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306 results on '"Wu, P-E"'

1. Fertility protection during chemotherapy treatment by boosting the NAD(P)+ metabolome

Author

Ho, Wing-Hong Jonathan, Marinova, Maria B, Listijono, Dave R, Bertoldo, Michael J, Richani, Dulama, Kim, Lynn-Jee, Brown, Amelia, Riepsamen, Angelique H, Cabot, Safaa, Frost, Emily R, Bustamante, Sonia, Zhong, Ling, Selesniemi, Kaisa, Wong, Derek, Madawala, Romanthi, Marchante, Maria, Goss, Dale M, Li, Catherine, Araki, Toshiyuki, Livingston, David J, Turner, Nigel, Sinclair, David A, Walters, Kirsty A, Homer, Hayden A, Gilchrist, Robert B, and Wu, Lindsay E

Published
2024
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2. What Determines the Boundaries of H2O Maser Emission in an X-ray Illuminated Gas Disk ?

Author

Kuo, C. Y., Gao, F., Braatz, J. A., Pesce, D. W., Humphreys, E. M. L., Reid, M. J., Impellizzeri, C. M. V., Henkel, C., Wagner, J., and Wu, C. E.

Subjects
Astrophysics - Astrophysics of Galaxies, Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract

High precision mapping of H2O megamaser emission from active galaxies has revealed more than a dozen Keplerian H2O maser disks, which enable a ~4% uncertainty estimate of the Hubble constant as well as providing accurate masses for the central black holes. These disks often have well-defined inner and outer boundaries of maser emission on sub-parsec scales. In order to better understand the physical conditions that determine the inner and outer radii of a maser disk, we examine the distributions of gas density and X-ray heating rate in a warped molecular disk described by a power-law surface density profile. For a suitable choice of the disk mass, we find that the outer radius R_out of the maser disk predicted from our model can match the observed value, with R_out mainly determined by the maximum heating rate or the minimum density for efficient maser action, depending on the combination of the Eddington ratio, black hole mass, and disk mass. Our analysis also indicates that the inner radius for maser action is comparable to the dust sublimation radius, suggesting that dust may play a role in determining the inner radius of a maser disk. Finally, our model predicts that H2O gigamaser disks could exist at the centers of high-z quasars, with disk sizes of >~ 10-30 pc., Comment: Accepted by MNRAS, 17 pages, 8 figures, 2 tables

Published
2023

6. Rapidly improving ARDS differs clinically and biologically from persistent ARDS

Author

Valda Toro, Patricia L., Willmore, Andrew, Wu, Nelson E., Delucchi, Kevin L., Jauregui, Alejandra, Sinha, Pratik, Liu, Kathleen D., Hendrickson, Carolyn M., Sarma, Aartik, Neyton, Lucile P. A., Leligdowicz, Aleksandra, Langelier, Charles R., Zhuo, Hanjing, Jones, Chayse, Kangelaris, Kirsten N., Gomez, Antonio D., Matthay, Michael A., and Calfee, Carolyn S.

Published
2024
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9. Protein structure generation via folding diffusion

Author

Wu, Kevin E., Yang, Kevin K., Berg, Rianne van den, Zou, James Y., Lu, Alex X., and Amini, Ava P.

Subjects
Quantitative Biology - Biomolecules, Computer Science - Artificial Intelligence, I.2.0, J.3
Abstract

The ability to computationally generate novel yet physically foldable protein structures could lead to new biological discoveries and new treatments targeting yet incurable diseases. Despite recent advances in protein structure prediction, directly generating diverse, novel protein structures from neural networks remains difficult. In this work, we present a new diffusion-based generative model that designs protein backbone structures via a procedure that mirrors the native folding process. We describe protein backbone structure as a series of consecutive angles capturing the relative orientation of the constituent amino acid residues, and generate new structures by denoising from a random, unfolded state towards a stable folded structure. Not only does this mirror how proteins biologically twist into energetically favorable conformations, the inherent shift and rotational invariance of this representation crucially alleviates the need for complex equivariant networks. We train a denoising diffusion probabilistic model with a simple transformer backbone and demonstrate that our resulting model unconditionally generates highly realistic protein structures with complexity and structural patterns akin to those of naturally-occurring proteins. As a useful resource, we release the first open-source codebase and trained models for protein structure diffusion.

