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Article ; Online: Quantitative Measurement of Tau Aggregation in Genetically Modified Rats with Neurodegeneration.

Lee, YouJin / Morrow, Eric M

Methods in molecular biology (Clifton, N.J.)

2024 Volume 2761, Page(s) 291–299

Abstract: Animal models of neurodegenerative diseases have helped us to better understand the pathogenesis of neurodegenerative diseases. However, recent failure to translate pre-clinical model studies to the clinic urges us to develop more rigorous and faithful ... ...

Abstract	Animal models of neurodegenerative diseases have helped us to better understand the pathogenesis of neurodegenerative diseases. However, recent failure to translate pre-clinical model studies to the clinic urges us to develop more rigorous and faithful animal models in neurodegenerative diseases. As genetic manipulation of rats becomes much more accessible due to availability of CRISPR-Cas9 and other genomic editing toolboxes, rats have been emerging as a new model system for neurodegenerative diseases. Even though mouse models have been dominant over the last decades, rats may provide advantages over mice. Rats are more genetically and physiologically closer to humans than to mice. Also, certain rat models can represent deposition of tau, which is one of the key pathological features of Alzheimer's diseases and tauopathies. However, there is an unmet need for standardized, rigorous testing in rat models. We adopted two commonly used biochemical and immunofluorescence methods from mice and human postmortem brains to measure tau aggregation. Due to the intrinsic differences between mice and rats, e.g., size of rat brains, certain equipment is required for rat models to study tau pathologies. Along with specific tools, here we describe the detailed methods for rat models of neurodegenerative diseases.
MeSH term(s)	Animals ; Rats ; Mice ; Humans ; tau Proteins/genetics ; tau Proteins/metabolism ; Tauopathies/genetics ; Tauopathies/pathology ; Alzheimer Disease/genetics ; Alzheimer Disease/pathology ; Neurodegenerative Diseases/genetics ; Neurodegenerative Diseases/pathology ; Brain/metabolism ; Disease Models, Animal
Chemical Substances	tau Proteins
Language	English
Publishing date	2024-03-01
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-3662-6_21
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Calculating risk and prevalence ratios and differences in R: developing intuition with a hands-on tutorial and code.

Yorlets, Rachel R / Lee, Youjin / Gantenberg, Jason R

Annals of epidemiology

2023 Volume 86, Page(s) 104–109

Abstract: Epidemiologic research questions often focus on evaluating binary outcomes, yet curricula and scientific literature do not always provide clear guidance or examples on selecting and calculating an appropriate measure of association in these scenarios. ... ...

Abstract	Epidemiologic research questions often focus on evaluating binary outcomes, yet curricula and scientific literature do not always provide clear guidance or examples on selecting and calculating an appropriate measure of association in these scenarios. Reporting inappropriate measures may lead to misleading statistical conclusions. We present a hands-on tutorial that includes annotated code written in an open-source statistical programming language (R) showing readers how to apply, compare, and understand four methods used to estimate a risk or prevalence ratio (or difference), rather than presenting an odds ratio. We will provide guidance on when to use each method, discussing the strengths and limitations of each approach, and compare the results obtained across them. Ultimately, we aim to help trainees, public health researchers, and interdisciplinary professionals develop an intuition for these methods and empower them to implement and interpret these methods in their own research.
MeSH term(s)	Humans ; Logistic Models ; Prevalence ; Intuition ; Odds Ratio
Language	English
Publishing date	2023-08-10
Publishing country	United States
Document type	Journal Article
ZDB-ID	1074355-8
ISSN	1873-2585 ; 1047-2797
ISSN (online)	1873-2585
ISSN	1047-2797
DOI	10.1016/j.annepidem.2023.08.001
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Zs.A 3225: Show issues

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Article ; Online: Facility profiling under competing risks using multivariate prognostic scores: Application to kidneytransplant centers.

Lee, Youjin / Schaubel, Douglas E

Statistical methods in medical research

2021 Volume 31, Issue 3, Page(s) 563–575

Abstract: The performance of health care facilities (e.g. hospitals, transplant centers, etc.) is often evaluated through time-to-event outcomes. In this paper, we consider the case where, for each subject, the failure event is due to one of several mutually ... ...

Abstract	The performance of health care facilities (e.g. hospitals, transplant centers, etc.) is often evaluated through time-to-event outcomes. In this paper, we consider the case where, for each subject, the failure event is due to one of several mutually exclusive causes (competing risks). Since the distribution of patient characteristics may differ greatly by the center, some form of covariate adjustment is generally necessary in order for center-specific outcomes to be accurately compared (to each other or to an overall average). We propose a weighting method for comparing facility-specific cumulative incidence functions to an overall average. The method directly standardizes each facility's non-parametric cumulative incidence function through a weight function constructed from a multivariate prognostic score. We formally define the center effects and derive large-sample properties of the proposed estimator. We evaluate the finite sample performance of the estimator through simulation. The proposed method is applied to the end-stage renal disease setting to evaluate the center-specific pre-transplant mortality and transplant cumulative incidence functions from the Scientific Registry of Transplant Recipients.
MeSH term(s)	Computer Simulation ; Female ; Humans ; Incidence ; Kidney Failure, Chronic ; Male ; Prognosis ; Research Design
Language	English
Publishing date	2021-12-08
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1136948-6
ISSN	1477-0334 ; 0962-2802
ISSN (online)	1477-0334
ISSN	0962-2802
DOI	10.1177/09622802211052873
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Zs.A 3564: Show issues

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Article ; Online: Egg microneedles for transdermal vaccination of inactivated influenza virus.

