Browsing by Author "Liu, Y"
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Item Open Access A model-based simulation framework for coupled acoustics, elastodynamics, and damage with application to nano-pulse lithotripsy(International Journal of Solids and Structures, 2024-03-01) Liu, Y; Zhong, P; Lopez-Pamies, O; Dolbow, JEWe develop a model for solid objects surrounded by a fluid that accounts for the possibility of acoustic pressures giving rise to damage on the surface of the solid. The propagation of an acoustic pressure in the fluid domain is modeled by the acoustic wave equation. On the other hand, the response of the solid is described by linear elastodynamics coupled with a gradient damage model, one that is based on a cohesive-type phase-field description of fracture. The interaction between the acoustic pressure and the deformation and damage of the solid are represented by transmission conditions at the fluid–solid interface. The resulting governing equations are discretized using a finite-element/finite-difference method that pays particular attention to the spatial and temporal scales that need to be resolved. Results from model-based simulations are provided for a benchmark problem as well as for recent experiments in nano-pulse lithotripsy. A parametric study is performed to illustrate how damage develops in response to the driving force (magnitude and location of the acoustic source) as a function of the fracture resistance of the solid. The results are shown to be qualitatively consistent with experimental observations for the location and size of the damage fields on the solid surface. A study of limiting cases also suggests that both the threshold for damage and the critical fracture energy are important to consider in order to capture the transition from damage initiation to complete localization. A low-cycle fatigue model is proposed that degrades the fracture resistance of the solid as a function of accumulated tensile strain energy, and it is shown to be capable of capturing damage localization in simulations of multi-pulse nano-pulse lithotripsy.Item Open Access A wearable hydraulic shock absorber with efficient energy dissipation(International Journal of Mechanical Sciences, 2024-05-15) Cecchi, NJ; Liu, Y; Vegesna, RV; Zhan, X; Yang, W; Espinoza Campomanes, LA; Grant, GA; Camarillo, DBAdvances in shock absorber technology are often translated to wearable personal protective equipment (PPE) to protect humans from impact-related injuries. However, the effectiveness of PPE is limited by factors such as the tolerable size and weight of the PPE device and the environmental conditions in which the PPE will be used. In this study, we leveraged the energy dissipation of fluid flow using soft structures to prototype a novel, wearable hydraulic shock absorber — the Soft Hydraulic Shock. The Soft Hydraulic Shock achieved an efficient energy absorption ratio of 100 % across a range of impact loading conditions due to its fluid-based mechanism of energy absorption. In comparison, five state-of-the-art shock-absorbing technologies with similar dimensions and weights used in American football helmets were found to have average energy absorption ratios ranging from 74.0 % to 90.0 %, on average. Furthermore, the Soft Hydraulic Shock maintained a stable energy dissipation across a wide range of temperatures (-18 °C, 19.5 °C, 50 °C), while the energy dissipation of other shock absorbing technologies varied up to 20 % across these temperatures. Analyses of the behavior of the Soft Hydraulic Shock with different design parameters and impact loadings were further explored with a validated finite element model of the device. Finally, the Soft Hydraulic Shock demonstrated the ability to significantly mitigate brain injury risk (average 23.9 % reduction in Head Acceleration Response Metric) when implemented into a full helmet system. The results of this study demonstrate the promise of wearable hydraulic shock absorbers and provide a platform for further optimizing their performance.Item Open Access Depression in pregnancy, infant birth weight and DNA methylation of imprint regulatory elements.