The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides (...) access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)

La philosophie cartésienne, en dépit des efforts souvent tentés pour l'exposer suivant une dialectique unilinéaire, n'est point à strictement parler, un système. On la nommerait assez bien, un pluralisme, en ce sens que son contenu ne se laisse ni dériver d'un seul principe ni enfermer dans une seule formule. Pluralisme cohérent, faudrait-il ajouter : non seulement parce que les oppositions qui s'y révèlent ne sont pas (quoi qu'on en ait dit) de formelles contradictions, mais surtout parce que chacun des termes (...) opposés n'y a été admis qu'en vertu d'une même attitude d'esprit, la docilité à l'évidence. Se plier en toutes choses à ce qu'on voit ; l'enregistrer comme on le voit, à quelque ordre qu'il appartienne, sans y rien mêler de sa sensibilité propre : voilà l'attitude cartésienne, telle qu'elle se manifeste dans la théorie de la méthode, comme aussi dans le Cogito et dans les démarches qui en procèdent. C'est l'attitude empirique, au sens premier et authentique du mot : ceux-là seuls répugnent à en convenir que des associations invétérées conduisent toujours à confondre empirique et sensualiste. En sorte que, si nous voulons à toute force caractériser la philosophie de Descartes par un nom, le nom qui lui siérait le mieux serait, tout paradoxe à part, celui d'empirisme - empirisme radical et intégral. (shrink)

Le. Jansénisme. Convient-il, dans une Histoire des Religions, de consacrer un chapitre au « jansénisme » ? On pourrait se le demander. Car tous ceux qui ont coutume d'être appelés « Jansénistes » s'accordent à répudier ce nom de « secte ...

Background The prioritization protocols for accessing adult critical care in the extreme pandemic context contain tiebreaker criteria to facilitate decision-making in the allocation of resources between patients with a similar survival prognosis. Besides being controversial, little is known about the public acceptability of these tiebreakers. In order to better understand the public opinion, Quebec and Ontario’s protocols were presented to the public in a democratic deliberation during the summer of 2022. Objectives (1) To explore the perspectives of Quebec and Ontario (...) citizens regarding tiebreakers, identifying the most acceptable ones and their underlying values. (2) To analyze these results considering other public consultations held during the pandemic on these criteria. Methods This was an exploratory qualitative study. The design involved an online democratic deliberation that took place over two days, simultaneously in Quebec and Ontario. Public participants were selected from a community sample which excluded healthcare workers. Participants were first presented the essential components of prioritization protocols and their related issues (training session day 1). They subsequently deliberated on the acceptability of these criteria (deliberation session day 2). The deliberation was then subject to thematic analysis. Results A total of 47 participants from the provinces of Quebec (n = 20) and Ontario (n = 27) took part in the online deliberation. A diverse audience participated excluding members of the healthcare workforce. Four themes were identified: (1) Priority to young patients - the life cycle - a preferred tiebreaker; (2) Randomization - a tiebreaker of last resort; (3) Multiplier effect of most exposed healthcare workers - a median acceptability tiebreaker, and (4) Social value – a less acceptable tiebreaker. Conclusion Life cycle was the preferred tiebreaker as this criterion respects intergenerational equity, which was considered relevant when allocating scarce resources to adult patients in a context of extreme pandemic. Priority to young patients is in line with other consultations conducted around the world. Additional studies are needed to further investigate the public acceptability of tiebreaker criteria. (shrink)

© Copyright 2015, Mary Ann Liebert, Inc..Signal transducer and activator of transcription factor 3 is hyperactivated in head and neck squamous cell carcinomas. Cumulative evidence indicates that IL-6 production by HNSCC cells and/or stromal cells in the tumor microenvironment activates STAT3 and contributes to tumor progression and drug resistance. A library of 94,491 compounds from the Molecular Library Screening Center Network was screened for the ability to inhibit interleukin-6 -induced pSTAT3 activation. For contractual reasons, the primary high-content screening campaign was (...) conducted over several months in 3 distinct phases; 1,068 primary HCS actives remained after cytotoxic or fluorescent outliers were eliminated. One thousand one hundred eighty-seven compounds were cherry-picked for confirmation; actives identified in the primary HCS and compounds selected by a structural similarity search of the remaining MLSCN library using hits identified in phases I and II of the screen. Actives were confirmed in pSTAT3 IC50 assays, and an IFNγ-induced pSTAT1 activation assay was used to prioritize selective inhibitors of STAT3 activation that would not inhibit STAT1 tumor suppressor functions. Two hundred three concentration-dependent inhibitors of IL-6-induced pSTAT3 activation were identified and 89 of these also produced IC50s against IFN-γ-induced pSTAT1 activation. Forty-nine compounds met our hit criteria: they reproducibly inhibited IL-6-induced pSTAT3 activation by ≥70% at 20 μM; their pSTAT3 activation IC50s were ≤25 μM; they were ≥2-fold selective for pSTAT3 inhibition over pSTAT1 inhibition; a cross target query of PubChem indicated that they were not biologically promiscuous; and they were ≥90% pure. Twenty-six chemically tractable hits that passed filters for nuisance compounds and had acceptable drug-like and ADME-Tox properties by computational evaluation were purchased for characterization. The hit structures were distributed among 5 clusters and 8 singletons. Twenty-four compounds inhibited IL-6-induced pSTAT3 activation with IC50s ≤20 μM and 13 were ≥3-fold selective versus inhibition of pSTAT1 activation. Eighteen hits inhibited the growth of HNSCC cell lines with average IC50s ≤ 20 μM. Four chemical series were progressed into lead optimization: the guanidinoquinazolines, the triazolothiadiazines, the amino alcohols, and an oxazole-piperazine singleton. (shrink)

