The role of phylogeny in the spatial distributions and assembly of mountain plant communities.

A major challenge in community ecology is a thorough understanding of the processes that govern the assembly and composition of communities in time and space. The growing threat of climate change to the vascular plant biodiversity of fragile ecosystems such as mountains has made it equally imperative to develop comprehensive methodologies to provide insights into how communities are assembled. In this perspective, the primary objective of this PhD thesis is to contribute to the theoretical and methodological development of community ecology, by proposing new solutions to better detect the ecological and evolutionary processes that govern community assembly. As phylogenetic trees provide by far, the most advanced tools to integrate the spatial, ecological and evolutionary dynamics of plant communities, they represent the cornerstone on which this work was based. In this thesis, I proposed new solutions to: (i) reveal trends in community assembly on phylogenies, depicted by the transition of signals at the nodes of the different species and lineages responsible for community assembly, (ii) contribute to evidence the importance of evolutionarily labile traits in the distribution of mountain plant species. More precisely, I demonstrated that phylogenetic and functional compositional turnover in plant communities was driven by climate and human land use gradients mostly influenced by evolutionarily labile traits, (iii) predict and spatially project the phylogenetic structure of communities using species distribution models, to identify the potential distribution of phylogenetic diversity, as well as areas of high evolutionary potential along elevation. The altitudinal setting of the Diablerets mountains (Switzerland) provided an appropriate model for this study. The elevation gradient served as a compression of large latitudinal variations similar to a collection of islands within a single area, and allowed investigations on a large number of plant communities. Overall, this thesis highlights that stochastic and deterministic environmental filtering processes mainly influence the phylogenetic structure of plant communities in mountainous areas. Negative density-dependent processes implied through patterns of phylogenetic overdispersion were only detected at the local scale, whereas environmental filtering implied through phylogenetic clustering was observed at both the regional and local scale. Finally, the integration of indices of phylogenetic community ecology with species distribution models revealed the prospects of providing novel and insightful explanations on the potential distribution of phylogenetic biodiversity in high mountain areas. These results generally demonstrate the usefulness of phylogenies in inferring assembly processes, and are worth considering in the theoretical and methodological development of tools to better understand phylogenetic community structure.

Lire l'oral : pour une typologie linguistique des représentations écrites de l'oralité (le cas du français)

Cette thèse propose de passer en revue les modalités de la représentation écrite de l'oralité en français. La pratique littéraire constitue le matériau et l'horizon de la théorisation. La problématique - comment l'écrit représente-t-il l'oral ? - est d'abord située et reformulée dans le cadre de la linguistique de la parole (I). Les rapports entre oralité et scripturalité sont ensuite étudiés sous trois angles. L'angle biotechnologique compare la matérialité et l'affordance des signaux graphiques et des signaux acoustiques (II 1). L'examen sémiotique reconnaît dans le français écrit un système dit phonographique dont la fonction est de représenter l'expression des signes du français oral. Sont analysées alors les relations entre les systèmes de signes impliqués, la diversité des actualisations possibles du système phonographique (effets d'écoute), ainsi que diverses sémiotiques analogiques (II 2). On étudie ensuite le rôle de la prosodie dans la lecture. La position adoptée est la suivante : bien qu'elle soit facultative dans l'activité de lecture, la prosodie est spécialement sollicitée par des écrits qu'on peut caractériser linguistiquement. L'interprétation prosodique apporte à ces écrits un surcroît de signification en même temps qu'il produit un mode spécifique de représentation de l'oral appelé effet prosodique (II 3). L'angle sémantique est esquissé finalement : il conduit à dégager deux modalités de représentation supplémentaire. Pour la première, l'oral se situe sur le plan sémantico-référentiel de l'expression écrite (écrire à propos d'oral) ; pour la seconde, l'oral est un extérieur discursif modalisant le dire écrit : l'écrit est reconnu comme énoncé à la manière de l'oral (effet de style oral). - This PhD thesis attempts to review the modalities of orality in written representation. Literary writings act as the material for theorization. First of all, the thesis statement - how does writing represent oral - is situated and then, reformulated within the frame of linguistique de la parole (the linguistic field of speech) (I). The connections between orality and writing are then studied under three angles. The biotechnological angle compares the materiality and the affordance of graphic signs and acoustic signals (II 1). A semiotic examination acknowledges, in French, a phonographical system whose function is to represent the expression of French oral signs. Thus, the relationships between the systems of implicated signs, the diversity of possible actualisations of the phonographic system (voice effects), as well as various analogical semiotics are analysed (II 2). Furthermore, the role of prosody is studied within reading. The stand taken is the following : even though it is optional during a reading activity, prosody is especially sought-after by linguistically characterised writings. The prosodie interpretation brings to these writings a surge of signification while producing a specific mode of oral representation called the prosodie effects (II 3). The semantic angle is finally drawn : it leads to two additional modalities of representation. For the first part, speech is located on the semantic and referential plan of the written expression (writing about speech); as for the second part, spoken language is a discursive exteriority : writing is recognised as an oral-like utterance {oral-like effect).