Kang, Geonwoo / Kim, Minkyung / Lee, Youjin / Yang, Huisuk / Seong, Baik-Lin / Jung, Hyungil

Biomaterials science

2024 Volume 12, Issue 4, Page(s) 907–918

Abstract: The use of dissolving microneedles (DMNs) is a drug delivery technique in which drug dissolution occurs once it is administered into the skin. The skin is a remarkable site for vaccination due to its significant immunologic properties. Compared to the ... ...

Abstract	The use of dissolving microneedles (DMNs) is a drug delivery technique in which drug dissolution occurs once it is administered into the skin. The skin is a remarkable site for vaccination due to its significant immunologic properties. Compared to the traditional hypodermic intramuscular (IM) injection, vaccination
MeSH term(s)	Animals ; Mice ; Injections, Intradermal ; Vaccination/methods ; Skin ; Influenza Vaccines ; Orthomyxoviridae ; Drug Delivery Systems
Chemical Substances	Influenza Vaccines
Language	English
Publishing date	2024-02-13
Publishing country	England
Document type	Journal Article
ZDB-ID	2693928-9
ISSN	2047-4849 ; 2047-4830
ISSN (online)	2047-4849
ISSN	2047-4830
DOI	10.1039/d3bm01635h
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Article ; Online: Network Dependence Can Lead to Spurious Associations and Invalid Inference

Lee, Youjin / Ogburn, Elizabeth L.

Journal of the American Statistical Association. 2021 July 3, v. 116, no. 535 p.1060-1074

2021

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 ... ...

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. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.
Keywords	autocorrelation ; coronary disease ; medicine ; psychology ; social networks ; statistical inference ; variance ; Confounding ; Replication ; Statistical dependence
Language	English
Dates of publication	2021-0703
Size	p. 1060-1074.
Publishing place	Taylor & Francis
Document type	Article ; Online
ZDB-ID	2064981-2
ISSN	1537-274X
ISSN	1537-274X
DOI	10.1080/01621459.2020.1782219
Database	NAL-Catalogue (AGRICOLA)

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Article: Potential Probiotic

Lee, Youjin / Werlinger, Pia / Suh, Joo-Won / Cheng, Jinhua

Microorganisms

2022 Volume 10, Issue 5

Abstract: Hyperuricemia is a metabolic disorder caused by increased uric acid (UA) synthesis or decreased UA excretion. Changes in eating habits have led to an increase in the consumption of purine-rich foods, which is closely related to hyperuricemia. Therefore, ... ...

Abstract	Hyperuricemia is a metabolic disorder caused by increased uric acid (UA) synthesis or decreased UA excretion. Changes in eating habits have led to an increase in the consumption of purine-rich foods, which is closely related to hyperuricemia. Therefore, decreased purine absorption, increased UA excretion, and decreased UA synthesis are the main strategies to ameliorate hyperuricemia. This study aimed to screen the lactic acid bacteria (LAB) with purine degrading ability and examine the serum UA-lowering effect in a hyperuricemia mouse model. As a result,
Language	English
Publishing date	2022-04-20
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2720891-6
ISSN	2076-2607
ISSN	2076-2607
DOI	10.3390/microorganisms10050851
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Article ; Online: Amygdala electrical stimulation for operant conditioning in rat navigation.

Lee, Youjin / Kim, Soonyoung / Cho, Yoon Kyung / Kong, Chanho / Chang, Jin Woo / Jun, Sang Beom

Biomedical engineering letters

2023 Volume 14, Issue 2, Page(s) 291–306

Abstract: There have been several attempts to navigate the locomotion of animals by neuromodulation. The most common method is animal training with electrical brain stimulation for directional cues and rewards; the basic principle is to activate dopamine-mediated ... ...

Abstract	There have been several attempts to navigate the locomotion of animals by neuromodulation. The most common method is animal training with electrical brain stimulation for directional cues and rewards; the basic principle is to activate dopamine-mediated neural reward pathways such as the medial forebrain bundle (MFB) when the animal correctly follows the external commands. In this study, the amygdala, which is the brain region responsible for fear modulation, was targeted for punishment training. The brain regions of MFB, amygdala, and barrel cortex were electrically stimulated for reward, punishment, and directional cues, respectively. Electrical stimulation was applied to the amygdala of rats when they failed to follow directional commands. First, two different amygdala regions, i.e., basolateral amygdala (BLA) and central amygdala (CeA), were stimulated and compared in terms of behavior responses, success and correction rates for training, and gene expression for learning and memory. Then, the training was performed in three groups: group R (MFB stimulation for reward), group P (BLA stimulation for punishment), and group RP (both MFB and BLA stimulation for reward and punishment). In group P, after the training, RNA sequencing was conducted to detect gene expression and demonstrate the effect of punishment learning. Group P showed higher success rates than group R, and group RP exhibited the most effective locomotion control among the three groups. Gene expression results imply that BLA stimulation can be more effective as a punishment in the learning process than CeA stimulation. We developed a new method to navigate rat locomotion behaviors by applying amygdala stimulation.
Language	English
Publishing date	2023-12-23
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2602422-6
ISSN	2093-985X ; 2093-9868
ISSN (online)	2093-985X
ISSN	2093-9868
DOI	10.1007/s13534-023-00336-1
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Article ; Online: Learning from Solar Energy Conversion: Biointerfaces for Artificial Photosynthesis and Biological Modulation.

