Multiple-centre clinical evaluation of an ultrafast single-tube assay for SARS-CoV-2 RNA

OBJECTIVE

To evaluate the performance of an ultrafast single-tube nucleic acid isothermal amplification detection assay for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA using clinical samples from multiple centres.

METHODS

A reverse transcription recombinase-aided amplification (RT-RAA) assay for SARS-CoV-2 was conducted within 15 minutes at 39°C with portable instruments after addition of extracted RNA. The clinical performance of RT-RAA assay was evaluated using 947 clinical samples from five institutions in four regions of China; approved commercial fluorescence quantitative real-time PCR (qRT-PCR) kits were used for parallel detection. The sensitivity and specificity of RT-RAA were compared and analysed.

RESULTS

The RT-RAA test results of 926 samples were consistent with those of qRT-PCR (330 were positive, 596 negative); 21 results were inconsistent. The sensitivity and specificity of RT-RAA was 97.63% (330/338, 95% confidence interval (CI) 95.21 to 98.90) and 97.87% (596/609, 95% CI 96.28 to 98.81) respectively. The positive and negative predictive values were 96.21% (330/343, 95% CI 93.45 to 97.88) and 98.68% (596/604, 95% CI 97.30 to 99.38) respectively. The total coincidence rate was 97.78% (926/947, 95% CI 96.80 to 98.70), and the kappa was 0.952 (p < 0.05).

CONCLUSIONS

With comparable sensitivity and specificity to the commercial qRT-PCR kits, RT-RAA assay for SARS-CoV-2 exhibited the distinctive advantages of simplicity and rapidity in terms of operation and turnaround time.

Vagococcus xieshaowenii sp. nov., isolated from snow finch (Montifringilla taczanowskii) cloacal content

A Gram-stain-positive, coccus-shaped, non-motile bacterium, designated CF-49^T, was isolated from the cloacal content of a snow finch, which was incidentally captured in a plateau pika burrow on the Qinghai-Tibet Plateau, PR China. Analysis of the 16S rRNA gene sequence showed that strain CF-49^T was closely related to Vagococcus elongatus CCUG 51432^T (96.5 % similarity), Vagococcus fluvialis NCFB 2497^T (96.0 %) and Vagococcus lutrae CCUG 39187^T (95.9 %), whereas the similarity to another isolate (CF-210) was 99.9 %. Strains CF-49^T and CF-210 grew optimally at 37 °C and pH 7.0 and in the presence of 0.5 % (w/v) NaCl. Acid was produced from N-acetylglucosamine, cellobiose, d-fructose, d-glucose, d-mannose, d-mannitol, maltose, d-ribose and salicin. The cell-wall peptidoglycan type was A4α (l-Lys-d-Asp). The major cellular fatty acids (>10 %) were C_16 : 0 (35.6 %), C_14 : 0 (17.3 %), C_18 : 1 ω9c (16.2 %) and C_16 : 1 ω9c (10.6 %). The predominant respiratory quinone was menaquinone MK-7 (68.8 %). The G+C content of the genomic DNA was 35.9 mol%. Digital DNA-DNA hybridization of strain CF-49^T with V. fluvialis DSM 5731^T, V. elongatus CCUG 51432^Tand V. lutrae CCUG 39187^T resulted in relatedness values of 21.4, 23.3 and 24.6 %, respectively. Based on results from polyphasic analyses, our two isolates are proposed to represent a novel species in the genus Vagococcus, with the name Vagococcus xieshaowenii. The type strain is CF-49^T (=CGMCC 1.6436^T=GDMCC 1.1588^T=JCM 33477^T).

Nocardioides yefusunii sp. nov., isolated from Equus kiang (Tibetan wild ass) faeces

Two Gram-stain-positive, irregular rod-shaped (0.2-0.5×1.3-2.5 um) strains, HY056^T and HY057, were isolated from the faeces of Equus kiang (the largest of the wild asses) collected at different regions from the Qinghai-Tibetan Plateau of PR China. Phylogenetic analyses indicated that strains HY056^T and HY057 belong to the genus Nocardioides by sharing a similarity ranging from 96.3 to 97.0 % in the 16S rRNA gene sequence and forming a distinct cluster with Nocardioides daphniae JCM 16608^T, Nocardioides houyundeii 78^T, Nocardioides solisilvae Ka25^T and Nocardioides gilvus XZ17^T. The digital DNA-DNA hybridization value of strain HY056^T was 96.9 % with strain HY057, but less than 30.0 % with the above four closest relatives. MK-8(H₄) was the predominant (91.6 %) respiratory quinone. The cell wall contained ll-2,6-diaminopimelic acid as the diamino acid of the peptidoglycan. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phospholipid. The predominant fatty acids (>10.0 %) were C_18 : 1ω9c and iso-C_16:0. The DNA G+C contents of strains HY056^T and HY057 were 68.9 and 69.1 mol%, respectively. β-Glucosidase expression was positive, and acid was produced from d-fructose. Strain HY056^T (=CGMCC 4.7563^T=JCM 33399^T) is assigned as the type strain of a novel species within the genus Nocardioides, for which the name Nocardioidesyefusunii sp. nov is proposed.

