Subspace confinement : how good is your qubit?

The basic operating element of standard quantum computation is the qubit, an isolated two-level system that can be accurately controlled, initialized and measured. However, the majority of proposed physical architectures for quantum computation are built from systems that contain much more complicated Hilbert space structures. Hence, defining a qubit requires the identification of an appropriate controllable two-dimensional sub-system. This prompts the obvious question of how well a qubit, thus defined, is confined to this subspace, and whether we can experimentally quantify the potential leakage into states outside the qubit subspace. We demonstrate how subspace leakage can be characterized using minimal theoretical assumptions by examining the Fourier spectrum of the oscillation experiment

Avian Resistance to Campylobacter jejuni Colonization Is Associated with an Intestinal Immunogene Expression Signature Identified by mRNA Sequencing

peer-reviewedThis research was funded by the The Irish Department of Agriculture and Food’s Food Institutional Research Measure (http://www.agriculture.gov.ie/ research/foodinstitutionalresearchmeasurefirm) – Grant No: 06_RDD_486.Campylobacter jejuni is the most common cause of human bacterial gastroenteritis and is associated with several post-infectious manifestations, including onset of the autoimmune neuropathy Guillain-Barré syndrome, causing significant morbidity and mortality. Poorly-cooked chicken meat is the most frequent source of infection as C. jejuni colonizes the avian intestine in a commensal relationship. However, not all chickens are equally colonized and resistance seems to be genetically determined. We hypothesize that differences in immune response may contribute to variation in colonization levels between susceptible and resistant birds. Using high-throughput sequencing in an avian infection model, we investigate gene expression associated with resistance or susceptibility to colonization of the gastrointestinal tract with C. jejuni and find that gut related immune mechanisms are critical for regulating colonization. Amongst a single population of 300 4-week old chickens, there was clear segregation in levels of C. jejuni colonization 48 hours post-exposure. RNAseq analysis of caecal tissue from 14 C. jejuni-susceptible and 14 C. jejuni-resistant birds generated over 363 million short mRNA sequences which were investigated to identify 219 differentially expressed genes. Significantly higher expression of genes involved in the innate immune response, cytokine signaling, B cell and T cell activation and immunoglobulin production, as well as the renin-angiotensin system was observed in resistant birds, suggesting an early active immune response to C. jejuni. Lower expression of these genes in colonized birds suggests suppression or inhibition of a clearing immune response thus facilitating commensal colonization and generating vectors for zoonotic transmission. This study describes biological processes regulating C. jejuni colonization of the avian intestine and gives insight into the differential immune mechanisms incited in response to commensal bacteria in general within vertebrate populations. The results reported here illustrate how an exaggerated immune response may be elicited in a subset of the population, which alters host-microbe interactions and inhibits the commensal state, therefore having wider relevance with regard to inflammatory and autoimmune disease

Critical Timescales for Burrowing in Undersea Substrates via Localized Fluidization, Demonstrated by RoboClam: A Robot Inspired by Atlantic Razor Clams

The Atlantic razor clam (Ensis directus) burrows into underwater soil by using motions of its shell to locally fluidize the surrounding substrate. The energy associated with movement through fluidized soil — characterized by a depth-independent density and viscosity — scales linearly with depth. In contrast, moving through static soil requires energy that scales with depth squared. For E. directus, this translates to a 10X reduction in the energy required to reach observed burrow depths. For engineers, localized fluidization offers a mechanically simple and purely kinematic method to dramatically reduce burrowing energy. This concept is demonstrated with RoboClam, an E. directus-inspired robot. Using a genetic algorithm to generate digging kinematics, RoboClam has achieved localized fluidization and burrowing performance comparable to that of the animal, with a linear energy-depth relationship. In this paper, we present the critical timescales and associated kinematics necessary for achieving localized fluidization, which are calculated from soil parameters and validated via RoboClam and E. directus testing.Battelle Memorial InstituteBluefin RoboticsChevron Corporatio

Evidence of the adaptive evolution of immune genes in chicken

The basis for understanding the characteristics of gene functional categories in chicken has been enhanced by the ongoing sequencing of the zebra finch genome, the second bird species to be extensively sequenced. This sequence provides an avian context for examining how variation in chicken has evolved since its divergence from its common ancestor with zebra finch as well as well as a calibrating point for studying intraspecific diversity within chicken. Immune genes have been subject to many selective processes during their evolutionary history: this gene class was investigated here in a set of orthologous chicken and zebra finch genes with functions assigned from the human ortholog. Tests demonstrated that nonsynonymous sites at immune genes were highly conserved both in chicken and on the avian lineage. McDonald-Kreitman tests provided evidence of adaptive evolution and a higher rate of selection on fixation of nonsynonymous substitutions at immune genes compared to that at non-immune genes. Further analyses showed that GC content was much higher in chicken than in zebra finch genes, and was significantly elevated in both species' immune genes. Pathogen challenges are likely to have driven the selective forces that have shaped variation at chicken immune genes, and continue to restrict diversity in this functional class

PVR: Patch-to-Volume Reconstruction for Large Area Motion Correction of Fetal MRI

