Publications

Iron and manganese mobilisation due to dam height increase for a tropical reservoir in South East Asia

The aim of this research was the analysis of the effect of a dam height raise on the water quality of a tropical reservoir used for drinking water purposes in South East Asia. Analyses of iron, manganese, pH and ammonia were performed over a 5-year period from daily water sampling at the reservoir. In addition, high-frequency monitoring data of nitrate, ammonium, pH and blue-green algae were obtained using a monitoring probe. The results showed that due to the raising of the reservoir water level, previously oxic sediments became submerged, triggering an increase in iron and manganese in particular due to the establishment of reducing conditions. Manganese concentrations with values up to 4 mg L−1 are now exceeding guideline values. The analysis strongly indicated that both iron and manganese have a seasonal component with higher iron and manganese concentrations during the wet season. Over a three-year period afterwards, concentrations did not go back to pre-raise levels. The change in water quality was accompanied by a change in pH from previous values of around 5 to pH values of around 6.5. Geochemical simulations confirmed the theory that the increasing concentrations of iron and manganese are due to the dissolution of MnO2 and ferric oxyhydroxides oxidising organic matter in the process. This study showed that changes in reservoir water levels with the establishment of reducing conditions can have long-term effects on the water quality of a reservoir.

Strategic information sharing in supply chain with value-perceived consumers

Purpose: Information sharing is one of essential collaboration methods for building effective system-level disruption responses and communication for supply chain resilience. However, supply chain members are often reluctant to share the members’ business information for fear of losing competitiveness. To facilitate the cooperation among these members, the supply chain members’ should be made aware of the value of information. As a result, the purpose of this paper is to quantify the benefit of information sharing and evaluate its magnitude under various factors. Design/methodology/approach: In this paper, information sharing is measured in a two-stage supply chain containing a manufacturer and a retailer. A demand function is constructed as a linear combination of a first-order autoregressive [AR(1)] process, the retail and reference prices. The values of information sharing are quantified for four scenarios: (1) no information sharing, (2) full information sharing, (3) limited information sharing and (4) partial information sharing. Based on the four scenarios, the conditions for valuable information sharing are determined. In addition, the impact of several demand parameters on the usefulness of information sharing is analyzed. Findings: When the demand function is a pure AR(1) process (i.e. there is no impact from the retail and reference prices), information sharing is always valuable regardless of the autoregressive coefficient. Under the influence of the retail price and consumer behavior via the reference price, information sharing is not always beneficial. The boundaries for useful information sharing are analytically constructed. In addition to full information sharing, this study also quantifies the value of information under a partial sharing scheme. The results indicate that the information is more valuable as long as the information is inducible. Originality/value: This study highlights several specific conditions for a beneficial information sharing agreement in consideration of consumer behaviors. These conditions enable supply chain members to design a sustainable partnership.

The global burden of adolescent and young adult cancer in 2019: a systematic analysis for the Global Burden of Disease Study 2019

Background: In estimating the global burden of cancer, adolescents and young adults with cancer are often overlooked, despite being a distinct subgroup with unique epidemiology, clinical care needs, and societal impact. Comprehensive estimates of the global cancer burden in adolescents and young adults (aged 15–39 years) are lacking. To address this gap, we analysed results from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2019, with a focus on the outcome of disability-adjusted life-years (DALYs), to inform global cancer control measures in adolescents and young adults. Methods: Using the GBD 2019 methodology, international mortality data were collected from vital registration systems, verbal autopsies, and population-based cancer registry inputs modelled with mortality-to-incidence ratios (MIRs). Incidence was computed with mortality estimates and corresponding MIRs. Prevalence estimates were calculated using modelled survival and multiplied by disability weights to obtain years lived with disability (YLDs). Years of life lost (YLLs) were calculated as age-specific cancer deaths multiplied by the standard life expectancy at the age of death. The main outcome was DALYs (the sum of YLLs and YLDs). Estimates were presented globally and by Socio-demographic Index (SDI) quintiles (countries ranked and divided into five equal SDI groups), and all estimates were presented with corresponding 95% uncertainty intervals (UIs). For this analysis, we used the age range of 15–39 years to define adolescents and young adults. Findings: There were 1·19 million (95% UI 1·11–1·28) incident cancer cases and 396 000 (370 000–425 000) deaths due to cancer among people aged 15–39 years worldwide in 2019. The highest age-standardised incidence rates occurred in high SDI (59·6 [54·5–65·7] per 100 000 person-years) and high-middle SDI countries (53·2 [48·8–57·9] per 100 000 person-years), while the highest age-standardised mortality rates were in low-middle SDI (14·2 [12·9–15·6] per 100 000 person-years) and middle SDI (13·6 [12·6–14·8] per 100 000 person-years) countries. In 2019, adolescent and young adult cancers contributed 23·5 million (21·9–25·2) DALYs to the global burden of disease, of which 2·7% (1·9–3·6) came from YLDs and 97·3% (96·4–98·1) from YLLs. Cancer was the fourth leading cause of death and tenth leading cause of DALYs in adolescents and young adults globally. Interpretation: Adolescent and young adult cancers contributed substantially to the overall adolescent and young adult disease burden globally in 2019. These results provide new insights into the distribution and magnitude of the adolescent and young adult cancer burden around the world. With notable differences observed across SDI settings, these estimates can inform global and country-level cancer control efforts. Funding: Bill & Melinda Gates Foundation, American Lebanese Syrian Associated Charities, St Baldrick’s Foundation, and the National Cancer Institute.

Incidence, Mortality and Survival Analysis of Epithelial Ovarian Cancer in Brunei Darussalam

Background: This study provides population-based study of cancer incidence, mortality and survival rates for women diagnosed with epithelial ovarian cancer (EOC), and evaluate the prognostic factors of EOC patients survival in Brunei Darussalam. Methods: This is a retrospective study of patients diagnosed with EOC between 1st January 2007 and 31st December 2017 in Brunei Darussalam. Crude, age-specific, age-standardized incidence and mortality rates per 100,000 women were calculated. Kaplan-Meier method was used to determine the overall 5-years survival rate. Log-rank test was used to examine the differences in survival between groups. The multivariable Cox Proportional Hazard regression models were used to estimate the hazard ratio for overall survival and to identify the prognostic factors. Results: A total of 207 patients were included in the study. The crude incidence and mortality rates were 9.7 and 3.6 per 100,000 respectively while the age-standardized incidence and mortality rates were 11.3 (95% CI: 9.7,12.9) and 4.5 (95% CI: 3.4,5.6) per 100,000 respectively in the period 2007-2017. The overall mean age at diagnosis was 48.4 (standard deviation=15.3) years. The overall survival rates at 1, 3, and 5 years for EOC patients were 79.7%, 69.7%, and 61.4% respectively. Age at diagnosis, cancer stage, and histology were significant prognostic factors for patients’ survival. Older age at diagnosis (≥70 years vs <40 years), regional or advanced stage (vs localized stage) and having undifferentiated or other epithelial ovarian (vs serous carcinoma) were associated with having higher hazard of death. Conclusion: Early detection of disease should be emphasized through public education and raising awareness to improve survival rates of patients with EOC.

