Displaying publications 1 - 20 of 54 in total

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  1. Pok KY, Squires RC, Tan LK, Takasaki T, Abubakar S, Hasebe F, et al.
    Western Pac Surveill Response J, 2015 Jun 30;6(2):73-81.
    PMID: 26306220 DOI: 10.5365/WPSAR.2015.6.1.017
    Accurate laboratory testing is a critical component of dengue surveillance and control. The objective of this programme was to assess dengue diagnostic proficiency among national-level public health laboratories in the World Health Organization (WHO) Western Pacific Region.
  2. Soh LT, Squires RC, Tan LK, Pok KY, Yang H, Liew C, et al.
    Western Pac Surveill Response J, 2016 04 22;7(2):26-34.
    PMID: 27508088 DOI: 10.5365/WPSAR.2016.7.1.002
    OBJECTIVE: To conduct an external quality assessment (EQA) of dengue and chikungunya diagnostics among national-level public health laboratories in the Asia Pacific region following the first round of EQA for dengue diagnostics in 2013.

    METHODS: Twenty-four national-level public health laboratories performed routine diagnostic assays on a proficiency testing panel consisting of two modules. Module A contained serum samples spiked with cultured dengue virus (DENV) or chikungunya virus (CHIKV) for the detection of nucleic acid and DENV non-structural protein 1 (NS1) antigen. Module B contained human serum samples for the detection of anti-DENV antibodies.

    RESULTS: Among 20 laboratories testing Module A, 17 (85%) correctly detected DENV RNA by reverse transcription polymerase chain reaction (RT-PCR), 18 (90%) correctly determined serotype and 19 (95%) correctly identified CHIKV by RT-PCR. Ten of 15 (66.7%) laboratories performing NS1 antigen assays obtained the correct results. In Module B, 18/23 (78.3%) and 20/20 (100%) of laboratories correctly detected anti-DENV IgM and IgG, respectively. Detection of acute/recent DENV infection by both molecular (RT-PCR) and serological methods (IgM) was available in 19/24 (79.2%) participating laboratories.

    DISCUSSION: Accurate laboratory testing is a critical component of dengue and chikungunya surveillance and control. This second round of EQA reveals good proficiency in molecular and serological diagnostics of these diseases in the Asia Pacific region. Further comprehensive diagnostic testing, including testing for Zika virus, should comprise future iterations of the EQA.

  3. Roslan A, Kamsani SH, Nay TW, Tan KL, Hakim N, Tan AM, et al.
    Med J Malaysia, 2018 12;73(6):388-392.
    PMID: 30647209
    OBJECTIVE: Cardiac amyloidosis is under diagnosed and its prevalence is unknown. This is a retrospective, nonrandomised, single centre study of patients with endomyocardial biopsy-proven cardiac amyloidosis focusing on their echocardiographic and electrocardiogram (ECG) presentations. This is the first case series in Malaysia on this subject.

    METHODS: We identified all of our endomyocardial biopsyproven cardiac amyloidosis patients from January 2010 to January 2018 and reviewed their medical records. All patients echocardiographic and ECG findings reviewed and analysed comparing to basic mean population value.

    RESULTS: In total there are 13 biopsy-proven cardiac amyloidosis patients. All of the biopsies shows light chain (AL) amyloid. Majority of the patients (8, 61.5%) is male, and most of our patients (8, 61.5%) is Chinese. All seven patients on whom we performed deformation imaging have apical sparing pattern on longitudinal strain echocardiogram. Mean ejection fraction is 49.3%, (SD=7.9). All patients have concentric left ventricular hypertrophy and right ventricular hypertrophy. Diastolic dysfunction was present in all of our patients with nine out of 13 patients (69.2%) having restrictive filling patterns (E/A ≥2.0 E/e' ≥15). On electrocardiogram, 12 (92%) patients have prolonged PR interval (median 200ms, IQR 76.50ms) and 9 (69.2%) patients have pseudoinfarct pattern.

    CONCLUSION: Echocardiography plays an important role in diagnosing cardiac amyloidosis. The findings of concentric left ventricular hypertrophy with preserved ejection fraction without increased in loading condition should alert the clinician towards its possibility. This is further supported by right ventricular hypertrophy and particularly longitudinal strain imaging showing apical sparing pattern.

