614 results on '"Lee, Youjin"'
Search Results
2. A Causal Framework for Evaluating Heterogeneous Policy Mechanisms Using Difference-in-Differences
- Author
-
Hettinger, Gary, Lee, Youjin, and Mitra, Nandita
- Subjects
Statistics - Methodology - Abstract
In designing and evaluating public policies, policymakers and researchers often hypothesize about the mechanisms through which a policy may affect a population and aim to assess these mechanisms in practice. For example, when studying an excise tax on sweetened beverages, researchers might explore how cross-border shopping, economic competition, and store-level price changes differentially affect store sales. However, many policy evaluation designs, including the difference-in-differences (DiD) approach, traditionally target the average effect of the intervention rather than the underlying mechanisms. Extensions of these approaches to evaluate policy mechanisms often involve exploratory subgroup analyses or outcome models parameterized by mechanism-specific variables. However, neither approach studies the mechanisms within a causal framework, limiting the analysis to associative relationships between mechanisms and outcomes, which may be confounded by differences among sub-populations exposed to varying levels of the mechanisms. Therefore, rigorous mechanism evaluation requires robust techniques to adjust for confounding and accommodate the interconnected relationship between stores within competitive economic landscapes. In this paper, we present a framework for evaluating policy mechanisms by studying Philadelphia beverage tax. Our approach builds on recent advancements in causal effect curve estimators under DiD designs, offering tools and insights for assessing policy mechanisms complicated by confounding and network interference.
- Published
- 2024
3. Difference-in-Differences for Health Policy and Practice: A Review of Modern Methods
- Author
-
Feng, Shuo, Ganguli, Ishani, Lee, Youjin, Poe, John, Ryan, Andrew, and Bilinski, Alyssa
- Subjects
Statistics - Applications ,Economics - Econometrics - Abstract
Difference-in-differences (DiD) is the most popular observational causal inference method in health policy, employed to evaluate the real-world impact of policies and programs. To estimate treatment effects, DiD relies on the "parallel trends assumption", that on average treatment and comparison groups would have had parallel trajectories in the absence of an intervention. Historically, DiD has been considered broadly applicable and straightforward to implement, but recent years have seen rapid advancements in DiD methods. This paper reviews and synthesizes these innovations for medical and health policy researchers. We focus on four topics: (1) assessing the parallel trends assumption in health policy contexts; (2) relaxing the parallel trends assumption when appropriate; (3) employing estimators to account for staggered treatment timing; and (4) conducting robust inference for analyses in which normal-based clustered standard errors are inappropriate. For each, we explain challenges and common pitfalls in traditional DiD and modern methods available to address these issues.
- Published
- 2024
4. Imaging thermally fluctuating N\`eel vectors in van der Waals antiferromagnet NiPS3
- Author
-
Lee, Youjin, Kim, Chaebin, Son, Suhan, Cui, Jingyuan, Park, Giung, Zhang, Kai-Xuan, Oh, Siwon, Cheong, Hyeonsik, Kleibert, Armin, and Park, Je-Geun
- Subjects
Condensed Matter - Materials Science ,Condensed Matter - Mesoscale and Nanoscale Physics - Abstract
Studying antiferromagnetic domains is essential for fundamental physics and potential spintronics applications. Despite its importance, few systematic studies have been performed on van der Waals (vdW) antiferromagnets (AFMs) domains with high spatial resolutions, and direct probing of the N\`eel vectors remains challenging. In this work, we found a multidomain in vdW AFM NiPS3, a material extensively investigated for its exotic magnetic exciton. We employed photoemission electron microscopy combined with the X-ray magnetic linear dichroism (XMLD-PEEM) to image the NiPS3's magnetic structure. The nanometer-spatial resolution of XMLD-PEEM allows us to determine local N\`eel vector orientations and discover thermally fluctuating N\'eel vectors that are independent of the crystal symmetry even at 65 K, well below TN of 155 K. We demonstrate a Ni ions' small in-plane orbital moment anisotropy is responsible for the weak magneto-crystalline anisotropy. The observed multidomain's thermal fluctuations may explain the broadening of magnetic exciton peaks at higher temperatures.
- Published
- 2024
5. Giant Linear Dichroism Controlled by Magnetic Field in FePS$_3$
- Author
-
Zhou, Xu-Guang, Yang, Zhuo, Lee, Youjin, Park, Jaena, Kohama, Yoshimitsu, Kindo, Koichi, Matsuda, Yasuhiro H., Park, Je-Geun, Janson, Oleg, and Miyata, Atsuhiko
- Subjects
Condensed Matter - Materials Science ,Condensed Matter - Strongly Correlated Electrons - Abstract
Magnetic-field control of fundamental optical properties is a crucial challenge in the engineering of multifunctional microdevices. Van der Waals (vdW) magnets retaining a magnetic order even in atomically thin layers, offer a promising platform for hosting exotic magneto-optical functionalities owing to their strong spin-charge coupling. Here, we demonstrate that a giant optical anisotropy can be controlled by magnetic fields in the vdW magnet FePS$_3$. The giant linear dichroism ($\sim$11%), observed below $T_{\text{N}}\!\sim\!120$ K, is nearly fully suppressed in a wide energy range from 1.6 to 2.0 eV, following the collapse of the zigzag magnetic order above 40 T. This remarkable phenomenon can be explained as a result of symmetry changes due to the spin order, enabling minority electrons of Fe$^{2+}$ to hop in a honeycomb lattice. The modification of spin-order symmetry by external fields provides a novel route for controllable anisotropic optical micro-devices., Comment: 5 pages, 4 figures
- Published
- 2024
6. Multiply Robust Difference-in-Differences Estimation of Causal Effect Curves for Continuous Exposures
- Author
-
Hettinger, Gary, Lee, Youjin, and Mitra, Nandita
- Subjects
Statistics - Methodology - Abstract
Researchers commonly use difference-in-differences (DiD) designs to evaluate public policy interventions. While methods exist for estimating effects in the context of binary interventions, policies often result in varied exposures across regions implementing the policy. Yet, existing approaches for incorporating continuous exposures face substantial limitations in addressing confounding variables associated with intervention status, exposure levels, and outcome trends. These limitations significantly constrain policymakers' ability to fully comprehend policy impacts and design future interventions. In this work, we propose new estimators for causal effect curves within the DiD framework, accounting for multiple sources of confounding. Our approach accommodates misspecification of a subset of treatment, exposure, and outcome models while avoiding any parametric assumptions on the effect curve. We present the statistical properties of the proposed methods and illustrate their application through simulations and a study investigating the heterogeneous effects of a nutritional excise tax under different levels of accessibility to cross-border shopping.
- Published
- 2024
7. Statistical and Causal Robustness for Causal Null Hypothesis Tests
- Author
-
Yang, Junhui, Bhattacharya, Rohit, Lee, Youjin, and Westling, Ted
- Subjects
Statistics - Methodology - Abstract
Prior work applying semiparametric theory to causal inference has primarily focused on deriving estimators that exhibit statistical robustness under a prespecified causal model that permits identification of a desired causal parameter. However, a fundamental challenge is correct specification of such a model, which usually involves making untestable assumptions. Evidence factors is an approach to combining hypothesis tests of a common causal null hypothesis under two or more candidate causal models. Under certain conditions, this yields a test that is valid if at least one of the underlying models is correct, which is a form of causal robustness. We propose a method of combining semiparametric theory with evidence factors. We develop a causal null hypothesis test based on joint asymptotic normality of K asymptotically linear semiparametric estimators, where each estimator is based on a distinct identifying functional derived from each of K candidate causal models. We show that this test provides both statistical and causal robustness in the sense that it is valid if at least one of the K proposed causal models is correct, while also allowing for slower than parametric rates of convergence in estimating nuisance functions. We demonstrate the effectiveness of our method via simulations and applications to the Framingham Heart Study and Wisconsin Longitudinal Study.
