The ability of a 3-gene host signature in blood to distinguish tuberculous meningitis from other brain infections

BACKGROUND

Tuberculous meningitis (TBM) is difficult to diagnose. We investigated whether a 3-gene host response signature in blood can distinguish TBM from other brain infections.

METHODS

The expression of 3 genes (Dual specificity phosphatase 3- DUSP3, Guanylate-binding protein- GBP5, Krupple-like factor 2- KLF2) was analysed by RNA sequencing of archived whole blood from four cohorts of Vietnamese adults: 281 with TBM; 279 with pulmonary tuberculosis; 50 with other brain infections; and 30 healthy controls. 'TB scores' (combined 3-gene expression) were calculated following published methodology and discriminatory performance compared using area under a receiver operator characteristic curve (AUC).

RESULTS

GBP5 was upregulated in TBM compared to other brain infections (p < 0.001), with no difference in DUSP3 and KLF2 expression. The diagnostic performance of GBP5 alone (AUC 0.74 (95% CI 0.67-0.81)) was slightly better than the 3-gene TB score (AUC 0.66, 95% CI 0.58-0.73) in TBM. Both GBP5 expression and TB score were higher in HIV-positive participants (P < 0.001), with good diagnostic performance of GBP5 alone (AUC 0.86, 95% CI 0.80-0.93).

CONCLUSION

The 3-gene host signature in whole blood has the ability to discriminate TBM from other brain infections, including in HIV-positive individuals. Validation in large prospective diagnostic study is now required.

Synthesis of benzo[a]carbazole derivatives via intramolecular cyclization using Brønsted acidic carbonaceous material as the catalyst

In this work, a new procedure for the synthesis of benzo[a]carbazole from 1,3-diketones, primary amines, phenylglyoxal monohydrate, and malononitrile employing a solid acidic catalyst has been developed. The multicomponent reaction provided 3-cyanoacetamide pyrrole as an intermediate and then the formation of benzo[a]carbazole via intramolecular ring closure. The reaction was carried out for 2 h at 240 °C, resulting in the desired product with 73% yield. Acidic sites on the solid acid catalyst, made from rice husk-derived amorphous carbon with a sulfonic acid core (AC-SO3H), provided the best activity. Acidic sites on the surface of the catalyst, including carboxylic, phenolic, and sulfonic acids, were 4.606 mmol g-1 of the total acidity. AC-SO3H demonstrated low cost, low toxicity, porosity, stability, and flexibility of tuning and reusability.

Fe2O3/diatomite materials as efficient photo-Fenton catalysts for ciprofloxacin removal

In this study, we used Fe₂O₃/diatomite material system toward ciprofloxacin (CIP) photo-Fenton removal in water under visible light (vis) excitation. The characterization of Fe₂O₃/diatomite catalysts was determined by X-ray diffraction patterns, Fourier-transform infrared analysis, inductively coupled plasma mass spectrometry, and scanning electron microscopy. The photo-Fenton catalytic activity of the Fe₂O₃/diatomite was appraised by the removal efficiency of the CIP throughout the effect of the H₂O₂ with various parameters such as initial pH, catalyst amount, and H₂O₂ amount. The results indicate that 0.2 gL^-1 Fe₂O₃/diatomite catalysts achieved the highest performance at approximately 90.03% with a 50 μL H₂O₂ concentration. Furthermore, the Fe₂O₃/diatomite catalysts have high stability, with over 80% CIP removed after five cycles. This study is inspired to develop a potential material for photo-Fenton degradation of antibiotics in wastewater.

A New Pathway for the Preparation of Pyrano[2,3-c]pyrazoles and molecular Docking as Inhibitors of p38 MAP Kinase

We report a new pathway to synthesize pyrano[2,3-c]pyrazoles and their binding mode to p38 MAP kinase. Pyrano[2,3-c]pyrazole derivatives have been prepared through a four-component reaction of benzyl alcohols, ethyl acetoacetate, phenylhydrazine, and malononitrile in the presence of sulfonated amorphous carbon and eosin Y as catalysts. All products were characterized by melting point, ¹H and ¹³C NMR, and HRMS (ESI). The products were screened in silico for their binding activities to both the ATP-binding pocket and the lipid-binding pocket of p38 MAP kinase, using a structure-based flexible docking provided by the engine ADFR. The results showed that eight synthesized compounds had a higher affinity to the lipid pocket than to the other target site, which implied potential applications as allosteric inhibitors. Finally, the most biologically active compound, 5, had a binding affinity comparable to those of other proven lipid pocket inhibitors, with affinity to the target pocket reaching -10.9932 kcal/mol, and also had the best binding affinity to the ATP-binding pockets in all of our products. Thus, our research provides a novel pathway for synthesizing pyrano[2,3-c]pyrazoles and bioinformatic evidence for their biological capability to block p38 MAP kinase pockets, which could be useful for developing cancer or immune drugs.

Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam

A second cluster of COVID-19 cases imported from Europe occured in Vietnam from early March 2020. We describe 44 SARS-CoV-2 RT-PCR positive patients (cycle threshold value <30) admitted to the National Hospital for Tropical Diseases in Hanoi between March 6 and April 15 2020. Whole SARS-CoV-2 genomes from these patients were sequenced using Illumina Miseq and analysed for common genetic variants and relationships to local and globally circulating strains. Results showed that 32 cases were Vietnamese with a median age of 37 years (range 15-74 years), and 23 were male. Most cases were acquired outside Vietnam, mainly from the UK (n = 15), other European countries (n = 14), Russia (n = 6) and countries in Asia (n = 3). No cases had travelled from China. Forty-one cases had symptoms at admission, typically dry cough (n = 36), fever (n = 20), sore throat (n = 14) and diarrhoea (n = 12). Hospitalisation was long with a median of 25 days, most commonly from 20-29 days. All SARS-CoV-2 genomes were similar (92-100% sequence homology) to the reference sequence Wuhan_1 (NC_045512), and 32 strains belonged to the B.1.1 lineage. The three most common variants were linked, and included C3037T, C14408T (nsp12: P323L) and A23403G (S: D614G) mutations. This group of mutations often accompanied variant C241T (39/44 genomes) or GGG 28881..28883 AAC (33/44 genomes). The prevalence of the former reflected probable European origin of viruses, and the transition D614G was dominant in Vietnam. New variants were identified; however, none could be associated with disease severity.

Distribution of gamma radiation dose rate related with natural radionuclides in all of Vietnam and radiological risk assessment of the built-up environment

A built-up environment utilizes building materials containing natural radionuclides that will change radiological risks. While radiological risks have been estimated from the activity concentrations of natural radionuclides in soil, it is important to evaluate the changes of these risks for the built-up environment using these building materials. Based on the direct measurements of absorbed dose rate in air and calculation of absorbed dose rate in air from activity concentrations in soil for all of Vietnam which has undergone significant economic growth in recent decades, the changes of absorbed dose rate in air and radiological risks before and after construction of many artificial structures were investigated. The results showed that the absorbed dose rates in air were clearly changed by the urbanization, and the difference ratio for all of Vietnam ranged from 0.5 to 2.1, meaning that the artificial structures have been acting as shielding materials to terrestrial gamma-rays or radiation sources. However, changes in annual effective dose in the built-up environment were small, and there was no new radiation risk from the built-up environment for Vietnam.

EFFECTIVE DOSE DUE TO TERRESTRIAL GAMMA RADIATION ESTIMATED IN SOUTHERN VIETNAM BY CAR-BORNE SURVEY TECHNIQUE

Absorbed dose rates in air from natural radionuclides were measured by a car-borne survey in southern Vietnam. The mean absorbed dose rate in air for southern Vietnam, which consists of the south-east region and the Mekong River Delta region, was 64 ± 18 nGy h-1, while rates for the two regions were 61 ± 17 and 66 ± 19 nGy h-1, respectively. These dose rates were respectively 1.2, 2.1 and 0.9 times the measured values that were calculated on the basis of activity concentrations of soil samples in a previous study. It was considered that measured dose rate in the south-east region was influenced by the presence of artificial structures such as high-rise buildings and roads. The effective dose due to terrestrial gamma radiation for southern Vietnam was calculated to be 0.55 mSv y-1 which is 1.2 times higher than the world-wide average of 0.48 mSv y-1.

Development and evaluation of a non-ribosomal random PCR and next-generation sequencing based assay for detection and sequencing of hand, foot and mouth disease pathogens

Background

Hand, foot and mouth disease (HFMD) has become a major public health problem across the Asia-Pacific region, and is commonly caused by enterovirus A71 (EV-A71) and coxsackievirus A6 (CV-A6), CV-A10 and CV-A16. Generating pathogen whole-genome sequences is essential for understanding their evolutionary biology. The frequent replacements among EV serotypes and a limited numbers of available whole-genome sequences hinder the development of overlapping PCRs for whole-genome sequencing.

