On the question of proportionality of the count of observed Scrapie cases and the size of holding

Background: The present paper investigates the question of a suitable basic model for the number of scrapie cases in a holding and applications of this knowledge to the estimation of scrapie-ffected holding population sizes and adequacy of control measures within holding. Is the number of scrapie cases proportional to the size of the holding in which case it should be incorporated into the parameter of the error distribution for the scrapie counts? Or, is there a different - potentially more complex - relationship between case count and holding size in which case the information about the size of the holding should be better incorporated as a covariate in the modeling? Methods: We show that this question can be appropriately addressed via a simple zero-truncated Poisson model in which the hypothesis of proportionality enters as a special offset-model. Model comparisons can be achieved by means of likelihood ratio testing. The procedure is illustrated by means of surveillance data on classical scrapie in Great Britain. Furthermore, the model with the best fit is used to estimate the size of the scrapie-affected holding population in Great Britain by means of two capture-recapture estimators: the Poisson estimator and the generalized Zelterman estimator. Results: No evidence could be found for the hypothesis of proportionality. In fact, there is some evidence that this relationship follows a curved line which increases for small holdings up to a maximum after which it declines again. Furthermore, it is pointed out how crucial the correct model choice is when applied to capture-recapture estimation on the basis of zero-truncated Poisson models as well as on the basis of the generalized Zelterman estimator. Estimators based on the proportionality model return very different and unreasonable estimates for the population sizes. Conclusion: Our results stress the importance of an adequate modelling approach to the association between holding size and the number of cases of classical scrapie within holding. Reporting artefacts and speculative biological effects are hypothesized as the underlying causes of the observed curved relationship. The lack of adjustment for these artefacts might well render ineffective the current strategies for the control of the disease.

Oligosaccharide-mediated inhibition of the adhesion of pathogenic Escherichia coli strains to human gut epithelial cells in vitro

The aim of the study was to investigate the ability of pectic oligosaccharides (POS) to inhibit adhesion of three strains of verotoxigenic Escherichia coli, three strains of enteropathogenic E. coli, and one nonclinical strain of Desulfovibrio desulfuricans to human intestinal epithelial cell cultures. Lactobacillus acidophilus and Lactobacillus gasseri were included for comparison. Attachment wits determined in the human HT29 cell line by viable Count of adherent bacteria. POS in buffer at pH 7.2 were antiadhesive at a dose of 2.5 mg ml(-1), reducing adhesion of enteropathogenic E. coli and verotoxigenic E. coli strains to less than 30% of control values. Concentrations resulting in 50% inhibition ranged from 0.15 to 0.46 mg ml(-1). L. acidophilus was not significantly affected. but adhesion of L. gasseri was reduced to 29% of the control value. POS reduced the adhesion of D. desulfuricans to 0.33% of the control value. POS also had a protective effect against E. coli verocytotoxins VT1 and VT2 at concentrations of 0.01 and 1 mu g ml(-1), respectively.

The use of gaseous ozone and gas packaging to control populations of Salmonella infantis and Pseudomonas aeruginosa on the skin of chicken portions

Chilled breasts of chicken were inoculated with Salmonella infantis or Pseudomonas aeruginosa and then given one of the following treatments: (i) exposure to gaseous ozone (>2000 ppm for up to 30 min); (ii) storage under 70% CO2:30% N-2; and (iii) exposure to gaseous ozone (>2000 ppm for 15 min) followed by storage under 70% CO2:30% N-2; all storage at 7degreesC. Gaseous ozone reduced the counts of samnonellae by 97(Y,, and pseudomonads by 95%, but indigenous coliforms were unaffected. Under the modified atmosphere, the cell count of S. infantis was reduced by 72% following initial exposure and then stabilised, coliforms grew, but Ps. aeruginosa behaved like S. infantis-initial reduction (58%) followed by stability. Exposure to gaseous ozone followed by gas packaging allowed survival of S. infantis, Ps. aeruginosa and coliforms over 9 days at 7degreesC, but there was no evidence of any sensory deterioration. It is proposed that the latter treatment could, in a modified form perhaps, be used to reduce the contamination of chicken carcasses with salmonellae and improve their shelf-life. (C) 2004 Elsevier Ltd. All rights reserved.

