Displaying publications 1 - 20 of 368 in total

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  1. Lim LY, Ab Majid AH
    Data Brief, 2020 Aug;31:105903.
    PMID: 32637504 DOI: 10.1016/j.dib.2020.105903
    Tapinoma indicum is a household pest that is widely distributed in Asian countries. It is known as nuisance pest that causes annoyance and disturbance by constructing nests and foraging in building for food and water. This article documents the draft genome dataset of T. indicum collected in Penang Island, Malaysia using the next-generation sequencing known as the Illumina platform. This article presents the pair-end 150 bp genome dataset and the quality of the sequencing result. This dataset provides the information for further understanding of T. indicum in the molecular aspect and the opportunity to develop a novel method for pest control and regulation. The dataset is available under Sequence Read Archive (SRA) databases with the accession number SRR10848807.
  2. Ashigar MA, Ab Majid AH
    Data Brief, 2020 Aug;31:106037.
    PMID: 32728606 DOI: 10.1016/j.dib.2020.106037
    Metagenomic datasets of the microbial DNA of workers of a Pheidole decarinata Santschi (Hymenoptera: Formicidae) around houses with three replicates were presented. Next-generation sequencing of the microbial DNA was performed on an Illumina Miseq platform. QIIME (version 1.9.1) was used to analyze the raw fastq files. Metagenome of the three (3) samples consist of 333,708 sequences representing 137,359,149 bps with an average length of 413.67 bps. The sequence data is available at the NCBI SRA with the bioproject number PRJNA632430. Community analysis revealed Proteobacteria was the predominant (84.77%) microbial community present in the microbial DNA of workers of the P. decarinata.
  3. Lim L, Ab Majid AH
    Data Brief, 2020 Jun;30:105575.
    PMID: 32368598 DOI: 10.1016/j.dib.2020.105575
    The metagenomic datasets of the microbial DNA from tropical bed bugs (Cimex hemipterus) after feeding on human blood were presented. Next-generation sequencing of the community DNA was carried out on an Illumina Miseq platform and the raw fastq files were analyzed using QIIME (version 1.9.1). The metagenome of three samples comprised of 108,198 sequences representing 44,646,263 bps with a mean length of 412.63 bps. The sequence data is accessible at the NCBI SRA under the bioproject number PRJNA600667. Community analysis showed Proteobacteria was the most abundance (more than 99%) microbial community that present in the guts of fully fed tropical bed bugs.
  4. Shamsuri QS, Ab Majid AH
    Data Brief, 2023 Apr;47:108993.
    PMID: 36875219 DOI: 10.1016/j.dib.2023.108993
    In this paper, we present the metagenomic dataset of gut microbial DNA of the lower group of subterranean termites, i.e. Coptotermes gestroi, and the higher groups, i.e. Globitermes sulphureus and Macrotermes gilvus, in Penang, Malaysia. Two replicates of each species were sequenced using Next-Generation Sequencing (Illumina MiSeq) and analysed via QIIME2. The results returned with 210,248 sequences in C. gestroi, 224,972 in G. sulphureus, and 249,549 in M. gilvus. The sequence data were deposited in the NCBI Sequence Read Archive (SRA) under BioProject number of PRJNA896747. The community analysis showed that Bacteroidota is the most abundant phylum in C. gestroi and M. gilvus, while Spirochaetota is prevalent in G. sulphureus.
  5. Taibukahn N, Ab Majid AH
    Data Brief, 2023 Apr;47:109024.
    PMID: 36936641 DOI: 10.1016/j.dib.2023.109024
    The metagenomics dataset presented here is based on bacterial 16S rDNA gene amplicons of DNA extracted from tropical bed bugs (Cimex hemipterus). Amplicon-based sequencing was performed using the Illumina MiSeq platform, and the raw sequence data were analyzed using QIIME (version 2022.8.3). The metagenome sequence comprised ten samples that include C1 (133 511bps), C2 (108 920bps), CH1 (106 562bps), CH2 (101 778bps), P1 (103 618bps), P2 (133 258bps), T1 (113 558bps), T2 (133 952bps), TM1 (125 335bps), and TM2 (118 345bps). The sequence data is readily accessible at the NCBI SRA under bio project PRJNA918835. The most abundant microbial community present in the C. hemipterus is the Proteobacteria, with more than 99% of the abundance.
  6. Dominic MIS, Ab Majid AH
    Data Brief, 2023 Aug;49:109301.
