From weak Allee effect to no Allee effect in Richards’ growth models

Population dynamics have been attracting interest since many years. Among the considered models, the Richards’ equations remain one of the most popular to describe biological growth processes. On the other hand, Allee effect is currently a major focus of ecological research, which occurs when positive density dependence dominates at low densities. In this chapter, we propose the dynamical study of classes of functions based on Richards’ models describing the existence or not of Allee effect. We investigate bifurcation structures in generalized Richards’ functions and we look for the conditions in the (β, r) parameter plane for the existence of a weak Allee effect region. We show that the existence of this region is related with the existence of a dovetail structure. When the Allee limit varies, the weak Allee effect region disappears when the dovetail structure also disappears. Consequently, we deduce the transition from the weak Allee effect to no Allee effect to this family of functions. To support our analysis, we present fold and flip bifurcation curves and numerical simulations of several bifurcation diagrams.

Sovereignty and power relations in the thought of Marsilius of Padua and William of Ockham a comparison.

pp. 229-253

Evolution of the Human Immunodeficiency Virus Type 2 Envelope in the First Years of Infection is Associated with the Dynamics of the Neutralizing Antibody Response

Background: Differently from HIV-1, HIV-2 disease progression usually takes decades without antiretroviral therapy and the majority of HIV-2 infected individuals survive as elite controllers with normal CD4+ T cell counts and low or undetectable plasma viral load. Neutralizing antibodies (Nabs) are thought to play a central role in HIV-2 evolution and pathogenesis. However, the dynamic of the Nab response and resulting HIV-2 escape during acute infection and their impact in HIV-2 evolution and disease progression remain largely unknown. Our objective was to characterize the Nab response and the molecular and phenotypic evolution of HIV-2 in association with Nab escape in the first years of infection in two children infected at birth. Results: CD4+ T cells decreased from about 50% to below 30% in both children in the first five years of infection and the infecting R5 viruses were replaced by X4 viruses within the same period. With antiretroviral therapy, viral load in child 1 decreased to undetectable levels and CD4+ T cells recovered to normal levels, which have been sustained at least until the age of 12. In contrast, viral load increased in child 2 and she progressed to AIDS and death at age 9. Beginning in the first year of life, child 1 raised high titers of antibodies that neutralized primary R5 isolates more effectively than X4 isolates, both autologous and heterologous. Child 2 raised a weak X4-specific Nab response that decreased sharply as disease progressed. Rate of evolution, nucleotide and amino acid diversity, and positive selection, were significantly higher in the envelope of child 1 compared to child 2. Rates of R5-to-X4 tropism switch, of V1 and V3 sequence diversification, and of convergence of V3 to a β-hairpin structure were related with rate of escape from the neutralizing antibodies. Conclusion: Our data suggests that the molecular and phenotypic evolution of the human immunodeficiency virus type 2 envelope are related with the dynamics of the neutralizing antibody response providing further support for a model in which Nabs play an important role in HIV-2 pathogenesis.

