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.

[Influential factors related to the long-term effect of periodontal-orthodontic treatment in patients with aggressive periodontitis and malocclusion]

Objective: To investigate the influential factors related to the long-term effect of periodontal-orthodontic treatment in patients with aggressive periodontitis (AgP). Methods: A retrospective analysis was conducted in 25 AgP patients, who have received periodontal-orthodontic treatment in Peking University School and Hospital of Stomatology. Changes in the ratio of the residual alveolar bone height (RBH) was measured at three time points: baseline (T0), post orthodontic treatment (T1), and the last re-visit 3 years after orthodontic treatment (T2). Root abnormity was evaluated by observing periapical radiographs, and its relationship with alveolar bone loss after orthodontic treatment was analyzed. A multi-level analysis on factors related to the clinical outcome (alveolar bone height change) was performed. Results: Totally 693 teeth of 25 patients at T0 and T1 and 368 teeth of 14 patients at T2 were investigated. During the periodontal-orthodontic treatment, the RBH was mainly influenced by root abnormity (estimation value -2.392), tooth position (estimation value for upper teeth vs. lower teeth 3.139, and anterior teeth vs. posterior teeth -3.469) and the baseline RBH at T0 (estimation value -0.391) (P<0.05). Teeth with root abnormity, teeth in mandibular and anterior area, and teeth with higher RBH showed less change in T1-T0 RBH values. In the long-term follow-up, RBH was mainly influenced by tooth position (estimation value for upper teeth vs. lower teeth 3.735, and anterior teeth vs. posterior teeth -5.318), the baseline RBH and probing depth (PD) at T0. Teeth in mandibular and anterior area, teeth with higher RBH (estimation value -0.498) and PD (estimation value -1.594) (P<0.05) showed less change in T0-T2 RBH values. Conclusions: During orthodontic treatment, teeth with abnormal root, lower teeth, anterior teeth, and teeth with high RBH were unfavorable factors for bone gain. In the long-term observation, lower teeth, anterior teeth, teeth with high RBH and PD at first visit were unfavorable factors for bone gain.

Liquid-phase mega-electron-volt ultrafast electron diffraction

The conversion of light into usable chemical and mechanical energy is pivotal to several biological and chemical processes, many of which occur in solution. To understand the structure-function relationships mediating these processes, a technique with high spatial and temporal resolutions is required. Here, we report on the design and commissioning of a liquid-phase mega-electron-volt (MeV) ultrafast electron diffraction instrument for the study of structural dynamics in solution. Limitations posed by the shallow penetration depth of electrons and the resulting information loss due to multiple scattering and the technical challenge of delivering liquids to vacuum were overcome through the use of MeV electrons and a gas-accelerated thin liquid sheet jet. To demonstrate the capabilities of this instrument, the structure of water and its network were resolved up to the 3 rd hydration shell with a spatial resolution of 0.6 Å; preliminary time-resolved experiments demonstrated a temporal resolution of 200 fs.

Integrated analysis of different mRNA and miRNA profiles in human hypopharyngeal squamous cell carcinoma sensitive and resistant to chemotherapy

The purpose of this study was to identify potential miRNAs and mRNAs involved in chemotherapy insensitivity in hypopharyngeal squamous cell carcinoma (HSCC) and to explore the underlying mechanisms involved to provide diagnostic markers and therapeutic targets for HSCC. We used microarrays to identify differences in both the mRNA and miRNA expression profiles between a group (twelve patients) sensitive to chemotherapy and a resistant group (nine patients). We then employed bioinformatics tools to examine the functions and pathways involved. The genes and miRNAs most related to chemotherapy sensitivity in HSCC were screened. Finally, a miRNA-mRNA-phenotype network was constructed with an integrated analysis based on the identified miRNAs and mRNAs. Nine differentially expressed miRNAs and one hundred differentially expressed mRNAs were identified, and the functions of these genes and miRNAs were predicted. Bioinformatics analysis revealed a regulatory network consisting of eight genes and two miRNAs that influenced HSCC chemosensitivity. According to our analysis, CCL4L1 may be a potential molecular marker for HSCC chemotherapy, and excess CCL4L1 leads to the upregulation of PRAME and the downregulation of miR-375, thus decreasing HSPB8 expression and promoting chemotherapy sensitivity. Our work provides reliable data for further studies investigating the mechanism of HSCC chemotherapy sensitivity.

