSION: With the advantages of sensitivity, specificity, rapid detection, cost-effectiveness, and convenience, this qq-PCR assay has potential for clinical use for rapid discrimination between SARS-CoV-2, SARS-CoV and seasonal HCoVs.

A New Multiplex Genetic Detection Assay Method for the Rapid Semi-Quantitative Detection of Six Common Curable Sexually Transmitted Pathogens From the Genital Tract.

Background: Sexually transmitted infections (STIs) are some of the most common communicable conditions and exert impact on the health and lives of many hundreds of millions of people across the world every year. Screening high-risk populations and conducting comprehensive detection tests would lead to a significant improvement in preventing the transmission of STIs and help us to provide rapid treatment to those affected. Here, we successfully established and validated a novel high-throughput multiplex gene detection system (HMGS) for the simultaneous and semiquantitative detection of six important curable sexually transmitted pathogens in a single reaction from secretions samples. Method: Fluorescently labeled primers were designed to target specific conserved and single-copy gene fragments of Ureaplasma urealyticum (U. urealyticum), Mycoplasma hominis (M. hominis), Chlamydia trachomatis (C. trachomatis), Neisseria gonorrhoeae (N. gonorrhoeae), Trichomonas vaginalis (T. vaginalis), and Treponema pallidum (T. pallidum). The specificity and sensitivity of the STI-HMGS was validated and optimized using plasmids and quantitative genomic DNA. Next, we validated the performances of the STI-HMGS for clinical application by testing samples of clinical secretions collected from patients who visited the gynecology and urology outpatient clinics of our reproductive medicine center. Results derived from the STI-HMGS were then compared with three approved commercialized kits that used to detect U. urealyticum, C. trachomatis and N. gonorrhoeae, respectively, followed by further validation with Sanger sequencing for all pathogens. Finally, a comprehensive analysis of epidemiology was performed among different subgroups to investigate the association between infection rates and clinically-relevant information. Results: The sensitivity of STI-HMGS for six target genes was 10 copies/µL. Data derived from the detection of 381 clinical secretions demonstrated that the STI-HMGS exhibited high concordance rate compared with approved commercialized kits and almost 100% sensitivity and specificity for the detection of six sexually transmitted pathogens when validated by Sanger sequencing. Semi-quantitative analysis found that STIs caused by N. gonorrhoeae had a significantly higher (P<0.05) pathogen load than the other pathogens. Infections caused by C. trachomatis were significantly more common in younger individuals (P<0.05). We also found that U. urealyticum infections were more likely to happen in females; while the males were more affected by N. gonorrhoeae (P<0.05). Conclusions: STI-HMGS proved to be an efficient method for the semi-quantitative detection of six important curable sexually transmitted pathogens and therefore represents an alternative method for the clinical detection and monitoring of STIs.

Prospective case-control study of enterovirus detection differences in children's cerebrospinal fluid between multiplex PCR and real-time RT-PCR assay.

BACKGROUND: Viral encephalitis is common in childhood. It is an acute brain parenchymal inflammation caused by a variety of viral infection, and enterovirus accounts for the majority. Due to atypical clinical manifestations, pathogenic testing is important for assisting clinical diagnosis. The purpose of this study was to evaluate the performance of the multiplex PCR assay compared with quantitative real-time PCR for enterovirus detection. METHODS: A prospective case-control study was performed involving 103 pediatric patients suspected for viral encephalitis and cerebrospinal fluid (CSF) samples were collected and tested for 9 pathogens using multiplex PCR assay during April to November in 2018. In parallel, an aliquot of samples was tested for enterovirus infection by real-time PCR assay. RESULTS: There were 85.4% children were confirmed as viral encephalitis on discharge, the remaining ones were diagnosed as other CNS diseases, such as epilepsy. The specificity of the two methods was the same as that of the clinical diagnosis, but the sensitivity and consistency with clinical diagnosis of multiplex PCR were both higher than the real-time PCR. Besides of enterovirus, multiplex PCR could also detect coinfection of enterovirus with Epstein-Barr virus and mumps virus. CONCLUSION: Results of multiplex PCR method are more consistent with the clinical diagnosis and are superior to real-time PCR for detecting enterovirus in CSF.

Application of Coblation Tonsillectomy with Inferior Pole Capsule Preservation in Pediatric Patients.

