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  1. Benzo(a)pyrene degradation and microbial community responses in composted soil
    Zhu F, Storey S, Ashaari MM, Clipson N, Doyle E
    Environ Sci Pollut Res Int, 2017 Feb;24(6):5404-5414.
    PMID: 28025788 DOI: 10.1007/s11356-016-8251-3
    Benzo(a)pyrene degradation was compared in soil that was either composted, incubated at a constant temperature of 22 °C, or incubated under a temperature regime typical of a composting process. After 84 days, significantly more (61%) benzo(a)pyrene was removed from composted soil compared to soils incubated at a constant temperature (29%) or at composting temperatures (46%). Molecular fingerprinting approaches indicated that in composted soils, bacterial community changes were driven by both temperature and organic amendment, while fungal community changes were primarily driven by temperature. Next-generation sequencing data revealed that the bacterial community in composted soil was dominated by Actinobacteria (order Actinomycetales), Firmicutes (class Bacilli), and Proteobacteria (classes Gammaproteobacteria and Alphaproteobacteria), regardless of whether benzo(a)pyrene was present or not. The relative abundance of unclassified Actinomycetales (Actinobacteria) was significantly higher in composted soil when degradation was occurring, indicating a potential role for these organisms in benzo(a)pyrene metabolism. This study provides baseline data for employing straw-based composting strategies for the removal of high molecular weight PAHs from soil and contributes to the knowledge of how microbial communities respond to incubation conditions and pollutant degradation.
  2. The effect of metformin on carotid intima-media thickness (CIMT): A systematic review and meta-analysis of randomized clinical trials
    Chen Y, Li H, Ye Z, Găman MA, Tan SC, Zhu F
    Eur J Pharmacol, 2020 Nov 05;886:173458.
    PMID: 32763300 DOI: 10.1016/j.ejphar.2020.173458
    Metformin administration has been reported to influence the carotid intima-media thickness (CIMT) in humans. However, since previously conducted studies have yielded inconsistent results, the exact effect of metformin on CIMT remains unclear. Causes that could lead to inconsistency in reported research could be the duration and dose of the intervention, as well as the sample size. To address this inconsistency, we conducted a systematic review and meta-analysis to evaluate the influence of metformin on CIMT in human subjects. We identified eligible studies by searching several electronic databases (EMBASE, PubMed-MEDLINE, Web of Science and Google Scholar) up to December 12, 2019. Data were pooled using the random-effects model. Combining data from 1087 participants (9 studies), our meta-analysis revealed that the administration of metformin resulted in a significant reduction in CIMT (WMD = -0.049 mm; 95% CI: -0.095, -0.004). Stratified analyses showed that an intervention lasting ≥12 months (WMD: -0.084 mm, 95% CI: -0.145, -0.024) and an intake of metformin ≤1500 mg/day (WMD: -0.081 mm, 95% CI: -0.132, -0.029) resulted in a significantly greater reduction in CIMT. However, an intervention duration of less than 12 months and an intake of metformin ˃1500 mg/day yielded no significant effects on CIMT. The results of the current study confirm that metformin administration is associated with a significant reduction in CIMT. Taking into account that CIMT reflects the burden of atherosclerosis, the clinical utility of metformin might also be related to its anti-atherogenic effects.
  3. Effects of high-voltage electrostatic field (HVEF) on frozen shrimp (Solenocera melantho) based on UPLC-MS untargeted metabolism
    Liu J, Zhu F, Yang J, Wang Y, Ma X, Lou Y, et al.
    Food Chem, 2023 Jun 15;411:135499.
    PMID: 36696717 DOI: 10.1016/j.foodchem.2023.135499
    Shrimp meat is prone to autolysis and decay due to the abundance of endogenous enzymes and contamination from microorganisms. HVEF freezing can slow the spoilage of shrimp, producing small and uniform ice crystals, resulting in less damage to muscle tissue. In this study, HVEF technique was used to freeze the shrimp (Solenocera melantho), and the UPLC-MS metabolic technique was used to investigate the metabolites of frozen shrimp meat. Compared with the control group, 367 differential metabolites were identified in the HVEF group. Mapping them to the KEGG database, there were 108 with KEGG ID. Purine metabolism and pyrimidine metabolism were the most enriched pathways. In addition, phosphatidylcholines (PCs), inosine (HxR), and l-valine were identified as potential biomarkers associated with lipid, nucleotide, and organic acid metabolism, respectively. Overall, HVEF can improve freezing quality of shrimp meat by slowing down the metabolism of substances in the muscle of S. melantho.
  4. Actual and estimated adenoma detection rates: a 2-year monocentric colonoscopic screening outcome in Shenzhen, China
    Zeng L, Chua EG, Xiong Y, Ding S, Ai H, Hou Z, et al.
    JGH Open, 2020 Aug;4(4):707-712.
    PMID: 32782960 DOI: 10.1002/jgh3.12322
    Background and Aim: While adenoma detection rate (ADR) is an important quality metric for screening colonoscopy, it remains difficult to be accessed due to the lack of integrated endoscopy and pathology databases. Hence, the use of an adenoma-to-polyp detection rate quotient and polyp detection rate (PDR) has been proposed to predict ADR. This study aimed to examine the usefulness of estimated ADR across different colonic segments in two age groups for Shenzhen people in China.