(Epigenetics : official journal of the DNA Methylation Society, 2012-07) Liu, Y; Murphy, SK; Murtha, AP; Fuemmeler, BF; Schildkraut, J; Huang, Z; Overcash, F; Kurtzberg, J; Jirtle, R; Iversen, ES; Forman, MR; Hoyo, CDepressed mood in pregnancy has been linked to low birth weight (LBW, 4,500 g) infants had 5.9% higher methylation at the PLAGL1 DMR compared with normal birth weight infants. Our findings confirm that severe maternal depressed mood in pregnancy is associated with LBW, and that MEG3 and IGF2 plasticity may play important roles.Item Open Access Differential item functioning in the Unified Dyskinesia Rating Scale (UDysRS)(Movement Disorders, 2017) Luo, S; Liu, Y; Teresi, JA; Stebbins, GT; Goetz, CGItem Open Access Effects of FOXO genotypes on longevity: a biodemographic analysis.(J Gerontol A Biol Sci Med Sci, 2010-12) Zeng, Y; Cheng, L; Chen, H; Cao, H; Hauser, ER; Liu, Y; Xiao, Z; Tan, Q; Tian, XL; Vaupel, JWBased on data from 760 centenarians and 1060 middle-age controls (all Han Chinese), this article contributes biodemographic insights and syntheses concerning the magnitude of effects of the FOXO genotypes on longevity. We also estimate independent and joint effects of the genotypes of FOXO1A and FOXO3A genes on long-term survival, considering carrying or not-carrying the minor allele of the single-nucleotide polymorphism of another relevant gene. We found substantial gender differences in the independent effects; positive effects of FOXO3A and negative effects of FOXO1A largely compensate each other if one carries both, although FOXO3A has a stronger impact. Ten-year follow-up cohort analysis shows that at very advanced ages 92-110, adjusted for various confounders, positive effects of FOXO3A on survival remain statistically significant, but no significant effects of FOXO1A alone; G × G interactions between FOXO1A-209 and FOXO3A-310 or FOXO3A-292 decrease survival likelihood by 32%-36% (p < .05); G × E interactions between FOXO1A-209 and regular exercise increase survival likelihood by 31%-32% (p < .05).Item Open Access Erratum: Large meta-analysis of genome-wide association studies identifies five loci for lean body mass.(Nat Commun, 2017-11-07) Zillikens, MC; Demissie, S; Hsu, Y - H; Yerges-Armstrong, LM; Chou, W - C; Stolk, L; Livshits, G; Broer, L; Johnson, T; Koller, DL; Kutalik, Z; Luan, J; Malkin, I; Ried, JS; Smith, AV; Thorleifsson, G; Vandenput, L; Hua Zhao, J; Zhang, W; Aghdassi, A; Åkesson, K; Amin, N; Baier, LJ; Barroso, I; Bennett, DA; Bertram, L; Biffar, R; Bochud, M; Boehnke, M; Borecki, IB; Buchman, AS; Byberg, L; Campbell, H; Campos Obanda, N; Cauley, JA; Cawthon, PM; Cederberg, H; Chen, Z; Cho, NH; Jin Choi, H; Claussnitzer, M; Collins, F; Cummings, SR; De Jager, PL; Demuth, I; Dhonukshe-Rutten, RAM; Diatchenko, L; Eiriksdottir, G; Enneman, AW; Erdos, M; Eriksson, JG; Eriksson, J; Estrada, K; Evans, DS; Feitosa, MF; Fu, M; Garcia, M; Gieger, C; Girke, T; Glazer, NL; Grallert, H; Grewal, J; Han, B - G; Hanson, RL; Hayward, C; Hofman, A; Hoffman, EP; Homuth, G; Hsueh, W - C; Hubal, MJ; Hubbard, A; Huffman, KM; Husted, LB; Illig, T; Ingelsson, E; Ittermann, T; Jansson, J - O; Jordan, JM; Jula, A; Karlsson, M; Khaw, K - T; Kilpeläinen, TO; Klopp, N; Kloth, JSL; Koistinen, HA; Kraus, WE; Kritchevsky, S; Kuulasmaa, T; Kuusisto, J; Laakso, M; Lahti, J; Lang, T; Langdahl, BL; Launer, LJ; Lee, J - Y; Lerch, MM; Lewis, JR; Lind, L; Lindgren, C; Liu, Y; Liu, T; Liu, Y; Ljunggren, Ö; Lorentzon, M; Luben, RN; Maixner, W; McGuigan, FE; Medina-Gomez, C; Meitinger, T; Melhus, H; Mellström, D; Melov, S; Michaëlsson, K; Mitchell, BD; Morris, AP; Mosekilde, L; Newman, A; Nielson, CM; O'Connell, JR; Oostra, BA; Orwoll, ES; Palotie, A; Parker, SCJ; Peacock, M; Perola, M; Peters, A; Polasek, O; Prince, RL; Räikkönen, K; Ralston, SH; Ripatti, S; Robbins, JA; Rotter, JI; Rudan, I; Salomaa, V; Satterfield, S; Schadt, EE; Schipf, S; Scott, L; Sehmi, J; Shen, J; Soo Shin, C; Sigurdsson, G; Smith, S; Soranzo, N; Stančáková, A; Steinhagen-Thiessen, E; Streeten, EA; Styrkarsdottir, U; Swart, KMA; Tan, S - T; Tarnopolsky, MA; Thompson, P; Thomson, CA; Thorsteinsdottir, U; Tikkanen, E; Tranah, GJ; Tuomilehto, J; van Schoor, NM; Verma, A; Vollenweider, P; Völzke, H; Wactawski-Wende, J; Walker, M; Weedon, MN; Welch, R; Wichmann, H - E; Widen, E; Williams, FMK; Wilson, JF; Wright, NC; Xie, W; Yu, L; Zhou, Y; Chambers, JC; Döring, A; van Duijn, CM; Econs, MJ; Gudnason, V; Kooner, JS; Psaty, BM; Spector, TD; Stefansson, K; Rivadeneira, F; Uitterlinden, AG; Wareham, NJ; Ossowski, V; Waterworth, D; Loos, RJF; Karasik, D; Harris, TB; Ohlsson, C; Kiel, DPA correction to this article has been published and is linked from the HTML version of this article.Item Open Access FLAME: A Fast Large-scale Almost Matching Exactly Approach to Causal Inference(2017-08-01) Wang, T; Morucci, M; Awan, MU; Liu, Y; Roy, S; Rudin, C; Volfovsky, AA classical problem in causal inference is that of matching, where treatment units need to be matched to control units. Some of the main challenges in developing matching methods arise from the tension among (i) inclusion of as many covariates as possible in defining the matched groups, (ii) having matched groups with enough treated and control units for a valid estimate of Average Treatment Effect (ATE) in each group, and (iii) computing the matched pairs efficiently for large datasets. In this paper we propose a fast and novel method for approximate and exact matching in causal analysis called FLAME (Fast Large-scale Almost Matching Exactly). We define an optimization objective for match quality, which gives preferences to matching on covariates that can be useful for predicting the outcome while encouraging as many matches as possible. FLAME aims to optimize our match quality measure, leveraging techniques that are natural for query processing in the area of database management. We provide two implementations of FLAME using SQL queries and bit-vector techniques.Item Open Access Gender-, age-, and race/ethnicity-based differential item functioning analysis of the movement disorder society–sponsored revision of the Unified Parkinson’s disease rating scale(Movement Disorders, 2016) Goetz, CG; Liu, Y; Stebbins, GT; Wang, L; Tilley, BC; Teresi, JA; Merkitch, D; Luo, SItem Open Access Genetic variants in the folate metabolic pathway genes predict melanoma-specific survival.(The British journal of dermatology, 2020-01-18) Dai, W; Liu, H; Liu, Y; Xu, X; Qian, D; Luo, S; Cho, E; Zhu, D; Amos, CI; Fang, S; Lee, JE; Li, X; Nan, H; Li, C; Wei, QBACKGROUND:Folate metabolism plays an important role in DNA methylation and nucleic acid synthesis and thus may function as a regulatory factor in cancer development. Genome-wide association studies (GWAS) have identified some single-nucleotide polymorphisms (SNPs) associated with cutaneous melanoma-specific survival (CMSS), but no SNPs were found in genes involved in the folate metabolic pathway. OBJECTIVE:To examine associations between SNPs in folate metabolic pathway genes and CMSS. METHODS:We comprehensively evaluated 2,645 (422 genotyped and 2,223 imputed) common SNPs in folate metabolic pathway genes from a published GWAS of 858 patients from The University of Texas M.D. Anderson Cancer Center and performed the validation in another GWAS of 409 patients from the Nurses' Health Study and Health Professionals Follow-up Study, in which 95/858 (11.1%) and 