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

Neoclassical theory versus new economic geography. Competing explanations of cross-regional variation in economic development

This paper uses data for 255 NUTS-2 European regions over the period 1995-2003 to test the relative explanatory performance of two important rival theories seeking to explain variations in the level of economic development across regions, namely the neoclassical model originating from the work of Solow (1956) and the so-called Wage Equation, which is one of a set of simultaneous equations consistent with the short-run equilibrium of new economic geography (NEG) theory, as described by Fujita, Krugman and Venables (1999). The rivals are non-nested, so that testing is accomplished both by fitting the reduced form models individually and by simply combining the two rivals to create a composite model in an attempt to identify the dominant theory. We use different estimators for the resulting panel data model to account variously for interregional heterogeneity, endogeneity, and temporal and spatial dependence, including maximum likelihood with and without fixed effects, two stage least squares and feasible generalised spatial two stage least squares plus GMM; also most of these models embody a spatial autoregressive error process. These show that the estimated NEG model parameters correspond to theoretical expectation, whereas the parameter estimates derived from the neoclassical model reduced form are sometimes insignificant or take on counterintuitive signs. This casts doubt on the appropriateness of neoclassical theory as a basis for explaining cross-regional variation in economic development in Europe, whereas NEG theory seems to hold in the face of competition from its rival. (authors' abstract

Protein folding causes an arrest of preprotein translocation into mitochondria in vivo

With vital yeast cells, a hybrid protein consisting of the amino- terminal third of the precursor to cytochrome b2 and of the entire dihydrofolate reductase was arrested on the import pathway into mitochondria. Accumulation of the protein in the mitochondrial membranes was achieved by inducing a stable tertiary structure of the dihydrofolate reductase domain. Thereby, three salient features of mitochondrial protein uptake in vivo were demonstrated: its posttranslational character; the requirement for unfolding of precursors; and import through translocation contact sites. The permanent occupation of translocation sites by the fusion protein inhibited the import of other precursors; it did, however, not lead to leakage of mitochondrial ions, implying the existence of a channel that is sealed around the membrane spanning polypeptide segment

Self-Averaging Expectation Propagation

We investigate the problem of approximate Bayesian inference for a general class of observation models by means of the expectation propagation (EP) framework for large systems under some statistical assumptions. Our approach tries to overcome the numerical bottleneck of EP caused by the inversion of large matrices. Assuming that the measurement matrices are realizations of specific types of ensembles we use the concept of freeness from random matrix theory to show that the EP cavity variances exhibit an asymptotic self-averaging property. They can be pre-computed using specific generating functions, i.e. the R- and/or S-transforms in free probability, which do not require matrix inversions. Our approach extends the framework of (generalized) approximate message passing -- assumes zero-mean iid entries of the measurement matrix -- to a general class of random matrix ensembles. The generalization is via a simple formulation of the R- and/or S-transforms of the limiting eigenvalue distribution of the Gramian of the measurement matrix. We demonstrate the performance of our approach on a signal recovery problem of nonlinear compressed sensing and compare it with that of EP.Comment: 12 page

Energy-related air pollution in Malta : black carbon measurements by use of a mobile aethalometer

Black Carbon (BC) is the component of fine particulate matter that is associated with energy use. It affects human health and is a significant contributor to climate change. Black Carbon (BC) concentrations in the atmosphere have been assessed by gathering 130 air samples in Malta, recording more than 230 hours of real-time data. A mobile micro-Aethalometer (microAeth AE51) was used for the measurements. Samples were taken under various conditions, from clean rural areas to the most polluted roads. Results showed that the highest levels of exposure to BC pollution are experienced in enclosed areas such as parking lots and inside motor vehicles while driving. The results also showed that the highest levels of BC concentration in the Maltese islands occur during the morning and the afternoon. These two periods coincide with the peaks in road traffic. All results indicated that the main source of BC in the Maltese islands comes from land transportation, and mostly from diesel engines.Bajada New Energy, General Membrane, EcoGroup, Econetique, Energy Investment, JMV Vibro Blocks, Solar Engineering, Solar Solutionspeer-reviewe