OBJECTIVES/HYPOTHESIS: To evaluate the application and advantages of coblation tonsillectomy with inferior pole capsule preservation in pediatric patients with tonsillar hypertrophy and recurrent tonsillitis. STUDY DESIGN: Retrospective chart review. METHODS: A total of 726 children who were diagnosed with either tonsillar hypertrophy or recurrent tonsillitis were included. Children were divided into two groups according to the surgical technique: conventional coblation tonsillectomy and coblation tonsillectomy with inferior pole capsule preservation. The duration of surgery, intraoperative hemorrhage volume, and postoperative pain, as well as postoperative hemorrhage data in the format of time, location, and degree were compared between the two groups. RESULTS: Of the 726 children included, conventional coblation tonsillectomy was performed in 320 children, coblation tonsillectomy with inferior pole capsule preservation was performed in 406 children. There were no significant differences in duration of surgery or intraoperative hemorrhage volume between the two groups. Children who underwent coblation tonsillectomy with inferior pole capsule preservation showed a remarkable improvement in postoperative pain on days 3 and 5 postoperatively. Additionally, the coblation tonsillectomy with inferior pole capsule preservation group exhibited a significantly lower total postoperative hemorrhage rate, secondary hemorrhage rate, and hemorrhage rate in the inferior pole compared with that in the conventional coblation tonsillectomy group. During the 1-year follow-up period, no cases of tonsillar re-hypertrophy or recurrent tonsillitis were observed in either group. CONCLUSION: For pediatric tonsillar hypertrophy and recurrent tonsillitis, coblation tonsillectomy with inferior pole capsule preservation is a safe and effective technique, capable of reducing postoperative pain and hemorrhage, especially secondary hemorrhage at the inferior pole. LEVEL OF EVIDENCE: 3b Laryngoscope, 131:1157-1162, 2021.

[Application of combined intracapsular and extracapsular hypothermic plasma tonsillectomy in reducing intraoperative and postoperative hemorrhage in children with OSA].

Objective:The aim of this study is to explore the application and advantages of combined intrathecal and extrathecal hypothermic plasma tonsillectomy in reducing intraoperative and postoperative hemorrhage in OSA children. Method:We retrospectively reviewed 726 cases who were diagnosed as OSA. All patients were divided into two groups according to the surgical method: 320 cases by total tonsillectomy and 406 cases by combined extracapsular and intracapsular tonsillectomy. The intro operative bleeding volume, post operative haemorrhage data as time, location and degree in the two groups were compared. Result:There was no statistical difference in the intro operative bleeding volume in the two groups [（9.3±4.6） mL]vs [（7.6±3.5） mL], t=12.687, P=0.235. Two patients who underwent combined extracapsular and intracapsular tonsillectomy presented with post operative haemorrhage, the total post operative haemorrhage rate was significantly decreased that in the total tonsillectomy group（14 cases）（χ²=10.779, P=0.001）. The 2 patients in combined extracapsular and intracapsular tonsillectomy group were secondary haemorrhage, with location in the upper pole and medium, grade A haemorrhage; while in the 14 cases in in the total tonsillectomy group, there were 2 cases presented with primary haemorrhage and 12 cases with secondary haemorrhage; with regard to location of haemorrhage, 1 in the upper pole, 2 in the medium, 11 in the lower pole; 5 cases presented with grade A haemorrhage, 8 with grade B haemorrhage and 1 with grade C haemorrhage. The haemorrhage rate at 7 days after surgery （χ²=5.697, P=0.017）, at the lower pole（χ²=11.961, P=0.001） and grade B（χ²=8.097, P=0.004） were all significantly decreases in the combined extracapsular and intracapsular tonsillectomy group. Conclusion:Plasma tonsillectomy combined with intrathecal and extrathecal hypothermic tonsillectomy is a safe and effective method, which has obvious advantages in reducing the postoperative hemorrhage, especially the secondary hemorrhage of Subtonsillar Pole.

Development and validation of a multiplex-PCR based assay for the detection of 18 pathogens in the cerebrospinal fluid of hospitalized children with viral encephalitis.

