Estimating equations for spatially correlated data in multi-dimensional space

We use the quasilikelihood concept to propose an estimatingequation for spatial data with correlation across the studyregion in a multi-dimensional space. With appropriate mixingconditions, we develop a central limit theorem for a randomfield under various L_p metrics. The consistency and asymptoticnormality of quasilikelihood estimators can then be derived.We also conduct simulations to evaluate the performance of theproposed estimating equation, and a dataset from East LansingWoods is used to illustrate the method.     

Semiparametric regression estimation in the presence of dependent censoring

We propose a semiparametric estimation procedure for estimatingthe regression of an outcome Y, measured at the end of a fixedfollow-up period, on baseline explanatory variables X, measuredprior to start of follow-up, in the presence of dependent censoringgiven X. The proposed estimators are consistent when the dataare ‘missing at random’ but not ‘missing completelyat random’ (Rubin, 1976), and do not require full specificationof the complete data likelihood. Specifically, we assume thatthe probability of censoring at time t is independent of theoutcome Y conditional on the recorded history up to t of a vectorof time-dependent covariates that are correlated with Y. Ourestimators can be used to adjust for dependent censoring andnonrandom noncompliance in randomised trials studying the effectof a treatment on the mean of a response variable of interest.Even with independent censoring, our methods allow the investigatorto increase efficiency by exploiting the correlation of theoutcome with a vector of time-dependent covariates.     

Combining multiple positive training sets to generate confidence scores for protein-protein interactions

Motivation: High-throughput experimental and computational methodsare generating a wealth of protein–protein interactiondata for a variety of organisms. However, data produced by currentstate-of-the-art methods include many false positives, whichcan hinder the analyses needed to derive biological insights.One way to address this problem is to assign confidence scoresthat reflect the reliability and biological significance ofeach interaction. Most previously described scoring methodsuse a set of likely true positives to train a model to scoreall interactions in a dataset. A single positive training set,however, may be biased and not representative of true interactionspace. Results: We demonstrate a method to score protein interactionsby utilizing multiple independent sets of training positivesto reduce the potential bias inherent in using a single trainingset. We used a set of benchmark yeast protein interactions toshow that our approach outperforms other scoring methods. Ourapproach can also score interactions across data types, whichmakes it more widely applicable than many previously proposedmethods. We applied the method to protein interaction data fromboth Drosophila melanogaster and Homo sapiens. Independent evaluationsshow that the resulting confidence scores accurately reflectthe biological significance of the interactions. Contact: rfinley{at}wayne.edu Supplementary information: Supplementary data are availableat Bioinformatics Online. Associate Editor: Burkhard Rost     

持续治理飞蝗灾害的新对策

该文通过对飞蝗Locusta migratoria为害特性的描述以及本世纪我国飞蝗防治历史的回顾,对各个时期的飞蝗治理策略的特点及不足进行了分析,并在总结我国近几年飞蝗生物治理理论研究与实践的基础上,提出了21世纪我国飞蝗生物治理的对策,即逐步扩大采用生物防治措施,增强如蝗虫微孢子虫生物防治制剂及天敌的控制作用,在飞蝗虫口密度中等或较低时,采用生物防治制剂为主,阻止或延缓中、低密度的飞蝗向高密度群居型的发展进程;在飞蝗虫口密度高时,可采用化防(昆虫生长调节剂等)与生防(如微孢子虫)配合使用,以迅速压低虫口密度,防治其迁飞为害,同时也可使蝗虫微孢子虫疾病长期流行于蝗群中,抑制飞蝗种群数量的增长。并积极探讨信息化合物对飞蝗行为的调控作用。     

A New Model Relating Crop Yield and Plant Arrangement

A new model is proposed which relates the weight of plants totheir spatial arrangement. The weight of each plant is calculatedas the integral of the function f(r) = L(cr² + 1)^–2 overan area allocated to it, r being distance from the plant, withL and c parameters to be specified. The model is thus concise,general, in that it can be used to describe the effects of anyspatial arrangement on plant weight, and the parameters L andc have a biological interpretation. It is also consistent withthe commonly-used relationship between plant weight (w) anddensity (p), w^–1 = a+bp. We show for carrots (Daucus carota L.) and red beet (Beta vulgarisL.), that the mean weights fitted by the model agree as wellwith the experimentally observed mean plot weight as those fittedby more complex models with more parameters, some of which arenot as general. We show also that the parameter c can be predictedfrom the time from sowing to harvest, with good results whentested on sets of data independent of those to which the modelhad been fitted. The assumptions on which the model is based,its application, and extensions to it are discussed. Crop yield, plant density, plant arrangement, carrot, Daucus carota L., red beet, Beta vulgaris L., soya bean, Glycine max L., mathematical model     

Zooplankton in the Ligurian Sea: Part II. Exploration of their physical and biological forcing functions during summer 2000