We developed and evaluated a non-ribosomal random PCR (rPCR) and next-generation sequencing based assay for sequence-independent whole-genome amplification and sequencing of HFMD pathogens. A total of 16 EV-A71/CV-A6/CV-A10/CV-A16 PCR positive rectal/throat swabs (Cp values: 20.9–33.3) were used for assay evaluation.

Results

Our assay evidently outperformed the conventional rPCR in terms of the total number of EV-A71 reads and the percentage of EV-A71 reads: 2.6 % (1275/50,000 reads) vs. 0.1 % (31/50,000) and 6 % (3008/50,000) vs. 0.9 % (433/50,000) for two samples with Cp values of 30 and 26, respectively. Additionally the assay could generate genome sequences with the percentages of coverage of 94–100 % of 4 different enterovirus serotypes in 73 % of the tested samples, representing the first whole-genome sequences of CV-A6/10/16 from Vietnam, and could assign correctly serotyping results in 100 % of 24 tested specimens. In all but three the obtained consensuses of two replicates from the same sample were 100 % identical, suggesting that our assay is highly reproducible.

Conclusions

In conclusion, we have successfully developed a non-ribosomal rPCR and next-generation sequencing based assay for sensitive detection and direct whole-genome sequencing of HFMD pathogens from clinical samples.

Electronic supplementary material

The online version of this article (doi:10.1186/s12985-016-0580-9) contains supplementary material, which is available to authorized users.

Impact on ambient dose rate in metropolitan Tokyo from the Fukushima Daiichi Nuclear Power Plant accident

A car-borne survey was made in metropolitan Tokyo, Japan, in December 2014 to estimate external dose. This survey was conducted for all municipalities of Tokyo and the results were compared with measurements done in 2003. The ambient dose rate measured in the whole area of Tokyo in December 2014 was 60 nGy h(-1) (23-142 nGy h(-1)), which was 24% higher than the rate in 2003. Higher dose rates (>70 nGy h(-1)) were observed on the eastern and western ends of Tokyo; furthermore, the contribution ratio from artificial radionuclides ((134)Cs and (137)Cs) to ambient dose rate in eastern Tokyo was twice as high as that of western Tokyo. Based on the measured ambient dose rate, the effective dose rate after the accident was estimated to be 0.45 μSv h(-1) in Tokyo. This value was 22% higher than the value before the accident as of December 2014.

Human blood dendritic cells from allergic subjects have impaired capacity to produce interferon-alpha via Toll-like receptor 9

BACKGROUND

High-affinity IgE receptor (Fc epsilon RI) expression on blood dendritic cells reportedly correlates with serum IgE levels. Our studies demonstrate that plasmacytoid dendritic cells (pDCs) secrete pro-inflammatory cytokines (IL-6, TNF-alpha) following Fc epsilon RI stimulation - a mode of activation that simultaneously reduces expression of Toll-like receptor 9 (TLR9). Whether or not TLR9 and/or Fc epsilon RI levels and their function on dendritic cells relate to allergic status is unknown.

OBJECTIVE

The aim of this study is to compare the innate (TLR9-mediated) immune response of human pDCs to TLR9 and Fc epsilon RI alpha receptor expression in allergic and non-allergic subjects.

METHODS

Basophil-depleted mononuclear cell fractions containing pDCs were prepared from peripheral blood of allergic and non-allergic subjects. Intracellular TLR9 and surface Fc epsilon RI alpha expression in blood dendritic cell antigen-2-positive cells were determined by flow cytometry. Activating anti-IgE antibody, anti-Fc epsilon RI alpha antibody, and TLR9 agonist were used to stimulate cell suspensions, with cytokine levels determined by ELISA.

RESULTS

No difference in the frequency of pDCs was detected among allergic (n=9) vs. non-allergic (n=11) subjects (P=0.261). While there was also no difference in the baseline expression of TLR9, pDCs from allergic subjects produced sixfold less IFN-alpha when stimulated with CpG (P=0.002). Conversely, there was higher Fc epsilon RI alpha expression (P=0.01) on the pDCs of allergic subjects.