- Published
- 2023
8. Time-of-flight detection of terahertz phonon-polariton
- Author
-
Luo, Tianchuang, Ilyas, Batyr, Hoegen, A. von, Lee, Youjin, Park, Jaena, Park, Je-Geun, and Gedik, Nuh
- Published
- 2024
- Full Text
- View/download PDF
9. Amygdala electrical stimulation for operant conditioning in rat navigation
- Author
-
Lee, Youjin, Kim, Soonyoung, Cho, Yoon Kyung, Kong, Chanho, Chang, Jin Woo, and Jun, Sang Beom
- Published
- 2024
- Full Text
- View/download PDF
10. Policy effect evaluation under counterfactual neighborhood interventions in the presence of spillover
- Author
-
Lee, Youjin, Hettinger, Gary, and Mitra, Nandita
- Subjects
Statistics - Methodology - Abstract
Policy interventions can spill over to units of a population that are not directly exposed to the policy but are geographically close to the units receiving the intervention. In recent work, investigations of spillover effects on neighboring regions have focused on estimating the average treatment effect of a particular policy in an observed setting. Our research question broadens this scope by asking what policy consequences would the treated units have experienced under hypothetical exposure settings. When we only observe treated unit(s) surrounded by controls -- as is common when a policy intervention is implemented in a single city or state -- this effect inquires about the policy effects under a counterfactual neighborhood policy status that we do not, in actuality, observe. In this work, we extend difference-in-differences (DiD) approaches to spillover settings and develop identification conditions required to evaluate policy effects in counterfactual treatment scenarios. These causal quantities are policy-relevant for designing effective policies for populations subject to various neighborhood statuses. We develop doubly robust estimators and use extensive numerical experiments to examine their performance under heterogeneous spillover effects. We apply our proposed method to investigate the effect of the Philadelphia beverage tax on unit sales.
- Published
- 2023
11. Estimation of Policy-Relevant Causal Effects in the Presence of Interference with an Application to the Philadelphia Beverage Tax
- Author
-
Hettinger, Gary, Roberto, Christina, Lee, Youjin, and Mitra, Nandita
- Subjects
Statistics - Methodology - Abstract
To comprehensively evaluate a public policy intervention, researchers must consider the effects of the policy not just on the implementing region, but also nearby, indirectly-affected regions. For example, an excise tax on sweetened beverages in Philadelphia was shown to not only be associated with a decrease in volume sales of taxed beverages in Philadelphia, but also an increase in sales in bordering counties not subject to the tax. The latter association may be explained by cross-border shopping behaviors of Philadelphia residents and indicate a causal effect of the tax on nearby regions, which may offset the total effect of the intervention. To estimate causal effects in this setting, we extend difference-in-differences methodology to account for such interference between regions and adjust for potential confounding present in quasi-experimental evaluations. Our doubly robust estimators for the average treatment effect on the treated and neighboring control relax standard assumptions on interference and model specification. We apply these methods to evaluate the change in volume sales of taxed beverages in 231 Philadelphia and bordering county stores due to the Philadelphia beverage tax. We also use our methods to explore the heterogeneity of effects across geographic features.
- Published
- 2023
12. Giant magnetic anisotropy in the atomically thin van der Waals antiferromagnet FePS3
- Author
-
Lee, Youjin, Son, Suhan, Kim, Chaebin, Kang, Soonmin, Shen, Junying, Kenzelmann, Michel, Delley, Bernard, Savchenko, Tatiana, Parchenko, Sergii, Na, Woongki, Choi, Ki-Young, Kim, Wondong, Cheong, Hyeonsik, Derlet, Peter M., Kleibert, Armin, and Park, Je-Geun
- Subjects
Condensed Matter - Mesoscale and Nanoscale Physics - Abstract
Van der Waals (vdW) magnets are an ideal platform for tailoring two-dimensional (2D) magnetism with immense potential for spintronics applications and are intensively investigated. However, little is known about the microscopic origin of magnetic order in these antiferromagnetic systems. We used X-ray photoemission electron microscopy to address the electronic and magnetic properties of the vdW antiferromagnet FePS3 down to the monolayer. Our experiments reveal a giant out-of-plane magnetic anisotropy of 22 meV per Fe ion, accompanied by unquenched magnetic orbital moments. Moreover, our calculations suggest that the Ising magnetism in FePS3 is a visible manifestation of spin-orbit entanglement of the Fe 3d electron system.
- Published
- 2022
13. Quantitative Measurement of Tau Aggregation in Genetically Modified Rats with Neurodegeneration
- Author
-
Lee, YouJin, primary and Morrow, Eric M., additional
- Published
- 2024
- Full Text
- View/download PDF
14. Early lysosome defects precede neurodegeneration with amyloid-β and tau aggregation in NHE6-null rat brain.
- Author
-
Lee, YouJin, Miller, Morgan R, Fernandez, Marty A, Berg, Elizabeth L, Prada, Adriana M, Ouyang, Qing, Schmidt, Michael, Silverman, Jill L, Young-Pearse, Tracy L, and Morrow, Eric M
- Subjects
Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) ,Acquired Cognitive Impairment ,Brain Disorders ,Alzheimer's Disease ,Neurosciences ,Neurodegenerative ,Rare Diseases ,Aging ,Dementia ,2.1 Biological and endogenous factors ,Aetiology ,Neurological ,Alzheimer Disease ,Amyloid beta-Peptides ,Animals ,Ataxia ,Brain ,Disease Models ,Animal ,Epilepsy ,Genetic Diseases ,X-Linked ,Hippocampus ,Intellectual Disability ,Lysosomes ,Male ,Microcephaly ,Ocular Motility Disorders ,Rats ,Sodium-Hydrogen Exchangers ,tau Proteins ,rat model ,lysosomes ,neurodegeneration ,tau ,amyloid beta ,Medical and Health Sciences ,Psychology and Cognitive Sciences ,Neurology & Neurosurgery - Abstract
Loss-of-function mutations in the X-linked endosomal Na+/H+ exchanger 6 (NHE6) cause Christianson syndrome in males. Christianson syndrome involves endosome dysfunction leading to early cerebellar degeneration, as well as later-onset cortical and subcortical neurodegeneration, potentially including tau deposition as reported in post-mortem studies. In addition, there is reported evidence of modulation of amyloid-β levels in experimental models wherein NHE6 expression was targeted. We have recently shown that loss of NHE6 causes defects in endosome maturation and trafficking underlying lysosome deficiency in primary mouse neurons in vitro. For in vivo studies, rat models may have an advantage over mouse models for the study of neurodegeneration, as rat brain can demonstrate robust deposition of endogenously-expressed amyloid-β and tau in certain pathological states. Mouse models generally do not show the accumulation of insoluble, endogenously-expressed (non-transgenic) tau or amyloid-β. Therefore, to study neurodegeneration in Christianson syndrome and the possibility of amyloid-β and tau pathology, we generated an NHE6-null rat model of Christianson syndrome using CRISPR-Cas9 genome-editing. Here, we present the sequence of pathogenic events in neurodegenerating NHE6-null male rat brains across the lifespan. NHE6-null rats demonstrated an early and rapid loss of Purkinje cells in the cerebellum, as well as a more protracted neurodegenerative course in the cerebrum. In both the cerebellum and cerebrum, lysosome deficiency is an early pathogenic event, preceding autophagic dysfunction. Microglial and astrocyte activation also occur early. In the hippocampus and cortex, lysosome defects precede loss of pyramidal cells. Importantly, we subsequently observed biochemical and in situ evidence of both amyloid-β and tau aggregation in the aged NHE6-null hippocampus and cortex (but not in the cerebellum). Tau deposition is widely distributed, including cortical and subcortical distributions. Interestingly, we observed tau deposition in both neurons and glia, as has been reported in Christianson syndrome post-mortem studies previously. In summary, this experimental model is among very few examples of a genetically modified animal that exhibits neurodegeneration with deposition of endogenously-expressed amyloid-β and tau. This NHE6-null rat will serve as a new robust model for Christianson syndrome. Furthermore, these studies provide evidence for linkages between endolysosome dysfunction and neurodegeneration involving protein aggregations, including amyloid-β and tau. Therefore these studies may provide insight into mechanisms of more common neurodegenerative disorders, including Alzheimer's disease and related dementias.
