Displaying publications 421 - 440 of 759 in total

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  1. Gubbiyappa KS, Barua A, Das B, Vasudeva Murthy CR, Baloch HZ
    Indian J Pharmacol, 2016 Oct;48(Suppl 1):S41-S46.
    PMID: 28031607 DOI: 10.4103/0253-7613.193313
    OBJECTIVES: Flipped classroom (FC) is a pedagogical model to engage students in learning process by replacing the didactic lectures. Using technology, lectures are moved out of the classroom and delivered online as means to provide interaction and collaboration. Poll Everywhere is an audience response system (ARS) which can be used in an FC to make the activities more interesting, engaging, and interactive. This study aims to study the perception of undergraduate pharmacy students on FC activity using Poll Everywhere ARS and to study the effectiveness of FC activity as a teaching-learning tool for delivering complementary medicine module in the undergraduate pharmacy program.

    MATERIALS AND METHODS: In this nonrandomized trial on interrupted time series study, flipped class was conducted on group of 112 students of bachelor of pharmacy semester V. The topic selected was popular herbal remedies of the complementary medicine module. Flipped class was conducted with audio and video presentation in the form of a quiz using ten one-best-answer type of multiple-choice questions covering the learning objectives. Audience response was captured using web-based interaction with Poll Everywhere. Feedback was obtained from participants at the end of FC activity and debriefing was done.

    RESULTS: Randomly selected 112 complete responses were included in the final analysis. There were 47 (42%) male and 65 (58%) female respondents. The overall Cronbach's alpha of feedback questionnaire was 0.912. The central tendencies and dispersions of items in the questionnaire indicated the effectiveness of FC. The low or middle achievers of quiz session (pretest) during the FC activity were three times (95% confidence interval [CI] = 1.1-8.9) at the risk of providing neutral or negative feedback than high achievers (P = 0.040). Those who gave neutral or negative feedback on FC activity were 3.9 times (95% CI = 1.3-11.8) at the risk of becoming low or middle achievers during the end of semester examination (P = 0.013). The multivariate analysis of "Agree" or "Disagree" and "Agree" or "Strongly Agree" was statistically significant.

    CONCLUSION: This study provides insight on how the pharmacy students learn and develop their cognitive functions. The results revealed that the FC activity with Poll Everywhere is an effective teaching-learning method.

    Matched MeSH terms: Software*
  2. Tan SY, Dutta A, Jakubovics NS, Ang MY, Siow CC, Mutha NV, et al.
    BMC Bioinformatics, 2015;16:9.
    PMID: 25591325 DOI: 10.1186/s12859-014-0422-y
    Yersinia is a Gram-negative bacteria that includes serious pathogens such as the Yersinia pestis, which causes plague, Yersinia pseudotuberculosis, Yersinia enterocolitica. The remaining species are generally considered non-pathogenic to humans, although there is evidence that at least some of these species can cause occasional infections using distinct mechanisms from the more pathogenic species. With the advances in sequencing technologies, many genomes of Yersinia have been sequenced. However, there is currently no specialized platform to hold the rapidly-growing Yersinia genomic data and to provide analysis tools particularly for comparative analyses, which are required to provide improved insights into their biology, evolution and pathogenicity.
    Matched MeSH terms: Software*
  3. Abdullah A, Deris S, Mohamad MS, Anwar S
    PLoS One, 2013;8(4):e61258.
    PMID: 23593445 DOI: 10.1371/journal.pone.0061258
    One of the key aspects of computational systems biology is the investigation on the dynamic biological processes within cells. Computational models are often required to elucidate the mechanisms and principles driving the processes because of the nonlinearity and complexity. The models usually incorporate a set of parameters that signify the physical properties of the actual biological systems. In most cases, these parameters are estimated by fitting the model outputs with the corresponding experimental data. However, this is a challenging task because the available experimental data are frequently noisy and incomplete. In this paper, a new hybrid optimization method is proposed to estimate these parameters from the noisy and incomplete experimental data. The proposed method, called Swarm-based Chemical Reaction Optimization, integrates the evolutionary searching strategy employed by the Chemical Reaction Optimization, into the neighbouring searching strategy of the Firefly Algorithm method. The effectiveness of the method was evaluated using a simulated nonlinear model and two biological models: synthetic transcriptional oscillators, and extracellular protease production models. The results showed that the accuracy and computational speed of the proposed method were better than the existing Differential Evolution, Firefly Algorithm and Chemical Reaction Optimization methods. The reliability of the estimated parameters was statistically validated, which suggests that the model outputs produced by these parameters were valid even when noisy and incomplete experimental data were used. Additionally, Akaike Information Criterion was employed to evaluate the model selection, which highlighted the capability of the proposed method in choosing a plausible model based on the experimental data. In conclusion, this paper presents the effectiveness of the proposed method for parameter estimation and model selection problems using noisy and incomplete experimental data. This study is hoped to provide a new insight in developing more accurate and reliable biological models based on limited and low quality experimental data.
    Matched MeSH terms: Software*
  4. Chan KL, Rosli R, Tatarinova TV, Hogan M, Firdaus-Raih M, Low EL
    BMC Bioinformatics, 2017 Jan 27;18(Suppl 1):1426.
    PMID: 28466793 DOI: 10.1186/s12859-016-1426-6
    BACKGROUND: Gene prediction is one of the most important steps in the genome annotation process. A large number of software tools and pipelines developed by various computing techniques are available for gene prediction. However, these systems have yet to accurately predict all or even most of the protein-coding regions. Furthermore, none of the currently available gene-finders has a universal Hidden Markov Model (HMM) that can perform gene prediction for all organisms equally well in an automatic fashion.

