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Optimizing Genetic Algorithm Parameters for Multiple Sequence Alignment Based on Structural Information 基于结构信息的多序列比对遗传算法参数优化
Pub Date : 2016-01-01 DOI: 10.12988/ASB.2016.51250
M. R. K. Sueno, J. Addawe
Multiple sequence alignments (MSAs) are commonly used approaches in the analysis of sequence structure relationships. MSA is generally the alignment of three or more protein or nucleic acid sequences that maximises the similarities between sequences. In this paper, we use genetic algorithm to compute multiple sequence alignment using the structural information as the scoring scheme implemented in the program Multiobjective Optimizer for Sequence Alignments based on Structural Evaluations (MOSAStrE). We performed numerical experiments on datasets obtained from benchmark alignment database (BAliBASE) to solve multiple sequence alignment. To test the performance of the proposed algorithm, numerical simulations were carried out in deciding the appropriate set of parameter values for the
多序列比对(Multiple sequence alignment, MSAs)是分析序列结构关系的常用方法。MSA通常是三个或更多的蛋白质或核酸序列的比对,以最大限度地提高序列之间的相似性。在基于结构评价的序列比对多目标优化器(MOSAStrE)程序中,我们采用遗传算法以结构信息作为评分方案来计算多个序列比对。在基准比对数据库(BAliBASE)的数据集上进行数值实验,求解多序列比对问题。为了测试所提算法的性能,在确定合适的参数值集时进行了数值模拟
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引用次数: 2
Effect of red and blue light-emitting diodes on germination, morphological and anatomical features of Brassica napus 红色和蓝色发光二极管对甘蓝型油菜萌发及形态解剖特征的影响
Pub Date : 2016-01-01 DOI: 10.12988/ASB.2016.6832
P. F. Tehrani, A. Majd, H. Mahmoodzadeh, T. N. Satari
Effect of red and blue light on seed germination, anatomical and ultrastructural features of chloroplasts were studied in oilseed rape (Brassica napus ‘Modena’). Oilseed rape seeds were germinated in 2, 4 and 8 h light under various light emitting-diodes (LED) treatments: white light (control), red light (638 nm) and blue light (450 nm) in the laboratory. In greenhouse experiment, potted plants were grown under 4, 8 and 12 days of blue and red lights and white light at the background. The photoperiod of 16 h and 28/18 °C day/night temperature and 30 % relative humidity were maintained in the greenhouse. Seed germination percentage under red light increased significantly when compared with the control; however, blue light decreased significantly germination percentage of oilseed rape seeds. Red and blue lights had negative effect on shoot and seminal root growth of oilseed rape in all the treatments. In greenhouse experiment, shoot length, plant biomass, stem diameter, were significantly increased by blue light treatment. It seems blue light treatment induces higher photosynthesis in leaves and produced higher biomass of the whole plant in this treatment than the control or red light treatment. 174 P. Farrokh Tehrani et al.
研究了红蓝光对油菜种子萌发、叶绿体解剖和超微结构特征的影响。实验采用白光(对照)、红光(638 nm)和蓝光(450 nm)三种不同的发光二极管(LED)处理,分别在2、4和8 h下对油菜种子进行萌发。在温室试验中,盆栽植物分别在4、8和12 d的蓝、红、白光背景下生长。温室内光周期为16 h,昼夜温度28/18℃,相对湿度30%。与对照相比,红光处理下种子发芽率显著提高;而蓝光则显著降低了油菜种子的发芽率。在所有处理中,红、蓝光对油菜茎、种根生长均有不利影响。在温室试验中,蓝光处理显著提高了植株的茎长、生物量和茎粗。与对照和红光处理相比,蓝光处理诱导叶片的光合作用更高,植株的生物量也更高。[4] P. Farrokh Tehrani等。
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引用次数: 14
Calcium Oxalate Crystal (CaOx) Composition at Different Growth Stages of Petiole in Vitis Vinifera (Vitaceae) 葡萄叶柄不同生长时期草酸钙晶体(CaOx)组成
Pub Date : 2016-01-01 DOI: 10.12988/ASB.2016.51146
Şenay Süngü Şeker, M. Akbulut, G. Şenel
Most plants accumulate inorganic inclusions called calcium oxalate crystals (CaOx) in both vegetative and reproductive organs. In these studies, the similarities and differences for the type and distribution of calcium oxalate (CaOx) crystals were examined in both young and mature petiole Vitis vinifera L. (Vitaceae). Transverse, radial, and tangential sections were obtained from epidermis, cortex, xylem and phloem tissue of different specimens. Crystal measurements of young and mature petiole were statically analyzed. Significant differences were determined between young and mature petiole in terms of distribution in the tissues and varieties of crystal.
