Seed,dispersal, microsite,habitat and recruitment limitation: identification of terms and concepts in studies of limitations

Recently, there is an increase in number of studies concerned with the effect of various types of limitations on species local population size and distribution pattern at the landscape scale. The terminology used to describe these limitations is, however, very inconsistent. Since the different terms often appear in conclusions of the papers, the inconsistency in their use obscures the message of these papers. In this study, we review the current uses of these terms, identify the basic concepts involved in the discussion of a limitation and link the concepts with the currently used terms. Finally, we discuss the experimental approaches used to assess the different types of limitations. We differentiated four basic concepts resulting from the combination of limitation by environment versus ability to grow and spread, and two spatial scales (local and regional scale). The two concepts at each spatial scale are expected to form a gradient of all possible combinations of the two respective types of limitations. In the considerations of various experimental approaches used to assess these limitations, we conclude that sowing experiments, i.e. seed addition into existing populations or seed introduction into unoccupied habitats, are the only reliable types of evidence for the different types of limitations.     

Text Mining the History of Medicine

Historical text archives constitute a rich and diverse source of information, which is becoming increasingly readily accessible, due to large-scale digitisation efforts. However, it can be difficult for researchers to explore and search such large volumes of data in an efficient manner. Text mining (TM) methods can help, through their ability to recognise various types of semantic information automatically, e.g., instances of concepts (places, medical conditions, drugs, etc.), synonyms/variant forms of concepts, and relationships holding between concepts (which drugs are used to treat which medical conditions, etc.). TM analysis allows search systems to incorporate functionality such as automatic suggestions of synonyms of user-entered query terms, exploration of different concepts mentioned within search results or isolation of documents in which concepts are related in specific ways. However, applying TM methods to historical text can be challenging, according to differences and evolutions in vocabulary, terminology, language structure and style, compared to more modern text. In this article, we present our efforts to overcome the various challenges faced in the semantic analysis of published historical medical text dating back to the mid 19^th century. Firstly, we used evidence from diverse historical medical documents from different periods to develop new resources that provide accounts of the multiple, evolving ways in which concepts, their variants and relationships amongst them may be expressed. These resources were employed to support the development of a modular processing pipeline of TM tools for the robust detection of semantic information in historical medical documents with varying characteristics. We applied the pipeline to two large-scale medical document archives covering wide temporal ranges as the basis for the development of a publicly accessible semantically-oriented search system. The novel resources are available for research purposes, while the processing pipeline and its modules may be used and configured within the Argo TM platform.     

National interests and international collaboration: tensions and ambiguity among Finns towards usages of tissue samples

Recent trends in biobanking indicate that the practices associated with the collection and use of human tissue samples and related health information are increasingly becoming premised on networks of biobanks. These networks and partnerships often involve international collaborations, as well as public–private partnerships. This article reports on the results of a study of people's attitudes towards biobanking and the biomedical use of tissue samples in Finland. Three approaches were used to study these attitudes: a population-based survey, focus group interviews among members of patient organizations and short interviews with research participants. In particular, we look at the attitudes of respondents in these three studies towards the use of tissue samples and use them as a catalyst to discuss two dimensions of biomedical research: public/private and domestic/international. Our discussion highlights how notions of value related to the use of tissue samples vary and provide contrasting perspectives and ambiguity that people may have towards various types of research partnerships and the benefits that may arise from them.     

Functional morphology and evolutionary biology

In this study the relationship between functional morpholoy and evolutionary biology is analysed by confronting the main concepts in both disciplines.Rather than only discussing this connection theoretically, the analysis is carried out by introducing important practical and experimental studies, which use aspects from both disciplines. The mentioned investigations are methodologically analysed and the consequences for extensions of the relationship are worked out. It can be shown that both disciplines have a large domain of their own and also share a large common ground. Many disagreements among evolutionary biologists can be reduced to differences in general philosophy (idealism vs. realism), selection of phenomenona (structure vs. function), definition of concepts (natural selection) and the position of the concept theory as an explaining factor (neutralists vs. selectionists, random variation, determinate selection, etc.).The significance of functional morphology for evolutionary biology, and vice versa depends on these differences. For a neo-Darwinian evolutionary theory, contributions from functional and ecological morphology are indispensable. Of ultimate importance are the notions of internal selection and constraints in the constructions determining further development. In this context the concepts of random variation and natural selection need more detailed definition.The study ends with a recommendation for future research founded in a system-theoretical or structuralistic conception.     