  4. Hapuarachchi HC, Bandara KB, Sumanadasa SD, Hapugoda MD, Lai YL, Lee KS, et al.
    J Gen Virol, 2010 Apr;91(Pt 4):1067-76.
    PMID: 19955565 DOI: 10.1099/vir.0.015743-0
    Chikungunya fever swept across many South and South-east Asian countries, following extensive outbreaks in the Indian Ocean Islands in 2005. However, molecular epidemiological data to explain the recent spread and evolution of Chikungunya virus (CHIKV) in the Asian region are still limited. This study describes the genetic Characteristics and evolutionary relationships of CHIKV strains that emerged in Sri Lanka and Singapore during 2006-2008. The viruses isolated in Singapore also included those imported from the Maldives (n=1), India (n=2) and Malaysia (n=31). All analysed strains belonged to the East, Central and South African (ECSA) lineage and were evolutionarily more related to Indian than to Indian Ocean Islands strains. Unique genetic characteristics revealed five genetically distinct subpopulations of CHIKV in Sri Lanka and Singapore, which were likely to have emerged through multiple, independent introductions. The evolutionary network based on E1 gene sequences indicated the acquisition of an alanine to valine 226 substitution (E1-A226V) by virus strains of the Indian sublineage as a key evolutionary event that contributed to the transmission and spatial distribution of CHIKV in the region. The E1-A226V substitution was found in 95.7 % (133/139) of analysed isolates in 2008, highlighting the widespread establishment of mutated CHIKV strains in Sri Lanka, Singapore and Malaysia. As the E1-A226V substitution is known to enhance the transmissibility of CHIKV by Aedes albopictus mosquitoes, this observation has important implications for the design of vector control strategies to fight the virus in regions at risk of chikungunya fever.
  5. Chia BL, Tan LK
    Am J Cardiol, 1984 May 01;53(9):1413.
    PMID: 6538741
  6. Tan LK, Ooi PT, Carniel E, Thong KL
    PLoS One, 2014;9(8):e106329.
    PMID: 25170941 DOI: 10.1371/journal.pone.0106329
    Y. enterocolitica and Y. pseudotuberculosis are important food borne pathogens. However, the presence of competitive microbiota makes the isolation of Y. enterocolitica and Y. pseudotuberculosis from naturally contaminated foods difficult. We attempted to evaluate the performance of a modified Cefsulodin-Irgasan-Novobiocin (CIN) agar in the differentiation of Y. enterocolitica from non-Yersinia species, particularly the natural intestinal microbiota. The modified CIN enabled the growth of Y. enterocolitica colonies with the same efficiency as CIN and Luria-Bertani agar. The detection limits of the modified CIN for Y. enterocolitica in culture medium (10 cfu/ml) and in artificially contaminated pork (10(4) cfu/ml) were also comparable to those of CIN. However, the modified CIN provided a better discrimination of Yersinia colonies from other bacteria exhibiting Yersinia-like colonies on CIN (H2S-producing Citrobacter freundii, C. braakii, Enterobacter cloacae, Aeromonas hydrophila, Providencia rettgeri, and Morganella morganii). The modified CIN exhibited a higher recovery rate of Y. enterocolitica from artificially prepared bacterial cultures and naturally contaminated samples compared with CIN. Our results thus demonstrated that the use of modified CIN may be a valuable means to increase the recovery rate of food borne Yersinia from natural samples, which are usually contaminated by multiple types of bacteria.
  7. Wong YQ, Tan LK, Seow P, Tan MP, Abd Kadir KA, Vijayananthan A, et al.
    PLoS One, 2017;12(6):e0179895.
    PMID: 28658309 DOI: 10.1371/journal.pone.0179895
    OBJECTIVES: This study assesses the whole brain microstructural integrity of white matter tracts (WMT) among older individuals with a history of falls compared to non-fallers.

    METHODS: 85 participants (43 fallers, 42 non-fallers) were evaluated with conventional MRI and diffusion tensor imaging (DTI) sequences of the brain. DTI metrics were obtained from selected WMT using tract-based spatial statistics (TBSS) method. This was followed by binary logistic regression to investigate the clinical variables that could act as confounding elements on the outcomes. The TBSS analysis was then repeated, but this time including all significant predictor variables from the regression analysis as TBSS covariates.

