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Fulltext Scientific misconduct encountered by APAME journals: an online survey

Looi LM, Wong LX, Koh CC

Malays J Pathol, 2015 Dec;37(3):213-8.
PMID: 26712665 MyJurnal

In June 2015, invitations were sent by email to 151 APAME journals to participate in an online survey with an objective of gaining insight into the common publication misconduct encountered by APAME editors. The survey, conducted through SurveyMonkey over a 20-day-period, comprised 10 questions with expansions to allow anecdotes limited to 400 characters, estimated to take less than 10 minutes to complete. Only one invitation was issued per journal, targeting (in order of priority) editors, editorial board members and editorial staff, and limited by email availability. 54 (36%) journals responded. 98% of respondents held Editor or Editorial Board positions. All respondent journals have editorial policies on publication ethics and 96% provide instructions related to ethics. 45% use anti-plagiarism software to screen manuscripts, the most popular being iThenticate, CrossCheck and Turnitin. Up to 50% of journals had encountered studies without IRB approval. Author misconduct encountered were (in rank order): plagiarism (75%), duplicate publication (58%), unjustified authorship (39%), authorship disputes (33%), data falsification (29%), data/image manipulation (27%), conflict of interest (25%), copyright violation (17%) and breach of confidentiality (10%). Reviewer misconduct encountered were: conflict of interest (19%), plagiarism (17%), obstructive behavior (17%), abusive language (13%) and breach of confidentiality (13%). Notwithstanding the limitations of the survey and the response rate, a few insights have been gained: (1) the need for strengthening the ethical culture of researchers/authors and reviewers, (2) anti-plagiarism software can improve plagiarism detection by about 15%, and (3) the need for technical support to detect plagiarism, duplicate publication and image manipulation.
Fulltext Response: Scientific misconduct encountered by APAME journals: insight?

Looi LM, Wong LX, Koh CC

Malays J Pathol, 2016 Apr;38(1):73.
PMID: 27126670
Process Optimisation of Ultrasound-Assisted Extraction of Oligosaccharides from Coconut Husk

Tang SL, Hii SL, Koh CC

ScientificWorldJournal, 2023;2023:9427831.
PMID: 37096240 DOI: 10.1155/2023/9427831

A fractional factorial design was used to investigate the ultrasound-assisted extraction (UAE) of oligosaccharides from coconut husk, an agroindustry by-product. The effects of five key influencing parameters (X 1, incubation temperature; X 2, extraction duration; X 3, ultrasonicator power; X 4, NaOH concentration; X 5, solid-to-liquid ratio) were studied. Total carbohydrate content (TC), total reducing sugar (TRS), and degree of polymerisation (DP) were the dependent variables. The optimal extraction condition was attained when oligosaccharides with a desired DP of 3.72 were extracted when the coconut husk in a liquid-to-solid ratio of 127 mL/g was treated with 1.05 percent (w/v) of NaOH solution at an incubation temperature of 30.4°C for 5 min using an ultrasonicator power of 248 W. The optimised parameters for oligosaccharide extraction from coconut husk reported in this study could be useful for the effective isolation of these compounds for prebiotic research.
Fulltext Isolation of Prebiotics from Artocarpus integer's Seed

Wong JC, Hii SL, Koh CC

Int J Food Sci, 2021;2021:9940078.
PMID: 34336997 DOI: 10.1155/2021/9940078

There has been a high amount of attention given to prebiotics due to their significant physiological function and health benefits. Prebiotics contain nondigestible compounds that allow specific changes, both in the growth and in the activity of bacteria in the host gastrointestinal tract, that provide benefits upon the host by promoting a healthy digestive system and preventing disease. This study aims at investigating the potential prebiotic activity of bioactive compounds extracted from the seeds of an underutilized indigenous plant Artocarpus integer (A. integer). The optimum microwave-assisted extraction conditions were a microwave power of 1500 W, extraction time of 180 s, and solvent-to-sample ratio of 1000 : 1. The maximum amount of the total carbohydrate content extracted from A. integer was 787 mg/L. The percentage hydrolysis levels of A. integer extract in gastric juice at pH 1, 2, 3, and 4 were 6.14%, 7.12%, 8.98%, and 10.23%, respectively. For enzymatic digestion, the percentage of hydrolysis was 0.16% at pH 7. A. integer extract was found to support the growth of probiotics such as L. acidophilus and L. casei. After 72 hours of incubation, L. acidophilus achieved 6.96 log10 CFU, whereas L. casei reached 8.33 log10 CFU. The study makes an important contribution to the development of the use of Sarawakian underutilized plants and to the identification of new sources of prebiotic materials to be used in food.
Fulltext Correlation of p16INK4a immunoexpression and human papillomavirus (HPV) detected by in-situ hybridization in cervical squamous neoplasia