Cancer Incidence, Mortality, Years of Life Lost, Years Lived With Disability, and Disability-Adjusted Life Years for 29 Cancer Groups From 2010 to 2019 A Systematic Analysis for the Global Burden of Disease Study 2019

IMPORTANCE The Global Burden of Diseases, Injuries, and Risk Factors Study 2019 (GBD 2019) provided systematic estimates of incidence, morbidity, and mortality to inform local and international efforts toward reducing cancer burden. OBJECTIVE To estimate cancer burden and trends globally for 204 countries and territories and by Sociodemographic Index (SDI) quintiles from 2010 to 2019. EVIDENCE REVIEW The GBD 2019 estimation methods were used to describe cancer incidence, mortality, years lived with disability, years of life lost, and disability-adjusted life years (DALYs) in 2019 and over the past decade. Estimates are also provided by quintiles of the SDI, a composite measure of educational attainment, income per capita, and total fertility rate for those younger than 25 years. Estimates include 95% uncertainty intervals (UIs). FINDINGS In 2019, there were an estimated 23.6 million (95% UI, 22.2-24.9 million) new cancer cases (17.2 million when excluding nonmelanoma skin cancer) and 10.0 million (95% UI, 9.36-10.6 million) cancer deaths globally, with an estimated 250 million (235-264 million) DALYs due to cancer. Since 2010, these represented a 26.3% (95% UI, 20.3%-32.3%) increase in new cases, a 20.9% (95% UI, 14.2%-27.6%) increase in deaths, and a 16.0% (95% UI, 9.3%-22.8%) increase in DALYs. Among 22 groups of diseases and injuries in the GBD 2019 study, cancer was second only to cardiovascular diseases for the number of deaths, years of life lost, and DALYs globally in 2019. Cancer burden differed across SDI quintiles. The proportion of years lived with disability that contributed to DALYs increased with SDI, ranging from 1.4% (1.1%-1.8%) in the low SDI quintile to 5.7% (4.2%-7.1%) in the high SDI quintile. While the high SDI quintile had the highest number of new cases in 2019, the middle SDI quintile had the highest number of cancer deaths and DALYs. From 2010 to 2019, the largest percentage increase in the numbers of cases and deaths occurred in the low and low-middle SDI quintiles. CONCLUSIONS AND RELEVANCE The results of this systematic analysis suggest that the global burden of cancer is substantial and growing, with burden differing by SDI. These results provide comprehensive and comparable estimates that can potentially inform efforts toward equitable cancer control around the world.

Advocating Blended Learning for University Undergraduate Level Mathematical Instruction Beyond Covid-19

Institutional mathematics education has long been traditional in its ways of being teacher-centric, a tradition which perhaps dates back to the Ancient Greece. Much like the society in those days, where there was a wary public feeling about the rigidness of the mathematical instruction in Pythagoras’ school, mathematics educators find themselves in a similar position in the common era of 2020. Unlike the Ancient Greece however, the battle is for the sustained delivery of a comprehensive mathematics education in the midst of the Covid-19 pandemic. It would be fair to say that mathematics departments across all levels of the education sector have been affected drastically; more so on instructors who favour the traditional “chalk and talk” method of instruction. In this article, we share several lessons learned in the delivery of mathematical instruction at undergraduate university level during the Covid-19 pandemic, drawing on our experience at Universiti Brunei Darussalam. These include specific methods for implementing online learning effectively, the pros and cons of such methods, and how we can use computer based tools to make learning more conducive. We highly think that these implementations are beneficial to be adapted by mathematics departments anywhere as a means of adapting to the new realities post Covid-19.

Survival of colorectal cancer patients in Brunei Darussalam: comparison between 2002–09 and 2010–17

Background: Colorectal cancer (CRC) is a major cause of cancer-related mortality worldwide. It is the second leading cause of cancer death in men and women in Brunei Darussalam in 2017, posing a major burden on society. Methods: This retrospective cohort study (n = 1035 patients diagnosed with CRC in Brunei Darussalam from 1st January 2002 until 31st December 2017) aims to compare the overall survival rates of CRC patients (2002–2017), to compare survival rates between two study periods (2002–2009 and 2010–2017) and to identify prognostic factors of CRC. Kaplan-Meier estimator and log-rank tests were performed to analyse the overall survival rates of CRC patients. Multiple Cox regression was performed to determine the prognostic factors of CRC with adjusted hazard ratios (Adj. HRs) reported. Results: The 1-, 3- and 5-year survival rates of CRC patients are 78.6, 62.5, and 56.0% respectively from 2002 to 2017. The 1-, 3-, and 5-year survival rates of CRC patients for 2002–2009 are 82.2, 69.6, and 64.7%; 77.0, 59.1, and 51.3% for 2010–2017 respectively. A significant difference in CRC patients’ survival rate was observed between the two study periods, age groups, ethnic groups, cancer stages, and sites of cancer (p < 0.05). The Adjusted Hazard Ratios (Adj. HRs) were significantly higher in the 2010–17 period (Adj. HR = 1.78, p < 0.001), older age group (≥ 60 years) (Adj. HR = 1.93, p = 0.005), distant cancer (Adj. HR = 4.69, p < 0.010), tumor at transverse colon and splenic flexure of colon (Adj. HR = 2.44, p = 0.009), and lower in the Chinese(Adj. HR = 0.63, p = 0.003). Conclusion: This study highlights the lower survival rates of CRC patients in 2010–2017, Malays, older patients, distant cancer, and tumors located at the latter half of the proximal colon (transverse colon), and predominantly LCRC (splenic flexure, descending colon, sigmoid colon, overlapping lesion colon and colon (NOS), as well as the rectosigmoid junction and rectum (NOS)). Age, ethnicity, cancer stage, and tumor location are significant prognostic factors for CRC. These findings underscore the importance of public health policies and programmes to enhance awareness on CRC from screening to developing strategies for early detection and management, to reduce CRC-associated mortality.

Learning-detailed 3D face reconstruction based on convolutional neural networks from a single image

The efficiency of convolutional neural networks (CNNs) facilitates 3D face reconstruction, which takes a single image as an input and demonstrates significant performance in generating a detailed face geometry. The dependence of the extensive scale of labelled data works as a key to making CNN-based techniques significantly successful. However, no such datasets are publicly available that provide an across-the-board quantity of face images with correspondingly explained 3D face geometry. State-of-the-art learning-based 3D face reconstruction methods synthesize the training data by using a coarse morphable model of a face having non-photo-realistic synthesized face images. In this article, by using a learning-based inverse face rendering, we propose a novel data-generation technique by rendering a large number of face images that are photo-realistic and possess distinct properties. Based on the real-time fine-scale textured 3D face reconstruction comprising decently constructed datasets, we can train two cascaded CNNs in a coarse-to-fine manner. The networks are trained for actual detailed 3D face reconstruction from a single image. Experimental results demonstrate that the reconstruction of 3D face shapes with geometry details from only one input image can efficiently be performed by our method. Furthermore, the results demonstrate the efficiency of our technique to pose, expression and lighting dynamics.

Identification and Classification of Driving Behaviour at Signalized Intersections Using Support Vector Machine

When the drivers approaching signalized intersections (onset of yellow signal), the drivers would enter into a zone, where they will be in uncertain mode assessing their capabilities to stop or cross the intersection. Therefore, any improper decision might lead to a right-angle or back-end crash. To avoid a right-angle collision, drivers apply the harsh brakes to stop just before the signalized intersection. But this may lead to a back-end crash when the following driver encounters the former’s sudden stopping decision. This situation gets multifaceted when the traffic is heterogeneous, containing various types of vehicles. In order to reduce this issue, this study’s primary objective is to identify the driving behaviour at signalized intersections based on the driving features (parameters). The secondary objective is to classify the outcome of driving behaviour (safe stopping and unsafe stopping) at the signalized intersection using a support vector machine (SVM) technique. Turning moments are used to identify the zones and label them accordingly for further classification. The classification of 50 instances is identified for training and testing using a 70%–30% rule resulted in an accuracy of 85% and 86%, respectively. Classification performance is further verified by random sampling using five cross-validation and 30 iterations, which gave an accuracy of 97% and 100% for training and testing. These results demonstrate that the proposed approach can help develop a pre-warning system to alert the drivers approaching signalized intersections, thus reducing back-end crash and accidents.

