Estimating the capacity for improvement in risk prediction with a marker

Consider a set of baseline predictors X to predict a binaryoutcome D and let Y be a novel marker or predictor. This paperis concerned with evaluating the performance of the augmentedrisk model P(D = 1|Y,X) compared with the baseline model P(D= 1|X). The diagnostic likelihood ratio, DLR_X(y), quantifiesthe change in risk obtained with knowledge of Y = y for a subjectwith baseline risk factors X. The notion is commonly used inclinical medicine to quantify the increment in risk predictiondue to Y. It is contrasted here with the notion of covariate-adjustedeffect of Y in the augmented risk model. We also propose methodsfor making inference about DLR_X(y). Case–control studydesigns are accommodated. The methods provide a mechanism toinvestigate if the predictive information in Y varies with baselinecovariates. In addition, we show that when combined with a baselinerisk model and information about the population distributionof Y given X, covariate-specific predictiveness curves can beestimated. These curves are useful to an individual in decidingif ascertainment of Y is likely to be informative or not forhim. We illustrate with data from 2 studies: one is a studyof the performance of hearing screening tests for infants, andthe other concerns the value of serum creatinine in diagnosingrenal artery stenosis.     

Chromosomal Mapping of Genes in theRBCS Family in Arabidopsis thaliana

In Arabidopsis thaliana, four genes have been identified inthe RBCS gene family, one being assigned to subfamily RBCS-Aand the other three to subfamily RBCS-B (1B, 2B and 3B). Todetermine the chromosomal location ofthese genes, hybridizationanalysis with CIC YAC high-density filters was carried out forthe RBCS-A gene, and CAPS analysis for the three RBCS-B genes,based on the finding that restriction fragment length polymorphismis present in the upstream region of the gene RBCS-3B. The RBCS-Agene was mapped at 100.8 cM from the top of chromosome 1 andthe three RBCS-B genes at 62.70 cM from the top of chromosome5.     

Electrophoretic Variation in Esterases, Peroxidases and Acid Phosphatases in Some Native Greek Taxa of the Genera Hordeum and Taeniatherum

Horizontal starch gel electrophoresis has been applied to thestudy of esterase, peroxidase and acid phosphatase patternsin seven taxa, namely Hordeum diploids (2n=14) (H. marinum,H. marinum I and H. hystrix), tetraploids (2n=28) (H. bulbosumand H. murinum subsp. leporinum) and Taeniatherum (2n=14) (T.caput-medusae and T. caput-medusae I) in order to elucidatetheir phylogenetic relationships. On the basis of our experimentalresults the seven taxa may be placed in the following threegroups; (1) diploid Hordeum (H. marinum, H. marinum I, H. hystrix);(2) tetraploid Hordeum (H. bulbosum, H. murinum subsp. leporinum);(3) Taeniatherum (T. caput-medusae, T. caput-medusae I). Esterase, peroxidase and acid phosphatase patterns of the twoHordeum diploid taxa (H. marinum and H. marinum I) are verysimilar suggesting their close phylogenetic relationship; thesame is true for both the taxa of the genus Taeniatherum (T.caput-medusae and T. caput-medusae I). The taxa of the Taeniatherumgroup compared with the diploid Hordeum (H. marinum, H. marinumI, H. hystrix) and the tetraploid Hordeum (H. bulbosum, H. murinumsubsp. leporinum) show a lower degree of phylogenetic relationshipand seem to be equally distant from them. The tetraploid Hordeumgroup shows a higher phylogenetic relationship with diploidHordeum group than with the Taeniatherum group. These results confirm that the genus Taeniatherum, previouslyconsidered as part of the genus Hordeum, should be regardedas a separate genus. Gramineae (Poaceae), Hordeum L., Taeniatherum Nevski., esterase, peroxidase and acid phosphatase patterns, phylogenetic relationships     