Cheah PL, Koh CC, Nazarina AR, Teoh KH, Looi LM

Malays J Pathol, 2016 Apr;38(1):33-8.
PMID: 27126662 MyJurnal

Persistence and eventual integration of high-risk HPV (hrHPV) into the cervical cell is crucial to the progression of cervical neoplasia and it would be beneficial to morphologically identify this transformation in routine surgical pathology practice. Increased p16(INK4a) (p16) expression is a downstream event following HPV E7 binding to pRB. A study was conducted to assess the correlation between hrHPV detection using a commercial in-situ hybridization assay (Ventana INFORM HPV ISH) and p16 immunoexpression (CINtec Histology Kit) in cervical squamous intraepithelial lesions and squamous carcinoma. 27 formalin-fixed, paraffin-embedded cervical low-grade squamous intraepithelial lesions (LSIL), 21 high-grade squamous intraepithelial lesions (HSIL) and 51 squamous carcinoma (SCC) were interrogated. hrHPV was significantly more frequent in HSIL (76.2%) and SCC (88.2%) compared to LSIL(37.0%). p16 expression was similarly more frequent in HSIL (95.2%) and SCC (90.2%) compared to LSIL(3.7%). That the rates of hrHPV when compared with p16 expression were almost equivalent in HSIL and SCC while p16 was expressed in only 1 of the 10 LSIL with hrHPV, are expected considering the likelihood that transformation has occurred in HSIL and SCC but does not occur in majority of LSIL.
Cyclooxygenase-2 (COX2) expression in adenocarcinoma surpasses that of squamous cell carcinoma in the uterine cervix

Marutha Muthu AK, Cheah PL, Koh CC, Chew MF, Toh YF, Looi LM

Malays J Pathol, 2017 Dec;39(3):251-255.
PMID: 29279587 MyJurnal

Over the years, adenocarcinoma (ADC), which has a worse prognosis than squamous cell carcinoma (SCC) of the cervix, has shown an increasing trend. Cyclooxygenase-2 (COX2) expression which has been associated with worse prognosis in several solid cancers was studied for its association with SCC and ADC of the cervix. 35 histologically re-confirmed SCC and 35 ADC were immunohistochemically stained for COX2 using a mouse monoclonal antibody to COX2 (1:100; Dako: Clone CX-294) on a Ventana Benchmark XT. The histoscore was computed as intensity of staining, semi-quantitated on a scale of 0-3 with 0 = negative, 1 = weak, 2 = moderate and 3 = strong staining intensity; multiplied by percentage of immunopositivity on a scale of 0-4 with 0 = <1%, 1 = 1-25%, 2 = 26-50%, 3 = 51-75% and 4 = ≥75% of immunopositive tumour cells. Histoscore 1-3/12 was considered as low and ≥4/12 as high COX2 expression. SCC affected Chinese more than Malays, while Malays had more ADC (p = 0.032). Mean age at presentation of SCC (57.5 years) was about a decade later than ADC at 47.9 years (p = 0.002). 30/35 (85.7%) of SCC and 34/35 (97.1%) of ADC expressed COX2. Histoscores of ADC (median = 4.0, IQR = 3.0-6.0) was significantly higher (p = 0.014) than those of SCC (median = 3.0, IQR = 2.0-3.0). High histoscores (≥4/12) were more frequent in ADC (55.9%) compared with SCC (26.7%) (p = 0.018), implicating COX2, either directly or indirectly, as a possible player in influencing the poorer outcome of ADC compared with SCC.
Screening for microsatellite instability in colorectal carcinoma: Practical utility of immunohistochemistry and PCR with fragment analysis in a diagnostic histopathology setting

Cheah PL, Li J, Looi LM, Koh CC, Lau TP, Chang SW, et al.

