Novel Method of Full-Length RNA-seq That Expands the Identification of Non-Polyadenylated RNAs Using Nanopore Sequencing.

The occurrence of diseases displayed transcriptome alteration, including both coding and non-coding transcripts. The third-generation sequencing (TGS) technologies allow for intensive and comprehensive research of the transcriptome. However, the present standard TGS RNA sequencing method is unable to detect many of the non-polyadenylated [non-poly(A)] RNAs. To obtain more complete transcriptome information, we presented a new comprehensive sequencing approach by performing conventional poly(A) RNA-sequencing combined with the sequencing of non-poly(A) RNA fraction which was tailed by poly(U) on HepG2 and HL-7702 cell lines, enabling the detection of multiple categories of non-poly(A) RNAs excluded by the existing standard approach. Moreover, the length distribution of the full-splice match transcripts was longer than that assembled by short-reads, which contributed to characterizing alternative splicing events and provided a comprehensive portrait of transcriptional complexity. Besides the detection of genes with differential expression patterns in the poly(A) library between HepG2 and HL-7702, we also found a cancer-related non-coding gene in the poly(U) data, that is, growth arrest special 5 (GAS5). Collectively, our results suggested that the novel method effectively captured both poly(A) and non-poly(A) transcripts in the tested cell lines and allowed a deeper exploration of the transcriptome.

Identification of full-length circular nucleic acids using long-read sequencing technologies.

Unlike the traditional perception in genomic DNA or linear RNA, circular nucleic acids are a class of functional biomolecules with a circular configuration and are often observed in nature. These circular molecules encompass the full spectrum of size and play an important role in organisms, making circular nucleic acids research worthy. Due to the low abundance of most types of circular nucleic acids and the disadvantages of short-read sequencing platforms, accurate and full-length circular nucleic acid sequencing and identification is difficult. In this review, we have provided insights into full-length circular nucleic acid detection methods using long-read sequencing technologies, with a focus on the experimental and bioinformatics strategies to obtain accurate sequences.

Effect of different cooling regimes on the mechanical properties of cementitious composites subjected to high temperatures.

The influence of different cooling regimes (quenching in water and cooling in air) on the residual mechanical properties of engineered cementitious composite (ECC) subjected to high temperature up to 800°C was discussed in this paper. The ECC specimens are exposed to 100, 200, 400, 600, and 800°C with the unheated specimens for reference. Different cooling regimens had a significant influence on the mechanical properties of postfire ECC specimens. The microstructural characterization was examined before and after exposure to fire deterioration by using scanning electron microscopy (SEM). Results from the microtest well explained the mechanical properties variation of postfire specimens.

The placement of percutaneous retrograde acetabular posterior column screw based on imaging anatomical study of acetabular posterior column corridor.

OBJECTIVE: To explore the entry point, orientation, and fixation range of retrograde acetabular posterior column screw. METHOD: The computed tomography data of 100 normal adult pelvises (50 males and 50 females, respectively) were collected and pelvis three-dimensional (3D) reconstruction was performed by using Mimics software and the 3D model was imported into Geomagic Studio software. The perspective of acetabular posterior column was carried out orienting from ischial tuberosity to iliac fossa in the Mimics software. Virtual screw was inserted perpendicular to the transverse section of acetabular posterior column corridor, and the maximum screw diameter, entry point, orientation, exit point were measured. The screw fixation range, the easy-to-penetrate sites, and intraoperative optimal fluoroscopic views were assessed. RESULTS: The acetabular posterior column corridor showed a triangular-prism shape. The virtual screw entry point was located at the midline between the medial and lateral edges of the ischial tuberosity. The distance between the entry point and the distal ischial tuberosity was around 13 mm. The distances between the exit point and the true pelvis rim, and ipsilateral anterior sacroiliac joint line were (19.33 ± 2.60) mm and (23.65 ± 2.42) mm in males, respectively. As for females, those two data were (17.63 ± 2.00) mm and (24.94 ± 2.39) mm, respectively. The maximum diameters of screws were (17.21 ± 1.41) mm in males and (15.54 ± 1.51) mm in females. The angle between the retrograde posterior column screw and the sagittal plane was lateral inclination (10.52 ± 3.04)° in males, and that was lateral inclination (7.72 ± 2.99)° in females. Correspondingly, the angle between the screw and the coronal plane was anterior inclination (15.00 ± 4.92)° in males, and that was anterior inclination (12.94 ± 4.72)° in females. Retrograde acetabular posterior column screw through ischial tuberosity can fix the acetabular posterior column fractures which were not 4 cm above the femoral head center. The easy-to-penetrate sites were located at the transition between the posterior acetabular wall and the ischium, the middle of the acetabulum, and 1 cm below the greater sciatic notch, respectively. The iliac oblique 10°, iliac oblique 60°, and obturator oblique 60° views were the intraoperative optimal fluoroscopic views to assess whether the screw was safely inserted. CONCLUSION: Retrograde acetabular posterior column screw entry point is located at the midline between the medial and lateral edges of the ischial tuberosity, which is 1.3 cm far from the distal ischial tuberosity. The screw direction is about 10° lateral inclination and 15° anterior inclination, which can fix the acetabular posterior column fractures which were not 4 cm above the femoral head center.

