A scaled sample space cube used to illustrate attributable fractions

A three-dimensional graphic method is proposed for displaying the association structure between multiple explanatory variables and their relation to a categorical response. The method combines the techniques of mosaic displays and scaled Venn diagrams, and is especially useful for illustrating attributable fractions in epidemiology. The primary purpose is to show the reduction of disease risk in a population if the joint exposure distribution or the conditional risk function is modified, and the method can be extended to illustrate the potential effects of successive removal of exposures on the overall risk of disease. The scaled sample space cube may be used for communicating the difficult concept of attributable fraction to statisticians, the medical community and the general public in an easily understandable way. Demonstrations of the method use theoretical models as well as data from the Hordaland study on the effect of smoking and occupational exposure on obstructive lung disease. Also, the general principle of adding a third dimension to a mosaic display, instead of using shading or colouring, to show an attribute of a cell in a multiway contingency table, can be helpful for other purposes, as in residual analysis of a loglinear model fitting.     

RATE OF O2 PRODUCTION DERIVED FROM PULSE‐AMPLITUDE‐MODULATED FLUORESCENCE: TESTING THREE BIOOPTICAL APPROACHES AGAINST MEASURED O2‐PRODUCTION RATE1

Light absorption by phytoplankton is both species specific and affected by photoacclimational status. To estimate oxygenic photosynthesis from pulse‐amplitude‐modulated (PAM) fluorescence, the amount of quanta absorbed by PSII needs to be quantified. We present here three different biooptical approaches to estimate the fraction of light absorbed by PSII: (1) the factor 0.5, which implies that absorbed light is equally distributed among PSI and PSII; (2) the fraction of chl a in PSII, determined as the ratio between the scaled red‐peak fluorescence excitation and the red absorption peak; and (3) the measure of light absorbed by PSII, determined from the scaling of the fluorescence excitation spectra to the absorption spectra by the “no‐overshoot” procedure. Three marine phytoplankton species were used as test organisms: Prorocentrum minimum (Pavill.) J. Schiller (Dinophyceae), Prymnesium parvum cf. patelliferum (J. C. Green, D. J. Hibberd et Pienaar) A. Larsen (Haptophyceae), and Phaeodactylum tricornutum Bohlin (Bacillariophyceae). Photosynthesis versus irradiance (P vs. E) parameters calculated using the three approaches were compared with P versus E parameters obtained from simultaneously measured rates of oxygen production. Generally, approach 1 underestimated, while approach 2 overestimated the gross O₂‐production rate calculated from PAM fluorescence. Approach 3, in principle the best approach to estimate quanta absorbed by PSII, was also superior according to observations. Hence, we recommend approach 3 for estimation of gross O₂‐production rates based on PAM fluorescence measurements.     

Temporal scales of density‐dependent habitat selection in a large grazing herbivore

Habitat selection is a density‐dependent process, but little is known regarding how this relationship may vary across different temporal scales. Over long time scales, grazing shapes the structure, diversity and functioning of terrestrial ecosystems, and grazing‐induced changes in forage production over time are likely to affect the level of density dependence in habitat selection. In this fully‐replicated, landscape‐scale experiment, we investigated how density‐dependent habitat selection by a large grazing herbivore, sheep Ovis aries, develops over the time scale of a decade. We also address an often‐neglected challenge in habitat selection studies; namely, whether there is variation in use within a particular habitat or vegetation type and why. We found clear evidence of density dependence in habitat selection, with a wider use of habitats at high density. Despite a change in the standing biomass of high‐productivity vegetation at high herbivore density over the years, with herb biomass declining and graminoid biomass increasing, there was no clear evidence that these grazing‐induced changes in habitat over the years were strong enough to affect the level of density‐dependent habitat selection. The difference in selection for high versus low‐productivity habitats remained similar, despite annual fluctuations in the strength of selection. We found strong variation in selection within each vegetation type, even when vegetation types were mapped at a fine‐resolution scale. Our study shows that despite the interactive effects of herbivores and habitats, they are not always sufficiently strong enough to affect the level of density‐dependent habitat selection.     

