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Remote protein homology detection and fold recognition using two-layer support vector machine classifiers

Muda HM, Saad P, Othman RM

Comput Biol Med, 2011 Aug;41(8):687-99.
PMID: 21704312 DOI: 10.1016/j.compbiomed.2011.06.004

Remote protein homology detection and fold recognition refer to detection of structural homology in proteins where there are small or no similarities in the sequence. To detect protein structural classes from protein primary sequence information, homology-based methods have been developed, which can be divided to three types: discriminative classifiers, generative models for protein families and pairwise sequence comparisons. Support Vector Machines (SVM) and Neural Networks (NN) are two popular discriminative methods. Recent studies have shown that SVM has fast speed during training, more accurate and efficient compared to NN. We present a comprehensive method based on two-layer classifiers. The 1st layer is used to detect up to superfamily and family in SCOP hierarchy using optimized binary SVM classification rules. It used the kernel function known as the Bio-kernel, which incorporates the biological information in the classification process. The 2nd layer uses discriminative SVM algorithm with string kernel that will detect up to protein fold level in SCOP hierarchy. The results obtained were evaluated using mean ROC and mean MRFP and the significance of the result produced with pairwise t-test was tested. Experimental results show that our approaches significantly improve the performance of remote protein homology detection and fold recognition for all three different version SCOP datasets (1.53, 1.67 and 1.73). We achieved 4.19% improvements in term of mean ROC in SCOP 1.53, 4.75% in SCOP 1.67 and 4.03% in SCOP 1.73 datasets when compared to the result produced by well-known methods. The combination of first layer and second layer of BioSVM-2L performs well in remote homology detection and fold recognition even in three different versions of datasets.
Lipofuscin Level in Eyestalk Blue Swimming Crab, Portunus pelagicus at Different Sexes

Ghani Hilmi M, Ikhwanuddin M

Pak J Biol Sci, 2020 Jan;23(5):708-714.
PMID: 32363828 DOI: 10.3923/pjbs.2020.708.714

BACKGROUND AND OBJECTIVE: The accumulation of lipofuscin (LF) is an alternative technique to identify age of crustacean species. However, the exact sites and the level of the LF concentration were unknown especially for different sexes of blue swimming crab, Portunus pelagicus. Thus, the present study was aimed to identify which part of the eyestalk of P. pelagicus contains more LF levels in order to establish a specific target part of samples.
MATERIALS AND METHODS: Thus, crab samples for this study were sampled from the wild habitat at Setiu wetlands, Terengganu, Malaysia. A total of 100 samples of with the same size (80±5 mm carapace width) were sampled and the eyestalk dissected for LF extraction. The determination of LF sites and levels in the eyestalks organ was taken from the area between the distal tangential layer (DTL) and proximal tangential layer (PTL). The lower part of the eyestalk was taken from the PTL until the end of the eyestalk.
RESULTS: The upper part of the crab's eyestalk was higher in the males crabs compared to the females crabs. LF index also shown that the upper part of crab's eyestalk have higher concentration compared to the lower part.
CONCLUSION: The left crab's eyestalk had the higher LF index especially in males compared to females but the total concentration was higher in female crabs. Knowing which part has highly dense accumulation of LF helps in LF detection of the tissue and further helps for age determination for this species.
Chromosomes of gaur cross domestic cattle hybrids

Bongso TA, Hilmi M, Sopian M, Zulkifli S

Res Vet Sci, 1988 Mar;44(2):251-4.
PMID: 3387680

The chromosomes of five gaur (Bos gaurus hubbacki) domestic cattle (B indicus cross B taurus) hybrids (three females, two males) were studied using the leucocyte culture method and centromeric (C) banding technique. All the hybrids had a diploid chromosome number of 2n = 58, made up of two submetacentric autosomes (different in size) and 54 acrocentric autosomes, most of which could be arranged in pairs in descending order of size. The sex (X) chromosomes in females were a pair of submetacentric chromosomes smaller than the submetacentric autosomes. The Y chromosome in males was a small submetacentric chromosome. The C banding patterns were useful in identifying the X and Y chromosomes and the inherited submetacentric autosomes from the gaur sire. Phenotypically, the hybrids resembled normal B indicus cross B taurus calves except for the presence of a distinct hump-like dorsal ridge containing the spinous processes of the third to 11th thoracic vertebrae, upright 'deer-like' ears and long lean legs. The potential of these hybrids as important genetic resources for meat production is stressed.
Karyotype of Malayan Gaur (Bos gaurus hubbacki), Sahiwal-Friesian cattle and Gaur x cattle hybrid backcrosses

