Santa Fe Institute

About: Santa Fe Institute is a nonprofit organization based out in Santa Fe, New Mexico, United States. It is known for research contribution in the topics: Population & Context (language use). The organization has 558 authors who have published 4558 publications receiving 396015 citations. The organization is also known as: SFI.

Recurrent Signature Patterns in HIV-1 B Clade Envelope Glycoproteins Associated with either Early or Chronic Infections

Abstract: Here we have identified HIV-1 B clade Envelope (Env) amino acid signatures from early in infection that may be favored at transmission, as well as patterns of recurrent mutation in chronic infection that may reflect common pathways of immune evasion. To accomplish this, we compared thousands of sequences derived by single genome amplification from several hundred individuals that were sampled either early in infection or were chronically infected. Samples were divided at the outset into hypothesis-forming and validation sets, and we used phylogenetically corrected statistical strategies to identify signatures, systematically scanning all of Env. Signatures included single amino acids, glycosylation motifs, and multi-site patterns based on functional or structural groupings of amino acids. We identified signatures near the CCR5 co-receptor-binding region, near the CD4 binding site, and in the signal peptide and cytoplasmic domain, which may influence Env expression and processing. Two signatures patterns associated with transmission were particularly interesting. The first was the most statistically robust signature, located in position 12 in the signal peptide. The second was the loss of an N-linked glycosylation site at positions 413–415; the presence of this site has been recently found to be associated with escape from potent and broad neutralizing antibodies, consistent with enabling a common pathway for immune escape during chronic infection. Its recurrent loss in early infection suggests it may impact fitness at the time of transmission or during early viral expansion. The signature patterns we identified implicate Env expression levels in selection at viral transmission or in early expansion, and suggest that immune evasion patterns that recur in many individuals during chronic infection when antibodies are present can be selected against when the infection is being established prior to the adaptive immune response.

Populational adaptive evolution, chemotherapeutic resistance and multiple anti-cancer therapies

Abstract: Resistance to chemotherapies, particularly to anticancer treatments, is an increasing medical concern. Among the many mechanisms at work in cancers, one of the most important is the selection of tumor cells expressing resistance genes or phenotypes. Motivated by the theory of mutation-selection in adaptive evolution, we propose a model based on a continuous variable that represents the expression level of a resistance gene (or genes, yielding a phenotype) influencing in healthy and tumor cells birth/death rates, effects of chemotherapies (both cytotoxic and cytostatic) and mutations. We extend previous work by demonstrating how qualitatively different actions of chemotherapeutic and cytostatic treatments may induce different levels of resistance. The mathematical interest of our study is in the formalism of constrained Hamilton–Jacobi equations in the framework of viscosity solutions. We derive the long-term temporal dynamics of the fittest traits in the regime of small mutations. In the context of adaptive cancer management, we also analyse whether an optimal drug level is better than the maximal tolerated dose.

The Barrier of Objects: From Dynamical Systems to Bounded Organizations

Abstract: ion Ax ∪ {x : τ ′} e : τ A λx.e : τ ′ → τ Let A e : σ Ax ∪ {x : σ} e′ : τ A (let x = e in e′) : τ The meaning of the Taut-rule is simply that a free variable has the type assigned to it in the boundary condition. If there is no assignment the expression x is not typable, and is barred from the universe. The meaning of rule App is also clear. It is useful, however, to know how the rule is implemented, since it introduces an important concept. Suppose that we have an object e whose type has been established to be σ, and that we want to apply it to an object e′ of type τ ′. For this to be possible e must have a type of the form τ ′ → τ where τ stands for a generic unknown type of (e)e′ that needs to be determined. Hence, for the interaction (e)e′ to be possible e’s established type σ and the required type τ ′ → τ must be made equal. This may be possible, since σ and τ ′ may contain type variables which can be made more specific in order to satisfy the equality. This means we must look for some type substitution T of the free variables in σ and in τ ′ → τ such that Tσ = T (τ ′ → τ). T is called a unifier, and the procedure for finding T is called unification. It boils down to solving a set of equations. For details about how this procedure is carried out the reader is referred to any standard textbook on type theory. The point is that a

The impact of imitation on vaccination behavior in social contact networks.

Abstract: Previous game-theoretic studies of vaccination behavior typically have often assumed that populations are homogeneously mixed and that individuals are fully rational. In reality, there is heterogeneity in the number of contacts per individual, and individuals tend to imitate others who appear to have adopted successful strategies. Here, we use network-based mathematical models to study the effects of both imitation behavior and contact heterogeneity on vaccination coverage and disease dynamics. We integrate contact network epidemiological models with a framework for decision-making, within which individuals make their decisions either based purely on payoff maximization or by imitating the vaccination behavior of a social contact. Simulations suggest that when the cost of vaccination is high imitation behavior may decrease vaccination coverage. However, when the cost of vaccination is small relative to that of infection, imitation behavior increases vaccination coverage, but, surprisingly, also increases the magnitude of epidemics through the clustering of non-vaccinators within the network. Thus, imitation behavior may impede the eradication of infectious diseases. Calculations that ignore behavioral clustering caused by imitation may significantly underestimate the levels of vaccination coverage required to attain herd immunity.

Domestication as a model system for niche construction theory

Abstract: Niche Construction Theory (NCT) provides a powerful conceptual framework for understanding how and why humans and target species entered into domesticatory relationships that have transformed Earth's biota, landforms, and atmosphere, and shaped the trajectory of human cultural development. NCT provides fresh perspective on how niche-constructing behaviors of humans and plants and animals promote co-evolutionary interactions that alter selection pressures and foster genetic responses in domesticates. It illuminates the role of niche-altering activities in bequeathing an ecological inheritance that perpetuates the co-evolutionary relationships leading to domestication, especially as it pertains to traditional ecological knowledge and the transmission of learned behaviors aimed at enhancing returns from local environments. NCT also provides insights into the contexts and mechanisms that promote cooperative interactions in both humans and target species needed to sustain niche-constructing activities, ensuring that these activities pro- duce an ecological inheritance in which domesticates play an increasing role. A NCT perspective contributes to on-going debates in the social sciences over explanatory frameworks for domestication, in particular as they pertain to issues of reciprocal causa- tion, co-evolution, and the role of human intentionality. Reciprocally, domestication provides a model system for evaluating on-going debates in evolutionary biology con- cerning the impact of niche construction, phenotypic plasticity, extra-genetic inheritance, and developmental bias in shaping the direction and tempo of evolutionary change.