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Datasets are sometimes divided into distinct subsets, e.g. due to multi-center sampling, or to variations in instruments, questionnaire item ordering or mode of administration, and the data analyst then needs to assess whether a joint analysis is meaningful. The Principal Component Analysis-based Data Structure Comparisons (PCADSC) tools are three new non-parametric, visual diagnostic tools for investigating differences in structure for two subsets of a dataset through covariance matrix comparisons by use of principal component analysis. The PCADCS tools are demonstrated in a data example using European Social Survey data on psychological well-being in three countries, Denmark, Sweden, and Bulgaria. The data structures are found to be different in Denmark and Bulgaria, and thus a comparison of for example mean psychological well-being scores is not meaningful. However, when comparing Denmark and Sweden, very similar data structures, and thus comparable concepts of well-being, are found. Therefore, inter-country comparisons are warranted for these countries. [ABSTRACT FROM AUTHOR]

The exponential race model embodied in the theory of visual attention (TVA) and the power law generalization of the sample size model (SSPL) provide competing accounts of the mechanisms that determine how exposure duration, set size, and attention influence how many items enter visual short-term memory (VSTM). In the exponential race model, items compete for entry into VSTM in a processing race with exponentially distributed processing times. The most recent version of the sample size model assumes that target sensitivity measured by d′ increases monotonically as a function of exposure duration and decreases as a power function of set size. Here we compare the two models in a new experiment with letters and Gabor patches and with data from five previously published experiments. This was done by applying TVA to the two-alternative forced-choice method (2AFC), which forms the basis of the experimental work on the sample size model. Both models fitted individual participants' proportions of correct trials quite well, and overall the fits by the two models were almost indistinguishable. This was confirmed by formal pairwise comparison of TVA and SSPL by the Akaike information criterion and the Bayesian information criterion measures. Public Significance Statement: This study compares two popular models of selection of visual stimuli into visual short-term memory (VSTM): the exponential race model contained in the theory of visual attention (TVA) and the power law extension of the sample size model (SSPL) that is based on signal detection theory. To assess the models, we used the time course of stimulus entry into VSTM as a dependent variable in six experiments. Despite their differences, the models performed equally well and provided good accounts of the experimental data. [ABSTRACT FROM AUTHOR]

A physiologically based nonhomogeneous Poisson counter model of visual identification is presented. The model was developed in the framework of a Theory of Visual Attention (Bundesen, 1990; Kyllingsbæk, Markussen, & Bundesen, 2012) and meant for modeling visual identification of objects that are mutually confusable and hard to see. The model assumes that the visual system's initial sensory response consists in tentative visual categorizations, which are accumulated by leaky integration of both transient and sustained components comparable with those found in spike density patterns of early sensory neurons. The sensory response (tentative categorizations) feeds independent Poisson counters, each of which accumulates tentative object categorizations of a particular type to guide overt identification performance. We tested the model's ability to predict the effect of stimulus duration on observed distributions of responses in a nonspeeded (pure accuracy) identification task with eight response alternatives. The time courses of correct and erroneous categorizations were well accounted for when the event-rates of competing Poisson counters were allowed to vary independently over time in a way that mimicked the dynamics of receptive field selectivity as found in neurophysiological studies. Furthermore, the initial sensory response yielded theoretical hazard rate functions that closely resembled empirically estimated ones. Finally, supplied with a Naka-Rushton type contrast gain control, the model provided an explanation for Bloch's law. [ABSTRACT FROM AUTHOR]