    RESULTS: The mean diffusivity (MD) and axial diffusivity (AD) and to a lesser extent radial diffusivity (RD) values of the projection fibers and commissural bundles were significantly different in fallers (p < 0.05) compared to non-fallers. However, the final logistic regression model obtained showed that only functional reach, white matter lesion volume, hypertension and orthostatic hypotension demonstrated statistical significant differences between fallers and non-fallers. No significant differences were found in the DTI metrics when taking into account age and the four variables as covariates in the repeated analysis.

    CONCLUSION: This DTI study of 85 subjects, do not support DTI metrics as a singular factor that contributes independently to the fall outcomes. Other clinical and imaging factors have to be taken into account.

  8. Liew YM, McLaughlin RA, Chan BT, Abdul Aziz YF, Chee KH, Ung NM, et al.
    Phys Med Biol, 2015 Apr 7;60(7):2715-33.
    PMID: 25768708 DOI: 10.1088/0031-9155/60/7/2715
    Cine MRI is a clinical reference standard for the quantitative assessment of cardiac function, but reproducibility is confounded by motion artefacts. We explore the feasibility of a motion corrected 3D left ventricle (LV) quantification method, incorporating multislice image registration into the 3D model reconstruction, to improve reproducibility of 3D LV functional quantification. Multi-breath-hold short-axis and radial long-axis images were acquired from 10 patients and 10 healthy subjects. The proposed framework reduced misalignment between slices to subpixel accuracy (2.88 to 1.21 mm), and improved interstudy reproducibility for 5 important clinical functional measures, i.e. end-diastolic volume, end-systolic volume, ejection fraction, myocardial mass and 3D-sphericity index, as reflected in a reduction in the sample size required to detect statistically significant cardiac changes: a reduction of 21-66%. Our investigation on the optimum registration parameters, including both cardiac time frames and number of long-axis (LA) slices, suggested that a single time frame is adequate for motion correction whereas integrating more LA slices can improve registration and model reconstruction accuracy for improved functional quantification especially on datasets with severe motion artefacts.
  9. Lau YS, Tan LK, Chan CK, Chee KH, Liew YM
    Phys Med Biol, 2021 Dec 31;66(24).
    PMID: 34911053 DOI: 10.1088/1361-6560/ac4348
    Percutaneous coronary intervention (PCI) with stent placement is a treatment effective for coronary artery diseases. Intravascular optical coherence tomography (OCT) with high resolution is used clinically to visualize stent deployment and restenosis, facilitating PCI operation and for complication inspection. Automated stent struts segmentation in OCT images is necessary as each pullback of OCT images could contain thousands of stent struts. In this paper, a deep learning framework is proposed and demonstrated for the automated segmentation of two major clinical stent types: metal stents and bioresorbable vascular scaffolds (BVS). U-Net, the current most prominent deep learning network in biomedical segmentation, was implemented for segmentation with cropped input. The architectures of MobileNetV2 and DenseNet121 were also adapted into U-Net for improvement in speed and accuracy. The results suggested that the proposed automated algorithm's segmentation performance approaches the level of independent human obsevers and is feasible for both types of stents despite their distinct appearance. U-Net with DenseNet121 encoder (U-Dense) performed best with Dice's coefficient of 0.86 for BVS segmentation, and precision/recall of 0.92/0.92 for metal stent segmentation under optimal crop window size of 256.
  10. Fum WKS, Md Shah MN, Raja Aman RRA, Abd Kadir KA, Wen DW, Leong S, et al.
    Phys Eng Sci Med, 2023 Dec;46(4):1535-1552.
    PMID: 37695509 DOI: 10.1007/s13246-023-01317-5
