Yan Zhang

Publications

2 Accurate HLA Typing at High-Digit Resolution from NGS Data

Authors: Yan Zhang, Yazhi Huang, Jing Yang, Dingge Ying, Vorasuk Shotelersuk, Nattiya Hirankarn, Pak Chung Sham, Yu Lung Lau, Wanling Yang

Abstract:

Human leukocyte antigen (HLA) typing from next generation sequencing (NGS) data has the potential for applications in clinical laboratories and population genetic studies. Here we introduce a novel technique for HLA typing from NGS data based on read-mapping using a comprehensive reference panel containing all known HLA alleles and de novo assembly of the gene-specific short reads. An accurate HLA typing at high-digit resolution was achieved when it was tested on publicly available NGS data, outperforming other newly-developed tools such as HLAminer and PHLAT.

Keywords: whole exome sequencing, human leukocyte antigens, HLA typing, next generation sequencing

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1 An Eulerian Numerical Method and its Application to Explosion Problems

Authors: Li Hao, Yan Zhang, Jingan Cui

Abstract:

The Eulerian numerical method is proposed to analyze the explosion in tunnel. Based on this method, an original software M-MMIC2D is developed by Cµ program language. With this software, the explosion problem in the tunnel with three expansion-chambers is numerically simulated, and the results are found to be in full agreement with the observed experimental data.

Keywords: Numerical Simulation, Tunnel, shock wave, Eulerian method

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Abstracts

4 Combination of Plantar Pressure and Star Excursion Balance Test for Evaluation of Dynamic Posture Control on High-Heeled Shoes

Authors: Yan Zhang, Jan Awrejcewicz, Lin Fu

Abstract:

High-heeled shoes force the foot into plantar flexion position resulting in foot arch rising and disturbance of the articular congruence between the talus and tibiofibular mortice, all of which may increase the challenge of balance maintenance. Plantar pressure distribution of the stance limb during the star excursion balance test (SEBT) contributes to the understanding of potential sources of reaching excursions in SEBT. The purpose of this study is to evaluate the dynamic posture control while wearing high-heeled shoes using SEBT in a combination of plantar pressure measurement. Twenty healthy young females were recruited. Shoes of three heel heights were used: flat (0.8 cm), low (4.0 cm), high (6.6 cm). The testing grid of SEBT consists of three lines extending out at 120° from each other, which were defined as anterior, posteromedial, and posterolateral directions. Participants were instructed to stand on their dominant limb with the heel in the middle of the testing grid and hands on hips and to reach the non-stance limb as far as possible towards each direction. The distal portion of the reaching limb lightly touched the ground without shifting weight. Then returned the reaching limb to the beginning position. The excursion distances were normalized to leg length. The insole plantar measurement system was used to record peak pressure, contact area, and pressure-time integral of the stance limb. Results showed that normalized excursion distance decreased significantly as heel height increased. The changes of plantar pressure in SEBT as heel height increased were more obvious in the medial forefoot (MF), medial midfoot (MM), rearfoot areas. At MF, the peak pressure and pressure-time integral of low and high shoes increased significantly compared with that of flat shoes, while the contact area decreased significantly as heel height increased. At MM, peak pressure, contact area, and pressure-time integral of high and low shoes were significantly lower than that of flat shoes. To reduce posture instability, the stance limb plantar loading shifted to medial forefoot. Knowledge of this study identified dynamic posture control deficits while wearing high-heeled shoes and the critical role of the medial forefoot in dynamic balance maintenance.

Keywords: Plantar Pressure, dynamic posture control, high-heeled shoes, star excursion balance test

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3 AIPM:An Integrator and Pull Request Matching Model in Github

Authors: Li Xu, Yan Zhang, Zhifang Liao, Yanbing Li, Xiaoping Fan, Jinsong Wu

Abstract:

Pull Request (PR) is the primary method for code contributions from the external contributors in Github. PR review is an essential part of open source software developments for maintaining the quality of software. Matching a new PR of an appropriate integrator will make the PR review more effective. However, PR and integrator matching are now organized manually in Github. To reduce this cost, we presented an AIPM model to predict highly relevant integrator of incoming PRs. AIPM uses topic model to extract topics from the PRs, and builds a one-to-one correspondence between topics and integrators. Then, AIPM finds the most suitable integrator according to the maximum entry of the topic-document distribution. On average, AIPM can reach a precision of 60%, and even in some projects, can reach a precision of 80%.

