Bo Markussen

Impact assessment revisited: improving the theoretical basis for management of invasive alien species

The theoretical underpinnings of the assessment of invasive alien species impacts need to be improved. At present most approaches are unreliable to quantify impact at regional scales and do not allow for comparison of different invasive species. There are four basic problems that need to be addressed: (1) Some impacted ecosystem traits are spatially not additive; (2) invader effects may increase non-linearly with abundance or there may be effect thresholds impairing estimates of linear impact models; (3) the abundance and impact of alien species will often co-vary with environmental variation; and (4) the total invaded range is an inappropriate measure for quantifying regional impact because the habitat area available for invasion can vary markedly among invasive species. Mathematical models and empirical data using an invasive alien plant species (Heracleum mantegazzianum) indicate that ignoring these issues leads to impact estimates almost an order of magnitude from the real values. Thus, we propose a habitat-sensitive formula for regional impact assessment that is unaffected by non-linearity. Furthermore, we make some statistical suggestions on how to assess invader effects properly and we discuss the quantification of the invaded range. These improvements are crucial for impact assessment with the overall aim of prioritizing management of invasive species.

Probabilistic environmental risk characterization of pharmaceuticals in sewage treatment plant discharges

The occurrence of pharmaceuticals in different water bodies and the findings of effects on aquatic organisms in ecotoxicity tests have raised concerns about environmental risks of pharmaceuticals in receiving waters. Due to the fact that the amount of ecotoxicological studies has increased significantly during the last decade, probabilistic approaches for risk characterization of these compounds may be feasible. This approach was evaluated by applying it to 22 human-used pharmaceuticals covering both pharmaceuticals with a high volume and high ecotoxicity, using ecotoxicological effect data from laboratory studies and comparing these to monitoring data on the effluents from sewage treatment plants in Europe and pharmaceutical sales quantities. We found that for 19 of the 22 selected pharmaceuticals the existing data were sufficient for probabilistic risk characterizations. The subsequently modeled ratios between monitored concentrations and low-effect concentrations were mostly above a factor of 100. Compared to the current paradigm for EU environmental risk assessment where a safety factor of 10 or 100 might have been used it seems that for the modeled compounds theres a low environmental risk. However, similarly calculated ratios for five pharmaceuticals (propranolol, ibuprofen, furosemide, ofloxacin, and ciprofloxacin) were below 100, while ibuprofen and ciprofloxacin are considered to be of high concern due to lack of ecotoxicity studies. This paper shows that by applying probabilistic approaches, existing data can be used to execute a comprehensive study on probability of impacts, thereby contributing to a more comprehensive environmental risk assessment of pharmaceuticals.

Genetic Variation in Virulence among Chalkbrood Strains Infecting Honeybees

Ascosphaera apis causes chalkbrood in honeybees, a chronic disease that reduces the number of viable offspring in the nest. Although lethal for larvae, the disease normally has relatively low virulence at the colony level. A recent study showed that there is genetic variation for host susceptibility, but whether Ascosphaera apis strains differ in virulence is unknown. We exploited a recently modified in vitro rearing technique to infect honeybee larvae from three colonies with naturally mated queens under strictly controlled laboratory conditions, using four strains from two distinct A. apis clades. We found that both strain and colony of larval origin affected mortality rates. The strains from one clade caused 12–14% mortality while those from the other clade induced 71–92% mortality. Larvae from one colony showed significantly higher susceptibility to chalkbrood infection than larvae from the other two colonies, confirming the existence of genetic variation in susceptibility across colonies. Our results are consistent with antagonistic coevolution between a specialized fungal pathogen and its host, and suggest that beekeeping industries would benefit from more systematic monitoring of this chronic stress factor of their colonies.

Factors associated with Coxiella burnetii antibody positivity in Danish dairy cows

