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Maurice Ling

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I am interested in life itself. My approach towards understanding the many mysteries of life is through the use of bioinformatics and computational biology - the interdisciplinary area of biology, computer science, and statistics.

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Papers by Maurice Ling

A computational model to derive certain human cognitive mind functions

The aim of this paper is to understand the human mind functions such that we can simulate them in... more The aim of this paper is to understand the human mind functions such that we can simulate them into a computational model for making cognitive systems more intelligent. We then present this model with formulae using a top-down approach. We propose that the human thought process, which is the fundamental unit for the human mind and all the different emotions coming from it, can be implemented as a computational model to a reasonable extent. Furthermore, we argue that our model has the ability to derive certain mind functions such as dreams, distraction, etc. The model utilizes a top-down approach for understanding the factors involved in the thought process while explaining the factors involved. We also propose interpretations of certain mind functions such as dreams, distraction, etc. We also present the formulae's application against certain hypothetical small sets of data which explains how this model identifies certain cognitive mind functions. The authors are intending to make continuous improvements in this framework as more scientific advances happen in the understanding of the human cognitive functions.

Sequence Composition

Elsevier eBooks, 2019

Science/Education Portraits VII: Statistical Methods Used in 1081 Papers Published in Year 2020 Across 12 Life Science Journals Under BioMed Central

Acta Scientific Nutritional Health, Feb 26, 2021

Statistics is an integral part of biology and is required for all undergraduate life science curr... more Statistics is an integral part of biology and is required for all undergraduate life science curriculum. However, are biology students trained in statistical skills required in the field? Despite studies listing various commonly statistical methods used in specialised branches of life sciences; such as, immunology and tropical biology; there is a lack of study on the common statistical methods used in life science in general. Here, we examine 1081 articles across 12 life sciences journals under BioMed Central, published in 2020, to elucidate the common statistical methods used in current life science research, as a basis to recommend an updated syllabus to all institutions that educate biologists. 72.7% of the examined articles contains identifiable statistical methods and a total of 2431 instances were identified. Our findings show that the first 3 out of 15 categories of methods; parametric comparison of means (25.38% of instances), correlation/regression (18.88%), and post-hoc test (10.32%); accounts for 54.59% of the instances. In terms of individual methods, the top 8 methods account for 52.04% of the instances-(a) t-test (13.00%), (b) ANOVA (12.26%), (c) unspecified (likely to be Pearson's correlation) and Pearson's correlation (9.79%), (d) Benjamini and Hochberg's False Discovery Rate (FDR) (4.77%), (e) Tukey's HSD (4.36%), (f) Kruskal-Wallis Test (2.96%), (g) Mann-Whitney U Test (2.80%), and (h) Chi Square Test (2.10%). These findings may have an impact on future curriculum design.

Characterization of Transcriptional Activities

Transcription is the first stage of gene expression, leading to the eventual determination the pr... more Transcription is the first stage of gene expression, leading to the eventual determination the protein abundance and affecting metabolism. Hence, there is a need to measure and characterize transcriptional activities accurately. This article discusses the experimental techniques to characterizing transcriptional activities from a single-gene approach (quantitative PCR) to highthroughput methods (microarray technology and next generation sequencing). Computational approaches to predicting relative transcript abundance from sequence features and gene coexpression network will be described. As a proxy to protein / enzyme abundance, transcriptional activities are critical in developing simulatable biochemical models, which can then to test biological hypotheses before laboratory experimentation.

