Browsing by Author "Qian, Feng"

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    The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies
    Shi, Leming; Jones, Wendell D.; Jensen, Roderick V.; Harris, Stephen C.; Perkins, Roger G.; Goodsaid, Federico M.; Guo, Lei; Croner, Lisa J.; Boysen, Cecilie; Fang, Hong; Qian, Feng; Amur, Shashi; Bao, Wenjun; Barbacioru, Catalin C.; Bertholet, Vincent; Cao, Xiaoxi M.; Chu, Tzu-Ming; Collins, Patrick J.; Fan, Xiao-hui; Frueh, Felix W.; Fuscoe, James C.; Guo, Xu; Han, Jing; Herman, Damir; Hong, Huixiao; Kawasaki, Ernest S.; Li, Quan-Zhen; Luo, Yuling; Ma, Yunqing; Mei, Nan; Peterson, Ron L.; Puri, Raj K.; Shippy, Richard; Su, Zhenqiang; Sun, Yongming A.; Sun, Hongmei; Thorn, Brett; Turpaz, Yaron; Wang, Charles; Wang, Sue J.; Warrington, Janet A.; Willey, James C.; Wu, Jie; Xie, Qian; Zhang, Liang; Zhang, Lu; Zhong, Sheng; Wolfinger, Russell D.; Tong, Weida (2008-08-12)
    Background Reproducibility is a fundamental requirement in scientific experiments. Some recent publications have claimed that microarrays are unreliable because lists of differentially expressed genes (DEGs) are not reproducible in similar experiments. Meanwhile, new statistical methods for identifying DEGs continue to appear in the scientific literature. The resultant variety of existing and emerging methods exacerbates confusion and continuing debate in the microarray community on the appropriate choice of methods for identifying reliable DEG lists. Results Using the data sets generated by the MicroArray Quality Control (MAQC) project, we investigated the impact on the reproducibility of DEG lists of a few widely used gene selection procedures. We present comprehensive results from inter-site comparisons using the same microarray platform, cross-platform comparisons using multiple microarray platforms, and comparisons between microarray results and those from TaqMan - the widely regarded "standard" gene expression platform. Our results demonstrate that (1) previously reported discordance between DEG lists could simply result from ranking and selecting DEGs solely by statistical significance (P) derived from widely used simple t-tests; (2) when fold change (FC) is used as the ranking criterion with a non-stringent P-value cutoff filtering, the DEG lists become much more reproducible, especially when fewer genes are selected as differentially expressed, as is the case in most microarray studies; and (3) the instability of short DEG lists solely based on P-value ranking is an expected mathematical consequence of the high variability of the t-values; the more stringent the P-value threshold, the less reproducible the DEG list is. These observations are also consistent with results from extensive simulation calculations. Conclusion We recommend the use of FC-ranking plus a non-stringent P cutoff as a straightforward and baseline practice in order to generate more reproducible DEG lists. Specifically, the P-value cutoff should not be stringent (too small) and FC should be as large as possible. Our results provide practical guidance to choose the appropriate FC and P-value cutoffs when selecting a given number of DEGs. The FC criterion enhances reproducibility, whereas the P criterion balances sensitivity and specificity.
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    Harnessing multi-layered soil to design seismic metamaterials with ultralow frequency band gaps
    Chen, Yanyu; Qian, Feng; Scarpa, Fabrizio; Zuo, Lei; Zhuang, Xiaoying (Elsevier, 2019-04-23)
    Phononic metamaterials are capable ofmanipulatingmechanicalwave propagation in applications ranging from nanoscale heat transfer to noise and vibration mitigation. The design of phononic metamaterials to control lowfrequency vibrations, such as those induced by ground transportation and low-amplitude seismic waves, however, remains a challenge. Here we propose a new design methodology to generate seismic metamaterials that can attenuate surface waves below 10 Hz. Our design concept evolves around the engineering of the multilayered soil, the use of conventional construction materials, and operational construction constraints. The proposed seismic metamaterials are constructed by periodically varying concrete piles in the host multi-layered soil. We first validate the design concept and the numerical models by performing a lab-scale experiment on the low-amplitude surface wave propagation in a finite-size seismic metamaterial. To the best of the Authors' knowledge, this is one of the few attempts made to date to experimentally understand the vibration mitigation capability of seismic metamaterials.We then numerically demonstrate that the multi-layered seismic metamaterials can attenuate surface waves over a wide frequency range, with the incident wave energy being confined within the softest layer of the shallow layered seismic metamaterials. In addition to the localized wave energy distribution, deep layered seismic metamaterials exhibit broadband cut-off band gaps up to 7.2 Hz due to the strongly imposed constraint between piles and surrounding soil. Furthermore, these cut-off band gaps strongly depend on the constraint between the piles and the bottomlayer of the soil and hence can be tuned by tailoring the foundation stiffness.We also evidence the possibility to create constant wave band gaps by introducing hollow concrete piles with pile volume fraction b10% in the deep layered seismic metamaterials. The findings reported here open new avenues to protect engineering structures from low-frequency seismic vibrations.