    In fluoroscopy-guided interventions (FGIs), obtaining large quantities of labelled data for deep learning (DL) can be difficult. Synthetic labelled data can serve as an alternative, generated via pseudo 2D projections of CT volumetric data. However, contrasted vessels have low visibility in simple 2D projections of contrasted CT data. To overcome this, we propose an alternative method to generate fluoroscopy-like radiographs from contrasted head CT Angiography (CTA) volumetric data. The technique involves segmentation of brain tissue, bone, and contrasted vessels from CTA volumetric data, followed by an algorithm to adjust HU values, and finally, a standard ray-based projection is applied to generate the 2D image. The resulting synthetic images were compared to clinical fluoroscopy images for perceptual similarity and subject contrast measurements. Good perceptual similarity was demonstrated on vessel-enhanced synthetic images as compared to the clinical fluoroscopic images. Statistical tests of equivalence show that enhanced synthetic and clinical images have statistically equivalent mean subject contrast within 25% bounds. Furthermore, validation experiments confirmed that the proposed method for generating synthetic images improved the performance of DL models in certain regression tasks, such as localizing anatomical landmarks in clinical fluoroscopy images. Through enhanced pseudo 2D projection of CTA volume data, synthetic images with similar features to real clinical fluoroscopic images can be generated. The use of synthetic images as an alternative source for DL datasets represents a potential solution to the application of DL in FGIs procedures.
  11. Hizam DA, Tan LK, Saad M, Muaadz A, Ung NM
    Phys Eng Sci Med, 2024 Apr 22.
    PMID: 38647633 DOI: 10.1007/s13246-024-01411-2
    This study aims to assess the accuracy of automatic atlas-based contours for various key anatomical structures in prostate radiotherapy treatment planning. The evaluated structures include the bladder, rectum, prostate, seminal vesicles, femoral heads and penile bulb. CT images from 20 patients who underwent intensity-modulated radiotherapy were randomly chosen to create an atlas library. Atlas contours of the seven anatomical structures were generated using four software packages: ABAS, Eclipse, MIM, and RayStation. These contours were then compared to manual delineations performed by oncologists, which served as the ground truth. Evaluation metrics such as dice similarity coefficient (DSC), mean distance to agreement (MDA), and volume ratio (VR) were calculated to assess the accuracy of the contours. Additionally, the time taken by each software to generate the atlas contour was recorded. The mean DSC values for the bladder exhibited strong agreement (>0.8) with manual delineations for all software except for Eclipse and RayStation. Similarly, the femoral heads showed significant similarity between the atlas contours and ground truth across all software, with mean DSC values exceeding 0.9 and MDA values close to zero. On the other hand, the penile bulb displayed only moderate agreement with the ground truth, with mean DSC values ranging from 0.5 to 0.7 for all software. A similar trend was observed in the prostate atlas contours, except for MIM, which achieved a mean DSC of over 0.8. For the rectum, both ABAS and MIM atlases demonstrated strong agreement with the ground truth, resulting in mean DSC values of more than 0.8. Overall, MIM and ABAS outperformed Eclipse and RayStation in both DSC and MDA. These results indicate that the atlas-based segmentation employed in this study produces acceptable contours for the anatomical structures of interest in prostate radiotherapy treatment planning.
  12. Azlan CA, Wong JHD, Tan LK, A D Huri MSN, Ung NM, Pallath V, et al.
    Phys Med, 2020 Dec;80:10-16.
    PMID: 33070007 DOI: 10.1016/j.ejmp.2020.10.002
    PURPOSE: We present the implementation of e-learning in the Master of Medical Physics programme at the University of Malaya during a partial lockdown from March to June 2020 due to the COVID-19 pandemic.

