IsoTree: A New Framework for De novo Transcriptome Assembly from RNA-seq Reads

High-throughput sequencing of mRNA has made the deep and efficient probing of transcriptome more affordable. However, the vast amounts of short RNA-seq reads make de novo transcriptome assembly an algorithmic challenge. In this work, we present IsoTree, a novel framework for transcripts reconstruction in the absence of reference genomes. Unlike most of de novo assembly methods that build de Bruijn graph or splicing graph by connecting $k-mers$ which are sets of overlapping substrings generated from reads, IsoTree constructs splicing graph by connecting reads directly. For each splicing graph, IsoTree applies an iterative scheme of mixed integer linear program to build a prefix tree, called isoform tree. Each path from the root node of the isoform tree to a leaf node represents a plausible transcript candidate which will be pruned based on the information of paired-end reads. Experiments showed that in most cases IsoTree performs better than other leading transcriptome assembly programs. IsoTree is available at https://github.com/Jane110111107/IsoTree

Mechanically enhanced electrical conductivity of polydimethylsiloxane-based composites by a hot embossing process

Electrically conductive polymer composites are in high demand for modern technologies, however, the intrinsic brittleness of conducting conjugated polymers and the moderate electrical conductivity of engineering polymer/carbon composites have highly constrained their applications. In this work, super high electrical conductive polymer composites were produced by a novel hot embossing design. The polydimethylsiloxane (PDMS) composites containing short carbon fiber (SCF) exhibited an electrical percolation threshold at 0.45 wt % and reached a saturated electrical conductivity of 49 S/m at 8 wt % of SCF. When reducing the sample thickness from 1.0 to 0.1 mm by the hot embossing process, a compression-induced percolation threshold occurred at 0.3 wt %, while the electrical conductivity was further enhanced to 378 S/m at 8 wt % SCF. Furthermore, the addition of a second nanofiller of 1 wt %, such as carbon nanotube or conducting carbon black, further increased the electrical conductivity of the PDMS/SCF (8 wt %) composites to 909 S/m and 657 S/m, respectively. The synergy of the densified conducting filler network by the mechanical compression and the hierarchical micro-/nano-scale filler approach has realized super high electrically conductive, yet mechanically flexible, polymer composites for modern flexible electronics applications

An anchoring array assembly method for enhancing the electrical conductivity of composites of polypropylene and hybrid fillers

Constructing an interconnected filler-filler network in a polymer matrix is essential for enhancing the electrical conductivity of polymer composites. This work describes an Anchoring Array Assembly method for distribution of copper particles (CP) and carbon fibers (CF) in a polypropylene (PP) matrix. Constrained by a predesigned array anchoring template, the CP distribution achieved a high packing density in the PP matrix during compression molding which is key for filling the gaps between CFs, as well as for forming an interconnected hybrid filler network. Using the fixed array anchoring design, the dispersion and flow behavior of the conductive fillers and the polymer matrix are critical. When the inclination angle between the groove of the anchor mold and the horizontal plane was greater than 11.5 °, the migration of CP in the molten PP when in the anchor mold during the hot embossing process is restricted. The most conductive composites were obtained when the CPs were densely arranged in a triangular format. The conductive filler network was determined by the preset dense triangular "island-bridge" structure of the customized microarray mold. The conductivity of the composites prepared by the anchoring array assembly method reached 137.70 S/m, some 52 times higher than that prepared by traditional hot embossing methods with the same filler loading

Variable Optical Attenuator Based on Long-Range Surface Plasmon Polariton Multimode Interference Coupler

The fabrication and characterization of a thermal variable optical attenuator based on long-range surface plasmon polariton (LRSPP) waveguide with multimode interference architecture were investigated. The surface morphology and waveguide configuration of Au stripe were studied by atomic force microscopy. The fluctuation of refractive index of poly(methyl-methacrylate-glycidyl-methacrylate) polymer cladding was confirmed to be less than 3×10-4 within 8 h curing at 120°C. The end-fire excitation of LRSPP mode guiding at 1550 nm along Au stripe indicated that the extinction ratio of attenuator was about 12 dB at a driving power of 69 mW. The measured optical rise time and fall time are 0.57 and 0.87 ms, respectively. These favorable properties promise potentials of this plasmonic device in the application of optical interconnection

Inhibition of IL-18-mediated myeloid derived suppressor cell accumulation enhances anti-PD1 efficacy against osteosarcoma cancer