大多数植物在营养器官和生殖器官中积累称为草酸钙晶体(CaOx)的无机包裹体。在这些研究中,草酸钙(CaOx)晶体的类型和分布在年轻和成熟叶柄葡萄(Vitis vinifera L.)的异同进行了研究。对不同标本的表皮、皮层、木质部和韧皮部组织进行横向、径向和切向切片。对幼叶柄和成熟叶柄的晶体测量进行了静态分析。幼叶柄和成熟叶柄在组织中的分布和晶体的种类有显著差异。
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引用次数: 2
Association of prevalent Leptospira species with different rodents of three northern provinces in Iran using microscopic agglutination test 用显微凝集试验分析伊朗北部三省流行钩端螺旋体与不同啮齿动物的关系
Pub Date : 2016-01-01 DOI: 10.12988/ASB.2016.625
B. Esfandiari, H. Nahrevanian, M. Pourshafie, M. Gouya, P. Khaki, E. Mostafavi, J. Darvish, S. M. Bidhendi, H. Hanifi, M. Gharakhani
Purpose: Leptospirosis as a zoonotic disease is caused by Leptospira bacteria. Transmission occurs by contact with contaminated biological fluids of the infected animals. Rodents are major sources of infection for humans or other animals. The disease is distributed mainly in tropical regions with rainfall like northern part of Iran. The aim of this study was to find association of prevalent Leptospira species with different rodents of three Northern Provinces in Iran using microscopic agglutination test (MAT). Methods: In this study, 404 rodents were captured alive at 10 different parts of each Mazandaran, Gilan and Golestan Provinces. Identification of the infecting serovars and the antibody titers were done by MAT in the sera samples using a panel of 20 strains of live Leptospira spp. as the source of antigens. RESULTS: Antibodies against one or more serovars were detected in 94 (23.27%) sera at dilution ≥1:200 and 76.73% were detected to be negative. The prevalent Leptospira serovars were detected as L. autumnalis (25.53%), L. serjoehardjo (24.47%) and L. cynopteri (6.38%). The majority of rodents were identified during this study in three provinces included Rattus norvegicus (67.33%), Apodemus sylvaticus (13.86%) and Rattus rattus (13.61%). The common prevalent rodent in three provinces was Rattus norvegicus, which was associated with L. serjoehardjo in Mazandaran (81.8%), L. autumnalis in Gilan (67.2%) and L. canicula in Golestan (50.0%). Conclusion: The dominant srovars of leptospira were L. autumnalis, L. serjoehardjo and L. cynopteri and the most prevalent rodents as reservoir were Rattus norvegicus, Apodemus sylvaticus and Rattus rattus in three Northern provinces of Iran. The results indicated a moderate prevalence of leptospirosis in rodents during this study in north of Iran. This study provided the first epidemiological data about the association between leptospirosis with rodents in Iran.
