Parametric inference of recombination in HIV genomes

Recombination is an important event in the evolution of HIV. It affects the global spread of the pandemic as well as evolutionary escape from host immune response and from drug therapy within single patients. Comprehensive computational methods are needed for detecting recombinant sequences in large databases, and for inferring the parental sequences. We present a hidden Markov model to annotate a query sequence as a recombinant of a given set of aligned sequences. Parametric inference is used to determine all optimal annotations for all parameters of the model. We show that the inferred annotations recover most features of established hand-curated annotations. Thus, parametric analysis of the hidden Markov model is feasible for HIV full-length genomes, and it improves the detection and annotation of recombinant forms. All computational results, reference alignments, and C++ source code are available at http://bio.math.berkeley.edu/recombination/.Comment: 20 pages, 5 figure

THE INFLUENCE OF DEPRESSIVE SYMPTOMS ON FATHERS’ BEHAVIORS AND ATTITUDES

The present study examines the impact of young, poor, unwed fathers on their family by investigating the influence of depressive symptom frequency on fathers’ relationship with their children and partners. Couples from seven American cities with populations over 200,000 were recruited and interviewed about such areas of life as romantic and parental relationships, health, and employment at the hospital within 24 hours after the birth of their child. An Item Response Theory (IRT) within-group analysis of the 1,759 African-, Caucasian-, Hispanic-, Asian-, and Native American fathers in the study yielded a 3-class clustering of depressive symptoms. Class 1 fathers had the lowest frequency of depressive symptom expression; class 2 fathers had a low frequency; and class 3 fathers had low to medium rates of depressive symptoms. Multivariate statistics revealed that depressive class membership predicted domestic violence toward fathers’ partners but not affection toward their children. The importance of the parental behavior of teaching children about life, however, varied by class, with class 2 fathers most highly endorsing this behavior. Implications of young, unwed, poor fathers' behaviors and attitudes toward their children and romantic partners will be discussed in terms of men's contributions to family life.

A time dependent relation between EUV solar flare light-curves from lines with differing formation temperatures

Extreme ultraviolet (EUV) solar flare emissions evolve in time as the emitting plasma heats and then cools. Although accurately modeling this evolution has been historically difficult, especially for empirical relationships, it is important for understanding processes at the Sun, as well as for their influence on planetary atmospheres. With a goal to improve empirical flare models, a new simple empirical expression is derived to predict how cool emissions will evolve based on the evolution of a hotter emission. This technique is initially developed by studying 12 flares in detail observed by the EUV Variability Experiment (EVE) onboard the Solar Dynamics Observatory (SDO). Then, over 1100 flares observed by EVE are analyzed to validate these relationships. The Cargill and Enthalpy Based Thermal Evolution of Loops (EBTEL) flare cooling models are used to show that this empirical relationship implies the energy radiated by a population of hotter formed ions is approximately proportional to the energy exciting a population of cooler formed ions emitting when the peak formation temperatures of the two lines are up to 72% of each other and above 2 MK. These results have practical implications for improving flare irradiance empirical modeling and for identifying key emission lines for future monitoring of flares for space weather operations; and also provide insight into the cooling processes of flare plasma.Comment: Final version accepted for publication by the Journal of Space Weather and Space Climate on 23 November 201

The Formation of Low-Mass Double White Dwarfs through an Initial Phase of Stable Non-Conservative Mass Transfer

Although many double white dwarfs (DWDs) have been observed, the evolutionary channel by which they are formed from low-mass/long-period red-giant-main-sequence (RG-MS) binaries remains uncertain. The canonical explanations involve some variant of double common-envelope (CE) evolution, however it has been found that such a mechanism cannot produce the observed distribution. We present a model for the initial episode of mass transfer (MT) in RG-MS binaries, and demonstrate that their evolution into double white dwarfs need not arise through a double-CE process, as long as the initial primary's core mass (Md,c) does not exceed 0.46M$_{\odot}$. Instead, the first episode of dramatic mass loss may be stable, non-conservative MT. We find a lower bound on the fraction of transferred mass that must be lost from the system in order to provide for MT, and demonstrate the feasibility of this channel in producing observed low-mass (with M$_{d,c}$ < 0.46M$_{\odot}$) DWD systems.Comment: 2 pages, 1 figure, Conference Proceedings for the International Conference on Binaries, Mykonos, Greec

FearNot! An Anti-Bullying Intervention: Evaluation of an Interactive Virtual Learning Environment

Original paper can be found at: http://www.aisb.org.uk/publications/proceedings.shtm

The Prelude to and Aftermath of the Giant Flare of 2004 December 27: Persistent and Pulsed X-ray Properties of SGR 1806-20 from 1993 to 2005

