一种基于后缀排序快速实现Burrows-Wheeler变换的方法

近年来,Bzip2压缩算法凭借其在压缩率方面的优势,得到了越来越多的应用,Bzip2的核心算法是Burrows-Wheeler变换(BWT),BWT能有效的将数据中相同的字符聚集到一起,为进一步压缩创造条件。在硬件实现BWT时,常用的基于后缀排序的算法能有效克服BWT消耗存储资源大的问题,该文对基于后缀排序实现BWT的方法进行了详细分析,并且在此基础上提出了一种快速实现BWT的方法后缀段算法。仿真结果表明后缀段算法在处理速度上比传统的基于后缀排序的算法有很大的提高。

A Review of the Engineering Role of Burrowing Animals: Implication of Chinese Pangolin as an Ecosystem Engineer

Ecosystem engineers are organisms that alter the distribution of resources in the environment by creating,modifying,maintaining and/or destroying the habitat.They can affect the structure and function of the whole ecosystem furthermore.Burrowing engineers are an important group in ecosystem engineers as they play a critical role in soil translocation and habitat creation in various types of environment.However,few researchers have systematically summarized and analyzed the studies of burrowing engineers.We reviewing the existing ecological studies of burrowing engineer about their interaction with habitat through five directions:(1)soil turnover;(2)changing soil physicochemical properties;(3)changing plant community structure;(4)providing limited resources for commensal animals;and/or(5)affecting animal communities.The Chinese pangolin(Manis pentadactyla)is a typical example of burrowing mammals,in part(5),we focus on the interspecific relationships among burrow commensal species of Chinese pangolin.The engineering effects vary with environmental gradient,literature indicates that burrowing engineer play a stronger role in habitat transformation in the tropical and subtropical areas.The most common experiment method is comparative measurements(include different spatial and temporal scale),manipulative experiment is relatively few.We found that most of the engineering effects had positive feedback to the local ecosystem,increased plant abundance and resilience,increased biodiversity and consequently improved ecosystem functioning.With the global background of dramatic climate change and biodiversity loss in recent decades,we recommend future studies should improving knowledge of long-term engineering effects on population scale and landscape scale,exploring ecological cascades through trophic and engineering pathways,to better understand the attribute of the burrowing behavior of engineers to restore ecosystems and habitat creation.The review is presented as an aid to systematically expound the engineering effect of burrowing animals in the ecosystem,and provided new ideas and advice for planning and implementing conservation management.

Effect of mangrove restoration on crab burrow density in Luoyangjiang Estuary,China

Background:Mangrove restoration seeks to restore or rebuild degraded mangrove systems.The methods of mangrove restoration include ecological projects and restoration-oriented technologies,the latter of which are designed to restore the structure,processes as well as related physical,chemical and biological characteristics of wetlands and to ensure the provision of ecosystem services.As important components of mangrove ecosystem,benthic organisms and crabs play a key role in nutrient cycling.In addition,mangrove restoration,such as vegetation restoration measures,can lead to changes in the benthic faunal communities.This study investigates whether the presence of different mangrove species,age and canopy cover of mangrove communities affect the density of crab burrows.Methods:The Luoyangjiang Estuary,in the southeast of Fujian Province,was selected as our research area.A survey,covering 14 sites,was conducted to investigate the impacts of mangrove restoration on the density of crab burrows in four rehabilitated forests with different stand ages and canopy.Results:It was found that differences in vegetation types had a large impact on crab density and that the density of crab burrows was lower on exposed beaches(non-mangrove)than under mature Kandelia candel,Aegiceras corniculatum and Avicennia marina communities.In general,the amount of leaf litter and debris on mangrove mudflats was greater than on the beaches as food sources for crabs.Two-factor analysis of variance(ANOVA)shows that changes in mangrove species and age since restoration had different effects on crab burrow density.The effect of canopy cover was highly significant on crab burrow density.Conclusions:The results suggest that in the process of mangrove restoration the combined effects of mangrove stand age,canopy cover and other factors should be taken into account.This study further supports the findings of the future scientific research and practice on mangrove restoration and management measures.