BACKGROUND: The Applied Biosystems 3500 Genetic Analyzer (ABI3500) allows for automated capillary electrophoresis on multiple targets. So far, the application of this method for detecting cerebrospinal fluid pathogens has hardly been reported. METHODS: To assess the performance of multiplex-PCR assay for 18 pathogens detection, 127 CSF samples from hospitalized children with suspected viral encephalitis were prospectively collected from April to November 2018. The Sanger sequencing was applied to verify this assay. RESULTS: All of the 18 target pathogens can be identified by multiplex-PCR assay at 104 copies (or CFU/mL) of each virus, bacterium and fungus. In contrast, 10 control microorganisms failed to be amplified. Approximately 68.5 % of the cases tested had positive results, the enterovirus accounted for the majority of the positive cases (63.8 %). Agreement between multiplex-PCR and sequencing was 91.49 %. CONCLUSIONS: Our findings suggest that the ABI3500-based multiplex-PCR detection kit could be a valuable diagnostic tool for pathogen detection in CSF of children with suspected viral encephalitis.

Remaining Useful Life Estimation of Insulated Gate Biploar Transistors (IGBTs) Based on a Novel Volterra k-Nearest Neighbor Optimally Pruned Extreme Learning Machine (VKOPP) Model Using Degradation Data.

The insulated gate bipolar transistor (IGBT) is a kind of excellent performance switching device used widely in power electronic systems. How to estimate the remaining useful life (RUL) of an IGBT to ensure the safety and reliability of the power electronics system is currently a challenging issue in the field of IGBT reliability. The aim of this paper is to develop a prognostic technique for estimating IGBTs' RUL. There is a need for an efficient prognostic algorithm that is able to support in-situ decision-making. In this paper, a novel prediction model with a complete structure based on optimally pruned extreme learning machine (OPELM) and Volterra series is proposed to track the IGBT's degradation trace and estimate its RUL; we refer to this model as Volterra k-nearest neighbor OPELM prediction (VKOPP) model. This model uses the minimum entropy rate method and Volterra series to reconstruct phase space for IGBTs' ageing samples, and a new weight update algorithm, which can effectively reduce the influence of the outliers and noises, is utilized to establish the VKOPP network; then a combination of the k-nearest neighbor method (KNN) and least squares estimation (LSE) method is used to calculate the output weights of OPELM and predict the RUL of the IGBT. The prognostic results show that the proposed approach can predict the RUL of IGBT modules with small error and achieve higher prediction precision and lower time cost than some classic prediction approaches.

Characterization of the relationship between polar and lateral flagellar structural genes in the deep-sea bacterium Shewanella piezotolerans WP3.

Bacteria with a dual flagellar system, which consists of a polar flagellum (PF) and several lateral flagella (LF), have been identified in diverse environments. Nevertheless, whether and how these two flagellar systems interact with each other is largely unknown. In the present study, the relationship between the structural genes for the PF and LF of the deep-sea bacterium Shewanella piezotolerans WP3 was investigated by genetic, phenotypic and phylogenetic analyses. The mutation of PF genes induced the expression of LF genes and the production of LF in liquid medium, while the defective LF genes led to a decrease in PF gene transcription. However, the level of PF flagellin remained unchanged in LF gene mutants. Further investigation showed that the flgH2 gene (encoding LF L-ring protein) can compensate for mutations of the flgH1 gene (encoding PF L-ring protein), but this compensation does not occur between the flagellar hook-filament junction proteins (FlgL1, FlgL2). Swarming motility was shown to specifically require LF genes, and PF genes cannot substitute for the LF genes in the lateral flagella synthesis. Considering the importance of flagella-dependent motility for bacterial survival in the abyssal sediment, our study thus provided a better understanding of the adaptation strategy of benthic bacteria.

Expression of Nogo receptor 1 in the regeneration process of the mouse olfactory epithelium.

Nogo receptor 1 (NgR1) is the most important Nogo-A receptor. By its interaction with myelin-associated inhibitory proteins, NgR1 inhibits the regeneration of axons and is extensively expressed in the central nervous system. However, the expression of NgR1 in regenerable neurons, such as olfactory neurons, and its expression in the regeneration progress of olfactory neurons have not been reported. In this study, we demonstrated that NgR1 was expressed in the cell bodies of certain mature olfactory receptor neurons (ORNs) but was not expressed in immature ORNs in the olfactory epithelium (OE) of normal adult mice. On day 21 after OE injury, NgR1 was expressed not only in the cell bodies of mature ORNs but also in the cell bodies of glial fibrillary acidic protein (GFAP)-positive cells in the top and submucosal layers of the OE. On day 48 after model establishment, NgR1 expression decreased in the cell bodies of the GFAP-positive cells. On day 56 after model establishment, no NgR1 expression was found in the cell bodies of the GFAP-positive cells, and NgR1 was again expressed only in the mature ORNs. Our results demonstrated that NgR1 expression is upregulated in the OE after injury, which suggests that NgR1 might be involved in the regeneration of the OE.