我国尖音库蚊复合组蚊虫的杂交及其与Wolbachia感染的关系

为了了解我国尖音库蚊复合组蚊虫间杂交卵的不孵化现象和明确该现象与共生微生物Wolbachia感染的关系,对该复合组实验室种群4个亚种进行了笼内杂交和抗生素处理后的杂交。试验表明: 在复合组蚊虫中骚扰库蚊Culex pipiens molestus与淡色库蚊Cx. Pipiens pallens、致倦库蚊Cx. Ipiens quinquefasciatus与尖音库蚊Cx. Pipiens pipiens之间存在有单向胞质不融合现象,骚扰库蚊的雄虫与尖音库蚊、致倦库蚊和淡色库蚊的雌虫杂交卵的孵化率分别为0.06%、0.46%和0.19%;该胞质不融合现象可以通过抗生素处理而消除,处理后骚扰库蚊雄虫与其余3个亚种雌虫F₃杂交卵的孵化率均有提高,分别为89.49%（t=3.90×10^-28＜t_0.01=2.704）、23.39%（t=9.15×10^-7＜t_0.01=2.660_）和22.27%（t=5.08×10^-4＜t_0.01=2.750）,并可因抗生素处理而产生新的不融合类型。     

Predation impact of Cyclops vicinus on the rotifer community in Lake Constance in spring

The predation impact of Cyclops vicinus on rotifers was studiedunder near-natural conditions in small enclosures to evaluatewhether copepod predation is responsible for the decline ofrotifers in Lake Constance in spring. Cyclops vicinus fed selectivelyon Synchaeta spp.; Keratella and Polyarthra spp. were not selectedfor. Predation rates increased with prey density up to a maximumof 37 Synchueta day^–1 at a density of 1.6 x 10⁶ Synchaetam^–2, i.e. at -1200 Synchaeta l^–1. Calculation ofcropping rates suggests that Cyclops alone can control the abundanceof Synchaeta in spring, i.e. that mainly Cyclops is responsiblefor the decline of Synchaeta species in Lake Constance in May.     

Potential Dry Matter and Water Import Rates in the Tomato Fruit in Relationship to Fruit Size

The tomato fruit was compared to a sphere with a radius R. Radialgrowth rates in the fruit (F_IW and F_ID) due to water importor to dry matter import, respectively, which are also the waterimport rate or dry matter import rate per unit surface areaof fruit, were calculated from two sets of published results.This data referred to fruits which swelled in such a way thatthe availability of assimilates had little effect on growth.Two varieties differentiated the two series of results and inone series, three trials were differentiated by the salinityof the nutrient solution. In all trials, it was found that F_IW and F_ID decreased whenR increased. Two phases were observed for F_IW: after a firstphase, F_IW decreased more quickly and almost linearly when Rincreased. F_ID was constant or decreased with respect to R.Except at the beginning of growth at the greatest salinity,there were clearly linear regressions between F_IW and F_ID suchas F_ID = aF_IW-b; where b was lower with higher salinity. Thechanges of the concentration of imported dry matter (F_ID/F_IWwere examined in terms of R and F_IW/R. The mechanisms controllingthe changes in F_IW and F_ID were discussed. The results suggestedfruit radius was an important parameter of these mechanisms.Thus, water import rate and dry matter import rate could eachbe considered to be the product of two factors: fruit surfacearea, which is directly dependent on fruit radius, and waterimport rate or dry matter import rate per unit of fruit surfacearea.Copyright 1993, 1999 Academic Press Dry matter, fruit growth, logistic model, sink size, tomato, water transfer     

Variation in Photosynthesis and Enzyme Activity in Cenchrus ciliaris L.

