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Fulltext A dataset of visualization methods to assessing soil profile using RES2DINV and VOXLER software

Yasir SF, Jani J, Mukri M

Data Brief, 2019 Jun;24:103821.
PMID: 30976635 DOI: 10.1016/j.dib.2019.103821

This data illustration the similarity and accuracy of two subsurface profile analysis software which is RES2DINV and VOXLER. Electrical resistivity imaging methods was conducted as a geophysical technique to get subsurface profile were borehole had previously been made in the same locations. The General Department of Geoscience (JMG) conducted the drilling of the borehole in three locations which is Kampung Bangkahulu, Gemas, Kampung Semerbok, Rembau and Felda Bukit Rokan Utara. The 2D resistivity image from RES2DINV and the 3D image from VOXLER was highly matching the subsurface profile compared with borehole data log. The depth of the resistivity was 76.8, 87.2 and 39.4 respectively for the sites. This two software gave more clearly interpreted result for investigate the sub ground and geological formations.

Matched MeSH terms: Software
A decision support system for automatic screening of non-proliferative diabetic retinopathy

Reza AW, Eswaran C

J Med Syst, 2011 Feb;35(1):17-24.
PMID: 20703589 DOI: 10.1007/s10916-009-9337-y

The increasing number of diabetic retinopathy (DR) cases world wide demands the development of an automated decision support system for quick and cost-effective screening of DR. We present an automatic screening system for detecting the early stage of DR, which is known as non-proliferative diabetic retinopathy (NPDR). The proposed system involves processing of fundus images for extraction of abnormal signs, such as hard exudates, cotton wool spots, and large plaque of hard exudates. A rule based classifier is used for classifying the DR into two classes, namely, normal and abnormal. The abnormal NPDR is further classified into three levels, namely, mild, moderate, and severe. To evaluate the performance of the proposed decision support framework, the algorithms have been tested on the images of STARE database. The results obtained from this study show that the proposed system can detect the bright lesions with an average accuracy of about 97%. The study further shows promising results in classifying the bright lesions correctly according to NPDR severity levels.

Matched MeSH terms: Software
A direction-sensitive underwater blast detector and its application for managing blast fishing

Woodman GH, Wilson SC, Li VY, Renneberg R

Mar Pollut Bull, 2004 Dec;49(11-12):964-73.
PMID: 15556182

Little is known about the spatial and temporal distribution of blast fishing which hampers enforcement against this activity. We have demonstrated that a triangular array of hydrophones 1 m apart is capable of detecting blast events whilst effectively rejecting other sources of underwater noise such as snapping shrimp and nearby boat propellers. A total of 13 blasts were recorded in Sepangor bay, North of Kota Kinabalu, Sabah, Malaysia from 7th to 15th July 2002 at distances estimated to be up to 20 km, with a directional uncertainty of 0.2 degrees . With such precision, a network of similar hydrophone arrays has potential to locate individual blast events by triangulation to within 30 m at a range of 10 km.

Matched MeSH terms: Software*
Fulltext A discrete event simulation model for evaluating the performances of an m/g/c/c state dependent queuing system

Khalid R, Nawawi MK, Kawsar LA, Ghani NA, Kamil AA, Mustafa A

PLoS One, 2013;8(4):e58402.
PMID: 23560037 DOI: 10.1371/journal.pone.0058402

M/G/C/C state dependent queuing networks consider service rates as a function of the number of residing entities (e.g., pedestrians, vehicles, and products). However, modeling such dynamic rates is not supported in modern Discrete Simulation System (DES) software. We designed an approach to cater this limitation and used it to construct the M/G/C/C state-dependent queuing model in Arena software. Using the model, we have evaluated and analyzed the impacts of various arrival rates to the throughput, the blocking probability, the expected service time and the expected number of entities in a complex network topology. Results indicated that there is a range of arrival rates for each network where the simulation results fluctuate drastically across replications and this causes the simulation results and analytical results exhibit discrepancies. Detail results that show how tally the simulation results and the analytical results in both abstract and graphical forms and some scientific justifications for these have been documented and discussed.

Matched MeSH terms: Software*
A fourth-order compact finite difference scheme for the goursat problem

Mohd Agos Salim Nasir, Ahmad Izani Md Ismail

Sains Malaysiana, 2013;42:341-346.

