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.

Are rare species rare or just overlooked? Assessing the distribution of the freshwater bryozoan, Lophopus crystallinus

Given the widespread degradation of freshwater habitats, assessing the distributions of species that may be negatively or positively impacted should be of general interest. However, determining distributions of freshwater organisms that are small and patchily distributed and attached or sedentary is particularly problematic, as it is time consuming, inaccurate, and nearly impossible when the focal species is rare. Here we illustrate the use of indirect sampling approaches to survey the distribution of the rare freshwater bryozoan Lophopus crystallinus, a priority species in the UK Biodiversity Action Plan [Anonymous, 1999. UK Biodiversity Group Tranche 2 Action Plans. Invertebrates, Vol. 4. Environment Agency, Peterborough, pp. 437-439.1. By utilising two complementary methods for sampling bryozoan propagules (statoblasts), namely the collection of debris samples and sediment cores, we achieved an efficient and integrative sampling of habitats across spatial and temporal scales. Analysis of 154 debris samples, encompassing 62 rivers and lakes, identified at least 16 new populations while analysis of 26 sediment cores provided evidence of current or very recent (in the last 10-20 years) occurrence in a further six localities. These results represent a more than 10-fold increase in the current recorded distribution of the species in the UK. Logistic regression analysis provided evidence that L. crystallinus is generally found in lowland sites and is tolerant of eutrophication. Our study exemplifies how integrative and indirect sampling approaches can greatly aid in assessing the conservation status of rare aquatic species and reveals, in this case, that the focal species is less rare than previously appreciated. (c) 2006 Elsevier Ltd. All rights reserved.

Bayesian decision procedures for binary and continuous bivariate dose-escalation studies

In this paper, Bayesian decision procedures are developed for dose-escalation studies based on binary measures of undesirable events and continuous measures of therapeutic benefit. The methods generalize earlier approaches where undesirable events and therapeutic benefit are both binary. A logistic regression model is used to model the binary responses, while a linear regression model is used to model the continuous responses. Prior distributions for the unknown model parameters are suggested. A gain function is discussed and an optional safety constraint is included. Copyright (C) 2006 John Wiley & Sons, Ltd.

Detecting non-multiplicative genotype relative risks from transmissions of parental alleles to affected children

The differential transmission of alleles from parents to affected children indicates that the locus under investigation is either directly involved in the occurrence of the disease or that there are allelic associations with other loci that are directly involved. Conditional logistic regression applied to a diallelic locus leads to a test with two degrees of freedom. The power of a single degree of freedom test to detect non-multiplicative allelic effects is discussed here.

Association between ovarian follicle development and pregnancy rates in dairy cows undergoing spontaneous oestrous cycles

Ovarian follicle development continues in a wave-like manner during the bovine oestrous cycle giving rise to variation in the duration of ovulatory follicle development. The objectives of the present study were to determine whether a relationship exists between the duration of ovulatory follicle development and pregnancy rates following artificial insemination (AI) in dairy cows undergoing spontaneous oestrous cycles, and to identify factors influencing follicle turnover and pregnancy rate and the relationship between these two variables. Follicle development was monitored by daily transrectal ultrasonography from 10 days after oestrus until the subsequent oestrus in 158 lactating dairy cows. The cows were artificially inseminated following the second observed oestrus and pregnancy was diagnosed 35 days later. The predominant pattern of follicle development was two follicle waves (74.7%) with three follicle waves in 22.1% of oestrous cycles and four or more follicle waves in 3.2% of oestrous cycles. The interval from ovulatory follicle emergence to oestrus (EOI) was 3 days longer (P < 0.0001) in cows with two follicle waves than in those with three waves. Ovulatory follicles from two-wave oestrous cycles grew more slowly but were approximately 2 mm larger (P < 0.0001) on the day of oestrus. Twin ovulations were observed in 14.2% of oestrous cycles and occurred more frequently (P < 0.001) in three-wave oestrous cycles; consequently EOI was shorter in cows with twin ovulations. Overall, 57.0% of the cows were diagnosed pregnant 35 days after AI. Linear logistic regression analysis revealed an inverse relationship between EOI and the proportion of cows diagnosed pregnant, among all cows (n = 158; P < 0.01) and amongst those with single ovulations (n = 145; P < 0.05). Mean EOI was approximately I day shorter (P < 0.01) in cows that became pregnant than in non-pregnant cows; however, pregnancy rates did not differ significantly among cows with different patterns of follicle development. These findings confirm and extend previous observations in pharmacologically manipulated cattle and show, for the first time, that in dairy cows undergoing spontaneous oestrous cycles, natural variation in the duration of post-emergence ovulatory follicle development has a significant effect on pregnancy rate, presumably reflecting variation in oocyte developmental competence.

