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Predictive modelling of colossal ATR-FTIR spectral data using PLS-DA: empirical differences between PLS1-DA and PLS2-DA algorithms

Lee LC, Jemain AA

Analyst, 2019 Apr 08;144(8):2670-2678.
PMID: 30849143 DOI: 10.1039/c8an02074d

In response to our review paper [L. C. Lee et al., Analyst, 2018, 143, 3526-3539], we present a study that compares empirical differences between PLS1-DA and PLS2-DA algorithms in modelling a colossal ATR-FTIR spectral dataset. Over the past two decades, partial least squares-discriminant analysis (PLS-DA) has gained wide acceptance and huge popularity in the field of applied research, partly due to its dimensionality reduction capability and ability to handle multicollinear and correlated variables. To solve a K-class problem (K > 2) using PLS-DA and high-dimensional data like infrared spectra, one can construct either K one-versus-all PLS1-DA models or only one PLS2-DA model. The aim of this work is to explore empirical differences between the two PLS-DA algorithms in modeling a colossal ATR-FTIR spectral dataset. The practical task is to build a prediction model using the imbalanced, high dimensional, colossal and multi-class ATR-FTIR spectra of blue gel pen inks. Four different sub-datasets were prepared from the principal dataset by considering the raw and asymmetric least squares (AsLS) preprocessed forms: (a) Raw-global region; (b) Raw-local region; (c) AsLS-global region; and (d) AsLS-local region. A series of 50 models which includes the first 50 PLS components incrementally was constructed repeatedly using the four sub-datasets. Each model was evaluated using six different variants of v-fold cross validation, autoprediction and external testing methods. As a result, each PLS-DA algorithm was represented by a number of figures of merit. The differences between PLS1-DA and PLS2-DA algorithms were assessed using hypothesis tests with respect to model accuracy, stability and fitting. On the other hand, confusion matrices of the two PLS-DA algorithms were inspected carefully for assessment of model parsimony. Overall, both the algorithms presented satisfactory model accuracy and stability. Nonetheless, PLS1-DA models showed significantly higher accuracy rates than PLS2-DA models, whereas PLS2-DA models seem to be much more stable compared to PLS1-DA models. Eventually, PLS2-DA also proved to be less prone to overfitting and is more parsimonious than PLS1-DA. In conclusion, the relatively high accuracy of the PLS1-DA algorithm is achieved at the cost of rather low parsimony and stability, and with an increased risk of overfitting.
Influence of sanitary conditions on the field performance of chlorpyrifos-based baits against American cockroaches, Periplaneta americana (L.) (Dictyoptera: Blattidae)

Lee CY, Lee LC

J Vector Ecol, 2000 Dec;25(2):218-21.
PMID: 11217220

The role of sanitation in performance of insecticidal bait stations containing 0.5% chlorpyrifos against the American cockroach, Periplaneta americana (L.), was investigated in residential premises. Test sites were chosen from three locations in Penang Island, Malaysia, and clustered according to their sanitary conditions. Results indicated that at 1-week post-treatment, houses with good sanitary conditions showed a significantly faster reduction (P > 0.05) in the number of cockroaches trapped (> 95%) than those with moderate and poor conditions. At 6 weeks post-treatment, all houses treated with insecticidal baits showed no significant difference in terms of reduction rate of cockroach numbers (P > 0.05), irrespective of sanitary condition. However, the bait performance in houses with poor sanitary conditions could not be sustained up to 12-week post-treatment.
Partial least squares-discriminant analysis (PLS-DA) for classification of high-dimensional (HD) data: a review of contemporary practice strategies and knowledge gaps

Lee LC, Liong CY, Jemain AA

Analyst, 2018 Jul 23;143(15):3526-3539.
PMID: 29947623 DOI: 10.1039/c8an00599k

Partial least squares-discriminant analysis (PLS-DA) is a versatile algorithm that can be used for predictive and descriptive modelling as well as for discriminative variable selection. However, versatility is both a blessing and a curse and the user needs to optimize a wealth of parameters before reaching reliable and valid outcomes. Over the past two decades, PLS-DA has demonstrated great success in modelling high-dimensional datasets for diverse purposes, e.g. product authentication in food analysis, diseases classification in medical diagnosis, and evidence analysis in forensic science. Despite that, in practice, many users have yet to grasp the essence of constructing a valid and reliable PLS-DA model. As the technology progresses, across every discipline, datasets are evolving into a more complex form, i.e. multi-class, imbalanced and colossal. Indeed, the community is welcoming a new era called big data. In this context, the aim of the article is two-fold: (a) to review, outline and describe the contemporary PLS-DA modelling practice strategies, and (b) to critically discuss the respective knowledge gaps that have emerged in response to the present big data era. This work could complement other available reviews or tutorials on PLS-DA, to provide a timely and user-friendly guide to researchers, especially those working in applied research.
Retrospective study on tension-free vaginal tape obturator (TVT-O)