Soil organic carbon (SOC) is broadly recognised as an important parameter affecting soil quality, and can therefore contribute to improving a number of soil properties that influence crop yield. Previous research generally indicates that soil organic carbon has positive effects on crop yields, but in many studies it is difficult to separate the effect of nutrients from the effect of SOC in itself. The aim of this study was to analyze whether the SOC content, in itself, has a significant effect on potential yields of commonly grown cereals across a wider range of soil types in Denmark. The study draws on historical data sets from the Danish national field trials consisting of 560 winter wheat ( Triticum aestivum L.) trials and 309 spring barley ( Hordeum vulgare L.) trials conducted over the past 20 and 17 years, respectively. We hypothesised that for these two crops, the potential grain yield, the yield with no fertiliser N application and the N use efficiency would be positively affected by SOC level. A statistical model was developed to explore relationships between SOC and potential yield, yields at zero N application and N use efficiency (NUE). The model included a variety of variables and aimed to elucidate the sole effect of SOC by controlling for potential confounding variables. No significant effect of SOC on potential winter wheat was found, whilst for spring barley, only for the course sandy loam soil type was a borderline significantly positive effect of SOC on potential yields found. The relationship between unfertilized plot yields and SOC was positive for winter wheat, although not significant, whilst for spring barley a significant positive effect of SOC was found only for the coarse sandy soil type, and a borderline significant positive effect of SOC was found for the coarse sandy loam soil type. A significant negative relationship was found between SOC and NUE for both winter wheat and spring barley. Based on the large dataset analyzed, we cautiously challenge the importance of SOC in contributing to crop productivity in contexts with similar soils and climate, and we speculate that in situations where nutrient limitation does not occur, SOC levels above 1% may be sufficient to sustain yields. In light of the findings presented in this study, further work should be conducted which can further elucidate the effect of SOC on yields. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

A goodness-of-fit test for continuous-time models is developed that examines if the parameter estimates are consistent with another for different sampling frequencies. The test compares parameter estimates obtained from estimating functions for downsamples of the data. We prove asymptotic results for stationary and ergodic processes, and apply the downsampling test to linear drift diffusions. Simulations indicate that the test is quite powerful in detecting non-Markovian deviations from the linear drift diffusions. [ABSTRACT FROM AUTHOR]

Abstract: 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 there’s 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. [Copyright &y& Elsevier]

Abstract: We construct the Laplace approximation of the Lebesgue density for a discrete partial observation of a multi-dimensional stochastic differential equation. This approximation may be computed integrating systems of ordinary differential equations. The construction of the Laplace approximation begins with the definition of the point of minimum energy. We show how such a point can be defined in the Cameron–Martin space as a maximum a posteriori estimate of the underlying Brownian motion given the observation of a finite-dimensional functional. The definition of the MAP estimator is possible via a renormalization of the densities of piecewise linear approximations of the Brownian motion. Using the renormalized Brownian density the Laplace approximation of the integral over all Brownian paths can be defined. The developed theory provides a method for performing approximate maximum likelihood estimation. [Copyright &y& Elsevier]

Analyzing the progression of Alzheimer's disease (AD) is challenging due to lacking sensitivity in currently available measures. AD stages are typically defined based on cognitive cut-offs, but this results in heterogeneous patient groups. More accurate modeling of the continuous progression of the disease would enable more accurate patient prognosis. To address these issues, we propose a new multivariate continuous-time disease progression (MCDP) model. The model is formulated as a nonlinear mixed-effects model that aligns patients based on their predicted disease progression along a continuous latent disease timeline. The model is evaluated using long-term follow-up data from 2152 participants in the Alzheimer's Disease Neuroimaging Initiative. The MCDP model was used to simultaneously model three cognitive scales; the Alzheimer's Disease Assessment Scale-cognitive subscale, the Mini-Mental State Examination, and the Clinical Dementia Rating scale-sum of boxes. Compared with univariate modeling and previously proposed multivariate disease progression models, the MCDP model showed superior ability to predict future patient trajectories. Finally, based on the multivariate disease timeline estimated using the MCDP model, the sensitivity of the individual items of the cognitive scales along the different stages of disease was analyzed. The analysis showed that delayed memory recall items had the highest sensitivity in the early stages of disease, whereas language and attention items were sensitive later in disease. [ABSTRACT FROM AUTHOR]

Background and aims: Root distribution over the soil profile is important for crop resource uptake. Using machine learning (ML), this study investigated whether measured square root of planar root length density (Sqrt_pRLD) at different soil depths were related to uptake of isotope tracer (15N) and drought stress indicator (13C) in wheat, to reveal root function. Methods: In the RadiMax semi-field root-screening facility 95 winter wheat genotypes were phenotyped for root growth in 2018 and 120 genotypes in 2019. Using the minirhizotron technique, root images were acquired across a depth range from 80 to 250 cm in May, June, and July and RL was extracted using a convolutional neural network. We developed ML models to explore whether the Sqrt_pRLD estimates at different soil depths were predictive of the uptake of deep soil nitrogen - using deep placement of 15N tracer as well as natural abundance of 13C isotope. We analyzed the correlations to tracer levels to both a parametrized root depth estimation and an ML approach. We further analyzed the genotypic effects on root function using mediation analysis. Results: Both parametrized and ML models demonstrated clear correlations between Sqrt_pRLD distribution and resource uptake. Further, both models demonstrated that deep roots at approx. 150 to 170 cm depth were most important for explaining the plant content of 15N and 13C isotopes. The correlations were higher in 2018. Conclusions: The results demonstrated that, parametrized models and ML-based analysis provided complementary insight into the importance of deep rooting for water and nitrogen uptake. [ABSTRACT FROM AUTHOR]

