Publications by authors named "Anthony Wong"

135 Publications

Enabling a learning healthcare system with automated computer protocols that produce replicable and personalized clinician actions.

J Am Med Inform Assoc 2021 Feb 16. Epub 2021 Feb 16.

Institute for Healthcare Improvement, Boston, Massachusetts, USA.

Clinical decision-making is based on knowledge, expertise, and authority, with clinicians approving almost every intervention-the starting point for delivery of "All the right care, but only the right care," an unachieved healthcare quality improvement goal. Unaided clinicians suffer from human cognitive limitations and biases when decisions are based only on their training, expertise, and experience. Electronic health records (EHRs) could improve healthcare with robust decision-support tools that reduce unwarranted variation of clinician decisions and actions. Current EHRs, focused on results review, documentation, and accounting, are awkward, time-consuming, and contribute to clinician stress and burnout. Decision-support tools could reduce clinician burden and enable replicable clinician decisions and actions that personalize patient care. Most current clinical decision-support tools or aids lack detail and neither reduce burden nor enable replicable actions. Clinicians must provide subjective interpretation and missing logic, thus introducing personal biases and mindless, unwarranted, variation from evidence-based practice. Replicability occurs when different clinicians, with the same patient information and context, come to the same decision and action. We propose a feasible subset of therapeutic decision-support tools based on credible clinical outcome evidence: computer protocols leading to replicable clinician actions (eActions). eActions enable different clinicians to make consistent decisions and actions when faced with the same patient input data. eActions embrace good everyday decision-making informed by evidence, experience, EHR data, and individual patient status. eActions can reduce unwarranted variation, increase quality of clinical care and research, reduce EHR noise, and could enable a learning healthcare system.
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http://dx.doi.org/10.1093/jamia/ocaa294DOI Listing
February 2021

The genomic characterisation and comparison of Bacillus cereus strains isolated from indoor air.

Gut Pathog 2021 Jan 30;13(1). Epub 2021 Jan 30.

Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.

Background: Bacillus cereus is ubiquitous in nature, found in environments such as soil, plants, air, and part of the insect and human gut microbiome. The ability to produce endospores and biofilms contribute to their pathogenicity, classified in two types of food poisoning: diarrheal and emetic syndromes. Here we report gap-free, whole-genome sequences of two B. cereus strains isolated from air samples and analyse their emetic and diarrheal potential.

Results: Genome assemblies of the B. cereus strains consist of one chromosome and seven plasmids each. The genome size of strain SGAir0260 is 6.30-Mb with 6590 predicted coding sequences (CDS) and strain SGAir0263 is 6.47-Mb with 6811 predicted CDS. Macrosynteny analysis showed 99% collinearity between the strains isolated from air and 90.2% with the reference genome. Comparative genomics with 57 complete B. cereus genomes suggests these strains from air are closely associated with strains isolated from foodborne illnesses outbreaks. Due to virulence potential of B. cereus and its reported involvement in nosocomial infections, antibiotic resistance analyses were performed and confirmed resistance to ampicillin and fosfomycin, with susceptibility to ciprofloxacin, tetracycline and vancomycin in both strains.

Conclusion: Phylogenetic analysis combined with detection of haemolytic (hblA, hblC, and hblD) and non-haemolytic (nheA, nheB, and nheC) enterotoxin genes in both air-isolated strains point to the diarrheic potential of the air isolates, though not emetic. Characterization of these airborne strains and investigation of their potential disease-causing genes could facilitate identification of environmental sources of contamination leading to foodborne illnesses and nosocomial infections transported by air.
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http://dx.doi.org/10.1186/s13099-021-00399-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7847026PMC
January 2021

Rationale and design of the ADAPT-TAVR trial: a randomised comparison of edoxaban and dual antiplatelet therapy for prevention of leaflet thrombosis and cerebral embolisation after transcatheter aortic valve replacement.

BMJ Open 2021 Jan 5;11(1):e042587. Epub 2021 Jan 5.

Division of Cardiology, Asan Medical Center, Songpa-gu, Seoul, The Republic of Korea

Introduction: Optimal antithrombotic strategy following transcatheter aortic valve replacement (TAVR) is still unknown. We hypothesised that the direct factor Xa inhibitor edoxaban can potentially prevent subclinical leaflet thrombosis and cerebral embolisation compared with conventional dual antiplatelet therapy (DAPT) in patients undergoing TAVR.

