Effective population size of an indigenous Swiss cattle breed estimated from linkage disequilibrium

Effective population size is an important parameter for the assessment of genetic diversity within a livestock population and its development over time. If pedigree information is not available, linkage disequilibrium (LD) analysis might offer an alternative perspective for the estimation of effective population size. In this study, 128 individuals of the Swiss Eringer breed were genotyped using the Illumina BovineSNP50 beadchip. We set bin size at 50 kb for LD analysis, assuming that LD for proximal single nucleotide polymorphism (SNP)-pairs reflects distant breeding history while LD from distal SNP-pairs would reflect near history. Recombination rates varied among different regions of the genome. The use of physical distances as an approximation of genetic distances (e.g. setting 1 Mb = 0.01 Morgan) led to an upward bias in LD-based estimates of effective population size for generations beyond 50, while estimates for recent history were unaffected. Correction for restricted sample size did not substantially affect these results. LD-based actual effective population size was estimated in the range of 87-149, whereas pedigree-based effective population size resulted in 321 individuals. For conservation purposes, requiring knowledge of recent history (<50 generations), approximation assuming constant recombination rate seemed adequate.

Current patch test results with the European baseline series and extensions to it from the 'European Surveillance System on Contact Allergy' network, 2007-2008

The pattern of contact sensitization to the supposedly most important allergens assembled in the baseline series differs between countries, presumably at least partly because of exposure differences. Objectives. To describe the prevalence of contact sensitization to allergens tested in consecutive patients in the years 2007 and 2008, and to discuss possible differences.

The European baseline series in 10 European Countries, 2005/2006--results of the European Surveillance System on Contact Allergies (ESSCA)

BACKGROUND: Continual surveillance based on patch test results has proved useful for the identification of contact allergy. OBJECTIVES: To provide a current view on the spectrum of contact allergy to important sensitizers across Europe. PATIENTS/METHODS: Clinical and patch test data of 19 793 patients patch tested in 2005/2006 in the 31 participating departments from 10 European countries (the European Surveillance System on Contact Allergies' (ESSCA) www.essca-dc.org) were descriptively analysed, aggregated to four European regions. RESULTS: Nickel sulfate remains the most common allergen with standardized prevalences ranging from 19.7% (central Europe) to 24.4% (southern Europe). While a number of allergens shows limited variation across the four regions, such as Myroxylon pereirae (5.3-6.8%), cobalt chloride (6.2-8.8%) or thiuram mix (1.7-2.4%), the differences observed with other allergens may hint on underlying differences in exposures, for example: dichromate 2.4% in the UK (west) versus 4.5-5.9% in the remaining EU regions, methylchloroisothiazolinone/methylisothiazolinone 4.1% in the South versus 2.1-2.7% in the remaining regions. CONCLUSIONS: Notwithstanding residual methodological variation (affecting at least some 'difficult' allergens) tackled by ongoing efforts for standardization, a comparative analysis as presented provides (i) a broad overview on contact allergy frequencies and (ii) interesting starting points for further, in-depth investigation.

Prevalence and prognostic significance of TMPRSS2-ERG gene fusion in lymph node positive prostate cancers.

BACKGROUND TMPRSS2-ERG gene fusion is the most frequent genetic alteration in prostate cancer. However, information about its distribution in lymph node positive prostate cancers and the prognostic significance in these advanced tumors is unknown. METHODS Gene fusion status was determined by fluorescence in situ hybridization on a tissue-microarray constructed from 119 hormone-naïve nodal positive, surgically treated prostate cancers containing samples from the primary tumors and corresponding lymph node metastases. Data were correlated with various tumor features (Gleason score, stage, cancer volume, nodal tumor burden) and biochemical recurrence-free, disease-specific, and overall survival. RESULTS TMPRSS2-ERG fusion was detected in 43.5% of the primary tumors. Conversely, only 29.9% of the metastasizing components showed the fusion. Concordance in TMPRSS2-ERG status between primary tumors and metastases was 70.9% (Kappa 0.39); 20.9% and 8.1% of the patients showed the mutation solely in their primary tumors and metastases, respectively. TMPRSS2-ERG fusion was not correlated with specific histopathological tumor features but predicted favorable biochemical recurrence-free, disease-specific and overall survival independently when present in the primary tumor (P < 0.05 each). CONCLUSION TMPRSS2-ERG fusion is more frequent in primary prostate cancer than in corresponding metastases suggesting no selection of fusion-positive cells in the metastatic process. The gene fusion in primary tumors independently predicts favorable outcome.