Published
2022

11. Identification of chromosome ploidy and analysis of breeding system of different Rosa odorata

Author

HOU Qiumei, ZHOU Yan, YANG Shuo, ZHANG Jiajia, ZHOU Hongying, and WU Hong􀆳e

Subjects
rosa odorata, chromosome ploidy, floral syndrome, breeding system, Biology (General), QH301-705.5, Botany, QK1-989
Abstract

Abstract [Objective] Rosa odorata is an important germplasm resource of Rosa, which has high value of appreciation and utilization. In order to promote the development and utilization of the germplasm resources, the chromosome ploidy, floral synthesis, and characteristics of breeding systems of different R. odorata were studied. [Methods] The chromosome ploidy, pollen vitality, stigma vitality, and flower characteristics of 9 R. odorata were observed and determined by flow cytometer and outcrossing analysis. We also analyzed the breeding systems. [Results] (1) 9 R. odorata were identified as diploid, and their flowers were bisexual with bright colors and mostly double or semi-double petals. Male and female flowers of 5 varieties were matured at different time. (2) 9 R. odorata pollen vitalities were low, with the highest vitality of 35.47%. The outcrossing index (OCI) of all varieties was ≥4, and pollen volume-ovule ratio (P/O) values ranged from 6 709 to 75 521. [Conclusion] The breeding system of 9 R. odorata is mainly outcrossing, and the breeding system is affected by many factors, such as the number of pollen grains and petals.

Published
2024
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14. Use of Machine Learning for Dosage Individualization of Vancomycin in Neonates

Author

Tang, Bo-Hao, Zhang, Jin-Yuan, Allegaert, Karel, Hao, Guo-Xiang, Yao, Bu-Fan, Leroux, Stephanie, Thomson, Alison H., Yu, Ze, Gao, Fei, Zheng, Yi, Zhou, Yue, Capparelli, Edmund V., Biran, Valerie, Simon, Nicolas, Meibohm, Bernd, Lo, Yoke-Lin, Marques, Remedios, Peris, Jose-Esteban, Lutsar, Irja, Saito, Jumpei, Jacqz-Aigrain, Evelyne, van den Anker, John, Wu, Yue-E., and Zhao, Wei

Published
2023
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16. Emotion Regulation, Parasympathetic Function, and Psychological Well-Being.

Author

Brown, Ryan, Chen, Michelle, Paoletti, Jensine, Dicker, Eva, Wu-Chung, E, LeRoy, Angie, Majd, Marzieh, Suchting, Robert, Fagundes, Christopher, and Thayer, Julian

Subjects
depression, emotion regulation, heart rate variability (HRV), perceived stress, resilience
Abstract

The negative emotions generated following stressful life events can increase ones risk of depressive symptoms and promote higher levels of perceived stress. The process model of emotion regulation can help distinguish between adaptive and maladaptive emotion regulation strategies to determine who may be at the greatest risk of worse psychological health across the lifespan. Heart rate variability (HRV) may affect these relationships as it indexes aspects of self-regulation, including emotion and behavioral regulation, that enable an individual to dynamically adapt to the changing demands of both internal and external environments. In this study, we expected individual differences in resting vagally mediated HRV to moderate the influence of emotion regulatory strategies among our sample of 267 adults. We found support for the hypothesis that higher vagally mediated HRV buffers against the typical adverse effects of expressive suppression when evaluating depressive symptoms and found weak support when considering perceived stress. There was no evidence for an interaction between cognitive reappraisal and vagally mediated HRV but there was a significant, negative association between cognitive reappraisal and depressive symptoms and perceived stress. Future work may determine if intervening on either emotion regulation strategies or HRV may change these within-persons over time.

