A Minimum-Labeling Approach for Reconstructing Protein Networks across Multiple Conditions

The sheer amounts of biological data that are generated in recent years have driven the development of network analysis tools to facilitate the interpretation and representation of these data. A fundamental challenge in this domain is the reconstruction of a protein-protein subnetwork that underlies a process of interest from a genome-wide screen of associated genes. Despite intense work in this area, current algorithmic approaches are largely limited to analyzing a single screen and are, thus, unable to account for information on condition-specific genes, or reveal the dynamics (over time or condition) of the process in question. Here we propose a novel formulation for network reconstruction from multiple-condition data and devise an efficient integer program solution for it. We apply our algorithm to analyze the response to influenza infection in humans over time as well as to analyze a pair of ER export related screens in humans. By comparing to an extant, single-condition tool we demonstrate the power of our new approach in integrating data from multiple conditions in a compact and coherent manner, capturing the dynamics of the underlying processes.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

A Cooperative Sequential Adsorption Model in Two Dimensions with Experimental Applications for Ionic Self-Assembly of Nanoparticles

Self-assembly of nanoparticles is an important tool in nanotechnology, with numerous applications including thin films, electronics, and drug delivery. We study the deposition of ionic nanoparticles on a glass substrate both experimentally and theoretically. Our theoretical model consists of a stochastic cooperative adsorption and evaporation process on a two-dimensional lattice. By exploring the relationship between the initial concentration of nanoparticles in the colloidal solution and the density of particles deposited on the substrate, we relate the deposition rate of our theoretical model to the concentration.Comment: 7 pages, 6 figures; v2: major revisio

Inactivation of a CRF-dependent amygdalofugal pathway reverses addiction-like behaviors in alcohol-dependent rats.

The activation of a neuronal ensemble in the central nucleus of the amygdala (CeA) during alcohol withdrawal has been hypothesized to induce high levels of alcohol drinking in dependent rats. In the present study we describe that the CeA neuronal ensemble that is activated by withdrawal from chronic alcohol exposure contains ~80% corticotropin-releasing factor (CRF) neurons and that the optogenetic inactivation of these CeA CRF+ neurons prevents recruitment of the neuronal ensemble, decreases the escalation of alcohol drinking, and decreases the intensity of somatic signs of withdrawal. Optogenetic dissection of the downstream neuronal pathways demonstrates that the reversal of addiction-like behaviors is observed after the inhibition of CeA CRF projections to the bed nucleus of the stria terminalis (BNST) and that inhibition of the CRFCeA-BNST pathway is mediated by inhibition of the CRF-CRF1 system and inhibition of BNST cell firing. These results suggest that the CRFCeA-BNST pathway could be targeted for the treatment of excessive drinking in alcohol use disorder

Extremely red objects in the UKIDSS Ultra Deep Survey Early Data Release

We construct a sample of extremely red objects (EROs) within the UKIDSS Ultra Deep Survey by combining the Early Data Release with optical data from the Subaru/XMM–Newton Deep Field. We find a total of 3715 objects over 2013 arcmin2 with R−K > 5.3 and K≤ 20.3, which is a higher surface density than found by previous studies. This is partly due to our ability to use a small aperture in which to measure colours, but is also the result of a genuine overdensity of objects compared to other fields. We separate our sample into passively evolving and dusty star-forming galaxies using their RJK colours and investigate their radio properties using a deep radio map. The dusty population has a higher fraction of individually detected radio sources and a higher mean radio flux density among the undetected objects, but the passive population has a higher fraction of bright radio sources, suggesting that active galactic nuclei are more prevalent among the passive ERO population

Dry anaerobic digestion of organic waste: A review of operational parameters and their impact on process performance.

open access articleDry digestion is a suitable technology for treating organic wastes with varying composition such as the organic fraction of municipal solids waste. Yet, there is a need for further research to overcome some of the disadvantages associated with the high total solids content of the process. Optimisation of inoculum to substrate ratio, feedstock composition and size, liquid recirculation, bed compaction and use of bulking agents are some of the parameters that need further investigation in batch dry anaerobic digestion, to limit localised inhibition effects and avoid process instability. In addition, further attention on the relation between feedstock composition, organic loading rate and mixing regimes is required for continuous dry anaerobic digestion systems. This paper highlights all the areas where knowledge is scarce and value can be added to increase dry anaerobic digestion performance and expansion