    PMID: 37346927 DOI: 10.1016/j.dib.2023.109301
    Periplaneta americana is a cosmopolitan pest cockroach endemic to tropical and subtropical climates. It occurs frequently in urban sewer and wastewater system and transit in human proximities, spreading pathogens that causes serious public health concerns such as asthma, allergies, and others. By using the Next-generation Sequencing (NGS) known as Illumina NovaSeq 6000, this article documents for the draft genome data set of P. americana collected in Penang Island, Malaysia. This article displays the pair-end 150 bp genome dataset and results on the sequence quality. This genome dataset presents the information for further understanding of P. americana populations at molecular level and the opportunity to develop effective control and management strategies for the species. This dataset is available under Sequence Read Archive (SRA) databases with the SRR23867103.
  7. Kamarudin SAA, Ahmad F, Hasan N, Hisham SN, Yusof SN, Abu Hassan A, et al.
    Data Brief, 2024 Feb;52:109974.
    PMID: 38229927 DOI: 10.1016/j.dib.2023.109974
    In Malaysia, rice mutant varieties that are genetically altered to confer resistance against blast disease have been substantially developed through mutational breeding program. However, due to the limited accessible information on the mutant lines, mutant gene variants corresponding to the disease resistance and other useful agronomic traits are yet to be exploited. Here, we conducted whole genome re-sequencing of blast resistance with kernel elongation traits in mutant line, Mahsuri Mutant (87,639,446 bp raw reads), and its parental line, Mahsuri (85,156,783 bp raw reads) using Illumina Novaseq 6000 sequencing platform with 30x sequencing coverage. The generated genome sequences are aimed to facilitate the discovery of causal mutation and single nucleotide polymorphisms (SNPs) related to the intended traits. The identified SNPs can be further employed to develop allele-specific SNP molecular markers to locate the mutant gene regions. The NGS data obtained (FASTQ format) of the parental and mutant lines have been deposited in the National Center for Biotechnology Information (NCBI) database under sequence read archive (SRA) xwith accession numbers SRR24388814 (Mahsuri) and SRR22952097 (Mahsuri Mutant) respectively.
  8. Mahat N, Tah J, Vidalakis C, Khamaksorn A, Thinnukool O, Abd Malek MI
    Data Brief, 2021 Dec;39:107556.
    PMID: 34825028 DOI: 10.1016/j.dib.2021.107556
    This data paper shows the perspectives by developers of housing on factors of the sustainable construction adoption. The Data was collected by using formal Likert scale questionnaire as main instrument. Simple random sampling was used to assign questionnaires to respondents. Data samples were evaluated using index and rating. The data will provide information on the most variables that considered as main factors for sustainable construction adoption. The importance between variables can provide information that will contribute to the expedition of sustainable practise in housing projects in Malaysia.
  9. Kadir MA, Haris NSH, Yusof MSM, Kassim K, Abdul Razak FI
    Data Brief, 2023 Dec;51:109635.
    PMID: 37840994 DOI: 10.1016/j.dib.2023.109635
    This paper provided the dataset obtained from spectroscopic, crystallography and DFT of a new compound namely 1,2-bis[N,N'-6-(4-pyridylmethylamido)pyridyl-2-carboxyamido]butane. This compound is prepared from the reaction between N-6-[(4-pyridylmethylamino)carbonyl]-pyridine-2-carboxylic acid methyl ester with butane-1,4-diamine. The preparation of this compound is modified from the method described in our article [1]. In this work, we present data characterization of 1,2-bis[N,N'-6-(4-pyridylmethylamido)pyridyl-2-carboxyamido]butane from Fourier Transform Infrared (FTIR), 1H Nuclear Magnetic Resonance (1 H NMR), NOESY NMR, 13C Nuclear Magnetic Resonance (13C NMR), and elemental analysis (CHNS). The structure of this molecule is also analysed by X-ray crystallography and DFT studies. A single-crystal X-ray diffraction investigation was carried out by using Bruker SMART Apex II Duo CCD area-detector diffractometers with MoKα radiation (wavelength of λ = 0.71073 Å). The optimized energy was indicated with GaussView 5.0 and Gaussian 16 software package programme.
  10. Abd Manan TSB, Khan T, Wan Mohtar WHM, Beddu S, Mohd Kamal NL, Yavari S, et al.
    Data Brief, 2020 Jun;30:105518.