Multiplication of Trypanosoma pacifica (Euglenozoa: Kinetoplastea) in English sole, Parophrys vetulus, from Oregon coastal waters

Multiplication of Trypanosoma pacifica was common in the fish host from observations of live flagellates and Giemsa-stained blood smears. Multiplication began with the elongation of the kinetoplast, thickening of the posterior portion of the body, and appearance of a new flagellum near the kinetoplast. The new flagellum was very rigid when less than 3 microm in length, but it became flexible as it elongated. When the new flagellum was approximately 12 microm in length, cell division began and the kinetoplast also began to divide. The timing of nuclear division was variable. Generally, it did not occur until division of the kinetoplast had begun, but occasionally binucleate individuals were observed before cell or kinetoplast division was apparent. As division continued, 1 nucleus migrated past the dividing kinetoplast into the future daughter trypanosome. Finally, the kinetoplast completed division and the trypanosomes separated. Cell division was unequal, with the daughter trypanosome being smaller than the parent and with a more weakly developed undulating membrane.     

High BRAF Mutation Frequency and Marked Survival Differences in Subgroups According to KRAS/BRAF Mutation Status and Tumor Tissue Availability in a Prospective Population-Based Metastatic Colorectal Cancer Cohort

RAS and BRAF mutations impact treatment and prognosis of metastatic colorectal cancer patients (mCRC), but the knowledge is based on trial patients usually not representative for the general cancer population. Patient characteristics, treatment and efficacy according to KRAS, BRAF and MSI status were analyzed in a prospectively collected unselected population-based cohort of 798 non-resectable mCRC patients. The cohort contained many patients with poor performance status (39% PS 2-4) and elderly (37% age>75), groups usually not included in clinical trials. Patients without available tissue micro array (TMA) (42%) had worse prognostic factors and inferior survival (all patients; 7m vs 11m, chemotherapy-treated;12m vs 17m). The 92 patients (21%) with BRAF mutation had a poor prognosis regardless of microsatellite instability, but receipt of 1-2^nd chemotherapy was similar to wildtype BRAF patients. Median survival in this cohort varied from 1 month in BRAF mutated patients not given chemotherapy to 26 months in wildtype KRAS/BRAF patients <75 years in good PS. TMA availability, BRAF mutation and KRAS mutation were all independent prognostic factors for survival. The observed 21% BRAF mutation incidence is higher than the previously and repeatedly reported incidence of 5-12% in mCRC. Screening for BRAF mutations before selection of treatment is relevant for many patients, especially outside clinical trials. A BRAF mutation only partly explained the very poor prognosis of many mCRC patients. Survival in unselected metastatic colorectal cancer patients is extremely variable and subgroups have an extremely short survival compared to trial patients. Patients without available TMA had worse prognostic factors and shorter survival, which questions the total generalizability of present TMA studies and implies that we lack information on the biologically worst mCRC cases. Lack of available tissue is an important underexposed issue which introduces sample bias, and this should be recognized more clearly when conclusions are made from translational mCRC studies.     

Sea ice loss increases genetic isolation in a high Arctic ungulate metapopulation

Sea ice loss may have dramatic consequences for population connectivity, extinction–colonization dynamics, and even the persistence of Arctic species subject to climate change. This is of particular concern in face of additional anthropogenic stressors, such as overexploitation. In this study, we assess the population‐genetic implications of diminishing sea ice cover in the endemic, high Arctic Svalbard reindeer (Rangifer tarandus platyrhynchus) by analyzing the interactive effects of landscape barriers and reintroductions (following harvest‐induced extirpations) on their metapopulation genetic structure. We genotyped 411 wild reindeer from 25 sampling sites throughout the entire subspecies' range at 19 microsatellite loci. Bayesian clustering analysis showed a genetic structure composed of eight populations, of which two were admixed. Overall population genetic differentiation was high (mean F_ST = 0.21). Genetic diversity was low (allelic richness [AR] = 2.07–2.58; observed heterozygosity = 0.23–0.43) and declined toward the outer distribution range, where populations showed significant levels of inbreeding. Coalescent estimates of effective population sizes and migration rates revealed strong evolutionary source–sink dynamics with the central population as the main source. The population genetic structure was best explained by a landscape genetics model combining strong isolation by glaciers and open water, and high connectivity by dispersal across winter sea ice. However, the observed patterns of natural isolation were strongly modified by the signature of past harvest‐induced extirpations, subsequent reintroductions, and recent lack of sea ice. These results suggest that past and current anthropogenic drivers of metapopulation dynamics may have interactive effects on large‐scale ecological and evolutionary processes. Continued loss of sea ice as a dispersal corridor within and between island systems is expected to increase the genetic isolation of populations, and thus threaten the evolutionary potential and persistence of Arctic wildlife.     

