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1. See Behind Walls in Real-time Using Aerial Drones and Augmented Reality

Author

Yang, Sikai, Yang, Kang, Chen, Yuning, Zhao, Fan, and Du, Wan

Subjects
Computer Science - Multiagent Systems, Computer Science - Computer Vision and Pattern Recognition, Computer Science - Human-Computer Interaction
Abstract

This work presents ARD2, a framework that enables real-time through-wall surveillance using two aerial drones and an augmented reality (AR) device. ARD2 consists of two main steps: target direction estimation and contour reconstruction. In the first stage, ARD2 leverages geometric relationships between the drones, the user, and the target to project the target's direction onto the user's AR display. In the second stage, images from the drones are synthesized to reconstruct the target's contour, allowing the user to visualize the target behind walls. Experimental results demonstrate the system's accuracy in both direction estimation and contour reconstruction., Comment: 6 pages

Published
2024

2. MARLP: Time-series Forecasting Control for Agricultural Managed Aquifer Recharge

Author

Chen, Yuning, Yang, Kang, An, Zhiyu, Holder, Brady, Paloutzian, Luke, Bali, Khaled, and Du, Wan

Subjects
Computer Science - Machine Learning, Electrical Engineering and Systems Science - Systems and Control
Abstract

The rapid decline in groundwater around the world poses a significant challenge to sustainable agriculture. To address this issue, agricultural managed aquifer recharge (Ag-MAR) is proposed to recharge the aquifer by artificially flooding agricultural lands using surface water. Ag-MAR requires a carefully selected flooding schedule to avoid affecting the oxygen absorption of crop roots. However, current Ag-MAR scheduling does not take into account complex environmental factors such as weather and soil oxygen, resulting in crop damage and insufficient recharging amounts. This paper proposes MARLP, the first end-to-end data-driven control system for Ag-MAR. We first formulate Ag-MAR as an optimization problem. To that end, we analyze four-year in-field datasets, which reveal the multi-periodicity feature of the soil oxygen level trends and the opportunity to use external weather forecasts and flooding proposals as exogenous clues for soil oxygen prediction. Then, we design a two-stage forecasting framework. In the first stage, it extracts both the cross-variate dependency and the periodic patterns from historical data to conduct preliminary forecasting. In the second stage, it uses weather-soil and flooding-soil causality to facilitate an accurate prediction of soil oxygen levels. Finally, we conduct model predictive control (MPC) for Ag-MAR flooding. To address the challenge of large action spaces, we devise a heuristic planning module to reduce the number of flooding proposals to enable the search for optimal solutions. Real-world experiments show that MARLP reduces the oxygen deficit ratio by 86.8% while improving the recharging amount in unit time by 35.8%, compared with the previous four years., Comment: Accepted by KDD 2024

Published
2024
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3. Profiling ovarian cancer tumor and microenvironment during disease progression for cell-based immunotherapy design

Author

Li, Yan-Ruide, Ochoa, Christopher J, Zhu, Yichen, Kramer, Adam, Wilson, Matthew, Fang, Ying, Chen, Yuning, Singh, Tanya, Di Bernardo, Gabriella, Zhu, Enbo, Lee, Derek, Moatamed, Neda A, Bando, Joanne, Zhou, Jin J, Memarzadeh, Sanaz, and Yang, Lili

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Immunology, Ovarian Cancer, Vaccine Related, Cancer, Rare Diseases, Immunization, Orphan Drug, Clinical Research, Good Health and Well Being, Therapy
Abstract

Ovarian cancer (OC) is highly lethal due to late detection and frequent recurrence. Initial treatments, comprising surgery and chemotherapy, lead to disease remission but are invariably associated with subsequent relapse. The identification of novel therapies and an improved understanding of the molecular and cellular characteristics of OC are urgently needed. Here, we conducted a comprehensive analysis of primary tumor cells and their microenvironment from 16 chemonaive and 10 recurrent OC patient samples. Profiling OC tumor biomarkers allowed for the identification of potential molecular targets for developing immunotherapies, while profiling the microenvironment yielded insights into its cellular composition and property changes between chemonaive and recurrent samples. Notably, we identified CD1d as a biomarker of the OC microenvironment and demonstrated its targeting by invariant natural killer T (iNKT) cells. Overall, our study presents a comprehensive immuno-profiling of OC tumor and microenvironment during disease progression, guiding the development of immunotherapies for OC treatment, especially for recurrent disease.

