Automated Seed-Based Region Growing Using The Moving K-Means Clustering For The Detection Of Mammographic Microcalcifications.

Mammography is by far the proven method of early detection of breast cancer. However, mammography is not without its problems. It is amongst the most difficult of radiological images to interpret as the images are of low contrast and features indicative of abnormalities are very subtle and minute. In this study, a new method of automated edge detection technique is proposed to detect the abnormalities in a region of interest in a mammogram

Conceptual Framework of Al-Ghazali Epistemology Knowledge in Media Education

The upheaval of the digital age has made media education an essential component in determining the belief, thought, and behavior of media practitioners. The task of the century is to raise a generation of educated people, especially those with knowledge, skills, and attitudes that go beyond what is taught in standard media curricula. As a result, the emphasis in media education needs to change from dualistic thinking to the idea of the absolute truth of knowledge. This calls for a deeper comprehension of what education means. Determining the meaning of education, the idea of knowledge from Al Ghazali's philosophical standpoint, and its connection to human nature and Islamic ideas is the goal of this articles. A conceptual framework for the epistemology of knowledge in media education is suggested in light of the review. Keywords: Epistemology; Media Education; Al Ghazali; Secularism eISSN: 2398-4287 © 2020. The Authors. They are published for AMER ABRA CE-Bs by E-International Publishing House, Ltd., UK. This is an open-access article under the CC-BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). Peer-review under the responsibility of AMER (Association of Malaysian Environment-Behaviour Researchers), ABRA (Association of Behavioural Researchers on Asians), and cE-Bs (Centre for Environment-Behaviour Studies), Faculty of Architecture, Planning & Surveying, Universiti Teknologi MARA, Malaysia. DOI: https://doi.org/10.21834/ebpj.v7iSI7.376

Characterization of thermostable beta-1,4-galactanase and its application in hydrolysis of pectin from sweet potato (Ipomoea batatas (l.) lam) peels

Galactooligosaccharides (GOS) synthesis has received much attention due to its prebiotic function. Beta-1,4-galactanase responsible for the hydrolysis of galactan plays an important role in producing GOS from biodegradation of this pectin component. In this study, beta-1,4-galactanase (BgcGC) from a thermophilic Geobacillus mahadii Geo-05 was heterologously expressed in Escherichia coli (E. coli) and characterized. The optimum temperature of BgcGC was at 60°C and stable from 20-60°C while optimum pH was at 6 and stable from pH 4-10. BgcGC showed high catalytic efficiency towards potato galactan (873.8 ml mg-1 s-1) and lupin galactan (1694.4 ml mg-1 s-1). The activity of BgcGC was not significantly affected with the presence of 100 mM K+, Tween-20 and 2-mercaptoethanol. Application of BgcGC towards pectin-containing galactan oligomer extracted from sweet potato peels resulted in galactose and GOS synthesis as revealed by high performance liquid chromatography analysis. Thus, this enzyme has a potential to be one of the enzyme candidates involves in pectin complex degradation to produce GOS

Reproductive biology of estuarine catfish, Arius argyropleuron (Siluriformes: Ariidae) in the northern part of Peninsular Malaysia

A preliminary study on reproductive biology of estuarine catfish, Arius argyropleuron was conducted using samples collected from Merbok estuary which is located in the northern part of peninsular Malaysia. The fish samples were collected in March-December 2009 using a barrier nets deployed on mudflat opposite vegetation of mangroves. Testes and ovaries were classified base on volume relative to abdominal cavity, gonad forms, size of gonad, colors and oocytes diameter. The gonado-somatic indices showed that the fish matured throughout the year with major spawning peak for females occurred in April and minor peak in July, whereas males recorded a higher peak in November. Absolute fecundity of mature ovary was ranged from 19 to 87 eggs and was linearly related to fish length and power function to fish body weight. Three groups of eggs for the ovary in stage II and two groups in stage III were recorded. The length at first maturity for both males and females was approximately 22.5 cm in fork length. Keywords: Arius argyropleuron, Merbok estuary, peninsular Malaysia, reproductive biolog

