HIV and AIDS in the Russian Federation : prisons as a case study of risk environments and agency

This thesis explores Russian prisons as risk environments for the spread of HIV through intravenous drug use. The Russian HIV epidemic is extremely fast growing, and though exact prevalence rates are unknown, the epidemic is now considered generalized as estimated prevalence rates exceed one percent of the Russian population. After decades of foreign-aid and interventions in African nations have largely failed to address the HIV epidemic, social scientists now attribute HIV infection to risk environments created by low levels of social cohesion and a lack of agency. Within my research, I explore Russian male prisons and the role risk environments and agency play in the spread of HIV. I review recently published literature, government statistics, as well as reports published by non-governmental organizations. I then analyze and interpret these data, draw conclusions and inferences regarding the spread of HIV within Russian prison risk environments.Russian, East European, and Eurasian Studie

Phylogenetic patterns recover known HIV epidemiological relationships and reveal common transmission of multiple variants.

The growth of human immunodeficiency virus (HIV) sequence databases resulting from drug resistance testing has motivated efforts using phylogenetic methods to assess how HIV spreads1-4. Such inference is potentially both powerful and useful for tracking the epidemiology of HIV and the allocation of resources to prevention campaigns. We recently used simulation and a small number of illustrative cases to show that certain phylogenetic patterns are associated with different types of epidemiological linkage5. Our original approach was later generalized for large next-generation sequencing datasets and implemented as a free computational pipeline6. Previous work has claimed that direction and directness of transmission could not be established from phylogeny because one could not be sure that there were no intervening or missing links involved7-9. Here, we address this issue by investigating phylogenetic patterns from 272 previously identified HIV transmission chains with 955 transmission pairs representing diverse geography, risk groups, subtypes, and genomic regions. These HIV transmissions had known linkage based on epidemiological information such as partner studies, mother-to-child transmission, pairs identified by contact tracing, and criminal cases. We show that the resulting phylogeny inferred from real HIV genetic sequences indeed reveals distinct patterns associated with direct transmission contra transmissions from a common source. Thus, our results establish how to interpret phylogenetic trees based on HIV sequences when tracking who-infected-whom, when and how genetic information can be used for improved tracking of HIV spread. We also investigate limitations that stem from limited sampling and genetic time-trends in the donor and recipient HIV populations

Unsupervised learning with contrastive latent variable models

In unsupervised learning, dimensionality reduction is an important tool for data exploration and visualization. Because these aims are typically open-ended, it can be useful to frame the problem as looking for patterns that are enriched in one dataset relative to another. These pairs of datasets occur commonly, for instance a population of interest vs. control or signal vs. signal free recordings.However, there are few methods that work on sets of data as opposed to data points or sequences. Here, we present a probabilistic model for dimensionality reduction to discover signal that is enriched in the target dataset relative to the background dataset. The data in these sets do not need to be paired or grouped beyond set membership. By using a probabilistic model where some structure is shared amongst the two datasets and some is unique to the target dataset, we are able to recover interesting structure in the latent space of the target dataset. The method also has the advantages of a probabilistic model, namely that it allows for the incorporation of prior information, handles missing data, and can be generalized to different distributional assumptions. We describe several possible variations of the model and demonstrate the application of the technique to de-noising, feature selection, and subgroup discovery settings

Neutrino Mixings in SO(10) with Type II Seesaw and theta_{13}

We analyze a class of supersymmetric SO(10) grand unified theories with type II seesaw for neutrino masses, where the contribution to PMNS matrix from the neutrino sector has an exact tri-bi-maximal (TBM) form, dictated by a broken S_4 symmetry. The Higgs fields that determine the fermion masses are two 10 fields and one 126 field, with the latter simultaneously contributing to neutrino as well as charged fermion masses. Fitting charged fermion masses and the CKM mixings lead to corrections to the TBM mixing that determine the final PMNS matrix with the predictions theta_{13} ~ 4-6 degrees and the Dirac CP phase to be between -10 and +15 degrees. We also show correlations between various mixing angles which can be used to test the model.Comment: 16 pages, 4 figures, 2 tables; typos corrected in Eq. (4) and Table I

Love, Will, and the Intellectual Ascents

Augustine’s accounts of his so-called mystical experiences in conf. 7.10.16, 17.23, and 9.10.24 are puzzling. The primary problem is that, although in all three accounts he claims to have seen “that which is,” we have no satisfactory account of what “that which is” is supposed to be. I shall be arguing that, contrary to a common interpretation, Augustine’s intellectual “seeing” of “being” in Books 7 and 9 was not a vision of the Christian God as a whole, nor of one of the divine persons, each of whom is equally God, according to Augustine. This becomes clear when we attend to the fact that Augustine is appropriating a specific meaning of “that which is” or “being” used by Plotinus in his account of the lover of Beauty. This resolution, however, leads to a second question. Is there anything distinctively Christian about any, or all, of Augustine’s ascents? On the one hand, it would be odd if there were not, given that the Confessions are addressed to the Christian God. On the other hand, upon close inspection we find that the allegedly specific “Christian” characteristics that modern commentators have identified in the ascents of conf. 7 and 9 also occur in the Neoplatonists. I will argue that there is in fact one important difference between Augustine and the Neoplatonists here that has not been pointed out in these prior interpretations