The Proverbial Bourdieu: Habitus and the Politics of Representation in the Ethnography of Kabylia

Since the 1970s, anthropologists have been centrally concerned with the relationship of ethnographic representation to political and historical context. Interestingly, the work of Pierre Bourdieu has largely escaped such contextualization, despite the significance of Bourdieu's ideas to anthropological theorizing. Today, many of Bourdieu's central concepts float free from the context out of which they arose—the Kabyle region of Algeria. This article addresses this omission by reading Bourdieu's early works against each other to reconstitute aspects of his methodology and fieldwork. Focusing on his choice to represent the Kabyles of his early work in prose, and those in his later work via proverbs, I suggest that key premises of Bourdieu's theory may not be supported by historical and ethnographic evidence. I consider how Bourdieu's position as a young social scientist grappling with ethnographic responsibilities in colonial wartime led him to privilege his interlocutors' accounts in some studies while expunging them from others. [Keywords: Bourdieu, represented speech, literacy, Algeria, Berbers]     

Normativity, agency, and life

There is an immense philosophical literature dealing with the notions of normativity and agency, as well as a sizeable and rapidly growing scientific literature on the topic of autonomous agents. However, there has been very little cross-fertilization between these two literatures. As a result, the philosophical literature tends to assume a somewhat outdated mechanistic image of living things, resulting in a quasi-dualistic picture in which only human beings, or the higher animals, can be normative agents properly speaking. From this perspective, the project of 'naturalizing normativity' becomes almost a contradiction in terms. At the same time, the scientific literature tends to misuse 'normativity,' 'agency,' and related terms, assuming that it is meaningful to ascribe these concepts to 'autonomous agents' conceived of as physical systems whose behavior is to be explained in terms of ordinary physical law. From this perspective, the true depth of the difficulty involved in understanding what makes living systems distinctive qua physical systems becomes occluded. In this essay, I begin the attempt to remedy this situation. After some preliminary discussion of terminology and situating of my project within the contemporary philosophical landscape, I make a distinction between two different aspects of the project of naturalizing normativity: (1) the 'Scope Problem,' which consists in saying how widely in nature our concept of normative agency may properly be applied; and (2) the 'Ground Problem,' which consists in rationalizing the phenomenon of normative agency in terms of the rest of our knowledge of nature. Then, in the remainder of this paper, I argue that the Scope Problem ought to be resolved in favor of attributing normative agency, in the proper sense of those words, to living things as such. The Ground Problem will be discussed in a companion paper at a later time.     

On the Numerous Concepts in Invasion Biology

The study of biological invasions has triggered the production of a diversity of concepts. The terminology has, however, often been applied inconsistently and inaccurately. This article lists and assesses the most commonly used terms and concepts in invasion ecology. In each case the most coherent definition and use is suggested.     

Gypsies and health care.

Gypsies in the United States are not a healthy group. They have a high incidence of heart disease, diabetes mellitus, and hypertension. When they seek medical care, Gypsies often come into conflict with medical personnel who find their behavior confusing, demanding, and chaotic. For their part, Gypsies are often suspicious of non-Gypsy people and institutions, viewing them as a source of disease and uncleanliness. Gypsy ideas about health and illness are closely related to notions of good and bad fortune, purity and impurity, and inclusion and exclusion from the group. These basic concepts affect everyday life, including the way Gypsies deal with eating and washing, physicians and hospitals, the diagnosis of illness, shopping around for cures, and coping with birth and death.     

Oxidative muscular injury and its relevance to hyperthyroidism

In experimental hyperthyroidism, acceleration of lipid peroxidation occurs in heart and slow-oxidative muscles, suggesting the contribution of reactive oxygen species to the muscular injury caused by thyroid hormones. This article reviews various models of oxidative muscular injury and considers the relevance of the accompanying metabolic derangements to thyrotoxic myopathy and cardiomyopathy, which are the major complications of hyperthyroidism. The muscular injury models in which reactive oxygen species are supposed to play a role are ischemia/reperfusion syndrome, exercise-induced myopathy, heart and skeletal muscle diseases related to the nutritional deficiency of selenium and vitamin E and related disorders, and genetic muscular dystrophies. These models provide evidence that mitochondrial function and the glutathione-dependent antioxidant system are important for the maintenance of the structural and functional integrity of muscular tissues. Thyroid hormones have a profound effect on mitochondrial oxidative activity, synthesis and degradation of proteins and vitamin E, the sensitivity of the tissues to catecholamine, the differentiation of muscle fibers, and the levels of antioxidant enzymes. The large volume of circumstantial evidence presented here indicates that hyperthyroid muscular tissues undergo several biochemical changes that predispose them to free radical-mediated injury.     

The family of mammalian small heat shock proteins (HSPBs): implications in protein deposit diseases and motor neuropathies

A number of neurological and muscular disorders are characterized by the accumulation of aggregate-prone proteins and are referred to as protein deposit or protein conformation diseases. Besides some sporadic forms, most of them are genetically inherited in an autosomal dominant manner, although recessive forms also exist. Although genetically very heterogeneous, some of these diseases are the result of mutations in some members of the mammalian small heat shock protein family (sHSP/HSPB), which are key players of the protein quality control system and participate, together with other molecular chaperones and co-chaperones, in the maintenance of protein homeostasis. Thus, on one hand upregulation of specific members of the HSPB family can exert protective effects in protein deposit diseases, such as the polyglutamine diseases. On the other hand, mutations in the HSPBs lead to neurological and muscular disorders, which may be due to a loss-of-function in protein quality control and/or to a gain-of-toxic function, resulting from the aggregation-proneness of the mutants. In this review we summarize the current knowledge about some of the best characterized functions of the HSPBs (e.g. role in cytoskeleton stabilization, chaperone function, anti-aggregation and anti-apoptotic activities), also highlighting differences in the properties of the various HSPBs and how these may counteract protein aggregation diseases. We also describe the mutations in the various HSPBs associated with neurological and muscular disorders and we discuss how gain-of-toxic function mechanisms (e.g. due to the mutated HSPB protein instability and aggregation) and/or loss-of-function mechanisms can contribute to HSPB-associated pathologies. This article is part of a Directed Issue entitled: Small HSPs in physiology and pathology.     