P5392Epicardium derived cells promote sympathetic ganglionic outgrowth towards myocardium in vitro

Background

The autonomic nerve system is essential to maintain homeostasis in the body. In the heart, autonomic innervation is important for adjusting the physiology to the continuously changing demands such as stress responses. After cardiac damage, excessive neurite outgrowth, referred to as autonomic hyperinnervation, can occur which is related to ventricular arrhythmias and sudden cardiac death. The cellular basis for this hyperinnervation is as yet unresolved. Here we hypothesize a role for epicardium derived cells (EPDCs) in stimulating sympathetic neurite outgrowth.

Purpose

To investigate the potential role of adult EPDCs in promoting sympathetic ganglionic outgrowth towards adult myocardium.

Method

Fetal murine superior cervical ganglia were dissected and co-cultured with activated adult mesenchymal epicardium-derived cells (EPDCs) or/and adult myocardium in a 3D collagen gel culture system. Four experiment groups were included: Group 1: Vehicle cultures (ganglia cultured without EPDC/myocardium) (n=48); Group 2: ganglia co-cultured with EPDCs (n=38); Group 3: ganglia co-cultured with myocardium (n=95); and group 4: ganglia co-cultured with both EPDCs and myocardium (n=96). The occurrence of neurite outgrowth was assessed in each group. The density of neurites that showed directional sprouting (i.e. sprouting towards myocardium) was assessed as well with a semi-automatic quantification method. Finally, sub-analyses were made by taking gender into account.

Results

Cervical ganglia cultured with EPDCs alone (group 2) showed increased neurite outgrowth compared to vehicle cultures (group 1), however the neurites did not show directional sprouting towards EPDCs. When co-cultured with myocardium (group 3), directional neurite outgrowth towards myocardium was observed. Compared to the ganglia-myocardium co-cultures, directional outgrowth was significantly increased in co-cultures combining myocardium and EPDCs (group 4), and the neurite density was also significantly augmented. Comparison between males and female ganglia demonstrated that more neurite outgrowth occurred in female-derived ganglia than in male-derived ganglia under the same co-culture conditions.

Conclusion

Activated adult EPDCs promote sympathetic ganglionic outgrowth in vitro. Sex differences exist in the response of ganglia to EPDCs, and female-derived ganglia appear more sensitive to EPDC-signalling. Results support a role of EPDCs in cardiac autonomic innervation and open avenues for exploring of their role in ventricular hyperinnervation after cardiac damage.

Comparing micropercutaneous nephrolithotomy and retrograde intrarenal surgery in treating 1-2 cm solitary renal stones in pediatric patients younger than 3 years

INTRODUCTION

To compare the effects of micropercutaneous nephrolithotomy (micro-PCNL) and retrograde intrarenal surgery (RIRS) in treating 1-2 cm solitary renal stones in pediatric patients aged less than 3 years.

PATIENTS AND METHODS

A retrospective analysis was performed on data from 57 children younger than 3 years who received micro-PCNL and RIRS surgery in the authors hospital from October 2016 to August 2018. The patients were divided into group 1, the micro-PCNL group, and group 2, the RIRS group. Peri-operative data including surgical time, number of anesthesia sessions, stone-free rate (SFR), and complications were analyzed.

RESULTS

There were 27 patients in group 1 and 30 patients in group 2, and the patients' mean ages were 19 ± 9.9 months and 21 ± 7.8 months, respectively (P = 0.462). The stone size was 1.6 ± 0.3 cm in group 1 and 1.7 ± 0.2 cm in group 2 (P = 0.217); the mean surgical time was 52 ± 7 min in group 1 and 48 ± 9 min in group 2 (P = 0.163), and the mean lithotripsy time was 21 ± 4 min in group 1 and 23 ± 5 min in group 2 (P = 0.148); and the SFR at 1 month after surgery was 88.9% in group 1 and 86.7% in group 2 (P = 0.799). The number of anesthesia sessions for patients was 1.4 ± 0.5 in group 1 and 2.7 ± 0.5 in group 2 (P < 0.001). The complication rate was 14.8% and 16.7% in group 1 and group 2, respectively (P = 0.714). None of the patients needed conversion to the 12-14 F mini-PCNL.