Quality testing of spectrum-based valency descriptors for polycyclic aromatic hydrocarbons with applications

In this paper, we investigate the prediction potential of commonly occurring eigenvalues-based descriptors which are related to chemical matrices corresponding to valency of vertices. The normal boiling point has been chosen to be representative of van-der-Waals and intermolecular type interactions, whereas, the standard enthalpy/heat of formation is selected to represent thermal properties, for our comparative testing. First, we propose a unified computational method to calculate commonly occurring eigenvalues-based valency descriptors. Experimental results show that our proposed method possesses less algorithmic and computational complexities and is more computationally diverse. The proposed method is used to calculate commonly occurring eigenvalues-based descriptors to investigate their correlation ability with the experimental data for the two chosen physicochemical properties. The Randić energy shows the best correlation among all the commonly occurring eigenvalues-based descriptors. Experimental results show some unexpected outcomes as the correlation ability of the well-known adjacency energy and the Laplacian & signless Laplacian Estrada indices is weak. Unlike their reputation among researchers, the harmonic energy and Estrada index outperformed all the well-known eigenvalues-based descriptors. The results warrant further usage of the harmonic energy and Estrada index in the structure-activity and structure-property models. Our study contributes towards putting forward the best spectrum-based topological descriptors while mentioning the ones which do not deserve further attention of researchers. Applications to certain families of titania nanotubes are presented.

Quality testing of spectrum-based distance descriptors for polycyclic aromatic hydrocarbons with applications to carbon nanotubes and nanocones

In this paper, we investigate the predictive potential of commonly occurring spectrum-based distance descriptors which are based on eigenvalues of distance-related chemical matrices. For our comparative testing, the normal boiling point has been chosen to be representative of van-der-Waals and intermolecular type interactions, whereas, the standard enthalpy/heat of formation is selected to represent thermal properties. We introduce three new chemical matrices and results show that the spectral descriptors based on these new matrices outperform the existing well-studied spectral descriptors. A computational method is used to calculate commonly occurring spectrum-based distance descriptors to investigate their correlation ability with the experimental data for the two chosen physicochemical properties for lower polycyclic aromatic hydrocarbons. By providing the list of the five best spectrum-based distance descriptors, our study contributes towards putting forward the best spectrum-based topological descriptors while mentioning the ones which do not deserve further attention of researchers. Applications of our results to certain families of carbon polyhex nanotubes and one-hexagonal nanocones have been presented. The results can potentially be used to determine certain physicochemical of these nanotubes and nanocones theoretically with higher accuracy and negligible error.

Latent class analysis: Insights about design and analysis of schistosomiasis diagnostic studies

Various global health initiatives are currently advocating the elimination of schistosomiasis within the next decade. Schistosomiasis is a highly debilitating tropical infectious disease with severe burden of morbidity and thus operational research accurately evaluating diagnostics that quantify the epidemic status for guiding effective strategies is essential. Latent class models (LCMs) have been generally considered in epidemiology and in particular in recent schistosomiasis diagnostic studies as a flexible tool for evaluating diagnostics because assessing the true infection status (via a gold standard) is not possible. However, within the biostatistics literature, classical LCM have already been criticised for real-life prob-lems under violation of the conditional independence (CI) assumption and when applied to a small number of diagnostics (i.e. most often 3-5 diagnostic tests). Solutions of relaxing the CI assumption and accounting for zero-inflation, as well as collecting partial gold standard information, have been proposed, offering the potential for more robust model estimates. In the current article, we examined such approaches in the context of schistosomiasis via analysis of two real datasets and extensive simulation studies. Our main conclusions highlighted poor model fit in low prevalence settings and the necessity of collecting partial gold standard information in such settings in order to improve the accuracy and reduce bias of sensitivity and specificity estimates.

Predictive potential of spectrum-based topological descriptors for measuring the π-electronic energy of benzenoid hydrocarbons with applications to boron triangular and boron α-nanotubes

In this paper, we determine the efficiency of all commonly occurring eigenvalues-based topological descriptors for measuring the π-electronic energy of lower polycyclic aromatic hydrocarbons. Results show some favorable outcomes as the spectrum-based descriptors such as the adjacency energy, the arithmetic-geometric energy, the geometric-arithmetic energy, and the adjacency Estrada index have the best correlation coefficients greater than 0.999 among all others. However, certain well-known spectrum-based descriptors such as the adjacency, Laplacian & signless Laplacian spectral radii, and the first & second Zagreb Estrada indices show considerably weak performance. Poor performances of the first & second Zagreb Estrada indices are, in general, unexpected. The arithmetic-geometric and geometric-arithmetic energies with correlation coefficients 0.99997 and 0.99996, respectively, are warranted for further use in quantitative structure activity/property relationship (QSAR/QSPR) models. Based on our comparative testing, we generate a priority list of the top five spectrum-based topological descriptors for measuring the π-electronic energy. These best preforming descriptors are then studied for certain infinite families of boron triangular and boron α-nanotubes. The results help in determining the π-electronic energy of these families of boron nanotubes. Combining our results with similar results studied in literature, we conclude that among all the classes of topological descriptors, spectrum-based descriptors are the best in correlating the π-electronic energy.

Global, regional, and national burden of respiratory tract cancers and associated risk factors from 1990 to 2019: a systematic analysis for the Global Burden of Disease Study 2019

Background Prevention, control, and treatment of respiratory tract cancers are important steps towards achieving target 3.4 of the UN Sustainable Development Goals (SDGs)—a one-third reduction in premature mortality due to non-communicable diseases by 2030. We aimed to provide global, regional, and national estimates of the burden of tracheal, bronchus, and lung cancer and larynx cancer and their attributable risks from 1990 to 2019. Methods Based on the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2019 methodology, we evaluated the incidence, mortality, years lived with disability, years of life lost, and disability-adjusted life-years (DALYs) of respiratory tract cancers (ie, tracheal, bronchus, and lung cancer and larynx cancer). Deaths from tracheal, bronchus, and lung cancer and larynx cancer attributable to each risk factor were estimated on the basis of risk exposure, relative risks, and the theoretical minimum risk exposure level input from 204 countries and territories, stratified by sex and Socio-demographic Index (SDI). Trends were estimated from 1990 to 2019, with an emphasis on the 2010-19 period. Findings Globally, there were 2·26 million (95% uncertainty interval 2·07 to 2·45) new cases of tracheal, bronchus, and lung cancer, and 2·04 million (1·88 to 2·19) deaths and 45·9 million (42·3 to 49·3) DALYs due to tracheal, bronchus, and lung cancer in 2019. There were 209 000 (194 000 to 225 000) new cases of larynx cancer, and 123 000 (115 000 to 133 000) deaths and 3·26 million (3·03 to 3·51) DALYs due to larynx cancer globally in 2019. From 2010 to 2019, the number of new tracheal, bronchus, and lung cancer cases increased by 23·3% (12·9 to 33·6) globally and the number of larynx cancer cases increased by 24·7% (16·0 to 34·1) globally. Global age-standardised incidence rates of tracheal, bronchus, and lung cancer decreased by 7·4% (−16·8 to 1·6) and age-standardised incidence rates of larynx cancer decreased by 3 ·0% (−10·5 to 5·0) in males over the past decade; however, during the same period, age-standardised incidence rates in females increased by 0·9% (−8·2 to 10·2) for tracheal, bronchus, and lung cancer and decreased by 0·5% (−8·4 to 8·1) for larynx cancer. Furthermore, although age-standardised incidence and death rates declined in both sexes combined from 2010 to 2019 at the global level for tracheal, bronchus, lung and larynx cancers, some locations had rising rates, particularly those on the lower end of the SDI range. Smoking contributed to an estimated 64·2% (61·9–66·4) of all deaths from tracheal, bronchus, and lung cancer and 63·4% (56·3–69·3) of all deaths from larynx cancer in 2019. For males and for both sexes combined, smoking was the leading specific risk factor for age-standardised deaths from tracheal, bronchus, and lung cancer per 100 000 in all SDI quintiles and GBD regions in 2019. However, among females, household air pollution from solid fuels was the leading specific risk factor in the low SDI quintile and in three GBD regions (central, eastern, and western sub-Saharan Africa) in 2019. Interpretation The numbers of incident cases and deaths from tracheal, bronchus, and lung cancer and larynx cancer increased globally during the past decade. Even more concerning, age-standardised incidence and death rates due to tracheal, bronchus, lung cancer and larynx cancer increased in some populations—namely, in the lower SDI quintiles and among females. Preventive measures such as smoking control interventions, air quality management programmes focused on major air pollution sources, and widespread access to clean energy should be prioritised in these settings.