In this paper we present a novel method for the correction of motion artifacts that are present in fetal Magnetic Resonance Imaging (MRI) scans of the whole uterus. Contrary to current slice-to-volume registration (SVR) methods, requiring an inflexible anatomical enclosure of a single investigated organ, the proposed patch-to-volume reconstruction (PVR) approach is able to reconstruct a large field of view of non-rigidly deforming structures. It relaxes rigid motion assumptions by introducing a specific amount of redundant information that is exploited with parallelized patch-wise optimization, super-resolution, and automatic outlier rejection. We further describe and provide an efficient parallel implementation of PVR allowing its execution within reasonable time on commercially available graphics processing units (GPU), enabling its use in the clinical practice. We evaluate PVR's computational overhead compared to standard methods and observe improved reconstruction accuracy in presence of affine motion artifacts of approximately 30% compared to conventional SVR in synthetic experiments. Furthermore, we have evaluated our method qualitatively and quantitatively on real fetal MRI data subject to maternal breathing and sudden fetal movements. We evaluate peak-signal-to-noise ratio (PSNR), structural similarity index (SSIM), and cross correlation (CC) with respect to the originally acquired data and provide a method for visual inspection of reconstruction uncertainty. With these experiments we demonstrate successful application of PVR motion compensation to the whole uterus, the human fetus, and the human placenta.Comment: 10 pages, 13 figures, submitted to IEEE Transactions on Medical Imaging. v2: wadded funders acknowledgements to preprin

Simulation of Many-Body Fermi Systems on a Universal Quantum Computer

We provide fast algorithms for simulating many body Fermi systems on a universal quantum computer. Both first and second quantized descriptions are considered, and the relative computational complexities are determined in each case. In order to accommodate fermions using a first quantized Hamiltonian, an efficient quantum algorithm for anti-symmetrization is given. Finally, a simulation of the Hubbard model is discussed in detail.Comment: Submitted 11/7/96 to Phys. Rev. Lett. 10 pages, 0 figure

Multi-level personalization of neuromusculoskeletal models to estimate physiologically plausible knee joint contact forces in children

Neuromusculoskeletal models are a powerful tool to investigate the internal biomechanics of an individual. However, commonly used neuromusculoskeletal models are generated via linear scaling of generic templates derived from elderly adult anatomies and poorly represent a child, let alone children with a neuromuscular disorder whose musculoskeletal structures and muscle activation patterns are profoundly altered. Model personalization can capture abnormalities and appropriately describe the underlying (altered) biomechanics of an individual. In this work, we explored the effect of six different levels of neuromusculoskeletal model personalization on estimates of muscle forces and knee joint contact forces to tease out the importance of model personalization for normal and abnormal musculoskeletal structures and muscle activation patterns. For six children, with and without cerebral palsy, generic scaled models were developed and progressively personalized by (1) tuning and calibrating musculotendon units' parameters, (2) implementing an electromyogram-assisted approach to synthesize muscle activations, and (3) replacing generic anatomies with image-based bony geometries, and physiologically and physically plausible muscle kinematics. Biomechanical simulations of gait were performed in the OpenSim and CEINMS software on ten overground walking trials per participant. A mixed-ANOVA test, with Bonferroni corrections, was conducted to compare all models' estimates. The model with the highest level of personalization produced the most physiologically plausible estimates. Model personalization is crucial to produce physiologically plausible estimates of internal biomechanical quantities. In particular, personalization of musculoskeletal anatomy and muscle activation patterns had the largest effect overall. Increased research efforts are needed to ease the creation of personalized neuromusculoskeletal models

Multi-Substrate Burrowing Performance and Constitutive Modeling of RoboClam: A Biomimetic Robot Based on Razor Clams

The Atlantic razor clam (Ensis directus) reduces burrowing drag by using motions of its shell to fluidize a thin layer of substrate around its body. We have developed RoboClam, a robot that digs using the same mechanisms as Ensis, to explore how localized fluidization burrowing can be extended to engineering applications. In this work we present burrowing performance results of RoboClam in two distinctly different substrates: ideally granular 1mm soda lime glass beads and cohesive ocean mudflat soil. Using a genetic algorithm to optimize RoboClam’s kinematics, the machine was able to burrow in both substrates with a power law relationship between digging energy and depth of n = 1.17. Pushing through static soil has a theoretical energy-depth power law of n = 2, which means that Ensis-inspired burrowing motions can provide exponentially higher energy efficiency. We propose a theoretical constitutive model that describes how a fluidized region should form around a contracting body in virtually any type of saturated soil. The model predicts fluidization to be a relatively local effect, extending only two to three characteristic lengths away from the body, depending on friction angle and coefficient of lateral earth pressure, two commonly measured soil parameters.Battelle Memorial InstituteBluefin RoboticsChevron Corporatio

Nonlinear quantum mechanics implies polynomial-time solution for NP-complete and #P problems

If quantum states exhibit small nonlinearities during time evolution, then quantum computers can be used to solve NP-complete problems in polynomial time. We provide algorithms that solve NP-complete and #P oracle problems by exploiting nonlinear quantum logic gates. It is argued that virtually any deterministic nonlinear quantum theory will include such gates, and the method is explicitly demonstrated using the Weinberg model of nonlinear quantum mechanics.Comment: 10 pages, no figures, submitted to Phys. Rev. Let