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  • 1
  • 2
    Publication Date: 2020-10-05
    Description: Motivation Researchers and practitioners use a number of popular sequence comparison tools that use many alignment-based techniques. Due to high time and space complexity and length-related restrictions, researchers often seek alignment-free tools. Recently, some interesting ideas, namely, Minimal Absent Words (MAW) and Relative Absent Words (RAW), have received much interest among the scientific community as distance measures that can give us alignment-free alternatives. This drives us to structure a framework for analyzing biological sequences in an alignment-free manner. Results In this application note, we present ADACT (Alignment-free Dissimilarity Analysis & Comparison Tool), a simple web based tool that computes the analogy among sequences using a varied number of indexes through the distance matrix, species relation list and phylogenetic tree. This tool basically combines absent word (MAW or RAW) computation, dissimilarity measures, species relationship and thus brings all required software in one platform for the ease of researchers and practitioners alike in the field of bioinformatics. We have also developed a restful API. Availability ADACT has been hosted at http://research.buet.ac.bd/ADACT/
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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    Publication Date: 2021-06-01
    Print ISSN: 0308-597X
    Electronic ISSN: 1872-9460
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Political Science , Law
    Published by Elsevier
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  • 5
    Publication Date: 2020-12-14
    Description: Atmospheric CO2 (c(a)) rise changes the physiology and possibly growth of tropical trees, but these effects are likely modified by climate. Such c(a) x climate interactions importantly drive CO2 fertilization effects of tropical forests predicted by global vegetation models, but have not been tested empirically. Here we use tree-ring analyses to quantify how c(a) rise has shifted the sensitivity of tree stem growth to annual fluctuations in rainfall and temperature. We hypothesized that c(a) rise reduces drought sensitivity and increases temperature sensitivity of growth, by reducing transpiration and increasing leaf temperature. These responses were expected for cooler sites. At warmer sites, c(a) rise may cause leaf temperatures to frequently exceed the optimum for photosynthesis, and thus induce increased drought sensitivity and stronger negative effects of temperature. We tested these hypotheses using measurements of 5,318 annual rings from 129 trees of the widely distributed (sub-)tropical tree species, Toona ciliata. We studied growth responses during 1950-2014, a period during which c(a) rose by 28%. Tree-ring data were obtained from two cooler (mean annual temperature: 20.5-20.7 degrees C) and two warmer (23.5-24.8 degrees C) sites. We tested c(a) x climate interactions, using mixed-effect models of ring-width measurements. Our statistical models revealed several significant and robust c(a) x climate interactions. At cooler sites (and seasons), c(a) x climate interactions showed good agreement with hypothesized growth responses of reduced drought sensitivity and increased temperature sensitivity. At warmer sites, drought sensitivity increased with increasing c(a), as predicted, and hot years caused stronger growth reduction at high c(a). Overall, c(a) rise has significantly modified sensitivity of Toona stem growth to climatic variation, but these changes depended on mean climate. Our study suggests that effects of c(a) rise on tropical tree growth may be more complex and less stimulatory than commonly assumed and require a better representation in global vegetation models.
    Type: info:eu-repo/semantics/article
    Format: application/pdf
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  • 6
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    In:  http://aquaticcommons.org/id/eprint/16429 | 12051 | 2015-03-27 09:27:05 | 16429 | Bangladesh Fisheries Research Institute
    Publication Date: 2021-07-05
    Description: Highest growth of prawn was obtained with Feed B (743 kg/ha) with highest survival rate (60.88%) followed by Feed A where production and survival rate was 659 kg/ha and 53.50%, respectively. Feed A contained 30% dry ground cow viscera, 40% oil cake, 20% rice-bran and 10% heat bran. Feed conversion ratios were found to be 7.60:1 for Feed A and 6.46:1 for Feed B, which indicated that Feed B was more efficiently utilized by the prawn than Feed A. Statistical analysis revealed that the differences in production of prawns among the treatments were highly significant (P〈 0.01).