ChatGPT (Feb 13 Version) is a Chinese Room

arXiv (Cornell University), Feb 18, 2023

ChatGPT has gained both positive and negative publicity after reports suggesting that it is able ... more ChatGPT has gained both positive and negative publicity after reports suggesting that it is able to pass various professional and licensing examinations. This suggests that ChatGPT may pass Turing Test in the near future. However, a computer program that passing Turing Test can either mean that it is a Chinese Room or artificially conscious. Hence, the question of whether the current state of ChatGPT is more of a Chinese Room or approaching artificial consciousness remains. Here, I demonstrate that the current version of ChatGPT (Feb 13 version) is a Chinese Room. Despite potential evidence of cognitive connections, ChatGPT exhibits critical errors in causal reasoning. At the same time, I demonstrate that ChatGPT can generate all possible categorical responses to the same question and response with erroneous examples; thus, questioning its utility as a learning tool. I also show that ChatGPT is capable of artificial hallucination, which is defined as generating confidently wrong replies. It is likely that errors in causal reasoning leads to hallucinations. More critically, ChatGPT generates false references to mimic real publications. Therefore, its utility is cautioned.

Low Classification Accuracy by Logistic Regression, Support Vector Classifier,and Multi-Layer Perceptron, But Not Decision Tree, on Random Attributesfrom Hadamard Matrix

EC Clinical and Medical Case Reports, Nov 28, 2020

The use of machine learning classifiers is increasing with evidence of overtaking human judgement... more The use of machine learning classifiers is increasing with evidence of overtaking human judgement. This can be risky if workings and implications of machine learning classifiers remain a black box. Here, a case where a balanced and algorithmically generated data set, Hadamard matrix, classifies poorer than random using logistic regression (accuracy < 17.4%), support vector classifier (accuracy < 23.4%) and in most cases of multi-layer perceptron (accuracy < 27.9%) but not in decision tree (accuracy > 77.3%); despite perfect (100%) internal classification accuracy for both support vector classifier and multi-layer perceptron; is reported. This suggests a systematic and yet currently unexplained source of error.

Consistency between Saccharomyces cerevisiae S288C Genome Scale Models (iND750 and iMM904)

Acta scientific microbiology, Mar 1, 2023

Saccharomyces cerevisiae is an important experimental organism for industrial and scientific rese... more Saccharomyces cerevisiae is an important experimental organism for industrial and scientific research with S. cerevisiae S288C as the first eukaryote genome sequenced. Genome-scale metabolic models (GSMs) are computational tools to explore metabolic engineering requirements. Currently, there are 2 major GSMs of S. cerevisiae S288C, iND750 and iMM904, which raises the question of whether they are consistent to each other. Here, we compare iND750 and iMM904 by examining the fluxomic changes resulting from single reaction knockouts. 40.5% to 50.3% (n = 637) of the reactions are common in both GSMs. Of which, 64 (10.0% of common reactions, or between 4.1% and 5.2% of the total reactions in each GSM) reaction knockouts resulted in significant fluxomic changes. This is significantly lower (t =-15.882, df = 30, p-value = 3.82E-16) from expected using randomization test, suggesting that iND750 and iMM904 are likely to be consistent with each other from the perspective of common reactions.

Simulation Suggests that One-Off Simple Supplementation from the Wildinto Captive Population May Not Increase Captive Genetic Diversity

EC Veterinary Science, Jun 30, 2021

Coffee as a Potential Nutraceutical

EC Nutrition, Feb 27, 2021

Global coffee production nearly doubled over the last decade, making coffee one of the most popul... more Global coffee production nearly doubled over the last decade, making coffee one of the most popular beverage in current society. However, recent consumer studies suggest concerns of potential health detriments from regular coffee consumption. Given its popularity, any health benefits or detriment can have substantial public health impact. Here, we examined several potential benefits and risks with regards to coffee drinking. Evidence is non-conclusive in several cases and warrants further studies. Despite so, there is likely more health benefits than harm, especially when moderation is applied. Hence, we are in the view that coffee is a potential nutraceutical when consumed in moderation and with adequate hydration.