基于扩展Burrows-Wheeler算法重构禽流感病毒的进化树

基于核苷酸的物理化学性质,利用扩展Burrows-Wheeler算法和Burrows-Wheeler相似性分布,对80种H5NI病毒的DNA序列的HA片段进行相似性比较,同时构建序列进化树,得到较好的结果.通过分析禽流感病毒之间的相似度关系,可为研究禽流感区域蔓延的特点提供一定的理论依据.

The hypoxia adaptation of small mammals to plateau and underground burrow conditions

Oxygen is one of the important substances for the survival of most life systems on the earth,and plateau and underground burrow systems are two typical hypoxic environments.Small mammals living in hypoxic environments have evolved different adaptation strategies,which include increased oxygen delivery,metabolic regulation of physiological responses and other physiological responses that change tissue oxygen utilization.Multiomics predictions have also shown that these animals have evolved different adaptations to extreme environments.In particular,vascular endothelial growth factor(VEGF)and erythropoietin(EPO),which have specific functions in the control of O_(2) delivery,have evolved adaptively in small mammals in hypoxic environments.Naked mole-rats and blind mole-rats are typical hypoxic model animals as they have some resistance to cancer.This review primarily summarizes the main living environment of hypoxia tolerant small mammals,as well as the changes of phenotype,physiochemical characteristics and gene expression mode of their long-term living in hypoxia environment.

The Habitats, Burrowing Behavior, Physiology Adaptation and Life Cycle of Spadefoot Toads (<i>Pelobates syriacus, Boettge</i>r, 1869) at the Southern Limit of Its Distribution in Israel

The present study describes the habitats, life cycle, larvae growth, burrowing behavior and terrestrial adaptation of Spadefoot toads in Israel based on observations and data collected during more than 30 years in northern Israel. The distribution area in Israel is from the north in the Upper Galilee and Golan Heights (annual rainfall range of 500 - 1000 mm) to the southern coastal plain (annual rainfall of about 250 mm). Among the 51 different breeding places of amphibians, only ponds where water was available for a few months were used by Spadefoot toads and metamorphosed populations were found around these ponds. The larvae underwent metamorphosis during the summer and autumn in northern Israel, and during the spring in central and southern Israel. A negative correlation exists between the percentage of toads burrowing and soil moisture levels, with greater burrowing behavior occurring under dry conditions. The plasma concentration increased during burrowing by electrolytes and urea accumulations. The burrowing behavior helped Spadefoot toads survive in this area at the southern border of its distribution.

The effect of substrate grain size on burrowing ability and distribution characteristics of Perinereis aibuhitensis

Perinereis aibuhitensis(Grube, 1878) lives in marine sediments of estuary or shoal areas, where substrate has some crucial environmental factors affecting its burrowing and distribution. In order to provide basic data for the habitat selection and suitability evaluations of the artificial aquaculture of P. aibuhitensis, this paper conducted a quantified analysis of its burrowing ability and explored its behavioral preferences in different substrates,including mud(<75 μm), fine sand(125–250 μm), medium sand(250–500 μm), coarse sand(500–2 000 μm), gravel(2 000–4 000 μm) and ceramsite(4 000–8 000 μm). The research results revealed that substrate grain size significantly affected the burrowing time, burrowing rate, burrowing depth and distribution rate(P<0.01).Moreover, P. aibuhitensis demonstrated preferential selections relating to substrate grain sizes, had higher burrowing ability in ceramsite, mud and fine sand compared with other substrates. The strongest burrowing ability and the highest distribution rate were observed in ceramsite. The study indicated that P. aibuhitensis was sensitive to substrate grain size, which also had an impact on its burrowing process and population distribution.In the natural sea, substrates mainly composed of mud and fine sand are fit for aquaculture and stock enhancement. Based on behavioral preferences and ecological rehabilitation function of P. aibuhitensis, this paper proposes a symbiotic system of marine animals and halophytes, and constructs an ecosystem model of"Marine fish-Halophytes-Perinereis aibuhitensis" with P. aibuhitensis as the link.