[Evaluation and cumulative characteristics of heavy metals in soil-Uncaria rhynchophylla system of different functional areas].

Soil and Uncaria rhynchophylla in different functional areas were selected for the study,the content of heavy metals such as As, Cd, Cu, Cr, Pb, and Hg in soil and U. rhynchophylla was discussed, the characteristics of their accumulation in the U.rhynchophylla was analyzed, the contamination levels of heavy metals in soil in different functional areas was evaluated. The results showed that content of Cu, As, Pb and Cr in soil was being cropland>woodland>wasteland, content of Cd was being woodland>cropland>wasteland, content of Hg was being cropland>woodland>wasteland. According to quality standard of soil environment, soil Cd in woodland, cropland and wasteland all exceeded the state-level standards, soil Cd in woodland exceeded the secondary standard, soil Hg in cropland and wasteland all exceeded the state-level standards. According to technical conditions of green food producing area, soil Cd in woodland exceeded the limit value of standard. According to Green Trade Standards of Importing Exporting Medicinal Plants Preparations,the content of heavy metals of U.rhynchophylla in cropland,woodland and wasteland were correspond to the specification. From the single factor pollution index, the soil in woodland was polluted by Cd. From the comprehensive pollution index, the soils in different functional areas were not contaminated by heavy metals. The enrichment coefficient of heavy metals such as As, Cu, Cr, and Pb in hook of U.rhynchophylla was being wasteland>woodland>cropland, the enrichment coefficient of Cu in hook of U. rhynchophylla in wasteland was more than 1. Except Cu, the enrichment coefficient of other heavy metals was low.

Multiple Genetic Analysis System-Based Antibiotic Susceptibility Testing in Helicobacter pylori and High Eradication Rate With Phenotypic Resistance-Guided Quadruple Therapy.

Antibiotics resistance in Helicobacter pylori (H. pylori) is the major factor for eradication failure. Molecular tests including fluorescence in situ hybridization, PCR-restriction fragment length polymorphism, and dual priming oligonucleotide-PCR (DPO-PCR) play critical roles in the detection of antibiotic susceptibility; however, limited knowledge is known about application of multiple genetic analysis system (MGAS) in the area of H. pylori identification and antibiotics resistance detection.The aim of this study is to determine the antibiotics resistance using different molecular tests and evaluate the treatment outcomes of E-test-based genotypic resistance.A total of 297 patients with dyspepsia complaint were recruited for gastroscopies. Ninety patients with H. pylori culture positive were randomly divided into 2 groups (test group and control group). E-test, general PCR, and MGAS assay were performed in test group. Patients in control group were treated with empirical therapy (rabeprazole + bismuth potassium citrate + amoxicillin [AMX] + clarithromycin [CLR]), whereas patients in test group received quadruple therapy based on E-test results twice daily for 14 consecutive days. The eradication effect of H. pylori was confirmed by C-urea breath test after at least 4 weeks when treatment was finished.Rapid urease test showed 46.5% (128/297) patients with H. pylori infection, whereas 30.3% (90/297) patients were H. pylori culture positive. E-test showed that H. pylori primary resistance rate to CLR, AMX, metronidazole, tetracycline, and levofloxacin (LVX) was 40.0% (18/45), 4.4% (2/45), 53.3% (24/45), 0% (0/45), and 55.6% (25/45), respectively. In addition, there are many multidrug resistant (MDR) phenotypes, and the MDR strains have higher minimum inhibitory concentration than their single-drug resistant counterparts. Considering E-test as the reference test, the sensitivities of general PCR and MGAS in detecting CLR resistance were 83.3% (15/18) and 94.4% (17/18), whereas in detecting LVX resistance were 100% (25/25) and 83.3% (15/18), respectively. Finally, the eradication rate in test group was significantly higher than that in control group as demonstrated by intention-to-treat analysis and per-protocol analysis.MGAS is a promising assay for H. pylori identification and antibiotic susceptibility testing. Phenotypic resistance-guided quadruple therapy showed a high efficacy in treating patients with H. pylori infection.