Back-of-the-Envelope Guide (A Tutorial) to 10 Intracellular Landscapes

MOJ proteomics & bioinformatics, Feb 6, 2018

Copy number landscape 4 often refers to copy number variation (CNV), which is the differences bet... more Copy number landscape 4 often refers to copy number variation (CNV), which is the differences between the numbers of copies of one or more nucleotides within individuals in the same species. The repeats can range from a few bases; such as, polyglutamine repeats; 5 to entire genes; such as alpha-amylase 6 and neutrophil cytosolic factor 1. 7 CNV can be a result when sections of a genome are duplicated/ repeated or deleted; 8,9 which exists in both higher eukaryotes, such as humans, 10 and prokaryotes, such as Escherichia coli; 11 and is implicated in several disease phenotypes. 8 For example, CNV in neutrophil cytosolic factor 1 has been implicated in rheumatoid arthritis 7 and CNV in protease has been implicated in anthropogenic toxins in arthropods 12 as differences in copy number may have an

Resistance Maintained in Digital Organisms despite Guanine/Cytosine-Based Fitness Cost and Extended De-Selection: Implications to Microbial Antibiotics Resistance

arXiv (Cornell University), Feb 19, 2023

Two Cellular Resource Based Models Linking Growth and Parts Characteristics Aids the Study and Optimization of Synthetic Gene Circuits

arXiv (Cornell University), Feb 19, 2023

A major challenge in synthetic genetic circuit development is the inter-dependency between hetero... more A major challenge in synthetic genetic circuit development is the inter-dependency between heterologous gene expressions by circuits and host's growth rate. Increasing heterologous gene expression increases burden to the host, resulting in host growth reduction; which reduces overall heterologous protein abundance. Hence, it is difficult to design predictable genetic circuits. Here, we develop two biophysical models; one for promoter, another for RBS; to correlate heterologous gene expression and growth reduction. We model cellular resource allocation in E. coli to describe the burden, as growth reduction, caused by genetic circuits. To facilitate their uses in genetic circuit design, inputs to the model are common characteristics of biological parts [e.g. relative promoter strength (RPU) and relative ribosome binding sites strength (RRU)]. The models suggest that E. coli 's growth rate reduces linearly with increasing RPU/RRU of the genetic circuits; thus, providing 2 handy models taking parts characteristics as input to estimate growth rate reduction for fine tuning genetic circuit design in silico prior to construction. Our promoter model correlates well with experiments using various genetic circuits, both single and double expression cassettes, up to a relative promoter unit of 3.7 with a 60% growth rate reduction (average R 2 ∼0.9).

A 5-Year Systematic Review (2018 to 2022) on The Effectiveness of Mediterranean Diet in Preventing Alzheimer’s Disease

Acta Scientific Nutritional Health, Feb 1, 2023

Alzheimer's disease (AD) is an age-related neuronal disorder characterized by abnormal levels of ... more Alzheimer's disease (AD) is an age-related neuronal disorder characterized by abnormal levels of proteins, beta amyloid (Aβ) and tau, resulting in gradual loss of cognitive functions due to impaired network of neurons in the brain. Past literature has proposed dietary interventions through administration of Mediterranean Diet (MD) as a solution to prevent AD development. A systematic review on the effectiveness of MD in preventing AD is executed up to July 3, 2022, using PubMed as source database within the last 5 years between 2018 to 2022. 131 articles were identified, and 26 articles were included in this review. After analysing the articles, 5 themes were identified to examine the effectiveness of MD: namely, (a) MD adherence and AD risk (b) MD and AD pathological development, (c) MD and cognitive health (d) Mediterranean-DASH Intervention for Neurodegenerative Delay (MIND) diet, and (e) Diet-microbe interaction. MD adherence is a vital factor in achieving successful dietary intervention. Various covariates and demographics affect adherence level. Differing evidence from literature discuss MD's efficacy in preventing AD. MD is concluded to be effective to a certain extent in preventing Alzheimer's disease due to various factors such as adherence levels, demographics etc and further longitudinal and randomised control trials (RCT) are warranted.

