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.     

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     

Water Import Rate in Tomato Fruit: A Resistance Model

A model of the water import rate in tomato fruit is proposed.It compares the fruit to a hollow sphere (P) with external radiusR and internal radius R_G, corresponding to pericarp, and containingan internal spherical part (G). The pathway limiting water inputrate at any point I at a distance r from the fruit centre wasassumed to be proportional: (a) in P, to the length of the arcwhich has a radius r and which goes from I to the pedicel extension;(b) in G, to r. The water input rate at I was modelled basedon a law similar to Darcy's law which takes into account thedifference between the water potential at entry of fruit andthe water potential at point I. This latter potential was thesum of fruit osmotic potential and pressure potential due toresistance of tissue to deformation. This potential was proportionalto R-r or R_G -r. The model was expressed at fruit level by alaw such that water mass imported per unit time per unit surfacearea of fruit (f_rw) was a linear function of R. The model wascompared to linear regressions of this rate in terms of R whichhad been found during fruit swelling from published results,and which were obtained at different values of nutrient solutionsalinity. The results suggested that water input in tomato fruitis conditioned by passive forces depending on fruit size.Copyright1994, 1999 Academic Press Fruit, growth, model, resistance, salinity, size, tomato, transfer, water     

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.     

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     

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。     

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.     

Violent Spore Release in Some Fungi Imperfecti

Violent spore discharge in the Hyphomycetes Alternaria tenuis,Memnoniella supsimplex, Curvularia lunata, C. geniculata, Corynesporacassiicola, and Zygophiala jamaicensis occurs after transferfrom a humid to a dry atmosphere. Mechanisms of discharge aresuggested.     

The FLOWERING LOCUS T/TERMINAL FLOWER 1 family in Lombardy poplar

Genes in the FLOWERING LOCUS T (FT) and TERMINAL FLOWER 1 (TFL1)family have been shown to be important in the control of theswitch between vegetative and reproductive growth in severalplant species. We isolated nine members of the FT/TFL1 familyfrom Lombardy poplar (Populus nigra var. italica Koehne). Sequenceanalysis of the members of the FT/TFL1 family revealed considerablehomology within their coding regions both among family membersand to the members of the same family in Arabidopsis, tomatoand grapevine. Moreover, members of this family in all fourspecies examined display a common exon–intron organization.Phylogenetic analysis revealed that the genes fall into fourdifferent clades: two into the TFL1 clade; five into the FTclade; and one each into the MOTHER OF FT AND TFL1 and BROTHEROF FT AND TFL1 clades. One gene in the TFL1 clade, PnTFL1, isexpressed in vegetative meristems, and transgenic Arabidopsisthat ectopically expressed PnTFL1 had a late-flowering phenotype.The expression patterns of two genes in the FT clade, PnFT1and PnFT2, suggested a role for them in the promotion of flowering,and transgenic Arabidopsis that ectopically expressed eitherPnFT1 or PnFT2 had an early-flowering phenotype.     

Internode Length in Pisum: Variation in Response to a Daylength Extension with Incandescent Light

Lines representing a range of internode length and floweringgenotypes in Pisum sativum L. were grown in 8 h of daylightfollowed by either 16 h of darkness or incandescent light. Thestem elongation response index (RI = length in 24 h ÷length in 8 h) was least in the very short internode nana types,which are grossly deficient in gibberellins (GAs), and the verylong internode slender types, which behave as if saturated withGAs. The common tall (genotype Le) and dwarf (le) types (lepartially blocks conversion of GA₂₀ to the active form, GA₁)were all markedly responsive but the peak RI (based on the mostresponsive internode) was less in tall lines (1.79 to 2.78)than in dwarf lines (2.32 to 5.01) and the peak RI tended tooccur about three to four internodes earlier in tall than indwarf lines. The cry⁸ mutation reduced the RI. (Duplicate lengthloci La and Cry are probably concerned with GA reception.) Amongle dwarf lines, genotype La cry⁸, was generally less responsivethan La Cry, La cry^c and la Cry. Data from crosses showed thaton either an le La or le la background cry⁸ segregates had alower RI than cry⁸ segregates. On an le la background, cry⁸plants were shorter than cry^c plants, cry⁸ was partially dominantto cry⁸ and segregation was clear only in long days. On an lela background, cry^c plants were shorter than cry^c plants, cry⁸was partially dominant to cry⁸ and segregation was clear inlong or short days. The very high peak RI (5.0) of the microcryptodwarfline, L57, appeared to result, in part, from a marked foreshorteningof internodes 4 to 10 in the 8 h regime. In the 24 h regimeL57 (lm) had a fairly similar growth pattern to normal (Lm)cryptodwarf types. The peak RI tended to occur at a lower internode in early thanlate flowering lines, especially among dwarf types, and genotypeswith a day neutral flowering habit (genotype sn or dne) wereless responsive than their photoperiodic counterparts (Sn Dne). White fluorescent light, given as a daylength extension, wasmuch less effective than incandescent light at stimulating stemelongation suggesting control through the phytochrome equilibrium(P_tr/P_total). Pisum sativum, garden pea, daylength extension, flowering, genotype, gibberellin, hormone receptor, incandescent light, internode length, phytochrome, stem elongation     

