Journal of bio-science最新文献

{"title":"Performance evaluation of different machine learning algorithms in presence of outliers using gene expression data","authors":"M. Shahjaman, M. Rashid, M. Asifuzzaman, H. Akter, S. Islam, M. Mollah","doi":"10.3329/jbs.v28i0.44712","DOIUrl":"https://doi.org/10.3329/jbs.v28i0.44712","url":null,"abstract":"Classification of samples into one or more populations is one of the main objectives of gene expression data (GED) analysis. Many machine learning algorithms were employed in several studies to perform this task. However, these studies did not consider the outliers problem. GEDs are often contaminated by outliers due to several steps involve in the data generating process from hybridization of DNA samples to image analysis. Most of the algorithms produce higher false positives and lower accuracies in presence of outliers, particularly for lower number of replicates in the biological conditions. Therefore, in this paper, a comprehensive study has been carried out among five popular machine learning algorithms (SVM, RF, Naive Bayes, k-NN and LDA) using both simulated and real gene expression datasets, in absence and presence of outliers. Three different rates of outliers (5%, 10% and 50%) and six performance indices (TPR, FPR, TNR, FNR, FDR and AUC) were considered to investigate the performance of five machine learning algorithms. Both simulated and real GED analysis results revealed that SVM produced comparatively better performance than the other four algorithms (RF, Naive Bayes, k-NN and LDA) for both small-and-large sample sizes. \u0000J. bio-sci. 28: 69-80, 2020","PeriodicalId":90580,"journal":{"name":"Journal of bio-science","volume":"28 1","pages":"69-80"},"PeriodicalIF":0.0,"publicationDate":"2019-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3329/jbs.v28i0.44712","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45749468","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Estimation of genetic variability, heritability and correlation for some quantitative traits in wheat (Triticum aestivum L.)","authors":"F. Haydar, M. Ahamed, A. Siddique, Gm Uddin, KL Biswas, Mf Alam","doi":"10.3329/jbs.v28i0.44713","DOIUrl":"https://doi.org/10.3329/jbs.v28i0.44713","url":null,"abstract":"Seventeen genotypes of wheat were used in this study the results showed significant differences in respect of yield and other yield contributing characters. Highest phenotypic and genotypic coefficients of variations were observed in plant height and lowest values were observed in spike length in both cases.Heritability estimated was found to be high in case of grain yield/plant and this was followed by 100 grain weight. Significant positive correlation was found in plant height with number of fertile tillers/plant and grain yield/plant, fertile tillers/plant with spike length, spike length with grain yield and grain yield with 100 grain weight. Negative correlation was found in plant height with 100 grain weight. Plant height, fertile tillers/plant, spike length and 100 grain weight appeared to be the effective criteria for improvement of yield of wheat. \u0000J. bio-sci. 28: 81-86, 2020","PeriodicalId":90580,"journal":{"name":"Journal of bio-science","volume":"28 1","pages":"81-86"},"PeriodicalIF":0.0,"publicationDate":"2019-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3329/jbs.v28i0.44713","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45078010","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic variability, heritability and genetic advance of some yield contributing characters in lablab bean (Lablab purpureus L. Sweet)","authors":"N. Afsan, A. Roy","doi":"10.3329/jbs.v28i0.44706","DOIUrl":"https://doi.org/10.3329/jbs.v28i0.44706","url":null,"abstract":"Eleven genotypes of lablab bean were put into trial in four consecutive years to evaluate genetic variability among characters. Genotypic and phenotypic coefficient of variability, heritability and genetic advance as percent of mean were estimated for four yield contributing characters i.e. number of flowers per plant, number of pods per plant, average number of seed per pod and average pod weight (gm). The range of variation was highly pronounced in all the four characters. Without grouping the presence of wide range of variation in these characters indicate that they are quantitative in nature and are under polygenic in control. Mean with standard error showed differences between the varieties and co-efficient of variability in percentage (CV%) indicates certain degree of variability for the characters studied which are prerequisite in breeding research. Genotypes were found to be