Myeloid derived suppressor cells (MDSC) are very important in tumor immune evasion and they dramatically increased in peripheral blood of patients with osteosarcoma cancer. The association between MDSC and various cytokines has been studied in the peripheral blood. However, little is known about the mechanism drawing MDSC into tumor parenchyma. This study was to analyze the correlation between MDSC subsets and interleukin 18 (IL-18) level in osteosarcoma tumor model and its effect on the immunotherapy. MDSC were isolated from the blood and parenchyma and analyzed in the osteosarcoma tumor model. IL-18 levels were detected by enzyme-linked immunosorbent assay (ELISA) assay, real-time PCR, western blot and flow cytometry. Moreover, combination treatment with IL-18 inhibition and anti-PD1 was conducted to assess the therapeutic effects of IL-18 blockade. Results showed MDSC levels had a positive correlation with IL-18, suggesting IL-18 may attract MDSC into the parenchyma. IL-18 gene and protein expression significantly increased in blood and tumor lysates of tumor-bearing mice. Anti-IL-18 treatment significantly decreased G-MDSC and M-MDSC in the peripheral blood and tumor. Furthermore, combination therapy decreased the tumor burden and increased CD4+ and CD8+ T cell infiltration, as well as the production of interferon gamma (IFNγ) and granzyme B. Our study revealed a possible correlation between MDSC subsets and IL-18 inducing MDSC migration into the tumor tissue, in addition to provide the potential target to enhance the efficacy of immunotherapy in patients with osteosarcoma. Keywords: Osteosarcoma, Myeloid derived suppressor cells, Anti-PD1, IL-1

Recent Progress in Metal-Based Nanoparticles Mediated Photodynamic Therapy

Photodynamic therapy (PDT) is able to non-invasively treat and diagnose various cancers and nonmalignant diseases by combining light, oxygen, and photosensitizers (PSs). However, the application of PDT is hindered by poor water solubility and limited light-penetration depth of the currently available photosensitizers (PSs). Water solubility of PSs is crucial for designing pharmaceutical formulation and administration routes. Wavelength of light source at visible range normally has therapeutic depth less than 1 mm. In this review, focus is on the recent research progress of metal-based nanoparticles being applied in PDT. The potential toxicity of these nanoscales and future directions are further discussed

Conductive Polymer Composites from Renewable Resources: An Overview of Preparation, Properties, and Applications

This article reviews recent advances in conductive polymer composites from renewable resources, and introduces a number of potential applications for this material class. In order to overcome disadvantages such as poor mechanical properties of polymers from renewable resources, and give renewable polymer composites better electrical and thermal conductive properties, various filling contents and matrix polymers have been developed over the last decade. These natural or reusable filling contents, polymers, and their composites are expected to greatly reduce the tremendous pressure of industrial development on the natural environment while offering acceptable conductive properties. The unique characteristics, such as electrical/thermal conductivity, mechanical strength, biodegradability and recyclability of renewable conductive polymer composites has enabled them to be implemented in many novel and exciting applications including chemical sensors, light-emitting diode, batteries, fuel cells, heat exchangers, biosensors etc. In this article, the progress of conductive composites from natural or reusable filling contents and polymer matrices, including (1) natural polymers, such as starch and cellulose, (2) conductive filler, and (3) preparation approaches, are described, with an emphasis on potential applications of these bio-based conductive polymer composites. Moreover, several commonly-used and innovative methods for the preparation of conductive polymer composites are also introduced and compared systematically

Utilization of Melt Fracture Phenomenon for the Preparation of Shark Skin Structured Hydrophobic Film

With the application of biomimetic shark skin microstructures with hydrophobicity in microfluidics, sensors and self-cleaning materials, microstructure processing methods are increasing. The preparation process has higher requirements for processing cost and efficiency. In this paper, linear low-density polyethylene (LLDPE) hydrophobic films were prepared with the help of melt fracture phenomenon. The equipment is a self-made single screw extruder. By adjusting the process parameters, the biomimetic shark skin structured LLDPE films with good hydrophobic property can be obtained. The surface microstructure shape of the product is related to kinds of additive, die temperature and screw speed. When AC5 was selected as an additive, the optimal processing parameter was found to be 160 °C die temperature and 80 r/min screw speed. A contact angle of 133° was obtained in this situation. In addition, the influences of die temperature and screw speed on the size of shark skin structure were also systematically investigated in this paper. It was found that the microstructure surface with hierarchical roughness had a better hydrophobic property

Recent Advances in Preparation, Mechanisms, and Applications of Thermally Conductive Polymer Composites: A Review

At present, the rapid accumulation of heat and the heat dissipation of electronic equipment and related components are important reasons that restrict the miniaturization, high integration, and high power of electronic equipment. It seriously affects the performance and life of electronic devices. Hence, improving the thermal conductivity of polymer composites (TCPCs) is the key to solving this problem. Compared with manufacturing intrinsic thermally conductive polymer composites, the method of filling the polymer matrix with thermally conductive fillers can better-enhance the thermal conductivity (λ) of the composites. This review starts from the thermal conduction mechanism and describes the factors affecting the λ of polymer composites, including filler type, filler morphology and distribution, and the functional surface treatment of fillers. Next, we introduce the preparation methods of filled thermally conductive polymer composites with different filler types. In addition, some commonly used thermal-conductivity theoretical models have been introduced to better-analyze the thermophysical properties of polymer composites. We discuss the simulation of λ and the thermal conduction process of polymer composites based on molecular dynamics and finite element analysis methods. Meanwhile, we briefly introduce the application of polymer composites in thermal management. Finally, we outline the challenges and prospects of TCPCs