    Methods: We retrospectively analyzed 7329 colonoscopy procedures performed by 12 endoscopists between January 2012 and February 2014. The PDR, actual ADR, and estimated ADR of the entire, proximal, and distal colon, and within each colonic segment, in two patient age groups: <50 and ≥50 years, were calculated for each endoscopist.

    Results: The overall polyp and adenoma prevalence rates were 19.1 and 9.3%, respectively. The average age of adenoma-positive patients was significantly higher than that of adenoma-negative patients (54 ± 12.6 years vs 42.9 ± 13.2 years, respectively). A total of 1739 polyps were removed, among which 826 were adenomas. More adenomatous polyps were found in the proximal colon (60.4%, 341/565) than in the distal colon (40.9%, 472/1154). Overall, both actual and estimated ADR correlated strongly at the entire colon level and within most colonic segments, except for the cecum and rectum. In both age groups, these parameters correlated strongly within the traverse colon and descending colon.

    Conclusion: Caution should be exercised when predicting ADR within the sigmoid colon and rectum.

  5. Fulltext Interferon Regulatory Factors IRF1 and IRF7 Directly Regulate Gene Expression in Bats in Response to Viral Infection
    Irving AT, Zhang Q, Kong PS, Luko K, Rozario P, Wen M, et al.
    Cell Rep, 2020 11 03;33(5):108345.
    PMID: 33147460 DOI: 10.1016/j.celrep.2020.108345
    Bat cells and tissue have elevated basal expression levels of antiviral genes commonly associated with interferon alpha (IFNα) signaling. Here, we show Interferon Regulatory Factor 1 (IRF1), 3, and 7 levels are elevated in most bat tissues and that, basally, IRFs contribute to the expression of type I IFN ligands and high expression of interferon regulated genes (IRGs). CRISPR knockout (KO) of IRF 1/3/7 in cells reveals distinct subsets of genes affected by each IRF in an IFN-ligand signaling-dependent and largely independent manner. As the master regulators of innate immunity, the IRFs control the kinetics and maintenance of the IRG response and play essential roles in response to influenza A virus (IAV), herpes simplex virus 1 (HSV-1), Melaka virus/Pteropine orthoreovirus 3 Melaka (PRV3M), and Middle East respiratory syndrome-related coronavirus (MERS-CoV) infection. With its differential expression in bats compared to that in humans, this highlights a critical role for basal IRF expression in viral responses and potentially immune cell development in bats with relevance for IRF function in human biology.
  6. Fulltext The combinatorial diversity of KIR and HLA class I allotypes in Peninsular Malaysia
    Tao S, Kichula KM, Harrison GF, Farias TDJ, Palmer WH, Leaton LA, et al.
    Immunology, 2021 Apr;162(4):389-404.
    PMID: 33283280 DOI: 10.1111/imm.13289
    Killer cell immunoglobulin-like receptors (KIRs) interact with polymorphic human leucocyte antigen (HLA) class I molecules, modulating natural killer (NK) cell functions and affecting both the susceptibility and outcome of immune-mediated diseases. The KIR locus is highly diverse in gene content, copy number and allelic polymorphism within individuals and across geographical populations. To analyse currently under-represented Asian and Pacific populations, we investigated the combinatorial diversity of KIR and HLA class I in 92 unrelated Malay and 75 Malaysian Chinese individuals from the