Published
2023

5. Satellite downlink scheduling under breakpoint resume mode

Author

Chang, Zhongxiang, Chen, Yuning, and Zhou, Zhongbao

Subjects
Computer Science - Artificial Intelligence
Abstract

A novel problem called satellite downlink scheduling problem (SDSP) under breakpoint resume mode (SDSP-BRM) is studied in our paper. Compared to the traditional SDSP where an imaging data has to be completely downloaded at one time, SDSP-BRM allows the data of an imaging data be broken into a number of pieces which can be downloaded in different playback windows. By analyzing the characteristics of SDSP-BRM, we first propose a mixed integer programming model for its formulation and then prove the NP-hardness of SDSP-BRM. To solve the problem, we design a simple and effective heuristic algorithm (SEHA) where a number of problem-tailored move operators are proposed for local searching. Numerical results on a set of well-designed scenarios demonstrate the efficiency of the proposed algorithm in comparison to the general purpose CPLEX solver. We conduct additional experiments to shed light on the impact of the segmental strategy on the overall performance of the proposed SEHA.

Published
2022

13. Widely tunable cavity-enhanced frequency combs

Author

Silfies, Myles C., Kowzan, Grzegorz, Chen, Yuning, Lewis, Neomi, Hou, Ryan, Baehre, Robin, Gross, Tobias, and Allison, Thomas K.

Subjects
Physics - Optics, Physics - Applied Physics
Abstract

We describe the cavity-enhancement of frequency combs over a wide tuning range of 450-700 nm (> 7900 cm$^{-1}$), covering nearly the entire visible spectrum. Tunable visible frequency combs from a synchronously-pumped optical parametric oscillator are coupled into a 4-mirror, dispersion-managed cavity with a finesse of 600 to 1400. An intracavity absorption path length enhancement greater than 190 is obtained over the entire tuning range, while preserving intracavity spectral bandwidths capable of supporting sub-200 fs pulse durations. These tunable cavity-enhanced frequency combs can find many applications in nonlinear optics and spectroscopy.

Published
2020
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21. Tunable visible frequency combs from a Yb-fiber-laser-pumped optical parametric oscillator

Author

Chen, Yuning, Silfies, Myles C., Kowzan, Grzegorz, Bautista, Jose Miguel, and Allison, Thomas K.

Subjects
Physics - Optics
Abstract

We present a 100 MHz repetition rate Yb-fiber-laser-pumped synchronously pumped optical parametric oscillator (SPOPO) delivering tunable frequency combs covering almost the entire visible spectral range. By intracavity doubling both the signal and idler combs and using collinear residual pump light, nearly continuous tuning over the range of 420-700 nm is achieved with only small gaps near the OPO degeneracy condition. Output powers range from 10 mW to 200 mW, depending on wavelength, with pulse durations below 150 fs without external compression. Frequency locking of all three collinearly outcoupled combs (pump, doubled signal, and doubled idler) to a femtosecond enhancement cavity facilitates direct comparison of their optical phase noise and phase modulation transfer functions. In the singly-resonant OPO, optical phase modulation of the pump comb is transferred nearly completely to the non-resonant idler comb. This results in a resonant signal comb with reduced optical phase noise and also enables high-bandwidth modulation on the idler comb via phase modulation of the pump.

Published
2019
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25. Author Correction: Genetic meta-analysis of diagnosed Alzheimer’s disease identifies new risk loci and implicates Aβ, tau, immunity and lipid processing