- Published
- 2022
15. Multiferroic-enabled magnetic exciton in 2D quantum entangled van der Waals antiferromagnet NiI2
- Author
-
Son, Suhan, Lee, Youjin, Kim, Jae Ha, Kim, Beom Hyun, Kim, Chaebin, Na, Woongki, Ju, Hwiin, Park, Sudong, Nag, Abhishek, Zhou, Ke-Jin, Son, Young-Woo, Kim, Hyeongdo, Noh, Woo-Suk, Park, Jae-Hoon, Lee, Jong Seok, Cheong, Hyeonsik, Kim, Jae Hoon, and Park, Je-Geun
- Subjects
Condensed Matter - Strongly Correlated Electrons - Abstract
Matter-light interaction is at the center of diverse research fields from quantum optics to condensed matter physics, opening new fields like laser physics. A magnetic exciton is one such rare example found in magnetic insulators. However, it is relatively rare to observe that external variables control matter-light interaction. Here, we report that the broken inversion symmetry of multiferroicity can act as an external knob enabling the magnetic exciton in van der Waals antiferromagnet NiI2. We further discover that this magnetic exciton arises from a transition between Zhang-Rice-triplet and Zhang-Rice-singlet's fundamentally quantum entangled states. This quantum entanglement produces an ultra-sharp optical exciton peak at 1.384 eV with a 5 meV linewidth. Our work demonstrates that NiI2 is two-dimensional magnetically ordered with an intrinsically quantum entangled ground state., Comment: 26 pages, 10 figures. Accepted for publication in Advanced Materials
- Published
- 2021
16. Association of nightmares with cardio-cerebrovascular disease, hypertension and hyperlipidemia in older adults: A population-based cross-sectional study
- Author
-
Lee, Youjin, Park, Dasom, Kim, Soriul, Shin, Chol, and Suh, Sooyeon
- Published
- 2024
- Full Text
- View/download PDF
17. Distinguishing nontuberculous mycobacterial lung disease and Mycobacterium tuberculosis lung disease on X-ray images using deep transfer learning
- Author
-
Park, Minwoo, Lee, Youjin, Kim, Sangil, Kim, Young-Jin, Kim, Shin Young, Kim, Yeongsic, and Kim, Hyun-Min
- Published
- 2023
- Full Text
- View/download PDF
18. Highly efficient nonvolatile magnetization switching and multi-level states by current in single van der Waals topological ferromagnet Fe3GeTe2
- Author
-
Zhang, Kaixuan, Lee, Youjin, Coak, Matthew J., Kim, Junghyun, Son, Suhan, Hwang, Inho, Ko, Dong-Su, Oh, Youngtek, Jeon, Insu, Kim, Dohun, Zeng, Changgan, Lee, Hyun-Woo, and Park, Je-Geun
- Subjects
Condensed Matter - Materials Science ,Condensed Matter - Other Condensed Matter ,Physics - Applied Physics ,Quantum Physics - Abstract
Robust multi-level spin memory with the ability to write information electrically is a long-sought capability in spintronics, with great promise for applications. Here we achieve nonvolatile and highly energy-efficient magnetization switching in a single-material device formed of van-der-Waals topological ferromagnet Fe3GeTe2, whose magnetic information can be readily controlled by a tiny current. Furthermore, the switching current density and power dissipation are about 400 and 4000 times smaller than those of the existing spin-orbit-torque magnetic random access memory based on conventional magnet/heavy-metal systems. Most importantly, we also demonstrate multi-level states, switched by electrical current, which can dramatically enhance the information capacity density and reduce computing costs. Thus, our observations combine both high energy efficiency and large information capacity density in one device, showcasing the potential applications of the emerging field of van-der-Waals magnets in the field of spin memory and spintronics., Comment: Accepted by Advanced Functional Materials; 28 pages, 5 main figures, 4 supporting figures
- Published
- 2021
- Full Text
- View/download PDF
19. Gigantic current control of coercive field and magnetic memory based on nm-thin ferromagnetic van der Waals Fe3GeTe2
- Author
-
Zhang, Kaixuan, Han, Seungyun, Lee, Youjin, Coak, Matthew J., Kim, Junghyun, Hwang, Inho, Son, Suhan, Shin, Jeacheol, Lim, Mijin, Jo, Daegeun, Kim, Kyoo, Kim, Dohun, Lee, Hyun-Woo, and Park, Je-Geun
- Subjects
Condensed Matter - Materials Science ,Condensed Matter - Mesoscale and Nanoscale Physics ,Physics - Applied Physics - Abstract
Controlling magnetic states by a small current is essential for the next-generation of energy-efficient spintronic devices. However, it invariably requires considerable energy to change a magnetic ground state of intrinsically quantum nature governed by fundamental Hamiltonian, once stabilized below a phase transition temperature. We report that surprisingly an in-plane current can tune the magnetic state of nm-thin van der Waals ferromagnet Fe3GeTe2 from a hard magnetic state to a soft magnetic state. It is the direct demonstration of the current-induced substantial reduction of the coercive field. This surprising finding is possible because the in-plane current produces a highly unusual type of gigantic spin-orbit torque for Fe3GeTe2. And we further demonstrate a working model of a new nonvolatile magnetic memory based on the principle of our discovery in Fe3GeTe2, controlled by a tiny current. Our findings open up a new window of exciting opportunities for magnetic van der Waals materials with potentially huge impacts on the future development of spintronic and magnetic memory., Comment: 61 pages, 4 main figures, 14 supporting figures
- Published
- 2021
- Full Text
- View/download PDF
20. Possible persistence of multiferroic order down to bilayer limit of van der Waals material NiI$_{2}$
- Author
-
Ju, Hwiin, Lee, Youjin, Kim, Kwang-Tak, Choi, In Hyeok, Roh, Chang Jae, Son, Suhan, Park, Pyeongjae, Kim, Jae Ha, Jung, Taek Sun, Kim, Jae Hoon, Kim, Kee Hoon, Park, Je-Geun, and Lee, Jong Seok
- Subjects
Condensed Matter - Materials Science - Abstract
Realizing a state of matter in two dimensions has repeatedly proven a novel route of discovering new physical phenomena. Van der Waals (vdW) materials have been at the center of these now extensive research activities. They offer a natural way of producing a monolayer of matter simply by mechanical exfoliation. This work demonstrates that the possible multiferroic state with coexisting antiferromagnetic and ferroelectric orders possibly persists down to the bilayer flake of NiI$_{2}$. By exploiting the optical second-harmonic generation technique, both magnitude and direction of the ferroelectric order, arising from the cycloidal spin order, are successfully traced. The possible multiferroic state's transition temperature decreases from 58 K for the bulk to about 20 K for the bilayer. Our observation will spur extensive efforts to demonstrate multi-functionality in vdW materials, which have been tried mostly by using heterostructures of singly ferroic ones until now.
- Published
- 2021
- Full Text
- View/download PDF
21. Ultraviolet light scattering by a silicon Bethe hole
- Author
-
Lee Dukhyung, Lee Youjin, and Kim Dai-Sik
- Subjects
scattering ,bethe hole ,magnetic dipole ,uv plasmonics ,silicon ,Physics ,QC1-999 - Abstract
Bethe’s theory predicts that scattering by a small hole on a thin perfect electric conductor (PEC) is presented as radiation by an in-plane magnetic dipole of the incident magnetic field direction. Even in the near-infrared range where metals are no more PEC, the magnetic dipole radiation of Bethe holes has been demonstrated. However, such Bethe holes’ nature has not been addressed yet in the ultraviolet (UV) range where conductivity of metals becomes severely deteriorated. Meanwhile, UV plasmonics has been elevating its importance in spectroscopy and photochemistry, recognizing silicon (Si) as an alternative plasmonic metal featuring the interband transition in the UV range. In this work, we expanded the Bethe’s theory’s prediction to the UV range by investigating Si Bethe holes theoretically and experimentally in terms of the scattering pattern and polarization. Simulation results showed that the scattered field distribution resembles that of an in-plane magnetic dipole, and the dipole direction at oblique incidence is roughly given as the incident magnetic field direction with a deviation angle which can be predicted from the Fresnel equations. Simulation with various diameters showed that the magnetic dipole nature maintains with a diameter less than the quarter-wavelength and multipoles becomes noticeable for diameters larger than the half-wavelength. We performed scattering polarization measurement at 69-degree incidence, which confirms the theoretical analysis. The features of Si Bethe holes demonstrated here will be useful for designing UV plasmonic metasurfaces.