Populations of Cenchrus ciliaris differ significantly in relativegrowth-rate (R), net assimilation rate (E), and leaf-area ratio(F). Differences in R were related to differences in E ratherthan in F. The populations also differed in the rate of apparentphotosynthesis of individual leaves as measured by infra-redgas analysis. Warburg and ^l4CO₂ techniques. Temperature andlight-response measurements revealed optimum temperature forphotosynthesis of 35 °C and the rate in most populationscontinued to increase up to the highest levels of irradianceemployed (200 W m²). The relative order of the populations wassimilar in all methods of analysis, but there was no relationshipevident between leaf photosynthesis and E derived from growthanalysis. The activity of the enzyme PEP carboxylase, expressedin terms of unit leaf area, was correlated with photosyntheticrate of the leaf. Activities of PEP carboxylase and of proteinsynthesis in vitro expressed on a basis of soluble protein contentwere correlated with E, but no such relationship was found forthe enzymes acid phosphatase and alanine--ketoglutarate aminotransferase.     

Wide-Range Distribution of Insertion Sequences Identified in B. halodurans among Bacilli and a New Transposon Disseminated in Alkaliphilic and Thermophilic Bacilli

All of the insertion sequences (ISs) except for IS663 and agroup II intron identified in the alkaliphilic Bacillus haloduransC-125 genome were also detected in nine other strains of thesame species by PCR and Southern blot analysis. The transposaseof IS653 identified in the genomes of the 10 strains of B. haloduranswas found to have become the most diversified of all ISs identifiedin the genomes of 10 strains. A new IS element designated IS661belonging to the IS1380 family with inverted repeats (IRs) 17bp in length was present within IS658 identified in the genomeof B. halodurans A59. In addition, a new transposon designatedTn3271bh was identified within the IS642 element in the A59genome, which is similar to a transposon identified in thermophilicGeobacillus stearothermophilus T-6. The new transposon, Tn3271bh,generated an 8-bp duplication of the target site sequence andcarries a 21-bp IR. On the other hand, all kinds of ISs exceptfor IS643 and IS658 were distributed in the genome of obligatelyalkaliphilic Bacillus alcalophilus. Three ISs (IS652, IS653,and IS660) and a group II intron (Bh.Int) were widely dispersedin other Bacillus species without a correlation with the phylogeneticplacement based on 16S rDNA sequences.     

Interannual variability in a predator-prey interaction: climate, chaetognaths and copepods in the southeastern Bering Sea

The interaction of the chaetognath Sagitta elegans with thecopepod community of the southeast Bering Sea middle shelf wasexamined in relation to environmental conditions during 1995–1999.Predation impact was estimated for 2 years, 1995 and 1997, usinggut content analysis, experimentally derived digestion time(DT) and abundances of chaetognaths and prey. Pseudocalanusconcentrations correlated with water temperature and Calanusmarshallae with sea ice extent. Sagitta elegans were less abundantbut individuals were larger in 1995, when C. marshallae predominated,compared to 1997, when Pseudocalanus and Acartia were the primaryprey. Predation by S. elegans removed <1% standing stockday^–1 of Pseudocalanus or C. marshallae in 1995 and 1.7to 2.3% of Pseudocalanus in 1997. The percent of the copepodcommunity biomass required by chaetognaths was estimated tobe <1% in 1995 compared with 8–12% in 1997. Calanusmarshallae may be more vulnerable than Pseudocalanus to cumulativepredation effects because of its reproductive strategy. Theeffect of chaetognath predation on the copepod community dependson which copepod species is predominant and its susceptibilityto cumulative predation effects, as well as on daily predationimpact, both of which varied between years with different climaticconditions.     

Effect of Water Stress on Pigment Formation in Quercus Species

The effect of water stress in three Quercus species belongingto different habitats is investigated. Chlorophyll concentrationdecreased in all Quercus species with the greatest decreaseoccurring in Quercus robur. An increase of total carotenoidcontent was observed in Quercus coccifera and Quercus ilex,while in Q. robur water stress effected a carotenoid contentreduction. Anthocyanins increased with decreasing relative watercontent in the three Quercus species, the largest increase occurringin Q. coccifera. A correlation between xerophytic characterand pigment concentration is discussed.     

