PseudoFuN: Deriving functional potentials of pseudogenes from integrative relationships with genes and microRNAs across 32 cancers

BACKGROUND: Long thought "relics" of evolution, not until recently have pseudogenes been of medical interest regarding regulation in cancer. Often, these regulatory roles are a direct by-product of their close sequence homology to protein-coding genes. Novel pseudogene-gene (PGG) functional associations can be identified through the integration of biomedical data, such as sequence homology, functional pathways, gene expression, pseudogene expression, and microRNA expression. However, not all of the information has been integrated, and almost all previous pseudogene studies relied on 1:1 pseudogene-parent gene relationships without leveraging other homologous genes/pseudogenes. RESULTS: We produce PGG families that expand beyond the current 1:1 paradigm. First, we construct expansive PGG databases by (i) CUDAlign graphics processing unit (GPU) accelerated local alignment of all pseudogenes to gene families (totaling 1.6 billion individual local alignments and >40,000 GPU hours) and (ii) BLAST-based assignment of pseudogenes to gene families. Second, we create an open-source web application (PseudoFuN [Pseudogene Functional Networks]) to search for integrative functional relationships of sequence homology, microRNA expression, gene expression, pseudogene expression, and gene ontology. We produce four "flavors" of CUDAlign-based databases (>462,000,000 PGG pairwise alignments and 133,770 PGG families) that can be queried and downloaded using PseudoFuN. These databases are consistent with previous 1:1 PGG annotation and also are much more powerful including millions of de novo PGG associations. For example, we find multiple known (e.g., miR-20a-PTEN-PTENP1) and novel (e.g., miR-375-SOX15-PPP4R1L) microRNA-gene-pseudogene associations in prostate cancer. PseudoFuN provides a "one stop shop" for identifying and visualizing thousands of potential regulatory relationships related to pseudogenes in The Cancer Genome Atlas cancers. CONCLUSIONS: Thousands of new PGG associations can be explored in the context of microRNA-gene-pseudogene co-expression and differential expression with a simple-to-use online tool by bioinformaticians and oncologists alike

Lane estimation for autonomous vehicles using vision and LIDAR

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2010.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Cataloged from student submitted PDF version of thesis.Includes bibliographical references (p. 109-114).Autonomous ground vehicles, or self-driving cars, require a high level of situational awareness in order to operate safely and eciently in real-world conditions. A system able to quickly and reliably estimate the location of the roadway and its lanes based upon local sensor data would be a valuable asset both to fully autonomous vehicles as well as driver assistance technologies. To be most useful, the system must accommodate a variety of roadways, a range of weather and lighting conditions, and highly dynamic scenes with other vehicles and moving objects. Lane estimation can be modeled as a curve estimation problem, where sensor data provides partial and noisy observations of curves. The number of curves to estimate may be initially unknown and many of the observations may be outliers and false detections (e.g., due to tree shadows or lens are). The challenge is to detect lanes when and where they exist, and to update the lane estimates as new observations are received. This thesis describes algorithms for feature detection and curve estimation, as well as a novel curve representation that permits fast and ecient estimation while rejecting outliers. Locally observed road paint and curb features are fused together in a lane estimation framework that detects and estimates all nearby travel lanes.(cont.) The system handles roads with complex geometries and makes no assumptions about the position and orientation of the vehicle with respect to the roadway. Early versions of these algorithms successfully guided a fully autonomous Land Rover LR3 through the 2007 DARPA Urban Challenge, a 90km urban race course, at speeds up to 40 km/h amidst moving traffic. We evaluate these and subsequent versions with a ground truth dataset containing manually labeled lane geometries for every moment of vehicle travel in two large and diverse datasets that include more than 300,000 images and 44km of roadway. The results illustrate the capabilities of our algorithms for robust lane estimation in the face of challenging conditions and unknown roadways.by Albert S. Huang.Ph.D