A high-order uniform Cartesian grid compact finite difference scheme for the Goursat problem is developed. The basic idea of high-order compact schemes is to find the compact approximations to the derivatives terms by differentiating centrally the governing equations. Our compact scheme will approximate the derivative terms by involving the higher terms and reducing the number of grid points. The compact finite difference scheme is given for general form of the Goursat problem in uniform domain and illustrates the performance by applying a linear problem. Numerical experiments have been conducted with the new scheme and encouraging results have been obtained. In this paper we present the compact finite difference scheme for the Goursat problem. With the aid of computational software the scheme was programmed for determining the relative errors of linear Goursat problem.

Matched MeSH terms: Software
Fulltext A low power and low ripple CMOS high voltage generator for RFID transponder EEPROM

Rahman LF, Marufuzzaman M, Alam L, Sidek LM, Reaz MBI

PLoS One, 2020;15(2):e0225408.
PMID: 32023244 DOI: 10.1371/journal.pone.0225408

A high-voltage generator (HVG) is an essential part of a radio frequency identification electrically erasable programmable read-only memory (RFID-EEPROM). An HVG circuit is used to generate a regulated output voltage that is higher than the power supply voltage. However, the performance of the HVG is affected owing to the high-power dissipation, high-ripple voltage and low-pumping efficiency. Therefore, a regulator circuit consists of a voltage divider, comparator and a voltage reference, which are respectively required to reduce the ripple voltage, increase pumping efficiency and decrease the power dissipation of the HVG. Conversely, a clock driving circuit consists of the current-starved ring oscillator (CSRO), and the non- overlapping clock generator is required to drive the clock signals of the HVG circuit. In this study, the Mentor Graphics EldoSpice software package is used to design and simulate the HVG circuitry. The results showed that the designed CSRO dissipated only 4.9 μW at 10.2 MHz and that the phase noise was only -119.38 dBc/Hz at 1 MHz. Moreover, the proposed charge pump circuit was able to generate a maximum VPP of 13.53 V and it dissipated a power of only 31.01 μW for an input voltage VDD of 1.8 V. After integrating all the HVG modules, the results showed that the regulated HVG circuit was also able to generate a higher VPP of 14.59 V, while the total power dissipated was only 0.12 mW with a chip area of 0.044 mm2. Moreover, the HVG circuit produced a pumping efficiency of 90% and reduced the ripple voltage to <4 mV. Therefore, the integration of all the proposed modules in HVG ensured low-ripple programming voltages, higher pumping efficiency, and EEPROMs with lower power dissipation, and can be extensively used in low-power applications, such as in non-volatile memory, radiofrequency identification transponders, on-chip direct current DC-DC converters.

Matched MeSH terms: Software*
A low-cost, high-quality method for remote recording of presentations

Tan LK, Wong JH, Ng KH

AJR Am J Roentgenol, 2006 Mar;186(3):898-901.
PMID: 16498128

The purpose of this article was to develop a low-cost method for high-quality remote capturing and recording of multimedia presentations.

Matched MeSH terms: Software*
Fulltext A low-loss and compact single-layer butler matrix for a 5G base station antenna

Idrus II, Abdul Latef T, Aridas NK, Abu Talip MS, Yamada Y, Abd Rahman T, et al.

PLoS One, 2019;14(12):e0226499.
PMID: 31841536 DOI: 10.1371/journal.pone.0226499

Researchers are increasingly showing interest in the application of a Butler matrix for fifth-generation (5G) base station antennas. However, the design of the Butler matrix is challenging at millimeter wave because of the very small wavelength. The literature has reported issues of high insertion losses and incorrect output phases at the output ports of the Butler matrix, which affects the radiation characteristics. To overcome these issues, the circuit elements of the Butler matrix such as the crossover, the quadrature hybrid and the phase shifter must be designed using highly accurate dimensions. This paper presents a low-loss and compact single-layer 8 × 8 Butler matrix operating at 28 GHz. The optimum design of each circuit element is also demonstrated in detail. The designed Butler matrix was fabricated to validate the simulated results. The measured results showed return losses of less than -10 dB at 28 GHz. The proposed Butler matrix achieved a low insertion loss and a low phase error of ± 2 dB and ± 10°, respectively. In sum, this work obtained a good agreement between the simulated and measured results.

Matched MeSH terms: Software
A method for control of an implantable rotary blood pump for heart failure patients using noninvasive measurements

Lim E, Alomari AH, Savkin AV, Dokos S, Fraser JF, Timms DL, et al.