Expression of PHA polymerase genes of Pseudomonas putida in Escherichia coli and its effect on PHA formation

Poly-3-hydroxyalkanoates (PHAs) are synthesized by many bacteria as intracellular storage material. The final step in PHA biosynthesis is catalyzed by two PHA polymerases (phaC) in Pseudomonas putida. The expression of these two phaC genes (phaC1 and phaC2)was studied in Escherichia coli, either under control of the native promoter or under control of an external promoter. It was found that the two phaC genes are not expressed in E. coli without an external promoter. During heterologous expression of phaC from Plac on a high copy number plasmid, a rapid reduction of the number of colony forming units was observed, especially for phaC2. It appears that the plasmid instability was partially caused by high-level production of PHA polymerase. Subsequently, tightly regulated phaC2 expression systems on a low copy number vector were applied in E. coli. This resulted in PHA yields of over 20 of total cell dry weight, which was 2 fold higher than that obtained from the system where phaC2 is present on a high copy number vector. In addition, the PHA monomer composition differed when different gene expression systems or different phaC genes were applie

Overexpression and characterization of medium-chain-length polyhydroxyalkanoate granule bound polymerases from Pseudomonas putida GPo1

<p>Abstract</p> <p>Background</p> <p>Polyhydroxyalkanoates (PHA) are synthesized by many bacteria in the cytoplasm as storage compounds for energy and carbon. The key enzymes for PHA biosynthesis are PHA polymerases, which catalyze the covalent linkage of 3-hydroxyacyl coenzymeA thioesters by transesterification with concomitant release of CoA. <it>Pseudomonas putida </it>GPo1 and many other <it>Pseudomonas </it>species contain two different class II polymerases, encoded by <it>phaC1 </it>and <it>phaC2</it>. Although numerous studies have been carried out on PHA polymerases and they are well characterized at the molecular level, the biochemical properties of the class II polymerases have not been studied in detail. Previously we and other groups purified the polymerases, however, the activities of the purified enzymes were several magnitude lower than the granule-bound enzymes. It is problematic to study the intrinsic properties of these enzymes with such low activities, although they are pure.</p> <p>Results</p> <p>PHA polymerase 1 (PhaC1) and PHA polymerase 2 (PhaC2) from <it>P. putida </it>GPo1 were overexpressed in the PHA-negative host <it>P. putida </it>GPp104 and purified from isolated PHA granules. Only minor activity (two to three orders of magnitude lower than that of the granule bound proteins) could be recovered when the enzymes were purified to homogeneity. Therefore, kinetic properties and substrate ranges were determined for the granule bound polymerases. The polymerases differed significantly with respect to their association with PHA granules, enzyme kinetics and substrate specificity. PhaC2 appeared to bind PHA granules more tightly than PhaC1. When <it>R</it>-3-hydroxyoctanoic acid was used as substrate, the granule-bound PhaC1 exhibited a <it>Km </it>of 125 (± 35) μM and a <it>V</it>max of 40.8 (± 6.2) U/mg PhaC1, while a <it>Km </it>of 37 (± 10) μM and a <it>V</it>max of 2.7 (± 0.7) U/mg PhaC2 could be derived for the granule-bound PhaC2. Granule-bound PhaC1 showed a strong preference for medium chain length (mcl-) 3-hydroxyacly-CoAs, with highest affinity towards 3-hydroxydecanoyl-CoA (40 U/mg PhaC1). Granule-bound PhaC2 demonstrated a far broader specificity ranging from short chain length up to long chain length substrates. Activity increased with increasing chain length with a maximum activity for 3-hydroxyacyl-CoAs containing 12 or more C-atoms.</p> <p>Conclusion</p> <p>The kinetic properties and substrate ranges were determined for both granule bound polymerases. Evidence was provided for the first time that two PHA polymerases exhibited significant differences in granule release and in vitro activity profiles, suggesting that there are substantial functional differences between granule bound PhaC1 and PhaC2.</p

Influence of growth stage on activities of polyhydroxyalkanoate (PHA) polymerase and PHA depolymerase in Pseudomonas putida U