家蚕保存系统红色卵的遗传分析

用遗传背景清楚的家蚕Bombyx mori红卵（re）、白卵(w-2、pe)、第4褐卵（b-4）的标志基因系统和正常型黑卵系统与我国家蚕基因库保存的20个红色卵系统杂交,进行顺反测验,分析了它们的卵色支配基因及遗传规律。结果发现：①在03-310系统中存在家蚕卵色新突变pink egg,与红卵re 等位,基因符号为re^p,表型特征为：卵淡红色,成虫蛾眼也为淡红色;②6个系统为红卵（re）的纯合系统,还有５个系统除具有re／re基因型外,还具有支配白色卵或浅红色或橙红色卵的突变基因;③２个系统为第4褐卵（b4）的纯合系统; ④6个系统的红褐色卵为母性影响遗传;⑤发现家蚕卵色基因b-4和r-e的互补关系,b-4/b-4 re/re基因型表现为新的卵色——橙黄色。     

Evidence of Three Subspecies in Trifolium nigrescens Viv.

Germplasm accessions of Trifolium nigrescens Viv. were foundto belong to three distinct taxa which differed in morphology,hybrid seed-set in crosses among themselves and with white clover(T. repens L.), chromosomal distribution of rDNA genes, andrDNA internally transcribed spacer (ITS) region sequences. Thesetaxonomic groups correspond with T. nigrescens ssp. nigrescens,T. nigrescens ssp. petrisavii var.petrisavii and var. meneghinianum.The existence of var. meneghinianum has been rejected or ignoredin recent taxonomic treatments. The present study indicatesthat it is very distinctive and warrants at least subspeciesstatus. Phylogenetic analysis based on ITS sequences and podmorphology placed ssp. nigrescens as progenitor to the others.ITS sequences placed white clover closer to ssp. petrisaviibut neither DNA sequences nor rDNA chromosome locations clearlyshowed whether var. petrisavii or var. meneghinianum was closerto white clover. In contrast, results of hybridization studiesshowed that ssp. nigrescens gave full seed-set when pollinatedwith T. repens whereas both ssp. petrisavii var. petrisaviiand ssp. petrisavii var. meneghinianum gave poor seed-set. Allthree taxa showed close relationships with white clover andnone can clearly be shown to be a direct ancestor of T. repens.Copyright 2001 Annals of Botany Company Fabaceae, Trifolium nigrescens, Trifolium repens, internal transcribed spacer region (ITS), nuclear ribosomal DNA, interspecific hybridization     

Coupling of nauplii release in barnacles with phytoplankton blooms: a parallel strategy to that of spawning in urchins and mussels

We examined the coupling between the release of nauplii in Semibalanusbalanoides and phytoplankton blooms, and compared it with themechanism synchronizing spawning with phytoplankton abundancein green sea urchins (Strongylocentrotus droebachiensis) andblue mussels (Mytilus edulis). Close contact with phytoplanktoncells is required to stimulate the release of nauplii in Semibalanus,whereas spawning in urchins and mussels is triggered by an extracellularmetabolite of phytoplankton. The response is concentration dependentand positively correlated with the frequency of moulting Themoulting rate in Semibalanus is reported to be directly correlatedwith food intake and thus larval release should be proportionalto feeding activity. The release of Semibalanus nauplii is morestrongly stimulated by the diatom Skeletonema costatum thanby Phaeodactylum tricornutum, whereas the highest response isobtained in treatments with nauplii of Artemia salina. We suggestthat these differences are related to size of the planktonicparticles (Artemia nauplii < Skeletonema < Phaeodactylum)Exposure to air, as occurs in the intertidal zone, does notinfluence significantly larval release Larval release in otherCrustacea may similarly be coupled to phytoplankton abundance.     