Processus et fonctions psychiques de l'écriture : de la création littéraire au groupe à médiation

Ce travail porte sur l'étude des processus et fonctions psychiques de la création littéraire et de l'écriture dans une perspective psychanalytique, à partir d'une méthodologie de recherche qualitative exploratoire. Un premier volet de la recherche s'attache à étudier les processus et fonctions psychiques dans la création littéraire à partir de six entretiens semi-structurés avec des écrivains romands publiés. Les entretiens sont analysés en profondeur à partir de la méthodologie qualitative Interpretative Phenomenological Analysis (Smith, Flowers & Larkin, 2009). Un second volet de la recherche étudie les processus et fonctions psychiques de l'écriture dans un atelier de groupe à médiation écriture prenant place dans un Centre de Jour pour adultes, à partir de l'élaboration de deux cas. L'articulation des analyses de ces expériences d'écriture dans les deux contextes étudiés permet de mettre en évidence des enjeux de continuité/discontinuité dans le passage du premier mouvement créateur de l'écriture - le « miroir-papier » - vers le mouvement de la publication/lecture - le « miroir-lecteur ». Ces enjeux de partage invitent à penser le travail créateur de l'écriture à partir de la notion de « Moi- peau » (Anzieu, 1995) et à préciser cinq fonctions psychiques de l'écriture : transformation ; protection ; échange ; réassurance narcissique ; partage. Un accent particulier est porté sur la fonction de protection, dans la tension qu'elle entretient avec celle de transformation, au travers de la mise en évidence de six formes d'enveloppes d'écriture protectrice. Finalement, les analyses mettent en évidence la manière dont cette tension entre un investissement défensif de l'écriture et un investissement de transformation se déploie par des voies singulières en vue d'une tentative de résolution du conflit subjectif interne entre les exigences du « public intérieur » (De M'Uzan, 1964) et la rencontre avec l'objet réel. Ces pistes d'analyses permettent de préciser les modalités de contribution de l'écriture aux processus de symbolisation et d'enrichir la pratique du champ des médiations thérapeutiques de repères d'appréciation clinique. - Based on an exploratory qualitative research methodology, this work focuses on the psychical processes and functions of literary creation and writing from a psychoanalytic perspective. The first part of the research investigates psychical processes and functions in creative writing through the analysis of six semi-structured interviews with published Swiss writers. The interviews are analyzed according to the exploratory qualitative methodology Interpretative Phenomenological Analysis (Smith, Flowers & Larkin, 2009). The second area of research examines the processes of writing in the context of an art-therapy writing group that took place in an adult day center. The observations lead to the elaboration of two case studies. The joint analysis of these writing experiences highlights issues of continuity/discontinuity in passing from the first creative writing movement - the « mirror-paper » - to the final publication/reading of the work - the «mirror-reader». These issues enable us to understand the creative writing processes from the concept of the « skin-ego » (Anzieu, 1995). Five functions of writing are proposed: transformation, protection, exchange, narcissistic reassurance, and sharing. An emphasis on the tension between the protection and the transformation functions is highlighted through the identification of six forms of protective writing psychical envelopes. Finally, the analysis shows how this tension between a defensive and a transformative investment in writing takes place in an attempt to resolve the internal conflict between the « inner audience » (De M'Uzan, 1964) and the encounter with the real object. This study clarifies the way creative writing can contribute to symbolization and can enrich clinical assessment in the field of art-therapy.

