18,914 research outputs found
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
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