The role of fungi in the precipitation of calcite : relationships between fungal filaments, nanofibres, and needle fibre calcite

RésuméLes champignons sont impliqués dans les cycles biogéochimiques de différentes manières. En particulier, ils sont reconnus en tant qu'acteurs clés dans la dégradation de la matière organique, comme fournisseurs d'éléments nutritifs via l'altération des minéraux mais aussi comme grands producteurs d'acide oxalique et de complexes oxalo-métalliques. Toutefois, peu de choses sont connues quant à leur contribution à la genèse d'autres types de minéraux, tel que le carbonate de calcium (CaCO3). Le CaCO3 est un minéral ubiquiste dans de nombreux écosystèmes et il joue un rôle essentiel dans les cycles biogéochimiques du carbone (C) et du calcium (Ca). Le CaCO3 peut être d'origine physico-chimique ou biogénique et de nombreux organismes sont connus pour contrôler ou induire sa biominéralisation. Les champignons ont souvent été soupçonnés d'être impliqué dans ce processus, cependant il existe très peu d'informations pour étayer cette hypothèse.Cette thèse a eu pour but l'étude de cet aspect négligé de l'impact des champignons dans les cycles biogéochimiques, par l'exploration de leur implication potentielle dans la formation d'un type particulier de CaCO3 secondaires observés dans les sols et dans les grottes des environnements calcaires. Dans les grottes, ces dépôts sont appelés moonmilk, alors que dans les sols on les appelle calcite en aiguilles. Cependant ces deux descriptions correspondent en fait au même assemblage microscopique de deux habitus particulier de la calcite: la calcite en aiguilles (au sens strict du terme cette fois-ci) et les nanofibres. Ces deux éléments sont des habitus aciculaires de la calcite, mais présentent des dimensions différentes. Leur origine, physico-chimique ou biologique, est l'objet de débats intenses depuis plusieurs années déjà.L'observation d'échantillons environnementaux avec des techniques de microscopie (microscopie électronique et micromorphologie), ainsi que de la microanalyse EDX, ont démontré plusieurs relations intéressantes entre la calcite en aiguilles, les nanofibres et des éléments organiques. Premièrement, il est montré que les nanofibres peuvent être organiques ou minérales. Deuxièmement, la calcite en aiguilles et les nanofibres présentent de fortes analogies avec des structures hyphales, ce qui permet de confirmer l'hypothèse de leur origine fongique. En outre, des expériences en laboratoire ont confirmé l'origine fongique des nanofibres, par des digestions enzymatiques d'hyphes fongiques. En effet, des structures à base de nanofibres, similaires à celles observées dans des échantillons naturels, ont pu être produites par cette approche. Finalement, des enrichissements en calcium ont été mesurés dans les parois des hyphes et dans des inclusions intrahyphales provenant d'échantillons naturels de rhizomorphes. Ces résultats suggèrent une implication de la séquestration de calcium dans la formation de la calcite en aiguilles et/ou des nanofibres.Plusieurs aspects restent à élucider, en particulier la compréhension des processus physiologiques impliqués dans la nucléation de calcite dans les hyphes fongiques. Cependant, les résultats obtenus dans cette thèse ont permis de confirmer l'implication des champignons dans la formation de la calcite en aiguilles et des nanofibres. Ces découvertes sont d'une grande importance dans les cycles biogéochimiques puisqu'ils apportent de nouveaux éléments dans le cycle couplé C-Ca. Classiquement, les champignons sont considérés comme étant impliqués principalement dans la minéralisation de la matière organique et dans l'altération minérale. Cette étude démontre que les champignons doivent aussi être pris en compte en tant qu'agents majeurs de la genèse de minéraux, en particulier de CaCO3. Ceci représente une toute nouvelle perspective en géomycologie quant à la participation des champignons au cycle biologique du C. En effet, la présence de ces précipitations de CaCO3 secondaires représente un court-circuit dans le cycle biologique du C puisque du C inorganique du sol se retrouve piégé dans de la calcite plutôt que d'être retourné dans l'atmosphère.AbstractFungi are known to be involved in biogeochemical cycles in numerous ways. In particular, they are recognized as key players in organic matter recycling, as nutrient suppliers via mineral weathering, as well as large producers of oxalic acid and metal-oxalate. However, little is known about their contribution to the genesis of other types of minerals such as calcium carbonate (CaCO3). Yet, CaC03 are ubiquitous minerals in many ecosystems and play an essential role in the biogeochemical cycles of both carbon (C) and calcium (Ca). CaC03 may be physicochemical or biogenic in origin and numerous organisms have been recognized to control or induce calcite biomineralization. While fungi have often been suspected to be involved in this process, only scarce information support this hypothesis.This Ph.D. thesis aims at investigating this disregarded aspect of fungal impact on biogeochemical cycles by exploring their possible implication in the formation of a particular type of secondary CaC03 deposit ubiquitously observed in soils and caves from calcareous environments. In caves, these deposits are known as moonmilk, whereas in soils, they are known as Needle Fibre Calcite (NFC - sensu lato). However, they both correspond to the same microscopic assemblage of two distinct and unusual habits of calcite: NFC {sensu stricto) and nanofibres. Both features are acicular habits of calcite displaying different dimensions. Whether these habits are physicochemical or biogenic in origin has been under discussion for a long time.Observations of natural samples using microscopic techniques (electron microscopy and micromorphology) and EDX microanalyses have demonstrated several interesting relationships between NFC, nanofibres, and organic features. First, it has shown that nanofibres can be either organic or minera! in nature. Second, both nanofibres and NFC display strong structural analogies with fungal hyphal features, supporting their fungal origin. Furthermore, laboratory experiments have confirmed the fungal origin of nanofibres through an enzymatic digestion of fungal hyphae. Indeed, structures made of nanofibres with similar features as those observed in natural samples have been produced. Finally, calcium enrichments have been measured in both cell walls and intrahyphal inclusions of hyphae from rhizomorphs sampled in the natural environment. These results point out an involvement of calcium sequestration in nanofibres and/or NFC genesis.Several aspects need further investigation, in particular the understanding of the physiological processes involved in hyphal calcite nucleation. However, the results obtained during this study have allowed the confirmation of the implication of fungi in the formation of both NFC and nanofibres. These findings are of great importance regarding global biogeochemical cycles as they bring new insights into the coupled C and Ca cycles. Conventionally, fungi are considered to be involved in organic matter mineralization and mineral weathering. In this study, we demonstrate that they must also be considered as major agents in mineral genesis, in particular CaC03. This is a completely new perspective in geomycology regarding the role of fungi in the short-term (or biological) C cycle. Indeed, the presence of these secondary CaC03 precipitations represents a bypass in the short- term carbon cycle, as soil inorganic C is not readily returned to the atmosphere.

