The complete mitochondrial genome of Paragonimus ohirai (Paragonimidae: Trematoda: Platyhelminthes) and its comparison with P. Westermani congeners and other trematodes

We present the complete mitochondrial genome of Paragonimus ohirai Miyazaki, 1939 and compare its features with those of previously reported mitochondrial genomes of the pathogenic lung-fluke, Paragonimus westermani, and other members of the genus. The circular mitochondrial DNA molecule of the single fully sequenced individual of P. ohirai was 14,818 bp in length, containing 12 protein-coding, two ribosomal RNA and 22 transfer RNA genes. As is common among trematodes, an atp8 gene was absent from the mitogenome of P. ohirai and the 50 end of nad4 overlapped with the 30 end of nad4L by 40 bp. Paragonimusohirai and four forms/strains of P. westermani from South Korea and India, exhibited remarkably different base compositions and hence codon usage in protein-coding genes. In the fully sequenced P. ohirai individual, the non-coding region started with two long identical repeats (292 bp each), separated by tRNAGlu. These were followed by an array of six short tandem repeats (STR), 117 bp each. Numbers of the short tandem repeats varied among P. ohirai individuals. A phylogenetic tree inferred from concatenated mitochondrial protein sequences of 50 strains encompassing 42 species of trematodes belonging to 14 families identified a monophyletic Paragonimidae in the class Trematoda. Characterization of additional mitogenomes in the genus Paragonimus will be useful for biomedical studies and development of molecular tools and mitochondrial markers for diagnostic, identification, hybridization and phylogenetic/epidemiological/evolutionary studies

The ribosomal transcription units of Haplorchis pumilio and H. taichui and the use of 28S rDNA sequences for phylogenetic identification of common heterophyids in Vietnam

Background: Heterophyidiasis is now a major public health threat in many tropical countries. Species in the trematode family Heterophyidae infecting humans include Centrocestus formosanus, Haplorchis pumilio, H. taichui, H. yokogawai, Procerovum varium and Stellantchasmus falcatus. For molecular phylogenetic and systematic studies on trematodes, we need more prospective markers for taxonomic identification and classification. This study provides near-complete ribosomal transcription units (rTU) from Haplorchis pumilio and H. taichui and demonstrates the use of 28S rDNA sequences for identification and phylogenetic analysis. Results: The near-complete ribosomal transcription units (rTU), consisting of 18S, ITS1, 5.8S, ITS2 and 28S rRNA genes and spacers, from H. pumilio and H. taichui from human hosts in Vietnam, were determined and annotated. Sequence analysis revealed tandem repetitive elements in ITS1 in H. pumilio and in ITS2 in H. taichui. A phylogenetic tree inferred from 28S rDNA sequences of 40 trematode strains/species, including 14 Vietnamese heterophyid individuals, clearly confirmed the status of each of the Vietnamese species: Centrocestus formosanus, Haplorchis pumilio, H. taichui, H. yokogawai, Procerovum varium and Stellantchasmus falcatus. However, the family Heterophyidae was clearly not monophyletic, with some genera apparently allied with other families within the superfamily Opisthorchioidea (i. e. Cryptogonimidae and Opisthorchiidae). These families and their constituent genera require substantial re-evaluation using a combination of morphological and molecular data. Our new molecular data will assist in such studies. Conclusions: The 28S rDNA sequences are conserved among individuals within a species but varied between genera. Based on analysis of 40 28S rDNA sequences representing 19 species in the superfamily Opisthorchioidea and an outgroup taxon (Alaria alata, family Diplostomidae), six common human pathogenic heterophyids were identified and clearly resolved. The phylogenetic tree inferred from these sequences again confirmed anomalies in molecular placement of some members of the family Heterophyidae and demonstrates the need for reappraisal of the entire superfamily Opisthorchioidea. The new sequences provided here supplement those already available in public databases and add to the array of molecular tools that can be used for the diagnosis of heterophyid species in human and animal infections