Biodiversity and functional metagenomic profiling of microbial communities in Tasik Kenyir, Terengganu

Tasik Kenyir located in the state of Terengganu is the largest artificial lake in Southeast Asia with mean-depth of 37 m. This lake plays an important role in maintaining the biodiversity in the surrounding environment. Microbial communities in the lake are important, as most of the nutrients are recycled through the “microbial loop”. Thus, understanding the connection between the diversity composition and functional role of aquatic microbial community is crucial for proper lake management. This study aims to determine the diversity and functions of microbial assemblages in Tasik Kenyir by means of shotgun metagenomics analysis. Briefly, water samples were collected from pristine and disturbed areas. Metagenome DNA were then extracted directly and subjected to clone-independent sequencing. Data sequences of all samples were analyzed and functional annotated using bioinformatics software MEGAN6. Analysis showed up to 41 phyla that had been detected from the water samples with the presence of dominant bacterial populations of more than 90% in all samples. Proteobacteria was the most dominant phylum, representing more than 70% of the microbiome in all samples. Other taxa such as Bacteriodetes, Terrabacteria group, Verrucomicrobia, Planctomycetes and Chloroflexi were also found as part of the microbial communities. The first sample from the disturbed area, TKSA1 had 3% of total contigs read assigned to genera Pseudomonas while the other samples appeared to be more homogeneous. The lake also appeared to contain a mixture of autotrophs and heterotrophs capable of performing main biogeochemical cycles. Findings of the present study has provided us valuable information on the microbial diversity structures and their functions in the nutrient processing pathways that occurred in the Tasik Kenyir environment and thus sheds light on the importance of freshwater microbial communities for ecosystem and human health

Transcriptomic analysis on susceptibility of different inbred chicken lines towards very virulent infectious bursal disease virus infection

Infectious bursal disease virus (IBDV) is an economically important virus which affects the poultry industry worldwide. The virus is a causative agent for Gumboro disease which can cause high mortality rate in young chickens by infecting and destroying actively dividing IgM-bearing B lymphocytes in the bursa of Fabricius leading to immunosuppression. Previous studies have identified differential expression of immune-mediated genes related to inflammatory response in chickens with different genetic susceptibility to IBDV infections. However, the mechanisms of genetic resistance against IBD are not known. RNA sequencing through next-generation sequencing (NGS) technologies provide an excellent platform to study differentially expressed genes of known or unknown function to better define effective mechanism of host resistance. Therefore, this study is aimed at investigating susceptibility of different inbred chicken lines toward very virulent IBDV through transcriptomic analysis. This analysis allows for quantification of gene expression and identification of possible single nucleotide polymorphisms (SNPs), indels, and novel protein-coding sequence. RNA isolated from bursa of day 3 IBDV-infected and control chickens were used for Illumina sequencing. Bioinformatics analysis of this data will allow function annotation of differentially expressed genes, indicating possible roles in the response to infection. Gene of interest, virus detection and copy number variation between different lines will be validated using qPCR. Genes of interest that exhibit novel SNP and/or indels will be validated using siRNA experiments. This study is expected to provide information that able to decipher the genetic resistance of chickens towards IBDV infection

Representative candidate of gelatinase encoded gene in Enterobacter aerogenes (Strain EA1) for hydrolyzing porcine gelatin