A practical approach to a multi-level analysis with a sparse binary outcome within a large surgical trial

Objectives: To assess the potential source of variation that surgeon may add to patient outcome in a clinical trial of surgical procedures. Methods: Two large (n = 1380) parallel multicentre randomized surgical trials were undertaken to compare laparoscopically assisted hysterectomy with conventional methods of abdominal and vaginal hysterectomy; involving 43 surgeons. The primary end point of the trial was the occurrence of at least one major complication. Patients were nested within surgeons giving the data set a hierarchical structure. A total of 10% of patients had at least one major complication, that is, a sparse binary outcome variable. A linear mixed logistic regression model (with logit link function) was used to model the probability of a major complication, with surgeon fitted as a random effect. Models were fitted using the method of maximum likelihood in SAS((R)). Results: There were many convergence problems. These were resolved using a variety of approaches including; treating all effects as fixed for the initial model building; modelling the variance of a parameter on a logarithmic scale and centring of continuous covariates. The initial model building process indicated no significant 'type of operation' across surgeon interaction effect in either trial, the 'type of operation' term was highly significant in the abdominal trial, and the 'surgeon' term was not significant in either trial. Conclusions: The analysis did not find a surgeon effect but it is difficult to conclude that there was not a difference between surgeons. The statistical test may have lacked sufficient power, the variance estimates were small with large standard errors, indicating that the precision of the variance estimates may be questionable.

Modelling habitat selection and distribution of the critically endangered Jerdon's courser Rhinoptilus bitorquatus in scrub jungle: an application of a new tracking method

1. Jerdon's courser Rhinoptilus bitorquatus is a nocturnally active cursorial bird that is only known to occur in a small area of scrub jungle in Andhra Pradesh, India, and is listed as critically endangered by the IUCN. Information on its habitat requirements is needed urgently to underpin conservation measures. We quantified the habitat features that correlated with the use of different areas of scrub jungle by Jerdon's coursers, and developed a model to map potentially suitable habitat over large areas from satellite imagery and facilitate the design of surveys of Jerdon's courser distribution. 2. We used 11 arrays of 5-m long tracking strips consisting of smoothed fine soil to detect the footprints of Jerdon's coursers, and measured tracking rates (tracking events per strip night). We counted the number of bushes and trees, and described other attributes of vegetation and substrate in a 10-m square plot centred on each strip. We obtained reflectance data from Landsat 7 satellite imagery for the pixel within which each strip lay. 3. We used logistic regression models to describe the relationship between tracking rate by Jerdon's coursers and characteristics of the habitat around the strips, using ground-based survey data and satellite imagery. 4. Jerdon's coursers were most likely to occur where the density of large (>2 m tall) bushes was in the range 300-700 ha(-1) and where the density of smaller bushes was less than 1000 ha(-1). This habitat was detectable using satellite imagery. 5. Synthesis and applications. The occurrence of Jerdon's courser is strongly correlated with the density of bushes and trees, and is in turn affected by grazing with domestic livestock, woodcutting and mechanical clearance of bushes to create pasture, orchards and farmland. It is likely that there is an optimal level of grazing and woodcutting that would maintain or create suitable conditions for the species. Knowledge of the species' distribution is incomplete and there is considerable pressure from human use of apparently suitable habitats. Hence, distribution mapping is a high conservation priority. A two-step procedure is proposed, involving the use of ground surveys of bush density to calibrate satellite image-based mapping of potential habitat. These maps could then be used to select priority areas for Jerdon's courser surveys. The use of tracking strips to study habitat selection and distribution has potential in studies of other scarce and secretive species.