On 2004 December 27, a highly-energetic giant flare was recorded from the magnetar candidate SGR 1806-20. In the months preceding this flare, the persistent X-ray emission from this object began to undergo significant changes. Here, we report on the evolution of key spectral and temporal parameters prior to and following this giant flare. Using the Rossi X-ray Timing Explorer, we track the pulse frequency of SGR 1806-20 and find that the spin-down rate of this SGR varied erratically in the months before and after the flare. Contrary to the giant flare in SGR 1900+14, we find no evidence for a discrete jump in spin frequency at the time of the December 27th flare (|dnu/nu| < 5 X 10^-6). In the months surrounding the flare, we find a strong correlation between pulsed flux and torque consistent with the model for magnetar magnetosphere electrodynamics proposed by Thompson, Lyutikov & Kulkarni (2002). As with the flare in SGR 1900+14, the pulse morphology of SGR 1806-20 changes drastically following the flare. Using the Chandra X-ray Observatory and other publicly available imaging X-ray detector observations, we construct a spectral history of SGR 1806-20 from 1993 to 2005. The usual magnetar persistent emission spectral model of a power-law plus a blackbody provides an excellent fit to the data. We confirm the earlier finding by Mereghetti et al. (2005) of increasing spectral hardness of SGR 1806-20 between 1993 and 2004. Contrary to the direct correlation between torque and spectral hardness proposed by Mereghetti et al., we find evidence for a sudden torque change that triggered a gradual hardening of the energy spectrum on a timescale of years. Interestingly, the spectral hardness, spin-down rate, pulsed, and phase-averaged of SGR 1806-20 all peak months before the flare epoch.Comment: 37 pages, 8 figures, 8 tables. Accepted for publication in ApJ. To appear in the Oct 20 2006 editio

Temperature dependent graphene suspension due to thermal Casimir interaction

Thermal effects contributing to the Casimir interaction between objects are usually small at room temperature and they are difficult to separate from quantum mechanical contributions at higher temperatures. We propose that the thermal Casimir force effect can be observed for a graphene flake suspended in a fluid between substrates at the room temperature regime. The properly chosen materials for the substrates and fluid induce a Casimir repulsion. The balance with the other forces, such as gravity and buoyancy, results in a stable temperature dependent equilibrium separation. The suspended graphene is a promising system due to its potential for observing thermal Casimir effects at room temperature.Comment: 5 pages, 4 figures, in APL production 201

Non Local Electron-Phonon Correlations in a Dispersive Holstein Model

Due to the dispersion of optical phonons, long range electron-phonon correlations renormalize downwards the coupling strength in the Holstein model. We evaluate the size of this effect both in a linear chain and in a square lattice for a time averaged {\it e-ph} potential, where the time variable is introduced according to the Matsubara formalism. Mapping the Holstein Hamiltonian onto the time scale we derive the perturbing source current which appears to be non time retarded. This property permits to disentangle phonon and electron coordinates in the general path integral for an electron coupled to dispersive phonons. While the phonon paths can be integrated out analytically, the electron path integrations have to be done numerically. The equilibrium thermodynamic properties of the model are thus obtained as a function of the electron hopping value and of the phonon spectrum parameters. We derive the {\it e-ph} corrections to the phonon free energy and show that its temperature derivatives do not depend on the {\it e-ph} effective coupling hence, the Holstein phonon heat capacity is strictly harmonic. A significant upturn in the low temperature total heat capacity over $T$ ratio is attributed to the electron hopping which largely contributes to the action.Comment: Phys.Rev.B (2005

Sustainable valorisation of organic urban wastes : insights from African case studies

Understanding the problems and potentials of the organic waste stream is perhaps the single most important step that city authorities in Africa could take in moving towards sustainable, affordable, effective and efficient waste management. This publication presents four examples of recent attempts to manage organic waste sustainably in the African context. The participants in the ‘Nairobi organic urban waste’ project have structured this case exercise in order to use the case studies as object lessons, to harvest genuine insights into the feasibility of a variety of ways to successfully and sustainably valorise urban organic waste streams. Three contemporary case examples of compost production are presented. These include composting by a community-based organisation in the Kenyan private sector and by a public-private partnership in Malawi. In all three cases, the project and case study focus is on the relations between city waste and the agricultural supply chain. A fourth case study describes the technical and economic potential to produce and use biogas from urban organic waste

The structural invisibility of outsiders: the role of migrant labour in the meat-processing industry

This article examines the role of migrant workers in meat-processing factories in the UK. Drawing on materials from mixed methods research in a number of case study towns across Wales, we explore the structural and spatial processes that position migrant workers as outsiders. While state policy and immigration controls are often presented as a way of protecting migrant workers from work-based exploitation and ensuring jobs for British workers, our research highlights that the situation ‘on the ground’ is more complex. We argue that ‘self-exploitation’ among the migrant workforce is linked to the strategies of employers and the organisation of work, and that hyper-flexible work patterns have reinforced the spatial and social invisibilities of migrant workers in this sector. While this creates problems for migrant workers, we conclude that it is beneficial to supermarkets looking to supply consumers with the regular supply of cheap food to which they have become accustomed