Echinacea purpurea: An overview of mechanism, efficacy, and safety in pediatric upper respiratory infections and otitis media

Pediatric upper respiratory infections (URIs) and otitis media (OM) significantly impact the health of children globally. Echinacea purpurea, known for its immunomodulatory, anti-inflammatory, and antimicrobial properties, has been historically used to treat various ailments, suggesting its potential as an adjunctive treatment in pediatric respiratory conditions. This narrative review synthesizes literature from January 2000 to December 2023 on the efficacy and safety of E. purpurea in treating pediatric URIs, including OM. It focuses on clinical trials and empirical studies that explore the mechanisms of action, such as the modulation of cytokine production, inhibition of NF-κB signaling, and antimicrobial effects. The analysis reveals mixed outcomes regarding the efficacy of E. purpurea in pediatric populations, attributed partly to variability in study designs and lack of standardized treatment protocols. While some studies report reduced severity and duration of respiratory symptoms, others indicate minimal or no significant difference compared to placebo. The review also highlights the need for specifically designed products that cater to the unique physiological and metabolic needs of children. Rigorous, well-designed clinical trials are crucial for establishing clear guidelines on the use of E. purpurea in pediatric respiratory care, ensuring its safe and effective application in improving health outcomes for children

Smoke-free environment policy in Vietnam: What did people see and how did they react when they visited various public places?

Introduction: Since Vietnam has signed WHO framework on tobacco control (FCTC) in 2003 and has issued tobacco control law in 2013, there has been little research concerning about what impacts smoke-free regulations have had on public compliance. The objective of this study was to assess public exposure to secondhand smoke and reaction toward smoke-free policy regulations in Vietnam and the associated factor. Methods: Using the design of GATS (Global Adult Tobacco Survey), a nationally representative sample of 8,996 adults were approached for data collection. Logistic regression was used to examine the associated factor.Results: The study revealed that the prevalence of respondents exposed to secondhand smoke was much higher in bars/café/tea shops (90.07%) and restaurants (81.81%) than in any other public places, universities (36.70%), government buildings (31.12%), public transport (20.04%), healthcare facilities (17.85%) and schools (15.84%). 13.23% of respondents saw smokers violate smoke-free regulations. Among those who saw them violate smoke-free regulations, just one-third cautioned them to stop smoking. Strikingly, a higher rate of cautioning smokers to stop smoking was observed among the older, married, and better educated respondents. Respondents who were married, better educated and in lower economic status were more likely to remind smokers to stop smoking.Conclusions: The study has called for strengthening two of the six MPOWER (Monitor, Protect, Offer, Warn, Enforce and Raise) components of the tobacco free initiative introduced by WHO, Monitoring tobacco use and prevention policies and Protecting people from tobacco smoke

Surveillance and treatment of primary hepatocellular carcinoma (aka. STOP HCC): protocol for a prospective cohort study of high-risk patients for HCC using GALAD-score.