Malays J Pathol, 2019 Aug;41(2):91-100.
PMID: 31427545

Since 2014, the National Comprehensive Cancer Network (NCCN) has recommended that colorectal carcinoma (CRC) be universally tested for high microsatellite instability (MSI-H) which is present in 15% of such cancers. Fidelity of resultant microsatellites during DNA replication is contingent upon an intact mismatch repair (MMR) system and lack of fidelity can result in tumourigenesis. Prior to commencing routine screening for MSI-H, we assessed two commonly used methods, immunohistochemical (IHC) determination of loss of MMR gene products viz MLH1, MSH2, MSH6 and PMS2 against PCR amplification and subsequent fragment analysis of microsatellite markers, BAT25, BAT26, D2S123, D5S346 and D17S250 (Bethesda markers) in 73 unselected primary CRC. 15.1% (11/73) were categorized as MSI-H while deficient MMR (dMMR) was detected in 16.4% (12/73). Of the dMMR, 66.7% (8/12) were classified MSI-H, while 33.3% (4/12) were microsatellite stable/low microsatellite instability (MSS/MSI-L). Of the proficient MMR (pMMR), 95.1% (58/61) were MSS/MSI-L and 4.9% (3/61) were MSI-H. The κ value of 0.639 (standard error =0.125; p = 0.000) indicated substantial agreement between detection of loss of DNA mismatch repair using immunohistochemistry and the detection of downstream microsatellite instability using PCR. After consideration of advantages and shortcomings of both methods, it is our opinion that the choice of preferred technique for MSI analysis would depend on the type of laboratory carrying out the testing.
FISHing for 1p19q codel in oligodendroglioma

Kong PL, Cheah PL, Mun KS, Chiew SF, Lau TP, Koh CC, et al.

Malays J Pathol, 2020 Dec;42(3):369-376.
PMID: 33361717

Together with isocitrate dehydrogenase (IDH) mutation, co-deletion of 1p19q (1p19q codel) is a prerequisite for diagnosis of oligodendroglioma, making it imperative that histopathology laboratories introduce testing for 1p19q codel. To date there is still no consensus reference range and cut-offs that confirm deletion of 1p or 19q. We embarked on determining our reference range in 11 formalinfixed, paraffin-embedded non-neoplastic brain tissue using fluorescence in situ hybridisation (FISH) with the Vysis 1p36/1q25 and 19q13/19p13 FISH Probe Kit (Abbott Molecular Inc., USA). At same time we attempted to validate our methodology in 13 histologically-confirmed IDH-mutant oligodendrogliomas. For 1p, percentage cells with deletion (range=8-23%; mean±SD = 15.73±5.50%) and target: control (1p36:1q25) ratio (range = 0.89-0.96; mean±SD = 0.92±0.03) in non-neoplastic brain, differed significantly (p<0.000) from oligodendroglioma (percentage cells with deletion: range = 49-100%; mean±SD = 82.46±15.21%; target:control ratio range:0.50-0.76; mean±SD = 0.59±0.08). For 19q, percentage cells with deletion (range = 7-20%; mean±SD = 12.00±3.49%) and target:control (19q13/19p13) ratio (range:0.90-0.97; mean±SD = 0.94±0.02) in non-neoplastic brain also differed significantly from oligodendroglioma (percentage cells with deletion: range = 45-100%; mean±SD = 82.62±18.13%; target:control ratio range:0.50-0.78; mean±SD = 0.59±0.09). Using recommended calculation method, for diagnosis of 1p deletion, percentage of cells showing deletion should be >32-33% and/or target:control ratio <0.83. For 19q, percentage of cells showing deletion should be >22% and target:control ratio <0.88. Using these cut-offs all 13 oligodendroglioma demonstrated 1p19q codel.
Esophageal squamous cell carcinomas in a Malaysian cohort show a lack of association with human papillomavirus

Cheah PL, Koh CC, Khang TF, Goh KL, Lau PC, Chin KF, et al.

J Dig Dis, 2018 May;19(5):272-278.
PMID: 29722130 DOI: 10.1111/1751-2980.12605

OBJECTIVE: With an age-standardized incidence rate of 2 per 100 000, esophageal cancer is not common among Malaysians, but they are nevertheless important due to its poor prognosis. The study is to clarify whether the human papillomavirus (HPV) is associated with esophageal cancer in Malaysians as there has been no report to date on this in Malaysians and other South East Asians.
METHODS: Altogether 67 esophageal squamous cell carcinomas histologically diagnosed between 1 January 2004 and 31 December 2014 at the Department of Pathology, University of Malaya Medical Center, Malaysia were considered for HPV analysis using two commercially available methods, polymerase chain reaction with flow-through hybridization (21 HPV GenoArray Diagnostic Kit) and multiplex real-time polymerase chain reaction (Anyplex II HPV28 Detection). The DNA amplifiability of the formalin-fixed, paraffin-embedded tumor was checked by amplification of a 268 bp segment of the human β-globin gene (GH20/PC04) prior to HPV detection.
RESULTS: HPV detection was finally carried out in 51 patients. HPV16 was detected in the moderately differentiated, stage IV lower esophageal tumor of a 32-year-old Malaysian-born Chinese woman by both methods. Except for a predilection for Indians, the clinical characteristics of esophageal squamous cell carcinomas in this Malaysian cohort were generally similar to those of other populations.
CONCLUSION: It appears that HPV is rare and an unlikely oncovirus in esophageal squamous cell carcinomas of Malaysians.