Design and fabrication of infrared filters for remote sounding instrumentation

Cooled infrared filters have been used in pressure modulation and filter radiometry to measure the dynamics, temperature distribution and concentrations of atmospheric elements in various satellite radiometers. Invariably such instruments use precision infrared bandpass filters and coatings for spectral selction, often operating at cryogenic temperatures. More recent developments in the use of spectrally-selective cooled detectors in focal plane arrays have simplified the optical layout and reduced the component count of radiometers but have placed additional demands on both the spectral and physical performance requirements of the filters. This paper describes and contrasts the more traditional radiometers using discrete detectors with those which use focal plane detector array technology, with particular emphasis on the function of the filters and coatings in the two cases. Additionally we discuss the spectral techniques and materials used to fabricate infrared coatings and filters for use in space optics, and give examples of their application in the fabrication of some demanding long wavelength dichroics and filters. We also discuss the effects of the space environment on the stability and durability of high performance infrared filters and materials exposed to low Earth orbit for 69 months on the NASA Long Duration Exposure Facility (LDEF).

A molecular, morphological and cytological investigation of the identity of non-native Ludwigia (Onagraceae) populations in Britain

A combined molecular, morphological and cytological analysis was used to study the identity and number of species of Ludwigia section Oligospermum occurring in British waterways. Only one taxon was identified for which the name L. grandiflora subsp. hexapetala (Hook. & Arn.) G.L. Nesom & Kartesz is preferred. A chromosome count of 2n = 80 was made for all plants tested and DNA evidence demonstrates that at least two clones are present in Britain. Morphological characters to differentiate L.grandiflora subsp. hexapetala and L. peploides subsp. montevidensis (Spreng.) P.H. Raven are provided. Though the production of fruit in Britain by apparently isolated populations is noted, repeated introduction into the wild from gardens is judged to be primarily responsible for the British distribution of the taxon. Legislative implications are considered and an amendment to Schedule 9 of the UK Wildlife and Countryside Act (1981) is strongly advocated.

Back to basics: how measures of lexical diversity can help discriminate between CEFR levels

This study contributes to ongoing discussions on how measures of lexical diversity (LD) can help discriminate between essays from second language learners of English, whose work has been assessed as belonging to levels B1 to C2 of the Common European Framework of Reference (CEFR). The focus is in particular on how different operationalisations of what constitutes a “different word” (type) impact on the LD measures themselves and on their ability to discriminate between CEFR levels. The results show that basic measures of LD, such as the number of different words, the TTR (Templin 1957) and the Index of Guiraud (Guiraud 1954) explain more variance in the CEFR levels than sophisticated measures, such as D (Malvern et al. 2004), HD-D (McCarthy and Jarvis 2007) and MTLD (McCarthy 2005) provided text length is kept constant across texts. A simple count of different words (defined as lemma’s and not as word families) was the best predictor of CEFR levels and explained 22 percent of the variance in overall scores on the Pearson Test of English Academic in essays written by 176 test takers.

Design, implementation and interpretation of in vitro batchculture experiments to assess enteric methane mitigation in ruminants—a review