Author

Kunkle, Brian W, Grenier-Boley, Benjamin, Sims, Rebecca, Bis, Joshua C, Damotte, Vincent, Naj, Adam C, Boland, Anne, Vronskaya, Maria, van der Lee, Sven J, Amlie-Wolf, Alexandre, Bellenguez, Céline, Frizatti, Aura, Chouraki, Vincent, Martin, Eden R, Sleegers, Kristel, Badarinarayan, Nandini, Jakobsdottir, Johanna, Hamilton-Nelson, Kara L, Moreno-Grau, Sonia, Olaso, Robert, Raybould, Rachel, Chen, Yuning, Kuzma, Amanda B, Hiltunen, Mikko, Morgan, Taniesha, Ahmad, Shahzad, Vardarajan, Badri N, Epelbaum, Jacques, Hoffmann, Per, Boada, Merce, Beecham, Gary W, Garnier, Jean-Guillaume, Harold, Denise, Fitzpatrick, Annette L, Valladares, Otto, Moutet, Marie-Laure, Gerrish, Amy, Smith, Albert V, Qu, Liming, Bacq, Delphine, Denning, Nicola, Jian, Xueqiu, Zhao, Yi, Del Zompo, Maria, Fox, Nick C, Choi, Seung-Hoan, Mateo, Ignacio, Hughes, Joseph T, Adams, Hieab H, Malamon, John, Sanchez-Garcia, Florentino, Patel, Yogen, Brody, Jennifer A, Dombroski, Beth A, Naranjo, Maria Candida Deniz, Daniilidou, Makrina, Eiriksdottir, Gudny, Mukherjee, Shubhabrata, Wallon, David, Uphill, James, Aspelund, Thor, Cantwell, Laura B, Garzia, Fabienne, Galimberti, Daniela, Hofer, Edith, Butkiewicz, Mariusz, Fin, Bertrand, Scarpini, Elio, Sarnowski, Chloe, Bush, Will S, Meslage, Stéphane, Kornhuber, Johannes, White, Charles C, Song, Yuenjoo, Barber, Robert C, Engelborghs, Sebastiaan, Sordon, Sabrina, Voijnovic, Dina, Adams, Perrie M, Vandenberghe, Rik, Mayhaus, Manuel, Cupples, L Adrienne, Albert, Marilyn S, De Deyn, Peter P, Gu, Wei, Himali, Jayanadra J, Beekly, Duane, Squassina, Alessio, Hartmann, Annette M, Orellana, Adelina, Blacker, Deborah, Rodriguez-Rodriguez, Eloy, Lovestone, Simon, Garcia, Melissa E, Doody, Rachelle S, Munoz-Fernadez, Carmen, Sussams, Rebecca, Lin, Honghuang, Fairchild, Thomas J, and Benito, Yolanda A

Subjects
Biochemistry and Cell Biology, Biological Sciences, Alzheimer Disease Genetics Consortium, European Alzheimer’s Disease Initiative, Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium, Genetic and Environmental Risk in AD/Defining Genetic, Polygenic and Environmental Risk for Alzheimer’s Disease Consortium, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology, Genetics
Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2019

26. Genetic meta-analysis of diagnosed Alzheimer’s disease identifies new risk loci and implicates Aβ, tau, immunity and lipid processing

Author

Kunkle, Brian W, Grenier-Boley, Benjamin, Sims, Rebecca, Bis, Joshua C, Damotte, Vincent, Naj, Adam C, Boland, Anne, Vronskaya, Maria, van der Lee, Sven J, Amlie-Wolf, Alexandre, Bellenguez, Céline, Frizatti, Aura, Chouraki, Vincent, Martin, Eden R, Sleegers, Kristel, Badarinarayan, Nandini, Jakobsdottir, Johanna, Hamilton-Nelson, Kara L, Moreno-Grau, Sonia, Olaso, Robert, Raybould, Rachel, Chen, Yuning, Kuzma, Amanda B, Hiltunen, Mikko, Morgan, Taniesha, Ahmad, Shahzad, Vardarajan, Badri N, Epelbaum, Jacques, Hoffmann, Per, Boada, Merce, Beecham, Gary W, Garnier, Jean-Guillaume, Harold, Denise, Fitzpatrick, Annette L, Valladares, Otto, Moutet, Marie-Laure, Gerrish, Amy, Smith, Albert V, Qu, Liming, Bacq, Delphine, Denning, Nicola, Jian, Xueqiu, Zhao, Yi, Del Zompo, Maria, Fox, Nick C, Choi, Seung-Hoan, Mateo, Ignacio, Hughes, Joseph T, Adams, Hieab H, Malamon, John, Sanchez-Garcia, Florentino, Patel, Yogen, Brody, Jennifer A, Dombroski, Beth A, Naranjo, Maria Candida Deniz, Daniilidou, Makrina, Eiriksdottir, Gudny, Mukherjee, Shubhabrata, Wallon, David, Uphill, James, Aspelund, Thor, Cantwell, Laura B, Garzia, Fabienne, Galimberti, Daniela, Hofer, Edith, Butkiewicz, Mariusz, Fin, Bertrand, Scarpini, Elio, Sarnowski, Chloe, Bush, Will S, Meslage, Stéphane, Kornhuber, Johannes, White, Charles C, Song, Yuenjoo, Barber, Robert C, Engelborghs, Sebastiaan, Sordon, Sabrina, Voijnovic, Dina, Adams, Perrie M, Vandenberghe, Rik, Mayhaus, Manuel, Cupples, L Adrienne, Albert, Marilyn S, De Deyn, Peter P, Gu, Wei, Himali, Jayanadra J, Beekly, Duane, Squassina, Alessio, Hartmann, Annette M, Orellana, Adelina, Blacker, Deborah, Rodriguez-Rodriguez, Eloy, Lovestone, Simon, Garcia, Melissa E, Doody, Rachelle S, Munoz-Fernadez, Carmen, Sussams, Rebecca, Lin, Honghuang, Fairchild, Thomas J, and Benito, Yolanda A