CONCLUSIONS

Impaired TLR9-dependent immune responses in human pDCs are associated with allergic status and inversely correlated with Fc epsilon RI alpha expression. This impaired innate immune response among dendritic cells of allergic subjects may lead to more targeted therapeutic approaches and could provide a better understanding of the mechanisms underlying conventional and CpG-based immunotherapy.

Cotton wool plaques in non-familial late-onset Alzheimer disease

Cotton wool plaques (CWP) are large, ball-like plaques lacking dense amyloid cores that displace adjacent structures. They were first described in a Finnish kindred with early-onset Alzheimer disease (AD) with spastic paraparesis due to a presenilin-1 delta9 mutation. We describe a case of sporadic late-onset AD with numerous neocortical CWP as well as severe amyloid angiopathy and marked leukoencephalopathy, compared with 16 cases of late-onset AD with similar degrees of amyloid angiopathy and leukoencephalopathy. The cases were studied with histologic methods and with single and double immunostaining for beta-amyloid (Abeta), paired helical filaments-tau (PHF-tau), neurofilament (NF), glial fibrillary acidic protein (GFAP), HLA-DR, and amyloid precursor protein (APP). We found that CWP were well-circumscribed amyloid deposits infiltrated by ramified microglia and surrounded by dystrophic neurites that were immunopositive for APP, but only weakly for NF and PHF-tau. Abeta1-12 was diffuse throughout the CWP, while Abeta37-42 was peripherally located and Abeta20-40 more centrally located. Two of the 16 late-onset AD cases also had CWP, but they were also admixed with diffuse plaques and plaques with dense amyloid cores. Pyramidal tract degeneration was not a consistent finding or a prominent feature in any case. The results suggest that CWP are not specific for early-onset familial AD with spastic paraparesis.

Relationship of the extended tau haplotype to tau biochemistry and neuropathology in progressive supranuclear palsy

Two extended haplotypes of the tau gene (H1 and H2) have been described. The frequency of H1 haplotype is increased in progressive supranuclear palsy (PSP). PSP is associated with filamentous tau lesions in neurons and glia, which are reportedly composed exclusively of tau isoforms with four repeats in the microtubule-binding domain (4R tau). To determine the influence of the tau haplotype on tau isoform composition and neuropathology, we studied 25 PSP cases and 6 Alzheimer's disease patients matched for age, sex, and postmortem delay. In the basal ganglia, tau and amyloid burdens were determined to see if there was an effect of concurrent Alzheimer-type pathology, and the ratio of 4R to 3R tau was measured in detergent-insoluble tau fractions. Insoluble tau from PSP was not composed exclusively of 4R tau. All brains had a mixture of 4R and 3R tau, but the ratio was different in Alzheimer's disease and PSP. In Alzheimer's disease there was less 4R than 3R tau, whereas the ratio was reversed in PSP. In PSP cases with concurrent Alzheimer-type pathology, the ratio of 4R to 3R was intermediate between Alzheimer's disease and PSP. The H1 haplotype had no effect on the 4R to 3R ratio or on tau and amyloid burdens. In summary, the H1 haplotype does not have a major influence on the pathological or biochemical phenotype of PSP.

A randomized, placebo-controlled trial of granulocyte colony-stimulating factor administration to newborn infants with neutropenia and clinical signs of early-onset sepsis

OBJECTIVE

To determine whether recombinant human granulocyte colony-stimulating factor (G-CSF) administration: 1) accelerates production of neutrophils; 2) increases bone marrow stored and precursor neutrophils; and 3) is safe in newborn infants with neutropenia and clinical signs of early-onset sepsis.

STUDY DESIGN

We randomized 20 infants with neutropenia and clinical signs of early-onset sepsis in the first 3 days of life to receive G-CSF (10 microg/kg/d) or placebo for 3 days. Entry criteria included neutropenia as defined by Manroe criteria, an elevated immature to total neutrophil ratio [(I/T) >/=0.25], and a requirement for ventilatory support. Cultures were obtained and antibiotics initiated on all study infants. Circulating absolute neutrophil count (ANC), I/T ratio, bone marrow neutrophil storage pool (NSP) and neutrophil proliferative pool (NPP), and plasma G-CSF concentrations were evaluated. Also, severity of illness as determined using the Score for Neonatal Acute Physiology (SNAP), morbidity, and mortality were recorded.

