Hierarchical and High-Girth QC LDPC Codes

We present a general approach to designing capacity-approaching high-girth low-density parity-check (LDPC) codes that are friendly to hardware implementation. Our methodology starts by defining a new class of "hierarchical" quasi-cyclic (HQC) LDPC codes that generalizes the structure of quasi-cyclic (QC) LDPC codes. Whereas the parity check matrices of QC LDPC codes are composed of circulant sub-matrices, those of HQC LDPC codes are composed of a hierarchy of circulant sub-matrices that are in turn constructed from circulant sub-matrices, and so on, through some number of levels. We show how to map any class of codes defined using a protograph into a family of HQC LDPC codes. Next, we present a girth-maximizing algorithm that optimizes the degrees of freedom within the family of codes to yield a high-girth HQC LDPC code. Finally, we discuss how certain characteristics of a code protograph will lead to inevitable short cycles, and show that these short cycles can be eliminated using a "squashing" procedure that results in a high-girth QC LDPC code, although not a hierarchical one. We illustrate our approach with designed examples of girth-10 QC LDPC codes obtained from protographs of one-sided spatially-coupled codes.Comment: Submitted to IEEE Transactions on Information THeor

A format for phylogenetic placements

We have developed a unified format for phylogenetic placements, that is, mappings of environmental sequence data (e.g. short reads) into a phylogenetic tree. We are motivated to do so by the growing number of tools for computing and post-processing phylogenetic placements, and the lack of an established standard for storing them. The format is lightweight, versatile, extensible, and is based on the JSON format which can be parsed by most modern programming languages. Our format is already implemented in several tools for computing and post-processing parsimony- and likelihood-based phylogenetic placements, and has worked well in practice. We believe that establishing a standard format for analyzing read placements at this early stage will lead to a more efficient development of powerful and portable post-analysis tools for the growing applications of phylogenetic placement.Comment: Documents version 3 of the forma

Monitoring of a Southern Giant Petrel Macronectes giganteus population on the Frazier Islands, Wilkes Land, Antarctica

Abstract Since 1956, Southern Giant Petrels on the Frazier Islands, East Antarctica, have been counted with different census techniques, sometimes varying within seasons and among islands, which hindered analysis of the data. Protective measures for the islands from 1986 onwards have increased the need for reliable long-term census data, but reduced the ways to collect these data. Published and unpublished data were re-examined, and population trends were reconstructed based on two relatively standardised techniques: the number of active chicks (AC) and the number of apparently occupied nests (AON) around hatching. AC-values from Nelly Island from 1959 to 1998 indicate substantial periodic fluctuations, but no consistent long-term change. Since the late 1970s, AC-values on the other two islands and AON-values suggest that the breeding population may have grown by 35%. This recent growth, however, is within the extent of periodic fluctuations observed in Southern Giant Petrel population that is stable over the long term

Probing ISM Structure in Trumpler 14 & Carina I Using The Stratospheric Terahertz Observatory 2

We present observations of the Trumpler 14/Carina I region carried out using the Stratospheric Terahertz Observatory 2 (STO2). The Trumpler 14/Carina I region is in the west part of the Carina Nebula Complex, which is one of the most extreme star-forming regions in the Milky Way. We observed Trumpler 14/Carina I in the 158 $\mu$m transition of [C\,{\sc ii}] with a spatial resolution of 48$''$ and a velocity resolution of 0.17 km s$^{-1}$. The observations cover a 0.25$^\circ$ by 0.28$^\circ$ area with central position {\it l} = 297.34$^\circ$, {\it b} = -0.60$^\circ$. The kinematics show that bright [C\,{\sc ii}] structures are spatially and spectrally correlated with the surfaces of CO clouds, tracing the photodissociation region and ionization front of each molecular cloud. Along 7 lines of sight that traverse Tr 14 into the dark ridge to the southwest, we find that the [C\,{\sc ii}] luminosity from the HII region is 3.7 times that from the PDR. In same los we find in the PDRs an average ratio of 1:4.1:5.6 for the mass in atomic gas:dark-CO gas: molecular gas traced by CO. Comparing multiple gas tracers including HI 21cm, [C\,{\sc ii}], CO, and radio recombination lines, we find that the HII regions of the Carina Nebula Complex are well-described as HII regions with one-side freely expanding towards us, consistent with the champagne model of ionized gas evolution. The dispersal of the GMC in this region is dominated by EUV photoevaporation; the dispersal timescale is 20-30 Myr.Comment: ApJ accepte

The Bolocam Galactic Plane Survey: Survey Description and Data Reduction

We present the Bolocam Galactic Plane Survey (BGPS), a 1.1 mm continuum survey at 33" effective resolution of 170 square degrees of the Galactic Plane visible from the northern hemisphere. The survey is contiguous over the range -10.5 < l < 90.5, |b| < 0.5 and encompasses 133 square degrees, including some extended regions |b| < 1.5. In addition to the contiguous region, four targeted regions in the outer Galaxy were observed: IC1396, a region towards the Perseus Arm, W3/4/5, and Gem OB1. The BGPS has detected approximately 8400 clumps over the entire area to a limiting non-uniform 1-sigma noise level in the range 11 to 53 mJy/beam in the inner Galaxy. The BGPS source catalog is presented in a companion paper (Rosolowsky et al. 2010). This paper details the survey observations and data reduction methods for the images. We discuss in detail the determination of astrometric and flux density calibration uncertainties and compare our results to the literature. Data processing algorithms that separate astronomical signals from time-variable atmospheric fluctuations in the data time-stream are presented. These algorithms reproduce the structure of the astronomical sky over a limited range of angular scales and produce artifacts in the vicinity of bright sources. Based on simulations, we find that extended emission on scales larger than about 5.9' is nearly completely attenuated (> 90%) and the linear scale at which the attenuation reaches 50% is 3.8'. Comparison with other millimeter-wave data sets implies a possible systematic offset in flux calibration, for which no cause has been discovered. This presentation serves as a companion and guide to the public data release through NASA's Infrared Processing and Analysis Center (IPAC) Infrared Science Archive (IRSA). New data releases will be provided through IPAC IRSA with any future improvements in the reduction.Comment: Accepted for publication in Astrophysical Journal Supplemen

