Uncertainty quantification for radiation measurements: Bottom-up error variance estimation using calibration information.

One example of top-down uncertainty quantification (UQ) involves comparing two or more measurements on each of multiple items. One example of bottom-up UQ expresses a measurement result as a function of one or more input variables that have associated errors, such as a measured count rate, which individually (or collectively) can be evaluated for impact on the uncertainty in the resulting measured value. In practice, it is often found that top-down UQ exhibits larger error variances than bottom-up UQ, because some error sources are present in the fielded assay methods used in top-down UQ that are not present (or not recognized) in the assay studies used in bottom-up UQ. One would like better consistency between the two approaches in order to claim understanding of the measurement process. The purpose of this paper is to refine bottom-up uncertainty estimation by using calibration information so that if there are no unknown error sources, the refined bottom-up uncertainty estimate will agree with the top-down uncertainty estimate to within a specified tolerance. Then, in practice, if the top-down uncertainty estimate is larger than the refined bottom-up uncertainty estimate by more than the specified tolerance, there must be omitted sources of error beyond those predicted from calibration uncertainty. The paper develops a refined bottom-up uncertainty approach for four cases of simple linear calibration: (1) inverse regression with negligible error in predictors, (2) inverse regression with non-negligible error in predictors, (3) classical regression followed by inversion with negligible error in predictors, and (4) classical regression followed by inversion with non-negligible errors in predictors. Our illustrations are of general interest, but are drawn from our experience with nuclear material assay by non-destructive assay. The main example we use is gamma spectroscopy that applies the enrichment meter principle. Previous papers that ignore error in predictors have shown a tendency for inverse regression to have lower error variance than classical regression followed by inversion. This paper supports that tendency both with and without error in predictors. Also, the paper shows that calibration parameter estimates using error in predictor methods perform worse than without using error in predictor methods in the case of inverse regression, but perform better than without using error in predictor methods in the case of classical regression followed by inversion. Both inverse and classical regression involve the ratio of dependent random variables; therefore, the assumed error distribution(s) will matter in parameter estimation and in uncertainty calculations. Mainly for that reason, calibration using a single predictor is distinct from simple regression, and it has not been thoroughly treated in the literature, nor in the ISO Guide to the Expression of Uncertainty in Measurements (GUM). Our refined approach is based on simulation, because we illustrate that analytical approximations are not adequate when there are, for example, 10 or fewer calibration measurements, which is common in calibration applications, each consisting of measured responses from known quantities.

Simultaneous estimation of computer model parameters and model bias.

Estimation of computer model parameters using field data is sometimes attempted in the presence of model bias. In this paper, using simulated field data, a vector-valued model bias is fit simultaneously with a scalar model calibration parameter. Our main finding is that simultaneous estimation of a bias vector and a scalar calibration parameter can be sensitive to assumptions made prior to data collection. Possible implications of this finding are considered in two examples of process monitoring for nuclear safeguards.

Impact of spectral smoothing on gamma radiation portal alarm probabilities.

Gamma detector counts are included in radiation portal monitors (RPM) to screen for illicit nuclear material. Gamma counts are sometimes smoothed to reduce variance in the estimated underlying true mean count rate, which is the "signal" in our context. Smoothing reduces total error variance in the estimated signal if the bias that smoothing introduces is more than offset by the variance reduction. An empirical RPM study for vehicle screening applications is presented for unsmoothed and smoothed gamma counts in low-resolution plastic scintillator detectors and in medium-resolution NaI detectors.

Surface motility and associated surfactant production in Agrobacterium vitis.

