Displaying publications 1 - 20 of 120 in total

  1. Wongrattanakamon P, Lee VS, Nimmanpipug P, Jiranusornkul S
    Data Brief, 2016 Dec;9:35-42.
    PMID: 27626051 DOI: 10.1016/j.dib.2016.08.004
    The data is obtained from exploring the modulatory activities of bioflavonoids on P-glycoprotein function by ligand-based approaches. Multivariate Linear-QSAR models for predicting the induced/inhibitory activities of the flavonoids were created. Molecular descriptors were initially used as independent variables and a dependent variable was expressed as pFAR. The variables were then used in MLR analysis by stepwise regression calculation to build the linear QSAR data. The entire dataset consisted of 23 bioflavonoids was used as a training set. Regarding the obtained MLR QSAR model, R of 0.963, R (2)=0.927, [Formula: see text], SEE=0.197, F=33.849 and q (2)=0.927 were achieved. The true predictabilities of QSAR model were justified by evaluation with the external dataset (Table 4). The pFARs of representative flavonoids were predicted by MLR QSAR modelling. The data showed that internal and external validations may generate the same conclusion.
  2. Nejat P, Calautit JK, Majid MZ, Hughes BR, Jomehzadeh F
    Data Brief, 2016 Dec;9:252-6.
    PMID: 27660813 DOI: 10.1016/j.dib.2016.08.042
    This article presents the datasets which were the results of the study explained in the research paper 'Anti-short-circuit device: a new solution for short-circuiting in windcatcher and improvement of natural ventilation performance' (P. Nejat, J.K. Calautit, M.Z. Abd. Majid, B.R. Hughes, F. Jomehzadeh, 2016) [1] which introduces a new technique to reduce or prevent short-circuiting in a two-sided windcatcher and also lowers the indoor CO2 concentration and improve the ventilation distribution. Here, we provide details of the numerical modeling set-up and data collection method to facilitate reproducibility. The datasets includes indoor airflow, ventilation rates and CO2 concentration data at several points in the flow field. The CAD geometry of the windcatcher models are also included.
  3. Samsir SA, Bunawan H, Yen CC, Noor NM
    Data Brief, 2016 Sep;8:1438-42.
    PMID: 27617279 DOI: 10.1016/j.dib.2016.08.016
    In this dataset, we present 15 Simple Sequence Repeat (SSR) markers with the motifs (AC)n, (GA)n, and (AC)n(AG)n using a ISSR-Suppression-PCR technique in order to discriminate Garcinia mangostana from diverse geographical origins in Peninsular Malaysia. A few loci showed differences between 3 and 6 bp in allele size, indicating that there are some polymorphisms between individuals correlating to the number of SSR repeats that may be useful for differentiate of genotypes. Collectively, these data show that the ISSR-Suppression-PCR is a valuable method to illustrate genetic variation of selected G. mangostana in Malaysia.
  4. Low CF, Bunawan H
    Data Brief, 2016 Sep;8:1454-61.
    PMID: 27617282 DOI: 10.1016/j.dib.2016.08.025
    In this article, nine complete genomes of viruses from the genus Alphanodavirus and Betanodavirus (Family Nodaviridae) were comparatively analyzed and the data of their evolutionary origins and relatedness are reported. The nucleotide sequence alignment of the complete genomes from all species and their deduced evolutionary relationships are presented. High sequence similarity within the genus Betanodavirus compared to the genus Alphanodavirus was revealed in multiple sequence alignment of the Nodaviridae genomes. The amino acid sequence similarity for both RNA1 and RNA2 ORF is more conserved in Betanodavirus, compared to Alphanodavirus. The conserved and variable regions within the virus genome that were defined based on the multiple sequence alignments are presented in this dataset.
  5. Nejat P, Calautit JK, Abd Majid MZ, Hughes BR, Zeynali I, Jomehzadeh F
    Data Brief, 2016 Dec;9:448-452.