Analysis of Roman pottery graffiti by high resolution capture and 3D laser profilometry

The graffiti on pottery discovered on the site of Aventicum (Avenches, VD/Switzerland) form the largest corpus of minor inscriptions of the Roman Empire studied until now. Indeed, a total of 1828 graffiti have been found. The reading and the recording of the inscriptions are generally dependent on the state of conservation of the graffito and its support. In numerous cases, only a pale shadow of the inscription is visible, which makes traditional observations, such as visual observations with the naked eye, unsuitable for its decipherment. Consequently, advanced techniques have been applied for enhancing the readability of such inscriptions. In our paper we show the efficiency of 3D laser profilometry as well as high resolution photography as powerful means to decipher illegible engraved inscriptions. The use of such analyses to decipher graffiti on pottery or on other materials enables a better understanding of minor inscriptions and improves the knowledge of the daily life of ancient populations substantially.

Large scale assessment of regulatory evolution and transcriptome complexity in mammals

AbstractIn addition to genetic changes affecting the function of gene products, changes in gene expression have been suggested to underlie many or even most of the phenotypic differences among mammals. However, detailed gene expression comparisons were, until recently, restricted to closely related species, owing to technological limitations. Thus, we took advantage of the latest technologies (RNA-Seq) to generate extensive qualitative and quantitative transcriptome data for a unique collection of somatic and germline tissues from representatives of all major mammalian lineages (placental mammals, marsupials and monotremes) and birds, the evolutionary outgroup.In the first major project of my thesis, we performed global comparative analyses of gene expression levels based on these data. Our analyses provided fundamental insights into the dynamics of transcriptome change during mammalian evolution (e.g., the rate of expression change across species, tissues and chromosomes) and allowed the exploration of the functional relevance and phenotypic implications of transcription changes at a genome-wide scale (e.g., we identified numerous potentially selectively driven expression switches).In a second project of my thesis, which was also based on the unique transcriptome data generated in the context of the first project we focused on the evolution of alternative splicing in mammals. Alternative splicing contributes to transcriptome complexity by generating several transcript isoforms from a single gene, which can, thus, perform various functions. To complete the global comparative analysis of gene expression changes, we explored patterns of alternative splicing evolution. This work uncovered several general and unexpected patterns of alternative splicing evolution (e.g., we found that alternative splicing evolves extremely rapidly) as well as a large number of conserved alternative isoforms that may be crucial for the functioning of mammalian organs.Finally, the third and final project of my PhD consisted in analyzing in detail the unique functional and evolutionary properties of the testis by exploring the extent of its transcriptome complexity. This organ was previously shown to evolve rapidly both at the phenotypic and molecular level, apparently because of the specific pressures that act on this organ and are associated with its reproductive function. Moreover, my analyses of the amniote tissue transcriptome data described above, revealed strikingly widespread transcriptional activity of both functional and nonfunctional genomic elements in the testis compared to the other organs. To elucidate the cellular source and mechanisms underlying this promiscuous transcription in the testis, we generated deep coverage RNA-Seq data for all major testis cell types as well as epigenetic data (DNA and histone methylation) using the mouse as model system. The integration of these complete dataset revealed that meiotic and especially post-meiotic germ cells are the major contributors to the widespread functional and nonfunctional transcriptome complexity of the testis, and that this "promiscuous" spermatogenic transcription is resulting, at least partially, from an overall transcriptionally permissive chromatin state. We hypothesize that this particular open state of the chromatin results from the extensive chromatin remodeling that occurs during spermatogenesis which ultimately leads to the replacement of histones by protamines in the mature spermatozoa. Our results have important functional and evolutionary implications (e.g., regarding new gene birth and testicular gene expression evolution).Generally, these three large-scale projects of my thesis provide complete and massive datasets that constitute valuables resources for further functional and evolutionary analyses of mammalian genomes.

Effects of age, birth cohort and period of death on Swiss cancer mortality, 1951-1984.