CONCLUSIONS

The results of this study showed that the surgical effects and complications from micro-PCNL and RIRS in treating young children with 1-2 cm solitary renal stones were similar. However, micro-PCNL reduced the need to prestent before surgery and allowed lower anesthesia sessions. Therefore, micro-PCNL is an effective alternative method for 1-2 cm solitary renal stones in patients below 3 years of age.

Multiple abiotic stress, nitrate availability and the growth of wheat

In the field, wheat experiences a combination of physical and nutrient stresses. There has been a tendency to study root impedance and water stress in separation and less is known about how they might interact. In this study, we investigated the effect of root impedance on the growth of three wheat varieties (Cadenza, Xi19 and Battalion) at different levels of nitrate availability, from 0-20 mM nitrate, in sand culture. This model system allows soil strength to be increased while maintaining adequate water availability. In a separate pot experiment, we grew the same wheat varieties in a loamy sand where soil was allowed to dry sufficiently to both reduce water potential and increase root impedance. This pot experiment also had a range of nitrate availabilities 0-20 mM nitrate. Once the seedlings were established we limited water supply to apply a matric potential of approximately -200 kPa to the roots. Soil drying increased the penetrometer resistance from approximately 300 kPa to more than 1 MPa. There were differences between the two experimental systems; growth was smaller in the soil-based experiment compared to the sand culture. However, the effects of the experimental treatment, root impedance or water withholding, relative to the control were comparable. Our data confirmed that leaf elongation in Cadenza (carrying the tall Rht allele) was the most sensitive to root impedance. Leaf stunting occurred irrespective of nitrate availability. Leaf elongation in the Xi19 and Battalion (carrying the semi-dwarf Rht allele) was less sensitive to root impedance and drought than Candenza. We suggest that the critical stress in a pot experiment where the soil was allowed to dry to approximately -200 kPa was root impedance and not water availability.

Making global river ecosystem health assessments objective, quantitative and comparable

Assessing and comparing global river ecosystem health in an objective and quantitative way remains a major challenge. In this study the widely-used semi-quantitative methods Rapid Biological assessment Protocols (RBPs) was used to determine the health of rivers. The findings were then compared to the results derived from our new UAV (Unmanned aerial vehicles) orthophotographic imagery method. This method quantitatively and objectively assesses river ecosystem health. As a comparison, our method was used to quantitatively measure distance and areas of a range of hydrological and biological attributes thus improving the accuracy of distance- and area-related indices, consequently avoiding subjective errors in these estimations that is fraught in methods like the RBPs. To strengthen the objectivity of the assessment the weights of these indices were objectively determined using the entropy weighting method. This new method was then tested using 9551 UAV orthophotographs taken over six field campaigns. It performed satisfactorily, showing that in our study area the health status of mountain rivers was the best with the highest score of 0.94 out of 1.0. Temporally, the health of the river was better in summer (0.65) compared with that in autumn (0.40). Changes in river ecosystem health were driven by variations in biology and water quality. In contrast the outputs of RBPs, especially in relation to distance and area indices, had ~ 20% uncertainty due to visual errors and subjectivity in estimations by observers. The UAV orthophotographic imaging method proposed in this study can improve the ability to compare the health of rivers across different periods and regions throughout the globe.

Clinical utility of quantitative dual-energy CT iodine maps and CT morphological features in distinguishing small-cell from non-small-cell lung cancer

AIM

To evaluate the clinical usefulness of quantitative dual-energy (DE) computed tomography (CT) iodine enhancement metrics combined with morphological CT features in distinguishing small-cell lung cancer (SCLC) from non-small-cell lung cancer (NSCLC).

MATERIALS AND METHODS

One hundred and six untreated lung cancer patients who underwent DECT before biopsy or surgery were prospectively enrolled. Twenty-seven routine CT descriptors, including tumour location, size, shape, margin, enhancement heterogeneity, and internal and surrounding structures, and associated findings were assessed and DECT parameters were measured in all patients. Multiple logistic regression analyses were applied to identify independent predictors of SCLC. The area under the receiver operating characteristic curve was compared between CT features combined with DECT metrics and CT features alone for distinguishing SCLC from NSCLC.

