A context-free and a 1-counter geodesic language for a Baumslag-Solitar group

We give a language of unique geodesic normal forms for the Baumslag-Solitar group BS(1,2) that is context-free and 1-counter. We discuss the classes of context-free, 1-counter and counter languages, and explain how they are inter-related

Increased Concentration of Polyvalent Phospholipids in the Adsorption Domain of a Charged Protein

We studied the adsorption of a charged protein onto an oppositely charged membrane, composed of mobile phospholipids of differing valence, using a statistical-thermodynamical approach. A two-block model was employed, one block corresponding to the protein-affected region on the membrane, referred to as the adsorption domain, and the other to the unaffected remainder of the membrane. We calculated the protein-induced lipid rearrangement in the adsorption domain as arising from the interplay between the electrostatic interactions in the system and the mixing entropy of the lipids. Equating the electrochemical potentials of the lipids in the two blocks yields an expression for the relations among the various lipid fractions in the adsorption domain, indicating a sensitive dependence of lipid fraction on valence. This expression is a result of the two-block picture but does not depend on further details of the protein-membrane interaction. We subsequently calculated the lipid fractions themselves using the Poisson-Boltzmann theory. We examined the dependence of lipid enrichment, i.e., the ratio between the lipid fractions inside and outside the adsorption domain, on various parameters such as ionic strength and lipid valence. Maximum enrichment was found for lipid valence of about (-3) to (-4) in physiological conditions. Our results are in qualitative agreement with recent experimental studies on the interactions between peptides having a domain of basic residues and membranes containing a small fraction of the polyvalent phosphatidylinositol 4,5-bisphosphate (PIP2). This study provides theoretical support for the suggestion that proteins adsorbed onto membranes through a cluster of basic residues may sequester PIP2 and other polyvalent lipids.Comment: 25 pages, 12 figure

Marine Protected Areas as a Risk Management Tool

There is considerable debate in the literature about the usefulness of Marine Protected Areas as fishery management tools. While most economists have found that it is unlikely that marine reserves will improve steady-state yields, some biologists have shown that protected areas have the potential to reduce uncertainty. Most of the work on uncertainty has focused on exogenous environmental variability; the probability of collapse can be reduced with protected areas, but this comes at the cost of lower yields. Here we consider single-owner management with spatial closures under growth and production-function parameter uncertainty. There are many reasons to suspect that estimates of fishery growth parameters are highly uncertain: intrinsic variability, lack of data, weak identification, and technological change to name a few. If a single owner does not know growth parameters very well then it is difficult to determine optimal extraction paths. Traditional optimal management utilizes a single control variable, catch. When growth and production parameters are uncertain we consider the expected benefits of utilizing a second control variable: fraction of area harvested. We show that even in a deterministic dynamical system, if parameters are unknown, expected harvests can be improved with protected areas. Under some parameterizations, unique optimal reserve and fleet sizes exist

Solenoid and non-solenoid protein recognition using stationary wavelet packet transform

Motivation: Solenoid proteins are emerging as a protein class with properties intermediate between structured and intrinsically unstructured proteins. Containing repeating structural units, solenoid proteins are expected to share sequence similarities. However, in many cases, the sequence similarities are weak and non-detectable. Moreover, solenoids can be degenerated and widely vary in the number of units. So that it is difficult to detect them. Recently, several solenoid repeats detection methods have been proposed, such as self-alignment of the sequence, spectral analysis and discrete Fourier transform of sequence. Although these methods have shown good performance on certain data sets, they often fail to detect repeats with weak similarities. In this article, we propose a new approach to recognize solenoid repeats and non-solenoid proteins using stationary wavelet packet transform (SWPT). Our method associates with three advantages: (i) naturally representing five main factors of protein structure and properties by wavelet analysis technique; (ii) extracting novel wavelet features that can capture hidden components from solenoid sequence similarities and distinguish them from global proteins; (iii) obtaining statistics features that capture repeating motifs of solenoid proteins

