抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Convergence of Probability Measures. By P. Billingsley. Chichester, Sussex, Wiley, 1968. xii, 253 p. 9 1/4“. 117s.

Convergence of Probability Measures

BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

“Bioinformatics” 특집을 내면서

Model checking of linear temporal logic (LTL) specifications with respect to pushdown systems has been shown to be a useful tool for analysis of programs with potentially recursive procedures. LTL, however, can specify only regular properties, and properties such as correctness of procedures with respect to pre and post conditions, that require matching of calls and returns, are not regular. We introduce a temporal logic of calls and returns (CaRet) for specification and algorithmic verification of correctness requirements of structured programs. The formulas of CaRet are interpreted over sequences of propositional valuations tagged with special symbols call and ret. Besides the standard global temporal modalities, CaRet admits the abstract-next operator that allows a path to jump from a call to the matching return. This operator can be used to specify a variety of non-regular properties such as partial and total correctness of program blocks with respect to pre and post conditions. The abstract versions of the other temporal modalities can be used to specify regular properties of local paths within a procedure that skip over calls to other procedures. CaRet also admits the caller modality that jumps to the most recent pending call, and such caller modalities allow specification of a variety of security properties that involve inspection of the call-stack. Even though verifying context-free properties of pushdown systems is undecidable, we show that model checking CaRet formulas against a pushdown model is decidable. We present a tableau construction that reduces our model checking problem to the emptiness problem for a Buchi pushdown system. The complexity of model checking CaRet formulas is the same as that of checking LTL formulas, namely, polynomial in the model and singly exponential in the size of the specification.

https://repository.upenn.edu/cgi/viewcontent.cgi?article=1186&context=cis_papers

A Temporal Logic of Nested Calls and Returns

Real and Complex Analysis

In the ambient logic of classical second order propositional calculus, we solve the specification problem for a family of excluded middle like tautologies. These are shown to be realized by sequential simulations of specific communication schemes for which they provide a safe typing mechanism.

Disjunctive Tautologies as Synchronisation Schemes

A language of formal proteins, the K-calculus, is introduced. Interactions are modeled at the domain level, bonds are represented by means of shared names, and reactions are required to satisfy a causality requirement of monotonicity.An example of a simplified signalling pathway is introduced to illustrate how standard biological events can be expressed in our protein language. A more comprehensive example, the lactose operon, is also developed, bringing some confidence in the formalism considered as a modeling language.Then a finer-grained concurrent model, the mK-calculus, is considered, where interactions have to be at most binary. We show how to embed the coarser-grained language in the latter, a properly which we call self-assembly.Finally we show how the finer-grained language can itself be encoded in π-calculus, a standard foundational language for concurrency theory.

/pdf/formal-molecular-biology-2eepqk8kjk.pdf

Formal molecular biology

Investigating Girard's new propositionnal calculus which aims at a large scale study of computation, we stumble quickly on that question: What is a multiplicative connective? We give here a detailed answer together with our motivations and expectations.

The structure of multiplicatives

One obtains in this paper a process algebra RCCS, in the style of CCS, where processes can backtrack. Backtrack, just as plain forward computation, is seen as a synchronization and incurs no additional cost on the communication structure. It is shown that, given a past, a computation step can be taken back if and only if it leads to a causally equivalent past.

/pdf/reversible-communicating-systems-43j3i8ss9x.pdf

Reversible communicating systems

Intracellular processes rarely work in isolation but continually interact with the rest of the cell. In microbes, for example, we now know that gene expression across the whole genome typically changes with growth rate. The mechanisms driving such global regulation, however, are not well understood. Here we consider three trade-offs that, because of limitations in levels of cellular energy, free ribosomes, and proteins, are faced by all living cells and we construct a mechanistic model that comprises these trade-offs. Our model couples gene expression with growth rate and growth rate with a growing population of cells. We show that the model recovers Monod’s law for the growth of microbes and two other empirical relationships connecting growth rate to the mass fraction of ribosomes. Further, we can explain growth-related effects in dosage compensation by paralogs and predict host–circuit interactions in synthetic biology. Simulating competitions between strains, we find that the regulation of metabolic pathways may have evolved not to match expression of enzymes to levels of extracellular substrates in changing environments but rather to balance a trade-off between exploiting one type of nutrient over another. Although coarse-grained, the trade-offs that the model embodies are fundamental, and, as such, our modeling framework has potentially wide application, including in both biotechnology and medicine.

https://www.pnas.org/content/pnas/112/9/E1038.full.pdf

Vincent Danos

Papers

Disjunctive Tautologies as Synchronisation Schemes

Formal molecular biology

The structure of multiplicatives

Reversible communicating systems

Mechanistic links between cellular trade-offs, gene expression, and growth.