Swiss death certification data over the period 1951-1984 for total cancer mortality and 30 major cancer sites in the population aged 25 to 74 years were analysed using a log-linear Poisson model with arbitrary constraints on the parameters to isolate the effects of birth cohort, calendar period of death and age. The overall pattern of total cancer mortality in males was stable for period values and showed some moderate decreases in cohort values restricted to the generations born after 1930. Cancer mortality trends were more favourable in females, with steady, though moderate, declines in both cohort and period values. According to the estimates from the model, the worst affected generation for male lung cancer was that born around 1910, and a flattening of trends or some moderate decline was observed for more recent cohorts, although this decline was considerably more limited than in other European countries. There were decreases in cohort and period values for stomach, intestine and oesophageal cancer in both sexes and (cervix) uteri in females. Increases were observed in both cohort and period trends for pancreas and liver in males and for several other neoplasms, including prostate, brain, leukaemias and lymphomas, restricted, however, for the latter sites, to the earlier cohorts and hence partly attributable to improved diagnosis and certification in the elderly. Although age values for lung cancer in females were around 10-times lower than in males, upward trends in female lung cancer cohort values were observed in subsequent cohorts and for period values from the late 1960's onwards. Therefore, future trends in female lung cancer mortality should continue to be monitored. The application of these age/period/cohort models thus provides a summary guide for the reading and interpretation of cancer mortality trends, although it cannot replace careful inspection of single age-specific rates.

How can we teach EBM in clinical practice? : an analysis of barriers to implementation of on-the-job EBM teaching and learning.

Introduction: Evidence-based medicine (EBM) improves the quality of health care. Courses on how to teach EBM in practice are available, but knowledge does not automatically imply its application in teaching. We aimed to identify and compare barriers and facilitators for teaching EBM in clinical practice in various European countries. Methods: A questionnaire was constructed listing potential barriers and facilitators for EBM teaching in clinical practice. Answers were reported on a 7-point Likert scale ranging from not at all being a barrier to being an insurmountable barrier. Results: The questionnaire was completed by 120 clinical EBM teachers from 11 countries. Lack of time was the strongest barrier for teaching EBM in practice (median 5). Moderate barriers were the lack of requirements for EBM skills and a pyramid hierarchy in health care management structure (median 4). In Germany, Hungary and Poland, reading and understanding articles in English was a higher barrier than in the other countries. Conclusion: Incorporation of teaching EBM in practice faces several barriers to implementation. Teaching EBM in clinical settings is most successful where EBM principles are culturally embedded and form part and parcel of everyday clinical decisions and medical practice.

Optical crop sensor for variable-rate nitrogen fertilization in corn: i - plant nutrition and dry matter production

Variable-rate nitrogen fertilization (VRF) based on optical spectrometry sensors of crops is a technological innovation capable of improving the nutrient use efficiency (NUE) and mitigate environmental impacts. However, studies addressing fertilization based on crop sensors are still scarce in Brazilian agriculture. This study aims to evaluate the efficiency of an optical crop sensor to assess the nutritional status of corn and compare VRF with the standard strategy of traditional single-rate N fertilization (TSF) used by farmers. With this purpose, three experiments were conducted at different locations in Southern Brazil, in the growing seasons 2008/09 and 2010/11. The following crop properties were evaluated: above-ground dry matter production, nitrogen (N) content, N uptake, relative chlorophyll content (SPAD) reading, and a vegetation index measured by the optical sensor N-Sensor® ALS. The plants were evaluated in the stages V4, V6, V8, V10, V12 and at corn flowering. The experiments had a completely randomized design at three different sites that were analyzed separately. The vegetation index was directly related to above-ground dry matter production (R² = 0.91; p<0.0001), total N uptake (R² = 0.87; p<0.0001) and SPAD reading (R² = 0.63; p<0.0001) and inversely related to plant N content (R² = 0.53; p<0.0001). The efficiency of VRF for plant nutrition was influenced by the specific climatic conditions of each site. Therefore, the efficiency of the VRF strategy was similar to that of the standard farmer fertilizer strategy at sites 1 and 2. However, at site 3 where the climatic conditions were favorable for corn growth, the use of optical sensors to determine VRF resulted in a 12 % increase in N plant uptake in relation to the standard fertilization, indicating the potential of this technology to improve NUE.