Adbullah MH, Idris I, Hilmi M

Pak J Biol Sci, 2009 Jun 15;12(12):896-901.
PMID: 19777782

Interspecific hybridization has been reported for a wide variety of vertebrate species either spontaneous or by organized crossing of bovine species. The hybrids were often carrying intermediate characters genetically and phenotypically of the parents. Thus, status information of both aspects is valuable in animal production for selection and breeding management. The Gaur-cattle hybrids was reported to be superior in production value compared to their parent cattle but fertility status was still questionable. The project was abandoned due to their fertility issue and the hybrids were kept within the cattle in a dairy farm. Cytogenetic status and breeding record of the remaining herd were unavailable since then. The herd was then translocated to a deer farm (PTH Lenggong) and kept freely in the paddock. Recently, two female calves were born via inter se mating. Peripheral blood cultures of Malayan Gaur, Sahiwal-Friesian cattle and Gaur x cattle hybrid backcrosses were analyzed via Giemsa stained metaphase. The Gaur and cattle were having diploid chromosome number (2n) of 56 and 60, respectively. Interestingly, the backcrosses from the hybrids by cattle bulls were found to have two chromosome arrangements, which are 2n = 58 and 2n = 60.
Fulltext Blood haematology, serum thyroid hormones and glutathione peroxidase status in kacang goats fed inorganic iodine and selenium supplemented diets

Aghwan ZA, Sazili AQ, Alimon AR, Goh YM, Hilmi M

Asian-Australas J Anim Sci, 2013 Nov;26(11):1577-82.
PMID: 25049744 DOI: 10.5713/ajas.2013.13180

The effects of dietary supplementation of selenium (Se), iodine (I), and a combination of both on the blood haematology, serum free thyroxine (FT4) and free triiodothyronine (FT3) hormones and glutathione peroxidase enzyme (GSH-Px) activity were examined on twenty four (7 to 8 months old, 22±1.17 kg live weight) Kacang crossbred male goats. Animals were randomly assigned to four dietary treatments (6 animals in each group). Throughout 100 d of feeding trial, the animals of control group (CON) received a basal diet, while the other three groups were offered basal diet supplemented with 0.6 mg/kg diet DM Se (SS), or 0.6 mg/kg diet DM I (PI), or a combination of both Se and I, each at 0.6 mg/kg diet DM (SSPI). The haematological attributes which are haemoglobin (Hb), red blood cell (RBC), packed cell volume (PCV), mean cell volume (MCV), white blood cells (WBC), band neutrophils (B Neut), segmented neutrophils (S Neut), lymphocytes (Lymph), monocytes (Mono), eosinophils (Eosin) and basophils (Baso) were similar among the four treatment groups, while serum levels of Se and I increased significantly (p<0.05) in the supplemented groups. The combined dietary supplementation of Se and I (SSPI) significantly increased serum FT3 in the supplemented animals. Serum GSH-Px activity increased significantly in the animals of SS and SSPI groups. It is concluded that the dietary supplementation of inorganic Se and I at a level of 0.6 mg/kg DM increased serum Se and I concentration, FT3 hormone and GSH-Px activity of Kacang crossbred male goats.
Liquefaction of kenaf (Hibiscus cannabinus L.) core for wood laminating adhesive

Juhaida MF, Paridah MT, Mohd Hilmi M, Sarani Z, Jalaluddin H, Mohamad Zaki AR

Bioresour Technol, 2010 Feb;101(4):1355-60.
PMID: 19833509 DOI: 10.1016/j.biortech.2009.09.048

