MyMedR

Displaying all 7 publications

Abstract:

Sort:

A systematic literature review on unnecessary diagnostic testing: The role of ICT use

Bai L, Gao S, Burstein F, Kerr D, Buntine P, Law N

Int J Med Inform, 2020 11;143:104269.
PMID: 32927268 DOI: 10.1016/j.ijmedinf.2020.104269

BACKGROUND: The negative impact of unnecessary diagnostic tests on healthcare systems and patients has been widely recognized. Medical researchers in various countries have been devoting effort to reduce unnecessary diagnostic tests by using different types of interventions, including information and communications technology-based (ICT-based) intervention, educational intervention, audit and feedback, the introduction of guidelines or protocols, and the reward and punishment of staff. We conducted a review of ICT based interventions and a comparative analysis of their relative effectiveness in reducing unnecessary tests.
METHOD: A systematic Boolean search in PubMed, EMBase and EBSCOhost research databases was performed. Keyword search and citation analysis were also conducted. Empirical studies reporting ICT based interventions, and their implications on relative effectiveness in reducing unnecessary diagnostic tests (pathology tests or medical imaging) were evaluated independently by two reviewers based on a rigorously developed coding protocol.
RESULTS: 92 research articles from peer-reviewed journals were identified as eligible. 47 studies involved a single-method intervention and 45 involved multi-method interventions. Regardless of the number of interventions involved in the studies, ICT-based interventions were utilized by 71 studies and 59 of them were shown to be effective in reducing unnecessary testing. A clinical decision support (CDS) tool appeared to be the most adopted ICT approach, with 46 out of 71 studies using CDS tools. The CDS tool showed effectiveness in reducing test volume in 38 studies and reducing cost in 24 studies.
CONCLUSIONS: This review investigated five frequently utilized intervention methods, ICT-based, education, introduction of guidelines or protocols, audit and feedback, and reward and punishment. It provides in-depth analysis of the efficacy of different types of interventions and sheds insights about the benefits of ICT based interventions, especially those utilising CDS tools, to reduce unnecessary diagnostic testing. The replicability of the studies is limited due to the heterogeneity of the studies in terms of context, study design, and targeted types of tests.
Real-time and visual sensing devices based on pH-control assembled lanthanide-barium nano-cluster

Liu M, Li H, Bai L, Zheng K, Zhao Z, Chen Z, et al.

J Hazard Mater, 2021 07 05;413:125291.
PMID: 33588337 DOI: 10.1016/j.jhazmat.2021.125291

Real-time and visual monitoring of pollutants in the air is of great importance since they are usually cannot be seen, smelled, or touched. Lanthanide nano-cluster is a kind of luminescent sensor for various species. However, controlling synthesis of lanthanide nano-cluster remains experimentally challenging. In this work, four series of lanthanide-barium (Ln-Ba) nano-clusters of Dy2Ba (1), Tb2Ba2 (2), Ln4Ba3 (Ln = Tb, 3a; Eu, 3b), Tb4Ba4 (4) were assembled through precisely controlling the pH of the reactant solutions. The work features the first example that the number of cluster's nuclei changes regularly with the pH. Moreover, investigation reveals that nano-cluster 3a is a highly selective and sensitive sensor towards acetylacetone (acac) and aniline. Interestingly, easy-to-use sensing devices of test paper, agarose gel, and five kinds of film on CaCO3, polyfoam, coin, mask, and wall that based on 3a were fabricated by facile methods. The seven sensing devices showed remarkable ability to sense aniline and acac vapors with visibility to the naked eyes. This is the first work on multiple real-time and visual sensing devices based on the lanthanide nano-cluster.
Degradation of MicroRNA miR-466d-3p by Japanese Encephalitis Virus NS3 Facilitates Viral Replication and Interleukin-1β Expression

Jiang H, Bai L, Ji L, Bai Z, Su J, Qin T, et al.