Methods And Analysis: The ADAPT-TAVR trial is an international, multicentre, randomised, open-label, superiority trial comparing edoxaban-based strategy and DAPT strategy in patients without an indication for oral anticoagulation who underwent successful TAVR. A total of 220 patients are randomised (1:1 ratio), 1-7 days after successful TAVR, to receive either edoxaban (60 mg daily or 30 mg daily if patients had dose-reduction criteria) or DAPT using aspirin (100 mg daily) plus clopidogrel (75 mg daily) for 6 months. The primary endpoint was an incidence of leaflet thrombosis on four-dimensional, volume-rendered cardiac CT imaging at 6 months post-TAVR. The key secondary endpoints were the number of new lesions and new lesion volume on brain diffusion-weighted MRI and the changes in neurological and neurocognitive function assessment between immediate post-TAVR and 6 months of study drug administration. Detailed clinical information on thromboembolic and bleeding events were also assessed.

Ethics And Dissemination: Ethic approval has been obtained from the Ethics Committee/Institutional Review Board of Asan Medical Center (approval number: 2017-1317) and this trial is also approved by National Institute of Food and Drug Safety Evaluation of Republic of Korea (approval number: 31511). Results of this study will be disseminated in scientific publication in reputed journals.

Trial Registration Number: NCT03284827.
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http://dx.doi.org/10.1136/bmjopen-2020-042587DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7786793PMC
January 2021

Factors associated with frailty transition at different follow-up intervals: A scoping review.

Geriatr Nurs 2020 Nov 2. Epub 2020 Nov 2.

School of Nursing, The Hong Kong Polytechnic University, Hong Kong SAR.

Frailty is a dynamic process. Identifying the factors associated with frailty transition may increase the opportunities for success in interventions for frailty. This scoping review, following Arksey and O'Malley's methodological framework, aimed to identify the factors associated with frailty transition and the rate of frailty transition among community-dwelling older people. A literature search was conducted. Among the included studies, 5, 13, and 3 involved follow-up intervals of 2-3 years (short term), 4-6 years (intermediate term), and >6 years (long term), respectively. Reportedly, life course characteristics, diseases, and psychological factors were related to frailty transitions at all follow-up intervals. Physical factors were related to frailty transition at both short and intermediate follow-up intervals, while social factors were related to frailty transition at intermediate follow-up intervals. The rate of improvement in frailty seemed to decrease, and that of worsening seemed to increase when the follow-up intervals lengthened.
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http://dx.doi.org/10.1016/j.gerinurse.2020.10.005DOI Listing
November 2020

Analysis of DNA variants in miRNAs and miRNA 3'UTR binding sites in female infertility patients.

Lab Invest 2020 Oct 17. Epub 2020 Oct 17.

Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.

Early human embryogenesis relies on maternal gene products accumulated during oocyte growth and maturation, until around day-3 post-fertilization when human zygotic genome activation occurs. The maternal-to-zygotic transition (MZT) is a tightly coordinated process of selective maternal transcript clearance and new zygotic transcript production. If MZT is disrupted, it will lead to developmental arrest and pregnancy loss. It is well established that microRNA (miRNA) mutations disrupt regulation of their target transcripts. We hypothesize that some cases of embryonic arrest and pregnancy loss could be explained by the mutations in the maternal genome that affect miRNA-target transcript pairs. To this end, we examined mutations within miRNAs or miRNA binding sites in the 3' untranslated regions (3'UTR) of target transcripts. Using whole-exome sequencing data from 178 women undergoing in vitro fertilization (IVF) procedures, we identified 1197 variants in miRNA genes, including 93 single nucleotide variants (SNVs) and 19 small insertions/deletions (INDELs) within the seed region of 100 miRNAs. Eight miRNA seed-region variants were significantly enriched among our patients when compared to a normal population. Within predicted 3'UTR miRNA binding sites, we identified 7393 SNVs and 1488 INDELs. Between our patients and a normal population, 52 SNVs and 30 INDELs showed significant association in the single-variant testing, whereas 51 genes showed significant association in the gene-burden analysis for genes that are expressed in preimplantation embryos. Interestingly, we found that many genes with disrupted 3'UTR miRNA binding sites follow gene expression patterns resembling MZT. In addition, some of these variants showed dramatic allele frequency difference between the patient and the normal group, offering potential utility as biomarkers for screening patients prior to IVF procedures.
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http://dx.doi.org/10.1038/s41374-020-00498-xDOI Listing
October 2020

Recommendations for patient similarity classes: results of the AMIA 2019 workshop on defining patient similarity.

J Am Med Inform Assoc 2020 Nov;27(11):1808-1812

The Ohio State University, Columbus, Ohio, USA.