Subjects
Biochemistry and Cell Biology, Genetics, Biological Sciences, Neurodegenerative, Dementia, Alzheimer's Disease, Aging, Prevention, Brain Disorders, Neurosciences, Clinical Research, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Human Genome, Acquired Cognitive Impairment, 2.1 Biological and endogenous factors, Aetiology, Inflammatory and immune system, Neurological, Aged, Alzheimer Disease, Amyloid beta-Peptides, Case-Control Studies, Female, Genetic Loci, Genetic Predisposition to Disease, Genetic Testing, Genome-Wide Association Study, Haplotypes, Humans, Immunity, Lipid Metabolism, Lipids, Male, tau Proteins, Alzheimer Disease Genetics Consortium (ADGC), European Alzheimer’s Disease Initiative (EADI), Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium (CHARGE), Genetic and Environmental Risk in AD/Defining Genetic, Polygenic and Environmental Risk for Alzheimer’s Disease Consortium (GERAD/PERADES), Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

Risk for late-onset Alzheimer's disease (LOAD), the most prevalent dementia, is partially driven by genetics. To identify LOAD risk loci, we performed a large genome-wide association meta-analysis of clinically diagnosed LOAD (94,437 individuals). We confirm 20 previous LOAD risk loci and identify five new genome-wide loci (IQCK, ACE, ADAM10, ADAMTS1, and WWOX), two of which (ADAM10, ACE) were identified in a recent genome-wide association (GWAS)-by-familial-proxy of Alzheimer's or dementia. Fine-mapping of the human leukocyte antigen (HLA) region confirms the neurological and immune-mediated disease haplotype HLA-DR15 as a risk factor for LOAD. Pathway analysis implicates immunity, lipid metabolism, tau binding proteins, and amyloid precursor protein (APP) metabolism, showing that genetic variants affecting APP and Aβ processing are associated not only with early-onset autosomal dominant Alzheimer's disease but also with LOAD. Analyses of risk genes and pathways show enrichment for rare variants (P = 1.32 × 10-7), indicating that additional rare variants remain to be identified. We also identify important genetic correlations between LOAD and traits such as family history of dementia and education.

Published
2019

27. Multimorbidity Prevalence and Its Association with Health Service Utilization and Medical Costs among Middle-aged and Older Chinese People

Author

Xiaoru FAN, Sha CHEN, Yuning SHI, Chun HAO

Subjects
multiple chronic conditions, facilities and services utilization, fees, medical, quantile regression, Medicine
Abstract

Background The high prevalence of multimorbidity among middle-aged and older adults has become a serious issue needing to be addressed by China's healthcare system. The number of chronic diseases is related to health service utilization and medical costs, but there is still a lack of relevant national surveys in China. Objective To understand the prevalence and features of multimorbidity and to examine its associations with health service utilization and medical costs among middle-aged and older Chinese adults. Methods Data were collected from the 2018 wave of China Health and Retirement Longitudinal Study (CHARLS) during April to October 2021, involving 16 674 Chinese adults (≥45 years old) . Multimorbidity was defined as the coexistence of two or more of the self-reported 14 chronic conditions. Health service utilization was measured using inpatient service utilization in the past year and outpatient service utilization in the past month. Medical costs were measured using total inpatient cost and out-of-pocket (OOP) cost for inpatient care in the past one year, total outpatient costs and OOP cost for outpatient care in the past one month. Logistic regression was used to estimate the association between the number of chronic diseases and health service utilization. Quantile regression was adopted to estimate the association between the number of chronic diseases and medical costs. Results Of all participants, 9 561 (57.34%) had multimorbidity. 2 624 (15.74%) had utilized inpatient services in the past year, and 2 588 (15.52%) used outpatient services in the past one month. Inpatient service utilization, outpatient service utilization, total inpatient cost, OOP cost for inpatient care, total outpatient cost, and OOP cost for outpatient care varied significantly by the number of chronic diseases (P

Published
2022
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31. The Expression Profiles and Clinical Significance of Mixed Lineage Kinases in Glioma.