- Published
- 2023
- Full Text
- View/download PDF
22. Observation of plateau-like magnetoresistance in twisted Fe3GeTe2/Fe3GeTe2 junction
- Author
-
Kim, Junghyun, Son, Suhan, Coak, Matthew. J., Hwang, Inho, Lee, Youjin, Zhang, Kaixuan, and Park, Je-Geun
- Subjects
Condensed Matter - Materials Science ,Condensed Matter - Strongly Correlated Electrons - Abstract
Controlling the stacking of van der Waals (vdW) materials is found to produce exciting new findings, since hetero- or homo- structures have added the diverse possibility of assembly and manipulated functionalities. However, so far, the homostructure with a twisted angle based on the magnetic vdW materials remains unexplored. Here, we achieved a twisted magnetic vdW Fe3GeTe2/Fe3GeTe2 junction with broken crystalline symmetry. A clean and metallic vdW junction is evidenced by the temperature-dependent resistance and the linear I-V curve. Unlike the pristine FGT, a plateau-like magnetoresistance (PMR) is observed in the magnetotransport of our homojunction due to the antiparallel magnetic configurations of the two FGT layers. The PMR ratio is found to be ~0.05% and gets monotonically enhanced as temperature decreases like a metallic giant magnetoresistance (GMR). Such a tiny PMR ratio is at least three orders of magnitude smaller than the tunneling magnetoresistance (TMR) ratio, justifying our clean metallic junction without a spacer. Our findings demonstrate the feasibility of the controllable homostructure and shed light on future spintronics using magnetic vdW materials., Comment: 10 pages, 4 figures, accepted for publication in Journal of Applied physics
- Published
- 2020
23. Doubly Robust Nonparametric Instrumental Variable Estimators for Survival Outcomes
- Author
-
Lee, Youjin, Kennedy, Edward H., and Mitra, Nandita
- Subjects
Statistics - Methodology - Abstract
Instrumental variable (IV) methods allow us the opportunity to address unmeasured confounding in causal inference. However, most IV methods are only applicable to discrete or continuous outcomes with very few IV methods for censored survival outcomes. In this work we propose nonparametric estimators for the local average treatment effect on survival probabilities under both nonignorable and ignorable censoring. We provide an efficient influence function-based estimator and a simple estimation procedure when the IV is either binary or continuous. The proposed estimators possess double-robustness properties and can easily incorporate nonparametric estimation using machine learning tools. In simulation studies, we demonstrate the flexibility and efficiency of our proposed estimators under various plausible scenarios. We apply our method to the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial for estimating the causal effect of screening on survival probabilities and investigate the causal contrasts between the two interventions under different censoring assumptions.
- Published
- 2020
24. Two Robust Tools for Inference about Causal Effects with Invalid Instruments
- Author
-
Kang, Hyunseung, Lee, Youjin, Cai, T. Tony, and Small, Dylan S.
- Subjects
Statistics - Methodology ,Statistics - Applications - Abstract
Instrumental variables have been widely used to estimate the causal effect of a treatment on an outcome. Existing confidence intervals for causal effects based on instrumental variables assume that all of the putative instrumental variables are valid; a valid instrumental variable is a variable that affects the outcome only by affecting the treatment and is not related to unmeasured confounders. However, in practice, some of the putative instrumental variables are likely to be invalid. This paper presents two tools to conduct valid inference and tests in the presence of invalid instruments. First, we propose a simple and general approach to construct confidence intervals based on taking unions of well-known confidence intervals. Second, we propose a novel test for the null causal effect based on a collider bias. Our two proposals, especially when fused together, outperform traditional instrumental variable confidence intervals when invalid instruments are present, and can also be used as a sensitivity analysis when there is concern that instrumental variables assumptions are violated. The new approach is applied to a Mendelian randomization study on the causal effect of low-density lipoprotein on the incidence of cardiovascular diseases.
- Published
- 2020
25. Efficient generation of isogenic primary human myeloid cells using CRISPR-Cas9 ribonucleoproteins
- Author
-
Hiatt, Joseph, Cavero, Devin A, McGregor, Michael J, Zheng, Weihao, Budzik, Jonathan M, Roth, Theodore L, Haas, Kelsey M, Wu, David, Rathore, Ujjwal, Meyer-Franke, Anke, Bouzidi, Mohamed S, Shifrut, Eric, Lee, Youjin, Kumar, Vigneshwari Easwar, Dang, Eric V, Gordon, David E, Wojcechowskyj, Jason A, Hultquist, Judd F, Fontaine, Krystal A, Pillai, Satish K, Cox, Jeffery S, Ernst, Joel D, Krogan, Nevan J, and Marson, Alexander
- Subjects
Biological Sciences ,Biotechnology ,Genetics ,Infectious Diseases ,Stem Cell Research ,2.1 Biological and endogenous factors ,Aetiology ,Animals ,CRISPR-Cas Systems ,Genome ,Humans ,Mice ,Myeloid Cells ,Ribonucleoproteins ,CRISPR ,Cas9 ,dendritic cells ,electroporation ,host-pathogen interactions ,knockout ,macrophages ,monocytes ,myeloid cells ,ribonculeoproteins ,Biochemistry and Cell Biology ,Medical Physiology ,Biological sciences - Abstract
Genome engineering of primary human cells with CRISPR-Cas9 has revolutionized experimental and therapeutic approaches to cell biology, but human myeloid-lineage cells have remained largely genetically intractable. We present a method for the delivery of CRISPR-Cas9 ribonucleoprotein (RNP) complexes by nucleofection directly into CD14+ human monocytes purified from peripheral blood, leading to high rates of precise gene knockout. These cells can be efficiently differentiated into monocyte-derived macrophages or dendritic cells. This process yields genetically edited cells that retain transcript and protein markers of myeloid differentiation and phagocytic function. Genetic ablation of the restriction factor SAMHD1 increased HIV-1 infection >50-fold, demonstrating the power of this system for genotype-phenotype interrogation. This fast, flexible, and scalable platform can be used for genetic studies of human myeloid cells in immune signaling, inflammation, cancer immunology, host-pathogen interactions, and beyond, and could facilitate the development of myeloid cellular therapies.
- Published
- 2021
26. XYZeq: Spatially resolved single-cell RNA sequencing reveals expression heterogeneity in the tumor microenvironment
- Author
-
Lee, Youjin, Bogdanoff, Derek, Wang, Yutong, Hartoularos, George C, Woo, Jonathan M, Mowery, Cody T, Nisonoff, Hunter M, Lee, David S, Sun, Yang, Lee, James, Mehdizadeh, Sadaf, Cantlon, Joshua, Shifrut, Eric, Ngyuen, David N, Roth, Theodore L, Song, Yun S, Marson, Alexander, Chow, Eric D, and Ye, Chun Jimmie
- Subjects
Biological Sciences ,Bioinformatics and Computational Biology ,Regenerative Medicine ,Stem Cell Research ,Biotechnology ,Genetics ,Stem Cell Research - Nonembryonic - Non-Human ,Cancer ,Human Genome ,Underpinning research ,1.1 Normal biological development and functioning ,Generic health relevance ,Animals ,Gene Expression Profiling ,Mice ,Neoplasms ,Sequence Analysis ,RNA ,Single-Cell Analysis ,Transcriptome ,Tumor Microenvironment ,Exome Sequencing - Abstract
Single-cell RNA sequencing (scRNA-seq) of tissues has revealed remarkable heterogeneity of cell types and states but does not provide information on the spatial organization of cells. To better understand how individual cells function within an anatomical space, we developed XYZeq, a workflow that encodes spatial metadata into scRNA-seq libraries. We used XYZeq to profile mouse tumor models to capture spatially barcoded transcriptomes from tens of thousands of cells. Analyses of these data revealed the spatial distribution of distinct cell types and a cell migration-associated transcriptomic program in tumor-associated mesenchymal stem cells (MSCs). Furthermore, we identify localized expression of tumor suppressor genes by MSCs that vary with proximity to the tumor core. We demonstrate that XYZeq can be used to map the transcriptome and spatial localization of individual cells in situ to reveal how cell composition and cell states can be affected by location within complex pathological tissue.