Low but contrasting neutral genetic differentiation shaped by winter temperature in European great tits

Gene flow is usually thought to reduce genetic divergence and impede local adaptation by homogenising gene pools between populations. However, evidence for local adaptation and phenotypic differentiation in highly mobile species, experiencing high levels of gene flow, is emerging. Assessing population genetic structure at different spatial scales is thus a crucial step towards understanding mechanisms underlying intraspecific differentiation and diversification. Here, we studied the population genetic structure of a highly mobile species – the great tit Parus major – at different spatial scales. We analysed 884 individuals from 30 sites across Europe including 10 close-by sites (< 50 km), using 22 microsatellite markers. Overall we found a low but significant genetic differentiation among sites (FST = 0.008). Genetic differentiation was higher, and genetic diversity lower, in south-western Europe. These regional differences were statistically best explained by winter temperature. Overall, our results suggest that great tits form a single patchy metapopulation across Europe, in which genetic differentiation is independent of geographical distance and gene flow may be regulated by environmental factors via movements related to winter severity. This might have important implications for the evolutionary trajectories of sub-populations, especially in the context of climate change, and calls for future investigations of local differences in costs and benefits of philopatry at large scales.

A Comparative Analysis of Hedging in a Corpus of Two Written Legal Discourse Genres

Esta tesis doctoral, que es la culminación de mis estudios de doctorado impartidos por el Departamento de Lingüística Aplicada a la Ciencia y a la Tecnología de la Universidad Politécnica de Madrid, aborda el análisis del uso de la matización (hedging) en el lenguaje legal inglés siguiendo los postulados y principios de la análisis crítica de género (Bhatia, 2004) y empleando las herramientas de análisis de córpora WordSmith Tools versión 6 (Scott, 2014). Como refleja el título, el estudio se centra en la descripción y en el análisis contrastivo de las variedades léxico-sintácticas de los matizadores del discurso (hedges) y las estrategias discursivas que con ellos se llevan a cabo, además de las funciones que éstas desempeñan en un corpus de sentencias del Tribunal Supremo de EE. UU., y de artículos jurídicos de investigación americanos, relacionando, en la medida posible, éstas con los rasgos determinantes de los dos géneros, desde una perspectiva socio-cognitiva. El elemento innovador que ofrece es que, a pesar de los numerosos estudios que se han podido realizar sobre los matizadores del discurso en el inglés general (Lakoff, 1973; Hübler, 1983; Clemen, 1997; Markkanen and Schröder, 1997; Mauranen, 1997; Fetzer 2010; y Finnegan, 2010 entre otros) académico (Crompton, 1997; Meyer, 1997; Skelton, 1997; Martín Butragueňo, 2003) científico (Hyland, 1996a, 1996c, 1998c, 2007; Grabe and Kaplan, 1997; Salager-Meyer, 1997 Varttala, 2001) médico (Prince, 1982; Salager-Meyer, 1994; Skelton, 1997), y, en menor medida el inglés legal (Toska, 2012), no existe ningún tipo de investigación que vincule los distintos usos de la matización a las características genéricas de las comunicaciones profesionales. Dentro del lenguaje legal, la matización confirma su dependencia tanto de las expectativas a macro-nivel de la comunidad de discurso, como de las intenciones a micro-nivel del escritor de la comunicación, variando en función de los propósitos comunicativos del género ya sean éstos educativos, pedagógicos, interpersonales u operativos. El estudio pone de relieve el uso predominante de los verbos modales epistémicos y de los verbos léxicos como matizadores del discurso, estos últimos divididos en cuatro tipos (Hyland 1998c; Palmer 1986, 1990, 2001) especulativos, citativos, deductivos y sensoriales. La realización léxico-sintáctica del matizador puede señalar una de cuatro estrategias discursivas particulares (Namsaraev, 1997; Salager-Meyer, 1994), la indeterminación, la despersonalización, la subjectivisación, o la matización camuflada (camouflage hedging), cuya incidencia y función varia según género. La identificación y cuantificación de los distintos matizadores y estrategias empleados en los diferentes géneros del discurso legal puede tener implicaciones