Development of a Basic Chemistry Conversational Corpus

Acta Scientific Nutritional Health, Feb 1, 2023

Chatbot technology can be an important tool and supplement to education, leading to explorations ... more Chatbot technology can be an important tool and supplement to education, leading to explorations in this area. Corpus-based chatbot building has a relatively low entry barrier as it only requires a relevant corpus to train a chatbot engine. The corpus is a set of human-readable questions and answers and may be an amalgamation of existing corpora. However, a suitable chemistry-based chatbot corpus catering for a freshman general chemistry course addressing inorganic and physical chemistry has not been developed. In this study, we present a basic chemistry conversational corpus consisting of 998 pairs of questions and answers, focused on a freshman general chemistry course addressing inorganic and physical chemistry. Ten human raters evaluated the responses of a chatbot trained on the corpus and suggests that the corpus resulted in better response than random (t = 17.4, p-value = 1.86E-53). However, only 20 of the 50 test questions show better responses compared to random (difference in mean score ≥ 1.9, paired t-test p-value ≤ 0.0324), suggesting that the corpus provides better responses to certain questions rather than overall better responses, with questions related to definitions and computational procedures answered more accurately. Hence, this provides a baseline for future corpora development.

Survey of Antisense Transcription

Elsevier eBooks, 2019

Reconstruction of Protein-Protein Interaction Pathways by Mining Subject-Verb-Objects Intermediates

Springer eBooks, Sep 18, 2007

The exponential increase in publication rate of new articles is limiting access of researchers to... more The exponential increase in publication rate of new articles is limiting access of researchers to relevant literature. This has prompted the use of text mining tools to extract key biological information. Previous studies have reported extensive modification of existing generic text processors to process biological text. However, this requirement for modification had not been examined. In this study, we have constructed Muscorian, using MontyLingua, a generic text processor. It uses a two-layered generalization-specialization paradigm previously proposed where text was generically processed to a suitable intermediate format before domain-specific data extraction techniques are applied at the specialization layer. Evaluation using a corpus and experts indicated 86-90% precision and approximately 30% recall in extracting proteinprotein interactions, which was comparable to previous studies using either specialized biological text processing tools or modified existing tools. Our study had also demonstrated the flexibility of the two-layered generalizationspecialization paradigm by using the same generalization layer for two specialized information extraction tasks.

Science/Education Portraits III: Perceived Prevalence of Data Fabrication and/or Falsification in Research

Advances in biotechnology & microbiology, Dec 7, 2018

Data fabrication or falsification are considered as "deadly sins" with high impact, above plagiar... more Data fabrication or falsification are considered as "deadly sins" with high impact, above plagiarism, on scientific truth and public confidence. What is the estimated prevalence of data fabrication or falsification? A meta-survey published a decade ago estimated 14.12% of respondents having knowledge of a colleague who fabricated or falsified research data, or who altered or modified research data. This mini-review updates this meta-survey by examining surveys from 2009 to 2018. Results suggests that 17.7% of responses indicated knowledge of fellow scientist's acts of data fabrication or data falsification. This is consistent with that of a decade ago, which suggests a critical need to address the worst type of research misconduct-data fabrication and falsification.

Grand challenges in bioinformatics education and training

Nature Biotechnology

Science/Education Portraits VIII: Duoethnography of First-Generation Bioscience Undergraduates in a Private Education Institute in Singapore

Acta Scientific Microbiology

It has been well-recognized that first-generation undergraduate faces unique challenges. This is ... more It has been well-recognized that first-generation undergraduate faces unique challenges. This is made worse by being a firstgeneration undergraduate in a private education institution (PEI), commonly characterized by lesser resources as compared to public education institution, during COVID-19 associated social restrictions. Currently, there is no study to on first-generation university undergraduates pursuing their undergraduate education via a PEI in Singapore during this COVID-19 pandemic. In this article, we document the journey, challenges, and triumphs of three first-generation bioscience undergraduates in Singapore pursuing their bachelor's degree in a PEI during the pandemic using duo ethnographical approach. Our analysis suggests that challenges faced by first-generation undergraduate in a PEI in Singapore during COVID-19 associated restrictions can be seen as sum of challenges faced by first-generation undergraduate and challenges faced by in the education sector during COVID-19 associated restrictions; but the resourcefulness, resilience, and adaptability of first-generation undergraduate are also evident.

