Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth-death SIR model

The evolution of RNA viruses such as HIV, Hepatitis C and Influenza virus occurs so rapidly that the viruses' genomes contain information on past ecological dynamics. Hence, we develop a phylodynamic method that enables the joint estimation of epidemiological parameters and phylogenetic history. Based on a compartmental susceptible-infected-removed (SIR) model, this method provides separate information on incidence and prevalence of infections. Detailed information on the interaction of host population dynamics and evolutionary history can inform decisions on how to contain or entirely avoid disease outbreaks. We apply our Birth-Death SIR method (BDSIR) to two viral data sets. First, five human immunodeficiency virus type 1 clusters sampled in the United Kingdom between 1999 and 2003 are analyzed. The estimated basic reproduction ratios range from 1.9 to 3.2 among the clusters. All clusters show a decline in the growth rate of the local epidemic in the middle or end of the 90's. The analysis of a hepatitis C virus (HCV) genotype 2c data set shows that the local epidemic in the C\'ordoban city Cruz del Eje originated around 1906 (median), coinciding with an immigration wave from Europe to central Argentina that dates from 1880--1920. The estimated time of epidemic peak is around 1970.Comment: Journal link: http://rsif.royalsocietypublishing.org/content/11/94/20131106.ful

Epigenetic Profiling Reveals a Developmental Decrease in Promoter Accessibility During Cortical Maturation in vivo

Axon regeneration in adult central nervous system (CNS) is limited in part by a developmental decline in the ability of injured neurons to re-express needed regeneration associated genes (RAGs). Adult CNS neurons may lack appropriate pro-regenerative transcription factors, or may display chromatin structure that restricts transcriptional access to RAGs. Here we performed epigenetic profiling around the promoter regions of key RAGs, and found progressive restriction across a time course of cortical maturation. These data identify a potential intrinsic constraint to axon growth in adult CNS neurons. Neurite outgrowth from cultured postnatal cortical neurons, however, proved insensitive to treatments that improve axon growth in other cell types, including combinatorial overexpression of AP1 factors, overexpression of histone acetyltransferases, and pharmacological inhibitors of histone deacetylases. This insensitivity could be due to intermediate chromatin closure at the time of culture, and highlights important differences in cell culture models used to test potential pro-regenerative interventions

Planetary nebulae after common-envelope phases initiated by low-mass red giants

It is likely that at least some planetary nebulae are composed of matter which was ejected from a binary star system during common-envelope (CE) evolution. For these planetary nebulae the ionizing component is the hot and luminous remnant of a giant which had its envelope ejected by a companion in the process of spiralling-in to its current short-period orbit. A large fraction of CE phases which end with ejection of the envelope are thought to be initiated by low-mass red giants, giants with inert, degenerate helium cores. We discuss the possible end-of-CE structures of such stars and their subsequent evolution to investigate for which structures planetary nebulae are formed. We assume that a planetary nebula forms if the remnant reaches an effective temperature greater than 30 kK within 10^4 yr of ejecting its envelope. We assume that the composition profile is unchanged during the CE phase so that possible remnant structures are parametrized by the end-of-CE core mass, envelope mass and entropy profile. We find that planetary nebulae are expected in post-CE systems with core masses greater than about 0.3 solar masses if remnants end the CE phase in thermal equilibrium. We show that whether the remnant undergoes a pre-white dwarf plateau phase depends on the prescribed end-of-CE envelope mass. Thus, observing a young post-CE system would constrain the end-of CE envelope mass and post-CE evolution.Comment: Published in MNRAS. 12 pages, 12 figures. Minor changes to match published versio

Synthetic aperture radar imagery of airports and surrounding areas: Study of clutter at grazing angles and their polarimetric properties