AIMS: Agrobacterium vitis is the causal agent of crown gall of grapevine. Surface motility (swarming), an important mechanism for bacterial colonization of new environments and a previously unknown behaviour of Ag. vitis, was demonstrated. METHODS: Surface motility assays were performed on half-strength potato dextrose agar (Difco) containing 0.75% agar. To test for surfactant production, a drop-collapse test was used. Quorum-sensing (QS) negative and complemented mutants were tested for swarming activity. RESULTS: Ninety-one Agrobacterium strains representing -Agrobacterium tumefaciens (17 strains), Agrobacterium rhizogenes (14 strains) and Ag. vitis (60 strains) were tested for swarming and production of surfactant. All Ag. vitis strains expressed a surface-related motility. In contrast, none of 17 strains of Ag. tumefaciens or 14 strains of Ag. rhizogenes exhibited this behaviour. Surface motility in Ag. vitis was associated with surfactant secretion; both of which are regulated by a QS system previously associated with induction of a hypersensitive response on tobacco and necrosis on grape. An aviR (belongs to luxR family) mutant was surface motility negative and did not produce surfactant. An avsI mutant (autoinducer synthase) was also surface motility negative and was complemented with an Ag. tumefaciens clone expressing avsI. CONCLUSIONS: Agrobacterium vitis is able to produce a characteristic swarming phenotype that is regulated by a complex QS system. SIGNIFICANCE AND IMPACT OF THE STUDY: Swarming activity is unique to Ag. vitis among Agrobacterium sp. and may be associated with the ability of the pathogen to colonize grapevines.

Multiple-component radiation-measurement error models.

Measurement error modeling and assessment are crucial to any assay method. Realistic error models prioritize future efforts to reduce key error components and provide a way to estimate total ("random" and "systematic") measurement error. This paper describes multiple-component error models for radiation-based assay, gives example applications, and describes strategies for choosing and then fitting error models.

A Pectate Lyase Homolog, xagP, in Xanthomonas axonopodis pv. glycines Is Associated with Hypersensitive Response Induction on Tobacco.

ABSTRACT Xanthomonas axonopodis pv. glycines is the causal agent of bacterial pustule disease of soybeans. A transposon insertional mutant (KU-P-M670) of X. axonopodis pv. glycines derived from wild-type strain KU-P-34017 lost the ability to induce the hypersensitive response (HR) on tobacco and pepper but retained its HR induction capacity on cucumber, sesame, and tomato. The mutation also resulted in loss of ability to cause a potato soft rot and express pectolytic activity at pH 6.5. An approximate 1.4-kb DNA fragment carrying the transposon insertion contained a single open reading frame that showed high homology with PSTRU-3, a pectate lyase gene in X. axonopodis pv. malvacearum. Complemented KU-P-M670 regained HR induction on tobacco and also pectolytic activity. Treatment of plants with inhibitors of eukaryotic metabolism blocked HR induction by wild-type strains and by complemented KU-P-M670. The presence of the pectate lyase homolog, which we designated xagP, in 26 X. axonopodis pv. glycines strains was highly correlated with their ability to induce an HR on tobacco. To our knowledge, this is the first study indicating a role for a functional pectate lyase in induction of a plant HR.

Statistical evaluation of FRAM gamma-ray isotopic analysis data.

High-purity germanium (HPGe) detector gamma-ray spectra were analyzed using the FRAM (fixed energy, response function analysis with multiple efficiencies) gamma-ray isotopic analysis software. The analyses are based on multiple measurements of samples having well-documented isotopic composition from mass spectrometry measurements. Statistical analyses of the FRAM results are reported, the errors in FRAM analyses arising from the choice of detector type and the energy region are discussed, and the errors that resulted from sample-dependent and analysis-dependent effects are quantified.

Effect of Wound Position, Auxin, and Agrobacterium vitis Strain F2/5 on Wound Healing and Crown Gall in Grapevine.

ABSTRACT Agrobacterium vitis is the causal agent of crown gall disease in grapevine, which can be severe in many regions worldwide. Vitis vinifera cultivars are highly susceptible to freeze injury, providing the wounds necessary for infection by A. vitis. Wound position in relation to the uppermost bud of cuttings was determined to be important in tumor development. Inoculated wounds below buds developed tumors, whereas wounds opposite the bud did not, implying that indole-3-aectic acid flow contributes to tumor formation. If auxin was applied to wounds prior to inoculation with a tumorigenic A. vitis strain, all sites of inoculation developed tumors, accompanied by an increased amount of callus in the cambium. Wounds inoculated with an A. vitis biological control strain F2/5 prior to application of the pathogen did not develop galls. A closer examination of these wounds determined that callus cells formed in the cambium during wound healing are susceptible to transformation by the pathogen. Although the mechanism by which F2/5 prevents transformation is unknown, our observations suggest that F2/5 inhibits normal wound healing by inducing necrosis in the cambium.

