An iterative algorithm for parametrization of shortest length shift registers over finite rings

The construction of shortest feedback shift registers for a finite sequence S_1,...,S_N is considered over the finite ring Z_{p^r}. A novel algorithm is presented that yields a parametrization of all shortest feedback shift registers for the sequence of numbers S_1,...,S_N, thus solving an open problem in the literature. The algorithm iteratively processes each number, starting with S_1, and constructs at each step a particular type of minimal Gr\"obner basis. The construction involves a simple update rule at each step which leads to computational efficiency. It is shown that the algorithm simultaneously computes a similar parametrization for the reciprocal sequence S_N,...,S_1.Comment: Submitte

Niche overlap across landscape variability in summer between two large herbivores using eDNA metabarcoding.

Understanding the relationship between a species feeding strategy and its environment (trophic ecology) is critical to assess environmental requirements and improve management policies. However, measuring trophic interactions remains challenging. Among the available methods, quantifying the plant composition of a species' diet indicates how species use their environment and their associated niche overlap. Nevertheless, most studies focusing on herbivore trophic ecology ignore the influence that landscape variability may have. Here, we explored how landscape variability influences diet composition through niche overlap. We used eDNA metabarcoding to quantify the diet composition of two large herbivores of the Bialowieza Forest, red deer (Cervus elaphus) and European bison (Bison bonasus) to investigate how increasing habitat quality (i.e. higher abundance of deciduous forage species) and predation risk (i.e. density of wolf in the area) influence their diet composition and niche partitioning. Our findings indicate diet composition is non-homogeneous across the landscape, both within and between species. Red deer showed greater diet variability and lower niche overlap within species compared to bison. We detected a reduction of niche overlap for red deer with increasing predation risk, leading to more dissimilar diets, suggesting their feeding behaviour is affected by wolf presence. This correlation was not found for bison, which are rarely predated by wolf. Higher habitat quality was associated with higher niche overlap only within bison, probably due to their suboptimal feeding strategy as browsers. These results show the importance of integrating environment-induced diet variation in studies aimed at determining the landscape usage or niche overlap of a species

Density-dependent switches in diet:a likely mechanism for negative feedbacks on goose population increase?

Goose grazing on arctic tundra vegetation has shown both positive and negative effects on subsequent foraging conditions. To understand the potential of a density-dependent feedback on herbivore population size, the relation between grazing pressure and future foraging conditions is essential. We studied the effect of increasing grazing pressure of barnacle geese (Branta leucopsis) on Spitsbergen. During the establishment of a breeding colony in the period 1992-2004, the proportion of graminoids decreased in the diet of wild geese, while the percentage of mosses increased. Grazing trials with captive geese in an unexploited area showed a similar shift in diet composition. High-quality food plants were depleted within years and over years. Intake rate declined too and as consequence, metabolisable energy intake rate (MEIR) decreased rapidly with increasing grazing pressure. During three successive years of experimental grazing, MEIR decreased at all levels of grazing pressure and declined below minimal energetic requirements when grazing exceeded natural levels of grazing pressure. This suggests that foraging conditions rapidly decline with increasing grazing pressure in these low-productive habitats. The potential for density-dependent feedbacks on local population increase is discussed

Aerial dissemination of Clostridium difficile spores inside and outside a pig farm

In both human and veterinary medicine Clostridium difficile infections are increasingly reported. The observation that aerial dissemination occurs in a hospital environment and can pla a role in the transmission of human C. difficile infection, resulted in the present study to the occurence of airborne C. difficile in, and nearby a pig farm with a high prevalence of C. difficile

Variety of Clostridium difficile PCR ribotypes in pigs arriving at the slaughterhouse

Food products of animal origin might play a role in interspecies transmission of C. difficile. In pigs, Clostridium difficile can cause neonatal enteritis and can be isolated from faeces from both diseased and healthy animals. To determine the prevalence of C. difficile in Dutch pigs arriving at the slaughterhouse a pilot study was conducted at one slaughterhouse in the Netherlands. Rectal faecal samples were taken from fifty slaughtering pigs from ten farms just after the pigs were sedated. These samples were examined using a real time PCR (BD GeneOhmTM Cdiff Assay), in combination with culturing after enrichment. Using real time PCR, none of the faecal samples were found to be positive for C. difficile while after culturing 14 samples (coming from pigs from nine different farms) were found to be positive for C. difficile. The positive samples derived from 9 different farms and encompassed seven different ribotypes

Recreation reduces tick density through fine-scale risk effects on deer space-use