Artif Organs, 2011 Aug;35(8):E174-80.
PMID: 21843286 DOI: 10.1111/j.1525-1594.2011.01268.x

We propose a deadbeat controller for the control of pulsatile pump flow (Q(p) ) in an implantable rotary blood pump (IRBP). Noninvasive measurements of pump speed and current are used as inputs to a dynamical model of Q(p) estimation, previously developed and verified in our laboratory. The controller was tested using a lumped parameter model of the cardiovascular system (CVS), in combination with the stable dynamical models of Q(p) and differential pressure (head) estimation for the IRBP. The control algorithm was tested with both constant and sinusoidal reference Q(p) as input to the CVS model. Results showed that the controller was able to track the reference input with minimal error in the presence of model uncertainty. Furthermore, Q(p) was shown to settle to the desired reference value within a finite number of sampling periods. Our results also indicated that counterpulsation yields the minimum left ventricular stroke work, left ventricular end diastolic volume, and aortic pulse pressure, without significantly affecting mean cardiac output and aortic pressure.

Matched MeSH terms: Software
Fulltext A mobile ferromagnetic shape detection sensor using a Hall sensor array and magnetic imaging

Misron N, Shin NW, Shafie S, Marhaban MH, Mailah NF

Sensors (Basel), 2011;11(11):10474-89.
PMID: 22346653 DOI: 10.3390/s111110474

This paper presents a mobile Hall sensor array system for the shape detection of ferromagnetic materials that are embedded in walls or floors. The operation of the mobile Hall sensor array system is based on the principle of magnetic flux leakage to describe the shape of the ferromagnetic material. Two permanent magnets are used to generate the magnetic flux flow. The distribution of magnetic flux is perturbed as the ferromagnetic material is brought near the permanent magnets and the changes in magnetic flux distribution are detected by the 1-D array of the Hall sensor array setup. The process for magnetic imaging of the magnetic flux distribution is done by a signal processing unit before it displays the real time images using a netbook. A signal processing application software is developed for the 1-D Hall sensor array signal acquisition and processing to construct a 2-D array matrix. The processed 1-D Hall sensor array signals are later used to construct the magnetic image of ferromagnetic material based on the voltage signal and the magnetic flux distribution. The experimental results illustrate how the shape of specimens such as square, round and triangle shapes is determined through magnetic images based on the voltage signal and magnetic flux distribution of the specimen. In addition, the magnetic images of actual ferromagnetic objects are also illustrated to prove the functionality of mobile Hall sensor array system for actual shape detection. The results prove that the mobile Hall sensor array system is able to perform magnetic imaging in identifying various ferromagnetic materials.

Matched MeSH terms: Software
A more elaborative way to check codon quality: an open source program

Shardiwal RK, Sohrab SS

Int J Bioinform Res Appl, 2010;6(3):223-9.
PMID: 20615831

Relative Synonymous Codon Usage (RSCU) and Relative Adaptiveness of a Codon (RAC) table bias importance in gene expression are well documented in the literature. However, to improve the gene expression we need to figure out which codons are optimal for the expression in order to synthesise an appropriate DNA sequence. An alternative to the manual approach, which is obviously a tedious task, is to set up software on your computer to perform this. Though such kinds of programs are available on the internet, none of them are open-source libraries. Here, one can use our Perl program to do his or her task more easily and efficiently. It is free for everyone.

Matched MeSH terms: Software*
A morphometric approach to morphology analysis of palatal rugae in sibling groups

Tey SN, Syed Mohamed AMF, Marizan Nor M

J Forensic Sci, 2024 Jan;69(1):189-198.
PMID: 37706423 DOI: 10.1111/1556-4029.15380

Recent advances in imaging technologies, such as intra-oral surface scanning, have rapidly generated large datasets of high-resolution three-dimensional (3D) sample reconstructions. These datasets contain a wealth of phenotypic information that can provide an understanding of morphological variation and evolution. The geometric morphometric method (GMM) with landmarks and the development of sliding and surface semilandmark techniques has greatly enhanced the quantification of shape. This study aimed to determine whether there are significant differences in 3D palatal rugae shape between siblings. Digital casts representing 25 pairs of full siblings from each group, male-male (MM), female-female (FF), and female-male (FM), were digitized and transferred to a GM system. The palatal rugae were determined, quantified, and visualized using GMM computational tools with MorphoJ software (University of Manchester). Principal component analysis (PCA) and canonical variates analysis (CVA) were employed to analyze palatal rugae shape variability and distinguish between sibling groups based on shape. Additionally, regression analysis examined the potential impact of shape on palatal rugae. The study revealed that the palatal rugae shape covered the first nine of the PCA by 71.3%. In addition, the size of the palatal rugae has a negligible impact on its shape. Whilst palatal rugae are known for their individuality, it is noteworthy that three palatal rugae (right first, right second, and left third) can differentiate sibling groups, which may be attributed to genetics. Therefore, it is suggested that palatal rugae morphology can serve as forensic identification for siblings.