Femtosecond Compression Dynamics and Timing Jitter Suppression in a THz-driven Electron Bunch Compressor

We present the first demonstration of THz driven bunch compression and timing stabilization of a relativistic electron beam. Quasi-single-cycle strong field THz radiation is used in a shorted parallel-plate structure to compress a few-fC beam with 2.5 MeV kinetic energy by a factor of 2.7, producing a 39 fs rms bunch length and a reduction in timing jitter by more than a factor of 2 to 31 fs rms. This THz driven technique offers a significant improvement to beam performance for applications like ultrafast electron diffraction, providing a critical step towards unprecedented timing resolution in ultrafast sciences, and other accelerator applications using femtosecond-scale electron beams.

TaqMan real-time PCR for detecting bovine viral diarrhea virus

The present study was aimed to establish a novel TaqMan real-time PCR (RTm-PCR) for detecting and typing bovine viral diarrhea virus (BVDV), and also to develop a diagnostic protocol which simplifies sample collection and processing. Universal primers and TaqMan-MGB probes were designed from the known sequences of conserved 5' - and 3'-untranslated regions (5'UTR, 3'UTR) of the NADL strain of BVDV. Prior to optimizing the assay, cDNAs were transcribed in vitro to make standard curves. The sensitivity, specificity and stability (reproducibility) were evaluated. The RTm-PCR was tested on the 312 feces specimens collected from persistently infected (PI) calves. The results showed the optimum conditions for RTm-PCR were 17.0 μmol/L primer, 7.5 μmol/L probe and 51.4°C annealing temperature. The established TaqMan RTm-PCR assay could specially detect BVDV without detecting any other viruses. Its detection limit was 1.55×100 copies/μL for viral RNA. It was 10000-fold higher than conventional PCR with excellent specificity and reproducibility. 312 samples were tested using this method and universal PCR from six dairy farms, respectively. Positive detections were found in 49 and 44 feces samples, respectively. The occurrence rate was 89.80%. In conclusion, the established TaqMan RTm-PCR could rapidly detect BVDV and effectively identify PI cattle. The detection limit of RTm-PCR was 1.55 copies/μL. It will be beneficial for enhancing diagnosis and therapy efficacy and reduce losses in cattle farms.

Prospective study of perceived dietary salt intake and the risk of non-alcoholic fatty liver disease

BACKGROUND

A high sodium intake is associated with obesity and metabolic syndrome. However, little is known regarding whether greater salt intake is a potential risk factor for non-alcoholic fatty liver disease (NAFLD). We thus prospectively investigated whether individuals with higher perceived dietary salt intake had a higher risk of developing NAFLD.

METHODS

The present study included 35 023 participants (22 629 men and 12 394 women) from the Kailuan study who were free of NAFLD at baseline (2006) and who did not drink alcohol at baseline and during follow-up (2006-2014; follow-rate 95.2%). NAFLD was defined as a participant who had been diagnosed with fatty liver at least twice by ultrasound tests conducted every 2 years during follow-up. Dietary salt intake was determined by a self-report question and was classified into three categories: low (<6 g day^-1 ), medium (6-9 g day^-1 ) or high (≥10 g day^-1 ). Cox proportional models were used to estimate the risk of NAFLD, adjusting for potential confounders, such as age, sex, education, physical activity, smoking, income, occupation, marriage, body mass index, waist circumference and blood pressure, as well as serum concentrations of glutamic-pyruvic transaminase, glucose, total cholesterol and triglyceride.

RESULTS

During 8 years of follow-up, we identified 5102 incident NAFLD cases. After adjusting for potential confounders, the hazard ratio (95% conference interval) for NAFLD was 1.12 (1.00, 1.26) for medium salt intake and 1.19 (1.02,1.39) for high salt consumption (P trend = 0.03) relative to the low salt consumption group.

