Wood-inhabiting Basidiomycetes in the Caucasus Region : Systematics and Biogeography

The Caucasus region is a hotspot of biodiversity and is one of the few areas in the Northern Hemisphere which harbor Pleistocene glacial refugia. The region encompasses Armenia, Azerbaijan, Georgia, the southernmost European Russia, NE Turkey, and northern Iran. The study on fungal composition of the Caucasus region and its connection and possible contribution to the present mycota of Europe has largely escaped empirical scrutiny. Using taxonomic surveys, phylogenetic reconstruction methods, haplotype analysis, and similarity tests, this study has aimed to, 1) summarize the knowledge on the occurrence of corticioids and polypores in the Caucasus region, 2) resolve the phylogenetic relationships of selected, resupinate wood-inhabiting basidiomycetes for which the Caucasus region is currently the mere, or one of the noteworthy areas of distribution, and, 3) assess the similarity of Caucasian corticioid fungi to those of Europe and important areas in the Northern Hemisphere, and to examine the significance of the Caucasus region as a glacial refugium for these fungi. This study provides the first catalogue of corticioids and polypores (635 species) occurring in the Caucasus region. The phylogeny and systematics of the Caucasian resupinate taxa in focus has been resolved and the usefulness of some morphological characters has been re-evaluated. In this context, four new genera and two new species were described and five new combinations were proposed, two of which were supplemented with modern descriptions. The species composition of corticioids in the Caucasus region is found to be distinctly more similar to Europe and North America than to East Asia and India. The highest molecular diversity and within population pairwise distance for Peniophorella praetermissa has been detected in the Caucasus and East Asia, with the isolates of the latter area being highly divergent from the European ones. This, and the assignment of root haplotype to the Caucasian isolates in a haplotype network for Phlebia tuberucalta and P. livida, call attention to the role of the Caucasus region in shaping the current mycota of Europe.

Publishing in the Networked World: Transforming the Nature of Communication, 14th International Conference on Electronic Publishing 16-18 June 2010, Helsinki, Finland

The title of the 14th International Conference on Electronic Publishing (ELPUB), “Publishing in the networked world: Transforming the nature of communication”, is a timely one. Scholarly communication and scientific publishing has recently been undergoing subtle changes. Published papers are no longer fixed physical objects, as they once were. The “convergence” of information, communication, publishing and web technologies along with the emergence of Web 2.0 and social networks has completely transformed scholarly communication and scientific papers turned to living and changing entities in the online world. The themes (electronic publishing and social networks; scholarly publishing models; and technological convergence) selected for the conference are meant to address the issues involved in this transformation process. We are pleased to present the proceedings book with more than 30 papers and short communications addressing these issues. What you hold in your hands is a by-product and the culmination of almost a Year long work of many people including conference organizers, authors, reviewers, editors and print and online publishers. The ELPUB 2010 conference was organized and hosted by the Hanken School of Economics in Helsinki, Finland. Professors Turid Hedlund of Hanken School of Economics and Yaşar Tonta of Hacettepe University Department of Information Management (Ankara, Turkey) served as General Chair and Program Chair, respectively. We received more than 50 submissions from several countries. All submissions were peer-reviewed by members of an international Program Committee whose contributions proved most valuable and appreciated. The 14th ELPUB conference carries on the tradition of previous conferences held in the United Kingdom (1997 and 2001), Hungary (1998), Sweden (1999), Russia (2000), the Czech Republic (2002), Portugal (2003), Brazil (2004), Belgium (2005), Bulgaria (2006), Austria (2007), Canada (2008) and Italy (2009). The ELPUB Digital Library, http://elpub.scix.net serves as archive for the papers presented at the ELPUB conferences through the years. The 15th ELPUB conference will be organized by the Department of Information Management of Hacettepe University and will take place in Ankara, Turkey, from 14-16 June 2011. (Details can be found at the ELPUB web site as the conference date nears by.) We thank Marcus Sandberg and Hannu Sääskilahti for copyediting, Library Director Tua Hindersson – Söderholm for accepting to publish the online as well as the print version of the proceedings. Thanks also to Patrik Welling for maintaining the conference web site and Tanja Dahlgren for administrative support. We warmly acknowledge the support in organizing the conference to colleagues at Hanken School of Economics and our sponsors.

