Browsing by Author "Wang, S"

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    A participatory framework for feasibility assessments of climate change resilience strategies for smallholders: lessons from coffee cooperatives in Latin America
    (International Journal of Agricultural Sustainability) Shapiro-Garza, E; King, D; Rivera-Aguirre, A; Wang, S; Finley-Lezcano, J
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    Behavior of Raman modes in InPBi alloys under hydrostatic pressure
    (AIP Advances, 2019-03) Zheng, C; Wang, X; Ning, J; Ding, K; Sun, B; Wang, S; Xu, S
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    High Multiplicity Infection by HIV-1 in Men Who Have Sex with Men.
    (PLoS pathogens, 2010) Li, H; Bar, KJ; Wang, S; Decker, JM; Chen, Y; Sun, C; Salazar Gonzalez, JF; Salazar, MG; Learn, GH; Morgan, CJ; Schumacher, JE; Hraber, P; Giorgi, EE; Bhattacharya, T; Korber, BT; Perelson, AS; Eron, JJ; Cohen, MS; Hicks, CB; Haynes, BF; Markowitz, M; Keele, BF; Hahn, BH; Shaw, GM
    Elucidating virus-host interactions responsible for HIV-1 transmission is important for advancing HIV-1 prevention strategies. To this end, single genome amplification (SGA) and sequencing of HIV-1 within the context of a model of random virus evolution has made possible for the first time an unambiguous identification of transmitted/founder viruses and a precise estimation of their numbers. Here, we applied this approach to HIV-1 env analyses in a cohort of acutely infected men who have sex with men (MSM) and found that a high proportion (10 of 28; 36%) had been productively infected by more than one virus. In subjects with multivariant transmission, the minimum number of transmitted viruses ranged from 2 to 10 with viral recombination leading to rapid and extensive genetic shuffling among virus lineages. A combined analysis of these results, together with recently published findings based on identical SGA methods in largely heterosexual (HSX) cohorts, revealed a significantly higher frequency of multivariant transmission in MSM than in HSX [19 of 50 subjects (38%) versus 34 of 175 subjects (19%); Fisher's exact p = 0.008]. To further evaluate the SGA strategy for identifying transmitted/founder viruses, we analyzed 239 overlapping 5' and 3' half genome or env-only sequences from plasma viral RNA (vRNA) and blood mononuclear cell DNA in an MSM subject who had a particularly well-documented virus exposure history 3-6 days before symptom onset and 14-17 days before peak plasma viremia (47,600,000 vRNA molecules/ml). All 239 sequences coalesced to a single transmitted/founder virus genome in a time frame consistent with the clinical history, and a molecular clone of this genome encoded replication competent virus in accord with model predictions. Higher multiplicity of HIV-1 infection in MSM compared with HSX is consistent with the demonstrably higher epidemiological risk of virus acquisition in MSM and could indicate a greater challenge for HIV-1 vaccines than previously recognized.
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    Multidimensional mechanism design: Finite-dimensional approximations and efficient computation
    (Operations Research, 2010-07-01) Belloni, A; Lopomo, G; Wang, S
    Multidimensional mechanism design problems have proven difficult to solve by extending techniques from the onedimensional case. This paper considers mechanism design problems with multidimensional types when the seller's cost function is not separable across buyers. By adapting results obtained by Border [Border, K. 1991. Implementation of reduced form auctions: A geometric approach. Econometrica 59 1175-1187], we transform the seller's problem into a representation that only involves "interim" variables and eliminates the dimensionality dependence on the number of buyers. We show that the associated infinite-dimensional optimization problem posed by the theoretical model can be approximated arbitrarily well by a sequence of finite-dimensional linear programming problems. We provide an efficient-i.e., terminating in polynomial time in the problem size-method to compute the separation oracle associated with the Border constraints and incentive compatibility constraints. This implies that our finite-dimensional approximation is solvable in polynomial time. Finally, we illustrate how the numerical solutions of the finite-dimensional approximations can provide insights into the nature of optimal solutions to the infinite-dimensional problem in particular cases. ©2010 INFORMS.
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    Nanoscale Resonance Energy Transfer-Based Devices for Probabilistic Computing
    (IEEE Micro, 2015-09-01) Lebeck, AR; Dwyer, CL; Wang, S
    © 1981-2012 IEEE.Despite the theoretical advances in probabilistic computing, a fundamental mismatch persists between the deterministic hardware that traditional computers use and the stochastic nature of probabilistic algorithms. In this article, the authors propose Resonance Energy Transfer (RET) between chromophores as an enabling technology for probabilistic computing functional units. As a natural continuous-time Markov chain, RET networks can physically implement efficient samplers with arbitrary probability distributions and have great potential for accelerating probabilistic algorithms.