In vitro fermentation techniques (IVFT) have been widely used to evaluate the nutritivevalue of feeds for ruminants and in the last decade to assess the effect of different nutritionalstrategies on methane (CH4) production. However, many technical factors may influencethe results obtained. The present review has been prepared by the ‘Global Network’ FACCE-JPI international research consortium to provide a critical evaluation of the main factorsthat need to be considered when designing, conducting and interpreting IVFT experimentsthat investigate nutritional strategies to mitigate CH4emission from ruminants. Given theincreasing and wide-scale use of IVFT, there is a need to critically review reports in the lit-erature and establish what criteria are essential to the establishment and implementationof in vitro techniques. Key aspects considered include: i) donor animal species and numberof animal used, ii) diet fed to donor animals, iii) collection and processing of rumen fluidas inoculum, iv) choice of substrate and incubation buffer, v) incubation procedures andCH4measurements, vi) headspace gas composition and vii) comparability of in vitro andin vivo measurements. Based on an evaluation of experimental evidence, a set of techni-cal recommendations are presented to harmonize IVFT for feed evaluation, assessment ofrumen function and CH4production.

Cloacibacterium normanense gen. nov., sp nov., a novel bacterium in the family Flavobacteriaceae isolated from municipal wastewater

Phenotypic and phylogenetic studies were performed on three isolates of an unknown Gram-negative, facultatively anaerobic, non-motile, yellow-pigmented, rod-shaped organism isolated from raw sewage. 16S rRNA gene sequence analysis indicated that these strains were members of the Bergeyella-Chryseobacterium-Riemerella branch of the family Flavobacteriaceae. The unknown bacterium was readily distinguished from reference strains by 16S rRNA gene sequencing and biochemical tests. The organism contained menaquinone MK-6 as the predominant respiratory quinone and had a DNA G + C content of 31 mol%. A most probable number-PCR approach was developed to detect, and estimate the numbers of, this organism. Untreated wastewater from one plant yielded an estimated count of 1.4 x 10(5) cells ml(-1), and untreated wastewater from a second plant yielded an estimated count of 1.4 x 10(4) cells ml(-1). Signal was not detected from treated effluent or from human stool specimens. On the basis of the results of the study presented, it is proposed that the unknown bacterium be classified in a novel genus Cloacibacterium, as Cloacibacterium normanense gen. nov., sp. nov., which is also the type species. The type strain of Cloacibacterium normanense is strain NRS1(T) (=CCUG 46293(T)=CIP 108613(T) =ATCC BAA-825(T) = DSM 15886(T)).

Non-word repetition in adolescents with Specific Language Impairment and Autism plus Language Impairments: a qualitative analysis

Non-word repetition (NWR) was investigated in adolescents with typical development, Specific Language Impairment (SLI) and Autism Plus language Impairment (ALI) (n = 17, 13, 16, and mean age 14;4, 15;4, 14;8 respectively). The study evaluated the hypothesis that poor NWR performance in both groups indicates an overlapping language phenotype (Kjelgaard & Tager-Flusberg, 2001). Performance was investigated both quantitatively, e.g. overall error rates, and qualitatively, e.g. effect of length on repetition, proportion of errors affecting phonological structure, and proportion of consonant substitutions involving manner changes. Findings were consistent with previous research (Whitehouse, Barry, & Bishop, 2008) demonstrating a greater effect of length in the SLI group than the ALI group, which may be due to greater short-term memory limitations. In addition, an automated count of phoneme errors identified poorer performance in the SLI group than the ALI group. These findings indicate differences in the language profiles of individuals with SLI and ALI, but do not rule out a partial overlap. Errors affecting phonological structure were relatively frequent, accounting for around 40% of phonemic errors, but less frequent than straight Consonant-for-Consonant or vowel-for-vowel substitutions. It is proposed that these two different types of errors may reflect separate contributory mechanisms. Around 50% of consonant substitutions in the clinical groups involved manner changes, suggesting poor auditory-perceptual encoding. From a clinical perspective algorithms which automatically count phoneme errors may enhance sensitivity of NWR as a diagnostic marker of language impairment. Learning outcomes: Readers will be able to (1) describe and evaluate the hypothesis that there is a phenotypic overlap between SLI and Autism Spectrum Disorders (2) describe differences in the NWR performance of adolescents with SLI and ALI, and discuss whether these differences support or refute the phenotypic overlap hypothesis, and (3) understand how computational algorithms such as the Levenshtein Distance may be used to analyse NWR data.