Rajendra M, Han HC, Lee LC, Tseng LA, Wong HF

Int Urogynecol J, 2012 Mar;23(3):327-34.
PMID: 21892684 DOI: 10.1007/s00192-011-1552-7

INTRODUCTION AND HYPOTHESIS: We aim to report the 3-year outcome and complications of the tension-free vaginal tape obturator (TVT-O) in treating female stress urinary incontinence (SUI).
METHODS: Retrospective analysis for complications and outcome of surgery was performed in 419 women undergoing the TVT-O from 2004 to 2006.
RESULTS: Three patients (0.8%) with an isolated TVT-O had a blood loss of more than 200 ml. Two patients (0.5%) had bladder perforation. Out of 11 readmitted patients (2.6%), 10 were due to voiding difficulty. Six patients (1.4%) required tape loosening or division. Persistent pain occurred in 3.6% and erosion in 2.4% of patients. One hundred eighty-five patients (44.2%) came for follow-up at 3 years. The actual subjective and objective success rates were 89.7% and 99.9% at 3 years follow-up, respectively. With imputation, the 3-year subjective and objective success rates were 86.9% and 97.4%, respectively.
CONCLUSIONS: The TVT-O is effective in treating female SUI with minimal complications.
Use of the Gynecare Prolift system in surgery for pelvic organ prolapse: 1-year outcome

Vaiyapuri GR, Han HC, Lee LC, Tseng LA, Wong HF

Int Urogynecol J, 2011 Jul;22(7):869-77.
PMID: 21479713 DOI: 10.1007/s00192-011-1400-9

INTRODUCTION AND HYPOTHESIS: This retrospective study reports the 1-year outcome in women who underwent mesh-augmented Prolift surgery performed from 2006 to 2008. There were a total of 254 patients, with 128, 106 and 20 patients receiving total, anterior and posterior Prolift, respectively.
METHODS: Incidence of thigh pain was lower in 2008 compared to 2006 and 2007 (p < 0.0001). The percentage of patients requiring blood transfusions (p = 0.09), duration of IDC ≥ 7 days (p = 0.27), wound dehiscence and re-operation rate were lower in 2008 in contrast to 2006 and 2007 (p = 0.43). Only 209 patients (82.3%) were available for review at 1 year. There were two (1.0%) cases of recurrent vault prolapse.
RESULTS: The subjective and objective cure rates at 1 year after this mesh implant surgery in 2006, 2007 and 2008 were 92.1% and 92.1%; 97.0% and 92.4% and 100% and 97%, respectively. The mesh erosion rate was remarkably lower in 2008 as compared to 2007 and 2006 (p < 0.001).
CONCLUSIONS: This synthetic mesh-augmented implant surgery is effective and safe, and surgical outcome appears related to the learning curve of the surgeon.
Fulltext Forensic profiling of non-volatile organic compounds in soil using ultra-performance liquid chromatography: a pilot study

Lee LC, Ishak AA, Nai Eyan AA, Zakaria AF, Kharudin NS, Noor NAM

Forensic Sci Res, 2022;7(4):761-773.
PMID: 36817254 DOI: 10.1080/20961790.2021.1899407

Soil is of particular interest to the forensic community because it can be used as valuable associative evidence to link a suspect to a victim or a crime scene. Liquid chromatography is a powerful analytical tool for organic compound analysis. Recently, high-performance liquid chromatography (HPLC) has proven to be an efficient method for forensic soil analysis, especially in discriminating soils from proximity locations. However, ultra-performance liquid chromatography (UPLC), which is much more sensitive than HPLC, has never been explored in this context. This study proposed a UPLC method for profiling non-volatile organic compounds in three Malaysian soils (red, brown and yellowish-brown soils). The three soils were analysed separately to assess the effects of individual chromatographic parameters: (a) elution programme (isocratic vs. two gradient programmes); (b) flow rate (0.1 vs. 0.2 mL/min); (c) extraction solvent (acetonitrile vs. methanol) and (d) detection wavelength (230 vs. 254 nm). The injection volume and total run time were set to 5 µL and 35 min, respectively. Consequently, each soil sample gave 24 different chromatograms. Results showed that the most desirable chromatographic parameters were (a) isocratic elution; (b) flow rate at 0.2 mL/min and (c) acetonitrile extraction solvent. The proposed UPLC system is expected to be a feasible method for profiling non-volatile organic compounds in soil, and is more chemical-efficient than a comparable HPLC system.
Fulltext Retrospective study of transobturator polypropylene mesh kit for the management of pelvic organ prolapse

