Reconstructing gene regulatory networks with a memetic-neural hybrid based on fuzzy cognitive maps

Reconstructing gene regulatory networks (GRNs) plays an important role in identifying the complicated regulatory relationships, uncovering regulatory patterns in cells, and gaining a systematic view for biological processes. In order to reconstruct large-scale GRNs accurately, in this paper, we first use fuzzy cognitive maps (FCMs), which are a kind of cognition fuzzy influence graphs based on fuzzy logic and neural networks, to model GRNs. Then, a novel hybrid method is proposed to reconstruct GRNs from time series expression profiles using memetic algorithm (MA) combined with neural network (NN), which is labeled as MANN_FCM-GRN. In MANN_FCM-GRN, the MA is used to determine regulatory connections in GRNs and the NN is used to determine the interaction strength of the regulatory connections. In the experiments, the performance of MANN_FCM-GRN is validated on both synthetic data and the benchmark dataset DREAM3 and DREAM4. The experimental results demonstrate the efficacy of MANN_FCM-GRN and show that MANN_FCM-GRN can reconstruct GRNs with high accuracy without expert knowledge. The comparison with existing algorithms also shows that MANN_FCM-GRN outperforms ant colony optimization, non-linear Hebbian learning, and real-coded genetic algorithms.

     

Relationship Between Shipping Accessibility and Maritime Transport Demand: the Case of Mainland China

Networks and Spatial Economics - The relationship between shipping accessibility and maritime transport demand is studied based on the relationship between production and consumption and stochastic...     

MPE: a mobility pattern embedding model for predicting next locations

World Wide Web - The wide spread use of positioning and photographing devices gives rise to a deluge of traffic trajectory data (e.g., vehicle passage records and taxi trajectory data), with each...     

芽孢杆菌Bacillus sp.dwc-2对模拟地下水中U(Ⅵ)的还原行为研究

在厌氧条件下研究了西南地区一种典型土壤微生物芽孢杆菌Bacillus sp.dwc-2对模拟地下水中U(Ⅵ)的还原行为，重点考察了时间、无机阴离子、腐殖酸（HA）及富里酸（FA）对还原的影响，并利用TEM、EDS、SAED和XPS对还原后的样品进行了表征。结果表明：在pH=7.0、c_NaHCO3=5 mmol/L和T=303 K条件下，Bacillus sp.dwc-2对U(Ⅵ)的还原率随时间的增加而增加，24 h内最大还原率为12.2%，此后则随时间的增加逐渐降低；HA和FA对U(Ⅵ)的微生物还原行为有一定影响，其中HA和FA浓度为25 mg/L时，U(Ⅵ)的还原在24 h最明显，其还原率分别为14.2%和16.2%，但随着HA和FA浓度的继续增加，因在U(Ⅵ)离子与HA、FA形成的配合物表面形成致密的腐殖层，抑制了电子的转移，阻止了U(Ⅵ)的还原。此外，研究表明HCO₃^-也会抑制U(Ⅵ)的还原。TEM-SAED和XPS分析证实了还原过程中U(Ⅳ)的存在。上述结果可为真实环境中微生物还原U(Ⅵ)提供基础数据和参考。     

Blocked crystallization in capped ultrathin polymer films studied by molecular simulations

The crystallization of capped ultrathin polymer films is closely dependent on film thickness and interfacial interaction. Using dynamic Monte Carlo simulations, the crystallization behaviors of polymer films confined between two substrates were investigated. The crystallization rate of confined polymers is reduced with high interfacial interactions. Above a critical strength of interfacial interaction, polymer crystallization in the thin film is inhibited within the simulation time scales. An increase in film thickness leads to a rise in critical interfacial interaction. In thicker films, the chains have more space to change conformation to form crystal stems. In addition, there are fewer absorbed segments in confined chains for the thicker films, and thus the chains have stronger ability to adjust their conformation. Therefore an increase in film thickness can cause a reduction in the entropic barrier required for the formation of crystals and thus an increase in the critical interfacial interaction. © 2018 Society of Chemical Industry     

Chemotherapy response of pancreatic cancer by diffusion-weighted imaging (DWI) and intravoxel incoherent motion DWI (IVIM-DWI) in an orthotopic mouse model

Magnetic Resonance Materials in Physics, Biology and Medicine - To investigate the value of using diffusion-weighted imaging (DWI) and intravoxel incoherent motion DWI (IVIM-DWI) to assess the...     

Macroscopic and Microscopic Structures of Cesium Lead Iodide Perovskite from Atomistic Simulations

A first‐principles‐based effective Hamiltonian is developed and employed to investigate finite‐temperature structural properties of a prototype of perovskite halides, that is CsPbI₃. Such simulations, when using first‐principles‐extracted coefficients, successfully reproduce the existence of an orthorhombic Pnma state and its iodine octahedral tilting angles around room temperature. However, they also yield a direct transformation from Pnma to cubic $Pm\overline{3}m$ upon heating, unlike measurements that reported the occurrence of an intermediate long‐range‐tilted tetragonal P4/mbm phase in‐between the orthorhombic and cubic phases. Such disagreement, which may cast some doubts about the extent to which first‐principle methods can be trusted to mimic hybrid perovskites, can be resolved by “only” changing one short‐range tilting parameter in the whole set of effective Hamiltonian coefficients. In such a case, some reasonable values of this specific parameter result in the predictions that i) the intermediate P4/mbm state originates from fluctuations over many different tilted states; and ii) the cubic $Pm\overline{3}m$ phase is highly locally distorted and develops strong transverse antiphase correlation between first‐nearest neighbor iodine octahedral tiltings, before undergoing a phase transition to P4/mbm under cooling.     

亲子乐园空调送风方式的数值模拟研究

大型综合室内亲子乐园属于高大空间,设有游乐设施和游戏的特殊性使得对空间的舒适性要求一致,但是送风气流遇阻严重,室内存在较多气流死角,影响室内空气质量和儿童健康。因此其空调设计不仅需要考虑温度、风速的空间均匀度,还要考虑各点的空气龄和PMV-PPD指标。以天津某亲子乐园为研究对象,利用scSTREAM软件对适用于该房间的辐射供冷加新风、置换通风、混合通风三种空调方式的送风效果进行数值模拟分析,从流场的均匀性、人员的热舒适性等方面对模拟结果进行探讨,研究结果表明辐射供冷加新风方式的空间均匀性和PMV指标最佳,混合通风方式的空气龄最小。     

Recent Advances in Conjugated Polymers for Visible-Light-Driven Water Splitting

With the ambition of solving the challenges of the shortage of fossil fuels and their associated environmental pollution, visible-light-driven splitting of water into hydrogen and oxygen using semiconductor photocatalysts has emerged as a promising technology to provide environmentally friendly energy vectors. Among the current library of developed photocatalysts, organic conjugated polymers present unique advantages of sufficient light-absorption efficiency, excellent stability, tunable electronic properties, and economic applicability. As a class of rising photocatalysts, organic conjugated polymers offer high flexibility in tuning the framework of the backbone and porosity to fulfill the requirements for photocatalytic applications. In the past decade, significant progress has been made in visible-light-driven water splitting employing organic conjugated polymers. The recent development of the structural design principles of organic conjugated polymers (including linear, crosslinked, and supramolecular self-assembled polymers) toward efficient photocatalytic hydrogen evolution, oxygen evolution, and overall water splitting is described, thus providing a comprehensive reference for the field. Finally, current challenges and perspectives are also discussed.