RESULTS

Circulating ANC increased in both G-CSF and placebo recipients by day 1. Also, the I/T neutrophil ratio decreased in both G-CSF and placebo recipients. There were no significant differences in the ANC or I/T ratio between the two groups during the study period. Similarly, bone marrow NSP and NPP did not differ between G-CSF and placebo recipients at study entry or day 2. No differences were observed in the secondary outcome measures including severity of illness, morbidity, and mortality.

CONCLUSIONS

Administration of recombinant G-CSF to infants with neutropenia and clinical signs of early-onset sepsis did not increase circulating ANC, or bone marrow NSP and NPP compared with placebo. No differences were observed between G-CSF and placebo recipients in severity of illness, morbidity, or mortality. No adverse effects of G-CSF administrations were noted.

Specific aspartic acid-rich sequences are responsible for silver staining of nucleolar proteins

Ag-NOR proteins are silver-stainable proteins in the nucleolar organizer regions and are used to distinguish benign from malignant tumors. B23 and C23 are the two major Ag-NOR proteins. This study shows that only one of the two acidic clusters of B23 is responsible for its silver staining property. Fusion of this region of B23 (amino acids 161-188) to glutathione S-transferase produced an Ag-NOR positive fusion protein. The same result was obtained when amino acids 233-277 of C23 was fused with glutathione S-transferase. The aspartate residues, but not the glutamate residues, were found to be primarily responsible for the silver staining of the acidic clusters.

Comparison of bone mineral density in both hips

Dual-photon absorptiometry (DPA) was performed on both hips of 40 patients to determine if the calculated bone-mineral density (BMD) of one hip could be used to predict the BMD of the opposite hip. For the Ward triangle, femoral neck, and greater trochanter the correlation coefficients between the BMD of the two hips was .920, .917, and .843, and the standard errors (SE) of the estimate for the linear regression of the left hip on to the right were 0.067, 0.063, and 0.077 g cm-2. The absolute error of predicting one hip from the other was not a function of BMD and thus the relative error increases with lower BMD values. The relative errors were 17%, 8%, and 7% for BMDs of 0.4, 0.8, and 1.0 g cm-2, respectively. The interobserver variability was small, with an r value of .96 and an SE of the estimate value of 0.036 g cm-2. The relative error in the mild-to-moderate osteoporosis categories was 2.5 times the precision of the instrument, indicating that the asymmetry of BMD is due to real differences between hips. Therefore the BMD of one hip cannot be used to predict that of the other with sufficient accuracy to discriminate clinically relevant trends in BMD.

99mTc-glucoheptonate for quantitation of differential renal function

Differential renal function was calculated by using 99mTc-glucoheptonate (Tc-GH) in 51 patients. Computer-acquired background-corrected individual renal function was calculated by using both the 1-3-min uptake counts and the 2-4-hr delayed static counts. The degree of correlation between the two was high (r = .96). An equally high correlation was noted in 16 children who were 12 years old or younger, in 15 patients with renal size disparity greater than 60/40%, and in six patients with abnormal creatinine clearances. Ten patients had a 30-min dynamic 99mTc-DTPA study followed immediately by the injection of Tc-GH and acquisition of delayed static images 2-4 hr later. A high degree of correlation (r = .99) was seen between the 1-3-min differential function obtained by using Tc-DTPA and the 2-4-hr delayed differential function obtained by using Tc-GH. This study shows that Tc-GH is a clinically useful and valid tool for calculation of differential renal function and that Tc-GH combines many of the best aspects of Tc-DTPA and Tc-DMSA.

Oral colonization and susceptibility testing of Pseudomonas aeruginosa oral isolates from cystic fibrosis patients

Microbial samples from the oral cavities of cystic fibrosis (C.F.) patients and 20 age-matched normal control subjects were characterized. Mucoid variant Pseudomonas aeruginosa was isolated from the tongue, buccal mucosa, and saliva of C.F. patients only. Analysis of the data suggests that the oral cavity is a potential reservoir for this organism. Aspiration and cross-contamination from this reservoir may be important in perpetuating chronic pulmonary infection in C.F. patients. Susceptibility testing was performed on 20 mucoid variant P. aeruginosa oral isolates obtained from the patients according to standardized broth dilution procedures. The in vitro antimicrobial effects of sodium fluoride, stannous fluoride, and chlorhexidine were measured. Analysis of the data suggests that clinically safe and achievable levels of chlorhexidine and stannous fluoride may be antimicrobial.