Computational approaches for whole-transcriptome cancer analysis based on RNA sequencing data

RNA-Seq (Whole Transcriptome Shotgun Sequencing) provides an ideal platform to study the complete set of transcripts for a specific developmental stage or physiological condition. It reveals not only expression-level changes, but also structural changes in the coding sequences, including gene rearrangements. In this dissertation, I present my contributions to the development of computational tools for the robust and efficient analysis of RNA-seq data to support cancer research. To automate the laborious and computationally intensive procedure of RNA-seq data management, I worked on the development of Hydra, an RNA-seq pipeline for the parallel processing and quality control of large numbers of samples. With user-friendly reports on quality control and running checkpoints, Hydra makes the data processing procedure fast, efficient and reliable. Here, I report my application of the pipeline to the analysis of patient-derived lymphoma xenograft samples, to show Hydra’s ability to detect abnormalities (e.g., mouse tissue contamination) in the sequencing data. Because fusions play an important role in carcinogenesis, fusion detection has become an important area of methodological research. Several computational methods have been developed to identify fusion transcripts from RNA-seq data. However, all these methods require realignment to the transcriptome, a computationally expensive task, unnecessary in many cases. Here, I present QueryFuse, a novel gene-specific fusion-detection algorithm for aligned RNA-seq data. It is designed to help biologists find and/or computationally validate fusions of interest quickly, and to annotate the detected events with visualization and detailed properties of the supporting reads. By focusing the fusion detection on read pairs aligned to query genes, we can not only reduce realignment time, but also afford to use a more accurate but computationally expensive local aligner. In the extensive evaluation I performed, I obtained comparable or better results compared with two widely adopted tools (deFuse and TophatFusion) on two simulated datasets, as well as on cell line datasets with known fusions. Finally, I contributed to the identification of a novel fusion event in lymphoma, with potential therapeutic implications in clinical samples. I validated this fusion in silico by my putative reference method before experimental validation

Long term bond strength and chloride resistance of epoxy and concrete overlays

There has been an increasing need to extend the service life of bridges due to deteriorating conditions of infrastructure and associated fiscal limitations. To protect bridge deck against deterioration, as well as to improve bridge performance through better maintenance practices, a better understanding of performance of the recently developed thin epoxy overlay and the well-adopted low slump dense concrete (LSDC) overlay is desired. To evaluate the performance of these two overlays, the following objectives are proposed: to evaluate the initial and long-term bond strength of overlays; to assess the chloride resistance of overlays and to identify factors that affect the initial performance of overlays. To fulfill these objectives, six existing bridges were chosen to install the two overlay types, and field inspections were performed on selected bridges to document substrate surface conditions; substrate cores were extracted and tested by both ASTM C642 and ASTM C666 to evaluate their porosity and durability to cyclic freezing condition; on-site pull-off tests (ASTM C1583) were conducted to assess the initial bond strength of overlays; laboratory pull-off tests (ASTM C1583) were conducted under cyclic freezing conditions to evaluate long-term bond strength and salt-ponding tests (AASHTO T259) were performed to assess chloride resistance. The results from these testing efforts indicated that the initial bond strength of both overlays are good; the long-term bond strength of thin epoxy overlay decreased sharply after 300th F/T cycles, whereas the bond performance of the LSDC overlay remained unchanged; chloride resistance of the epoxy overlay is much better than LSDC overlay and the percentage of air voids of the substrate concrete was seen to have an effect on the initial performance of the overlays

Continuous Versatile Jumping Using Learned Action Residuals

Jumping is essential for legged robots to traverse through difficult terrains. In this work, we propose a hierarchical framework that combines optimal control and reinforcement learning to learn continuous jumping motions for quadrupedal robots. The core of our framework is a stance controller, which combines a manually designed acceleration controller with a learned residual policy. As the acceleration controller warm starts policy for efficient training, the trained policy overcomes the limitation of the acceleration controller and improves the jumping stability. In addition, a low-level whole-body controller converts the body pose command from the stance controller to motor commands. After training in simulation, our framework can be deployed directly to the real robot, and perform versatile, continuous jumping motions, including omni-directional jumps at up to 50cm high, 60cm forward, and jump-turning at up to 90 degrees. Please visit our website for more results: https://sites.google.com/view/learning-to-jump.Comment: To be presented at L4DC 202