The ecology and evolution of tooth wear in red deer and moose

Differences in body size and diet type (browser–grazer continuum) have formed functional traits of ruminants, including tooth design. Grazers and mixed-feeders eat a more fibrous diet than browsers, which arguably increase tooth wear. Tooth wear has also been suggested to increase with body size. Moreover, for species with large distribution ranges, different populations may be exposed to very different ecological factors affecting diet and thus tooth wear rates. Therefore, evolutionary history and contemporary ecological conditions, both operating through diet, may be important for patterns of tooth wear. Here, we compare inter- and intraspecific rates of tooth wear in multiple populations of one large browser (moose Alces alces ) and one mixed-feeder (red deer Cervus elaphus ) covering the main distribution range of each species in Norway. We found that the mixed-feeding red deer wore teeth faster than the larger and browsing moose, suggesting that feeding-type was more important than body size for patterns of wear. There was substantial spatial variation in tooth wear rates, but the inter-specific difference in wear was consistent. Molar wear rates, but not incisors wear rates, in the browser were less variable between populations than in the mixed-feeder. There was no close link between incisor and molar wear rates at the population level. Our findings are consistent with the view that both evolution related to diet type and current ecological conditions (being proxies for within-species variation in diet quality) are important for patterns of tooth wear.     

Effects of enrichment items on activity and social interactions in domestic horses (Equus caballus)

The aim of this study was to investigate the use of items intended to provide enrichment during turnout, both for individual and group kept horses in an attempt to reduce the amount of passive behaviours. The study was divided into two parts, where study 1 involved eight horses rotated through eight individual paddocks, each containing one of seven enrichment items and one paddock being kept without item, functioning as a control. The horses’ item-directed behaviours; passive behaviours or other non-item related activities were scored using instantaneous sampling, every minute for 1 h at the beginning and the end of the turnout period. Study 2 involved six horse groups (3–6 horses) and the same scoring methods and ethogram as in study 1. The four items that the horses interacted the most with during study 1 (straw STRA, ball filled with concentrates CBALL, branches BRAN and scratching pole POLE) are investigated in study 2. In addition, the amount of social interactions was recorded.Both horses kept individually (P < 0.05) and in groups (P < 0.0001) performed significantly more item-directed behaviours towards edible items like STRA and CBALL than other objects. There was, however, no overall relation between the numbers of item-directed behaviours and the number of passive behaviours observed, indicating that the enrichment items did not alone reduce the amount of passive behaviours during turnout periods. Such a reduction was, however, only apparent when horses spent more time eating green leaves growing on the paddock surface (R = ?0.97 study 1, R = ?0.67 study 2, P < 0.0001). Access to STRA in group kept horses also seemed to reduce the amount of agonistic behaviours (P < 0.0001). In conclusion, if grass is not available in paddocks, the provision of roughage reduces the amount of passive behaviours in singly kept horses and it also reduces the risk of agonistic interactions between horses kept in group.     

Molecular tools for the detection and identification of Ichthyobodo spp. (Kinetoplastida), important fish parasites

Ichthyobodo spp. are ectoparasitic flagellates of fish that may cause disease (ichthyobodosis), a common problem affecting the aquaculture industry worldwide. Ichthyobodosis in farmed fish is often associated with a range of other infectious agents and diagnosis in for example gill disease may be difficult. Sensitive and effective methods for detection and identification of Ichthyobodo spp. are needed to aid diagnosis of ichthyobodosis and epizootiological studies on Ichthyobodo spp. We have designed a specific quantitative real-time PCR assay targeting SSU rDNA for the detection of Ichthyobodo spp. infections. Also, several novel primer sets are presented for use in identification of Ichthyobodo spp. through PCR and sequencing. These PCR methods have been optimized and tested on samples from wild caught and farmed fish from different geographical areas in Norway. The real-time PCR assay has been tested for sensitivity and efficiency, and we present data demonstrating its use for absolute quantification of Ichthyobodo salmonis in tissue samples through RT-qPCR and qPCR. We demonstrate the use of the described set of molecular tools for the detection and sequencing of Ichthyobodo spp. from farmed and wild fish, and also show that they may aid the discovery of new Ichthyobodo species. The detection of light Ichthyobodo spp. infections through microscopy is time consuming and less sensitive compared to PCR methods. Initial real-time PCR testing and subsequent sequencing of positive samples is a powerful method that will increase diagnostic precision, aid carrier detection and promote species discoveries in the Ichthyobodonidae. Our preliminary observations indicate a high Ichthyobodo spp. diversity.