    PMID: 27709121
    The data presented in this article were the basis for the study reported in the research articles entitled "Evaluation of a two-sided windcatcher integrated with wing wall (as a new design) and comparison with a conventional windcatcher" (P. Nejat, J.K. Calautit, M.Z.A. Majid, B.R. Hughes, I. Zeynali, F. Jomehzadeh, 2016) [1] which presents the effect of wing wall on the air flow distribution under using the windcatchers as a natural ventilation equipment. Here, we detail the wind tunnel testing and numerical set-up used for obtaining the data on ventilation rates and indoor airflow distribution inside a test room with a two-sided windcatcher and wing wall. Three models were integrated with wing wall angled at 30°, 45° and 60° and another windcatcher was a conventional two-sided device. The computer-aided design (CAD) three-dimensional geometries which were produced using Solid Edge modeler are also included in the data article.
  6. Alhammami M, Ooi CP, Tan WH
    Data Brief, 2017 Jun;12:480-484.
    PMID: 28508027 DOI: 10.1016/j.dib.2017.04.026
    We present in this paper a novel dataset (MMU VAAC) for violent actions against children recognition. This original dataset has been recorded using Microsoft Kinect with the usage of a child mannequin. MMU VAAC dataset contains skeleton joints, depth, and RGB modalities.
  7. Ling HL, Rahmat Z, Murad AMA, Mahadi NM, Illias RM
    Data Brief, 2017 Oct;14:35-40.
    PMID: 28761915 DOI: 10.1016/j.dib.2017.07.026
    Bacillus lehensis G1 is a cyclodextrin glucanotransferase (CGTase) producer, which can degrade starch into cyclodextrin. Here, we present the proteomics data of B. lehensis cultured in starch-containing medium, which is related to the article "Proteome-based identification of signal peptides for improved secretion of recombinant cyclomaltodextrin glucanotransferase in Escherichia coli" (Ling et. al, in press). This dataset was generated to better understand the secretion of proteins involved in starch utilization for bacterial sustained growth. A 2-DE proteomic technique was used and the proteins were tryptically digested followed by detection using MALDI-TOF/TOF. Proteins were classified into functional groups using the information available in SubtiList webserver (http://genolist.pasteur.fr/SubtiList/).
  8. Toni B, Monfared HH, Mat Isa MN, Md Isa N, Ismail I, Zainal Z
    Data Brief, 2017 Oct;14:260-266.
    PMID: 28795103 DOI: 10.1016/j.dib.2017.07.043
    Drought stress is the main abiotic factor affecting rice production. Rain-fed upland rice which is grown on unbounded fields and totally dependent on rainfall for moisture is more prone to drought stress compared to rice from other ecosystems. However, upland rice has adapted to this limited water condition, thus are more drought tolerant than rice from other ecosystems. We performed the first transcriptome sequencing of drought tolerant indica upland rice cultivar Kuku Belang to identify differentially expressed genes related to drought tolerance mechanism. Raw reads for non-treated and PEG-treated Oryza sativa subspecies indica cv. Kuku Belang were deposited in the NCBI SRA database with accession number SRP074520 (https://www.ncbi.nlm.nih.gov/sra?term=SRP074520).
  9. Tan LW, Tan CS, Rahman ZA, Goh HH, Ismail I, Zainal Z
    Data Brief, 2017 Oct;14:267-271.
    PMID: 28795104 DOI: 10.1016/j.dib.2017.07.047
    The dataset presented in this article describes microarray experiment of Auxin-binding protein 57, Abp57-overexpressing transgenic rice. The gene expression profiles were generated using Affymetrix GeneChip® Rice (Cn) Gene 1.0 ST Arrays. Total RNA from seedlings tissue of transgenic rice and wildtype, which serve as control were used as starting materials for microarray experiment. Detailed experimental methods and data analysis were described here. The raw and normalized microarray data were deposited into Gene Expression Omnibus (GEO) under accession number GSE99055.
