`Operational' Energy Conditions

I show that a quantized Klein-Gordon field in Minkowski space obeys an `operational' weak energy condition: the energy of an isolated device constructed to measure or trap the energy in a region, plus the energy it measures or traps, cannot be negative. There are good reasons for thinking that similar results hold locally for linear quantum fields in curved space-times. A thought experiment to measure energy density is analyzed in some detail, and the operational positivity is clearly manifested. If operational energy conditions do hold for quantum fields, then the negative energy densities predicted by theory have a will-o'-the-wisp character: any local attempt to verify a total negative energy density will be self-defeating on account of quantum measurement difficulties. Similarly, attempts to drive exotic effects (wormholes, violations of the second law, etc.) by such densities may be defeated by quantum measurement problems. As an example, I show that certain attempts to violate the Cosmic Censorship principle by negative energy densities are defeated. These quantum measurement limitations are investigated in some detail, and are shown to indicate that space-time cannot be adequately modeled classically in negative energy density regimes.Comment: 18 pages, plain Tex, IOP macros. Expanded treatment of measurement problems for space-time, with implications for Cosmic Censorship as an example. Accepted by Classical and Quantum Gravit

Unitary relations in time-dependent harmonic oscillators

For a harmonic oscillator with time-dependent (positive) mass and frequency, an unitary operator is shown to transform the quantum states of the system to those of a harmonic oscillator system of unit mass and time-dependent frequency, as well as operators. For a driven harmonic oscillator, it is also shown that, there are unitary transformations which give the driven system from the system of same mass and frequency without driving force. The transformation for a driven oscillator depends on the solution of classical equation of motion of the driven system. These transformations, thus, give a simple way of finding exact wave functions of a driven harmonic oscillator system, provided the quantum states of the corresponding system of unit mass are given.Comment: Submitted to J. Phys.

Centralized Modularity of N-Linked Glycosylation Pathways in Mammalian Cells

Glycosylation is a highly complex process to produce a diverse repertoire of cellular glycans that are attached to proteins and lipids. Glycans are involved in fundamental biological processes, including protein folding and clearance, cell proliferation and apoptosis, development, immune responses, and pathogenesis. One of the major types of glycans, N-linked glycans, is formed by sequential attachments of monosaccharides to proteins by a limited number of enzymes. Many of these enzymes can accept multiple N-linked glycans as substrates, thereby generating a large number of glycan intermediates and their intermingled pathways. Motivated by the quantitative methods developed in complex network research, we investigated the large-scale organization of such N-linked glycosylation pathways in mammalian cells. The N-linked glycosylation pathways are extremely modular, and are composed of cohesive topological modules that directly branch from a common upstream pathway of glycan synthesis. This unique structural property allows the glycan production between modules to be controlled by the upstream region. Although the enzymes act on multiple glycan substrates, indicating cross-talk between modules, the impact of the cross-talk on the module-specific enhancement of glycan synthesis may be confined within a moderate range by transcription-level control. The findings of the present study provide experimentally-testable predictions for glycosylation processes, and may be applicable to therapeutic glycoprotein engineering

Restrictions on negative energy density in a curved spacetime

Recently a restriction ("quantum inequality-type relation") on the (renormalized) energy density measured by a static observer in a "globally static" (ultrastatic) spacetime has been formulated by Pfenning and Ford for the minimally coupled scalar field, in the extension of quantum inequality-type relation on flat spacetime of Ford and Roman. They found negative lower bounds for the line integrals of energy density multiplied by a sampling (weighting) function, and explicitly evaluate them for some specific spacetimes. In this paper, we study the lower bound on spacetimes whose spacelike hypersurfaces are compact and without boundary. In the short "sampling time" limit, the bound has asymptotic expansion. Although the expansion can not be represented by locally invariant quantities in general due to the nonlocal nature of the integral, we explicitly evaluate the dominant terms in the limit in terms of the invariant quantities. We also make an estimate for the bound in the long sampling time limit.Comment: LaTex, 23 Page

Generalization of the Darboux transformation and generalized harmonic oscillators

The Darbroux transformation is generalized for time-dependent Hamiltonian systems which include a term linear in momentum and a time-dependent mass. The formalism for the $N$-fold application of the transformation is also established, and these formalisms are applied for a general quadratic system (a generalized harmonic oscillator) and a quadratic system with an inverse-square interaction up to N=2. Among the new features found, it is shown, for the general quadratic system, that the shape of potential difference between the original system and the transformed system could oscillate according to a classical solution, which is related to the existence of coherent states in the system

Flux-sum analysis: a metabolite-centric approach for understanding the metabolic network

<p>Abstract</p> <p>Background</p> <p>Constraint-based flux analysis of metabolic network model quantifies the reaction flux distribution to characterize the state of cellular metabolism. However, metabolites are key players in the metabolic network and the current reaction-centric approach may not account for the effect of metabolite perturbation on the cellular physiology due to the inherent limitation in model formulation. Thus, it would be practical to incorporate the metabolite states into the model for the analysis of the network.</p> <p>Results</p> <p>Presented herein is a metabolite-centric approach of analyzing the metabolic network by including the turnover rate of metabolite, known as flux-sum, as key descriptive variable within the model formulation. By doing so, the effect of varying metabolite flux-sum on physiological change can be simulated by resorting to mixed integer linear programming. From the results, we could classify various metabolite types based on the flux-sum profile. Using the <it>i</it>AF1260 <it>in silico </it>metabolic model of <it>Escherichia coli</it>, we demonstrated that this novel concept complements the conventional reaction-centric analysis.</p> <p>Conclusions</p> <p>Metabolite flux-sum analysis elucidates the roles of metabolites in the network. In addition, this metabolite perturbation analysis identifies the key metabolites, implicating practical application which is achievable through metabolite flux-sum manipulation in the areas of biotechnology and biomedical research.</p

Parathyroid gland detection using an intraoperative autofluorescence handheld imager – early feasibility study

IntroductionParathyroid glands may be compromised during thyroid surgery which can lead to hypoparathyroidism and hypocalcemia. Identifying the parathyroid glands relies on the surgeon’s experience and the only way to confirm their presence was through tissue biopsy. Near infrared autofluorescence technology offers an opportunity for real-time, non-invasive identification of the parathyroid glands.MethodsWe used a new research prototype (hANDY-I) developed by Optosurgical, LLC. It offers coaxial excitation light and a dual-Red Green Blue/Near Infrared sensor that guides anatomical landmarks and can aid in identification of parathyroid glands by showing a combined autofluorescence and colored image simultaneously.ResultsWe tested the imager during 23 thyroid surgery cases, where initial clinical feasibility data showed that out of 75 parathyroid glands inspected, 71 showed strong autofluorescence signal and were correctly identified (95% accuracy) by the imager.ConclusionsThe hANDY-I prototype demonstrated promising results in this feasibility study by aiding in real-time visualization of the parathyroid glands. However, further testing by conducting randomized clinical trials with a bigger sample size is required to study the effect on levels of hypoparathyroidism and hypocalcemia

Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing

An amendment to this paper has been published and can be accessed via a link at the top of the paper.(undefined)info:eu-repo/semantics/publishedVersio

The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli

Background: Escherichia coli is a model prokaryote, an important pathogen, and a key organism for industrial biotechnology. E. coli W (ATCC 9637), one of four strains designated as safe for laboratory purposes, has not been sequenced. E. coli W is a fast-growing strain and is the only safe strain that can utilize sucrose as a carbon source. Lifecycle analysis has demonstrated that sucrose from sugarcane is a preferred carbon source for industrial bioprocesses