Of (Biological) Models and Simulations

arXiv (Cornell University), Feb 19, 2023

All models are wrong, but some are useful. Box and Draper [1]. All models are right… Most are use... more

A computational model to derive certain human cognitive mind functions

The aim of this paper is to understand the human mind functions such that we can simulate them in... more The aim of this paper is to understand the human mind functions such that we can simulate them into a computational model for making cognitive systems more intelligent. We then present this model with formulae using a top-down approach. We propose that the human thought process, which is the fundamental unit for the human mind and all the different emotions coming from it, can be implemented as a computational model to a reasonable extent. Furthermore, we argue that our model has the ability to derive certain mind functions such as dreams, distraction, etc. The model utilizes a top-down approach for understanding the factors involved in the thought process while explaining the factors involved. We also propose interpretations of certain mind functions such as dreams, distraction, etc. We also present the formulae's application against certain hypothetical small sets of data which explains how this model identifies certain cognitive mind functions. The authors are intending to make continuous improvements in this framework as more scientific advances happen in the understanding of the human cognitive functions.

Sequence Composition

Elsevier eBooks, 2019

Science/Education Portraits VII: Statistical Methods Used in 1081 Papers Published in Year 2020 Across 12 Life Science Journals Under BioMed Central

Acta Scientific Nutritional Health, Feb 26, 2021

Statistics is an integral part of biology and is required for all undergraduate life science curr... more Statistics is an integral part of biology and is required for all undergraduate life science curriculum. However, are biology students trained in statistical skills required in the field? Despite studies listing various commonly statistical methods used in specialised branches of life sciences; such as, immunology and tropical biology; there is a lack of study on the common statistical methods used in life science in general. Here, we examine 1081 articles across 12 life sciences journals under BioMed Central, published in 2020, to elucidate the common statistical methods used in current life science research, as a basis to recommend an updated syllabus to all institutions that educate biologists. 72.7% of the examined articles contains identifiable statistical methods and a total of 2431 instances were identified. Our findings show that the first 3 out of 15 categories of methods; parametric comparison of means (25.38% of instances), correlation/regression (18.88%), and post-hoc test (10.32%); accounts for 54.59% of the instances. In terms of individual methods, the top 8 methods account for 52.04% of the instances-(a) t-test (13.00%), (b) ANOVA (12.26%), (c) unspecified (likely to be Pearson's correlation) and Pearson's correlation (9.79%), (d) Benjamini and Hochberg's False Discovery Rate (FDR) (4.77%), (e) Tukey's HSD (4.36%), (f) Kruskal-Wallis Test (2.96%), (g) Mann-Whitney U Test (2.80%), and (h) Chi Square Test (2.10%). These findings may have an impact on future curriculum design.

Characterization of Transcriptional Activities

Transcription is the first stage of gene expression, leading to the eventual determination the pr... more Transcription is the first stage of gene expression, leading to the eventual determination the protein abundance and affecting metabolism. Hence, there is a need to measure and characterize transcriptional activities accurately. This article discusses the experimental techniques to characterizing transcriptional activities from a single-gene approach (quantitative PCR) to highthroughput methods (microarray technology and next generation sequencing). Computational approaches to predicting relative transcript abundance from sequence features and gene coexpression network will be described. As a proxy to protein / enzyme abundance, transcriptional activities are critical in developing simulatable biochemical models, which can then to test biological hypotheses before laboratory experimentation.

ChatGPT (Feb 13 Version) is a Chinese Room

arXiv (Cornell University), Feb 18, 2023

ChatGPT has gained both positive and negative publicity after reports suggesting that it is able ... more ChatGPT has gained both positive and negative publicity after reports suggesting that it is able to pass various professional and licensing examinations. This suggests that ChatGPT may pass Turing Test in the near future. However, a computer program that passing Turing Test can either mean that it is a Chinese Room or artificially conscious. Hence, the question of whether the current state of ChatGPT is more of a Chinese Room or approaching artificial consciousness remains. Here, I demonstrate that the current version of ChatGPT (Feb 13 version) is a Chinese Room. Despite potential evidence of cognitive connections, ChatGPT exhibits critical errors in causal reasoning. At the same time, I demonstrate that ChatGPT can generate all possible categorical responses to the same question and response with erroneous examples; thus, questioning its utility as a learning tool. I also show that ChatGPT is capable of artificial hallucination, which is defined as generating confidently wrong replies. It is likely that errors in causal reasoning leads to hallucinations. More critically, ChatGPT generates false references to mimic real publications. Therefore, its utility is cautioned.