Malay Peninsula. We identified substantial allelic and structural diversity of the KIR locus in both populations and characterized novel variations at each analysis level. The Malay population is more diverse than Malay Chinese, likely representing a unique history including admixture with immigrating populations spanning several thousand years. Characterizing the Malay population are KIR haplotypes with large structural variants present in 10% individuals, and KIR and HLA alleles previously identified in Austronesian populations. Despite the differences in ancestries, the proportion of HLA allotypes that serve as KIR ligands is similar in each population. The exception is a significantly reduced frequency of interactions of KIR2DL1 with C2+ HLA-C in the Malaysian Chinese group, caused by the low frequency of C2+ HLA. One likely implication is a greater protection from preeclampsia, a pregnancy disorder associated with KIR2DL1, which shows higher incidence in the Malay than in the Malaysian Chinese. This first complete, high-resolution, characterization of combinatorial diversity of KIR and HLA in Malaysians will form a valuable reference for future clinical and population studies.
  7. Fulltext Incidence and outcome of SARS-CoV-2 reinfection in the pre-Omicron era: A global systematic review and meta-analysis
    Ismail NF, Rahman AE, Kulkarni D, Zhu F, Wang X, Del Carmen Morales G, et al.
    J Glob Health, 2023 Nov 24;13:06051.
    PMID: 37994839 DOI: 10.7189/jogh.13.06051
    BACKGROUND: With the emergence of new variants and sub-lineages of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), reinfections can significantly impact herd immunity, vaccination policies, and decisions on other public health measures. We conducted a systematic review and meta-analysis to synthesise the global evidence on SARS-CoV-2 reinfections in the pre-Omicron era.

    METHODS: We searched five global databases (MEDLINE, Embase, CINAHL Plus, Global Health, WHO COVID-19) on 12 May 2022 and 28 July 2023 and three Chinese databases (CNKI, Wanfang, CQvip) on 16 October 2022 for articles reporting incidence and outcomes of SARS-CoV-2 reinfection before the period of Omicron (B.1.1.529) predominance. We assessed risk of bias using Joanna Briggs Institute critical appraisal tools and conducted meta-analyses with random effects models to estimate the proportion of SARS-CoV-2 reinfection among initially infected cases and hospitalisation and mortality proportions among reinfected ones.

    RESULTS: We identified 7593 studies and extracted data from 64 included ones representing 21 countries. The proportion of SARS-CoV-2 reinfection was 1.16% (95% confidence interval (CI) = 1.01-1.33) based on 11 639 247 initially infected cases, with ≥45 days between the two infections. Healthcare providers (2.28%; 95% CI = 1.37-3.40) had a significantly higher risk of reinfection than the general population (1.00%; 95% CI = 0.81-1.20), while young adults aged 18 to 35 years (1.01%; 95% CI = 0.8-1.25) had a higher reinfection burden than other age groups (children <18 years old: 0.57%; 95% CI = 0.39-0.79, older adults aged 36-65 years old: 0.53%; 95% CI = 0.41-0.65, elderly >65 years old: 0.37%; 95% CI = 0.15-0.66). Among the reinfected cases, 8.12% (95% CI = 5.30-11.39) were hospitalised, 1.31% (95% CI = 0.29-2.83) were admitted to the intensive care unit, and 0.71% (95% CI = 0.02-2.01) died.