Quantitative ultrasound in the management of osteoporosis: the 2007 ISCD Official Positions

Dual-energy X-ray absorptiometry (DXA) is commonly used in the care of patients for diagnostic classification of osteoporosis, low bone mass (osteopenia), or normal bone density; assessment of fracture risk; and monitoring changes in bone density over time. The development of other technologies for the evaluation of skeletal health has been associated with uncertainties regarding their applications in clinical practice. Quantitative ultrasound (QUS), a technology for measuring properties of bone at peripheral skeletal sites, is more portable and less expensive than DXA, without the use of ionizing radiation. The proliferation of QUS devices that are technologically diverse, measuring and reporting variable bone parameters in different ways, examining different skeletal sites, and having differing levels of validating data for association with DXA-measured bone density and fracture risk, has created many challenges in applying QUS for use in clinical practice. The International Society for Clinical Densitometry (ISCD) 2007 Position Development Conference (PDC) addressed clinical applications of QUS for fracture risk assessment, diagnosis of osteoporosis, treatment initiation, monitoring of treatment, and quality assurance/quality control. The ISCD Official Positions on QUS resulting from this PDC, the rationale for their establishment, and recommendations for further study are presented here.

Influence of emergence timing of weeds on the establishment of woody natives and ground cover species

Les invasions biològiques són produïdes per espècies transportades per l'home fora de la regió d'origen a altres regions on s'estableixen i expandeixen. Són actualment de les majors causes de perduda de biodiversitat, amb el canvi d'usos del sòl, tret rellevant en zones insulars. Comprendre mecanismes de competència amb les espècies autòctones és clau per gestionar el problema. L’experiment evidencia diferències de creixement de 7 plantes natives australianes (3 espècies d’eucaliptus, 3 espècies d’acàcia, 1 pasturatge natiu), competint intraespecífica (entre mateixa espècie) i interespecíficament (acàcies o eucaliptus convivint amb pasturatge natiu) plantejant tres tractaments (sense males herbes, males herbes i males herbes a posteriori) per definir la naturalesa de la interacció dels diferents tipus funcionals d'espècies. S’analitzen tendències temporals de creixement de plàntules, així com la supervivència. S’ha detectat una moderada correlació entre taxes de creixement d’espècies i mida de la llavor, (p ≈ 0.6), així com una correlació entre la supervivència i la humitat del sòl (p ≈ 0.5); efectes estacionals. A curt termini i en escenari de primavera la convivència amb males herbes reporta creixement nul. Tractaments sense males herbes, presenten major supervivència en escenaris en competència interespecífica. A llarg termini les espècies amb major supervivència són les que conviuen amb pasturatge natiu i sense males herbes, indicant un efecte beneficiós en espècies millor adaptades a la sequera (E. loxophleba).

Quantifying the level of eusociality

The evolution of animal societies in which some individuals forego direct reproduction to help others to reproduce poses an evolutionary paradox. Societies where all individuals reproduce equally and societies where a single individual completely monopolizes reproduction represent the end points of a continuum of variance in the reproductive output among group members. This led Sherman et al. (1995) to propose that cooperative breeding and eusociality (a term originally applied only to insects) are not discrete phenomena. Rather they form a continuum whose main difference is the extent to which individuals forego their own reproductive opportunity to help other members of the group. Here we present a new index: the eusociality index. It quantifies the decrease in direct reproduction of group members as a resut of altruistic acts directed to other members of the group (i.e. a measure of the level of eusociality). The rationale for this index lies in the fundamental duality of the reproductive process, in which organisms supply two distinct elements: (i) genetic material (genes); and (ii) power (energy). In non-eusocial animals, all individuals transmit genes and power in the same ratio (notwithstanding individual variance in offspring size and parental investment). By contrast, amongst eusocial animals some individuals contribute proportionally more to gene transfer, and others more to energy, resulting in high interindividual variation in the ratio of gene to power transfer.