Enterobacter aerogenes (Strain EA1) was characterised as gelatinase species-specific bacterium to porcine and fish gelatin. This bacterium offers the possibility of enzymes production to each species gelatin. In this study, a bioinformatic analysis toward genome sequence of E. aerogenes was perfomed to determine genes encoded for gelatinase. E. aerogenes were partially genome sequenced resulting in 5.0 mega basepair total size of sequence. From pre-process pipeline, 78.58% of high quality reads was obtained for E. aerogenes. Genome assembly produced 120 contigs with 55.17% of GC base content. Protein prediction analysis determined 4705 genes from E. aerogenes. Two gelatinase candidate target genes selected from E. aerogenes were NODE_9_length_26866_cov_148.013245_12 containing 1029 bp sequence and NODE_24_length_155103_cov_177.082458_62 containing 717 bp sequence with highest similarity identity percentage against gelatinase enzyme available in Swiss-Prot and NCBI online database. Then, primers were designed for each target genes based on the open reading frame of selected genes. The expected gene candidate showed, 1029 bp and 717 bp amplicons for gen NODE_9_12 and gene NODE_24_62, respectively. Thus, gelatinase candidate encoded genes of E. aerogenes were identified for hydrolyzing porcine gelatin

Dynamic QoS: Automatically Modifying QoS Queue's Maximum Bandwidth Rate-Limit of Network Devices for Network Improvement

The heterogeneous data traffic of today's network is a huge challenge to existing best-effort network technology, particularly in the context of large Ethernet, which handles hundreds to thousands of users. The existing conventional best-effort network technology is no longer efficient to handle the diversity of traffic types in the network and requires network management equipment such as Quality of Service (QOS). Usually, QOS is implemented on the gateway router. However, for better network performance and management, to guarantee high priority for sensitive traffic like video conferencing, Voice over Internet Protocol (VoIP), and streaming media within an internal network, it is nice to have QoS implemented on each router in the LAN network, starting from the access router to the gateway router. This paper is to demonstrate the effectiveness of the proposed dynamic QoS that has been developed and deployed in the LAN, purposely to provide adequate bandwidth for sensitive traffic when the network utilization is high and congested, by automatically modifying the QoS Queue's Maximum Bandwidth Rate-Limit of the best-effort traffic queue of the related router. The performance of the proposed developed dynamic QoS was evaluated via a comparison study before and after the dynamic QoS was presented in the network simulation environment that was built using Mininet. Results from the testing show that the developed dynamic QoS can improve the network's performance by automatically giving the appropriate bandwidth for sensitive traffic on the fly while needed/on demand

Pencirian jujukan genom mitokondria spesies Rafflesia (Rafflesiaceae) di Semenanjung Malaysia

Rafflesia terkenal sebagai tumbuhan yang menghasilkan bunga tunggal yang terbesar di dunia. Namun, ia semakin jarang ditemui dan ialah spesies dalam bahaya. Sistem pengelasan spesies Rafflesia ialah komponen penting dalam usaha pemuliharaan lazimnya bergantung kepada pencirian morfologi bunga. Walau bagaimanapun, pendekatan molekul, termasuk yang berasaskan kepada jujukan genom mitokondria (mtDNA), berupaya menyediakan kaedah pengelasan yang lebih berkesan. Untuk meneroka kemungkinan ini, jujukan mtDNA empat spesies Rafflesia di Semenanjung Malaysia, iaitu R. cantleyi, R. azlanii, R. kerrii dan R. sharifah-hapsahiae telah dihimpun dan dicirikan dalam kajian ini. Bacaan jujukan mtDNA untuk setiap spesies kajian pada mulanya telah ditentukan masing-masing daripada set data genom keseluruhan menggunakan pendekatan pemetaan berbantukan rujukan. Proses penghimpunan secara de novo dan perancahan kemudiannya telah dijalankan ke atas bacaan jujukan yang telah dikenal pasti untuk menghasilkan jujukan mtDNA bagi R. cantleyi (441,992 pb), R. azlanii (472,723 pb), R. kerrii (500,932 pb) dan R. sharifah-hapsahiae (453,747 pb). Seterusnya, anotasi mtDNA bagi setiap spesies telah mengenal pasti sekurang-kurangnya 31 gen pengekodan protein, enam gen tRNA dan tiga rRNA. Perbandingan gen mitokondria mendapati bahawa beberapa gen seperti cob, rpl10, mttB dan ccmB mempamerkan orientasi yang berbeza dalam spesies Rafflesia yang tertentu manakala analisis penjajaran jujukan berganda menunjukkan jujukan gen nad1 adalah berbeza antara keempat-empat spesies Rafflesia yang dikaji. Analisis filogenetik dengan menggunakan jujukan bagi tujuh gen pengekodan protein yang terpelihara berupaya membezakan spesies Rafflesia yang dikaji. Kesimpulannya, hasil pencirian jujukan mDNA menunjukkan bahawa jujukan gen mitokondria yang khusus berupaya membezakan spesies Rafflesia yang dikaji dan berpotensi untuk digunakan bagi tujuan pengenalpastian serta pengelasan spesies Rafflesia dalam usaha pemuliharaan organisma yang unik ini