RESULTS

Histology revealed NSCLC in 80 and SCLC in 26 patients. In univariate analysis, 12 morphological CT features and two DECT metrics differed significantly between NSCLC and SCLC. When DECT parameters were combined with CT features for multivariate analysis, the independent predictors of SCLC were large tumour size, central location, confluent mediastinal lymphadenopathy, homogeneous enhancement, absence of coarse spiculation, and lower iodine density and iodine ratio (all p<0.05). The area under the receiver operating characteristic curve was improved from 0.908 to 0.981 after adding DECT metrics compared with CT features alone (p=0.007).

CONCLUSION

The combination of DECT measures and CT morphological features can be used to distinguish SCLC from NSCLC, with higher diagnostic performance compared with CT morphological features alone.

[Diagnostic and prognostic implications of MAML2 gene translocation in primary pulmonary mucoepidermoid carcinoma]

Objective: To investigate MAML2 gene-translocation in primary pulmonary mucoepidermoid carcinoma (PMEC) and pulmanary adenosquamous carcinoma, and the optimal diagnostic immunohistiochemical (IHC) panel in distinguishing PMEC from adenosqumous carcinoma. Methods: Twenty-four cases of PMEC and 44 adenosqumous carcinoma diagnosed in the Guangdong General Hospital were tested for MAML2 translocation by fluorescent in-situ hybridization (FISH) using tissue array. An IHC panel including TTF1, Napsin A, CK5/6, p63, p40 and Ki-67 was performed on the cohort. The clinical data for all cases were collected and all PMEC patients had follow-up information. Results: The patients' age ranged form 6 to 73 years, with a median age of 32 years. The male to female ratio was 1.4∶1.0. MAML2 translocation was found in 16/24 (66.7%) cases of PMEC whereas all 44 cases adenosqumous carcinoma were negative for translocation. All the cases of the PMEC were negative for TTF1 and Napsin A but positive for CK5/6, p63 and p40 in the intermediate cells and epidermal-like cells. In most PMEC cases, the Ki-67 expression index was lower than 10%. In contrast, most cases of adenosqumous carcinomas expressed TTF1 and Napsin A in the adenomatous component and CK5/6, p63 and p40 in the squamous component, which expression pattern was different from that of PMEC. Based on IHC staining, 2 cases of highly invasive ALK-positive adenocarcinoma mimicing PMEC were also found in the study. Conclusions: MAML2 gene translocation can be detected in about two-third of PMEC. Translocation of MAML2 gene and lower morphology grading are associated with good prognosis. The combined use of IHC antibodies panel is helpful to distinguish PMEC from the adenosqumous carcinoma and adenocarcinoma mimicing PMEC.

Correction to: Inhibition of cathepsin B by caspase-3 inhibitors blocks programmed cell death in Arabidopsis

We thank D Nicholson for initial advice on caspase activity purification and B Turk for advice on recombinant cathepsin B. We thank N Atanasova for cell death assays. The Bioimaging Facility microscopes used in this study were purchased with grants from BBSRC, Wellcome Trust and the University of Manchester Strategic Fund. Special thanks go to D Knight in the Faculty Biomolecular Analysis facility. We thank P Birch and M Kim for improving the manuscript. The project was partially funded by BBSRC Grants 34/P14516, BB/K009478/1 and China National High-Tech Research and Development Programme(863 programme)NO. 2015AA020903.

Spirometra erinaceieuropaei severely infect frogs and snakes from food markets in Guangdong, China: implications a highly risk for zoonotic sparganosis

Sparganosis is a parasitic disease caused by plerocercoid larvae of the genus Spirometra. In China, the main source of sparganosis is from Guangdong, 16.1% of the country's human sparganosis cases occur in this province. Frequent international trade of amphibians and reptiles in Guangdong may introduce new species of Spirometra into the local market. In this study, a large-scale, high-intensity sampling survey was conducted to find out the causative species and epidemic situation of Sparganosis in Guangdong. The prevalence of sparganum infection in five species of frogs (Boulengerana guentheri, Fejervarya multistriata, Hoplobatrachus chinensis, Pelophylax nigromaculatus and Quasipaa spinosa) and nine species of snakes (Elaphe carinata, Lycodon rufozonatum, Hypsiscopus plumbea, Ptyas dhumnades, P. korros, P. mucosa, Naja atra, Sinonatrix annularis and Xenochrophis piscator) was investigated in Guangdong, Southern China from May 2014 to August 2015. The results showed that 9.8% (50/511) of the frogs and 40.8% (141/ 346) of snakes were found to be infected by plerocercoids (spargana). To identify the species of the collected spargana, a partial sequence of the mitochondrial cytochrome c oxidase subunit1 gene (cox1) was amplified and sequenced. Phylogenetic analysis identified all the spargana specimens as Spirometra erinaceieuropaei. Our study indicated that S. erinaceieuropaei, a highly pathogenic parasite, is the only causative agent of sparganosis in Guangdong, China. This study suggests that the large numbers of frogs and snakes in food markets in Guangdong may impact public health in China by transmitting S. erinaceieuropaei sparganum. Additional steps should be considered by the governments and public health agencies to prevent the risk of food-associated Spirometra infections in humans in China.