Is blood still thicker than water? A life-course perspective on the transformation of family and friends' roles in personal networks

This thesis addresses the issue of the moving boundaries between family and friends' roles in personal networks, adopting a life-course perspective and using Switzerland as a case study. In a period of major changes in personal life happening in contemporary Western societies, understanding the organization of personal networks intertwined with the unfolding of individual life courses is of prime importance in facing new challenges with regard to social integration. The data stem from a representative national survey carried out in 2011 named Family tiMes, including 803 individuals born either in 1950-1955 or in 1970-1975. An innovative research design was adopted, combing cross-sectional ego-centered network data and retrospective longitudinal life-course data. The results show continuing boundaries between family and friends' roles and that family keeps a prominent role in personal networks despite the notable importance of friendship ties. One relationship stands out above all, that with the partner, followed quite a few steps behind by those with children. Regarding life courses, de-standardization tendencies were found in family formation and also a persistent gendering of occupational trajectories. Two kinds of life trajectories are particularly intertwined with personal networks, co-residence and partnership trajectories, both related to the unfolding of family life. In particular, transition to parenthood functions as a turning point in individuals' lives, deeply transforming their sociability. Finally, a twofold pluralization process was identified, affecting simultaneously the organization of personal networks and the unfolding of individual life courses. This thesis contributes to the literature on the sociology of family and personal life, and to fruitful interlinkage between the network approach and the life-course perspective.

Induced pluripotent stem cells as a promising tool to study the effect of interleukin-22 in multiple sclerosis