significantly different for all characters in analysis of variance. Low differences between PVC and GVC shows that these traits are less influenced by environment and the effect of heritable components were high. High heritability coupled with high genetic advance as percent of mean was recorded by number of flowers per plant, number of pods per plant and average pod weight (g) indicates additive action of genes controlling them. \u0000J. bio-sci. 28: 13-20, 2020","PeriodicalId":90580,"journal":{"name":"Journal of bio-science","volume":"28 1","pages":"13-20"},"PeriodicalIF":0.0,"publicationDate":"2019-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3329/jbs.v28i0.44706","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44068202","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Management practices in the beel aquaculture system at Rajshahi, northwest Bangladesh","authors":"S. Akter, Ali, Mmr Mondol","doi":"10.3329/jbs.v28i0.44709","DOIUrl":"https://doi.org/10.3329/jbs.v28i0.44709","url":null,"abstract":"Open aquatic system such as beel is an important freshwater resource for agriculture and aquaculture.This study was conducted (July-December 2014) to describe the beel aquaculture management practices in the Hagla Beel at Bagmara upazila under Rajshahi district.The Beel fish farming area was 20.25 ha and irregular in shape with average depth 1.5 m. During the study period, the measured water quality parameters of the beel were within the suitable range for aquaculture. Eight genera of phytoplankton and eight genera of zooplankton were identified from the beel water body. Four native and 4 exotic fish species with sizes ranging from 0.15-1.11 kg were stocked for growing in the beel. At the end of culture period, the production of fish was 2,622.15 kg/ha and cost-benefit ratio (CBR) was 1:1.42. Environmental problems such as increasing of water temperature and decreasing of water level during summer, and parasitic diseases were some of the risks in beel fish farming system. The results of this study should be useful for beel aquaculture, and for the farmers and resource manager for harnessing maximum benefits from the beel resources in Bangladesh. \u0000J. bio-sci. 28: 43-50, 2020","PeriodicalId":90580,"journal":{"name":"Journal of bio-science","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3329/jbs.v28i0.44709","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69504308","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Application of plant extracts for pest management in tea: a study on tea leaf’s thrips, Scirtothrips bispinosus","authors":"M. Azad, I. Ahmad, A. Mainuddin","doi":"10.3329/jbs.v28i0.44714","DOIUrl":"https://doi.org/10.3329/jbs.v28i0.44714","url":null,"abstract":"Medicinal plant extract contains bioactive molecules and these molecules are benefited to mitigate, eradicate or cure diseases. In advent to search for new medicinally important plant, the current paper deals to select the most effective and promising plants which are suitable for controlling tea leaf’s thrips (Scirtothrips bispinosus) based on extracts concentration and death affect over time. To fulfill the specific objectives, five medicinal plants extracts viz. Ipomoea crassicaulis, Lantana camara, Ipomoea hederaceaa, Glycosmis arborea, and Justicia gendarussa had been used with four different concentrations. From statistical analysis using One-way ANOVA and post hoc test, it was found that Ipomoea crassicaulis and Lantana camara are the most promising of all the experimented plants extracts based on both time and concentration. In the study, average mortality was found 0.47, 1.67, 1.93 and 2.53 for concentration of 1%, 5%, 10% and 15% respectively. Analysis based on different concentrations reveals that average mortality of thrips increases significantly with the increase of concentrations. Coefficient of variance was found minimum for Ipomoea crassicaulis and Lantana camara plants with range of 5.44 to 6.71 based on time and concentration. So, it could be concluded that these two plants are the most effective plants for controlling the tea thrips. For the other plants, ranks were found as Ipomoea hederaceaa, Glycosmis arborea and Justicia gendarussa respectively as well. \u0000J. bio-sci. 28: 87-93, 2020","PeriodicalId":90580,"journal":{"name":"Journal of bio-science","volume":"28 1","pages":"87-93"},"PeriodicalIF":0.0,"publicationDate":"2019-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3329/jbs.v28i0.44714","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45939514","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of planting method on yield and yield attributing