Geometry Constrained Weakly Supervised Object Localization

We propose a geometry constrained network, termed GC-Net, for weakly supervised object localization (WSOL). GC-Net consists of three modules: a detector, a generator and a classifier. The detector predicts the object location defined by a set of coefficients describing a geometric shape (i.e. ellipse or rectangle), which is geometrically constrained by the mask produced by the generator. The classifier takes the resulting masked images as input and performs two complementary classification tasks for the object and background. To make the mask more compact and more complete, we propose a novel multi-task loss function that takes into account area of the geometric shape, the categorical cross-entropy and the negative entropy. In contrast to previous approaches, GC-Net is trained end-to-end and predict object location without any post-processing (e.g. thresholding) that may require additional tuning. Extensive experiments on the CUB-200-2011 and ILSVRC2012 datasets show that GC-Net outperforms state-of-the-art methods by a large margin. Our source code is available at https://github.com/lwzeng/GC-Net.Comment: This paper (ID 5424) is accepted to ECCV 202

Selection for Replicases in Protocells

PMCID: PMC3649988This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Improved Unsteady RANS Models Applied to Jet Transverse to a Pipe Flow

An unsteady RANS model is developed in order to simulate the complex situations involving both free and bounded flows. This model tuned to catch coherent flow structures is developed both in the k-ε and k-l approaches. The full 3D geometry of a round jet exiting from a reservoir into a pipe has been computed. Periodic conditions are applied in order to compare with an experiments consisting of eight jets exiting in a cross pipe flow. Improvement has been obtained with this URANS turbulence model compared to RANS and good agreement compared with experiments has been obtained. Unsteady phenomena are reproduced by the model and provide more insight into the physical properties of the flow and of the transport of a passive scalar

Glyoxal yield from isoprene oxidation and relation to formaldehyde: chemical mechanism, constraints from SENEX aircraft observations, and interpretation of OMI satellite data

Glyoxal (CHOCHO) is produced in the atmosphere by the oxidation of volatile organic compounds (VOCs). Like formaldehyde (HCHO), another VOC oxidation product, it is measurable from space by solar backscatter. Isoprene emitted by vegetation is the dominant source of CHOCHO and HCHO in most of the world. We use aircraft observations of CHOCHO and HCHO from the SENEX campaign over the southeast US in summer 2013 to better understand the CHOCHO time-dependent yield from isoprene oxidation, its dependence on nitrogen oxides (NOx  ≡  NO + NO2), the behavior of the CHOCHO–HCHO relationship, the quality of OMI CHOCHO satellite observations, and the implications for using CHOCHO observations from space as constraints on isoprene emissions. We simulate the SENEX and OMI observations with the Goddard Earth Observing System chemical transport model (GEOS-Chem) featuring a new chemical mechanism for CHOCHO formation from isoprene. The mechanism includes prompt CHOCHO formation under low-NOx conditions following the isomerization of the isoprene peroxy radical (ISOPO2). The SENEX observations provide support for this prompt CHOCHO formation pathway, and are generally consistent with the GEOS-Chem mechanism. Boundary layer CHOCHO and HCHO are strongly correlated in the observations and the model, with some departure under low-NOx conditions due to prompt CHOCHO formation. SENEX vertical profiles indicate a free-tropospheric CHOCHO background that is absent from the model. The OMI CHOCHO data provide some support for this free-tropospheric background and show southeast US enhancements consistent with the isoprene source but a factor of 2 too low. Part of this OMI bias is due to excessive surface reflectivities assumed in the retrieval. The OMI CHOCHO and HCHO seasonal data over the southeast US are tightly correlated and provide redundant proxies of isoprene emissions. Higher temporal resolution in future geostationary satellite observations may enable detection of the prompt CHOCHO production under low-NOx conditions apparent in the SENEX data

