Hasil untuk "q-bio.CB"

H. Huberti, W. Hayes

K. Hoffer

L. Gambardella, M. Dorigo

E. Ukkonen

We study approximate string matching in connection with two string distance functions that are computable in linear time. The first function is based on the so-called $q$-grams. An algorithm is given for the associated string matching problem that finds the locally best approximate occurences of pattern $P$, $|P|=m$, in text $T$, $|T|=n$, in time $O(n\log (m-q))$. The occurences with distance $\leq k$ can be found in time $O(n\log k)$. The other distance function is based on finding maximal common substrings and allows a form of approximate string matching in time $O(n)$. Both distances give a lower bound for the edit distance (in the unit cost model), which leads to fast hybrid algorithms for the edit distance based string matching.

Thomas Ernst

K. Coyne, D. Revicki, T. Hunt et al.

A. Al-Tamimi, F. Lewis, M. Abu-Khalaf

J. Aardoom, A. Dingemans, Margarita C T Slof Op't Landt et al.

P. DeMarzo, Michael J. Fishman, Zhiguo He et al.

K. Simons, J. Fellers, H. Trick et al.

Ariel Nikas, Hasan Ahmed, Mia R. Moore et al.

Antibodies and humoral memory are key components of the adaptive immune system. We consider and computationally model mechanisms by which humoral memory present at baseline might instead increase infection load; we refer to this effect as EI-HM (enhancement of infection by humoral memory). We first consider antibody dependent enhancement (ADE) in which antibody enhances the growth of the pathogen, typically a virus, and typically at intermediate "Goldilocks" levels of antibody. Our ADE model reproduces ADE in vitro and enhancement of infection in vivo from passive antibody transfer. But notably the simplest implementation of our ADE model never results in EI-HM. Adding complexity, by making the cross-reactive antibody much less neutralizing than the de novo generated antibody or by including a sufficiently strong non-antibody immune response, allows for ADE-mediated EI-HM. We next consider the possibility that cross-reactive memory causes EI-HM by crowding out a possibly superior de novo immune response. We show that, even without ADE, EI-HM can occur when the cross-reactive response is both less potent and "directly" (i.e. independently of infection load) suppressive with regard to the de novo response. In this case adding a non-antibody immune response to our computational model greatly reduces or completely eliminates EI-HM, which suggests that "crowding out" is unlikely to cause substantial EI-HM. Hence, our results provide examples in which simple models give qualitatively opposite results compared to models with plausible complexity. Our results may be helpful in interpreting and reconciling disparate experimental findings, especially from dengue, and for vaccination.

F. Russo, A. Tenore, M. R. Mattei et al.

A multiscale mathematical model describing the genesis and ecology of algal-bacterial photogranules and the metals biosorption on their solid matrix within a sequencing batch reactor (SBR) is presented. The granular biofilm is modelled as a spherical free boundary domain with radial symmetry and a vanishing initial value. The free boundary evolution is governed by an ODE accounting for microbial growth, attachment and detachment phenomena. The model is based on systems of PDEs derived from mass conservation principles. Specifically, two systems of nonlinear hyperbolic PDEs model the growth of attached species and the dynamics of free adsorption sites; and two systems of quasi-linear parabolic PDEs govern the diffusive transport and conversion of nutrients and metals. The model is completed with systems of impulsive ordinary differential equations (IDEs) describing the evolution of dissolved substrates, metals, and planktonic and detached biomasses within the granular-based SBR. All main phenomena involved in the process are considered in the mathematical model. Moreover, the dual effect of metal presence on the formation process of photogranules is accounted: metal stimulates the production of EPS by sessile species and negatively affects the metabolic activities of microbial species. To describe the effects related to metal presence, a stimulation term for EPS production and an inhibition term for metal are included in all microbial kinetics. The model is used to examine the role of the microbial species and EPS in the adsorption process, and the effect of metal concentration and adsorption proprieties of biofilm components on the metal removal. Numerical results show that the model accurately describes the photogranules evolution and ecology and confirm the applicability of algal-bacterial photogranules systems for metal-rich wastewater treatment.

Belén Villalonga

I. Aganj, C. Lenglet, G. Sapiro et al.

M. Ablikim, M. Achasov, X. Ai et al.

We extract the e+e− → π+π− cross section in the energy range between 600 and 900 MeV, exploiting the method of initial state radiation. A data set with an integrated luminosity of 2.93 fb−1 taken at a centerof-mass energy of 3.773 GeV with the BESIII detector at the BEPCII collider is used. The cross section is measured with a systematic uncertainty of 0.9%. We extract the pion form factor |Fπ| as well as the contribution of the measured cross section to the leading-order hadronic vacuum polarization contribution to (g − 2)μ. We find this value to be a μ (600 − 900 MeV) = (368.2 ± 2.5stat ± 3.3sys) · 10−10, which is between the corresponding values using the BaBar or KLOE data.