CHANGING STRUCTURES IN THE BARLEY PRODUCTION AND MALTING INDUSTRIES OF THE UNITED STATES AND CANADA

Substantial changes have taken place recently in the regulation of agricultural trade in North America. The effect of these changes on trade in agricultural commodities is of particular interest to producers and policymakers in the Northern Plains and Rockies region. In this paper, we discuss specifically the malt barley production, malting, and brewing industries in light of these new trade agreements and their ramifications. We evaluate the incentives that free trade provides for mergers between barley malting firms, and then we assess the consequences of these mergers on the realized gains from trade for consumers, barley producers, and malting firms. The globalization of markets has fundamentally changed the world in which economic agents operate. Trade has been liberalized through multilateral world-wide agreements such as the General Agreement on Trade and Tariffs (GATT) and through regional free trade agreements such as those within the European Union, the Canadian/United States Trade Agreement (CUSTA), and the North American Free Trade Agreement (NAFTA). A striking phenomena which has accompanied trade liberalization has been the international merger of firms and the creation of many jointly owned multinational operations. There are two distinct types of malt barley that differ in their yield and in their production areas in North America. Montana and the Canadian provinces grow primarily high-quality two row barley, while North Dakota and Minnesota produce primarily six row malting varieties. Two row barley yields more malt per bushel for maltsters, but it is more prone to disease for barley producers. The opening of the border between the United States and Canada has made large quantities of two row barley available to U.S. malting firms and brewers. The trade policy literature suggests that trade liberalization will have a profound impact on domestic policy choice, making the costs of any government action to increase market prices above the prevailing world price more expensive. Open borders should also provide discipline on how industries price in the domestic market. With import restrictions such as tariffs in place, the non-competitive industry structures that raise prices in the domestic market can exist with limited fear of foreign competition. With freer trade, however, the industry faces more potential competition. When a free trade policy merges formally distinct markets for which stable industry structures exist, this creates additional incentives for mergers within the newly combined industry that reduce these gains from free trade. This analysis was motivated by observing the malting barley industry in Canada and the United States. In 1985, prior to CUSTA, the two domestic markets for barley malt were distinctly separated by import license requirements into Canada and import tariffs in the United States. As such, both countries had large malting industries, but there was little trade flow between the two countries in malting barley, in barley malt, or in beer. Four firms controlled 90 percent of the Canadian malting market, and six firms controlled over 80 percent of the U.S. malting market before CUSTA. As a result of mergers after CUSTA, five firms owned 90 percent of the malting capacity in North America. Economies of scale and elimination of high cost plants often drive industry consolidation. Interestingly enough, despite all of the merger activity among malting firms, there were very few plant closures and very little new capacity built. Even new entrants to either the United States or Canadian industries purchased the assets of existing firms, rather than building new plants. We review relevant literature for firm behavior and report the results of a model for the incentives for plant mergers in the North American malting industry following CUSTA. We evaluate malting firm profits, the changes in malting margins, the price effects, and the overall welfare effects of the creation of the free trade area and subsequent mergers within the industry. We found that free trade, in the absence of mergers, increases output in both countries and reduces malting margins leading to large gains for consumers and producers of malt barley. The agreement, however, also increases incentives for mergers. With the mergers that took place, we show that merging barley malting firms have incentives to decrease output by about 21 percent, while their producers' surplus increased by approximately 34 percent. The net benefits of free trade to consumers and input suppliers are reduced by mergers, while the profits of merging firms are increased by them. Overall, with free trade and mergers, there is still a net social gain relative to pre-CUSTA. Malt production in Canada increases by over 12 percent, while that in the U.S. is slightly lower, leaving North American consumers, firms, and barley producers better off.malting barley, industry concentration, free trade agreement, Industrial Organization, Q1, F1,

Origins of choice-related activity in mouse somatosensory cortex.

During perceptual decisions about faint or ambiguous sensory stimuli, even identical stimuli can produce different choices. Spike trains from sensory cortex neurons can predict trial-to-trial variability in choice. Choice-related spiking is widely studied as a way to link cortical activity to perception, but its origins remain unclear. Using imaging and electrophysiology, we found that mouse primary somatosensory cortex neurons showed robust choice-related activity during a tactile detection task. Spike trains from primary mechanoreceptive neurons did not predict choices about identical stimuli. Spike trains from thalamic relay neurons showed highly transient, weak choice-related activity. Intracellular recordings in cortex revealed a prolonged choice-related depolarization in most neurons that was not accounted for by feed-forward thalamic input. Top-down axons projecting from secondary to primary somatosensory cortex signaled choice. An intracellular measure of stimulus sensitivity determined which neurons converted choice-related depolarization into spiking. Our results reveal how choice-related spiking emerges across neural circuits and within single neurons

Composable computation in discrete chemical reaction networks

We study the composability of discrete chemical reaction networks (CRNs) that stably compute (i.e., with probability 0 of error) integer-valued functions $f:\mathbb{N}^d\to\mathbb{N}$. We consider output-oblivious CRNs in which the output species is never a reactant (input) to any reaction. The class of output-oblivious CRNs is fundamental, appearing in earlier studies of CRN computation, because it is precisely the class of CRNs that can be composed by simply renaming the output of the upstream CRN to match the input of the downstream CRN. Our main theorem precisely characterizes the functions $f$ stably computable by output-oblivious CRNs with an initial leader. The key necessary condition is that for sufficiently large inputs, $f$ is the minimum of a finite number of nondecreasing quilt-affine functions. (An affine function is linear with a constant offset; a quilt-affine function is linear with a periodic offset)