Fast Searching in Packed Strings

Given strings $P$ and $Q$ the (exact) string matching problem is to find all positions of substrings in $Q$ matching $P$. The classical Knuth-Morris-Pratt algorithm [SIAM J. Comput., 1977] solves the string matching problem in linear time which is optimal if we can only read one character at the time. However, most strings are stored in a computer in a packed representation with several characters in a single word, giving us the opportunity to read multiple characters simultaneously. In this paper we study the worst-case complexity of string matching on strings given in packed representation. Let $m \leq n$ be the lengths $P$ and $Q$, respectively, and let $\sigma$ denote the size of the alphabet. On a standard unit-cost word-RAM with logarithmic word size we present an algorithm using time O\left(\frac{n}{\log_\sigma n} + m + \occ\right). Here \occ is the number of occurrences of $P$ in $Q$. For $m = o(n)$ this improves the $O(n)$ bound of the Knuth-Morris-Pratt algorithm. Furthermore, if $m = O(n/\log_\sigma n)$ our algorithm is optimal since any algorithm must spend at least \Omega(\frac{(n+m)\log \sigma}{\log n} + \occ) = \Omega(\frac{n}{\log_\sigma n} + \occ) time to read the input and report all occurrences. The result is obtained by a novel automaton construction based on the Knuth-Morris-Pratt algorithm combined with a new compact representation of subautomata allowing an optimal tabulation-based simulation.Comment: To appear in Journal of Discrete Algorithms. Special Issue on CPM 200

Yersinia enterocolitica strains associated with human infections in Switzerland 2001-2010

Yersinia enterocolitica infections are common in humans. However, very scarce data are available on the different biotypes and virulence factors of human strains, which has proved to be problematic to assess the clinical significance of the isolated strains. In this study, the presence of the ail gene and distribution of different bio- and serotypes among human Y. enterocolitica strains and their possible relation to the genotype and antimicrobial resistance were studied. In total, 128 Y. enterocolitica strains isolated from human clinical samples in Switzerland during 2001-2010 were characterised. Most (75 out of 128) of the Y. enterocolitica strains belonged to biotypes 2, 3 or 4 and carried the ail gene. One of the 51 strains that belonged to biotype 1A was also ail positive. Most of the ail-positive strains belonged to bioserotype 4/O:3 (47 out of 76) followed by 2/O:9 (22 out of 76). Strains of bioserotype 4/O:3 were dominant among patients between 20 and 40years old and strains of biotype 1A dominate in patients over 40years. Strains belonging to biotypes 2, 3 and 4, which all carried the ail gene, exhibited a high homogeneity with PFGE typing. Y. enterocolitica 2/O:5,27 and 2/O:9 strains showed resistance to amoxicillin/clavulanic acid and cefoxitin, but Y. enterocolitica 4/O:3 strains did no

Discrete-Ordinates Modelling of the Radiative Heat Transfer in a Pilot-Scale Rotary Kiln

This paper presents work focused on the development, evaluation and use of a 3D model for investigation of the radiative heat transfer in rotary kilns. The model applies a discrete-ordinates method to solve the radiative transfer equation considering emission, absorption and scattering of radiation by gas species and particles for cylindrical and semi-cylindrical enclosures. Modelling input data on temperature, particle distribution and gas composition in the radial, axial and angular directions are experimentally gathered in a down-scaled version of a rotary kiln. The model is tested in its capability to predict the radiative intensity and heat flux to the inner wall of the furnace and good agreement was found when compared to measurements. Including the conductive heat transfer through the furnace wall, the model also satisfactorily predicts the intermediate wall temperature. The work also includes a first study on the effect of the incident radiative heat flux to the different surfaces while adding a cold bed material. With further development of the model, it can be used to study the heat transfer in full-scale rotary kilns

Pathogenic Yersinia enterocolitica O:3 isolated from a hunted wild alpine ibex

Occurrence of Yersinia spp. in wild ruminants was studied and the strains were characterized to get more information on the epidemiology of enteropathogenic Yersinia in the wildlife. In total, faecal samples of 77 red deer, 60 chamois, 55 roe deer and 27 alpine ibex were collected during 3 months of the hunting season in 2011. The most frequently identified species was Y. enterocolitica found in 13%, 10%, 4% and 2% of roe deer, red deer, alpine ibex and chamois, respectively. Interestingly, one Y. enterocolitica O:3 strain, isolated from an alpine ibex, carried the important virulence genes located on the virulence plasmid (yadA and virF) and in the chromosome (ail, hreP, myfA and ystA). Most of the Y. enterocolitica strains belonged to biotype 1A of which 14 were ystB positive. Further studies are needed to clarify the importance of alpine ibex as a reservoir of pathogenic Y. enterocolitic

A comparative analysis of meat inspection data as an information source of the health and welfare of broiler chickens based on Finnish data