Comparison of modelled and monitored deposition fluxes of sulphur and nitrogen to ICP-forest sites in Europe

The EMEP MSC-W Eulerian chemical transport model, and its predictions of deposition of acidifying and eutrophying pollutants over Europe, play a key role in the development of emission control strategies for Europe. It is important that this model is tested against observational data. Here we compare the results of the EMEP model with measured data from 160 sites of the European Union/ICP Forest (Level II) monitoring network, for the years 1997 and 2000. This comparison comprises: (a) Precipitation amount, (b) Total deposition of SO42- to coniferous and deciduous forests, (c) Wet deposition of SO42-, NO3- and NH4+ in open field sites, and (d) Concentrations of SO42-, NO3- and NH4+ in precipitation. Concerning precipitation, the EMEP model and ICP network showed very similar overall levels (within 4% for 1997 and 11% for 2000). The correlation was, however, poor (r2=0.15-0.23). This can be attributed largely to the influence of a few outliers, combined with a small range of rainfall amounts for most points. Correlations between modelled and observed deposition values in this study were rather high (r2 values between 0.4-0.8 for most components and years), with mean values across all sites being within 30%. The EMEP model tends to give somewhat lower values for SO42-, NO3- and NH4+ wet deposition to ICP, but differences in mean values were within 20% in 1997 and 30% in 2000. Modelled and observed concentrations of SO 42-, NO3- and NH4+ in precipitation are very similar on average (differences of 0-14%), with good correlation between modelled and observed data (r 2=0.50-0.78). Differences between the EMEP model and ICP measurements are thought to arise from a mixture of problems with both the observations and model. However, the overall conclusion is that the EMEP model performs rather well in reproducing patterns of S and N deposition to European forests

Carbonaceous aerosols in Norwegian urban areas

Little is known regarding levels and source strength of carbonaceous aerosols in Scandinavia. In the present study, ambient aerosol (PM<sub>10</sub> and PM<sub>2.5</sub>) concentrations of elemental carbon (EC), organic carbon (OC), water-insoluble organic carbon (WINSOC), and water-soluble organic carbon (WSOC) are reported for a curbside site, an urban background site, and a suburban site in Norway in order to investigate their spatial and seasonal variations. Aerosol filter samples were collected using tandem filter sampling to correct for the positive sampling artefact introduced by volatile and semivolatile OC. Analyses were performed using the thermal optical transmission (TOT) instrument from Sunset Lab Inc., which corrects for charring during analysis. Finally, we estimated the relative contribution of OC from wood burning based on the samples content of levoglucosan. <br><br> Levels of EC varied by more than one order of magnitude between sites, likely due to the higher impact of vehicular traffic at the curbside and the urban background sites. In winter, the level of particulate organic carbon (OC<sub><i>p</i></sub>) at the suburban site was equal to (for PM<sub>10</sub>) or even higher (for PM<sub>2.5</sub>) than the levels observed at the curbside and the urban background sites. This finding was attributed to the impact of residential wood burning at the suburban site in winter, which was confirmed by a high mean concentration of levoglucosan (407 ng m<sup>−3</sup>). This finding indicates that exposure to primary combustion derived OC<sub><i>p</i></sub> could be equally high in residential areas as in a city center. It is demonstrated that OC<sub><i>p</i></sub> from wood burning (OC<sub>wood</sub>) accounted for almost all OC<sub><i>p</i></sub> at the suburban site in winter, allowing a new estimate of the ratio TC<sub><i>p</i></sub>/levoglucosan for both PM<sub>10</sub> and PM<sub>2.5</sub>. Particulate carbonaceous material (PCM=Organic matter+Elemental matter) accounted for 46–83% of PM<sub>10</sub> at the sites studied, thus being the major fraction