Dung and nest surveys: estimating decay rates

1. Wildlife managers often require estimates of abundance. Direct methods of estimation are often impractical, especially in closed-forest environments, so indirect methods such as dung or nest surveys are increasingly popular. 2. Dung and nest surveys typically have three elements: surveys to estimate abundance of the dung or nests; experiments to estimate the production (defecation or nest construction) rate; and experiments to estimate the decay or disappearance rate. The last of these is usually the most problematic, and was the subject of this study. 3. The design of experiments to allow robust estimation of mean time to decay was addressed. In most studies to date, dung or nests have been monitored until they disappear. Instead, we advocate that fresh dung or nests are located, with a single follow-up visit to establish whether the dung or nest is still present or has decayed. 4. Logistic regression was used to estimate probability of decay as a function of time, and possibly of other covariates. Mean time to decay was estimated from this function. 5. Synthesis and applications. Effective management of mammal populations usually requires reliable abundance estimates. The difficulty in estimating abundance of mammals in forest environments has increasingly led to the use of indirect survey methods, in which abundance of sign, usually dung (e.g. deer, antelope and elephants) or nests (e.g. apes), is estimated. Given estimated rates of sign production and decay, sign abundance estimates can be converted to estimates of animal abundance. Decay rates typically vary according to season, weather, habitat, diet and many other factors, making reliable estimation of mean time to decay of signs present at the time of the survey problematic. We emphasize the need for retrospective rather than prospective rates, propose a strategy for survey design, and provide analysis methods for estimating retrospective rates.

Patented biologically-inspired technological innovations: A twenty year view

Publication rate of patents can be a useful measure of innovation and productivity in fields of science and technology. To assess the growth in industrially-important research, I conducted an appraisal of patents published between 1985 and 2005 on online databases using keywords chosen to select technologies arising as a result of biological inspiration. Whilst the total number of patents increased over the period examined, those with biomimetic content had increased faster as a proportion of total patent publications. Logistic regression analysis reveals that we may be a little over half way through an initial innovation cycle inspired by biological systems.

Assessment of long chain n-3 polyunsaturated fatty acid status and clinical outcome in adults receiving home parenteral nutrition

Background & aims: Long term parenteral nutrition rarely supplies the long chain n-3 polyunsaturated fatty acids (PUFA), eicosapentaenoic acid (EPA), docosapentaenoic acid (DPA) and docosahexaenoic acid (DHA). The aim of this study was to assess long chain n-3 PUFA status in patients receiving home parenteral. nutrition (HPN). Methods: Plasma phospholipid fatty acids were measured in 64 adult HPN patients and compared with 54 age, sex and BMI matched controls. Logistic regression analysis was used to identify factors related to plasma fatty acid fractions in the HPN patients, and to identify factors associated with the risk of clinical. complications. Results: Plasma phospholipid fractions of EPA, DPA and DHA were significantly tower in patients receiving HPN. Factors independently associated with tow fractions included high parenteral energy provision, tow parenteral lipid intake, tow BMI and prolonged duration of HPN. Long chain n-3 PUFA fractions were not associated with incidence of either central venous catheter associated infection or central venous thrombosis. However, the fraction of EPA were inversely associated with plasma alkaline phosphatase concentrations. Conclusions: This study demonstrates abnormal long chain n-3 PUFA profiles in patients receiving HPN. Reduced fatty acid intake may be partly responsible. Fatty acid metabolism may also be altered. (C) 2008 Elsevier Ltd and European Society for Clinical Nutrition and Metabolism. All rights reserved.

Children's representation of family mealtime in the context of maternal eating disorders

Background Recent research provides evidence for specific disturbance in feeding and growth in children of mothers with eating disorders. Aim To investigate the impact of maternal eating disorders during the post-natal year on the internal world of children, as expressed in children's representations of self and their mother in pretend mealtime play at 5 years of age. Methods Children of mothers with eating disorders (n = 33) and a comparison group (n = 24) were videotaped enacting a family mealtime in pretend play. Specific classes of children's play representations were coded blind to group membership. Univariate analyses compared the groups on representations of mother and self. Logistic regression explored factors predicting pretend play representations. Results Positive representations of the mother expressed as feeding, eating or body shape themes were more frequent in the index group. There were no other significant group differences in representations. In a logistic regression analysis, current maternal eating psychopathology was the principal predictor of these positive maternal representations. Marital criticism was associated with negative representations of the mother. Conclusions These findings suggest that maternal eating disorders may influence the development of a child's internal world, such that they are more preoccupied with maternal eating concerns. However, more extensive research on larger samples is required to replicate these preliminary findings.

New evidence on the green building rent and price premium

This paper investigates the effect of voluntary eco-certification on the rental and sale prices of US commercial office properties. Hedonic and logistic regressions are used to test whether there are rental and sale price premiums for LEED and Energy Star certified buildings. The results of the hedonic analysis suggest that there is a rental premium of approximately 6% for LEED and Energy Star certification. A sale price premium of approximately 35% was found for 127 price observations involving LEED rated buildings and 31% for 662 buildings involving Energy Star rated buildings. When compared to samples of similar buildings identified by a binomial logistic regression for LEED-certified buildings, the existence of a rent and sales price premium is confirmed albeit with differences regarding the magnitude of the premium. Overall, the results of this study confirm that LEED and Energy Star buildings exhibit higher rental rates and sales prices per square foot controlling for a large number of location- and property-specific factors.

