Three-dimensional topological lattice models with surface anyons

We study a class of three dimensional exactly solvable models of topological matter first put forward by Walker and Wang [arXiv:1104.2632v2]. While these are not models of interacting fermions, they may well capture the topological behavior of some strongly correlated systems. In this work we give a full pedagogical treatment of a special simple case of these models, which we call the 3D semion model: We calculate its ground state degeneracies for a variety of boundary conditions, and classify its low-lying excitations. While point defects in the bulk are confined in pairs connected by energetic strings, the surface excitations are more interesting: the model has deconfined point defects pinned to the boundary of the lattice, and these exhibit semionic braiding statistics. The surface physics is reminiscent of a $\nu=1/2$ bosonic fractional quantum Hall effect in its topological limit, and these considerations help motivate an effective field theoretic description for the lattice models as variants of $bF$ theories. Our special example of the 3D semion model captures much of the behavior of more general `confined Walker-Wang models'. We contrast the 3D semion model with the closely related 3D version of the toric code (a lattice gauge theory) which has deconfined point excitations in the bulk and we discuss how more general models may have some confined and some deconfined excitations. Having seen that there exist lattice models whose surfaces have the same topological order as a bosonic fractional quantum Hall effect on a confining bulk, we construct a lattice model whose surface has similar topological order to a fermionic quantum hall effect. We find that in these models a fermion is always deconfined in the three dimensional bulk

Radio Properties of Low Redshift Broad Line Active Galactic Nuclei

The question as to whether the distribution of radio-loudness in active galactic nuclei (AGN) is actually bimodal has been discussed extensively in the literature. Futhermore, there have been claims that radio-loudness depends on black hole mass and Eddington ratio. We investigate these claims using the low redshift broad line AGN sample of Greene & Ho (2007), which consists of 8434 objects at z < 0.35 from the Sloan Digital Sky Survey Fourth Data Release (SDSS DR4). We obtained radio fluxes from the Very Large Array Faint Images of the Radio Sky at Twenty-Centimeters (FIRST) survey for the SDSS AGN. Out of the 8434 SDSS AGN, 821 have corresponding observed radio fluxes in the FIRST survey. We calculated the radio-loudness parameter (R) for all objects above the FIRST detection limit (1 mJy), and an upper limit to R for the undetected objects. Using these data, the question of radio bimodality is investigated for different subsets of the total sample. We find no clear demarcation between the radio-loud (RL, R > 10) and radio-quiet (RQ, R < 10) objects, but instead fill in a more radio-intermediate population in a continuous fashion for all subsamples. We find that 4.7% of the AGN in the flux-limited subsample are RL based on core radio emission alone. We calculate the radio-loud fraction (RLF) as both a function of black hole mass and Eddington ratio. The RLF decreases (from 13% to 2%) as Eddington ratio increases over 2.5 order of magnitude. The RLF is nearly constant (~5%) over 4 decades in black hole mass, except for an increase at masses greater than 10^8 solar masses. We find for the FIRST detected subsample that 367 of the RL AGN have black hole masses less than 10^8 solar masses, a large enough number to indicate that RL AGN are not a product of only the most massive black holes in the local universe.Comment: 28 pages, 14 figures, accepted to A

Radio Properties of Low Redshift Broad Line Active Galactic Nuclei Including Extended Radio Sources

We present a study of the extended radio emission in a sample of 8434 low redshift (z < 0.35) broad line active galactic nuclei (AGN) from the Sloan Digital Sky Survey (SDSS). To calculate the jet and lobe contributions to the total radio luminosity, we have taken the 846 radio core sources detected in our previous study of this sample and performed a systematic search in the Faint Images of the Radio Sky at Twenty-centimeters (FIRST) database for extended radio emission that is likely associated with the optical counterparts. We found 51 out of 846 radio core sources have extended emission (> 4" from the optical AGN) that is positively associated with the AGN, and we have identified an additional 12 AGN with extended radio emission but no detectable radio core emission. Among these 63 AGN, we found 6 giant radio galaxies (GRGs), with projected emission exceeding 750 kpc in length, and several other AGN with unusual radio morphologies also seen in higher redshift surveys. The optical spectra of many of the extended sources are similar to that of typical broad line radio galaxy spectra, having broad H$\alpha$ emission lines with boxy profiles and large M_BH. With extended emission taken into account, we find strong evidence for a bimodal distribution in the radio-loudness parameter R, where the lower radio luminosity core-only sources appear as a population separate from the extended sources, with a dividing line at log(R) $\approx 1.75$. This dividing line ensures that these are indeed the most radio-loud AGN, which may have different or extreme physical conditions in their central engines when compared to the more numerous radio quiet AGN.Comment: 25 pages, 6 figures, accepted to A