Towards Multiculturalism in Turkish Public Service Broadcasting

The announcement of Turkey as a European Union (EU) candidate country in the Helsinki Summit (10, 11 December 1999) marked a distinct change of identity policy and attitudes towards its citizens. A result in the shift of mindset has been the launch of the first public service broadcasting TV channel for Kurdish people on the 1st of January 2009. TRT 6 (Şeş) broadcasting in unofficial Kurdish language is run by Turkish Radio and Television Corporation (TRT). The thesis attempts to elaborate on the discussions surrounding the launch of TRT 6, Turkey’s first public service broadcasting TV channel for its Kurdish citizens. The research aims at finding the discourses of multiculturalism and public service broadcasting through the mainstream Turkish newspapers, Cumhuriyet, Hurriyet, Sabah, Taraf and Zaman. The method used for the research is Critical Discourse Analysis (CDA) and the representative newspapers of the Turkish print media are under the question: How has the launch of TRT 6, as the first public service broadcasting channel of Turkey in Kurdish language, been discussed by Turkish daily newspapers in terms of multiculturalism and minority media? The most significant results of the research is that the concerning newspapers have mostly discussed the launch of TRT 6 in the same line with their political affiliation. Thus it is comprehensively concluded that the selected newspapers proved holding a high level of political parallelism, and low professionalism. However, it should be noted that Taraf differs itself from others while challenging the hegemonic discourses embedded in the articles of the other newspapers. Moreover, the study detected three types of discourses: Pro-multiculturalism discourse, Unification discourse, and Assimilation discourse. It can be concluded that in Turkey, media owners and even individual journalists have incentives to form ideological alliances with political parties, and media appears to be an instrument of power struggle. Today, Turkey seems to restore Kurdish identity in its identity policy and aims to proceed with the negotiation for membership of the European Union (EU). The country still strives to transform from the traditional nation-state to a multiethnic democratic state, with multiculturalism as a policy discussed throughout the two terms that the AKP government has been in power. However, this transformation is not an easy process because of the deep-rooted traditions of the nation-state structure that has also polarized the Turkish press.

Campylobacter jejuni and C. coli in Finnish poultry production

Campylobacter, mainly Campylobacter jejuni and C. coli, are worldwide recognized as a major cause of bacterial food-borne gastroenteritis. Epidemiological studies have shown handling or eating of poultry to be significant risk factors for human infections. Campylobacter contamination can occur at all stages of a poultry meat production cycle. The aim of this thesis was to study the occurrence and diversity of Campylobacter in broiler and turkey production in Finland. In summer 1999, 2.9 % of slaughtered broiler flocks were Campylobacter-positive. From the isolated strains 94 % were C. jejuni and 6% were C. coli. During years 2005-2006 one turkey parent flock, the hatchery, six different commercial turkey farms and different stages of the slaughterhouse were monitored during one and the half year. No Campylobacter were detected in either of the samples from the turkey parent flock or from the hatchery using the culture method. Instead PCR detected DNA of Campylobacter from the turkey parent flock and samples from the hatchery. Six out of 12 commercial turkey flocks were found negative at the farm level but only two of those were negative at slaughter. Campylobacter-positive samples within the flock at slaughter were detected between 0% and 94% with evisceration and chilling water being the most critical stages for contamination. All of Campylobacter isolates were shown to be C. jejuni. Campylobacter-positive turkey flocks were colonized by a limited number of Campylobacter genotypes both at the farm and slaughter level. In conclusion, in our first study in 1999 a low prevalence of Campylobacter in Finnish broiler flocks was detected and it has remained at a low level during the study period until the present. In the turkey meat production, we found that flocks which were negative at the farm became contaminated with Campylobacter at the slaughter process. These results suggest that proper and efficient cleaning and disinfection of slaughter and processing premises are needed to avoid cross-contamination. Prevention of colonization at the farm by a high level of biosecurity control and hygiene may be one of the most efficient ways to reduce the amount of Campylobacter-positive poultry meat in Finland. With a persistent low level of Campylobacter-positive flocks, it could be speculated that the use of logistic slaughtering, according to Campylobacter status at farm, might have be advantageous in reducing Campylobacter contamination of retail poultry products. However, the significance of the domestic poultry meat for human campylobacteriosis in Finland should be evaluated.