Characterization of Agrobacterium vitis Strains Isolated from Turkish Grape Cultivars in the Central Anatolia Region.

Crown gall was detected in several vineyards in the Central Anatolia region of Turkey. Vineyards were planted to cultivars of grape that originated in Turkey and that were not grafted. The predominant species isolated from galls consisted of tumorigenic strains of Agrobacterium vitis. They were identified based on reactions to standard biochemical and physiological tests, by polymerase chain reaction amplification of specific Ti plasmid and chromosomal sequences, and by reaction to a species-specific monoclonal antibody. All strains utilized octopine, suggesting that they may carry similar types of Ti plasmids. Some of the strains exhibited a differential host range compared with others and were less virulent based on the numbers of galls that they induced on grape. When grapevines were treated with nontumorigenic A. vitis strain F2/5 prior to inoculation with the Turkish A. vitis strains, crown gall was effectively controlled. The genetic diversity of strains was evaluated by comparing DNA fingerprints that were generated by restriction enzyme digestion of the intergenic spacer region that lies between 16S and 23S rRNA genes. They segregated into two main groups, one that is similar to previously identified A. vitis strains carrying octopine type Ti plasmids and one that was more similar to strains carrying nopaline and vitopine Ti plasmids. The strains of A. vitis from Turkey may represent ancestral forms of the pathogen that will provide insight into the evolution of the bacterium.

A chimeric activator of transcription that uses two DNA-binding domains to make simultaneous contact with pairs of recognition sites.

Many well-known transcriptional regulatory proteins are composed of at least two independently folding domains and, typically, only one of these is a DNA-binding domain. However, some transcriptional regulators have been described that have more than one DNA-binding domain. Regulators with a single DNA-binding domain often bind co-operatively to the DNA in homotypic or heterotypic combinations, and two or more DNA-binding domains of a single regulatory protein can also bind co-operatively to suitably positioned recognition sequences. Here, we examine the behaviour of a chimeric activator of transcription with two different DNA-binding domains, that of the bacteriophage lambda cI protein and that of the Escherichia coli cyclic AMP receptor protein. We show that these two DNA-binding moieties, when present in the same molecule, can bind co-operatively to a pair of cognate recognition sites located upstream of a test promoter, thereby permitting the chimera to function as a particularly strong activator of transcription from this promoter. Our results show how such a bivalent DNA-binding protein can be used to regulate transcription differentially from promoters that bear either one or both recognition sites.

The origin of acquired immune deficiency syndrome: Darwinian or Lamarckian?

The subtypes of human immunodeficiency virus type 1 (HIV-1) group M exhibit a remarkable similarity in their between-subtype distances, which we refer to as high synchrony. The shape of the phylogenetic tree of these subtypes is referred to as a sunburst to distinguish it from a simple star phylogeny. Neither a sunburst pattern nor a comparable degree of symmetry is seen in a natural process such as in feline immunodeficiency virus evolution. We therefore have undertaken forward-process simulation studies employing coalescent theory to investigate whether such highly synchronized subtypes could be readily produced by natural Darwinian evolution. The forward model includes both classical (macro) and molecular (micro) epidemiological components. HIV-1 group M subtype synchrony is quantified using the standard deviation of the between-subtype distances and the average of the within-subtype distances. Highly synchronized subtypes and a sunburst phylogeny are not observed in our simulated data, leading to the conclusion that a quasi-Lamarckian, punctuated event occurred. The natural transfer theory for the origin of human acquired immune deficiency syndrome (AIDS) cannot easily be reconciled with these findings and it is as if a recent non-Darwinian process took place coincident with the rise of AIDS in Africa.

Maximally selected measures of evidence of disease clusters.

