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.

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 rnicrohabitats 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.

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.

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 Kondelio condel, Aegiceros corniculatum and Avicennio morina communities. In general, the amount of leaf litter and debris on mangrove mudfiats 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 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.

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.

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.

Alpine grassland degradation intensifies the burrowing behavior of small mammals:evidence for a negative feedback loop

Globally,grassland degradation is an acute ecological problem.In alpine grassland on the Tibetan Plateau,increased densities of various small mammals in degraded grassland are assumed to intensify the degradation process and these mammals are subject to lethal control.However,whether the negative impact of small mammals is solely a result of population size or also a result of activity and behavior has not been tested.In this study,we use plateau pika as a model to compare population size,core area of colony,and the number of burrow entrances and latrines between lightly and severely degraded grassland.We test whether the alleged contribution of pika to grassland degradation is a result of increased population size or increased burrowing activities of individuals in response to lower food abundance.We found that grassland degradation resulted in lower plant species richness,plant height,and biomass.Furthermore,the overall population size of pika was not significantly affected by location in lightly and severely degraded grassland.However,pika core areas in severely grassland degradation were significantly larger and had significantly higher densities of burrows and latrines.Our study provides convincing evidence that habitat-induced changes in the behavior of small,burrowing mammals,such as pika,can exacerbate grassland degradation.This finding has significant implications for managing small mammals and restoring degraded grassland ecosystems.

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.

Calcite Cements in Burrows and Their Influence on Reservoir Property of the Donghe Sandstone, Tarim Basin, China

Abundant burrows of Skolithos linearis, Palaeophycus tubularis, and Taenidium barretti are preserved in the Upper Devonian Donghe sandstone of Tarim basin, China. They are commonly highlighted in core by the color of the burrow fill in contrast to the surrounding matrix and have dif-ferent textures and fabrics from the matrix. There are three kinds of calcite cements in burrows, microcrystalline-crystalline calcite cement, mosaic calcite cement, and ferroan calcite cement. Microcrystalline-crystalline calcite cement is widely distributed in the lower part of the Donghe sand-stone, but it is rare in burrows filling. It displays a globule structure under burial cementation and sel-dom replaces the quartz grains in shallow burial depth stage. Mosaiccalcite cement is widespread in the Donghe sansdtone reservoir of North Tarim basin. It shows chrysoidine, orange and bright orange lu-minescence, and intensely replaces the quartz grains, forming in early diagenetic and shallow burial depth stage. Ferroan calcite is asymmetrically distributed in the Donghe sandstone reservoir of Central Tarim basin. It fills the remanent pores in the shape of mosaic and replaces the quartz grains, matrix, and early calcite cement, forming in late diagenetic and deep burial depth stage. The burrows filled with white calcite cements have low oil saturation or may be oil-stained. In contrast, there is high oil saturation in the sandstone reservoir where the bioturbation is sparse or not present. With increased bioturbation, the porosity, permeability, and oil saturation decrease; thus, bioturbation intensity and reservoir property appear to be negatively correlated.

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.

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。

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.

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.

Determination of the burrow shapes of Cardisoma guanhumi on Vieques,Puerto Rico

Objective:To determine the burrow morphology of Cardisoma guanhumi and to determine if a battery-powered fiber optic camera could be used to investigate these burrows.Methods:A portable fiber optic camera was used to investigate 116 active burrows.All burrows were categorized according to shape.The diameter of each burrow was also recorded and biomass calculations were completed at each study site.Results:Analysis showed that different study sites were more likely to have particular burrow shapes than expected.Three main types of burrows were classified as horizontal slide,short and shallow,and inverted-S.A Pearson Chi-square analysis revealed that burrow shape was not equally distributed across study sites(χ^(2)=61.05,df=18,P<0.0001).Biomass calculations showed that different sized animals inhabited different study sites(ANOVA;df=7,MS=158.3,F=13.9,P<0.0001).The fiber optic camera was useful in determining burrow morphology and occupancy non-destructively.Conclusions:As the locations of juvenile individuals of this species are poorly known,and the species is both ecologically and economically important where it occurs,a greater understanding of burrow morphology and size segregation may help agencies be responsible for managing this natural resource to do so effectively.

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.

Stephen Burrows：China is now the largest beer market in the world

Stephen Burrows, the Chief Executive Officer and President of Anheuser-Busch International Inc, joined Anheuser-Busch (A-B), producer of Budweiser beer, 26 years ago, starting as an entry-level salesman for the brewery. Anheuser-Busch International, the international beer subsidiary of Anheuser-Busch Companies, is responsible for A-B's foreign beer operations and equity investments.