Vietnam and Saudi Arabia have high disease burden of primary hepatocellular carcinoma (HCC). Early detection in asymptomatic patients at risk for HCC is a strategy to improve survival outcomes in HCC management. GALAD score, a serum-based panel, has demonstrated promising clinical utility in HCC management. However, in order to ascertain its potential role in the surveillance of the early detection of HCC, GALAD needs to be validated prospectively for clinical surveillance of HCC (i.e., phase IV biomarker validation study). Thus, we propose to conduct a phase IV biomarker validation study to prospectively survey a cohort of patients with advanced fibrosis or compensated cirrhosis, irrespective of etiologies, using semi-annual abdominal ultrasound and GALAD score for five years. We plan to recruit a cohort of 1,600 patients, male or female, with advanced fibrosis or cirrhosis (i.e., F3 or F4) and MELD ≤ 15, in Vietnam and Saudi Arabia (n = 800 each). Individuals with a liver mass ≥ 1 cm in diameter, elevated alpha-fetoprotein (AFP) (≥ 9 ng/mL), and/or elevated GALAD score (≥ -0.63) will be scanned with dynamic contrast-enhanced magnetic resonance imaging (MRI), and a diagnosis of HCC will be made by Liver Imaging Reporting and Data System (LiRADS) assessment (LiRADS-5). Additionally, those who do not exhibit abnormal imaging findings, elevated AFP titer, and/or elevated GALAD score will obtain a dynamic contrast-enhanced MRI annually for five years to assess for HCC. Only MRI nearest to the time of GALAD score measurement, ultrasound and/or AFP evaluation will be included in the diagnostic validation analysis. MRI will be replaced with an abdominal computed tomography scan when MRI results are poor due to patient conditions such as movement etc. Gadolinium-ethoxybenzyl-diethylenetriamine pentaacetic acid-enhanced MRI will not be carried out in study sites in both countries. Bootstrap resampling technique will be used to account for repeated measures to estimate standard errors and confidence intervals. Additionally, we will use the Cox proportional hazards regression model with covariates tailored to the hypothesis under investigation for time-to-HCC data as predicted by time-varying biomarker data. The present work will evaluate the performance of GALAD score in early detection of liver cancer. Furthermore, by leveraging the prospective cohort, we will establish a biorepository of longitudinally collected biospecimens from patients with advanced fibrosis or cirrhosis to be used as a reference set for future research in early detection of HCC in the two countries. Name of the registry: ClinicalTrials.gov Registration date: 22 April 2022 Trial registration number: NCT05342350 URL of trial registry record

Efficient Hamiltonian Monte Carlo for large data sets by data subsampling

Bayesian statistics carries out inference about the unknown parameters in a statistical model using their posterior distribution, which in many cases is computationally intractable. Therefore, simulation methods such as Markov Chain Monte Carlo (MCMC) and Sequential Monte Carlo (SMC) are frequently used to approximate the posterior distribution. SMC has the attractive ability to accurately estimate the marginal likelihood, although it is computationally more expensive than MCMC. Nevertheless, both methods require efficient Markov moves to deal with complex, high dimensional problems. While Hamiltonian Monte Carlo (HMC) is a remedy in many cases, it also increases the computational cost of the algorithms appreciably, especially for large data sets. This thesis presents some novel methods that focus on speeding up inference by combining HMC and data subsampling. The first contribution is a Metropolis within Gibbs algorithm that successfully speeds up standard HMC by orders of magnitude in two large data examples. I then show that the new approach can be incorporated into other HMC implementations such as the No-U-Turn sampler. The next contribution is an extension of the first method to SMC for Bayesian static models, which gives comparable result to full data SMC in terms of accuracy but is much faster in several model settings. The final contribution shows that the subsampling HMC scheme can also be applied to a thermodynamic integration method to estimate the marginal likelihood

Detection of the Potential Inactivation of Tetrodotoxin by Lactic Acid Bacterial Exopolysaccharide

Screening for compounds that can neutralize the toxicity of tetrodotoxin (TTX) or reduce its negative effects is necessary. Our study tested the TTX detoxification capacity of exopolysaccharide (EPS) extracted from lactic acid bacteria. EPS of Leuconostoc mesenteroides N3 isolated from the Vung Tau sea (Vietnam), Lactobacillus plantarum PN05, and Lactobacillus rhamnosus PN04 were used in the study. To more completely evaluate the importance of EPS in detoxification, EPS samples of Leuconostoc mesenteroides N3, Lactobacillus plantarum PN05 and Lactobacillus rhamnosus PN04 were also tested. The majority of EPS of these bacteria contained glucose; this was observed using thin layer chromatography (TLC) and high-performance liquid chromatography (HPLC) analysis. As observed with FTIR analysis, only EPS of Lactobacillus plantarum PN05 contained methyl groups. The results indicated that detoxification of TTX in mice could be obtained at an optimal dose of 248 µg EPS from Leuconostoc mesenteroides incubated with 54 µg cuprous oxide for 40 min or 148 µg EPS Lactobacillus rhamnosus incubated with 55 µg cuprous oxide for 40 min, while EPS from Lactobacillus plantarum showed TTX detoxification capacity without cuprous oxide combination. Consequently, EPS from Lactobacillus plantarum PN05 can be used in TTX prevention. This is the first report on the importance of lactic acid bacteria in TTX detoxification