The comprehensive, reliable, and comparable meat inspection (MI) data of broiler chickens (i.e. broilers) are essential for the monitoring and surveillance of broiler health and welfare at the national and European Union (EU) levels. We compared the condemnation causes issued to broiler carcasses during MI in four large Finnish broiler slaughterhouses (SHs) by investigating the similarities and differences between local MI instructions used in the SHs. The way in which MI condemnations were recorded in the Finnish Food Authority's (FFA's) MI statistics were also explored. We additionally analysed the FFA's official MI data from the 2015-2019 period. The study showed that the MI criteria used in the SHs differed from one another regarding how severe or extensive a broiler defect or disease must be to cause condemnation during MI. In Finland, the annual total condemnation prevalence of whole broilers varied between 2.6% and 4.8% in 2015-2019, and a significant difference was observed between the SHs' monthly total condemnation prevalences, except in two SH pairs. Mistakes in recording the FFA's MI statistics and differences in the SH operators' reasons to reject broilers from the food chain affect the comparability of the condemnation prevalences between the SHs. Only half of the SHs partially condemned broiler carcasses and collected data concerning these condemnations. Cellulitis (0.3-1.0%), ascites (0.3-0.4%), and body cavity disorders (0.2-0.3%) were the most common causes for condemning whole broiler carcasses in 2015-2019. The MI data can be used for monitoring and surveillance purposes only once the differences between the SH data and data reliability are known. Although the harmonization of all condemnation causes is impossible, harmonizing the condemnations of carcasses with diseases that most threaten broiler health and welfare and cause the largest economic losses would be important.Peer reviewe

Prerequisites of inspection conditions for uniform post-mortem inspection in broiler chicken slaughterhouses in Finland

Meat inspection of broiler chickens (broiler) in the European Union is regulated by common legislation to secure meat safety. However, the legislation is general in nature and proper post-mortem inspection (PMI) of every carcass and visceral organs of broilers is challenging in slaughterhouses (SHs) with a high slaughter line speed. The aim of this study was to investigate the on-site organization and possible differences of the PMI in four Finnish SHs, which slaughter over 99% of broilers in Finland. Our results show that the meat inspector's available inspection time per broiler in the PMI varied between 0.28 and 0.90 s, with the shortest available inspection time in the SH with the highest slaughter line speed and the longest available inspection time in the SH with the slowest line speed. We observed that only part of the total inspection time per broiler could be used for true PMI in most (3/4) SHs, as the meat inspectors also performed other tasks during the PMI. We observed deficiencies in the visual inspection of broiler carcasses; in particular, the proper inspection of all or most of the body cavities was impossible in all SHs during the PMI. Some deficiencies in facilities (e.g. in recording system) were observed. Moreover, lighting properties varied between the SHs and a significant difference between illumination conditions at the first inspection stations in the SHs was observed. This study considered the prerequisites for proper PMI and revealed that the PMI of broilers was not completely uniform in Finland. The results emphasize the need for more precise guidelines and recommendations, especially for inspection time and lighting at inspection stations.Peer reviewe

Approximate string matching with reduced alphabet

Peer reviewe

Roux-En Y Gastric Bypass Surgery Induces Genome-Wide Promoter-Specific Changes in DNA Methylation in Whole Blood of Obese Patients

Context DNA methylation has been proposed to play a critical role in many cellular and biological processes. Objective To examine the influence of Roux-en-Y gastric bypass (RYGB) surgery on genome-wide promoter-specific DNA methylation in obese patients. Promoters are involved in the initiation and regulation of gene transcription. Methods Promoter-specific DNA methylation in whole blood was measured in 11 obese patients (presurgery BMI >35 kg/m2, 4 females), both before and 6 months after RYGB surgery, as well as once only in a control group of 16 normal-weight men. In addition, body weight and fasting plasma glucose were measured after an overnight fast. Results The mean genome-wide distance between promoter-specific DNA methylation of obese patients at six months after RYGB surgery and controls was shorter, as compared to that at baseline (p<0.001). Moreover, postsurgically, the DNA methylation of 51 promoters was significantly different from corresponding values that had been measured at baseline (28 upregulated and 23 downregulated, P<0.05 for all promoters, Bonferroni corrected). Among these promoters, an enrichment for genes involved in metabolic processes was found (n = 36, P<0.05). In addition, the mean DNA methylation of these 51 promoters was more similar after surgery to that of controls, than it had been at baseline (P<0.0001). When controlling for the RYGB surgery-induced drop in weight (-24% of respective baseline value) and fasting plasma glucose concentration (-16% of respective baseline value), the DNA methylation of only one out of 51 promoters (~2%) remained significantly different between the pre-and postsurgery time points. Conclusions Epigenetic modifications are proposed to play an important role in the development of and predisposition to metabolic diseases, including type II diabetes and obesity. Thus, our findings may form the basis for further investigations to unravel the molecular effects of gastric bypass surgery. Clinical Trial ClinicalTrials.gov NCT0173074

Dynamic and approximate pattern matching in 2D

International audienc