La sclérose en plaques (SEP) est une maladie démyélinisante du système nerveux central (SNC) provoquant des pertes motrices, sensitives et cognitives. La SEP se déclare chez le jeune adulte ayant des prédispositions génétiques, mais semble induite, par des facteurs environnementaux. La SEP touche principalement les femmes et sa prévalence dans les zones à haut risque, tel que la Suisse, est de 0.1%. Bien que son étiologie exacte reste méconnue, nous savons que la maladie est médiée par des lymphocytes T autoréactifs périphériques, qui infiltrent le SNC où ils activent d'autres cellules immunitaires ainsi que les cellules du SNC elles-mêmes, créant un foyer inflammatoire, qui va attaquer et finir par tuer les oligodendrocytes et les neurones. Les épisodes inflammatoires sont entrecoupés par des phases de rémission associées à une guérison partielle des lésions. Cette première phase de la maladie, comprenant des épisodes inflammatoires et de rémissions est appelé SEP récurrente-rémittente (SEP-RR) et touche 90% des patients. Elle évolue, dans deux-tiers des cas, vers une SEP secondaire progressive (SEP-SP), qui est caractérisée par une progression constante de la maladie, associée à une réduction de l'inflammation mais une augmentation de la neurodégénérescence. Les patients souffrants de SEP primaire progressive (SEP-PP) développent directement les symptômes de la phase progressive de la maladie. Les thérapies disponibles ont considérablement amélioré l'évolution de la maladie des patients SEP-RR, en agissant sur une diminution de la réponse immunitaire et donc de l'inflammation. Cependant, ces traitements sont inefficaces chez les patients SEP-SP et SEP-PP, n'agissant pas sur la neurodégénérescence. IL-22, une cytokine sécrétée notoirement par les cellules Th17, a été associée à la SEP en contribuant à la perméabilisation de la barrière hémato-encéphalique et à l'inflammation du SNC, qui sont des étapes clés de la pathogenèse de la maladie. En outre, le gène codant pour un inhibiteur puissant d'IL- 22, 'IL-22 binding protein' (IL-22BP), a été démontré comme un facteur de risque de la SEP. Ces indices nous ont poussés à nous intéresser de plus près au rôle de l'IL-22 dans la SEP. Nous avons pu montrer qu'IL-22 et IL-22BP étaient augmentées dans le sang des patients SEP par rapport à des sujets sains. Nous avons trouvé qu'IL-22 cible spécifiquement les astrocytes dans le SNC et que son récepteur est particulièrement exprimé dans les lésions des patient SEP. Contre toute attente, nous avons pu montrer que l'IL-22 semble soutenir la survie des astrocytes. Cette découverte, suggérant qu'IL-22 serait protecteur pour le SNC et pour la SEP, confirme de récentes publications et ouvre la voie à de potentielles applications thérapeutiques. En parallèle, dans le but de mieux comprendre l'immunopathogenèse de la SEP, nous avons développé les techniques de culture de cellules souches pluripotentes induites (iPSC). Nos iPSC sont dérivées du sang des donneurs et acquièrent toutes les propriétés des cellules souches embryonnaires après induction. Les iPSC peuvent ensuite être différenciées en différents types de cellules, dont les cellules du SNC. Nous avons ainsi pu obtenir avec succès des neurones, dérivés de cellules du sang, en passant par le stade des iPSC. La prochaine étape consiste à générer des cultures d'astrocytes et d'oligodendrocytes et ainsi obtenir les principales cellules du SNC, le but étant de former de véritables 'cerveaux-en-culture'. Cet outil semble particulièrement adapté à l'étude de l'activité de diverses molécules sur les cellules du SNC, comme par exemple l'IL-22 et d'autres molécules ayant un potentiel intérêt thérapeutique au niveau du SNC. Le but ultime étant de développer des co-cultures de cellules du SNC avec des cellules immunitaires autologues, de patients SEP et de sujets sains, afin de mettre en évidence l'attaque des cellules du SNC par des leucocytes autoréactifs. Ce projet prospectif a permis d'accroître nos connaissance sur des aspects immunitaires de la SEP et à pour but de mieux comprendre l'immunopathogenèse de la SEP afin d'élaborer de nouvelles stratégies thérapeutiques. -- La sclérose en plaques est une maladie auto-inflammatoire du système nerveux central conduisant à la destruction de la myéline, indispensable à la conduction nerveuse, et finalement à la mort des neurones eux-mêmes. Cela a pour conséquence des pertes motrices, sensorielles et cognitives, qui ont tendance à s'aggraver au fil de la maladie. Elle se déclare chez le jeune adulte, entre l'âge de 20 et 40 ans, et prédomine chez la femme. En Suisse, environ une personne sur l'OOO est atteinte de sclérose en plaques. Les causes exactes de cette maladie, qui incluent des facteurs génétiques et environnementaux, sont encore mal connues. Des traitements de plus en plus efficaces ont été développés ces dernières années et ont permis de drastiquement améliorer l'évolution de la maladie chez les patients atteints de sclérose en plaques. Cependant, ces traitements ne sont efficaces que sur certaines catégories de patients et peuvent engendrer de lourds effets secondaires. Ces thérapies agissent presque exclusivement sur les cellules du système immunitaire en les désactivant partiellement, mais pas sur les cellules nerveuses, qui sont pourtant celles qui conditionnent le devenir du patient. Le développement de médicaments protégeant ou permettant la régénération des cellules du système nerveux central est donc primordial. L'étude de l'interleukine-22 nous a permis de montrer que cette cytokine ('hormone' du système immunitaire) pouvait cibler spécifiquement les astrocytes, des cellules gliales qui jouent un rôle central dans le maintien de l'équilibre du système nerveux central. Nos recherches ont montré que cette interleukine-22 permettrait une meilleure survie des astrocytes durant la phase aiguë de la maladie et aurait aussi des propriétés neuroprotectrices. En parallèle, nous sommes en train de développer un nouveau modèle in vitro d'étude de la sclérose en plaques grâce à la technologie des cellules souches pluripotentes induites. Ces cellules souches sont induites à partir de cellules du sang du donneur et acquièrent toutes les caractéristiques des cellules souches embryonnaires présentes dans un organisme en formation. Ainsi, ces cellules souches pluripotentes ont, par exemple, la capacité de se différencier en cellules du système nerveux central. Nous avons pu, de cette manière, obtenir des neurones. Le but ultime serait de pouvoir reconstituer une ébauche de cerveau in vitro, en cultivant ensemble différents types de cellules du système nerveux central, afin d'y réaliser des expériences avec des cellules immunitaires du même donneur. Ces travaux ont pour but d'améliorer notre compréhension de la pathogenèse de la sclérose en plaques et de permettre le développement de nouvelles stratégies thérapeutiques. --Multiple sclerosis (MS) is a demyelinating disease of the central nervous system leading to cognitive, sensitive and motor disabilities. MS occurs in genetically predisposed young adults with probable environmental triggers. MS affects predominantly women and its prevalence in high risk area such as Switzerland is 0.1%. Though its exact aetiology remains undetermined, we know that autoreactive T cells from de periphery are reactivated and recruited into the central nervous system (CNS) were they further activate other immune cells and resident cells, creating inflammatory foci, where oligodendrocytes and neurons are insulted and, eventually, killed. Inflammatory episodes, called relapses, are interspersed with remission phases where partial recovery of the lesions occurs. This first phase of the disease, occurring in 90% of the patients, is called relapsing-remitting MS (RR-MS) and is leading, in two-third of the cases, to secondary-progressive MS (SP-MS), where there is a continuous steady progression of the disease, associated with reduced inflammation but increased neurodegeneration. Primary-progressive MS (PP-MS) patients experience directly this progressive phase of the disease. Whereas disease modifying therapies have dramatically ameliorated the disease course of RR-MS patients by dampening immunity and, in turn, inflammation, treatments of SP-MS and PP-MS patients, who suffer primarily from the neurodegenerative aspect of the disease, are still inexistent. IL-22, a pro-inflammatory Th17 cell cytokine, has been associated with MS by participating to blood-brain barrier infiltration and CNS inflammation, which are crucial steps in MS pathogenesis. In addition, the gene coding for IL-22 binding protein (IL-22BP), which is a potent secreted IL-22 inhibitor, has been associated with MS risk. These findings call for further investigation on the role of IL-22 in MS. We detected increased IL-22 and IL-22BP in the blood of MS patients as compared to healthy controls. Acting exclusively on cells of nonhematopoietic origin, we found that IL-22 targets specifically astrocytes in the CNS and that its receptor is highly expressed in the lesion of MS patients. Unexpectedly, we found that IL-22 seems to promote survival of astrocytes. This finding, suggesting that IL-22 might be protective for the CNS in the context of MS, is consistent with recent publications and might open putative therapeutic applications at the CNS level. In parallel, with the aim of better understanding the immunopathogenesis of MS, we developed induced pluripotent stem cell (iPSC) techniques. IPSC are derived from blood cells of the donors and bear embryonic stem cell properties. IPSC can be differentiated into various cell types including CNS cells. We successfully obtained neurons derived from the donor blood cells, through iPSC. We further aim at developing astrocytes and oligodendrocytes cultures to recreate a 'brain-in-a-dish'. This would be a powerful tool to test the activity of various compounds on CNS cells, including IL-22 and other putative neuroprotective drugs. Ultimately, the goal is to develop co-cultures of CNS cells with autologous immune cells of MS patients as well as healthy controls to try to expose evidence of CNS cells targeted by autoreactive leukocytes. This prospective project has increased our knowledge of immune aspects of MS and further aims at better understanding the immunopathology of MS in order to pave the way to the elaboration of new therapeutic strategies.

Is the presence of an intrathecal synthesis of immunoglobulins associated with neurocognitive impairment in HIV-infected patients?