  10. Rosli MAF, Azizan KA, Baharum SN, Goh HH
    Data Brief, 2017 Oct;14:295-297.
    PMID: 28795107 DOI: 10.1016/j.dib.2017.07.068
    Hybridisation plays a significant role in the evolution and diversification of plants. Hybridisation among Nepenthes species is extensive, either naturally or man-made. To investigate the effects of hybridisation on the chemical compositions, we carried out metabolomics study on pitcher tissue of Nepenthes ampullaria, Nepenthes rafflesiana and their hybrid, Nepenthes × hookeriana. Pitcher samples were harvested and extracted in methanol:chloroform:water via sonication-assisted extraction before analysed using LC-TOF-MS. MS data were analysed using XCMS online version 2.2.5. This is the first MS data report towards the profiling, identification and comprehensive comparison of metabolites present in Nepenthes species.
  11. Shariat BS, Meng Q, Mahmud AS, Wu Z, Bakhtiari R, Zhang J, et al.
    Data Brief, 2017 Aug;13:562-568.
    PMID: 28706965 DOI: 10.1016/j.dib.2017.06.017
    Functionally graded NiTi structures benefit from the combination of the smart properties of NiTi and those of functionally graded structures. This article provides experimental data for thermomechanical deformation behaviour of microstructurally graded, compositionally graded and geometrically graded NiTi alloy components, related to the research article entitled "Functionally graded shape memory alloys: design, fabrication and experimental evaluation" (Shariat et al., 2017) [1]. Stress-strain variation of microstructurally graded NiTi wires is presented at different heat treatment conditions and testing temperatures. The complex 4-way shape memory behaviour of a compositionally graded NiTi strip during one complete thermal cycle is demonstrated. The effects of geometrical design on pseudoelastic behaviour of geometrically graded NiTi plates over tensile loading cycles are presented on the stress-strain diagrams.
  12. Osman BE, Khalik WMAWM
    Data Brief, 2018 Oct;20:999-1003.
    PMID: 30225314 DOI: 10.1016/j.dib.2018.08.178
    The main goal of this research work is to measure the concentration levels of organochlorine residue in soil. The potential health risk of this pollutant on human was also determined. 10 samples were taken from a lowland paddy field situated in Kelantan, Malaysia. Physical parameters namely soil pH, organic carbon content, water content and particle size were identified to evaluate the quality of soil from the agriculture site. Soxhlet extraction and florisil clean-up process were applied to isolate 10 targeted organochlorine compounds prior to the final determination using a gas chromatography-electron capture detector. Soil from the lowland has characteristics such as slightly acidic, low organic carbon content, high water content and texture dominated by the sandy type. Concentration levels of six detected organochlorine pesticides were calculated in µg/kg. Hazard quotient value in all samples was less than the acceptable risk level HQ ≤ 1, thus reflecting the status of soil in the subjected area as unlikely to pose any adverse health effects.
  13. Olalere OA, Abdurahman NH, Yunus RBM, Alara OR
    Data Brief, 2018 Aug;19:1627-1630.
    PMID: 30229034 DOI: 10.1016/j.dib.2018.06.034
    This paper contains data from the elemental and phytochemical profiling of black pepper oleoresin extracts using the LC-MS QToF and ICP-MS analysis. In recent years studies have shown the medicinal properties of extracts from these two cultivars of Piper nigrum. The medicinal properties are attributed to the presence of many secondary metabolites and mineral element in them. The phytochemical profiling was conducted using a Liquid Chromatography equipped with an electrospray time-of-flight mass spectrometer detectors. The mass spectrometer was equipped with an electrospray ionization sources operated in positive ion mode. The alkaloid compounds in the optimized black pepper extract were tentatively characterized in accordance with their ions׳ mass fragmentation.
  14. Yusup Y, Kayode JS, Alkarkhi AFM
    Data Brief, 2018 Aug;19:1477-1481.