characters in chickpea (Cicer arietinum L.)","authors":"Alam, F. Haydar, A. Hoque","doi":"10.3329/jbs.v28i0.44716","DOIUrl":"https://doi.org/10.3329/jbs.v28i0.44716","url":null,"abstract":"The experiment was conducted to study the effect of planting method on yield and yield attributing characters in chickpea. A randomized complete block design was adopted for the experiment with three replications. Four variety viz. BAU-1, BINA Chola-4, BINA Chola-5 and BINA Chola-9 and two planting method i.e. line sowing and ridge sowing were used in the experiment. The highest seed yield (1.81 ton/ha) was obtained from BINA Chola-4 and the lowest one (1.31 ton/ha) was found in BARI Chola-9. The seed yield was higher in ridge sowing (1.57ton/ha) and the lower (1.53 ton/ha) in line sowing. The highest seed yield (1.83 ton/ha) was obtained from BINA Chola-4 with ridge sowing and the lowest (1.30 ton/ha) was obtained from BARI Chola-9 in line sowing. It is concluded that ridge sowing is better than line sowing for the yield of chickpea. \u0000J. bio-sci. 28: 105-110, 2020","PeriodicalId":90580,"journal":{"name":"Journal of bio-science","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3329/jbs.v28i0.44716","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46473392","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessment of present environmental status of the Ratargul Swamp forest Sylhet","authors":"T. Siddika, M. Azad, M. Sujan, M. Hasan","doi":"10.3329/jbs.v28i0.44710","DOIUrl":"https://doi.org/10.3329/jbs.v28i0.44710","url":null,"abstract":"This study aims to find out the present environmental status and issues that have emerged in the recent time due to change in human activities, resource extraction and human dependency on the forest. This study is based on both qualitative and quantitative approach with Participatory Rural Appraisal (PRA) tools and random sampling of 260 respondents, six focus group discussions (FGDs), six key informants interviews (KIIs). The result suggests that about 90% of poor and middle-classhouseholds are depended on the income from tourism, agriculture or boat riding activities. Both the local people and tourists’activities are responsible for decreasing environmental condition by plastic pollution, land cover and land use change, water follows control, road and building construction and violence of rules and regulation. The south and east boundaries, and the center of the forest are mainly facing land use and land cover changes between the years of 2005 to 2018. For sustainable management, local communities should be aware of the importance of swamp forest and have to find out alternative income sources to reduce pressure on swamp forest in terms of resources extraction and forest degradation. \u0000J. bio-sci. 28: 51-57, 2020","PeriodicalId":90580,"journal":{"name":"Journal of bio-science","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3329/jbs.v28i0.44710","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47609497","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prevalence and PCR based molecular characterization of goat pox virus from field outbreaks of Multan and Bahawalnagar, Pakistan","authors":"A. Ijaz, F. Jabeen, A. Ashraf, S. Naz","doi":"10.3329/jbs.v28i0.44715","DOIUrl":"https://doi.org/10.3329/jbs.v28i0.44715","url":null,"abstract":"This study was designed to check the prevalence and PCR-based molecular characterization of goat pox virus (GTPV) in the Multan and Bahwalnagar regions of Punjab, Pakistan. Capripox virus (CPPV) is the cause of goat pox (GTP) and sheep pox (SPP) disease, it highly affects the morbidity and mortality rate of goats and sheep. In this study, the 80 tissues and blood samples of goats were collected on age basis from the goat farms, slaughter houses, tanneries and domestic animals. The epidemiological data was also collected. The collected samples were processed for DNA extraction. We characterized the goat pox virus (GTPV) with specific primers of P32 gene by PCR. Then each amplified product was analyzed by agarose gel electrophoresis visualized by UV fluorescence light. This study showed that Infants of goats (2-10 months) in Multan showed 25% while adult goat in Multan showed 14.2 % positive results. In Bahawlnagar, the affected infants of goats (2-10 months) found were 31.25% while adult infected goats were 11.1%. Both primers were equally effective for the characterization of unknown samples. The most effected goats were adult female and infants. \u0000J. bio-sci. 28: 95-103, 2020","PeriodicalId":90580,"journal":{"name":"Journal of