Author

Huang, Jin, Liu, Yuankun, Wang, Gaosong, Chen, Yuning, Shen, Yifan, Zhang, Jiahao, Ji, Wei, Shao, Junfei, and Capasso, Raffaele

Subjects
LEUCINE zippers, GLIOBLASTOMA multiforme, PROTEIN kinases, DISEASE risk factors, OVERALL survival
Abstract

Mixed lineage kinases (MLKs), comprising seven members: MLK1‐4, dual leucine zipper kinase (DLK), leucine zipper kinase (LZK), and sterile alpha motif and leucine zipper containing kinase (ZAK), belong to the mitogen‐activated protein kinase kinase kinase (MAP3K) family. These kinases are implicated in the progression of numerous cancers by activating mitogen‐activated protein kinase (MAPK) cascades or functioning as ser/thr and tyr kinases. However, their specific roles in glioma remain elusive. In the present study, we utilized bioinformatics approaches to investigate the expression patterns of MLKs in low‐grade gliomas (LGG) and glioblastoma multiforme (GBM). Additionally, we analyzed their clinical significance and delved into the potential mechanisms underlying MLK activity as well as their association with tumor‐immune infiltrating cells (TIICs) in glioma. Furthermore, we conducted in vitro studies to elucidate the functional roles of MLK1‐2 in glioma. Our findings revealed that the expressions of MLK1‐2 were conspicuously downregulated in GBM and positively correlated with patients' overall survival. Conversely, ZAK exhibited an opposing trend. Notably, our newly devised risk score model exhibited superior performance in predicting patient prognoses. Moreover, we analyzed the potential mechanisms of MLK activity and its interplay with tumor immune infiltration. Last, we validated the antitumor effect of MLK1‐2 at the in vitro level. In summary, our study sheds new insights into the roles of MLKs in glioma, particularly MLK1‐2, and their potential as therapeutic targets. [ABSTRACT FROM AUTHOR]

Published
2024
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40. Generation of allogeneic CAR-NKT cells from hematopoietic stem and progenitor cells using a clinically guided culture method

Author

Li, Yan-Ruide, primary, Zhou, Yang, additional, Yu, Jiaji, additional, Kim, Yu Jeong, additional, Li, Miao, additional, Lee, Derek, additional, Zhou, Kuangyi, additional, Chen, Yuning, additional, Zhu, Yichen, additional, Wang, Yu-Chen, additional, Li, Zhe, additional, Yu, Yanqi, additional, Dunn, Zachary Spencer, additional, Guo, Wenbin, additional, Cen, Xinjian, additional, Husman, Tiffany, additional, Bajpai, Aarushi, additional, Kramer, Adam, additional, Wilson, Matthew, additional, Fang, Ying, additional, Huang, Jie, additional, Li, Shuo, additional, Zhou, Yonggang, additional, Zhang, Yuchong, additional, Hahn, Zoe, additional, Zhu, Enbo, additional, Ma, Feiyang, additional, Pan, Calvin, additional, Lusis, Aldons J., additional, Zhou, Jin J., additional, Seet, Christopher S., additional, Kohn, Donald B., additional, Wang, Pin, additional, Zhou, Xianghong Jasmine, additional, Pellegrini, Matteo, additional, Puliafito, Benjamin R., additional, Larson, Sarah M., additional, and Yang, Lili, additional

Published
2024
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42. Genome-Wide Analysis of Trehalose-6-Phosphate Phosphatase Gene Family and Their Expression Profiles in Response to Abiotic Stress in Groundnut

Author

Liu, Yue, primary, Wang, Xin, additional, Ouyang, Lei, additional, Yao, Ruonan, additional, Wang, Zhihui, additional, Kang, Yanping, additional, Yan, Liying, additional, Chen, Yuning, additional, Huai, Dongxin, additional, Wang, Qianqian, additional, Jiang, Huifang, additional, Lei, Yong, additional, and Liao, Boshou, additional

Published
2024
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46. Learning to Construct a Solution for the Agile Satellite Scheduling Problem With Time-Dependent Transition Times

