Harmonic Analysis of Boolean Networks: Determinative Power and Perturbations

Consider a large Boolean network with a feed forward structure. Given a probability distribution on the inputs, can one find, possibly small, collections of input nodes that determine the states of most other nodes in the network? To answer this question, a notion that quantifies the determinative power of an input over the states of the nodes in the network is needed. We argue that the mutual information (MI) between a given subset of the inputs X = {X_1, ..., X_n} of some node i and its associated function f_i(X) quantifies the determinative power of this set of inputs over node i. We compare the determinative power of a set of inputs to the sensitivity to perturbations to these inputs, and find that, maybe surprisingly, an input that has large sensitivity to perturbations does not necessarily have large determinative power. However, for unate functions, which play an important role in genetic regulatory networks, we find a direct relation between MI and sensitivity to perturbations. As an application of our results, we analyze the large-scale regulatory network of Escherichia coli. We identify the most determinative nodes and show that a small subset of those reduces the overall uncertainty of the network state significantly. Furthermore, the network is found to be tolerant to perturbations of its inputs

PEPPo: Using a Polarized Electron Beam to Produce Polarized Positrons

An experiment demonstrating a new method for producing polarized positrons has been performed at the CEBAF accelerator at Jefferson Laboratory. The PEPPo (Polarized Electrons for Polarized Positrons) concept relies on the production of polarized e+/e− pairs originating from the bremsstrahlung radiation of a longitudinally polarized electron beam interacting within a 1.0 mm tungsten pair-production target. This paper describes preliminary results of measurements using an 8.2 MeV/c electron beam with polarization 84% to generate positrons in the range of 3.1 to 6.2 MeV/c with polarization as high as ∼80%

Heterogeneous freezing of droplets with immersed mineral dust particles – measurements and parameterization

During the measurement campaign FROST (FReezing Of duST), LACIS (Leipzig Aerosol Cloud Interaction Simulator) was used to investigate the immersion freezing behavior of size selected, coated and uncoated Arizona Test Dust (ATD) particles with a mobility diameter of 300 nm. Particles were coated with succinic acid (C4H6O4), sulfuric acid (H2SO4) and ammonium sulfate ((NH4)2SO4). Ice fractions at mixed-phase cloud temperatures ranging from 233.15 K to 239.15 K (±0.60 K) were determined for all types of particles. In this temperature range, pure ATD particles and those coated with C4H6O4 or small amounts of H2SO4 were found to be the most efficient ice nuclei (IN). ATD particles coated with (NH4)2SO4 were the most inefficient IN. Since the supercooled droplets were highly diluted before freezing occurred, a freezing point suppression due to the soluble material on the particles (and therefore in the droplets) cannot explain this observation. Therefore, it is reasonable to assume that the coatings lead to particle surface alterations which cause the differences in the IN abilities. Two different theoretical approaches based on the stochastic and the singular hypotheses were applied to clarify and parameterize the freezing behavior of the particles investigated. Both approaches describe the experimentally determined results, yielding parameters that can subsequently be used to compare our results to those from other studies. However, we cannot clarify at the current state which of the two approaches correctly describes the investigated immersion freezing process. But both approaches confirm the assumption that the coatings lead to particle surface modifications lowering the nucleation efficiency. The stochastic approach interprets the reduction in nucleation rate from coating as primarily due to an increase in the thermodynamic barrier for ice formation (i.e., changes in interfacial free energies). The singular approach interprets the reduction as resulting from a reduced surface density of active sites

Production of highly-polarized positrons using polarized electrons at MeV energies

The Polarized Electrons for Polarized Positrons experiment at the injector of the Continuous Electron Beam Accelerator Facility has demonstrated for the first time the efficient transfer of polarization from electrons to positrons produced by the polarized bremsstrahlung radiation induced by a polarized electron beam in a high-$Z$ target. Positron polarization up to 82\% have been measured for an initial electron beam momentum of 8.19~MeV/$c$, limited only by the electron beam polarization. This technique extends polarized positron capabilities from GeV to MeV electron beams, and opens access to polarized positron beam physics to a wide community.Comment: 5 pages, 4 figure