The complete mitogenome of the Asian lung fluke Paragonimus skrjabini miyazakii and its implications for the family Paragonimidae (Trematoda: Platyhelminthes)

The complete circular mitogenome of Paragonimus skrjabini miyazakii (Platyhelminthes: Paragonimidae) from Japan, obtained by PacBio long-read sequencing, was 17 591 bp and contained 12 protein-coding genes (PCGs), 2 mitoribosomal RNA and 22 transfer RNA genes. The atp8 gene was absent, and there was a 40 bp overlap between nad4L and nad4. The long non-coding region (4.3 kb) included distinct types of long and short repeat units. The pattern of base usage for PCGs and the mtDNA coding region overall in Asian and American Paragonimus species (P. s. miyazakii, P. heterotremus, P. ohirai and P. kellicotti) and the Indian form of P. westermani was T > G > A > C. On the other hand, East-Asian P. westermani used T> G > C > A. Five Asian and American Paragonimus species and P. westermani had TIT/Phe, TTG/Leu and GTT/Val as the most frequently used codons, whereas the least-used codons were different in each species and between regional forms of P. westermani. The phylogenetic tree reconstructed from a concatenated alignment of amino acids of 12 PCGs from 36 strains/26 species/5 families of trematodes confirmed that the Paragonimidae is monophyletic, with 100% nodal support. Paragonimus skrjabini miyazakii was resolved as a sister to P. heterotrernus. The P. westermani lade was clearly separate from remaining congeners. The latter Glade was comprised of 2 subclades, one of the East-Asian and the other of the Indian Type 1 samples. Additional mitogenomes in the Paragonimidae are needed for genomic characterization and are useful for diagnostics, identification and genetic/ phylogenetic/ epidemiological/ evolutionary studies of the Paragonimidae

A complete mitochondrial genome from Echinochasmus japonicus supports the elevation of Echinochasminae Odhner, 1910 to family rank (Trematoda: Platyhelminthes)

The complete mitochondrial (mt) genome of the trematode Echinochasmus japonicus Tanabe, 1926 was fully determined and annotated. The circular mt molecule of this species is 15,865 bp in length, containing 12 protein-coding genes (arranged in the following order: cox3-cob-nad4L-nad4-atp6-nad2-nad1-nad3-cox1-cox2-nad6-nad5), two ribosomal RNA genes (rrnL and rrnS) and 22 transfer RNA genes (trnH; trnQ; trnF; trnM; trnV; trnA; trnD; trnN; trnP; trnI; trnK; trnS1(AGN); trnW; trnT; trnC; trnL1(CUN); trnS2(UCN); trnL2(UUN); trnG; and trnE). The atp8 gene is absent. The 3′ end of nad4L overlaps the 5′ end of nad4 by 40 bp. An array of eight identical tandem repeats (240 bp each) was found between trnG and trnE in the long non-coding region of the individual worm sequenced. Numbers of these repeats varied among E. japonicus samples. Phylogenetic analysis of concatenated mt protein sequences of 40 trematode species/strains supports the elevation of Echinochasminae Odhner, 1910 to family rank, close to the families Echinostomatidae and Fasciolidae. As echinochasmid and echinostomatid species can parasitize humans, the future characterization of additional mt genomes is needed for development of mt markers for identification and phylogenetic, population, epidemiological and hybridization studies