    METHODS: Teaching and Learning (T&L) activities were conducted virtually on e-learning platforms. The students' experience and feedback were evaluated after 15 weeks.

    RESULTS: We found that while students preferred face-to-face, physical teaching, they were able to adapt to the new norm of e-learning. More than 60% of the students agreed that pre-recorded lectures and viewing videos of practical sessions, plus answering short questions, were beneficial. Certain aspects, such as hands-on practical and clinical experience, could never be replaced. The e-learning and study-from-home environment accorded a lot of flexibility. However, students also found it challenging to focus because of distractions, lack of engagement and mental stress. Technical problems, such as poor Internet connectivity and limited data plans, also compounded the problem.

    CONCLUSION: We expect e-learning to prevail in future. Hybrid learning strategies, which includes face-to-face classes and e-learning, will become common, at least in the medical physics programme of the University of Malaya even after the pandemic.

  13. Fum WKS, Wong JHD, Tan LK
    Phys Med, 2021 Apr;84:228-240.
    PMID: 33849785 DOI: 10.1016/j.ejmp.2021.03.004
    PURPOSE: This systematic review aims to understand the dose estimation approaches and their major challenges. Specifically, we focused on state-of-the-art Monte Carlo (MC) methods in fluoroscopy-guided interventional procedures.

    METHODS: All relevant studies were identified through keyword searches in electronic databases from inception until September 2020. The searched publications were reviewed, categorised and analysed based on their respective methodology.

    RESULTS: Hundred and one publications were identified which utilised existing MC-based applications/programs or customised MC simulations. Two outstanding challenges were identified that contribute to uncertainties in the virtual simulation reconstruction. The first challenge involves the use of anatomical models to represent individuals. Currently, phantom libraries best balance the needs of clinical practicality with those of specificity. However, mismatches of anatomical variations including body size and organ shape can create significant discrepancies in dose estimations. The second challenge is that the exact positioning of the patient relative to the beam is generally unknown. Most dose prediction models assume the patient is located centrally on the examination couch, which can lead to significant errors.

    CONCLUSION: The continuing rise of computing power suggests a near future where MC methods become practical for routine clinical dosimetry. Dynamic, deformable phantoms help to improve patient specificity, but at present are only limited to adjustment of gross body volume. Dynamic internal organ displacement or reshaping is likely the next logical frontier. Image-based alignment is probably the most promising solution to enable this, but it must be automated to be clinically practical.

  14. Chuah SH, Md Sari NA, Chew BT, Tan LK, Chiam YK, Chan BT, et al.
    Phys Med, 2020 Oct;78:137-149.
    PMID: 33007738 DOI: 10.1016/j.ejmp.2020.08.022
    Differential diagnosis of hypertensive heart disease (HHD) and hypertrophic cardiomyopathy (HCM) is clinically challenging but important for treatment management. This study aims to phenotype HHD and HCM in 3D + time domain by using a multiparametric motion-corrected personalized modeling algorithm and cardiac magnetic resonance (CMR). 44 CMR data, including 12 healthy, 16 HHD and 16 HCM cases, were examined. Multiple CMR phenotype data consisting of geometric and dynamic variables were extracted globally and regionally from the models over a full cardiac cycle for comparison against healthy models and clinical reports. Statistical classifications were used to identify the distinctive characteristics and disease subtypes with overlapping functional data, providing insights into the challenges for differential diagnosis of both types of disease. While HCM is characterized by localized extreme hypertrophy of the LV, wall thickening/contraction/strain was found to be normal and in sync, though it was occasionally exaggerated at normotrophic/less severely hypertrophic regions during systole to preserve the overall ejection fraction (EF) and systolic functionality. Additionally, we observed that hypertrophy in HHD could also be localized, although at less extreme conditions (i.e. more concentric). While fibrosis occurs mostly in those HCM cases with aortic obstruction, only minority of HHD patients were found affected by fibrosis. We demonstrate that subgroups of HHD (i.e. preserved and reduced EF: HHDpEF & HHDrEF) have different 3D + time CMR characteristics. While HHDpEF has cardiac functions in normal range, dilation and heart failure are indicated in HHDrEF as reflected by low LV wall thickening/contraction/strain and synchrony, as well as much reduced EF.
  15. Kuan SW, Chua KH, Tan EW, Tan LK, Loch A, Kee BP
    PeerJ, 2022;10:e13265.
    PMID: 35441061 DOI: 10.7717/peerj.13265
    Cardiomyopathy (CMP) constitutes a diverse group of myocardium diseases affecting the pumping ability of the heart. Genetic predisposition is among the major factors affecting the development of CMP. Globally, there are over 100 genes in autosomal and mitochondrial DNA (mtDNA) that have been reported to be associated with the pathogenesis of CMP. However, most of the genetic studies have been conducted in Western countries, with limited data being available for the Asian population. Therefore, this study aims to investigate the mutation spectrum in the mitochondrial genome of 145 CMP patients in Malaysia. Long-range PCR was employed to amplify the entire mtDNA, and whole mitochondrial genome sequencing was conducted on the MiSeq platform. Raw data was quality checked, mapped, and aligned to the revised Cambridge Reference Sequence (rCRS). Variants were named, annotated, and filtered. The sequencing revealed 1,077 variants, including 18 novel and 17 CMP and/or mitochondrial disease-associated variants after filtering. In-silico predictions suggested that three of the novel variants (m.8573G>C, m.11916T>A and m.11918T>G) in this study are potentially pathogenic. Two confirmed pathogenic variants (m.1555A>G and m.11778G>A) were also found in the CMP patients. The findings of this study shed light on the distribution of mitochondrial mutations in Malaysian CMP patients. Further functional studies are required to elucidate the role of these variants in the development of CMP.
  16. Ramli N, Lim CH, Rajagopal R, Tan LK, Seow P, Ariffin H
    Pediatr Radiol, 2020 08;50(9):1277-1283.
    PMID: 32591982 DOI: 10.1007/s00247-020-04717-x
    BACKGROUND: Intrathecal and intravenous chemotherapy, specifically methotrexate, might contribute to neural microstructural damage.

