Template-dependent multiple displacement amplification for profiling human circulating RNA

Multiple displacement amplification (MDA) is widely used in whole-genome/transcriptome amplification. However, template-independent amplification (TIA) in MDA is a commonly observed phenomenon, particularly when using high concentrations of random hexamer primers and extended incubation times. Here, we demonstrate that the use of random pentamer primers with 5´ ends blocked by a C18 spacer results in MDA solely in a template-dependent manner, a technique we have named tdMDA. Together with an optimized procedure for the removal of residual genomic DNA during RNA extraction, tdMDA was used to profile circulating RNA from 0.2 mL of patient sera. In comparison to regular MDA, tdMDA demonstrated a lack of quantifiable DNA amplification in the negative control, a remarkable reduction of unmapped reads from Illumina sequencing (7 ± 10.9% versus 58.6 ± 39%, P = 0.006), and increased mapping rates of the serum transcriptome (26.9 ± 7.9% versus 5.8 ± 8.2%, P = 3.8 × 10-4). Transcriptome profiles could be used to separate patients with chronic hepatitis C virus (HCV) infection from those with HCV-associated hepatocellular carcinoma (HCC). We conclude that tdMDA should facilitate RNA-based liquid biopsy, as well as other genome studies with biological specimens having ultralow amounts of genetic material. </jats:p

Landau-Zener Tunnelling in a Nonlinear Three-level System

We present a comprehensive analysis of the Landau-Zener tunnelling of a nonlinear three-level system in a linearly sweeping external field. We find the presence of nonzero tunnelling probability in the adiabatic limit (i.e., very slowly sweeping field) even for the situation that the nonlinear term is very small and the energy levels keep the same topological structure as that of linear case. In particular, the tunnelling is irregular with showing an unresolved sensitivity on the sweeping rate. For the case of fast-sweeping fields, we derive an analytic expression for the tunnelling probability with stationary phase approximation and show that the nonlinearity can dramatically influence the tunnelling probability when the nonlinear "internal field" resonate with the external field. We also discuss the asymmetry of the tunnelling probability induced by the nonlinearity. Physics behind the above phenomena is revealed and possible application of our model to triple-well trapped Bose-Einstein condensate is discussed.Comment: 8 pages, 8 figure

From Operator Algebras to Superconformal Field Theory

We make a review on the recent progress in the operator algebraic approach to (super)conformal field theory. We discuss representation theory, classification results, full and boundary conformal field theories, relations to supervertex operator algebras and Moonshine, connections to subfactor theory and noncommutative geometry

Impatient Queuing for Intelligent Task Offloading in Multi-Access Edge Computing

Multi-access edge computing (MEC) emerges as an essential part of the upcoming Fifth Generation (5G) and future beyond-5G mobile communication systems. It adds computational power towards the edge of cellular networks, much closer to energy-constrained user devices, and therewith allows the users to offload tasks to the edge computing nodes for low-latency applications with very-limited battery consumption. However, due to the high dynamics of user demand and server load, task congestion may occur at the edge nodes resulting in long queuing delay. Such delays can significantly degrade the quality of experience (QoE) of some latency-sensitive applications, raise the risk of service outage, and cannot be efficiently resolved by conventional queue management solutions. In this article, we study a latency-outage critical scenario, where users intend to limit the risk of latency outage. We propose an impatience-based queuing strategy for such users to intelligently choose between MEC offloading and local computation, allowing them to rationally renege from the task queue. The proposed approach is demonstrated by numerical simulations to be efficient for generic service model, when a perfect queue status information is available. For the practical case where the users obtain only imperfect queue status information, we design an optimal online learning strategy to enable its application in Poisson service scenarios.Comment: To appear in IEEE Transactions on Wireless Communication

Intelectin contributes to allergen-induced IL-25, IL-33, and TSLP expression and type 2 response in asthma and atopic dermatitis.