The use of Bluetooth in Linux and location aware computing

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2005.Includes bibliographical references (p. 87-89).The Bluetooth specification describes a robust and powerful technology for short-range wireless communication. Unfortunately, the specification is immense and complicated, presenting a formidable challenge for novice developers. Currently, there is a lack of satisfactory technical documentation describing Bluetooth application development and the parts of the Bluetooth specification that are relevant to software developers. This thesis explains Bluetooth programming in the context of Internet programming and shows how most concepts in Internet programming are easily translated to Bluetooth. It describes how these concepts can be implemented in the GNU/Linux operating system using the BlueZ Bluetooth protocol stack and libraries. A Python extension module is presented that was created to assist in rapid development and deployment of Bluetooth applications. Finally, an inexpensive and trivially deployed infrastructure for location aware computing is presented, with a series of experiments conducted to determine how best to exploit such an infrastructure.by Albert Shuyu Huang.S.M

Enhanced Short Text Modeling: Leveraging Large Language Models for Topic Refinement

Crafting effective topic models for brief texts, like tweets and news headlines, is essential for capturing the swift shifts in social dynamics. Traditional topic models, however, often fall short in accurately representing the semantic intricacies of short texts due to their brevity and lack of contextual data. In our study, we harness the advanced capabilities of Large Language Models (LLMs) to introduce a novel approach termed "Topic Refinement". This approach does not directly involve itself in the initial modeling of topics but focuses on improving topics after they have been mined. By employing prompt engineering, we direct LLMs to eliminate off-topic words within a given topic, ensuring that only contextually relevant words are preserved or substituted with ones that fit better semantically. This method emulates human-like scrutiny and improvement of topics, thereby elevating the semantic quality of the topics generated by various models. Our comprehensive evaluation across three unique datasets has shown that our topic refinement approach significantly enhances the semantic coherence of topics.Comment: 6 pages, 4 figure

Comparison of multi-field coupling numerical simulation in hot dry rock thermal exploitation of enhanced geothermal systems

 In order to alleviate the environmental crisis and improve energy structure, countries from all over the world have focused on the hot dry rock geothermal resources with great potential and with little pollution. The geothermal heat production from Enhanced Geothermal System (EGS) comes with complex multi-field coupling process, and it is of great significance to study the temporal and spatial evolution of geothermal reservoir. In this work, a practical numerical model is established to simulate the heat production process in EGS, and the comparison of thermal-hydraulic (TH), thermal-hydraulic-mechanical (THM) and thermal-hydraulic-mechanical-chemical (THMC) coupling in geothermal reservoir is analyzed. The results show that the stable production stage of the three cases is approximately 5 years; however, compared with TH and THMC coupling, the service-life for THM coupling decreased by 1140 days and 332 days, respectively. The mechanical enhanced effects are offset by the chemical precipitation, and the precipitation from SiO2 is much larger than the dissolution of calcite.Cited as: Chen, S., Ding, B., Gong, L., Huang, Z., Yu, B., Sun, S. Comparison of multi-field coupling numerical simulation in hot dry rock thermal exploitation of enhanced geothermal systems. Advances in Geo-Energy Research, 2019, 3(4): 396-409, doi: 10.26804/ager.2019.04.0

Type I interferon signaling facilitates the development of IL-10-producing effector CD8+ T cells during influenza virus infection

Recent evidence has suggested that IL-10-producing effector CD8+ T cells play an important role in regulating excessive inflammation during acute viral infections. However, the cellular and molecular cues regulating the development of IL-10-producing effector CD8+ T cells are not completely defined. Here, we show that type I interferons (IFNs) are required for the development of IL-10-producing effector CD8+ T cells during influenza virus infection in mice. We find that type I IFNs can enhance IL-27 production by lung APCs, thereby facilitating IL-10-producing CD8+ T-cell development through a CD8+ T-cell-nonautonomous way. Surprisingly, we also demonstrate that direct type I IFN signaling in CD8+ T cells is required for the maximal generation of IL-10-producing CD8+ T cells. Type I IFN signaling in CD8+ T cells, in cooperation with IL-27 and IL-2 signaling, promotes and sustains the expression of IFN regulatory factor 4 (IRF4) and B-lymphocyte-induced maturation protein-1 (Blimp-1), two transcription factors required for the production of IL-10 by effector CD8+ T cells. Our data reveal a critical role of the innate antiviral effector cytokines in regulating the production of a regulatory cytokine by effector CD8+ T cells during respiratory virus infection