One of the main concepts in quantum physics is a density matrix, which is a symmetric positive definite matrix of trace one. Finite probability distributions can be seen as a special case when the density matrix is restricted to be diagonal. We develop a probability calculus based on these more general distributions that includes definitions of joints, conditionals and formulas that relate these, including analogs of the Theorem of Total Probability and various Bayes rules for the calculation of posterior density matrices. The resulting calculus parallels the familiar “conventional” probability calculus and always retains the latter as a special case when all matrices are diagonal. We motivate both the conventional and the generalized Bayes rule with a minimum relative entropy principle, where the Kullbach-Leibler version gives the conventional Bayes rule and Umegaki’s quantum relative entropy the new Bayes rule for density matrices. Whereas the conventional Bayesian methods maintain uncertainty about which model has the highest data likelihood, the generalization maintains uncertainty about which unit direction has the largest variance. Surprisingly the bounds also generalize: as in the conventional setting we upper bound the negative log likelihood of the data by the negative log likelihood of the MAP estimator.

Ebola virus (EBOV) causes a severe, often fatal disease in humans and nonhuman primates. Within the past decade, EBOV has caused two large and difficult-to-control outbreaks, one of which recently ended in the Democratic Republic of the Congo. Bats are the likely reservoir of EBOV, but little is known of their relationship with the virus. We perform serial passages of EBOV in human and bat cells and use circular sequencing to compare the short-term evolution of the virus. Virus populations passaged in bat cells have sequence markers indicative of host RNA editing enzyme activity, including evidence for ADAR editing of the EBOV glycoprotein. Multiple regions in the EBOV genome appear to have undergone adaptive evolution when passaged in bat and human cells. Individual mutated viruses are rescued and characterized. Our results provide insight into the host species-specific evolution of EBOV and highlight the adaptive flexibility of the virus.

Extinction of the woolly mammoth in Beringia has long been subject to research and speculation. Here we use a new geo-referenced database of radiocarbon-dated evidence to show that mammoths were abundant in the open-habitat of Marine Isotope Stage 3 (∼45-30 ka). During the Last Glacial Maximum (∼25-20 ka), northern populations declined while those in interior Siberia increased. Northern mammoths increased after the glacial maximum, but declined at and after the Younger Dryas (∼12.9-11.5 ka). Remaining continental mammoths, now concentrated in the north, disappeared in the early Holocene with development of extensive peatlands, wet tundra, birch shrubland and coniferous forest. Long sympatry in Siberia suggests that humans may be best seen as a synergistic cofactor in that extirpation. The extinction of island populations occurred at ∼4 ka. Mammoth extinction was not due to a single cause, but followed a long trajectory in concert with changes in climate, habitat and human presence.

The experimental data on fragment multiplicities, their energy and charge distributions, the emission times are considered for the nuclear multifragmentation process induced by relativistic light projectiles (protons, helium) and heavy ions. With light projectiles, the multifragmentation is a pure "thermal" process, well described by the statistical models. Heavy-ion-induced multifragmentation is influenced by dynamic effects related first of all to the compression of the system in the collision. But statistical models can also be applied to rendering the partition of the system if the excitation energy is less than 10 MeV/nucleon and compression is modest. For the central collision of heavy ions the statistical approach fails to describe the data.

Phase transition in highly excited nucleus is treated in terms of thermo-dynamics of microensembles. The emission of intermediate mass fragments from pure thermally excited heavy nucleus 197Au is an indication of the liquid to fog phase transition. Evidence of the spinodal decomposition of the heavy nuclear system is found and its relation to the multisaddle transition configuration and freeze-out state is presented.

We present the high-quality genome sequence of a ∼45,000-year-old modern human male from Siberia. This individual derives from a population that lived before-or simultaneously with-the separation of the populations in western and eastern Eurasia and carries a similar amount of Neanderthal ancestry as present-day Eurasians. However, the genomic segments of Neanderthal ancestry are substantially longer than those observed in present-day individuals, indicating that Neanderthal gene flow into the ancestors of this individual occurred 7,000-13,000 years before he lived. We estimate an autosomal mutation rate of 0.4 × 10(-9) to 0.6 × 10(-9) per site per year, a Y chromosomal mutation rate of 0.7 × 10(-9) to 0.9 × 10(-9) per site per year based on the additional substitutions that have occurred in present-day non-Africans compared to this genome, and a mitochondrial mutation rate of 1.8 × 10(-8) to 3.2 × 10(-8) per site per year based on the age of the bone.

The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived^1-8. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000-30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located.

We present measurements of the branching fraction and time-dependent CP asymmetries in B0→J/ψπ0 decays based on (231.8±2.6) ×106Υ(4S)→BB̄ decays collected with the BABAR detector at the SLAC PEP-II asymmetric-energy B factory. We obtain a branching fraction B(B0→J/ψπ0)=(1.94±0.22(stat)±0.17(syst))×10-5. We also measure the CP asymmetry parameters C=-0.21±0.26(stat)±0. 06(syst) and S=-0.68±0.30(stat)±0.04(syst). © 2006 The American Physical Society.