An advanced fragment analysis-based individualized subtype classification of pediatric acute lymphoblastic leukemia.

Pediatric acute lymphoblastic leukemia (ALL) is the most common neoplasm and one of the primary causes of death in children. Its treatment is highly dependent on the correct classification of subtype. Previously, we developed a microarray-based subtype classifier based on the relative expression levels of 62 marker genes, which can predict 7 different ALL subtypes with an accuracy as high as 97% in completely independent samples. Because the classifier is based on gene expression rank values rather than actual values, the classifier enables an individualized diagnosis, without the need to reference the background distribution of the marker genes in a large number of other samples, and also enables cross platform application. Here, we demonstrate that the classifier can be extended from a microarray-based technology to a multiplex qPCR-based technology using the same set of marker genes as the advanced fragment analysis (AFA). Compared to microarray assays, the new assay system makes the convenient, low cost and individualized subtype diagnosis of pediatric ALL a reality and is clinically applicable, particularly in developing countries.

Synergetic effect of metal nickel and graphene as a cocatalyst for enhanced photocatalytic hydrogen evolution via dye sensitization.

Exploiting new, low-cost and efficient electrocatalysts for hydrogen evolution reaction (HER) is important to resolve the energy crisis and environment pollution. In this work, graphene decorated with Ni nanoparticles (NPs) were synthesized via one-pot reduction using graphene oxide (GO, the obtained composite was denoted as GN) as a precursor. The as-prepared composite GN exhibits much better electrocatalytic and dye-sensitized HER activities than single Ni and reduced graphene oxide (RGO), namely, a great synergetic effect of RGO and Ni for HER. The coupling of metal Ni with the defect carbons of RGO plays a key role in the synergetic effect. The structure of GN composites is another key factor to the synergetic effect. The highest apparent quantum yield (AQY) for dye-sensitized photocatalytic hydrogen evolution at 470 nm reaches 30.3% under the optimal conditions.

Thermococcus eurythermalis sp. nov., a conditional piezophilic, hyperthermophilic archaeon with a wide temperature range for growth, isolated from an oil-immersed chimney in the Guaymas Basin.

A conditional piezophilic, hyperthermophilic archaeon showing growth over a wide range of temperature, pH and pressure was isolated from an oil-immersed hydrothermal chimney at a depth of 2006.9 m in the Guaymas Basin. Enrichment and isolation of strain A501(T) were performed at 80 °C at 0.1 MPa. Cells of isolate A501(T) were irregular motile cocci with a polar tuft of flagella and generally 0.6-2.6 µm in diameter. Growth was detected over the range 50-100 °C (optimal growth at 85 °C) at atmospheric pressure and was observed at 102 °C at a pressure of 10 MPa. At 85 °C, growth was observed at a pressure of 0.1-70 MPa (optimum pressure 0.1 MPa-30 MPa), while at 95 °C, the pressure allowing growth ranged from 0.1 MPa to 50 MPa (optimum pressure 10 MPa). Cells of strain A501(T) grew at pH 4-9 (optimum pH 7.0) and a NaCl concentration of 1.0-5.0 % (w/v) (optimum concentration 2.5 % NaCl). This isolate was an anaerobic chemo-organoheterotroph and was able to utilize yeast extract, peptone, tryptone and starch as the single carbon source for growth. Elemental sulfur and cysteine stimulated growth; however, these molecules were not necessary. The DNA G+C content of the complete genome was 53.47 mol%. The results of 16S rRNA gene sequence analysis indicated that strain A501(T) belongs to the genus Thermococcus. There was no significant similarity between strain A501(T) and the phylogenetically related species of the genus Thermococcus based on complete genome sequence alignments and calculation of the average nucleotide identity and the tetranucleotide signature frequency correlation coefficient. These results indicate that strain A501(T) represents a novel species, Thermococcus eurythermalis sp. nov. The type strain is A501(T) ( = CGMCC 7834(T) = JCM 30233(T)).