- Published
- 2021
27. Somatosensory ECoG-based brain–machine interface with electrical stimulation on medial forebrain bundle
- Author
-
Cho, Yoon Kyung, Koh, Chin Su, Lee, Youjin, Park, Minkyung, Kim, Tae Jun, Jung, Hyun Ho, Chang, Jin Woo, and Jun, Sang Beom
- Published
- 2023
- Full Text
- View/download PDF
28. Partially Pooled Propensity Score Models for Average Treatment Effect Estimation with Multilevel Data
- Author
-
Lee, Youjin, Nguyen, Trang Q., and Stuart, Elizabeth A.
- Subjects
Statistics - Applications - Abstract
Causal inference analyses often use existing observational data, which in many cases has some clustering of individuals. In this paper we discuss propensity score weighting methods in a multilevel setting where within clusters individuals share unmeasured confounders that are related to treatment assignment and the potential outcomes. We focus in particular on settings where models with fixed cluster effects are either not feasible or not useful due to the presence of a large number of small clusters. We found, both through numerical experiments and theoretical derivations, that a strategy of grouping clusters with similar treatment prevalence and estimating propensity scores within such cluster groups is effective in reducing bias from unmeasured cluster-level covariates under mild conditions on the outcome model. We apply our proposed method in evaluating the effectiveness of center-based pre-school program participation on children's achievement at kindergarten, using the Early Childhood Longitudinal Study, Kindergarten data.
- Published
- 2019
29. Network Dependence Can Lead to Spurious Associations and Invalid Inference
- Author
-
Lee, Youjin and Ogburn, Elizabeth L.
- Subjects
Statistics - Applications - Abstract
Researchers across the health and social sciences generally assume that observations are independent, even while relying on convenience samples that draw subjects from one or a small number of communities, schools, hospitals, etc. A paradigmatic example of this is the Framingham Heart Study (FHS). Many of the limitations of such samples are well-known, but the issue of statistical dependence due to social network ties has not previously been addressed. We show that, along with anticonservative variance estimation, this can result in spurious associations due to network dependence. Using a statistical test that we adapted from one developed for spatial autocorrelation, we test for network dependence in several of the thousands of influential papers that have been published using FHS data. Results suggest that some of the many decades of research on coronary heart disease, other health outcomes, and peer influence using FHS data may suffer from spurious associations, error-prone point estimates, and anticonservative inference due to unacknowledged network dependence. These issues are not unique to the FHS; as researchers in psychology, medicine, and beyond grapple with replication failures, this unacknowledged source of invalid statistical inference should be part of the conversation.
- Published
- 2019
30. Evaluation of SARS-CoV-2 serology assays reveals a range of test performance
- Author
-
Whitman, Jeffrey D, Hiatt, Joseph, Mowery, Cody T, Shy, Brian R, Yu, Ruby, Yamamoto, Tori N, Rathore, Ujjwal, Goldgof, Gregory M, Whitty, Caroline, Woo, Jonathan M, Gallman, Antonia E, Miller, Tyler E, Levine, Andrew G, Nguyen, David N, Bapat, Sagar P, Balcerek, Joanna, Bylsma, Sophia A, Lyons, Ana M, Li, Stacy, Wong, Allison Wai-yi, Gillis-Buck, Eva Mae, Steinhart, Zachary B, Lee, Youjin, Apathy, Ryan, Lipke, Mitchell J, Smith, Jennifer Anne, Zheng, Tina, Boothby, Ian C, Isaza, Erin, Chan, Jackie, Acenas, Dante D, Lee, Jinwoo, Macrae, Trisha A, Kyaw, Than S, Wu, David, Ng, Dianna L, Gu, Wei, York, Vanessa A, Eskandarian, Haig Alexander, Callaway, Perri C, Warrier, Lakshmi, Moreno, Mary E, Levan, Justine, Torres, Leonel, Farrington, Lila A, Loudermilk, Rita P, Koshal, Kanishka, Zorn, Kelsey C, Garcia-Beltran, Wilfredo F, Yang, Diane, Astudillo, Michael G, Bernstein, Bradley E, Gelfand, Jeffrey A, Ryan, Edward T, Charles, Richelle C, Iafrate, A John, Lennerz, Jochen K, Miller, Steve, Chiu, Charles Y, Stramer, Susan L, Wilson, Michael R, Manglik, Aashish, Ye, Chun Jimmie, Krogan, Nevan J, Anderson, Mark S, Cyster, Jason G, Ernst, Joel D, Wu, Alan HB, Lynch, Kara L, Bern, Caryn, Hsu, Patrick D, and Marson, Alexander
- Subjects
Biological Sciences ,Biomedical and Clinical Sciences ,Clinical Sciences ,Biodefense ,Pneumonia & Influenza ,Prevention ,Clinical Research ,Infectious Diseases ,Lung ,Vaccine Related ,Pneumonia ,Emerging Infectious Diseases ,Detection ,screening and diagnosis ,4.1 Discovery and preclinical testing of markers and technologies ,4.2 Evaluation of markers and technologies ,Infection ,Good Health and Well Being ,Adult ,Aged ,Aged ,80 and over ,Antibodies ,Viral ,Betacoronavirus ,Biotechnology ,COVID-19 ,COVID-19 Testing ,Chromatography ,Affinity ,Clinical Laboratory Techniques ,Coronavirus Infections ,Enzyme-Linked Immunosorbent Assay ,Female ,Humans ,Immunoglobulin G ,Immunoglobulin M ,Male ,Middle Aged ,Pandemics ,Pneumonia ,Viral ,Point-of-Care Testing ,Reverse Transcriptase Polymerase Chain Reaction ,SARS-CoV-2 ,Sensitivity and Specificity ,Young Adult - Abstract
Appropriate use and interpretation of serological tests for assessments of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exposure, infection and potential immunity require accurate data on assay performance. We conducted a head-to-head evaluation of ten point-of-care-style lateral flow assays (LFAs) and two laboratory-based enzyme-linked immunosorbent assays to detect anti-SARS-CoV-2 IgM and IgG antibodies in 5-d time intervals from symptom onset and studied the specificity of each assay in pre-coronavirus disease 2019 specimens. The percent of seropositive individuals increased with time, peaking in the latest time interval tested (>20 d after symptom onset). Test specificity ranged from 84.3% to 100.0% and was predominantly affected by variability in IgM results. LFA specificity could be increased by considering weak bands as negative, but this decreased detection of antibodies (sensitivity) in a subset of SARS-CoV-2 real-time PCR-positive cases. Our results underline the importance of seropositivity threshold determination and reader training for reliable LFA deployment. Although there was no standout serological assay, four tests achieved more than 80% positivity at later time points tested and more than 95% specificity.