Impact of Human Disturbance on Fiddler Crab (<i>Uca tangeri</i>) Burrow Morphology, Distribution and Chemistry at Eagle Island, Niger Delta, Nigeria

Fiddler crabs are described as ecosystem engineers because of their burrow constructing ability. It was hypothesized that human activity will impact crab burrows. The study area was delineated into lowly, medium and highly impacted plots. Crab holes were randomly counted and their width, length and surface area estimated. Burrow soils were collected and analyzed for Cadmium (Cd), Lead (Pb) and Zinc (Zn) using spectrophotometric method (HACH DR 890 colorimeter). The result indicates that burrow width was significantly different between impacted plots (P < 0.05). Lowly impacted plot had the largest width while highly impacted plot had the smallest width. In contrast, there was no significant difference in burrow length (P > 0.05), but highly impacted plot has the longest length while lowly impacted plot has the shortest length. Again, the surface area of crab burrow varies significantly (P < 0.05), and lowly impacted plot had the largest area (507.95 ± 61.84 cm2) followed by medium (390.30 ± 57.65 cm2) and high (265.16 ± 30.85 cm2) impacted plots. Similarly, lowly impacted area has more number of burrows (n = 55) followed by medium (n = 30) and highly (n = 23) impacted plots. Highly impacted plot had the highest Cd and Pb concentration whereas lowly impacted plot had the highest Zn concentration. This implies that burrow morphology and chemistry exemplify the level of anthropogenic impact.

Large Tetrapod Burrows from the Permian Naobaogou Formation of the Daqingshan Area, Nei Mongol, China

Two new tetrapod burrow casts from the Naobaogou Formation(Middle or Late Permian)of Nei Mongol,China are described.It marks the first pre-Cenozoic tetrapod burrow from China,and one of the earliest records of tetrapod burrows.Comparison to other Permian and Triassic burrows suggests that these burrows were created by tetrapod slightly smaller than Lystrosaurus.Deduced from the morphology and sizes of two burrows and known tetrapods of the Naobaogou Formation,the burrow should be the production of a therapsid,most likely a dicynodon.These burrows indicate a seasonal climate and this area was semiarid or arid during that time.

Burrow Characteristics and Microhabitat Use of the Turpan Wonder Gecko Teratoscincus roborowskii (Squamata, Gekkonidae)

Burrow structural charactersitcs and microhabitat use of the Turpan wonder gecko Teratoscincus roborowskii(Gekkonidae) were studied between April and September of 2013 in the Turpan Eremophytes Botanic Garden,in the Turpan Depression of Western China.Burrow depth,entrance orientation,entrance height and width were observed.We assessed microhabitat selection and noted differences in microhabitat use among males,females,and juveniles.The magnitude of selection was measured using Jacobs' index of selectivity.Entrance height and width of the burrows of adults were significantly larger than those of juveniles,but the difference in burrow depth was not significant.The directional orientation of the burrow entrance showed a preference for the north-northeast and south-southeast,which were likely influenced by local prevailing winds and sunlight.Both the adult and juvenile geckos prefer to construct their burrows in sandy soil within a layer of loose soil whose thickness is greater than 30 cm.A majority of the burrows were located within 20 m of the nearest plant.Nearly half(48%) of the entrances of juveniles were located within 5 m of the nearest vegetation,significantly different from those of the adults.Results showed that the Turpan wonder gecko did not utilize microhabitats according to their availability,but rather that it preferred microhabitats which contained dead wood or the caper bush.Our results suggested that burrow characteristics and microhabitat selection were important factors in T.roborowskii adaptation to harsh and arid desert habitats.