Entomophthoralean fungi are insect pathogenic fungi and are characterized by their active discharge of infective conidia that infect insects. Our aim was to study the effects of temperature on the discharge and to characterize the variation in the associated temporal pattern of a newly discovered Pandora species with focus on peak location and shape of the discharge. Mycelia were incubated at various temperatures in darkness, and conidial discharge was measured over time. We used a novel modification of a statistical model (pavpop), that simultaneously estimates phase and amplitude effects, into a setting of generalized linear models. This model is used to test hypotheses of peak location and discharge of conidia. The statistical analysis showed that high temperature leads to an early and fast decreasing peak, whereas there were no significant differences in total number of discharged conidia. Using the proposed model we also quantified the biological variation in the timing of the peak location at a fixed temperature. [ABSTRACT FROM AUTHOR]

Water availability is often described as one of the main drivers of phenology of tropical dry forests but experimental studies to identify the cues triggering phenological changes are few. In a greenhouse trial, we exposed seedlings of thirteen origins, seven from West and six from East Africa, respectively, of Adansonia digitata L.(baobab) to a well‐watered control treatment and a water withholding treatment in combination with exposure to three different daylengths (11.5, 12.0, and 12.5 hr). Responses were measured in terms of meristematic activity, number of leaves, and height growth followed over 6.5 months. Multi‐level mixed‐effects statistical models were used to analyze how environmental and inter‐population variables affected phenological behavior. Flushing was influenced by the daylength with the lowest degree of meristematic activity observed in the short daylength treatment. Daylength also influenced the number of leaves through an interaction with the water regime. The water regime influenced all variables through interactions with the origins. Seedlings subjected to water stress had higher meristematic activity, but initially lower numbers of leaves than continuously watered plants. Height growth in continuously watered plants was fastest or at par with water‐stressed plants, depending on the origin. Origins from West Africa tended to have higher meristematic activity and their phenology was found to be less influenced by water withholding than East African origins. There were no signs of significant differences between origins in their response to photoperiod. In conclusion, baobab seedlings show opportunistic behavior, setting leaves when water is available, but larger activity is found when days are long. We discuss the results in terms of triggering factors for baobab phenology and adaptation to specific environmental conditions at the site of origins. There are very few studies on triggering factors for phenology of dry zone tropical tree species, and even fewer studies that investigate how phenology is varying among origins in common garden experiments. In this study, we tested 13 baobab origins and their phenological response to drought stress and different daylengths. Our results demonstrate that both water availability and daylength influence flushing of leaves, and that origin react differently to these signals. [ABSTRACT FROM AUTHOR]

Many butterfly populations respond negatively to land-use intensification in human-dominated landscapes. Networks of protected sites have been established with the aim to halt species loss. We undertook annual surveys of all occurrence sites of 22 uncommon butterfly species in eastern Denmark during the period 2014–2019 and compared to a systematic atlas survey done 1989–1993, in order to assess trends in regional occupancy of species. Three out of 22 species went regionally extinct between 1993 and 2015. One species sustained a single population through the study period. Logistic regression for the remaining 18 species showed 10 to be in strong decline from 1993 to 2015, two showed a declining trend and six had stable trends. For all species except one, the declining trend continued 2015–2019. For five species, a sustained strong decline was evident. In 1993, the total count of occurrence sites for all 22 butterfly species was 565, which by 2019 had declined to 158 sites (a 72 % loss over 26 years). From 2015 to 2019 alone, the total count of occurrence sites shrank from 200 to 158 (a 21 % decline over just four years). Legal protection of areas (Natura 2000 and Danish Nature Protection Act §3) was, unexpectedly, not associated with lower probability of local extinction for butterfly population. The observed sustained decline across species suggests an overall low efficiency of the network of protected sites, probably due to a combination of misguided management regimes and payment of extinction debts from the past. [ABSTRACT FROM AUTHOR]