Atmospheric sulfur cycling in the southeastern Pacific – longitudinal distribution, vertical profile, and diel variability observed during VOCALS-REx

Dimethylsulfide (DMS) emitted from the ocean is a biogenic precursor gas for sulfur dioxide (SO<sub>2</sub>) and non-sea-salt sulfate aerosols (SO<sub>4</sub><sup>2−</sup>). During the VAMOS-Ocean-Cloud-Atmosphere-Land Study Regional Experiment (VOCALS-REx) in 2008, multiple instrumented platforms were deployed in the Southeastern Pacific (SEP) off the coast of Chile and Peru to study the linkage between aerosols and stratocumulus clouds. We present here observations from the NOAA Ship <i>Ronald H. Brown</i> and the NSF/NCAR C-130 aircraft along ~20° S from the coast (70° W) to a remote marine atmosphere (85° W). While SO<sub>4</sub><sup>2−</sup> and SO<sub>2</sub> concentrations were distinctly elevated above background levels in the coastal marine boundary layer (MBL) due to anthropogenic influence (~800 and 80 pptv, respectively), their concentrations rapidly decreased west of 78° W (~100 and 25 pptv). In the remote region, entrainment from the free troposphere (FT) increased MBL SO<sub>2</sub> burden at a rate of 0.05 ± 0.02 μmoles m<sup>−2</sup> day<sup>−1</sup> and diluted MBL SO<sub>4</sub><sup>2</sup> burden at a rate of 0.5 ± 0.3 μmoles m<sup>−2</sup> day<sup>−1</sup>, while the sea-to-air DMS flux (3.8 ± 0.4 μmoles m<sup>−2</sup> day<sup>−1</sup>) remained the predominant source of sulfur mass to the MBL. In-cloud oxidation was found to be the most important mechanism for SO<sub>2</sub> removal and in situ SO<sub>4</sub><sup>2−</sup> production. Surface SO<sub>4</sub><sup>2−</sup> concentration in the remote MBL displayed pronounced diel variability, increasing rapidly in the first few hours after sunset and decaying for the rest of the day. We theorize that the increase in SO<sub>4</sub><sup>2−</sup> was due to nighttime recoupling of the MBL that mixed down cloud-processed air, while decoupling and sporadic precipitation scavenging were responsible for the daytime decline in SO<sub>4</sub><sup>2−</sup>

Prospecting environmental mycobacteria: combined molecular approaches reveal unprecedented diversity

Background: Environmental mycobacteria (EM) include species commonly found in various terrestrial and aquatic environments, encompassing animal and human pathogens in addition to saprophytes. Approximately 150 EM species can be separated into fast and slow growers based on sequence and copy number differences of their 16S rRNA genes. Cultivation methods are not appropriate for diversity studies; few studies have investigated EM diversity in soil despite their importance as potential reservoirs of pathogens and their hypothesized role in masking or blocking M. bovis BCG vaccine. Methods: We report here the development, optimization and validation of molecular assays targeting the 16S rRNA gene to assess diversity and prevalence of fast and slow growing EM in representative soils from semi tropical and temperate areas. New primer sets were designed also to target uniquely slow growing mycobacteria and used with PCR-DGGE, tag-encoded Titanium amplicon pyrosequencing and quantitative PCR. Results: PCR-DGGE and pyrosequencing provided a consensus of EM diversity; for example, a high abundance of pyrosequencing reads and DGGE bands corresponded to M. moriokaense, M. colombiense and M. riyadhense. As expected pyrosequencing provided more comprehensive information; additional prevalent species included M. chlorophenolicum, M. neglectum, M. gordonae, M. aemonae. Prevalence of the total Mycobacterium genus in the soil samples ranged from 2.3×107 to 2.7×108 gene targets g−1; slow growers prevalence from 2.9×105 to 1.2×107 cells g−1. Conclusions: This combined molecular approach enabled an unprecedented qualitative and quantitative assessment of EM across soil samples. Good concordance was found between methods and the bioinformatics analysis was validated by random resampling. Sequences from most pathogenic groups associated with slow growth were identified in extenso in all soils tested with a specific assay, allowing to unmask them from the Mycobacterium whole genus, in which, as minority members, they would have remained undetected

Deep-Ocean dissolved organic matter reactivity along the Mediterranea Sea: does size matter?