CONCLUSIONS

A perceived high salt intake was associated with a higher future risk of NAFLD.

Methionine and arginine supplementation alter inflammatory and oxidative stress responses during lipopolysaccharide challenge in bovine mammary epithelial cells in vitro

Mastitis, inflammation of the udder, is one of the most common diseases hampering milk yield of dairy cows. Methionine (Met) and arginine (Arg) are key nutrients with potential to regulate inflammation and oxidative stress. The aim of this study was to evaluate the effect of increased supply of Met and Arg on mRNA and protein abundance associated with innate immune response and redox balance during lipopolysaccharide (LPS) stimulation in primary bovine mammary epithelial cells (BMEC). Primary BMEC (n = 4 replicates per treatment) were pre-incubated for 12 h in media with the following amino acid combinations: ideal profile of amino acids (control; Con), increased Met supply (incMet), increased Arg supply (incArg), and increased supply of Met and Arg (incMetArg). Subsequently, cells were challenged with or without LPS (1 µg/mL) and incubated for 6 h. Data were analyzed as a 2 × 2 × 2 factorial using the MIXED procedure of SAS 9.4 (SAS Institute Inc., Cary, NC). The downregulation of SLC36A1 and SLC7A1 mRNA abundance induced by LPS was attenuated in the incArg cultures. Although challenge with LPS led to lower abundance of proteins related to the antioxidant response (NFE2L2, NQO1, GPX1), lower levels of ATG7, and lower mRNA abundance of GPX3, we found little effect in cultures with incMet or incArg. Cultures with incMet, incArg, or incMetArg led to attenuation of the upregulation of SOD2 and NOS2 induced by LPS. Abundance of phosphorylated p65 (RELA) was greater after LPS stimulation, but the response was attenuated in cultures with incMet. The greater ratio of pRELA to total RELA in responses to LPS was also attenuated in cultures with incMetArg. The greater mRNA abundance of the proinflammatory cytokine IL1B induced by LPS was attenuated in cultures with incMet, and the same trend induced by LPS on CXCL2 was also alleviated in cultures with incArg. Overall, the data suggest that greater supply of Met and Arg alleviated the proinflammatory responses triggered by LPS through controlling the abundance of proinflammatory cytokines and chemokines and activity of NF-κB. Little benefit on oxidative stress induced by LPS challenge in BMEC was detected with greater supply of Met and Arg.

Transmission of multidrug-resistant tuberculosis in Shanghai: roles of residential status

SETTING

Shanghai is a mega city where 39% of the population comprises internal migrants.

OBJECTIVE

To examine the different roles played by migrants and permanent residents in the transmission of multidrug-resistant tuberculosis (MDR-TB).

DESIGN

We conducted a population-based cohort study to assess MDR-TB transmission in Shanghai between 1 January 2009 and 31 December 2012 using genotyping and geospatial analyses.

RESULTS

A total of 367 MDR-TB cases formed the study cohort. Significant differences between MDR-TB cases who were internal migrants and those who were permanent residents were found with regard to age, sex, region, genetic characteristics and treatment outcomes. Permanent residents had a higher transmission rate than internal migrants (OR 3.36, 95%CI 1.86-6.09). Permanent residents and genotypic clustering cases had similar clusters in central downtown and some parts of suburban areas. Most of the clusters of internal migrants were found in rural areas bordering suburban areas. Clusters of genotypic non-clustering cases showed patterns that closely matched those of internal migrants, suggesting acquired drug resistance in migrants.

CONCLUSION

In Shanghai, permanent residents were significantly associated with recent transmission of MDR-TB in central downtown areas. Clustered cases of internal migrants in rural areas were most likely to have contracted MDR-TB through acquired resistance.