    Keywords: Aquaculture ; diets ; prawn culture ; artificial feeding ; feed efficiency ; feeding equipment ; Macrobrachium rosenbergii ; Golda chingri ; survival ; Bangladesh
    Repository Name: AquaDocs
    Type: article
    Format: application/pdf
    Format: application/pdf
    Format: 151-155
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  • 7
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    In:  http://aquaticcommons.org/id/eprint/22538 | 18721 | 2018-04-23 11:10:27 | 22538 | Iranian Fisheries Science Research Institute
    Publication Date: 2021-07-07
    Description: Euglenophyte bloom is a common problem in most of the aquaculture ponds in Bangladesh. In the present study we conducted an experiment to control euglenophyte bloom for getting better fish production using duckweed (Lemna minor) and lime. The experiment was carried out using four treatments, i.e., ponds were supplied with duckweed (T1), lime treatment (T2), both duckweed and lime (T3) and without supply of duckweed and lime (T4). Rohu, catla, mrigal, silver carp and silver barb were stocked and their gut contents were analyzed monthly. The ranges of water quality parameters were analyzed within the productive limit during the experimental period. The mean abundance of euglenophyte was significantly highest in T4 (17.62 ± 1.97 × 104 cells/L), followed by T2 (2.96 ± 0.20 × 104 cells/L), T1 (1.94 ± 0.35 × 104 cells/L) and T3 (1.53 ± 0.42 × 104 cells/L). Gut content analysis revealed that considerable amount of euglenophyte were consumed by silver carp and silver barb, but not preferred by rohu, catla and mrigal. The gross yields of fish were 2133.37, 1967.76, 2816.52 and 1725.62 kg/ha/5 months in T1, T2, T3 and T4, respectively. The highest fish production in T3 and lowest fish production in T4 indicated the use of duckweed and lime is economically sustainable for controlling euglenophytes bloom, maintaining water quality and getting higher fish production.
    Keywords: Aquaculture ; Biology ; Environment ; Euglenophytes ; Bloom ; Duckweed ; Production ; Pond ; Water quality ; Lime ; Bangladesh
    Repository Name: AquaDocs
    Type: article , TRUE
    Format: application/pdf
    Format: application/pdf
    Format: 602-617
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  • 8
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    In:  http://aquaticcommons.org/id/eprint/22700 | 18721 | 2018-05-16 20:29:56 | 22700 | Iranian Fisheries Science Research Institute
    Publication Date: 2021-07-09
    Description: Effects of salinity on fertilization, embryonic stage, and early larval development and growth performances of short-spined white sea urchin, Salmacis sphaeroides were conducted under a controlled laboratory condition. The experiment was carried out with seven salinity treatments (15, 20, 25, 30, 35, 40 and 45 PSU), each of which was triplicated. Significantly highest fertilization success was achieved at 30 PSU, followed by those at 25, 35, 20, 40 and 45 PSU, while the lowest value was obtained at 15 PSU, decreased with increasing and decreasing salinities (p〈.05).The time required to reach these embryonic and larval stages was increased with the salinity deviations from 30 till the extent to 25 and 35 PSU. No significant differences (p〉.05) were noted among these three salinity levels on prism larval length and width. However, significance differences (p〉.05) were noted in morphometric characters of 2-arm and 4-arm pluteus larvae. The findings of the this study indicate that S. sphaeroides is stenohaline and do not survive and develop out of the range from 25 to 35 PSU.