    RESULTS: We present an automated gene prediction pipeline, Seqping that uses self-training HMM models and transcriptomic data. The pipeline processes the genome and transcriptome sequences of the target species using GlimmerHMM, SNAP, and AUGUSTUS pipelines, followed by MAKER2 program to combine predictions from the three tools in association with the transcriptomic evidence. Seqping generates species-specific HMMs that are able to offer unbiased gene predictions. The pipeline was evaluated using the Oryza sativa and Arabidopsis thaliana genomes. Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis showed that the pipeline was able to identify at least 95% of BUSCO's plantae dataset. Our evaluation shows that Seqping was able to generate better gene predictions compared to three HMM-based programs (MAKER2, GlimmerHMM and AUGUSTUS) using their respective available HMMs. Seqping had the highest accuracy in rice (0.5648 for CDS, 0.4468 for exon, and 0.6695 nucleotide structure) and A. thaliana (0.5808 for CDS, 0.5955 for exon, and 0.8839 nucleotide structure).

    CONCLUSIONS: Seqping provides researchers a seamless pipeline to train species-specific HMMs and predict genes in newly sequenced or less-studied genomes. We conclude that the Seqping pipeline predictions are more accurate than gene predictions using the other three approaches with the default or available HMMs.

    Matched MeSH terms: Software*
  5. Mienda BS
    J Biomol Struct Dyn, 2017 Jul;35(9):1863-1873.
    PMID: 27251747 DOI: 10.1080/07391102.2016.1197153
    Genome-scale metabolic models (GEMs) have been developed and used in guiding systems' metabolic engineering strategies for strain design and development. This strategy has been used in fermentative production of bio-based industrial chemicals and fuels from alternative carbon sources. However, computer-aided hypotheses building using established algorithms and software platforms for biological discovery can be integrated into the pipeline for strain design strategy to create superior strains of microorganisms for targeted biosynthetic goals. Here, I described an integrated workflow strategy using GEMs for strain design and biological discovery. Specific case studies of strain design and biological discovery using Escherichia coli genome-scale model are presented and discussed. The integrated workflow presented herein, when applied carefully would help guide future design strategies for high-performance microbial strains that have existing and forthcoming genome-scale metabolic models.
    Matched MeSH terms: Software
  6. Lim AC, Chong VC, Wong CS, Muniandy SV
    PeerJ, 2015;3:e1471.
    PMID: 26734507 DOI: 10.7717/peerj.1471
    Background. Syngnathid fishes produce three kinds of sounds, named click, growl and purr. These sounds are generated by different mechanisms to give a consistent signal pattern or signature which is believed to play a role in intraspecific and interspecific communication. Commonly known sounds are produced when the fish feeds (click, purr) or is under duress (growl). While there are more acoustic studies on seahorses, pipefishes have not received much attention. Here we document the differences in feeding click signals between three species of pipefishes and relate them to cranial morphology and kinesis, or the sound-producing mechanism. Methods. The feeding clicks of two species of freshwater pipefishes, Doryichthys martensii and Doryichthys deokhathoides and one species of estuarine pipefish, Syngnathoides biaculeatus, were recorded by a hydrophone in acoustic dampened tanks. The acoustic signals were analysed using time-scale distribution (or scalogram) based on wavelet transform. A detailed time-varying analysis of the spectral contents of the localized acoustic signal was obtained by jointly interpreting the oscillogram, scalogram and power spectrum. The heads of both Doryichthys species were prepared for microtomographical scans which were analysed using a 3D imaging software. Additionally, the cranial bones of all three species were examined using a clearing and double-staining method for histological studies. Results. The