A survey of the biological and physical oceanography of theLigurian Sea was conducted in the late summer of 2000. Forty-onestations were sampled for nutrients, oxygen, fluorescence andhydrographic information. Acoustic backscatter measurementswere used to estimate abundance of small (<5 mm) zooplanktonbiovolume versus depth and the distribution of northern krill,Meganyctiphanes norvegica. Net-tow and underwater video datawere collected to identify the zooplankton present. These datawere used to analyze the Ligurian Sea ecosystem for physicaland biological linkages that control zooplankton abundance anddistribution. Results are compared with those from a similarstudy conducted in 1999. Hydrographic sampling showed a domeof dense water in the southwestern middle of the basin. Thehighest chlorophyll a (Chl a) concentrations were measured inthis area, while small zooplankton biovolume was evenly distributedthroughout the survey. Integrated values of Chl a and smallzooplankton biovolume in 2000 were greater than in 1999. Meganyctiphanesnorvegica, siphonophores and salps were the dominant componentsof the macrozooplankton population in the upper 200 m. In thesampled depth strata, siphonophore abundance did not changeduring the day, while M. norvegica were only caught at night.Acoustic backscatter data show that higher densities of M. norvegicaoccurred in deeper water and in the western and southwesternareas of the Ligurian Sea.     

Interactions Between Physical and Biological Constraints in the Structure of the Inflorescences of the Araceae

A study of the inflorescences ofMonsteraandAnthuriumwas usedto establish a relationship between biological and physicalconstraints for the structure of plant organs. The physicalconstraint between flowers in the compact inflorescences ofAnthuriumandMonsteraisexpressed by Aboav-Weaire's law. The application of this lawto inflorescences indicates a linear relationship between thenumber of sides of a flower and the number of sides of neighbouringflowers. However, the slope of this straight line is significantlyhigher forAnthuriumandMonsterathan that expected in theory.This deviation from the law is attributable to a biologicalcause that can be estimated using Aboav-Weaire's law. Actingalone, the biological constraint tends to produce four-sidedflowers. The equilibrium between biological and physical constraintsreduces the number of sides per flower from six (theoreticalvalue) to 5.9 (inAnthurium) or 5.8 (inMonstera) with a varianceof the measures less than that expected in theory. Furthermore,when flower density in an inflorescence increases (towards themiddle of the inflorescence inMonsteraand towards the lowersection forAnthurium) the number of sides approaches six (i.e.the physical constraint dominates). When flower density decreases(towards the top of the inflorescence) the number of sides approaches5.5 (i.e. the biological constraint dominates). The geometryof the inflorescences ofAnthuriumandMonsterais the result ofthe joint action of biological and physical constraints.Copyright1998 Annals of Botany Company Monstera,Anthurium, Araceae, Aboav-Weaire, inflorescence, constraint, flower.     

The Photosynthesis and Cell Shape Rhythms can be Naturally Uncoupled from the Biological Clock in Euglena gracilis

A naturally occurring population of Euglena (Klebs Strain Z)cells, with unusual biological clock properties, has been isolated.The photosynthesis reactions, which are usually controlled bythe biological clock, are uncoupled from the clock in the newpopulation. The rate of oxygen evolution is influenced predominantlyby the environmental growth parameters instead of the biologicalclock. In addition, the rhythm in cellular shape has a differenttiming from the control population and can be temporarily uncoupledfrom the clock by lowering the light intensity used for growth Key words: Biological clock, photosynthesis, Euglena     

Analysis of Organ Specificity of a Low Temperature Responsive Gene Family in Rye (Secale cereale L.)

The barley (Hordeum vulgare L.) low temperature responsive geneblt14 was used as a probe, to isolate two different cognateclones (rlt1412; rlt1421) from a rye (Secale cereale L.) cDNAlibrary prepared from low temperature-treated (6°C day/2°C night) shoot meristems of the cultivar, Puma. Northernblot analysis revealed that low temperature expression of rlt1412is highest in root tissues whereas, rlt1421 shows greatest mRNAaccumulation in mature leaf tissues. There is a relationshipbetween the steady-state levels of these mRNA species and thefrost hardiness of Puma (North American cultivar) and Rhayader(UK cultivar) such that the expression ofboth genes is higherin the more frost hardy cultivar, Puma, compared with Rhayader. DNA and predicted amino acid sequence analysis indicated thatthe rye and barley clones encode small proteins with consensusN-terminal signal sequences whose biological function is atpresent unknown. The relevant sequences are lodged in the EMBL data base. Key words: Rye, cold, cDNA, organ specificity, low temperature genes     

Selection and control of Deborah numbers in plankton ecology

The Deborah number (De) is widely used to characterize processestaking place in deforming continua. De=(the time scale of aprocess)/(the time scale of deformation). When De >>lthe process thus takes place in a functionally fluid medium,but when De <<1 the regime is functionally solid. De hasbeen used to refine concepts in three pelagic processes. Dispersionof dividing cells may be characterized by De, and may be regulatedby means of secretions. Dispersion of microzones by diffusionand shear is characterized. The characteristic time of microzonesis shown to depend on the concentration. Because microzonessmear Out along the shear, to prevent nutrient-seekers and predatorsusing them as scent trails, organisms may convolute their microzonesby swimming, particularly across the shear. In a predator-preymodel, it has been shown that when De, (shear rate) (time takento swim radius of detection sphere), >2.6, not all the perceivedprey is accessible. More economical hunting strategies and thoseallowing access to more of the perceived prey, require bettersensory and navigational abilities. When De >2.6, the predatorwill perceive a greater flux of accessible prey when it swimsacross the shear than when it swims in the other two dimensions.De may help to understand many more biological processes indeforming media.