Author

Chen, Ming, Du, Yonghao, Tang, Ke, Xing, Lining, Chen, Yuning, and Chen, Yingwu

Abstract

The agile earth observation satellite scheduling problem (AEOSSP) with time-dependent transition times is a complex combinational optimization problem that has emerged from the development of large-scale satellite management techniques. To address this problem, we propose a deep reinforcement learning-based construction model (DRL-CM) that consists of five parts: 1) a Markov decision process (MDP); 2) a feature engineering; 3) a constructive heuristic neural network (CHNN); 4) an RL training method; and 5) an evaluation system. Specifically, the CHNN comprises six modules containing three special components that we propose: a dynamic encoder, a dynamic global layer, and a two-stage attention layer. First, we build the MDP of the AEOSSP and the feature engineering with effective features required for decision-making. Second, we design the CHNN to function as the MDP policy and train it with an RL model. Finally, we propose a comprehensive evaluation system for the validation of our model. The experimental results indicate that the proposed DRL-CM outperforms the state-of-the-art algorithm in terms of both optimization speed and quality. In addition, the feature engineering and network architecture built in our model are verified to be effective in comprehensive experiments.

Published
2024
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48. Human whole-exome genotype data for Alzheimer’s disease

Author

Leung, Yuk Yee, Naj, Adam C., Chou, Yi Fan, Valladares, Otto, Schmidt, Michael, Hamilton-Nelson, Kara, Wheeler, Nicholas, Lin, Honghuang, Gangadharan, Prabhakaran, Qu, Liming, Clark, Kaylyn, Kuzma, Amanda B., Lee, Wan Ping, Cantwell, Laura, Nicaretta, Heather, van der Lee, Sven, English, Adam, Kalra, Divya, Muzny, Donna, Skinner, Evette, Doddapeneni, Harsha, Dinh, Huyen, Hu, Jianhong, Santibanez, Jireh, Jayaseelan, Joy, Worley, Kim, Gibbs, Richard A., Lee, Sandra, Dugan-Perez, Shannon, Korchina, Viktoriya, Nasser, Waleed, Liu, Xiuping, Han, Yi, Zhu, Yiming, Liu, Yue, Khan, Ziad, Zhu, Congcong, Sun, Fangui Jenny, Jun, Gyungah R., Chung, Jaeyoon, Farrell, John, Zhang, Xiaoling, Banks, Eric, Gupta, Namrata, Gabriel, Stacey, Butkiewicz, Mariusz, Benchek, Penelope, Smieszek, Sandra, Song, Yeunjoo, Vardarajan, Badri, Reitz, Christiane, Reyes-Dumeyer, Dolly, Tosto, Giuseppe, De Jager, Phillip L., Barral, Sandra, Ma, Yiyi, Beiser, Alexa, Liu, Ching Ti, Dupuis, Josee, Lunetta, Kathy, Cupples, L. Adrienne, Choi, Seung Hoan, Chen, Yuning, Mez, Jesse, Vanderspek, Ashley, Ikram, M. Arfan, Ahmad, Shahzad, Faber, Kelley, Foroud, Tatiana, Mlynarski, Elisabeth, Schmidt, Helena, Schmidt, Reinhold, Kunkle, Brian, Rajabli, Farid, Beecham, Gary, Vance, Jeffrey M., Adams, Larry D., Cuccaro, Michael, Mena, Pedro, Booth, Briana M., Renton, Alan, Goate, Alison, Marcora, Edoardo, Stine, Adam, Feolo, Michael, Launer, Lenore J., Koboldt, Daniel C., Wilson, Richard K., van Duijn, Cornelia, Amin, Najaf, Kapoor, Manav, Salerno, William, Bennett, David A., Xia, Li Charlie, Malamon, John, Mosley, Thomas