The epithelial and epidermal innate cytokines IL-25, IL-33, and thymic stromal lymphopoietin (TSLP) have pivotal roles in the initiation of allergic inflammation in asthma and atopic dermatitis (AD). However, the mechanism by which the expression of these innate cytokines is regulated remains unclear. Intelectin (ITLN) is expressed in airway epithelial cells and promotes allergic airway inflammation. We hypothesized that ITLN is required for allergen-induced IL-25, IL-33, and TSLP expression. In two asthma models, Itln knockdown reduced allergen-induced increases in Il-25, Il-33, and Tslp and development of type 2 response, eosinophilic inflammation, mucus overproduction, and airway hyperresponsiveness. Itln knockdown also inhibited house dust mite (HDM)-induced early upregulation of Il-25, Il-33, and Tslp in a model solely inducing airway sensitization. Using human airway epithelial cells, we demonstrated that HDM-induced increases in ITLN led to phosphorylation of epidermal growth factor receptor and extracellular-signal regulated kinase, which were required for induction of IL-25, IL-33, and TSLP expression. In two AD models, Itln knockdown suppressed expression of Il-33, Tslp, and Th2 cytokines and eosinophilic inflammation. In humans, ITLN1 expression was significantly increased in asthmatic airways and in lesional skin of AD. We conclude that ITLN contributes to allergen-induced Il-25, Il-33, and Tslp expression in asthma and AD

3D Geometric Analysis of Tubular Objects based on Surface Normal Accumulation

This paper proposes a simple and efficient method for the reconstruction and extraction of geometric parameters from 3D tubular objects. Our method constructs an image that accumulates surface normal information, then peaks within this image are located by tracking. Finally, the positions of these are optimized to lie precisely on the tubular shape centerline. This method is very versatile, and is able to process various input data types like full or partial mesh acquired from 3D laser scans, 3D height map or discrete volumetric images. The proposed algorithm is simple to implement, contains few parameters and can be computed in linear time with respect to the number of surface faces. Since the extracted tube centerline is accurate, we are able to decompose the tube into rectilinear parts and torus-like parts. This is done with a new linear time 3D torus detection algorithm, which follows the same principle of a previous work on 2D arc circle recognition. Detailed experiments show the versatility, accuracy and robustness of our new method.Comment: in 18th International Conference on Image Analysis and Processing, Sep 2015, Genova, Italy. 201

Enhance the Efficiency of Heuristic Algorithm for Maximizing Modularity Q

Modularity Q is an important function for identifying community structure in complex networks. In this paper, we prove that the modularity maximization problem is equivalent to a nonconvex quadratic programming problem. This result provide us a simple way to improve the efficiency of heuristic algorithms for maximizing modularity Q. Many numerical results demonstrate that it is very effective.Comment: 9 pages, 3 figure

Representations of Conformal Nets, Universal C*-Algebras and K-Theory

We study the representation theory of a conformal net A on the circle from a K-theoretical point of view using its universal C*-algebra C*(A). We prove that if A satisfies the split property then, for every representation \pi of A with finite statistical dimension, \pi(C*(A)) is weakly closed and hence a finite direct sum of type I_\infty factors. We define the more manageable locally normal universal C*-algebra C*_ln(A) as the quotient of C*(A) by its largest ideal vanishing in all locally normal representations and we investigate its structure. In particular, if A is completely rational with n sectors, then C*_ln(A) is a direct sum of n type I_\infty factors. Its ideal K_A of compact operators has nontrivial K-theory, and we prove that the DHR endomorphisms of C*(A) with finite statistical dimension act on K_A, giving rise to an action of the fusion semiring of DHR sectors on K_0(K_A)$. Moreover, we show that this action corresponds to the regular representation of the associated fusion algebra.Comment: v2: we added some comments in the introduction and new references. v3: new authors' addresses, minor corrections. To appear in Commun. Math. Phys. v4: minor corrections, updated reference