The statistical description of ground clutter at an airport and in the surrounding area is addressed. These data are being utilized in a program to detect microbursts. Synthetic aperture radar data were collected at the Denver Stapleton Airport. Mountain terrain data were examined to determine if they may potentially contribute to range ambiguity problems and degrade microburst detection. Results suggest that mountain clutter may not present a special problem source. The examination of clutter at small grazing angles was continued by examining data collected at especially low altitudes. Cultural objects such as buildings produce strong sources of backscatter at angles of about 85 deg, with responses of 30 dB to 60 dB above the background. Otherwise there are a few sources which produce significant scatter. The polarization properties of hydrospheres and clutter were examined with the intent of determining the optimum polarization. This polarization was determined to be dependent upon the ratio of VV and HH polarizations of both rain and ground clutter

Beyond postcolonial: expression of self and exploration of the infinite in the writing of Jorge Luis Borges

Studies of postcolonial literature often focus on works that pertain to the East such as African or Indian nations. Written works such as Things Fall Apart by Chinua Achebe, and film such as Bollywood or Nollywood offer perspective for students of English Literature on the struggle of Eastern writers and filmmakers for acceptance into the canon. Some critics, such as Edna Aizenberg, have addressed the question of whether postcolonialism should include Latin American writers. In this work, I contend that Argentine writer Jorge Luis Borges does have a place in postcolonial studies, although I assert that he takes postcolonialism to a new level - beyond the politically charged works of most postcolonial writers. This essay explores the effects that Borges\u27 life has had on his works, as well as his ability to convey the essence of his homeland with a style that combines the tropes of the center with those of Latin America, and in so doing, shows how Borges has transcended the barriers of the European canon for Latin American writers --Document

Values, nation building and control: The Singapore mass media in the next lap

1990 marked a significant change in the political history of Singapore – it was the year Mr. Lee Kuan Yew handed over his role as Singapore’s leader to Mr. Goh Chok Tong. Termed “The Next Lap”, this new period of Singapore’s history was heralded in as a period of change and new directions for Singapore and Singaporeans. This thesis explores the introduction of the Next Lap, the promises of positive changes and the potential effect this new era may have on the Singapore Government’s intimate relationship with and control of the media as a Nation Building apparatus. It looks at the Government’s continued desire to control the media and struggle to re-negotiate its position due to the development of new media technologies, such as satellite television, which have the ability to elude direct control over its broadcasting capacity.The mass media in Singapore have always been strictly controlled through the practice of censorship, strict broadcasting guidelines (and severe penalties for those who do not abide by these guidelines) as well as self-censorship. Through strict control of the mass media, the Government has been able to use it to promote desirable values which have been identified as crucial to the process of Nation Building. These values include putting the nation before community and the community before self, the importance of the family as the basic unit of society and racial and religious harmony. However, recently there have been signs that the Singapore Government has realised the need to make some changes to their broadcasting policies. The change coincided with the transfer of leadership from the former Prime Minister, Lee Kuan Yew, to the current Prime Minister, Goh Chok Tong. When he came into office, Prime Minister Goh promised that there would be more openness. This thesis examines how the policy of \u27openness\u27 applies to the mass media and the possible consequences of the changes implicit in the new policy on the mass media. Results of the change in political climate are reflected in the recent introduction of three pay television channels in Singapore and a review of the censorship laws. To many Singaporeans, this is a welcome: sign, an opportunity for more choice. To the Government, it involves an important question: To what degree should they relax control over the media and bow to the demands of the public for more freedom and choice. The relationship between the Next Lap and the mass media will be examined through the application of Hobsbawm\u27s (1983) theory of invented traditions\u27, Bhabha\u27s (1990a) discussions on the difficulties of locating a nation1 s cultural identity and Foucault\u27s (1979) analysis on the art of government. By applying these theories, I will show that the Next Lap.is an ongoing process of Singapore political and social construction. With the apparent change in the political climate in Singapore, it is timely to explore the relationship between the Government and the mass media after 25 years of independence. By looking at the important social. and political variables, I will show that the relaxation of mass media in the Next Lap represents a continuation of the Singaporean government\u27s \u27desire to control the media for Nation Building activities