    PMID: 30229020 DOI: 10.1016/j.dib.2018.06.020
    Air-sea flux exchanges influence the climate condition and the global carbon-moisture cycle. It is imperative to understand the fundamentals of the natural systems at the tropical coastal ocean and how the transformation takes place over the time. Hence, latent and sensible heat fluxes, microclimate variables, and surface water temperature data were collected using eddy covariance instruments mounted on a platform at a tropical coastal ocean station from November 2015 to October 2017. The research data is to gain the needful knowledge of the energy exchanges in the tropical climatic environment to further improve predictive algorithms or models. Therefore, it is intended that this data report will offer appropriate information for the Monsoonal, and diurnal patterns of latent (LE) and sensible (H) heats and hence, establish the relationship between microclimate variables on the energy fluxes at the peninsular Malaysian tropical coastal ocean.
  15. Gunasekaran D, Bunawan H, Ismail I, Noor NM
    Data Brief, 2018 Aug;19:1423-1427.
    PMID: 30229014 DOI: 10.1016/j.dib.2018.06.025
    In this dataset, we differentiate four different tissues of Cosmos caudatus Kunth (leaves, flowers, stem and root) obtained from UKM Bangi plot, based on Fourier transform-infrared spectroscopy. Different tissues of C. caudatus demonstrated the position and intensity of characteristic peaks at 4000-450 cm-1. Principal component analysis (PCA) shows three main groups were formed. The samples from leaves and flowers were found to be clustered together in one group, while the samples from stems and roots were clustered into two separate groups, respectively. This data provides an insight into the fingerprint identification and distribution of metabolites in the different organs of this species.
  16. Kayode JS, Yusup Y, Nawawi MNM, Ariffin KS, Kalil AE, Tagwa MG
    Data Brief, 2018 Oct;20:1525-1531.
    PMID: 30258956 DOI: 10.1016/j.dib.2018.09.014
    Energy Dispersive X-ray Analysis, EDX mapping, Scanning Electron Microscope, SEM, together with X-ray Fluorescence Analysis, XRF, was carried out to extract the needed data from some metamorphic rock samples in part of the Nigerian Southwestern Precambrian Basement Complex, NSPBC. The foremost aim is to obtain the detail subsurface geological structures of the rocks within the area and to enhanced understanding of the processes and the types of metamorphic evolution in the area. The techniques involved qualitative and quantitative data analysis of the major, minor and radioactive elements present in the samples of rocks analyzed. The data helped to experimentally evaluate the rocks microstructures, and to also explore the development of magmatic and metamorphic mechanisms for the recognition of textual associations in the area. Applications of the EDX, SEM, and XRF data analysis are effortlessly done to determine the varied mixtures of Si, Al, Ca, Fe, K, Mg, and Na, in the presence of O existing in the rocks samples.The data helped in the classification and perceptive of these rocks and it was considered as a necessary tool in the knowledge of the metamorphism and origin of the Basement Complex rocks through measurement of the intensity of the emitted X-ray and its characteristics.
  17. Bharudin I, Abdul Rahim SN, Abu Bakar MF, Ibrahim SN, Kamaruddin S, Latif MT, et al.
    Data Brief, 2018 Aug;19:2416-2419.