Vaiyapuri GR, Han HC, Lee LC, Tseng AL, Wong HF

Singapore Med J, 2012 Oct;53(10):664-70.
PMID: 23112018

This retrospective study assessed the surgical outcomes of patients for whom the transobturator polypropylene mesh kit was used for the management of pelvic organ prolapse (Gynecare Prolift) in a tertiary urogynaecological centre in Singapore from January 1, 2006 to December 31, 2007.
First record of the fungal genus Neodevriesia Quaedvl. & Crous (Ascomycota, Dothideomycetes, Neodevriesiaceae) isolated from scleractinian corals of Perhentian Islands, Malaysia

Lee LC, Rizman-Idid M, Alias SA, Palaniveloo K, Gu H

Biodivers Data J, 2022;10:e81533.
PMID: 36761577 DOI: 10.3897/BDJ.10.e81533

Fungal species members of the genus Neodevriesia have been known to occur in marine environments. This report documents the first record of the fungal genus Neodevriesia isolated from scleractinian corals. Three isolated strains were identified from a phylogenetic tree that was constructed, based on the nuclear ribosomal internal transcribed spacer and partial large subunit (ITS + LSU) DNA sequences. Isolates were closely related to both Neodevriesiashakazului (Crous) Crous and Neodevriesiaqueenslandica (Crous, R.G. Shivas & McTaggart) Crous, but formed a distinct clade with strong support that implies a potentially genetic variant of a known species or even a novel species. These findings contribute to the fungal diversity checklist in Malaysia and knowledge about marine fungi associated with scleractinian corals.
Fulltext Comparing baseline correction algorithms in discriminating brownish soils from five proximity locations based on UPLC and PLS-DA methods

Ahmad MAB, Lee LC, Mohd Rosdi NAN, Abd Hamid NB, Ishak AA, Sino H

Forensic Sci Res, 2023 Dec;8(4):313-320.
PMID: 38405627 DOI: 10.1093/fsr/owad045

Soil is commonly collected from an outdoor crime scene, and thus it is helpful in linking a suspect and a victim to a crime scene. The chemical profiles of soils can be acquired via chemical instruments such as Ultra-Performance Liquid Chromatography (UPLC). However, the UPLC chromatogram often interferes with an unstable baseline. In this paper, we compared the performance of five baseline correction (BC) algorithms, i.e. asymmetric least squares (AsLS), fill peak, iterative restricted least squares, median window (MW), and modified polynomial fitting, in discriminating 30 chromatograms of brownish soils by five locations of origin, i.e. PP, HK, KU, BL, and KB. The performances of the preprocessed sub-datasets were first visually inspected through the mean chromatograms and then further explored via scores plots of principal component analysis (PCA). Eventually, the predictive performances of the partial least squares-discriminant analysis (PLS-DA) models estimated from 1 000 pairs of training and testing samples (i.e. prepared via iterative random resampling split at 75:25) were studied to identify the best BC method. Mean raw chromatograms of the 10 soil samples were different from each other, with evident fluctuated baselines. AsLS and MW corrected chromatograms demonstrated the most significant improvement compared with the raw counterpart. Meanwhile, the scores plot of PCA revealed that most of the sub-datasets produced three separate clusters. Then, the sub-datasets were modelled via the PLS-DA technique. MW emerged as the excellent BC method based on the mean prediction accuracy estimated using 1 000 pairs of training and testing samples. In conclusion, MW outperformed the other BC methods in correcting the UPLC data of soil.
KEY POINTS: UPLC data of soil interfere with baseline drifts.BC can improve the quality of the pixel-level UPLC data.MW emerges as the most desired algorithm in improving the quality of UPLC data of soil.
A Critical Review of Soil Sampling and Data Analysis Strategies for Source Tracing of Soil in Forensic Investigations