MicroRNA-543 functions as an osteogenesis promoter in human periodontal ligament-derived stem cells by inhibiting transducer of ERBB2, 2

BACKGROUND AND OBJECTIVE

Previous research has indicated that altered expression of microRNAs (miRNAs) is in connection with osteogenesis of human periodontal ligament-derived stem cells (hPDLSCs). We investigated the mechanisms by which miR-543 promotes osteogenic differentiation of hPDLSCs.

MATERIAL AND METHODS

First, the expression of miR-543 in hPDLSCs cultured with or without an osteogenic inductive cocktail was explored. Then, the function of miR-543 during osteogenesis of hPDLSCs was investigated by overexpressing and inhibiting miR-543. Next, 3 databases were used to predict target genes of miR-543 and a luciferase report was used to validate the direct regulation of miR-543 on the target gene. Further, a rescue experiment using co-transfection of miR-543 mimic and target mimic was performed to evaluate whether overexpressing the target gene could partly rescue the efficiency of overexpressing miR-543 on osteogenesis in hPDLSCs.

RESULTS

miR-543 was upregulated during osteogenic differentiation of hPDLSCs. Functional experiments showed that overexpressing miR-543 could enhance osteogenesis, while inhibiting miR-543 resulted in reduced formation of mineralized nodules. The transducer of ERBB2, 2 (TOB2) was identified as a target gene of miR-543 and luciferase report revealed that miR-543 interacts directly with the 3'-untranslated repeat sequence of TOB2 mRNA. Overexpression of miR-543 inhibited the expression of TOB2 in both mRNA and protein levels while inhibiting miR-543 increased. Furthermore, the rescue experiment confirmed the promotional role of miR-543 TOB2 expression could be abrogated by overexpressing TOB2, which also had the effect of reducing osteogenic differentiation.

CONCLUSION

Our research confirmed that miR-543 is a promoter of osteogenesis in hPDLSCs, acting by inhibiting its target gene TOB2, which suggests that miR-543 may be a potential therapy for bone loss in periodontitis.

Preoperative CT texture analysis of gastric cancer: correlations with postoperative TNM staging

AIM

To explore the role of computed tomography (CT) texture analysis in predicting pathologic stage of gastric cancers.

MATERIALS AND METHODS

Preoperative enhanced CT images of 153 patients (112 men, 41 women) with gastric cancers were reviewed retrospectively. Regions of interest (ROIs) were manually drawn along the margin of the lesion on the section where it appeared largest on the arterial and venous CT images, which yielded texture parameters, including mean, maximum frequency, mode, skewness, kurtosis, and entropy. Correlations between texture parameters and pathological stage were analysed with Spearman's correlation test. The diagnostic performance of CT texture parameters in differentiating different stages was evaluated using receiver operating characteristic (ROC) analysis.

RESULTS

Maximum frequency in the arterial phase and mean, maximum frequency, mode in the venous phase correlated positively with T stage, N stage, and overall stage (all p<0.05) of gastric cancer. Entropy in the venous phase also correlated positively with N stage (p=0.009) and overall stage (p=0.032). Skewness in the arterial phase had the highest area under the ROC curve (AUC) of 0.822 in identifying early from advanced gastric cancers. Multivariate analysis identified four parameters, including maximum frequency, skewness, entropy in the venous phase, and differentiation degree from biopsy, for predicting lymph node metastasis of gastric cancer. The multivariate model could distinguish gastric cancers with and without lymph node metastasis with an AUC of 0.892.

CONCLUSION

Multiple CT texture parameters, especially those in the venous phase, correlated well with pathological stage and hold great potential in predicting lymph node metastasis of gastric cancers.