pedagógicos para los estudiantes de derecho no nativos que tienen que demostrar una competencia adecuada en su uso y procesamiento. ABSTRACT This doctoral thesis, which represents the culmination of my doctoral studies undertaken in the Department of Linguistics Applied to Science and Technology of the Universidad Politécnica de Madrid, focusses on the analysis of hedging in legal English following the principles of Critical Genre Analysis (Bhatia, 2004), and using WordSmith Tools version 6 (Scott, 2014) corpus analysis tools. As the title suggests, this study centers on the description and contrastive analysis of lexico-grammatical realizations of hedges and the discourse strategies which they can indicate, as well as the functions they can carry out, in a corpus of U.S. Supreme Court opinions and American law review articles. The study relates realization, incidence and function of hedging to the predominant generic characteristics of the two genres from a socio-cognitive perspective. While there have been numerous studies on hedging in general English (Lakoff, 1973; Hübler, 1983; Clemen, 1997; Markkanen and Schröder, 1997; Mauranen, 1997; Fetzer 2010; and Finnegan, 2010 among others) academic English (Crompton, 1997; Meyer, 1997; Skelton, 1997; Martín Butragueňo, 2003) scientific English (Hyland, 1996a, 1996c, 1998c, 2007; Grabe and Kaplan, 1997; Salager-Meyer, 1997 Varttala, 2001) medical English (Prince, 1982; Salager-Meyer, 1994; Skelton, 1997), and, to a lesser degree, legal English (Toska, 2012), this study is innovative in that it links the different realizations and functions of hedging to the generic characteristics of a particular professional communication. Within legal English, hedging has been found to depend on not only the macro-level expectations of the discourse community for a specific genre, but also on the micro-level intentions of the author of a communication, varying according to the educational, pedagogical, interpersonal or operative purposes the genre may have. The study highlights the predominance of epistemic modal verbs and lexical verbs as hedges, dividing the latter into four types (Hyland, 1998c; Palmer, 1986, 1990, 2001): speculative, quotative, deductive and sensorial. Lexical-grammatical realizations of hedges can signal one of four discourse strategies (Namsaraev, 1997; Salager-Meyer, 1994), indetermination, depersonalization, subjectivization and camouflage hedging, as well as fulfill a variety of functions. The identification and quantification of the different hedges and hedging strategies and functions in the two genres may have pedagogical implications for non-native law students who must demonstrate adequate competence in the production and interpretation of hedged discourse.

Georeferenced standardized apparent wave power along the coastline of Cabrera National Park for analysis of essential habitats of littoral species

Wind- induced exposure is one of the major forces shaping the geomorphology and biota in coastal areas. The effect of wave exposure on littoral biota is well known in marine environments (Ekebon et al., 2003; Burrows et al., 2008). In the Cabrera Archipelago National Park wave exposure has demostrated to have an effect on the spatial distribution of different stages of E.marginatus (Alvarez et al., 2010). Standarized average wave exposures during 2008 along the Cabrera Archipelago National park coast line were calculated to be applied in studies of littoral species distribution within the archipelago. Average wave exposure (or apparent wave power) was calculated for points located 50 m equidistant on the coastline following the EXA methodology (EXposure estimates for fragmented Archipelagos) (Ekebon et al., 2003). The average wave exposures were standardized from 1 to 100 (minimum and maximum in the area), showing coastal areas with different levels of mea wave exposure during the year. Input wind data (direction and intensity) from 2008 was registered at the Cabrera mooring located north of Cabrera Archipelago. Data were provided by IMEDEA (CSIC-UIB, TMMOS http://www.imedea.uib-csic.es/tmoos/boyas/). This cartography has been developed under the framework of the project EPIMHAR, funded by the National Park's Network (Spanish Ministry of Environment, Maritime and Rural Affairs, reference: 012/2007 ). Part of this work has been developed under the research programs funded by "Fons de Garantia Agrària i Pesquera de les Illes Balears (FOGAIBA)".

