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Stress analysis of femoral bone resorption with implant

Solehuddin Shuib, Sahari, B.B., Wong, Shaw Voon, Arumugam, Manohar, Halim Kadarman, A.

CREAM : Current Research in Malaysia (Penyelidikan Terkini di Malaysia), 2013;2(2):23-41.
MyJurnal

Bone is a living tissue. It continuously reproduces its structure and its growth depends partly upon the applied mechanical load. After an implant is inserted, the load equilibrium is disturbed, leading to bone resorption and the stress shielding phenomena. Aseptic loosening is the main contributor for hip prosthesis failure. The purpose of the study is to determine the effect of bone resorption on the stress values and hence obtain a better understanding of the behavior of the stress adaptive bone-remodeling. The bone material used for the analysis was assumed to be isotropic and linearly elastic, and the external loads applied comprised of a femoral head load and an abductor load. A Finite element computer program for evaluating the changes in bone's density and modulus was developed. The values of stress for bone, cement mantle in medial, and lateral positions of Total Hip Replacement (THR) are presented. The failure mechanisms of THR with bone resorption observed the implant loosening since stress is reduced.

Matched MeSH terms: Software
ENRI: A tool for selecting structure-based virtual screening target conformations

Akbar R, Jusoh SA, Amaro RE, Helms V

Chem Biol Drug Des, 2017 May;89(5):762-771.
PMID: 27995760 DOI: 10.1111/cbdd.12900

Finding pharmaceutically relevant target conformations from an arbitrary set of protein conformations remains a challenge in structure-based virtual screening (SBVS). The growth in the number of available conformations, either experimentally determined or computationally derived, obscures the situation further. While the inflated conformation space potentially contains viable druggable targets, the increase of conformational complexity, as a consequence, poses a selection problem. To address this challenge, we took advantage of machine learning methods, namely an over-sampling and a binary classification procedure, and present a novel method to select druggable receptor conformations. Specifically, we trained a binary classifier on a set of nuclear receptor conformations, wherein each conformation was labeled with an enrichment measure for a corresponding SBVS. The classifier enabled us to formulate suggestions and identify enriching SBVS targets for six of seven nuclear receptors. Further, the classifier can be extended to other proteins of interest simply by feeding new training data sets to the classifier. Our work, thus, provides a methodology to identify pharmaceutically interesting receptor conformations for nuclear receptors and other drug targets.

Matched MeSH terms: Software*
Fulltext Microwave synthesis, crystal structure, antioxidant, and antimicrobial study of new 6-heptyl-5,6-dihydrobenzo[4,5]imidazo[1,2-c]quinazoline compound

Hasan HA, Abdulmalek E, Rahman MBA, Shaari KB, Yamin BM, Chan KW

Chem Cent J, 2018 Dec 20;12(1):145.
PMID: 30570683 DOI: 10.1186/s13065-018-0509-z

BACKGROUND: Although the development of antibiotic and antioxidant manufacturing, the problem of bacterial resistance and food and/or cosmetics oxidation still needs more efforts to design new derivatives which can help to minimize these troubles. Benzimidazo[1,2-c]quinazolines are nitrogen-rich heterocyclic compounds that possess many pharmaceutical properties such as antimicrobial, anticonvulsant, immunoenhancer, and anticancer.
RESULTS: A comparative study between two methods, (microwave-assisted and conventional heating approaches), was performed to synthesise a new quinazoline derivative from 2-(2-aminophenyl)-1H-benzimidazole and octanal to produce 6-heptyl-5,6-dihydrobenzo[4,5]imidazo[1,2-c]quinazoline (OCT). The compound was characterised using FTIR, 1H and 13C NMR, DIMS, as well as X-ray crystallography. The most significant peak in the 13C NMR spectrum is C-7 at 65.5 ppm which confirms the cyclisation process. Crystal structure analysis revealed that the molecule grows in the monoclinic crystal system P21/n space group and stabilised by an intermolecular hydrogen bond between the N1-H1A…N3 atoms. The crystal packing analysis showed that the molecule adopts zig-zag one dimensional chains. Fluorescence study of OCT revealed that it produces blue light when expose to UV-light and its' quantum yield equal to 26%. Antioxidant activity, which included DPPH· and ABTS·+ assays was also performed and statistical analysis was achieved via a paired T-test using Minitab 16 software with P

Matched MeSH terms: Software
Development of a novel mathematical model using a group contribution method for prediction of ionic liquid toxicities

Ismail Hossain M, Samir BB, El-Harbawi M, Masri AN, Abdul Mutalib MI, Hefter G, et al.