不同干扰强度高原鼠兔对高寒草甸土壤温室气体通量变化的影响

高原鼠兔通过取食植物、排泄粪尿及掘土等行为对土壤理化性质及土壤微生物产生广泛干扰,进而可能会影响高寒草甸土壤温室气体排放。本研究选择高密度组(H)、低密度组(L)、对照组(CK)3种鼠兔干扰强度的高寒草甸为研究对象,揭示温室气体排放速率对不同高原鼠兔干扰强度的响应规律及主要调控因素。结果表明,H组高寒草甸土壤CO_(2)排放速率为596.66 mg·(m^(2)·h)^(-1),显著低于CK组的695.45 mg·(m^(2)·h)^(-1)(P<0.05)。高原鼠兔干扰强度、地上生物量、土壤pH和土壤含水量是影响CO_(2)排放速率的主要调控因素。H组高寒草甸CH_(4)吸收速率为-43.46mg·(m^(2)·h)^(-1),显著低于L组的4.92mg·(m^(2)·h)^(-1)(P<0.05),H和L组高寒草甸N_(2)O排放速率分别为8.03、-2.39μg·(m^(2)·h)^(-1),均显著高于CK组的-16.69μg·(m^(2)·h)^(-1)(P<0.05)。土壤硝态氮和铵态氮含量、pH和含水量是影响CH_(4)吸收和N_(2)O排放的重要因素。因此,高原鼠兔干扰强度是影响温室气体排放速率的因素之一,进一步研究高原鼠兔对高寒草甸土壤温室气体排放速率的影响具有重要意义。

Burrow morphology of Uca uruguayensis and Uca leptodactylus(Decapoda:Ocypodidae)from a subtropical mangrove forest in the western Atlantic

The continuous excavation of burrows by fiddler crabs generates bioturbation in the sediment,which can be estimated from burrow morphology.The aim of the present study was to describe the burrow morphology of Uca uruguayensis and U.leptodactylus and its relationship with demography of resident individuals and to estimate the level of bioturbation in the sediment generated by each species.For all individuals from each of the 2 species,sex was determined and the carapace width(CW;mm)measured.Burrows were characterized according to burrow diameter(BD;mm),maximum burrow depth(MBD;mm)and burrow volume(BV;cm^(3)).The density of each species in the study area was also evaluated.In both species,the males were larger and occupied burrows with higher BV compared to females.Differences between sexes in relation to the burrow characteristics might reflect sexual dimorphism within the group and are probably related to the fact that males use the burrows for mating.BD and BV showed significant positive relationships with the size of resident crabs.The amount of sediment removed per burrow was estimated from mean BV:10.78 cm^(3)of sediment/burrow for U.uruguayensis and 12.38 cm^(3)of sediment/burrow for U.leptodactylus.Despite the density and depth differences between the 2 species,the similarity in burrow volume suggests that U.uruguayensis and U.leptodactylus present the same importance in terms of the bioturbation process.Burrow morphology is highly associated with characteristics of the occupant,although extrinsic factors should also be considered,and its description can provide estimates on the bioturbation generated by Uca species in mangrove forests.

Motion Characteristics of the Appendages of Mole Crickets during Burrowing

Mole crickets,Gryllotalpa orientalis,have a pair of fully specialized forelegs for burrowing and employ an efficient underground excavating pattern,which provides excellent biological example for design of bionic underground excavation equipment.In this study,the excavating pattern and kinematic features of mole crickets were obtained by using high-speed motion capture system and employing a transparent hydrogel as the analogue for soil.The two-dimensional motion characteristics of the forelegs of mole crickets during burrowing were captured and analyzed.The results show that the forelegs of the mole cricket employ a unique excavating pattern,which consists of foreword digging and horizontal expansion.We label this pattern a digging-expanding mode.An excavating cycle includes the digging and expanding motion of the forelegs,rotation caused by the midlegs and hindlegs,and forward thrust by the hindlegs.The excavating motion of the left and right forelegs is alternately carried out.This study can inspire the design of bionic tunnelling mechanisms and underground excavation equipment.

Burrowing Richardson's ground squirrels affect plant seedling assemblages via environmental but not seed bank changes