The aim of the study was to identify associations between the level of Coxiella burnetii (C. burnetii) antibodies in individual milk samples and cow and herd level factors in Danish dairy cows. The study, designed as a prospective cross sectional study with follow up, included 24 herds identified by a stratified random sampling procedure according to the level of C. burnetii antibodies in one bulk tank milk (BTM) sample at the beginning of the study. Ten herds were BTM positive, ten herds were BTM negative and four herds had an intermediate level. The samples were tested with an ELISA and results determined as S/P (sample to positive control) values. Three cross sectional studies of all lactating cows within each herd were then conducted during an 11 months follow up period with collection of a total of 5829 milk samples from 3116 cows. Each sample was tested with the same ELISA as used for BTM testing, and cows were considered test positive for S/P values ≥ 40, and otherwise negative. Individual cow information was extracted from the Danish Cattle Database and herd information was obtained from a telephone interview with each farmer. From multivariable logistic regression analysis accounting for hierarchical structures in the data it was concluded that odds for seropositivity increased with Danish Holstein breed, increasing number of parity and high milk protein contents, but decreased with increasing milk yield and high milk fat contents. Cows were at a higher risk during summer than other seasons. Among the herd level factors, herd size, tie stall housing system, quarantine of newly purchased animals and good hygienic precautions taken by the veterinarian before entering into the stable were also significantly associated with reduced odds of C. burnetii antibody positivity. The prevalence of test positive cows was almost constant during the study period in herds which were initially BTM positive and BTM intermediate, whilst the prevalence of positive cows in a few of the initial BTM negative herds changed from almost zero to higher than 60%. This indicates that herd infections last quite long and that test negative herds may convert to positive due to a few latently infected cows or due to transmissions from other herds.

Mechanisms of topoisomerase I (TOP1) gene copy number increase in a stage III colorectal cancer patient cohort.

Background Topoisomerase I (Top1) is the target of Top1 inhibitor chemotherapy. The TOP1 gene, located at 20q12-q13.1, is frequently detected at elevated copy numbers in colorectal cancer (CRC). The present study explores the mechanism, frequency and prognostic impact of TOP1 gene aberrations in stage III CRC and how these can be detected by fluorescent in situ hybridization (FISH). Methods Nine CRC cell line metaphase spreads were analyzed by FISH with a TOP1 probe in combination with a reference probe covering either the centromeric region of chromosome 20 (CEN-20) or chromosome 2 (CEN-2). Tissue sections from 154 chemonaive stage III CRC patients, previously studied with TOP1/CEN-20, were analyzed with TOP1/CEN-2. Relationships between biomarker status and overall survival (OS), time to recurrence (TTR) in CRC and time to local recurrence (LR; rectal cancer only) were determined. Results TOP1 aberrations were observed in four cell line metaphases. In all cell lines CEN-2 was found to reflect chromosomal ploidy levels and therefore the TOP1/CEN-2 probe combination was selected to identify TOP1 gene gains (TOP1/CEN-2≥1.5). One hundred and three patients (68.2%) had TOP1 gain, of which 15 patients (14.6%) harbored an amplification (TOP1/CEN-20≥2.0). TOP1 gene gain did not have any association with clinical endpoints, whereas TOP1 amplification showed a non-significant trend towards longer TTR (multivariate HR: 0.50, p = 0.08). Once amplified cases were segregated from other cases of gene gain, non-amplified gene increases (TOP1/CEN-2≥1.5 and TOP1/CEN-20<2.0) showed a trend towards shorter TTR (univariate HR: 1.57, p = 0.07). Conclusions TOP1 gene copy number increase occurs frequently in stage III CRC in a mechanism that often includes CEN-20. Using CEN-2 as a measurement for tumor ploidy levels, we were able to discriminate between different mechanisms of gene gain, which appeared to differ in prognostic impact. TOP1 FISH guidelines have been updated.

Potential of GLMM in modelling invasive spread

Utilization of Generalized Linear Mixed Models (GLMM) in invasion biology has increased exponentially during the last 5-10 years. GLMM are useful tools that can handle data with various distributions as well as s patial or temporal dependence which are involved in many study designs. We review the c urrent state-of-the-art of GLMM with special focus on applications in invasion biol ogy. This review covers all steps of data analysis with GLMM. We address frequently encountered practical problems, such as failure of convergence, and put some emphasis on validation of model assumptions. Further, we point towards possibilities of analysin g zero-heavy data using combined GLMM. More detailed insight into practical applicat ions of GLMM is provided in three worked examples in the supplementary material. Regarding applications of GLMM in invasion biology, a literature analysis showed that random effects are mostly used to account for non-independence of observations due to study design, but rarely for estimation of random variation. There may be some potential in using random-effect estimation more consciously, like in some recent st udies of genetic variation of invasive species. Often, invasion biologists have to deal wi th count data or proportions. In such cases, several methods of parameter estimation are available, but their suitability depends on characteristics of the data at hand and, hence, they should be chosen carefully. Also repeated measures are common in invasion biology. In GLMM frameworks, the auto-correlation of such data can b e modelled by structured co-variance matrices. This opportunity, however, has seldom bee n used.