bio-science","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3329/jbs.v28i0.44715","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41596726","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation of microbial quality and pathogenic potentiality of enterobacteria in poultry feeds","authors":"S. Islam, N. Tanjila, M. Begum","doi":"10.3329/jbs.v28i0.44711","DOIUrl":"https://doi.org/10.3329/jbs.v28i0.44711","url":null,"abstract":"The present investigation has been carried out to assess the microbial safety and pathogenic potentialities of enterobacteria in poultry feeds. From the results it was observed that total aerobic plate count of poultry feeds samples were recorded as 2.8 × 105 to 5.8 × 109 cfu/g and 100% samples contained ≥106 cfu/g while the highest mean of cfu was counted as log10 8.797/gm. Large number of coliforms were recorded in different poultry feed samples and the ranges of cfu were counted as 1.2 × 104 to 5.2 × 107/g while average 75% samples were contaminated with coliform bacteria with ≥104 cfu/g and the highest mean of cfu was counted as log10 6.103/g. The ranges of cfu of Escherichia coli were 1.03 × 102 to 1.09 × 105/g and 70% samples contained ≥102 cfu/g while the highest mean of cfu was counted as log10 4.493/gm. But the ranges of cfu of total Salmonella sp. were recorded as 1.02 × 101 to 5.25 × 104/g and 50% samples contained ≥102 cfu/g and the highest mean of cfu was counted as log10 3.665/g. Total 29 enterobacterial isolates were isolated from the feed by using selected media. On the basis of morphological characteristics and biochemical test results the isolates were identified as Salmonella sp., Shigella sp., Klebsiella sp., Citrobacter sp., Proteus sp., Enterobacter sp. and Escherichia coli. These isolates were tested on blood agar medium and only seven isolates showed positive β-hemolytic activity.In virulence efficacy test, only hemolytic positive isolates were ingested to chicken and observed that E. coli (SGE-1), Klebsiella sp. (SSE-6) and Salmonella sp. (JSS-9) isolates were highly toxic because the experimental chickens were died after 3 days of ingestion of the bacteria, two isolates showed loose motion symptom after 15 days while other isolates showed little sickness. All the selected isolates showed positive hem-agglutination reactivity in poultry RBC. The results indicate that the poultry feeds were highly contaminated with pathogenic enterobacteria which are risk to public health. \u0000J. bio-sci. 28: 59-68, 2020","PeriodicalId":90580,"journal":{"name":"Journal of bio-science","volume":"28 1","pages":"59-68"},"PeriodicalIF":0.0,"publicationDate":"2019-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3329/jbs.v28i0.44711","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48818428","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Isolation of bacteria from diesel contaminated soil for diesel remediation","authors":"O. A. Oyewole, S. S. L. Zobeashia, O. Oladoja, I. Musa, IT Terhemba","doi":"10.3329/jbs.v28i0.44708","DOIUrl":"https://doi.org/10.3329/jbs.v28i0.44708","url":null,"abstract":"This study is aimed at isolating bacterial species that inhabit diesel contaminated soil and also screened these isolates for the ability to be used for remediating diesel contaminated environment using their potential to degrade diesel as carbon and energy source. Top soil sample was collected from an ancient diesel-powered generator house in Minna, Nigeria, in a sterilized plastic container while diesel oil was obtained from local petrol bunk. Four bacterial isolates were isolated from the diesel contaminated soil sample and were screened for their ability to degrade diesel using mineral salt medium (MSM). The isolates with highest biodegradation potential were identified as Bacillus subtilis and Bacillus cereus. The optimum pH (5, 6, 7 and 8) and hydrocarbon concentration (1%, 2%, 5% and 10%) of the isolate was determined by spectrophotometry and the result revealed that the optimum pH for biodegradation of diesel by Bacillus subtilis and Bacillus cereus, was 7 (1.170) and 8 (1.745) respectively while the optimum hydrocarbon concentration degradation for both isolates was 5% (2.22) and 1% (2.37) respectively. The results of this study showed that these isolates were able to degrade diesel and can be useful for large scale bioremediation of diesel contaminated soils.","PeriodicalId":90580,"journal":{"name":"Journal of bio-science","volume":"28 1","pages":"33-41"},"PeriodicalIF":0.0,"publicationDate":"2019-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3329/jbs.v28i0.44708","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47791792","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}