- Published
- 2020
31. Test performance evaluation of SARS-CoV-2 serological assays
- Author
-
Whitman, Jeffrey D, Hiatt, Joseph, Mowery, Cody T, Shy, Brian R, Yu, Ruby, Yamamoto, Tori N, Rathore, Ujjwal, Goldgof, Gregory M, Whitty, Caroline, Woo, Jonathan M, Gallman, Antonia E, Miller, Tyler E, Levine, Andrew G, Nguyen, David N, Bapat, Sagar P, Balcerek, Joanna, Bylsma, Sophia A, Lyons, Ana M, Li, Stacy, Wong, Allison Wai-yi, Gillis-Buck, Eva Mae, Steinhart, Zachary B, Lee, Youjin, Apathy, Ryan, Lipke, Mitchell J, Smith, Jennifer Anne, Zheng, Tina, Boothby, Ian C, Isaza, Erin, Chan, Jackie, Acenas, Dante D, Lee, Jinwoo, Macrae, Trisha A, Kyaw, Than S, Wu, David, Ng, Dianna L, Gu, Wei, York, Vanessa A, Eskandarian, Haig Alexander, Callaway, Perri C, Warrier, Lakshmi, Moreno, Mary E, Levan, Justine, Torres, Leonel, Farrington, Lila A, Loudermilk, Rita, Koshal, Kanishka, Zorn, Kelsey C, Garcia-Beltran, Wilfredo F, Yang, Diane, Astudillo, Michael G, Bernstein, Bradley E, Gelfand, Jeffrey A, Ryan, Edward T, Charles, Richelle C, Iafrate, A John, Lennerz, Jochen K, Miller, Steve, Chiu, Charles Y, Stramer, Susan L, Wilson, Michael R, Manglik, Aashish, Ye, Chun Jimmie, Krogan, Nevan J, Anderson, Mark S, Cyster, Jason G, Ernst, Joel D, Wu, Alan HB, Lynch, Kara L, Bern, Caryn, Hsu, Patrick D, and Marson, Alexander
- Subjects
Infectious Diseases ,Vaccine Related ,Clinical Research ,Pneumonia ,Lung ,Pneumonia & Influenza ,Biodefense ,Prevention ,Emerging Infectious Diseases ,Detection ,screening and diagnosis ,4.2 Evaluation of markers and technologies ,Infection ,Good Health and Well Being - Abstract
Background:Serological tests are crucial tools for assessments of SARS-CoV-2 exposure, infection and potential immunity. Their appropriate use and interpretation require accurate assay performance data. Method:We conducted an evaluation of 10 lateral flow assays (LFAs) and two ELISAs to detect anti-SARS-CoV-2 antibodies. The specimen set comprised 128 plasma or serum samples from 79 symptomatic SARS-CoV-2 RT-PCR-positive individuals; 108 pre-COVID-19 negative controls; and 52 recent samples from individuals who underwent respiratory viral testing but were not diagnosed with Coronavirus Disease 2019 (COVID-19). Samples were blinded and LFA results were interpreted by two independent readers, using a standardized intensity scoring system. Results:Among specimens from SARS-CoV-2 RT-PCR-positive individuals, the percent seropositive increased with time interval, peaking at 81.8-100.0% in samples taken >20 days after symptom onset. Test specificity ranged from 84.3-100.0% in pre-COVID-19 specimens. Specificity was higher when weak LFA bands were considered negative, but this decreased sensitivity. IgM detection was more variable than IgG, and detection was highest when IgM and IgG results were combined. Agreement between ELISAs and LFAs ranged from 75.7-94.8%. No consistent cross-reactivity was observed. Conclusion:Our evaluation showed heterogeneous assay performance. Reader training is key to reliable LFA performance, and can be tailored for survey goals. Informed use of serology will require evaluations covering the full spectrum of SARS-CoV-2 infections, from asymptomatic and mild infection to severe disease, and later convalescence. Well-designed studies to elucidate the mechanisms and serological correlates of protective immunity will be crucial to guide rational clinical and public health policies.
- Published
- 2020
32. Pooled Knockin Targeting for Genome Engineering of Cellular Immunotherapies
- Author
-
Roth, Theodore L, Li, P Jonathan, Blaeschke, Franziska, Nies, Jasper F, Apathy, Ryan, Mowery, Cody, Yu, Ruby, Nguyen, Michelle LT, Lee, Youjin, Truong, Anna, Hiatt, Joseph, Wu, David, Nguyen, David N, Goodman, Daniel, Bluestone, Jeffrey A, Ye, Chun Jimmie, Roybal, Kole, Shifrut, Eric, and Marson, Alexander
- Subjects
Biomedical and Clinical Sciences ,Oncology and Carcinogenesis ,Immunology ,Biotechnology ,Human Genome ,Immunization ,Genetics ,Gene Therapy ,Vaccine Related ,Cancer ,5.2 Cellular and gene therapies ,Underpinning research ,Development of treatments and therapeutic interventions ,1.1 Normal biological development and functioning ,Animals ,Blood Cells ,CRISPR-Cas Systems ,Clustered Regularly Interspaced Short Palindromic Repeats ,Gene Knock-In Techniques ,Genetic Engineering ,Humans ,Immunotherapy ,Mice ,Mice ,Inbred NOD ,Mice ,SCID ,RNA ,Guide ,Kinetoplastida ,Single-Cell Analysis ,T-Lymphocytes ,Transcriptome ,CRISPR ,cell therapy ,human T cell ,knockins ,pooled screen ,single-cell RNA-seq ,Biological Sciences ,Medical and Health Sciences ,Developmental Biology ,Biological sciences ,Biomedical and clinical sciences - Abstract
Adoptive transfer of genetically modified immune cells holds great promise for cancer immunotherapy. CRISPR knockin targeting can improve cell therapies, but more high-throughput methods are needed to test which knockin gene constructs most potently enhance primary cell functions in vivo. We developed a widely adaptable technology to barcode and track targeted integrations of large non-viral DNA templates and applied it to perform pooled knockin screens in primary human T cells. Pooled knockin of dozens of unique barcoded templates into the T cell receptor (TCR)-locus revealed gene constructs that enhanced fitness in vitro and in vivo. We further developed pooled knockin sequencing (PoKI-seq), combining single-cell transcriptome analysis and pooled knockin screening to measure cell abundance and cell state ex vivo and in vivo. This platform nominated a novel transforming growth factor β (TGF-β) R2-41BB chimeric receptor that improved solid tumor clearance. Pooled knockin screening enables parallelized re-writing of endogenous genetic sequences to accelerate discovery of knockin programs for cell therapies.
- Published
- 2020
33. Causal inference, social networks, and chain graphs
- Author
-
Ogburn, Elizabeth L., Shpitser, Ilya, and Lee, Youjin
- Subjects
Statistics - Methodology - Abstract
Traditionally, statistical and causal inference on human subjects rely on the assumption that individuals are independently affected by treatments or exposures. However, recently there has been increasing interest in settings, such as social networks, where individuals may interact with one another such that treatments may spill over from the treated individual to their social contacts and outcomes may be contagious. Existing models proposed for causal inference using observational data from networks of interacting individuals have two major shortcomings. First, they often require a level of granularity in the data that is practically infeasible to collect in most settings, and second, the models are high-dimensional and often too big to fit to the available data. In this paper we illustrate and justify a parsimonious parameterization for network data with interference and contagion. Our parameterization corresponds to a particular family of graphical models known as chain graphs. We argue that, in some settings, chain graph models approximate the marginal distribution of a snapshot of a longitudinal data generating process on interacting units. We illustrate the use of chain graphs for causal inference about collective decision making in social networks using data from U.S. Supreme Court decisions between 1994 and 2004 and in simulations.
- Published
- 2018
34. Quality improvement of outpatient clinical chemistry tests through a novel middleware-laboratory information system solution
- Author
-
Park, Minwoo, Kim, Young-Jin, Jung, Dawoon, Kim, Yeongsic, Kim, Hyun-Min, Lee, Youjin, and Choi, In Young
- Published
- 2023
- Full Text
- View/download PDF
35. A large CRISPR-induced bystander mutation causes immune dysregulation.
- Author
-
Simeonov, Dimitre R, Brandt, Alexander J, Chan, Alice Y, Cortez, Jessica T, Li, Zhongmei, Woo, Jonathan M, Lee, Youjin, Carvalho, Claudia MB, Indart, Alyssa C, Roth, Theodore L, Zou, James, May, Andrew P, Lupski, James R, Anderson, Mark S, Buaas, F William, Rokhsar, Daniel S, and Marson, Alexander
- Subjects
T-Lymphocytes ,Cells ,Cultured ,Animals ,Mice ,Inbred NOD ,DNA Damage ,DNA Repair ,Gene Expression Regulation ,Gene Duplication ,Base Sequence ,Mutation ,T-Lymphocytes ,Regulatory ,Interleukin-2 Receptor alpha Subunit ,CRISPR-Cas Systems ,Gene Editing ,Cells ,Cultured ,Mice ,Inbred NOD ,Regulatory - Abstract
A persistent concern with CRISPR-Cas9 gene editing has been the potential to generate mutations at off-target genomic sites. While CRISPR-engineering mice to delete a ~360 bp intronic enhancer, here we discovered a founder line that had marked immune dysregulation caused by a 24 kb tandem duplication of the sequence adjacent to the on-target deletion. Our results suggest unintended repair of on-target genomic cuts can cause pathogenic "bystander" mutations that escape detection by routine targeted genotyping assays.