Abstract: Plants produce a multitude of metabolites that contribute to their fitness and survival and play a role in local adaptation to environmental conditions. The effects of environmental variation are particularly well studied within the genus Plantago; however, previous studies have largely focused on targeting specific metabolites. Studies exploring metabolome‐wide changes are lacking, and the effects of natural environmental variation and herbivory on the metabolomes of plants growing in situ remain unknown. An untargeted metabolomic approach using ultra‐high‐performance liquid chromatography–mass spectrometry, coupled with variation partitioning, general linear mixed modeling, and network analysis was used to detect differences in metabolic phenotypes of Plantago major in fifteen natural populations across Denmark. Geographic region, distance, habitat type, phenological stage, soil parameters, light levels, and leaf area were investigated for their relative contributions to explaining differences in foliar metabolomes. Herbivory effects were further investigated by comparing metabolomes from damaged and undamaged leaves from each plant. Geographic region explained the greatest number of significant metabolic differences. Soil pH had the second largest effect, followed by habitat and leaf area, while phenological stage had no effect. No evidence of the induction of metabolic features was found between leaves damaged by herbivores compared to undamaged leaves on the same plant. Differences in metabolic phenotypes explained by geographic factors are attributed to genotypic variation and/or unmeasured environmental factors that differ at the regional level in Denmark. A small number of specialized features in the metabolome may be involved in facilitating the success of a widespread species such as Plantago major into such wide range of environmental conditions, although overall resilience in the metabolome was found in response to environmental parameters tested. Untargeted metabolomic approaches have great potential to improve our understanding of how specialized plant metabolites respond to environmental change and assist in adaptation to local conditions. [ABSTRACT FROM AUTHOR]

• Intrinsic resistance in wild strawberry plantations inhibited generalist aphid population. • Plant genotypes that were resistant against a chewing beetle (Galerucella tenella), conveyed resistance to generalist aphid only. • There were more specialists aphids on high diversity plots. • Anthocorids and Lacewing adults were more on high diversity plots, whereas other specialist predators followed aphid prey. Ecological theory hypothesizes that plant trait diversity may be as important as the presence of specific functional traits (e.g., resistance) for the herbivore and predator communities within a population. We used experimental populations of wild woodland strawberry (Fragaria vesca) to test whether the degree of plant genotypic diversity and/or the existence of specific resistance traits play a role in the host plant's community structure specifically, the community of generalist and specialist aphids and their natural enemies. In 2019, we studied the aphid abundance and relative predator abundance in an experimental field site in Alnarp, Southern Sweden; the field consisted of plots planted with combinations of 20 different wild strawberry genotypes. These strawberry genotypes were previously identified as either susceptible to or resistant against the herbivorous beetle (Galerucella tenella). Two aphid species, Chaetosiphon fragaefolii (specialist) and the exotic Aphis gossypii (generalist) were found in the plots and of the two species A. gossypii was dominant. The abundance of the specialist aphid (C. fragaefolii) was highest in susceptible plots with high genotypic diversity, while the generalist (A. gossypii) was highest in plots with a mix of resistant and susceptible plants with high genotypic diversity. Anthocorid predators, developed significantly higher population densities in strawberry plots with high genotypic diversity. Overall, predator abundance showed a positive correlation with aphid abundance. These results show that the specific functional trait of resistance as well as plant diversity affected aphids. Knowledge about these effects can be important factors to consider when designing strawberry plantings less susceptible to aphids. [ABSTRACT FROM AUTHOR]

The coffee research community has maintained a long ongoing debate regarding the implications of shade trees in coffee production. Historically, there has been contrasting results and opinions on this matter, thus recommendations for the use of shade (namely in coffee agroforestry systems) are often deemed controversial, particularly due to potential yield declines and farmers' income. This study is one of the first demonstrating how several Coffea arabica cultivars respond differently to shade with respect to yield. By standardising more than 200 coffee yield data from various in-field trials, we assembled the so-called "Ristretto" data pool, a one of a kind, open-source dataset, consolidating decades of coffee yield data under shaded systems. With this standardised dataset, our meta-analysis demonstrated significant genotypic heterogeneity in response to shade, showing neutral, inverted U-shaped and decreasing trends between yield and shade cover amongst 18 different cultivars. These findings encourage the examination of C. arabica at the cultivar level when assessing suitability for agroforestry systems. Comparison of productivity is also encouraged across a range of low to moderate shade levels (10–40%), in order to help elucidate potential unknown optimal shade levels for coffee production. [ABSTRACT FROM AUTHOR]