Detection of regulator genes and eQTLs in gene networks

Genetic differences between individuals associated to quantitative phenotypic traits, including disease states, are usually found in non-coding genomic regions. These genetic variants are often also associated to differences in expression levels of nearby genes (they are "expression quantitative trait loci" or eQTLs for short) and presumably play a gene regulatory role, affecting the status of molecular networks of interacting genes, proteins and metabolites. Computational systems biology approaches to reconstruct causal gene networks from large-scale omics data have therefore become essential to understand the structure of networks controlled by eQTLs together with other regulatory genes, and to generate detailed hypotheses about the molecular mechanisms that lead from genotype to phenotype. Here we review the main analytical methods and softwares to identify eQTLs and their associated genes, to reconstruct co-expression networks and modules, to reconstruct causal Bayesian gene and module networks, and to validate predicted networks in silico.Comment: minor revision with typos corrected; review article; 24 pages, 2 figure

Physical activity to improve cognition in older adults: can physical activity programs enriched with cognitive challenges enhance the effects? A systematic review and meta-analysis

: EPHPP quality rating scores (DOCX 38 kb

Regulation of the vapBC-1 Toxin-Antitoxin Locus in Nontypeable Haemophilus influenzae

Nontypeable Haemophilus influenzae (NTHi) are human-adapted commensal bacteria that can cause a number of chronic mucosal infections, including otitis media and bronchitis. One way for these organisms to survive antibiotic therapy and cause recurrent disease is to stop replicating, as most antimicrobials target essential biosynthetic pathways. Toxin-antitoxin (TA) gene pairs have been shown to facilitate entry into a reversible bacteriostatic state. Characteristically, these operons encode a protein toxin and an antitoxin that associate following translation to form a nontoxic complex, which then binds to and regulates the cognate TA promoter. Under stressful conditions, the labile antitoxin is degraded and the complex disintegrates, freeing the stable toxin to facilitate growth arrest. How these events affected the regulation of the TA locus, as well as how the transcription of the operon was subsequently returned to its normal state upon resumption of growth, was not fully understood. Here we show that expression of the NTHi vapBC-1 TA locus is repressed by a complex of VapB-1 and VapC-1 under conditions favorable for growth, and activated by the global transactivator Factor for Inversion Stimulation (Fis) upon nutrient upshift from stationary phase. Further, we demonstrate for the first time that the VapC-1 toxin alone can bind to its cognate TA locus control region and that the presence of VapB-1 directs the binding of the VapBC-1 complex in the transcriptional regulation of vapBC-1

Smoking Cessation Quitlines in Europe: Matching Services to Callers' Characteristics

<p>Abstract</p> <p>Background</p> <p>Telephone quitlines offer a wide range of services to callers, including advice and counsel, and information on pharmacotherapy for smoking cessation. But, little is known about what specific quitline services are offered to smokers and whether these services are appropriately matched to characteristics of smokers. This study examines how quitline services are matched to callers' level of addiction, educational level, stage-of-change with quitting, and whether they are referred by a doctor or other health professional.</p> <p>Methods</p> <p>Between February 2005 and April 2006, 3,585 callers to seven European quitlines responded to our survey. During the course of and immediately after the call, quitline counsellors collected descriptive data on callers' characteristics and the services they used. We then conducted four logistic regression analyses to examine the relationship between quitline services and the four caller characteristics.</p> <p>Results</p> <p>Forty three percent of all callers received information on pharmacotherapy - most often nicotine patches and nicotine gum - from the counsellor. As we predicted, these callers were the heavy smokers. There was a direct correlation between the length of the conversations between the counsellor and the educational level of the smoker: the lower the education of the smoker, the shorter the call. However, we found no significant association between any other type of service and the educational level of caller. We also found a correlation between the smoker's stage of quitting and the type of advice a counsellor gives. Smokers in the action stage of quitting were more likely to receive advice (in two quitlines) or counselling (in two quitlines) than those in the preparation stage, who were less likely to be referred (in three quitlines). Very few of the total number of calls (10.7%) were from referrals by health professionals. Referred callers were more likely to receive counselling, but this was found only in four of seven quitlines.</p> <p>Conclusion</p> <p>Most of the services quitlines offer to smokers favour heavy smokers and those at a more advanced stage of cessation, but not based on their educational level. Thus, we recommend that European quitlines extend and tailor their services to include less-educated smokers.</p