S-AMP for Non-linear Observation Models

Recently we extended Approximate message passing (AMP) algorithm to be able to handle general invariant matrix ensembles. In this contribution we extend our S-AMP approach to non-linear observation models. We obtain generalized AMP (GAMP) algorithm as the special case when the measurement matrix has zero-mean iid Gaussian entries. Our derivation is based upon 1) deriving expectation propagation (EP) like algorithms from the stationary-points equations of the Gibbs free energy under first- and second-moment constraints and 2) applying additive free convolution in free probability theory to get low-complexity updates for the second moment quantities.Comment: 6 page

S-AMP: Approximate Message Passing for General Matrix Ensembles

In this work we propose a novel iterative estimation algorithm for linear observation systems called S-AMP whose fixed points are the stationary points of the exact Gibbs free energy under a set of (first- and second-) moment consistency constraints in the large system limit. S-AMP extends the approximate message-passing (AMP) algorithm to general matrix ensembles. The generalization is based on the S-transform (in free probability) of the spectrum of the measurement matrix. Furthermore, we show that the optimality of S-AMP follows directly from its design rather than from solving a separate optimization problem as done for AMP.Comment: 5 pages, 1 figur

Dynamical Functional Theory for Compressed Sensing

We introduce a theoretical approach for designing generalizations of the approximate message passing (AMP) algorithm for compressed sensing which are valid for large observation matrices that are drawn from an invariant random matrix ensemble. By design, the fixed points of the algorithm obey the Thouless-Anderson-Palmer (TAP) equations corresponding to the ensemble. Using a dynamical functional approach we are able to derive an effective stochastic process for the marginal statistics of a single component of the dynamics. This allows us to design memory terms in the algorithm in such a way that the resulting fields become Gaussian random variables allowing for an explicit analysis. The asymptotic statistics of these fields are consistent with the replica ansatz of the compressed sensing problem.Comment: 5 pages, accepted for ISIT 201

In silico prediction of mutant HIV-1 proteases cleaving a target sequence

HIV-1 protease represents an appealing system for directed enzyme re-design, since it has various different endogenous targets, a relatively simple structure and it is well studied. Recently Chaudhury and Gray (Structure (2009) 17: 1636 -- 1648) published a computational algorithm to discern the specificity determining residues of HIV-1 protease. In this paper we present two computational tools aimed at re-designing HIV-1 protease, derived from the algorithm of Chaudhuri and Gray. First, we present an energy-only based methodology to discriminate cleavable and non cleavable peptides for HIV-1 proteases, both wild type and mutant. Secondly, we show an algorithm we developed to predict mutant HIV-1 proteases capable of cleaving a new target substrate peptide, different from the natural targets of HIV-1 protease. The obtained in silico mutant enzymes were analyzed in terms of cleavability and specificity towards the target peptide using the energy-only methodology. We found two mutant proteases as best candidates for specificity and cleavability towards the target sequence

Multipole Expansion for Relativistic Coulomb Excitation

We derive a general expression for the multipole expansion of the electro-magnetic interaction in relativistic heavy-ion collisions, which can be employed in higher-order dynamical calculations of Coulomb excitation. The interaction has diagonal as well as off-diagonal multipole components, associated with the intrinsic and relative coordinates of projectile and target. A simple truncation in the off-diagonal components gives excellent results in first-order perturbation theory for distant collisions and for beam energies up to 200 MeV/nucleon.Comment: 3 figures, Accepted for publication in Phys. Rev.

Redox characteristics of the eukaryotic cytosol

AbstractThe eukaryotic cytoplasm has long been regarded as a cellular compartment in which the reduced state of protein cysteines is largely favored. Under normal conditions, the cytosolic low-molecular weight redox buffer, comprising primarily of glutathione, is highly reducing and reactive oxygen species (ROS) and glutathionylated proteins are maintained at very low levels. In the present review, recent progress in the understanding of the cytosolic thiol–disulfide redox metabolism and novel analytical approaches to studying cytosolic redox properties are discussed. We will focus on the yeast model organism, Saccharomyces cerevisiae, where the combination of genetic and biochemical approaches has brought us furthest in understanding the mechanisms underlying cellular redox regulation. It has been shown in yeast that, in addition to the enzyme glutathione reductase, other mechanisms may exist for restricting the cytosolic glutathione redox potential to a relatively narrow interval. Several mutations in genes involved in cellular redox regulation cause ROS accumulation but only moderate decreases in the cytosolic glutathione reducing power. The redox regulation in the cytosol depends not only on multiple cytosolic factors but also on the redox homeostasis of other compartments like the secretory pathway and the mitochondria. Possibly, the cytosol is not just a reducing compartment surrounding organelles with high oxidative activity but also a milieu for regulation of the redox status of more than one compartment. Although much has been learned about redox homeostasis and oxidative stress response several important aspects of the redox regulation in the yeast cytosol are still unexplained