    PMID: 32382595 DOI: 10.1016/j.dib.2020.105518
    Perak River basin is in Perak state of Peninsular Malaysia. In this research, the river stretch serves as water intake for domestic, agricultural and industrial purposes in Perak Tengah, Hilir Perak and Manjung regions. It is located in mixed use area whilst exposing the river to anthropogenic elements. The sampling locations were conducted at selected points of Perak River namely Tanjung Belanja Bridge (TBB), Water Treatment Plant Parit (WTPP), Parit Town discharge (PTD), Water Treatment Plant Senin (WTPS) and Water Treatment Plant Kepayang (WTPK). The existence of aromatic hydrocarbons in freshwater samples was pre-assessed via qualification analysis; specific ultraviolet absorbance (SUVA254) method at 254 nm of wavelength. The SUVA dataset were 48.38 L/mg-m (TBB), 50.54 L/mg-m (WTPP), 8.05 L/mg-m (PTD), 85.75 L/mg-m (WTPS) and 217.39 L/mg-m (WTPK). The SUVA254 values of fresh water at the river basin have exceeded the water quality standards value equivalent to 2.0 L/mg-m permitted by the Environmental Protection Agency of United States. The exceeding values were an indication of a large portion of aromatic compounds in the water. Qualification analyses evident the existence of water pollutants at treacherous concentrations for public health in freshwater samples of Perak River basin. Thus, this research has presented important findings towards further research and countermeasure for a better alternative of water treatment in Malaysia.
  11. Najmuddin MF, Haris H, Othman N, Zahari F, Mohd-Ridwan AR, Md-Zain BM, et al.
    Data Brief, 2020 Aug;31:105727.
    PMID: 32548216 DOI: 10.1016/j.dib.2020.105727
    Morphism refer to polymorphic species, in which multiple colour variants coexist within a population. Morphism in primates is common and langurs also exhibit certain characteristics of morphism, such as conspicuous natal coats. Banded langurs (Presbytis femoralis) and dusky leaf monkey (Trachypithecus obscurus) exhibits the same characteristics of conspicuous natal coats, but these coats are only limited to infants and changed when they reached adulthood. This article reports the first discovery of rare brown morph of two adult male banded langurs and one leucistic adult female dusky leaf monkey in Malaysia. We also conducted a systematic literature search to review the diversity of morphism in leaf monkey globally.
  12. Fakhrul-Hatta SNN, Nelson BR, Shafie NJ, Zahidin MA, Abdullah MT
    Data Brief, 2018 Dec;21:2089-2094.
    PMID: 30533456 DOI: 10.1016/j.dib.2018.11.058
    This data article informs about Chiropteran diversity, new records, ecosystem services and possible pathogen carriers in fragmented forests (sub-divided by utility corridors, man-made structures, untouched and secondary plantations) within districts Setiu (Setiu Research Station), Hulu Terengganu (Saok and Lasir waterfalls) and Besut (Gunung Tebu Forest Reserve) of state Terengganu, Peninsular Malaysia. These bats were captured using harp traps and mist nets that were set 10 m apart across flyways, streams and less cluttered trees in the 50 m × 50 m transect zones (identified at each site). All animals were distinguished by morphology and gender before their release at the site of capture. The data comprise of five bat family groups Hipposideridae, Megadermatidae, Pteropodidae, Rhinolophidae and Vespertilionidae. It is interesting to note that untouched Saok Waterfalls is home to wide variety of bats listed (68.8%), followed by secondary forests of Gunung Tebu Forest Reserve (24.8%), untouched Lasir Waterfalls (4.8%) and lastly, Setiu Research Station as least favored (1.6%). Chiroptera like Cynopterus brachyotis (n = 23, 37.7%), Hipposideros bicolor (n = 6, 9.8%) and Scotophilus kuhli (n = 6, 9.8%) were most dominant in the checklist whereas Hipposideros armiger, Murina suilla and Scotophilus kuhlii are new data records in the fragmented forests of Terengganu. The data were interpret into Shannon, Simpson, Margalef, Menhinik and Evenness indices to individually or collectively distinguish chiropteran variety in Terengganu State whereas weight-forearm length (W/FA) informs about chiropteran Body Condition Index (-0.25 to 0.25). The function of bats were also identified to distinguish service providers (pollination and forests regeneration) and zoonotic pathogen carriers (in particular to Leptospira bacteria, Nipah virus and Sindbis virus).
  13. Zahidin MA, Jalil NA, Naharuddin NM, Abd Rahman MR, Gani M, Abdullah MT
    Data Brief, 2019 Aug;25:104133.