Low Classification Accuracy by Logistic Regression, Support Vector Classifier,and Multi-Layer Perceptron, But Not Decision Tree, on Random Attributesfrom Hadamard Matrix

EC Clinical and Medical Case Reports, Nov 28, 2020

The use of machine learning classifiers is increasing with evidence of overtaking human judgement... more The use of machine learning classifiers is increasing with evidence of overtaking human judgement. This can be risky if workings and implications of machine learning classifiers remain a black box. Here, a case where a balanced and algorithmically generated data set, Hadamard matrix, classifies poorer than random using logistic regression (accuracy < 17.4%), support vector classifier (accuracy < 23.4%) and in most cases of multi-layer perceptron (accuracy < 27.9%) but not in decision tree (accuracy > 77.3%); despite perfect (100%) internal classification accuracy for both support vector classifier and multi-layer perceptron; is reported. This suggests a systematic and yet currently unexplained source of error.

Consistency between Saccharomyces cerevisiae S288C Genome Scale Models (iND750 and iMM904)

Acta scientific microbiology, Mar 1, 2023

Saccharomyces cerevisiae is an important experimental organism for industrial and scientific rese... more Saccharomyces cerevisiae is an important experimental organism for industrial and scientific research with S. cerevisiae S288C as the first eukaryote genome sequenced. Genome-scale metabolic models (GSMs) are computational tools to explore metabolic engineering requirements. Currently, there are 2 major GSMs of S. cerevisiae S288C, iND750 and iMM904, which raises the question of whether they are consistent to each other. Here, we compare iND750 and iMM904 by examining the fluxomic changes resulting from single reaction knockouts. 40.5% to 50.3% (n = 637) of the reactions are common in both GSMs. Of which, 64 (10.0% of common reactions, or between 4.1% and 5.2% of the total reactions in each GSM) reaction knockouts resulted in significant fluxomic changes. This is significantly lower (t =-15.882, df = 30, p-value = 3.82E-16) from expected using randomization test, suggesting that iND750 and iMM904 are likely to be consistent with each other from the perspective of common reactions.

Simulation Suggests that One-Off Simple Supplementation from the Wildinto Captive Population May Not Increase Captive Genetic Diversity

EC Veterinary Science, Jun 30, 2021

Coffee as a Potential Nutraceutical

EC Nutrition, Feb 27, 2021

Global coffee production nearly doubled over the last decade, making coffee one of the most popul... more Global coffee production nearly doubled over the last decade, making coffee one of the most popular beverage in current society. However, recent consumer studies suggest concerns of potential health detriments from regular coffee consumption. Given its popularity, any health benefits or detriment can have substantial public health impact. Here, we examined several potential benefits and risks with regards to coffee drinking. Evidence is non-conclusive in several cases and warrants further studies. Despite so, there is likely more health benefits than harm, especially when moderation is applied. Hence, we are in the view that coffee is a potential nutraceutical when consumed in moderation and with adequate hydration.