A two-level analysis of the determinants of direct democratic choices in European, immigration and foreign policy in Switzerland

This article employs a unique data set - covering 25 popular votes on foreign, European and immigration/asylum policy held between 1992 and 2006 in Switzerland - in order to examine the conditional impact of context upon utilitarian, cultural, political and cognitive determinants of individual attitudes toward international openness. Our results reveal clear patterns of cross-level interactions between individual determinants and the project-related context of the vote. Thus, although party cues and political competence have a strong impact on individuals' support for international openness, this impact is substantially mediated by the type of coalition that is operating within the party elite. Similarly, subjective utilitarian and cultural considerations influence the voters' decision in interaction with the content of the proposal submitted to the voters as well as with the framing of the voting campaign.

A process for mining science & technology documents databases, illustrated for the case of "knowledge discovery and data mining"

This paper presents a process of mining research & development abstract databases to profile current status and to project potential developments for target technologies, The process is called "technology opportunities analysis." This article steps through the process using a sample data set of abstracts from the INSPEC database on the topic o "knowledge discovery and data mining." The paper offers a set of specific indicators suitable for mining such databases to understand innovation prospects. In illustrating the uses of such indicators, it offers some insights into the status of knowledge discovery research*.

Frost Action in Rocks and Concrete, HR-258, 1986

The objectives of the project were to develop methodologies for (i) prediction and measurement of the magnitude of pressure which develops within pores of saturated porous materials upon freezing, (ii) determination of pore structure (pore size distribution) of porous materials; (iii) prediction and measurement of the rate with which pore ice grows; and (iv) prediction of frost susceptibility of porous materials with varying pore structures. As with all research endeavors solution of one problem leads to another one and this project was no exception. Emergence of new problems and the measures taken as the work progressed were discussed in progress reports submitted to the board. This final report will discuss only the conclusive finds and suggest measures to be taken for future investigations. The theory discussed in the proposal is not repeated in this report for the sake of brevity. However, the paper published as part of this project containing the theory is attached as Appendix I for the reader interested in the theory. In conformity with the objectives, this report consists of four parts. In accordance with the project contract two ice porosimeters were built and one will be delivered to the Iowa DOT after training of a DOT technician under the supervision of Mr. Wendell Dubberke with assistance from ISU researchers. During the training period debugging and further improvements in software will continue.

Examination of Heterogeneous Crossing Sequences Between Toner and Rollerball Pen Strokes by Digital Microscopy and 3-D Laser Profilometry

The determination of line crossing sequences between rollerball pens and laser printers presents difficulties that may not be overcome using traditional techniques. This research aimed to study the potential of digital microscopy and 3-D laser profilometry to determine line crossing sequences between a toner and an aqueous ink line. Different paper types, rollerball pens, and writing pressure were tested. Correct opinions of the sequence were given for all case scenarios, using both techniques. When the toner was printed before the ink, a light reflection was observed in all crossing specimens, while this was never observed in the other sequence types. The 3-D laser profilometry, more time-consuming, presented the main advantage of providing quantitative results. The findings confirm the potential of the 3-D laser profilometry and demonstrate the efficiency of digital microscopy as a new technique for determining the sequence of line crossings involving rollerball pen ink and toner. With the mass marketing of laser printers and the popularity of rollerball pens, the determination of line crossing sequences between such instruments is encountered by forensic document examiners. This type of crossing presents difficulties with optical microscopic line crossing techniques involving ballpoint pens or gel pens and toner (1-4). Indeed, the rollerball's aqueous ink penetrates through the toner and is absorbed by the fibers of the paper, leaving the examiner with the impression that the toner is above the ink even when it is not (5). Novotny and Westwood (3) investigated the possibility of determining aqueous ink and toner crossing sequences by microscopic observation of the intersection before and after toner removal. A major disadvantage of their study resides in destruction of the sample by scraping off the toner line to see what was underneath. The aim of this research was to investigate the ways to overcome these difficulties through digital microscopy and three-dimensional (3-D) laser profilometry. The former was used as a technique for the determination of sequences between gel pen and toner printing strokes, but provided less conclusive results than that of an optical stereomicroscope (4). 3-D laser profilometry, which allows one to observe and measure the topography of a surface, has been the subject of a number of recent studies in this area. Berx and De Kinder (6) and Schirripa Spagnolo (7,8) have tested the application of laser profilometry to determine the sequence of intersections of several lines. The results obtained in these studies overcome disadvantages of other methods applied in this area, such as scanning electron microscope or the atomic force microscope. The main advantages of 3-D laser profilometry include the ease of implementation of the technique and its nondestructive nature, which does not require sample preparation (8-10). Moreover, the technique is reproducible and presents a high degree of freedom in the vertical axes (up to 1000 μm). However, when the paper surface presents a given roughness, if the pen impressions alter the paper with a depth similar to the roughness of medium, the results are not always conclusive (8). It becomes difficult in this case to distinguish which characteristics can be imputed to the pen impressions or the quality of the paper surface. This important limitation is assessed by testing different types of paper of variable quality (of different grammage and finishing) and the writing pressure. The authors will therefore assess the limits of 3-D laser profilometry technique and determine whether the method can overcome such constraints. Second, the authors will investigate the use of digital microscopy because it presents a number of advantages: it is efficient, user-friendly, and provides an objective evaluation and interpretation.