Identifying cancer specific signaling pathways based on the dysregulation between genes.

A large collection of studies has shown that the occurrence of cancer is related to the functional dysfunction of the pathways. Identification of cancer-related pathways could help researchers understand the mechanisms of complex diseases well. Whereas, most current signaling pathway analysis methods take no account of the gene interaction variations within pathways. Furthermore, considering that some pathways have connection with two or more cancer types, while some are likely to be cancer-type specific pathways. Identifying cancer-type specific pathways contributes to interpreting the different mechanisms of different cancer types. In this study, we first proposed a pathway analysis method named Pathway Analysis of Intergenic Regulation (PAIGR) to identify pathways with dysregulation between genes and compared the performance of this method with four existing methods on four colorectal cancer (CRC) datasets. The results showed that PAIGR could find cancer-related pathways more accurately. Moreover, in order to explore the relationship between the identified pathways and the cancer type, we constructed a pathway interaction network, in which nodes and edges represented pathways and interactions between pathways respectively. Highly connected pathways were considered to play a central role in an extensive range of biological processes, while sparsely connected pathways are considered to have certain specificity. Our results showed that pathways identified by PAIGR had a low nodal degree (i.e., a few numbers of interactions), which suggested that most of these pathways were cancer-type specific.

Amphiphilic Polymer-Modified Uniform CuFeSe2 Nanoparticles for CT/MR Dual-Modal Imaging.

Recently, magnetic photothermal nanomaterials have attracted much attention in the diagnosis and treatment of cancer. In this study, we developed the ultrasmall magnetic CuFeSe2 nanoparticles for CT/MR dual-modal imaging. By controlling the reaction time and condition, CuFeSe2 nanoparticles were synthesized by a simple directly aqueous method. After modification with copolymer methoxy polyethylene glycol-polycaprolactone (MPEG-PCL), the obtained MPEG-PCL@CuFeSe2 nanoparticles showed excellent water solubility, colloidal stability, and biocompatibility. In addition, they also exhibited superparamagnetism and X-ray's characteristics. For these properties, they will become ideal nanomaterials for CT/MR dual-modal imaging.

The mechanism and detection of alternative splicing events in circular RNAs.

Circular RNAs (circRNAs) are considered as functional biomolecules with tissue/development-specific expression patterns. Generally, a single gene may generate multiple circRNA variants by alternative splicing, which contain different combinations of exons and/or introns. Due to the low abundance of circRNAs as well as overlapped with their linear counterparts, circRNA enrichment protocol is needed prior to sequencing. Compared with numerous algorithms, which use back-splicing reads for detection and functional characterization of circRNAs, original bioinformatic analyzing tools have been developed to large-scale determination of full-length circRNAs and accurate quantification. This review provides insights into the complexity of circRNA biogenesis and surveys the recent progresses in the experimental and bioinformatic methodologies that focus on accurately full-length circRNAs identification.

A Prediction Model of the Concrete Cracking Induced by the Non-Uniform Corrosion of the Steel Reinforcement.

This paper investigates the influence of non-uniform corrosion in the transversal direction of the steel reinforcement on the cracking propagation of the concrete cover. An analytical model is proposed for the prediction of the corrosion-induced cracking performance. Both the thick cylinder theory of the concrete and the effect of transversal non-uniform corrosion of the steel reinforcement are involved by considering the corrosion layer of the corrosion products and a layer of concrete with the corrosion products filled with the pores. A three-stage corrosion-induced cracking of the concrete is proposed: corrosion without expansive stress to the concrete, corrosion with expansive stress to the adjacent concrete, as well as the corrosion-induced cracking of the concrete. By considering the non-uniform corrosion of the steel reinforcement and the tensile stress induced by the volumetric expansion of the corrosion products, the cracking initiation resulting from the non-uniform corrosion was involved in the prediction model. The models were also validated by the experimental results from both the corroded specimens and the existing literature, which would be helpful for the evaluation of the existing reinforced concrete constructions in the marine environment.

Parameter Screening Study for Optimizing the Static Properties of Nanoparticle-Stabilized CO2 Foam Based on Orthogonal Experimental Design.