48/409 (11.5%) patients died of cutaneous melanoma, respectively. RESULTS:We identified two independent SNPs (MTHFD1 rs1950902 G>A and ALPL rs10917006 C>T) to be associated with CMSS in both datasets, and their meta-analysis yielded an allelic hazards ratio of 1.75 (95% confidence interval=1.32-2.32, P=9.96×10-5 ) and 2.05 (1.39-3.01, P=2.84×10-4 ), respectively. The genotype-phenotype correlation analyses provided additional support for biologic plausibility of these two variants' roles in tumour progression, suggesting that variation in SNP-related mRNA expression levels is likely to be the mechanism underlying the observed associations with CMSS. CONCLUSION:Two possibly functional genetic variants, MTHFD1 rs1950902 and ALPL rs10917006, were likely to be independently or jointly associated with CMSS, which may add to personalized treatment in the future, once further validated.Item Open Access Implementing diffusion-weighted MRI for body imaging in prospective multicentre trials: current considerations and future perspectives.(European radiology, 2018-03) deSouza, NM; Winfield, JM; Waterton, JC; Weller, A; Papoutsaki, M-V; Doran, SJ; Collins, DJ; Fournier, L; Sullivan, D; Chenevert, T; Jackson, A; Boss, M; Trattnig, S; Liu, YFor body imaging, diffusion-weighted MRI may be used for tumour detection, staging, prognostic information, assessing response and follow-up. Disease detection and staging involve qualitative, subjective assessment of images, whereas for prognosis, progression or response, quantitative evaluation of the apparent diffusion coefficient (ADC) is required. Validation and qualification of ADC in multicentre trials involves examination of i) technical performance to determine biomarker bias and reproducibility and ii) biological performance to interrogate a specific aspect of biology or to forecast outcome. Unfortunately, the variety of acquisition and analysis methodologies employed at different centres make ADC values non-comparable between them. This invalidates implementation in multicentre trials and limits utility of ADC as a biomarker. This article reviews the factors contributing to ADC variability in terms of data acquisition and analysis. Hardware and software considerations are discussed when implementing standardised protocols across multi-vendor platforms together with methods for quality assurance and quality control. Processes of data collection, archiving, curation, analysis, central reading and handling incidental findings are considered in the conduct of multicentre trials. Data protection and good clinical practice are essential prerequisites. Developing international consensus of procedures is critical to successful validation if ADC is to become a useful biomarker in oncology.• Standardised acquisition/analysis allows quantification of imaging biomarkers in multicentre trials. • Establishing "precision" of the measurement in the multicentre context is essential. • A repository with traceable data of known provenance promotes further research.Item Open Access Individuals with mutations in XPNPEP3, which encodes a mitochondrial protein, develop a nephronophthisis-like nephropathy.(J Clin Invest, 2010-03) O'Toole, JF; Liu, Y; Davis, EE; Westlake, CJ; Attanasio, M; Otto, EA; Seelow, D; Nurnberg, G; Becker, C; Nuutinen, M; Kärppä, M; Ignatius, J; Uusimaa, J; Pakanen, S; Jaakkola, E; van den Heuvel, LP; Fehrenbach, H; Wiggins, R; Goyal, M; Zhou, W; Wolf, MT; Wise, E; Helou, J; Allen, SJ; Murga Zamalloa, CA; Ashraf, S; Chaki, M; Heeringa, S; Chernin, G; Hoskins, BE; Chaib, H; Gleeson, J; Kusakabe, T; Suzuki, T; Isaac, RE; Quarmby, LM; Tennant, B; Fujioka, H; Tuominen, H; Hassinen, I; Lohi, H; van Houten, JL; Rotig, A; Sayer, JA; Rolinski, B; Freisinger, P; Madhavan, SM; Herzer, M; Madignier, F; Prokisch, H; Nurnberg, P; Jackson, PK; Jackson, P; Khanna, H; Katsanis, N; Hildebrandt, FThe