sound characteristics of the feeding click of the pipefish is species-specific, appearing to be dependent on three bones: the supraoccipital, 1st postcranial plate and 2nd postcranial plate. The sounds are generated when the head of the Dorichthyes pipefishes flexes backward during the feeding strike, as the supraoccipital slides backwards, striking and pushing the 1st postcranial plate against (and striking) the 2nd postcranial plate. In the Syngnathoides pipefish, in the absence of the 1st postcranial plate, the supraoccipital rubs against the 2nd postcranial plate twice as it is pulled backward and released on the return. Cranial morphology and kinesis produce acoustic signals consistent with the bone strikes that produce sharp energy spikes (discrete or merged), or stridulations between bones that produce repeated or multimodal sinusoidal waveforms. Discussion. The variable structure of the sound-producing mechanism explains the unique acoustic signatures of the three species of pipefish. The differences in cranial bone morphology, cranial kinesis and acoustic signatures among pipefishes (and seahorses) could be attributed to independent evolution within the Syngnathidae, which warrants further investigation.
    Matched MeSH terms: Software
  7. Che Lah EF, Yaakop S, Ahamad M, Md Nor S
    Zookeys, 2015.
    PMID: 25685009 DOI: 10.3897/zookeys.478.8037
    Blood meal analysis (BMA) from ticks allows for the identification of natural hosts of ticks (Acari: Ixodidae). The aim of this study is to identify the blood meal sources of field collected on-host ticks using PCR analysis. DNA of four genera of ticks was isolated and their cytochrome b (Cyt b) gene was amplified to identify host blood meals. A phylogenetic tree was constructed based on data of Cyt b sequences using Neighbor Joining (NJ) and Maximum Parsimony (MP) analysis using MEGA 5.05 for the clustering of hosts of tick species. Twenty out of 27 samples showed maximum similarity (99%) with GenBank sequences through a Basic Local Alignment Search Tool (BLAST) while 7 samples only showed a similarity range of between 91-98%. The phylogenetic trees showed that the blood meal samples were derived from small rodents (Leopoldamyssabanus, Rattustiomanicus and Sundamysmuelleri), shrews (Tupaiaglis) and mammals (Tapirusindicus and Prionailurusbengalensis), supported by 82-88% bootstrap values. In this study, Cyt b gene as a molecular target produced reliable results and was very significant for the effective identification of ticks' blood meal. The assay can be used as a tool for identifying unknown blood meals of field collected on-host ticks.
    Matched MeSH terms: Software
  8. Marufuzzaman M, Reaz MB, Ali MA, Rahman LF
    Methods Inf Med, 2015;54(3):262-70.
    PMID: 25604028 DOI: 10.3414/ME14-01-0061
    OBJECTIVES: The goal of smart homes is to create an intelligent environment adapting the inhabitants need and assisting the person who needs special care and safety in their daily life. This can be reached by collecting the ADL (activities of daily living) data and further analysis within existing computing elements. In this research, a very recent algorithm named sequence prediction via enhanced episode discovery (SPEED) is modified and in order to improve accuracy time component is included.

    METHODS: The modified SPEED or M-SPEED is a sequence prediction algorithm, which modified the previous SPEED algorithm by using time duration of appliance's ON-OFF states to decide the next state. M-SPEED discovered periodic episodes of inhabitant behavior, trained it with learned episodes, and made decisions based on the obtained knowledge.

    RESULTS: The results showed that M-SPEED achieves 96.8% prediction accuracy, which is better than other time prediction algorithms like PUBS, ALZ with temporal rules and the previous SPEED.

    CONCLUSIONS: Since human behavior shows natural temporal patterns, duration times can be used to predict future events more accurately. This inhabitant activity prediction system will certainly improve the smart homes by ensuring safety and better care for elderly and handicapped people.