目的:钩端螺旋体病是一种由钩端螺旋体引起的人畜共患疾病。通过接触受感染动物的受污染的生物体液传播。啮齿动物是人类或其他动物的主要感染源。该病主要分布在多雨的热带地区,如伊朗北部。本研究的目的是利用显微凝集试验(MAT)发现伊朗北部三省流行的钩端螺旋体与不同啮齿动物的关系。方法:在马赞达兰省、吉兰省和戈列斯坦省各10个不同地点捕获活鼠404只。用20株活钩端螺旋体作为抗原来源,用MAT对血清样本进行感染血清型鉴定和抗体滴度测定。结果:94份(23.27%)血清在稀释度≥1:20 00时检出一种或多种血清型抗体,76.73%血清阴性。检出流行的钩端螺旋体血清型为秋季钩端螺旋体(25.53%)、serjohardjo钩端螺旋体(24.47%)和钩端螺旋体(6.38%)。调查中发现的鼠类以褐家鼠(67.33%)、森林姬鼠(13.86%)和家鼠(13.61%)居多。三省常见流行鼠为褐家鼠,与马赞达兰省serjoehardjo鼠(81.8%)、吉兰省秋季鼠(67.2%)和戈列斯坦省canicula鼠(50.0%)为伴。结论:伊朗北部三省钩端螺旋体的优势鼠种为秋季L.、serjoehardjo L.和cynopteri .,主要宿主鼠为褐家鼠、森林姬鼠和家鼠。结果表明,在本研究期间,伊朗北部啮齿动物中钩端螺旋体病的流行程度中等。本研究首次提供了伊朗钩端螺旋体病与啮齿动物之间关系的流行病学数据。
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引用次数: 3
The effect of manure and the bioaccumulation of heavy metals Hg, Cu and Zn at ex-gold mining land on the growth of silk tree (Paraserinthes falcataria (L.) Nielsen) in Bombana, Southeast Sulawesi 前金矿废弃地粪肥及重金属Hg、Cu、Zn的生物积累对蚕树生长的影响尼尔森)在邦巴纳,苏拉威西岛东南部
Pub Date : 2016-01-01 DOI: 10.12988/ASB.2016.6411
S. Ambardini, Darwis, L. Safuan, A. Zaeni, A. Sani
One of the negative effects of gold mining activity is soil contamination by heavy metal. The aims of this study were two folds; to assess the effect of manures (cow, goat, chicken) (i) on the growth of silk tree (Paraserianthes falcataria (L.) Nielsen) and (ii) on the bioaccumulation of heavy metals (Hg, Cu, Zn) in the plant organs of the silk tree planted in the ex-gold mining land in Bombana. This is an experimental research design with a completely randomized 78 Sri Ambardini et al. design consisting of one control (without manure) and 4 treatments (cow, goat and chicken manures) with 5 repplicates. The plant growth parameters observed are plant height, stem diameter, number of leaves, leaf area, and metal content of Hg, Zn, and Cu in plant organs. ANOVA with Duncan Multiple Range Test (DMRT) were used for the analysis. The results showed that the treatment with manure has an impact on the parameter of plant growth and bioaccumulation of Hg, Cu and Zn in the plant organs. DMRT showed that the treatment with manures has a significant influence on the growth and bioaccumulation of Hg, Cu, and Zn in the plants. The manure with cows was better in supporting growth of silk tree compared to those with chicken, goat as well as control. Treatment with manure reduced bioaccumulation of Hg but increased bioaccumulation of Cu and Zn in the plant organs. The bioaccumulation of Hg, Cu and Zn was found the highest in the root than in the stem and leaves. The total bioaccumulation of Zn in plant organs was the highest compared with that of Cu and Hg. Keyword: Manure, Growth, Heavy Metals, Silk Tree, Ex-Gold Mining Land
金矿开采活动的负面影响之一是重金属污染土壤。这项研究的目的有两个方面;评价牛粪、羊粪、鸡粪对蚕树(Paraserianthes falcataria)生长的影响。Nielsen)和(ii) Bombana前金矿土地上种植的蚕树植物器官中重金属(Hg, Cu, Zn)的生物积累。这是一个完全随机的78个Sri Ambardini等人设计的实验研究设计,包括一个对照(无粪便)和4个处理(牛、山羊和鸡粪便),有5个重复。观察植株的生长参数为株高、茎粗、叶数、叶面积和植株各器官中汞、锌、铜的金属含量。方差分析采用Duncan多元极差检验(DMRT)。结果表明,有机肥处理对植物生长参数及各器官中汞、铜、锌的生物积累均有影响。DMRT结果表明,有机肥处理对植株生长和汞、铜、锌的生物积累有显著影响。牛粪对蚕树生长的促进作用优于鸡粪、羊粪和对照。有机肥处理减少了汞的生物积累,但增加了铜和锌在植物器官中的生物积累。汞、铜和锌的生物积累在根中最高,在茎和叶中次之。与Cu和Hg相比,植物器官中Zn的总生物积累量最高。关键词:粪肥,生长,重金属,蚕树,前金矿地