Published
2022

17. Shared and distinct biological circuits in effector, memory and exhausted CD8+ T cells revealed by temporal single-cell transcriptomics and epigenetics

Author

Giles, Josephine R., Ngiow, Shin Foong, Manne, Sasikanth, Baxter, Amy E., Khan, Omar, Wang, Ping, Staupe, Ryan, Abdel-Hakeem, Mohamed S., Huang, Hua, Mathew, Divij, Painter, Mark M., Wu, Jennifer E., Huang, Yinghui Jane, Goel, Rishi R., Yan, Patrick K., Karakousis, Giorgos C., Xu, Xiaowei, Mitchell, Tara C., Huang, Alexander C., and Wherry, E. John

Published
2022
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21. Expansion of Luminal Progenitor Cells in the Aging Mouse and Human Prostate

Author

Crowell, Preston D, Fox, Jonathan J, Hashimoto, Takao, Diaz, Johnny A, Navarro, Héctor I, Henry, Gervaise H, Feldmar, Blake A, Lowe, Matthew G, Garcia, Alejandro J, Wu, Ye E, Sajed, Dipti P, Strand, Douglas W, and Goldstein, Andrew S

Subjects
Biochemistry and Cell Biology, Biological Sciences, Stem Cell Research - Nonembryonic - Human, Stem Cell Research - Nonembryonic - Non-Human, Stem Cell Research, Prostate Cancer, Cancer, Regenerative Medicine, Urologic Diseases, Aging, Aetiology, Underpinning research, 1.1 Normal biological development and functioning, 2.1 Biological and endogenous factors, Adolescent, Adult, Animals, Antigens, Neoplasm, Cell Adhesion Molecules, Cell Proliferation, Humans, Male, Mice, Mice, Inbred C57BL, Middle Aged, Organoids, Prostate, Prostatic Hyperplasia, Stem Cells, Young Adult, aging, basal, epithelium, luminal, organoid, progenitor, Medical Physiology, Biological sciences
Abstract

Aging is associated with loss of tissue mass and a decline in adult stem cell function in many tissues. In contrast, aging in the prostate is associated with growth-related diseases including benign prostatic hyperplasia (BPH). Surprisingly, the effects of aging on prostate epithelial cells have not been established. Here we find that organoid-forming progenitor activity of mouse prostate basal and luminal cells is maintained with age. This is caused by an age-related expansion of progenitor-like luminal cells that share features with human prostate luminal progenitor cells. The increase in luminal progenitor cells may contribute to greater risk for growth-related disease in the aging prostate. Importantly, we demonstrate expansion of human luminal progenitor cells in BPH. In summary, we define a Trop2+ luminal progenitor subset and identify an age-related shift in the luminal compartment of the mouse and human prostate epithelium.

Published
2019

24. Drug Clearance in Neonates: A Combination of Population Pharmacokinetic Modelling and Machine Learning Approaches to Improve Individual Prediction

Author

Tang, Bo-Hao, Guan, Zheng, Allegaert, Karel, Wu, Yue-E., Manolis, Efthymios, Leroux, Stephanie, Yao, Bu-Fan, Shi, Hai-Yan, Li, Xiao, Huang, Xin, Wang, Wen-Qi, Shen, A.-Dong, Wang, Xiao-Ling, Wang, Tian-You, Kou, Chen, Xu, Hai-Yan, Zhou, Yue, Zheng, Yi, Hao, Guo-Xiang, Xu, Bao-Ping, Thomson, Alison H., Capparelli, Edmund V., Biran, Valerie, Simon, Nicolas, Meibohm, Bernd, Lo, Yoke-Lin, Marques, Remedios, Peris, Jose-Esteban, Lutsar, Irja, Saito, Jumpei, Burggraaf, Jacobus, Jacqz-Aigrain, Evelyne, van den Anker, John, and Zhao, Wei

Published
2021
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28. CD8+ T cells contribute to survival in patients with COVID-19 and hematologic cancer