H., Satizabal, Claudia, Jan Bressler, Bressler, Jian, Xueqiu, Nato, Alejandro Q., Horimoto, Andrea R., Wang, Bowen, Psaty, Bruce, Witten, Daniela, Tsuang, Debby, Blue, Elizabeth, Wijsman, Ellen, Sohi, Harkirat, Nguyen, Hiep, Bis, Joshua C., Rice, Kenneth, Brown, Lisa, Dorschner, Michael, Saad, Mohamad, Navas, Pat, Nafikov, Rafael, Thornton, Timothy, Day, Tyler, Haut, Jacob, Sha, Jin, Zhang, Nancy, Iqbal, Taha, Zhao, Yi, Below, Jennifer E., Larson, David E., Appelbaum, Elizabeth, Waligorski, Jason, Antonacci-Fulton, Lucinda, Fulton, Robert S., Haines, Jonathan, Farrer, Lindsay, Seshadri, Sudha, Brkanac, Zoran, Cruchaga, Carlos, Pericak-Vance, Margaret, Mayeux, Richard P., Bush, William S., Destefano, Anita, Martin, Eden, Schellenberg, Gerard D., Wang, Li San, Leung, Yuk Yee, Naj, Adam C., Chou, Yi Fan, Valladares, Otto, Schmidt, Michael, Hamilton-Nelson, Kara, Wheeler, Nicholas, Lin, Honghuang, Gangadharan, Prabhakaran, Qu, Liming, Clark, Kaylyn, Kuzma, Amanda B., Lee, Wan Ping, Cantwell, Laura, Nicaretta, Heather, van der Lee, Sven, English, Adam, Kalra, Divya, Muzny, Donna, Skinner, Evette, Doddapeneni, Harsha, Dinh, Huyen, Hu, Jianhong, Santibanez, Jireh, Jayaseelan, Joy, Worley, Kim, Gibbs, Richard A., Lee, Sandra, Dugan-Perez, Shannon, Korchina, Viktoriya, Nasser, Waleed, Liu, Xiuping, Han, Yi, Zhu, Yiming, Liu, Yue, Khan, Ziad, Zhu, Congcong, Sun, Fangui Jenny, Jun, Gyungah R., Chung, Jaeyoon, Farrell, John, Zhang, Xiaoling, Banks, Eric, Gupta, Namrata, Gabriel, Stacey, Butkiewicz, Mariusz, Benchek, Penelope, Smieszek, Sandra, Song, Yeunjoo, Vardarajan, Badri, Reitz, Christiane, Reyes-Dumeyer, Dolly, Tosto, Giuseppe, De Jager, Phillip L., Barral, Sandra, Ma, Yiyi, Beiser, Alexa, Liu, Ching Ti, Dupuis, Josee, Lunetta, Kathy, Cupples, L. Adrienne, Choi, Seung Hoan, Chen, Yuning, Mez, Jesse, Vanderspek, Ashley, Ikram, M. Arfan, Ahmad, Shahzad, Faber, Kelley, Foroud, Tatiana, Mlynarski, Elisabeth, Schmidt, Helena, Schmidt, Reinhold, Kunkle, Brian, Rajabli, Farid, Beecham, Gary, Vance, Jeffrey M., Adams, Larry D., Cuccaro, Michael, Mena, Pedro, Booth, Briana M., Renton, Alan, Goate, Alison, Marcora, Edoardo, Stine, Adam, Feolo, Michael, Launer, Lenore J., Koboldt, Daniel C., Wilson, Richard K., van Duijn, Cornelia, Amin, Najaf, Kapoor, Manav, Salerno, William, Bennett, David A., Xia, Li Charlie, Malamon, John, Mosley, Thomas H., Satizabal, Claudia, Jan Bressler, Bressler, Jian, Xueqiu, Nato, Alejandro Q., Horimoto, Andrea R., Wang, Bowen, Psaty, Bruce, Witten, Daniela, Tsuang, Debby, Blue, Elizabeth, Wijsman, Ellen, Sohi, Harkirat, Nguyen, Hiep, Bis, Joshua C., Rice, Kenneth, Brown, Lisa, Dorschner, Michael, Saad, Mohamad, Navas, Pat, Nafikov, Rafael, Thornton, Timothy, Day, Tyler, Haut, Jacob, Sha, Jin, Zhang, Nancy, Iqbal, Taha, Zhao, Yi, Below, Jennifer E., Larson, David E., Appelbaum, Elizabeth, Waligorski, Jason, Antonacci-Fulton, Lucinda, Fulton, Robert S., Haines, Jonathan, Farrer, Lindsay, Seshadri, Sudha, Brkanac, Zoran, Cruchaga, Carlos, Pericak-Vance, Margaret, Mayeux, Richard P., Bush, William S., Destefano, Anita, Martin, Eden, Schellenberg, Gerard D., and Wang, Li San