    Keywords: Biology ; Fisheries ; Salmacis sphaeroides ; Sea urchin ; Salinity ; Embryo ; Larvae development ; Malaysia
    Repository Name: AquaDocs
    Type: article , TRUE
    Format: application/pdf
    Format: application/pdf
    Format: 456-468
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  • 9
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    In:  http://aquaticcommons.org/id/eprint/22752 | 18721 | 2018-05-19 19:20:20 | 22752 | Iranian Fisheries Science Research Institute
    Publication Date: 2021-07-09
    Description: An experiment was undertaken to develop a suitable seed production technique for Sperata aor in captivity. Naturally produced fry of aor was reared at different densities in nine nursery ponds 0.012 ha in size with an average depth of 0.8 m each. Three stocking densities tested, each of which was triplicated. Fry of aor stocked at 100,000/ha was designated as treatment-1 (T1), 150,000/ha as treatment-2 (T2) and 200,000/ha as treatment-3 (T3). All stocked fry were from the same age group with mean length and weight of 1.78 ± 0.28 cm and 0.24 ± 0.05 g, respectively. Fry in all the treatments were fed with SABINCO nursery feed (32.06% crude protein) for the first 14 days and starter-I (31.53% crude protein) for days 15 to 56. Physico-chemical parameters and plankton population of pond water were within the optimal level being better in T1 than those in T2 and T3. Growth in terms of final weight and length, weight and length gain, specific growth rate, daily growth rate, and survival of fingerlings were significantly higher in T1 followed by T2 and T3. Food conversion rate was significantly lower in T1 than in T2 and T3. Significantly higher number of fingerlings was produced in T3 than those in T2 and T1. Despite this, consistently higher net benefits were achieved from T1 than from T2 and T3. This is the first time report that stocking of 100,000 fry/ha appears to be the most suitable density for rearing of aor fingerlings in nursery ponds.
    Keywords: Biology ; Fisheries ; Sperata aor ; Fry ; Stocking density ; Fingerling ; Growth ; Production ; Genetics ; Malaysia
    Repository Name: AquaDocs
    Type: article , TRUE
    Format: application/pdf
    Format: application/pdf
    Format: 1-14
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  • 10
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    In:  http://aquaticcommons.org/id/eprint/22785 | 18721 | 2018-05-22 18:06:23 | 22785 | Iranian Fisheries Science Research Institute
    Publication Date: 2021-07-10
    Description: Diadema setosum (Leske, 1778), is one of the common echinoids widely distributed in the Indo-West Pacific Ocean, where it occurs from the Red Sea, Persian Gulf and the east coast of Africa to Japan, Australia and Malaysia. To investigate the developmental basis of morphological changes in embryos and larvae, we documented the ontogeny of D. setosum in a controlled laboratory condition at the Institute of Bioscience, Universiti Putra Malaysia, during July–September, 2012. Matured gametes were obtained from the adult individuals and the eggs fertilized at limited sperm concentration (10^-5 dilution). The obtained embryos were then reared at 24-25°C. First cleavage (2-cell), 4-cell, 8-cell, 16-cell, 32-cell and multi-cell (Morulla) stages were attained at 01.20, 02.14, 02.44, 03.09, 03.32 and 03.54 h after fertilization, respectively. Blastulae with a mean length of 111.47±1.88 µm (mean±SD) hatched 08.45 h after sperm entry. Gastrula formed 16.36 h post-fertilization and the archenteron extended constantly, while the ectodermal red-pigmented cells migrated synchronously to the apical plate. The pluteus larva started to feed unicellular algae (Chaetoceros calcitrans) in 2 d, grew continuously, and finally attained metamorphic competence within 35 d after fertilization. Induction of metamorphosis took approximately 1 h 30 min from attachment on the substratum to the complete resorption of larval tissues and the development of complete juvenile structure with adult spines, extended tubefeet and well-developed pedicellaria, the whole event usually took place within 1 d post-settlement. The newly formed juvenile (473.16 ± 6.96 µm, n=30) with a complete adult structure then grew on coralline algae to 3-month old juvenile, which represents the "sea urchin seed" for stocking in grow-out culture. This study represents the first successful investigation on embryonic, larval and early juvenile development of D. setosum. The findings would greatly be helpful towards the development of breeding and seed production techniques for aquaculture of sea urchins.
    Keywords: Aquaculture ; Biology ; Fisheries ; Sea urchin ; Diadema setosum ; Embryo ; Larva ; Juvenile ; Development ; Pulau Pangkor ; aquaculture ; Pacific Ocean ; Red Sea ; Persian Gulf ; Africa ; Japan ; Australia ; Malaysia
    Repository Name: AquaDocs
    Type: article , TRUE
    Format: application/pdf
    Format: application/pdf
    Format: 409-424
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