Campylobacter jejuni and C.coli in Finnish poultry production

Campylobacter, mainly Campylobacter jejuni and C. coli, are worldwide recognized as a major cause of bacterial food-borne gastroenteritis (World Health Organization 2010). Epidemiological studies have shown handling or eating of poultry to be significant risk factors for human infections. Campylobacter contamination can occur at all stages of a poultry meat production cycle. In summer 1999, every broiler flock from all three major Finnish poultry slaughterhouses was studied during a five month period. Caecal samples were taken in the slaughterhouses from five birds per flock. A total of 1 132 broiler flocks were tested and 33 (2.9%) of those were Campylobacter-positive. Thirty-one isolates were identified as C. jejuni and two isolates were C. coli. The isolates were serotyped for heat-stable antigens (HS) and genotyped by pulsed-field gel electrophoresis (PFGE). The most common serotypes found were HS 6,7, 12 and 4-complex. Using a combination of SmaI and KpnI patterns, 18 different PFGE types were identified. Thirty-five Finnish C. jejuni strains with five SmaI/SacII PFGE types selected among human and chicken isolates from 1997 and 1998 were used for comparison of their PFGE patterns, amplified fragment length polymorphism (AFLP) patterns, HaeIII ribotypes, and HS serotypes. The discriminatory power of PFGE, AFLP and ribotyping with HaeIII were shown to be at the same level for this selected set of strains, and these methods assigned the strains into the same groups. The PFGE and AFLP patterns within a genotype were highly similar, indicating genetic relatedness. An HS serotype was distributed among different genotypes, and different serotypes were identified within one genotype. From one turkey parent flock, the hatchery, six different commercial turkey farms (together 12 flocks) and from 11 stages at the slaughterhouse a total of 456 samples were collected during one and the half year. For the detection of Campylobacter both conventional culture and a PCR method were used. No Campylobacter were detected in either of the samples from the turkey parent flock or from the hatchery samples using the culture method. Instead PCR detected DNA of Campylobacter in five faecal samples from the turkey parent flock and in one fluff and an eggshell sample. Six out of 12 commercial turkey flocks were found negative at the farm level but only two of those were negative at slaughter. Campylobacter-positive samples within the flock at slaughter were detected between 0% and 94%, with evisceration and chilling water being the most critical stages for contamination. All of a total of 121 Campylobacter isolates were shown to be C. jejuni using a multiplex PCR assay. PFGE analysis of all isolates with KpnI restriction enzyme resulted in 11 PFGE types (I-XI) and flaA-SVR typing yielded nine flaA-SVR alleles. Three Campylobacter-positive turkey flocks were colonized by a limited number of Campylobacter genotypes both at the farm and slaughter level.In conclusion, in our first study in 1999 a low prevalence of Campylobacter in Finnish broiler flocks was detected and it has remained at a low level during the study period until the present. In the turkey meat production, we found that flocks which were negative at the farm became contaminated with Campylobacter at the slaughter process. These results suggest that proper and efficient cleaning and disinfection of slaughter and processing premises are needed to avoid cross-contamination. Prevention of colonization at the farm by a high level of biosecurity control and hygiene may be one of the most efficient ways to reduce the amount of Campylobacter-positive poultry meat in Finland. In Finland, with a persistent low level of Campylobacter-positive flocks, it could be speculated that the use of logistic slaughtering, according to Campylobacter status at farm, might have be advantageous in reducing Campylobacter contamination of retail poultry products. However, the significance of the domestic poultry meat for human campylobacteriosis in Finland should be evaluated.