- Published
- 2019
36. Testing for Network and Spatial Autocorrelation
- Author
-
Lee, Youjin and Ogburn, Elizabeth L.
- Subjects
Statistics - Applications - Abstract
Testing for dependence has been a well-established component of spatial statistical analyses for decades. In particular, several popular test statistics have desirable properties for testing for the presence of spatial autocorrelation in continuous variables. In this paper we propose two contributions to the literature on tests for autocorrelation. First, we propose a new test for autocorrelation in categorical variables. While some methods currently exist for assessing spatial autocorrelation in categorical variables, the most popular method is unwieldy, somewhat ad hoc, and fails to provide grounds for a single omnibus test. Second, we discuss the importance of testing for autocorrelation in data sampled from the nodes of a network, motivated by social network applications. We demonstrate that our proposed statistic for categorical variables can both be used in the spatial and network setting.
- Published
- 2017
- Full Text
- View/download PDF
37. Network Dependence Testing via Diffusion Maps and Distance-Based Correlations
- Author
-
Lee, Youjin, Shen, Cencheng, Priebe, Carey E., and Vogelstein, Joshua T.
- Subjects
Statistics - Methodology - Abstract
Deciphering the associations between network connectivity and nodal attributes is one of the core problems in network science. The dependency structure and high-dimensionality of networks pose unique challenges to traditional dependency tests in terms of theoretical guarantees and empirical performance. We propose an approach to test network dependence via diffusion maps and distance-based correlations. We prove that the new method yields a consistent test statistic under mild distributional assumptions on the graph structure, and demonstrate that it is able to efficiently identify the most informative graph embedding with respect to the diffusion time. The methodology is illustrated on both simulated and real data.
- Published
- 2017
- Full Text
- View/download PDF
38. Syngas production for Fischer-Tropsch process via co-electrolytic processes of CO2 reduction and NH3 oxidation
- Author
-
Choi, Minjun, Kim, Jin Won, Chung, Sunki, Lee, Youjin, Bong, Sungyool, and Lee, Jaeyoung
- Published
- 2022
- Full Text
- View/download PDF
39. Testing for Network and Spatial Autocorrelation
- Author
-
Lee, Youjin, Ogburn, Elizabeth L., Masuda, Naoki, editor, Goh, Kwang-Il, editor, Jia, Tao, editor, Yamanoi, Junichi, editor, and Sayama, Hiroki, editor
- Published
- 2020
- Full Text
- View/download PDF
40. Discovery of stimulation-responsive immune enhancers with CRISPR activation
- Author
-
Simeonov, Dimitre R, Gowen, Benjamin G, Boontanrart, Mandy, Roth, Theodore L, Gagnon, John D, Mumbach, Maxwell R, Satpathy, Ansuman T, Lee, Youjin, Bray, Nicolas L, Chan, Alice Y, Lituiev, Dmytro S, Nguyen, Michelle L, Gate, Rachel E, Subramaniam, Meena, Li, Zhongmei, Woo, Jonathan M, Mitros, Therese, Ray, Graham J, Curie, Gemma L, Naddaf, Nicki, Chu, Julia S, Ma, Hong, Boyer, Eric, Van Gool, Frederic, Huang, Hailiang, Liu, Ruize, Tobin, Victoria R, Schumann, Kathrin, Daly, Mark J, Farh, Kyle K, Ansel, K Mark, Ye, Chun J, Greenleaf, William J, Anderson, Mark S, Bluestone, Jeffrey A, Chang, Howard Y, Corn, Jacob E, and Marson, Alexander
- Subjects
Biological Sciences ,Biomedical and Clinical Sciences ,Immunology ,Human Genome ,Genetics ,Autoimmune Disease ,Animals ,Antigens ,CD ,Antigens ,Differentiation ,T-Lymphocyte ,Autoimmunity ,CRISPR-Cas Systems ,Cell Differentiation ,Cell Line ,Chromatin ,Clustered Regularly Interspaced Short Palindromic Repeats ,Enhancer Elements ,Genetic ,Female ,Gene Expression Regulation ,Humans ,Interleukin-2 Receptor alpha Subunit ,Lectins ,C-Type ,Mice ,Receptors ,Antigen ,T-Cell ,Th17 Cells ,General Science & Technology - Abstract
The majority of genetic variants associated with common human diseases map to enhancers, non-coding elements that shape cell-type-specific transcriptional programs and responses to extracellular cues. Systematic mapping of functional enhancers and their biological contexts is required to understand the mechanisms by which variation in non-coding genetic sequences contributes to disease. Functional enhancers can be mapped by genomic sequence disruption, but this approach is limited to the subset of enhancers that are necessary in the particular cellular context being studied. We hypothesized that recruitment of a strong transcriptional activator to an enhancer would be sufficient to drive target gene expression, even if that enhancer was not currently active in the assayed cells. Here we describe a discovery platform that can identify stimulus-responsive enhancers for a target gene independent of stimulus exposure. We used tiled CRISPR activation (CRISPRa) to synthetically recruit a transcriptional activator to sites across large genomic regions (more than 100 kilobases) surrounding two key autoimmunity risk loci, CD69 and IL2RA. We identified several CRISPRa-responsive elements with chromatin features of stimulus-responsive enhancers, including an IL2RA enhancer that harbours an autoimmunity risk variant. Using engineered mouse models, we found that sequence perturbation of the disease-associated Il2ra enhancer did not entirely block Il2ra expression, but rather delayed the timing of gene activation in response to specific extracellular signals. Enhancer deletion skewed polarization of naive T cells towards a pro-inflammatory T helper (TH17) cell state and away from a regulatory T cell state. This integrated approach identifies functional enhancers and reveals how non-coding variation associated with human immune dysfunction alters context-specific gene programs.
- Published
- 2017
41. Temperature-Dependent Hole Transfer from Photoexcited Quantum Dots to Molecular Species: Evidence for Trap-Mediated Transfer
- Author
-
Olshansky, Jacob H, Balan, Arunima D, Ding, Tina X, Fu, Xiao, Lee, Youjin V, and Alivisatos, A Paul
- Subjects
Engineering ,Nanotechnology ,quantum dots ,charge transfer ,cadmium selenide ,hole traps ,temperature dependence ,ferrocene ,Nanoscience & Nanotechnology - Abstract
The effect of temperature on the rate of hole transfer from photoexcited quantum dots (QDs) is investigated by measuring the driving force dependence of the charge transfer rate for different sized QDs across a range of temperatures from 78 to 300 K. Spherical CdSe/CdS core/shell QDs were used with a series of ferrocene-derived molecular hole acceptors with an 800 meV range in electrochemical potential. Time-resolved photoluminescence measurements and photoluminescence quantum yield measurements in an integrating sphere were both performed from 78 to 300 K to obtain temperature-dependent rates for a series of driving forces as dictated by the nature of the molecular acceptor. For both QD sizes studied and all ligands, the Arrhenius plot of hole transfer exhibited an activated (linear) regime at higher temperatures and a temperature-independent regime at low temperatures. The extracted activation energies in the high-temperature regime were consistent across all ligands for a given QD size. This observation is not consistent with direct charge transfer from the QD valence band to the ferrocene acceptor. Instead, a model in which charge transfer is mediated by a shallow and reversible trap more accurately fits the experimental results. Implications for this observed trap-mediated transfer are discussed including as a strategy to more efficiently extract charge from QDs.