En publiant en 1965 Le Péché et la durée de l’ange, le P. Guérard des Lauriers, o. p. (1898-1989) offrait une contribution majeure à un débat qui divisait les thomistes. En 1946 en effet, la parution de Surnaturel du P. de Lubac avait remis en cause, textes de Thomas d’Aquin à l’appui, la thèse de l’impeccabilité naturelle de l’ange, jusqu’alors (presque) unanimement reçue dans l’École thomiste. Deux interprétations de Thomas d’Aquin polarisèrent alors le débat : la raison de la peccabilité (...) de l’ange est à rechercher ou bien dans son élévation à l’ordre surnaturel ( De malo, q. 16, a. 4), ou bien dans la structure même de la créature angélique ( Summa theologiae I a Pars, q. 63, a. 1). Servi par une herméneutique renouvelée des textes de Thomas sur la peccabilité de l’ange, et fort d’un redéploiement d’une doctrine thomiste de la liberté, articulée dans sa double dimension de spécification et d’exercice, Guérard établit que le fondement de la liberté des créatures spirituelles – et donc leur peccabilité – se situe au cœur de leur constitution métaphysique, dans la distinction réelle entre nature et personne, sans qu’intervienne nécessairement la distinction des ordres naturel et surnaturel. Son analyse pénétrante et novatrice le conduit à mettre au jour une structure du libre arbitre, laquelle intègre et unit sans confusion les deux ordres de réalité engagés dans l’acte libre : le métaphysique et le moral. Il offre ainsi une contribution de premier plan à l’élaboration d’une philosophie contemporaine de la liberté, attestant par-là la fécondité de la tradition thomiste. (shrink)

Considering the persisting disagreement between the common sense philosophers and the sceptics, it seems that they are faced with a deep epistemic disagreement. Taking stock from Wittgenstein’s On Certainty, one generally thinks that deep epistemic disagreements cannot be rationally resolved. Hinge epistemology, inherited from Wittgenstein, is also considered as an illuminating detour to understand common sense epistemology. But is there really a deep epistemic disagreement between the common sense philosophers and the sceptics? Could it not be considered that they share (...) a common background? If so, is the rational resolution of their disagreement logically possible? What rational means can common sense use to convince someone of the privileged status of an epistemic principle? Relying on Reid’s, Alston’s and Lynch’s arguments, I show that common sense epistemology is a more promising approach than hinge epistemology, because it is driven by an optimism about reason in the solving of deep epistemic disagreements. (shrink)

The pivotal problem of comorbidity research lies in the psychometric foundation it rests on, that is, latent variable theory, in which a mental disorder is viewed as a latent variable that causes a constellation of symptoms. From this perspective, comorbidity is a (bi)directional relationship between multiple latent variables. We argue that such a latent variable perspective encounters serious problems in the study of comorbidity, and offer a radically different conceptualization in terms of a network approach, where comorbidity is hypothesized to (...) arise from direct relations between symptoms of multiple disorders. We propose a method to visualize comorbidity networks and, based on an empirical network for major depression and generalized anxiety, we argue that this approach generates realistic hypotheses about pathways to comorbidity, overlapping symptoms, and diagnostic boundaries, that are not naturally accommodated by latent variable models: Some pathways to comorbidity through the symptom space are more likely than others; those pathways generally have the same direction (i.e., from symptoms of one disorder to symptoms of the other); overlapping symptoms play an important role in comorbidity; and boundaries between diagnostic categories are necessarily fuzzy. (shrink)