    CONCLUSIONS: Our data suggest a relatively low risk of SARS-CoV-2 reinfection in the pre-Omicron era, but the risk of hospitalisation was relatively high among the reinfected cases. Considering the possibility of underdiagnosis, the reinfection burden may be underestimated.

    REGISTRATION: PROSPERO: CRD42023449712.

  8. Fulltext Epidemiology and clinical features of SARS-CoV-2 infection in children and adolescents in the pre-Omicron era: A global systematic review and meta-analysis
    Kulkarni D, Ismail NF, Zhu F, Wang X, Del Carmen Morales G, Srivastava A, et al.
    J Glob Health, 2024 Mar 01;14:05003.
    PMID: 38419461 DOI: 10.7189/jogh.14.05003
    METHODS: We searched MEDLINE, Embase, Global Health, CINAHL, China National Knowledge Infrastructure, Wanfang, CQvip, and the World Health Organization (WHO) COVID-19 global literature databases for primary studies recruiting children aged ≤18 years with a diagnosis of SARS-CoV-2 infection confirmed either by molecular or antigen tests. We used the Joanna Briggs Institute critical appraisal tools to appraise the study quality and conducted meta-analyses using the random effects model for all outcomes except for race/ethnicity as risk factors of SARS-CoV-2 infection.

    RESULTS: We included 237 studies, each reporting at least one of the study outcomes. Based on data from 117 studies, the pooled SARS-CoV-2 positivity rate was 9.30% (95% confidence interval (CI) = 7.15-11.73). Having a comorbidity was identified as a risk factor for SARS-CoV-2 infection (risk ratio (RR) = 1.33; 95% CI = 1.04-1.71) based on data from 49 studies. Most cases in this review presented with mild disease (n = 50; 52.47% (95% CI = 44.03-60.84)). However, 20.70% of paediatric SARS-CoV-2 infections were hospitalised (67 studies), 7.19% required oxygen support (57 studies), 4.26% required intensive care (93 studies), and 2.92% required assisted ventilation (63 studies). The case fatality ratio (n = 119) was 0.87% (95% CI = 0.54-1.28), which included in-hospital and out-of-hospital deaths.

    CONCLUSIONS: Our data showed that children were at risk for SARS-CoV-2 infections and severe outcomes in the pre-Omicron era. These findings underscore the need for effective vaccination strategies for the paediatric population to protect against the acute and long-term sequelae of COVID-19.

    REGISTRATION: PROSPERO: CRD42022327680.

  9. Fulltext Accuracy and Cost-effectiveness of Technology-Assisted Dietary Assessment Comparing the Automated Self-administered Dietary Assessment Tool, Intake24, and an Image-Assisted Mobile Food Record 24-Hour Recall Relative to Observed Intake: Protocol for a Randomized Crossover Feeding Study
    Whitton C, Healy JD, Collins CE, Mullan B, Rollo ME, Dhaliwal SS, et al.
    JMIR Res Protoc, 2021 Dec 16;10(12):e32891.
    PMID: 34924357 DOI: 10.2196/32891
    BACKGROUND: The assessment of dietary intake underpins population nutrition surveillance and nutritional epidemiology and is essential to inform effective public health policies and programs. Technological advances in dietary assessment that use images and automated methods have the potential to improve accuracy, respondent burden, and cost; however, they need to be evaluated to inform large-scale use.

    OBJECTIVE: The aim of this study is to compare the accuracy, acceptability, and cost-effectiveness of 3 technology-assisted 24-hour dietary recall (24HR) methods relative to observed intake across 3 meals.