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引用次数: 1
Biochemical association between essential trace elements and susceptibility to malaria in outbred mice after inhibition with dexamethasone or induction with lipopolysaccharide 地塞米松抑制或脂多糖诱导后近交种小鼠必需微量元素与疟疾易感性的生化关系
Pub Date : 2016-01-01 DOI: 10.12988/ASB.2016.6516
M. Modaresinejad, H. Nahrevanian, S. Khatami, E. Bagheri
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引用次数: 2
Nutlet micromorphology study of some species of Thymus L. (Lamiaceae) in NE Iran 伊朗东北部部分胸腺属植物坚果微形态研究
Pub Date : 2016-01-01 DOI: 10.12988/ASB.2016.663
Elahe Tabassi, Mahmoud Zokaei, A. Jafari, J. Vaezi
In the present study, nutlet micromorphological features of five Thymus species growing in NE Iran were examined. For this purpose, nutlet shape and ornamentation were assessed using SEM. The results indicated that theP/E of nutlet, abscission scar position, cell shape, anticlinal wall and periclinal surface varied among the studied species. Finally an identification key was prepared basis on the mentioned characteristics for species under study.
本研究对生长在伊朗东北部的5种胸腺的坚果微形态特征进行了研究。为此,利用扫描电镜对坚果的形状和纹饰进行了评估。结果表明,不同种属的小核、脱落疤痕位置、细胞形状、背斜壁和外周表面的p /E存在差异。最后根据上述特征编制了被研究物种的鉴定密钥。
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引用次数: 3
Control of the Applicability of the Dipole Approximation for Gold Nanoparticles 偶极近似对金纳米粒子适用性的控制
Pub Date : 2015-09-01 DOI: 10.12988/ASB.2015.5532
D. Barchiesi, T. Grosges
Gold nanoparticles are widely used for biomedical applications such as cancer therapy, drug delivery and high resolution imaging of biological tissues (spectroscopy, Surface Enhanced Raman spectroscopy, uo
金纳米颗粒广泛应用于生物医学领域,如癌症治疗、药物输送和生物组织的高分辨率成像(光谱学、表面增强拉曼光谱等)
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引用次数: 2
A population-based case-control study to evaluate the role of codon 164 of beta 2-adrenergic receptor gene polymorphism in Iranian PCOS patients 一项基于人群的病例对照研究,评估β 2-肾上腺素能受体基因多态性密码子164在伊朗PCOS患者中的作用
Pub Date : 2015-01-01 DOI: 10.12988/ASB.2015.41271
Shahla Lotfi, T. Naji, A. Shakoori, D. N. Inanlou
Polycystic ovary syndrome (PCOS) is a common endocrine disorder. This syndrome is a genetic disorder that involves about 5 to 10 percent of women in reproductive age. The purpose of this study was to investigate the effect of codon 164 of beta-2 adrenergic receptor (NM- _000024.5:c.491C>T) polymorphism in patients with PCOS. The normal form of this codon isACC and when polymorphism occurs, it changes to the ADRB2rs1800888 (Thr164Ile) with codon ATC. This case-control study consisted of 14 Iranian patients (mean age 26.86±1.03), along with 13 healthy controls, from Infertility Center of Valie Asre, Imam Khomaini Hospital Complex in May 2013 until Feb 2014. Data analysis was done by statistical software SPSS, version 19.0. The result shows that, two persons of control group and one individual of patient group had polymorphism codon 164. The P-value greater than 0.05 (P>0.05) demonstrated that there is no correlation between Thr164Ile polymorphism and PCOS.