Defining patient-to-patient similarity is essential for the development of precision medicine in clinical care and research. Conceptually, the identification of similar patient cohorts appears straightforward; however, universally accepted definitions remain elusive. Simultaneously, an explosion of vendors and published algorithms have emerged and all provide varied levels of functionality in identifying patient similarity categories. To provide clarity and a common framework for patient similarity, a workshop at the American Medical Informatics Association 2019 Annual Meeting was convened. This workshop included invited discussants from academics, the biotechnology industry, the FDA, and private practice oncology groups. Drawing from a broad range of backgrounds, workshop participants were able to coalesce around 4 major patient similarity classes: (1) feature, (2) outcome, (3) exposure, and (4) mixed-class. This perspective expands into these 4 subtypes more critically and offers the medical informatics community a means of communicating their work on this important topic.
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http://dx.doi.org/10.1093/jamia/ocaa159DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7671612PMC
November 2020

NRG Oncology Updated International Consensus Atlas on Pelvic Lymph Node Volumes for Intact and Postoperative Prostate Cancer.

Int J Radiat Oncol Biol Phys 2021 Jan 27;109(1):174-185. Epub 2020 Aug 27.

Medical College of Wisconsin, Department of Radiation Oncology, Milwaukee, Wisconsin.

Purpose: In 2009, the Radiation Therapy Oncology Group (RTOG) genitourinary members published a consensus atlas for contouring prostate pelvic nodal clinical target volumes (CTVs). Data have emerged further informing nodal recurrence patterns. The objective of this study is to provide an updated prostate pelvic nodal consensus atlas.

Methods And Materials: A literature review was performed abstracting data on nodal recurrence patterns. Data were presented to a panel of international experts, including radiation oncologists, radiologists, and urologists. After data review, participants contoured nodal CTVs on 3 cases: postoperative, intact node positive, and intact node negative. Radiation oncologist contours were analyzed qualitatively using count maps, which provided a visual assessment of controversial regions, and quantitatively analyzed using Sorensen-Dice similarity coefficients and Hausdorff distances compared with the 2009 RTOG atlas. Diagnostic radiologists generated a reference table outlining considerations for determining clinical node positivity.

Results: Eighteen radiation oncologists' contours (54 CTVs) were included. Two urologists' volumes were examined in a separate analysis. The mean CTV for the postoperative case was 302 cm, intact node positive case was 409 cm, and intact node negative case was 342 cm. Compared with the original RTOG consensus, the mean Sorensen-Dice similarity coefficient for the postoperative case was 0.63 (standard deviation [SD] 0.13), the intact node positive case was 0.68 (SD 0.13), and the intact node negative case was 0.66 (SD 0.18). The mean Hausdorff distance (in cm) for the postoperative case was 0.24 (SD 0.13), the intact node positive case was 0.23 (SD 0.09), and intact node negative case was 0.33 (SD 0.24). Four regions of CTV controversy were identified, and consensus for each of these areas was reached.

Conclusions: Discordance with the 2009 RTOG consensus atlas was seen in a group of experienced NRG Oncology and international genitourinary radiation oncologists. To address areas of variability and account for new data, an updated NRG Oncology consensus contour atlas was developed.
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http://dx.doi.org/10.1016/j.ijrobp.2020.08.034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7736505PMC
January 2021

Factors Associated With Improving or Worsening the State of Frailty: A Secondary Data Analysis of a 5-Year Longitudinal Study.

J Nurs Scholarsh 2020 09 1;52(5):515-526. Epub 2020 Aug 1.

Honorary Professor, Centre for Gerontological Nursing, School of Nursing, The Hong Kong Polytechnic University, Kowloon, Hong Kong.

Purpose: This study aims to examine the frailty transition patterns of older adults recruited from both community and residential care settings within a 5-year period, and to identify the physical and psychosocial factors associated with the transitions.

Design: This study is a secondary data analysis of a longitudinal study for tracking the change of health status of older adults 60 years of age or older. Participants who had undergone at least two assessments during 2013-2017 were selected for analysis. Guided by the Gobben's Frailty Model, biopsychosocial predictors were comprehensively identified from the literature, and their relationship to frailty state transition was explored.

Methods: We compared the baseline characteristics of participants at the frail, pre-frail, and robust states (categorized using the Fried Frailty Index). A generalized estimating equation was used to identify factors associated with an improvement or a deterioration in frailty. The probability of transitions between frailty states was calculated.

Findings: Among the 306 participants, 19% (n = 59) improved and 30% (n = 92) declined in frailty within the project period. Sleep difficulties (odds ratio [OR] = 1.76; 95% confidence interval [CI]: 1.07-2.90; p = .027), better cognitive status (OR = 0.80-0.84; 95% CI: 0.66-0.98 and 0.73-2.73; p = .031 and .018), good nutritional status (OR = 0.74; 95% CI: 0.59-0.91; p = .005), slow mobility (OR = 1.03-1.13; 95% CI: 1.00-1.05 and 1.03-1.25; p = .047 and .014), hearing impairment (OR = 2.83; 95% CI: 1.00-8.01; p = .05), better quality of health-physical domain (OR = 0.95; 95% CI: 0.92-0.99; p = .006), and better functional ability (OR = 0.85-0.97; 95% CI: 0.79-0.92 and 0.96-0.99; p < .001 and p = .003) were significant associated factors in the worsening group. More physical activity (OR = 1.01; 95% CI: 1.00-1.01 and 1.01-1.02; p = .026 and p < .001), hearing impairment (OR = 0.26; 95% CI: 0.08-0.86; p = .028), and slow mobility (OR = 0.93; 95% CI: 0.87-1.00; p = .037) were significant associated factors in the improvement group.

