Hierarchical community structure in networks

Modular and hierarchical structures are pervasive in real-world complex systems. A great deal of effort has gone into trying to detect and study these structures. Important theoretical advances in the detection of modular, or "community", structures have included identifying fundamental limits of detectability by formally defining community structure using probabilistic generative models. Detecting hierarchical community structure introduces additional challenges alongside those inherited from community detection. Here we present a theoretical study on hierarchical community structure in networks, which has thus far not received the same rigorous attention. We address the following questions: 1)~How should we define a valid hierarchy of communities? 2)~How should we determine if a hierarchical structure exists in a network? and 3)~how can we detect hierarchical structure efficiently? We approach these questions by introducing a definition of hierarchy based on the concept of stochastic externally equitable partitions and their relation to probabilistic models, such as the popular stochastic block model. We enumerate the challenges involved in detecting hierarchies and, by studying the spectral properties of hierarchical structure, present an efficient and principled method for detecting them.Comment: 22 pages, 12 figure

Genome-Wide Characterization of the Phosphate Starvation Response in Schizosaccharomyces pombe

Background: Inorganic phosphate is an essential nutrient required by organisms for growth. During phosphate starvation, Saccharomyces cerevisiae activates the phosphate signal transduction (PHO) pathway, leading to expression of the secreted acid phosphatase, PHO5. The fission yeast, Schizosaccharomyces pombe, regulates expression of the ScPHO5 homolog (pho1+) via a non-orthologous PHO pathway involving genetically identified positive (pho7+) and negative (csk1+) regulators. The genes induced by phosphate limitation and the molecular mechanism by which pho7+ and csk1+ function are unknown. Here we use a combination of molecular biology, expression microarrays, and chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) to characterize the role of pho7+ and csk1+ in the PHO response. Results: We define the set of genes that comprise the initial response to phosphate starvation in S. pombe. We identify a conserved PHO response that contains the ScPHO5 (pho1+), ScPHO84 (SPBC8E4.01c), and ScGIT1 (SPBC1271.09) orthologs. We identify members of the Pho7 regulon and characterize Pho7 binding in response to phosphate-limitation and Csk1 activity. We demonstrate that activation of pho1+ requires Pho7 binding to a UAS in the pho1+ promoter and that Csk1 repression does not regulate Pho7 enrichment. Further, we find that Pho7-dependent activation is not limited to phosphate-starvation, as additional environmental stress response pathways require pho7+ for maximal induction. Conclusions: We provide a global analysis of the transcriptional response to phosphate limitation in S. pombe. Our results elucidate the conserved core regulon induced in response to phosphate starvation in this ascomycete distantly related to S. cerevisiae and provide a better understanding of flexibility in environmental stress response networks.Chemistry and Chemical BiologyMolecular and Cellular Biolog

The C-Band All-Sky Survey (C-BASS): Constraining diffuse Galactic radio emission in the North Celestial Pole region

The C-Band All-Sky Survey C-BASS is a high-sensitivity all-sky radio survey at an angular resolution of 45 arcmin and a frequency of 4.7 GHz. We present a total intensity 4.7 GHz map of the North Celestial Pole (NCP) region of sky, above declination +80 deg, which is limited by source confusion at a level of ~0.6 mK rms. We apply the template-fitting (cross-correlation) technique to WMAP and Planck data, using the C-BASS map as the synchrotron template, to investigate the contribution of diffuse foreground emission at frequencies ~20-40 GHz. We quantify the anomalous microwave emission (AME) that is correlated with far-infrared dust emission. The AME amplitude does not change significantly (<10%) when using the higher frequency C-BASS 4.7 GHz template instead of the traditional Haslam 408 MHz map as a tracer of synchrotron radiation. We measure template coefficients of $9.93\pm0.35$ and $9.52\pm0.34$ K per unit $\tau_{353}$ when using the Haslam and C-BASS synchrotron templates, respectively. The AME contributes $55\pm2\,\mu$K rms at 22.8 GHz and accounts for ~60% of the total foreground emission. Our results suggest that a harder (flatter spectrum) component of synchrotron emission is not dominant at frequencies >5 GHz; the best-fitting synchrotron temperature spectral index is $\beta=-2.91\pm0.04$ from 4.7 to 22.8 GHz and $\beta=-2.85\pm0.14$ from 22.8 to 44.1 GHz. Free-free emission is weak, contributing ~$7\,\mu$K rms (~7%) at 22.8 GHz. The best explanation for the AME is still electric dipole emission from small spinning dust grains.Comment: 18 pages, 6 figures, version matches version accepted by MNRA