Haemostatic alterations in a group of canine cancer patients are associated with cancer type and disease progression

BackgroundHaemostatic alterations are commonly detected in human and canine cancer patients. Previous studies have described haemostatic dysfunction in canine patients with haemangiosarcomas and carcinomas, and haemostasis has been assessed in dogs with various malignant and benign neoplasias. Few studies have addressed the effect of cancer type and progression of disease on the presence of haemostatic alterations in canine patients. The objective of the present study was to evaluate haemostatic variables of coagulation and fibrinolysis in a group of canine cancer patients, and to compare haemostatic changes to the cancer type and progression of disease.MethodsThe study population consisted of 71 dogs with malignant neoplasia presented to the University Hospital for Companion Animals, Faculty of Life Sciences, University of Copenhagen, Denmark. The study was designed as a prospective observational study evaluating the haemostatic function in canine cancer patients stratified according to type of cancer disease and disease progression. The coagulation response was evaluated by thromboelastrography (TEG), platelet count, activated partial thromboplastin time (aPTT), prothombin time (PT), fibrinogen and antithrombin (AT); and fibrinolysis by d-dimer and plasminogen.ResultsHypercoagulability was the most common haemostatic dysfunction found. Non mammary carcinomas had increased clot strength (TEG G), aPTT and fibrinogen compared to the other groups. When stratifying the patients according to disease progression dogs with distant metastatic disease exhibited significantly increased fibrinogen, and d-dimer compared to dogs with local invasive and local non-invasive cancers.ConclusionHypercoagulability was confirmed as the most common haemostatic abnormality in canine cancer patients and haemostatic dysfunction in canine cancer patients was found related to the cancer type and progression of disease. Increase in TEG G, aPTT and fibrinogen were observed in non-mammary carcinomas and were speculated to overall represent a proinflammatory response associated with the disease. Dogs with distant metastatic disease exhibited increased fibrinogen and d-dimer. Future studies are needed to elucidate the clinical importance of these results.

Leaching of Cryptosporidium parvum Oocysts, Escherichia coli, and a Salmonella enterica Serovar Typhimurium Bacteriophage through Intact Soil Cores following Surface Application and Injection of Slurry

ABSTRACT Increasing amounts of livestock manure are being applied to agricultural soil, but it is unknown to what extent this may be associated with contamination of aquatic recipients and groundwater if microorganisms are transported through the soil under natural weather conditions. The objective of this study was therefore to evaluate how injection and surface application of pig slurry on intact sandy clay loam soil cores influenced the leaching of Salmonella enterica serovar Typhimurium bacteriophage 28B, Escherichia coli, and Cryptosporidium parvum oocysts. All three microbial tracers were detected in the leachate on day 1, and the highest relative concentration was detected on the fourth day (0.1 pore volume). Although the concentration of the phage 28B declined over time, the phage was still found in leachate at day 148. C. parvum oocysts and chloride had an additional rise in the relative concentration at a 0.5 pore volume, corresponding to the exchange of the total pore volume. The leaching of E. coli was delayed compared with that of the added microbial tracers, indicating a stronger attachment to slurry particles, but E. coli could be detected up to 3 months. Significantly enhanced leaching of phage 28B and oocysts by the injection method was seen, whereas leaching of the indigenous E. coli was not affected by the application method. Preferential flow was the primary transport vehicle, and the diameter of the fractures in the intact soil cores facilitated transport of all sizes of microbial tracers under natural weather conditions.

Testing a Poisson counter model for visual identification of briefly presented, mutually confusable single stimuli in pure accuracy tasks.

The authors propose and test a simple model of the time course of visual identification of briefly presented, mutually confusable single stimuli in pure accuracy tasks. The model implies that during stimulus analysis, tentative categorizations that stimulus i belongs to category j are made at a constant Poisson rate, v(i, j). The analysis is continued until the stimulus disappears, and the overt response is based on the categorization made the greatest number of times. The model was evaluated by Monte Carlo tests of goodness of fit against observed probability distributions of responses in two extensive experiments and also by quantifications of the information loss of the model compared with the observed data by use of information theoretic measures. The model provided a close fit to individual data on identification of digits and an apparently perfect fit to data on identification of Landolt rings.

Large deformation diffeomorphisms with application to optic flow

Using standard statistical assumptions we derive a stochastic differential equation generating flows of diffeomorphisms. These stochastic processes provide a generative model for non-rigid registration and image warping problems. We give a mathematically rigorous derivation of the renormalized Brownian density in context of maximum a posteriori estimation of the underlying Brownian motions driving the warp flow. The second part of the paper combines the prior model with a likelihood model for image sequences. The combined model is employed to study the warp field for an image sequence of turbulent smoke.