N. Mottram, C. Newton

This paper aims to provide an introduction to a basic form of the Q-tensor approach to modelling liquid crystals, which has seen increased interest in recent years. The increase in interest in this type of modelling approach has been driven by investigations into the fundamental nature of defects and new applications of liquid crystals such as bistable displays and colloidal systems for which a description of defects and disorder is essential. The work in this paper is not new research, rather it is an introductory guide for anyone wishing to model a system using such a theory. A more complete mathematical description of this theory, including a description of flow effects, can be found in numerous sources but the books by Virga and Sonnet and Virga are recommended. More information can be obtained from the plethora of papers using such approaches, although a general introduction for the novice is lacking. The first few sections of this paper will detail the development of the Q-tensor approach for nematic liquid crystalline systems and construct the free energy and governing equations for the mesoscopic dependent variables. A number of device surface treatments are considered and theoretical boundary conditions are specified for each instance. Finally, an example of a real device is demonstrated.

Marco Santorelli, Pranav Bhamidipati, Andriu Kavanagh et al.

During organismal development, biochemical reaction networks sense and respond to mechanical forces to coordinate embryonic patterning with embryo morphogenesis. Factors such as cortical tension, cell density, and matrix mechanical properties influence differentiation and cell fate decisions by modulating gene regulatory signaling networks. A major goal in synthetic development is to construct gene regulatory circuits that program the patterning and morphogenesis of synthetic multicellular structures. However, in the synthetic context, little is known regarding how the physical properties of the growth environment impact the behavior of synthetic gene circuits. Here, we exploit physical-chemical coupling observed in a synthetic patterning circuit in order to control the size and spatial distribution of patterned synthetic cell sheets. We show that cell density attenuates the propagation of signal between neighboring cells in a multicellular sheet containing a contact-dependent patterning circuit based on the synNotch signaling system. Density-dependent attenuation leads to a signal propagation wave that exhibits distinct qualitative phases of persistent propagation, transient propagation, and no propagation. Through computational modeling, we demonstrate that cell growth parameters determine the phase of propagation observed within a growing cell sheet. Using growth-modulating drugs and spatial density gradients, we control the size of synNotch-activated cell populations and generate tissue-scale activation gradients and kinematic waves. Our study reveals that density-dependent synNotch activity can be exploited to control a synthetic multicellular patterning circuit. More broadly, we show that synthetic gene circuits can be critically impacted by their physical context, providing an alternate means for programming circuit behavior.

Devavrat Shah, Qiaomin Xie

We consider model-free reinforcement learning for infinite-horizon discounted Markov Decision Processes (MDPs) with a continuous state space and unknown transition kernel, when only a single sample path under an arbitrary policy of the system is available. We consider the Nearest Neighbor Q-Learning (NNQL) algorithm to learn the optimal Q function using nearest neighbor regression method. As the main contribution, we provide tight finite sample analysis of the convergence rate. In particular, for MDPs with a $d$-dimensional state space and the discounted factor $\gamma \in (0,1)$, given an arbitrary sample path with "covering time" $ L $, we establish that the algorithm is guaranteed to output an $\varepsilon$-accurate estimate of the optimal Q-function using $\tilde{O}\big(L/(\varepsilon^3(1-\gamma)^7)\big)$ samples. For instance, for a well-behaved MDP, the covering time of the sample path under the purely random policy scales as $ \tilde{O}\big(1/\varepsilon^d\big),$ so the sample complexity scales as $\tilde{O}\big(1/\varepsilon^{d+3}\big).$ Indeed, we establish a lower bound that argues that the dependence of $ \tilde{\Omega}\big(1/\varepsilon^{d+2}\big)$ is necessary.

F. Delduc, M. Magro, B. Vicedo

A bstractA procedure is developed for constructing deformations of integrable σ-models which are themselves classically integrable. When applied to the principal chiral model on any compact Lie group F, one recovers the Yang-Baxter σ-model introduced a few years ago by C. Klimčík. In the case of the symmetric space σ-model on F/G we obtain a new one-parameter family of integrable σ-models. The actions of these models correspond to a deformation of the target space geometry and include a torsion term. An interesting feature of the construction is the q-deformation of the symmetry corresponding to left multiplication in the original models, which becomes replaced by a classical q-deformed Poisson-Hopf algebra. Another noteworthy aspect of the deformation in the coset σ-model case is that it interpolates between a compact and a non-compact symmetric space. This is exemplified in the case of the SU(2)/U(1) coset σ-model which interpolates all the way to the SU(1, 1)/U(1) coset σ-model.

Yunxiao Chen, Jingchen Liu, Gongjun Xu et al.