Back-of-the-Envelope Guide (A Tutorial) to 10 Intracellular Landscapes

MOJ proteomics & bioinformatics, Feb 6, 2018

Copy number landscape 4 often refers to copy number variation (CNV), which is the differences bet... more Copy number landscape 4 often refers to copy number variation (CNV), which is the differences between the numbers of copies of one or more nucleotides within individuals in the same species. The repeats can range from a few bases; such as, polyglutamine repeats; 5 to entire genes; such as alpha-amylase 6 and neutrophil cytosolic factor 1. 7 CNV can be a result when sections of a genome are duplicated/ repeated or deleted; 8,9 which exists in both higher eukaryotes, such as humans, 10 and prokaryotes, such as Escherichia coli; 11 and is implicated in several disease phenotypes. 8 For example, CNV in neutrophil cytosolic factor 1 has been implicated in rheumatoid arthritis 7 and CNV in protease has been implicated in anthropogenic toxins in arthropods 12 as differences in copy number may have an

Resistance Maintained in Digital Organisms despite Guanine/Cytosine-Based Fitness Cost and Extended De-Selection: Implications to Microbial Antibiotics Resistance

arXiv (Cornell University), Feb 19, 2023

Two Cellular Resource Based Models Linking Growth and Parts Characteristics Aids the Study and Optimization of Synthetic Gene Circuits

arXiv (Cornell University), Feb 19, 2023

A major challenge in synthetic genetic circuit development is the inter-dependency between hetero... more A major challenge in synthetic genetic circuit development is the inter-dependency between heterologous gene expressions by circuits and host's growth rate. Increasing heterologous gene expression increases burden to the host, resulting in host growth reduction; which reduces overall heterologous protein abundance. Hence, it is difficult to design predictable genetic circuits. Here, we develop two biophysical models; one for promoter, another for RBS; to correlate heterologous gene expression and growth reduction. We model cellular resource allocation in E. coli to describe the burden, as growth reduction, caused by genetic circuits. To facilitate their uses in genetic circuit design, inputs to the model are common characteristics of biological parts [e.g. relative promoter strength (RPU) and relative ribosome binding sites strength (RRU)]. The models suggest that E. coli 's growth rate reduces linearly with increasing RPU/RRU of the genetic circuits; thus, providing 2 handy models taking parts characteristics as input to estimate growth rate reduction for fine tuning genetic circuit design in silico prior to construction. Our promoter model correlates well with experiments using various genetic circuits, both single and double expression cassettes, up to a relative promoter unit of 3.7 with a 60% growth rate reduction (average R 2 ∼0.9).

A 5-Year Systematic Review (2018 to 2022) on The Effectiveness of Mediterranean Diet in Preventing Alzheimer’s Disease

Acta Scientific Nutritional Health, Feb 1, 2023

Alzheimer's disease (AD) is an age-related neuronal disorder characterized by abnormal levels of ... more Alzheimer's disease (AD) is an age-related neuronal disorder characterized by abnormal levels of proteins, beta amyloid (Aβ) and tau, resulting in gradual loss of cognitive functions due to impaired network of neurons in the brain. Past literature has proposed dietary interventions through administration of Mediterranean Diet (MD) as a solution to prevent AD development. A systematic review on the effectiveness of MD in preventing AD is executed up to July 3, 2022, using PubMed as source database within the last 5 years between 2018 to 2022. 131 articles were identified, and 26 articles were included in this review. After analysing the articles, 5 themes were identified to examine the effectiveness of MD: namely, (a) MD adherence and AD risk (b) MD and AD pathological development, (c) MD and cognitive health (d) Mediterranean-DASH Intervention for Neurodegenerative Delay (MIND) diet, and (e) Diet-microbe interaction. MD adherence is a vital factor in achieving successful dietary intervention. Various covariates and demographics affect adherence level. Differing evidence from literature discuss MD's efficacy in preventing AD. MD is concluded to be effective to a certain extent in preventing Alzheimer's disease due to various factors such as adherence levels, demographics etc and further longitudinal and randomised control trials (RCT) are warranted.