Author

Bange, Erin M., Han, Nicholas A., Wileyto, Paul, Kim, Justin Y., Gouma, Sigrid, Robinson, James, Greenplate, Allison R., Hwee, Madeline A., Porterfield, Florence, Owoyemi, Olutosin, Naik, Karan, Zheng, Cathy, Galantino, Michael, Weisman, Ariel R., Ittner, Caroline A. G., Kugler, Emily M., Baxter, Amy E., Oniyide, Olutwatosin, Agyekum, Roseline S., Dunn, Thomas G., Jones, Tiffanie K., Giannini, Heather M., Weirick, Madison E., McAllister, Christopher M., Babady, N. Esther, Kumar, Anita, Widman, Adam J., DeWolf, Susan, Boutemine, Sawsan R., Roberts, Charlotte, Budzik, Krista R., Tollett, Susan, Wright, Carla, Perloff, Tara, Sun, Lova, Mathew, Divij, Giles, Josephine R., Oldridge, Derek A., Wu, Jennifer E., Alanio, Cécile, Adamski, Sharon, Garfall, Alfred L., Vella, Laura A., Kerr, Samuel J., Cohen, Justine V., Oyer, Randall A., Massa, Ryan, Maillard, Ivan P., Maxwell, Kara N., Reilly, John P., Maslak, Peter G., Vonderheide, Robert H., Wolchok, Jedd D., Hensley, Scott E., Wherry, E. John, Meyer, Nuala J., DeMichele, Angela M., Vardhana, Santosha A., Mamtani, Ronac, and Huang, Alexander C.

Published
2021
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33. Genome-wide, integrative analysis implicates microRNA dysregulation in autism spectrum disorder

Author

Wu, Ye E, Parikshak, Neelroop N, Belgard, T Grant, and Geschwind, Daniel H

Subjects
Biological Psychology, Biomedical and Clinical Sciences, Neurosciences, Psychology, Human Genome, Intellectual and Developmental Disabilities (IDD), Brain Disorders, Biotechnology, Mental Health, Genetics, Autism, Pediatric, Aetiology, 2.1 Biological and endogenous factors, Mental health, Autism Spectrum Disorder, Computational Biology, Down-Regulation, Female, Gene Expression Profiling, Genome-Wide Association Study, Humans, Male, MicroRNAs, Oligonucleotide Array Sequence Analysis, RNA, Messenger, Up-Regulation, Cognitive Sciences, Neurology & Neurosurgery, Biological psychology
Abstract

Genetic variants conferring risk for autism spectrum disorder (ASD) have been identified, but the role of post-transcriptional mechanisms in ASD is not well understood. We performed genome-wide microRNA (miRNA) expression profiling in post-mortem brains from individuals with ASD and controls and identified miRNAs and co-regulated modules that were perturbed in ASD. Putative targets of these ASD-affected miRNAs were enriched for genes that have been implicated in ASD risk. We confirmed regulatory relationships between several miRNAs and their putative target mRNAs in primary human neural progenitors. These include hsa-miR-21-3p, a miRNA of unknown CNS function that is upregulated in ASD and that targets neuronal genes downregulated in ASD, and hsa_can_1002-m, a previously unknown, primate-specific miRNA that is downregulated in ASD and that regulates the epidermal growth factor receptor and fibroblast growth factor receptor signaling pathways involved in neural development and immune function. Our findings support a role for miRNA dysregulation in ASD pathophysiology and provide a rich data set and framework for future analyses of miRNAs in neuropsychiatric diseases.

Published
2016

39. Surface optical phonon modes in ternary aligned crystalline InGaN-GaN multi-quantum well nanopillar arrays

Author

Wu, S. -E., Dhara, S., Hsueh, T. -H., Lai, Y. -F., Wang, C. -Y., and Liu, C. -P.