An extension of an over-dispersion test for count data

While over-dispersion in capture–recapture studies is well known to lead to poor estimation of population size, current diagnostic tools to detect the presence of heterogeneity have not been specifically developed for capture–recapture studies. To address this, a simple and efficient method of testing for over-dispersion in zero-truncated count data is developed and evaluated. The proposed method generalizes an over-dispersion test previously suggested for un-truncated count data and may also be used for testing residual over-dispersion in zero-inflation data. Simulations suggest that the asymptotic distribution of the test statistic is standard normal and that this approximation is also reasonable for small sample sizes. The method is also shown to be more efficient than an existing test for over-dispersion adapted for the capture–recapture setting. Studies with zero-truncated and zero-inflated count data are used to illustrate the test procedures.

The calculation of force constants and normal co-ordinates--VII Normal co-ordinates in the E species of allene

Force constant and normal co-ordinate calculations are reported for the E species vibrations of the allene molecule. Data on the fundamental vibration frequencies of allene-h4, allene-d4 and allene-1.1-d2 and on the five experimentally determined Coriolis zeta constants of C3H4 and C3D4, were used in a force constant refinement procedure. Allowing for product and sum rules this gives 21 independent data which were used to refine to the most general harmonic force field (10 parameters) with one constraint (in the absence of any constraints the refinement was not satisfactory). The results have been used to calculate the complete ζz Coriolis interaction matrix for the allene-1.1-d2 molecule, and hence to calculate the expected rotational structure of the perpendicular bending vibrations of this molecule; the good agreement obtained with the observed spectra is a check on our results.

Estimating the hidden number of scrapie affected holdings in great Britain using a simple, truncated count model allowing for heterogeneity.

None of the current surveillance streams monitoring the presence of scrapie in Great Britain provide a comprehensive and unbiased estimate of the prevalence of the disease at the holding level. Previous work to estimate the under-ascertainment adjusted prevalence of scrapie in Great Britain applied multiple-list capture–recapture methods. The enforcement of new control measures on scrapie-affected holdings in 2004 has stopped the overlapping between surveillance sources and, hence, the application of multiple-list capture–recapture models. Alternative methods, still under the capture–recapture methodology, relying on repeated entries in one single list have been suggested in these situations. In this article, we apply one-list capture–recapture approaches to data held on the Scrapie Notifications Database to estimate the undetected population of scrapie-affected holdings with clinical disease in Great Britain for the years 2002, 2003, and 2004. For doing so, we develop a new diagnostic tool for indication of heterogeneity as well as a new understanding of the Zelterman and Chao’s lower bound estimators to account for potential unobserved heterogeneity. We demonstrate that the Zelterman estimator can be viewed as a maximum likelihood estimator for a special, locally truncated Poisson likelihood equivalent to a binomial likelihood. This understanding allows the extension of the Zelterman approach by means of logistic regression to include observed heterogeneity in the form of covariates—in case studied here, the holding size and country of origin. Our results confirm the presence of substantial unobserved heterogeneity supporting the application of our two estimators. The total scrapie-affected holding population in Great Britain is around 300 holdings per year. None of the covariates appear to inform the model significantly.

Estimating the hidden number of scrapie affected holdings in great Britain using a simple, truncated count model allowing for heterogeneity

