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COMPUTATIONAL INFERENCE TECHNIQUE FOR MINING STRUCTURED MOTIFS
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A Health Education Video in an Indigenous Nigerian Language to Dispel Misconceptions Associated with Reversal of Eruption Sequence of Anterior Teeth
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EPIDEMIOLOGICAL STUDIES ON DRACUNCULIASIS IN OYO STATE, NIGERIA
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Page will reload when a filter is selected or excluded.- DNA Binding Site 1 results 1
- One of the major challenges in bioinformatics is the development of efficient computational tools for mining patterns. Structured motifs, like DNA binding sites in organisms with peculiarities in their genomic sequence like malaria parasite, Plasmodium falciparum have not been mined by existing structured motifs extraction tools. There is a need to develop faster computational tools to mine these DNA binding sites which are viable drug targets. This work was aimed at developing an algorithm for mining structured motifs in the genome of P. falciparum. The Gene Enrichment Motif Searching (GEMS) method for mining simple motifs was modified by incorporating the time efficient implementation of the suffix tree data structure with suffix links. This enables an improved searching speed, while adding an optimized position-weight matrix computation using the hypergeometric-based scoring function. This algorithm, Suffix Tree Gene Enrichment Motif Searching (STGEMS) was implemented in C programming language on Linux platform. An empirical evaluation of the sensitivity of STGEMS was conducted by comparing the similarity check mechanism of the GEMS algorithm for mining simple motifs with that used in another popular algorithm for extracting structured motifs, a Multi-Objective Genetic Algorithm Motif Discovery (MOGAMOD). The output of STGEMS algorithm was validated by comparing the motifs discovered with those obtained using biological experiments. A further validation was done by applying the STGEMS and GEMS algorithm to selected metabolic pathways and the results were compared. The STGEMS algorithm was tested with four sets of genes from the intraerythrocytic development cycle of P. falciparum. The speed of execution was evaluated using three simple motif discovery tools: Expectation Maximization Motif Elicitation(MEME), Gene Enrichment Motif Search (GEMS), and WEEDER as well as two structured motif discovery tools: RISOTTO and EXMOTIF on four different gene sizes.The high sensitivity of STGEMS in mining structured motifs from sequences in P. falciparum was proven empirically by its ability to identify 91% of the motifs in the sequences while MOGAMOD could not identify any motif. This validated the high sensitivity of the similarity check mechanism employed, in contrast with that used in MOGAMOD. The STGEMS algorithm identified 90% of the binding sites in P. falciparum which were similar to those obtained in biological experiments. On the selected metabolic pathways, STGEMS discovered all the simple motifs identified by GEMS, in addition to the structured motifs which GEMS could not identify. The empirical runtimes of STGEMS, MEME, WEEDER, GEMS, RISOTTO and EXMOTIF were respectively 20, 35, 26, 25, 28, 30 seconds for 20,000 base pair (bp), 32, 43, 44, 45, 42, 40 seconds for 40,000 bp, 41, 55, 56, 55, 52, 50 seconds for 60,000 bp and 54, 68, 69, 65, 67, 61 seconds for 80,000 bp respectively. The proposition resulted in a linear asymptotic runtime of O(N) at each iteration of the algorithm. The suffix tree gene enrichment motif searching algorithm developed was time efficient and successful in mining structured motifs like DNA binding sites in Plasmodium 15 falciparum. This will aid a faster drug target discovery pipeline for the design of effective anti malaria drugs. 1 results 1
- Research findings conducted in Nigeria have revealed grave misconceptions regarding eruption of maxillary anterior teeth before the mandibular ones in children as affected individuals are believed to be evil, carriers of misfortune and their families are deemed cursed. Such children are stigmatized, abandoned and may be gotten rid of. A twenty three minute culturally appropriate video in the Yoruba language titled “Baba Yoyin” (meaning male tooth extractor -traditional dentist ) was developed to demystify the Nigerian community about misconceptions associated with reversal of eruption sequence of teeth and educate them about hazards associated with patronizing traditional dentists and the need to visit a dentist/doctor for advice. In the pre -production stage, the video was designed and planned and the cast , crew and appropriate locations for shooting the film shooting were selected . In the production stage, filming was done with several wide, medium and close shots. At post production, the film was edited with a sound mix comprising of sound effects and music. Computer graphic effects were added digitally. This video was produced in Yoruba, an indigenous Nigerian language to serve as a culturally appropriate community dental health education tool targeting nursing mothers, pregnant women, and traditional birth attendants from the lower social class in south western Nigeria. The storyline in this video tape will be translated into Igbo and Hausa , the two other major Nigerian languages. This videotape can be repeated in other African settings whose societies experience similar misconceptions about tooth eruption 1 results 1