<p>Abstract</p> <p>Background</p> <p>Medium chain length (mcl-) polyhydroxyalkanoates (PHA) are synthesized by many bacteria in the cytoplasm as storage compounds for energy and carbon. The key enzymes for PHA metabolism are PHA polymerase (PhaC) and depolymerase (PhaZ). Little is known of how mcl-PHA accumulation and degradation are controlled. It has been suggested that overall PHA metabolism is regulated by the β-oxidation pathway of which the flux is governed by intracellular ratios of [NADH]/[NAD] and [acetyl-CoA]/[CoA]. Another level of control could relate to modulation of the activities of PhaC and PhaZ. In order to investigate the latter, assays for <it>in vitro </it>activity measurements of PhaC and PhaZ in crude cell extracts are necessary.</p> <p>Results</p> <p>Two <it>in vitro </it>assays were developed which allow the measurement of PhaC and PhaZ activities in crude cell extracts of <it>Pseudomonas putida </it>U. Using the assays, it was demonstrated that the activity of PhaC decreased 5-fold upon exponential growth on nitrogen limited medium and octanoate. In contrast, the activity of PhaZ increased only 1.5-fold during growth. One reason for the changes in the enzymatic activity of PhaC and PhaZ could relate to a change in interaction with the phasin surface proteins on the PHA granule. SDS-PAGE analysis of isolated PHA granules demonstrated that during growth, the ratio of [phasins]/[PHA] decreased. In addition, it was found that after eliminating phasins (PhaF and PhaI) from the granules PhaC activity decreased further.</p> <p>Conclusion</p> <p>Using the assays developed in this study, we followed the enzymatic activities of PhaC and PhaZ during growth and correlated them to the amount of phasins on the PHA granules. It was found that in <it>P. putida </it>PhaC and PhaZ are concomitantly active, resulting in parallel synthesis and degradation of PHA. Moreover PhaC activity was found to be decreased, whereas PhaZ activity increased during growth. Availability of phasins on PHA granules affected the activity of PhaC.</p

Poly(3-hydroxyalkanoate) polymerase synthesis and in vitro activity in recombinant Escherichia coli and Pseudomonas putida

We tested the synthesis and in vitro activity of the poly(3-hydroxyalkanoate) (PHA) polymerase 1 from Pseudomonas putida GPo1 in both P. putida GPp104 and Escherichia coli JMU193. The polymerase encoding gene phaC1 was expressed using the inducible PalkB promoter. It was found that the production of polymerase could be modulated over a wide range of protein levels by varying inducer concentrations. The optimal inducer dicyclopropylketone concentrations for PHA production were at 0.03% (v/v) for P. putida and 0.005% (v/v) for E. coli. Under these concentrations the maximal polymerase level synthesized in the E. coli host (6% of total protein) was about three- to fourfold less than that in P. putida (20%), whereas the maximal level of PHA synthesized in the E. coli host (8% of total cell dry weight) was about fourfold less than that in P. putida (30%). In P. putida, the highest specific activity of polymerase was found in the mid-exponential growth phase with a maximum of 40U/g polymerase, whereas in E. coli, the maximal specific polymerase activity was found in the early stationary growth phase (2U/g polymerase). Our results suggest that optimal functioning of the PHA polymerase requires factors or a molecular environment that is available in P. putida but not in E. col

One-step synthesis of N-succinimidyl-4-[¹⁸F]Fluorobenzoate ([¹⁸F]SFB)

Herein, we present a one-step labeling procedure of N-succinimidyl-4-[18F]-fluorobenzoate ([18F]SFB) starting from spirocyclic iodonium ylide precursors. Precursor syntheses succeeded via a simple one-pot, two-step synthesis sequence, in yields of approximately 25%. Subsequent 18F-nucleophilic aromatic labeling was performed, and radiochemical incorporations (RCCs) from 5&ndash;35% were observed. Purification could be carried out using HPLC and subsequent solid phase extraction. Radiochemical purity (RCP) of &gt;95% was determined. The total synthesis time, including purification and formulation, was no longer than 60 min. In comparison to the established 3-step synthesis route of [18F]SFB, this one-step approach avoids formation of volatile radioactive side-products and simplifies automatization