DNA sequence polymorphisms in a panel of eight candidate bovine imprinted genes and their association with performance traits in Irish Holstein-Friesian cattle

peer-reviewedBackground: Studies in mice and humans have shown that imprinted genes, whereby expression from one of the two parentally inherited alleles is attenuated or completely silenced, have a major effect on mammalian growth, metabolism and physiology. More recently, investigations in livestock species indicate that genes subject to this type of epigenetic regulation contribute to, or are associated with, several performance traits, most notably muscle mass and fat deposition. In the present study, a candidate gene approach was adopted to assess 17 validated single nucleotide polymorphisms (SNPs) and their association with a range of performance traits in 848 progeny-tested Irish Holstein-Friesian artificial insemination sires. These SNPs are located proximal to, or within, the bovine orthologs of eight genes (CALCR, GRB10, PEG3, PHLDA2, RASGRF1, TSPAN32, ZIM2 and ZNF215) that have been shown to be imprinted in cattle or in at least one other mammalian species (i.e. human/mouse/pig/sheep). Results: Heterozygosities for all SNPs analysed ranged from 0.09 to 0.46 and significant deviations from Hardy-Weinberg proportions (P ≤ 0.01) were observed at four loci. Phenotypic associations (P ≤ 0.05) were observed between nine SNPs proximal to, or within, six of the eight analysed genes and a number of performance traits evaluated, including milk protein percentage, somatic cell count, culled cow and progeny carcass weight, angularity, body conditioning score, progeny carcass conformation, body depth, rump angle, rump width, animal stature, calving difficulty, gestation length and calf perinatal mortality. Notably, SNPs within the imprinted paternally expressed gene 3 (PEG3) gene cluster were associated (P ≤ 0.05) with calving, calf performance and fertility traits, while a single SNP in the zinc finger protein 215 gene (ZNF215) was associated with milk protein percentage (P ≤ 0.05), progeny carcass weight (P ≤ 0.05), culled cow carcass weight (P ≤ 0.01), angularity (P ≤ 0.01), body depth (P ≤ 0.01), rump width (P ≤ 0.01) and animal stature (P ≤ 0.01). Conclusions: Of the eight candidate bovine imprinted genes assessed, DNA sequence polymorphisms in six of these genes (CALCR, GRB10, PEG3, RASGRF1, ZIM2 and ZNF215) displayed associations with several of the phenotypes included for analyses. The genotype-phenotype associations detected here are further supported by the biological function of these six genes, each of which plays important roles in mammalian growth, development and physiology. The associations between SNPs within the imprinted PEG3 gene cluster and traits related to calving, calf performance and gestation length suggest that this domain on chromosome 18 may play a role regulating pre-natal growth and development and fertility. SNPs within the bovine ZNF215 gene were associated with bovine growth and body conformation traits and studies in humans have revealed that the human ZNF215 ortholog belongs to the imprinted gene cluster associated with Beckwith-Wiedemann syndrome--a genetic disorder characterised by growth abnormalities. Similarly, the data presented here suggest that the ZNF215 gene may have an important role in regulating bovine growth. Collectively, our results support previous work showing that (candidate) imprinted genes/loci contribute to heritable variation in bovine performance traits and suggest that DNA sequence polymorphisms within these genes/loci represents an important reservoir of genomic markers for future genetic improvement of dairy and beef cattle populations.Department of Agriculture, Fisheries and Food Ireland - Research Stimulus Fund (project numbers: RSF-06-406, RSF-06-0353 and RSF-06-0409); Science Foundation Ireland - Investigator Programme Grants(SFI/01/F.1/B028; SFI/08/IN.1/B1931, 07/SRC/B1156 (MPM)