The Course of Conflict. A Study in the Thought of Paul Ricoeur

Esta tese leva a cabo uma clarificação conceptual e uma reconstrução histórica da noção de conflito, tal como ela aparece na filosofia. Num primeiro momento, analisa-se o fenómeno do conflito na fonte Grega (em Homero, Heraclito, Platão, nas tragédias gregas e nas formas de interação agonística no espaço público) e na filosofia moderna (principalmente em Kant, Hegel e Marx). Num segundo momento, estabelece-se, nos seus traços gerais, uma cartografia da recuperação desta noção na contemporaneidade através da discussão das contribuições provenientes da teoria crítica (Habermas, Honneth, Hunyadi), da sociologia pragmática (Boltanski, Thévenot) e da filosofia política anglo-saxónica (Rawls, Walzer, Taylor), entre outras. Estas partes iniciais da tese desembocam numa análise aprofundada da obra do filósofo francês Paul Ricoeur e das muitas instanciações do conflito nessa obra, naquilo a que chamo o “percurso do conflito” no pensamento de Ricoeur. Neste “percurso do conflito” o objetivo é duplo: por um lado, provar que o conflito é a pedra de toque não só da filosofia de Ricoeur, mas também de um grande conjunto de outros autores; por outro lado, que é necessário reavaliar o papel desta noção no debate contemporâneo e que nesse contexto a filosofia de Ricoeur e as suas análises finas e plurais podem ser de uma grande utilidade. Assim sendo, este “percurso do conflito” divide-se em três partes, as quais lidam com diferentes tipos de conflito: conflitos “existenciais”, “hermenêuticos” e “práticos”. Ao longo destas partes, várias disciplinas são chamadas à colação, como a hermenêutica, a psicanálise e a filosofia prática (ética, filosofia política e filosofia social), numa tentativa de esclarecer os diferentes fenómenos em causa. Em última instância, chega-se à conclusão que o conflito é inevitável em filosofia, tal como na vida, mas que este não é (pelo menos não em todas as suas formas e instanciações) um fenómeno estritamente negativo; por vezes, os conflitos podem ser criativos e positivos. Porém, aceitar este facto implica igualmente consentir que o reconhecimento dos conflitos está intrinsecamente ligado à busca de soluções para eles, formas de lidar com eles e torná-los criativos e positivos. Para que possa ser compreendido, em traços gerais, como é que estes procedimentos funcionam, esta tese elabora uma tipologia de diferentes tipos de conflito e respetivas formas de lidar com eles, mediando-os, conciliando-os ou, nalguns casos, apenas aceitando a sua existência e mesmo multiplicando-os. A busca da melhor solução tem sempre de ser operada caso a caso. Nas partes finais da tese, e partindo das análises de Ricoeur e dos outro autores apresentadas ao longo da mesma, delineia-se o projeto de uma filosofia social hermenêutica e argumenta-se que aquilo de que precisamos hoje em dia é de uma nova crítica da razão, uma “crítica da razão miserável” que possa repensar o mundo social em novos termos e que, ao fazê-lo, possa evitar os perigos do reducionismo nas suas múltiplas formas.

Science progress in the twentieth century : a quarterly journal of scientific work & thought.

v. 3 (1908-1909)

Science progress in the twentieth century : a quarterly journal of scientific work & thought.

v. 10 (1915-1916)

Science progress in the twentieth century : a quarterly journal of scientific work & thought.

v. 4 (1909-1910)

Science progress in the twentieth century : a quarterly journal of scientific work & thought.

v. 2 (1907-1908)

Science progress in the twentieth century : a quarterly journal of scientific work & thought.

v. 8 (1913-1914)

Science progress in the twentieth century : a quarterly journal of scientific work & thought.

v. 1 (1907)

Science progress in the twentieth century : a quarterly journal of scientific work & thought.

v. 9 (1914-1915)

Science progress in the twentieth century : a quarterly journal of scientific work & thought.

v. 6 (1911-1912)

Science progress in the twentieth century : a quarterly journal of scientific work & thought.

v. 7 (1912-1913)

Weak systems of Gandy, Jensen and Devlin

In Part I, we formulate and examine some systems that have arisen in the study of the constructible hierarchy; we find numerous transitive models for them, among which are supertransitive models containing all ordinals that show that Devlin's system BS lies strictly between Gandy's systems PZ and BST'; and we use our models to show that BS fails to handle even the simplest rudimentary functions, and is thus inadequate for the use intended for it in Devlin's treatise. In Part II we propose and study an enhancement of the underlying logic of these systems, build further models to show where the previous hierarchy of systems is preserved by our enhancement; and consider three systems that might serve for Devlin's purposes: one the enhancement of a version of BS, one a formulation of Gandy-Jensen set theory, and the third a subsystem common to those two. In Part III we give new proofs of results of Boffa by constructing three models in which, respectively, TCo, AxPair and AxSing fail; we give some sufficient conditions for a set not to belong to the rudimentary closure of another set, and thus answer a question of McAloon; and we comment on Gandy's numerals and correct and sharpen other of his observations.

The identity type weak factorisation system

We show that the classifying category C(T)of a dependent type theory T with axioms for identity types admits a nontrivial weak factorisation system. After characterising this weak factorisation system explicitly, we relate it to the homotopy theory of groupoids.