Development of a Basic Chemistry Conversational Corpus

Acta Scientific Nutritional Health, Feb 1, 2023

Chatbot technology can be an important tool and supplement to education, leading to explorations ... more Chatbot technology can be an important tool and supplement to education, leading to explorations in this area. Corpus-based chatbot building has a relatively low entry barrier as it only requires a relevant corpus to train a chatbot engine. The corpus is a set of human-readable questions and answers and may be an amalgamation of existing corpora. However, a suitable chemistry-based chatbot corpus catering for a freshman general chemistry course addressing inorganic and physical chemistry has not been developed. In this study, we present a basic chemistry conversational corpus consisting of 998 pairs of questions and answers, focused on a freshman general chemistry course addressing inorganic and physical chemistry. Ten human raters evaluated the responses of a chatbot trained on the corpus and suggests that the corpus resulted in better response than random (t = 17.4, p-value = 1.86E-53). However, only 20 of the 50 test questions show better responses compared to random (difference in mean score ≥ 1.9, paired t-test p-value ≤ 0.0324), suggesting that the corpus provides better responses to certain questions rather than overall better responses, with questions related to definitions and computational procedures answered more accurately. Hence, this provides a baseline for future corpora development.

Survey of Antisense Transcription

Elsevier eBooks, 2019

Reconstruction of Protein-Protein Interaction Pathways by Mining Subject-Verb-Objects Intermediates

Springer eBooks, Sep 18, 2007

The exponential increase in publication rate of new articles is limiting access of researchers to... more The exponential increase in publication rate of new articles is limiting access of researchers to relevant literature. This has prompted the use of text mining tools to extract key biological information. Previous studies have reported extensive modification of existing generic text processors to process biological text. However, this requirement for modification had not been examined. In this study, we have constructed Muscorian, using MontyLingua, a generic text processor. It uses a two-layered generalization-specialization paradigm previously proposed where text was generically processed to a suitable intermediate format before domain-specific data extraction techniques are applied at the specialization layer. Evaluation using a corpus and experts indicated 86-90% precision and approximately 30% recall in extracting proteinprotein interactions, which was comparable to previous studies using either specialized biological text processing tools or modified existing tools. Our study had also demonstrated the flexibility of the two-layered generalizationspecialization paradigm by using the same generalization layer for two specialized information extraction tasks.

Science/Education Portraits III: Perceived Prevalence of Data Fabrication and/or Falsification in Research

Advances in biotechnology & microbiology, Dec 7, 2018

Data fabrication or falsification are considered as "deadly sins" with high impact, above plagiar... more Data fabrication or falsification are considered as "deadly sins" with high impact, above plagiarism, on scientific truth and public confidence. What is the estimated prevalence of data fabrication or falsification? A meta-survey published a decade ago estimated 14.12% of respondents having knowledge of a colleague who fabricated or falsified research data, or who altered or modified research data. This mini-review updates this meta-survey by examining surveys from 2009 to 2018. Results suggests that 17.7% of responses indicated knowledge of fellow scientist's acts of data fabrication or data falsification. This is consistent with that of a decade ago, which suggests a critical need to address the worst type of research misconduct-data fabrication and falsification.

Grand challenges in bioinformatics education and training

Nature Biotechnology

Science/Education Portraits VIII: Duoethnography of First-Generation Bioscience Undergraduates in a Private Education Institute in Singapore

Acta Scientific Microbiology

It has been well-recognized that first-generation undergraduate faces unique challenges. This is ... more It has been well-recognized that first-generation undergraduate faces unique challenges. This is made worse by being a firstgeneration undergraduate in a private education institution (PEI), commonly characterized by lesser resources as compared to public education institution, during COVID-19 associated social restrictions. Currently, there is no study to on first-generation university undergraduates pursuing their undergraduate education via a PEI in Singapore during this COVID-19 pandemic. In this article, we document the journey, challenges, and triumphs of three first-generation bioscience undergraduates in Singapore pursuing their bachelor's degree in a PEI during the pandemic using duo ethnographical approach. Our analysis suggests that challenges faced by first-generation undergraduate in a PEI in Singapore during COVID-19 associated restrictions can be seen as sum of challenges faced by first-generation undergraduate and challenges faced by in the education sector during COVID-19 associated restrictions; but the resourcefulness, resilience, and adaptability of first-generation undergraduate are also evident.

Of (Biological) Models and Simulations

arXiv (Cornell University), Feb 19, 2023

All models are wrong, but some are useful. Box and Draper [1]. All models are right… Most are use... more