Lee, Youjin V / Tian, Bozhi

Nano letters

2019 Volume 19, Issue 4, Page(s) 2189–2197

Abstract: Three seemingly distinct directions of nanomaterials research, photovoltaics, biofuel production, and biological modulation, have been sequentially developed over the past several decades. In this Mini Review, we discuss how the insights gleaned from ... ...

Abstract	Three seemingly distinct directions of nanomaterials research, photovoltaics, biofuel production, and biological modulation, have been sequentially developed over the past several decades. In this Mini Review, we discuss how the insights gleaned from nanomaterials-based solar energy conversion can be adapted to biointerface designs. Because of their size- and shape-dependent optical properties and excellent synthetic control, nanomaterials have shown unique technological advantages as the light absorbers or energy transducers. Biocompatible nanomaterials have also been incorporated into biological systems including biomolecules, bacteria, and eukaryotic cells for a large collection of fundamental studies and applications. For the photocatalytic biofuel production, either isolated bacterial enzymes or the entire bacteria have been hybridized with the nanomaterials, where functions from both parts are synergistically integrated. Likewise, interfacing nanomaterials with eukaryotic systems, whether in individual cells or tissues, has enabled optical modulation of cellular behavior and the construction of active cellular materials. Here we survey different approaches in which nanomaterials are used to elicit electrical or mechanical changes in single cells or cellular assemblies via photoelectrochemical or photothermal processes. We end this Mini Review with the discussion of future nongenetic modulation at the intracellular level.
MeSH term(s)	Bacteria ; Biocompatible Materials/chemistry ; Biofuels ; Catalysis ; Electron Transport ; Eukaryota ; Nanostructures/chemistry ; Photosynthesis ; Solar Energy ; Sunlight
Chemical Substances	Biocompatible Materials ; Biofuels
Language	English
Publishing date	2019-03-21
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ISSN	1530-6992
ISSN (online)	1530-6992
DOI	10.1021/acs.nanolett.9b00388
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Article ; Online: Doubly robust nonparametric instrumental variable estimators for survival outcomes.

Lee, Youjin / Kennedy, Edward H / Mitra, Nandita

Biostatistics (Oxford, England)

2021 Volume 24, Issue 2, Page(s) 518–537

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 ...

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 article, we propose nonparametric estimators for the local average treatment effect on survival probabilities under both covariate-dependent and outcome-dependent 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 double robustness 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.
MeSH term(s)	Humans ; Computer Simulation ; Causality ; Probability
Language	English
Publishing date	2021-11-18
Publishing country	England
Document type	Journal Article
ZDB-ID	2031500-4
ISSN	1468-4357 ; 1465-4644
ISSN (online)	1468-4357
ISSN	1465-4644
DOI	10.1093/biostatistics/kxab036
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Zs.A 6259: Show issues

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Article ; Online: Time-of-flight detection of terahertz phonon-polariton.

Luo, Tianchuang / Ilyas, Batyr / Hoegen, A von / Lee, Youjin / Park, Jaena / Park, Je-Geun / Gedik, Nuh

Nature communications

2024 Volume 15, Issue 1, Page(s) 2276

Abstract: A polariton is a fundamental quasiparticle that arises from strong light-matter interaction and as such has attracted wide scientific and practical interest. When light is strongly coupled to the crystal lattice, it gives rise to phonon-polaritons (PPs), ...

Abstract	A polariton is a fundamental quasiparticle that arises from strong light-matter interaction and as such has attracted wide scientific and practical interest. When light is strongly coupled to the crystal lattice, it gives rise to phonon-polaritons (PPs), which have been proven useful in the dynamical manipulation of quantum materials and the advancement of terahertz technologies. Yet, current detection and characterization methods of polaritons are still limited. Traditional techniques such as Raman or transient grating either rely on fine-tuning of external parameters or complex phase extraction techniques. To overcome these inherent limitations, we propose and demonstrate a technique based on a time-of-flight measurement of PPs. We resonantly launch broadband PPs with intense terahertz fields and measure the time-of-flight of each spectral component with time-resolved second harmonic generation. The time-of-flight information, combined with the PP attenuation, enables us to resolve the real and imaginary parts of the PP dispersion relation. We demonstrate this technique in the van der Waals magnets NiI
Language	English
Publishing date	2024-03-13
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-46515-1
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