    OBJECTIVE: To assess, by diffusion tensor imaging, microstructural integrity of white matter in paediatric patients with acute lymphoblastic leukaemia (ALL) following intrathecal and intravenous chemotherapy.

    MATERIALS AND METHODS: Eleven children diagnosed with de novo ALL underwent MRI scans of the brain with diffusion tensor imaging (DTI) prior to commencement of chemotherapy and at 12 months after diagnosis, using a 3-tesla (T) MRI scanner. We investigated the changes in DTI parameters in white matter tracts before and after chemotherapy using tract-based spatial statistics overlaid on the International Consortium of Brain Mapping DTI-81 atlas. All of the children underwent formal neurodevelopmental assessment at the two study time points.

    RESULTS: Whole-brain DTI analysis showed significant changes between the two time points, affecting several white matter tracts. The tracts demonstrated longitudinal changes of decreasing mean and radial diffusivity. The neurodevelopment of the children was near compatible for age at the end of ALL treatment.

    CONCLUSION: The quantification of white matter tracts changes in children undergoing chemotherapy showed improving longitudinal values in DTI metrics (stable fractional anisotropy, decreasing mean and radial diffusivity), which are incompatible with deterioration of microstructural integrity in these children.

  17. Tan LK, Chua EH, Mohd Ghazali S, Cheah YK, Jayaraj VJ, Kee CC
    Nutrients, 2023 Dec 08;15(24).
    PMID: 38140302 DOI: 10.3390/nu15245043
    The healthy eating plate concept has been introduced in many countries, including Malaysia, as a visual guide for the public to eat healthily. The relationship between Malaysian Healthy Plate (MHP) and adequate fruit and vegetable (FV) intake among morbid Malaysian adults is unknown. Hence, we investigated the relationship between awareness of the MHP and FV intake among morbid Malaysian adults. National survey data on 9760 morbid Malaysian adults aged 18 years and above were analyzed. The relationship between awareness of MHP and FV intake among Malaysian adults with obesity, diabetes mellitus, hypertension, and hypercholesterolemia were determined using multivariable logistic regression controlling for sociodemographic characteristics and lifestyle risk factors. Our data demonstrated that MHP awareness is associated with adequate FV intake among the Malaysian adults with abdominal obesity (adjusted odds ratio (aOR): 1.86, 95% confidence interval (CI): 1.05-3.29), diabetes mellitus (aOR: 4.88, 95% CI: 2.13-22.18), hypertension (aOR: 4.39, 95% CI: 1.96-9.83), and hypercholesterolemia (aOR: 4.16, 95% CI: 1.48-11.72). Our findings indicated the necessity for ongoing efforts by policymakers, healthcare professionals, and nutrition educators to promote the concept of MHP and ensure that morbid Malaysian adults consume a sufficient intake of FV or adopt a healthy eating pattern to achieve and maintain optimal health.
  18. Ho WS, Balan G, Puthucheary S, Kong BH, Lim KT, Tan LK, et al.
    Microb Drug Resist, 2012 Aug;18(4):408-16.
    PMID: 22394084 DOI: 10.1089/mdr.2011.0222
    The emergence of Escherichia coli resistant to extended-spectrum cephalosporins (ESCs) is of concern as ESC is often used to treat infections by Gram-negative bacteria. One-hundred and ten E. coli strains isolated in 2009-2010 from children warded in a Malaysian tertiary hospital were analyzed for their antibiograms, carriage of extended-spectrum beta-lactamase (ESBL) and AmpC genes, possible inclusion of the beta-lactamase genes on an integron platform, and their genetic relatedness. All E. coli strains were sensitive to carbapenems. About 46% of strains were multidrug resistant (MDR; i.e., resistant to ≥3 antibiotic classes) and almost half (45%) were nonsusceptible to ESCs. Among the MDR strains, high resistance rates were observed for ampicillin (98%), tetracycline (75%), and