    PMID: 31321260 DOI: 10.1016/j.dib.2019.104133
    Tarsier is an endangered nocturnal primate in the family Tarsiidae and is an endemic to Sundaic islands of Philippine (Carlito syrichta), Sulawesi (Tarsius tarsier-complex) and Borneo (Cephalopachus bancanus). Recent records indicated that most molecular studies were done on the Eastern Tarsier and little information for the other group of tarsiers. Here, we present a partial cytochrome b data set of C. bancanus in Sarawak, Malaysian Borneo. Standard mist nets were deployed at strategic locations in various habitat types. A total of 18 individuals were caught, measured and weighed. Approximately, 2 × 2 mm of tissue samples were taken and preserved in molecular grade alcohol. Out of 18, only 11 samples were screened with partial mtDNA (cytochrome b) and the DNA sequences were registered in the GenBank (accession numbers: KY794797-KY794807). Phylogenetic trees were constructed with 20 additional mtDNA sequences downloaded from GenBank. The data are valuable for the management authorities to regulate the type of management units for the metapopulation to sustain population genetics integrity of tarsiers in the range countries across the Sunda Shelf.
  14. Jusoh H, Sabariah Binti Abd Manan T, Beddu S, Osman SBS, Jusoh MNH, Mohtar WHMW, et al.
    Data Brief, 2020 Aug;31:105868.
    PMID: 32637485 DOI: 10.1016/j.dib.2020.105868
    Soil requires load bearing impact assessment for stability. Therefore, this study aims to utilize the multi-channel analysis surface wave (MASW) for soil subsurface investigation and profiling around Peninsular Malaysia. The standard penetration test (SPT) was conducted for comparison between factual N-value and computed N-value from shear wave velocity (Vs ) obtained from MASW using the Imai and Tonouchi equation. The correlation coefficient (R) and coefficient of determination, (R2 ), showed strong relationship between factual N-value and computed N-value. The model of Vs and factual N-value data distribution is non-normal but the analyzed relationship shows a significant level of p-value < 0.05. The R2 for each location of Vs -N-value relationship are ranging from 0.5 to 0.9.
  15. Beddu S, Abd Manan TSB, Zainoodin MM, Khan T, Wan Mohtar WHM, Nurika O, et al.
    Data Brief, 2020 Aug;31:105843.
    PMID: 32596432 DOI: 10.1016/j.dib.2020.105843
    Coal combustion by-products (CCPs) (i.e. fly (FA) and bottom (BA) ashes) generated by power plants contain heavy metals. This research presents leaching properties of coal ashes (FA and BA) collected from Jimah coal-fired power station, Port Dickson, Negeri Sembilan using USEPA standard methods namely toxicity characteristic leaching procedure (TCLP), and synthetic precipitation leaching procedure (SPLP). Heavy metals like lead (Pb), zinc (Zn), copper (Cu) and arsenic (As) were quantified using atomic absorption spectrometer (AAS). The leached of heavy metals fluxes were Cu < Zn < Pb < As. As leached the most whilst indicating of possible contamination from As. Overall, the ranges of leached concentration were adhered to permissible limits of hazardous waste criteria for metal (Pb and As) and industrial effluent (Zn and Cu). The presented data has potential reuse as reference for the coal ash concrete mixed design application in construction industries.
  16. Khalib NKA, Shafie NJ, Basri HH, Nelson BR, Abdullah MT
    Data Brief, 2018 Dec;21:1514-1520.
    PMID: 30480062 DOI: 10.1016/j.dib.2018.10.061
    This data article is about non-volant small mammal (squirrel, rat and tree shrew) capture from fragmented forest understories within sub-urban areas of Setiu (Peladang Agro Resort and Setiu Wetland Research Station) and inhabited areas of Hulu Terengganu (Saok and Lasir waterfalls) that are situated in Terengganu State, Peninsular Malaysia. Fruits like banana and oil palm were individually placed into each cage before the cages were fastened onto three to five meter height tree branches. The traps were also spatially distributed about ten meters from each other. Under this installation, fifty baited traps were used during the twenty-four nights of sample collection. All animals caught were distinguished by morphology and released at the same location it was caught. The understory data comprise of seven non-volant mammal species from family groups Sciuridae, Muridae and Tupaiidae. Overall, Callosciurus notatus (n = 17, 39%) were dominant in the capture pool from all sites. Comparatively, Sundascriurus tenuis (n = 2, 4%) and Rattus rattus (n = 4, 9.3%) were restricted to Saok Waterfalls and Setiu Wetland. Banana and oil palm fruits did not attract any small mammals during the Lasir Waterfall (Hulu Terengganu) survey. All data were interpret into Shannon, Simpson, Margalef, Menhinik and Evenness indices to individually or collectively distinguish small mammal variety in Terengganu State.