Small-angle X-ray and neutron scattering have become increasingly popular owing to improvements in instrumentation and developments in data analysis, sample handling and sample preparation. For some time, it has been suggested that a more systematic approach to the quantification of the information content in small-angle scattering data would allow for a more optimal experiment planning and a more reliable data analysis. In the present article, it is shown how ray-tracing techniques in combination with a statistically rigorous data analysis provide an appropriate platform for such a systematic quantification of the information content in scattering data. As examples of applications, it is shown how the exposure time at different instrumental settings or contrast situations can be optimally prioritized in an experiment. Also, the gain in information by combining small-angle X-ray and neutron scattering is assessed. While solution small-angle scattering data of proteins and protein-lipid complexes are used as examples in the present case study, the approach is generalizable to a wide range of other samples and experimental techniques. The source code for the algorithms and ray-tracing components developed for this study has been made available on-line. [ABSTRACT FROM AUTHOR]

Optimizing crops water use is essential for ensuring food production under future climate scenarios. Therefore, new cultivars that are capable of maintaining production under limited water resource are needed. This study screened for clonal differences in intrinsic water use efficiency (WUE i ) within a dihaploid potato ( Solanum tuberosum L.) mapping population under well-watered (WW) and drought-stress (DS) conditions. The factorial dependency of WUE i on several plant bio-physiological traits was analyzed, and clonal difference of WUE i was compared. Significant differences in WUE i were found among the clones within the population. Under WW the two clones showing the highest WUE i were significantly different from the two lowest WUE i performing clones. This could only be seen as a trend under DS. Under WW, WUE i differences were closely associated to net photosynthetic rate ( A n ) and nitrogen isotope composition ( δ 15 N) in the leaf biomass, but did not relate to stomatal conductance ( g s ) and carbon isotope composition ( δ 13 C) in the leaf biomass. A n was found to correlate significantly with leaf nitrogen concentration ([N] leaf ) and chlorophyll content index (CCI) under WW. Leaf abscisic acid concentration did not correspond to the changes in g s , indicating that other factors might have been involved in controlling g s among the different clones. Collectively, the clonal differences in WUE i were attributed mainly to the variation in A n , which in turn was influenced by plant N metabolism. Clones with high WUE i could be potentially used as material in future breeding programs. Furthermore CCI seemed to be a reliable tool in estimating the clonal A n and thereby WUE i . [ABSTRACT FROM AUTHOR]

Deep rooting winter wheat genotypes can reduce nitrate leaching losses and increase N uptake. We aimed to investigate which deep root traits are correlated to deep N uptake and to estimate genetic variation in root traits and deep 15N tracer uptake. In 2 years, winter wheat genotypes were grown in RadiMax, a semifield root‐screening facility. Minirhizotron root imaging was performed three times during the main growing season. At anthesis, 15N was injected via subsurface drip irrigation at 1.8 m depth. Mature ears from above the injection area were analysed for 15N content. From minirhizotron image‐based root length data, 82 traits were constructed, describing root depth, density, distribution and growth aspects. Their ability to predict 15N uptake was analysed with the least absolute shrinkage and selection operator (LASSO) regression. Root traits predicted 24% and 14% of tracer uptake variation in 2 years. Both root traits and genotype showed significant effects on tracer uptake. In 2018, genotype and the three LASSO‐selected root traits predicted 41% of the variation in tracer uptake, in 2019 genotype and one root trait predicted 48%. In both years, one root trait significantly mediated the genotype effect on tracer uptake. Deep root traits from minirhizotron images can predict deep N uptake, indicating the potential to breed deep‐N‐uptake‐genotypes. Summary Statement: Root traits of winter wheat were constructed from minirhizotron image data. Root traits predicted 24% of 15N tracer uptake, which was injected at anthesis at 1.8 m depth, and explained genotypic variation in tracer uptake. [ABSTRACT FROM AUTHOR]

Highlights: [•] We consider models for data that require warping, but contains systematic differences. [•] Fixed effects, systematic differences and data warping are estimated simultaneously. [•] All hyperparameters in the model can be estimated by maximum likelihood estimation. [•] Results on simulated data show near-optimal behavior of the method. [•] The method clearly outperform conventional two-stage registration/modeling procedures. [Copyright &y& Elsevier]