autosomal recessive kidney disease nephronophthisis (NPHP) constitutes the most frequent genetic cause of terminal renal failure in the first 3 decades of life. Ten causative genes (NPHP1-NPHP9 and NPHP11), whose products localize to the primary cilia-centrosome complex, support the unifying concept that cystic kidney diseases are "ciliopathies". Using genome-wide homozygosity mapping, we report here what we believe to be a new locus (NPHP-like 1 [NPHPL1]) for an NPHP-like nephropathy. In 2 families with an NPHP-like phenotype, we detected homozygous frameshift and splice-site mutations, respectively, in the X-prolyl aminopeptidase 3 (XPNPEP3) gene. In contrast to all known NPHP proteins, XPNPEP3 localizes to mitochondria of renal cells. However, in vivo analyses also revealed a likely cilia-related function; suppression of zebrafish xpnpep3 phenocopied the developmental phenotypes of ciliopathy morphants, and this effect was rescued by human XPNPEP3 that was devoid of a mitochondrial localization signal. Consistent with a role for XPNPEP3 in ciliary function, several ciliary cystogenic proteins were found to be XPNPEP3 substrates, for which resistance to N-terminal proline cleavage resulted in attenuated protein function in vivo in zebrafish. Our data highlight an emerging link between mitochondria and ciliary dysfunction, and suggest that further understanding the enzymatic activity and substrates of XPNPEP3 will illuminate novel cystogenic pathways.Item Open Access Mechanosensitive neurons on the internal reproductive tract contribute to egg-laying-induced acetic acid attraction in Drosophila.(Cell Rep, 2014-10-23) Gou, B; Liu, Y; Guntur, A; Stern, U; Yang, CSelecting a suitable site to deposit their eggs is an important reproductive need of Drosophila females. Although their choosiness toward egg-laying sites is well documented, the specific neural mechanism that activates females' search for attractive egg-laying sites is not known. Here, we show that distention and contraction of females' internal reproductive tract triggered by egg delivery through the tract plays a critical role in activating such search. We found that females start to exhibit acetic acid (AA) attraction prior to depositing each egg but no attraction when they are not laying eggs. Artificially distending the reproductive tract triggers AA attraction in non-egg-laying females, whereas silencing the mechanosensitive neurons we identified that can sense the contractile status of the tract eliminates such attraction. Our work uncovers the circuit basis of an important reproductive need of Drosophila females and provides a simple model for dissecting the neural mechanism that underlies a reproductive need-induced behavioral modification.Item Open Access Synthesis of copper nanocatalysts with tunable size using diblock copolymer solution micelles(Journal of Physical Chemistry C, 2010-04-08) Liu, Y; Lor, C; Fu, Q; Pan, D; Lei, D; Liu, J; Lu, JSelf-assembled solution micelles prepared from polystyrene-b-poly(4- vinylpyridine) (PS-b-P4VP) and polystyrene-b-poly(2-vinylpyridine) (PS-b-P2VP), have been employed as templates to synthesize copper nanocatalysts which are regarded as an excellent catalyst system for 1D nanomaterial synthesis. We have demonstrated that uniform-sized nanoparticles with diameters ranging from 1 to 15 nm have been generated. We have revealed that nanocatalyst size can be rationally tailored by adjusting the interaction between copper precursors and ligands and metal sequestration time. Ordered arrays of copper nanocatalysts derived from depositing a monolayer of solution micelles exhibit excellent thermal stability and do not agglomerate during the thermal treatment at 850 °C, typical growth temperature for 1D nanomaterial using the chemical vapor deposition technique. High-density and aligned single-walled