A myocybernetic control model of skeletal muscle

A mathematical model of skeletal muscle is presented which contains the two physiological control parameters stimulation rate and motor unit recruitment. The model is complete in the sense that it adequately describes all possible contractive states normally occurring in living muscle. The modelling procedure relies entirely on established myo-physiological facts and each assumption made is substantiated by experimental data. Extensive simulation studies reveal that the model is capable of correctly predicting practically all known phenomena of the muscular force-output. A simplified version of the model is also presented, particularly suitable for inclusion as the driving structure in complex musculoskeletal link systems. This version was successfully tested in the prediction of an optimal human motion. The present control model is believed to fill a gap in the literature on models of muscle, and may be expected to provide a sound basis for research into the optimal control aspects of muscular contraction, and to stimulate such research.     

Plant–pathogen interactions: will the understanding of common mechanisms lead to the unification of concepts?

Plant-pathogen interactions are still classically described using concepts that make a distinction between qualitative and quantitative aspects linked to these concepts. This article first describes these aspects, using the terminology associated with them. It then presents some recent experimental observations that demonstrate that such concepts share either common or closely related mechanisms at the cellular and molecular levels. The emergence of a more global vision and understanding of the interactions between plants and their parasites is discussed.     

Survivin study: What is the next wave?

Survivin, a novel member of inhibitor of apoptosis (IAP) protein family, is aberrantly expressed in cancer but undetectable in normal, differentiated adult tissues. Current studies suggest that survivin is implicated in both control of apoptosis and regulation of cell division. However, due to some inconsistent observations on survivin subcellular localization, there is debate about survivin's function in regulating apoptosis, cell division, or both. This review will discuss concepts, experimental methods, and interesting results that unify the different notions about survivin localization and function or point out gaps of knowledge about controversial issues. The author also intends to review various aspects of survivin studies, which were not emphasized or sufficiently discussed in previous reviews on survivin, and update recent developments that may reveal new applications of disease-oriented therapeutics in the coming years.     

Breast Tumor Heterogeneity: Cancer Stem Cells or Clonal Evolution?

Breast tumors are composed of a variety of cell types with distinct morphologies and behaviors. It is not clear how this tumor heterogeneity comes about. Two popular concepts that attempt to explain this are the cancer stem cell hypothesis and the clonal evolution model. Each of these ideas has been investigated for some time, leading to the accumulation of numerous findings that are used to support one or the other. Although the two views share some similarities, they are fundamentally different notions with very different clinical implications. Analysis of the research backing each concept, along with a review of the results of our recent study investigating putative breast cancer stem cells, suggests how the cancer stem cell hypothesis and the clonal evolution model may be involved in generating breast tumor heterogeneity. An understanding of this process will allow the development of more effective ways to treat and prevent breast cancer.     

Utility and precision of Silurian graptolite biozones

The various past uses of the assemblage-zone and biozone concepts are reviewed and a modern definition of biozone is given. Silurian biozones are related to the recentideas on standard reference (graptolite) zones (SRZs) and primary biozones (PBs). Use of evolving lineages, interregna, numerical notation systems, and chronozones are discussed. Precision in correlation of the Silurian biozones is described in terms of the Ordovician-Silurian boundary and the Wenlock-Ludlow (Silurian) boundary. A number of recommendations are made with respect to all zonal concepts, essentially giving prime importance to the use of biozones. □ Biozones, standard reference zones, primary biozones, chronozones, graptolites.     

The visual system as a constraint on the survival and success of specific artworks

Why should vision science turn its gaze towards artworks? One possibility is that understanding visual processing might yield some fundamental insight into the nature of art. However, there are many examples of phenomena that can be seen - such as automobiles, clouds or leaves - but which are not explained in any deep sense by the properties of human visual perception. We examine one art historical question that might benefit from knowledge about the visual system: why do some artworks 'survive' historically while others fade into the dustbin of time? One possible reason, suggested by studies of rapid visual categorization, is that some objects are recognized more quickly and easily than others and thus are less culturally specific in terms of pictorial representation. A second, related, explanation is that many artistic techniques use the eyes as a channel to evoke other senses, cognition, emotions and the motor system. 'Art' is a social and historical construct - after all, the concept of 'fine art' was invented in the 18th century - and thus many aspects of artistic appreciation are specific to particular cultural and historical contexts. Some great works, however, may be adopted by successive generations because of an ability to appeal to a shared perceptual system.