How is hope to be found amid the ethical and political dilemmas of modern life? Writer and philosopher Mary Zournazi brought her questions to some of the most thoughtful intellectuals at work today. She discusses "joyful revolt" with Julia Kristeva, the idea of "the rest of the world" with Gayatri Spivak, the "art of living" with Michel Serres, the "carnival of the senses" with Michael Taussig, the relation of hope to passion and to politics with Chantal Mouffe and Ernesto Laclau. (...) A dozen stimulating minds weigh in with their visions of a better social and political order. The result is a collaboration - of writing, of thinking, and of politics - that demonstrates more clearly than any single-authored project could how ideas encountering one another can produce the vision needed for social change. (shrink)

The building of a global model of carcinogenesis is one of modern biology’s greatest challenges. The traditional somatic mutation theory is now supplemented by a new approach, called the Tissue Organization Field Theory. According to TOFT, the original source of cancer is loss of tissue organization rather than genetic mutations. In this paper, we study the argumentative strategy used by the advocates of TOFT to impose their view. In particular, we criticize their claim of incompatibility used to justify the necessity (...) to definitively reject SMT. First, we note that since it is difficult to build a non-ambiguous experimental demonstration of the superiority of TOFT, its partisans add epistemological and metaphysical arguments to the debate. This argumentative strategy allows them to defend the necessity of a paradigm shift, with TOFT superseding SMT. To do so, they introduce a notion of incompatibility, which they actually use as the Kuhnian notion of incommensurability. To justify this so-called incompatibility between the two theories of cancer, they move the debate to a metaphysical ground by assimilating the controversy to a fundamental opposition between reductionism and organicism. We show here that this argumentative strategy is specious, because it does not demonstrate clearly that TOFT is an organicist theory. Since it shares with SMT its vocabulary, its ontology and its methodology, it appears that a claim of incompatibility based on this metaphysical plan is not fully justified in the present state of the debate. We conclude that it is more cogent to argue that the two theories are compatible, both biologically and metaphysically. We propose to consider that TOFT and SMT describe two distinct and compatible causal pathways to carcinogenesis. This view is coherent with the existence of integrative approaches, and suggests that they have a higher epistemic value than the two theories taken separately. (shrink)

In this paper, I address the charge that the category species should be abandoned in biological work. The widespread appeal to species in scientific discourse provides a presumption in favor of the category’s usefulness, but a defeasible presumption. Widely acknowledged troubles attend species: these troubles might render the concept unusable by showing that ‘species’ is equivocal or meaningless or in some similar way fatally flawed. Further, there might be better alternatives to species. I argue that the presumption in favor of (...) species is not defeated on these scores. Troubles attending species, which arise on account of contextual variation attending the use of ‘species’, do not indicate that the concept is unusable. And alternatives to the use of ‘species’, which have been proposed in connection with rank-free systematics and in connection with conservation efforts, fail to provide a proper replacement for species. (shrink)

This paper is devoted to computer modelling of the development and regeneration of multicellular biological structures. Some species are able to regenerate parts of their body after amputation damage, but the global rules governing cooperative cell behaviour during morphogenesis are not known. Here, we consider a simplified model organism, which consists of tissues formed around special cells that can be interpreted as stem cells. We assume that stem cells communicate with each other by a set of signals, and that the (...) values of these signals depend on the distance between cells. Thus the signal distribution characterizes location of stem cells. If the signal distribution is changed, then the difference between the initial and the current signal distribution affects the behaviour of stem cells—e.g. as a result of an amputation of a part of tissue the signal distribution changes which stimulates stem cells to migrate to new locations, appropriate for regeneration of the proper pattern. Moreover, as stem cells divide and form tissues around them, they control the form and the size of regenerating tissues. This two-level organization of the model organism, with global regulation of stem cells and local regulation of tissues, allows its reproducible development and regeneration. (shrink)

Systems biology is today such a widespread discipline that it becomes difficult to propose a clear definition of what it really is. For some, it remains restricted to the genomic field. For many, it designates the integrated approach or the corpus of computational methods employed to handle the vast amount of biological or medical data and investigate the complexity of the living. Although defining systems biology might be difficult, on the other hand its purpose is clear: systems biology, with its (...) emerging subfields systems medicine and systems pharmacology, clearly aims at making sense of complex observations/experimental and clinical datasets to improve our understanding of diseases and their treatments without putting aside the context in which they appear and develop. In this short review, we aim to specifically focus on these new subfields with the new theoretical tools and approaches that were developed in the context of cancer. Systems pharmacology and medicine now give hope for major improvements in cancer therapy, making personalized medicine closer to reality. As we will see, the current challenge is to be able to improve the clinical practice according to the paradigm shift of systems sciences. (shrink)