Chemosphere, 2011 Oct;85(6):990-4.
PMID: 21794892 DOI: 10.1016/j.chemosphere.2011.06.088

A new mathematical model has been developed that expresses the toxicities (EC₅₀ values) of a wide variety of ionic liquids (ILs) towards the freshwater flea Daphnia magna by means of a quantitative structure-activity relationship (QSAR). The data were analyzed using summed contributions from the cations, their alkyl substituents and anions. The model employed multiple linear regression analysis with polynomial model using the MATLAB software. The model predicted IL toxicities with R²=0.974 and standard error of estimate of 0.028. This model affords a practical, cost-effective and convenient alternative to experimental ecotoxicological assessment of many ILs.

Matched MeSH terms: Software
Patients with congenital hypothyroidism demonstrate different altered expression of plasma fibrinogen and haptoglobin polypeptide chains

Yong PH, Junit SM, Harun F, Hashim OH

Clin Biochem, 2006 Feb;39(2):126-32.
PMID: 16412408

To compare the plasma protein profiles of treated and untreated congenital hypothyroidism (CH) patients with those of normal control infants.

Matched MeSH terms: Software
Fulltext Efficacy of WINROP as a Screening Tool for Retinopathy of Prematurity in the East Coast of Malaysia

Lim ZD, Oo KT, Tai ELM, Shatriah I

Clin Ophthalmol, 2020;14:1101-1106.
PMID: 32425496 DOI: 10.2147/OPTH.S247820

Purpose: To evaluate the efficacy of the "weight, insulin-like growth factor 1, neonatal retinopathy of prematurity" (WINROP) algorithm in predicting retinopathy of prematurity (ROP) requiring treatment in Malaysia.
Participants: This was a retrospective study involving premature infants with gestational age less than 32 weeks treated from September 2016 to March 2019 in Hospital Universiti Sains Malaysia. Clinical diagnosis was made based on Early Treatment Retinopathy of Prematurity study. Participants' weekly weight gain since birth was entered in the website (http://winrop.com), along with date of birth, gestational age and final clinical examination outcome. WINROP software signals an alarm if an infant is at high risk of developing ROP requiring treatment during weight data entry. By using the alarm status, the sensitivity and specificity of this algorithm for predicting ROP requiring treatment were obtained.
Results: Ninety-two infants were included in this study. An alarm was detected in 67 infants (72.8%). There were a total of 53 infants (54.6%) with no ROP, 15 (16.3%) of whom developed stage 1 ROP, 10 (10.8%) who developed stage 2 ROP and 14 infants (15.2%) who developed stage 3 ROP. In our study, WINROP sensitivity was 95.2% and specificity was 33.8%.
Conclusion: WINROP is recommended as an initial screening tool for premature infants at risk of developing treatment-requiring ROP in Malaysia. It may help to alert clinicians managing severely ill infants when clinical examinations are less possible.

Matched MeSH terms: Software
Dimensional profile of oral mucosa around combined tooth-implant-supported bridgework in macaque mandible

Siar CH, Toh CG, Ali TB, Seiz D, Ong ST

Clin Oral Implants Res, 2012 Apr;23(4):438-46.
PMID: 21435011 DOI: 10.1111/j.1600-0501.2010.02145.x

A stable oral mucosa is crucial for long-term survival and biofunctionality of implants. Most of this evidence is derived from clinical and animal studies based solely on implant-supported prosthesis. Much less is known about the dimensions and relationships of this soft tissue complex investing tooth-implant-supported bridgework (TISB). The aim here was to obtain experimental evidence on the dimensional characteristics of oral mucosa around TISB with two different abutment designs.

Matched MeSH terms: Software
Fulltext Effects of antihypertensive drugs on alveolar bone loss in patients with chronic periodontitis: a retrospective study

AL-Bayaty, F.H., Omar Emad Ibrahim, William, C., Khairuddin, N.A.