None of the current surveillance streams monitoring the presence of scrapie in Great Britain provide a comprehensive and unbiased estimate of the prevalence of the disease at the holding level. Previous work to estimate the under-ascertainment adjusted prevalence of scrapie in Great Britain applied multiple-list capture-recapture methods. The enforcement of new control measures on scrapie-affected holdings in 2004 has stopped the overlapping between surveillance sources and, hence, the application of multiple-list capture-recapture models. Alternative methods, still under the capture-recapture methodology, relying on repeated entries in one single list have been suggested in these situations. In this article, we apply one-list capture-recapture approaches to data held on the Scrapie Notifications Database to estimate the undetected population of scrapie-affected holdings with clinical disease in Great Britain for the years 2002, 2003, and 2004. For doing so, we develop a new diagnostic tool for indication of heterogeneity as well as a new understanding of the Zelterman and Chao's lower bound estimators to account for potential unobserved heterogeneity. We demonstrate that the Zelterman estimator can be viewed as a maximum likelihood estimator for a special, locally truncated Poisson likelihood equivalent to a binomial likelihood. This understanding allows the extension of the Zelterman approach by means of logistic regression to include observed heterogeneity in the form of covariates-in case studied here, the holding size and country of origin. Our results confirm the presence of substantial unobserved heterogeneity supporting the application of our two estimators. The total scrapie-affected holding population in Great Britain is around 300 holdings per year. None of the covariates appear to inform the model significantly.

Equivalence of truncated count mixture distributions and mixtures of truncated count distributions

This article is about modeling count data with zero truncation. A parametric count density family is considered. The truncated mixture of densities from this family is different from the mixture of truncated densities from the same family. Whereas the former model is more natural to formulate and to interpret, the latter model is theoretically easier to treat. It is shown that for any mixing distribution leading to a truncated mixture, a (usually different) mixing distribution can be found so. that the associated mixture of truncated densities equals the truncated mixture, and vice versa. This implies that the likelihood surfaces for both situations agree, and in this sense both models are equivalent. Zero-truncated count data models are used frequently in the capture-recapture setting to estimate population size, and it can be shown that the two Horvitz-Thompson estimators, associated with the two models, agree. In particular, it is possible to achieve strong results for mixtures of truncated Poisson densities, including reliable, global construction of the unique NPMLE (nonparametric maximum likelihood estimator) of the mixing distribution, implying a unique estimator for the population size. The benefit of these results lies in the fact that it is valid to work with the mixture of truncated count densities, which is less appealing for the practitioner but theoretically easier. Mixtures of truncated count densities form a convex linear model, for which a developed theory exists, including global maximum likelihood theory as well as algorithmic approaches. Once the problem has been solved in this class, it might readily be transformed back to the original problem by means of an explicitly given mapping. Applications of these ideas are given, particularly in the case of the truncated Poisson family.

Restricted expression of NADPH oxidase/peroxidase gene (Duox) in zone VII of the ascidian endostyle

The ascidian Ciona intestinalis, a marine invertebrate chordate, is an emerging model system for developmental and evolutionary studies. The endostyle, one of the characteristic organs of ascidians, is a pharyngeal structure with iodine-concentrating and peroxidase activities and is therefore considered to be homologous to the follicular thyroid of higher vertebrates. We have previously reported that a limited part of the endostyle (zone VII) is marked by the expression of orthologs of the thyroid peroxidase (TPO) and thyroid transcription factor-2 (TTF-2/FoxE) genes. In this study, we have identified the Ciona homolog of NADPH oxidase/peroxidase (Duox), which provides hydrogen peroxide (H2O2) for iodine metabolism by TPO in the vertebrate thyroid. Expression patterns assessed by in situ hybridization have revealed that Ciona Duox (Ci-Duox) is predominantly expressed in the dorsal part of zone VII of the endostyle. Furthermore, two-color fluorescent in situ hybridization with Ci-Duox and Ciona TPO (CiTPO) has revealed that the ventral boundary of the Ci-Duox domain of expression is more dorsal than that of CiTPO. We have also characterized several genes, such as Ci-Fgf8/17/18, 5HT7, and Ci-NK4, which are predominantly expressed in the ventral part of zone VII, in a region complementary to the Ci-Duox expression domain. These observations suggest that, at the molecular level, zone VII has a complex organization that might have some impact on the specification of cell types and functions in this thyroid-equivalent element of the ascidian endostyle.