Subjects
Condensed Matter - Materials Science
Abstract

The optical properties of focused ion beam-engraved perfectly aligned and spatially controlled multi-quantum-well InGaN-GaN nanopillars were investigated. Crystalline MQW nanopillars with a diameter of 30 to 95 nm and high aspect ratios showed a maximum of three-fold enhancement in emission intensity per unit active area. A light emitting contour map of Taiwan is drawn with a nanopillar structure to demonstrate the site control of the technique adopted in the present study. Raman scattering studies were used to characterize the newly created surfaces. Unknown peaks in GaN and InGaN nanostructures are identified for surface optical (SO) phonon modes with proper assignments of wave vectors using multiple excitations, and the SO mode for the ternary phase is reported for the first time., Comment: 18 Pages; 8 Figures Including TOC; Acepted in J. Raman Spectroscopy

Published
2009
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40. Flux Qubits and Readout Device with Two Independent Flux Lines

Author

Plourde, B. L. T., Robertson, T. L., Reichardt, P. A., Hime, T., Linzen, S., Wu, C. -E., and Clarke, John

Subjects
Condensed Matter - Superconductivity
Abstract

We report measurements on two superconducting flux qubits coupled to a readout Superconducting QUantum Interference Device (SQUID). Two on-chip flux bias lines allow independent flux control of any two of the three elements, as illustrated by a two-dimensional qubit flux map. The application of microwaves yields a frequency-flux dispersion curve for 1- and 2-photon driving of the single-qubit excited state, and coherent manipulation of the single-qubit state results in Rabi oscillations and Ramsey fringes. This architecture should be scalable to many qubits and SQUIDs on a single chip., Comment: 5 pages, 4 figures, higher quality figures available upon request. Submitted to PRL

Published
2005
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41. Entangling flux qubits with a bipolar dynamic inductance

Author

Plourde, B. L. T., Zhang, J., Whaley, K. B., Wilhelm, F. K., Robertson, T. L., Hime, T., Linzen, S., Reichardt, P. A., Wu, C. -E., and Clarke, John

Subjects
Quantum Physics
Abstract

We propose a scheme to implement variable coupling between two flux qubits using the screening current response of a dc Superconducting QUantum Interference Device (SQUID). The coupling strength is adjusted by the current bias applied to the SQUID and can be varied continuously from positive to negative values, allowing cancellation of the direct mutual inductance between the qubits. We show that this variable coupling scheme permits efficient realization of universal quantum logic. The same SQUID can be used to determine the flux states of the qubits., Comment: 4 pages, 4 figures

Published
2004
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42. Accelerated aging in HIV/AIDS: novel biomarkers of senescent human CD8+ T cells.

Author

Chou, Jennifer P, Ramirez, Christina M, Wu, Jennifer E, and Effros, Rita B

Subjects
CD8-Positive T-Lymphocytes, Humans, HIV Infections, DNA Primers, Flow Cytometry, Base Sequence, Aging, Middle Aged, Real-Time Polymerase Chain Reaction, Biomarkers, Cellular Senescence, Cell Aging, General Science & Technology
Abstract

Clinical evaluation of immune reconstitution and health status during HIV-1 infection and anti-retroviral therapy (ART) is largely based on CD4+ T cell counts and viral load, measures that fail to take into account the CD8+ T cell subset, known to show features of accelerated aging in HIV disease. Here, we compare adenosine deaminase (ADA), glucose uptake receptor 1 (GLUT1), and leucine-rich repeat neuronal 3 (LRRN3) to CD38 expression and telomerase activity, two strong predictors of HIV disease progression. Our analysis revealed that reduced ADA, telomerase activity and LRRN3 gene expression were significantly associated with high CD38 and HLA-DR in CD8+ T cells, with % ADA+ cells being the most robust predictor of CD8+ T cell activation. Our results suggest that ADA, LRRN3 and telomerase activity in CD8+ T cells may serve as novel, clinically relevant biomarkers of immune status in HIV-1 infection, specifically by demonstrating the degree to which CD8+ T cells have progressed to the end stage of replicative senescence. Since chronological aging itself leads to the accumulation of senescent CD8+ T cells, the prolonged survival and resultant increased age of the HIV+ population may synergize with the chronic immune activation to exacerbate both immune decline and age-associated pathologies. The identification and future validation of these new biomarkers may lead to fresh immune-based HIV treatments.