Compendium of Oral Science, 2018;5(1):26-36.
MyJurnal

Objective: This retrospective study aims to evaluate the possible effects of antihypertensive drugs on alveolar bone loss in patients with chronic periodontitis. Methods: 50 patients on antihypertensive drugs selected as the experimental group and 50 patients with chronic periodontitis with no known systemic illnesses as control group were randomly selected as the study samples. Orthopantomographs were obtained, calibration and assessment of alveolar bone loss was performed by using the computer software program available in the faculty, through radiographic linear measurement procedure. Premolars, first and second molars of both maxilla and mandible were measured from the most apical point to the cementoenamel junction for mesial and distal aspects in the form of millimetres and percentile of the root length. Data was statistically analyzed using independent t-test and Analysis of Covariance in SPSS Version 23 with significance at P-value, p

Matched MeSH terms: Software
Fulltext Digitalized bite mark analysis for the undergraduate dental students

Mohd Yusmiaidil Putera Mohd Yusof

Compendium of Oral Science, 2015;2(1):1-5.
MyJurnal

In legal system, the admissibility of bite mark injury has proven to give more positive impact when current tech-nologies are adapted to its analysis. The early exposure of the digitalized bite mark analysis during the under-graduate dental program is beneficial to stimulate interests and provide guidance among the professional den-tists. The step-by-step bite mark analysis partly adapted from KU Leuven, Belgium is emphasized by delivering the illustrated practical techniques using computer software Adobe Photoshop®. The overlays analysis demon-strated its practicality as easy to use and offered opportunities to learn through unconventional mode of teach-ing. The incorporation of bite mark injury analysis to the undergraduate dental learning is highly recommended

Matched MeSH terms: Software
Fulltext Feasibility of using latex examination gloves as dental dam: a tensile strength study

Budi Aslinie Md Sabri, Nur Hidayah Mohd Radzi, Fatimatuz Zahira Abdul Hadi, Ikmal HishamIsmai

Compendium of Oral Science, 2015;2(1):6-13.
MyJurnal

Objective: To evaluate feasibility of hand gloves as a rubber dam isolation alternative, in respect of physical properties. Materials and Methods: A randomized controlled trial study design was used. Three types of gloves were tested with two types of a rubber dam used as the control group. Cut-out pattern of dumb-bell shapes were made from 35 samples for each type of groups and tensile strength were tested using Universal Testing Machine and the Trapezium X software. All tests for physical requirements were performed in accord-ance with American Society for Testing and Materials D412, Standard Test Methods for Vulcanized Rubber and Thermoplastic Rubbers and Thermoplastic Elastomers-Tension. Findings were analyzed by analysis of vari-ance (ANOVA) and differences were compared using a Tukey-Kramer interval calculated at the 0.05 signifi-cance level. Results: Heavy gauge rubber dam has the highest Mean (calculated at the 0.05 significance level) except for maximum stress calculated at entire area. Medium-gauge rubber dam has significantly higher tensile strength (44.5075 N/mm2) when compared to heavy-gauge rubber dam (35.7787 N/mm2) although it was 0.09mm thinner. Discovery 2020 Powder Free Latex Examination Gloves with tensile strength value of 28.5922 N/mm2 (±3.27366) is more than the minimum requirement specified by American Federal Specification ZZ-R90B Rubber Dam (Dental, 1985) (4000 pounds per square inch or 27.6 N/mm2). For all variable tested, all groups are significantly different from each other. The mean square between the groups was quite large. Conclusion: This study shows that there are significant differences between the physical strength of latex gloves when com-pared to rubber dam. However, the comparison between thickness and tensile strength among various rubber dam, did not correspond proportionately. Only one type of rubber gloves met the minimum requirement but that is just one aspect. In view of these mixed results, more research is needed before we can conclude that it is feasable that we use hand gloves to replace rubber dam.

Matched MeSH terms: Software
Fulltext Reliability of the pressure indicating film for occlusal force analysis: a pilot study

Idris R.I, Tasri, N,I, Yusof, S.F., Lim, T.W., Shoji, Y.