Correlation Ability of Degree-Based Topological Indices for Physicochemical Properties of Polycyclic Aromatic Hydrocarbons with Applications

Several chemical and medical experimentation reveals a dependence of physicochemical and biological properties of a compound on its molecular structure. Molecular/topological descriptors/indices retrieve this dependence by employing mathematical/statistical tools to generate quantitative structure property/activity relationship (QSAR/QSPR) models. QSAR/QSPR models are regression models which theoretically relate a physicochemical/biological property to a molecular descriptor. By converting a compound to a chemical graph, graph-theoretic topological indices use algorithmic graph theory to generate QSAR/QSPR models. Degree-related molecular indices have been well-known for correlating better with certain physicochemical characteristics of compounds. In this paper, we conduct a comparative analysis to put forward the best degree-based index for correlating with physicochemical characteristics of polycyclic aromatic hydrocarbons. Two different computational techniques have been put forward and then used to conduct our comparative analysis. Our comparative testing generates several favorable and unexpected conclusions as the well-known indices such as the augmented Zagreb index, the atom-bond connectivity index, the geometric arithmetic index deliver relatively poor performance. Moreover, exceptional performance of the generalized variants of Randić and sum-connectivity indices is somehow unexpected as they significantly outperform the well-studied and well-researched degree-based indices. This warrants to study further the general Randić and sum-connectivity indices for QSAR/QSPR models. Applications to certain families of carbon polyhex aromatic nanotubes are reported.

A computer-based method to determine predictive potential of distance-spectral descriptors for measuring the π-electronic energy of benzenoid hydrocarbons with applications

Graph signal processing deals with signals whose domain, defined by a graph, is irregular. The total π -electron energy or simply the π -electronic energy, as calculated within the Hückel tight-binding molecular orbital approximation, is one of the important quantum-theoretical characteristic of conjugated molecules. In this paper, we propose an efficient computer-assisted computational method to determine eigenvalues-based distance descriptors for chemical compounds which are then used to learn to quantitative relationship between the activity/property and the structure (QSAR/QSPR) of compound. Comparisons with other similar methods show that our proposed method possesses less algorithmic and computational complexities and is more computationally diverse. The proposed method is used to determine predictive potential of eigenvalues-based distance descriptors for measuring the π -electronic energy of benzenoid hydrocarbons. Importantly, we propose three new chemical matrices and, unexpectedly, results show that the spectral descriptors defined based on new chemical matrices outperform all the well-known descriptors in the literature. Specifically, our proposed second atom-bond connectivity Estrada index show the best correlation coefficient of 0.9997. Applications of our computational method to certain infinite families of carbon nanotubes and carbon nanocones are presented. The obtained results can potentially be used to determine the π -electronic energy of these nanotubes and nanocones theoretically with higher accuracy and negligible error.

Quality testing of distance-based molecular descriptors for benzenoid hydrocarbons

In this paper, we investigate the prediction power of all the well-known distance-based molecular structure descriptors in the literature for 22 lower polycyclic aromatic hydrocarbons (PAHs). The standard enthalpy/heat of formation is chosen to be the representative of thermal properties, whereas, the normal boiling point is selected to represent intermolecular and van-der-Waals type interactions. First, we present a computational technique to compute distance-based, eccentricity-based, degree-distance-based and degree based topological descriptors. The proposed method extends certain existing techniques in the literature. The proposed method is used to compute various distance-based descriptors for the 22 PAHs and then we develop the regression models with their normal boiling point and standard enthalpy of formation. Experimental results reveal some unexpected outcomes as the correlation ability of some well-known distance-based descriptors such as the Wiener and the Szeged indices is rather weak. Unlike their reputation among researchers, the second atomic-bond connectivity index and the fourth geometric-arithmetic index yield the best performance with correlation coefficients greater than 0.95. The results warrant further usage of the second atom-bond connectivity index in the structure-activity and structure-property models. Our study contributes towards slowing down the proliferation of distance-based topological descriptors.

Factors associated with participation in stool based colorectal screening in Brunei Darussalam

Colorectal cancers (CRC) continues to increase worldwide and is associated with significant morbidity and mortality. CRC can be prevented through early detection using several modalities. However, like any screening program participation remains suboptimal. This study assessed the factors associated with participation in a stool based CRC screening that was carried out as part of an Integrated Health Screening Survey for civil servants. Materials and Methods: Civil servants who participated in a health survey (N=10,756, mean age 48.08 ± 5.26 years old) were studied. Demographic factors (gender, age groups, marital status, employment status, body mass index [BMI] categories, smoking status, personal and family history of cancers) were analyzed to assess for features associated with willingness to participate in this fecal immunohistochemistry test (FIT) screening for CRC. Comorbid conditions studied were cardiac disease, diabetes mellitus, dyslipidemia, hypertension and stroke. Multivariate analysis was performed to evaluate variables associated with participation in CRC screening programme. Results: Of the invited 10,756 participants, 7,360 returned a stool specimen giving a participation rate of 68.4%. Those who participated were significantly older (<40 [41.3%], 40-44 [64.6%], 45-49 [68.8%], 50-54 years [70.6%], 55-59 years [72.4%] and >60 years [77.8%], p<0.001 for trend), being of professional employment (p=0.010) and presence of comorbid conditions (p=0.003). There were no significant differences between gender, race, marital status, BMI categories, personal history of cancer, family history of cancer, and smoking status (all p values >0.05). Multivariate analyses showed that older age (45-49, 50-54, 55-59 and >60) and employment status (professional) remained significant factors associated with participation in a stool based CRC screening. Conclusions: Our study showed that older age and professional employment status were significantly associated with willingness to participate in a stool based CRC screening.

Survival rates and associated factors of colorectal cancer patients in Brunei Darussalam

Background: Colorectal cancer (CRC) is the third most common cancer in both men and women. In most Asian countries, both the incidence and mortality rates of CRC are gradually increasing. In Brunei Darussalam, CRC ranks first and second in lifetime risk among men and women respectively. This study aims to report the overall survival rates and associated factors of CRC in Brunei Darussalam. Methods: This is a retrospective study examining CRC data for the period 2007 to 2017 retrieved from a population based cancer registry in Brunei Darussalam. A total of 728 patients were included in the analysis. Kaplan Meier method was used to estimate survival rates. Univariate analysis using log-rank test was used to examine the differences in survival between groups. Multivariate analysis using Cox PH regression was used to estimate hazard of death and obtain significant predictors that influence CRC patients’ survival. Results: The median survival time for colorectal, colon and rectal cancer patients were 57.0, 85.8 and 40.0 months respectively. The overall 1-, 3- and 5- year survival rates for CRC patients were 78.0%, 57.7% and 49.6% respectively. In univariate analysis, age at diagnosis, ethnicity, cancer stage, tumour location and histology were found to have significant difference in CRC patients’ survival. In the Cox PH analysis, older age (=70 years), cancer stage, ethnicity and other histological type were determined as associated factors of CRC patients’ survival. Conclusion: This study found the overall 5-year survival rate of CRC in Brunei Darussalam is similar to that in some Asian countries such as Singapore and Malaysia. However, more efforts need to be carried out in order to raise awareness of CRC and improve the survival of CRC patients.

Distance-based topological descriptors for measuring the π-electronic energy of benzenoid hydrocarbons with applications to carbon nanotubes

In this paper, we provide efficient regression models for correlating the π-electronic energies of carbon nanotubes and nanocones. First, a computational technique for determining distance-based, eccentricity-based, degree-distance-based, and degree-based molecular descriptors is proposed. Then, the application of our technique has been explained for the family of fibonacenes. Importantly, we use the proposed computational technique to determine commonly occurring distance-based molecular descriptors and generate regression models to determine their correlation with the π-electronic energies of lower polycyclic aromatic hydrocarbons (PAHs). Unlike its reputation among chemical graph theorists and reticular chemists, the fourth version of the geometric–arithmetic index outperforms all the distance-based descriptors having the correlation coefficient 0.999. This warrants further usage of the fourth geometric–arithmetic index in quantitative structure-activity relationship models. To ensure the applicability of our proposed study, we use the proposed computational technique to compute analytically explicit expressions for certain distance-based molecular descriptors for certain infinite families of carbon nanotubes and carbon nanocones. Our results assist in correlating the π-electronic energies of underlying chemical structures of these nanotubes and nanocones.