A VLBI receiving system for the South Pole Telescope

The Event Horizon Telescope (EHT) is a very-long-baseline interferometry (VLBI) experiment that aims to observe supermassive black holes with an angular resolution that is comparable to the event horizon scale. The South Pole occupies an important position in the array, greatly increasing its north-south extent and therefore its resolution. The South Pole Telescope (SPT) is a 10-meter diameter, millimeter-wavelength telescope equipped for bolometric observations of the cosmic microwave background. To enable VLBI observations with the SPT we have constructed a coherent signal chain suitable for the South Pole environment. The dual-frequency receiver incorporates state-of-the-art SIS mixers and is installed in the SPT receiver cabin. The VLBI signal chain also includes a recording system and reference frequency generator tied to a hydrogen maser. Here we describe the SPT VLBI system design in detail and present both the lab measurements and on-sky results.Comment: 14 pages, 11 figures, to appear in the Proceedings of the SPIE (SPIE Astronomical Telescopes + Instrumentation 2018; Millimeter, Submillimeter, and Far-Infrared Detectors and Instrumentation for Astronomy IX

Increased diversification rates follow shifts to bisexuality in liverworts

Shifts in sexual systems are one of the key drivers of species diversification. In contrast to angiosperms, unisexuality prevails in bryophytes. Here, we test the hypotheses that bisexuality evolved from an ancestral unisexual condition and is a key innovation in liverworts. We investigate whether shifts in sexual systems influence diversification using hidden state speciation and extinction analysis (HiSSE). This new method compares the effects of the variable of interest to the best-fitting latent variable, yielding robust and conservative tests. We find that the transitions in sexual systems are significantly biased toward unisexuality, even though bisexuality is coupled with increased diversification. Sexual systems are strongly conserved deep within the liverwort tree but become much more labile toward the present. Bisexuality appears to be a key innovation in liverworts. Its effects on diversification are presumably mediated by the interplay of high fertilization rates, massive spore production and long-distance dispersal, which may separately or together have facilitated liverwort speciation, suppressed their extinction, or both. Importantly, shifts in liverwort sexual systems have the opposite effect when compared to angiosperms, leading to contrasting diversification patterns between the two groups. The high prevalence of unisexuality among liverworts suggests, however, a strong selection for sexual dimorphism

Fish Oil-Derived Fatty Acids in Pregnancy and Wheeze and Asthma in Offspring

© 2016 Massachusetts Medical Society. Bisgaard, H., Stokholm, J., Chawes, B. L., Vissing, N. H., Bjarnadóttir, E., Schoos, A.-M. M., … Bønnelykke, K. (2016). Fish Oil–Derived Fatty Acids in Pregnancy and Wheeze and Asthma in Offspring. New England Journal of Medicine, 375(26), 2530–2539. https://doi.org/10.1056/NEJMoa1503734BACKGROUND Reduced intake of n-3 long-chain polyunsaturated fatty acids (LCPUFAs) may be a contributing factor to the increasing prevalence of wheezing disorders. We assessed the effect of supplementation with n-3 LCPUFAs in pregnant women on the risk of persistent wheeze and asthma in their offspring. METHODS We randomly assigned 736 pregnant women at 24 weeks of gestation to receive 2.4 g of n-3 LCPUFA (fish oil) or placebo (olive oil) per day. Their children formed the Copenhagen Prospective Studies on Asthma in Childhood 2010 (COPSAC 2010) cohort and were followed prospectively with extensive clinical phenotyping. Neither the investigators nor the participants were aware of group assignments during follow-up for the first 3 years of the children's lives, after which there was a 2-year follow-up period during which only the investigators were unaware of group assignments. The primary end point was persistent wheeze or asthma, and the secondary end points included lower respiratory tract infections, asthma exacerbations, eczema, and allergic sensitization. RESULTS A total of 695 children were included in the trial, and 95.5% completed the 3-year, double-blind follow-up period. The risk of persistent wheeze or asthma in the treatment group was 16.9%, versus 23.7% in the control group (hazard ratio, 0.69; 95% confidence interval [CI], 0.49 to 0.97; P=0.035), corresponding to a relative reduction of 30.7%. Prespecified subgroup analyses suggested that the effect was strongest in the children of women whose blood levels of eicosapentaenoic acid and docosahexaenoic acid were in the lowest third of the trial population at randomization: 17.5% versus 34.1% (hazard ratio, 0.46; 95% CI, 0.25 to 0.83; P=0.011). Analyses of secondary end points showed that supplementation with n-3 LCPUFA was associated with a reduced risk of infections of the lower respiratory tract (31.7% vs. 39.1%; hazard ratio, 0.75; 95% CI, 0.58 to 0.98; P=0.033), but there was no statistically significant association between supplementation and asthma exacerbations, eczema, or allergic sensitization. CONCLUSIONS Supplementation with n-3 LCPUFA in the third trimester of pregnancy reduced the absolute risk of persistent wheeze or asthma and infections of the lower respiratory tract in offspring by approximately 7 percentage points, or one third. (Funded by the Lund-beck Foundation and others; ClinicalTrials.gov number, NCT00798226.)Lundbeck Foundatio