Compendium of Oral Science, 2019;6(1):9-14.
MyJurnal

Objective: : The aim of this study was to evaluate the reliability of the pressure indicating film in measuring pressure exerted on it with and without Polyethylene (PE) sleeve as infection control purposes, and to analyze the pressure produced with its software for occlusal force study. Materials and Methods: The optimization of the pressure indicating film for occlusal force analysis commenced with the design and calibration of this sheet. The film was designed into horseshoe shape to suit the shape of maxillary and mandibular arches. The calibration was initiated with 5 different types of pressure which were 15 MPa, 25 MPa, 30 MPa, 35 MPa and 45 MPa exerted on two groups of the film: (i) with PE sleeve and (ii) without PE sleeve. Three readings were recorded for each group and mean value was documented. Then, the films were calibrated by its software for pressure analysis. Results: There was no significance difference found between the film with and without PE sleeve during the calibration stage (P>0.05). In all groups of pressure, there was no significant difference documented between pressure exerted and read out value. Conclusion: The results suggested that the film can be used for occlusal force analysis and improvement of the film with addition of PE sleeve for hygienic purpose is suitable to form the basis of clinical occlusal forces study.

Matched MeSH terms: Software
Fulltext Performance of dental undergraduate students using international caries detection and assessment system (icdas)

Sanus,M,A,, Nordin,M,A,, Rusli,M,R,, Mohamed,Z,N,h,

Compendium of Oral Science, 2020;7(1):13-19.
MyJurnal

Abstract
Objectives: This study aimed to assess intra- and inter-examiner reliability of International Caries Detection
and Assessment System (ICDAS) and modified epidemiology ICDAS (MOD) code by undergraduate dental
students with different clinical experiences.
Methods: A total of 150 dental undergraduate students with varying clinical experiences (0, 1 and 2 years of
clinical experience) were recruited. Participants received training through a theoretical lecture on ICDAS criteria
by an experienced National Benchmark Group (NBG) examiner and underwent e-learning program prior to
ICDAS calibration. Visual examination on extracted permanent teeth (N= 45) with different location and stages
of caries progression ranging from ICDAS scores 0 to 6, was performed using the ICDAS criteria. The
assessments were repeated after one hour. The data were analysed to evaluate inter-examiner and
intra-examiner reliability in the form of kappa scores using SPSS 23 Software.
Results: Mean kappa values for intra- and inter-examiner reliability for ICDAS code, were between 0.41 to
0.60, and 0.61 to 0.80 respectively. For MOD code, mean kappa values for intra- and inter-examiner reliability
were between 0.61 to 0.80. Good intra-examiner agreement (>0.61) was observed in both ICDAS and MOD
code for all groups.
Conclusion: All students performed similar agreement, therefore, clinical experience within 2 years does not
influence the performance of visual inspection in detecting caries using ICDAS. The results of the study shows
that ICDAS and modified epidemiology ICDAS codes has good reproducibility and is feasible to be used as a
tool in clinical practice as well as patient education.

Matched MeSH terms: Software
Fulltext Automatic detection and quantification of WBCs and RBCs using iterative structured circle detection algorithm

Alomari YM, Sheikh Abdullah SN, Zaharatul Azma R, Omar K

Comput Math Methods Med, 2014;2014:979302.
PMID: 24803955 DOI: 10.1155/2014/979302

Segmentation and counting of blood cells are considered as an important step that helps to extract features to diagnose some specific diseases like malaria or leukemia. The manual counting of white blood cells (WBCs) and red blood cells (RBCs) in microscopic images is an extremely tedious, time consuming, and inaccurate process. Automatic analysis will allow hematologist experts to perform faster and more accurately. The proposed method uses an iterative structured circle detection algorithm for the segmentation and counting of WBCs and RBCs. The separation of WBCs from RBCs was achieved by thresholding, and specific preprocessing steps were developed for each cell type. Counting was performed for each image using the proposed method based on modified circle detection, which automatically counted the cells. Several modifications were made to the basic (RCD) algorithm to solve the initialization problem, detecting irregular circles (cells), selecting the optimal circle from the candidate circles, determining the number of iterations in a fully dynamic way to enhance algorithm detection, and running time. The validation method used to determine segmentation accuracy was a quantitative analysis that included Precision, Recall, and F-measurement tests. The average accuracy of the proposed method was 95.3% for RBCs and 98.4% for WBCs.