carbon nanotubes with uniform diameter have been synthesized using the chemical vapor deposition technique. The average diameter is 1.4 nm, which is on the same order of catalyst size, around 2.0 nm. The combination of tunable size and spacing with superb thermal stability and outstanding catalytic activity offered by this new copper nanocatalyst system will enable growth of high-yield 1D nanomaterials with controllable diameter and spacing consistently and reproducible properties. It also paves a new path to study the effect of nanocatalyst size on 1D nanomaterial synthesis and their properties. © 2010 American Chemical Society.Item Open Access Translational models of mild traumatic brain injury tissue biomechanics(Current Opinion in Biomedical Engineering, 2022-12-01) Zhan, X; Oeur, A; Liu, Y; Zeineh, MM; Grant, GA; Margulies, SS; Camarillo, DBTraumatic brain injury (TBI) is a global health concern. Mild TBI (mTBI) which accounts for the majority of TBI cases, is hard to detect since often the imaging is normal but can still cause brain damage and long-term sequelae. Physiologically, acute primary damage to the brain is thought to be caused by tissue deformation from the inertial movement of the brain after rapid head rotation. Respecting tissue biomechanics, animal models are often used to understand the pathophysiology of mTBI. We have reviewed the literature focusing on connecting biomechanics with mTBI pathologies at the tissue scale using neuroimaging, neurobehavioral tests, and pathologies across species, particularly studies using strain and strain rate. These studies have found strain and strain rate predict mTBI pathology and strain is generalizable across species, including small animals, large animals, and humans. We propose that researchers can leverage tissue-level strain and strain rate to bridge biomechanics and mTBI pathology.Item Open Access Warm season heavy rainfall events over the Huaihe River Valley and their linkage with wintertime thermal condition of the tropical oceans(Climate Dynamics, 2015) Li, L; Li, W; Tang, Q; Zhang, P; Liu, YWarm season heavy rainfall events over the Huaihe River Valley (HRV) of China are amongst the top causes of agriculture and economic loss in this region. Thus, there is a pressing need for accurate seasonal prediction of HRV heavy rainfall events. This study improves the seasonal prediction of HRV heavy rainfall by implementing a novel rainfall framework, which overcomes the limitation of traditional probability models and advances the statistical inference on HRV heavy rainfall events. The framework is built on a three-cluster Normal mixture model, whose distribution parameters are sampled using Bayesian inference and Markov Chain Monte Carlo algorithm. The three rainfall clusters reflect probability behaviors of light, moderate, and heavy rainfall, respectively. Our analysis indicates that heavy rainfall events make the largest contribution to the total amount of seasonal precipitation. Furthermore, the interannual variation of summer precipitation is attributable to the variation of heavy rainfall frequency over the HRV. The heavy rainfall frequency, in turn, is influenced by sea surface temperature anomalies (SSTAs) over the north Indian Ocean, equatorial western Pacific, and the tropical Atlantic. The tropical SSTAs modulate the HRV heavy rainfall events by influencing atmospheric circulation favorable for the onset and maintenance of heavy rainfall events. Occurring 5 months prior to the summer season, these tropical SSTAs provide potential sources of prediction skill for heavy rainfall events over the HRV. Using these preceding SSTA signals, we show that the support vector machine algorithm can predict HRV heavy rainfall satisfactorily. The improved prediction skill has important implication for the nation’s disaster early warning system.