Matched MeSH terms: Software
A new approach for arrhythmia classification using deep coded features and LSTM networks

Yildirim O, Baloglu UB, Tan RS, Ciaccio EJ, Acharya UR

Comput Methods Programs Biomed, 2019 Jul;176:121-133.
PMID: 31200900 DOI: 10.1016/j.cmpb.2019.05.004

BACKGROUND AND OBJECTIVE: For diagnosis of arrhythmic heart problems, electrocardiogram (ECG) signals should be recorded and monitored. The long-term signal records obtained are analyzed by expert cardiologists. Devices such as the Holter monitor have limited hardware capabilities. For improved diagnostic capacity, it would be helpful to detect arrhythmic signals automatically. In this study, a novel approach is presented as a candidate solution for these issues.
METHODS: A convolutional auto-encoder (CAE) based nonlinear compression structure is implemented to reduce the signal size of arrhythmic beats. Long-short term memory (LSTM) classifiers are employed to automatically recognize arrhythmias using ECG features, which are deeply coded with the CAE network.
RESULTS: Based upon the coded ECG signals, both storage requirement and classification time were considerably reduced. In experimental studies conducted with the MIT-BIH arrhythmia database, ECG signals were compressed by an average 0.70% percentage root mean square difference (PRD) rate, and an accuracy of over 99.0% was observed.
CONCLUSIONS: One of the significant contributions of this study is that the proposed approach can significantly reduce time duration when using LSTM networks for data analysis. Thus, a novel and effective approach was proposed for both ECG signal compression, and their high-performance automatic recognition, with very low computational cost.

Matched MeSH terms: Software
Fulltext A new graph-based molecular descriptor using the canonical representation of the molecule

Hentabli H, Saeed F, Abdo A, Salim N

ScientificWorldJournal, 2014;2014:286974.
PMID: 25140330 DOI: 10.1155/2014/286974

Molecular similarity is a pervasive concept in drug design. The basic idea underlying molecular similarity is the similar property principle, which states that structurally similar molecules will exhibit similar physicochemical and biological properties. In this paper, a new graph-based molecular descriptor (GBMD) is introduced. The GBMD is a new method of obtaining a rough description of 2D molecular structure in textual form based on the canonical representations of the molecule outline shape and it allows rigorous structure specification using small and natural grammars. Simulated virtual screening experiments with the MDDR database show clearly the superiority of the graph-based descriptor compared to many standard descriptors (ALOGP, MACCS, EPFP4, CDKFP, PCFP, and SMILE) using the Tanimoto coefficient (TAN) and the basic local alignment search tool (BLAST) when searches were carried.

Matched MeSH terms: Software
Fulltext A new method of mark detection for software-based optical mark recognition

Loke SC, Kasmiran KA, Haron SA

PLoS One, 2018;13(11):e0206420.
PMID: 30412588 DOI: 10.1371/journal.pone.0206420

Software optical mark recognition (SOMR) is the process whereby information entered on a survey form or questionnaire is converted using specialized software into a machine-readable format. SOMR normally requires input fields to be completely darkened, have no internal labels, or be filled with a soft pencil, otherwise mark detection will be inaccurate. Forms can also have print and scan artefacts that further increase the error rate. This article presents a new method of mark detection that improves over existing techniques based on pixel counting and simple thresholding. Its main advantage is that it can be used under a variety of conditions and yet maintain a high level of accuracy that is sufficient for scientific applications. Field testing shows no software misclassification in 5695 samples filled by trained personnel, and only two misclassifications in 6000 samples filled by untrained respondents. Sensitivity, specificity, and accuracy were 99.73%, 99.98%, and 99.94% respectively, even in the presence of print and scan artefacts, which was superior to other methods tested. A separate direct comparison for mark detection showed a sensitivity, specificity, and accuracy respectively of 99.7%, 100.0%, 100.0% (new method), 96.3%, 96.0%, 96.1% (pixel counting), and 99.9%, 99.8%, 99.8% (simple thresholding) on clean forms, and 100.0%, 99.1%, 99.3% (new method), 98.4%, 95.6%, 96.2% (pixel counting), 100.0%, 38.3%, 51.4% (simple thresholding) on forms with print artefacts. This method is designed for bubble and box fields, while other types such as handwriting fields require separate error control measures.