Worldwide, the incidence of HIV-associated dementia has decreased However, the prevalence of HIV-associated neurocognitive disorders (HAND), mostly the milder forms, i.e. mild neurocognitve disorders (MND) and asymptomatic neurocognitive impairments (ANI) has increased in the combined antiretroviral therapy (cART) era. Indeed, 20% to 60% of well- treated HIV-infected patients, i.e. with undetectable HIV viremia, still present HAND in the cART era. HAND are characterized by psychomotor slowing, memory loss, and attention deficit. Possible explanations for this paradoxical phenomenon encompass: increased survival of HIV- infected patients thank to cART, low grade inflammation of the brain insufficient penetrance of antiretroviral drugs through the blood brain barrier (BBB), or on the contrary, toxic effect of some antiretroviral drugs. These somewhat contradictory hypotheses underline our poor understanding of HAND physiopathology. Here, we aim at determining whether the intrathecal synthesis of immunoglobulins G (IgG), hereafter referred as cerebrospinal fluid oligoclonal band (CSF OB), may help us in better understanding the immunopathogenesis of cognitive disorders. By analogy with other infection, such as syphilis or neuroborreliosis (9, 10), one can assume that, in the case of HIV-infected patients, the CSF OB are directed against HIV proteins (11). Nevertheless, in the case of HIV, the meaning of such CSF OB is unclear. Indeed, it is unknown whether this intrathecal inflammatory reaction is beneficial (viral control) or harmful (brain parenchyma destruction by the different inflammatory factors). Here, we looked at the association between CSF OB and cognitive disorders in HIV-infected patients, hypothesizing that if these CSF OB are protective, one should see an inverse correlation with the presence of cognitive disorders.

The Pursuit of Efficient Copyright Licensing : How Some Rights Reserved Attempts to Solve the Problems of All Rights Reserved

This dissertation analyses the growing pool of copyrighted works, which are offered to the public using Creative Commons licensing. The study consist of analysis of the novel licensing system, the licensors, and the changes of the "all rights reserved" —paradigm of copyright law. Copyright law reserves all rights to the creator until seventy years have passed since her demise. Many claim that this endangers communal interests. Quite often the creators are willing to release some rights. This, however, is very difficult to do and needs help of specialized lawyers. The study finds that the innovative Creative Commons licensing scheme is well suited for low value - high volume licensing. It helps to reduce transaction costs on several le¬vels. However, CC licensing is not a "silver bullet". Privacy, moral rights, the problems of license interpretation and license compatibility with other open licenses and collecting societies remain unsolved. The study consists of seven chapters. The first chapter introduces the research topic and research questions. The second and third chapters inspect the Creative Commons licensing scheme's technical, economic and legal aspects. The fourth and fifth chapters examine the incentives of the licensors who use open licenses and describe certain open business models. The sixth chapter studies the role of collecting societies and whether two institutions, Creative Commons and collecting societies can coexist. The final chapter summarizes the findings. The dissertation contributes to the existing literature in several ways. There is a wide range of prior research on open source licensing. However, there is an urgent need for an extensive study of the Creative Commons licensing and its actual and potential impact on the creative ecosystem.

Development of research networks : the case of social capital

The aim of this study is to explore how a new concept appears inscientific discussion and research, how it diffuses to other fields and out of the scientific communities, and how the networks are formed around the concept. Text and terminology take the interest of a reader in the digital environment. Texts create networks where the terminology used is dependent on the ideas, viewsand paradigms of the field. This study is based mainly on bibliographic data. Materials for bibliometric studies have been collected from different databases. The databases are also evaluated and their quality and coverage are discussed. The thesauri of those databases that have been selected for a more in depth study have also been evaluated. The material selected has been used to study how long and in which ways an innovative publication, which can be seen as a milestone in a specific field, influences the research. The concept that has been chosen as a topic for this research is Social Capital, because it has been a popular concept in different scientific fields as well as in everyday speech and the media. It seemed to be a `fashion concept´ that appeared in different situations at the Millennium. The growth and diffusion of social capital publications has been studied. The terms connected with social capital in different fields and different stages of the development have also been analyzed. The methods that have been used in this study are growth and diffusion analysis, content analysis, citation analysis, coword analysis and cocitation analysis. One method that can be used tounderstand and to interpret results of these bibliometric studies is to interview some key persons, who are known to have a gatekeeper position in the diffusion of the concept. Thematic interviews with some Finnish researchers and specialists that have influenced the diffusion of social capital into Finnish scientificand social discussions provide background information. iv The Milestone Publications on social capital have been chosen and studied. They give answers to the question "What is Social Capital?" By comparing citations to Milestone Publications with the growth of all social capital publications in a database, we can drawconclusions about the point at which social capital became generally approved `tacit knowledge´. The contribution of the present study lies foremost in understanding the development of network structures around a new concept that has diffused in scientific communities and also outside them. The network means both networks of researchers, networks of publications and networks of concepts that describe the research field. The emphasis has been on the digital environment and onthe socalled information society that we are now living in, but in this transitional stage, the printed publications are still important and widely used in social sciences and humanities. The network formation is affected by social relations and informal contacts that push new ideas. This study also gives new information about using different research methods, like bibliometric methods supported by interviews and content analyses. It is evident that interpretation of bibliometric maps presupposes qualitative information and understanding of the phenomena under study.