  17. Zahidin MA, Omar WBW, Taib WRW, Japning JRR, Abdullah MT
    Data Brief, 2018 Dec;21:2609-2615.
    PMID: 30761343 DOI: 10.1016/j.dib.2018.10.158
    Orang Asli is the aboriginal people in Peninsular Malaysia who have been recognized as indigenous to the country and still practicing traditional lifestyle. The molecular interest on the Orang Asli started when the earliest prehistoric migration occurred approximately 200 kya and entering Peninsular Malaysia 50 kya in stages. A total of three groups of Orang Asli present in Peninsular Malaysia, namely, Negrito also known as Semang, Senoi and Proto Malays. Through records, there is no research has been conducted on mtDNA variations in the Semoq Beri population, one of the tribes in Senoi group. In this report, variations of mtDNA were analysed in the population in Hulu Terengganu as an initial effort to establish the genetic characterisation and elucidating the history of Orang Asli expansion in Peninsular Malaysia. An array of mtDNA parameters was estimated and the observed polymorphisms with their respective haplogroups in comparison to rCRS were inferred respectively. The DNA sequences are registered in the NCBI with accession numbers KY853670-KY853753.
  18. Afiq Ramlee MN, Hussin MF, Roslan A, Rosmidi FH, Pesiu E, Aisyah A Rahim N, et al.
    Data Brief, 2020 Apr;29:105328.
    PMID: 32181296 DOI: 10.1016/j.dib.2020.105328
    This data article presents the diversity of flora and selected fauna in Tasik Kenyir, Malaysia. This man-made lake once suffered huge loss of biodiversity for allowing an earth-dam construction during 1980s. Series of publications on different types of target taxa have been published separately after the post-dam construction. A biodiversity assessment was conducted in Tasik Kenyir from March 2015 until February 2016. The one year assessment were compiled with the previous published data to document and updated the biodiversity checklist in the lake. The data show that Tasik Kenyir is occupied by 113 tree species, 217 butterfly species, 35 bee species, 26 reptile species, 267 aves species and 153 mammal species. The micro-climate data was downloaded from the Malaysian Meteorological Department and analysed in R Studio to highlight the relationship between climate data and biodiversity data.
  19. Rovie-Ryan JJ, Gani M, Lee YP, Gan HM, Abdullah MT
    Data Brief, 2019 Aug;25:104058.
    PMID: 31211204 DOI: 10.1016/j.dib.2019.104058
    This data article presents the first complete mitochondrial genome (mitogenome) of an endangered slow loris subspecies, Nycticebus coucang insularis Robinson, 1917 from Tioman Island, Pahang. Once considered as extinct, an individual of the subspecies was captured alive from the island during the 2016 Biodiversity Inventory Programme as highlighted in the related research article entitled "Rediscovery of Nycticebus coucang insularis Robinson, 1917 (Primates: Lorisidae) at Tioman Island and its mitochondrial genetic assessment" Rovie-Ryan et al., 2018. Using MiSeq™ sequencing system, the entire mitogenome recovered is 16,765 bp in length, made up of 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and one control region. The mitogenome has been deposited at DDBJ/EMBL/GenBank under the accession number NC_040292.1/MG515246.
  20. Yung DTC, Jani R, Azizi R, Ramli MN, Haidi Y, Zainudin AN, et al.
    Data Brief, 2020 Apr;29:105082.
    PMID: 31993462 DOI: 10.1016/j.dib.2019.105082
    In this data article we present the determinations of the diet preference and growth of a pair of the giant panda, Ailuropoda melanoleuca (David, 1869) from Zoo Negara Malaysia. Once considered as endangered, the captive giant pandas were given with nine species of local bamboo in separate indoor enclosures. We recorded data between May 25, 2014 and December 31, 2016 and analysed it based on food preference, the pattern toward food consumption and body weights using SPSS v25.0 (IBM, USA). Data on the bamboo preference, daily average bamboo provided and consumed, and factors predicting of body weight per individual are reported in this article. The data highlight correlation between panda growth (kg) to the part of bamboo consumed (kg) and exhibit the pattern of preferred part of food (i.e.: either the leaf, culm or shoots of bamboo variety) for panda consumptions. The food consumption toward the body weight was modelled using logistic regression analysis to help determine the pattern of food consumption and body weight of giant panda in the future and based on regression model 1, only consumed variable is significance to the model.
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