J Virol, 2020 07 16;94(15).
PMID: 32461319 DOI: 10.1128/JVI.00294-20

Japanese encephalitis virus (JEV) infection alters microRNA (miRNA) expression in the central nervous system (CNS). However, the mechanism contributing to miRNA regulation in the CNS is not known. We discovered global degradation of mature miRNA in mouse brains and neuroblastoma (NA) cells after JEV infection. Integrative analysis of miRNAs and mRNAs suggested that several significantly downregulated miRNAs and their targeted mRNAs were clustered into an inflammation pathway. Transfection with miRNA 466d-3p (miR-466d-3p) decreased interleukin-1β (IL-1β) expression and inhibited JEV replication in NA cells. However, miR-466d-3p expression increased after JEV infection in the presence of cycloheximide, indicating that viral protein expression reduced miR-466d-3p expression. We generated all the JEV coding proteins and demonstrated NS3 helicase protein to be a potent miRNA suppressor. The NS3 proteins of Zika virus, West Nile virus, and dengue virus serotype 1 (DENV-1) and DENV-2 also decreased miR-466d-3p expression. Results from helicase-blocking assays and in vitro unwinding assays demonstrated that NS3 could unwind pre-miR-466d and induce miRNA dysfunction. Computational models and an RNA immunoprecipitation assay revealed arginine-rich domains of NS3 to be crucial for pre-miRNA binding and degradation of host miRNAs. Importantly, site-directed mutagenesis of conserved residues in NS3 revealed that R226G and R202W reduced the binding affinity and degradation of pre-miR-466d. These results expand the function of flavivirus helicases beyond unwinding duplex RNA to degrade pre-miRNAs. Hence, we revealed a new mechanism for NS3 in regulating miRNA pathways and promoting neuroinflammation.IMPORTANCE Host miRNAs have been reported to regulate JEV-induced inflammation in the CNS. We found that JEV infection could reduce expression of host miRNA. The helicase region of the NS3 protein bound specifically to miRNA precursors and could lead to incorrect unwinding of miRNA precursors, thereby reducing the expression of mature miRNAs. This observation led to two major findings. First, our results suggested that JEV NS3 protein induced miR-466d-3p degradation, which promoted IL-1β expression and JEV replication. Second, arginine molecules on NS3 were the main miRNA-binding sites, because we demonstrated that miRNA degradation was abolished if arginines at R226 and R202 were mutated. Our study provides new insights into the molecular mechanism of JEV and reveals several amino acid sites that could be mutated for a JEV vaccine.
Fulltext A reference genome of Commelinales provides insights into the commelinids evolution and global spread of water hyacinth (Pontederia crassipes)

Huang Y, Guo L, Xie L, Shang N, Wu D, Ye C, et al.

Gigascience, 2024 Jan 02;13.
PMID: 38486346 DOI: 10.1093/gigascience/giae006

Commelinales belongs to the commelinids clade, which also comprises Poales that includes the most important monocot species, such as rice, wheat, and maize. No reference genome of Commelinales is currently available. Water hyacinth (Pontederia crassipes or Eichhornia crassipes), a member of Commelinales, is one of the devastating aquatic weeds, although it is also grown as an ornamental and medical plant. Here, we present a chromosome-scale reference genome of the tetraploid water hyacinth with a total length of 1.22 Gb (over 95% of the estimated size) across 8 pseudochromosome pairs. With the representative genomes, we reconstructed a phylogeny of the commelinids, which supported Zingiberales and Commelinales being sister lineages of Arecales and shed lights on the controversial relationship of the orders. We also reconstructed ancestral karyotypes of the commelinids clade and confirmed the ancient commelinids genome having 8 chromosomes but not 5 as previously reported. Gene family analysis revealed contraction of disease-resistance genes during polyploidization of water hyacinth, likely a result of fitness requirement for its role as a weed. Genetic diversity analysis using 9 water hyacinth lines from 3 continents (South America, Asia, and Europe) revealed very closely related nuclear genomes and almost identical chloroplast genomes of the materials, as well as provided clues about the global dispersal of water hyacinth. The genomic resources of P. crassipes reported here contribute a crucial missing link of the commelinids species and offer novel insights into their phylogeny.
Transcriptional landscape of B cell precursor acute lymphoblastic leukemia based on an international study of 1,223 cases

Li JF, Dai YT, Lilljebjörn H, Shen SH, Cui BW, Bai L, et al.

