GRATIS: Deep Learning Graph Representation with Task-specific Topology and Multi-dimensional Edge Features

Graph is powerful for representing various types of real-world data. The topology (edges' presence) and edges' features of a graph decides the message passing mechanism among vertices within the graph. While most existing approaches only manually define a single-value edge to describe the connectivity or strength of association between a pair of vertices, task-specific and crucial relationship cues may be disregarded by such manually defined topology and single-value edge features. In this paper, we propose the first general graph representation learning framework (called GRATIS) which can generate a strong graph representation with a task-specific topology and task-specific multi-dimensional edge features from any arbitrary input. To learn each edge's presence and multi-dimensional feature, our framework takes both of the corresponding vertices pair and their global contextual information into consideration, enabling the generated graph representation to have a globally optimal message passing mechanism for different down-stream tasks. The principled investigation results achieved for various graph analysis tasks on 11 graph and non-graph datasets show that our GRATIS can not only largely enhance pre-defined graphs but also learns a strong graph representation for non-graph data, with clear performance improvements on all tasks. In particular, the learned topology and multi-dimensional edge features provide complementary task-related cues for graph analysis tasks. Our framework is effective, robust and flexible, and is a plug-and-play module that can be combined with different backbones and Graph Neural Networks (GNNs) to generate a task-specific graph representation from various graph and non-graph data. Our code is made publicly available at https://github.com/SSYSteve/Learning-Graph-Representation-with-Task-specific-Topology-and-Multi-dimensional-Edge-Features

The Function of MicroRNAs in B-Cell Development, Lymphoma, and Their Potential in Clinical Practice

B-cell formation, development, and differentiation are complex processes regulated by several mechanisms. Recently, there has been growing evidence indicating that microRNAs (miRNAs) are important for normal B-cell lineage development. miRNAs are small non-coding RNA molecules, about 20–22 nucleotide in length, that play an important role in regulating gene expression. They pair with specific messenger RNAs (mRNAs), resulting in mRNAs translational repression or degradation. Here, we review current research about the function of miRNAs in the aspects of B-cell physiology and pathology. We start by introducing the process of miRNA biogenesis. We will then focus on the role of miRNAs during B-cell lineage commitment and development in the bone marrow, followed by a discussion of miRNAs’ role in subsequent peripheral B-cell activation, proliferation, and final differentiation (including B-cell central tolerance and autoimmunity). We list and describe several examples to illustrate miRNAs’ role in the development of B-cell lymphoma, both as oncogenes and tumor suppressor genes. Finally, we delineate the potential value of miRNAs in diagnosing B-cell lymphoma, predicting clinical outcomes, and modulating the efficiency of anticancer treatments. Despite the vast amount of research conducted on miRNAs in recent years, it is still necessary to increase and further strengthen studies on miRNAs and their targets to promote a better understanding on B-cell development and as a result, construct more effective treatments against B-cell disease

Selection of HBsAg-Specific DNA Aptamers Based on Carboxylated Magnetic Nanoparticles and Their Application in the Rapid and Simple Detection of Hepatitis B Virus Infection

Aptamers are short single-stranded DNA or RNA oligonucleotides and can be selected from synthetic combinatorial libraries in vitro. They have a high binding affinity and specificity for their targets. Agarose gels, nitrocellulose membranes, and adsorptive microplates are often used as carriers to immobilize targets in the SELEX (systematic evolution of ligands by exponential enrichment) process, but the subsequent separation step is tedious and time-consuming. Therefore, we used magnetic nanoparticles (MNPs) as carriers to immobilize the target, hepatitis B surface antigen (HBsAg), which is convenient for fast magnetic separation. In this study, we first selected DNA aptamers against HBsAg by immobilizing HBsAg on the surface of carboxylated MNPs. The ssDNA library of each selection round was prepared by asymmetric PCR amplification for the next selection round. To obtain aptamer sequences, the final selected products were purified by gel electrophoresis, then cloned, and sequenced. DNA aptamers that specifically bind to HBsAg were successfully obtained after 13 selection rounds. The selected aptamers were used to construct a chemiluminescence aptasensor based on magnetic separation and immunoassay to detect HBsAg from pure protein or actual serum samples. There was a linear relationship between HBsAg concentration and chemiluminescent intensity in the range of 1–200 ng/mL. The aptasensor worked well even in the presence of interfering substances and was highly specific in the detection of HBsAg in serum samples, with a detection limit 0.1 ng/mL lower than the 0.5 ng/mL limit of an ELISA in use at the hospital. This aptasensor can contribute to better detection of hepatitis B virus infection

Influence of Molecular Weight on Structure and Catalytic Characteristics of Ordered Mesoporous Carbon Derived from Lignin

Bio-renewable lignin has been used as a carbon source for the preparation of porous carbon materials. Nevertheless, up to now, there are few studies about the influence of molecular weight of lignin on the structure and morphology of the ordered mesoporous carbon. Here, we synthesized the ordered mesoporous carbon derived from different molecular weights of lignin and Pluronic F127. Fortunately, we found that molecular weight is an important factor for obtaining highly ordered channels, high specific surface area, and ordered mesoporous carbon. More importantly, the narrow well-defined mesoporous channel could exert a spatial restriction effect to some extent, which can serve as nanoreactors for efficient reactions and enhance catalytic performance. The highly ordered mesoporous carbon from lignin is a good candidate for Fischer–Tropsch synthesis catalyst supports

Additively Manufactured Macroporous Titanium with Silver-Releasing Micro-/Nanoporous Surface for Multipurpose Infection Control and Bone Repair – A Proof of Concept

Restoring large-scale bone defects, where osteogenesis is slow while infections lurk, with biomaterials represents a formidable challenge in orthopedic clinics. Here, we propose a scaffold-based multipurpose anti-infection and bone repairing strategy to meet such restorative needs. To do this, personalized multifunctional titanium meshes were produced through an advanced additive manufacturing process and dual “TiO₂–poly­(dopamine)/Ag (nano)” post modifications, yielding macroporous constructs with micro-/nanoporous walls and nanosilver bullets immobilized/embedded therein. Ultrahigh loading capacity and durable release of Ag⁺ were accomplished. The scaffolds were active against planktonic/adherent bacteria (Gram-negative and positive) for up to 12 weeks. Additionally, they not only defended themselves from biofilm colonization but also helped destroy existing biofilms, especially in combination with antibiotics. Further, the osteoblasts/bacteria coculture study displayed that the engineered surfaces aided MG-63 cells to combat bacterial invasion. Meanwhile, the scaffolds elicited generally acceptable biocompatibility (cell adhesion, proliferation, and viability) and hastened osteoblast differentiation and maturation (alkaline phosphatase production, matrix secretion, and calcification), by synergy of micro-/nanoscale topological cues and bioactive catecholamine chemistry. Although done ex vivo, these studies reveal that our three-in-one strategy (infection prophylaxis, infection fighting, and bone repair) has great potential to simultaneously prevent/combat infections and bridge defected bone. This work provides new thoughts to the use of enabling technologies to design biomaterials that resolve unmet clinical needs