Matched MeSH terms: Software
Fulltext A new split based searching for exact pattern matching for natural texts

Hakak S, Kamsin A, Shivakumara P, Idna Idris MY, Gilkar GA

PLoS One, 2018;13(7):e0200912.
PMID: 30048486 DOI: 10.1371/journal.pone.0200912

Exact pattern matching algorithms are popular and used widely in several applications, such as molecular biology, text processing, image processing, web search engines, network intrusion detection systems and operating systems. The focus of these algorithms is to achieve time efficiency according to applications but not memory consumption. In this work, we propose a novel idea to achieve both time efficiency and memory consumption by splitting query string for searching in Corpus. For a given text, the proposed algorithm split the query pattern into two equal halves and considers the second (right) half as a query string for searching in Corpus. Once the match is found with second halves, the proposed algorithm applies brute force procedure to find remaining match by referring the location of right half. Experimental results on different S1 Dataset, namely Arabic, English, Chinese, Italian and French text databases show that the proposed algorithm outperforms the existing S1 Algorithm in terms of time efficiency and memory consumption as the length of the query pattern increases.

Matched MeSH terms: Software
Fulltext A novel N-input voting algorithm for X-by-wire fault-tolerant systems

Karimi A, Zarafshan F, Al-Haddad SA, Ramli AR

ScientificWorldJournal, 2014;2014:672832.
PMID: 25386613 DOI: 10.1155/2014/672832

Voting is an important operation in multichannel computation paradigm and realization of ultrareliable and real-time control systems that arbitrates among the results of N redundant variants. These systems include N-modular redundant (NMR) hardware systems and diversely designed software systems based on N-version programming (NVP). Depending on the characteristics of the application and the type of selected voter, the voting algorithms can be implemented for either hardware or software systems. In this paper, a novel voting algorithm is introduced for real-time fault-tolerant control systems, appropriate for applications in which N is large. Then, its behavior has been software implemented in different scenarios of error-injection on the system inputs. The results of analyzed evaluations through plots and statistical computations have demonstrated that this novel algorithm does not have the limitations of some popular voting algorithms such as median and weighted; moreover, it is able to significantly increase the reliability and availability of the system in the best case to 2489.7% and 626.74%, respectively, and in the worst case to 3.84% and 1.55%, respectively.

Matched MeSH terms: Software*; Software Design
Fulltext A novel alternative method for 3D visualisation in Parasitology: the construction of a 3D model of a parasite from 2D illustrations

Teo BG, Sarinder KK, Lim LH

Trop Biomed, 2010 Aug;27(2):254-64.
PMID: 20962723 MyJurnal

Three-dimensional (3D) models of the marginal hooks, dorsal and ventral anchors, bars and haptoral reservoirs of a parasite, Sundatrema langkawiense Lim & Gibson, 2009 (Monogenea) were developed using the polygonal modelling method in Autodesk 3ds Max (Version 9) based on two-dimensional (2D) illustrations. Maxscripts were written to rotate the modelled 3D structures. Appropriately orientated 3D haptoral hard-parts were then selected and positioned within the transparent 3D outline of the haptor and grouped together to form a complete 3D haptoral entity. This technique is an inexpensive tool for constructing 3D models from 2D illustrations for 3D visualisation of the spatial relationships between the different structural parts within organisms.

Matched MeSH terms: Software*
Fulltext A novel and improved method of predicting hand grip strength in the adult Malaysian population

Kamarul T, Ahmad TS, Loh WY

Med J Malaysia, 2006 Dec;61 Suppl B:37-44.
PMID: 17600991

Hand grip strength measurement is a recognized part of hand function assessment. The standard measurement using the Jamar dynamometer and comparing these results to the recommended normal values suggested by the manufacturers of the Jamar was questioned as these values were based on Western population. A study comparing a novel method of predicting grip strength using our software was conducted on 25 normal subjects using the LIDO kinetic workset (Group A and B ). These results were then compared against our predictive software (Group A) and the expected values supplied together with the Jamar Dynamometer (Group B). In another group, 22 normal subjects were tested using the Jamar (Group C and D) and then matched against the predicted values using their recommended chart (Group C). The last group (Group D) was tested using the Jamar but the values attained were compared to the results from our software. In group A, the predictability of our predictive method was 100% (both R & L) as compared to (R = 64%, L = 68%) in group B, (R = 27.3%, L = 59.1%) in group C and (R = 81.8%, L = 86.4%) in group D. The differences between the predictability of both methods were statistically significant. The data collected using both the Jamar and the LIDO kinetic workset correlated well to the data from our software but not to the values suggested by the manufacturers of Jamar. We conclude that our method of predicting hand grip values are superior to that suggested by the manufacturers of dynamometers. The standard reference for hand grip strength provided by the manufacturers is less accurate in predicting the grip strength of our local population.

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

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