Proc Natl Acad Sci U S A, 2018 12 11;115(50):E11711-E11720.
PMID: 30487223 DOI: 10.1073/pnas.1814397115

Most B cell precursor acute lymphoblastic leukemia (BCP ALL) can be classified into known major genetic subtypes, while a substantial proportion of BCP ALL remains poorly characterized in relation to its underlying genomic abnormalities. We therefore initiated a large-scale international study to reanalyze and delineate the transcriptome landscape of 1,223 BCP ALL cases using RNA sequencing. Fourteen BCP ALL gene expression subgroups (G1 to G14) were identified. Apart from extending eight previously described subgroups (G1 to G8 associated with MEF2D fusions, TCF3-PBX1 fusions, ETV6-RUNX1-positive/ETV6-RUNX1-like, DUX4 fusions, ZNF384 fusions, BCR-ABL1/Ph-like, high hyperdiploidy, and KMT2A fusions), we defined six additional gene expression subgroups: G9 was associated with both PAX5 and CRLF2 fusions; G10 and G11 with mutations in PAX5 (p.P80R) and IKZF1 (p.N159Y), respectively; G12 with IGH-CEBPE fusion and mutations in ZEB2 (p.H1038R); and G13 and G14 with TCF3/4-HLF and NUTM1 fusions, respectively. In pediatric BCP ALL, subgroups G2 to G5 and G7 (51 to 65/67 chromosomes) were associated with low-risk, G7 (with ≤50 chromosomes) and G9 were intermediate-risk, whereas G1, G6, and G8 were defined as high-risk subgroups. In adult BCP ALL, G1, G2, G6, and G8 were associated with high risk, while G4, G5, and G7 had relatively favorable outcomes. This large-scale transcriptome sequence analysis of BCP ALL revealed distinct molecular subgroups that reflect discrete pathways of BCP ALL, informing disease classification and prognostic stratification. The combined results strongly advocate that RNA sequencing be introduced into the clinical diagnostic workup of BCP ALL.
Pan-Asian adapted ESMO Clinical Practice Guidelines for the diagnosis, treatment and follow-up of patients with biliary tract cancer

Chen LT, Vogel A, Hsu C, Chen MH, Fang W, Pangarsa EA, et al.

ESMO Open, 2024 Aug;9(8):103647.
PMID: 39232586 DOI: 10.1016/j.esmoop.2024.103647

The European Society for Medical Oncology (ESMO) Clinical Practice Guidelines for the diagnosis, treatment and follow-up of patients with biliary tract cancer (BTC), published in late 2022 were adapted in December 2023, according to established standard methodology, to produce the Pan-Asian adapted (PAGA) ESMO consensus guidelines for the management of Asian patients with BTC. The adapted guidelines presented in this manuscript represent the consensus opinions reached by a panel of Asian experts in the treatment of patients with BTC representing the oncological societies of China (CSCO), Indonesia (ISHMO), India (ISMPO), Japan (JSMO), Korea (KSMO), Malaysia (MOS), the Philippines (PSMO), Singapore (SSO), Taiwan (TOS) and Thailand (TSCO), co-ordinated by ESMO and the Taiwan Oncology Society (TOS). The voting was based on scientific evidence and was independent of the current treatment practices, drug access restrictions and reimbursement decisions in the different regions of Asia. Drug access and reimbursement in the different regions of Asia are discussed separately in the manuscript. The aim is to provide guidance for the optimisation and harmonisation of the management of patients with BTC across the different countries and regions of Asia, drawing on the evidence provided by both Western and Asian trials, whilst respecting the differences in screening practices and molecular profiling, as well as age and stage at presentation. Attention is drawn to the disparity in the drug approvals and reimbursement strategies, between the different countries.
Fulltext Australian vegetated coastal ecosystems as global hotspots for climate change mitigation

Serrano O, Lovelock CE, B Atwood T, Macreadie PI, Canto R, Phinn S, et al.

Nat Commun, 2019 10 02;10(1):4313.
PMID: 31575872 DOI: 10.1038/s41467-019-12176-8

Policies aiming to preserve vegetated coastal ecosystems (VCE; tidal marshes, mangroves and seagrasses) to mitigate greenhouse gas emissions require national assessments of blue carbon resources. Here, we present organic carbon (C) storage in VCE across Australian climate regions and estimate potential annual CO2 emission benefits of VCE conservation and restoration. Australia contributes 5-11% of the C stored in VCE globally (70-185 Tg C in aboveground biomass, and 1,055-1,540 Tg C in the upper 1 m of soils). Potential CO2 emissions from current VCE losses are estimated at 2.1-3.1 Tg CO2-e yr-1, increasing annual CO2 emissions from land use change in Australia by 12-21%. This assessment, the most comprehensive for any nation to-date, demonstrates the potential of conservation and restoration of VCE to underpin national policy development for reducing greenhouse gas emissions.