Nanoparticle (NP)-stabilized foam technology has found potential applications in CO2 enhanced oil recovery (EOR) and greenhouse gas geological storage practices and accordingly attracts lots of research interest. To screen the optimal formula for the satisfactory foam performance, orthogonal experimental design (OED) is used in this paper for the complex multifactor multilevel system consisting of five influential factors of NP size, surfactant concentration, NP concentration, temperature, and salinity at four different levels in the range of 7-40 nm, 0-0.15 wt %, 0-0.2 wt %, 25-55 °C, and 0-3 wt %, respectively. Based on the orthogonal principle, only 16 experiments were performed to analyze the effect of various factors on the foam height and foam half-life properties. In addition to showing that the influence of the single factor on foam static properties, OED results reveal that the surfactant concentration and temperature are dominating factors on foamability and stability of the NP-stabilized CO2 foam, respectively. Finally, NP-stabilized CO2 foam with satisfactory static characteristics is obtained with the OED recommended composition of a 0.15 wt % surfactant concentration, 0.1 wt % NP concentration, and NP size of 7 nm in 1 wt % saline solution at temperatures of 30 and 50 °C, validating that the OED method could substantially facilitate the laboratory screening and optimization process for a successful NP-stabilized CO2 foam application.

Flexural Fatigue Properties of Ultra-High Performance Engineered Cementitious Composites (UHP-ECC) Reinforced by Polymer Fibers.

In recent years, the application of engineered cementitious composites (ECCs) in structures subjected to cyclic fatigue loading, such as highway bridges, has gained widespread attention. However, most existing ECCs do not have sufficient strength and ductility, which limits their applications, especially in highway bridge structures under high-stress. In this work, an ultra-high performance engineered cementitious composite (UHP-ECC) was configured, which had a compressive strength of approximately 120 MPa, a tensile strength of up to 12 MPa, and a tensile strain capacity of more than 8%. This paper presents a study of the fatigue performance of UHP-ECC at four different fatigue stress levels through the four-point bending test. The mid-span deflection of the specimen was monitored along with the crack opening displacement (COD) of the pure bending section at the bottom of the specimen, and the crack width. In addition, the dissipated energy was calculated at various stress levels. The progressive formation of cracks under static loading was monitored using the digital image correlation (DIC) technique. The fibers at the fractured surface of the specimens were observed and analyzed by environmental scanning electron microscopy, and the morphology of the fibers was obtained at different fatigue stress levels. Eventually, the fatigue life under different stress levels was obtained, and the relationship between the fatigue life and the stress level was established.

Mechanical Properties of Hybrid Ultra-High Performance Engineered Cementitous Composites Incorporating Steel and Polyethylene Fibers.

This paper presents the authors' newly developed hybrid ultra-high performance (HUHP) engineered cementitious composite (ECC) with steel (ST) and polyethylene (PE) fibers. From this point on it will be referred to as HUHP-ECC. The volumes of steel and PE fibers were adjusted to obtain different mechanical properties, including compressive strength, tensile, and flexural properties. We found that tensile and flexural properties, including bending strength and ductility indexes, increased with higher PE fiber amounts but reduced with the increased ST fiber volume. Notably, the compressive strength had the opposite tendency and decreased with increases in the PE volume. The ST fiber had a significantly positive effect on the compressive strength. The fluidity of HUHP-ECC improved with the increasing amount of ST fiber. The pseudo strain-hardening (PSH) values for all the HUHP-ECC mixtures were used to create an index indicating the ability of strain capacity; thus, the PSH values were calculated to explain the ductility of HUHP-ECC with different fiber volumes. Finally, the morphology of PE and ST fibers at the fracture surface was observed by an environmental scanning electron microscope (ESEM).

High-Salt Diet Has a Certain Impact on Protein Digestion and Gut Microbiota: A Sequencing and Proteome Combined Study.

High-salt diet has been considered to cause health problems, but it is still less known how high-salt diet affects gut microbiota, protein digestion, and passage in the digestive tract. In this study, C57BL/6J mice were fed low- or high-salt diets (0.25 vs. 3.15% NaCl) for 8 weeks, and then gut contents and feces were collected. Fecal microbiota was identified by sequencing the V4 region of 16S ribosomal RNA gene. Proteins and digested products of duodenal, jejunal, cecal, and colonic contents were identified by LC-MS-MS. The results indicated that the high-salt diet increased Firmicutes/Bacteroidetes ratio, the abundances of genera Lachnospiraceae and Ruminococcus (P < 0.05), but decreased the abundance of Lactobacillus (P < 0.05). LC-MS-MS revealed a dynamic change of proteins from the diet, host, and gut microbiota alongside the digestive tract. For dietary proteins, high-salt diet seemed not influence its protein digestion and absorption. For host proteins, 20 proteins of lower abundance were identified in the high-salt diet group in duodenal contents, which were involved in digestive enzymes and pancreatic secretion. However, no significant differentially expressed proteins were detected in jejunal, cecal, and colonic contents. For bacterial proteins, proteins secreted by gut microbiota were involved in energy metabolism, sodium transport, and protein folding. Five proteins (cytidylate kinase, trigger factor, 6-phosphogluconate dehydrogenase, transporter, and undecaprenyl-diphosphatase) had a higher abundance in the high-salt diet group than those in the low-salt group, while two proteins (acetylglutamate kinase and PBSX phage manganese-containing catalase) were over-expressed in the low-salt diet group than in the high-salt group. Consequently, high-salt diet may alter the composition of gut microbiota and has a certain impact on protein digestion.