Heat Shock Induced Change in Protein Ubiquitination in Chlamydomonas

Ubiquitin was purified from pea (Pisum sativum L.) and its antibodywas produced. Western blot analysis showed that the antibodycross-reacted with ubiquitins from a green alga Chlamydomonasreinhardtii, a brown alga Laminaria angustata and a red algaPorphyridium cruentum but not with ubiquitin from a blue-greenalga Synechococcus sp. In Chlamydomonas, the antibody also reactedwith some ubiquitinated proteins including 28- and 31-kDa polypeptides.The isoelectric points of Chlamydomonas ubiquitin and the 28-and 31-kDa ubiquitinated proteins were 8.0, 8.9 and 10.3, respectively.The ubiquitinated proteins, including the 28- and 31-kDa polypeptideswere detected after in vitro ATP-dependent ubiquitination ofChlamydomonas cell extract with ^l25I-labeled bovine ubiquitin.Heat treatment of Chlamydomonas cells (>40°C) causeddrastic increase of ubiquitinated proteins with high mol wt(>60kDa), and coordinated redistribution or decrease of otherubiquitinated proteins and free ubiquitin. Quantitative analysisrevealed that the 28- and 31-kDa ubiquitinated proteins showeddifferent responses against heat stress, i.e. the former beingmore sensitive than the latter. (Received July 10, 1988; Accepted October 4, 1988)     

Further Studies in Magnetotropism

Studies have been mode of the growth curvatures induced in theroots of Lepidium sativum, the coleoptiles of Avena saliva andthe sporangiophores of Phycomyces blakesleeanus by exposureto an intense magnetic gradient during continuous rotation ona slow klinostat (0.5 rpm). Attempts have been made to determinethe relationships of the curvature responses to the parametersof the magnetic field (H, dH/dx, and H. dH/dx). Analysis ofthe data was by a progressive regression analysis up to thethird order coupled with an analysis of variance to test theimprovement of fit at each stage. Response is characterizedby an initial lag (reaction time, T) followed by a constantrate of curvature down the magnetic gradient for the first 20or 30? of curvature. The reciprocal of T was the most satisfactorymeasure of response (i. e. a measure of the rate of inductionof the response while the organ was in a constant magnetic environment)and in Avena and Phycomyces was best fitted by linear regressionson log_edH/dx and on log_eH. dH/dx. For Lepidium, with much morevariable data, the best fit was with a linear regression onlog_eH. The significance of these results is discussed.     

Relationships Between Climate and Flowering of Eight Herbs in a Swedish Deciduous Forest

Effects of annual variation in rainfall, temperature and humidityon flowering abundance of eight temperate woodland plants (Anemonenemorosa, Cardamine bulbifera, Lamiastrum galeobdolon,Oxalisacetosella , Ranunculus ficaria, Stellaria holostea, Viola reichenbachianaand Viola riviniana) were studied during 12 consecutive years(1989–2000) in a hornbeam (Carpinus betulus) forest insoutheast Sweden. Above-average rainfall/humidity in late summerto early autumn of the preceding year increased flowering abundancein L. galeobdolon, O. acetosella, V. reichenbachiana, V. rivinianaand, especially, in R. ficaria, but not in S. holostea and A.nemorosa. Moreover, flowering of R. ficaria and O. acetosellawas positively related to rainfall/humidity during several partsof, or the entire, preceding year. On the contrary, floweringof S. holostea and A. nemorosa was closely related to low valuesof rainfall/humidity in autumn and/or winter of the precedingyear and also to low humidity in the current year in A. nemorosa.Two long periods (3–4 years) of increasing rainfall deficitcoincided with decreasing flowering abundance in most of thespecies, but not with decreasing vegetative development. Temperaturevariability was less consistently related to flowering. A coolperiod during the preceding summer or autumn seemed importantfor flowering in L. galeobdolon, O. acetosella and the Violaspecies, although these relations were, at least partly, causedby interactions with rainfall/humidity. No significant (P <0.05) correlations were found between flowering and the conditionsprevailing in April to May—the main flowering season—ofthe current year. Copyright 2001 Annals of Botany Company Climate, flowering, rainfall, temperature, Anemone nemorosa, Cardamine bulbifera, Lamiastrum galeobdolon, Oxalis acetosella, Ranunculus ficaria, Stellaria holostea, Viola reichenbachiana, Viola riviniana