Methods for construction and analysis of computational models in systems biology : applications to the modelling of the heat shock response and the self-assembly of intermediate filaments

Systems biology is a new, emerging and rapidly developing, multidisciplinary research field that aims to study biochemical and biological systems from a holistic perspective, with the goal of providing a comprehensive, system- level understanding of cellular behaviour. In this way, it addresses one of the greatest challenges faced by contemporary biology, which is to compre- hend the function of complex biological systems. Systems biology combines various methods that originate from scientific disciplines such as molecu- lar biology, chemistry, engineering sciences, mathematics, computer science and systems theory. Systems biology, unlike “traditional” biology, focuses on high-level concepts such as: network, component, robustness, efficiency, control, regulation, hierarchical design, synchronization, concurrency, and many others. The very terminology of systems biology is “foreign” to “tra- ditional” biology, marks its drastic shift in the research paradigm and it indicates close linkage of systems biology to computer science. One of the basic tools utilized in systems biology is the mathematical modelling of life processes tightly linked to experimental practice. The stud- ies contained in this thesis revolve around a number of challenges commonly encountered in the computational modelling in systems biology. The re- search comprises of the development and application of a broad range of methods originating in the fields of computer science and mathematics for construction and analysis of computational models in systems biology. In particular, the performed research is setup in the context of two biolog- ical phenomena chosen as modelling case studies: 1) the eukaryotic heat shock response and 2) the in vitro self-assembly of intermediate filaments, one of the main constituents of the cytoskeleton. The range of presented approaches spans from heuristic, through numerical and statistical to ana- lytical methods applied in the effort to formally describe and analyse the two biological processes. We notice however, that although applied to cer- tain case studies, the presented methods are not limited to them and can be utilized in the analysis of other biological mechanisms as well as com- plex systems in general. The full range of developed and applied modelling techniques as well as model analysis methodologies constitutes a rich mod- elling framework. Moreover, the presentation of the developed methods, their application to the two case studies and the discussions concerning their potentials and limitations point to the difficulties and challenges one encounters in computational modelling of biological systems. The problems of model identifiability, model comparison, model refinement, model inte- gration and extension, choice of the proper modelling framework and level of abstraction, or the choice of the proper scope of the model run through this thesis.

The role of IL-12 in experimental Trypanosoma cruzi infection

Host resistance to Trypanosoma cruzi infection is dependent on both natural and acquired immune responses. During the early acute phase of infection in mice, natural killer (NK) cell-derived IFN-g is involved in controlling intracellular parasite replication, mainly through the induction of nitric oxide biosynthesis by activated macrophages. We have shown that IL-12, a powerful inducer of IFN-g production by NK cells, is synthesized soon after trypomastigote-macrophage interaction. The role of IL-12 in the control of T. cruzi infection in vivo was determined by treating infected mice with anti-IL-12 monoclonal antibody (mAb) and analyzing both parasitemia and mortality during the acute phase of infection. The anti-IL-12 mAb-treated mice had higher levels of parasitemia and mortality compared to control mice. Also, treatment of infected mice with mAb specific for IFN-g or TNF-a inhibited the protective effect of exogenous IL-12. On the other hand, TGF-ß and IL-10 produced by infected macrophages inhibited the induction and effects of IL-12. Therefore, while IL-12, TNF-a and IFN-g correlate with resistance to T. cruzi infection, TGF-ß and IL-10 promote susceptibility. These results provide support for a role of innate immunity in the control of T. cruzi infection. In addition to its protective role, IL-12 may also be involved in the modulation of T. cruzi-induced myocarditis, since treatment of infected mice with IL-12 or anti-IL-12 mAb leads to an enhanced or decreased inflammatory infiltrate in the heart, respectively. Understanding the role of the cytokines produced during the acute phase of T. cruzi infection and their involvement in protection and pathogenesis would be essential to devise new vaccines or therapies.

The role of chemokines and chemokine receptors in eosinophil activation during inflammatory allergic reactions

Chemokines are important chemotactic cytokines that play a fundamental role in the trafficking of leukocytes to sites of inflammation. They are also potent cell-activating factors, inducing cytokine and histamine release and free radical production, a fact that makes them particularly important in the pathogenesis of allergic inflammation. The action of chemokines is regulated at the level of agonist production and processing as well as at the level of receptor expression and coupling. Therefore, an analysis of the ligands must necessarily consider receptors. Eosinophils are target cells involved in the allergic inflammatory response since they are able to release a wide variety of mediators including CC and CXC chemokines and express their receptors. These mediators could damage the airway epithelial cells and might be important to stimulate other cells inducing an amplification of the allergic response. This review focuses on recently emerging data pertaining to the importance of chemokines and chemokine receptors in promoting eosinophil activation and migration during the allergic inflammatory process. The analysis of the function of eosinophils and their chemokine receptors during allergic inflammation might be a good approach to understanding the determinants of asthma severity and to developing novel therapies.

An investigation of the nature and role of historicality in the thought of Dilthey and Heidegger