- Published
- 2017
42. Effect of Thermal Fluctuations on the Radiative Rate in Core/Shell Quantum Dots
- Author
-
Balan, Arunima D, Eshet, Hagai, Olshansky, Jacob H, Lee, Youjin V, Rabani, Eran, and Alivisatos, A Paul
- Subjects
Chemical Sciences ,Physical Chemistry ,Engineering ,Physical Sciences ,Nanotechnology ,Core/shell quantum dots ,temperature-dependent lifetime ,exciton dynamics ,electronic structure ,Nanoscience & Nanotechnology - Abstract
The effect of lattice fluctuations and electronic excitations on the radiative rate is demonstrated in CdSe/CdS core/shell spherical quantum dots (QDs). Using a combination of time-resolved photoluminescence spectroscopy and atomistic simulations, we show that lattice fluctuations can change the radiative rate over the temperature range from 78 to 300 K. We posit that the presence of the core/shell interface plays a significant role in dictating this behavior. We show that the other major factor that underpins the change in radiative rate with temperature is the presence of higher energy states corresponding to electron excitation into the shell. These effects should be present in other core/shell samples and should also affect other excited state rates, such as the rate of Auger recombination or the rate of charge transfer.
- Published
- 2017
43. Prognostic score‐based methods for estimating center effects based on survival probability: Application to post‐kidney transplant survival.
- Author
-
Lee, Youjin, Reese, Peter P., Tran, Amelia H., and Schaubel, Douglas E.
- Subjects
- *
KIDNEY transplantation , *SURVIVAL rate , *GRAFT survival , *PROBABILITY theory - Abstract
In evaluating the performance of different facilities or centers on survival outcomes, the standardized mortality ratio (SMR), which compares the observed to expected mortality has been widely used, particularly in the evaluation of kidney transplant centers. Despite its utility, the SMR may exaggerate center effects in settings where survival probability is relatively high. An example is one‐year graft survival among U.S. kidney transplant recipients. We propose a novel approach to estimate center effects in terms of differences in survival probability (ie, each center versus a reference population). An essential component of the method is a prognostic score weighting technique, which permits accurately evaluating centers without necessarily specifying a correct survival model. Advantages of our approach over existing facility‐profiling methods include a metric based on survival probability (greater clinical relevance than ratios of counts/rates); direct standardization (valid to compare between centers, unlike indirect standardization based methods, such as the SMR); and less reliance on correct model specification (since the assumed model is used to generate risk classes as opposed to fitted‐value based 'expected' counts). We establish the asymptotic properties of the proposed weighted estimator and evaluate its finite‐sample performance under a diverse set of simulation settings. The method is then applied to evaluate U.S. kidney transplant centers with respect to graft survival probability. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
44. Conversion of Layered WS2 Crystals into Mixed‐Domain Electrochemical Catalysts by Plasma‐Assisted Surface Reconstruction.
- Author
-
Park, Jiheon, Cho, Iaan, Jeon, Hotae, Lee, Youjin, Zhang, Jian, Lee, Dongwook, Cho, Min Kyung, Preston, Daniel J., Shong, Bonggeun, Kim, In Soo, and Lee, Won‐Kyu
- Published
- 2024
- Full Text
- View/download PDF
45. Snowflake relocated Cu2O electrocatalyst on Ag backbone template for the production of liquid C2+ chemicals from CO2
- Author
-
Lee, Youjin, primary, Choi, Minjun, additional, Bae, Sooan, additional, Tayal, Akhil, additional, Seo, Okkyun, additional, Lim, Hojoon, additional, Lee, Kug-Seung, additional, Jang, Jae Hyuck, additional, Jeong, Beomgyun, additional, and Lee, Jaeyoung, additional
- Published
- 2024
- Full Text
- View/download PDF
46. Amygdala electrical stimulation for operant conditioning in rat navigation
- Author
-
Lee, Youjin, primary, Kim, Soonyoung, additional, Cho, Yoon Kyung, additional, Kong, Chanho, additional, Chang, Jin Woo, additional, and Jun, Sang Beom, additional
- Published
- 2023
- Full Text
- View/download PDF
47. Joint modelling of competing risks and current status data : an application to a spontaneous labour study
- Author
-
Lee, Youjin, Wang, Mei-Cheng, Grantz, Katherine L., and Sundaram, Rajeshwari
- Published
- 2019
48. Hole Transfer from Photoexcited Quantum Dots: The Relationship between Driving Force and Rate
- Author
-
Olshansky, Jacob H., Ding, Tina X., Lee, Youjin V., Leone, Stephen R., and Alivisatos, A. Paul
- Published
- 2015
49. CRISPR screen in regulatory T cells reveals modulators of Foxp3
- Author
-
Cortez, Jessica T., Montauti, Elena, Shifrut, Eric, Gatchalian, Jovylyn, Zhang, Yusi, Shaked, Oren, Xu, Yuanming, Roth, Theodore L., Simeonov, Dimitre R., Zhang, Yana, Chen, Siqi, Li, Zhongmei, Woo, Jonathan M., Ho, Josephine, Vogel, Ian A., Prator, Grace Y., Zhang, Bin, Lee, Youjin, Sun, Zhaolin, Ifergan, Igal, Van Gool, Frédéric, Hargreaves, Diana C., Bluestone, Jeffrey A., Marson, Alexander, and Fang, Deyu
- Published
- 2020
- Full Text
- View/download PDF
50. Altered cofactor regulation with disease-associated p97/VCP mutations
- Author
-
Zhang, Xiaoyi, Gui, Lin, Zhang, Xiaoyan, Bulfer, Stacie L, Sanghez, Valentina, Wong, Daniel E, Lee, YouJin, Lehmann, Lynn, Lee, James Siho, Shih, Pei-Yin, Lin, Henry J, Iacovino, Michelina, Weihl, Conrad C, Arkin, Michelle R, Wang, Yanzhuang, and Chou, Tsui-Fen
- Subjects
Neurodegenerative ,2.1 Biological and endogenous factors ,Aetiology ,Adaptor Proteins ,Signal Transducing ,Adenosine Triphosphatases ,Adenosine Triphosphate ,Autophagy ,Bone Diseases ,Cell Cycle Proteins ,Cell Line ,Tumor ,Chromatography ,Gel ,Golgi Apparatus ,Homeostasis ,Humans ,Muscular Diseases ,Mutation ,Neurodegenerative Diseases ,Phenotype ,Protein Structure ,Tertiary ,Surface Plasmon Resonance ,Valosin Containing Protein ,AAA ATPase ,p97/VCP ,MSP1 ,p47 ,steady-state kinetics - Abstract
Dominant mutations in p97/VCP (valosin-containing protein) cause a rare multisystem degenerative disease with varied phenotypes that include inclusion body myopathy, Paget's disease of bone, frontotemporal dementia, and amyotrophic lateral sclerosis. p97 disease mutants have altered N-domain conformations, elevated ATPase activity, and altered cofactor association. We have now discovered a previously unidentified disease-relevant functional property of p97 by identifying how the cofactors p37 and p47 regulate p97 ATPase activity. We define p37 as, to our knowledge, the first known p97-activating cofactor, which enhances the catalytic efficiency (kcat/Km) of p97 by 11-fold. Whereas both p37 and p47 decrease the Km of ATP in p97, p37 increases the kcat of p97. In contrast, regulation by p47 is biphasic, with decreased kcat at low levels but increased kcat at higher levels. By deleting a region of p47 that lacks homology to p37 (amino acids 69-92), we changed p47 from an inhibitory cofactor to an activating cofactor, similar to p37. Our data suggest that cofactors regulate p97 ATPase activity by binding to the N domain. Induced conformation changes affect ADP/ATP binding at the D1 domain, which in turn controls ATPase cycling. Most importantly, we found that the D2 domain of disease mutants failed to be activated by p37 or p47. Our results show that cofactors play a critical role in controlling p97 ATPase activity, and suggest that lack of cofactor-regulated communication may contribute to p97-associated disease pathogenesis.
- Published
- 2015
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.