It is now common to read reports such as 'city A has a childhood cancer rate 30 per cent higher than the national average'. Because the details about how the data was examined can greatly impact the conclusions, the epidemiologist then wants to know more information, such as 'over what time period' and 'how many other cancer types were examined'. For example, city A might have calculated cancer rates for many age groups within different regions of the city over many time intervals, but reported only the highest cancer rate discovered in a particular group. We will refer to such selective reporting as 'maximally selecting measures of evidence of disease clustering', or less formally as 'fishing for statistical significance'. The objective of this paper is to study the behaviour of maximally selected statistics for measuring the extent of clustering in disease outbreaks. The original data is the time and location of each reported case of the disease. In some cases we are only given aggregates of the original data, such as the number of cases during a time period over a given region. We introduce new and review existing methods for correcting for the effect of making maximal selections in disease cluster detection. We consider three main cases with examples. We demonstrate via simulation and analytical approximations that some types of 'fishing' are simple to correct for while others are not.

Mutations that Affect Agrobacterium vitis-Induced Grape Necrosis also Alter Its Ability to Cause a Hypersensitive Response on Tobacco.

ABSTRACT Tn5-induced mutations in Agrobacterium vitis F2/5 resulted in both altered grape necrosis and tobacco leaf panel collapse phenotypes, suggesting that the underlying mechanisms of the reactions are related. The reaction on tobacco resembles the classical hypersensitive response (HR) caused by several plant pathogenic bacteria in that it is observable within 14 h, is inhibited by treatment of plants with metabolic inhibitors, and results in the inability to recover the pathogen from the necrotic zone. Strains of A. vitis differ with regard to their efficiency of causing the reaction on tobacco. An EcoRI fragment from one mutant, M6, which is necrosis-altered and HR-minus, was cloned and sequenced. Sequence analysis revealed that the Tn5 insertion occurred in a region that shares significant homology with genes involved in long chain fatty acid production by the marine bacteria Shewanella spp. and Moritella marina. Complementation of M6 with a cosmid clone from an F2/5 DNA library restored the tobacco HR and grape necrosis phenotypes.

Quasi-equilibrium theory for the distribution of rare alleles in a subdivided population: justification and implications.

This paper examines a quasi-equilibrium theory of rare alleles for subdivided populations that follow an island-model version of the Wright-Fisher model of evolution. All mutations are assumed to create new alleles. We present four results: (1) conditions for the theory to apply are formally established using properties of the moments of the binomial distribution; (2) approximations currently in the literature can be replaced with exact results that are in better agreement with our simulations; (3) a modified maximum likelihood estimator of migration rate exhibits the same good performance on island-model data or on data simulated from the multinomial mixed with the Dirichlet distribution, and (4) a connection between the rare-allele method and the Ewens Sampling Formula for the infinite-allele mutation model is made. This introduces a new and simpler proof for the expected number of alleles implied by the Ewens Sampling Formula.

DNA sequence elements located immediately upstream of the -10 hexamer in Escherichia coli promoters: a systematic study.

We have made a systematic study of how the activity of an Escherichia coli promoter is affected by the base sequence immediately upstream of the -10 hexamer. Starting with an activator-independent promoter, with a 17 bp spacing between the -10 and -35 hexamer elements, we constructed derivatives with all possible combinations of bases at positions -15 and -14. Promoter activity is greatest when the 'non-template' strand carries T and G at positions -15 and -14, respectively. Promoter activity can be further enhanced by a second T and G at positions -17 and -16, respectively, immediately upstream of the first 'TG motif'. Our results show that the base sequence of the DNA segment upstream of the -10 hexamer can make a significant contribution to promoter strength. Using published collections of characterised E.coli promoters, we have studied the frequency of occurrence of 'TG motifs' upstream of the promoters' -10 elements. We conclude that correctly placed 'TG motifs' are found at over 20% of E.coli promoters.

Characterization of plasmids that encode streptomycin-resistance in bacterial epiphytes of apple.