A study was carried out to produce polyurethane (PU) as a wood laminating adhesive from liquefied kenaf core (LKC) polyols by reacting it with toluene-2,4-diisocyanate (TDI) and 1,4-butanediol (BDO). The LKC polyurethane (LKCPU) adhesive has a molecular weight (MW) of 2666, viscosity of 5370 mPa s, and solids content of 86.9%. The average shear strength of the rubberwood (RW) bonded with LKCPU adhesive was 2.9 MPa. Most of the sheared specimens experienced a total adhesive failure. The formation of air bubbles through the liberation of carbon dioxide was observed to reduce the adhesive penetration and bonding strength which was obviously seen on the sheared specimens. The percentage of catalyst used can be varied based on the usage and working time needed. Nonetheless, the physical properties of LKCPU produced in this work had shown good potential as edge-bonding adhesive.
Randomized Controlled Trial Comparing Daycare and Overnight Stay Laparoscopic Cholecystectomy

Salleh AA, Affirul CA, Hairol O, Zamri Z, Azlanudin A, Hilmi MA, et al.

Clin Ter, 2015;166(3):e165-8.
PMID: 26152626 DOI: 10.7417/CT.2015.1848

BACKGROUND: This present study sought to review the feasibility and patients' satisfaction of laparoscopic cholecystectomy to be perform as daycare procedure.
MATERIAL AND METHODS: Sixty-two patients with symptomatic gallstones were recruited within a year. They were randomized into overnight stay and daycare groups. The outcomes and post-operative complications were analyzed.
RESULTS: Fifty-eight patients were eligible for analysis and four patients were excluded because of conversion to open cholecystectomy. All patients in daycare group reported no fever but two patients in the overnight stay group complaint of post-operative fever (p=0.150). The mean pain score using Visual Analogue Score (VAS) in daycare group was 2.93 but in the overnight stay was recorded as 3.59 (p=0.98). Five patients had post-operative nausea and vomiting (PONV) in daycare group compared to 2 patients in the overnight stay group (p=0.227). Patient's satisfaction were higher in the daycare group (p=0.160). All patients in daycare group were back at work within a week but in overnight stay, 11 patients had to stay off work for more than one week (p=0.01).
CONCLUSIONS: Daycare laparoscopic cholecystectomy is safe and feasible. The satisfaction of daycare surgery is higher than overnight stay group. Patients' selection is an important aspect of its success.
Identification of crossbred buffalo genotypes and their chromosome segregation patterns

Harisah M, Azmi TI, Hilmi M, Vidyadaran MK, Bongso TA, Nava ZM, et al.

Genome, 1989 Dec;32(6):999-1002.
PMID: 2628159

Chromosome analysis on different breed types of water buffaloes (Bubalus bubalis) was undertaken to identify their karyotypes and to determine the pattern of chromosome segregation in crossbred water buffaloes. Altogether, 75 purebred and 198 crossbred buffaloes including 118 from Malaysia and 80 from the Philippines, were analyzed in this study. The diploid chromosome number of the swamp buffalo from both countries was 48 and that of the river buffalo was 50, while all F1 hybrids exhibited 49 chromosomes. The F2 hybrids consisted of three different karyotype categories (2n = 48, 2n = 49, and 2n = 50), whereas the backcrosses included two different karyotype categories each, with 2n = 48 and 2n = 49 in the three quarters swamp types and 2n = 49 and 2n = 50 in the three quarters river types. Chi-square tests on pooled data from Malaysia and the Philippines indicated that the distribution of different karyotype categories of F2 animals did not deviate significantly from the 1:2:1 ratio expected if only balanced gametes with 24 and 25 chromosomes were produced by the F1 hybrids. In the three quarters swamp and three quarters river types, the respective karyotypic categories were in ratios approximating 1:1. The distribution of chromosome categories among the F2 hybrids and backcrosses suggests that only genetically balanced gametes of the F1 hybrids are capable of producing viable F2 and backcross generations.