    PMID: 30229114 DOI: 10.1016/j.dib.2018.07.020
    Lichen is a symbiotic organism that exists as a single composite body consisting of a mycobiont (fungus) and a photobiont (algae or a cyanobacterium). Many lichen species are considered as extremophiles due to their tolerance to radiation, desiccation, temperature and pollution. However, not all lichen species are tolerant to harsh environmental conditions as several species are sensitive for example to nitrogen, sulphur, acidity, heavy metals, halogens (e.g. fluoride) and ozone. Thus, to better understand why some lichens can withstand exposure to pollutants as opposed to those that are susceptible, we focused on the lichen species of Dirinaria known for their wide distribution in the tropics, subtropics and pantropical, and moderate tolerance to air pollution. Their moderate tolerance to air pollution affords them to thrive in good air quality environments as well as polluted air environments. Lichen samples of Dirinaria sp., UKM-J1 and UKM-K1, were respectively collected from two areas with different levels of air quality based on Air Pollutant Index or API (with index pollutant criteria of PM10, carbon monoxide, ozone, nitrogen dioxide and sulfur dioxide) in the outskirt of Jerantut (UKM-J1), a rural area in the middle of Peninsular Malaysia and the township of Klang (UKM-K1), in a busy area of the Klang Valley, Malaysia. API was monitored throughout 2012-2013 whereby the sample collection site in Klang showed markedly higher concentrations of pollutants in all the index pollutant criteria as compared to that of Jerantut. We performed transcriptome sequencing using Illumina RNA-seq technology and de novo assembly of the transcripts from the lichen samples. Raw reads from both libraries were deposited in the NCBI database with the accession number SRP138994.
  18. Taheri S, Abdullah TL, Noor YM, Padil HM, Sahebi M, Azizi P
    Data Brief, 2018 Aug;19:2452-2454.
    PMID: 30246104 DOI: 10.1016/j.dib.2018.07.038
    Curcuma alismatifolia, is an Asian crop from Zingiberaceae family, popularly used as ornamental plant in floriculture industry of Thailand and Cambodia. Different varieties with a wide range of colors can be found in species. Until now, few breeding programs have been done on this species and most commercially important cultivars are hybrids that are propagated vegetatively. In spite of other flowering plants, there is still lack of transcriptomic-based data on the functions of genes related to flower color in C. alismatifolia. The raw data presented in this article provides information on new original transcriptome data of two cultivars of C. alismatifolia by Illumina Hiseq. 4000 RNA-Seq technology which is the first ever report about this plant. The data is accessible via European Nucleotide Archive (ENA) under project number PRJEB18956.
  19. Samad AFA, Sajad M, Jani J, Murad AMA, Ismail I
    Data Brief, 2018 Oct;20:555-557.
    PMID: 30197911 DOI: 10.1016/j.dib.2018.08.034
    Degradome sequencing referred as parallel analysis of RNA ends (PARE) by modifying 5'-rapid amplification of cDNA ends (RACE) with deep sequencing method. Deep sequencing of 5' products allow the determination of cleavage sites through the mapping of degradome fragments against small RNAs (miRNA or siRNA) on a large scale. Here, we carried out degradome sequencing in medicinal plant, Persicaria minor, to identify cleavage sites in small RNA libraries in control (mock-inoculated) and Fusarium oxysporum treated plants. The degradome library consisted of both control and treated samples which were pooled together during library preparation and named as D4. The D4 dataset have been deposited at GenBank under accession number SRX3921398, https://www.ncbi.nlm.nih.gov/sra/SRX3921398.
  20. Dzulkefli NA, Zainol N
    Data Brief, 2018 Oct;20:1710-1720.
    PMID: 30263925 DOI: 10.1016/j.dib.2018.09.008
    In this article, five variables including type of substrates, sizes of substrates, mass ratio of spawn to substrates (SP/SS), temperature and pretreatment of substrates were used to model mycelium growth in Pleurotus sp. (oyster mushroom) cultivation by using agricultural wastes via two level factorial analysis. Two different substrates which were empty fruit bunch (EFB) and sugarcane bagasse (SB) were used. Analysis of Variance (ANOVA) for both mycelium extension rate (M) and nitrogen concentration in mycelium (N) showed that the confidence level was greater than 95% while p-value of both models were less than 0.05 which is significant. The coefficient of determination (R2) for both M and N were 0.8829 and 0.9819 respectively. From the experiment, the best condition to achieve maximum M (0.8 cm/day) and N (656 mg/L) was by using substrate B, 2.5 cm size of substrate, 1:14 for SP/SS, incubated at ambient temperature and application of steam treatment. The data showed that EFB can be used to replace sawdust as a media for the oyster mushroom cultivation. Data analysis was performed using Design Expert version 7.0.
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