- Reversal of eruption sequence 1 results 1
- Structured motifs 1 results 1
- Suffix tree 1 results 1
- The studies were designed to collect baseline information to form essential data base for effective planning and subsequent evaluation of guineaworm control programme in Oyo State. In order to establish the epidemiology of dracunculiasis and assess the impact of the disease on the economic life of the affected population, pretested questionnaire data sheets were administered to 2,415 individuals and 257 heads of household in eight different villages in Oyo State. The data analysis was done by using analysis of variance and coefficient of determination and multiple range tests, using the IBM computer, utilizing the SPSSH package. The survey of concurrent parasitic diseases was carried out in one village by examining faecal and blood samples of 287 individuals. The antibiogram and profile of bacteria associated with secondary infection was determined. Simple methods of chemical, biological and physical control of guineaworm vector under laboratory conditions were described. Of 2,415 individuals examined in eight villages of Oyo State in 1988, 76.9 per cent had history of dracunculiasis while the infection rate at the time of study was 47.9 per cent. There was no significant difference in the infection rate between the sexes. However, the risk of infection increased with age. Infection occurs at any age above 1 year and reinfection is common, indicating that on clinical grounds, no protective immunity is developed after infection. There was a general awareness by individuals that they were infected before the formation of the guineaworm bleb. Mean percentage of 18.9 ± 1 had the sympoms in 1 day. The sites of guineaworm emergence differ significantly for each victim (P < 0.05), and no anatomical part of the body was apparently exempted with regard to worm emergence. Majority of the affected people (a mean per cent of 54 ± 6.7) became clinically ill in the dry season; and also a mean per cent of 54.3 ± 2.3 suffered severe infection. 5 - 8 weeks was the most frequently occuring period of incapacitation. 54.5% of the victims had no form of assistance on the farm during the period of incapacitation. Majority of the heads of household held various wrong beliefs of causes and prevention of the diesease. 82 ± 3.6 per cent attributed the cause of guineaworm to the act of God and that there was no remedy for it. Only 6.53 per cent treated the drinking water before consumption. The disease has an adverse impact on agriculture, while an average of 20 - 41 per cent of the pupils were absent from school with attendant poor academic performances. Of 487 samples examined for concurrent parasitic disease 278 (57.1 per cent) were infected with one parasitic disease or the other: Ascariasis (43.7%), hook-worm disease (27.1%), strongyloidiasis (2.5%), trichuriasis (31%), Entamoeba histolvtical infection (3.9%) and plasmodiasis (43.7%). The haematocrit value of the individuals in the community was generally low (26 - 30%) whilst eosinophilia was a common feature. The health implication was discussed. Klebsiella sp., Streptococcus sp., Proteus sp. and Staphylococcus aureus were common bacterial agents isolated from guinea worm ulcers. The phage types of Staph, aureus (the commonest agents) isolated were resistant to both penicilline and tetracycline. The epidemiological importance of the various phage types was discussed. The ecology of the environment where the copepod intermediate hosts breed and transmit racunculiasis was described and discussed. Cyclopoid copepods died within 60 minutes when the ironment was manipulated to 24.6mg/l. oxidizable organic matter concentration from the natural average value of 12.5mg/l. It was shown that cyclopoid copepods became inactive at 4 - 6°C in 4 hours and later regained activity in 15 minutes at room temperature. The study showed that ponds in a study area had the highest density of cylops in November/December (1988) and lowest density in July/August (1988) with natural cyclops infection rate of 6.5% at the peak of transmission. It was also shown that the concentration of cyclops was greatest when water was drawn at the time the pond water was still and undisturbed, especially with the first caller at the pond, with attendant higher risk of infection. The study also revealed that population mobility occasioned by marriage, socio-cultural and economic life of the people contributed to the diffusion and control of the disease. A variety of chemicals found in natrual waters, or used in the treatment of water were added to pond water and their effects on the survival of the cyclopoid copepods were assessed. The possible use of such chemicals as calcium hypochlorite, potassium permanganate, lime, etc., in individual houses as a preventive measure against the transmission of the disease was discussed. Furthermore, the study revealed that indigenous fishes like Hemicromis fasciatus. Barbus occidentalis. Tilapia nilotica and T. galilea; were very useful biological control agents of the vector of Dracunculus. It is believed that provision of safe drinking water and good health education with active case search to monitor the intervention programme will reduce the disease prevalence. 1 results 1
- child health education 1 results 1
- video 1 results 1
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