Decode-and-forward relay beamforming for secrecy with imperfect CSI and multiple eavesdroppers

In this paper, we evaluate secrecy rates in cooperative relay beamforming in the presence of imperfect channel state information (CSI) and multiple eavesdroppers. A source-destination pair aided by.. out of.. relays, 1 <= k <= M, using decode-and-forward relay beamforming is considered. We compute the worst case secrecy rate with imperfect CSI in the presence of multiple eavesdroppers, where the number of eavesdroppers can be more than the number of relays. We solve the optimization problem for all possible relay combinations to find the secrecy rate and optimum source and relay weights subject to a total power constraint. We relax the rank-1 constraint on the complex semi-definite relay weight matrix and use S-procedure to reformulate the optimization problem that can be solved using convex semi-definite programming.

A Multi-phase Approach for Improving Information Diffusion in Social Networks

For maximizing influence spread in a social network, given a certain budget on the number of seed nodes, we investigate the effects of selecting and activating the seed nodes in multiple phases. In particular, we formulate an appropriate objective function for two-phase influence maximization under the independent cascade model, investigate its properties, and propose algorithms for determining the seed nodes in the two phases. We also study the problem of determining an optimal budget-split and delay between the two phases.

Prototype Selection on Large and Streaming Data

Since streaming data keeps coming continuously as an ordered sequence, massive amounts of data is created. A big challenge in handling data streams is the limitation of time and space. Prototype selection on streaming data requires the prototypes to be updated in an incremental manner as new data comes in. We propose an incremental algorithm for prototype selection. This algorithm can also be used to handle very large datasets. Results have been presented on a number of large datasets and our method is compared to an existing algorithm for streaming data. Our algorithm saves time and the prototypes selected gives good classification accuracy.

A Stochastic Approximation Algorithm for Quantile Estimation

In this paper, we present two new stochastic approximation algorithms for the problem of quantile estimation. The algorithms uses the characterization of the quantile provided in terms of an optimization problem in 1]. The algorithms take the shape of a stochastic gradient descent which minimizes the optimization problem. Asymptotic convergence of the algorithms to the true quantile is proven using the ODE method. The theoretical results are also supplemented through empirical evidence. The algorithms are shown to provide significant improvement in terms of memory requirement and accuracy.

Empirical Analysis of Sampling Based Estimators for Evaluating RBMs

The Restricted Boltzmann Machines (RBM) can be used either as classifiers or as generative models. The quality of the generative RBM is measured through the average log-likelihood on test data. Due to the high computational complexity of evaluating the partition function, exact calculation of test log-likelihood is very difficult. In recent years some estimation methods are suggested for approximate computation of test log-likelihood. In this paper we present an empirical comparison of the main estimation methods, namely, the AIS algorithm for estimating the partition function, the CSL method for directly estimating the log-likelihood, and the RAISE algorithm that combines these two ideas.

Analysis of critical excavation depth for a jointed rock slope using a face-to-face discrete element method

The critical excavation depth of a jointed rock slope is an important problem in rock engineering. This paper studies the critical excavation depth for two idealized jointed rock slopes by employing a face-to-face discrete element method (DEM). The DEM is based on the discontinuity analysis which can consider anisotropic and discontinuous deformations due to joints and their orientations. It uses four lump-points at each surface of rock blocks to describe their interactions. The relationship between the critical excavation depth D-s and the natural slope angle alpha, the joint inclination angle theta as well as the strength parameters of the joints c(r) ,phi(r) is analyzed, and the critical excavation depth obtained with this DEM and the limit equilibrium method (LEM) is compared. Furthermore, effects of joints on the failure modes are compared between DEM simulations and experimental observations. It is found that the DEM predicts a lower critical excavation depth than the LEM if the joint structures in the rock mass are not ignored.