The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids used is small

In the maximum parsimony (MP) and minimum evolution (ME) methods of phylogenetic inference, evolutionary trees are constructed by searching for the topology that shows the minimum number of mutational changes required (M) and the smallest sum of branch lengths (S), respectively, whereas in the maximum likelihood (ML) method the topology showing the highest maximum likelihood (A) of observing a given data set is chosen. However, the theoretical basis of the optimization principle remains unclear. We therefore examined the relationships of M, S, and A for the MP, ME, and ML trees with those for the true tree by using computer simulation. The results show that M and S are generally greater for the true tree than for the MP and ME trees when the number of nucleotides examined (n) is relatively small, whereas A is generally lower for the true tree than for the ML tree. This finding indicates that the optimization principle tends to give incorrect topologies when n is small. To deal with this disturbing property of the optimization principle, we suggest that more attention should be given to testing the statistical reliability of an estimated tree rather than to finding the optimal tree with excessive efforts. When a reliability test is conducted, simplified MP, ME, and ML algorithms such as the neighbor-joining method generally give conclusions about phylogenetic inference very similar to those obtained by the more extensive tree search algorithms.

Recognition principle of the TAP transporter disclosed by combinatorial peptide libraries

Transport of peptides across the membrane of the endoplasmic reticulum for assembly with MHC class I molecules is an essential step in antigen presentation to cytotoxic T cells. This task is performed by the major histocompatibility complex-encoded transporter associated with antigen processing (TAP). Using a combinatorial approach we have analyzed the substrate specificity of human TAP at high resolution and in the absence of any given sequence context, revealing the contribution of each peptide residue in stabilizing binding to TAP. Human TAP was found to be highly selective with peptide affinities covering at least three orders of magnitude. Interestingly, the selectivity is not equally distributed over the substrate. Only the N-terminal three positions and the C-terminal residue are critical, whereas effects from other peptide positions are negligible. A major influence from the peptide backbone was uncovered by peptide scans and libraries containing d amino acids. Again, independent of peptide length, critical positions were clustered near the peptide termini. These approaches demonstrate that human TAP is selective, with residues determining the affinity located in distinct regions, and point to the role of the peptide backbone in binding to TAP. This binding mode of TAP has implications in an optimized repertoire selection and in a coevolution with the major histocompatibility complex/T cell receptor complex.

The hard-soft acid-base principle in enzymatic catalysis: dual reactivity of phosphoenolpyruvate.

In this paper, the chemical reactivity of C3 of phosphoenolpyruvate (PEP) has been analyzed in terms of density functional theory quantified through quantum chemistry calculations. PEP is involved in a number of important enzymatic reactions, in which its C3 atom behaves like a base. In three different enzymatic reactions analyzed here, C3 sometimes behaves like a soft base and sometimes behaves like a hard base in terms of the hard-soft acid-base principle. This dual nature of C3 of PEP was found to be related to the conformational change of the molecule. This leads to a testable hypothesis: that PEP adopts particular conformations in the enzyme-substrate complexes of different PEP-using enzymes, and that the enzymes control the reactivity through controlling the dihedral angle between the carboxylate and the C==C double bond of PEP.

The resource consumption principle: attention and memory in volumes of neural tissue.

In the cerebral cortex, the small volume of the extracellular space in relation to the volume enclosed by synapses suggests an important functional role for this relationship. It is well known that there are atoms and molecules in the extracellular space that are absolutely necessary for synapses to function (e.g., calcium). I propose here the hypothesis that the rapid shift of these atoms and molecules from extracellular to intrasynaptic compartments represents the consumption of a shared, limited resource available to local volumes of neural tissue. Such consumption results in a dramatic competition among synapses for resources necessary for their function. In this paper, I explore a theory in which this resource consumption plays a critical role in the way local volumes of neural tissue operate. On short time scales, this principle of resource consumption permits a tissue volume to choose those synapses that function in a particular context and thereby helps to integrate the many neural signals that impinge on a tissue volume at any given moment. On longer time scales, the same principle aids in the stable storage and recall of information. The theory provides one framework for understanding how cerebral cortical tissue volumes integrate, attend to, store, and recall information. In this account, the capacity of neural tissue to attend to stimuli is intimately tied to the way tissue volumes are organized at fine spatial scales.