Childhood Cancer Survival in Brunei Darussalam

Background: This study aims to determine the survival rates for children and adolescents aged 0–19 years diagnosed with childhood cancer and to evaluate the associated factors for childhood cancer survival in Brunei Darussalam. Methods: The analysis was based on de-identified data of 263 childhood cancer for the period 2002 to 2017 retrieved from a population-based cancer registry. Overall survival was estimated using the Kaplan-Meier method. Univariate analysis, using the log-rank test, was used to examine the differences in survival between groups. Multivariate analysis, using the Cox Proportional Hazard (PH) regression model, was used to estimate the hazard ratios (HRs) and select the significant associated factors for childhood cancer patients’ survival. Results: The overall 1-, 5- and 10-year survival rates for all childhood cancers combined were 79.4%, 70.0% and 68.8% respectively. The most common types of cancer were leukemias, malignant epithelial neoplasms, lymphomas and tumours of the central nervous system (CNS). The 5-year survival estimates were highest for malignant epithelial neoplasms (84.2%) while the lowest was tumours of the CNS (44.1%). Log rank tests showed significant differences in childhood cancer patients’ survival between tumour types and period of diagnosis. In the Cox PH analysis, the presence of lymphomas, gonodal and germ cell neoplasms, and malignant epithelial neoplasms compared to leukemia; children aged 1–4 and 5–9 years compared to adolescents aged 15–19 years; and periods of diagnosis in 2002–2006 and 2007–2011 compared to 2012–2017 were significantly associated with lower hazard of death in this study. Conclusion: This study provides a baseline measurement of childhood cancer survival for monitoring and evaluation of cancer control programmes, to allow planning of cancer control program strategies such as surveillance, screening, and treatment to improve childhood survival rates in Brunei Darussalam.

BioHackathon 2015: Semantics of data for life sciences and reproducible research

We report on the activities of the 2015 edition of the BioHackathon, an annual event that brings together researchers and developers from around the world to develop tools and technologies that promote the reusability of biological data. We discuss issues surrounding the representation, publication, integration, mining and reuse of biological data and metadata across a wide range of biomedical data types of relevance for the life sciences, including chemistry, genotypes and phenotypes, orthology and phylogeny, proteomics, genomics, glycomics, and metabolomics. We describe our progress to address ongoing challenges to the reusability and reproducibility of research results, and identify outstanding issues that continue to impede the progress of bioinformatics research. We share our perspective on the state of the art, continued challenges, and goals for future research and development for the life sciences Semantic Web.

Predictive factors associated with survival rate of cervical cancer patients in Brunei Darussalam

Introduction: Cervical cancer is the third most prevalent cancer among women in Bru-nei Darussalam. This study aims to report the overall survival rates and associated factors of pa-tients diagnosed with malignant cervical cancer in Brunei Darussalam. Methods: A retrospective study of patients diagnosed with cervical cancer from 2007 to 2017 in Brunei Darussalam. The data were obtained from the population-based cancer registry in Brunei Darussalam. Kaplan-Meier survival analysis was used to estimate the overall survival rates at 1-, 3- and 5-year inter-vals while the log-rank test was used to assess differences in survival between groups. Cox Pro-portional Hazard (PH) regression analysis was used to examine the association of demographic and clinical factors on the survival of cervical cancer patients. Results: A total of 329 registered malignant cervical cancer cases were analyzed. The mean age at diagnosis of patients with cervi-cal cancer was 46.7 ± 12.2 years. There were 28.6% deaths and the overall survival rates at 1, 3 and 5 years were 85.4%, 72.6% and 68.6% respectively. Age at diagnosis, cancer stage and his-tology types were significant predictive factors for overall survival of the patients diagnosed with cervical cancers when analysed on both log rank tests and Cox PH model. Conclusion: Age at di-agnosis, cancer stage and histology types were significantly associated with the overall survival rates of cervical cancer patients in Brunei Darussalam. Early detection and management of cervi-cal cancer at early stages should be prioritized to improve the survival rate and quality of cancer care.

Five-year survival rate of breast cancer patients in Brunei Darussalam

Introduction: Breast cancer is the most common cancer and leading cause of cancer deaths among women worldwide. In Brunei Darussalam, breast cancer has the highest incidence rate among women. This study presents the survival rate of women diagnosed with breast cancer in Brunei Darussalam and explores the association between survival and demographic or clinical characteristics. Methods: This is a retrospective study of breast cancer diagnosed from 2007 to 2017 among women in Brunei Darussalam. Cancer data was retrieved from population based cancer registry. Kaplan-Meier survival analysis and Log rank test were applied to estimate the survival rates and the association between survival and important patients’ characteristics. Haz-ard ratios were derived using Cox Proportional Hazard model. Results: The survival rates of breast cancer patients at 1, 3 and 5 years were 89.5%, 79.2% and 72.0% respectively. The 5-year survival rates for cancer stages were 92.2% for localized, 76.9% for regional, and 21.4% for distant metastasis. Ethnicity, cancer stages and cancer stages-morphology interaction were sig-nificant independent predictors for breast cancer survival in Brunei Darussalam. Conclusion: The survival rate of women diagnosed with breast cancer in Brunei Darussalam and its significant pre-dictors are similar to those reported from other developed countries. Further studies on predic-tors such as health seeking behaviours and impact of different cancer treatment will provide fur-ther insight in improving survival rates of breast cancer through early cancer detection pro-grammes and strengthening of the healthcare service delivery.

BioHackathon series in 2013 and 2014: Improvements of semantic interoperability in life science data and services

Publishing databases in the Resource Description Framework (RDF) model is becoming widely accepted to maximize the syntactic and semantic interoperability of open data in life sciences. Here we report advancements made in the 6th and 7th annual BioHackathons which were held in Tokyo and Miyagi respectively. This review consists of two major sections covering: 1) improvement and utilization of RDF data in various domains of the life sciences and 2) meta-data about these RDF data, the resources that store them, and the service quality of SPARQL Protocol and RDF Query Language (SPARQL) endpoints. The first section describes how we developed RDF data, ontologies and tools in genomics, proteomics, metabolomics, glycomics and by literature text mining. The second section describes how we defined descriptions of datasets, the provenance of data, and quality assessment of services and service discovery. By enhancing the harmonization of these two layers of machine-readable data and knowledge, we improve the way community wide resources are developed and published. Moreover, we outline best practices for the future, and prepare ourselves for an exciting and unanticipatable variety of real world applications in coming years.

Valency-based topological descriptors of chemical networks and their applications

A topological descriptor/index (or molecular structure descriptor) is a numerical value associated with chemical constitution for correlation of chemical structure/network with various physical properties, chemical reactivity or biological activity. Quantitative structure–activity and structure–property relationships of chemical networks require expressions for the topological properties of these networks. Topological indices provide these expressions of topological properties. Valency-based topological descriptors are the oldest and most successful class of descriptors so far. A chemical graph/network is a representation of the structural formula of a chemical compound whose vertices correspond to the atoms of the compound and edges correspond to chemical bonds. In this paper, we study valency-based topological indices of chemical networks. By using some real world data, we performed certain comparative testings to investigate the performance of almost all well-known valency-based indices. Dependence on the molecular structure is studied for topological indices which are best in performance. We calculated explicit formulas for well-performed indices of some infinite families of carbon nanotubes, carbon nanocones and a newly proposed family of organic networks called tetrahedral diamond networks. Tetrahedral diamond networks arises by recurrently joining graphene layers in a diamond cluster. Significance and applicability of the obtained results are reported.