Pesäpuu palaa

Kansi ja välivignetit: Tapio Tapiovaara.

Ikuisesta runsaudensarvesta uppoaviin paratiisisaariin. Muuttuvan maailman kuvauksia suomalaisissa kaukomatkakertomuksissa

Nykypäivän matkakirjallisuuden suurimpia haasteita on se, miten yhdistää globalisoituvan maailman kuvaaminen lajityyppiin, jonka kuvastoa ovat perinteisesti hallinneet tallaamattomat polut, neitseelliset paratiisirannat sekä kulttuurien eksoottinen toiseus. Tämä tutkielma tarkastelee sitä, millaista kuvaa muuttuvasta maailmasta suomalaiset matkakirjailijat ovat luoneet. Tutkielma sijoittuu ekokriittisen sekä postkolonialistisen kirjallisuudentutkimuksen välimaastoon, jossa painottuu vahva kytkös konkreettiseen maailmaan. Kohdeteoksina on neljä kaukomatkakertomusta eri ajoilta: Tapio Hiisivaaran Myrkkynuolia, kahvia, banaaneja (1945), Tuomas Vennon Katoavaa Grönlantia (1960), Annikki Sankarin Afrikkalainen uni (1984) ja Pirkko Lindbergin SOS Tuvalu (2004). Kohdeteosten avulla käydään läpi eurooppalaisen maisemakuvauksen vanhoja traditioita, joita teokset sekä uusintavat että uudistavat. Matkailijan omat halut ja pelot ilmenevät usein matkakuvauksissa esimerkiksi paratiisien ja helvettien sekä ikuisen rauhan ja ajattomuuden teemoina, ja samankaltaisesti määrittyy myös matkailijan suhde muihin olentoihin. Matkalla tapahtuvat kohtaamiset rikkovat omien ennakkokäsitysten varaan rakennettuja olettamuksia, sillä äärimmäistä kuvaa voi pitää yllä vain, jos asioita tarkastelee etäältä. Kohdeteoksia vertailemalla piirtyy kuva maapallon muuttumisesta luonnonvaroiltaan yltäkylläisestä runsaudensarvesta saasteiden tahrimaksi maailmankyläksi. Pelko länsimaalaisen kulttuurin globaalista leviämisestä ilmenee kohdeteoksissa vahvana, mikä näkyy esimerkiksi primitiivisyyden ihannointina. Tulevaisuuden matkakuvauksissa ilmastonmuutos saattaa toisaalta voimistaa tätä vastakohta-asetelmaa, mutta toisaalta myös luoda yhtenäisempää, koko ihmiskunnan laajuista perspektiiviä. Yksi tärkeimmistä nykypäivän matkakirjallisuuden lajityyppiä uudistavista kerronnan tavoista on moniperspektiivisyys, joka nostaa esille myös kertojan kokemusmaailman ulkopuolisia näkökulmia. Sen valossa koskemattomien idyllienkään ei tarvitse olla matkakirjallisuudelta kiellettyjä aiheita, sillä ne voidaan nähdä vain yhtenä perspektiivin palasena sekä kaunokirjallisen ilmaisun tehokeinoina. Tutkielma osoittaa, miten konkreettisten paikkojen fiktiivisillä esityksillä on voima vahvistaa paikan tunnetta ja siten tuottaa läheistä suhdetta kaukaisiinkin paikkoihin.