Generalization of graph network inferences in higher-order probabilistic graphical models

Probabilistic graphical models provide a powerful tool to describe complex statistical structure, with many real-world applications in science and engineering from controlling robotic arms to understanding neuronal computations. A major challenge for these graphical models is that inferences such as marginalization are intractable for general graphs. These inferences are often approximated by a distributed message-passing algorithm such as Belief Propagation, which does not always perform well on graphs with cycles, nor can it always be easily specified for complex continuous probability distributions. Such difficulties arise frequently in expressive graphical models that include intractable higher-order interactions. In this paper we construct iterative message-passing algorithms using Graph Neural Networks defined on factor graphs to achieve fast approximate inference on graphical models that involve many-variable interactions. Experimental results on several families of graphical models demonstrate the out-of-distribution generalization capability of our method to different sized graphs, and indicate the domain in which our method gains advantage over Belief Propagation.Comment: 9 pages, 2 figure

Displacement mechanism of polymeric surfactant in chemical cold flooding for heavy oil based on microscopic visualization experiments

 In order to study the microscopic oil displacement mechanism of polymeric surfactant in chemical cold flooding for heavy oil, the indoor microscopic visualization displacement experiments were carried out. The flooding experiment of heavy oil was conducted by using water, osmotic modified oil displacing agent (a kind of polymeric surfactant) and water-in-oil emulsion (obtained by mixing polymeric surfactant and heavy oil) as displacing phases to study the mechanism of polymeric surfactant to enhance oil recovery in heavy oil reservoir. The experimental results show that the polymeric surfactant can increase the viscosity of the water phase, reduce the water-oil mobility ratio, expand the swept area, and there is no obvious fingering phenomenon which occurs during water flooding. The polymeric surfactant has the surfactant characteristics which can reduce the interfacial tension between oil and water to promote the formation of oil droplets with smaller droplet diameter. And the interfacial film composed of polymeric surfactant molecules will be formed on the surface of oil droplets to prevent the coalescence of oil droplets and improve the flow ability of oil phase. The water-in-oil emulsion can be miscible with the oil in heavy oil displacement process, and thus sweeps the areas such as the dead pores which cannot be swept by water and polymeric surfactant flooding, which increases the sweep efficiency to a certain extent.Cited as: Xu, F., Chen, Q., Ma, M., Wang, Y., Yu, F., Li, J. Displacement mechanism of polymeric surfactant in chemical cold flooding for heavy oil based on microscopic visualization experiments. Advances in Geo-Energy Research, 2020, 4(1): 77-85, doi: 10.26804/ager.2020.01.0

PgtE Enzyme of Salmonella enterica Shares the Similar Biological Roles to Plasminogen Activator (Pla) in Interacting With DEC-205 (CD205), and Enhancing Host Dissemination and Infectivity by Yersinia pestis

Yersinia pestis, the cause of plague, is a newly evolved Gram-negative bacterium. Through the acquisition of the plasminogen activator (Pla), Y. pestis gained the means to rapidly disseminate throughout its mammalian hosts. It was suggested that Y. pestis utilizes Pla to interact with the DEC-205 (CD205) receptor on antigen-presenting cells (APCs) to initiate host dissemination and infection. However, the evolutionary origin of Pla has not been fully elucidated. The PgtE enzyme of Salmonella enterica, involved in host dissemination, shows sequence similarity with the Y. pestis Pla. In this study, we demonstrated that both Escherichia coli K-12 and Y. pestis bacteria expressing the PgtE-protein were able to interact with primary alveolar macrophages and DEC-205-transfected CHO cells. The interaction between PgtE-expressing bacteria and DEC-205-expressing transfectants could be inhibited by the application of an anti-DEC-205 antibody. Moreover, PgtE-expressing Y. pestis partially re-gained the ability to promote host dissemination and infection. In conclusion, the DEC-205-PgtE interaction plays a role in promoting the dissemination and infection of Y. pestis, suggesting that Pla and the PgtE of S. enterica might share a common evolutionary origin.Peer reviewe

Neuromatch Academy: a 3-week, online summer school in computational neuroscience

Neuromatch Academy (https://academy.neuromatch.io; (van Viegen et al., 2021)) was designed as an online summer school to cover the basics of computational neuroscience in three weeks. The materials cover dominant and emerging computational neuroscience tools, how they complement one another, and specifically focus on how they can help us to better understand how the brain functions. An original component of the materials is its focus on modeling choices, i.e. how do we choose the right approach, how do we build models, and how can we evaluate models to determine if they provide real (meaningful) insight. This meta-modeling component of the instructional materials asks what questions can be answered by different techniques, and how to apply them meaningfully to get insight about brain function

Fabrication of Self-Propelled Micro- and Nanomotors Based on Janus Structures

Contains fulltext : 214599.pdf (publisher's version ) (Closed access)Abstract Delicate molecular and biological motors are tiny machines capable of achieving numerous vital tasks in biological processes. To gain a deeper understanding of their mechanism of motion, researchers from multiple backgrounds have designed and fabricated artificial micro- and nanomotors. These nano-/microscale motors can self-propel in solution by exploiting different sources of energy; thus showing tremendous potential in widespread applications. As one of the most common motor systems, Janus motors possess unique asymmetric structures and integrate different functional materials onto two sides. This review mainly focuses on the fabrication of different types of micro- and nanomotors based on Janus structures. Furthermore, some challenges still exist in the implementation of Janus motors in the biomedical field. With such common goals in mind, it is expected that the elaborate and multifunctional design of Janus motors will overcome their challenges in the near future

Bone-Targeting Prodrug Mesoporous Silica-Based Nanoreactor with Reactive Oxygen Species Burst for Enhanced Chemotherapy

Cancer remains a primary threat to human lives. Recently, amplification of tumor-associated reactive oxygen species (ROS) has been used as a boosting strategy to improve tumor therapy. Here, we report on a bone-targeting prodrug mesoporous silica-based nanoreactor for combined photodynamic therapy (PDT) and enhanced chemotherapy for osteosarcoma. Because of surface modification of a bone-targeting biphosphate moiety and the enhanced permeability and retention effect, the formed nanoreactor shows efficient accumulation in osteosarcoma and exhibits long-term retention in the tumor microenvironment. Upon laser irradiation, the loaded photosensitizer chlorin e6 (Ce6) produces in situ ROS, which not only works for PDT but also functions as a trigger for controlled release of doxorubicin (DOX) and doxycycline (DOXY) from the prodrugs based on a thioketal (TK) linkage. The released DOXY further promotes ROS production, thus perpetuating subsequent DOX/DOXY release and ROS burst. The ROS amplification induces long-term high oxidative stress, which increases the sensitivity of the osteosarcoma to chemotherapy, therefore resulting in enhanced tumor cell inhibition and apoptosis. The as-developed nanoreactor with combined PDT and enhanced chemotherapy based on ROS amplification shows significant promise as a potential platform for cancer treatment

Rational Design of Deep-Ultraviolet Nonlinear Optical Materials in Fluorooxoborates: Toward Optimal Planar Configuration

Rational Design of Deep-Ultraviolet Nonlinear Optical Materials in Fluorooxoborates: Toward Optimal Planar Configuratio