    Matched MeSH terms: Software Design
  9. Esmaeilpour M, Naderifar V, Shukur Z
    PLoS One, 2014;9(9):e106313.
    PMID: 25243670 DOI: 10.1371/journal.pone.0106313
    Over the last decade, design patterns have been used extensively to generate reusable solutions to frequently encountered problems in software engineering and object oriented programming. A design pattern is a repeatable software design solution that provides a template for solving various instances of a general problem.
    Matched MeSH terms: Software
  10. Mohebbi K, Ibrahim S, Zamani M, Khezrian M
    PLoS One, 2014;9(8):e104735.
    PMID: 25157872 DOI: 10.1371/journal.pone.0104735
    In this paper, a Semantic Web service matchmaker called UltiMatch-NL is presented. UltiMatch-NL applies two filters namely Signature-based and Description-based on different abstraction levels of a service profile to achieve more accurate results. More specifically, the proposed filters rely on semantic knowledge to extract the similarity between a given pair of service descriptions. Thus it is a further step towards fully automated Web service discovery via making this process more semantic-aware. In addition, a new technique is proposed to weight and combine the results of different filters of UltiMatch-NL, automatically. Moreover, an innovative approach is introduced to predict the relevance of requests and Web services and eliminate the need for setting a threshold value of similarity. In order to evaluate UltiMatch-NL, the repository of OWLS-TC is used. The performance evaluation based on standard measures from the information retrieval field shows that semantic matching of OWL-S services can be significantly improved by incorporating designed matching filters.
    Matched MeSH terms: Software
  11. Ang MY, Heydari H, Jakubovics NS, Mahmud MI, Dutta A, Wee WY, et al.
    Database (Oxford), 2014;2014.
    PMID: 25149689 DOI: 10.1093/database/bau082
    Fusobacterium are anaerobic gram-negative bacteria that have been associated with a wide spectrum of human infections and diseases. As the biology of Fusobacterium is still not well understood, comparative genomic analysis on members of this species will provide further insights on their taxonomy, phylogeny, pathogenicity and other information that may contribute to better management of infections and diseases. To facilitate the ongoing genomic research on Fusobacterium, a specialized database with easy-to-use analysis tools is necessary. Here we present FusoBase, an online database providing access to genome-wide annotated sequences of Fusobacterium strains as well as bioinformatics tools, to support the expanding scientific community. Using our custom-developed Pairwise Genome Comparison tool, we demonstrate how differences between two user-defined genomes and how insertion of putative prophages can be identified. In addition, Pathogenomics Profiling Tool is capable of clustering predicted genes across Fusobacterium strains and visualizing the results in the form of a heat map with dendrogram.
    Matched MeSH terms: Software
  12. Dzulkarnain AA, Wan Mhd Pandi WM, Wilson WJ, Bradley AP, Sapian F
    Int J Audiol, 2014 Aug;53(8):514-21.
    PMID: 24702636 DOI: 10.3109/14992027.2014.897763
    To determine if a computer simulation can be used to improve the ability of audiology students to analyse ABR waveforms.
    Matched MeSH terms: Software
  13. Ng KH, Yip CH, Taib NA
    Lancet Oncol, 2012 Apr;13(4):334-6.
    PMID: 22469115 DOI: 10.1016/S1470-2045(12)70093-1
    Matched MeSH terms: Software
  14. 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
  15. Mohamed-Hussein ZA, Harun S
    PMID: 19723303 DOI: 10.1186/1742-4682-6-18
    Polycystic ovary syndrome (PCOS) is a complex but frequently occurring endocrine abnormality. PCOS has become one of the leading causes of oligo-ovulatory infertility among premenopausal women. The definition of PCOS remains unclear because of the heterogeneity of this abnormality, but it is associated with insulin resistance, hyperandrogenism, obesity and dyslipidaemia. The main purpose of this study was to identify possible candidate genes involved in PCOS. Several genomic approaches, including linkage analysis and microarray analysis, have been used to look for candidate PCOS genes. To obtain a clearer view of the mechanism of PCOS, we have compiled data from microarray analyses. An extensive literature search identified seven published microarray analyses that utilized PCOS samples. These were published between the year of 2003 and 2007 and included analyses of ovary tissues as well as whole ovaries and theca cells. Although somewhat different methods were used, all the studies employed cDNA microarrays to compare the gene expression patterns of PCOS patients with those of healthy controls. These analyses identified more than a thousand genes whose expression was altered in PCOS patients. Most of the genes were found to be involved in gene and protein expression, cell signaling and metabolism. We have classified all of the 1081 identified genes as coding for either known or unknown proteins. Cytoscape 2.6.1 was used to build a network of protein and then to analyze it. This protein network consists of 504 protein nodes and 1408 interactions among those proteins. One hypothetical protein in the PCOS network was postulated to be involved in the cell cycle. BiNGO was used to identify the three main ontologies in the protein network: molecular functions, biological processes and cellular components. This gene ontology analysis identified a number of ontologies and genes likely to be involved in the complex mechanism of PCOS. These include the insulin receptor signaling pathway, steroid biosynthesis, and the regulation of gonadotropin secretion among others.