    METHODS: Using a controlled feeding study design, 24HR data collected using 3 methods will be obtained for comparison with observed intake. A total of 150 healthy adults, aged 18 to 70 years, will be recruited and will complete web-based demographic and psychosocial questionnaires and cognitive tests. Participants will attend a university study center on 3 separate days to consume breakfast, lunch, and dinner, with unobtrusive documentation of the foods and beverages consumed and their amounts. Following each feeding day, participants will complete a 24HR process using 1 of 3 methods: the Automated Self-Administered Dietary Assessment Tool, Intake24, or the Image-Assisted mobile Food Record 24-Hour Recall. The sequence of the 3 methods will be randomized, with each participant exposed to each method approximately 1 week apart. Acceptability and the preferred 24HR method will be assessed using a questionnaire. Estimates of energy, nutrient, and food group intake and portion sizes from each 24HR method will be compared with the observed intake for each day. Linear mixed models will be used, with 24HR method and method order as fixed effects, to assess differences in the 24HR methods. Reporting bias will be assessed by examining the ratios of reported 24HR intake to observed intake. Food and beverage omission and intrusion rates will be calculated, and differences by 24HR method will be assessed using chi-square tests. Psychosocial, demographic, and cognitive factors associated with energy misestimation will be evaluated using chi-square tests and multivariable logistic regression. The financial costs, time costs, and cost-effectiveness of each 24HR method will be assessed and compared using repeated measures analysis of variance tests.

    RESULTS: Participant recruitment commenced in March 2021 and is planned to be completed by the end of 2021.

    CONCLUSIONS: This protocol outlines the methodology of a study that will evaluate the accuracy, acceptability, and cost-effectiveness of 3 technology-enabled dietary assessment methods. This will inform the selection of dietary assessment methods in future studies on nutrition surveillance and epidemiology.

    TRIAL REGISTRATION: Australian New Zealand Clinical Trials Registry ACTRN12621000209897; https://tinyurl.com/2p9fpf2s.

    INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/32891.

  10. Fulltext Rapid Targeted Next-Generation Sequencing Platform for Molecular Screening and Clinical Genotyping in Subjects with Hemoglobinopathies
    Shang X, Peng Z, Ye Y, Asan, Zhang X, Chen Y, et al.
    EBioMedicine, 2017 Sep;23:150-159.
    PMID: 28865746 DOI: 10.1016/j.ebiom.2017.08.015
    Hemoglobinopathies are among the most common autosomal-recessive disorders worldwide. A comprehensive next-generation sequencing (NGS) test would greatly facilitate screening and diagnosis of these disorders. An NGS panel targeting the coding regions of hemoglobin genes and four modifier genes was designed. We validated the assay by using 2522 subjects affected with hemoglobinopathies and applied it to carrier testing in a cohort of 10,111 couples who were also screened through traditional methods. In the clinical genotyping analysis of 1182 β-thalassemia subjects, we identified a group of additional variants that can be used for accurate diagnosis. In the molecular screening analysis of the 10,111 couples, we detected 4180 individuals in total who carried 4840 mutant alleles, and identified 186 couples at risk of having affected offspring. 12.1% of the pathogenic or likely pathogenic variants identified by our NGS assay, which were undetectable by traditional methods. Compared with the traditional methods, our assay identified an additional at-risk 35 couples. We describe a comprehensive NGS-based test that offers advantages over the traditional screening/molecular testing methods. To our knowledge, this is among the first large-scale population study to systematically evaluate the application of an NGS technique in carrier screening and molecular diagnosis of hemoglobinopathies.
  11. Erratum to "The histology of ovarian cancer: Worldwide distribution and implications for international survival comparisons (CONCORD-2)" [Gynecol. Oncol. 144 (2017) 405-413]
    Matz M, Coleman MP, Sant M, Chirlaque MD, Visser O, Gore M, et al.
    Gynecol Oncol, 2017 Jul 05.
    PMID: 28687170 DOI: 10.1016/j.ygyno.2017.06.032
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