Concepts of quantum non-Markovianity: a hierarchy

Markovian approximation is a widely-employed idea in descriptions of the dynamics of open quantum systems (OQSs). Although it is usually claimed to be a concept inspired by classical Markovianity, the term quantum Markovianity is used inconsistently and often unrigorously in the literature. In this report we compare the descriptions of classical stochastic processes and quantum stochastic processes (as arising in OQSs), and show that there are inherent differences that lead to the non-trivial problem of characterizing quantum non-Markovianity. Rather than proposing a single definition of quantum Markovianity, we study a host of Markov-related concepts in the quantum regime. Some of these concepts have long been used in quantum theory, such as quantum white noise, factorization approximation, divisibility, Lindblad master equation, etc.. Others are first proposed in this report, including those we call past-future independence, no (quantum) information backflow, and composability. All of these concepts are defined under a unified framework, which allows us to rigorously build hierarchy relations among them. With various examples, we argue that the current most often used definitions of quantum Markovianity in the literature do not fully capture the memoryless property of OQSs. In fact, quantum non-Markovianity is highly context-dependent. The results in this report, summarized as a hierarchy figure, bring clarity to the nature of quantum non-Markovianity.Comment: Clarifications and references added; discussion of the related classical hierarchy significantly improved. To appear in Physics Report

A Gapless, Unambiguous Genome Sequence of the Enterohemorrhagic Escherichia coli O157:H7 Strain EDL933.

Escherichia coli EDL933 is the prototypic strain for enterohemorrhagic E. coli serotype O157:H7, associated with deadly food-borne outbreaks. Because the publicly available sequence of the EDL933 genome has gaps and >6,000 ambiguous base calls, we here present an updated high-quality, unambiguous genome sequence with no assembly gaps

Ultraviolet spectroscopy of narrow coronal mass ejections

We present Ultraviolet Coronagraph Spectrometer (UVCS) observations of 5 narrow coronal mass ejections (CMEs) that were among 15 narrow CMEs originally selected by Gilbert et al. (2001). Two events (1999 March 27, April 15) were "structured", i.e. in white light data they exhibited well defined interior features, and three (1999 May 9, May 21, June 3) were "unstructured", i.e. appeared featureless. In UVCS data the events were seen as 4-13 deg wide enhancements of the strongest coronal lines HI Ly-alpha and OVI (1032,1037 A). We derived electron densities for several of the events from the Large Angle Spectrometric Coronagraph (LASCO) C2 white light observations. They are comparable to or smaller than densities inferred for other CMEs. We modeled the observable properties of examples of the structured (1999 April 15) and unstructured (1999 May 9) narrow CMEs at different heights in the corona between 1.5 and 2 R(Sun). The derived electron temperatures, densities and outflow speeds are similar for those two types of ejections. They were compared with properties of polar coronal jets and other CMEs. We discuss different scenarios of narrow CME formation either as a jet formed by reconnection onto open field lines or CME ejected by expansion of closed field structures. Overall, we conclude that the existing observations do not definitively place the narrow CMEs into the jet or the CME picture, but the acceleration of the 1999 April 15 event resembles acceleration seen in many CMEs, rather than constant speeds or deceleration observed in jets.Comment: AASTeX, 22 pages, incl. 3 figures (2 color) and 3 tables. Accepted for publication in Ap.

Rapid purification of quantum systems by measuring in a feedback-controlled unbiased basis

Rapid-purification by feedback --- specifically, reducing the mean impurity faster than by measurement alone --- can be achieved by making the eigenbasis of the density matrix to be unbiased relative to the measurement basis. Here we further examine the protocol introduced by Combes and Jacobs [Phys.Rev.Lett. {\bf 96}, 010504 (2006)] involving continuous measurement of the observable $J_z$ for a $D$-dimensional system. We rigorously re-derive the lower bound $(2/3)(D+1)$ on the achievable speed-up factor, and also an upper bound, namely $D^2/2$, for all feedback protocols that use measurements in unbiased bases. Finally we extend our results to $n$ independent measurements on a register of $n$ qubits, and derive an upper bound on the achievable speed-up factor that scales linearly with $n$.Comment: v2: published versio

Catastrophic eruption of magnetic flux rope in the corona and solar wind with and without magnetic reconnection

It is generally believed that the magnetic free energy accumulated in the corona serves as a main energy source for solar explosions such as coronal mass ejections (CMEs). In the framework of the flux rope catastrophe model for CMEs, the energy may be abruptly released either by an ideal magnetohydrodynamic (MHD) catastrophe, which belongs to a global magnetic topological instability of the system, or by a fast magnetic reconnection across preexisting or rapidly-developing electric current sheets. Both ways of magnetic energy release are thought to be important to CME dynamics. To disentangle their contributions, we construct a flux rope catastrophe model in the corona and solar wind and compare different cases in which we either prohibit or allow magnetic reconnection to take place across rapidly-growing current sheets during the eruption. It is demonstrated that CMEs, even fast ones, can be produced taking the ideal MHD catastrophe as the only process of magnetic energy release. Nevertheless, the eruptive speed can be significantly enhanced after magnetic reconnection sets in. In addition, a smooth transition from slow to fast eruptions is observed when increasing the strength of the background magnetic field, simply because in a stronger field there is more free magnetic energy at the catastrophic point available to be released during an eruption. This suggests that fast and slow CMEs may have an identical driving mechanism.Comment: 7 pages, 4 figures, ApJ, in press (vol. 666, Sept. 2007