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    Piezoelectric Energy Harvesting for Powering Wireless Monitoring Systems
    Qian, Feng (Virginia Tech, 2020-06-26)
    The urgent need for a clean and sustainable power supply for wireless sensor nodes and low-power electronics in various monitoring systems and the Internet of Things has led to an explosion of research in substitute energy technologies. Traditional batteries are still the most widely used power source for these applications currently but have been blamed for chemical pollution, high maintenance cost, bulky volume, and limited energy capacity. Ambient energy in different forms such as vibration, movement, heat, wind, and waves otherwise wasted can be converted into usable electricity using proper transduction mechanisms to power sensors and low-power devices or charge rechargeable batteries. This dissertation focuses on the design, modeling, optimization, prototype, and testing of novel piezoelectric energy harvesters for extracting energy from human walking, bio-inspired bi-stable motion, and torsional vibration as an alternative power supply for wireless monitoring systems. To provide a sustainable power supply for health care monitoring systems, a piezoelectric footwear harvester is developed and embedded inside a shoe heel for scavenging energy from human walking. The harvester comprises of multiple 33-mode piezoelectric stacks within single-stage force amplification frames sandwiched between two heel-shaped aluminum plates taking and reallocating the dynamic force at the heel. The single-stage force amplification frame is designed and optimized to transmit, redirect, and amplify the heel-strike force to the inner piezoelectric stack. An analytical model is developed and validated to predict precisely the electromechanical coupling behavior of the harvester. A symmetric finite element model is established to facilitate the mesh of the transducer unit based on a material equivalent model that simplifies the multilayered piezoelectric stack into a bulk. The symmetric FE model is experimentally validated and used for parametric analysis of the single-stage force amplification frame for a large force amplification factor and power output. The results show that an average power output of 9.3 mW/shoe and a peak power output of 84.8 mW are experimentally achieved at the walking speed of 3.0 mph (4.8 km/h). To further improve the power output, a two-stage force amplification compliant mechanism is designed and incorporated into the footwear energy harvester, which could amplify the dynamic force at the heel twice before applied to the inner piezoelectric stacks. An average power of 34.3 mW and a peak power of 110.2 mW were obtained under the dynamic force with the amplitude of 500 N and frequency of 3 Hz. A comparison study demonstrated that the proposed two-stage piezoelectric harvester has a much larger power output than the state-of-the-art results in the literature. A novel bi-stable piezoelectric energy harvester inspired by the rapid shape transition of the Venus flytrap leaves is proposed, modeled and experimentally tested for the purpose of energy harvesting from broadband frequency vibrations. The harvester consists of a piezoelectric macro fiber composite (MFC) transducer, a tip mass, and two sub-beams with bending and twisting deformations created by in-plane pre-displacement constraints using rigid tip-mass blocks. Different from traditional ways to realize bi-stability using nonlinear magnetic forces or residual stress in laminate composites, the proposed bio-inspired bi-stable piezoelectric energy harvester takes advantage of the mutual self-constraint at the free ends of the two cantilever sub-beams with a pre-displacement. This mutual pre-displacement constraint bi-directionally curves the two sub-beams in two directions inducing higher mechanical potential energy. The nonlinear dynamics of the bio-inspired bi-stable piezoelectric energy harvester is investigated under sweeping frequency and harmonic excitations. The results show that the sub-beams of the harvester experience local vibrations, including broadband frequency components during the snap-through, which is desirable for large power output. An average power output of 0.193 mW for a load resistance of 8.2 kΩ is harvested at the excitation frequency of 10 Hz and amplitude of 4.0 g. Torsional vibration widely exists in mechanical engineering but has not yet been well exploited for energy harvesting to provide a sustainable power supply for structural health monitoring systems. A torsional vibration energy harvesting system comprised of a shaft and a shear mode piezoelectric transducer is developed in this dissertation to look into the feasibility of harvesting energy from oil drilling shaft for powering downhole sensors. A theoretical model of the torsional vibration piezoelectric energy harvester is derived and experimentally verified to be capable of characterizing the electromechanical coupling system and predicting the electrical responses. The position of the piezoelectric transducer on the surface of the shaft is parameterized by two variables that are optimized to maximize the power output. Approximate expressions of the voltage and power are derived by simplifying the theoretical model, which gives predictions in good agreement with analytical solutions. Based on the derived approximate expression, physical interpretations of the implicit relationship between the power output and the position parameters of the piezoelectric transducer are given.