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

Statistical physics has proven to be a fruitful framework to describe phenomena outside the realm of traditional physics. Recent years have witnessed an attempt by physicists to study collective phenomena emerging from the interactions of individuals as elementary units in social structures. A wide list of topics are reviewed ranging from opinion and cultural and language dynamics to crowd behavior, hierarchy formation, human dynamics, and social spreading. The connections between these problems and other, more traditional, topics of statistical physics are highlighted. Comparison of model results with empirical data from social systems are also emphasized.

Statistical physics of social dynamics

The structure and dynamics of multilayer networks

Many ``real-world'' networks are clearly defined while most ``social'' networks are to some extent subjective. Indeed, the accuracy of empirically-determined social networks is a question of some concern because individuals may have distinct perceptions of what constitutes a social link. One unambiguous type of connection is sexual contact. Here we analyze data on the sexual behavior of a random sample of individuals, and find that the cumulative distributions of the number of sexual partners during the twelve months prior to the survey decays as a power law with similar exponents $\alpha \approx 2.4$ for females and males. The scale-free nature of the web of human sexual contacts suggests that strategic interventions aimed at preventing the spread of sexually-transmitted diseases may be the most efficient approach.

The Web of Human Sexual Contacts

In the run-up to the recent financial crisis, an increasingly elaborate set of financial instruments emerged, intended to optimize returns to individual institutions with seemingly minimal risk. Essentially no attention was given to their possible effects on the stability of the system as a whole. Drawing analogies with the dynamics of ecological food webs and with networks within which infectious diseases spread, we explore the interplay between complexity and stability in deliberately simplified models of financial networks. We suggest some policy lessons that can be drawn from such models, with the explicit aim of minimizing systemic risk.

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Systemic risk in banking ecosystems

Our current view on how protein complexes assemble and disassemble at promoter sites is based on experimental data. For instance this data is provided by biochemical methods (e.g. ChIP-on-chip assays) or GFP-based assays. These two approaches suggest very different characteristics for protein recruitment processes that regulate and initiate gene transcription. Biochemical methods suggest a strictly ordered and consecutive protein recruitment while GFP-based assays draw a picture much closer to chaotic or stochastic recruitment. To understand the reason for these conflicting results, we design a generalized recruitment model (GRM) that allows to simulate all possible scenarios between strictly sequential recruitment and completely probabilistic recruitment. With this model we show that probabilistic, transient binding events that are visible in GFP experiments can not be detected by ChIP experiments. We demonstrate that sequential recruitment processes and probabilistic recruitment processes that contain “shortcuts” exhibit periodic dynamics and are hard to distinguish with standard ChIP measurements. Therefore we propose a simple experimental method that can be used to discriminate sequential from probabilistic recruitment processes. We discuss the limitations of this method.

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Protein Complex Formation: Computational Clarification of the Sequential versus Probabilistic Recruitment Puzzle

Recent attempts to understand the origin of social fragmentation are based on spin models which include terms accounting for two social phenomena: homophily -- the tendency for people with similar opinions to establish positive relations -- and social balance -- the tendency for people to establish balanced triadic relations. Spins represent attribute vectors that encode multiple (binary) opinions of individuals and social interactions between individuals can be positive or negative. Recent work suggests that large systems of N >> 1 individuals never reach a balanced state (where unbalanced triads with one or three hostile links remain), provided the number of attributes for each agent is less than O(N^2) [Phys. Rev. Lett. 125, 078302]. Here we show that this statement is overly restrictive. Within a Hamiltonian framework that minimizes individuals' social stress, we demonstrate that stationary, balanced, but fragmented states can be reached for any number of attributes, if, in addition to homophily, individuals take into account a significant fraction, q, of their triadic relations. Above a critical value q_c, balanced states result. This result also holds for sparse realistic social networks. Finally, in the limit of small q, our result agrees with that of [Phys. Rev. Lett. 125, 078302].

Balanced and fragmented phases in societies with homophily and social balance

The present invention relates to a composition comprising a plurality of polynucleotide probes. The composition can be used as hybridisable array elements in a microarray. The present invention also relates to a method for selecting polynucleotide probes for the composition. The present invention further relates to a composition comprising a plurality of polynucleotide probes for use in research and diagnostic applications, in particular for the diagnosis of diabetic microangiopathy. The present invention also relates to novel bio-markers and sets thereof that are useful in the diagnosis and treatment of diabetic microangiopathy.

Compositions for the detection of gene expression in diabetic microangiopathy

Traditionally evolution is seen as a process where from a pool of possible variations of a population (e.g. biological species or industrial goods) a few variations get selected which survive and proliferate, whereas the others vanish. Survival probability is typically associated with the 'fitness' of a particular variation. In this paper we argue that the notion of fitness is an a posteriori concept, in the sense that one can assign higher fitness to species that survive but one can generally not derive or even measure fitness - or fitness landscapes - per se. For this reason we think that in a 'physical' theory of evolution such notions should be avoided. In this spirit, here we propose a random matrix model of evolution where selection mechanisms are encoded in the interaction matrices of species. We are able to recover some key facts of evolution dynamics, such as punctuated equilibrium, i.e. the existence of intrinsic large extinctions events, and, at the same time, periods of dramatic diversification, as known e.g. from fossil records. Further, we comment on two fundamental technical problems of a 'physics of evolution', the non-closedness of its phase space and the problem of co-evolving boundary conditions, apparent in all systems subject to evolution.

Physics of Evolution: Selection without Fitness

Systems evolving according to the standard concept of biological or technological evolution are often described by catalytic evolution equations. We study the structure of these equations and find a deep relationship to classical thermodynamics. In particular we can demonstrate the existence of several distinct phases of evolutionary dynamics: a phase of fast growing diversity, one of stationary, finite diversity, and one of rapidly decaying diversity. While the first two phases have been subject to previous work, here we focus on the destructive aspects - in particular the phase diagram - of evolutionary dynamics. We further propose a dynamical model of diversity which captures spontaneous creation and destruction processes fully respecting the phase diagrams of evolutionary systems. The emergent timeseries show a Zipf law in the diversity dynamics, which is e.g. observable in actual economical data, e.g. in firm bankruptcy data. We believe the present model is a way to cast the famous qualitative picture of Schumpeterian economic evolution, into a quantifiable and testable framework.

Stefan Thurner

Papers

Protein Complex Formation: Computational Clarification of the Sequential versus Probabilistic Recruitment Puzzle

Balanced and fragmented phases in societies with homophily and social balance

Compositions for the detection of gene expression in diabetic microangiopathy

Physics of Evolution: Selection without Fitness

Towards a physics of evolution: Existence of gales of creative deconstruction in evolving technological networks