COMPARATIVE METAGENOMICS ANALYSIS OF PALM OIL MILL EFFLUENT (POME) USING THREE DIFFERENT BIOINFORMATICS PIPELINES

ABSTRACT: The substantial cost reduction and massive production of next-generation sequencing (NGS) data have contributed to the progress in the rapid growth of metagenomics. However, production of the massive amount of data by NGS has revealed the challenges in handling the existing bioinformatics tools related to metagenomics. Therefore, in this research we have investigated an equal set of DNA metagenomics data from palm oil mill effluent (POME) sample using three different freeware bioinformatics pipelines’ websites of metagenomics RAST server (MG-RAST), Integrated Microbial Genomes with Microbiome Samples (IMG/M) and European Bioinformatics Institute (EBI) Metagenomics, in term of the taxonomic assignment and functional analysis. We found that MG-RAST is the quickest among these three pipelines. However, in term of analysis of results, IMG/M provides more variety of phylum with wider percent identities for taxonomical assignment and IMG/M provides the highest carbohydrates, amino acids, lipids, and coenzymes transport and metabolism functional annotation beside the highest in total number of glycoside hydrolase enzymes. Next, in identifying the conserved domain and family involved, EBI Metagenomics would be much more appropriate. All the three bioinformatics pipelines have their own specialties and can be used alternately or at the same time based on the user’s functional preference. ABSTRAK: Pengurangan kos dalam skala besar dan pengeluaran data ‘next-generation sequencing’ (NGS) secara besar-besaran telah menyumbang kepada pertumbuhan pesat metagenomik. Walau bagaimanapun, pengeluaran data dalam skala yang besar oleh NGS telah menimbulkan cabaran dalam mengendalikan alat-alat bioinformatika yang sedia ada berkaitan dengan metagenomik. Justeru itu, dalam kajian ini, kami telah menyiasat satu set data metagenomik DNA yang sama dari sampel effluen kilang minyak sawit dengan menggunakan tiga laman web bioinformatik percuma iaitu dari laman web ‘metagenomics RAST server’ (MG-RAST), ‘Integrated Microbial Genomes with Microbiome Samples’ (IMG/M) dan ‘European Bioinformatics Institute’ (EBI) Metagenomics dari segi taksonomi dan analisis fungsi. Kami mendapati bahawa MG-RAST ialah yang paling cepat di antara ketiga-tiga ‘pipeline’, tetapi mengikut keputusan analisa, IMG/M mengeluarkan maklumat philum yang lebih pelbagai bersama peratus identiti yang lebih luas berbanding yang lain untuk pembahagian taksonomi dan IMG/M juga mempunyai bacaan tertinggi dalam hampir semua anotasi fungsional karbohidrat, amino asid, lipid, dan koenzima pengangkutan dan metabolisma malah juga paling tinggi dalam jumlah enzim hidrolase glikosida. Kemudian, untuk mengenal pasti ‘domain’ terpelihara dan keluarga yang terlibat, EBI metagenomics lebih bersesuaian. Ketiga-tiga saluran ‘bioinformatics pipeline’ mempunyai keistimewaan mereka yang tersendiri dan boleh digunakan bersilih ganti dalam masa yang sama berdasarkan pilihan fungsi penggun