Mohd Rosdi NANB, Abd Hamid N, Mohd Ali SF, Sino H, Lee LC

Crit Rev Anal Chem, 2024;54(8):3520-3558.
PMID: 37672265 DOI: 10.1080/10408347.2023.2253473

Soil is one type of Earth material demonstrating a wide range of physical, chemical, and biological properties. As the compositional profile of soil is a product of interaction between numerous abiotic and biotic components, it tends to be unique by its geographic origin. Hence, soil is paramount for predicting source or origin in forensic provenance and intelligence, food provenance, biosecurity, and archaeology. In the context of forensic investigation, source tracing of soil could be executed by a comparison or provenance analysis. Soil compositional fingerprints acquired using analytical methods must be carefully interpreted via suitable mathematical and statistical tools since multiple sources can contribute to the variability of soil other than its provenance. This article reviews recent trends in soil sampling and data interpretation strategies proposed for source tracing of soil evidence. Performances of soil provenance indicators are also described. Then, perspectives on possible research directions guiding forensic soil provenance are proposed. This timely critical review reveals the essential idea and gap in forensic soil provenance for stimulating the development of more efficient and effective provenance strategies.
Fulltext Improved Nylon 6,6 Nanofiber Membrane in A Tilted Panel Filtration System for Fouling Control in Microalgae Harvesting

Mat Nawi NI, Abd Halim NS, Lee LC, Wirzal MDH, Bilad MR, Nordin NAH, et al.

Polymers (Basel), 2020 Jan 21;12(2).
PMID: 31973178 DOI: 10.3390/polym12020252

The competitiveness of algae as biofuel feedstock leads to the growth of membrane filtration as one of promising technologies for algae harvesting. Nanofiber membrane (NFM) was found to be efficient for microalgae harvesting via membrane filtration, but it is highly limited by its weak mechanical strength. The main objective of this study is to enhance the applicability of nylon 6,6 NFM for microalgae filtration by optimizing the operational parameters and applying solvent vapor treatment to improve its mechanical strength. The relaxation period and filtration cycle could be optimized to improve the hydraulic performance. For a cycle of 5 min., relaxation period of ≤2 min shows the highest steady-state permeability of 365 ± 14.14 L m-2 h-1 bar-1, while for 10 min cycle, 3 min. of relaxation period was found optimum that yields permeability of 402 ± 34.47 L m-2 h-1 bar-1. The treated nylon 6,6 NFM was also used to study the effect of aeration rate. It is confirmed that the aeration rate enhances the steady-state performance for both intermittent and continuous mode of aeration. Remarkably, intermittent aeration shows 7% better permeability than the full aeration for all tested condition, which is beneficial for reducing the total energy consumption.
Fulltext Awareness, expectation and satisfaction towards ward pharmacy services among patients in medical wards: a multi-centre study in Perak, Malaysia

Ng CB, Chang CT, Ong SY, Mahmud M, Lee LC, Chew WY, et al.

BMC Health Serv Res, 2021 Oct 29;21(1):1175.
PMID: 34711230 DOI: 10.1186/s12913-021-07185-7

BACKGROUND: Patient's awareness and satisfaction towards ward pharmacy services may influence perception towards effectiveness and safety of drugs, affecting medication adherence and clinical outcome. Nevertheless, studies on local ward pharmacy services were lacking. This study evaluated awareness, expectation and satisfaction of ward pharmacy services among patients in medical wards and determined their association with demographic characteristics.
METHODS: This was a cross-sectional study using self-administered questionnaire conducted in medical wards of fourteen Perak state public hospitals from September to October 2020. In-patients aged ≥18 years old were included. The validated questionnaire had four domains. The student's t-test, one-way analysis of variance (ANOVA) and multiple linear regression were was employed to evaluate the association between patients' demographic characteristics with their awareness, expectation and satisfaction towards ward pharmacy services.
RESULTS: 467 patients agreed to participate (response rate = 83.8%) but only 441 were analysed. The mean age of the patients was 54.9 years. Majority was male (56.2%), Malay (77.3%), with secondary education (62.9%), rural resident (57.1%) and reported good medication adherence (61.6%). The mean awareness score was 49.6 out of 60. Patients were least aware about drug-drug interaction (3.85 ± 1.15) and proper storage of medications (3.98 ± 1.06). Elderly patients (β = - 2.82, P

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