Matched MeSH terms: Software
Fulltext First comprehensive in silico analysis of the functional and structural consequences of SNPs in human GalNAc-T1 gene

Mohamoud HS, Hussain MR, El-Harouni AA, Shaik NA, Qasmi ZU, Merican AF, et al.

Comput Math Methods Med, 2014;2014:904052.
PMID: 24723968 DOI: 10.1155/2014/904052

GalNAc-T1, a key candidate of GalNac-transferases genes family that is involved in mucin-type O-linked glycosylation pathway, is expressed in most biological tissues and cell types. Despite the reported association of GalNAc-T1 gene mutations with human disease susceptibility, the comprehensive computational analysis of coding, noncoding and regulatory SNPs, and their functional impacts on protein level, still remains unknown. Therefore, sequence- and structure-based computational tools were employed to screen the entire listed coding SNPs of GalNAc-T1 gene in order to identify and characterize them. Our concordant in silico analysis by SIFT, PolyPhen-2, PANTHER-cSNP, and SNPeffect tools, identified the potential nsSNPs (S143P, G258V, and Y414D variants) from 18 nsSNPs of GalNAc-T1. Additionally, 2 regulatory SNPs (rs72964406 and #x26; rs34304568) were also identified in GalNAc-T1 by using FastSNP tool. Using multiple computational approaches, we have systematically classified the functional mutations in regulatory and coding regions that can modify expression and function of GalNAc-T1 enzyme. These genetic variants can further assist in better understanding the wide range of disease susceptibility associated with the mucin-based cell signalling and pathogenic binding, and may help to develop novel therapeutic elements for associated diseases.

Matched MeSH terms: Software
Fulltext Multiple adaptive neuro-fuzzy inference system with automatic features extraction algorithm for cervical cancer recognition

Al-batah MS, Isa NA, Klaib MF, Al-Betar MA

Comput Math Methods Med, 2014;2014:181245.
PMID: 24707316 DOI: 10.1155/2014/181245

To date, cancer of uterine cervix is still a leading cause of cancer-related deaths in women worldwide. The current methods (i.e., Pap smear and liquid-based cytology (LBC)) to screen for cervical cancer are time-consuming and dependent on the skill of the cytopathologist and thus are rather subjective. Therefore, this paper presents an intelligent computer vision system to assist pathologists in overcoming these problems and, consequently, produce more accurate results. The developed system consists of two stages. In the first stage, the automatic features extraction (AFE) algorithm is performed. In the second stage, a neuro-fuzzy model called multiple adaptive neuro-fuzzy inference system (MANFIS) is proposed for recognition process. The MANFIS contains a set of ANFIS models which are arranged in parallel combination to produce a model with multi-input-multioutput structure. The system is capable of classifying cervical cell image into three groups, namely, normal, low-grade squamous intraepithelial lesion (LSIL) and high-grade squamous intraepithelial lesion (HSIL). The experimental results prove the capability of the AFE algorithm to be as effective as the manual extraction by human experts, while the proposed MANFIS produces a good classification performance with 94.2% accuracy.

Matched MeSH terms: Software
Fulltext Automated bone age assessment: motivation, taxonomies, and challenges

Mansourvar M, Ismail MA, Herawan T, Raj RG, Kareem SA, Nasaruddin FH

Comput Math Methods Med, 2013;2013:391626.
PMID: 24454534 DOI: 10.1155/2013/391626

Bone age assessment (BAA) of unknown people is one of the most important topics in clinical procedure for evaluation of biological maturity of children. BAA is performed usually by comparing an X-ray of left hand wrist with an atlas of known sample bones. Recently, BAA has gained remarkable ground from academia and medicine. Manual methods of BAA are time-consuming and prone to observer variability. This is a motivation for developing automated methods of BAA. However, there is considerable research on the automated assessment, much of which are still in the experimental stage. This survey provides taxonomy of automated BAA approaches and discusses the challenges. Finally, we present suggestions for future research.