trimethoprim/sulfamethoxazole (73%). Out of 110 strains, bla(TEM-1) (49.1%), bla(CTX-M) (11.8%), and bla(CMY-2) (6.4%) were detected. Twenty-one strains were ESBL producers. CTX-M-15 was the predominant CTX-M variant found and this is the first report of a CTX-M-27-producing E. coli strain from Malaysia. Majority (3.1%) of the strains harbored class 1 integron-encoded integrases with a predominance of aadA and dfr genes within the integron variable region. No gene cassette encoding ESBL genes was found and integrons were not significantly associated with ESBL or non-ESBL producers. Possible clonal expansion was observed for few CTX-M-15-positive strains but the O25-ST131 E. coli clone known to harbor CTX-M-15 was not detected while CMY-2-positive strains were genetically diverse.
  19. Tan LK, Liew YM, Lim E, McLaughlin RA
    Med Image Anal, 2017 Apr 12;39:78-86.
    PMID: 28437634 DOI: 10.1016/j.media.2017.04.002
    Automated left ventricular (LV) segmentation is crucial for efficient quantification of cardiac function and morphology to aid subsequent management of cardiac pathologies. In this paper, we parameterize the complete (all short axis slices and phases) LV segmentation task in terms of the radial distances between the LV centerpoint and the endo- and epicardial contours in polar space. We then utilize convolutional neural network regression to infer these parameters. Utilizing parameter regression, as opposed to conventional pixel classification, allows the network to inherently reflect domain-specific physical constraints. We have benchmarked our approach primarily against the publicly-available left ventricle segmentation challenge (LVSC) dataset, which consists of 100 training and 100 validation cardiac MRI cases representing a heterogeneous mix of cardiac pathologies and imaging parameters across multiple centers. Our approach attained a .77 Jaccard index, which is the highest published overall result in comparison to other automated algorithms. To test general applicability, we also evaluated against the Kaggle Second Annual Data Science Bowl, where the evaluation metric was the indirect clinical measures of LV volume rather than direct myocardial contours. Our approach attained a Continuous Ranked Probability Score (CRPS) of .0124, which would have ranked tenth in the original challenge. With this we demonstrate the effectiveness of convolutional neural network regression paired with domain-specific features in clinical segmentation.
  20. Tan LK, Liew YM, Lim E, Abdul Aziz YF, Chee KH, McLaughlin RA
    Med Biol Eng Comput, 2018 Jun;56(6):1053-1062.
    PMID: 29147835 DOI: 10.1007/s11517-017-1750-7
    In this paper, we develop and validate an open source, fully automatic algorithm to localize the left ventricular (LV) blood pool centroid in short axis cardiac cine MR images, enabling follow-on automated LV segmentation algorithms. The algorithm comprises four steps: (i) quantify motion to determine an initial region of interest surrounding the heart, (ii) identify potential 2D objects of interest using an intensity-based segmentation, (iii) assess contraction/expansion, circularity, and proximity to lung tissue to score all objects of interest in terms of their likelihood of constituting part of the LV, and (iv) aggregate the objects into connected groups and construct the final LV blood pool volume and centroid. This algorithm was tested against 1140 datasets from the Kaggle Second Annual Data Science Bowl, as well as 45 datasets from the STACOM 2009 Cardiac MR Left Ventricle Segmentation Challenge. Correct LV localization was confirmed in 97.3% of the datasets. The mean absolute error between the gold standard and localization centroids was 2.8 to 4.7 mm, or 12 to 22% of the average endocardial radius. Graphical abstract Fully automated localization of the left ventricular blood pool in short axis cardiac cine MR images.
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