Electrically Tunable Selective Reflection of Light from Ultraviolet to Visible and Infrared by Heliconical Cholesterics

Acknowledgements This work was supported by NSF DMR-1410378 and DMR-1121288. We thank V. Borshch for helping with preparation of illustrations, to Y. K. Kim for the help in experiments, V. A. Belyakov and S. V. Shiyanovskii for useful discussions.

Groups, information theory, and Einstein's likelihood principle

We propose a unifying picture where the notion of generalized entropy is related to information theory by means of a group-theoretical approach. The group structure comes from the requirement that an entropy be well defined with respect to the composition of independent systems, in the context of a recently proposed generalization of the Shannon-Khinchin axioms. We associate to each member of a large class of entropies a generalized information measure, satisfying the additivity property on a set of independent systems as a consequence of the underlying group law. At the same time, we also show that Einstein's likelihood function naturally emerges as a byproduct of our informational interpretation of (generally nonadditive) entropies. These results confirm the adequacy of composable entropies both in physical and social science contexts.

A integralidade no cuidado das pessoas vivendo com HIV e AIDS: a experiência do Centro de Referência e Treinamento em DST/AIDS da SES-SP

Ao assumir o compromisso com a prevenção e tratamento, baseada no princípio da integralidade, a estratégia brasileira, fez a diferença na resposta nacional à aids nas décadas de 1980/90 e criou um novo paradigma que mostrou-se avançado do ponto de vista técnico, ético e político, contribuindo para a mudança nas recomendações das agências internacionais (OMS\\Banco Mundial) - do \"não tratar e só prevenir\" do início dos anos 1990, para o \"Tratamento como Prevenção\", base da atual proposta dos 90/90/90. Essa estratégia de controle da epidemia concentra responsabilidade na Rede de Serviços, em um período de discussão sobre mudanças no modelo de atenção a ser priorizado no país. Características relevantes dos contextos político e programáticos permitiram uma maior efetivação do cuidado às PVHA no Estado de São Paulo. O objetivo do presente estudo é recuperar a história do Centro de Referência e Treinamento em DST/Aids (CRT) na gestão e organização programática do cuidado em HIV/Aids no Estado de São Paulo, no período de 1988 a 2015, interpretando-a sob a perspectiva dos aspectos facilitadores e limitadores da incorporação prática do princípio da integralidade às ações de saúde. Realizou-se, nesse sentido, uma revisão narrativa da literatura sobre o tema da integralidade no campo da Saúde Coletiva Brasileira nas últimas cinco décadas. Tomando por base o cotejamento com esse desenvolvimento conceitual, a trajetória do CRT foi analisada por meio de entrevistas com atores-chaves no processo da gestão e organização programática do cuidado das PVHA no Estado de São Paulo, e análise dos documentos produzidos no processo. Esta análise foi organizada em torno de dois grandes eixos temáticos: (1) a criação e estruturação do CRT, e (2) as relações entre o CRT, os Programas Municipais de DST/aids e a rede de serviços assistenciais no Estado de São Paulo. Entre os resultados do estudo, destacam-se o resgate e reflexão crítica sobre o desenvolvimento dos discursos tecnocientíficos sobre integralidade no contexto das propostas de reforma da saúde no Brasil; a incorporação desses construtos às propostas desenvolvidas pelo CRT, especialmente em torno aos conceitos de vulnerabilidade, cuidado, clínica ampliada e direitos humanos em saúde; e a identificação de arranjos institucionais, estratégias técnicas e configurações políticas que permitiram ao CRT o exercício articulado de três níveis de gestão do cuidado (das PVHA, dos serviços e da Rede) numa mesma plataforma. Conclui-se apontando alcances e limites na efetivação da integralidade, que se mostraram desiguais nos três níveis de gestão do cuidado. Aponta-se maiores avanços na dimensão gerencial da rede e as maiores dificuldades na efetivação da integralidade no cuidado das PVHA e na gestão dos serviços de saúde