    Matched MeSH terms: Software
  16. Ali A, Logeswaran R
    J Digit Imaging, 2007 Dec;20(4):352-66.
    PMID: 17372781
    This article proposes a set-up for a 3-dimensional ultrasound system using visual probe localization on the conventional 2-dimensional ultrasound machines readily available in most hospitals. A calibrated digital camera is used for probe-tracking (localization) purposes, whereas ultrasound probe calibration is implemented using a purpose-built phantom. The calibration steps and results are detailed here. The overall system is proven effective in clinical trials through scanning of human organs. Results obtained show successful, accurate 3-dimensional representations using this simple cost-effective set-up.
    Matched MeSH terms: Software Design
  17. Sim KS, Tso CP, Law KK
    Microsc Res Tech, 2008 Apr;71(4):315-24.
    PMID: 18172898 DOI: 10.1002/jemt.20558
    The mixed Lagrange time-delay estimation autoregressive (MLTDEAR) model is proposed as a solution to estimate image noise variance. The only information available to the proposed estimator is a corrupted image and the nature of additive white noise. The image autocorrelation function is calculated and used to obtain the MLTDEAR model coefficients; the relationship between the MLTDEAR and linear prediction models is utilized to estimate the model coefficients. The forward-backward prediction is then used to obtain the predictor coefficients; the MLTDEAR model coefficients and prior samples of zero-offset autocorrelation values are next used to predict the power of the noise-free image. Furthermore, the fundamental performance limit of the signal and noise estimation, as derived from the Cramer-Rao inequality, is presented.
    Matched MeSH terms: Software
  18. Logeswaran R, Eswaran C
    J Med Syst, 2006 Apr;30(2):133-8.
    PMID: 16705998
    Many medical examinations involve acquisition of a large series of slice images for 3D reconstruction of the organ of interest. With the paperless hospital concept and telemedicine, there is very heavy utilization of limited electronic storage and transmission bandwidth. This paper proposes model-based compression to reduce the load on such resources, as well as aid diagnosis through the 3D reconstruction of the structures of interest, for images acquired by various modalities, such as MRI, Ultrasound, CT, PET etc. and stored in the DICOM file format. An example implementation for the biliary track in MRCP images is illustrated in the paper. Significant compression gains may be derived from the proposed method, and a suitable mixture of the models and raw images would enhance the patient medical history archives as the models may be stored in the DICOM file format used in most medical archiving systems.
    Matched MeSH terms: Software
  19. Campbell P, Schneider CJ, Adnan AM, Zubaid A, Kunz TH
    Mol Phylogenet Evol, 2004 Dec;33(3):764-81.
    PMID: 15522802
    Taxonomic relationships within the Old World fruit bat genus, Cynopterus, have been equivocal for the better part of a century. While nomenclature has been revised multiple times on the basis of phenotypic characters, evolutionary relationships among taxa representing the entire geographic range of the genus have not been determined. We used mitochondrial DNA sequence data to infer phylogenetic relationships among the three most broadly distributed members of the genus: C. brachyotis, C. horsfieldi, and C. sphinx, and to assess whether C. brachyotis represents a single widespread species, or a complex of distinct lineages. Results clearly indicate that C. brachyotis is a complex of lineages. C. sphinx and C. horsfieldi haplotypes formed monophyletic groups nested within the C. brachyotis species complex. We identified six divergent mitochondrial lineages that are currently referred to C. brachyotis. Lineages from India, Myanmar, Sulawesi, and the Philippines are geographically well-defined, while in Malaysia two lineages, designated Sunda and Forest, are broadly sympatric and may be ecologically distinct. Demographic analyses of the Sunda and Forest lineages suggest strikingly different population histories, including a recent and rapid range expansion in the Sunda lineage, possibly associated with changes in sea levels during the Pleistocene. The resolution of the taxonomic issues raised in this study awaits combined analysis of morphometric characters and molecular data. However, since both the Indian and Malaysian Forest C. brachyotis lineages are apparently ecologically restricted to increasingly fragmented forest habitat, we suggest that reevaluation of the conservation status of populations in these regions should be an immediate goal.
    Matched MeSH terms: Software
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