In grassland ecosystems,burrowing mammals create disturbances,providing habitat for animal species and increasing plant community diversity.We investigated whether seedling assemblages on Richardson's ground squirrel Urocitellus richardsonii mounds result from seed rearrangement or environmental changes that favor germination of certain species over others.To test whether ground squirrels rearrange the seed bank by burrowing,we compared seed compositions among mounds,burrows,and undisturbed soil.To test whether ground squirrels change environmental conditions,we compared soil nitrate and bare ground cover on and off mounds.We also compared seedlings that germinated on mounds with seedlings that germinated on artificial disturbances from which we removed aboveground vegetation.Soil nitrate and bare ground cover were significantly higher on mounds than artificial disturbances.While seed richness and abundance did not differ among mounds,burrows,and undisturbed soil,seedling richness was reduced on mounds relative to artificial disturbances.Burrowing disturbance favors seedlings that can capitalize on bare ground availability but are less able to immobilize nitrate,as opposed to perennial species that immobilize more nitrate but take longer to establish.Our results suggest that Richardson's ground squirrels act as ecosystem engineers,although future research following succession on ground squirrel mounds is necessary to understand how they influence plant communities past the seedling stage.

The effects of two free-floating plants (Eichhornia crassipes and Pistia stratiotes) on the burrow morphology and water quality characteristics of pond loach (Misgurnus anguillicaudatus) habitat

Loach exhibit conspicuous drilling behaviors in the mud of shallow waters,yet their burrow morphology and the factors affecting this behavior have received little attention.We characterized the burrow morphology and water quality of the pond loach Misgurnus anguillicaudatus in three scenarios:in tanks without plants,tanks with the free-floating plant water hyacinth Eichhornia crassipes,and tanks with water lettuce Pistia stratiotes.Water hyacinth effectively removed water TN,COD,NO3-N and NH4-N,and water lettuce removed water TP and NH4-N.Water hyacinth and water lettuce markedly reduced water turbidity and DO,increased TOC and EC.Water hyacinth purified water more effectively than water lettuce,providing a suitable habitat for loach feeding,living and burrowing.The burrow structures were V-shaped,Y-shaped,inverted L-shaped,or complicated dendritic networks composed of multiple V shapes.The hyacinth treatment was characterized by the greatest burrow volume,length,depth,and structural complexity,but the opening size was reduced by dense root mat coverage.Burrows in the water lettuce treatment were characterized by intermediate volume,length,branches and sinuosity,but they had the largest opening and pit size.The control treatment had a flat bottom with the smallest,shortest burrows.This study indicates that free-floating plants improve habitat suitability and change burrow morphology and may be used to improve loach breeding methods。

舀种勺舌式胡麻精量穴播器设计与试验

针对胡麻播种机用种量大、播量变异系数大、播种不均匀的问题,基于胡麻种子物理特性和种植农艺要求,设计一种舀种勺舌式胡麻精量穴播器。通过分析穴播器工作原理确定穴播器组成、舀种勺结构参数范围及安装数量;对舀种勺舀种过程和清种过程进行力学分析,确定穴播器角速度范围;通过EDEM仿真过程得知,花纹内壁聚种斜槽在不影响舀种勺填充效果的同时,不仅可以提高仿真效率,还可以增大种子流动性,便于舀种勺充种。以穴播器角速度、舀种勺顶端过渡圆角半径、种室隔离板高度为试验因素,穴播器排种合格率、漏播率和重播率为试验指标,利用EDEM离散元仿真软件开展二次旋转正交组合试验,得到最优参数组合为:穴播器角速度2.9 rad/s、舀种勺顶端过渡圆角半径2.5 mm、种室隔离板高6.8 mm;将该舀种勺3D打印制作进行排种性能试验验证,台架试验得到该舀种勺排种合格率、漏播率和重播率平均值分别为87.00%、6.33%、6.67%;田间试验得到该舀种勺排种合格率为88.33%,漏播率为6.67%,重播率为5.00%;胡麻平均种植密度为50株/m^(2),其台架试验与田间试验结果基本一致,性能满足胡麻精量播种农艺要求。