La repetición, una interpretación psicoanalítica: Freud y Lacan

The following dissertation is framed by the psychoanalytic line of thought inaugurated by Sigmund Freud and rethought by Jacques Lacan. The starting point of this work is the notion of repetition, which finds its utmost reason in what Freud called compulsive repetition. The idea of repetition, besides being called by Lacan as one of the foundations of Psychoanalysis, articulates a series of theoretical landmarks which, in turn, constitute Psychoanalysis’ own arguments – whether linked to clinical practice or articulated around metapsychological reflection of the psychoanalytical field. This dissertation is gravitates around four specific theoretical moments: two Freudian ones and two Lacanian ones. The latter taking place during the period called “The return to Freud”, which comprises the period from 1953 to 1964. In this period, the postfreudian developments deviate from Freudian theory, as well as the psychoanalytic method, which is reviewed by poststructuralism. Altogether, the four moments being analyzed are: in Freud, the “repetition linked to the act” in 1914, and the “repetition as such” developed in Beyond the Pleasure Principle in 1920.In Lacan, the theory of “the insistence of the signifier” from 1955 and what he later named as the “failed encounter with the real” in 1964...

Application of Mathieu functions for the study of non-slanted reflection gratings

In this work we prensent an analysis of non-slanted reflection gratings by using exact solution of the second order differential equation derived from Maxwell equations, in terms of Mathieu functions. The results obtained by using this method will be compared to those obtained by using the well known Kogelnik's Coupled Wave Theory which predicts with great accuracy the response of the efficieny of the zero and first order for volume phase gratings, for both reflection and transmission gratings.

A acção de condenação à prática de acto devido : conhecimento e prova dos pressupostos de facto do acto

A acção de condenação à prática de acto devido corresponde à concretização, com o Código de Processo nos Tribunais Administrativos, do princípio da tutela jurisdicional efectiva previsto no art. 268º/4 da Constituição da República Portuguesa, assegurando aos particulares a obtenção de uma pronúncia condenatória na prática do acto administrativo que tenha sido recusado ou omitido. Esta pronúncia sofre as limitações decorrentes do princípio da separação de poderes, entre o Administrativo e o Judicial, nos termos expressos no art. 71º/2 do Código de Processo, que determina que quando a emissão do acto pretendido envolva a formulação de valorações próprias do exercício da função administrativa (…) o tribunal não pode determinar o conteúdo do acto a praticar, mas deve explicitar as vinculações a observar (…) na emissão do acto devido. À limitação enunciada acresce outra, sem reflexo no texto do Código mas que se impõe por via do mesmo princípio, e que respeita aos poderes do tribunal no conhecimento e determinação dos pressupostos do acto devido, nos casos em que estes são questionados em juízo. A determinação dos pressupostos de facto do acto devido pelo tribunal está limitada pela natureza da actividade instrutória procedimental, pelo (in)cumprimento do ónus da prova no procedimento pelo interessado, nos casos limitados em que este tem relevância e pelo princípio da decisão prévia administrativa, nos termos do qual é à Administração que compete o conhecimento e decisão das pretensões que lhe são dirigidas e cuja competência que lhe foi determinada pela lei. Os limites enunciados não prejudicam a sindicabilidade, pelos tribunais, dos actos de recolha e valoração das provas pela Administração, que, nos casos em que configurem espaços de margem de livre decisão administrativa, são sindicáveis nos termos em que pode ser controlada a actividade autodeterminada da Administração, sem qualquer limitação quanto aos meios de prova.