Keywords: topic model, pull Request, integrator matching, Github, open source project

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2 Predictive Maintenance: Machine Condition Real-Time Monitoring and Failure Prediction

Authors: Yan Zhang

Abstract:

Predictive maintenance is a technique to predict when an in-service machine will fail so that maintenance can be planned in advance. Analytics-driven predictive maintenance is gaining increasing attention in many industries such as manufacturing, utilities, aerospace, etc., along with the emerging demand of Internet of Things (IoT) applications and the maturity of technologies that support Big Data storage and processing. This study aims to build an end-to-end analytics solution that includes both real-time machine condition monitoring and machine learning based predictive analytics capabilities. The goal is to showcase a general predictive maintenance solution architecture, which suggests how the data generated from field machines can be collected, transmitted, stored, and analyzed. We use a publicly available aircraft engine run-to-failure dataset to illustrate the streaming analytics component and the batch failure prediction component. We outline the contributions of this study from four aspects. First, we compare the predictive maintenance problems from the view of the traditional reliability centered maintenance field, and from the view of the IoT applications. When evolving to the IoT era, predictive maintenance has shifted its focus from ensuring reliable machine operations to improve production/maintenance efficiency via any maintenance related tasks. It covers a variety of topics, including but not limited to: failure prediction, fault forecasting, failure detection and diagnosis, and recommendation of maintenance actions after failure. Second, we review the state-of-art technologies that enable a machine/device to transmit data all the way through the Cloud for storage and advanced analytics. These technologies vary drastically mainly based on the power source and functionality of the devices. For example, a consumer machine such as an elevator uses completely different data transmission protocols comparing to the sensor units in an environmental sensor network. The former may transfer data into the Cloud via WiFi directly. The latter usually uses radio communication inherent the network, and the data is stored in a staging data node before it can be transmitted into the Cloud when necessary. Third, we illustrate show to formulate a machine learning problem to predict machine fault/failures. By showing a step-by-step process of data labeling, feature engineering, model construction and evaluation, we share following experiences: (1) what are the specific data quality issues that have crucial impact on predictive maintenance use cases; (2) how to train and evaluate a model when training data contains inter-dependent records. Four, we review the tools available to build such a data pipeline that digests the data and produce insights. We show the tools we use including data injection, streaming data processing, machine learning model training, and the tool that coordinates/schedules different jobs. In addition, we show the visualization tool that creates rich data visualizations for both real-time insights and prediction results. To conclude, there are two key takeaways from this study. (1) It summarizes the landscape and challenges of predictive maintenance applications. (2) It takes an example in aerospace with publicly available data to illustrate each component in the proposed data pipeline and showcases how the solution can be deployed as a live demo.

Keywords: Internet of Things, Machine Learning, streaming data, Predictive Maintenance

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1 Accurate HLA Typing at High-Digit Resolution from NGS Data

Authors: Yan Zhang, Yazhi Huang, Jing Yang, Dingge Ying, Vorasuk Shotelersuk, Nattiya Hirankarn, Pak Chung Sham, Yu Lung Lau, Wanling Yang

Abstract:

Human leukocyte antigen (HLA) typing from next generation sequencing (NGS) data has the potential for applications in clinical laboratories and population genetic studies. Here we introduce a novel technique for HLA typing from NGS data based on read-mapping using a comprehensive reference panel containing all known HLA alleles and de novo assembly of the gene-specific short reads. An accurate HLA typing at high-digit resolution was achieved when it was tested on publicly available NGS data, outperforming other newly-developed tools such as HLAminer and PHLAT.

Keywords: Next Generation Sequencing, whole exome sequencing, human leukocyte antigens, HLA typing

Procedia PDF Downloads 351