Abstract: 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. [Copyright &y& Elsevier]

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. [ABSTRACT FROM AUTHOR]

Objective To investigate parameters causing canine thromboelastographic hypercoagulability and to investigate whether thromboelastography (TEG) with Cytochalasin D (Cyt D) added is related to parameters of platelet activity. Design Prospective observational study on hemostatic and inflammatory parameters. Data were collected between November 2012 and July 2013. Setting University teaching hospital. Animals Twenty-eight dogs suffering from diseases predisposing to thrombosis and 19 clinically healthy dogs. Diseased dogs were enrolled if they fulfilled inclusion criteria regarding age, size, informed client consent, and obtained a diagnosis of a disease that has been associated with thrombosis or hypercoagulability. Interventions None. Measurements and Main Results Parameters of coagulation and anticoagulation, fibrinolysis, and antifibrinolysis, platelet activity, inflammation, platelet count, and hematocrit were measured using CBC, TEG, platelet aggregation on multiplate, platelet activity on flow cytometry, and hemostatic and inflammatory markers on plasma and serum analyses. ANOVA and multilinear regression analyses indicated that especially hematocrit and the inflammatory parameters C-reactive protein and interleukin-8 showed best association with overall clot strength in diseased dogs with hypercoagulable TEG tracings. Ratios presumed to reflect platelet contribution to the TEG tracing obtained in TEG analyses with Cyt D were related especially with hematocrit and P-selectin expression of platelets measured after γ-Thrombin activation on flow cytometry. Conclusion Overall clot strength in TEG analyses of the hypercoagulable dogs included in the present study appears to be primarily associated with inflammation as well as hematocrit. Furthermore, the ratio between standard TEG analyses and TEG analyses with Cyt D may reflect some degree of platelet activity. [ABSTRACT FROM AUTHOR]

Aim: To understand how the integration of contextual spatial data on land cover and human infrastructure can help reduce spatial bias in sampling effort, and improve the utilization of citizen science-based species recording schemes. By comparing four different citizen science projects, we explore how the sampling design's complexity affects the role of these spatial biases. Location: Denmark, Europe. Methods: We used a point process model to estimate the effect of land cover and human infrastructure on the intensity of observations from four different citizen science species recording schemes. We then use these results to predict areas of under- and oversampling as well as relative biodiversity 'hotspots' and 'deserts', accounting for common spatial biases introduced in unstructured sampling designs. Results: We demonstrate that the explanatory power of spatial biases such as infrastructure and human population density increased as the complexity of the sampling schemes decreased. Despite a low absolute sampling effort in agricultural landscapes, these areas still appeared oversampled compared to the observed species richness. Conversely, forests and grassland appeared undersampled despite higher absolute sampling efforts. We also present a novel and effective analytical approach to address spatial biases in unstructured sampling schemes and a new way to address such biases, when more structured sampling is not an option. Main conclusions: We show that citizen science datasets, which rely on untrained amateurs, are more heavily prone to spatial biases from infrastructure and human population density. Objectives and protocols of mass-participating projects should thus be designed with this in mind. Our results suggest that, where contextual data is available, modelling the intensity of individual observation can help understand and quantify how spatial biases affect the observed biological patterns. [ABSTRACT FROM AUTHOR]

A central task in the analysis of human movement behavior is to determine systematic patterns and differences across experimental conditions, participants and repetitions. This is possible because human movement is highly regular, being constrained by invariance principles. Movement timing and movement path, in particular, are linked through scaling laws. Separating variations of movement timing from the spatial variations of movements is a well-known challenge that is addressed in current approaches only through forms of preprocessing that bias analysis. Here we propose a novel nonlinear mixed-effects model for analyzing temporally continuous signals that contain systematic effects in both timing and path. Identifiability issues of path relative to timing are overcome by using maximum likelihood estimation in which the most likely separation of space and time is chosen given the variation found in data. The model is applied to analyze experimental data of human arm movements in which participants move a hand-held object to a target location while avoiding an obstacle. The model is used to classify movement data according to participant. Comparison to alternative approaches establishes nonlinear mixed-effects models as viable alternatives to conventional analysis frameworks. The model is then combined with a novel factor-analysis model that estimates the low-dimensional subspace within which movements vary when the task demands vary. Our framework enables us to visualize different dimensions of movement variation and to test hypotheses about the effect of obstacle placement and height on the movement path. We demonstrate that the approach can be used to uncover new properties of human movement. [ABSTRACT FROM AUTHOR]

