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RISS 인기검색어
- 검색키워드
- 저자 : Golam Bari, A.T.M. (검색결과 15 건)
- 무료
- 기관 내 무료
- 유료
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Survey on Nucleotide Encoding Techniques and SVM Kernel Design for Human Splice Site Prediction
Bari, A.T.M. Golam,Reaz, Mst. Rokeya,Choi, Ho-Jin,Jeong, Byeong-Soo Korean Society for Bioinformatics 2012 Interdisciplinary Bio Central (IBC) Vol.4 No.4
Splice site prediction in DNA sequence is a basic search problem for finding exon/intron and intron/exon boundaries. Removing introns and then joining the exons together forms the mRNA sequence. These sequences are the input of the translation process. It is a necessary step in the central dogma of molecular biology. The main task of splice site prediction is to find out the exact GT and AG ended sequences. Then it identifies the true and false GT and AG ended sequences among those candidate sequences. In this paper, we survey research works on splice site prediction based on support vector machine (SVM). The basic difference between these research works is nucleotide encoding technique and SVM kernel selection. Some methods encode the DNA sequence in a sparse way whereas others encode in a probabilistic manner. The encoded sequences serve as input of SVM. The task of SVM is to classify them using its learning model. The accuracy of classification largely depends on the proper kernel selection for sequence data as well as a selection of kernel parameter. We observe each encoding technique and classify them according to their similarity. Then we discuss about kernel and their parameter selection. Our survey paper provides a basic understanding of encoding approaches and proper kernel selection of SVM for splice site prediction.
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Pankaj Kumar Jha,Md. Golam Shahi Alam,Md. Abdullah Al Mansur,Mohammad Rafiqul Islam Talukder,Nazmun Naher,A K M Anisur Rahman,David C. Hall,Farida Yeasmin Bari 사단법인 한국동물생명공학회 2020 한국동물생명공학회지 Vol.35 No.2
The effects of the number of frozen-thawed ram sperm per single and double intra-cervical artificial insemination (AI) on fertility in ewes were studied. A total of 89 non-pregnant ewes were synchronized for oestrus with two doses of 100 μg PGF2α (Cloprostenol) 9 days apart. The ewes were randomly assigned to one of four groups; D200 (n = 23; double AI with 200 × 106 sperm), S200 (n = 24; single AI with 200 × 106 sperm), D100 (n = 24; double AI with 100 × 106 sperm) and S100 (n = 18; single AI with 100 × 106 sperm). Ewes were inseminated within 12 to 18 h for single AI and, within 10 to 12 h and 16 to 18 h for double AI after the onset of oestrus. The onset of oestrus ranged from 28 to 76 h (54.33 ± 1.28 h). The high percentage (29.2%) of ewes showed oestrus between 51 to 60 h. The non-return rates were highest in group D200 (56.5%) and differed significantly (p < 0.05) from group S100 (11.1%). No ewes were pregnant in group S100, and the pregnancy rates among the remaining groups did not differ. The mean gestation period was 152.8 ± 0.5 days and no difference was observed among the groups. The lambing and multiple birth rates were 100% in group D200. The single and twin lambing was highest in group D100 (33.3%) and group D200 (83.3%), respectively. Only one triplet lambing and the highest lambing size (2.2 ± 0.2) was recorded in group D200. In conclusion, double AI with 200 × 106 sperm showed comparatively most practical for achieving high pregnancy rates and lambing performances in Bangladeshi ewes under field conditions.
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Pankaj Kumar Jha,Md. Golam Shahi Alam,Md. Abdullah Al Mansur,Mohammad Rafiqul Islam Talukder,Nazmun Naher,A. K. M. Anisur Rahman,David C. Hall,Farida Yeasmin Bari 한국동물생명공학회(구 한국동물번식학회) 2020 Journal of Animal Reproduction and Biotechnology Vol.35 No.2
The effects of the number of frozen-thawed ram sperm per single and double intra-cervical artificial insemination (AI) on fertility in ewes were studied. A total of 89 non-pregnant ewes were synchronized for oestrus with two doses of 100 μg PGF2α (Cloprostenol) 9 days apart. The ewes were randomly assigned to one of four groups; D200 (n = 23; double AI with 200 × 106 sperm), S200 (n = 24; single AI with 200 × 106 sperm), D100 (n = 24; double AI with 100 × 106 sperm) and S100 (n = 18; single AI with 100 × 106 sperm). Ewes were inseminated within 12 to 18 h for single AI and, within 10 to 12 h and 16 to 18 h for double AI after the onset of oestrus. The onset of oestrus ranged from 28 to 76 h (54.33 ± 1.28 h). The high percentage (29.2%) of ewes showed oestrus between 51 to 60 h. The non-return rates were highest in group D200 (56.5%) and differed significantly (p < 0.05) from group S100 (11.1%). No ewes were pregnant in group S100, and the pregnancy rates among the remaining groups did not differ. The mean gestation period was 152.8 ± 0.5 days and no difference was observed among the groups. The lambing and multiple birth rates were 100% in group D200. The single and twin lambing was highest in group D100 (33.3%) and group D200 (83.3%), respectively. Only one triplet lambing and the highest lambing size (2.2 ± 0.2) was recorded in group D200. In conclusion, double AI with 200 × 106 sperm showed comparatively most practical for achieving high pregnancy rates and lambing performances in Bangladeshi ewes under field conditions.