Published
2013

43. TOX transcriptionally and epigenetically programs CD8+ T cell exhaustion

Author

Khan, Omar, Giles, Josephine R., McDonald, Sierra, Manne, Sasikanth, Ngiow, Shin Foong, Patel, Kunal P., Werner, Michael T., Huang, Alexander C., Alexander, Katherine A., Wu, Jennifer E., Attanasio, John, Yan, Patrick, George, Sangeeth M., Bengsch, Bertram, Staupe, Ryan P., Donahue, Greg, Xu, Wei, Amaravadi, Ravi K., Xu, Xiaowei, Karakousis, Giorgos C., Mitchell, Tara C., Schuchter, Lynn M., Kaye, Jonathan, Berger, Shelley L., and Wherry, E. John

Published
2019
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44. Sustained CD28 Expression Delays Multiple Features of Replicative Senescence in Human CD8 T Lymphocytes

Author

Parish, Stanley T., Wu, Jennifer E., and Effros, Rita B.

Subjects
Biomedicine, Medical Microbiology, Internal Medicine, Infectious Diseases, Immunology, Human, T lymphocytes, CD28, CTLA-4, telomerase, replicative senescence
Abstract

CD28 costimulatory signal transduction in T lymphocytes is essential for optimal telomerase activity, stabilization of cytokine mRNAs, and glucose metabolism. During aging and chronic infection with HIV-1, there are increased proportions of CD8 T lymphocytes that lack CD28 expression and show additional features of replicative senescence. Moreover, the abundance of these cells correlates with decreased vaccine responsiveness, early mortality in the very old, and accelerated HIV disease progression. Here, we show that sustained expression of CD28, via gene transduction, retards the process of replicative senescence, as evidenced by enhanced telomerase activity, increased overall proliferative potential, and reduced secretion of pro-inflammatory cytokines. Nevertheless, the transduced cultures eventually do reach senescence, which is associated with increased CTLA-4 gene expression and a loss of CD28 cell surface expression. These findings further elucidate the central role of CD28 in the replicative senescence program, and may ultimately lead to novel therapies for diseases associated with replicative senescence.

Published
2010

47. The construction of the Ni/La2O2CO3 nanorods catalysts with enhanced low-temperature CO2 methanation activities.

Author

Yang, Hui, Wen, Xueying, Yin, Siyuan, Zhang, Yixin, Wu, Cai-e, Xu, Liang, Qiu, Jian, Hu, Xun, Xu, Leilei, and Chen, Mindong

Subjects
METHANATION, CATALYST supports, NANORODS, CATALYSTS, CARBON dioxide, X-ray diffraction
Abstract

[Display omitted] • The La based nanorod support was synthesized by the hydrothermal method. • The Ni-based supported catalysts were prepared by various methods. • The effects of support morphology and preparation method were studied. • The rod-shaped catalyst prepared by the deposition–precipitation method was the best. • The reaction mechanism of CO 2 methanation was investigated by the in-situ techniques. In this work, the La(OH) 3 nanorods were successfully synthesized by precisely regulating the parameters of the hydrothermal method. Then, a series of Ni-based CO 2 methanation catalysts were fabricated via the incipient-wetness impregnation and deposition–precipitation methods by employing the La(OH) 3 nanorods as the supports. The influences of the support morphology and the preparation method on the metal-support interaction, Ni dispersion, and the surface basicity were carefully investigated based on various techniques, such as XRD, SEM, H 2 -TPR, CO 2 -TPD, XPS, ect. It was found that the rod-shaped La(OH) 3 supported catalyst prepared by the deposition–precipitation method performed the optimum activity and stability. The reason for this could be derived from the confinement effect of the crystal plane of the rod-shaped support, which would promote the formation of the strong metal-support interaction and the construction of the Ni-La interface with high activity. Furthermore, the online-tandem TG-MS and in-situ DRIFTS technologies were used to investigate the thermal decomposition performance of the catalyst precursors in the calcination process and the reaction intermediates of the CO 2 methanation. Therefore, the fundamental roles of support morphology and catalyst preparation method were expected to direct the advancement of the Ni-based nanostructured catalysts with outstanding low-temperature performances. [ABSTRACT FROM AUTHOR]

Published
2023
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