Shade is one of the recommended management solutions to mitigate the effects of heat stress, which is a major challenge for cocoa production globally. Nevertheless, there are limited studies to verify this hypothesis. Here, we evaluate the effects of heat and shade on cocoa physiology using experimental plots with six-month old potted seedlings in a randomized complete block design. Infrared heaters were applied for one month to increase leaf temperatures by an average of 5–7 ºC (heat treatment) compared with no heat (unheated treatments), and shaded plants were placed under a shade net removing 60% of the light compared with no shade (sun treatments). Plants under heat treatments in sun and in shade showed severe reduction in photosynthesis. Measurements of chlorophyll fluorescence and photosynthetic light response curves indicated that heat caused damages at photosystem II and additionally resulted in lower rates of maximal photosynthesis. Temperature optima for photosynthesis were at 31–33 ºC with only small differences between treatments, and as light saturation was reached at low PAR levels of 325 – 380 µmol m−2 s−1 in shade and 427 – 521 µmol m−2 s−1 in sun, ambient rates of photosynthesis were comparable between sun and shade treatments. Heat treatments resulted in decreased concentrations of chlorophyll and changed pigment composition, reduced specific leaf areas, and plant biomass. While shade may benefit cocoa seedlings, our results indicate that the positive effects may not be sufficient to counteract the negative effects of increased temperatures on cocoa physiology. • Heat is imposed on six-month old cocoa seedlings and shade is provided. • Heat treated plants show severe reduction in photosynthesis and damages at photosystem II. • Heat decreases chlorophyll concentrations and pigment composition. • Shade improves cocoa physiology but has limited effects on heat. [ABSTRACT FROM AUTHOR]

Background: Polyacrylamide hydrogel (PAAG) was evaluated recently to treat osteoarthritis (OA) in horses with highly encouraging results; however no long term field-study was done to explore its clinical efficacy and lasting effect. The objective of this study was to evaluate the efficacy of PAAG in improving clinical signs of OA in horses. We hypothesized that lameness grade would significantly improve and the effect would last at least 2 years in osteoarthritic joints treated with PAAG. Forty three horses older than 2 years with OA in only one joint based on clinical evaluation, intra-articular anaesthesia and imaging (radiography) were included in this study. Horses were injected with 2 ml of PAAG into the affected joint and were followed up at 1, 3, 6, 12 and 24 months. Efficacy of PAAG was evaluated by blinded clinical assessment of lameness. Adverse reactions to joint injection were assessed. Data relating to case details, type of activity, joint and limb involved, lameness duration, lameness grading, previous joint treatment, joint effusion grading, radiographic grading, and owner assessment were recorded. Factors associated with the outcome measure “lameness grading” were analyzed using generalized linear mixed model for logistic regression. Results: At 1, 3, 6, 12 and 24 months follow-up, 59%, 69%, 79%, 81/% and 82.5% of horses were non-lame respectively. Reduction of joint effusion was observed over time. No side effect was observed in the treated joints. There was a significant decrease in lameness grade from baseline to 1, 3, 6, 12 and 24 months (P < 0.0001) and a significant positive association with joint effusion (P < 0.0001). Estimates for odds ratio (OR) showed that the effect of treatment increased over time (OR for lower lameness from month 1 to month 24 relative to baseline increased from 20 to 58). Conclusions: PAAG significantly alleviated lameness and joint effusion in osteoarthritic joints. PAAG is a safe and lasting (at least 24 months) OA treatment in horses. PAAG is a promising new treatment for OA in horses. [ABSTRACT FROM AUTHOR]