Introduction The question of the meaning, methods and philosophical manifestations of history is currently rife with contention. The problem that I will address in an exposition of the thought of Wilhelm Dilthey and Martin Heidegger, centers around the intersubjectivity of an historical world. Specifically, there are two interconnected issues. First, since all knowledge occurs to a person from within his or her historical age how can any person in any age make truth claims? In order to answer this concern we must understand the essence and role of history. Yet how can we come to an individual understanding ofwhat history is when the meanings that we use are themselves historically enveloped? But can we, we who are well aware of the knowledge that archaeology has dredged up from old texts or even from 'living' monuments of past ages, really neglect to notice these artifacts that exist within and enrich our world? Charges of wilful blindness would arise if any attempt were made to suggest that certain things of our world did not come down to us from the past. Thus it appears more important 2 to determine what this 'past' is and therefore how history operates than to simply derail the possibility for historical understanding. Wilhelm Dilthey, the great German historicist from the 19th century, did not question the existence of historical artifacts as from the past, but in treating knowledge as one such artifact placed the onus on knowledge to show itself as true, or meaningful, in light ofthe fact that other historical periods relied on different facts and generated different truths or meanings. The problem for him was not just determining what the role of history is, but moreover to discover how knowledge could make any claim as true knowledge. As he stated, there is a problem of "historical anarchy"!' Martin Heidegger picked up these two strands of Dilthey's thought and wanted to answer the problem of truth and meaning in order to solve the problem of historicism. This problem underscored, perhaps for the first time, that societal presuppositions about the past and present oftheir era are not immutable. Penetrating to the core of the raison d'etre of the age was an historical reflection about the past which was now conceived as separated both temporally and attitudinally from the present. But further than this, Heidegger's focus on asking the question of the meaning of Being meant that history must be ontologically explicated not merely ontically treated. Heidegger hopes to remove barriers to a genuine ontology by II 1 3 including history into an assessment ofprevious philosophical systems. He does this in order that the question of Being be more fully explicated, which necessarily for him includes the question of the Being of history. One approach to the question ofwhat history is, given the information that we get from historical knowledge, is whether such knowledge can be formalized into a science. Additionally, we can approach the question of what the essence and role of history is by revealing its underlying characteristics, that is, by focussing on historicality. Thus we will begin with an expository look at Dilthey's conception of history and historicality. We will then explore these issues first in Heidegger's Being and Time, then in the third chapter his middle and later works. Finally, we shall examine how Heidegger's conception may reflect a development in the conception of historicality over Dilthey's historicism, and what such a conception means for a contemporary historical understanding. The problem of existing in a common world which is perceived only individually has been philosophically addressed in many forms. Escaping a pure subjectivist interpretation of 'reality' has occupied Western thinkers not only in order to discover metaphysical truths, but also to provide a foundation for politics and ethics. Many thinkers accept a solipsistic view as inevitable and reject attempts at justifying truth in an intersubjective world. The problem ofhistoricality raises similar problems. We 4 -. - - - - exist in a common historical age, presumably, yet are only aware ofthe historicity of the age through our own individual thoughts. Thus the question arises, do we actually exist within a common history or do we merely individually interpret this as communal? What is the reality of history, individual or communal? Dilthey answers this question by asserting a 'reality' to the historical age thus overcoming solipsism by encasing individual human experience within the historical horizon of the age. This however does nothing to address the epistemological concern over the discoverablity of truth. Heidegger, on the other hand, rejects a metaphysical construel of history and seeks to ground history first within the ontology ofDasein, and second, within the so called "sending" of Being. Thus there can be no solipsism for Heidegger because Dasein's Being is necessarily "cohistorical", Being-with-Others, and furthermore, this historical-Being-in-the-worldwith- Others is the horizon of Being over which truth can appear. Heidegger's solution to the problem of solipsism appears to satisfy that the world is not just a subjective idealist creation and also that one need not appeal to any universal measures of truth or presumed eternal verities. Thus in elucidating Heidegger's notion of history I will also confront the issues ofDasein's Being-alongside-things as well as the Being of Dasein as Being-in-the-world so that Dasein's historicality is explicated vis-a-vis the "sending of Being" (die Schicken des S eins).