Biomechanical and Morphometric Differences in Triticum aestivum Seedlings Differing in Rht Gene-Dosage

Biomechanical and morphometric comparisons among coleoptilesfrom wheat seedlings differing in Rht gene-dosage (Rht = 0,2, 4 doses) are presented in an effort to evaluate the influenceof Rht on the mechanics of soil penetration by this organ. Rhtis known to reduce seedling establishment compared to the wildtype. Data from 3–7-day-old seedlings indicate that Rhtreduces tissue elastic modulus E, increases the second momentof area I, and decreases the slenderness ratio (l/r) of coleoptiles.Rht-relatedchanges in E and I are such that the flexural stiffness of coleoptilesfrom Rht plants does not differ significantly from the wildtype-hence the growing coleoptiles of all three genotypes haveequivalent biomechanical capacity to penetrate the soil. Rhtreduction of coleoptile slenderness ratios confers a capacityto safely sustain higher axial compressive loads compared tocoleoptiles with equivalent flexural stiffness but higher ratios.However, wild type seedlings produce longer coleoptiles andlonger subcrown internodes than Rht seedlings. Longer coleoptilesdeliver the crown node closer to the top of the soil beforethe crown node extends beyond the lateral confinement of thecoleoptile. This reduces the potential for buckling of the subcrowninternode and leaves due to the compressive loading of soil.Rht affects a variety of mechanical features whose influenceis dependent upon the stage of seedling growth and the degreeof soil compaction. However, at equivalent depths of burialwhich exceed the maximum length of coleoptiles and moderatesoil compaction, Rht is biomechanically disadvantageous to seedlingestablishment. Wheat, germination, biomechanics, Rht-gene     

Dry-matter Production and Photosynthesis in Pine Seedlings

Growth analysis and photosynthesis measurements were carriedout on first-year seedlings of Pinus radiata, P. contorta, andP. nigra. P. sylvestris was also included in two growth-analysisexperiments. There appeared to be no difference in relativegrowth-rate (RGR) between the species mentioned, except betweenP. radiata and P. nigra. It was found that when the level ofmineral nutrition was high, P. radiata had a higher RGR thanP. nigra and that the reverse was true at low mineral nutrientlevels. There was no difference in net assimilation rate (NAR)between the species, but NAR appeared to increase and decreasewith mineral nutrient supply. Net photosynthesis per unit of leaf was somewhat higher in P.radiata than in P. contorta; P. nigra had a lower photosyntheticrate than either P. radiata or P. contorta.     

Diet selection by copepods in the presence of cyanobacteria

Boeckella, the dominant calanoid in many Southern Hemispherelakes, can survive, grow and reproduce to varying extents onmonocultures of cyanobacteria. In this study, we determinedthe effects of algal and cyanobacterial foods of different nutritionalvalue and concentration on food preferences of adult femaleBoeckella trianiculata and Boeckella hamata. Four species ofcyanobacteria (Anabaena flos-aquae, Nostoc sp. 2, OscillatoriatenuisandMicrocystis aeruginosa) were offered alone and mixedwith equal biomasses of Cryptomonas sp., Choricystis or a cyanobacterium.Food preferences were calculated as ratios of the rates at whichthe copepods removed each food at high and low food concentrations.In high-concentration mixtures with cyanobacteria, Cryptomonaswas consistently preferred by both Boeckella spp. In low-concentrationmixtures, both Boeckella spp. preferred Anabaena and Nostoc,which they removed at high rates(81–142 ml mg^–1h^–1), although Cryptomonas was selected in preferenceto Oscillatoria and Microcystis. When fed mixtures of filamentouscyanobacteria, both species of Boeckella showed invariant discriminationagainst Nostoc, andshifts in preference between Anabaena andOscillatoria that were related to food concentration. Microcystis,the least favouredfood, appeared to have a toxic effect on B.triarticulata. ¹Present address: Nursing and Midwifery Department, Otago Polytechnic,Forth Street, Dunedin, New Zealand     

Leaf Properties Related to the Photosynthetic Response to Drought in Upland and Lowland Rice Varieties

Four upland and two lowland varieties were grown on floodedand dry soil in pots in a glasshouse. Photosynthetic rate (P),transpiration rate (T), and water content (W) of the secondexpanded leaf from the top of the main stem were measured undercontrolled aeration and illumination in a leaf chamber in thelaboratory, together with leaf area (La), dry matter content(DM), nitrogen content (N), stomatal frequency (Sf), and totalvessel cross-sectional area at the base of the leaf blade (Va).P/La was positively related to T/La and Sf/La among six varietieswhen they were grown on flooded soil. IR 8, a semidwarf indicalowland variety, showed the highest P/La with the highest Sf/Laand T/La. When grown on dry soil P/La was positively correlatedwith W/DM, the latter being negatively related to T/Va. Twoupland varieties, African Moroberekan and Brazilian IAC 1246,showed the highest P/La on dry soil, keeping a higher W/DM witha lower T/La and a lower T/Va. Daytime leaf diffusive conductance(l/r_L) and leaf water potential (_L) measured on the same orthe same stage leaf in the glasshouse were positively correlatedwith the W/DM measured in the laboratory among varieties grownon dry soil. Simultaneous observation of P, T and W in the laboratoryindicated nonstomatal reduction in P/La due to leaf water deficitin sensitive varieties, although these varieties also showeda markedly lower daytime l/r_L in the glasshouse as comparedwith resistant varieties. Oryza sativa L., rice, drought resistance, photosynthesis, transpiration, water deficit, stomatal frequency, vessel size     