Identifying and investigating pesticide application types to promote a more sustainable pesticide use: the case of smallholders in Boyacá, Colombia

The present paper investigates pesticide application types adopted by smallholder potato producers in the Department of Boyacá , Colombia. In this region, environmental, health and adverse economic effects due to pesticide mis- or over-use respectively have been observed. Firstly, pesticide application types were identified based on input-effectiveness. Secondly, their determinants of adoption were investigated. Finally suggestions were given to develop intervention options for transition towards a more sustainable pesticide use. Three application types were identified for fungicide and insecticide. The types differed in terms of input (intensity of pesticide application), effect (damage control), frequency of application, average quantity applied per application, chemical class, and productivity. Then, the determinants of different pesticide application types were investigated with a multinomial logistic regression approach and applying the integrative agent centred (IAC) framework. The area of the plot, attendance at training sessions and educational and income levels were among the most relevant determinants. The analysis suggested that better pesticide use could be fostered to reduce pesticide-related risks in the region. Intervention options were outlined, which may help in targeting this issue. They aim not only at educating farmers, but to change their social and institutional context, by involving other agents of the agricultural system (i.e. pesticide producers), facilitating new institutional settings (i.e. cooperatives) and targeting social dynamics (i.e. conformity to social norms).

Why don’t pesticide applicators protect themselves? Exploring the use of personal protective equipment among Colombian smallholders

The misuse of personal protective equipment (PPE) during pesticide application was investigated among smallholders in Colombia. The integrative agent-centered (IAC) framework and a logistic regression approach were adopted. The results suggest that the descriptive social norm was significantly influencing PPE use. The following were also important: (1) having experienced pesticide-related health problems; (2) age; (3) the share of pesticide application carried out; and (4) the perception of PPE hindering work. Interestingly, the influence of these factors differed for different pieces of PPE. Since conformity to the social norm is a source of rigidity in the system, behavioral change may take the form of a discontinuous transition. In conclusion, five suggestions for triggering a transition towards more sustainable PPE use are formulated: (1) diversifying targets/tools; (2) addressing structural aspects; (3) sustaining interventions in the long-term; (4) targeting farmers’ learning-by-experience; and (5) targeting PPE use on a collective level.

Dietary, lifestyle and clinico-pathological factors associated with APC mutations and promoter methylation in colorectal cancers from the EPIC-Norfolk Study

The tumour suppressor APC is the most commonly altered gene in colorectal cancer (CRC). Genetic and epigenetic alterations of APC may therefore be associated with dietary and lifestyle risk factors for CRC. Analysis of APC mutations in the extended mutation cluster region (codons 1276-1556) and APC promoter 1A methylation was performed on 185 archival CRC samples collected from participants of the European Prospective Investigation into Cancer (EPIC)-Norfolk Study, with the aim of relating these to high quality seven-day dietary and lifestyle data collected prospectively. Truncating APC mutations (APC+) and promoter 1A methylation (PM+) were identified in 43% and 23% of CRCs analysed, respectively. Distal CRCs were more likely than proximal CRCs to be APC+ or PM+ (P = 0.04). APC+ CRCs were more likely to be moderately/well differentiated and microsatellite stable than APC- CRCs (P = 0.05 and 0.03). APC+ CRC cases consumed more alcohol than their counterparts (P = 0.01) and PM+ CRC cases consumed lower levels of folate and fibre (P = 0.01 and 0.004). APC+ or PM+ CRC cases consumedhigher levels of processed meat and iron from red meat and red meat products (P=0.007 and 0.006). Specifically, CRC cases harbouring GC to AT transition mutations consumed higher levels of processed meat (35 versus 24 g/day, P = 0.04) and iron from red meat and red meat products (0.8 versus 0.6 mg/day, P = 0.05). In a logistic regression model adjusted for age, sex and cigarette smoking status, each 19g/day (1SD) increment increase in processed meat consumption was associated with cases with GC to AT mutations (OR 1.68, 95% CI 1.03-2.75). In conclusion, APC+ and PM+ CRCs may be influenced by diet and GC to AT mutations in APC are associated with processed meat consumption, suggesting a mechanistic link with dietary alkylating agents, such as N-nitroso compounds.