Gathering dust : A galaxy-wide study of dust emission from cloud complexes in NGC 300

© 2018 ESO. Reproduced with permission from Astronomy & Astrophysics. Content in the UH Research Archive is made available for personal research, educational, and non-commercial purposes only. Unless otherwise stated, all content is protected by copyright, and in the absence of an open license, permissions for further re-use should be sought from the publisher, the author, or other copyright holder.Aims. We use multi-band observations by the Herschel Space Observatory to study the dust emission properties of the nearby spiral galaxy NGC 300. We compile a first catalogue of the population of giant dust clouds (GDCs) in NGC 300, including temperature and mass estimates, and give an estimate of the total dust mass of the galaxy. Methods. We carried out source detection with the multiwavelength source extraction algorithm getsources. We calculated physical properties, including mass and temperature, of the GDCs from five-band Herschel PACS and SPIRE observations from 100 to 500 μm; the final size and mass estimates are based on the observations at 250 μm that have an effective spatial resolution of ~170 pc. We correlated our final catalogue of GDCs to pre-existing catalogues of HII regions to infer the number of GDCs associated with high-mass star formation and determined the Hα emission of the GDCs. Results. Our final catalogue of GDCs includes 146 sources, 90 of which are associated with known HII regions. We find that the dust masses of the GDCs are completely dominated by the cold dust component and range from ~1.1 × 10 3 to 1.4 × 10 4 M. The GDCs have effective temperatures of ~13-23 K and show a distinct cold dust effective temperature gradient from the centre towards the outer parts of the stellar disk. We find that the population of GDCs in our catalogue constitutes ~16% of the total dust mass of NGC 300, which we estimate to be about 5.4 × 10 6 M. At least about 87% of our GDCs have a high enough average dust mass surface density to provide sufficient shielding to harbour molecular clouds. We compare our results to previous pointed molecular gas observations in NGC 300 and results from other nearby galaxies and also conclude that it is very likely that most of our GDCs are associated with complexes of giant molecular clouds.Peer reviewe

The Mice at play in the CALIFA survey: A case study of a gas-rich major merger between first passage and coalescence

We present optical integral field spectroscopy (IFS) observations of the Mice, a major merger between two massive (>10^11Msol) gas-rich spirals NGC4676A and B, observed between first passage and final coalescence. The spectra provide stellar and gas kinematics, ionised gas properties and stellar population diagnostics, over the full optical extent of both galaxies. The Mice provide a perfect case study highlighting the importance of IFS data for improving our understanding of local galaxies. The impact of first passage on the kinematics of the stars and gas has been significant, with strong bars likely induced in both galaxies. The barred spiral NGC4676B exhibits a strong twist in both its stellar and ionised gas disk. On the other hand, the impact of the merger on the stellar populations has been minimal thus far: star formation induced by the recent close passage has not contributed significantly to the global star formation rate or stellar mass of the galaxies. Both galaxies show bicones of high ionisation gas extending along their minor axes. In NGC4676A the high gas velocity dispersion and Seyfert-like line ratios at large scaleheight indicate a powerful outflow. Fast shocks extend to ~6.6kpc above the disk plane. The measured ram pressure and mass outflow rate (~8-20Msol/yr) are similar to superwinds from local ULIRGs, although NGC4676A has only a moderate infrared luminosity of 3x10^10Lsol. Energy beyond that provided by the mechanical energy of the starburst appears to be required to drive the outflow. We compare the observations to mock kinematic and stellar population maps from a merger simulation. The models show little enhancement in star formation during and following first passage, in agreement with the observations. We highlight areas where IFS data could help further constrain the models.Comment: 23 pages, 13 figures, accepted to A&A. A version with a complete set of high resolution figures is available here: http://www-star.st-and.ac.uk/~vw8/resources/mice_v8_astroph.pd