Conclusions: Frailty is a crucial global public health issue. This study provides evidence for nurses to holistically consider the associated factors and to design effective interventions to combat frailty in our ageing society.

Clinical Relevance: Frailty is a transient state that can be reversed. Professional nurses working in both community and residential care settings should be able to identify older adults at risk and improve their health conditions appropriately.
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http://dx.doi.org/10.1111/jnu.12588DOI Listing
September 2020

Redox-Controlled Reactivity at Boron: Parallels to Frustrated Lewis/Radical Pair Chemistry.

Inorg Chem 2020 Jul 9;59(14):10343-10352. Epub 2020 Jul 9.

Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States.

We report the synthesis of new Lewis-acidic boranes tethered to redox-active vanadium centers, (PhN)V(μ-N)B(CF) () and (N(CHCHN(CF)))V(μ-N)B(CF) (). Redox control of the V couple resulted in switchable borane versus "hidden" boron radical reactivity, mimicking frustrated Lewis versus frustrated radical pair (FLP/FRP) chemistry, respectively. Whereas heterolytic FLP-type addition reactions were observed with the V complex () in the presence of a bulky phosphine, homolytic peroxide, or Sn-hydride bond cleavage reactions were observed with the V complex, [CoCp][(N(CHCHN(CF)))V(μ-N)B(CF)] (), indicative of boron radical anion character. The extent of radical character was probed by spectroscopic and computational means. Together, these results demonstrate that control of the V oxidation states allows these compounds to access reactivity observed in both FLP and FRP chemistry.
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http://dx.doi.org/10.1021/acs.inorgchem.0c01464DOI Listing
July 2020

The use of functional performance tests and simple anthropomorphic measures to screen for comorbidity in primary care.

Int J Older People Nurs 2020 Dec 7;15(4):e12333. Epub 2020 Jul 7.

School of Nursing, The Hong Kong Polytechnic University, Kowloon, Hong Kong.

Background: Many older adults are unaware that they have comorbid diseases. Increased adiposity and reduced muscle mass are identified as key contributors to many chronic diseases in older adults. Understanding the role they play in the development of comorbidities in older populations is of prime importance.

Objectives: To identify the optimal body shape associated with three common functional performance tests and to determine which anthropometric and functional performance test best explains comorbidity in a sample of older adults in Hong Kong.

Methods: A total of 432 older adults participated in this cross-sectional study. Researchers assessed their body height, body mass index, waist circumference, waist-to-hip ratio, handgrip strength (kg), functional reach (cm) and results in the timed-up-and-go (TUG) test (seconds). The Charlson Comorbidity Index was used to assess comorbidity.

Results: Allometric modelling indicated that the optimal body shape associated with all functional performance tests would have required the participants to be taller and leaner. The only variable that predicted comorbidity was the TUG test. The inclusion of body size/shape variables did not improve the prediction model.

Conclusion: Performance in the TUG test alone was found to be capable of identifying participants at risk of developing comorbidities. The TUG test has potential as a screening tool for the early detection of chronic diseases in older adults.

Implications For Practice: Many older people are unaware of their own co-existing illnesses when they consult physicians for a medical condition. TUG can be a quick and useful screening measure to alert nurses in primary care to the need to proceed with more detailed assessments. It is an especially useful screening measure in settings with high patient volumes and fiscal constraints. TUG is low cost and easy to learn and is therefore also relevant for nurses and health workers in low-resource, low-income countries.
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http://dx.doi.org/10.1111/opn.12333DOI Listing
December 2020

A Virion-Based Assay for Glycoprotein Thermostability Reveals Key Determinants of Filovirus Entry and Its Inhibition.

J Virol 2020 08 31;94(18). Epub 2020 Aug 31.

Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA

Ebola virus (EBOV) entry into cells is mediated by its spike glycoprotein (GP). Following attachment and internalization, virions traffic to late endosomes where GP is cleaved by host cysteine proteases. Cleaved GP then binds its cellular receptor, Niemann-Pick C1. In response to an unknown cellular trigger, GP undergoes conformational rearrangements that drive fusion of viral and endosomal membranes. The temperature-dependent stability (thermostability) of the prefusion conformers of class I viral fusion glycoproteins, including those of filovirus GPs, has provided insights into their propensity to undergo fusion-related rearrangements. However, previously described assays have relied on soluble glycoprotein ectodomains. Here, we developed a simple enzyme-linked immunosorbent assay (ELISA)-based assay that uses the temperature-dependent loss of conformational epitopes to measure thermostability of GP embedded in viral membranes. The base and glycan cap subdomains of all filovirus GPs tested suffered a concerted loss of prefusion conformation at elevated temperatures but did so at different temperature ranges, indicating virus-specific differences in thermostability. Despite these differences, all of these GPs displayed reduced thermostability upon cleavage to GP conformers (GP). Surprisingly, acid pH enhanced, rather than decreased, GP thermostability, suggesting it could enhance viral survival in hostile endo/lysosomal compartments. Finally, we confirmed and extended previous findings that some small-molecule inhibitors of filovirus entry destabilize EBOV GP and uncovered evidence that the most potent inhibitors act through multiple mechanisms. We establish the epitope-loss ELISA as a useful tool for studies of filovirus entry, engineering of GP variants with enhanced stability for use in vaccine development, and discovery of new stability-modulating antivirals. The development of Ebola virus countermeasures is challenged by our limited understanding of cell entry, especially at the step of membrane fusion. The surface-exposed viral protein, GP, mediates membrane fusion and undergoes major structural rearrangements during this process. The stability of GP at elevated temperatures (thermostability) can provide insights into its capacity to undergo these rearrangements. Here, we describe a new assay that uses GP-specific antibodies to measure GP thermostability under a variety of conditions relevant to viral entry. We show that proteolytic cleavage and acid pH have significant effects on GP thermostability that shed light on their respective roles in viral entry. We also show that the assay can be used to study how small-molecule entry inhibitors affect GP stability. This work provides a simple and readily accessible assay to engineer stabilized GP variants for antiviral vaccines and to discover and improve drugs that act by modulating GP stability.
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http://dx.doi.org/10.1128/JVI.00336-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7459555PMC
August 2020

Impact of coronavirus disease 2019 (COVID-19) outbreak on outcome of myocardial infarction in Hong Kong, China.

Catheter Cardiovasc Interv 2021 02 5;97(2):E194-E197. Epub 2020 May 5.

Cardiology Division, Department of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, China.

Objective: To determine whether COVID-19 may adversely affect outcome of myocardial infarction (MI) patients in Hong Kong, China.

Background: The COVID-19 pandemic has infected thousands of people and placed enormous stress on healthcare system. Apart from being an infectious disease, it may affect human behavior and healthcare resource allocation which potentially cause treatment delay in MI.

Methods: This was a single center cross-sectional observational study. From November 1, 2019 to March 31, 2020, we compared outcome of patients admitted for acute ST-elevation MI (STEMI) and non-ST elevation MI (NSTEMI) before (group 1) and after (group 2) January 25, 2020 which was the date when Hong Kong hospitals launched emergency response measures to combat COVID-19.

Results: There was a reduction in daily emergency room attendance since January 25, 2020 (group 1,327/day vs. group 2,231/day) and 149 patients with diagnosis of MI were included into analysis (group 1 N = 85 vs. group 2 N = 64). For STEMI, patients in group 2 tended to have longer symptom-to-first medical contact time and more presented out of revascularization window (group 1 27.8 vs. group 2 33%). The primary composite outcome of in-hospital death, cardiogenic shock, sustained ventricular tachycardia or fibrillation (VT/VF) and use of mechanical circulatory support (MCS) was significantly worse in group 2 (14.1 vs. 29.7%, p = .02).

Conclusions: More MI patients during COVID-19 outbreak had complicated in-hospital course and worse outcomes. Besides direct infectious complications, cardiology community has to acknowledge the indirect effect of communicable disease on our patients and system of care.
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http://dx.doi.org/10.1002/ccd.28943DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7267252PMC
February 2021

Noninvasive ventricular tachycardia ablation: Should we apply the accelerator or the brake?

Heart Rhythm 2020 Aug 11;17(8):1249-1250. Epub 2020 Apr 11.

Electrophysiology Section, Division of Cardiology, Department of Medicine, University of California, San Francisco, San Francisco, California. Electronic address:

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http://dx.doi.org/10.1016/j.hrthm.2020.04.003DOI Listing
August 2020

Complete Genome Sequence of Penicillium oxalicum Strain SGAir0226 Isolated from Outdoor Tropical Air in Singapore.

Mycopathologia 2020 Jun 8;185(3):591-594. Epub 2020 Apr 8.

Nanyang Technological University, Singapore Centre for Environmental Life Sciences Engineering, Singapore, Singapore.