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Codon-based encoding for DNA sequence analysis
Jeong, B.S.,Golam Bari, A.T.M.,Rokeya Reaz, Mst.,Jeon, S.,Lim, C.G.,Choi, H.J. Academic Press 2014 Methods Vol.67 No.3
With the exponential growth of biological sequence data (DNA or Protein Sequence), DNA sequence analysis has become an essential task for biologist to understand the features, functions, structures, and evolution of species. Encoding DNA sequences is an effective method to extract the features from DNA sequences. It is commonly used for visualizing DNA sequences and analyzing similarities/dissimilarities between different species or cells. Although there have been many encoding approaches proposed for DNA sequence analysis, we require more elegant approaches for higher accuracy. In this paper, we propose a noble encoding approach for measuring the degree of similarity/dissimilarity between different species. Our approach can preserve the physiochemical properties, positional information, and the codon usage bias of nucleotides. An extensive performance study shows that our approach provides higher accuracy than existing approaches in terms of the degree of similarity.
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Azizunnesa,Begum Fatema Zohara,Farida Yeasmin Bari,Golam Shahi Alam 韓國受精卵移植學會 2013 한국동물생명공학회지 Vol.28 No.4
The study was set for one year to measure the effects of concentrate supplementation on reproductive performances and semen quality in indigenous rams. The study was conducted at the Department of Surgery and Obstetrics, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh during the period from May 2011 to April 2012. Forteen ram lambs (4∼5 months) were randomly divided into two equal groups (n=7); supplemented vs control. The animals of control group were maintained on natural grazing. Along with natural grazing the supplemented group was on supplemented feeding. The concentrate supplementation (Wheat bran, Crushed maize, Soy bean meal, Fish meal, DCP powder, Vitamin mineral premix, Salt) was provided @ 300 g/head /day to the supplemented group. Body weight, scrotal circumference, BCS and libido index were measured weekly. Age, body weight and scrotal circumference at puberty were recorded. Semen was collected once in a weak using artificial vagina and chilled at 5℃ for 48h for evaluation. Concentrate supplementation did not influence (p>0.05) body condition score, age, weight, scrotal circumference at puberty and libido index. Final body weight (kg), growth rate (g/d), scrotal circumference (cm) and scrotal growth rate (mm/15d) were significantly (p<0.05) higher in supplemented group of rams compared to control. Volume, concentration, motility and membrane potentiality of spermatozoa were varied significantly (p<0.05) in supplemented and control groups. However, density, mass motility, viability and sperm with normal acrosome, midpiece and tail were not differed insignificantly (p>0.05) in different observation times. It was concluded that concentrate supplementation with free grazing improved weight and scrotal circumference gain and semen production with increased quality in indigenous ram.
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Azizunnesa, Azizunnesa,Zohara, Begum Fatema,Bari, Farida Yeasmin,Alam, Md. Golam Shahi The Korean Society of Embryo Transfer 2013 한국동물생명공학회지 Vol.28 No.4
The study was set for one year to measure the effects of concentrate supplementation on reproductive performances and semen quality in indigenous rams. The study was conducted at the Department of Surgery and Obstetrics, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh during the period from May 2011 to April 2012. Forteen ram lambs (4~5 months) were randomly divided into two equal groups (n=7); supplemented vs control. The animals of control group were maintained on natural grazing. Along with natural grazing the supplemented group was on supplemented feeding. The concentrate supplementation (Wheat bran, Crushed maize, Soy bean meal, Fish meal, DCP powder, Vitamin mineral premix, Salt) was provided @ 300 g/head /day to the supplemented group. Body weight, scrotal circumference, BCS and libido index were measured weekly. Age, body weight and scrotal circumference at puberty were recorded. Semen was collected once in a weak using artificial vagina and chilled at $5^{\circ}C$ for 48h for evaluation. Concentrate supplementation did not influence (p>0.05) body condition score, age, weight, scrotal circumference at puberty and libido index. Final body weight (kg), growth rate (g/d), scrotal circumference (cm) and scrotal growth rate (mm/15d) were significantly (p<0.05) higher in supplemented group of rams compared to control. Volume, concentration, motility and membrane potentiality of spermatozoa were varied significantly (p<0.05) in supplemented and control groups. However, density, mass motility, viability and sperm with normal acrosome, midpiece and tail were not differed insignificantly (p>0.05) in different observation times. It was concluded that concentrate supplementation with free grazing improved weight and scrotal circumference gain and semen production with increased quality in indigenous ram.