Preventing Bias in Cluster Randomised Trials

Bruno Giraudeau and Philippe Ravaud discuss the difficulties in preventing selection bias and applying intention-to-treat analysis in cluster randomized trials, and propose some solutions

Insights into the content and spatial distribution of dust from the integrated spectral properties of galaxies

[Abridged] We present a new approach to investigate the content and spatial distribution of dust in structurally unresolved star-forming galaxies from the observed dependence of integrated spectral properties on galaxy inclination. We develop an innovative combination of generic models of radiative transfer (RT) in dusty media with a prescription for the spectral evolution of galaxies, via the association of different geometric components of galaxies with stars in different age ranges. We show that a wide range of RT models all predict a quasi-universal relation between slope of the attenuation curve at any wavelength and V-band attenuation optical depth in the diffuse interstellar medium (ISM), at all galaxy inclinations. This relation predicts steeper (shallower) dust attenuation curves than both the Calzetti and MW curves at small (large) attenuation optical depths, which implies that geometry and orientation effects have a stronger influence on the shape of the attenuation curve than changes in the optical properties of dust grains. We use our combined RT and spectral evolution model to interpret the observed dependence of the H\alpha/H\beta\ ratio and ugrizYJH attenuation curve on inclination in a sample of ~23 000 nearby star-forming galaxies. From a Bayesian MCMC fit, we measure the central face-on B-band optical depth of this sample to be tau_B\perp~1.8\pm0.2. We also quantify the enhanced optical depth towards newly formed stars in their birth clouds, finding this to be significantly larger in galaxies with bulges than in disc-dominated galaxies, while tau_B\perp is roughly similar in both cases. Finally, we show that neglecting the effect of geometry and orientation on attenuation can severely bias the interpretation of galaxy spectral energy distributions, as the impact on broadband colours can reach up to 0.3-0.4 mag at optical wavelengths and 0.1 mag at near-infrared ones.Comment: 32 pages, 3 tables, 41 figures, MNRAS in-pres

Bidirectional links between HIV and intimate partner violence in pregnancy: implications for prevention of mother-to-child transmission.

INTRODUCTION: Prevention of mother-to-child transmission (PMTCT) has the potential to eliminate new HIV infections among infants. Yet in many parts of sub-Saharan Africa, PMTCT coverage remains low, leading to unacceptably high rates of morbidity among mothers and new infections among infants. Intimate partner violence (IPV) may be a structural driver of poor PMTCT uptake, but has received little attention in the literature to date. METHODS: We conducted qualitative research in three Johannesburg antenatal clinics to understand the links between IPV and HIV-related health of pregnant women. We held focus group discussions with pregnant women (n=13) alongside qualitative interviews with health care providers (n=10), district health managers (n=10) and pregnant abused women (n=5). Data were analysed in Nvivo10 using a team-based approach to thematic coding. FINDINGS: We found qualitative evidence of strong bidirectional links between IPV and HIV among pregnant women. HIV diagnosis during pregnancy, and subsequent partner disclosure, were noted as a common trigger of IPV. Disclosure leads to violence because it causes relationship conflict, usually related to perceived infidelity and the notion that women are "bringing" the disease into the relationship. IPV worsened HIV-related health through poor PMTCT adherence, since taking medication or accessing health services might unintentionally alert male partners of the women's HIV status. IPV also impacted on HIV-related health via mental health, as women described feeling depressed and anxious due to the violence. IPV led to secondary HIV risk as women experienced forced sex, often with little power to negotiate condom use. Pregnant women described staying silent about condom negotiation in order to stay physically safe during pregnancy. CONCLUSIONS: IPV is a crucial issue in the lives of pregnant women and has bidirectional links with HIV-related health. IPV may worsen access to PMTCT and secondary prevention behaviours, thereby posing a risk of secondary transmission. IPV should be urgently addressed in antenatal care settings to improve uptake of PMTCT and ensure that goals of maternal and child health are met in sub-Saharan African settings