Penicillium oxalicum strain SGAir0226 was isolated from a tropical air sample collected in Singapore. The complete genome was assembled from long reads obtained from single-molecule real-time sequencing and was further polished and error corrected using short read sequencing data. The assembly comprises 20 contigs with a total length of 30.7 Mb. The genome was predicted to contain 8310 protein-coding genes, 237 tRNAs and 83 rRNAs.
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http://dx.doi.org/10.1007/s11046-019-00422-yDOI Listing
June 2020

Impact of Coronavirus Disease 2019 (COVID-19) Outbreak on ST-Segment-Elevation Myocardial Infarction Care in Hong Kong, China.

Circ Cardiovasc Qual Outcomes 2020 04 17;13(4):e006631. Epub 2020 Mar 17.

Cardiology Division, Department of Medicine (C.-C.F.T., S.L., A.W., A.Y., M.S., Y.-M.L., C.C., H.-F.T., C.-W.S.), Queen Mary Hospital, the University of Hong Kong, Hong Kong SAR, China.

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http://dx.doi.org/10.1161/CIRCOUTCOMES.120.006631DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7147280PMC
April 2020

Complete genome of strain SGAir0282 isolated from air in Singapore.

Gut Pathog 2020 27;12:12. Epub 2020 Feb 27.

1Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.

Background: complex (ECC) bacteria, such as , , , and , have been emerging as nosocomial pathogens. Many strains isolated from medical clinics were found to be resistant to antibiotics, and in the worst cases, acquired multidrug resistance. We present the whole genome sequence of SGAir0282, isolated from the outdoor air in Singapore, and its relevance to other ECC bacteria by in silico genomic analysis.

Results: Complete genome assembly of strain SGAir0282 was generated using PacBio RSII and Illumina MiSeq platforms, and the datasets were used for de novo assembly using Hierarchical Genome Assembly Process (HGAP) and error corrected with Pilon. The genome assembly consisted of a single contig of 4.71 Mb and with a G+C content of 55.5%. No plasmid was detected in the assembly. The genome contained 4371 coding genes, 83 tRNA and 25 rRNA genes, as predicted by NCBI's Prokaryotic Genome Annotation Pipeline (PGAP). Among the genes, the antibiotic resistance related genes were included: Streptothricin acetdyltransferase (SatA), fosfomycin resistance protein (FosA) and metal-dependent hydrolases of the beta-lactamase superfamily I (BLI).

Conclusion: Based on whole genome alignment and phylogenetic analysis, the strain SGAir0282 was identified to be . The strain possesses gene clusters for virulence, disease and defence, that can also be found in other multidrug resistant ECC type strains.
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http://dx.doi.org/10.1186/s13099-020-00350-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7045367PMC
February 2020

Comparing Metastatic Clear Cell Renal Cell Carcinoma Model Established in Mouse Kidney and on Chicken Chorioallantoic Membrane.

J Vis Exp 2020 02 8(156). Epub 2020 Feb 8.

Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles; Department of Urology, David Geffen School of Medicine, University of California, Los Angeles;

Metastatic clear cell renal cell carcinoma (ccRCC) is the most common subtype of kidney cancer. Localized ccRCC has a favorable surgical outcome. However, one third of ccRCC patients will develop metastases to the lung, which is related to a very poor outcome for patients. Unfortunately, no therapy is available for this deadly stage, because the molecular mechanism of metastasis remains unknown. It has been known for 25 years that the loss of function of the von Hippel-Lindau (VHL) tumor suppressor gene is pathognomonic of ccRCC. However, no clinically relevant transgenic mouse model of ccRCC has been generated. The purpose of this protocol is to introduce and compare two newly established animal models for metastatic ccRCC. The first is renal implantation in the mouse model. In our laboratory, the CRISPR gene editing system was utilized to knock out the VHL gene in several RCC cell lines. Orthotopic implantation of heterogeneous ccRCC populations to the renal capsule created novel ccRCC models that develop robust lung metastases in immunocompetent mice. The second model is the chicken chorioallantoic membrane (CAM) system. In comparison to the mouse model, this model is more time, labor, and cost-efficient. This model also supported robust tumor formation and intravasation. Due to the short 10 day period of tumor growth in CAM, no overt metastasis was observed by immunohistochemistry (IHC) in the collected embryo tissues. However, when tumor growth was extended by two weeks in the hatched chicken, micrometastatic ccRCC lesions were observed by IHC in the lungs. These two novel preclinical models will be useful to further study the molecular mechanism behind metastasis, as well as to establish new, patient-derived xenografts (PDXs) toward the development of novel treatments for metastatic ccRCC.
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http://dx.doi.org/10.3791/60314DOI Listing
February 2020

Renal Denervation in Asia: Consensus Statement of the Asia Renal Denervation Consortium.

Hypertension 2020 03 3;75(3):590-602. Epub 2020 Feb 3.

Cardiovascular Center and Division of Cardiology, Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan (T.-D.W.).