多囊卵巢综合征(PCOS)是一种常见的内分泌疾病。这种综合征是一种遗传性疾病,大约有5%到10%的育龄妇女患有这种疾病。本研究旨在探讨β -2肾上腺素能受体(NM- _000024.5:c.491C>T)密码子164多态性对PCOS患者的影响。该密码子的正常形式为acc,当多态性发生时,它变为密码子ATC的ADRB2rs1800888 (Thr164Ile)。本病例对照研究包括14名伊朗患者(平均年龄26.86±1.03岁),以及13名健康对照,这些患者于2013年5月至2014年2月在Imam Khomaini医院综合医院Valie Asre不孕不育中心就诊。数据分析采用SPSS 19.0版统计软件。结果表明,对照组2人,患者组1人存在多态性密码子164。P值大于0.05 (P>0.05)表明Thr164Ile多态性与PCOS无相关性。
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引用次数: 0
Physical and academic performance of vegetarian and non-vegetarian school girls (13–15 yrs) 素食及非素食女学生(13-15岁)的体能及学业表现
Pub Date : 2015-01-01 DOI: 10.12988/ASB.2015.41165
Priyanka Pareek, S. Ayesha
The study was undertaken to assess the physical and academic performance of vegetarian and non-vegetarian school girls. One hundred school going girls vegetarian (n=50) and non-vegetarian (n=50) in the age group of 13-15 years were selected purposively for the study. The data were collected through personal interview technique using the especially structured questionnaire. The general profile, status and educational details of the family, dietary habits and menarcheal profile of the subjects were collected. The height and weight of the subjects were measured by standardized methods. The BMI of the subjects were calculated and categorized accordingly. The academic performance of the girls was measured using the percentage marks obtained by the end of the academic year. Physical activity tests were conducted to assess the physical work capacity by noting the time taken and change in pulse rate after performing the activities as running (100m), jumping (25times) and touching toes (25times). In the study 32% nonvegetarian got higher scores followed by 26% of vegetarian. More than 10% vegetarian and non-vegetarian girls got lower score in academics. The mean difference in the time taken to complete the running and jumping activities came out to be non significant and the time taken to touch toes for vegetarian subjects was 80 Priyanka Pareek and Syeda Ayesha significantly lower as compared to non-vegetarian subjects. The difference was significant for the change in pulse rate after completing the running and jumping activities in both the groups, but difference was non-significant between the groups. In case of toe touching difference was non-significant for the change in pulse rate within both the groups, but difference was significant between the groups, It can be concluded as the non-vegetarian girls were found to be better physical performers. Academically, however they were better than their vegetarian correlates.
这项研究是为了评估素食和非素食女学生的身体和学业表现。有针对性地选择了年龄在13-15岁之间的100名吃素和不吃素的在校女生(n=50)进行研究。数据收集采用个人访谈技术,采用特别结构化的问卷调查。收集研究对象的一般情况、家庭状况和教育情况、饮食习惯和月经初潮情况。采用标准化方法测量受试者的身高和体重。计算受试者的BMI并进行分类。女生的学习成绩是用学年结束时获得的百分比分数来衡量的。进行体力活动测试,通过记录跑步(100米)、跳跃(25次)和触趾(25次)等活动所花费的时间和脉搏率变化来评估体力工作能力。在这项研究中,32%的非素食者得分更高,其次是26%的素食者。超过10%的素食和非素食女孩在学业上得分较低。完成跑步和跳跃活动所需的平均时间差异不显著,素食者触摸脚趾所需的时间为80,与非素食者相比,Priyanka Pareek和Syeda Ayesha显着降低。两组完成跑跳活动后脉搏率变化差异有显著性,组间差异无显著性。在接触脚趾的情况下,两组的脉搏变化差异不显著,但两组之间的差异显著,可以得出结论,非素食女孩的身体表现更好。然而,在学术上,他们比素食者要好。
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引用次数: 1
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Advanced Studies in Biology
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