Burden of hereditary transthyretin amyloidosis on quality of life

INTRODUCTION: Hereditary transthyretin (hATTR) amyloidosis is a progressive, degenerative disease, with peripheral neuropathy, cardiomyopathy, and other clinical manifestations. In this study we examine the impact of hATTR amyloidosis on quality of life (QOL). METHODS: Neuropathy-specific QOL, measured with the Norfolk QOL-Diabetic Neuropathy questionnaire, was compared between patients with hATTR amyloidosis and patients with type 2 diabetes, whereas generic QOL, measured with the 36-item Short Form Health Survey version 2 (SF-36v2), was compared between patients with hATTR amyloidosis, the general population, and patients with chronic diseases. RESULTS: Neuropathy-specific QOL for patients with hATTR amyloidosis was nearly equivalent to that of patients with type 2 diabetes with diabetic neuropathy accompanied by a history of ulceration, gangrene, or amputation. Generic QOL was worse than that seen in the general population, with physical functioning worse than that for patients with multiple sclerosis and congestive heart failure. DISCUSSION: Patients with hATTR amyloidosis show significant burden on QOL, particularly in physical functioning. Muscle Nerve 60: 169-175, 201

SSAGES : Software Suite for Advanced General Ensemble Simulations

Molecular simulation has emerged as an essential tool for modern-day research, but obtaining proper results and making reliable conclusions from simulations requires adequate sampling of the system under consideration. To this end, a variety of methods exist in the literature that can enhance sampling considerably, and increasingly sophisticated, effective algorithms continue to be developed at a rapid pace. Implementation of these techniques, however, can be challenging for experts and non-experts alike. There is a clear need for software that provides rapid, reliable, and easy access to a wide range of advanced sampling methods and that facilitates implementation of new techniques as they emerge. Here we present SSAGES, a publicly available Software Suite for Advanced General Ensemble Simulations designed to interface with multiple widely used molecular dynamics simulations packages. SSAGES allows facile application of a variety of enhanced sampling techniques—including adaptive biasing force, string methods, and forward flux sampling—that extract meaningful free energy and transition path data from all-atom and coarse-grained simulations. A noteworthy feature of SSAGES is a user-friendly framework that facilitates further development and implementation of new methods and collective variables. In this work, the use of SSAGES is illustrated in the context of simple representative applications involving distinct methods and different collective variables that are available in the current release of the suite. The code may be found at: https://github.com/MICCoM/SSAGES-public

Measurement of H₂O₂ within living drosophila during aging using a ratiometric mass spectrometry probe targeted to the mitochondrial matrix

Hydrogen peroxide (H&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;2&lt;/sub&gt;) is central to mitochondrial oxidative damage and redox signaling, but its roles are poorly understood due to the difficulty of measuring mitochondrial H&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;2&lt;/sub&gt; in vivo. Here we report a ratiometric mass spectrometry probe approach to assess mitochondrial matrix H&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;2&lt;/sub&gt; levels in vivo. The probe, MitoB, comprises a triphenylphosphonium (TPP) cation driving its accumulation within mitochondria, conjugated to an arylboronic acid that reacts with H&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;2&lt;/sub&gt; to form a phenol, MitoP. Quantifying the MitoP/MitoB ratio by liquid chromatography-tandem mass spectrometry enabled measurement of a weighted average of mitochondrial H&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;2&lt;/sub&gt; that predominantly reports on thoracic muscle mitochondria within living flies. There was an increase in mitochondrial H&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;2&lt;/sub&gt; with age in flies, which was not coordinately altered by interventions that modulated life span. Our findings provide approaches to investigate mitochondrial ROS in vivo and suggest that while an increase in overall mitochondrial H&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;2&lt;/sub&gt; correlates with aging, it may not be causative

Highly Active Ice-Nucleating Particles at the Summer North Pole

The amount of ice versus supercooled water in clouds is important for their radiative properties and role in climate feedbacks. Hence, knowledge of the concentration of ice-nucleating particles (INPs) is needed. Generally, the concentrations of INPs are found to be very low in remote marine locations allowing cloud water to persist in a supercooled state. We had expected the concentrations of INPs at the North Pole to be very low given the distance from open ocean and terrestrial sources coupled with effective wet scavenging processes. Here we show that during summer 2018 (August and September) high concentrations of biological INPs (active at\ua0&gt;−20\ub0C) were sporadically present at the North Pole. In fact, INP concentrations were sometimes as high as those recorded at mid-latitude locations strongly impacted by highly active biological INPs, in strong contrast to the Southern Ocean. Furthermore, using a balloon borne sampler we demonstrated that INP concentrations were often different at the surface versus higher in the boundary layer where clouds form. Back trajectory analysis suggests strong sources of INPs near the Russian coast, possibly associated with wind-driven sea spray production, whereas the pack ice, open leads, and the marginal ice zone were not sources of highly active INPs. These findings suggest that primary ice production, and therefore Arctic climate, is sensitive to transport from locations such as the Russian coast that are already experiencing marked climate change