Streptomycin resistance in strains of Pseudomonas syringae pv. papulans, Pantoea agglomerans and a yellow-pigmented, non-fluorescent Pseudomonas sp. (Py), isolated from apple orchards in New York and Washington states, is predominantly associated with strA-strB genes carried on conjugal plasmids (R plasmids). None of 128 resistant Erwinia amylovora strains from the eastern and western USA hybridized with a strA-strB probe, SMP3. Resistant Py strains transfered R plasmids to Ps. syringae pv. papulans and to Py in vitro at frequencies of 10(-1)-10(-2) per recipient cell whereas Ps. syringae pv. papulans transferred its plasmids at frequencies of 10(-2) to below detectable levels. Transfer of R plasmids to P. agglomerans was not detected and resistant P. agglomerans did not transfer their R plasmids to any recipients. R plasmids were found to be highly diverse as measured by DNA fingerprint analysis. Transfer-deficient transposon mutants of R plasmid pCPP519 were generated, and 3.9 kb EcoRI and 3.0 kb SmaI fragments that hybridized with a Tn5 probe were cloned and sequenced. The deduced amino acid sequences of the 3.9 kb fragment were similar to proteins involved in replication, nicking at oriT, and piliation in other bacteria.

Characterization of Agrobacterium vitis Strains Isolated from Feral Vitis riparia.

Agrobacterium vitis was isolated from roots of 41 of 66 feral Vitis riparia vines collected in three different regions of New York State. Two of the regions were more than 150 km from commercial vineyards. The strains were highly diverse as determined by DNA fingerprinting of the chromosomal region lying between the 16S and 23S rRNA genes. Of 24 strains examined, 15 different fingerprints were generated, and none was identical to fingerprints generated by previously identified groups of tumorigenic A. vitis strains. Results of physiological tests that were done to characterize strains from V. riparia conformed closely to those expected for A. vitis, except that 23 of 26 strains did not utilize tartrate. All strains were nontumorigenic, did not hybridize with a probe consisting of T-DNA genes, did not utilize octopine or nopaline, and carried zero to three plasmids. Of 26 strains, 7 inhibited A. vitis strain K306 from causing galls at wound sites on grape as well as or better than a previously studied nontumorigenic A. vitis strain, F2/5, that is known to have biological control activity.

Biological control of grape crown gall by strain f2/5 is not associated with agrocin production or competition for attachment sites on grape cells.

ABSTRACT Agrocin-minus mutants of nontumorigenic Agrobacterium vitis strain F2/5 controlled grape crown gall as well as the wild-type strain, indicating that agrocin is not a major factor in the mechanism of biological control. Relative levels of attachment to grape cells by tumorigenic and biocontrol strains were also measured. Attachment of tumorigenic strains (CG49 and K306) and biological control strains (F2/5 and agrocin-minus mutant 1077) was often reduced when mixtures of the strains were applied. However, high populations (10(3) to 10(5) CFU/ml) of all strains attached following mixed inoculations, suggesting that competition for attachment sites is also not a factor in the mechanism of biological control. Transfer of T-DNA to grape by CG49 was prevented or greatly inhibited in the presence of F2/5 or 1077 as measured by expression of the GUS reporter gene. The Ti plasmid virulence genes, however, were induced by exudates from grape shoots that had been inoculated with F2/5. Sonicated and autoclaved preparations of F2/5 and 1077 did not control crown gall or inhibit T-DNA transfer. Control by F2/5 is specific to grape, since gall formation on tomato, sunflower, and Kalanchoe daigremontiana were not inhibited.

Characterization of the Agrobacterium vitis pehA gene and comparison of the encoded polygalacturonase with the homologous enzymes from Erwinia carotovora and Ralstonia solanacearum.

DNA sequencing of the Agrobacterium vitis pehA gene revealed a predicted protein with an M(r) of 58,000 and significant similarity to the polygalacturonases of two other plant pathogens, Erwinia carotovora and Ralstonia (= Pseudomonas or Burkholderia) solanacearum. Sequencing of the N terminus of the PehA protein demonstrated cleavage of a 34-amino-acid signal peptide from pre-PehA. Mature PehA accumulated primarily in the periplasm of A. vitis and pehA+ Escherichia coli cells during exponential growth. A. vitis PehA released dimers, trimers, and monomers from polygalacturonic acid and caused less electrolyte leakage from potato tuber tissue than did the E. carotovora and R. solanacearum polygalacturonases.