Using Margin-based Region of Interest Technique with Multi-Task Convolutional Neural Network and Template Matching for Robust Face Detection and Tracking System

Real-time face detection and tracking systems suffer from low accuracy and slow processing speed that lead to poor robustness. This problem is vital in real-time setups including human robot interactions (HRI) and video analysis systems. This paper presents margin-based region of interest (MROI) approach to speed up the processing time. Further a hybrid approach is also presented that combines Multi-task Convolutional Neural Networks (MTCNN) with template matching to improve face detection accuracy. The MROI approach which is responsible to speed up the processing time is presented in two variants with fixed and dynamic margin concepts. Dataset used in this work comprises of twenty RGB video files. Each video file is fifteen seconds long and been created from real-life videos containing a person in lecture delivering environment. Each video file contains a person in which the person moves, turns head and the camera also moves. The highest face detection and tracking accuracy achieved in this paper is 99.31% with a processing time of 14.93 milliseconds per frame. The proposed hybrid algorithm significantly improves the ability to detect and track faces in sideway orientation apart from frontal face. The proposed algorithm has the ability to process above 65 frames per second (FPS). The system presented has increased FPS processing ability by more than 400% as well as given boost to the accuracy if compared to the conventional MTCNN full frame scanning techniques.

Cooperative “folding transition” in the sequence space facilitates function-driven evolution of protein families

In the protein sequence space, natural proteins form clusters of families which are characterized by their unique native folds whereas the great majority of random polypeptides are neither clustered nor foldable to unique structures. Since a given polypeptide can be either foldable or unfoldable, a kind of “folding transition” is expected at the boundary of a protein family in the sequence space. By Monte Carlo simulations of a statistical mechanical model of protein sequence alignment that coherently incorporates both short-range and long-range interactions as well as variable-length insertions to reproduce the statistics of the multiple sequence alignment of a given protein family, we demonstrate the existence of such transition between natural-like sequences and random sequences in the sequence subspaces for 15 domain families of various folds. The transition was found to be highly cooperative and two-state-like. Furthermore, enforcing or suppressing consensus residues on a few of the well-conserved sites enhanced or diminished, respectively, the natural-like pattern formation over the entire sequence. In most families, the key sites included ligand binding sites. These results suggest some selective pressure on the key residues, such as ligand binding activity, may cooperatively facilitate the emergence of a protein family during evolution. From a more practical aspect, the present results highlight an essential role of long-range effects in precisely defining protein families, which are absent in conventional sequence models.

Modeling and forecasting volatility series: With reference to gold price

The recent global financial crisis has highlighted the need for financial institutions to find and implement of appropriate models for risk measurement. There was a particular interest of investors to increase their positions in the gold market as the risk in equity and bond markets was increasing. This study evaluates the effectiveness of various volatility models with respect to modeling and forecasting market risk in the gold future market. For this study, last trading price of gold futures are considered from January 1990 to June 2014 with 6,373 observations. The gold futures volatility is modeled and forecasted using GARCH-class models with long memory and fat-tail distributions, by considering ARMA model as the conditional returns. The results reveal that ARMA(1,1) model provides best results for the conditional returns. Among the linear and non-linear GARCH-class models, EGARCH and FIEGARCH models are provided best results for in-sampling forecasting. Moreover, EGARCH model gives bit of higher performance than FIEGARCH model under model diagnostic tests. After that, futures price volatilities of gold are forecasted using EGARCH and FIEGARCH models. Furthermore, it was found that long memory effect is significant. Forecasting accuracy of GARCH-class models are compared with different distributions of innovations. The results indicate that GARCH model with skew t-distribution outperform those with normal distribution. For speculations and noise traders in futures market, both linear and nonlinear models should be taken into account.

Determining the relationship and influencing factors of high school students’ performances and achievements in mathematics

This study examined 86 high school (Year 11) students’ basic proficiencies in Mathematics were examined, and the connections between language proficiency, gender, family socio-economic background and family factors to their performances were also identified. A ‘proficiency test’ paper was developed to investigate students’ proficiency in Mathematics, and semi-structured interviews were utilized to gather data regarding parental involvement in students’ academic activities. Several different statistical tests were employed for the data analyse. Although the findings revealed a positive correlation between students’ proficiency test score and their yearly Mathematics achievements, the relationship between students’ basic proficiency in Mathematics and their gender were not found to be significant. The students’ English language literacy was significantly related to their achievements in Mathematics. And the students’ basic proficiency in Mathematics and parents’ income was significantly correlated, but the students’ proficiency and parents’ education was not significantly correlated. Students’ English language proficiency and parental involvement in terms of emotional or financial support (such as attending private tuition class) were also determined to be the contributing factors in the students’ achievement in Mathematics.

Neuro-symbolic representation learning on biological knowledge graphs

Motivation: Biological data and knowledge bases increasingly rely on Semantic Web technologies and the use of knowledge graphs for data integration, retrieval and federated queries. In the past years, feature learning methods that are applicable to graph-structured data are becoming available, but have not yet widely been applied and evaluated on structured biological knowledge. Results: We develop a novel method for feature learning on biological knowledge graphs. Our method combines symbolic methods, in particular knowledge representation using symbolic logic and automated reasoning, with neural networks to generate embeddings of nodes that encode for related information within knowledge graphs. Through the use of symbolic logic, these embeddings contain both explicit and implicit information. We apply these embeddings to the prediction of edges in the knowledge graph representing problems of function prediction, finding candidate genes of diseases, protein-protein interactions, or drug target relations, and demonstrate performance that matches and sometimes outperforms traditional approaches based on manually crafted features. Our method can be applied to any biological knowledge graph, and will thereby open up the increasing amount of Semantic Web based knowledge bases in biology to use in machine learning and data analytics.Availability and implementation: https://github.com/bio-ontology-research-group/walking-rdf-and-owl.Contact: robert.hoehndorf@kaust.edu.sa.Supplementary information: Supplementary data are available at Bioinformatics online.

Protein Data Bank Japan (PDBj): Updated user interfaces, resource description framework, analysis tools for large structures

The Protein Data Bank Japan (PDBj, http://pdbj.org), a member of the worldwide Protein Data Bank (ww- PDB), accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins.We herein outline the updated web user interfaces together with RESTful web services and the backend relational database that support the former. To enhance the interoperability of the PDB data, we have previously developed PDB/RDF, PDB data in the Resource Description Framework (RDF) format, which is now a wwPDB standard called wwPDB/RDF. We have enhanced the connectivity of the wwPDB/RDF data by incorporating various external data resources. Services for searching, comparing and analyzing the ever-increasing large structures determined by hybrid methods are also described.

Integrating the use of interdisciplinary learning activity task in creating students’ mathematical knowledge

This study investigated the use of interdisciplinary learning activity task to construct students‟ knowledge in Mathematics, specifically on the topic of scale drawing application. The learning activity task involved more than one academic discipline, which is Mathematics, English Language, Art, Geography and integrating the Brunei Darussalam national philosophy of the Malay Islamic Monarchy. A quantitative method using a pre-experimental design focusing on one-group pre-and post-test design was used for this study. The participants were selected from a convenient sample of 43 Year 9 students in one of the secondary schools in Brunei. The findings were also triangulated with the students‟ collected reflective journal artifact documents. Each student journal was analyzed using the identified learning activity stages within the RBC-model, where the R denotes Recognizing, B is Building with and C means Constructing. The results showed an improvement in the students‟ achievement, and they were able to construct the mathematics knowledge by means of collaboration among group members. Based on the findings, it is recommended that Mathematics teachers be encouraged and supported to design authentic and interdisciplinary learning activity that are learner centered catering to the different needs of our students and also to meet the 21st century skills demand.