Abstract: Antibodies to Coxiella burnetii have been found in the Danish dairy cattle population with high levels of herd and within herd seroprevalences. However, the prevalence of antibodies to C. burnetii in Danish beef cattle remains unknown. The objectives of this study were to (1) estimate the prevalence and (2) identify risk factors associated with C. burnetii seropositivity in Danish beef and dairy cattle based on sampling at slaughter. Eight hundred blood samples from slaughtered cattle were collected from six Danish slaughter houses from August to October 2012 following a random sampling procedure. Blood samples were tested by a commercially available C. burnetii antibody ELISA kit. A sample was defined positive if the sample-to-positive ratio was greater than or equal to 40. Animal and herd information were extracted from the Danish Cattle Database. Apparent (AP) and true prevalences (TPs) specific for breed, breed groups, gender and herd type; and breed-specific true prevalences with a random effect of breed was estimated in a Bayesian framework. A Bayesian logistic regression model was used to identify risk factors of C. burnetii seropositivity. Test sensitivity and specificity estimates from a previous study involving Danish dairy cattle were used to generate prior information. The prevalence was significantly higher in dairy breeds (AP=9.11%; TP=9.45%) than in beef breeds (AP=4.32%; TP=3.54%), in females (AP=9.10%; TP=9.40%) than in males (AP=3.62%; TP=2.61%) and in dairy herds (AP=15.10%; TP=16.67%) compared to beef herds (AP=4.54%; TP=3.66%). The Bayesian logistic regression model identified breed group along with age, and number of movements as contributors for C. burnetii seropositivity. The risk of seropositivity increased with age and increasing number of movements between herds. Results indicate that seroprevalence of C. burnetii is lower in cattle sent for slaughter than in Danish dairy cows in production units. A greater proportion of this prevalence is attributed to slaughtered cattle of dairy breeds or cattle raised in dairy herds rather than beef breeds. [Copyright &y& Elsevier]

Background: Platinum-based chemotherapy has long been used in the treatment of a variety of cancers and functions by inducing DNA damage. ERCC1 and ERCC4 are involved in the removal of this damage and have previously been implicated in resistance to platinum compounds. The aim of the current investigation is to determine the presence, frequency and prognostic impact of ERCC1 or ERCC4 gene copy number alterations in colorectal cancer (CRC).Methods: Fluorescent in situ hybridization probes directed at ERCC1 and ERCC4 with relevant reference probes were constructed. Probes were tested in a CRC cell line panel and in tumor sections from 152 stage III CRC chemonaive patients. Relationships between biomarker status and clinical endpoints (overall survival, time to recurrence, and local recurrence in rectal cancer) were analyzed by survival statistics.Results: ERCC1-19q13 copy number alterations were observed in a single cell line metaphase (HT29). In patient material, ERCC1-19q13 copy number gains (ERCC1-19q13/CEN-2 ≥ 1.5) were detected in 27.0% of specimens, whereas ERCC1-19q13 deletions (ERCC1-19q13/CEN-2 < 0.8) were only detected in 1.3%. ERCC1-19q13 gain was significantly associated with longer survival (multivariate analysis, HR: 0.45, 95% CI: 0.20-1.00, p = 0.049) in patients with colon tumors, but not rectal tumors. No ERCC4 aberrations were detected and scoring was discontinued after 50 patients.Conclusions: ERCC1-19q13 copy number gains occur frequently in stage III CRC and influences survival in patients with colon tumors. Future studies will investigate the effect of ERCC1-19q13 aberrations in a platinum-treated patient population with the aim of developing a predictive biomarker profile for oxaliplatin sensitivity in CRC. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Abstract: The risk for contamination of potatoes and groundwater through subsurface drip irrigation with low quality water was explored in 30 large-scale lysimeters containing repacked coarse sand and sandy loam soils. The human pathogens, Salmonella Senftenberg, Campylobacter jejuni and Escherichia coli O157:H7, and the virus indicator Salmonella Typhimurium bacteriophage 28B, were added weekly through irrigation tubes for one month with low irrigation rates (8 mm per week). In the following six months lysimeters were irrigated with groundwater free of pathogens. Two weeks after irrigation was started, phage 28B was detected in low concentrations (2 pfu ml−1) in leachate from both sandy loam soil and coarse sand lysimeters. After 27 days, phage 28B continued to be present in similar concentrations in leachate from lysimeters containing coarse sand, while no phage were found in lysimeters with sandy loam soil. The added bacterial pathogens were not found in any leachate samples during the entire study period of 212 days. Under the study conditions with repacked soil, limited macropores and low water velocity, bacterial pathogens seemed to be retained in the soil matrix and died-off before leaching to groundwater. However, viruses may leach to groundwater and represent a health risk as for some viruses only few virus particles are needed to cause human disease. The bacterial pathogens and the phage 28B were found on the potato samples harvested just after the application of microbial tracers was terminated. The findings of bacterial pathogens and phage 28 on all potato samples suggest that the main risk associated with subsurface drip irrigation with low quality water is faecal contamination of root crops, in particular those consumed raw. [Copyright &y& Elsevier]