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Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection
A mathematical model of random viral evolution and phylogenetic tree construction is developed and used to analyze 3,449 complete env sequences derived by single genome amplification from 102 subjects with acute HIV-1 (clade B) infection, suggesting a finite window of potential vulnerability of HIV- 1 to vaccine-elicited immune responses, although phenotypic properties of transmitted Envs pose a formidable defense.
Timing the ancestor of the HIV-1 pandemic strains.
Using a comprehensive full-length envelope sequence alignment, the date of the last common ancestor of the main group of HIV-1 is estimated to be 1931 (1915-41).
The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection
Kinetic analysis and mathematical modeling of virus immune escape showed that the contribution of CD8 T cell–mediated killing of productively infected cells was earlier and much greater than previously recognized and that it contributed to the initial decline of plasma virus in acute infection.
Chiral and deconfinement aspects of the QCD transition
We present results on the chiral and deconfinement properties of the QCD transition at finite temperature. Calculations are performed with 2 + 1 flavors of quarks using the p4, asqtad, and HISQ/tree
Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection
Viral properties associated with mucosal HIV-1 transmission and a limited set of rapidly evolving adaptive mutations driven primarily, but not exclusively, by early cytotoxic T cell responses are revealed.
On Mixup Training: Improved Calibration and Predictive Uncertainty for Deep Neural Networks
DNNs trained with mixup are significantly better calibrated and are less prone to over-confident predictions on out-of-distribution and random-noise data, suggesting that mixup be employed for classification tasks where predictive uncertainty is a significant concern.
Equation of state in ( 2+1 )-flavor QCD
We present results for the equation of state in ( 2 + 1 )-flavor QCD using the highly improved staggered quark action and lattices with temporal extent N τ = 6 , 8, 10, and 12. We show that these
Transmission of Single HIV-1 Genomes and Dynamics of Early Immune Escape Revealed by Ultra-Deep Sequencing
Traces of immune escape were observed in the earliest samples, suggesting that immune pressure is present and effective earlier than previously reported; quantifying the loss rate of the founder virus suggests a direct role for CD8 T-lymphocyte responses in viral containment after peak viremia.
Diversity Considerations in HIV-1 Vaccine Selection
Consensus or ancestor sequences could be used in vaccine design to minimize the genetic differences between vaccine strains and contemporary isolates, effectively reducing the extent of diversity by half.