Hybrid model with margin-based real-time face detection and tracking

Face detection and tracking algorithms mainly suffer from low accuracy, slow processing speed, and poor robustness when meet with real-time setup. The problem becomes crucial in real-time situations such as in human robot interactions (HRI) or video analysis. A margin-based region of interest (ROI) hybrid approach that combines Haar cascade and template matching for face detection and tracking is proposed in this paper to improve the detection accuracy and processing speed. To speed up the processing time, region of interests (ROIs) with fixed and dynamic margin concepts are used. A dataset comprising of ten RGB video streams of fifteen seconds have been created from real-life videos containing a person in lecture delivering environment. In each video, there exists person’s movement, face turning and camera movements. An accuracy of 97.96% with processing time of 10.76 ms per frame has been achieved. The proposed algorithm can detect and track faces in sideway orientation apart from frontal face. The proposed approach can process the video streams at the speed above 90 frames per second (FPS). The proposed approach reduces processing time by ten times and with a boost to accuracy in comparison to the conventional full frame scanning techniques.

VaProS: a database-integration approach for protein/genome information retrieval

Life science research now heavily relies on all sorts of databases for genome sequences, transcription, protein three-dimensional (3D) structures, protein–protein interactions, phenotypes and so forth. The knowledge accumulated by all the omics research is so vast that a computer-aided search of data is now a prerequisite for starting a new study. In addition, a combinatory search throughout these databases has a chance to extract new ideas and new hypotheses that can be examined by wet-lab experiments. By virtually integrating the related databases on the Internet, we have built a new web application that facilitates life science researchers for retrieving experts’ knowledge stored in the databases and for building a new hypothesis of the research target. This web application, named VaProS, puts stress on the interconnection between the functional information of genome sequences and protein 3D structures, such as structural effect of the gene mutation. In this manuscript, we present the notion of VaProS, the databases and tools that can be accessed without any knowledge of database locations and data formats, and the power of search exemplified in quest of the molecular mechanisms of lysosomal storage disease. VaProS can be freely accessed at http://p4d-info.nig.ac.jp/vapros/.

Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins

Background: The nuclear magnetic resonance (NMR) spectroscopic data for biological macromolecules archived at the BioMagResBank (BMRB) provide a rich resource of biophysical information at atomic resolution. The NMR data archived in NMR-STAR ASCII format have been implemented in a relational database. However, it is still fairly difficult for users to retrieve data from the NMR-STAR files or the relational database in association with data from other biological databases. Findings: To enhance the interoperability of the BMRB database, we present a full conversion of BMRB entries to two standard structured data formats, XML and RDF, as common open representations of the NMR-STAR data. Moreover, a SPARQL endpoint has been deployed. The described case study demonstrates that a simple query of the SPARQL endpoints of the BMRB, UniProt, and Online Mendelian Inheritance in Man (OMIM), can be used in NMR and structure-based analysis of proteins combined with information of single nucleotide polymorphisms (SNPs) and their phenotypes. Conclusions: We have developed BMRB/XML and BMRB/RDF and demonstrate their use in performing a federated SPARQL query linking the BMRB to other databases through standard semantic web technologies. This will facilitate data exchange across diverse information resources.

Common misconceptions of algebraic problems: Identifying trends and proposing possible remedial measures

Algebra is a fundamental concept in Mathematics at the secondary level. The focus of this study is on the four different main subtopics in algebra namely, factorisation, expansion, inequalities and algebraic application word problems. This study aims to investigate and identify misconceptions and common errors occurring among secondary school students as well as to suggest solutions to counter each respective common error found according to each subtopic. For the purpose of this study, a test paper was designed containing five questions. Each question consisted of one of the four main algebra subtopics and an additional fifth question on inequality. The test was disseminated to a mixed ability Year 10 class in Brunei Darussalam chosen by convenient sampling. The findings reported were from the qualitative analyses of the collected students’ work. Constant patterns of misconceptions and common errors emerging among the students were discerned and its findings were reported in this paper. According to the findings, generally, the students developed misconceptions that prevented them from achieving the required solutions. As a consequence, these misconceptions had strongly led the students towards the action of performing common errors in their workings. Hence, to overcome these consistently incorrect habits among students from arising in the future, the suggested solutions should be included in the teaching strategies as a guide for future educators of Mathematics.

An alternative approach to teaching: Implementing a cooperative learning strategy students team achievement division at the junior college level

In this action research study on junior college level (the equivalent of 11th and 12th grades in American schooling) students, an investigation was conducted to determine the effectiveness in implementing a cooperative learning strategy known as the Students Team Achievement Division (STAD). Data were collected quantitatively and qualitatively from two groups of 95 first year students in one of the junior colleges in Brunei Darussalam. In the first cycle, an achievement test was administered to Group 1 without STAD (N = 49) and Group 2 with STAD (N = 46). An independent sample t-test was later conducted to compare the two groups and the results showed that there was a significant difference in their mathematics scores; for Group 1 without STAD (M = 35.8%, SD = 19.9) and Group 2 with STAD (M = 45.6%, SD = 20.8) on conditions; t(93) = 2.347, p = 0.0211. The p-value indicated that this difference in mean was statistically significant. In addition, qualitative data was collected in the form of an unstructured interview in each of the two cycles. The findings revealed that the students were positive and satisfied with the STAD approach. Implementing the cooperative learning strategy STAD may be useful as an alternative teaching method for junior college level mathematics.

Persistent random walk of cells involving anomalous effects and random death

The purpose of this paper is to implement a random death process into a persistent random walk model which produces sub-ballistic superdiffusion (Lévy walk). We develop a stochastic two-velocity jump model of cell motility for which the switching rate depends upon the time which the cell has spent moving in one direction. It is assumed that the switching rate is a decreasing function of residence (running) time. This assumption leads to the power law for the velocity switching time distribution. This describes the anomalous persistence of cell motility: the longer the cell moves in one direction, the smaller the switching probability to another direction becomes. We derive master equations for the cell densities with the generalized switching terms involving the tempered fractional material derivatives. We show that the random death of cells has an important implication for the transport process through tempering of the superdiffusive process. In the long-time limit we write stationary master equations in terms of exponentially truncated fractional derivatives in which the rate of death plays the role of tempering of a Lévy jump distribution. We find the upper and lower bounds for the stationary profiles corresponding to the ballistic transport and diffusion with the death-rate-dependent diffusion coefficient. Monte Carlo simulations confirm these bounds.

Discovery year options and students’ preferences

In 2009, the Universiti Brunei Darussalam (UBD) made extensive changes to its curriculum from a majorcentric to a liberal arts style broad-based degree with emphasis on the soft-skill development. One of the important components of the new curriculum is the mandatory year out also known as the ‘Discovery Year’. The objectives of the discovery year is to promote real-world experiential and design-centric learning, and students are given the opportunity to gain community-based or international experience outside of the UBD campus. During the discovery year, students have a choice of four activities namely study abroad, internship, incubation and community outreach programme. Since the inception of the discovery year, study abroad has always been the first choice for most of our students. In 2011, the ratio of UBD students who did the study abroad programme was 4 out of 10. This proportion increased to 7 out of 10 in 2014. More importantly, around 90% of students who left Brunei chose the study abroad option. In this paper, we investigated the reasons behind why study abroad is and has always been the first choice, and also the reasons behind the increasing proportion. We also explored the benefits of study abroad from the perspectives of both the home and host universities. Furthermore, we examined the issues and challenges that hindered the students from taking other activities during discovery year. To conclude, the benefits of study abroad are an all encompassing one from raising the quality of education, improving the university’s ranking to fostering global citizens.

Specific non-local interactions are not necessary for recovering native protein dynamics

The elastic network model (ENM) is a widely used method to study native protein dynamics by normal mode analysis (NMA). In ENM we need information about all pairwise distances, and the distance between contacting atoms is restrained to the native value. Therefore ENM requires O(N2) information to realize its dynamics for a protein consisting of N amino acid residues. To see if (or to what extent) such a large amount of specific structural information is required to realize native protein dynamics, here we introduce a novel model based on only O(N ) restraints. This model, named the ‘contact number diffusion’ model (CND), includes specific distance restraints for only local (along the amino acid sequence) atom pairs, and semi-specific non-local restraints imposed on each atom, rather than atom pairs. The semi-specific non-local restraints are defined in terms of the non-local contact numbers of atoms. The CND model exhibits the dynamic characteristics comparable to ENM and more correlated with the explicit-solvent molecular dynamics simulation than ENM. Moreover, unrealistic surface fluctuations often observed in ENM were suppressed in CND. On the other hand, in some ligand-bound structures CND showed larger fluctuations of buried protein atoms interacting with the ligand compared to ENM. In addition, fluctuations from CND and ENM show comparable correlations with the experimental B-factor. Although there are some indications of the importance of some specific non-local interactions, the semi-specific non-local interactions are mostly sufficient for reproducing the native protein dynamics.