Altered interactions between pathogens, their hosts and vectors have potential consequences for human disease risk. Notably, tick-borne pathogens, many of which are associated with growing deer abundance, show global increasing prevalence and pose increasing challenges for disease prevention. Human activities can largely affect the patterns of deer space-use and can therefore be potential management tools to alleviate human-wildlife conflicts. Here, we tested how deer space-use patterns are influenced by human recreational activities, and how this in turn affects the spatial distribution of the sheep tick (Ixodes ricinus), a relevant disease vector of zoonoses such as Lyme borrelioses. We compared deer dropping and questing tick density on transects near (20 m) and further away from(100 m) forest trails that were either frequently used (open for recreation) or infrequently used (closed for recreation, but used by park managers). In contrast to infrequently used trails, deer dropping density was 31% lower near (20 m) than further away from (100 m) frequently used trails. Similarly, ticks were 62% less abundant near (20 m) frequently used trails compared to further away from (100 m) these trails, while this decline in tick numbers was only 14% near infrequently used trails. The avoidance by deer of areas close to human-used trails was thus associated with a similar reduction in questing tick density near these trails. As tick abundance generally correlates to pathogen prevalence, the use of trails for recreation may reduce tick-borne disease risk for humans on and near these trails. Our study reveals an unexplored effect of human activities on ecosystems and how this knowledge could be potentially used to mitigate zoonotic disease risk

First isolation of Clostridium difficile PCR ribotype 027 from a patient with severe persistent diarrhoea in Hungary

A recent Supplement to Clinical Microbiology and Infection entitled ‘Infection control measures to limit the spread of C. difficile’ pointed out that the incidence of C. difficile-associated diarrhoea (CDAD) has been increasing worldwide, and stressed the importance of research in the fields of epidemiology and infection control [1]. Since 2003, one of the main causes of the increasing prevalence of CDAD has been claimed to be the emergence of PCR ribotype 027/NAP1, which has caused epidemics in North America, the UK, the Netherlands, Belgium and France. The presence of PCR ribotype 027 in Austria, Japan, Ireland, Germany and Switzerland has also been reported recently [2,3]. The majority of publications have emphasized that the presence of this strain is usually associated with more severe symptoms and signs than those associated with the other more common toxinpositive strains [4,5]. Whereas PCR ribotype 027 was present in the population earlier, the majority of the historic strains were fluoroquinolone sensitive [6]. The overuse of antibiotics such as fluoroquinolones may lead to the selection and emergence of resistant strains, and may contribute to the spread of PCR ribotype 027, which is usually resistant to erythromycin. Here, the Eastern European spread of C. difficile PCR ribotype 027 is reported

Clostridium difficile Ribotype 027, Toxinotype III, the Netherlands

Outbreaks due to Clostridium difficile polymerase chain reaction (PCR) ribotype 027, toxinotype III, were detected in 7 hospitals in the Netherlands from April 2005 to February 2006. One hospital experienced at the same time a second outbreak due to a toxin A–negative C. difficile PCR ribotype 017 toxinotype VIII strain. The outbreaks are difficult to control

Presence of Clostridium difficile in pig faecal samples and wild animal species associated with pig farms

Aims: to determine the presence of Clostridium difficile on fattening pig farms in north-eastern Spain. Methods and results: Twenty-seven farms were sampled. Pools of pig faecal samples (n = 210), samples of intestinal content from common farm pest species (n = 95) and environment-related samples (n = 93) were collected. Isolates were tested for toxin genes of C. difficile, and typed by PCR-ribotyping and toxinotyping. The minimal inhibitory concentrations of six antimicrobial agents were determined using Etest. Thirty-four isolates were obtained from 12 farms, and 30 (88·2%) had toxin genes. Seven ribotypes were identified. Ribotype 078 and its variant 126 were predominant (52·9%). The same ribotypes were isolated from different animal species on the same farm. None of the isolates were resistant to metronidazole or vancomycin. Conclusions: Clostridium difficile was common within the pig farm environment. Most of the positive samples came from pest species or were pest-related environmental samples. Significance and Impact of the Study: Pest species were colonized with toxigenic and antimicrobial-resistant C. difficile strains of the same ribotypes that are found in humans and pigs. Rodents and pigeons may transmit toxigenic and antimicrobial-resistant C. difficile strains that are of the same ribotypes as those occuring in humans

Recreation reduces tick density through fine-scale risk effects on deer space-use

Altered interactions between pathogens, their hosts and vectors have potential consequences for human disease risk. Notably, tick-borne pathogens, many of which are associated with growing deer abundance, show global increasing prevalence and pose increasing challenges for disease prevention. Human activities can largely affect the patterns of deer space-use and can therefore be potential management tools to alleviate human-wildlife conflicts. Here, we tested how deer space-use patterns are influenced by human recreational activities, and how this in turn affects the spatial distribution of the sheep tick (Ixodes ricinus), a relevant disease vector of zoonoses such as Lyme borrelioses. We compared deer dropping and questing tick density on transects near (20 m) and further away from (100 m) forest trails that were either frequently used (open for recreation) or infrequently used (closed for recreation, but used by park managers). In contrast to infrequently used trails, deer dropping density was 31% lower near (20 m) than further away from (100 m) frequently used trails. Similarly, ticks were 62% less abundant near (20 m) frequently used trails compared to further away from (100 m) these trails, while this decline in tick numbers was only 14% near infrequently used trails. The avoidance by deer of areas close to human-used trails was thus associated with a similar reduction in questing tick density near these trails. As tick abundance generally correlates to pathogen prevalence, the use of trails for recreation may reduce tick-borne disease risk for humans on and near these trails. Our study reveals an unexplored effect of human activities on ecosystems and how this knowledge could be potentially used to mitigate zoonotic disease risk