Original research paperDespite of the major role ascribed to marine dissolved organic matter (DOM) in the global carbon cycle, the reactivity of this pool in the dark ocean is still poorly understood. Present hypotheses, posed within the size-reactivity continuum (SRC) and the microbial carbon pump (MCP) conceptual frameworks, need further empirical support. Here, we provide field evidence of the soundness of the SRC model. We sampled the high salinity core-of-flow of the Levantine Intermediate Water along its westward route through the entire Mediterranean Sea. At selected sites, DOM was size-fractionated in apparent high (aHMW) and low (aLMW) molecular weight fractions using an efficient ultrafiltration cell. A percentage decline of the aHMW DOM from 68–76% to 40–55% was observed from the Levantine Sea to the Strait of Gibraltar in parallel with increasing apparent oxygen utilization (AOU). DOM mineralization accounted for 30±3% of the AOU, being the aHMW fraction solely responsible for this consumption, verifying the SRC model in the field. We also demonstrate that, in parallel to this aHMW DOM consumption, fluorescent humic-like substances accumulate in both fractions and protein-like substances decline in the aLMW fraction, thus indicating that not only size matters and providing field support to the MCP modelHOTMIX (grant number CTM2011–30010-C02 01-MAR and 02-MAR) and the project FERMIO (MINECO, CTM2014-57334-JIN), both co-financed with FEDER funds; (reference BES-2012- 056175) from the Spanish Ministry of Economy, Industry and Competitivenes; the project MODMED from CSIC (PIE, 201730E020) and CSIC Program “Junta para la Ampliación de Estudios” co-financed by the ESF (reference JAE DOC 040)Versión del editor2,92

On the link between ocean biota emissions, aerosol, and maritime clouds: Airborne, ground, and satellite measurements off the coast of California

Surface, airborne, and satellite measurements over the eastern Pacific Ocean off the coast of California during the period between 2005 and 2007 are used to explore the relationship between ocean chlorophyll a, aerosol, and marine clouds. Periods of enhanced chlorophyll a and wind speed are coincident with increases in particulate diethylamine and methanesulfonate concentrations. The measurements indicate that amines are a source of secondary organic aerosol in the marine atmosphere. Subsaturated aerosol hygroscopic growth measurements indicate that the organic component during periods of high chlorophyll a and wind speed exhibit considerable water uptake ability. Increased average cloud condensation nucleus (CCN) activity during periods of increased chlorophyll a levels likely results from both size distribution and aerosol composition changes. The available data over the period of measurements indicate that the cloud microphysical response, as represented by either cloud droplet number concentration or cloud droplet effective radius, is likely influenced by a combination of atmospheric dynamics and aerosol perturbations during periods of high chlorophyll a concentrations

An Automated Phenotype-Driven Approach (GeneForce) for Refining Metabolic and Regulatory Models

Integrated constraint-based metabolic and regulatory models can accurately predict cellular growth phenotypes arising from genetic and environmental perturbations. Challenges in constructing such models involve the limited availability of information about transcription factor—gene target interactions and computational methods to quickly refine models based on additional datasets. In this study, we developed an algorithm, GeneForce, to identify incorrect regulatory rules and gene-protein-reaction associations in integrated metabolic and regulatory models. We applied the algorithm to refine integrated models of Escherichia coli and Salmonella typhimurium, and experimentally validated some of the algorithm's suggested refinements. The adjusted E. coli model showed improved accuracy (∼80.0%) for predicting growth phenotypes for 50,557 cases (knockout mutants tested for growth in different environmental conditions). In addition to identifying needed model corrections, the algorithm was used to identify native E. coli genes that, if over-expressed, would allow E. coli to grow in new environments. We envision that this approach will enable the rapid development and assessment of genome-scale metabolic and regulatory network models for less characterized organisms, as such models can be constructed from genome annotations and cis-regulatory network predictions