Exhaustive comparison and classification of ligand-binding surfaces in proteins

Many proteins function by interacting with other small molecules (ligands). Identification of ligand-binding sites (LBS) in proteins can therefore help to infer their molecular functions. A comprehensive comparison among local structures of LBSs was previously performed, in order to understand their relationships and to classify their structural motifs. However, similar exhaustive comparison among local surfaces of LBSs (patches) has never been performed, due to computational complexity. To enhance our understanding of LBSs, it is worth performing such comparisons among patches and classifying them based on similarities of their surface configurations and electrostatic potentials. In this study, we first developed a rapid method to compare two patches. We then clustered patches corresponding to the same PDB chemical component identifier for a ligand, and selected a representative patch from each cluster. We subsequently exhaustively as compared the representative patches and clustered them using similarity score, PatSim. Finally, the resultant PatSim scores were compared with similarities of atomic structures of the LBSs and those of the ligand-binding protein sequences and functions. Consequently, we classified the patches into 2000 well-characterized clusters. We found that about 63% of these clusters are used in identical protein folds, although about 25% of the clusters are conserved in distantly related proteins and even in proteins with cross-fold similarity. Furthermore, we showed that patches with higher PatSim score have potential to be involved in similar biological processes.

NPlug: An autonomous peak load controller

The Indian electricity sector, despite having the world’s fifth largest installed capacity, suffers from a 12.9% peaking shortage. This shortage could be alleviated, if a large number of deferrable loads, particularly the high powered ones, could be moved from on-peak to off-peak times. However, conventional Demand Side Management (DSM) strategies may not be suitable for India as the local conditions usually favor inexpensive solutions with minimal dependence on the pre-existing infrastructure. In this work, we present a completely autonomous DSM controller called the nPlug. nPlug is positioned between the wall socket and deferrable load(s) such as water heaters, washing machines, and electric vehicles. nPlugs combine local sensing and analytics to infer peak periods as well as supply-demand imbalance conditions. They schedule attached appliances in a decentralized manner to alleviate peaks whenever possible without violating the requirements of consumers. nPlugs do not require any manual intervention by the end consumer nor any communication infrastructure nor any enhancements to the appliances or the power grids. Some of nPlug’s capabilities are demonstrated using experiments on a combination of synthetic and real data collected from plug-level energy monitors. Our results indicate that nPlug can be an effective and inexpensive technology to address the peaking shortage. This technology could potentially be integrated into millions of future deferrable loads: appliances, electric vehicle (EV) chargers, heat pumps, water heaters, etc. © 1983-2012 IEEE.

Functional structural motifs for protein-ligand, protein-protein, and protein-nucleic acid interactions and their connection to supersecondary structures

Protein functions are mediated by interactions between proteins and other molecules. One useful approach to analyze protein functions is to compare and classify the structures of interaction interfaces of proteins. Here, we describe the procedures for compiling a database of interface structures and ef fi ciently comparing the interface structures. To do so requires a good understanding of the data structures of the Protein Data Bank (PDB). Therefore, we also provide a detailed account of the PDB exchange dictionary necessary for extracting data that are relevant for analyzing interaction interfaces and secondary structures. We identify recurring structural motifs by classifying similar interface structures, and we de fi ne a coarse-grained representation of supersecondary structures (SSS) which represents a sequence of two or three secondary structure elements including their relative orientations as a string of four to seven letters. By examining the correspondence between structural motifs and SSS strings, we show that no SSS string has particularly high propensity to be found interaction interfaces in general, indicating any SSS can be used as a binding interface. When individual structural motifs are examined, there are some SSS strings that have high propensity for particular groups of structural motifs. In addition, it is shown that while the SSS strings found in particular structural motifs for nonpolymer and protein interfaces are as abundant as in other structural motifs that belong to the same subunit, structural motifs for nucleic acid interfaces exhibit somewhat stronger preference for SSS strings. In regard to protein folds, many motif-speci fi c SSS strings were found across many folds, suggesting that SSS may be a useful description to investigate the universality of ligand binding modes.

Composite structural motifs of binding sites for delineating biological functions of proteins

Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at atomic resolution, and thereby to better understand the relation between protein interactions and biological functions, we conducted exhaustive all-against-all atomic structure comparisons of all known binding sites for ligands including small molecules, proteins and nucleic acids, and identified recurring elementary motifs. By integrating the elementary motifs associated with each subunit, we defined composite motifs that represent context-dependent combinations of elementary motifs. It is demonstrated that function similarity can be better inferred from composite motif similarity compared to the similarity of protein sequences or of individual binding sites. By integrating the composite motifs associated with each protein function, we define meta-composite motifs each of which is regarded as a time-independent diagrammatic representation of a biological process. It is shown that meta-composite motifs provide richer annotations of biological processes than sequence clusters. The present results serve as a basis for bridging atomic structures to higher-order biological phenomena by classification and integration of binding site structures.

Protein Data Bank Japan (PDBj): Maintaining a structural data archive and resource description framework format

The Protein Data Bank Japan (PDBj, http://pdbj.org) is a member of the worldwide Protein Data Bank (wwPDB) and accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins, which are summarized in this article. To enhance the interoperability of the PDB data, we have recently developed PDB/RDF, PDB data in the Resource Description Framework (RDF) format, along with its ontology in the Web Ontology Language (OWL) based on the PDB mmCIF Exchange Dictionary. Being in the standard format for the Semantic Web, the PDB/RDF data provide a means to integrate the PDB with other biological information resources.

Performance evaluation and optimization of nested high resolution weather simulations

Weather models with high spatial and temporal resolutions are required for accurate prediction of meso-micro scale weather phenomena. Using these models for operational purposes requires forecasts with sufficient lead time, which in turn calls for large computational power. There exists a lot of prior studies on the performance of weather models on single domain simulations with a uniform horizontal resolution. However, there has not been much work on high resolution nested domains that are essential for high-fidelity weather forecasts. In this paper, we focus on improving and analyzing the performance of nested domain simulations using WRF on IBM Blue Gene/P. We demonstrate a significant reduction (up to 29%) in runtime via a combination of compiler optimizations, mapping of process topology to the physical torus topology, overlapping communication with computation, and parallel communications along torus dimensions. We also conduct a detailed performance evaluation using four nested domain configurations to assess the benefits of the different optimizations as well as the scalability of different WRF operations. Our analysis indicates that the choice of nesting configuration is critical for good performance. To aid WRF practitioners in making this choice, we describe a performance modeling approach that can predict the total simulation time in terms of the domain and processor configurations with a very high accuracy (< 8%) using a regression-based model learned from empirical timing data.

nPlug: A smart plug for alleviating peak loads

The Indian electricity sector, despite having the world’s fifth largest installed capacity, suffers from a 12.9% peaking shortage. This shortage could be alleviated, if a large number of deferrable loads, particularly the high powered ones, could be moved from on-peak to off-peak times. However, conventional DSM strategies may not be suitable for India as the local conditions usually favor only inexpensive solutions with minimal dependence on the pre-existing infrastructure. In this work, we present nPlug, a smart plug that sits between the wall socket and deferrable loads such as water heaters, washing machines, and electric vehicles. nPlugs combine real-time sensing and analytics to infer peak periods as well as supply-demand imbalance and reschedule attached appliances in a decentralized manner to alleviate peaks whenever possible. They do not require any manual intervention by the end consumer nor any enhancements to the appliances or existing infrastructure. Some of nPlug’s capabilities are demonstrated using experiments on a combination of synthetic and real data collected from plug-level energy monitors. Our results indicate that nPlug can be an effective and inexpensive technology to address the peaking shortage. © 2012 ACM.