The Regulatory Functions of the rolB and rolC Genes of Agrobacterium rhizogenes are Conserved in the Homologous Genes (Ngrol) of Nicotiana glauca in Tobacco Genetic Tumors

To compare patterns of expression between the Ngrol genes ofN. glauca and the Rirol genes of Agrobacterium rhizogenes, weperformed fluorometric and histochemical analysis of transgenicgenetic tumors on the hybrid of Nicotiana glauca x N. langsdorffü(Fl) that harbored a rß- glucuronidase (GUS) reportergene fused to the promoter of NgrolB, NgrolC, RirolB or RirolC The promoters of NgrolB and NgrolCNgrolC had 2- to 3-fold loweractivity than those of RirolB and RirolC However, the changesin patterns of GUS activity caused by deletion of NgrolB andNgrolCpromoters were similar to those of RirolB and RirolC promoters.This result suggests that the cis-acting sequences that regulatethe level of expression of RirolB and RirolC are conserved inthe NgrolB and NgrolC promoters. Furthermore, an auxin dependent(NAA-dependent) increase in GUS activity was observed in thecase of NgrolB-GUS and RirolB-GUS. Histochemical analysis showedGUS activity encoded by both NgrolB-GUS and RirolB-GUS in normal-typeFl transgenic plants was located in meristematic zones, whilethat encoded by NgrolC-GUS and RirolC-GUS was detected mainlyin vascular systems of various organs. Thus, the patterns ofexpression of the Ngrol genes were the same as those of theRirol genes in terms of promotion by auxin and tissue-specificity,indicating that regulatory mechanisms for both sets of geneshave been conserved during the evolution of the genus Nicotianaafter transfer from a progenitor of Agrobacterium to that ofNicotiana. (Received May 2, 1995; Accepted June 13, 1995)     

Diversity of cycloidea -like Genes in Gesneriaceae in Relation to Floral Symmetry

Homology assessment of cycloidea -like genes was carried outin Gesneriaceae, a predominantly zygomorphic family in whichseveral independent reversals to actinomorphy have occurred,as a basis for further investigation of the control and evolutionof floral symmetry. Phylogenetic analysis of Gesneriaceae cycloidea(Gcyc)suggests that independent duplication and gene loss events haveoccurred during the evolution of this family after the splitfrom Scrophulariaceae. Comparison of Gcyc sequences betweenzygomorphic and naturally occurring actinomorphic taxa doesnot suggest that reversals to actinomorphy were caused in thesecases by loss of function of cyc -like genes. Examination offloral development in the nearly actinomorphic Ramonda myconidid not reveal any evidence of residual unequal dorso-ventraldifferentiation indicative of expression of Gcyc. This suggeststhat Gcyc may be expressed before primordia initiation in R.myconi, or may have additional functions not directly relatedto floral symmetry. Copyright 2000 Annals of Botany Company cycloidea, developmental gene, floral symmetry, Florist’s Gloxinia, Gcyc, Gesneriaceae,Ramonda myconi , Sinningia speciosa     

Stomatal Responses of Woody Seedlings to Flooding in Relation to Nutrient Status in Leaves

Ten-week-old woody seedlings of Gmelina arborea Roxb., Tectonagrandis L. (De Wild. & Th. Dur.) Merrill, and Nauclea diderrichiif., were subjected to 10 weeks flooding and a 5-week-long post-floodingperiod. Flooding induced the development of hypertrophied lenticels,adventitious roots, and root aerenchyma in Gmelina and Tectona,while it did not in Nauclea. All three species responded toflooding by first closing their stomata and reopening at differenttimes during the flooding period. The time and extent of reopeningwere earliest and greatest in Gmelina, followed by Tectona,and latest and smallest in Nauclea. Differences in stomatalconductance at the end of the flooding period paralleled theconcentrations of ethanol in roots and inorganic nutrients inleaves. After flooding was discontinued, stomatal conductanceincreased in Gmelina, but did not in the other species. Leafwater potentials and transpiration rates of flooded Gmelinaand Tectona plants were higher at week 8 than at week 2 whilethe reverse was the case in Nauclea. It is argued that whilepersistently small stomatal apertures during the post-floodingperiod in Nauclea may be a strategy to slow down the movementof accumulated toxic substances from the soil, the higher leafwater potential and transpiration in Gmelina and Tectona atweek 8 than at week 2 may represent recovery of shoot waterrelations resulting from adventitious roots development. Key words: Flooding, stomatal conductance, transpiration, adventitious roots, ethanol