Toward a Theory of Effective Supranational Adjudication

Supranational adjudication in Europe is a remarkable and surprising success. Europe\u27s two supranational courts -- the European Court of Justice (ECJ) and the European Court of Human Rights (ECHR) -- issue dozens of judgments each year with which defending national governments habitually comply in essentially the same manner as they would with domestic court rulings. These experiences stand in striking contrast to those of many international tribunals past and present. Can the European experience of supranational adjudication be transplanted beyond Europe? Professors Helfer and Slaughter argue that the effectiveness of the ECJ and the ECHR is linked to their power to hear claims brought by private parties directly against national governments or against other private parties. Such supranational jurisdiction has allowed the European courts to penetrate the surface of the state, to forge direct relationships not only with individual citizens but also with distinct government institutions such as national courts. Over time, this penetration and the deepening relationships between supranational jurists and domestic legal actors have led to the evolution of a community of law, a web of nominally apolitical relations among subnational and supranational legal actors. The simple provision of supranational jurisdiction, however, is not a guarantee of effective adjudication. Drawing on the observations of scholars, practitioners, and judges, Professors Helfer and Slaughter develop a checklist of factors that enhance the effectiveness of supranational adjudication. They distinguish among those factors that are within the control of member states; those that are within the control of the judges themselves; and those that may be beyond the control of either states or judges. Isolating the factors in this way provides both a rough metric for evaluating the effectiveness of other supranational tribunals and a potential set of prescriptions for judges on those tribunals seeking to enhance their institutions\u27 effectiveness. After developing the checklist, Professors Helfer and Slaughter use it to analyze the United Nations Human Rights Committee (UNHRC). Although the UNHRC was established expressly as a committee of experts rather than a court, analysis of its recent practice reveals that it is becoming increasingly court-like. Moreover, within the constraints imposed by severely limited resources, UNHRC members are independently following many of the checklist prescriptions for increased effectiveness. The next step is for the organization to enter into a sustained dialogue with its European counterparts, harmonizing its decisions with theirs in some areas while consciously preserving its own distinctive jurisprudence in others. Structured and regular interaction between these tribunals would add additional voices to an emerging transjudicial conversation, potentially laying the foundation for a global community of law

Equivalence of the long-wavelength approximation and the truncated Taylor expansion in relativistic Coulomb excitation

The long-wavelength approximation and the truncated Taylor expansion are frequently used in the theory of relativistic Coulomb excitation to obtain multipole expansions of the interaction. It is shown in this note that these two approximations are exactly equivalent.Comment: 5 page

Cross infection in a hospital ward and deposition of particles exhaled from a source patient

The cross infection in a hospital ward is studied. Deposition of particles exhaled from a source manikin is investigated in a full-scale hospital ward ventilated by downward directed ventilation. Deposition on vertical surfaces close to the source shows distribution of particles directed upwards in the room. Deposition at the four beds shows that particles smaller than 10 μm disperse evenly in the ward, indicating that particles smaller than this size are airborne. The influence of top and bottom extraction openings on dispersion of particles is investigated. Results show that vertical distribution in the room is not affected by the position of the return openings. Deposition of particles at the four beds gives some indication of a less wide spread of particles with the use of ceiling-mounted return openings, and thereby a better protection of patients compared with bottom return openings.postprint第五届居住建筑能源与环境国际研讨会 (EERB) & 第三届建筑环境与公共健康国际学术会议 (BEPH), 中国, 桂林, 2009年5月29至31日.The 5th International Workshop on Energy and Environment of Residential Buildings and the 3rd International Conference on Built Environment and Public Health (EERB-BEPH 2009), Guilin, China, 29-31 May 2009