CAJun: Continuous Adaptive Jumping using a Learned Centroidal Controller

We present CAJun, a novel hierarchical learning and control framework that enables legged robots to jump continuously with adaptive jumping distances. CAJun consists of a high-level centroidal policy and a low-level leg controller. In particular, we use reinforcement learning (RL) to train the centroidal policy, which specifies the gait timing, base velocity, and swing foot position for the leg controller. The leg controller optimizes motor commands for the swing and stance legs according to the gait timing to track the swing foot target and base velocity commands using optimal control. Additionally, we reformulate the stance leg optimizer in the leg controller to speed up policy training by an order of magnitude. Our system combines the versatility of learning with the robustness of optimal control. By combining RL with optimal control methods, our system achieves the versatility of learning while enjoys the robustness from control methods, making it easily transferable to real robots. We show that after 20 minutes of training on a single GPU, CAJun can achieve continuous, long jumps with adaptive distances on a Go1 robot with small sim-to-real gaps. Moreover, the robot can jump across gaps with a maximum width of 70cm, which is over 40% wider than existing methods.Comment: Please visit https://yxyang.github.io/cajun/ for additional result

Stable Internal Reference Genes for Normalizing Real-Time Quantitative PCR in Baphicacanthus cusia under Hormonal Stimuli and UV Irradiation, and in Different Plant Organs

Baphicacanthus cusia (Nees) Bremek, the plant source for many kinds of drugs in traditional Chinese medicine, is widely distributed in South China, especially in Fujian. Recent studies about B. cusia mainly focus on its chemical composition and pharmacological effects, but further analysis of the plant's gene functions and expression is required to better understand the synthesis of its effective compounds. Real-time quantitative polymerase chain reaction (RT-qPCR) is a powerful method for gene expression analysis. It is necessary to select a suitable reference gene for expression normalization to ensure the accuracy of RT-qPCR results. Ten candidate reference genes were selected from the transcriptome datasets of B. cusia in this study, and the expression stability was assessed across 60 samples representing different tissues and organs under various conditions, including ultraviolet (UV) irradiation, hormonal stimuli (jasmonic acid methyl ester and abscisic acid), and in different plant organs. By employing different algorithms, such as geNorm, NormFinder, and BestKeeper, which are complementary approaches based on different statistical procedures, 18S rRNA was found to be the most stable gene under UV irradiation and hormonal stimuli, whereas ubiquitin-conjugating enzyme E2 was the best suitable gene for different plant organs. This novel study aimed to screen for suitable reference genes and corresponding primer pairs specifically designed for gene expression studies in B. cusia, in particular for RT-qPCR analyses

Clinical efficacy and safety of robotic retroperitoneal lymph node dissection for testicular cancer: a systematic review and meta-analysis

BackgroundRetroperitoneal lymph node dissection (RPLND) is an effective treatment for testicular tumors. In recent years, with the development of robotics, many urological procedures performed via standard laparoscopy have been replaced by robots. Our objective was to compare the safety and efficacy of robotic retroperitoneal lymph node dissection (R-RPLND) versus Non-robotic retroperitoneal lymph node dissection (NR-RPLND) in testicular cancer.MethodsPubmed, Embase, Scopus, Cochrane Library, and Web of Science databases were searched for literature on robotic surgery for testicular germ cell tumors up to April 2023. The statistical and sensitivity analyses were performed using Review Manager 5.3. Meta-analysis was performed to calculate mean difference (MD), odds ratio(OR), and 95% confidence interval (CI) effect indicators.ResultsEight studies with 3875 patients were finally included in this study, 453 with R-RPLND and 3422 with open retroperitoneal lymph node dissection (O-RPLND)/laparoscopic retroperitoneal lymph node dissection (L-RPLND). The results showed that R-RPLND had lower rates of intraoperative blood loss (MD = -436.39; 95% CI -707.60 to -165.19; P = 0.002), transfusion (OR = 0.06; 95% CI 0.01 to 0.26; P = 0.0001), total postoperative complication rates (OR = 0.39; 95% CI 0.21 to 0.70; P = 0.002), and length of stay (MD=-3.74; 95% CI -4.69 to -2.78; P<0.00001). In addition, there were no statistical differences between the two groups regarding perioperative and oncological outcomes regarding total operative time, the incidence of postoperative complications grade≥III, abnormal ejaculation rate, lymph node yield, and postoperative recurrence rate.ConclusionsThe R-RPLND and O-RPLND/L-RPLND provide safe and effective retroperitoneal lymph node dissection for testicular cancer. Patients with R-RPLND have less intraoperative bleeding, shorter hospitalization period, fewer postoperative complications, and faster recovery. It should be considered a viable alternative to O-RPLND/L-RPLND.Systematic Review Registrationhttps://www.crd.york.ac.uk/PROSPERO, identifier CRD42023411696