The Asia Renal Denervation Consortium consensus conference of Asian physicians actively performing renal denervation (RDN) was recently convened to share up-to-date information and regional perspectives, with the goal of consensus on RDN in Asia. First- and second-generation trials of RDN have demonstrated the efficacy and safety of this treatment modality for lowering blood pressure in patients with resistant hypertension. Considering the ethnic differences of the hypertension profile and demographics of cardiovascular disease demonstrated in the SYMPLICITY HTN (Renal Denervation in Patients With Uncontrolled Hypertension)-Japan study and Global SYMPLICITY registry data from Korea and Taiwan, RDN might be an effective hypertension management strategy in Asia. Patient preference for device-based therapy should be considered as part of a shared patient-physician decision process. A practical population for RDN treatment could consist of Asian patients with uncontrolled essential hypertension, including resistant hypertension. Opportunities to refine the procedure, expand the therapy to other sympathetically mediated diseases, and explore the specific effects on nocturnal and morning hypertension offer a promising future for RDN. Based on available evidence, RDN should not be considered a therapy of last resort but as an initial therapy option that may be applied alone or as a complementary therapy to antihypertensive medication.
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http://dx.doi.org/10.1161/HYPERTENSIONAHA.119.13671DOI Listing
March 2020

Whole-Genome Sequence of Bacillus megaterium Strain SGAir0080, Isolated from an Indoor Air Sample.

Microbiol Resour Announc 2019 Dec 12;8(50). Epub 2019 Dec 12.

Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore

strain SGAir0080 was isolated from a tropical air sample in Singapore. Its genome was assembled using single-molecule real-time (SMRT) sequencing and MiSeq reads. It has one chromosome of 5.06 Mbp and seven plasmids (average length, 62.8 kbp). It possesses 5,339 protein-coding genes, 130 tRNAs, and 35 rRNAs.
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http://dx.doi.org/10.1128/MRA.01249-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6908797PMC
December 2019

Complete Genome Sequence of sp. Strain SGAir0471, Isolated from Singapore Air Samples.

Microbiol Resour Announc 2019 Nov 21;8(47). Epub 2019 Nov 21.

Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore

sp. strain SGAir0471 was isolated from tropical air samples collected in Singapore. The genome was assembled using PacBio RS II long reads and Illumina MiSeq short paired-end reads. The complete genome measures 3.53 Mb and consists of 3,151 protein-coding genes, 49 tRNAs, and 12 rRNAs.
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http://dx.doi.org/10.1128/MRA.00960-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6872882PMC
November 2019

Mouse- and patient-derived CAM xenografts for studying metastatic renal cell carcinoma.

Enzymes 2019 18;46:59-80. Epub 2019 Oct 18.

Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, United States; Department of Urology, David Geffen School of Medicine, University of California, Los Angeles, CA, United States. Electronic address:

Renal cell carcinoma is the seventh most common cancer in the United States, and its metastatic form has a very poor prognosis due to a lack of effective treatment and thorough understanding on metastatic mechanism. This chapter will demonstrate a novel concept that intratumoral heterogeneity is essential for metastasis in renal cell carcinoma. We will first introduce the in vitro system and the mouse model that led to the finding of the cooperative mechanism for metastasis. Then, the results from the CAM model illustrate the cooperative interactions that lead to metastasis also occur in this model. We believe that the CAM model, as a unique and sustainable system, can open up new opportunities to study the metastatic disease.
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http://dx.doi.org/10.1016/bs.enz.2019.08.009DOI Listing
November 2019

Microbial communities in the tropical air ecosystem follow a precise diel cycle.

Proc Natl Acad Sci U S A 2019 11 28;116(46):23299-23308. Epub 2019 Oct 28.

Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551 Singapore;

The atmosphere is vastly underexplored as a habitable ecosystem for microbial organisms. In this study, we investigated 795 time-resolved metagenomes from tropical air, generating 2.27 terabases of data. Despite only 9 to 17% of the generated sequence data currently being assignable to taxa, the air harbored a microbial diversity that rivals the complexity of other planetary ecosystems. The airborne microbial organisms followed a clear diel cycle, possibly driven by environmental factors. Interday taxonomic diversity exceeded day-to-day and month-to-month variation. Environmental time series revealed the existence of a large core of microbial taxa that remained invariable over 13 mo, thereby underlining the long-term robustness of the airborne community structure. Unlike terrestrial or aquatic environments, where prokaryotes are prevalent, the tropical airborne biomass was dominated by DNA from eukaryotic phyla. Specific fungal and bacterial species were strongly correlated with temperature, humidity, and CO concentration, making them suitable biomarkers for studying the bioaerosol dynamics of the atmosphere.
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http://dx.doi.org/10.1073/pnas.1908493116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6859341PMC
November 2019

Complete Genome Sequence of Micrococcus luteus Strain SGAir0127, Isolated from Indoor Air Samples from Singapore.

