Microbial imbalance in inflammatory bowel disease patients at different taxonomic levels

Background Inflammatory bowel disease (IBD), is a debilitating group of chronic diseases including Crohn’s Disease (CD) and ulcerative colitis (UC), which causes inflammation of the gut and affects millions of people worldwide. At different taxonomic levels, the structure of the gut microbiota is significantly altered in IBD patients compared to that of healthy individuals. However, it is unclear how these IBD-affected bacterial groups are related to other common bacteria in the gut, and how they are connected across different disease conditions at the global scale. Results In this study, using faecal samples from patients with IBD, we show through diversity analysis of the microbial community structure based on the 16S rRNA gene that the gut microbiome of IBD patients is less diverse compared to healthy individuals. Furthermore, we have identified which bacterial groups change in abundance in both CD and UC compared to healthy controls. A substantial imbalance was observed across four major bacterial phyla including Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria, which together constitute >98% of the gut microbiota. Next, we reconstructed a bacterial family co-abundance network based on the correlation of abundance profiles obtained from the public gut microbiome data of >22000 samples of faecal and gut biopsies taken from both diseased and healthy individuals. The data was compiled using the EBI metagenomics database [1]. By mapping IBD-altered bacterial families to the network, we show that the bacterial families which exhibit an increased abundance in IBD conditions are not well connected to other groups, implying that these families generally do not coexist together with common gut organisms. Whereas, the bacterial families whose abundance is reduced or did not change in IBD conditions compared to healthy conditions are very well connected to other bacterial groups, suggesting they are highly important groups of bacteria in the gut that can coexist with other bacteria across a range of conditions. Conclusions IBD patients exhibited a less diverse gut microbiome compared to healthy individuals. Bacterial groups which changed in IBD patients were found to be groups which do not co-exist well with common commensal gut bacteria, whereas bacterial groups which did not change in patients with IBD were found to commonly co-exist with commensal gut microbiota. This gives a potential insight into the dynamics of the gut microbiota in patients with IBD

Mapping the optimal route between two quantum states

A central feature of quantum mechanics is that a measurement is intrinsically probabilistic. As a result, continuously monitoring a quantum system will randomly perturb its natural unitary evolution. The ability to control a quantum system in the presence of these fluctuations is of increasing importance in quantum information processing and finds application in fields ranging from nuclear magnetic resonance to chemical synthesis. A detailed understanding of this stochastic evolution is essential for the development of optimized control methods. Here we reconstruct the individual quantum trajectories of a superconducting circuit that evolves in competition between continuous weak measurement and driven unitary evolution. By tracking individual trajectories that evolve between an arbitrary choice of initial and final states we can deduce the most probable path through quantum state space. These pre- and post-selected quantum trajectories also reveal the optimal detector signal in the form of a smooth time-continuous function that connects the desired boundary conditions. Our investigation reveals the rich interplay between measurement dynamics, typically associated with wave function collapse, and unitary evolution of the quantum state as described by the Schrodinger equation. These results and the underlying theory, based on a principle of least action, reveal the optimal route from initial to final states, and may enable new quantum control methods for state steering and information processing.Comment: 12 pages, 9 figure

Quantum Fluctuations in the Chirped Pendulum

An anharmonic oscillator when driven with a fast, frequency chirped voltage pulse can oscillate with either small or large amplitude depending on whether the drive voltage is below or above a critical value-a well studied classical phenomenon known as autoresonance. Using a 6 GHz superconducting resonator embedded with a Josephson tunnel junction, we have studied for the first time the role of noise in this non-equilibrium system and find that the width of the threshold for capture into autoresonance decreases as the square root of T, and saturates below 150 mK due to zero point motion of the oscillator. This unique scaling results from the non-equilibrium excitation where fluctuations, both quantum and classical, only determine the initial oscillator motion and not its subsequent dynamics. We have investigated this paradigm in an electrical circuit but our findings are applicable to all out of equilibrium nonlinear oscillators.Comment: 5 pages, 4 figure

Crohn's disease activity index and Vienna classification - Is it worthwhile to calculate before surgery?

Background: Crohn's disease (CD) patients with increased disease activity may reveal an increased risk for perioperative complications. The `Crohn's disease activity index' (CDAI) and the `Vienna classification' (VC) were developed for standardized disease activity estimations. The significance of these scores to predict extent, type and early outcome of surgery in CD patients was analyzed. Methods: In 179 surgically treated CD patients, the CDAI and VC were assessed from a prospective database. Relations of the scores with CD risk factors, type, number, location and complications of surgery were analyzed. Results: VC behavior and location subtypes were associated with distinct types of surgery (i.e. `strictureplasty' in `stricturing disease', `colon surgery' in `colon involvement'), but not with surgery type and extent or outcome. Surgery extent (i.e. with 5 vs. 3 `surgical sites' 425 +/- 25 vs. 223.3 +/- 25) and complications (357.1 +/- 36.9 (with) vs. 244.4 +/- 13 (without)) were associated with elevated CDAI levels; however, nicotine abuse remained the only significant risk factor for perioperative complications after multiple logistic regression. Conclusion: The significance of VC or CDAI for predicting the extent of surgery or complications is limited. None of the tested variables except preoperative nicotine abuse influenced the likelihood for perioperative complications. Copyright (c) 2006 S. Karger AG, Base

Quantum feedback control of a superconducting qubit: Persistent Rabi oscillations

The act of measurement bridges the quantum and classical worlds by projecting a superposition of possible states into a single, albeit probabilistic, outcome. The time-scale of this "instantaneous" process can be stretched using weak measurements so that it takes the form of a gradual random walk towards a final state. Remarkably, the interim measurement record is sufficient to continuously track and steer the quantum state using feedback. We monitor the dynamics of a resonantly driven quantum two-level system -- a superconducting quantum bit --using a near-noiseless parametric amplifier. The high-fidelity measurement output is used to actively stabilize the phase of Rabi oscillations, enabling them to persist indefinitely. This new functionality shows promise for fighting decoherence and defines a path for continuous quantum error correction.Comment: Manuscript: 5 Pages and 3 figures ; Supplementary Information: 9 pages and 3 figure