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Relationship between Semen Quality Parameters and Field Fertility of Bulls
Sushanto Kumar Rabidas,Anup Kumar Talukder,Md. Golam Shahi Alam,Farida Yeasmin Bari 사단법인 한국동물생명공학회 2012 한국동물생명공학회지 Vol.27 No.1
A study was conducted on four crossbred bulls, used as artificial insemination (AI) sires, to correlate their semen quality with their non return rate (NRR). Semen was collected once a week via an artificial vagina, diluted in egg yolk-citrate and maintained at +7℃ for three days. It was evaluated for sperm motility, viability, morphology immediately after collection and was examined daily for sperm motility, viability and morphology of acrosome, mid piece and tail for a total of three days. A total of 2016 cows were inseminated by two AI technicians. The proportions of sperm with normal heads were 83.4% (63.7~91.7%), the proportion of spermatozoa exhibiting normal morphology (acrosome, mid piece and tail), motility and viability were 89.2% (82.3~92.0%), 71.3% (61.7~75.0%) and 76.7% (65.7~85.0%), respectively in fresh ejaculates. Sperm motility and sperm viability was significantly (p<0.05) lower in Holstein-Friesian × Local bull than in other bulls during all three days of storage. The overall NRR for four bulls was 82.7% (72.9-87.5%). Bulls with higher sperm motility, viability and normal morphology of spermatozoa of individual bull had significantly (each p<0.05) higher NRR. The highest (p<0.01) NRR (87.5%) was observed in a Red Chittagong bull whose semen qualities were significantly (p<0.05) higher than Holstein-Friesian × Local bull (NNR 72.9%). The results of the present study concluded that NRR at 56 days post AI is related to parameters of semen quality. Therefore, semen evaluation may allow the discarding of bulls with poor fertility in an AI program
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Tapas Ghosh,Ashit Kumar Paul,Anup Kumar Talukder,M. Golam Shahi Alam,Farida Yeasmin Bari 사단법인 한국동물생명공학회 2012 한국동물생명공학회지 Vol.27 No.4
This study was designed to adopt two estrus synchronization protocols in zebu and crossbred heifers and their effects on pregnancy rate after timed artificial insemination (TAI). A number of 120 cyclic heifers were allotted for two different treatment groups and one control group. Heifers under protocol A were injected with GnRH at first day followed by a single dose of PGF2α at Day 11 and injection of GnRH at the day of AI; and heifers belonged to protocol B were treated with GnRH, two PGF_(2α) injections at 11 days apart and injection of GnRH at AI. AI was done at fixed time (within 72~96 hours after PGF_(2α) injection) in both protocols and pregnancy was confirmed by rectal palpation on 80~120 days of post AI. In control group; local heifers were conceived higher (30%) proportion than that of crossbred heifers (25%; p<0.05). In protocol A, the local breed were conceived higher (38.9%) proportion compared with crossbred (25%; p<0.05). In protocol B, local breed heifers were conceived higher (38.9%) proportion compared with crossbred heifers (33.3%; p<0.05). The overall pregnancy rate in protocol A and protocol B was 33.3% and 36.6%, respectively. The proportion of pregnancy rate of local heifers (38.9%; Protocol A) was significant (p<0.05) in comparison with local heifers (30%) in control group (p<0.05). The overall pregnancy rate between pooled control group (28.3%) and treatment group (35%) was significantly (p<0.05) differ from each other’s. Results of present study concluded that estrus synchronization followed by fixed time AI could be applied for higher pregnancy rate in zebu and crossbred heifers
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Ghosh, Tapas,Paul, Ashit Kumar,Talukder, Anup Kumar,Alam, M. Golam Shahi,Bari, Farida Yeasmin 韓國受精卵移植學會 2012 한국동물생명공학회지 Vol.27 No.4
This study was designed to adopt two estrus synchronization protocols in zebu and crossbred heifers and their effects on pregnancy rate after timed artificial insemination (TAI). A number of 120 cyclic heifers were allotted for two different treatment groups and one control group. Heifers under protocol A were injected with GnRH at first day followed by a single dose of at Day 11 and injection of GnRH at the day of AI; and heifers belonged to protocol B were treated with GnRH, two injections at 11 days apart and injection of GnRH at AI. AI was done at fixed time (within 72~96 hours after injection) in both protocols and pregnancy was confirmed by rectal palpation on 80~120 days of post AI. In control group; local heifers were conceived higher (30%) proportion than that of crossbred heifers (25%; p<0.05). In protocol A, the local breed were conceived higher (38.9%) proportion compared with crossbred (25%; p<0.05). In protocol B, local breed heifers were conceived higher (38.9%) proportion compared with crossbred heifers (33.3%; p<0.05). The overall pregnancy rate in protocol A and protocol B was 33.3% and 36.6%, respectively. The proportion of pregnancy rate of local heifers (38.9%; Protocol A) was significant (p<0.05) in comparison with local heifers (30%) in control group (p<0.05). The overall pregnancy rate between pooled control group (28.3%) and treatment group (35%) was significantly (p<0.05) differ from each other's. Results of present study concluded that estrus synchronization followed by fixed time AI could be applied for higher pregnancy rate in zebu and crossbred heifers.
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