Prosody and pragmatics in parenthetical insertions in catalan

This paper analyses the role of prosody in parenthetical insertions, a type of structure that is extremely common in both speech and writing. The materials under study come from a corpus of spontaneous speech acts in Central Catalan (with varying degrees of spontaneity) from which a corpus of oral parenthetical insertions has been compiled. The prototypical prosodic features of a parenthetical insertion in Catalan are: prosodic autonomy, limited extension, production in between pauses or final pause, tendency towards acceleration, fall in intensity, lower pitch range and, finally, falling or rising melodic pattern. While the final fall is the most frequent pattern in spontaneous conversations with a high degree of confidence between interlocutors, a final rising structure is found in interviews in which the degree of confidence between participants is smaller, their roles are unequal, and the interviewed constructs a narrative discourse. We thus suggest that the pitch contour of parenthetical insertions is related to formality and discourse typology (in this case, narrative vs. dialogue). Bearing in mind the discursive functions performed by these insertions, we propose a typology which classifies them with regards to two main functions: completion of information, and modalisation.

Lecture d'articles médicaux: quelques pièges à éviter [Reading medical articles--what pitfalls to avoid]

Critical reading and careful interpretation of results of the medical literature is a difficult task for primary care physicians. Being aware of common potential pitfalls that may bias results of a study is helpful. Among common pitfalls, odds ratios are often interpreted as relative risks, which overestimate the impact of a risk factor. Randomized controlled trials assessing the effectiveness of a new drug or a new target disease often use surrogate markers instead of clinical events as outcomes. Results of these trials should be considered with caution before using their results for clinical practice. For screening, observational studies often yield potentially biased or conflicting results. As clinical guidelines and expert opinions are often conflicting, primary care physicians should wait for results of large clinical trials in clinical events before changing their practice for screening or new drugs.

Access Management Research and Awareness Program : Phase IV, 1999

Access management involves balancing the dual roles that roadways must play - through travel and access to property and economic activity. When these roles are not in proper balance, the result is a roadway system that functions sub-optimally. Arterial routes that have a too high driveway density and provide overly extensive access to property have high crash rates and begin to suffer in terms of traffic operations. Such routes become congested, delays increase, and mean travel speeds decline. The Iowa access management research and awareness project has had four distinct phases. Phase I involved a detailed review of the extensive national access management literature so lessons learned elsewhere could be applied in Iowa. In Phase II original case study research was conducted in Iowa. Phase III of the project concentrated on outreach and education about access management. Phase IV of the Iowa access management project extended the work conducted during Phases II and III. The main work products for Phase IV were as follows: 1) three additional before and after case studies, illustrating the impacts of various access management treatments on traffic safety, traffic operations, and business vitality; 2) an access management handbook aimed primarily at local governments in Iowa; 3) a modular access management toolkit with brief descriptions of various access management treatments and considerations; and 4) an extensive outreach plan aimed at getting the results of Phases I through IV of the project out to diverse audiences in Iowa and elsewhere.