Microbiol Resour Announc 2019 Oct 10;8(41). Epub 2019 Oct 10.

Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore

strain SGAir0127 was isolated from indoor air samples collected in Singapore. The assembly, based on single-molecule real-time sequencing reads, resulted in two contigs, one chromosomal contig with a length of 2.57 Mbp and one nonchromosomal contig of 8.68 kbp. The genome has a total of 2,564 genes.
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http://dx.doi.org/10.1128/MRA.00646-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6787313PMC
October 2019

Complete Genome Sequence of sp. Strain SGAir0479, Isolated from Indoor Air Collected in Singapore.

Microbiol Resour Announc 2019 Oct 3;8(40). Epub 2019 Oct 3.

Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore

The complete genome sequence of sp. strain SGAir0479 is presented here. This organism was isolated from an air sample collected in an indoor location in Singapore. The consensus assembly generated one chromosome of 4.86 Mb (G+C content of 69.8%) and one plasmid of 104,493 bp.
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http://dx.doi.org/10.1128/MRA.00622-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6776762PMC
October 2019

Complete Genome Sequence of sp. Strain SGAir0095, Isolated from Tropical Air Samples Collected in Singapore.

Microbiol Resour Announc 2019 Sep 19;8(38). Epub 2019 Sep 19.

Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore

sp. strain SGAir0095 was isolated from tropical air samples collected in Singapore, and its complete genome was sequenced with a hybrid strategy using single-molecule real-time sequencing and short reads. The genome consists of one chromosome of 4.14 Mbp and encompasses 3,885 protein-coding genes, 39 rRNAs, and 101 tRNAs.
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http://dx.doi.org/10.1128/MRA.00604-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6753264PMC
September 2019

Genome Sequence of the Tropical Atmosphere Bacterium sp. Strain SGAir0037.

Microbiol Resour Announc 2019 Sep 12;8(37). Epub 2019 Sep 12.

Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore

The bacterial genus has been detected in marine and soil environments. Here, we report the genome sequence of sp. strain SGAir0037, which was isolated from outdoor air samples collected in Singapore. The genome comprises one chromosome of 5.26 Mb and one plasmid of 127 kb.
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http://dx.doi.org/10.1128/MRA.00610-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6742788PMC
September 2019

Complete Genome Sequence of Citricoccus sp. Strain SGAir0253, Isolated from Indoor Air in Singapore.

Microbiol Resour Announc 2019 Sep 12;8(37). Epub 2019 Sep 12.

Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore

sp. strain SGAir0253 was isolated from indoor air collected in Singapore. Its genome sequence was assembled using single-molecule real-time sequencing. It comprises one chromosome of 3.32 Mb and two plasmids of 137 kb and 99 kb. The genome consists of 2,950 protein-coding genes, 49 tRNAs, and 9 rRNAs.
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http://dx.doi.org/10.1128/MRA.00606-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6742787PMC
September 2019

Complete Genome Sequence of Streptomyces sp. Strain SGAir0924, an Actinobacterium Isolated from Outdoor Air in Singapore.

Microbiol Resour Announc 2019 Aug 29;8(35). Epub 2019 Aug 29.

Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore

sp. strain SGAir0924 was isolated from outdoor air collected in Singapore. Its genome was assembled using long reads generated by single-molecule real-time sequencing. The final assembly had one chromosome of 7.65 Mb and three plasmids with an average length of 142 kb. The genome contained 6,825 protein-coding genes, 68 tRNAs, and 18 rRNAs.
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http://dx.doi.org/10.1128/MRA.00899-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6715878PMC
August 2019

Complete Genome Sequence of sp. Strain SGAir0191, Isolated from Tropical Air Collected in Singapore.

Microbiol Resour Announc 2019 Aug 22;8(34). Epub 2019 Aug 22.

Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore

sp. strain SGAir0191 was isolated from an air sample collected in Singapore, and its genome was sequenced using a combination of long and short reads to generate a high-quality genome assembly. The complete genome is approximately 5.07 Mb with 4,370 protein-coding genes, 19 rRNAs, and 73 tRNAs.
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http://dx.doi.org/10.1128/MRA.00617-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6706683PMC
August 2019

Complete Genome Sequence of sp. Strain SGAir0570, Isolated from Tropical Air Collected in Singapore.

Microbiol Resour Announc 2019 Aug 22;8(34). Epub 2019 Aug 22.

Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore

sp. strain SGAir0570 was isolated from air samples collected in Singapore. Its genome was assembled using single-molecule real-time sequencing and MiSeq short reads. It has one chromosome with a length of 3.38 Mb and one 59.2-kb plasmid. It contains 3,170 protein-coding genes, 48 tRNAs, and 6 rRNAs.
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http://dx.doi.org/10.1128/MRA.00613-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6706682PMC
August 2019