Femtosecond gas-phase mega-electron-volt ultrafast electron diffraction

The development of ultrafast gas electron diffraction with nonrelativistic electrons has enabled the determination of molecular structures with atomic spatial resolution. It has, however, been challenging to break the picosecond temporal resolution barrier and achieve the goal that has long been envisioned-making space- and-time resolved molecular movies of chemical reaction in the gas-phase. Recently, an ultrafast electron diffraction (UED) apparatus using mega-electron-volt (MeV) electrons was developed at the SLAC National Accelerator Laboratory for imaging ultrafast structural dynamics of molecules in the gas phase. The SLAC gas-phase MeV UED has achieved 65 fs root mean square temporal resolution, 0.63 Å spatial resolution, and 0.22 Å-1 reciprocal-space resolution. Such high spatial-temporal resolution has enabled the capturing of real-time molecular movies of fundamental photochemical mechanisms, such as chemical bond breaking, ring opening, and a nuclear wave packet crossing a conical intersection. In this paper, the design that enables the high spatial-temporal resolution of the SLAC gas phase MeV UED is presented. The compact design of the differential pump section of the SLAC gas phase MeV UED realized five orders-of-magnitude vacuum isolation between the electron source and gas sample chamber. The spatial resolution, temporal resolution, and long-term stability of the apparatus are systematically characterized.

Short communication: Supply of methionine during late pregnancy enhances whole-blood innate immune response of Holstein calves partly through changes in mRNA abundance in polymorphonuclear leukocytes

The supply of methionine (Met) in late pregnancy can alter mRNA abundance of genes associated with metabolism and immune response in liver and polymorphonuclear leukocytes (PMN) of the neonatal calf. Whether prenatal supply of Met elicits postnatal effects on systemic inflammation and innate immune response of the calf is not well known. We investigated whether enhancing the maternal supply of Met via feeding ethyl-cellulose rumen-protected Met (RPM) was associated with differences in calf innate immune response mRNA abundance in PMN and systemic indicators of inflammation during the first 50 d of life. Calves (n = 14 per maternal diet) born to cows fed RPM at 0.09% of diet dry matter per day (MET) for the last 28 ± 2 d before calving or fed a control diet with no added Met (CON) were used. Blood for biomarker analysis and isolation of PMN for innate immune function assays and mRNA abundance was harvested at birth (before colostrum feeding) and at 7, 21 and 50 d of age. Whole blood was challenged with enteropathogenic bacteria (Escherichia coli 0118:H8) and phagocytosis and oxidative burst of neutrophils and monocytes were quantified via flow cytometry. Although concentration of haptoglobin and activity of myeloperoxidase among calves from both maternal groups increased markedly between 0 and 7 d of age followed by a decrease to baseline at d 21 the responses were lower in MET compared with CON calves. Nitric oxide concentration decreased markedly between 0 and 7 d regardless of maternal group but MET calves tended to have lower overall concentrations during the study. In vitro phagocytosis in stimulated neutrophils increased markedly over time in both CON and MET calves but responses were overall greater in MET calves. Oxidative burst in both neutrophils and monocytes increased over time regardless of maternal treatment. The mRNA abundance of lactate dehydrogenase (LDHA) signal transducer and activator of transcription 3 (STAT3) and S100 calcium binding protein A8 (S100A8) in PMN was overall greater in MET calves. Overall data suggest that increasing the maternal supply of Met during late pregnancy could affect the neonatal calf inflammatory status and innate immune response. Although changes in mRNA abundance could play a role in coordinating the immune response the exact mechanisms merit further study.

First Measurement of Near-Threshold J/ψ Exclusive Photoproduction off the Proton

We report on the measurement of the γp→J/ψp cross section from E_{γ}=11.8  GeV down to the threshold at 8.2 GeV using a tagged photon beam with the GlueX experiment. We find that the total cross section falls toward the threshold less steeply than expected from two-gluon exchange models. The differential cross section dσ/dt has an exponential slope of 1.67±0.39  GeV^{-2} at 10.7 GeV average energy. The LHCb pentaquark candidates P_{c}^{+} can be produced in the s channel of this reaction. We see no evidence for them and set model-dependent upper limits on their branching fractions B(P_{c}^{+}→J/ψp) and cross sections σ(γp→P_{c}^{+})×B(P_{c}^{+}→J/ψp).