不同底质和光周期对青蛤潜沙和摄食行为的影响

在(25±3)℃下,将2龄青蛤(Cyclina sinensis)放在30 cm×30 cm×30 cm的人工调控水温、光照和声音的养殖暗箱中,每箱放8个。开关箱盖上的LED光源模拟有光(12 h)和无光(12 h)条件,箱底铺10 cm厚全泥(含沙量0%组),沙泥比1∶3(25%沙组)、沙泥比1∶1(50%沙组)、沙泥比3∶1(75%沙组)和全沙(100%沙组),每天早晚各投喂小球藻1次,连续投喂3天,用摄像头拍摄记录青蛤在不同底质和光照时长下的潜沙行为和摄食活动,测定其消化酶和代谢酶的活性,研究光照对青蛤摄食和消化代谢的影响。结果发现青蛤的潜沙行为大致分为五个步骤:伸出水管,伸出斧足,竖壳,钻泥,潜沙;黑暗条件下潜沙时间较短。青蛤白天的摄食活动时长明显低于黑暗条件下,摄食活动时间主要集中在19:00—22:00;α-淀粉酶和丙酮酸激酶在自然光照组(12h黑暗∶12 h光照)中酶活达到最高,胃蛋白酶、己糖激酶和乳酸脱氢酶在24 h黑暗条件下酶活最高。实验结果表明,青蛤更喜在黑暗条件下的进行潜沙、摄食及体内消化代谢等活动。

底质对硬壳蛤(Mercenaria mercenaria)幼贝潜砂及相关酶活性的影响

为研究底质对硬壳蛤幼贝潜砂行为及相关酶活性的影响,设置5种底质,观察幼贝的潜砂过程,统计潜砂时间及潜砂率,测定呼吸代谢酶活性。结果表明:硬壳蛤幼贝潜砂率排序为泥组<粗砂泥组<细砂泥组<粗砂组<细砂组;10%硬壳蛤幼贝竖壳时间排序为粗砂组<细砂组<细砂泥组<泥组<粗砂泥组;10%硬壳蛤幼贝潜砂时间排序为粗砂组<细砂组<粗砂泥组<细砂泥组<泥组;Na^(+)-K^(+)-ATP酶活性排序为粗砂泥组<细砂组<粗砂组<泥组<细砂泥组;Ca^(2+)-Mg^(2+)-ATP酶活性排序为粗砂泥组<粗砂组<细砂组<细砂泥组<泥组;乳酸脱氢酶活性排序为细砂组<粗砂组<粗砂泥组<泥组<细砂泥组;琥珀酸脱氢酶活性排序为粗砂泥组<细砂泥组<泥组<细砂组<粗砂组。综合分析,细砂底质更适合于作为硬壳蛤幼贝养殖的底质。

Rodent burrow network dynamics under human-induced landscape transformation from desert to steppe in Kalmykian rangelands

Rodents play an important role in rangelands through the engineering of extensive burrow systems,which pro­vides key habitats for many animal and plant species.We have analyzed the long-term variation in the abun­dance and distribution of rodent burrows in grazing ecosystems of southern Russia(Kalmykia)under the land­scape change from desert to steppe caused by the drastic reduction of livestock after the collapse of the USSR in the early 1990s.We conducted burrow surveys in the“desert”(1980)and“steppe”(2017)periods on 193-km transects.We found considerable changes in burrow abundance and distribution,as well as evidence of desert habitat fragmentation and isolation caused by the expansion of tall-grass communities.Burrows of the open-dwelling diurnal ground squirrel(Spermophilus pygmaeus),the dominant and the keystone species during the“desert”period,almost completely disappeared from the rodent burrow network by 2017,indicating signifi­cant habitat loss.In contrast,the burrows of the folivorous social vole(Microtus socialis)which was rare in the 1980s,became abundant and ubiquitously distributed.The burrow density of the desert-dwelling psammophi­lous midday gerbil(Meriones meridianus)decreased,while the distances between occupied patches increased,indicating desert habitat fragmentation and loss of population connectivity.Burrows of the folivorous tamarisk gerbils(M.tamariscinus)were recorded only sporadically in both 1980 and 2017.The observed changes in the rodent burrow network,the key component of grazing ecosystems,correlate with rodent species ecology and can have long-term and important consequences for ecosystem functioning.

Clustering and presorting for parallel burrows wheeler-based compression

We describe practical improvements for parallel BWT-based lossless compressors frequently utilized in modern day big data applications.We propose a clustering-based data permutation approach for improving compression ratio for data with significant alphabet variation along with a faster string sorting approach based on the application of the O(n)complexity counting sort with permutation reindexing.