A study on the performance of flexible pavements on mature soil subgrades

The country has witnessed tremendous increase in the vehicle population and increased axle loading pattern during the last decade, leaving its road network overstressed and leading to premature failure. The type of deterioration present in the pavement should be considered for determining whether it has a functional or structural deficiency, so that appropriate overlay type and design can be developed. Structural failure arises from the conditions that adversely affect the load carrying capability of the pavement structure. Inadequate thickness, cracking, distortion and disintegration cause structural deficiency. Functional deficiency arises when the pavement does not provide a smooth riding surface and comfort to the user. This can be due to poor surface friction and texture, hydro planning and splash from wheel path, rutting and excess surface distortion such as potholes, corrugation, faulting, blow up, settlement, heaves etc. Functional condition determines the level of service provided by the facility to its users at a particular time and also the Vehicle Operating Costs (VOC), thus influencing the national economy. Prediction of the pavement deterioration is helpful to assess the remaining effective service life (RSL) of the pavement structure on the basis of reduction in performance levels, and apply various alternative designs and rehabilitation strategies with a long range funding requirement for pavement preservation. In addition, they can predict the impact of treatment on the condition of the sections. The infrastructure prediction models can thus be classified into four groups, namely primary response models, structural performance models, functional performance models and damage models. The factors affecting the deterioration of the roads are very complex in nature and vary from place to place. Hence there is need to have a thorough study of the deterioration mechanism under varied climatic zones and soil conditions before arriving at a definite strategy of road improvement. Realizing the need for a detailed study involving all types of roads in the state with varying traffic and soil conditions, the present study has been attempted. This study attempts to identify the parameters that affect the performance of roads and to develop performance models suitable to Kerala conditions. A critical review of the various factors that contribute to the pavement performance has been presented based on the data collected from selected road stretches and also from five corporations of Kerala. These roads represent the urban conditions as well as National Highways, State Highways and Major District Roads in the sub urban and rural conditions. This research work is a pursuit towards a study of the road condition of Kerala with respect to varying soil, traffic and climatic conditions, periodic performance evaluation of selected roads of representative types and development of distress prediction models for roads of Kerala. In order to achieve this aim, the study is focused into 2 parts. The first part deals with the study of the pavement condition and subgrade soil properties of urban roads distributed in 5 Corporations of Kerala; namely Thiruvananthapuram, Kollam, Kochi, Thrissur and Kozhikode. From selected 44 roads, 68 homogeneous sections were studied. The data collected on the functional and structural condition of the surface include pavement distress in terms of cracks, potholes, rutting, raveling and pothole patching. The structural strength of the pavement was measured as rebound deflection using Benkelman Beam deflection studies. In order to collect the details of the pavement layers and find out the subgrade soil properties, trial pits were dug and the in-situ field density was found using the Sand Replacement Method. Laboratory investigations were carried out to find out the subgrade soil properties, soil classification, Atterberg limits, Optimum Moisture Content, Field Moisture Content and 4 days soaked CBR. The relative compaction in the field was also determined. The traffic details were also collected by conducting traffic volume count survey and axle load survey. From the data thus collected, the strength of the pavement was calculated which is a function of the layer coefficient and thickness and is represented as Structural Number (SN). This was further related to the CBR value of the soil and the Modified Structural Number (MSN) was found out. The condition of the pavement was represented in terms of the Pavement Condition Index (PCI) which is a function of the distress of the surface at the time of the investigation and calculated in the present study using deduct value method developed by U S Army Corps of Engineers. The influence of subgrade soil type and pavement condition on the relationship between MSN and rebound deflection was studied using appropriate plots for predominant types of soil and for classified value of Pavement Condition Index. The relationship will be helpful for practicing engineers to design the overlay thickness required for the pavement, without conducting the BBD test. Regression analysis using SPSS was done with various trials to find out the best fit relationship between the rebound deflection and CBR, and other soil properties for Gravel, Sand, Silt & Clay fractions. The second part of the study deals with periodic performance evaluation of selected road stretches representing National Highway (NH), State Highway (SH) and Major District Road (MDR), located in different geographical conditions and with varying traffic. 8 road sections divided into 15 homogeneous sections were selected for the study and 6 sets of continuous periodic data were collected. The periodic data collected include the functional and structural condition in terms of distress (pothole, pothole patch, cracks, rutting and raveling), skid resistance using a portable skid resistance pendulum, surface unevenness using Bump Integrator, texture depth using sand patch method and rebound deflection using Benkelman Beam. Baseline data of the study stretches were collected as one time data. Pavement history was obtained as secondary data. Pavement drainage characteristics were collected in terms of camber or cross slope using camber board (slope meter) for the carriage way and shoulders, availability of longitudinal side drain, presence of valley, terrain condition, soil moisture content, water table data, High Flood Level, rainfall data, land use and cross slope of the adjoining land. These data were used for finding out the drainage condition of the study stretches. Traffic studies were conducted, including classified volume count and axle load studies. From the field data thus collected, the progression of each parameter was plotted for all the study roads; and validated for their accuracy. Structural Number (SN) and Modified Structural Number (MSN) were calculated for the study stretches. Progression of the deflection, distress, unevenness, skid resistance and macro texture of the study roads were evaluated. Since the deterioration of the pavement is a complex phenomena contributed by all the above factors, pavement deterioration models were developed as non linear regression models, using SPSS with the periodic data collected for all the above road stretches. General models were developed for cracking progression, raveling progression, pothole progression and roughness progression using SPSS. A model for construction quality was also developed. Calibration of HDM–4 pavement deterioration models for local conditions was done using the data for Cracking, Raveling, Pothole and Roughness. Validation was done using the data collected in 2013. The application of HDM-4 to compare different maintenance and rehabilitation options were studied considering the deterioration parameters like cracking, pothole and raveling. The alternatives considered for analysis were base alternative with crack sealing and patching, overlay with 40 mm BC using ordinary bitumen, overlay with 40 mm BC using Natural Rubber Modified Bitumen and an overlay of Ultra Thin White Topping. Economic analysis of these options was done considering the Life Cycle Cost (LCC). The average speed that can be obtained by applying these options were also compared. The results were in favour of Ultra Thin White Topping over flexible pavements. Hence, Design Charts were also plotted for estimation of maximum wheel load stresses for different slab thickness under different soil conditions. The design charts showed the maximum stress for a particular slab thickness and different soil conditions incorporating different k values. These charts can be handy for a design engineer. Fuzzy rule based models developed for site specific conditions were compared with regression models developed using SPSS. The Riding Comfort Index (RCI) was calculated and correlated with unevenness to develop a relationship. Relationships were developed between Skid Number and Macro Texture of the pavement. The effort made through this research work will be helpful to highway engineers in understanding the behaviour of flexible pavements in Kerala conditions and for arriving at suitable maintenance and rehabilitation strategies. Key Words: Flexible Pavements – Performance Evaluation – Urban Roads – NH – SH and other roads – Performance Models – Deflection – Riding Comfort Index – Skid Resistance – Texture Depth – Unevenness – Ultra Thin White Topping

Factors influencing the success of animal husbandry cooperatives: A case study in Southwest Iran

This survey study aimed at identifying the factors influencing the success of animal husbandry cooperatives in Southwest Iran. Using a questionnaire, the data were collected from 95 managing directors of the cooperatives who were chosen through a multi-stage stratified random sampling method. This study showed an essential need for a systemic framework to analyze the cooperatives’ success. The results showed that the “Honey Bee”, “Cattle (dairy)”, and “Lamb” cooperatives were the most successful among different kinds of the cooperatives. Also, among individual attributes, “interest”, “technical knowledge”, and “understanding the concept of cooperative”; among economic variables, “income” and “current investment”; and among external factors, “market access” have significant correlation with the success while structural variables have no significant relation. Furthermore, among all the factors, four variables (“interest”, “understanding the concept of cooperative”, “market access”, and “other incomes”) can explain the variations of the success.