Long-term yogurt consumption and risk of incident hypertension in adults

The Nurses' Health Study and Health Professionals Follow-up Study cohorts are supported by grants UM1 CA186107, UM1 CA176726, and UM1 CA167552 from the National Institutes of Health. The current analyses were supported by small grants from the National Dairy Council, the General Mills Bell Institute for Health and Nutrition, and the Boston Nutrition and Obesity Research Center. The Boston Nutrition Obesity Research Center is administratively based at Boston Medical Center and is funded by the National Institutes of Health (NIH/NIDDK) grant P30DK046200. (UM1 CA186107 - National Institutes of Health; UM1 CA176726 - National Institutes of Health; UM1 CA167552 - National Institutes of Health; small grants from the National Dairy Council; General Mills Bell Institute for Health and Nutrition; Boston Nutrition and Obesity Research Center; P30DK046200 - National Institutes of Health (NIH/NIDDK))Accepted manuscrip

RareVar: A Framework for Detecting Low-Frequency Single-Nucleotide Variants

Accurate identification of low-frequency somatic point mutations in tumor samples has important clinical utilities. Although high-throughput sequencing technology enables capturing such variants while sequencing primary tumor samples, our ability for accurate detection is compromised when the variant frequency is close to the sequencer error rate. Most current experimental and bioinformatic strategies target mutations with ≥5% allele frequency, which limits our ability to understand the cancer etiology and tumor evolution. We present an experimental and computational modeling framework, RareVar, to reliably identify low-frequency single-nucleotide variants from high-throughput sequencing data under standard experimental protocols. RareVar protocol includes a benchmark design by pooling DNAs from already sequenced individuals at various concentrations to target variants at desired frequencies, 0.5%-3% in our case. By applying a generalized, linear model-based, position-specific error model, followed by machine-learning-based variant calibration, our approach outperforms existing methods. Our method can be applied on most capture and sequencing platforms without modifying the experimental protocol

Preferential tau aggregation in von Economo neurons and fork cells in frontotemporal lobar degeneration with specific MAPT variants.

Tau aggregation is a hallmark feature in a subset of patients with frontotemporal dementia (FTD). Early and selective loss of von Economo neurons (VENs) and fork cells within the frontoinsular (FI) and anterior cingulate cortices (ACC) is observed in patients with sporadic behavioral variant FTD (bvFTD) due to frontotemporal lobar degeneration (FTLD), including FTLD with tau inclusions (FTLD-tau). Recently, we further showed that these specialized neurons show preferential aggregation of TDP-43 in FTLD-TDP. Whether VENs and fork cells are prone to tau accumulation in FTLD-tau remains unclear, and no previous studies of these neurons have focused on patients with pathogenic variants in the gene encoding microtubule-associated protein tau (FTLD-tau/MAPT). Here, we examined regional profiles of tau aggregation and neurodegeneration in 40 brain regions in 8 patients with FTLD-tau/MAPT and 7 with Pick's disease (PiD), a sporadic form of FTLD-tau that often presents with bvFTD. We further qualitatively assessed the cellular patterns of frontoinsular tau aggregation in FTLD-tau/MAPT using antibodies specific for tau hyperphosphorylation, acetylation, or conformational change. ACC and mid-insula were among the regions most affected by neurodegeneration and tau aggregation in FTLD-tau/MAPT and PiD. In these two forms of FTLD-tau, severity of regional neurodegeneration and tau protein aggregation were highly correlated across regions. In FTLD-tau/MAPT, VENs and fork cells showed disproportionate tau protein aggregation in patients with V337 M, A152T, and IVS10 + 16 variants, but not in patients with the P301L variant. As seen in FTLD-TDP, our data suggest that VENs and fork cells represent preferentially vulnerable neuron types in most, but not all of the MAPT variants we studied

Detection of skewed X-chromosome inactivation in Fragile X syndrome and X chromosome aneuploidy using quantitative melt analysis.

Methylation of the fragile X mental retardation 1 (FMR1) exon 1/intron 1 boundary positioned fragile X related epigenetic element 2 (FREE2), reveals skewed X-chromosome inactivation (XCI) in fragile X syndrome full mutation (FM: CGG > 200) females. XCI skewing has been also linked to abnormal X-linked gene expression with the broader clinical impact for sex chromosome aneuploidies (SCAs). In this study, 10 FREE2 CpG sites were targeted using methylation specific quantitative melt analysis (MS-QMA), including 3 sites that could not be analysed with previously used EpiTYPER system. The method was applied for detection of skewed XCI in FM females and in different types of SCA. We tested venous blood and saliva DNA collected from 107 controls (CGG < 40), and 148 FM and 90 SCA individuals. MS-QMA identified: (i) most SCAs if combined with a Y chromosome test; (ii) locus-specific XCI skewing towards the hypomethylated state in FM females; and (iii) skewed XCI towards the hypermethylated state in SCA with 3 or more X chromosomes, and in 5% of the 47,XXY individuals. MS-QMA output also showed significant correlation with the EpiTYPER reference method in FM males and females (P < 0.0001) and SCAs (P < 0.05). In conclusion, we demonstrate use of MS-QMA to quantify skewed XCI in two applications with diagnostic utility