C-Band All-Sky Survey: A First Look at the Galaxy

We present an analysis of the diffuse emission at 5 GHz in the first quadrant of the Galactic plane using two months of preliminary intensity data taken with the C-Band All Sky Survey (C-BASS) northern instrument at the Owens Valley Radio Observatory, California. Combining C-BASS maps with ancillary data to make temperature-temperature plots we find synchrotron spectral indices of $\beta = -2.65 \pm 0.05$ between 0.408 GHz and 5 GHz and $\beta = -2.72 \pm 0.09$ between 1.420 GHz and 5 GHz for $-10^{\circ} < |b| < -4^{\circ}$, $20^{\circ} < l < 40^{\circ}$. Through the subtraction of a radio recombination line (RRL) free-free template we determine the synchrotron spectral index in the Galactic plane ($|b| < 4^{\circ}$) to be $\beta = -2.56 \pm 0.07$ between 0.408 GHz and 5 GHz, with a contribution of $53 \pm 8$ per cent from free-free emission at 5\,GHz. These results are consistent with previous low frequency measurements in the Galactic plane. By including C-BASS data in spectral fits we demonstrate the presence of anomalous microwave emission (AME) associated with the HII complexes W43, W44 and W47 near 30 GHz, at 4.4 sigma, 3.1 sigma and 2.5 sigma respectively. The CORNISH VLA 5 GHz source catalogue rules out the possibility that the excess emission detected around 30\;GHz may be due to ultra-compact HII regions. Diffuse AME was also identified at a 4 sigma level within $30^{\circ} < l < 40^{\circ}$, $-2^{\circ} < b < 2^{\circ}$ between 5 GHz and 22.8 GHz.Comment: 16 pages, 9 figures, submitted to MNRAS, referee's corrections made, awaiting for final approval for publicatio

The C-Band All-Sky Survey (C-BASS): New Constraints on the Integrated Radio Spectrum of M 31

The Andromeda galaxy (M31) is our closest neighbouring spiral galaxy, making it an ideal target for studying the physics of the interstellar medium in a galaxy very similar to our own. Using new observations of M31 at 4.76GHz by the C-Band All-Sky Survey (C-BASS), and all available radio data at $1^\circ$ resolution, we produce the integrated spectrum and put new constraints on the synchrotron spectral index and anomalous microwave emission (AME) from M31. We use aperture photometry and spectral modelling to fit for the integrated spectrum of M31, and subtract a comprehensive model of nearby background radio sources. The AME in M31 is detected at $3\sigma$ significance with a peak near 30GHz and flux density $0.27\pm0.09$Jy. The synchrotron spectral index of M31 is flatter than our own Galaxy at $\alpha = -0.66 \pm 0.03$ with no strong evidence of spectral curvature. The emissivity of AME, averaged over the total emission from M31 is lower than typical AME sources in our Galaxy, implying that AME is not uniformly distributed throughout M31 and instead is likely confined to sub-regions -- this will need to be confirmed using future higher resolution observations around 20--30GHz.Comment: 16 pages, 6 figures, submitted to MNRA

Molecular Epidemiology of Early and Acute HIV Type 1 Infections in the United States Navy and Marine Corps, 2005–2010

The U.S. military represents a unique population within the human immunodeficiency virus 1 (HIV-1) pandemic. The last comprehensive study of HIV-1 in members of the U.S. Navy and Marine Corps (Sea Services) was completed in 2000, before large-scale combat operations were taking place. Here, we present molecular characterization of HIV-1 from 40 Sea Services personnel who were identified during their seroconversion window and initially classified as HIV-1 negative during screening. Protease/reverse transcriptase (pro/rt) and envelope (env) sequences were obtained from each member of the cohort. Phylogenetic analyses were carried out on these regions to determine relatedness within the cohort and calculate the most recent common ancestor for the related sequences. We identified 39 individuals infected with subtype B and one infected with CRF01_AE. Comparison of the pairwise genetic distance of Sea Service sequences and reference sequences in the env and pro/rt regions showed that five samples were part of molecular clusters, a group of two and a group of three, confirmed by single genome amplification. Real-time molecular monitoring of new HIV-1 acquisitions in the Sea Services may have a role in facilitating public health interventions at sites where related HIV-1 infections are identified

Closing in on a new treatment for sleeping sickness

A chemoproteomics approach has been employed to identify a kinase that could be used as a druggable target in efforts to develop new treatments for African sleeping sickness