Richard Lennan’s Tilling the Church treats ecclesial conflict, the possibility of change, and the tensions involved. He acknowledges the resistance to development within the Church’s structures. This resistance helps to explain the church’s distrust of women, which frustrates many Catholics. Cornell philosopher Kate Manne puts resistance to change in context by describing the social expectations of women, by showing that those who resist change feel entitled to do so, and by revealing how victimization is legitimated. “Tilling the church” is an (...) apt metaphor for transformation that does not sufficiently appreciate socially-mediated systems of privilege and vulnerability. (shrink)

A powerful argument that religious and theological issues should have no place in public morality issues such as euthanasia, assisted suicide, and abortion.

This article is an exploration of how the concept of relational autonomy might be applied in practice. The discussion uses the example of breast cancer nursing as a lens through which to consider how a view of autonomy as relational might affect the ways in which practitioners work with their clients.

Unlike some other reproductions of classic texts (1) We have not used OCR(Optical Character Recognition), as this leads to bad quality books with introduced typos. (2) In books where there are images such as portraits, maps, sketches etc We have endeavoured to keep the quality of these images, so they represent accurately the original artefact. Although occasionally there may be certain imperfections with these old texts, we feel they deserve to be made available for future generations to enjoy.

Lindquist et al. present a strong case for a constructionist account of emotion. First, we elaborate on the ramifications that a constructionist account of emotions might have for psychiatric disorders with emotional disturbances as core elements. Second, we reflect on similarities between Lindquist et al.'s model and recent attempts at formulating psychiatric disorders as networks of causally related symptoms.

In this article we present a new kind of computing device that uses biochemical reactions networks as building blocks to implement logic gates. The architecture of a computing machine relies on these generic and composable building blocks, computation units, that can be used in multiple instances to perform complex boolean functions. Standard logical operations are implemented by biochemical networks, encapsulated and insulated within synthetic vesicles called protocells. These protocells are capable of exchanging energy and information with each other through transmembrane (...) electron transfer. In the paradigm of computation we propose, protoputing, a machine can solve only one problem and therefore has to be built specifically. Thus, the programming phase in the standard computing paradigm is represented in our approach by the set of assembly instructions that directs the wiring of the protocells that constitute the machine itself. To demonstrate the computing power of protocellular machines, we apply it to solve a NP-complete problem, known to be very demanding in computing power, the 3-SAT problem. We show how to program the assembly of a machine that can verify the satisfiability of a given boolean formula. Then we show how to use the massive parallelism of these machines to verify in less than 20 min all the valuations of the input variables and output a fluorescent signal when the formula is satisfiable or no signal at all otherwise. (shrink)

This article examines women who have been antinuclear activists at the Three Mile Island nuclear power plant for two decades. Qualitative interviews focus on their perceived transformations over time that are based on gender and everyday experiences. They perceive gender as both a barrier and a facilitator to activism, even after 20 years. Women describe their technological education as one strategy to overcome the barrier of gender. On the other hand, they consider the gendered role of motherhood as a primary (...) catalyst for action. In addition, they discuss individual everyday experiences focused on the health concerns for family members that influenced their political activity. Over time, women linked personal transformations with increased political understanding and involvement. (shrink)

The majority of commentators agree on one thing: Our network approach might be the prime candidate for offering a new perspective on the origins of mental disorders. In our response, we elaborate on refinements (e.g., cognitive and genetic levels) and extensions (e.g., to Axis II disorders) of the network model, as well as discuss ways to test its validity.

Large sets of elements interacting locally and producing specific architectures reliably form a category that transcends the usual dividing line between biological and engineered systems. We propose to call them morphogenetically architected complex systems. While taking the emergence of properties seriously, the notion of MACS enables at the same time the design of operational means that allow controlling and even, paradoxically, programming this emergence. To demonstrate our claim, we first show that among all the self-organized systems studied in the field (...) of Artificial Life, the specificity of MACS essentially lies in the close relation between their emergent properties and functional properties. Second, we argue that to be a MACS a system does not need to display more than weak emergent properties. Third, since the notion of weak emergence is based on the possibility of simulation, whether computational or mechanistic via machines, we see MACS as good candidates to help design artificial self-architected systems but also harness and redesign living ones. (shrink)

Présentation des articles qui suivent : invoquer le sens commun, ce n’est pas supposer un abandon de la philosophie et de la raison, mais faire droit à une conception ajustée de la rationalité humaine. Les articles ici réunis s’inscrivent dans l’approche du sens commun comme instance régulatrice.