Abstract

The heterogeneity of the whole-exome sequencing (WES) data generation methods present a challenge to a joint analysis. Here we present a bioinformatics strategy for joint-calling 20,504 WES samples collected across nine studies and sequenced using ten capture kits in fourteen sequencing centers in the Alzheimer’s Disease Sequencing Project. The joint-genotype called variant-called format (VCF) file contains only positions within the union of capture kits. The VCF was then processed specifically to account for the batch effects arising from the use of different capture kits from different studies. We identified 8.2 million autosomal variants. 96.82% of the variants are high-quality, and are located in 28,579 Ensembl transcripts. 41% of the variants are intronic and 1.8% of the variants are with CADD > 30, indicating they are of high predicted pathogenicity. Here we show our new strategy can generate high-quality data from processing these diversely generated WES samples. The improved ability to combine data sequenced in different batches benefits the whole genomics research community.

Published
2024

49. The Association Between Diabetic Retinopathy and the Prevalence of Age-Related Macular Degeneration—The Kailuan Eye Study

Author

Zhang Yongpeng, Wang Yaxing, Zhou Jinqiong, Wang Qian, Yan Yanni, Yang Xuan, Yang Jingyan, Zhou Wenjia, Wang Ping, Shen Chang, Yang Ming, Luan Yanan, Wang Jinyuan, Wu Shouling, Chen Shuohua, Wang Haiwei, Fang Lijian, Wan Qianqian, Zhu Jingyuan, Nie Zihan, Chen Yuning, Xie Ying, Jost B. Jonas, and Wei Wenbin

Subjects
diabetes mellitus, diabetic retinopathy, age-related macular degeneration, prevalence, epidemiology, Public aspects of medicine, RA1-1270
Abstract

This study aimed to investigate the prevalence of age-related macular degeneration (AMD) in patients with diabetes mellitus (DM) and diabetic retinopathy (DR) and analyze whether DR is a risk factor for AMD. This population-based epidemiological study included 14,440 people from the Kailuan Eye Study in 2016, of whom 1,618 were patients with type 2 DM aged over 50 years, and 409 had DM with DR. We analyzed whether there were differences in the prevalence of AMD between DM with DR and DM without DR, and conducted a hierarchical statistical analysis according to different stages of DR. Using variable regression analysis, we explored whether DR constituted a risk factor for AMD. In the DM population, the prevalence of wet AMD in patients with DM with and without DR was 0. 3 and 0.2%, respectively, with no significant difference (P = 0.607). Meanwhile, the prevalence of dry AMD in patients with DM with and without DR was 20.8 and 16.0%, respectively, with a significant difference. In the subgroup analysis of dry AMD, the prevalence of early, middle, and late dry AMD in DM with DR was 14.4, 5.9, and 0.5%, respectively. In DM without DR, the prevalence of early, middle, and late dry AMD was 10.5, 4.8, and 0.7%, respectively (P = 0.031). In the subgroup analysis of DR staging, statistical analysis could not be performed because of the limited number of patients with PDR. In the variable regression analysis of risk factors for dry AMD, after adjusting for age, sex, body mass index, hypertension, and dyslipidemia, DR constituted the risk factor for dry AMD. In conclusion, DM did not constitute a risk factor for AMD, and the prevalence of wet AMD and dry AMD in patients with DM and DR was higher than that in patients with DM without DR (among which dry AMD was statistically significant). Multivariate regression analysis confirmed that DR is an independent risk factor for dry AMD. Reasonable control of DM and slowing down the occurrence and development of DR may effectively reduce the prevalence of AMD in patients with DM.

Published
2022
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50. Cavity-Enhanced Ultrafast Transient Absorption Spectroscopy

Author

Reber, Melanie A. R., Chen, Yuning, and Allison, Thomas K.

Subjects
Physics - Optics, Physics - Atomic Physics, Physics - Chemical Physics
Abstract

We present a new technique using a frequency comb laser and optical cavities for performing ultrafast transient absorption spectroscopy with improved sensitivity. Resonantly enhancing the probe pulses, we demonstrate a sensitivity of $\Delta$OD $ = 1 \times 10^{-9}/\sqrt{\mbox{Hz}}$ for averaging times as long as 30 s per delay point ($\Delta$OD$_{min} = 2 \times 10^{-10}$). Resonantly enhancing the pump pulses allows us to produce a high excitation fraction at high repetition-rate, so that signals can be recorded from samples with optical densities as low as OD $\approx 10^{-8}$, or column densities $< 10^{10}$ molecules/cm$^2$. This high sensitivity enables new directions for ultrafast spectroscopy.

Published
2015
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