Matched MeSH terms: Software
Fulltext Diagnosis of Lung Cancer by Fractal Analysis of Damaged DNA

Namazi H, Kiminezhadmalaie M

Comput Math Methods Med, 2015;2015:242695.
PMID: 26539245 DOI: 10.1155/2015/242695

Cancer starts when cells in a part of the body start to grow out of control. In fact cells become cancer cells because of DNA damage. A DNA walk of a genome represents how the frequency of each nucleotide of a pairing nucleotide couple changes locally. In this research in order to study the cancer genes, DNA walk plots of genomes of patients with lung cancer were generated using a program written in MATLAB language. The data so obtained was checked for fractal property by computing the fractal dimension using a program written in MATLAB. Also, the correlation of damaged DNA was studied using the Hurst exponent measure. We have found that the damaged DNA sequences are exhibiting higher degree of fractality and less correlation compared with normal DNA sequences. So we confirmed this method can be used for early detection of lung cancer. The method introduced in this research not only is useful for diagnosis of lung cancer but also can be applied for detection and growth analysis of different types of cancers.

Matched MeSH terms: Software
Fulltext A novel clinical decision support system using improved adaptive genetic algorithm for the assessment of fetal well-being

Ravindran S, Jambek AB, Muthusamy H, Neoh SC

Comput Math Methods Med, 2015;2015:283532.
PMID: 25793009 DOI: 10.1155/2015/283532

A novel clinical decision support system is proposed in this paper for evaluating the fetal well-being from the cardiotocogram (CTG) dataset through an Improved Adaptive Genetic Algorithm (IAGA) and Extreme Learning Machine (ELM). IAGA employs a new scaling technique (called sigma scaling) to avoid premature convergence and applies adaptive crossover and mutation techniques with masking concepts to enhance population diversity. Also, this search algorithm utilizes three different fitness functions (two single objective fitness functions and multi-objective fitness function) to assess its performance. The classification results unfold that promising classification accuracy of 94% is obtained with an optimal feature subset using IAGA. Also, the classification results are compared with those of other Feature Reduction techniques to substantiate its exhaustive search towards the global optimum. Besides, five other benchmark datasets are used to gauge the strength of the proposed IAGA algorithm.

Matched MeSH terms: Software
Fulltext Adaptive localization of focus point regions via random patch probabilistic density from whole-slide, Ki-67-stained brain tumor tissue

Alomari YM, Sheikh Abdullah SN, MdZin RR, Omar K

Comput Math Methods Med, 2015;2015:673658.
PMID: 25793010 DOI: 10.1155/2015/673658

Analysis of whole-slide tissue for digital pathology images has been clinically approved to provide a second opinion to pathologists. Localization of focus points from Ki-67-stained histopathology whole-slide tissue microscopic images is considered the first step in the process of proliferation rate estimation. Pathologists use eye pooling or eagle-view techniques to localize the highly stained cell-concentrated regions from the whole slide under microscope, which is called focus-point regions. This procedure leads to a high variety of interpersonal observations and time consuming, tedious work and causes inaccurate findings. The localization of focus-point regions can be addressed as a clustering problem. This paper aims to automate the localization of focus-point regions from whole-slide images using the random patch probabilistic density method. Unlike other clustering methods, random patch probabilistic density method can adaptively localize focus-point regions without predetermining the number of clusters. The proposed method was compared with the k-means and fuzzy c-means clustering methods. Our proposed method achieves a good performance, when the results were evaluated by three expert pathologists. The proposed method achieves an average false-positive rate of 0.84% for the focus-point region localization error. Moreover, regarding RPPD used to localize tissue from whole-slide images, 228 whole-slide images have been tested; 97.3% localization accuracy was achieved.

Matched MeSH terms: Software
Fulltext The Use of System Dynamics Methodology in Building a COVID-19 Confirmed Case Model

Mohd Yusoff MI

Comput Math Methods Med, 2020;2020:9328414.
PMID: 33224268 DOI: 10.1155/2020/9328414

Researchers used a hybrid model (a combination of health resource demand model and disease transmission model), Bayesian model, and susceptible-exposed-infectious-removed (SEIR) model to predict health service utilization and deaths and mixed-effect nonlinear regression. Further, they used the mixture model to predict the number of confirmed cases and deaths or to predict when the curve would flatten. In this article, we show, through scenarios developed using system dynamics methodology, besides close to real-world results, the detrimental effects of ignoring social distancing guidelines (in terms of the number of people infected, which decreased as the percentage of noncompliance decreased).

Matched MeSH terms: Software

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