How do we act justly in the world? How can we ethically respond to social and economic crisis and the desperation caused by violence and atrocity? Justice and Love is a philosophical dialogue on how to imagine and act in a more just world by theologian Rowan Williams and philosopher Mary Zournazi. Drawing on examples from the European Migrant Crisis to Brexit, the authors reflect on justice as a condition of being rather than cold fact. Looking at different religious and (...) philosophical traditions to enrich our language of justice, this book explores the love and patience needed for social healing and the imagination required to experience the world in new ways. (shrink)

The Enzymatic control reactions model was presented within the scope of fractional calculus. In order to accommodate the usual initial conditions, the fractional derivative used is in Caputo sense. The methodologies of the three analytical methods were used to derive approximate solution of the fractional nonlinear system of differential equations. Two methods use integral operator and the other one uses just an integral. Numerical results obtained exhibit biological behavior of real world problem.

Fundamental principles : the nature of the dispute -- Types of euthanasia -- Psychiatric assisted suicide -- Neonates -- Incompetent adults -- Human life is sacred -- The slippery slope -- Medical views -- Four methods of easing death and their effect on doctors -- Looking further ahead.

According to the received tradition, the language used to to refer to natural kinds in scientific discourse remains stable even as theories about these kinds are refined. In this illuminating book, Joseph LaPorte argues that scientists do not discover that sentences about natural kinds, like 'Whales are mammals, not fish', are true rather than false. Instead, scientists find that these sentences were vague in the language of earlier speakers and they refine the meanings of the relevant natural-kind terms to (...) make the sentences true. Hence, scientists change the meaning of these terms, This conclusions prompts LaPorte to examine the consequences of this change in meaning for the issue of incommensurability and for the progress of science. This book will appeal to students and professional in the philosophy of science, the philosophy of biology and the philosophy of language. (shrink)

This book arose out of a conference organised by the Fay Gale Centre for Research on Gender at The University of Adelaide honouring Carol Bacchi's work and is intended to make that work accessible to a range of audiences. - from the ...

RÉSUMÉLe mot «migrants» n'existait pas dans la langue des Hellènes; ils étaient plus familiers avec le vocable de l'exil et de l'asile. D'ailleurs, l'exil ne saurait se penser sans son corollaire, l'asile, comme le citoyen antique sans le barbare et la démocratie sans la tyrannie. À travers une métaphore située au carrefour de la fiction historique, de la philosophie politique et de la psychanalyse, cet article propose une réflexion sur l'exil comme condition fondamentale du sujet. L'exil est d'origine, car la (...) langue de l'enfance, la langue dite maternelle est d'abord une langue étrangère. L'exil intime porte la marque d'une universalité qui fonde l'expérience subjective.ABSTRACTThe word ‘migrants’ did not exist in the language of the Hellenes; they were more familiar with the terms ‘exile’ and ‘political asylum.’ Indeed, exile cannot be thought of without its corollary, political asylum, as the Ancient citizen cannot be thought of without the barbarian, and democracy without tyranny. Through a metaphor located at the crossroads of historical fiction, political philosophy and psychoanalysis, this article offers a reflection on exile as a fundamental condition of the subject. Exile is originary because the language of childhood, the so-called mother tongue, is originally a foreign language. Intimate exile bears the mark of a universality that founds subjective experience. (shrink)

This book presents the views of 22 women philosophers from outside the Greco-Roman and Judeo-Christian worlds. These eminent thinkers are from Mesopotamia, India, Tibet, China, Korea, Japan, Australia, America, the Philippines and Nigeria. Six philosophers, the earliest of whom predates the Greek pre-Socratics by two thousand years, lived at “the dawn of philosophy”; another six from late Antiquity through the Classical period; five more taught and wrote during the Middle Ages up to the Age of Exploration, and yet five others (...) were active during the modern period to the mid-twentieth century. Most belonged to major philosophical traditions: Hinduism, Buddhism, Confucianism, Taoism, Zen, or Sufism. The chapters of the book describe the life and views of the philosophers, outline the fundamental features of their respective schools, and contain translations of their writings. The book is intended for scholars of philosophy and women’s studies who wish to expand their knowledge of non-Western philosophical traditions and is ideally suited for undergraduate education. Comprehensive multilingual bibliographies of carefully documented sources offer scholars many promising resources for further research. (shrink)

An anthology of essays that discuss the ethics of money (including issues of wealth, income, expenditures, charity, debt, etc.) from a variety of Jewish perspectives.